diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml new file mode 100644 index 0000000..78b15aa --- /dev/null +++ b/.github/workflows/main.yml @@ -0,0 +1,18 @@ +name: CI +on: + pull_request: + branches: + - main + push: + branches: + - main +jobs: + build: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v1 + - name: Build and test with Docker + run: | + docker build --tag ci -f ./DOCKERFILE . + docker run --rm ci diff --git a/.gitignore b/.gitignore index f02fa59..b629069 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ *.pyc *.bak +.idea diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..589ee36 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,55 @@ +# EVOLVE Dockerfile for CI + +# Github Actions does not support GPU acceleration and the parallized amber pmemd engine is not available for free via conda. +# The unittests regarding this are not executed + + +FROM continuumio/miniconda3 + +# Setup a spot for the code +WORKDIR /evolve +# Install Python dependencies +COPY environment.yml environment.yml +RUN conda env create -f environment.yml + +# Activate environment +SHELL ["conda", "run", "-n", "evolve", "/bin/bash", "-c"] + + +# Copy necessary files +COPY share share/ +COPY unittests unittests/ +COPY main.py . +COPY evaluators.py . + +# This is necessary due to a bug in Docker +RUN true + +COPY src ./src/ + +# Set Environment variables +ENV PYTHONPATH="/evolve/:${PYTHONPATH}" + +ENV PATH="/opt/conda/envs/evolve/bin:$PATH" + +ENV CONDA_DEFAULT_ENV evolve + +ENV EVOLVE_GPU=FALSE + +SHELL ["conda", "run", "-n", "evolve", "/bin/bash", "-c"] + +# Chceck that openbabel is available +RUN echo "Make sure openbabel is installed:" +RUN python -c "from openbabel import openbabel" + +# Change to unittest directory +WORKDIR /evolve/unittests + + +# Execute tests +RUN ["python", "test_gaapi.py"] +RUN ["python", "test_openbabel.py"] +RUN ["python", "test_StartGA_Run.py"] + + +RUN ["/bin/bash"] \ No newline at end of file diff --git a/README.md b/README.md index 71f3691..25acd27 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,8 @@ EVOLVE is python3 based and depends on the following packages ``` pygmo amber18 +openmm +openbabel ``` ### Installing @@ -37,8 +39,7 @@ evaluator and a detailed instructions to run the tests in the [Documentation](ht * [openbabel](http://openbabel.org/) - Openbabel * [Amber](https://ambermd.org/) - to build toplogies -* [Gromacs](http://gromacs.com) - to run molecular dynamics -* [MDAnalysis](http://mdanalysis) - to run automated analysis of MD simulations +* [OpenMM](http://openmm.org) - to run molecular dynamics ## Contributing diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..6604d3d --- /dev/null +++ b/environment.yml @@ -0,0 +1,27 @@ +name: evolve +channels: + - conda-forge + - omnia + - defaults +dependencies: + - openbabel=3.1.0 + - numpy=1.18.4=py37h8960a57_0 + - openmm=7.4.1=py37_cuda101_rc_1 + - openmmtools=0.19.0=py37_1 + - pagmo=2.15.0=hec06268_1 + - pip=20.1.1=pyh9f0ad1d_0 + - ambertools=20.9 + - pygmo=2.15.0=py37h2566bc3_0 + - python=3.7.6=h8356626_5_cpython + - six=1.15.0=pyh9f0ad1d_0 + - sphinx=3.0.3=py_0 + - sphinxcontrib-applehelp=1.0.2=py_0 + - sphinxcontrib-bibtex=1.0.0=py_0 + - sphinxcontrib-devhelp=1.0.2=py_0 + - sphinxcontrib-htmlhelp=1.0.3=py_0 + - sphinxcontrib-jsmath=1.0.1=py_0 + - sphinxcontrib-napoleon=0.7=py_0 + - sphinxcontrib-qthelp=1.0.3=py_0 + - sphinxcontrib-serializinghtml=1.1.4=py_0 + - future + \ No newline at end of file diff --git a/evaluators.py b/evaluators.py index f264b0d..26dcc14 100755 --- a/evaluators.py +++ b/evaluators.py @@ -1,7 +1,11 @@ ''' -main.py +Evaluators in EVOLVE are functions that can call outprocesses and that return fitness values. + + + +.. codeauthor:: Nicholas Browning +.. codeauthor:: Simon Duerr dev@simonduerr.eu -@author: Nicholas Browning ''' from __future__ import print_function @@ -11,14 +15,29 @@ from src.gaapi import generators from src import constants as cnts import numpy as np -import openbabel +from openbabel import openbabel import src.outprocesses as op import os import subprocess import sys - +import time +import glob +from src import MoleculeInfo as mi def minimise_sidechain_ff(settings, individual): + ''' + Use openbabel to minimize the sidechain + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + individual: object + see :class:`src.gaapi.Inidividual` + + + ''' + from src import MoleculeInfo as mi constraints = openbabel.OBFFConstraints() @@ -70,6 +89,19 @@ def minimise_sidechain_ff(settings, individual): def getSidechainAngleAtoms(mol, sidechain_atoms): + ''' + + + + Parameters + ---------- + mol + sidechain_atoms + + Returns + ------- + + ''' angle_atom_dx = [] for obangle in openbabel.OBMolAngleIter(mol): @@ -183,7 +215,20 @@ def minimise_backbone_ff(settings, individual): ff.GetCoordinates(individual.mol) -def turbomol_scf_energy(settings, individuals, fitness_index): +def turbomol_scf_energy(settings, individuals, fitness_index): + ''' + Does a turbomole SCF calculation + + Parameters + ---------- + settings + individuals + fitness_index + + Returns + ------- + + ''' import subprocess for i in range (0, len(individuals)): @@ -223,6 +268,33 @@ def turbomol_scf_energy(settings, individuals, fitness_index): def amber_energy_minimize(settings, individual): + ''' + + This function performs necessary topology preparation and minimization of a pdb file. + + The following evaluators depend on this: + used in :meth:`helical_stability` + + Procedure: + + - write out mutated file from memory to pdb file on disk for amber + - :meth:`src.outprocesses.runtleap` + - :meth:`src.outprocesses.runPMEMD` + - convert rst file to pdb file using `ambpdb` + - read in the minimized structure as new pdb file and set as structure for :data:`individual` + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + individual : object + see :class:`src.gaapi.Individual.Individual` + + Returns + ------- + finalEnergy: float + amber energy after minimization + ''' import shutil directory = settings.output_path + "/amber_run" @@ -240,7 +312,7 @@ def amber_energy_minimize(settings, individual): obconv.SetOutFormat("pdb") obconv.WriteFile(individual.mol, directory + "/mol.pdb") - op.runtleap(work_dir=directory + "/", mol_file='mol.pdb', tleaptemp=settings.tleap_template, tleapin="leap.in") + op.runtleap(work_dir=directory + "/", mol_file='mol2.pdb', tleaptemp=settings.tleap_template, tleapin="leap.in") op.runPMEMD(work_dir=directory + "/", np=settings.mpi_procs, amberin=settings.amber_params) @@ -268,11 +340,174 @@ def amber_energy_minimize(settings, individual): individual.mol = molec finalEnergy = op.parseAmberEnergy(directory + "/amber.out") + f.close() + ferr.close() + fout.close() + return finalEnergy + +def openmm_energy_minimize(settings, individual): + ''' + + This function performs necessary topology preparation and minimization of a pdb file. + + The following evaluators depend on this: + used in :meth:`helical_stability` + + This uses OpenMM instead of Amber for the minimization. + There are options to either relax the structure using + + - a Steepest Descent Integrator + - Simulated Annealing + - using minimization, MD (100ps) and then minimization + + Procedure: + + - write out mutated file from memory to pdb file on disk for amber + - :meth:`src.outprocesses.runtleap` + - openmm + - read in the minimized structure as new pdb file and set as structure for :data:`individual` + + .. code-block:: none + + [EVALUATOR] + evaluators = helical_stability + tleap_template = /path/to/tleap_template.in + amber_params = /path/to/amber_minimization.in + dielectric = 80.0 + gpu_openmm = True + gpudeviceindex = 0 + simAnneal = False + md = False + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + individual : object + see :class:`src.gaapi.Individual.Individual` + + Returns + ------- + finalEnergy: float + amber energy after minimization + ''' + import shutil + # OpenMM Imports + import simtk.openmm as mm + import simtk.openmm.app as app + from parmed import load_file, unit as u + from parmed.openmm import StateDataReporter, NetCDFReporter + import openmmtools + + + directory = settings.output_path + "/amber_run" + if (os.path.exists(directory)): + shutil.rmtree(directory, ignore_errors=True) + + if not os.path.exists(directory): + os.makedirs(directory) + + # if (os.path.exists(directory + "/mol.pdb")): + # os.remove(directory + "/mol.pdb") + + obconv = openbabel.OBConversion() + obconv.SetOutFormat("pdb") + obconv.WriteFile(individual.mol, directory + "/mol.pdb") + + op.runtleap(work_dir=directory + "/", mol_file='mol_amber.pdb', tleaptemp=settings.tleap_template, tleapin="leap.in") + + tleapfiles = load_file(os.getcwd()+"/amber_run/mol.prmtop",os.getcwd()+"/amber_run/mol.inpcrd") + system = tleapfiles.createSystem(nonbondedMethod=app.NoCutoff,implicitSolvent=app.OBC2,) + + platform = mm.Platform.getPlatformByName('CUDA') + prop = dict(CudaPrecision='mixed') # Use mixed single/double precision + platform.setPropertyDefaultValue("CudaDeviceIndex", str(settings.gpudeviceindex)) + + if settings.md: + try: + # Energy Minimize, then 100ps of NVT, then Gradient Descent Minimization. + print("Using MD relaxation") + integrator = mm.LangevinIntegrator(300*u.kelvin,1.0/u.picoseconds,2.0*u.femtoseconds,) + sim = app.Simulation(tleapfiles.topology, system, integrator, platform, prop) + sim.context.setPositions(tleapfiles.positions) + sim.minimizeEnergy(maxIterations=2500) + sim.reporters.append(StateDataReporter(sys.stdout, 100000, step=True, potentialEnergy=True,kineticEnergy=True, temperature=True)) + sim.step(50000) + state = sim.context.getState(getEnergy=True,getPositions=True) + # Gradient Descent to get to potential energy well. + integrator = openmmtools.integrators.GradientDescentMinimizationIntegrator(initial_step_size=0.04 * u.angstroms) + sim = app.Simulation(tleapfiles.topology, system, integrator, platform, prop) + sim.context.setPositions(state.getPositions()) + sim.reporters.append(StateDataReporter(sys.stdout, 1000, step=True, potentialEnergy=True,kineticEnergy=True, temperature=True)) + sim.reporters.append(app.PDBReporter(directory +'/min.pdb', 10000)) + sim.step(15000) + state = sim.context.getState(getEnergy=True) + finalEnergy=state.getPotentialEnergy().value_in_unit(u.kilocalories_per_mole) + pass + except ValueError: + finalEnergy=999999 + pass + else: + integrator = openmmtools.integrators.GradientDescentMinimizationIntegrator(initial_step_size=0.04 * u.angstroms) + sim = app.Simulation(tleapfiles.topology, system, integrator, platform, prop) + sim.context.setPositions(tleapfiles.positions) + #sim.minimizeEnergy(maxIterations=1000) + sim.reporters.append(StateDataReporter(os.devnull, 15000, step=True, potentialEnergy=True,kineticEnergy=True, temperature=True)) + sim.reporters.append(app.PDBReporter(directory +'/min.pdb', 15000)) + sim.step(15000) + state = sim.context.getState(getEnergy=True,getPositions=True) + finalEnergy=state.getPotentialEnergy().value_in_unit(u.kilocalories_per_mole) + + obConversion = openbabel.OBConversion() + obConversion.SetInFormat("pdb") + + molec = openbabel.OBMol() + obConversion.ReadFile(molec, directory + '/min.pdb') + individual.mol = molec + + # ToDo: + # Implement settings for starting temperature and MD + if settings.simAnneal: + try: + minimized=state.getPositions() + integrator = mm.LangevinIntegrator(300.0*u.kelvin,1.0/u.picoseconds,1.0*u.femtoseconds) + sim = app.Simulation(tleapfiles.topology, system, integrator, platform, prop) + sim.context.setPositions(minimized) + sim.reporters.append(StateDataReporter(os.devnull, 2500, step=True, potentialEnergy=True,kineticEnergy=True, temperature=True)) + #sim.reporters.append(app.DCDReporter(name+'.dcd', 10000)) + for i in range(121): + integrator.setTemperature(3*(120-i)*u.kelvin) + sim.step(5000) + state = sim.context.getState(getEnergy=True) + finalEnergy=state.getPotentialEnergy().value_in_unit(u.kilocalories_per_mole) + pass + except ValueError: + finalEnergy=999999 + pass + + return finalEnergy def amber_energy_simplified(settings, individuals, fitness_index, pop_start=0): + ''' + + Remenant of Nick. Should probably be removed. + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + individuals : object + see :class:`src.gaapi.Individual.Individual` + fitness_index + pop_start + + Returns + ------- + + ''' for i in range(pop_start, len(individuals)): @@ -291,6 +526,47 @@ def amber_energy_simplified(settings, individuals, fitness_index, pop_start=0): def helical_stability(settings, individuals, fitness_index, pop_start=0): + ''' + Helical stability function that computes the stability using an implicit solvent minimized structure. + + First the evaluator checks whether the current individual is identical in composition to an already computed individual, if yes computation is skipped and fitness value is copied. + If no, :meth:`amber_energy_minimize` + + If GPU option is set, openmm_minimize is used. + + Then the add and negate energies and the inital energy will be added to the minimized energy + + To use this evaluator in the input file you need to include the following section in your file. + + .. code-block:: none + + [EVALUATOR] + evaluators = helical_stability + tleap_template = /path/to/tleap_template.in + amber_params = /path/to/amber_minimization.in + mpi_processors = 20 + dielectric = 80.0 + gpu_openmm = False + + + Reference: Perez et al., "EVOLVE: A Genetic Algorithm to Predict Protein Thermostability." + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + individuals : list + every item is an :class:`src.gaapi.Individual.Individual` + fitness_index : int + the index in the fitness list that helical_stability populates + pop_start : int + Defines with which individual to start + + + Returns + ------- + + ''' from src import constants from src import MoleculeInfo as mi directory = settings.output_path + "/amber_run" @@ -306,28 +582,57 @@ def helical_stability(settings, individuals, fitness_index, pop_start=0): break if (already_done != -1): - print("ALready computed: " , i, " -> member ", already_done) + print("Already computed: " , i, " -> member ", already_done) individuals[i].mol = openbabel.OBMol(individuals[already_done].mol) individuals[i].fitnesses = individuals[already_done].fitnesses + individuals[i].energies = individuals[already_done].energies continue add = 0.0 - negate = settings.initial_energy + negate = 0.0 + + #Entropy corrections + entropy_add=0.0 + entropy_negate=0.0 print("Minimising: ", i, [mi.getResType(individuals[i].mol.GetResidue(j)) for j in settings.composition_residue_indexes]) print("Rotamers: ", [cnts.selected_rotamers[v] for v in individuals[i].composition]) - finalEnergy = amber_energy_minimize(settings, individuals[i]) + if settings.gpu_openmm: + finalEnergy = openmm_energy_minimize(settings, individuals[i]) + else: + finalEnergy = amber_energy_minimize(settings, individuals[i]) for j in range (0, len(settings.composition_residue_indexes)): + #res = mi.getResType(individuals[i].mol.GetResidue(settings.composition_residue_indexes[j])) + #add += constants.energies['ALA'][settings.helical_dielectric] # TODO this won't work for a non poly ala protein!! + #negate += constants.energies[res][settings.helical_dielectric] res = mi.getResType(individuals[i].mol.GetResidue(settings.composition_residue_indexes[j])) - - add += constants.energies['ALA'][settings.helical_dielectric] # TODO this won't work for a non poly ala protein!! + add += constants.energies[str(settings.originalResidues[j])][settings.helical_dielectric] negate += constants.energies[res][settings.helical_dielectric] - + if settings.entropy_correction: + entropy_add+=constants.entropy_corrections[str(settings.originalResidues[j])][settings.entropy_correction] + entropy_negate+=constants.entropy_corrections[res][settings.entropy_correction] + + #print('add',str(settings.originalResidues[j]), constants.energies[str(settings.originalResidues[j])][settings.helical_dielectric]) + #print('negate',res,'-(', settings.initial_energy,'+', constants.energies[res][settings.helical_dielectric],')') + + if settings.write_energies: + individuals[i].setEnergies(settings.initial_energy, add, finalEnergy, negate) + + negate +=settings.initial_energy + print("min_energy:", finalEnergy, add, negate) finalEnergy += (add - negate) + if settings.entropy_correction: + print("Entropy Correction: ", (entropy_add - entropy_negate)) + finalEnergy+= (entropy_add - entropy_negate) + + + + + individuals[i].setFitness(fitness_index, finalEnergy) if (settings.solution_min_fitness is not None): @@ -335,4 +640,298 @@ def helical_stability(settings, individuals, fitness_index, pop_start=0): individuals[i].setFitness(fitness_index, 999999999.0) print('ind {}, fitness {}'.format(i, individuals[i].fitnesses)) + + + + +def stability_multi(settings, individuals, fitness_index, pop_start=0): + ''' + + This evaluator is used in conjunction with the :func:`evaluators.mmpbsa_multi`. + + It uses the total energy extracted from the mmpbsa calculation which is stored as the mean of all frames in `work_dir/evaluator_stability_multi.log` and the energy corrections developed by Perez et.al. + to calculate the stability of a mutant + Reference: Perez et al., "EVOLVE: A Genetic Algorithm to Predict Protein Thermostability. + + .. code-block:: none + + [GA_MULTIMMPBSA] + multi_individual = True + no_frames =12 + molecule_dir=./pdbs_rename/ + use_compute_cluster=False + compute_cluster_nodes=6 #(optional) + compute_cluster_ntasks=10 #(optional) + compute_cluster_queuename=nccr-short #(optional) + energy_calculator=pb + [EVALUATOR] + evaluators = mmpbsa_multi stability_multi + tleap_template =path/to/leap.in + amber_params =/path/to/min.in + mmpbsa_params=/path/to/mmpbsa.in + mpi_processors =24 + dielectric = 80.0 + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + individuals: list + list of :class:`src.gaapi.Individual.Individual` + fitness_index: int + integer designating the fitness index of this fitness (needed to update the correct value in the fitness list + pop_start: int + if only treating part of the population + + Returns + ------- + + ''' + from src import constants + from src import MoleculeInfo as mi + directory = settings.output_path + "/work_dir" + + for i in range(pop_start, len(individuals)): + + already_done = -1 + if (i > 0): + for j in range(0, i): + if (np.array_equal(individuals[j].composition, individuals[i].composition)): + already_done = j + break + if (already_done != -1): + print("Already computed: ", i, " -> member ", already_done) + individuals[i].fitnesses = individuals[already_done].fitnesses + continue + if (individuals[i].fitnesses[0] == 123456789): + # TODO set to max fitness in this generation to prevent replication + individuals[i].setFitness(0, 3) + individuals[i].setFitness(1, 100) + continue + + add = 0.0 + negate = settings.initial_energy + + print("Getting energy for ", i, [mi.getResType(individuals[i].mol[0].GetResidue(j)) for j in settings.composition_residue_indexes]) + + logfileStability = open(directory + "/evaluator_stability_multi.log") + # lines=logfileStability.readlines() + if individuals[i].stability == "NA": + print("Stability=NA, stability set to 100") + finalEnergy = 100 + pass + else: + finalEnergy = individuals[i].stability + for j in range(0, len(settings.composition_residue_indexes)): + res = mi.getResType(individuals[i].mol[0].GetResidue(settings.composition_residue_indexes[j])) + add += constants.energies[str(settings.originalResidues[j])][settings.helical_dielectric] + negate += constants.energies[res][settings.helical_dielectric] + # print "Residue:", res, "add", add, "negate", negate + print + add, negate, finalEnergy + finalEnergy += (add - negate) + logfileStability.close() + + # if (i+1==len(individuals)): + # truncate logfileStability after evaluation has finished + # logfileStability = open(directory+"/evaluator_stability_multi.log", "w") + # logfileStability.close() + + individuals[i].setFitness(fitness_index, finalEnergy) + print("Fitnes index:", fitness_index) + print("Fitness value:", finalEnergy) + print('ind {}, fitness {}'.format(i, individuals[i].fitnesses)) + + +def mmpbsa_multi(settings, individuals, fitness_index, pop_start=0): + ''' + + This evaluator is used in conjunction with the stability multi evaluator. + + It sets up the system (containing multiple frames) using leap, runs energy minimization (explicit solvent), + then runs an MMPBSA calculation and extracts total energy (used for :func:`evaluators.stability_multi`) and binding free energy. + + .. code-block:: none + + [GA_MULTIMMPBSA] + multi_individual = True + no_frames =12 + molecule_dir=./pdbs_rename/ + use_compute_cluster=False + compute_cluster_nodes=6 #(optional) + compute_cluster_ntasks=10 #(optional) + compute_cluster_queuename=nccr-short #(optional) + energy_calculator=pb + [EVALUATOR] + evaluators = mmpbsa_multi stability_multi + tleap_template =/path/to/leap.in + amber_params =/path/to/min.in + mmpbsa_params=/path/to/mmpbsa.in + mpi_processors =24 + dielectric = 80.0 + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + individuals: list + list of :class:`src.gaapi.Individual.Individual` + fitness_index: int + integer designating the fitness index of this fitness (needed to update the correct value in the fitness list + pop_start: int + if only treating part of the population + ''' + # create working directory for all different frames, this is needed to avoid output garbling from leap, pdb4amber and amber + work_dir = settings.output_path + "/work_dir" + logfile = open(work_dir + "/evaluator_mmpbsa_multi.log", "a") + # iterate over all invdividuals in the population + for i in range(pop_start, len(individuals)): + logfile.write("\n") + logfile.write("#" * 100) + logfile.write("\n") + individualStart = time.time() + # For each individual we determine whether it has already been computed in this population. Each combination of amino acids is only computed once per generation + already_done = -1 + if (i > 0): + for j in range(0, i): + if (np.array_equal(individuals[j].composition, individuals[i].composition)): + already_done = j + break + if (already_done != -1): + print("Already computed: ", i, " -> member ", already_done) + logfile.write("Already computed: " + str(i) + " -> member " + str(already_done)) + logfile.write("\n") + # Not sure why this was included for helical stability, we initialize a new instance of OBMol for each frame anyway so this is not needed for mmpbsa_multi + # individuals[i].mol = [None]*settings.no_frames + # for x in range(0, settings.no_frames): + # individuals[i].mol[x] = openbabel.OBMol(individuals[already_done].mol[x]) + individuals[i].fitnesses = individuals[already_done].fitnesses + # need to write the second fitness also to the stability logfile + # logfileStability = open(work_dir+"/evaluator_stability_multi.log", "a") + # logfileStability.write(str(individuals[already_done].fitnesses[1])+"\n") + # logfileStability.close() + continue + # check if work dir exists + if not os.path.exists(work_dir): + os.makedirs(work_dir) + # create subdirectories for all frames specified and if they exists delete all files in them + for frame in range(0, settings.no_frames): + if not os.path.exists(work_dir + "/frame" + str(frame)): + os.makedirs(work_dir + "/frame" + str(frame)) + if (os.path.exists(work_dir + "/frame" + str(frame) + "/mutated.pdb")): + for f in glob.glob(work_dir + "/frame" + str(frame) + "/*"): + os.remove(f) + pass + pass + # for each frame mutate to individual composition + # note that this required changing Individual.py + # With evaluator mmpbsa multi set, individual will not hold a single mol but multiple instances of OBmol + for x in range(0, settings.no_frames): + obconv = openbabel.OBConversion() + obconv.SetOutFormat("pdb") + obconv.WriteFile(individuals[i].mol[x], work_dir + "/frame" + str(x) + "/mutated.pdb") + pass + pass + + print("Individual ind {}".format(i)) + logfile.write("Individual ind {}".format(i)) + logfile.write("\n") + logfile.write("Individual composition:" + str([mi.getResType(individuals[i].mol[0].GetResidue(a)) for a in settings.composition_residue_indexes])) + logfile.write("\n") + logfile.close() + # running tleap for all frames. Inside this routine we change to every frame dir and run a seperate instance of leap + op.runtleapMultiInd(work_dir=work_dir, leap_inputfile=settings.tleap_template, n_frames=settings.no_frames) + # run pmemd using multipmemd version. Need to use pmemd.MPI because of force truncation in pmemd.cuda! + minReturnCode = op.runPMEMDMultiInd(work_dir=work_dir, np=settings.mpi_procs, amberin=settings.amber_params, + n_frames=settings.no_frames) + logfile = open(work_dir + "/evaluator_mmpbsa_multi.log", "a") + if minReturnCode == 0: + print("Setting individual fitness to 0 due to error in the minimization (Seg fault)") + finalEnergy = 0 + pass + else: + logfile.write("finished energy min") + logfile.write("\n") + logfile.close() + # Do mmpbsa calculation after frames have been minimized and converted to a solvent free pdb file. MMPBSA calculation can run on as many cores as there are frames. + finalEnergy = op.runMMPBSAMultiInd(work_dir=work_dir, mmpbsa_inputfile=settings.mmpbsa_params, + n_frames=settings.no_frames, + energy_evaluator=settings.energy_calculator) + logfile = open(work_dir + "/evaluator_mmpbsa_multi.log", "a") + logfile.write("finished MMPBSA min\n") + + # set fitness to absurd value in case something goes wrong in order to avoid replication of this composition + if (settings.solution_min_fitness is not None): + if (finalEnergy < settings.solution_min_fitness): + finalEnergy = 0 + # update fitness of individual with computed value from MMPBSA GB or PB calculatioN + individuals[i].setFitness(fitness_index, finalEnergy) + if fitness_index == 0: + individuals[i].setFitness(fitness_index + 1, 0) + pass + # read out energies from minimization and store in logfile in case evaluator stability multi is also used + frameEnergies = settings.no_frames * [None] + for frame in range(0, settings.no_frames): + # frameEnergies[frame]=op.parseAmberEnergy(work_dir+"/frame"+str(frame)+"/min.out."+"frame"+str(frame)) + frameEnergies[frame] = op.parseGBEnergy(work_dir + "/_MMPBSA_complex_gb.mdout." + str(frame)) + logfile.write("frame" + str(frame) + " energy:" + str(frameEnergies[frame]) + "\n") + if frameEnergies[frame] == 999: + print("Something went wrong with reading the minimization file") + continue + pass + if frameEnergies[frame] != 999: + stabilityEnergy = np.mean(frameEnergies) + logfile.write("Stability Energy (mean of all frames):" + str(stabilityEnergy) + "\n") + logfile.write("Stability Energy - Initial Energy:" + str(stabilityEnergy - settings.initial_energy) + "\n") + else: + stabilityEnergy = "NA" + + logfileStability = open(work_dir+"/evaluator_stability_multi.log", "a") + logfileStability.write(str(stabilityEnergy)+"\n") + logfileStability.close() + individuals[i].setStability(stabilityEnergy) + + print('ind {}, fitness {}'.format(i, individuals[i].fitnesses)) + logfile.write('ind {}, fitness {}\n'.format(i, individuals[i].fitnesses)) + individualEnd = time.time() + # read in new files + # update mols with minized molecules from work dir + + if settings.update_files == True: + for frame in range(0, settings.no_frames): + errorcatcher = 0 + obconv = openbabel.OBConversion() + pdbFile = openbabel.OBMol() + obconv.ReadFile(pdbFile, settings.output_path + "/work_dir/frame" + str(frame) + "/min_nosolv.pdb") + # TODO: this should only print once + try: + # test if pdb file is correct + testPDBfile = [mi.getResType(pdbFile.GetResidue(j)) for j in settings.composition_residue_indexes] + pass + except Exception as e: + print + "could not read pdb file", str(e) + individuals[i].setFitness(0, 123456789) + individuals[i].setFitness(1, 123456789) + errorcatcher = 1 + pass + # if minimization fails we cannot update with non exisiting pdb file + if errorcatcher == 0: + individuals[i].mol[frame] = pdbFile + pass + pass + logfile.write("Runtime of this ind: " + str(individualEnd - individualStart) + " sec.") + logfile.write("\n") + logfile.write("#" * 100) + logfile.write("\n") + if minReturnCode != 0: + os.remove( + work_dir + "/reference.frc") # This file is generated by MMPBSA and gets huge. Somehow MMPBSA does not remove it automatically + # Get a list of all the files with _MMPBSA + fileList = glob.glob(work_dir + "/_MMPBSA*") + # Iterate over the list of filepaths & remove each file. + for filePath in fileList: + os.remove(filePath) + pass + logfile.close() diff --git a/ga_main_decomp.py b/ga_main_decomp.py index 8c05929..b318acb 100755 --- a/ga_main_decomp.py +++ b/ga_main_decomp.py @@ -1,7 +1,8 @@ ''' -main.py -@author: Nicholas Browning +not sure what this dois? + +.. codeauthor:: Nicholas Browning ''' from __future__ import division from __future__ import print_function diff --git a/main.py b/main.py index da7d1c2..1636931 100755 --- a/main.py +++ b/main.py @@ -1,7 +1,11 @@ ''' -main.py +This is the main module of EVOLVE. -@author: Nicholas Browning +It initialises the genetic algorithm search, +determines initial fitnesses for each evaluator and then loops over the generations. + +.. codeauthor:: Nicholas Browning +.. codeauthor:: Simon Duerr dev@simonduerr.eu ''' from __future__ import division from __future__ import print_function @@ -11,11 +15,11 @@ from past.utils import old_div import numpy as np import argparse -import openbabel +from openbabel import openbabel import time import json import sys - +import os from src import constants as cnts from src import JobConfig from src.gaapi import Individual @@ -25,58 +29,150 @@ from src.gaapi import generators from src.gaapi import replacers from src import MoleculeInfo as mi +import src.outprocesses as op +from collections import Counter import evaluators as evals # import printResidueInfo as pri def mainLoop(settings): + ''' + + The main GA loop that initalises the optimizaion procedure with an empty parent population. + A seed population can be used (not implemented yet) + Then the initial fitness is determined and a parent population is created (if not seeded) + Its fitness is determined. + + In the main GA while loop, from each parent population a child generation is created + through the crossover and mutation operations, their fitness is determined and + the replacer operation is used to build the next parent generation. + + For single objective runs the comparison is made using simple sorting of the children and retention of a certain percentage of good solutions (elistism) + For multiobjective runs Deb et.al. NSGA2 algorithm is used which autmatically incorporates elistim. + + If you want to add your own evaluation function you want to add your method to evaluators.py and add corresponding methods to outprocesses and methods. + Your evaluator needs to be registered in operator_types. + + In order to bias the first parent population the generators file can be used. + For composotion optimization we currently implement random aminoacid rotamer subsitution (favors aas with many rotamers), unform (equal probability for each allowed amino acid) and swissprot (based on swissprot probability densities) + + Parameters + ---------- + settings: object + see :class:`src.JobConfig.Settings` + + ''' curr_iteration = -1 parent_population = [] ga = initialise_ga(settings) + - if ("helical_stability" in settings.evaluators): - print('Fitness of {}:'.format(settings.initial_molecule_path)) - initial_indiv = Individual.Individual(settings) - initial_indiv.init = True - - print("MINIMISING INITIAL STRUCTURE") - for k, eval in enumerate(ga["evaluators"]): - print("EVALUATORS {}".format(ga["evaluators"][k].__name__)) - eval(settings, [initial_indiv], k) - - with open(settings.output_path + '/initial_fitness.dat', 'w') as outfile: - json.dump(initial_indiv.fitnesses[0], outfile) - - settings.initial_energy = initial_indiv.fitnesses[0] - - print("INITIAL_ENERGY", settings.initial_energy) - - directory = settings.output_path + "/amber_run" - - obConversion = openbabel.OBConversion() - obConversion.SetInFormat("pdb") - - molec = openbabel.OBMol() - obConversion.ReadFile(molec, directory + '/min_struct.pdb') - - settings.initial_molecule = molec - + # if ("helical_stability" in settings.evaluators): + # print('Fitness of {}:'.format(settings.initial_molecule_path)) + # initial_indiv = Individual.Individual(settings) + # initial_indiv.init = True + # + # print("MINIMISING INITIAL STRUCTURE") + # for k, eval in enumerate(ga["evaluators"]): + # print("EVALUATORS {}".format(ga["evaluators"][k].__name__)) + # eval(settings, [initial_indiv], k) + # + # with open(settings.output_path + '/initial_fitness.dat', 'w') as outfile: + # json.dump(initial_indiv.fitnesses[0], outfile) + # + # settings.initial_energy = initial_indiv.fitnesses[0] + # + # print("INITIAL_ENERGY", settings.initial_energy) + # + # directory = settings.output_path + "/amber_run" + # + # obConversion = openbabel.OBConversion() + # obConversion.SetInFormat("pdb") + # + # molec = openbabel.OBMol() + # obConversion.ReadFile(molec, directory + '/min_struct.pdb') + # + # settings.initial_molecule = molec + # if settings.seed_population: # TODO - IMPLEMENT pass else: # generateInitialPopulation - + if settings.initial_fitness_computation: + # if multi individual we need to do this for every individual. + if (settings.multi_individual): + print('Fitness of initial frames:') + pass + else: + print('Fitness of {}:'.format(settings.initial_molecule_path)) + if not os.path.exists(settings.output_path + "/work_dir"): + os.makedirs(settings.output_path + "/work_dir") + f = open(settings.output_path + "/work_dir/evaluator_mmpbsa_multi.log", "w+") + f.close() + initial_indiv = Individual.Individual(settings) + initial_indiv.init = True + if (settings.multi_individual): + settings.originalResidues = [mi.getResType(initial_indiv.mol[0].GetResidue(j)) for j in settings.composition_residue_indexes] + else: + settings.originalResidues = [mi.getResType(initial_indiv.mol.GetResidue(j)) for j in settings.composition_residue_indexes] + + print("Original residues:", settings.originalResidues) + print(ga["evaluators"]) + for k, eval in enumerate(ga["evaluators"]): + print("EVALUATORS {}".format(ga["evaluators"][k].__name__)) + eval(settings, [initial_indiv], k) + print("evaluated", ga["evaluators"][k]) + + with open(settings.output_path + '/initial_fitness.dat', 'w') as outfile: + json.dump(str(initial_indiv.fitnesses), outfile) + + if (settings.multi_individual): + settings.initial_energy = initial_indiv.fitnesses[1] # TODO only works for multi mmpbsa for now + pass + else: + settings.initial_energy = initial_indiv.fitnesses[0] + + + print("INITIAL_ENERGY", settings.initial_energy) + + pass + parent_population = generators.initialisePopulation(settings) - + + + # TODO + # This should become similar to the way evaluators are chosen if (settings.composition_optimization): - if (settings.unbiased_protein_composition_generator): - print("Generating initial population composition from unbiased distribution") - generators.unbiased_protein_composition_generator(settings, parent_population) - else: - print("Generating initial population composition from uniform distribution") - generators.UniformCompositionGenerator(settings, parent_population) + generators.generate(settings, parent_population, ga["chosenGenerator"]) + #if (settings.unbiased_protein_composition_generator): + # print("Generating initial population composition from unbiased distribution") + # generators.unbiased_protein_composition_generator(settings, parent_population) + #elif (settings.swissprot_composition_generator): + # print("Generating initial population composition from swissprot probability distribution") + # generators.swissprot_composition_generator(settings, parent_population) + #else: + # print("Generating initial population composition from uniform distribution") + # generators.UniformCompositionGenerator(settings, parent_population) + + if (settings.multi_individual): + print("Resetting logfile in work dir\n "+settings.output_path + "/work_dir/evaluator_mmpbsa_multi.log") + if os.path.exists(settings.output_path + "/work_dir"): + try: + os.remove(settings.output_path + "/work_dir"+"/evaluator_mmpbsa_multi.log") + except OSError as e: # this would be "except OSError, e:" before Python 2.6 + os.makedirs(settings.output_path + "/work_dir") + f= open(settings.output_path + "/work_dir/evaluator_mmpbsa_multi.log","w+") + f.close() + if e.errno != errno.ENOENT: # errno.ENOENT = no such file or directory + raise # re-raise exception if a different error occurred + pass + + if (settings.use_compute_cluster): + print("Create folder for SLURM output\n "+settings.output_path + "/slurm") + if not os.path.exists(settings.output_path +"/slurm"): + os.makedirs(settings.output_path +"/slurm") if (settings.backbone_dihedral_optimization): if (settings.mc_generate_dihedrals): @@ -96,7 +192,14 @@ def mainLoop(settings): eval(settings, parent_population, i) curr_iteration = 0 - best_fitnesses = [np.min([p.fitnesses[0] for p in parent_population])] + # If multiobjevtive optimization the population will already be sorted, the fittest individual is always 0 + # For single objective the fittest individual is not 0 and needs to be identified + best_fitnesses = np.zeros(shape=(settings.max_iteration,1)) + if settings.no_evaluators==1: + best_fitnesses = [np.min([p.fitnesses[0] for p in parent_population])] + else: + best_fitnesses=[parent_population[0].fitnesses] + # TODO Need to implement convergence relative error for multi objective while (curr_iteration < settings.max_iteration): @@ -118,7 +221,15 @@ def mainLoop(settings): # evaluate - build new mol files, run amber minimisation/whatever else, update individuals with resulting dihedrals for j in range(0, len(child_population)): - child_population[j].mol = openbabel.OBMol(settings.initial_molecule) + if (settings.multi_individual): + child_population[j].mol = [None] * settings.no_frames + for frame, x in enumerate(settings.initial_molecule): + child_population[j].mol[frame] = openbabel.OBMol(x) + pass + pass + else: + child_population[j].mol = openbabel.OBMol(settings.initial_molecule) + pass child_population[j].applyComposition(settings) for i, eval in enumerate(ga["evaluators"]): @@ -128,29 +239,69 @@ def mainLoop(settings): # elitism parent_population = replacers.replace(settings, parent_population, child_population, ga["chosenReplacer"]) - best_fitnesses.append(min([p.fitnesses[0] for p in parent_population])) - curr_conv_relative_error = abs(old_div((best_fitnesses[curr_iteration + 1] - best_fitnesses[curr_iteration]), best_fitnesses[curr_iteration + 1])) - print("Convergence relative error: {}".format(curr_conv_relative_error)) + if settings.no_evaluators == 1: + best_fitnesses.append(min([p.fitnesses[0] for p in parent_population])) + curr_conv_relative_error = abs( + (best_fitnesses[curr_iteration + 1] - best_fitnesses[curr_iteration]) / best_fitnesses[ + curr_iteration + 1]) + print("Convergence relative error: {}".format(curr_conv_relative_error)) + pass + else: + #best_fitnesses.append(parent_population[0].fitnesses) + #print("Best Individual fitness", parent_population[0].fitnesses) + # TODO Need to implement convergence relative error for multi objective + pass curr_iteration += 1 - - np.savetxt(settings.output_path + '/fitnesses.dat', best_fitnesses, delimiter='\n') + settings.curr_iteration = curr_iteration + if settings.no_evaluators == 1: + np.savetxt(settings.output_path + '/fitnesses.dat', best_fitnesses, delimiter='\n') + if list(best_fitnesses).count(best_fitnesses[-1])>settings.convergence_cycles: + print(f"Reached convergence. Last {list(best_fitnesses).count(best_fitnesses[-1])} generations were identical.") + printIterationInfo(settings, curr_iteration, parent_population, True) + sys.exit(0) + else: + # in order to correctly write out with np savetext we need to reduce multidimensional fitness arrays to a 1d list + fitness_list = [] + fitness_line = '' + for fitness in best_fitnesses: + for fitness_ind in fitness: + fitness_line += str(fitness_ind) + " " + pass + fitness_list.append([fitness_line]) + fitness_line = '' + if settings.verbose: + print("BEST FITNESSES:", fitness_list) + pass + np.savetxt(settings.output_path + '/fitnesses.dat', fitness_list, delimiter='\n', fmt='%s') + + printIterationInfo(settings, curr_iteration, parent_population, True) print('Best GA fitnesses written in fitnesses.dat') def initialise_ga(settings): - from src.gaapi import operator_types ''' - chosenSelector = selectors.tournamentSelectionWOR - chosenMutator = mutators.polynomial_dihedral - chosenCrossover = crossovers.simulated_binary_dihedral - chosenReplacer = replacers.elitist_replace - evaluators = [evaluators.amber_energy]#[evaluators.testEnergyByMinimisation] + + Initalizes the GA program usign the settings object. + Picks the corresponding methods for the text strings in the input file that are stored in the settings object from operator_types + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + + Returns + ------- + dict + dictionary containing keys for chosen operations and the method or a list of methods respectively + + ''' + from src.gaapi import operator_types - chosenSelector, chosenMutator, chosenCrossover, chosenReplacer, evaluators = None, None, None, None, None + chosenSelector, chosenMutator, chosenCrossover, chosenReplacer,chosenGenerator, evaluators = None, None, None, None, None, None if (settings.selector == operator_types.TOURNAMENT_WOR): chosenSelector = selectors.tournamentSelectionWOR @@ -167,23 +318,64 @@ def initialise_ga(settings): if (settings.replacer == operator_types.ELITIST): chosenReplacer = replacers.elitist_replace - + + if (settings.replacer== operator_types.NSGA2): + chosenReplacer = replacers.non_dominated_sorting + + if (settings.generator== operator_types.SWISSPROT): + chosenGenerator = generators.swissprot_composition_generator + elif (settings.generator == operator_types.UNBIASED): + chosenGenerator=generators.unbiased_protein_composition_generator + else: + chosenGenerator = generators.UniformCompositionGenerator + evaluators = [] for k in settings.evaluators: - if ("openbabel_ff94" in k): - evaluators.append(evals.testEnergyByMinimisation) - elif ("helical_stability" in k): - evaluators.append(evals.helical_stability) - elif ("pmemd" in k): - evaluators.append(evals.amber_energy_simplified) + if k in operator_types.availableEvaluators: + evaluators.append(operator_types.availableEvaluators[k]) else: print("Could not parse evaluator from setting file") sys.exit() - return {'chosenSelector': chosenSelector, 'chosenMutator': chosenMutator, 'chosenCrossover': chosenCrossover, 'chosenReplacer': chosenReplacer, 'evaluators': evaluators} + if len(evaluators) > 1: + print("More than one evaluator is used. Automatically using non dominated sorting") + settings.no_evaluators = len(evaluators) + chosenReplacer = replacers.non_dominated_sorting + pass + + print(settings.composition_residue_indexes) + print(settings.composition_lower_bounds) + print(settings.composition_upper_bounds) + for i,res in enumerate(settings.composition_residue_indexes): + print("Resindex", res) + print(i) + print("First Rotamer",cnts.rotamers[settings.composition_lower_bounds[i]] ) + print("Last Rotamer",cnts.rotamers[settings.composition_upper_bounds[i]] ) + pass + + return {'chosenSelector': chosenSelector, 'chosenMutator': chosenMutator, 'chosenCrossover': chosenCrossover, 'chosenReplacer': chosenReplacer, 'chosenGenerator': chosenGenerator, 'evaluators': evaluators} def printIterationInfo(settings, curr_iteration, pop, ending): + """ + + Prints information about each ga run. + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + curr_iteration: int + index of current iteration + pop: list + contains :class:`src.gaapi.Individual.Individual` + ending: bool + to prematurely exit the calculation + + Returns + ------- + + """ print("CURRENT POPULATION") @@ -206,28 +398,47 @@ def printIterationInfo(settings, curr_iteration, pop, ending): print("Population Average Fitness(es):", np.mean([p.fitnesses for p in pop])) print("Population STD(s):", np.std([p.fitnesses for p in pop])) - print("Best individual:", min_indiv) + if settings.multi_individual: + print("no best individual for multi-objective runs") + else: + print("Best individual:", min_indiv) if (pop[min_indiv].composition_residue_indexes != None): - print("Best Individual Composition: ", [mi.getResType(pop[min_indiv].mol.GetResidue(j)) for j in settings.composition_residue_indexes]) - print("Best Individual Rotamers: ", [cnts.selected_rotamers[v] for v in pop[min_indiv].composition]) + if (settings.multi_individual): + #print("Best Individual Composition: ", [mi.getResType(pop[min_indiv].mol[0].GetResidue(j)) for j in settings.composition_residue_indexes]) + #print("Best Individual Rotamers: ", [cnts.selected_rotamers[v] for v in pop[min_indiv].composition]) + print("Utopia point individuals") + else: + print("Best Individual Composition: ", [mi.getResType(pop[min_indiv].mol.GetResidue(j)) for j in settings.composition_residue_indexes]) + print("Best Individual Rotamers: ", [cnts.selected_rotamers[v] for v in pop[min_indiv].composition]) if (pop[min_indiv].dihedral_residue_indexes != None): print('Best ind - PHIs, PSIs') print(pop[min_indiv].phi_dihedrals, pop[min_indiv].psi_dihedrals) print("Best ind - Fitness(es):", pop[min_indiv].fitnesses) + + if settings.write_energies: + print("writing energies to file") + op.writeEnergyLog(path=settings.output_path, energies=pop[min_indiv].energies, iteration=curr_iteration) obConversion = openbabel.OBConversion() obConversion.SetOutFormat("pdb") if (curr_iteration == settings.max_iteration or ending): print("OUT: FINAL MOLECULE in {}".format(settings.output_path + '/' + settings.output_file)) - obConversion.WriteFile(pop[min_indiv].mol, settings.output_path + '/' + settings.output_file) + if (settings.multi_individual): + obConversion.WriteFile(pop[min_indiv].mol[0], settings.output_path + '/' + settings.output_file) + else: + obConversion.WriteFile(pop[min_indiv].mol, settings.output_path + '/' + settings.output_file) elif (settings.store_intermediate_mol): print("OUT: INTERMEDIATE MOLECULE in {}".format(settings.output_path + '/' + "min_mol_iter_" + str(curr_iteration) + ".pdb")) - obConversion.WriteFile(pop[min_indiv].mol, settings.output_path + '/' + "min_mol_iter_" + str(curr_iteration) + ".pdb") + + if (settings.multi_individual): + obConversion.WriteFile(pop[min_indiv].mol[0],settings.output_path + '/' + "min_mol_iter_" + str(curr_iteration) + ".pdb") + else: + obConversion.WriteFile(pop[min_indiv].mol, settings.output_path + '/' + "min_mol_iter_" + str(curr_iteration) + ".pdb") if __name__ == '__main__': @@ -243,7 +454,7 @@ def printIterationInfo(settings, curr_iteration, pop, ending): print("-- END SETTINGS PRINT -- ") print("\n--- START MOLECULE PRINT --") - #pri.printResidueInfo(settings.initial_molecule) + #printResidueInfo(settings.initial_molecule) print("--- END MOLECULE PRINT --") print("\nRunning GA") diff --git a/set_dihedrals.py b/set_dihedrals.py index ff99783..541a88a 100755 --- a/set_dihedrals.py +++ b/set_dihedrals.py @@ -1,4 +1,8 @@ ''' + +what does this do? + + printMoleculeInfo @author: Nicholas Browning diff --git a/share/ALA/A01.mol2 b/share/ALA/A01.mol2 new file mode 100755 index 0000000..a8ef81d --- /dev/null +++ b/share/ALA/A01.mol2 @@ -0,0 +1,30 @@ +@MOLECULE +A01 + 10 9 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 A01 0.000000 + 2 H -1.9370 -0.7700 -0.4440 H 1 A01 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 A01 0.000000 + 4 HA 0.3490 0.9010 -0.5040 H 1 A01 0.000000 + 5 CB 0.5400 0.0010 1.4380 C.3 1 A01 0.000000 + 6 HB1 0.2060 -0.9000 1.9530 H 1 A01 0.000000 + 7 HB2 1.6300 0.0250 1.4170 H 1 A01 0.000000 + 8 HB3 0.1680 0.8790 1.9660 H 1 A01 0.000000 + 9 C 0.5510 -1.1980 -0.7660 C.1 1 A01 0.000000 + 10 O 0.0240 -2.3060 -0.6670 O.2 1 A01 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 9 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 9 10 1 +@SUBSTRUCTURE + 1 A01 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R01.mol2 b/share/ARG/R01.mol2 new file mode 100755 index 0000000..ecd0822 --- /dev/null +++ b/share/ARG/R01.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R01 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R01 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R01 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R01 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R01 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R01 0.000000 + 6 HB2 0.0790 -0.8460 1.9470 H 1 R01 0.000000 + 7 HB3 1.6140 -0.1510 1.3730 H 1 R01 0.000000 + 8 CG 0.2460 1.2770 2.2040 C.3 1 R01 0.000000 + 9 HG2 0.7010 2.1140 1.6730 H 1 R01 0.000000 + 10 HG3 -0.8340 1.4190 2.2470 H 1 R01 0.000000 + 11 CD 0.8050 1.2090 3.6160 C.3 1 R01 0.000000 + 12 HD2 0.3500 0.3670 4.1370 H 1 R01 0.000000 + 13 HD3 1.8840 1.0630 3.5640 H 1 R01 0.000000 + 14 NE 0.5340 2.4280 4.3710 N.3 1 R01 0.000000 + 15 HE 0.0220 3.1600 3.9000 H 1 R01 0.000000 + 16 CZ 0.9150 2.6280 5.6290 C.cat 1 R01 0.000000 + 17 NH1 0.6240 3.7700 6.2360 N.3 1 R01 0.000000 + 18 HH11 0.1130 4.4860 5.7400 H 1 R01 0.000000 + 19 HH12 0.9150 3.9190 7.1920 H 1 R01 0.000000 + 20 NH2 1.5840 1.6840 6.2770 N.3 1 R01 0.000000 + 21 HH21 1.8020 0.8140 5.8120 H 1 R01 0.000000 + 22 HH22 1.8720 1.8390 7.2330 H 1 R01 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R01 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R01 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R01 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R02.mol2 b/share/ARG/R02.mol2 new file mode 100755 index 0000000..bca0267 --- /dev/null +++ b/share/ARG/R02.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R02 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R02 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R02 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R02 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R02 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R02 0.000000 + 6 HB2 0.0790 -0.8460 1.9470 H 1 R02 0.000000 + 7 HB3 1.6140 -0.1510 1.3730 H 1 R02 0.000000 + 8 CG 0.2460 1.2770 2.2040 C.3 1 R02 0.000000 + 9 HG2 0.7010 2.1140 1.6730 H 1 R02 0.000000 + 10 HG3 -0.8340 1.4190 2.2470 H 1 R02 0.000000 + 11 CD 0.8050 1.2090 3.6160 C.3 1 R02 0.000000 + 12 HD2 0.3500 0.3670 4.1370 H 1 R02 0.000000 + 13 HD3 1.8840 1.0630 3.5640 H 1 R02 0.000000 + 14 NE 0.5340 2.4280 4.3710 N.3 1 R02 0.000000 + 15 HE -0.2860 2.4350 4.9600 H 1 R02 0.000000 + 16 CZ 1.2950 3.5170 4.3290 C.cat 1 R02 0.000000 + 17 NH1 2.3780 3.5400 3.5650 N.3 1 R02 0.000000 + 18 HH11 2.6220 2.7280 3.0160 H 1 R02 0.000000 + 19 HH12 2.9540 4.3690 3.5350 H 1 R02 0.000000 + 20 NH2 0.9700 4.5810 5.0520 N.3 1 R02 0.000000 + 21 HH21 0.1440 4.5600 5.6330 H 1 R02 0.000000 + 22 HH22 1.5500 5.4070 5.0180 H 1 R02 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R02 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R02 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R02 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R03.mol2 b/share/ARG/R03.mol2 new file mode 100755 index 0000000..24441c1 --- /dev/null +++ b/share/ARG/R03.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R03 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R03 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R03 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R03 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R03 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R03 0.000000 + 6 HB2 0.0790 -0.8460 1.9470 H 1 R03 0.000000 + 7 HB3 1.6140 -0.1510 1.3730 H 1 R03 0.000000 + 8 CG 0.2460 1.2770 2.2040 C.3 1 R03 0.000000 + 9 HG2 0.7010 2.1140 1.6730 H 1 R03 0.000000 + 10 HG3 -0.8340 1.4190 2.2470 H 1 R03 0.000000 + 11 CD 0.8050 1.2090 3.6160 C.3 1 R03 0.000000 + 12 HD2 0.3500 0.3670 4.1370 H 1 R03 0.000000 + 13 HD3 1.8840 1.0630 3.5640 H 1 R03 0.000000 + 14 NE 0.5340 2.4280 4.3710 N.3 1 R03 0.000000 + 15 HE 1.2560 3.1340 4.3820 H 1 R03 0.000000 + 16 CZ -0.5930 2.6620 5.0350 C.cat 1 R03 0.000000 + 17 NH1 -1.5600 1.7550 5.0380 N.3 1 R03 0.000000 + 18 HH11 -1.4370 0.8880 4.5350 H 1 R03 0.000000 + 19 HH12 -2.4160 1.9350 5.5440 H 1 R03 0.000000 + 20 NH2 -0.7490 3.8010 5.6950 N.3 1 R03 0.000000 + 21 HH21 -0.0090 4.4890 5.6920 H 1 R03 0.000000 + 22 HH22 -1.6070 3.9760 6.1990 H 1 R03 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R03 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R03 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R03 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R04.mol2 b/share/ARG/R04.mol2 new file mode 100755 index 0000000..adc10e5 --- /dev/null +++ b/share/ARG/R04.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R04 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R04 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R04 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R04 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R04 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R04 0.000000 + 6 HB2 0.0790 -0.8460 1.9470 H 1 R04 0.000000 + 7 HB3 1.6140 -0.1510 1.3730 H 1 R04 0.000000 + 8 CG 0.2460 1.2770 2.2040 C.3 1 R04 0.000000 + 9 HG2 0.7010 2.1140 1.6730 H 1 R04 0.000000 + 10 HG3 -0.8340 1.4190 2.2470 H 1 R04 0.000000 + 11 CD 0.8050 1.2090 3.6160 C.3 1 R04 0.000000 + 12 HD2 1.8700 0.9850 3.5650 H 1 R04 0.000000 + 13 HD3 0.6600 2.1740 4.1020 H 1 R04 0.000000 + 14 NE 0.1480 0.1790 4.4150 N.3 1 R04 0.000000 + 15 HE -0.6310 -0.3060 3.9940 H 1 R04 0.000000 + 16 CZ 0.5100 -0.1530 5.6500 C.cat 1 R04 0.000000 + 17 NH1 1.5290 0.4650 6.2310 N.3 1 R04 0.000000 + 18 HH11 2.0280 1.1870 5.7320 H 1 R04 0.000000 + 19 HH12 1.8020 0.2100 7.1700 H 1 R04 0.000000 + 20 NH2 -0.1470 -1.1040 6.3000 N.3 1 R04 0.000000 + 21 HH21 -0.9220 -1.5740 5.8540 H 1 R04 0.000000 + 22 HH22 0.1300 -1.3540 7.2390 H 1 R04 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R04 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R04 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R04 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R05.mol2 b/share/ARG/R05.mol2 new file mode 100755 index 0000000..c70eb31 --- /dev/null +++ b/share/ARG/R05.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R05 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R05 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R05 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R05 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R05 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R05 0.000000 + 6 HB2 0.0790 -0.8460 1.9470 H 1 R05 0.000000 + 7 HB3 1.6140 -0.1510 1.3730 H 1 R05 0.000000 + 8 CG 0.2460 1.2770 2.2040 C.3 1 R05 0.000000 + 9 HG2 0.4920 2.1290 1.5690 H 1 R05 0.000000 + 10 HG3 -0.8160 1.3020 2.4480 H 1 R05 0.000000 + 11 CD 1.0620 1.3470 3.4840 C.3 1 R05 0.000000 + 12 HD2 2.1180 1.2400 3.2370 H 1 R05 0.000000 + 13 HD3 0.8970 2.3150 3.9580 H 1 R05 0.000000 + 14 NE 0.6920 0.2950 4.4270 N.3 1 R05 0.000000 + 15 HE 1.2420 -0.5520 4.4150 H 1 R05 0.000000 + 16 CZ -0.3130 0.3870 5.2910 C.cat 1 R05 0.000000 + 17 NH1 -1.0540 1.4850 5.3330 N.3 1 R05 0.000000 + 18 HH11 -0.8520 2.2510 4.7070 H 1 R05 0.000000 + 19 HH12 -1.8170 1.5510 5.9920 H 1 R05 0.000000 + 20 NH2 -0.5750 -0.6220 6.1110 N.3 1 R05 0.000000 + 21 HH21 -0.0090 -1.4580 6.0750 H 1 R05 0.000000 + 22 HH22 -1.3400 -0.5500 6.7670 H 1 R05 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R05 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R05 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R05 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R06.mol2 b/share/ARG/R06.mol2 new file mode 100755 index 0000000..5e4a11b --- /dev/null +++ b/share/ARG/R06.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R06 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R06 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R06 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R06 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R06 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R06 0.000000 + 6 HB2 0.0790 -0.8460 1.9470 H 1 R06 0.000000 + 7 HB3 1.6140 -0.1510 1.3730 H 1 R06 0.000000 + 8 CG 0.2460 1.2770 2.2040 C.3 1 R06 0.000000 + 9 HG2 0.7010 2.1140 1.6730 H 1 R06 0.000000 + 10 HG3 -0.8340 1.4190 2.2470 H 1 R06 0.000000 + 11 CD 0.8050 1.2090 3.6160 C.3 1 R06 0.000000 + 12 HD2 1.8700 0.9850 3.5650 H 1 R06 0.000000 + 13 HD3 0.6600 2.1740 4.1020 H 1 R06 0.000000 + 14 NE 0.1480 0.1790 4.4150 N.3 1 R06 0.000000 + 15 HE -0.7840 0.3770 4.7480 H 1 R06 0.000000 + 16 CZ 0.6980 -0.9900 4.7260 C.cat 1 R06 0.000000 + 17 NH1 1.9200 -1.2810 4.3030 N.3 1 R06 0.000000 + 18 HH11 2.4300 -0.6120 3.7440 H 1 R06 0.000000 + 19 HH12 2.3350 -2.1710 4.5410 H 1 R06 0.000000 + 20 NH2 0.0240 -1.8660 5.4590 N.3 1 R06 0.000000 + 21 HH21 -0.9070 -1.6410 5.7800 H 1 R06 0.000000 + 22 HH22 0.4450 -2.7540 5.6940 H 1 R06 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R06 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R06 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R06 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R07.mol2 b/share/ARG/R07.mol2 new file mode 100755 index 0000000..894e4a2 --- /dev/null +++ b/share/ARG/R07.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R07 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R07 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R07 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R07 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R07 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R07 0.000000 + 6 HB2 0.0790 -0.8460 1.9470 H 1 R07 0.000000 + 7 HB3 1.6140 -0.1510 1.3730 H 1 R07 0.000000 + 8 CG 0.2460 1.2770 2.2040 C.3 1 R07 0.000000 + 9 HG2 0.7010 2.1140 1.6730 H 1 R07 0.000000 + 10 HG3 -0.8340 1.4190 2.2470 H 1 R07 0.000000 + 11 CD 0.8050 1.2090 3.6160 C.3 1 R07 0.000000 + 12 HD2 0.4960 2.1000 4.1630 H 1 R07 0.000000 + 13 HD3 0.4090 0.3230 4.1130 H 1 R07 0.000000 + 14 NE 2.2630 1.1370 3.6240 N.3 1 R07 0.000000 + 15 HE 2.7350 1.2160 2.7350 H 1 R07 0.000000 + 16 CZ 2.9970 0.9740 4.7200 C.cat 1 R07 0.000000 + 17 NH1 4.3190 0.9200 4.6300 N.3 1 R07 0.000000 + 18 HH11 4.7640 1.0030 3.7270 H 1 R07 0.000000 + 19 HH12 4.8750 0.7960 5.4650 H 1 R07 0.000000 + 20 NH2 2.4070 0.8630 5.9020 N.3 1 R07 0.000000 + 21 HH21 1.4000 0.9030 5.9660 H 1 R07 0.000000 + 22 HH22 2.9680 0.7390 6.7330 H 1 R07 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R07 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R07 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R07 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R08.mol2 b/share/ARG/R08.mol2 new file mode 100755 index 0000000..95d37d7 --- /dev/null +++ b/share/ARG/R08.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R08 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R08 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R08 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R08 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R08 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R08 0.000000 + 6 HB2 0.0790 -0.8460 1.9470 H 1 R08 0.000000 + 7 HB3 1.6140 -0.1510 1.3730 H 1 R08 0.000000 + 8 CG 0.2460 1.2770 2.2040 C.3 1 R08 0.000000 + 9 HG2 0.7010 2.1140 1.6730 H 1 R08 0.000000 + 10 HG3 -0.8340 1.4190 2.2470 H 1 R08 0.000000 + 11 CD 0.8050 1.2090 3.6160 C.3 1 R08 0.000000 + 12 HD2 0.4960 2.1000 4.1630 H 1 R08 0.000000 + 13 HD3 0.4090 0.3230 4.1130 H 1 R08 0.000000 + 14 NE 2.2630 1.1370 3.6240 N.3 1 R08 0.000000 + 15 HE 2.7690 1.9870 3.4200 H 1 R08 0.000000 + 16 CZ 2.9550 0.0330 3.8810 C.cat 1 R08 0.000000 + 17 NH1 4.2810 0.0630 3.8660 N.3 1 R08 0.000000 + 18 HH11 4.7610 0.9270 3.6590 H 1 R08 0.000000 + 19 HH12 4.8050 -0.7790 4.0620 H 1 R08 0.000000 + 20 NH2 2.3210 -1.0990 4.1530 N.3 1 R08 0.000000 + 21 HH21 1.3110 -1.1190 4.1650 H 1 R08 0.000000 + 22 HH22 2.8510 -1.9370 4.3480 H 1 R08 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R08 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R08 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R08 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R09.mol2 b/share/ARG/R09.mol2 new file mode 100755 index 0000000..e7b1f1e --- /dev/null +++ b/share/ARG/R09.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R09 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R09 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R09 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R09 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R09 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R09 0.000000 + 6 HB2 0.0790 -0.8460 1.9470 H 1 R09 0.000000 + 7 HB3 1.6140 -0.1510 1.3730 H 1 R09 0.000000 + 8 CG 0.2460 1.2770 2.2040 C.3 1 R09 0.000000 + 9 HG2 0.7010 2.1140 1.6730 H 1 R09 0.000000 + 10 HG3 -0.8340 1.4190 2.2470 H 1 R09 0.000000 + 11 CD 0.8050 1.2090 3.6160 C.3 1 R09 0.000000 + 12 HD2 0.4960 2.1000 4.1630 H 1 R09 0.000000 + 13 HD3 0.4090 0.3230 4.1130 H 1 R09 0.000000 + 14 NE 2.2630 1.1370 3.6240 N.3 1 R09 0.000000 + 15 HE 2.6810 0.2190 3.6770 H 1 R09 0.000000 + 16 CZ 3.0630 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b/share/ARG/R13.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R13 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R13 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R13 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R13 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R13 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R13 0.000000 + 6 HB2 0.1510 -0.8960 1.9200 H 1 R13 0.000000 + 7 HB3 1.6230 -0.0600 1.3700 H 1 R13 0.000000 + 8 CG 0.1430 1.2250 2.2420 C.3 1 R13 0.000000 + 9 HG2 -0.9390 1.3470 2.1850 H 1 R13 0.000000 + 10 HG3 0.4350 1.0650 3.2800 H 1 R13 0.000000 + 11 CD 0.8220 2.4770 1.7120 C.3 1 R13 0.000000 + 12 HD2 0.5900 2.5840 0.6530 H 1 R13 0.000000 + 13 HD3 0.4430 3.3430 2.2550 H 1 R13 0.000000 + 14 NE 2.2720 2.4230 1.8700 N.3 1 R13 0.000000 + 15 HE 2.8120 2.0970 1.0810 H 1 R13 0.000000 + 16 CZ 2.9160 2.7750 2.9780 C.cat 1 R13 0.000000 + 17 NH1 4.2390 2.6920 3.0300 N.3 1 R13 0.000000 + 18 HH11 4.7530 2.3610 2.2260 H 1 R13 0.000000 + 19 HH12 4.7260 2.9600 3.8740 H 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2.5750 1.3940 0.9900 C.3 1 R15 0.000000 + 12 HD2 2.2790 1.4930 -0.0540 H 1 R15 0.000000 + 13 HD3 2.1420 2.2100 1.5690 H 1 R15 0.000000 + 14 NE 4.0300 1.4810 1.0740 N.3 1 R15 0.000000 + 15 HE 4.4200 1.9410 1.8840 H 1 R15 0.000000 + 16 CZ 4.8620 0.9970 0.1570 C.cat 1 R15 0.000000 + 17 NH1 4.3820 0.3880 -0.9180 N.3 1 R15 0.000000 + 18 HH11 3.3840 0.2930 -1.0370 H 1 R15 0.000000 + 19 HH12 5.0170 0.0210 -1.6130 H 1 R15 0.000000 + 20 NH2 6.1720 1.1230 0.3190 N.3 1 R15 0.000000 + 21 HH21 6.5340 1.5880 1.1400 H 1 R15 0.000000 + 22 HH22 6.8020 0.7540 -0.3800 H 1 R15 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R15 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R15 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R15 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R16.mol2 b/share/ARG/R16.mol2 new file mode 100755 index 0000000..1e6d84c --- /dev/null +++ b/share/ARG/R16.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R16 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R16 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R16 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R16 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R16 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R16 0.000000 + 6 HB2 0.0980 0.8600 1.9400 H 1 R16 0.000000 + 7 HB3 0.1860 -0.9170 1.9070 H 1 R16 0.000000 + 8 CG 2.0510 0.0730 1.5290 C.3 1 R16 0.000000 + 9 HG2 2.3380 -0.0320 2.5760 H 1 R16 0.000000 + 10 HG3 2.4760 -0.7490 0.9530 H 1 R16 0.000000 + 11 CD 2.5750 1.3940 0.9900 C.3 1 R16 0.000000 + 12 HD2 2.2790 1.4930 -0.0540 H 1 R16 0.000000 + 13 HD3 2.1420 2.2100 1.5690 H 1 R16 0.000000 + 14 NE 4.0300 1.4810 1.0740 N.3 1 R16 0.000000 + 15 HE 4.5190 0.6880 1.4650 H 1 R16 0.000000 + 16 CZ 4.7410 2.5290 0.6710 C.cat 1 R16 0.000000 + 17 NH1 4.1290 3.5850 0.1530 N.3 1 R16 0.000000 + 18 HH11 3.1230 3.5890 0.0660 H 1 R16 0.000000 + 19 HH12 4.6720 4.3800 -0.1530 H 1 R16 0.000000 + 20 NH2 6.0610 2.5180 0.7870 N.3 1 R16 0.000000 + 21 HH21 6.5240 1.7120 1.1830 H 1 R16 0.000000 + 22 HH22 6.5990 3.3160 0.4800 H 1 R16 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R16 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R16 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R16 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R17.mol2 b/share/ARG/R17.mol2 new file mode 100755 index 0000000..2eaed44 --- /dev/null +++ b/share/ARG/R17.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R17 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R17 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R17 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R17 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R17 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R17 0.000000 + 6 HB2 0.0980 0.8600 1.9400 H 1 R17 0.000000 + 7 HB3 0.1860 -0.9170 1.9070 H 1 R17 0.000000 + 8 CG 2.0510 0.0730 1.5290 C.3 1 R17 0.000000 + 9 HG2 2.4740 -0.7880 1.0100 H 1 R17 0.000000 + 10 HG3 2.3860 0.9890 1.0430 H 1 R17 0.000000 + 11 CD 2.5130 0.0690 2.9770 C.3 1 R17 0.000000 + 12 HD2 3.5920 0.2180 3.0050 H 1 R17 0.000000 + 13 HD3 2.0210 0.8830 3.5090 H 1 R17 0.000000 + 14 NE 2.1960 -1.1880 3.6490 N.3 1 R17 0.000000 + 15 HE 1.3380 -1.2240 4.1800 H 1 R17 0.000000 + 16 CZ 2.9600 -2.2740 3.6030 C.cat 1 R17 0.000000 + 17 NH1 4.0920 -2.2590 2.9140 N.3 1 R17 0.000000 + 18 HH11 4.3710 -1.4210 2.4250 H 1 R17 0.000000 + 19 HH12 4.6710 -3.0860 2.8810 H 1 R17 0.000000 + 20 NH2 2.5890 -3.3720 4.2470 N.3 1 R17 0.000000 + 21 HH21 1.7260 -3.3790 4.7720 H 1 R17 0.000000 + 22 HH22 3.1720 -4.1970 4.2110 H 1 R17 0.000000 + 23 C 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5.0020 H 1 R23 0.000000 + 19 HH12 1.9720 2.7310 6.5500 H 1 R23 0.000000 + 20 NH2 2.8820 0.5460 5.7240 N.3 1 R23 0.000000 + 21 HH21 3.2110 -0.3040 5.2890 H 1 R23 0.000000 + 22 HH22 3.0220 0.7020 6.7120 H 1 R23 0.000000 + 23 C 0.5510 -1.1980 -0.7660 C.1 1 R23 0.000000 + 24 O 0.0240 -2.3060 -0.6670 O.2 1 R23 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 23 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 10 1 + 11 8 11 1 + 12 11 12 1 + 13 11 13 1 + 14 11 14 1 + 15 14 15 1 + 16 14 16 1 + 17 16 17 1 + 18 16 20 1 + 19 17 18 1 + 20 17 19 1 + 21 20 21 1 + 22 20 22 1 + 23 23 24 1 +@SUBSTRUCTURE + 1 R23 1 TEMP 0 **** **** 0 ROOT diff --git a/share/ARG/R24.mol2 b/share/ARG/R24.mol2 new file mode 100755 index 0000000..a684337 --- /dev/null +++ b/share/ARG/R24.mol2 @@ -0,0 +1,58 @@ +@MOLECULE +R24 + 24 23 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 R24 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R24 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 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--- /dev/null +++ b/share/HIP/HP3.mol2 @@ -0,0 +1,47 @@ +@MOLECULE +HP3 + 18 18 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 HP3 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 HP3 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 HP3 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 HP3 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 HP3 0.000000 + 6 HB2 0.1140 -0.8350 1.9910 H 1 HP3 0.000000 + 7 HB3 1.6230 -0.0820 1.4250 H 1 HP3 0.000000 + 8 CG 0.2050 1.2410 2.2020 C.2 1 HP3 0.000000 + 9 ND1 -1.0040 1.4240 2.8360 N.pl3 1 HP3 0.000000 + 10 HD1 -1.7590 0.7530 2.8390 H 1 HP3 0.000000 + 11 CE1 -1.0120 2.6050 3.4300 C.2 1 HP3 0.000000 + 12 HE1 -1.8860 2.9370 3.9890 H 1 HP3 0.000000 + 13 NE2 0.1460 3.1940 3.2040 N.pl3 1 HP3 0.000000 + 14 HE2 0.4240 4.1070 3.5350 H 1 HP3 0.000000 + 15 CD2 0.9260 2.3630 2.4380 C.2 1 HP3 0.000000 + 16 HD2 1.9280 2.6750 2.1420 H 1 HP3 0.000000 + 17 C 0.5510 -1.1980 -0.7660 C.1 1 HP3 0.000000 + 18 O 0.0240 -2.3060 -0.6670 O.2 1 HP3 0.000000 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diff --git a/share/LYS/K07.mol2 b/share/LYS/K07.mol2 new file mode 100755 index 0000000..186c3c0 --- /dev/null +++ b/share/LYS/K07.mol2 @@ -0,0 +1,54 @@ +@MOLECULE +K07 + 22 21 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 K07 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 K07 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 K07 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 K07 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 K07 0.000000 + 6 HB2 0.0790 -0.8460 1.9470 H 1 K07 0.000000 + 7 HB3 1.6140 -0.1510 1.3730 H 1 K07 0.000000 + 8 CG 0.2460 1.2770 2.2040 C.3 1 K07 0.000000 + 9 HG2 0.7010 2.1140 1.6730 H 1 K07 0.000000 + 10 HG3 -0.8340 1.4190 2.2470 H 1 K07 0.000000 + 11 CD 0.8050 1.2090 3.6160 C.3 1 K07 0.000000 + 12 HD2 0.4450 2.0730 4.1750 H 1 K07 0.000000 + 13 HD3 0.4450 0.2950 4.0890 H 1 K07 0.000000 + 14 CE 2.3250 1.2090 3.6080 C.3 1 K07 0.000000 + 15 HE2 2.6720 1.0560 4.6300 H 1 K07 0.000000 + 16 HE3 2.6640 0.3830 2.9830 H 1 K07 0.000000 + 17 NZ 2.8770 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1 K13 1 TEMP 0 **** **** 0 ROOT diff --git a/share/LYS/K14.mol2 b/share/LYS/K14.mol2 new file mode 100755 index 0000000..c15a3ea --- /dev/null +++ b/share/LYS/K14.mol2 @@ -0,0 +1,54 @@ +@MOLECULE +K14 + 22 21 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 K14 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 K14 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 K14 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 K14 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 K14 0.000000 + 6 HB2 0.0980 0.8600 1.9400 H 1 K14 0.000000 + 7 HB3 0.1860 -0.9170 1.9070 H 1 K14 0.000000 + 8 CG 2.0510 0.0730 1.5290 C.3 1 K14 0.000000 + 9 HG2 2.4740 -0.7880 1.0100 H 1 K14 0.000000 + 10 HG3 2.3860 0.9890 1.0430 H 1 K14 0.000000 + 11 CD 2.5130 0.0690 2.9770 C.3 1 K14 0.000000 + 12 HD2 2.0610 -0.7830 3.4840 H 1 K14 0.000000 + 13 HD3 3.5980 -0.0320 2.9950 H 1 K14 0.000000 + 14 CE 2.1120 1.3510 3.6870 C.3 1 K14 0.000000 + 15 HE2 2.5640 2.1900 3.1580 H 1 K14 0.000000 + 16 HE3 1.0260 1.4390 3.6460 H 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-1.4580 0.0000 0.0000 N.2 1 R16 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 R16 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 R16 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 R16 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 R16 0.000000 + 6 HB2 0.0980 0.8600 1.9400 H 1 R16 0.000000 + 7 HB3 0.1860 -0.9170 1.9070 H 1 R16 0.000000 + 8 CG 2.0510 0.0730 1.5290 C.3 1 R16 0.000000 + 9 HG2 2.3380 -0.0320 2.5760 H 1 R16 0.000000 + 10 HG3 2.4760 -0.7490 0.9530 H 1 R16 0.000000 + 11 CD 2.5750 1.3940 0.9900 C.3 1 R16 0.000000 + 12 HD2 2.2790 1.4930 -0.0540 H 1 R16 0.000000 + 13 HD3 2.1420 2.2100 1.5690 H 1 R16 0.000000 + 14 NE 4.0300 1.4810 1.0740 N.3 1 R16 0.000000 + 15 HE 4.5190 0.6880 1.4650 H 1 R16 0.000000 + 16 CZ 4.7410 2.5290 0.6710 C.cat 1 R16 0.000000 + 17 NH1 4.1290 3.5850 0.1530 N.3 1 R16 0.000000 + 18 HH11 3.1230 3.5890 0.0660 H 1 R16 0.000000 + 19 HH12 4.6720 4.3800 -0.1530 H 1 R16 0.000000 + 20 NH2 6.0610 2.5180 0.7870 N.3 1 R16 0.000000 + 21 HH21 6.5240 1.7120 1.1830 H 1 R16 0.000000 + 22 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19 16 18 1 + 20 18 19 1 + 21 20 21 1 +@SUBSTRUCTURE + 1 Y02 1 TEMP 0 **** **** 0 ROOT diff --git a/share/flat/Y03.mol2 b/share/flat/Y03.mol2 new file mode 100644 index 0000000..6cc5398 --- /dev/null +++ b/share/flat/Y03.mol2 @@ -0,0 +1,53 @@ +@MOLECULE +Y03 + 21 21 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 Y03 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 Y03 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 Y03 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 Y03 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 Y03 0.000000 + 6 HB2 0.1000 0.8600 1.9410 H 1 Y03 0.000000 + 7 HB3 0.1880 -0.9170 1.9090 H 1 Y03 0.000000 + 8 CG 2.0440 0.0730 1.5230 C.ar 1 Y03 0.000000 + 9 CD1 2.7080 1.2840 1.3810 C.ar 1 Y03 0.000000 + 10 HD1 2.1220 2.1860 1.2040 H 1 Y03 0.000000 + 11 CE1 4.0840 1.3590 1.4610 C.ar 1 Y03 0.000000 + 12 HE1 4.5960 2.3140 1.3470 H 1 Y03 0.000000 + 13 CZ 4.8180 0.2010 1.6900 C.ar 1 Y03 0.000000 + 14 OH 6.1890 0.2670 1.7720 O.3 1 Y03 0.000000 + 15 HH 6.5290 1.1570 1.6570 H 1 Y03 0.000000 + 16 CE2 4.1760 -1.0150 1.8350 C.ar 1 Y03 0.000000 + 17 HE2 4.7480 -1.9250 2.0140 H 1 Y03 0.000000 + 18 CD2 2.7990 -1.0710 1.7510 C.ar 1 Y03 0.000000 + 19 HD2 2.2840 -2.0260 1.8640 H 1 Y03 0.000000 + 20 C 0.5510 -1.1980 -0.7660 C.1 1 Y03 0.000000 + 21 O 0.0240 -2.3060 -0.6670 O.2 1 Y03 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 20 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 18 1 + 11 9 10 1 + 12 9 11 1 + 13 11 12 1 + 14 11 13 1 + 15 13 14 1 + 16 13 16 1 + 17 14 15 1 + 18 16 17 1 + 19 16 18 1 + 20 18 19 1 + 21 20 21 1 +@SUBSTRUCTURE + 1 Y03 1 TEMP 0 **** **** 0 ROOT diff --git a/share/flat/Y04.mol2 b/share/flat/Y04.mol2 new file mode 100644 index 0000000..2d7b44e --- /dev/null +++ b/share/flat/Y04.mol2 @@ -0,0 +1,53 @@ +@MOLECULE +Y04 + 21 21 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N -1.4580 0.0000 0.0000 N.2 1 Y04 0.000000 + 2 H -1.9370 -0.7700 -0.4450 H 1 Y04 0.000000 + 3 CA 0.0000 0.0000 0.0000 C.3 1 Y04 0.000000 + 4 HA 0.3690 0.8900 -0.5100 H 1 Y04 0.000000 + 5 CB 0.5360 0.0000 1.4330 C.3 1 Y04 0.000000 + 6 HB2 1.6230 0.0600 1.3720 H 1 Y04 0.000000 + 7 HB3 0.1500 0.8940 1.9220 H 1 Y04 0.000000 + 8 CG 0.1430 -1.2210 2.2340 C.ar 1 Y04 0.000000 + 9 CD1 0.9440 -2.3550 2.2420 C.ar 1 Y04 0.000000 + 10 HD1 1.8650 -2.3510 1.6590 H 1 Y04 0.000000 + 11 CE1 0.5930 -3.4740 2.9710 C.ar 1 Y04 0.000000 + 12 HE1 1.2290 -4.3590 2.9720 H 1 Y04 0.000000 + 13 CZ -0.5840 -3.4640 3.7100 C.ar 1 Y04 0.000000 + 14 OH -0.9420 -4.5740 4.4380 O.3 1 Y04 0.000000 + 15 HH -0.3090 -5.2920 4.3630 H 1 Y04 0.000000 + 16 CE2 -1.3970 -2.3450 3.7150 C.ar 1 Y04 0.000000 + 17 HE2 -2.3210 -2.3340 4.2920 H 1 Y04 0.000000 + 18 CD2 -1.0290 -1.2350 2.9800 C.ar 1 Y04 0.000000 + 19 HD2 -1.6630 -0.3480 2.9780 H 1 Y04 0.000000 + 20 C 0.5510 -1.1980 -0.7660 C.1 1 Y04 0.000000 + 21 O 0.0240 -2.3060 -0.6670 O.2 1 Y04 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 3 4 1 + 4 3 5 1 + 5 3 20 1 + 6 5 6 1 + 7 5 7 1 + 8 5 8 1 + 9 8 9 1 + 10 8 18 1 + 11 9 10 1 + 12 9 11 1 + 13 11 12 1 + 14 11 13 1 + 15 13 14 1 + 16 13 16 1 + 17 14 15 1 + 18 16 17 1 + 19 16 18 1 + 20 18 19 1 + 21 20 21 1 +@SUBSTRUCTURE + 1 Y04 1 TEMP 0 **** **** 0 ROOT diff --git a/share/off/ALA/A01.off b/share/off/ALA/A01.off new file mode 100644 index 0000000..cea9be1 --- /dev/null +++ b/share/off/ALA/A01.off @@ -0,0 +1,93 @@ +!!index array str + "A01" +!entry.A01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 0.033700 + "HA" "H1" 0 1 131075 4 1 0.082300 + "CB" "CT" 0 1 131075 5 6 -0.182500 + "HB1" "HC" 0 1 131075 6 1 0.060300 + "HB2" "HC" 0 1 131075 7 1 0.060300 + "HB3" "HC" 0 1 131075 8 1 0.060300 + "C" "C" 0 1 131075 9 6 0.597300 + "O" "O" 0 1 131075 10 8 -0.567900 +!entry.A01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB1" "HC" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.A01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.A01.unit.childsequence single int + 2 +!entry.A01.unit.connect array int + 1 + 9 +!entry.A01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 9 17 + 3 5 17 + 5 8 17 + 5 6 17 + 5 7 17 + 9 10 17 +!entry.A01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 +!entry.A01.unit.name single str + "" +!entry.A01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.444000 + 0.0 0.0 0.0 + 0.349000 0.901000 -0.504000 + 0.540000 0.001000 1.438000 + 0.206000 -0.900000 1.953000 + 1.630000 0.025000 1.417000 + 0.168000 0.879000 1.966000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.A01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.A01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "A01" 1 11 1 "?" 0 +!entry.A01.unit.residuesPdbSequenceNumber array int + 1 +!entry.A01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.A01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R01.off b/share/off/ARG/R01.off new file mode 100644 index 0000000..989868a --- /dev/null +++ b/share/off/ARG/R01.off @@ -0,0 +1,177 @@ +!!index array str + "R01" +!entry.R01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 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"A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 + "R" 1 "A" 20 + "R" 1 "A" 21 + "R" 1 "A" 22 + "R" 1 "A" 23 + "R" 1 "A" 24 +!entry.R01.unit.name single str + "default_name" +!entry.R01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.350000 0.367000 4.137000 + 1.884000 1.063000 3.564000 + 0.534000 2.428000 4.371000 + 0.022000 3.160000 3.900000 + 0.915000 2.628000 5.629000 + 0.624000 3.770000 6.236000 + 0.113000 4.486000 5.740000 + 0.915000 3.919000 7.192000 + 1.584000 1.684000 6.277000 + 1.802000 0.814000 5.812000 + 1.872000 1.839000 7.233000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R01" 1 25 1 "?" 0 +!entry.R01.unit.residuesPdbSequenceNumber array int + 1 +!entry.R01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R02.off b/share/off/ARG/R02.off new file mode 100644 index 0000000..e08f4fd --- /dev/null +++ b/share/off/ARG/R02.off @@ -0,0 +1,177 @@ +!!index array str + "R02" +!entry.R02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R02.unit.childsequence single int + 2 +!entry.R02.unit.connect array int + 1 + 23 +!entry.R02.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R02.unit.name single str + "default_name" +!entry.R02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.350000 0.367000 4.137000 + 1.884000 1.063000 3.564000 + 0.534000 2.428000 4.371000 + -0.285931 2.435072 4.960468 + 1.295000 3.517000 4.329000 + 2.378000 3.540000 3.565000 + 2.622312 2.728314 3.016118 + 2.954280 4.369367 3.535486 + 0.970000 4.581000 5.052000 + 0.143515 4.560085 5.632633 + 1.550255 5.407470 5.017987 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R02" 1 25 1 "?" 0 +!entry.R02.unit.residuesPdbSequenceNumber array int + 1 +!entry.R02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R03.off b/share/off/ARG/R03.off new file mode 100644 index 0000000..c93fecd --- /dev/null +++ b/share/off/ARG/R03.off @@ -0,0 +1,177 @@ +!!index array str + "R03" +!entry.R03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R03.unit.childsequence single int + 2 +!entry.R03.unit.connect array int + 1 + 23 +!entry.R03.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R03.unit.name single str + "default_name" +!entry.R03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.350000 0.367000 4.137000 + 1.884000 1.063000 3.564000 + 0.534000 2.428000 4.371000 + 1.255815 3.134164 4.382154 + -0.593000 2.662000 5.035000 + -1.560000 1.755000 5.038000 + -1.436650 0.888213 4.534752 + -2.416039 1.935212 5.543508 + -0.749000 3.801000 5.695000 + -0.008927 4.488699 5.691530 + -1.607095 3.975779 6.199014 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R03" 1 25 1 "?" 0 +!entry.R03.unit.residuesPdbSequenceNumber array int + 1 +!entry.R03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R04.off b/share/off/ARG/R04.off new file mode 100644 index 0000000..f5216dc --- /dev/null +++ b/share/off/ARG/R04.off @@ -0,0 +1,177 @@ +!!index array str + "R04" +!entry.R04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R04.unit.childsequence single int + 2 +!entry.R04.unit.connect array int + 1 + 23 +!entry.R04.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R04.unit.name single str + "default_name" +!entry.R04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 1.870246 0.985172 3.565192 + 0.660000 2.173733 4.102339 + 0.148000 0.179000 4.415000 + -0.631409 -0.305941 3.994092 + 0.510000 -0.153000 5.650000 + 1.529000 0.465000 6.231000 + 2.028169 1.187460 5.732328 + 1.801683 0.210165 7.169893 + -0.147000 -1.104000 6.300000 + -0.922262 -1.573529 5.853727 + 0.130417 -1.354115 7.238822 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R04" 1 25 1 "?" 0 +!entry.R04.unit.residuesPdbSequenceNumber array int + 1 +!entry.R04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R05.off b/share/off/ARG/R05.off new file mode 100644 index 0000000..4dc1489 --- /dev/null +++ b/share/off/ARG/R05.off @@ -0,0 +1,177 @@ +!!index array str + "R05" +!entry.R05.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R05.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R05.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R05.unit.childsequence single int + 2 +!entry.R05.unit.connect array int + 1 + 23 +!entry.R05.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R05.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R05.unit.name single str + "default_name" +!entry.R05.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.491983 2.129120 1.569226 + -0.816162 1.301519 2.448180 + 1.062000 1.347000 3.484000 + 2.117981 1.239532 3.237456 + 0.896970 2.314694 3.957914 + 0.692000 0.295000 4.427000 + 1.241607 -0.552110 4.414959 + -0.313000 0.387000 5.291000 + -1.054000 1.485000 5.333000 + -0.852135 2.250966 4.706630 + -1.817309 1.550877 5.991663 + -0.575000 -0.622000 6.111000 + -0.008985 -1.458057 6.075165 + -1.339894 -0.550058 6.767252 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R05.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R05.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R05" 1 25 1 "?" 0 +!entry.R05.unit.residuesPdbSequenceNumber array int + 1 +!entry.R05.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R05.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R06.off b/share/off/ARG/R06.off new file mode 100644 index 0000000..c167f1b --- /dev/null +++ b/share/off/ARG/R06.off @@ -0,0 +1,177 @@ +!!index array str + "R06" +!entry.R06.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R06.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R06.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R06.unit.childsequence single int + 2 +!entry.R06.unit.connect array int + 1 + 23 +!entry.R06.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R06.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R06.unit.name single str + "default_name" +!entry.R06.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 1.870246 0.985172 3.565192 + 0.660000 2.173733 4.102339 + 0.148000 0.179000 4.415000 + -0.784353 0.377256 4.748499 + 0.698000 -0.990000 4.726000 + 1.920000 -1.281000 4.303000 + 2.430280 -0.612158 3.744379 + 2.335305 -2.170741 4.541120 + 0.024000 -1.866000 5.459000 + -0.907240 -1.641198 5.779787 + 0.445285 -2.753871 5.693755 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R06.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R06.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R06" 1 25 1 "?" 0 +!entry.R06.unit.residuesPdbSequenceNumber array int + 1 +!entry.R06.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R06.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R07.off b/share/off/ARG/R07.off new file mode 100644 index 0000000..4dbc373 --- /dev/null +++ b/share/off/ARG/R07.off @@ -0,0 +1,177 @@ +!!index array str + "R07" +!entry.R07.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R07.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R07.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R07.unit.childsequence single int + 2 +!entry.R07.unit.connect array int + 1 + 23 +!entry.R07.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R07.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R07.unit.name single str + "default_name" +!entry.R07.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.496235 2.099591 4.162757 + 0.408850 0.323148 4.112581 + 2.263000 1.137000 3.624000 + 2.735040 1.215533 2.734719 + 2.997000 0.974000 4.720000 + 4.319000 0.920000 4.630000 + 4.764396 1.002855 3.727476 + 4.874568 0.795932 5.464727 + 2.407000 0.863000 5.902000 + 1.399564 0.903261 5.966030 + 2.967692 0.739321 6.733404 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R07.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R07.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R07" 1 25 1 "?" 0 +!entry.R07.unit.residuesPdbSequenceNumber array int + 1 +!entry.R07.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R07.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R08.off b/share/off/ARG/R08.off new file mode 100644 index 0000000..c43a414 --- /dev/null +++ b/share/off/ARG/R08.off @@ -0,0 +1,177 @@ +!!index array str + "R08" +!entry.R08.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R08.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R08.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R08.unit.childsequence single int + 2 +!entry.R08.unit.connect array int + 1 + 23 +!entry.R08.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R08.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R08.unit.name single str + "default_name" +!entry.R08.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.496235 2.099591 4.162757 + 0.408850 0.323148 4.112581 + 2.263000 1.137000 3.624000 + 2.768994 1.986894 3.420382 + 2.955000 0.033000 3.881000 + 4.281000 0.063000 3.866000 + 4.761146 0.926855 3.658617 + 4.804645 -0.778582 4.061840 + 2.321000 -1.099000 4.153000 + 1.310982 -1.118505 4.164533 + 2.850891 -1.936871 4.348174 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R08.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R08.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R08" 1 25 1 "?" 0 +!entry.R08.unit.residuesPdbSequenceNumber array int + 1 +!entry.R08.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R08.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R09.off b/share/off/ARG/R09.off new file mode 100644 index 0000000..9ae5851 --- /dev/null +++ b/share/off/ARG/R09.off @@ -0,0 +1,177 @@ +!!index array str + "R09" +!entry.R09.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R09.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R09.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R09.unit.childsequence single int + 2 +!entry.R09.unit.connect array int + 1 + 23 +!entry.R09.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R09.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R09.unit.name single str + "default_name" +!entry.R09.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.496235 2.099591 4.162757 + 0.408850 0.323148 4.112581 + 2.263000 1.137000 3.624000 + 2.681395 0.219436 3.677204 + 3.063000 2.197000 3.564000 + 2.546000 3.415000 3.492000 + 1.543335 3.534875 3.482697 + 3.157269 4.218177 3.446455 + 4.379000 2.034000 3.578000 + 4.769115 1.103821 3.634800 + 4.985390 2.840922 3.532468 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R09.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R09.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R09" 1 25 1 "?" 0 +!entry.R09.unit.residuesPdbSequenceNumber array int + 1 +!entry.R09.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R09.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R10.off b/share/off/ARG/R10.off new file mode 100644 index 0000000..85d8da6 --- /dev/null +++ b/share/off/ARG/R10.off @@ -0,0 +1,177 @@ +!!index array str + "R10" +!entry.R10.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R10.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R10.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R10.unit.childsequence single int + 2 +!entry.R10.unit.connect array int + 1 + 23 +!entry.R10.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R10.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R10.unit.name single str + "default_name" +!entry.R10.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.150519 -0.895845 1.920470 + 1.622690 -0.060148 1.369971 + 0.143000 1.225000 2.242000 + -0.939341 1.346689 2.184680 + 0.435295 1.064558 3.279899 + 0.822000 2.477000 1.712000 + 1.902202 2.344994 1.768288 + 0.528715 2.627058 0.672901 + 0.455000 3.665000 2.478000 + -0.184690 3.539114 3.249206 + 0.909000 4.888000 2.223000 + 1.749000 5.087000 1.218000 + 2.042705 4.307231 0.647482 + 2.092161 6.017919 1.027086 + 0.520000 5.908000 2.975000 + -0.121339 5.752011 3.739853 + 0.866217 6.836840 2.779310 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R10.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R10.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R10" 1 25 1 "?" 0 +!entry.R10.unit.residuesPdbSequenceNumber array int + 1 +!entry.R10.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R10.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R11.off b/share/off/ARG/R11.off new file mode 100644 index 0000000..3f316e1 --- /dev/null +++ b/share/off/ARG/R11.off @@ -0,0 +1,177 @@ +!!index array str + "R11" +!entry.R11.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R11.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R11.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R11.unit.childsequence single int + 2 +!entry.R11.unit.connect array int + 1 + 23 +!entry.R11.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R11.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R11.unit.name single str + "default_name" +!entry.R11.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.150519 -0.895845 1.920470 + 1.622690 -0.060148 1.369971 + 0.143000 1.225000 2.242000 + -0.939341 1.346689 2.184680 + 0.435295 1.064558 3.279899 + 0.822000 2.477000 1.712000 + 1.902202 2.344994 1.768288 + 0.528715 2.627058 0.672901 + 0.455000 3.665000 2.478000 + 1.075573 3.943381 3.224460 + -0.634000 4.392000 2.254000 + -1.469000 4.053000 1.281000 + -1.273896 3.241749 0.712143 + -2.296372 4.608050 1.113092 + -0.885000 5.457000 3.003000 + -0.246391 5.712105 3.743101 + -1.714146 6.008052 2.830480 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R11.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R11.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R11" 1 25 1 "?" 0 +!entry.R11.unit.residuesPdbSequenceNumber array int + 1 +!entry.R11.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R11.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R12.off b/share/off/ARG/R12.off new file mode 100644 index 0000000..36c1c7b --- /dev/null +++ b/share/off/ARG/R12.off @@ -0,0 +1,177 @@ +!!index array str + "R12" +!entry.R12.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R12.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R12.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R12.unit.childsequence single int + 2 +!entry.R12.unit.connect array int + 1 + 23 +!entry.R12.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R12.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R12.unit.name single str + "default_name" +!entry.R12.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.150519 -0.895845 1.920470 + 1.622690 -0.060148 1.369971 + 0.143000 1.225000 2.242000 + -0.939341 1.346689 2.184680 + 0.435295 1.064558 3.279899 + 0.822000 2.477000 1.712000 + 0.589789 2.584068 0.652734 + 0.443465 3.342788 2.255492 + 2.272000 2.423000 1.870000 + 2.653430 1.630526 2.366291 + 3.110000 3.344000 1.405000 + 2.640000 4.396000 0.749000 + 1.645369 4.494033 0.604463 + 3.279071 5.094651 0.396449 + 4.415000 3.210000 1.597000 + 4.768987 2.407007 2.097545 + 5.049363 3.911955 1.242391 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R12.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R12.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R12" 1 25 1 "?" 0 +!entry.R12.unit.residuesPdbSequenceNumber array int + 1 +!entry.R12.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R12.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R13.off b/share/off/ARG/R13.off new file mode 100644 index 0000000..a690d08 --- /dev/null +++ b/share/off/ARG/R13.off @@ -0,0 +1,177 @@ +!!index array str + "R13" +!entry.R13.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R13.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R13.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R13.unit.childsequence single int + 2 +!entry.R13.unit.connect array int + 1 + 23 +!entry.R13.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R13.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R13.unit.name single str + "default_name" +!entry.R13.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.150519 -0.895845 1.920470 + 1.622690 -0.060148 1.369971 + 0.143000 1.225000 2.242000 + -0.939341 1.346689 2.184680 + 0.435295 1.064558 3.279899 + 0.822000 2.477000 1.712000 + 0.589789 2.584068 0.652734 + 0.443465 3.342788 2.255492 + 2.272000 2.423000 1.870000 + 2.811918 2.097253 1.081212 + 2.916000 2.775000 2.978000 + 4.239000 2.692000 3.030000 + 4.753068 2.360937 2.226306 + 4.726269 2.960106 3.873508 + 2.237000 3.210000 4.030000 + 1.229667 3.273347 3.986234 + 2.730105 3.476844 4.870563 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R13.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R13.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R13" 1 25 1 "?" 0 +!entry.R13.unit.residuesPdbSequenceNumber array int + 1 +!entry.R13.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R13.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R14.off b/share/off/ARG/R14.off new file mode 100644 index 0000000..9031247 --- /dev/null +++ b/share/off/ARG/R14.off @@ -0,0 +1,177 @@ +!!index array str + "R14" +!entry.R14.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R14.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R14.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R14.unit.childsequence single int + 2 +!entry.R14.unit.connect array int + 1 + 23 +!entry.R14.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R14.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R14.unit.name single str + "default_name" +!entry.R14.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.338205 -0.031809 2.575940 + 2.475756 -0.749000 0.952535 + 2.575000 1.394000 0.990000 + 3.664403 1.368927 0.988576 + 2.214108 1.529599 -0.029623 + 2.134000 2.528000 1.797000 + 1.303131 3.016225 1.495169 + 2.754000 2.949000 2.894000 + 3.847000 2.329000 3.318000 + 4.205634 1.536700 2.804740 + 4.315768 2.651952 4.152731 + 2.280000 3.991000 3.564000 + 1.448171 4.461951 3.237021 + 2.753461 4.309306 4.397919 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R14.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R14.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R14" 1 25 1 "?" 0 +!entry.R14.unit.residuesPdbSequenceNumber array int + 1 +!entry.R14.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R14.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R15.off b/share/off/ARG/R15.off new file mode 100644 index 0000000..fead3a5 --- /dev/null +++ b/share/off/ARG/R15.off @@ -0,0 +1,177 @@ +!!index array str + "R15" +!entry.R15.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R15.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R15.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R15.unit.childsequence single int + 2 +!entry.R15.unit.connect array int + 1 + 23 +!entry.R15.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R15.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R15.unit.name single str + "default_name" +!entry.R15.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.338205 -0.031809 2.575940 + 2.475756 -0.749000 0.952535 + 2.575000 1.394000 0.990000 + 2.278826 1.493121 -0.053976 + 2.142334 2.210189 1.568702 + 4.030000 1.481000 1.074000 + 4.419862 1.940589 1.884305 + 4.862000 0.997000 0.157000 + 4.382000 0.388000 -0.918000 + 3.383724 0.293156 -1.037344 + 5.017021 0.021196 -1.612997 + 6.172000 1.123000 0.319000 + 6.533997 1.587599 1.139826 + 6.802067 0.754351 -0.379583 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R15.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R15.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R15" 1 25 1 "?" 0 +!entry.R15.unit.residuesPdbSequenceNumber array int + 1 +!entry.R15.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R15.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R16.off b/share/off/ARG/R16.off new file mode 100644 index 0000000..f2bb1fd --- /dev/null +++ b/share/off/ARG/R16.off @@ -0,0 +1,177 @@ +!!index array str + "R16" +!entry.R16.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R16.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R16.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R16.unit.childsequence single int + 2 +!entry.R16.unit.connect array int + 1 + 23 +!entry.R16.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R16.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R16.unit.name single str + "default_name" +!entry.R16.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.338205 -0.031809 2.575940 + 2.475756 -0.749000 0.952535 + 2.575000 1.394000 0.990000 + 2.278826 1.493121 -0.053976 + 2.142334 2.210189 1.568702 + 4.030000 1.481000 1.074000 + 4.518529 0.688319 1.464903 + 4.741000 2.529000 0.671000 + 4.129000 3.585000 0.153000 + 3.122910 3.589430 0.066068 + 4.671981 4.380339 -0.152657 + 6.061000 2.518000 0.787000 + 6.523530 1.711665 1.182650 + 6.598696 3.316390 0.479818 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R16.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R16.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R16" 1 25 1 "?" 0 +!entry.R16.unit.residuesPdbSequenceNumber array int + 1 +!entry.R16.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R16.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R17.off b/share/off/ARG/R17.off new file mode 100644 index 0000000..0618726 --- /dev/null +++ b/share/off/ARG/R17.off @@ -0,0 +1,177 @@ +!!index array str + "R17" +!entry.R17.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R17.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R17.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R17.unit.childsequence single int + 2 +!entry.R17.unit.connect array int + 1 + 23 +!entry.R17.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R17.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R17.unit.name single str + "default_name" +!entry.R17.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 3.592140 0.217653 3.005100 + 2.020854 0.883243 3.509035 + 2.196000 -1.188000 3.649000 + 1.337927 -1.224161 4.180237 + 2.960000 -2.274000 3.603000 + 4.092000 -2.259000 2.914000 + 4.370813 -1.420598 2.424981 + 4.670777 -3.086488 2.880864 + 2.589000 -3.372000 4.247000 + 1.725653 -3.378851 4.771628 + 3.171809 -4.196570 4.210614 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R17.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R17.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R17" 1 25 1 "?" 0 +!entry.R17.unit.residuesPdbSequenceNumber array int + 1 +!entry.R17.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R17.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R18.off b/share/off/ARG/R18.off new file mode 100644 index 0000000..7bd027e --- /dev/null +++ b/share/off/ARG/R18.off @@ -0,0 +1,177 @@ +!!index array str + "R18" +!entry.R18.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R18.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R18.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R18.unit.childsequence single int + 2 +!entry.R18.unit.connect array int + 1 + 23 +!entry.R18.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R18.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R18.unit.name single str + "default_name" +!entry.R18.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 3.592140 0.217653 3.005100 + 2.020854 0.883243 3.509035 + 2.196000 -1.188000 3.649000 + 1.793165 -1.924339 3.087451 + 2.404000 -1.417000 4.941000 + 2.083000 -2.592000 5.466000 + 1.680611 -3.310024 4.880921 + 2.242247 -2.763263 6.448918 + 2.932000 -0.471000 5.706000 + 3.175525 0.422837 5.303010 + 3.088862 -0.648887 6.688169 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R18.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R18.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R18" 1 25 1 "?" 0 +!entry.R18.unit.residuesPdbSequenceNumber array int + 1 +!entry.R18.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R18.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R19.off b/share/off/ARG/R19.off new file mode 100644 index 0000000..661c6a3 --- /dev/null +++ b/share/off/ARG/R19.off @@ -0,0 +1,177 @@ +!!index array str + "R19" +!entry.R19.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R19.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R19.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R19.unit.childsequence single int + 2 +!entry.R19.unit.connect array int + 1 + 23 +!entry.R19.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R19.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R19.unit.name single str + "default_name" +!entry.R19.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 2.082797 0.929451 3.488840 + 2.169534 -0.847447 3.457018 + 3.968000 0.138000 3.087000 + 4.467260 -0.734616 3.182343 + 4.665000 1.269000 3.068000 + 4.040000 2.431000 2.943000 + 3.033640 2.453439 2.862192 + 4.573201 3.289087 2.928837 + 5.986000 1.234000 3.175000 + 6.458569 0.346272 3.271258 + 6.513917 2.095393 3.160449 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R19.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R19.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R19" 1 25 1 "?" 0 +!entry.R19.unit.residuesPdbSequenceNumber array int + 1 +!entry.R19.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R19.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R20.off b/share/off/ARG/R20.off new file mode 100644 index 0000000..9e9cb54 --- /dev/null +++ b/share/off/ARG/R20.off @@ -0,0 +1,177 @@ +!!index array str + "R20" +!entry.R20.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R20.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R20.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R20.unit.childsequence single int + 2 +!entry.R20.unit.connect array int + 1 + 23 +!entry.R20.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R20.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R20.unit.name single str + "default_name" +!entry.R20.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 2.082797 0.929451 3.488840 + 2.169534 -0.847447 3.457018 + 3.968000 0.138000 3.087000 + 4.496320 0.180664 2.227426 + 4.629000 0.149000 4.239000 + 5.954000 0.214000 4.242000 + 6.456461 0.254775 3.366978 + 6.454448 0.222133 5.119670 + 3.966000 0.096000 5.386000 + 2.956893 0.047771 5.380849 + 4.473064 0.104769 6.259907 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R20.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R20.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R20" 1 25 1 "?" 0 +!entry.R20.unit.residuesPdbSequenceNumber array int + 1 +!entry.R20.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R20.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R21.off b/share/off/ARG/R21.off new file mode 100644 index 0000000..20bc586 --- /dev/null +++ b/share/off/ARG/R21.off @@ -0,0 +1,177 @@ +!!index array str + "R21" +!entry.R21.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R21.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R21.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R21.unit.childsequence single int + 2 +!entry.R21.unit.connect array int + 1 + 23 +!entry.R21.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R21.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R21.unit.name single str + "default_name" +!entry.R21.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 2.082797 0.929451 3.488840 + 2.169534 -0.847447 3.457018 + 3.968000 0.138000 3.087000 + 4.379783 1.051044 3.215817 + 4.772000 -0.918000 3.028000 + 4.264000 -2.130000 2.859000 + 3.264566 -2.248108 2.775478 + 4.878790 -2.930557 2.814739 + 6.084000 -0.758000 3.139000 + 6.467799 0.167630 3.267670 + 6.693546 -1.562553 3.093682 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R21.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R21.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R21" 1 25 1 "?" 0 +!entry.R21.unit.residuesPdbSequenceNumber array int + 1 +!entry.R21.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R21.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R22.off b/share/off/ARG/R22.off new file mode 100644 index 0000000..a23caca --- /dev/null +++ b/share/off/ARG/R22.off @@ -0,0 +1,177 @@ +!!index array str + "R22" +!entry.R22.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R22.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R22.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R22.unit.childsequence single int + 2 +!entry.R22.unit.connect array int + 1 + 23 +!entry.R22.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R22.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R22.unit.name single str + "default_name" +!entry.R22.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 2.104047 -0.808504 3.477174 + 3.601939 0.026203 3.002322 + 2.075000 1.263000 3.694000 + 2.561309 2.125924 3.497339 + 1.086000 1.280000 4.581000 + 0.427000 0.164000 4.862000 + 0.679199 -0.697698 4.399761 + -0.324566 0.180965 5.537040 + 0.757000 2.414000 5.184000 + 1.260594 3.262496 4.966983 + 0.004574 2.424185 5.858282 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R22.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R22.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R22" 1 25 1 "?" 0 +!entry.R22.unit.residuesPdbSequenceNumber array int + 1 +!entry.R22.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R22.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R23.off b/share/off/ARG/R23.off new file mode 100644 index 0000000..583e6f5 --- /dev/null +++ b/share/off/ARG/R23.off @@ -0,0 +1,177 @@ +!!index array str + "R23" +!entry.R23.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R23.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R23.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R23.unit.childsequence single int + 2 +!entry.R23.unit.connect array int + 1 + 23 +!entry.R23.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R23.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R23.unit.name single str + "default_name" +!entry.R23.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 2.104047 -0.808504 3.477174 + 3.601939 0.026203 3.002322 + 2.075000 1.263000 3.694000 + 1.601153 1.976854 3.159499 + 2.262000 1.463000 4.994000 + 1.829000 2.581000 5.561000 + 1.358076 3.277598 5.001738 + 1.972479 2.730853 6.549825 + 2.882000 0.546000 5.724000 + 3.210705 -0.304325 5.288628 + 3.022217 0.701654 6.712441 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R23.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R23.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R23" 1 25 1 "?" 0 +!entry.R23.unit.residuesPdbSequenceNumber array int + 1 +!entry.R23.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R23.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R24.off b/share/off/ARG/R24.off new file mode 100644 index 0000000..4264e6e --- /dev/null +++ b/share/off/ARG/R24.off @@ -0,0 +1,177 @@ +!!index array str + "R24" +!entry.R24.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R24.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R24.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R24.unit.childsequence single int + 2 +!entry.R24.unit.connect array int + 1 + 23 +!entry.R24.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R24.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R24.unit.name single str + "default_name" +!entry.R24.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 2.104047 -0.808504 3.477174 + 3.601939 0.026203 3.002322 + 2.075000 1.263000 3.694000 + 1.601153 1.976854 3.159499 + 2.262000 1.463000 4.994000 + 1.829000 2.581000 5.561000 + 1.358076 3.277598 5.001738 + 1.972479 2.730853 6.549825 + 2.882000 0.546000 5.724000 + 3.210705 -0.304325 5.288628 + 3.022217 0.701654 6.712441 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R24.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R24.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R24" 1 25 1 "?" 0 +!entry.R24.unit.residuesPdbSequenceNumber array int + 1 +!entry.R24.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R24.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R25.off b/share/off/ARG/R25.off new file mode 100644 index 0000000..b4ddf5f --- /dev/null +++ b/share/off/ARG/R25.off @@ -0,0 +1,177 @@ +!!index array str + "R25" +!entry.R25.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R25.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R25.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R25.unit.childsequence single int + 2 +!entry.R25.unit.connect array int + 1 + 23 +!entry.R25.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R25.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R25.unit.name single str + "default_name" +!entry.R25.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.622823 0.059818 1.369769 + 0.150928 0.895867 1.920470 + 0.143000 -1.225000 2.242000 + -0.945461 -1.276207 2.288750 + 0.526339 -2.112325 1.737899 + 0.708000 -1.159000 3.652000 + 0.485825 -2.093368 4.166805 + 1.788219 -1.024044 3.595652 + 0.138000 -0.055000 4.419000 + -0.599259 0.479462 3.982413 + 0.528000 0.284000 5.643000 + 1.493000 -0.398000 6.244000 + 1.929474 -1.174801 5.768748 + 1.787192 -0.137695 7.174866 + -0.049000 1.304000 6.263000 + -0.784096 1.821166 5.801673 + 0.249610 1.559787 7.193758 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R25.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R25.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R25" 1 25 1 "?" 0 +!entry.R25.unit.residuesPdbSequenceNumber array int + 1 +!entry.R25.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R25.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R26.off b/share/off/ARG/R26.off new file mode 100644 index 0000000..ae9f0e8 --- /dev/null +++ b/share/off/ARG/R26.off @@ -0,0 +1,177 @@ +!!index array str + "R26" +!entry.R26.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R26.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R26.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R26.unit.childsequence single int + 2 +!entry.R26.unit.connect array int + 1 + 23 +!entry.R26.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R26.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R26.unit.name single str + "default_name" +!entry.R26.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.622823 0.059818 1.369769 + 0.150928 0.895867 1.920470 + 0.143000 -1.225000 2.242000 + -0.945461 -1.276207 2.288750 + 0.526339 -2.112325 1.737899 + 0.708000 -1.159000 3.652000 + 1.794804 -1.102787 3.596087 + 0.323798 -0.267132 4.147199 + 0.340000 -2.329000 4.444000 + -0.476617 -2.250809 5.032924 + 1.009000 -3.477000 4.436000 + 2.085000 -3.612000 3.674000 + 2.393770 -2.840381 3.100364 + 2.591282 -4.486347 3.670260 + 0.599000 -4.488000 5.190000 + -0.221761 -4.381630 5.769384 + 1.109799 -5.359737 5.182000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R26.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R26.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R26" 1 25 1 "?" 0 +!entry.R26.unit.residuesPdbSequenceNumber array int + 1 +!entry.R26.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R26.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R27.off b/share/off/ARG/R27.off new file mode 100644 index 0000000..1feb64c --- /dev/null +++ b/share/off/ARG/R27.off @@ -0,0 +1,177 @@ +!!index array str + "R27" +!entry.R27.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R27.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R27.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R27.unit.childsequence single int + 2 +!entry.R27.unit.connect array int + 1 + 23 +!entry.R27.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.R27.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.R27.unit.name single str + "default_name" +!entry.R27.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.622823 0.059818 1.369769 + 0.150928 0.895867 1.920470 + 0.143000 -1.225000 2.242000 + -0.945461 -1.276207 2.288750 + 0.526339 -2.112325 1.737899 + 0.708000 -1.159000 3.652000 + 1.794804 -1.102787 3.596087 + 0.323798 -0.267132 4.147199 + 0.340000 -2.329000 4.444000 + -0.227284 -3.032488 3.993330 + 0.704000 -2.521000 5.708000 + 1.449000 -1.616000 6.327000 + 1.738081 -0.782604 5.835395 + 1.724467 -1.764231 7.287710 + 0.322000 -3.616000 6.349000 + -0.246515 -4.303104 5.874313 + 0.600533 -3.758344 7.309761 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.R27.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.R27.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "R27" 1 25 1 "?" 0 +!entry.R27.unit.residuesPdbSequenceNumber array int + 1 +!entry.R27.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R27.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ARG/R28.off b/share/off/ARG/R28.off new file mode 100644 index 0000000..19bf149 --- /dev/null +++ b/share/off/ARG/R28.off @@ -0,0 +1,177 @@ +!!index array str + "R28" +!entry.R28.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.263700 + "HA" "H1" 0 1 131075 4 1 0.156000 + "CB" "CT" 0 1 131075 5 6 -0.000700 + "HB2" "HC" 0 1 131075 6 1 0.032700 + "HB3" "HC" 0 1 131075 7 1 0.032700 + "CG" "CT" 0 1 131075 8 6 0.039000 + "HG2" "HC" 0 1 131075 9 1 0.028500 + "HG3" "HC" 0 1 131075 10 1 0.028500 + "CD" "CT" 0 1 131075 11 6 0.048600 + "HD2" "H1" 0 1 131075 12 1 0.068700 + "HD3" "H1" 0 1 131075 13 1 0.068700 + "NE" "N2" 0 1 131075 14 7 -0.529500 + "HE" "H" 0 1 131075 15 1 0.345600 + "CZ" "CA" 0 1 131075 16 6 0.807600 + "NH1" "N2" 0 1 131075 17 7 -0.862700 + "HH11" "H" 0 1 131075 18 1 0.447800 + "HH12" "H" 0 1 131075 19 1 0.447800 + "NH2" "N2" 0 1 131075 20 7 -0.862700 + "HH21" "H" 0 1 131075 21 1 0.447800 + "HH22" "H" 0 1 131075 22 1 0.447800 + "C" "C" 0 1 131075 23 6 0.734100 + "O" "O" 0 1 131075 24 8 -0.589400 +!entry.R28.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "H1" 0 -1 0.0 + "HD3" "H1" 0 -1 0.0 + "NE" "N2" 0 -1 0.0 + "HE" "H" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "NH1" "N2" 0 -1 0.0 + "HH11" "H" 0 -1 0.0 + "HH12" "H" 0 -1 0.0 + "NH2" "N2" 0 -1 0.0 + "HH21" "H" 0 -1 0.0 + "HH22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.R28.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.R28.unit.childsequence single int + 2 +!entry.R28.unit.connect array int + 1 + 23 +!entry.R28.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 17 18 17 + 17 19 17 + 16 17 17 + 16 20 17 + 14 15 17 + 14 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 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/dev/null +++ b/share/off/ASH/script.sh~ @@ -0,0 +1,38 @@ +#!/usr/bin/env bash + +END=5; +str=""; +for i in $(seq 1 $END); +do + +added=$(( $i + $END )) + +if [ $added -lt 10 ] +then +str="D0"; +else +str="D"; +fi + +echo "$str"; +val="$i"; + +regexSearch="$str$val"; + + + +regexReplace="$str$added"; + +filename="$regexReplace.off"; + +echo "added: $added"; +echo "regexSearch: $regexSearch"; +echo "regexReplace: $regexReplace"; +echo "fileName: $filename"; +sed -i "s/$regexSearch/$regexReplace/g" "$filename"; + + +done + + + diff --git a/share/off/ASN/N01.off b/share/off/ASN/N01.off new file mode 100644 index 0000000..822cc20 --- /dev/null +++ b/share/off/ASN/N01.off @@ -0,0 +1,117 @@ +!!index array str + "N01" +!entry.N01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 0.014300 + "HA" "H1" 0 1 131075 4 1 0.104800 + "CB" "CT" 0 1 131075 5 6 -0.204100 + "HB2" "HC" 0 1 131075 6 1 0.079700 + "HB3" "HC" 0 1 131075 7 1 0.079700 + "CG" "C" 0 1 131075 8 6 0.713000 + "OD1" "O" 0 1 131075 9 8 -0.593100 + "ND2" "N" 0 1 131075 10 7 -0.919100 + "HD21" "H" 0 1 131075 11 1 0.419600 + "HD22" "H" 0 1 131075 12 1 0.419600 + "C" "C" 0 1 131075 13 6 0.597300 + "O" "O" 0 1 131075 14 8 -0.567900 +!entry.N01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C" 0 -1 0.0 + "OD1" "O" 0 -1 0.0 + "ND2" "N" 0 -1 0.0 + "HD21" "H" 0 -1 0.0 + "HD22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.N01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.N01.unit.childsequence single int + 2 +!entry.N01.unit.connect array int + 1 + 13 +!entry.N01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 13 17 + 3 5 17 + 5 6 17 + 5 7 17 + 5 8 17 + 8 9 17 + 8 10 17 + 10 12 17 + 10 11 17 + 13 14 17 +!entry.N01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 +!entry.N01.unit.name single str + "" +!entry.N01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.111000 -0.850000 1.966000 + 1.621000 -0.098000 1.400000 + 0.186000 1.268000 2.186000 + -0.108000 2.299000 1.582000 + 0.216000 1.195000 3.511000 + -0.008000 2.010000 4.064000 + 0.463000 0.325000 3.960000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.N01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.N01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "N01" 1 15 1 "?" 0 +!entry.N01.unit.residuesPdbSequenceNumber array int + 1 +!entry.N01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.N01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ASN/N02.off b/share/off/ASN/N02.off new file mode 100644 index 0000000..8363db5 --- /dev/null +++ b/share/off/ASN/N02.off @@ -0,0 +1,117 @@ +!!index array str + "N02" +!entry.N02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 0.014300 + "HA" "H1" 0 1 131075 4 1 0.104800 + "CB" "CT" 0 1 131075 5 6 -0.204100 + "HB2" "HC" 0 1 131075 6 1 0.079700 + "HB3" "HC" 0 1 131075 7 1 0.079700 + "CG" "C" 0 1 131075 8 6 0.713000 + "OD1" "O" 0 1 131075 9 8 -0.593100 + "ND2" "N" 0 1 131075 10 7 -0.919100 + "HD21" "H" 0 1 131075 11 1 0.419600 + "HD22" "H" 0 1 131075 12 1 0.419600 + "C" "C" 0 1 131075 13 6 0.597300 + "O" "O" 0 1 131075 14 8 -0.567900 +!entry.N02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C" 0 -1 0.0 + "OD1" "O" 0 -1 0.0 + "ND2" "N" 0 -1 0.0 + "HD21" "H" 0 -1 0.0 + "HD22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.N02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.N02.unit.childsequence single int + 2 +!entry.N02.unit.connect array int + 1 + 13 +!entry.N02.unit.connectivity table int atom1x int atom2x int flags + 13 14 17 + 10 12 17 + 10 11 17 + 8 9 17 + 8 10 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 13 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.N02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.N02.unit.name single str + "" +!entry.N02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.111529 -0.850054 1.966336 + 1.621013 -0.097676 1.399461 + 0.186000 1.268000 2.186000 + 0.789000 2.318000 1.966000 + -0.792000 1.175000 3.077000 + -1.066542 1.989126 3.608071 + -1.257391 0.290514 3.220545 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.N02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.N02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "N02" 1 15 1 "?" 0 +!entry.N02.unit.residuesPdbSequenceNumber array int + 1 +!entry.N02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.N02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ASN/N03.off b/share/off/ASN/N03.off new file mode 100644 index 0000000..fb79cd7 --- /dev/null +++ b/share/off/ASN/N03.off @@ -0,0 +1,117 @@ +!!index array str + "N03" +!entry.N03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 0.014300 + "HA" "H1" 0 1 131075 4 1 0.104800 + "CB" "CT" 0 1 131075 5 6 -0.204100 + "HB2" "HC" 0 1 131075 6 1 0.079700 + "HB3" "HC" 0 1 131075 7 1 0.079700 + "CG" "C" 0 1 131075 8 6 0.713000 + "OD1" "O" 0 1 131075 9 8 -0.593100 + "ND2" "N" 0 1 131075 10 7 -0.919100 + "HD21" "H" 0 1 131075 11 1 0.419600 + "HD22" "H" 0 1 131075 12 1 0.419600 + "C" "C" 0 1 131075 13 6 0.597300 + "O" "O" 0 1 131075 14 8 -0.567900 +!entry.N03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C" 0 -1 0.0 + "OD1" "O" 0 -1 0.0 + "ND2" "N" 0 -1 0.0 + "HD21" "H" 0 -1 0.0 + "HD22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.N03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.N03.unit.childsequence single int + 2 +!entry.N03.unit.connect array int + 1 + 13 +!entry.N03.unit.connectivity table int atom1x int atom2x int flags + 13 14 17 + 10 12 17 + 10 11 17 + 8 9 17 + 8 10 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 13 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.N03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.N03.unit.name single str + "" +!entry.N03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.112403 -0.850141 1.966890 + 1.621033 -0.097142 1.398571 + 0.186000 1.268000 2.186000 + -0.499000 1.226000 3.207000 + 0.659000 2.402000 1.684000 + 0.456642 3.277945 2.144414 + 1.218724 2.383745 0.843830 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.N03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.N03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "N03" 1 15 1 "?" 0 +!entry.N03.unit.residuesPdbSequenceNumber array int + 1 +!entry.N03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.N03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ASN/N04.off b/share/off/ASN/N04.off new file mode 100644 index 0000000..e44103e --- /dev/null +++ b/share/off/ASN/N04.off @@ -0,0 +1,117 @@ +!!index array str + "N04" +!entry.N04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 0.014300 + "HA" "H1" 0 1 131075 4 1 0.104800 + "CB" "CT" 0 1 131075 5 6 -0.204100 + "HB2" "HC" 0 1 131075 6 1 0.079700 + "HB3" "HC" 0 1 131075 7 1 0.079700 + "CG" "C" 0 1 131075 8 6 0.713000 + "OD1" "O" 0 1 131075 9 8 -0.593100 + "ND2" "N" 0 1 131075 10 7 -0.919100 + "HD21" "H" 0 1 131075 11 1 0.419600 + "HD22" "H" 0 1 131075 12 1 0.419600 + "C" "C" 0 1 131075 13 6 0.597300 + "O" "O" 0 1 131075 14 8 -0.567900 +!entry.N04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C" 0 -1 0.0 + "OD1" "O" 0 -1 0.0 + "ND2" "N" 0 -1 0.0 + "HD21" "H" 0 -1 0.0 + "HD22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.N04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.N04.unit.childsequence single int + 2 +!entry.N04.unit.connect array int + 1 + 13 +!entry.N04.unit.connectivity table int atom1x int atom2x int flags + 13 14 17 + 10 12 17 + 10 11 17 + 8 9 17 + 8 10 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 13 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.N04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.N04.unit.name single str + "" +!entry.N04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.084753 0.829157 1.977141 + 0.257937 -0.940386 1.908682 + 2.044000 0.146000 1.491000 + 2.741000 -0.129000 0.516000 + 2.550000 0.583000 2.638000 + 3.548713 0.699165 2.734374 + 1.933985 0.796891 3.408900 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.N04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.N04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "N04" 1 15 1 "?" 0 +!entry.N04.unit.residuesPdbSequenceNumber array int + 1 +!entry.N04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.N04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ASN/N05.off b/share/off/ASN/N05.off new file mode 100644 index 0000000..5bb97bb --- /dev/null +++ b/share/off/ASN/N05.off @@ -0,0 +1,117 @@ +!!index array str + "N05" +!entry.N05.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 0.014300 + "HA" "H1" 0 1 131075 4 1 0.104800 + "CB" "CT" 0 1 131075 5 6 -0.204100 + "HB2" "HC" 0 1 131075 6 1 0.079700 + "HB3" "HC" 0 1 131075 7 1 0.079700 + "CG" "C" 0 1 131075 8 6 0.713000 + "OD1" "O" 0 1 131075 9 8 -0.593100 + "ND2" "N" 0 1 131075 10 7 -0.919100 + "HD21" "H" 0 1 131075 11 1 0.419600 + "HD22" "H" 0 1 131075 12 1 0.419600 + "C" "C" 0 1 131075 13 6 0.597300 + "O" "O" 0 1 131075 14 8 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"CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O" 0 -1 0.0 + "OE2" "OH" 0 -1 0.0 + "HE2" "HO" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.E12.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E12.unit.childsequence single int + 2 +!entry.E12.unit.connect array int + 1 + 15 +!entry.E12.unit.connectivity table int atom1x int atom2x int flags + 15 16 1 + 13 14 1 + 11 12 1 + 11 13 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 15 1 + 1 2 1 + 1 3 1 +!entry.E12.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.E12.unit.name single str + "" +!entry.E12.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 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0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLH/E13.off b/share/off/GLH/E13.off new file mode 100644 index 0000000..c2936be --- /dev/null +++ b/share/off/GLH/E13.off @@ -0,0 +1,129 @@ +!!index array str + "E13" +!entry.E13.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 0.014500 + "HA" "H1" 0 1 131072 4 1 0.077900 + "CB" "CT" 0 1 131072 5 6 -0.007100 + "HB2" "HC" 0 1 131072 6 1 0.025600 + "HB3" "HC" 0 1 131072 7 1 0.025600 + "CG" "CT" 0 1 131072 8 6 -0.017400 + "HG2" "HC" 0 1 131072 9 1 0.043000 + "HG3" "HC" 0 1 131072 10 1 0.043000 + "CD" "C" 0 1 131072 11 6 0.680100 + "OE1" "O" 0 1 131072 12 8 -0.583800 + "OE2" "OH" 0 1 131072 13 8 -0.651100 + "HE2" "HO" 0 1 131072 14 1 0.464100 + "C" "C" 0 1 131072 15 6 0.597300 + "O" "O" 0 1 131072 16 8 -0.567900 +!entry.E13.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O" 0 -1 0.0 + "OE2" "OH" 0 -1 0.0 + "HE2" "HO" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.E13.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E13.unit.childsequence single int + 2 +!entry.E13.unit.connect array int + 1 + 15 +!entry.E13.unit.connectivity table int atom1x int atom2x int flags + 15 16 1 + 13 14 1 + 11 12 1 + 11 13 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 15 1 + 1 2 1 + 1 3 1 +!entry.E13.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.E13.unit.name single str + "" +!entry.E13.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 1.622489 0.060011 1.369446 + 0.151000 0.896024 1.919842 + 0.143000 -1.225000 2.243000 + -0.945555 -1.269134 2.277667 + 0.525535 -2.105289 1.726417 + 0.692000 -1.190000 3.655000 + 1.663000 -0.443000 3.897000 + 0.151000 -1.910000 4.521000 + 0.596836 -1.788913 5.362527 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.E13.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 15 0 0 0 0 +!entry.E13.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "E13" 1 17 1 "p" 0 +!entry.E13.unit.residuesPdbSequenceNumber array int + 1 +!entry.E13.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E13.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLH/E14.off b/share/off/GLH/E14.off new file mode 100644 index 0000000..c2a346a --- /dev/null +++ b/share/off/GLH/E14.off @@ -0,0 +1,129 @@ +!!index array str + "E14" +!entry.E14.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 0.014500 + "HA" "H1" 0 1 131072 4 1 0.077900 + "CB" "CT" 0 1 131072 5 6 -0.007100 + "HB2" "HC" 0 1 131072 6 1 0.025600 + "HB3" "HC" 0 1 131072 7 1 0.025600 + "CG" "CT" 0 1 131072 8 6 -0.017400 + "HG2" "HC" 0 1 131072 9 1 0.043000 + "HG3" "HC" 0 1 131072 10 1 0.043000 + "CD" "C" 0 1 131072 11 6 0.680100 + "OE1" "O" 0 1 131072 12 8 -0.583800 + "OE2" "OH" 0 1 131072 13 8 -0.651100 + "HE2" "HO" 0 1 131072 14 1 0.464100 + "C" "C" 0 1 131072 15 6 0.597300 + "O" "O" 0 1 131072 16 8 -0.567900 +!entry.E14.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O" 0 -1 0.0 + "OE2" "OH" 0 -1 0.0 + "HE2" "HO" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.E14.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E14.unit.childsequence single int + 2 +!entry.E14.unit.connect array int + 1 + 15 +!entry.E14.unit.connectivity table int atom1x int atom2x int flags + 15 16 1 + 13 14 1 + 11 12 1 + 11 13 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 15 1 + 1 2 1 + 1 3 1 +!entry.E14.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.E14.unit.name single str + "" +!entry.E14.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 1.605274 0.203732 1.376036 + 0.039320 0.813520 1.961767 + 0.308000 -1.304000 2.181000 + 0.502183 -2.126090 1.492115 + 1.020448 -1.345075 3.004911 + -1.102000 -1.424000 2.726000 + -1.901000 -0.487000 2.518000 + -1.408000 -2.456000 3.359000 + -2.323127 -2.398074 3.643228 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.E14.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 15 0 0 0 0 +!entry.E14.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "E14" 1 17 1 "p" 0 +!entry.E14.unit.residuesPdbSequenceNumber array int + 1 +!entry.E14.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E14.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLH/renamescript.sh b/share/off/GLH/renamescript.sh new file mode 100644 index 0000000..b5dbd13 --- /dev/null +++ b/share/off/GLH/renamescript.sh @@ -0,0 +1,48 @@ +#!/usr/bin/env bash + +END=7; +filestr=""; +searchstr=""; +acid="E"; +for i in $(seq 1 $END); +do + +added=$(( $i + $END )) + +if [ $added -lt 10 ] +then +filestr=$acid"0"; +else +filestr="$acid"; +fi + +if [ $i -lt 10 ] +then +searchstr=$acid"0"; +else +searchstr="$acid"; +fi + +echo "$searchstr"; +echo "$filestr"; + +val="$i"; + +regexSearch="$searchstr$val"; + + + +regexReplace="$filestr$added"; + +filename="$regexReplace.off"; + +echo "added: $added"; +echo "regexSearch: $regexSearch"; +echo "regexReplace: $regexReplace"; +echo "fileName: $filename"; +sed -i "s/$regexSearch/$regexReplace/g" "$filename"; + + +done + + diff --git a/share/off/GLN/Q01.off b/share/off/GLN/Q01.off new file mode 100644 index 0000000..992994d --- /dev/null +++ b/share/off/GLN/Q01.off @@ -0,0 +1,135 @@ +!!index array str + "Q01" +!entry.Q01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.003100 + "HA" "H1" 0 1 131075 4 1 0.085000 + "CB" "CT" 0 1 131075 5 6 -0.003600 + "HB2" "HC" 0 1 131075 6 1 0.017100 + "HB3" "HC" 0 1 131075 7 1 0.017100 + "CG" "CT" 0 1 131075 8 6 -0.064500 + "HG2" "HC" 0 1 131075 9 1 0.035200 + "HG3" "HC" 0 1 131075 10 1 0.035200 + "CD" "C" 0 1 131075 11 6 0.695100 + "OE1" "O" 0 1 131075 12 8 -0.608600 + "NE2" "N" 0 1 131075 13 7 -0.940700 + "HE21" "H" 0 1 131075 14 2 0.425100 + "HE22" "H" 0 1 131075 15 2 0.425100 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.Q01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O" 0 -1 0.0 + "NE2" "N" 0 -1 0.0 + "HE21" "H" 0 -1 0.0 + "HE22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.Q01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Q01.unit.childsequence single int + 2 +!entry.Q01.unit.connect array int + 1 + 16 +!entry.Q01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 16 17 + 3 5 17 + 5 7 17 + 5 6 17 + 5 8 17 + 8 9 17 + 8 10 17 + 8 11 17 + 11 12 17 + 11 13 17 + 13 15 17 + 13 14 17 + 16 17 17 +!entry.Q01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 +!entry.Q01.unit.name single str + "" +!entry.Q01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.278000 2.204000 + 0.701000 2.117000 1.678000 + -0.834000 1.421000 2.251000 + 0.791000 1.240000 3.618000 + 0.973000 0.169000 4.196000 + 1.055000 2.415000 4.180000 + 1.420000 2.451000 5.121000 + 0.889000 3.267000 3.664000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.Q01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.Q01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "Q01" 1 18 1 "?" 0 +!entry.Q01.unit.residuesPdbSequenceNumber array int + 1 +!entry.Q01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Q01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLN/Q02.off b/share/off/GLN/Q02.off new file mode 100644 index 0000000..b739369 --- /dev/null +++ b/share/off/GLN/Q02.off @@ -0,0 +1,135 @@ +!!index array str + "Q02" +!entry.Q02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.003100 + "HA" "H1" 0 1 131075 4 1 0.085000 + "CB" "CT" 0 1 131075 5 6 -0.003600 + "HB2" "HC" 0 1 131075 6 1 0.017100 + "HB3" "HC" 0 1 131075 7 1 0.017100 + "CG" "CT" 0 1 131075 8 6 -0.064500 + "HG2" "HC" 0 1 131075 9 1 0.035200 + "HG3" "HC" 0 1 131075 10 1 0.035200 + "CD" "C" 0 1 131075 11 6 0.695100 + "OE1" "O" 0 1 131075 12 8 -0.608600 + "NE2" "N" 0 1 131075 13 7 -0.940700 + "HE21" "H" 0 1 131075 14 2 0.425100 + "HE22" "H" 0 1 131075 15 2 0.425100 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.Q02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O" 0 -1 0.0 + "NE2" "N" 0 -1 0.0 + "HE21" "H" 0 -1 0.0 + "HE22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.Q02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Q02.unit.childsequence single int + 2 +!entry.Q02.unit.connect array int + 1 + 16 +!entry.Q02.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 13 15 17 + 13 14 17 + 11 12 17 + 11 13 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.Q02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.Q02.unit.name single str + "" +!entry.Q02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.106755 -0.866518 1.936643 + 1.618317 -0.115241 1.371410 + 0.205000 1.258000 2.219000 + -0.874483 1.406920 2.206276 + 0.541517 1.125101 3.247665 + 0.871000 2.494000 1.648000 + 2.027000 2.450000 1.228000 + 0.140000 3.603000 1.629000 + 0.532602 4.457086 1.259674 + -0.805054 3.587588 1.984459 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.Q02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.Q02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "Q02" 1 18 1 "?" 0 +!entry.Q02.unit.residuesPdbSequenceNumber array int + 1 +!entry.Q02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Q02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLN/Q03.off b/share/off/GLN/Q03.off new file mode 100644 index 0000000..8f687ab --- /dev/null +++ b/share/off/GLN/Q03.off @@ -0,0 +1,135 @@ +!!index array str + "Q03" +!entry.Q03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.003100 + "HA" "H1" 0 1 131075 4 1 0.085000 + "CB" "CT" 0 1 131075 5 6 -0.003600 + "HB2" "HC" 0 1 131075 6 1 0.017100 + "HB3" "HC" 0 1 131075 7 1 0.017100 + "CG" "CT" 0 1 131075 8 6 -0.064500 + "HG2" "HC" 0 1 131075 9 1 0.035200 + "HG3" "HC" 0 1 131075 10 1 0.035200 + "CD" "C" 0 1 131075 11 6 0.695100 + "OE1" "O" 0 1 131075 12 8 -0.608600 + "NE2" "N" 0 1 131075 13 7 -0.940700 + "HE21" "H" 0 1 131075 14 2 0.425100 + "HE22" "H" 0 1 131075 15 2 0.425100 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.Q03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O" 0 -1 0.0 + "NE2" "N" 0 -1 0.0 + "HE21" "H" 0 -1 0.0 + "HE22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.Q03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Q03.unit.childsequence single int + 2 +!entry.Q03.unit.connect array int + 1 + 16 +!entry.Q03.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 13 15 17 + 13 14 17 + 11 12 17 + 11 13 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.Q03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.Q03.unit.name single str + "" +!entry.Q03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098575 0.860743 1.939499 + 0.185442 -0.916933 1.907160 + 2.051000 0.072000 1.529000 + 2.477169 -0.788256 1.013285 + 2.387969 0.989379 1.045342 + 2.545000 0.071000 2.962000 + 1.752000 0.016000 3.902000 + 3.861000 0.130000 3.133000 + 4.246591 0.132472 4.066443 + 4.470392 0.172715 2.328928 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.Q03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.Q03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "Q03" 1 18 1 "?" 0 +!entry.Q03.unit.residuesPdbSequenceNumber array int + 1 +!entry.Q03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Q03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLN/Q04.off b/share/off/GLN/Q04.off new file mode 100644 index 0000000..986d89e --- /dev/null +++ b/share/off/GLN/Q04.off @@ -0,0 +1,135 @@ +!!index array str + "Q04" +!entry.Q04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.003100 + "HA" "H1" 0 1 131075 4 1 0.085000 + "CB" "CT" 0 1 131075 5 6 -0.003600 + "HB2" "HC" 0 1 131075 6 1 0.017100 + "HB3" "HC" 0 1 131075 7 1 0.017100 + "CG" "CT" 0 1 131075 8 6 -0.064500 + "HG2" "HC" 0 1 131075 9 1 0.035200 + "HG3" "HC" 0 1 131075 10 1 0.035200 + "CD" "C" 0 1 131075 11 6 0.695100 + "OE1" "O" 0 1 131075 12 8 -0.608600 + "NE2" "N" 0 1 131075 13 7 -0.940700 + "HE21" "H" 0 1 131075 14 2 0.425100 + "HE22" "H" 0 1 131075 15 2 0.425100 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.Q04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O" 0 -1 0.0 + "NE2" "N" 0 -1 0.0 + "HE21" "H" 0 -1 0.0 + "HE22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.Q04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Q04.unit.childsequence single int + 2 +!entry.Q04.unit.connect array int + 1 + 16 +!entry.Q04.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 13 15 17 + 13 14 17 + 11 12 17 + 11 13 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.Q04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.Q04.unit.name single str + "" +!entry.Q04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098575 0.860743 1.939499 + 0.185442 -0.916933 1.907160 + 2.051000 0.072000 1.529000 + 2.341953 -0.030272 2.574232 + 2.477358 -0.748506 0.951032 + 2.607000 1.379000 0.997000 + 2.277000 2.454000 1.498000 + 3.455000 1.289000 -0.021000 + 3.856530 2.127372 -0.415852 + 3.694392 0.382665 -0.396453 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.Q04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.Q04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "Q04" 1 18 1 "?" 0 +!entry.Q04.unit.residuesPdbSequenceNumber array int + 1 +!entry.Q04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Q04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLN/Q05.off b/share/off/GLN/Q05.off new file mode 100644 index 0000000..074e29d --- /dev/null +++ b/share/off/GLN/Q05.off @@ -0,0 +1,135 @@ +!!index array str + "Q05" +!entry.Q05.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.003100 + "HA" "H1" 0 1 131075 4 1 0.085000 + "CB" "CT" 0 1 131075 5 6 -0.003600 + "HB2" "HC" 0 1 131075 6 1 0.017100 + "HB3" "HC" 0 1 131075 7 1 0.017100 + "CG" "CT" 0 1 131075 8 6 -0.064500 + "HG2" "HC" 0 1 131075 9 1 0.035200 + "HG3" "HC" 0 1 131075 10 1 0.035200 + "CD" "C" 0 1 131075 11 6 0.695100 + "OE1" "O" 0 1 131075 12 8 -0.608600 + "NE2" "N" 0 1 131075 13 7 -0.940700 + "HE21" "H" 0 1 131075 14 2 0.425100 + "HE22" "H" 0 1 131075 15 2 0.425100 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.Q05.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O" 0 -1 0.0 + "NE2" "N" 0 -1 0.0 + "HE21" "H" 0 -1 0.0 + "HE22" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.Q05.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Q05.unit.childsequence single int + 2 +!entry.Q05.unit.connect array int + 1 + 16 +!entry.Q05.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 13 15 17 + 13 14 17 + 11 12 17 + 11 13 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.Q05.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.Q05.unit.name single str + "" +!entry.Q05.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.622783 0.060096 1.369341 + 0.150842 0.896053 1.920059 + 0.143000 -1.225000 2.243000 + -0.944253 -1.279342 2.293499 + 0.528466 -2.113314 1.741630 + 0.692000 -1.190000 3.655000 + 1.050000 -0.130000 4.167000 + 0.758000 -2.354000 4.291000 + 1.115765 -2.391130 5.234731 + 0.450711 -3.197220 3.828107 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.Q05.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.Q05.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "Q05" 1 18 1 "?" 0 +!entry.Q05.unit.residuesPdbSequenceNumber array int + 1 +!entry.Q05.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Q05.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLU/E01.off b/share/off/GLU/E01.off new file mode 100644 index 0000000..9b5226e --- /dev/null +++ b/share/off/GLU/E01.off @@ -0,0 +1,123 @@ +!!index array str + "E01" +!entry.E01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.516300 + "H" "H" 0 1 131075 2 1 0.293600 + "CA" "CX" 0 1 131075 3 20 0.039700 + "HA" "H1" 0 1 131075 4 1 0.110500 + "CB" "CT" 0 1 131075 5 6 0.056000 + "HB2" "HC" 0 1 131075 6 1 -0.017300 + "HB3" "HC" 0 1 131075 7 1 -0.017300 + "CG" "CT" 0 1 131075 8 6 0.013600 + "HG2" "HC" 0 1 131075 9 1 -0.042500 + "HG3" "HC" 0 1 131075 10 1 -0.042500 + "CD" "C" 0 1 131075 11 6 0.805400 + "OE1" "O2" 0 1 131075 12 8 -0.818800 + "OE2" "O2" 0 1 131075 13 8 -0.818800 + "C" "C" 0 1 131075 14 6 0.536600 + "O" "O" 0 1 131075 15 8 -0.581900 +!entry.E01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O2" 0 -1 0.0 + "OE2" "O2" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.E01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E01.unit.childsequence single int + 2 +!entry.E01.unit.connect array int + 1 + 14 +!entry.E01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 14 17 + 3 5 17 + 5 7 17 + 5 6 17 + 5 8 17 + 8 10 17 + 8 9 17 + 8 11 17 + 11 12 17 + 11 13 17 + 14 15 17 +!entry.E01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 +!entry.E01.unit.name single str + "" +!entry.E01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.278000 2.204000 + 0.699000 2.108000 1.662000 + -0.835000 1.412000 2.235000 + 0.791000 1.240000 3.618000 + 1.225000 0.156000 4.060000 + 0.785000 2.297000 4.285000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.E01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.E01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "E01" 1 16 1 "?" 0 +!entry.E01.unit.residuesPdbSequenceNumber array int + 1 +!entry.E01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLU/E02.off b/share/off/GLU/E02.off new file mode 100644 index 0000000..67e2d13 --- /dev/null +++ b/share/off/GLU/E02.off @@ -0,0 +1,123 @@ +!!index array str + "E02" +!entry.E02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.516300 + "H" "H" 0 1 131075 2 1 0.293600 + "CA" "CX" 0 1 131075 3 20 0.039700 + "HA" "H1" 0 1 131075 4 1 0.110500 + "CB" "CT" 0 1 131075 5 6 0.056000 + "HB2" "HC" 0 1 131075 6 1 -0.017300 + "HB3" "HC" 0 1 131075 7 1 -0.017300 + "CG" "CT" 0 1 131075 8 6 0.013600 + "HG2" "HC" 0 1 131075 9 1 -0.042500 + "HG3" "HC" 0 1 131075 10 1 -0.042500 + "CD" "C" 0 1 131075 11 6 0.805400 + "OE1" "O2" 0 1 131075 12 8 -0.818800 + "OE2" "O2" 0 1 131075 13 8 -0.818800 + "C" "C" 0 1 131075 14 6 0.536600 + "O" "O" 0 1 131075 15 8 -0.581900 +!entry.E02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O2" 0 -1 0.0 + "OE2" "O2" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.E02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E02.unit.childsequence single int + 2 +!entry.E02.unit.connect array int + 1 + 14 +!entry.E02.unit.connectivity table int atom1x int atom2x int flags + 14 15 17 + 11 12 17 + 11 13 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 14 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.E02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.E02.unit.name single str + "" +!entry.E02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.106755 -0.866518 1.936643 + 1.618317 -0.115241 1.371410 + 0.205000 1.258000 2.219000 + -0.876946 1.388626 2.204732 + 0.538590 1.107153 3.245373 + 0.871000 2.494000 1.648000 + 2.045000 2.399000 1.235000 + 0.217000 3.558000 1.612000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.E02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.E02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "E02" 1 16 1 "?" 0 +!entry.E02.unit.residuesPdbSequenceNumber array int + 1 +!entry.E02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLU/E03.off b/share/off/GLU/E03.off new file mode 100644 index 0000000..a88b6ae --- /dev/null +++ b/share/off/GLU/E03.off @@ -0,0 +1,123 @@ +!!index array str + "E03" +!entry.E03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.516300 + "H" "H" 0 1 131075 2 1 0.293600 + "CA" "CX" 0 1 131075 3 20 0.039700 + "HA" "H1" 0 1 131075 4 1 0.110500 + "CB" "CT" 0 1 131075 5 6 0.056000 + "HB2" "HC" 0 1 131075 6 1 -0.017300 + "HB3" "HC" 0 1 131075 7 1 -0.017300 + "CG" "CT" 0 1 131075 8 6 0.013600 + "HG2" "HC" 0 1 131075 9 1 -0.042500 + "HG3" "HC" 0 1 131075 10 1 -0.042500 + "CD" "C" 0 1 131075 11 6 0.805400 + "OE1" "O2" 0 1 131075 12 8 -0.818800 + "OE2" "O2" 0 1 131075 13 8 -0.818800 + "C" "C" 0 1 131075 14 6 0.536600 + "O" "O" 0 1 131075 15 8 -0.581900 +!entry.E03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O2" 0 -1 0.0 + "OE2" "O2" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.E03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E03.unit.childsequence single int + 2 +!entry.E03.unit.connect array int + 1 + 14 +!entry.E03.unit.connectivity table int atom1x int atom2x int flags + 14 15 17 + 11 12 17 + 11 13 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 14 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.E03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.E03.unit.name single str + "" +!entry.E03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.106755 -0.866518 1.936643 + 1.618317 -0.115241 1.371410 + 0.205000 1.258000 2.219000 + 0.965428 1.382421 2.989806 + 0.244109 2.102410 1.531307 + -1.166000 1.196000 2.866000 + -1.856000 0.169000 2.698000 + -1.548000 2.175000 3.541000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.E03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.E03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "E03" 1 16 1 "?" 0 +!entry.E03.unit.residuesPdbSequenceNumber array int + 1 +!entry.E03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLU/E04.off b/share/off/GLU/E04.off new file mode 100644 index 0000000..d40102f --- /dev/null +++ b/share/off/GLU/E04.off @@ -0,0 +1,123 @@ +!!index array str + "E04" +!entry.E04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.516300 + "H" "H" 0 1 131075 2 1 0.293600 + "CA" "CX" 0 1 131075 3 20 0.039700 + "HA" "H1" 0 1 131075 4 1 0.110500 + "CB" "CT" 0 1 131075 5 6 0.056000 + "HB2" "HC" 0 1 131075 6 1 -0.017300 + "HB3" "HC" 0 1 131075 7 1 -0.017300 + "CG" "CT" 0 1 131075 8 6 0.013600 + "HG2" "HC" 0 1 131075 9 1 -0.042500 + "HG3" "HC" 0 1 131075 10 1 -0.042500 + "CD" "C" 0 1 131075 11 6 0.805400 + "OE1" "O2" 0 1 131075 12 8 -0.818800 + "OE2" "O2" 0 1 131075 13 8 -0.818800 + "C" "C" 0 1 131075 14 6 0.536600 + "O" "O" 0 1 131075 15 8 -0.581900 +!entry.E04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O2" 0 -1 0.0 + "OE2" "O2" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.E04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E04.unit.childsequence single int + 2 +!entry.E04.unit.connect array int + 1 + 14 +!entry.E04.unit.connectivity table int atom1x int atom2x int flags + 14 15 17 + 11 12 17 + 11 13 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 14 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.E04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.E04.unit.name single str + "" +!entry.E04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098575 0.860743 1.939499 + 0.185442 -0.916933 1.907160 + 2.051000 0.072000 1.529000 + 2.460326 -0.790218 1.002781 + 2.375526 0.986789 1.033701 + 2.545000 0.071000 2.962000 + 3.776000 0.126000 3.167000 + 1.701000 0.014000 3.881000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.E04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.E04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "E04" 1 16 1 "?" 0 +!entry.E04.unit.residuesPdbSequenceNumber array int + 1 +!entry.E04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/GLU/E05.off b/share/off/GLU/E05.off new file mode 100644 index 0000000..0c4d1ef --- /dev/null +++ b/share/off/GLU/E05.off @@ -0,0 +1,123 @@ +!!index array str + "E05" +!entry.E05.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.516300 + "H" "H" 0 1 131075 2 1 0.293600 + "CA" "CX" 0 1 131075 3 20 0.039700 + "HA" "H1" 0 1 131075 4 1 0.110500 + "CB" "CT" 0 1 131075 5 6 0.056000 + "HB2" "HC" 0 1 131075 6 1 -0.017300 + "HB3" "HC" 0 1 131075 7 1 -0.017300 + "CG" "CT" 0 1 131075 8 6 0.013600 + "HG2" "HC" 0 1 131075 9 1 -0.042500 + "HG3" "HC" 0 1 131075 10 1 -0.042500 + "CD" "C" 0 1 131075 11 6 0.805400 + "OE1" "O2" 0 1 131075 12 8 -0.818800 + "OE2" "O2" 0 1 131075 13 8 -0.818800 + "C" "C" 0 1 131075 14 6 0.536600 + "O" "O" 0 1 131075 15 8 -0.581900 +!entry.E05.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "C" 0 -1 0.0 + "OE1" "O2" 0 -1 0.0 + "OE2" "O2" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.E05.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.E05.unit.childsequence single int + 2 +!entry.E05.unit.connect array int + 1 + 14 +!entry.E05.unit.connectivity table int atom1x int atom2x int flags + 14 15 17 + 11 12 17 + 11 13 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 14 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.E05.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.E05.unit.name single str + "" +!entry.E05.unit.positions table dbl x dbl y dbl z + 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int c6x + 0 0 0 0 0 0 +!entry.HD1.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HD1" 1 18 1 "?" 0 +!entry.HD1.unit.residuesPdbSequenceNumber array int + 1 +!entry.HD1.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD1.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HID/HD2.off b/share/off/HID/HD2.off new file mode 100644 index 0000000..2eb7354 --- /dev/null +++ b/share/off/HID/HD2.off @@ -0,0 +1,136 @@ +!!index array str + "HD2" +!entry.HD2.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 0.018800 + "HA" "H1" 0 1 131075 4 1 0.088100 + 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+!entry.HD2.unit.childsequence single int + 2 +!entry.HD2.unit.connect array int + 1 + 16 +!entry.HD2.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 13 14 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HD2.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HD2.unit.name single str + "default_name" +!entry.HD2.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.112102 -0.834905 1.990461 + 1.622963 -0.082561 1.426889 + 0.205000 1.241000 2.202000 + 0.324000 1.322000 3.572000 + 0.638677 0.569175 4.167193 + -0.036000 2.529000 3.971000 + -0.012346 2.791641 5.028188 + -0.382000 3.234000 2.912000 + -0.241000 2.452000 1.792000 + -0.481017 2.858770 0.809100 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HD2.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HD2.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HD2" 1 18 1 "?" 0 +!entry.HD2.unit.residuesPdbSequenceNumber array int + 1 +!entry.HD2.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD2.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HID/HD3.off b/share/off/HID/HD3.off new file mode 100644 index 0000000..5e9f082 --- /dev/null +++ b/share/off/HID/HD3.off @@ -0,0 +1,136 @@ +!!index array str + "HD3" +!entry.HD3.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 0.018800 + "HA" "H1" 0 1 131075 4 1 0.088100 + "CB" "CT" 0 1 131075 5 6 -0.046200 + "HB2" "HC" 0 1 131075 6 1 0.040200 + "HB3" "HC" 0 1 131075 7 1 0.040200 + "CG" "CC" 0 1 131075 8 6 -0.026600 + "ND1" "NA" 0 1 131075 9 7 -0.381100 + "HD3" "H" 0 1 131075 10 1 0.364900 + "CE1" "CR" 0 1 131075 11 6 0.205700 + "HE1" "H5" 0 1 131075 12 1 0.139200 + "NE2" "NB" 0 1 131075 13 7 -0.572700 + "CD2" "CV" 0 1 131075 14 6 0.129200 + "HD2" "H4" 0 1 131075 15 1 0.114700 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HD3.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD3" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NB" 0 -1 0.0 + "CD2" "CV" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HD3.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD3.unit.childsequence single int + 2 +!entry.HD3.unit.connect array int + 1 + 16 +!entry.HD3.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 13 14 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HD3.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HD3.unit.name single str + "default_name" +!entry.HD3.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.113667 -0.835070 1.991400 + 1.623027 -0.081584 1.425339 + 0.205000 1.241000 2.202000 + -1.004000 1.424000 2.836000 + -1.758540 0.752673 2.839178 + -1.012000 2.605000 3.430000 + -1.886114 2.937425 3.989110 + 0.146000 3.194000 3.204000 + 0.926000 2.363000 2.438000 + 1.928204 2.675010 2.142366 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HD3.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HD3.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HD3" 1 18 1 "?" 0 +!entry.HD3.unit.residuesPdbSequenceNumber array int + 1 +!entry.HD3.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD3.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HID/HD4.off b/share/off/HID/HD4.off new file mode 100644 index 0000000..6486357 --- /dev/null +++ b/share/off/HID/HD4.off @@ -0,0 +1,136 @@ +!!index array str + "HD4" +!entry.HD4.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 0.018800 + "HA" "H1" 0 1 131075 4 1 0.088100 + "CB" "CT" 0 1 131075 5 6 -0.046200 + "HB2" "HC" 0 1 131075 6 1 0.040200 + "HB3" "HC" 0 1 131075 7 1 0.040200 + "CG" "CC" 0 1 131075 8 6 -0.026600 + "ND1" "NA" 0 1 131075 9 7 -0.381100 + "HD4" "H" 0 1 131075 10 1 0.364900 + "CE1" "CR" 0 1 131075 11 6 0.205700 + "HE1" "H5" 0 1 131075 12 1 0.139200 + "NE2" "NB" 0 1 131075 13 7 -0.572700 + "CD2" "CV" 0 1 131075 14 6 0.129200 + "HD2" "H4" 0 1 131075 15 1 0.114700 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HD4.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD4" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NB" 0 -1 0.0 + "CD2" "CV" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HD4.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD4.unit.childsequence single int + 2 +!entry.HD4.unit.connect array int + 1 + 16 +!entry.HD4.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 13 14 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HD4.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HD4.unit.name single str + "default_name" +!entry.HD4.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.149833 0.862015 1.976436 + 0.237483 -0.914965 1.944926 + 2.029000 0.072000 1.520000 + 2.838000 -1.032000 1.361000 + 2.504826 -1.967121 1.175081 + 4.102000 -0.669000 1.490000 + 4.900588 -1.404534 1.398165 + 4.143000 0.628000 1.725000 + 2.859000 1.116000 1.749000 + 2.681936 2.176443 1.931404 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HD4.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HD4.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HD4" 1 18 1 "?" 0 +!entry.HD4.unit.residuesPdbSequenceNumber array int + 1 +!entry.HD4.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD4.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HID/HD5.off b/share/off/HID/HD5.off new file mode 100644 index 0000000..e40000c --- /dev/null +++ b/share/off/HID/HD5.off @@ -0,0 +1,136 @@ +!!index array str + "HD5" +!entry.HD5.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 0.018800 + "HA" "H1" 0 1 131075 4 1 0.088100 + "CB" "CT" 0 1 131075 5 6 -0.046200 + "HB2" "HC" 0 1 131075 6 1 0.040200 + "HB3" "HC" 0 1 131075 7 1 0.040200 + "CG" "CC" 0 1 131075 8 6 -0.026600 + "ND1" "NA" 0 1 131075 9 7 -0.381100 + "HD5" "H" 0 1 131075 10 1 0.364900 + "CE1" "CR" 0 1 131075 11 6 0.205700 + "HE1" "H5" 0 1 131075 12 1 0.139200 + "NE2" "NB" 0 1 131075 13 7 -0.572700 + "CD2" "CV" 0 1 131075 14 6 0.129200 + "HD2" "H4" 0 1 131075 15 1 0.114700 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HD5.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD5" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NB" 0 -1 0.0 + "CD2" "CV" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HD5.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD5.unit.childsequence single int + 2 +!entry.HD5.unit.connect array int + 1 + 16 +!entry.HD5.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 13 14 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HD5.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HD5.unit.name single str + "default_name" +!entry.HD5.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.149821 0.861725 1.976888 + 0.237523 -0.915237 1.944464 + 2.029000 0.072000 1.520000 + 2.724000 -0.254000 2.663000 + 2.299390 -0.564235 3.525254 + 4.019000 -0.096000 2.447000 + 4.741091 -0.303932 3.236009 + 4.188000 0.319000 1.207000 + 2.959000 0.433000 0.605000 + 2.887915 0.766716 -0.430733 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HD5.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HD5.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HD5" 1 18 1 "?" 0 +!entry.HD5.unit.residuesPdbSequenceNumber array int + 1 +!entry.HD5.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD5.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HID/HD6.off b/share/off/HID/HD6.off new file mode 100644 index 0000000..d24ba97 --- /dev/null +++ b/share/off/HID/HD6.off @@ -0,0 +1,136 @@ +!!index array str + "HD6" +!entry.HD6.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 0.018800 + "HA" "H1" 0 1 131075 4 1 0.088100 + "CB" "CT" 0 1 131075 5 6 -0.046200 + "HB2" "HC" 0 1 131075 6 1 0.040200 + "HB3" "HC" 0 1 131075 7 1 0.040200 + "CG" "CC" 0 1 131075 8 6 -0.026600 + "ND1" "NA" 0 1 131075 9 7 -0.381100 + "HD6" "H" 0 1 131075 10 1 0.364900 + "CE1" "CR" 0 1 131075 11 6 0.205700 + "HE1" "H5" 0 1 131075 12 1 0.139200 + "NE2" "NB" 0 1 131075 13 7 -0.572700 + "CD2" "CV" 0 1 131075 14 6 0.129200 + "HD2" "H4" 0 1 131075 15 1 0.114700 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HD6.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD6" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NB" 0 -1 0.0 + "CD2" "CV" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HD6.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD6.unit.childsequence single int + 2 +!entry.HD6.unit.connect array int + 1 + 16 +!entry.HD6.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 13 14 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HD6.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HD6.unit.name single str + "default_name" +!entry.HD6.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.149795 0.861114 1.977836 + 0.237607 -0.915805 1.943494 + 2.029000 0.072000 1.520000 + 2.752000 1.141000 1.038000 + 2.349148 1.953426 0.593370 + 4.039000 0.930000 1.251000 + 4.779658 1.665739 0.939071 + 4.177000 -0.235000 1.853000 + 2.935000 -0.793000 2.032000 + 2.838713 -1.765939 2.514993 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HD6.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HD6.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HD6" 1 18 1 "?" 0 +!entry.HD6.unit.residuesPdbSequenceNumber array int + 1 +!entry.HD6.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD6.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HID/HD7.off b/share/off/HID/HD7.off new file mode 100644 index 0000000..e0e6aa3 --- /dev/null +++ b/share/off/HID/HD7.off @@ -0,0 +1,136 @@ +!!index array str + "HD7" +!entry.HD7.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 0.018800 + "HA" "H1" 0 1 131075 4 1 0.088100 + "CB" "CT" 0 1 131075 5 6 -0.046200 + "HB2" "HC" 0 1 131075 6 1 0.040200 + "HB3" "HC" 0 1 131075 7 1 0.040200 + "CG" "CC" 0 1 131075 8 6 -0.026600 + "ND1" "NA" 0 1 131075 9 7 -0.381100 + "HD7" "H" 0 1 131075 10 1 0.364900 + "CE1" "CR" 0 1 131075 11 6 0.205700 + "HE1" "H5" 0 1 131075 12 1 0.139200 + "NE2" "NB" 0 1 131075 13 7 -0.572700 + "CD2" "CV" 0 1 131075 14 6 0.129200 + "HD2" "H4" 0 1 131075 15 1 0.114700 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HD7.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD7" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NB" 0 -1 0.0 + "CD2" "CV" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HD7.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD7.unit.childsequence single int + 2 +!entry.HD7.unit.connect array int + 1 + 16 +!entry.HD7.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 13 14 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HD7.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HD7.unit.name single str + "default_name" +!entry.HD7.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.625309 0.029098 1.424214 + 0.154453 0.864630 1.976304 + 0.146000 -1.209000 2.224000 + -1.124000 -1.392000 2.727000 + -1.888351 -0.742392 2.609533 + -1.174000 -2.541000 3.378000 + -2.098977 -2.867306 3.852477 + 0.013000 -3.110000 3.315000 + 0.858000 -2.298000 2.599000 + 1.893890 -2.597267 2.436104 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HD7.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HD7.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HD7" 1 18 1 "?" 0 +!entry.HD7.unit.residuesPdbSequenceNumber array int + 1 +!entry.HD7.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD7.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HID/HD8.off b/share/off/HID/HD8.off new file mode 100644 index 0000000..45ecc84 --- /dev/null +++ b/share/off/HID/HD8.off @@ -0,0 +1,136 @@ +!!index array str + "HD8" +!entry.HD8.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 0.018800 + "HA" "H1" 0 1 131075 4 1 0.088100 + "CB" "CT" 0 1 131075 5 6 -0.046200 + "HB2" "HC" 0 1 131075 6 1 0.040200 + "HB3" "HC" 0 1 131075 7 1 0.040200 + "CG" "CC" 0 1 131075 8 6 -0.026600 + "ND1" "NA" 0 1 131075 9 7 -0.381100 + "HD8" "H" 0 1 131075 10 1 0.364900 + "CE1" "CR" 0 1 131075 11 6 0.205700 + "HE1" "H5" 0 1 131075 12 1 0.139200 + "NE2" "NB" 0 1 131075 13 7 -0.572700 + "CD2" "CV" 0 1 131075 14 6 0.129200 + "HD2" "H4" 0 1 131075 15 1 0.114700 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HD8.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD8" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NB" 0 -1 0.0 + "CD2" "CV" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HD8.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD8.unit.childsequence single int + 2 +!entry.HD8.unit.connect array int + 1 + 16 +!entry.HD8.unit.connectivity table int atom1x int atom2x int flags + 2 1 17 + 3 1 17 + 4 3 17 + 5 3 17 + 6 5 17 + 7 5 17 + 8 5 17 + 9 8 17 + 10 9 17 + 11 9 17 + 12 11 17 + 13 11 17 + 14 8 17 + 14 13 17 + 15 14 17 + 16 3 17 + 17 16 17 +!entry.HD8.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 +!entry.HD8.unit.name single str + "default_name" +!entry.HD8.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.625294 0.030031 1.425633 + 0.152996 0.864532 1.975435 + 0.146000 -1.209000 2.224000 + 0.769000 -2.429000 2.076000 + 1.528143 -2.612780 1.435728 + 0.217000 -3.304000 2.898000 + 0.572866 -4.333340 2.929691 + -0.739000 -2.698000 3.574000 + -0.805000 -1.387000 3.171000 + -1.540328 -0.715970 3.616169 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HD8.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HD8.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HD8" 1 18 1 "?" 0 +!entry.HD8.unit.residuesPdbSequenceNumber array int + 1 +!entry.HD8.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HD8.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIE/HE1.off b/share/off/HIE/HE1.off new file mode 100644 index 0000000..f5f8023 --- /dev/null +++ b/share/off/HIE/HE1.off @@ -0,0 +1,136 @@ +!!index array str + "HE1" +!entry.HE1.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.058100 + "HA" "H1" 0 1 131075 4 1 0.136000 + "CB" "CT" 0 1 131075 5 6 -0.007400 + "HB2" "HC" 0 1 131075 6 1 0.036700 + "HB3" "HC" 0 1 131075 7 1 0.036700 + "CG" "CC" 0 1 131075 8 6 0.186800 + "ND1" "NB" 0 1 131075 9 7 -0.543200 + "CE1" "CR" 0 1 131075 10 6 0.163500 + "HE1" "H5" 0 1 131075 11 1 0.143500 + "NE2" "NA" 0 1 131075 12 7 -0.279500 + "HE2" "H" 0 1 131075 13 1 0.333900 + "CD2" "CW" 0 1 131075 14 6 -0.220700 + "HD2" "H4" 0 1 131075 15 1 0.186200 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HE1.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NB" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HE1.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE1.unit.childsequence single int + 2 +!entry.HE1.unit.connect array int + 1 + 16 +!entry.HE1.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 16 17 + 3 5 17 + 5 6 17 + 5 7 17 + 5 8 17 + 8 14 17 + 8 9 17 + 9 10 17 + 10 11 17 + 10 12 17 + 12 13 17 + 12 14 17 + 14 15 17 + 16 17 17 +!entry.HE1.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 +!entry.HE1.unit.name single str + "default_name" +!entry.HE1.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.113000 -0.835000 1.991000 + 1.623000 -0.082000 1.426000 + 0.205000 1.241000 2.202000 + 0.760000 2.468000 1.910000 + 0.286000 3.372000 2.749000 + 0.607000 4.411000 2.681000 + -0.555000 2.779000 3.572000 + -1.070000 3.223000 4.319000 + -0.624000 1.445000 3.253000 + -1.271000 0.780000 3.826000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HE1.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HE1.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HE1" 1 18 1 "?" 0 +!entry.HE1.unit.residuesPdbSequenceNumber array int + 1 +!entry.HE1.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE1.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIE/HE2.off b/share/off/HIE/HE2.off new file mode 100644 index 0000000..bd57f32 --- /dev/null +++ b/share/off/HIE/HE2.off @@ -0,0 +1,136 @@ +!!index array str + "HE2" +!entry.HE2.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.058100 + "HA" "H1" 0 1 131075 4 1 0.136000 + "CB" "CT" 0 1 131075 5 6 -0.007400 + "HB2" "HC" 0 1 131075 6 1 0.036700 + "HB3" "HC" 0 1 131075 7 1 0.036700 + "CG" "CC" 0 1 131075 8 6 0.186800 + "ND1" "NB" 0 1 131075 9 7 -0.543200 + "CE1" "CR" 0 1 131075 10 6 0.163500 + "HE2" "H5" 0 1 131075 11 1 0.143500 + "NE2" "NA" 0 1 131075 12 7 -0.279500 + "H1" "H" 0 1 131075 13 1 0.333900 + "CD2" "CW" 0 1 131075 14 6 -0.220700 + "HD2" "H4" 0 1 131075 15 1 0.186200 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HE2.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NB" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE2" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HE2.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE2.unit.childsequence single int + 2 +!entry.HE2.unit.connect array int + 1 + 16 +!entry.HE2.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 12 13 17 + 12 14 17 + 10 11 17 + 10 12 17 + 9 10 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HE2.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HE2.unit.name single str + "default_name" +!entry.HE2.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.112102 -0.834905 1.990461 + 1.622963 -0.082561 1.426889 + 0.205000 1.241000 2.202000 + 0.324000 1.322000 3.572000 + -0.036000 2.529000 3.971000 + -0.012346 2.791641 5.028188 + -0.382000 3.234000 2.912000 + -0.700295 4.192675 2.912387 + -0.241000 2.452000 1.792000 + -0.481017 2.858770 0.809100 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HE2.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HE2.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HE2" 1 18 1 "?" 0 +!entry.HE2.unit.residuesPdbSequenceNumber array int + 1 +!entry.HE2.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE2.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIE/HE3.off b/share/off/HIE/HE3.off new file mode 100644 index 0000000..b4c907a --- /dev/null +++ b/share/off/HIE/HE3.off @@ -0,0 +1,136 @@ +!!index array str + "HE3" +!entry.HE3.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.058100 + "HA" "H1" 0 1 131075 4 1 0.136000 + "CB" "CT" 0 1 131075 5 6 -0.007400 + "HB2" "HC" 0 1 131075 6 1 0.036700 + "HB3" "HC" 0 1 131075 7 1 0.036700 + "CG" "CC" 0 1 131075 8 6 0.186800 + "ND1" "NB" 0 1 131075 9 7 -0.543200 + "CE1" "CR" 0 1 131075 10 6 0.163500 + "HE3" "H5" 0 1 131075 11 1 0.143500 + "NE2" "NA" 0 1 131075 12 7 -0.279500 + "HE2" "H" 0 1 131075 13 1 0.333900 + "CD2" "CW" 0 1 131075 14 6 -0.220700 + "HD2" "H4" 0 1 131075 15 1 0.186200 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HE3.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NB" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE3" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HE3.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE3.unit.childsequence single int + 2 +!entry.HE3.unit.connect array int + 1 + 16 +!entry.HE3.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 12 13 17 + 12 14 17 + 10 11 17 + 10 12 17 + 9 10 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HE3.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HE3.unit.name single str + "default_name" +!entry.HE3.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.113667 -0.835070 1.991400 + 1.623027 -0.081584 1.425339 + 0.205000 1.241000 2.202000 + -1.004000 1.424000 2.836000 + -1.012000 2.605000 3.430000 + -1.886114 2.937425 3.989110 + 0.146000 3.194000 3.204000 + 0.424398 4.106855 3.535000 + 0.926000 2.363000 2.438000 + 1.928204 2.675010 2.142366 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HE3.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HE3.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HE3" 1 18 1 "?" 0 +!entry.HE3.unit.residuesPdbSequenceNumber array int + 1 +!entry.HE3.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE3.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIE/HE4.off b/share/off/HIE/HE4.off new file mode 100644 index 0000000..1aaab9d --- /dev/null +++ b/share/off/HIE/HE4.off @@ -0,0 +1,136 @@ +!!index array str + "HE4" +!entry.HE4.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.058100 + "HA" "H1" 0 1 131075 4 1 0.136000 + "CB" "CT" 0 1 131075 5 6 -0.007400 + "HB2" "HC" 0 1 131075 6 1 0.036700 + "HB3" "HC" 0 1 131075 7 1 0.036700 + "CG" "CC" 0 1 131075 8 6 0.186800 + "ND1" "NB" 0 1 131075 9 7 -0.543200 + "CE1" "CR" 0 1 131075 10 6 0.163500 + "HE4" "H5" 0 1 131075 11 1 0.143500 + "NE2" "NA" 0 1 131075 12 7 -0.279500 + "HE2" "H" 0 1 131075 13 1 0.333900 + "CD2" "CW" 0 1 131075 14 6 -0.220700 + "HD2" "H4" 0 1 131075 15 1 0.186200 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HE4.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NB" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE4" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HE4.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE4.unit.childsequence single int + 2 +!entry.HE4.unit.connect array int + 1 + 16 +!entry.HE4.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 12 13 17 + 12 14 17 + 10 11 17 + 10 12 17 + 9 10 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HE4.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HE4.unit.name single str + "default_name" +!entry.HE4.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.149833 0.862015 1.976436 + 0.237483 -0.914965 1.944926 + 2.029000 0.072000 1.520000 + 2.838000 -1.032000 1.361000 + 4.102000 -0.669000 1.490000 + 4.900588 -1.404534 1.398165 + 4.143000 0.628000 1.725000 + 4.975678 1.182194 1.866021 + 2.859000 1.116000 1.749000 + 2.681936 2.176443 1.931404 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HE4.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HE4.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HE4" 1 18 1 "?" 0 +!entry.HE4.unit.residuesPdbSequenceNumber array int + 1 +!entry.HE4.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE4.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIE/HE5.off b/share/off/HIE/HE5.off new file mode 100644 index 0000000..ddac473 --- /dev/null +++ b/share/off/HIE/HE5.off @@ -0,0 +1,136 @@ +!!index array str + "HE5" +!entry.HE5.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.058100 + "HA" "H1" 0 1 131075 4 1 0.136000 + "CB" "CT" 0 1 131075 5 6 -0.007400 + "HB2" "HC" 0 1 131075 6 1 0.036700 + "HB3" "HC" 0 1 131075 7 1 0.036700 + "CG" "CC" 0 1 131075 8 6 0.186800 + "ND1" "NB" 0 1 131075 9 7 -0.543200 + "CE1" "CR" 0 1 131075 10 6 0.163500 + "HE5" "H5" 0 1 131075 11 1 0.143500 + "NE2" "NA" 0 1 131075 12 7 -0.279500 + "HE2" "H" 0 1 131075 13 1 0.333900 + "CD2" "CW" 0 1 131075 14 6 -0.220700 + "HD2" "H4" 0 1 131075 15 1 0.186200 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HE5.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NB" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE5" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HE5.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE5.unit.childsequence single int + 2 +!entry.HE5.unit.connect array int + 1 + 16 +!entry.HE5.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 12 13 17 + 12 14 17 + 10 11 17 + 10 12 17 + 9 10 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HE5.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HE5.unit.name single str + "default_name" +!entry.HE5.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.149821 0.861725 1.976888 + 0.237523 -0.915237 1.944464 + 2.029000 0.072000 1.520000 + 2.724000 -0.254000 2.663000 + 4.019000 -0.096000 2.447000 + 4.741091 -0.303932 3.236009 + 4.188000 0.319000 1.207000 + 5.071680 0.522991 0.762177 + 2.959000 0.433000 0.605000 + 2.887915 0.766716 -0.430733 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HE5.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HE5.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HE5" 1 18 1 "?" 0 +!entry.HE5.unit.residuesPdbSequenceNumber array int + 1 +!entry.HE5.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE5.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIE/HE6.off b/share/off/HIE/HE6.off new file mode 100644 index 0000000..82b2380 --- /dev/null +++ b/share/off/HIE/HE6.off @@ -0,0 +1,136 @@ +!!index array str + "HE6" +!entry.HE6.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.058100 + "HA" "H1" 0 1 131075 4 1 0.136000 + "CB" "CT" 0 1 131075 5 6 -0.007400 + "HB2" "HC" 0 1 131075 6 1 0.036700 + "HB3" "HC" 0 1 131075 7 1 0.036700 + "CG" "CC" 0 1 131075 8 6 0.186800 + "ND1" "NB" 0 1 131075 9 7 -0.543200 + "CE1" "CR" 0 1 131075 10 6 0.163500 + "HE6" "H5" 0 1 131075 11 1 0.143500 + "NE2" "NA" 0 1 131075 12 7 -0.279500 + "HE2" "H" 0 1 131075 13 1 0.333900 + "CD2" "CW" 0 1 131075 14 6 -0.220700 + "HD2" "H4" 0 1 131075 15 1 0.186200 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HE6.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NB" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE6" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HE6.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE6.unit.childsequence single int + 2 +!entry.HE6.unit.connect array int + 1 + 16 +!entry.HE6.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 12 13 17 + 12 14 17 + 10 11 17 + 10 12 17 + 9 10 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HE6.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HE6.unit.name single str + "default_name" +!entry.HE6.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.149795 0.861114 1.977836 + 0.237607 -0.915805 1.943494 + 2.029000 0.072000 1.520000 + 2.752000 1.141000 1.038000 + 4.039000 0.930000 1.251000 + 4.779658 1.665739 0.939071 + 4.177000 -0.235000 1.853000 + 5.048402 -0.657756 2.139889 + 2.935000 -0.793000 2.032000 + 2.838713 -1.765939 2.514993 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HE6.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HE6.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HE6" 1 18 1 "?" 0 +!entry.HE6.unit.residuesPdbSequenceNumber array int + 1 +!entry.HE6.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE6.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIE/HE7.off b/share/off/HIE/HE7.off new file mode 100644 index 0000000..cbc36d5 --- /dev/null +++ b/share/off/HIE/HE7.off @@ -0,0 +1,136 @@ +!!index array str + "HE7" +!entry.HE7.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.058100 + "HA" "H1" 0 1 131075 4 1 0.136000 + "CB" "CT" 0 1 131075 5 6 -0.007400 + "HB2" "HC" 0 1 131075 6 1 0.036700 + "HB3" "HC" 0 1 131075 7 1 0.036700 + "CG" "CC" 0 1 131075 8 6 0.186800 + "ND1" "NB" 0 1 131075 9 7 -0.543200 + "CE1" "CR" 0 1 131075 10 6 0.163500 + "HE7" "H5" 0 1 131075 11 1 0.143500 + "NE2" "NA" 0 1 131075 12 7 -0.279500 + "HE2" "H" 0 1 131075 13 1 0.333900 + "CD2" "CW" 0 1 131075 14 6 -0.220700 + "HD2" "H4" 0 1 131075 15 1 0.186200 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HE7.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NB" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE7" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HE7.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE7.unit.childsequence single int + 2 +!entry.HE7.unit.connect array int + 1 + 16 +!entry.HE7.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 12 13 17 + 12 14 17 + 10 11 17 + 10 12 17 + 9 10 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HE7.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HE7.unit.name single str + "default_name" +!entry.HE7.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.625309 0.029098 1.424214 + 0.154453 0.864630 1.976304 + 0.146000 -1.209000 2.224000 + -1.124000 -1.392000 2.727000 + -1.174000 -2.541000 3.378000 + -2.098977 -2.867306 3.852477 + 0.013000 -3.110000 3.315000 + 0.270576 -3.997500 3.722884 + 0.858000 -2.298000 2.599000 + 1.893890 -2.597267 2.436104 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HE7.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HE7.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HE7" 1 18 1 "?" 0 +!entry.HE7.unit.residuesPdbSequenceNumber array int + 1 +!entry.HE7.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE7.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIE/HE8.off b/share/off/HIE/HE8.off new file mode 100644 index 0000000..3a6106b --- /dev/null +++ b/share/off/HIE/HE8.off @@ -0,0 +1,136 @@ +!!index array str + "HE8" +!entry.HE8.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.058100 + "HA" "H1" 0 1 131075 4 1 0.136000 + "CB" "CT" 0 1 131075 5 6 -0.007400 + "HB2" "HC" 0 1 131075 6 1 0.036700 + "HB3" "HC" 0 1 131075 7 1 0.036700 + "CG" "CC" 0 1 131075 8 6 0.186800 + "ND1" "NB" 0 1 131075 9 7 -0.543200 + "CE1" "CR" 0 1 131075 10 6 0.163500 + "HE8" "H5" 0 1 131075 11 1 0.143500 + "NE2" "NA" 0 1 131075 12 7 -0.279500 + "HE2" "H" 0 1 131075 13 1 0.333900 + "CD2" "CW" 0 1 131075 14 6 -0.220700 + "HD2" "H4" 0 1 131075 15 1 0.186200 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.HE8.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NB" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE8" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HE8.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE8.unit.childsequence single int + 2 +!entry.HE8.unit.connect array int + 1 + 16 +!entry.HE8.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 14 15 17 + 12 13 17 + 12 14 17 + 10 11 17 + 10 12 17 + 9 10 17 + 8 14 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HE8.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HE8.unit.name single str + "default_name" +!entry.HE8.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.625294 0.030031 1.425633 + 0.152996 0.864532 1.975435 + 0.146000 -1.209000 2.224000 + 0.769000 -2.429000 2.076000 + 0.217000 -3.304000 2.898000 + 0.572866 -4.333340 2.929691 + -0.739000 -2.698000 3.574000 + -1.332007 -3.118638 4.275268 + -0.805000 -1.387000 3.171000 + -1.540328 -0.715970 3.616169 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HE8.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HE8.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HE8" 1 18 1 "?" 0 +!entry.HE8.unit.residuesPdbSequenceNumber array int + 1 +!entry.HE8.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HE8.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIP/HP1.off b/share/off/HIP/HP1.off new file mode 100644 index 0000000..2a12adb --- /dev/null +++ b/share/off/HIP/HP1.off @@ -0,0 +1,142 @@ +!!index array str + "HP1" +!entry.HP1.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.135400 + "HA" "H1" 0 1 131075 4 1 0.121200 + "CB" "CT" 0 1 131075 5 6 -0.041400 + "HB2" "HC" 0 1 131075 6 1 0.081000 + "HB3" "HC" 0 1 131075 7 1 0.081000 + "CG" "CC" 0 1 131075 8 6 -0.001200 + "ND1" "NA" 0 1 131075 9 7 -0.151300 + "HD1" "H" 0 1 131075 10 1 0.386600 + "CE1" "CR" 0 1 131075 11 6 -0.017000 + "HE1" "H5" 0 1 131075 12 1 0.268100 + "NE2" "NA" 0 1 131075 13 7 -0.171800 + "HE2" "H" 0 1 131075 14 1 0.391100 + "CD2" "CW" 0 1 131075 15 6 -0.114100 + "HD2" "H4" 0 1 131075 16 1 0.231700 + "C" "C" 0 1 131075 17 6 0.734100 + "O" "O" 0 1 131075 18 8 -0.589400 +!entry.HP1.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD1" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HP1.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP1.unit.childsequence single int + 2 +!entry.HP1.unit.connect array int + 1 + 17 +!entry.HP1.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 17 17 + 3 5 17 + 5 6 17 + 5 7 17 + 5 8 17 + 8 15 17 + 8 9 17 + 9 10 17 + 9 11 17 + 11 12 17 + 11 13 17 + 13 14 17 + 13 15 17 + 15 16 17 + 17 18 17 +!entry.HP1.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 +!entry.HP1.unit.name single str + "default_name" +!entry.HP1.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.113000 -0.835000 1.991000 + 1.623000 -0.082000 1.426000 + 0.205000 1.241000 2.202000 + 0.760000 2.468000 1.910000 + 1.424000 2.637000 1.168000 + 0.286000 3.372000 2.749000 + 0.607000 4.411000 2.681000 + -0.555000 2.779000 3.572000 + -1.070000 3.223000 4.319000 + -0.624000 1.445000 3.253000 + -1.271000 0.780000 3.826000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HP1.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HP1.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HP1" 1 19 1 "?" 0 +!entry.HP1.unit.residuesPdbSequenceNumber array int + 1 +!entry.HP1.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP1.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIP/HP2.off b/share/off/HIP/HP2.off new file mode 100644 index 0000000..e37b67c --- /dev/null +++ b/share/off/HIP/HP2.off @@ -0,0 +1,142 @@ +!!index array str + "HP2" +!entry.HP2.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.135400 + "HA" "H1" 0 1 131075 4 1 0.121200 + "CB" "CT" 0 1 131075 5 6 -0.041400 + "HB2" "HC" 0 1 131075 6 1 0.081000 + "HB3" "HC" 0 1 131075 7 1 0.081000 + "CG" "CC" 0 1 131075 8 6 -0.001200 + "ND1" "NA" 0 1 131075 9 7 -0.151300 + "HD1" "H" 0 1 131075 10 1 0.386600 + "CE1" "CR" 0 1 131075 11 6 -0.017000 + "HE1" "H5" 0 1 131075 12 1 0.268100 + "NE2" "NA" 0 1 131075 13 7 -0.171800 + "HE2" "H" 0 1 131075 14 1 0.391100 + "CD2" "CW" 0 1 131075 15 6 -0.114100 + "HD2" "H4" 0 1 131075 16 1 0.231700 + "C" "C" 0 1 131075 17 6 0.734100 + "O" "O" 0 1 131075 18 8 -0.589400 +!entry.HP2.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD1" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HP2.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP2.unit.childsequence single int + 2 +!entry.HP2.unit.connect array int + 1 + 17 +!entry.HP2.unit.connectivity table int atom1x int atom2x int flags + 17 18 17 + 15 16 17 + 13 14 17 + 13 15 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 15 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 17 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HP2.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HP2.unit.name single str + "default_name" +!entry.HP2.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.112102 -0.834905 1.990461 + 1.622963 -0.082561 1.426889 + 0.205000 1.241000 2.202000 + 0.324000 1.322000 3.572000 + 0.638677 0.569175 4.167193 + -0.036000 2.529000 3.971000 + -0.012346 2.791641 5.028188 + -0.382000 3.234000 2.912000 + -0.700295 4.192675 2.912387 + -0.241000 2.452000 1.792000 + -0.481017 2.858770 0.809100 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HP2.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HP2.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HP2" 1 19 1 "?" 0 +!entry.HP2.unit.residuesPdbSequenceNumber array int + 1 +!entry.HP2.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP2.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIP/HP3.off b/share/off/HIP/HP3.off new file mode 100644 index 0000000..d795ed5 --- /dev/null +++ b/share/off/HIP/HP3.off @@ -0,0 +1,142 @@ +!!index array str + "HP3" +!entry.HP3.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.135400 + "HA" "H1" 0 1 131075 4 1 0.121200 + "CB" "CT" 0 1 131075 5 6 -0.041400 + "HB2" "HC" 0 1 131075 6 1 0.081000 + "HB3" "HC" 0 1 131075 7 1 0.081000 + "CG" "CC" 0 1 131075 8 6 -0.001200 + "ND1" "NA" 0 1 131075 9 7 -0.151300 + "HD1" "H" 0 1 131075 10 1 0.386600 + "CE1" "CR" 0 1 131075 11 6 -0.017000 + "HE1" "H5" 0 1 131075 12 1 0.268100 + "NE2" "NA" 0 1 131075 13 7 -0.171800 + "HE2" "H" 0 1 131075 14 1 0.391100 + "CD2" "CW" 0 1 131075 15 6 -0.114100 + "HD2" "H4" 0 1 131075 16 1 0.231700 + "C" "C" 0 1 131075 17 6 0.734100 + "O" "O" 0 1 131075 18 8 -0.589400 +!entry.HP3.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD1" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HP3.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP3.unit.childsequence single int + 2 +!entry.HP3.unit.connect array int + 1 + 17 +!entry.HP3.unit.connectivity table int atom1x int atom2x int flags + 17 18 17 + 15 16 17 + 13 14 17 + 13 15 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 15 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 17 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HP3.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HP3.unit.name single str + "default_name" +!entry.HP3.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.113667 -0.835070 1.991400 + 1.623027 -0.081584 1.425339 + 0.205000 1.241000 2.202000 + -1.004000 1.424000 2.836000 + -1.758540 0.752673 2.839178 + -1.012000 2.605000 3.430000 + -1.886114 2.937425 3.989110 + 0.146000 3.194000 3.204000 + 0.424398 4.106855 3.535000 + 0.926000 2.363000 2.438000 + 1.928204 2.675010 2.142366 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HP3.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HP3.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HP3" 1 19 1 "?" 0 +!entry.HP3.unit.residuesPdbSequenceNumber array int + 1 +!entry.HP3.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP3.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIP/HP4.off b/share/off/HIP/HP4.off new file mode 100644 index 0000000..c995227 --- /dev/null +++ b/share/off/HIP/HP4.off @@ -0,0 +1,142 @@ +!!index array str + "HP4" +!entry.HP4.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.135400 + "HA" "H1" 0 1 131075 4 1 0.121200 + "CB" "CT" 0 1 131075 5 6 -0.041400 + "HB2" "HC" 0 1 131075 6 1 0.081000 + "HB3" "HC" 0 1 131075 7 1 0.081000 + "CG" "CC" 0 1 131075 8 6 -0.001200 + "ND1" "NA" 0 1 131075 9 7 -0.151300 + "HD1" "H" 0 1 131075 10 1 0.386600 + "CE1" "CR" 0 1 131075 11 6 -0.017000 + "HE1" "H5" 0 1 131075 12 1 0.268100 + "NE2" "NA" 0 1 131075 13 7 -0.171800 + "HE2" "H" 0 1 131075 14 1 0.391100 + "CD2" "CW" 0 1 131075 15 6 -0.114100 + "HD2" "H4" 0 1 131075 16 1 0.231700 + "C" "C" 0 1 131075 17 6 0.734100 + "O" "O" 0 1 131075 18 8 -0.589400 +!entry.HP4.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD1" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HP4.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP4.unit.childsequence single int + 2 +!entry.HP4.unit.connect array int + 1 + 17 +!entry.HP4.unit.connectivity table int atom1x int atom2x int flags + 17 18 17 + 15 16 17 + 13 14 17 + 13 15 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 15 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 17 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HP4.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HP4.unit.name single str + "default_name" +!entry.HP4.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.149833 0.862015 1.976436 + 0.237483 -0.914965 1.944926 + 2.029000 0.072000 1.520000 + 2.838000 -1.032000 1.361000 + 2.504826 -1.967121 1.175081 + 4.102000 -0.669000 1.490000 + 4.900588 -1.404534 1.398165 + 4.143000 0.628000 1.725000 + 4.975678 1.182194 1.866021 + 2.859000 1.116000 1.749000 + 2.681936 2.176443 1.931404 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HP4.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HP4.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HP4" 1 19 1 "?" 0 +!entry.HP4.unit.residuesPdbSequenceNumber array int + 1 +!entry.HP4.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP4.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIP/HP5.off b/share/off/HIP/HP5.off new file mode 100644 index 0000000..8829771 --- /dev/null +++ b/share/off/HIP/HP5.off @@ -0,0 +1,142 @@ +!!index array str + "HP5" +!entry.HP5.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.135400 + "HA" "H1" 0 1 131075 4 1 0.121200 + "CB" "CT" 0 1 131075 5 6 -0.041400 + "HB2" "HC" 0 1 131075 6 1 0.081000 + "HB3" "HC" 0 1 131075 7 1 0.081000 + "CG" "CC" 0 1 131075 8 6 -0.001200 + "ND1" "NA" 0 1 131075 9 7 -0.151300 + "HD1" "H" 0 1 131075 10 1 0.386600 + "CE1" "CR" 0 1 131075 11 6 -0.017000 + "HE1" "H5" 0 1 131075 12 1 0.268100 + "NE2" "NA" 0 1 131075 13 7 -0.171800 + "HE2" "H" 0 1 131075 14 1 0.391100 + "CD2" "CW" 0 1 131075 15 6 -0.114100 + "HD2" "H4" 0 1 131075 16 1 0.231700 + "C" "C" 0 1 131075 17 6 0.734100 + "O" "O" 0 1 131075 18 8 -0.589400 +!entry.HP5.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD1" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HP5.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP5.unit.childsequence single int + 2 +!entry.HP5.unit.connect array int + 1 + 17 +!entry.HP5.unit.connectivity table int atom1x int atom2x int flags + 17 18 17 + 15 16 17 + 13 14 17 + 13 15 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 15 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 17 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HP5.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HP5.unit.name single str + "default_name" +!entry.HP5.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.149821 0.861725 1.976888 + 0.237523 -0.915237 1.944464 + 2.029000 0.072000 1.520000 + 2.724000 -0.254000 2.663000 + 2.299390 -0.564235 3.525254 + 4.019000 -0.096000 2.447000 + 4.741091 -0.303932 3.236009 + 4.188000 0.319000 1.207000 + 5.071680 0.522991 0.762177 + 2.959000 0.433000 0.605000 + 2.887915 0.766716 -0.430733 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HP5.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HP5.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HP5" 1 19 1 "?" 0 +!entry.HP5.unit.residuesPdbSequenceNumber array int + 1 +!entry.HP5.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP5.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIP/HP6.off b/share/off/HIP/HP6.off new file mode 100644 index 0000000..ddd0a03 --- /dev/null +++ b/share/off/HIP/HP6.off @@ -0,0 +1,142 @@ +!!index array str + "HP6" +!entry.HP6.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.135400 + "HA" "H1" 0 1 131075 4 1 0.121200 + "CB" "CT" 0 1 131075 5 6 -0.041400 + "HB2" "HC" 0 1 131075 6 1 0.081000 + "HB3" "HC" 0 1 131075 7 1 0.081000 + "CG" "CC" 0 1 131075 8 6 -0.001200 + "ND1" "NA" 0 1 131075 9 7 -0.151300 + "HD1" "H" 0 1 131075 10 1 0.386600 + "CE1" "CR" 0 1 131075 11 6 -0.017000 + "HE1" "H5" 0 1 131075 12 1 0.268100 + "NE2" "NA" 0 1 131075 13 7 -0.171800 + "HE2" "H" 0 1 131075 14 1 0.391100 + "CD2" "CW" 0 1 131075 15 6 -0.114100 + "HD2" "H4" 0 1 131075 16 1 0.231700 + "C" "C" 0 1 131075 17 6 0.734100 + "O" "O" 0 1 131075 18 8 -0.589400 +!entry.HP6.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD1" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HP6.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP6.unit.childsequence single int + 2 +!entry.HP6.unit.connect array int + 1 + 17 +!entry.HP6.unit.connectivity table int atom1x int atom2x int flags + 17 18 17 + 15 16 17 + 13 14 17 + 13 15 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 15 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 17 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HP6.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HP6.unit.name single str + "default_name" +!entry.HP6.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.149795 0.861114 1.977836 + 0.237607 -0.915805 1.943494 + 2.029000 0.072000 1.520000 + 2.752000 1.141000 1.038000 + 2.349148 1.953426 0.593370 + 4.039000 0.930000 1.251000 + 4.779658 1.665739 0.939071 + 4.177000 -0.235000 1.853000 + 5.048402 -0.657756 2.139889 + 2.935000 -0.793000 2.032000 + 2.838713 -1.765939 2.514993 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HP6.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HP6.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HP6" 1 19 1 "?" 0 +!entry.HP6.unit.residuesPdbSequenceNumber array int + 1 +!entry.HP6.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP6.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIP/HP7.off b/share/off/HIP/HP7.off new file mode 100644 index 0000000..dfcc584 --- /dev/null +++ b/share/off/HIP/HP7.off @@ -0,0 +1,142 @@ +!!index array str + "HP7" +!entry.HP7.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.135400 + "HA" "H1" 0 1 131075 4 1 0.121200 + "CB" "CT" 0 1 131075 5 6 -0.041400 + "HB2" "HC" 0 1 131075 6 1 0.081000 + "HB3" "HC" 0 1 131075 7 1 0.081000 + "CG" "CC" 0 1 131075 8 6 -0.001200 + "ND1" "NA" 0 1 131075 9 7 -0.151300 + "HD1" "H" 0 1 131075 10 1 0.386600 + "CE1" "CR" 0 1 131075 11 6 -0.017000 + "HE1" "H5" 0 1 131075 12 1 0.268100 + "NE2" "NA" 0 1 131075 13 7 -0.171800 + "HE2" "H" 0 1 131075 14 1 0.391100 + "CD2" "CW" 0 1 131075 15 6 -0.114100 + "HD2" "H4" 0 1 131075 16 1 0.231700 + "C" "C" 0 1 131075 17 6 0.734100 + "O" "O" 0 1 131075 18 8 -0.589400 +!entry.HP7.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD1" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HP7.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP7.unit.childsequence single int + 2 +!entry.HP7.unit.connect array int + 1 + 17 +!entry.HP7.unit.connectivity table int atom1x int atom2x int flags + 17 18 17 + 15 16 17 + 13 14 17 + 13 15 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 15 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 17 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HP7.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HP7.unit.name single str + "default_name" +!entry.HP7.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.625309 0.029098 1.424214 + 0.154453 0.864630 1.976304 + 0.146000 -1.209000 2.224000 + -1.124000 -1.392000 2.727000 + -1.888351 -0.742392 2.609533 + -1.174000 -2.541000 3.378000 + -2.098977 -2.867306 3.852477 + 0.013000 -3.110000 3.315000 + 0.270576 -3.997500 3.722884 + 0.858000 -2.298000 2.599000 + 1.893890 -2.597267 2.436104 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HP7.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HP7.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HP7" 1 19 1 "?" 0 +!entry.HP7.unit.residuesPdbSequenceNumber array int + 1 +!entry.HP7.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP7.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/HIP/HP8.off b/share/off/HIP/HP8.off new file mode 100644 index 0000000..84efa0a --- /dev/null +++ b/share/off/HIP/HP8.off @@ -0,0 +1,142 @@ +!!index array str + "HP8" +!entry.HP8.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 6 -0.135400 + "HA" "H1" 0 1 131075 4 1 0.121200 + "CB" "CT" 0 1 131075 5 6 -0.041400 + "HB2" "HC" 0 1 131075 6 1 0.081000 + "HB3" "HC" 0 1 131075 7 1 0.081000 + "CG" "CC" 0 1 131075 8 6 -0.001200 + "ND1" "NA" 0 1 131075 9 7 -0.151300 + "HD1" "H" 0 1 131075 10 1 0.386600 + "CE1" "CR" 0 1 131075 11 6 -0.017000 + "HE1" "H5" 0 1 131075 12 1 0.268100 + "NE2" "NA" 0 1 131075 13 7 -0.171800 + "HE2" "H" 0 1 131075 14 1 0.391100 + "CD2" "CW" 0 1 131075 15 6 -0.114100 + "HD2" "H4" 0 1 131075 16 1 0.231700 + "C" "C" 0 1 131075 17 6 0.734100 + "O" "O" 0 1 131075 18 8 -0.589400 +!entry.HP8.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CC" 0 -1 0.0 + "ND1" "NA" 0 -1 0.0 + "HD1" "H" 0 -1 0.0 + "CE1" "CR" 0 -1 0.0 + "HE1" "H5" 0 -1 0.0 + "NE2" "NA" 0 -1 0.0 + "HE2" "H" 0 -1 0.0 + "CD2" "CW" 0 -1 0.0 + "HD2" "H4" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.HP8.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP8.unit.childsequence single int + 2 +!entry.HP8.unit.connect array int + 1 + 17 +!entry.HP8.unit.connectivity table int atom1x int atom2x int flags + 17 18 17 + 15 16 17 + 13 14 17 + 13 15 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 15 17 + 8 9 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 17 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.HP8.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.HP8.unit.name single str + "default_name" +!entry.HP8.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.625294 0.030031 1.425633 + 0.152996 0.864532 1.975435 + 0.146000 -1.209000 2.224000 + 0.769000 -2.429000 2.076000 + 1.528143 -2.612780 1.435728 + 0.217000 -3.304000 2.898000 + 0.572866 -4.333340 2.929691 + -0.739000 -2.698000 3.574000 + -1.332007 -3.118638 4.275268 + -0.805000 -1.387000 3.171000 + -1.540328 -0.715970 3.616169 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.HP8.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.HP8.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "HP8" 1 19 1 "?" 0 +!entry.HP8.unit.residuesPdbSequenceNumber array int + 1 +!entry.HP8.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.HP8.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ILE/I01.off b/share/off/ILE/I01.off new file mode 100644 index 0000000..ae84243 --- /dev/null +++ b/share/off/ILE/I01.off @@ -0,0 +1,147 @@ +!!index array str + "I01" +!entry.I01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.059700 + "HA" "H1" 0 1 131075 4 1 0.086900 + "CB" "CT" 0 1 131075 5 6 0.130300 + "HB" "HC" 0 1 131075 6 1 0.018700 + "CG2" "CT" 0 1 131075 7 6 -0.320400 + "HG21" "HC" 0 1 131075 8 80 0.088200 + "HG22" "HC" 0 1 131075 9 80 0.088200 + "HG23" "HC" 0 1 131075 10 80 0.088200 + "CG1" "CT" 0 1 131075 11 6 -0.043000 + "HG12" "HC" 0 1 131075 12 80 0.023600 + "HG13" "HC" 0 1 131075 13 80 0.023600 + "CD1" "CT" 0 1 131075 14 6 -0.066000 + "HD11" "HC" 0 1 131075 15 1 0.018600 + "HD12" "HC" 0 1 131075 16 1 0.018600 + "HD13" "HC" 0 1 131075 17 1 0.018600 + "C" "C" 0 1 131075 18 6 0.597300 + "O" "O" 0 1 131075 19 8 -0.567900 +!entry.I01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB" "HC" 0 -1 0.0 + "CG2" "CT" 0 -1 0.0 + "HG21" "HC" 0 -1 0.0 + "HG22" "HC" 0 -1 0.0 + "HG23" "HC" 0 -1 0.0 + "CG1" "CT" 0 -1 0.0 + "HG12" "HC" 0 -1 0.0 + "HG13" "HC" 0 -1 0.0 + "CD1" "CT" 0 -1 0.0 + "HD11" "HC" 0 -1 0.0 + "HD12" "HC" 0 -1 0.0 + "HD13" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.I01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.I01.unit.childsequence single int + 2 +!entry.I01.unit.connect array int + 1 + 18 +!entry.I01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 18 17 + 3 5 17 + 5 6 17 + 5 7 17 + 5 11 17 + 7 9 17 + 7 10 17 + 7 8 17 + 11 12 17 + 11 13 17 + 11 14 17 + 14 16 17 + 14 17 17 + 14 15 17 + 18 19 17 +!entry.I01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 +!entry.I01.unit.name single str + "" +!entry.I01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.765000 -0.453000 + 0.0 0.0 0.0 + 0.346000 0.895000 -0.517000 + 0.564000 -0.015000 1.433000 + 0.138000 -0.872000 1.954000 + 2.080000 -0.139000 1.408000 + 2.507000 0.718000 0.887000 + 2.460000 -0.169000 2.429000 + 2.362000 -1.055000 0.889000 + 0.195000 1.277000 2.165000 + 0.754000 2.086000 1.695000 + -0.873000 1.439000 2.017000 + 0.500000 1.248000 3.646000 + 1.568000 1.086000 3.795000 + 0.211000 2.198000 4.096000 + -0.059000 0.439000 4.117000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.I01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.I01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "I01" 1 20 1 "?" 0 +!entry.I01.unit.residuesPdbSequenceNumber array int + 1 +!entry.I01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.I01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ILE/I02.off b/share/off/ILE/I02.off new file mode 100644 index 0000000..2bec7f4 --- /dev/null +++ b/share/off/ILE/I02.off @@ -0,0 +1,147 @@ +!!index array str + "I02" +!entry.I02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.059700 + "HA" "H1" 0 1 131075 4 1 0.086900 + "CB" "CT" 0 1 131075 5 6 0.130300 + "HB" "HC" 0 1 131075 6 1 0.018700 + "CG2" "CT" 0 1 131075 7 6 -0.320400 + "HG21" "HC" 0 1 131075 8 80 0.088200 + "HG22" "HC" 0 1 131075 9 80 0.088200 + "HG23" "HC" 0 1 131075 10 80 0.088200 + "CG1" "CT" 0 1 131075 11 6 -0.043000 + "HG12" "HC" 0 1 131075 12 80 0.023600 + "HG13" "HC" 0 1 131075 13 80 0.023600 + "CD1" "CT" 0 1 131075 14 6 -0.066000 + "HD11" "HC" 0 1 131075 15 1 0.018600 + "HD12" "HC" 0 1 131075 16 1 0.018600 + "HD13" "HC" 0 1 131075 17 1 0.018600 + "C" "C" 0 1 131075 18 6 0.597300 + "O" "O" 0 1 131075 19 8 -0.567900 +!entry.I02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB" "HC" 0 -1 0.0 + "CG2" "CT" 0 -1 0.0 + "HG21" "HC" 0 -1 0.0 + "HG22" "HC" 0 -1 0.0 + "HG23" "HC" 0 -1 0.0 + "CG1" "CT" 0 -1 0.0 + "HG12" "HC" 0 -1 0.0 + "HG13" "HC" 0 -1 0.0 + "CD1" "CT" 0 -1 0.0 + "HD11" "HC" 0 -1 0.0 + "HD12" "HC" 0 -1 0.0 + "HD13" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.I02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.I02.unit.childsequence single int + 2 +!entry.I02.unit.connect array int + 1 + 18 +!entry.I02.unit.connectivity table int atom1x int atom2x int flags + 18 19 17 + 14 16 17 + 14 17 17 + 14 15 17 + 11 12 17 + 11 13 17 + 11 14 17 + 7 9 17 + 7 10 17 + 7 8 17 + 5 6 17 + 5 7 17 + 5 11 17 + 3 4 17 + 3 18 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.I02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.I02.unit.name single str + "" +!entry.I02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.765000 -0.453000 + 0.0 0.0 0.0 + 0.346000 0.895000 -0.517000 + 0.564000 -0.015000 1.433000 + 0.254030 -0.945226 1.908356 + 2.083000 0.060000 1.408000 + 2.393962 0.990356 0.932648 + 2.466209 0.027948 2.427737 + 2.480124 -0.784295 0.844618 + 0.032000 1.180000 2.228000 + -1.051187 1.073889 2.285522 + 0.457307 1.117256 3.229973 + 0.375000 2.520000 1.618000 + -0.049975 2.583659 0.615796 + -0.035393 3.317826 2.237332 + 1.458519 2.627026 1.560247 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.I02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.I02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "I02" 1 20 1 "?" 0 +!entry.I02.unit.residuesPdbSequenceNumber array int + 1 +!entry.I02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.I02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ILE/I03.off b/share/off/ILE/I03.off new file mode 100644 index 0000000..66ed7ac --- /dev/null +++ b/share/off/ILE/I03.off @@ -0,0 +1,147 @@ +!!index array str + "I03" +!entry.I03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.059700 + "HA" "H1" 0 1 131075 4 1 0.086900 + "CB" "CT" 0 1 131075 5 6 0.130300 + "HB" "HC" 0 1 131075 6 1 0.018700 + "CG2" "CT" 0 1 131075 7 6 -0.320400 + "HG21" "HC" 0 1 131075 8 80 0.088200 + "HG22" "HC" 0 1 131075 9 80 0.088200 + "HG23" "HC" 0 1 131075 10 80 0.088200 + "CG1" "CT" 0 1 131075 11 6 -0.043000 + "HG12" "HC" 0 1 131075 12 80 0.023600 + "HG13" "HC" 0 1 131075 13 80 0.023600 + "CD1" "CT" 0 1 131075 14 6 -0.066000 + "HD11" "HC" 0 1 131075 15 1 0.018600 + "HD12" "HC" 0 1 131075 16 1 0.018600 + "HD13" "HC" 0 1 131075 17 1 0.018600 + "C" "C" 0 1 131075 18 6 0.597300 + "O" "O" 0 1 131075 19 8 -0.567900 +!entry.I03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB" "HC" 0 -1 0.0 + "CG2" "CT" 0 -1 0.0 + "HG21" "HC" 0 -1 0.0 + "HG22" "HC" 0 -1 0.0 + "HG23" "HC" 0 -1 0.0 + "CG1" "CT" 0 -1 0.0 + "HG12" "HC" 0 -1 0.0 + "HG13" "HC" 0 -1 0.0 + "CD1" "CT" 0 -1 0.0 + "HD11" "HC" 0 -1 0.0 + "HD12" "HC" 0 -1 0.0 + "HD13" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.I03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.I03.unit.childsequence single int + 2 +!entry.I03.unit.connect array int + 1 + 18 +!entry.I03.unit.connectivity table int atom1x int atom2x int flags + 18 19 17 + 14 16 17 + 14 17 17 + 14 15 17 + 11 12 17 + 11 13 17 + 11 14 17 + 7 9 17 + 7 10 17 + 7 8 17 + 5 6 17 + 5 7 17 + 5 11 17 + 3 4 17 + 3 18 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.I03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.I03.unit.name single str + "" +!entry.I03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.765000 -0.453000 + 0.0 0.0 0.0 + 0.346000 0.895000 -0.517000 + 0.564000 -0.015000 1.433000 + 0.158817 0.845838 1.964179 + 0.157000 -1.292000 2.152000 + 0.561992 -2.153706 1.621280 + 0.546377 -1.277003 3.169793 + -0.930225 -1.363158 2.180639 + 2.092000 0.060000 1.406000 + 2.457796 -0.913792 1.080756 + 2.365722 0.815885 0.669463 + 2.710000 0.410000 2.741000 + 2.436751 -0.345486 3.478322 + 3.795150 0.444512 2.642111 + 2.344678 1.384191 3.067030 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.I03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.I03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "I03" 1 20 1 "?" 0 +!entry.I03.unit.residuesPdbSequenceNumber array int + 1 +!entry.I03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.I03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ILE/I04.off b/share/off/ILE/I04.off new file mode 100644 index 0000000..2055db3 --- /dev/null +++ b/share/off/ILE/I04.off @@ -0,0 +1,147 @@ +!!index array str + "I04" +!entry.I04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.059700 + "HA" "H1" 0 1 131075 4 1 0.086900 + "CB" "CT" 0 1 131075 5 6 0.130300 + "HB" "HC" 0 1 131075 6 1 0.018700 + "CG2" "CT" 0 1 131075 7 6 -0.320400 + "HG21" "HC" 0 1 131075 8 80 0.088200 + "HG22" "HC" 0 1 131075 9 80 0.088200 + "HG23" "HC" 0 1 131075 10 80 0.088200 + "CG1" "CT" 0 1 131075 11 6 -0.043000 + "HG12" "HC" 0 1 131075 12 80 0.023600 + "HG13" "HC" 0 1 131075 13 80 0.023600 + "CD1" "CT" 0 1 131075 14 6 -0.066000 + "HD11" "HC" 0 1 131075 15 1 0.018600 + "HD12" "HC" 0 1 131075 16 1 0.018600 + "HD13" "HC" 0 1 131075 17 1 0.018600 + "C" "C" 0 1 131075 18 6 0.597300 + "O" "O" 0 1 131075 19 8 -0.567900 +!entry.I04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB" "HC" 0 -1 0.0 + "CG2" "CT" 0 -1 0.0 + "HG21" "HC" 0 -1 0.0 + "HG22" "HC" 0 -1 0.0 + "HG23" "HC" 0 -1 0.0 + "CG1" "CT" 0 -1 0.0 + "HG12" "HC" 0 -1 0.0 + "HG13" "HC" 0 -1 0.0 + "CD1" "CT" 0 -1 0.0 + "HD11" "HC" 0 -1 0.0 + "HD12" "HC" 0 -1 0.0 + "HD13" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.I04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.I04.unit.childsequence single int + 2 +!entry.I04.unit.connect array int + 1 + 18 +!entry.I04.unit.connectivity table int atom1x int atom2x int flags + 18 19 17 + 14 16 17 + 14 17 17 + 14 15 17 + 11 12 17 + 11 13 17 + 11 14 17 + 7 9 17 + 7 10 17 + 7 8 17 + 5 6 17 + 5 7 17 + 5 11 17 + 3 4 17 + 3 18 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.I04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.I04.unit.name single str + "" +!entry.I04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.765000 -0.453000 + 0.0 0.0 0.0 + 0.346000 0.895000 -0.517000 + 0.564000 -0.015000 1.433000 + 0.158817 0.845838 1.964179 + 0.157000 -1.292000 2.152000 + 0.561992 -2.153706 1.621280 + 0.546377 -1.277003 3.169793 + -0.930225 -1.363158 2.180639 + 2.092000 0.060000 1.406000 + 2.441362 -0.084350 2.428238 + 2.445561 -0.760823 0.781488 + 2.629000 1.369000 0.870000 + 2.275872 2.190572 1.494010 + 3.718921 1.347447 0.881358 + 2.280071 1.514098 -0.152740 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.I04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.I04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "I04" 1 20 1 "?" 0 +!entry.I04.unit.residuesPdbSequenceNumber array int + 1 +!entry.I04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.I04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/ILE/I05.off b/share/off/ILE/I05.off new file mode 100644 index 0000000..96d3c12 --- /dev/null +++ b/share/off/ILE/I05.off @@ -0,0 +1,147 @@ +!!index array str + "I05" +!entry.I05.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.059700 + "HA" "H1" 0 1 131075 4 1 0.086900 + "CB" "CT" 0 1 131075 5 6 0.130300 + "HB" "HC" 0 1 131075 6 1 0.018700 + "CG2" "CT" 0 1 131075 7 6 -0.320400 + "HG21" "HC" 0 1 131075 8 80 0.088200 + "HG22" "HC" 0 1 131075 9 80 0.088200 + "HG23" "HC" 0 1 131075 10 80 0.088200 + "CG1" "CT" 0 1 131075 11 6 -0.043000 + "HG12" "HC" 0 1 131075 12 80 0.023600 + "HG13" "HC" 0 1 131075 13 80 0.023600 + "CD1" "CT" 0 1 131075 14 6 -0.066000 + "HD11" "HC" 0 1 131075 15 1 0.018600 + "HD12" "HC" 0 1 131075 16 1 0.018600 + "HD13" "HC" 0 1 131075 17 1 0.018600 + "C" "C" 0 1 131075 18 6 0.597300 + "O" "O" 0 1 131075 19 8 -0.567900 +!entry.I05.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB" "HC" 0 -1 0.0 + "CG2" "CT" 0 -1 0.0 + "HG21" "HC" 0 -1 0.0 + "HG22" "HC" 0 -1 0.0 + "HG23" "HC" 0 -1 0.0 + "CG1" "CT" 0 -1 0.0 + "HG12" "HC" 0 -1 0.0 + "HG13" "HC" 0 -1 0.0 + "CD1" "CT" 0 -1 0.0 + "HD11" "HC" 0 -1 0.0 + "HD12" "HC" 0 -1 0.0 + "HD13" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.I05.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.I05.unit.childsequence single int + 2 +!entry.I05.unit.connect array int + 1 + 18 +!entry.I05.unit.connectivity table int atom1x int atom2x int flags + 18 19 17 + 14 16 17 + 14 17 17 + 14 15 17 + 11 12 17 + 11 13 17 + 11 14 17 + 7 9 17 + 7 10 17 + 7 8 17 + 5 6 17 + 5 7 17 + 5 11 17 + 3 4 17 + 3 18 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.I05.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.I05.unit.name single str + "" +!entry.I05.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.765000 -0.453000 + 0.0 0.0 0.0 + 0.346000 0.895000 -0.517000 + 0.564000 -0.015000 1.433000 + 1.650918 0.026506 1.367783 + 0.057000 1.185000 2.218000 + -1.030305 1.144232 2.283770 + 0.481910 1.169882 3.221476 + 0.354504 2.103350 1.711972 + 0.133000 -1.289000 2.163000 + -0.941992 -1.218667 2.328248 + 0.344958 -2.128521 1.500391 + 0.833000 -1.502000 3.486000 + 0.621579 -0.662787 4.149394 + 0.474973 -2.424749 3.943025 + 1.908530 -1.572640 3.321537 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.I05.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.I05.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "I05" 1 20 1 "?" 0 +!entry.I05.unit.residuesPdbSequenceNumber array int + 1 +!entry.I05.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.I05.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LEU/L01.off b/share/off/LEU/L01.off new file mode 100644 index 0000000..7a7214a --- /dev/null +++ b/share/off/LEU/L01.off @@ -0,0 +1,147 @@ +!!index array str + "L01" +!entry.L01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.051800 + "HA" "H1" 0 1 131075 4 1 0.092200 + "CB" "CT" 0 1 131075 5 6 -0.110200 + "HB2" "HC" 0 1 131075 6 1 0.045700 + "HB3" "HC" 0 1 131075 7 1 0.045700 + "CG" "CT" 0 1 131075 8 6 0.353100 + "HG" "HC" 0 1 131075 9 1 -0.036100 + "CD1" "CT" 0 1 131075 10 6 -0.412100 + "HD11" "HC" 0 1 131075 11 1 0.100000 + "HD12" "HC" 0 1 131075 12 1 0.100000 + "HD13" "HC" 0 1 131075 13 1 0.100000 + "CD2" "CT" 0 1 131075 14 6 -0.412100 + "HD21" "HC" 0 1 131075 15 1 0.100000 + "HD22" "HC" 0 1 131075 16 1 0.100000 + "HD23" "HC" 0 1 131075 17 1 0.100000 + "C" "C" 0 1 131075 18 6 0.597300 + "O" "O" 0 1 131075 19 8 -0.567900 +!entry.L01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG" "HC" 0 -1 0.0 + "CD1" "CT" 0 -1 0.0 + "HD11" "HC" 0 -1 0.0 + "HD12" "HC" 0 -1 0.0 + "HD13" "HC" 0 -1 0.0 + "CD2" "CT" 0 -1 0.0 + "HD21" "HC" 0 -1 0.0 + "HD22" "HC" 0 -1 0.0 + "HD23" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.L01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.L01.unit.childsequence single int + 2 +!entry.L01.unit.connect array int + 1 + 18 +!entry.L01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 18 17 + 3 5 17 + 5 6 17 + 5 7 17 + 5 8 17 + 8 9 17 + 8 14 17 + 8 10 17 + 10 12 17 + 10 11 17 + 10 13 17 + 14 16 17 + 14 17 17 + 14 15 17 + 18 19 17 +!entry.L01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 +!entry.L01.unit.name single str + "" +!entry.L01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.106000 -0.878000 1.915000 + 1.616000 -0.124000 1.349000 + 0.230000 1.243000 2.271000 + -0.845000 1.423000 2.255000 + 0.690000 1.049000 3.708000 + 1.765000 0.869000 3.725000 + 0.463000 1.944000 4.287000 + 0.172000 0.194000 4.144000 + 0.943000 2.461000 1.705000 + 0.609000 2.635000 0.682000 + 0.712000 3.334000 2.315000 + 2.019000 2.288000 1.711000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.L01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.L01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "L01" 1 20 1 "?" 0 +!entry.L01.unit.residuesPdbSequenceNumber array int + 1 +!entry.L01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.L01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LEU/L02.off b/share/off/LEU/L02.off new file mode 100644 index 0000000..1facf17 --- /dev/null +++ b/share/off/LEU/L02.off @@ -0,0 +1,147 @@ +!!index array str + "L02" +!entry.L02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.051800 + "HA" "H1" 0 1 131075 4 1 0.092200 + "CB" "CT" 0 1 131075 5 6 -0.110200 + "HB2" "HC" 0 1 131075 6 1 0.045700 + "HB3" "HC" 0 1 131075 7 1 0.045700 + "CG" "CT" 0 1 131075 8 6 0.353100 + "HG" "HC" 0 1 131075 9 1 -0.036100 + "CD1" "CT" 0 1 131075 10 6 -0.412100 + "HD11" "HC" 0 1 131075 11 1 0.100000 + "HD12" "HC" 0 1 131075 12 1 0.100000 + "HD13" "HC" 0 1 131075 13 1 0.100000 + "CD2" "CT" 0 1 131075 14 6 -0.412100 + "HD21" "HC" 0 1 131075 15 1 0.100000 + "HD22" "HC" 0 1 131075 16 1 0.100000 + "HD23" "HC" 0 1 131075 17 1 0.100000 + "C" "C" 0 1 131075 18 6 0.597300 + "O" "O" 0 1 131075 19 8 -0.567900 +!entry.L02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG" "HC" 0 -1 0.0 + "CD1" "CT" 0 -1 0.0 + "HD11" "HC" 0 -1 0.0 + "HD12" "HC" 0 -1 0.0 + "HD13" "HC" 0 -1 0.0 + "CD2" "CT" 0 -1 0.0 + "HD21" "HC" 0 -1 0.0 + "HD22" "HC" 0 -1 0.0 + "HD23" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.L02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.L02.unit.childsequence single int + 2 +!entry.L02.unit.connect array int + 1 + 18 +!entry.L02.unit.connectivity table int atom1x int atom2x int flags + 18 19 17 + 14 16 17 + 14 17 17 + 14 15 17 + 10 12 17 + 10 11 17 + 10 13 17 + 8 9 17 + 8 14 17 + 8 10 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 18 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.L02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.L02.unit.name single str + "" +!entry.L02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + -0.141638 -0.630113 2.009083 + 1.517759 -0.471819 1.384329 + 0.661000 1.367000 2.110000 + 1.274940 2.015019 1.484356 + -0.709000 1.999000 2.300000 + -1.325076 1.351803 2.924420 + -0.598373 2.969960 2.782487 + -1.187965 2.129131 1.328865 + 1.317000 1.233000 3.475000 + 2.313010 0.805297 3.359268 + 1.396439 2.216012 3.938645 + 0.713281 0.581273 4.106281 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.L02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.L02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "L02" 1 20 1 "?" 0 +!entry.L02.unit.residuesPdbSequenceNumber array int + 1 +!entry.L02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.L02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LEU/L03.off b/share/off/LEU/L03.off new file mode 100644 index 0000000..28694a6 --- /dev/null +++ b/share/off/LEU/L03.off @@ -0,0 +1,147 @@ +!!index array str + "L03" +!entry.L03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.051800 + "HA" "H1" 0 1 131075 4 1 0.092200 + "CB" "CT" 0 1 131075 5 6 -0.110200 + "HB2" "HC" 0 1 131075 6 1 0.045700 + "HB3" "HC" 0 1 131075 7 1 0.045700 + "CG" "CT" 0 1 131075 8 6 0.353100 + "HG" "HC" 0 1 131075 9 1 -0.036100 + "CD1" "CT" 0 1 131075 10 6 -0.412100 + "HD11" "HC" 0 1 131075 11 1 0.100000 + "HD12" "HC" 0 1 131075 12 1 0.100000 + "HD13" "HC" 0 1 131075 13 1 0.100000 + "CD2" "CT" 0 1 131075 14 6 -0.412100 + "HD21" "HC" 0 1 131075 15 1 0.100000 + "HD22" "HC" 0 1 131075 16 1 0.100000 + "HD23" "HC" 0 1 131075 17 1 0.100000 + "C" "C" 0 1 131075 18 6 0.597300 + "O" "O" 0 1 131075 19 8 -0.567900 +!entry.L03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG" "HC" 0 -1 0.0 + "CD1" "CT" 0 -1 0.0 + "HD11" "HC" 0 -1 0.0 + "HD12" "HC" 0 -1 0.0 + "HD13" "HC" 0 -1 0.0 + "CD2" "CT" 0 -1 0.0 + "HD21" "HC" 0 -1 0.0 + "HD22" "HC" 0 -1 0.0 + "HD23" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.L03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.L03.unit.childsequence single int + 2 +!entry.L03.unit.connect array int + 1 + 18 +!entry.L03.unit.connectivity table int atom1x int atom2x int flags + 18 19 17 + 14 16 17 + 14 17 17 + 14 15 17 + 10 12 17 + 10 11 17 + 10 13 17 + 8 9 17 + 8 14 17 + 8 10 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 18 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.L03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.L03.unit.name single str + "" +!entry.L03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079460 0.858125 1.926254 + 0.168010 -0.919443 1.889113 + 2.056000 0.072000 1.588000 + 2.506344 -0.744610 1.023535 + 2.587000 1.399000 1.067000 + 2.136731 2.217265 1.629151 + 3.669884 1.429943 1.186163 + 2.335307 1.502660 0.010899 + 2.455000 -0.059000 3.049000 + 2.107096 -1.016728 3.436403 + 3.539957 -0.005468 3.136134 + 2.004043 0.750149 3.623158 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.L03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.L03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "L03" 1 20 1 "?" 0 +!entry.L03.unit.residuesPdbSequenceNumber array int + 1 +!entry.L03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.L03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LEU/L04.off b/share/off/LEU/L04.off new file mode 100644 index 0000000..8576155 --- /dev/null +++ b/share/off/LEU/L04.off @@ -0,0 +1,147 @@ +!!index array str + "L04" +!entry.L04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.051800 + "HA" "H1" 0 1 131075 4 1 0.092200 + "CB" "CT" 0 1 131075 5 6 -0.110200 + "HB2" "HC" 0 1 131075 6 1 0.045700 + "HB3" "HC" 0 1 131075 7 1 0.045700 + "CG" "CT" 0 1 131075 8 6 0.353100 + "HG" "HC" 0 1 131075 9 1 -0.036100 + "CD1" "CT" 0 1 131075 10 6 -0.412100 + "HD11" "HC" 0 1 131075 11 1 0.100000 + "HD12" "HC" 0 1 131075 12 1 0.100000 + "HD13" "HC" 0 1 131075 13 1 0.100000 + "CD2" "CT" 0 1 131075 14 6 -0.412100 + "HD21" "HC" 0 1 131075 15 1 0.100000 + "HD22" "HC" 0 1 131075 16 1 0.100000 + "HD23" "HC" 0 1 131075 17 1 0.100000 + "C" "C" 0 1 131075 18 6 0.597300 + "O" "O" 0 1 131075 19 8 -0.567900 +!entry.L04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG" "HC" 0 -1 0.0 + "CD1" "CT" 0 -1 0.0 + "HD11" "HC" 0 -1 0.0 + "HD12" "HC" 0 -1 0.0 + "HD13" "HC" 0 -1 0.0 + "CD2" "CT" 0 -1 0.0 + "HD21" "HC" 0 -1 0.0 + "HD22" "HC" 0 -1 0.0 + "HD23" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.L04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.L04.unit.childsequence single int + 2 +!entry.L04.unit.connect array int + 1 + 18 +!entry.L04.unit.connectivity table int atom1x int atom2x int flags + 18 19 17 + 14 16 17 + 14 17 17 + 14 15 17 + 10 12 17 + 10 11 17 + 10 13 17 + 8 9 17 + 8 14 17 + 8 10 17 + 5 6 17 + 5 7 17 + 5 8 17 + 3 4 17 + 3 18 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.L04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.L04.unit.name single str + "" +!entry.L04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.011686 0.803011 1.951050 + 0.244672 -0.959542 1.861066 + 2.046000 0.191000 1.592000 + 2.422429 0.750784 0.735715 + 2.359000 0.952000 2.871000 + 1.982478 0.393709 3.728238 + 3.437481 1.077571 2.965368 + 1.881359 1.931905 2.837977 + 2.754000 -1.153000 1.653000 + 2.564089 -1.706033 0.732973 + 3.826285 -0.994653 1.765784 + 2.379551 -1.723109 2.503003 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.L04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.L04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "L04" 1 20 1 "?" 0 +!entry.L04.unit.residuesPdbSequenceNumber array int + 1 +!entry.L04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.L04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K20.off b/share/off/LYN/K20.off new file mode 100644 index 0000000..a3ae66f --- /dev/null +++ b/share/off/LYN/K20.off @@ -0,0 +1,159 @@ +!!index array str + "K20" +!entry.K20.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K20.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K20.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K20.unit.childsequence single int + 2 +!entry.K20.unit.connect array int + 1 + 20 +!entry.K20.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K20.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K20.unit.name single str + "" +!entry.K20.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.079326 -0.845949 1.946730 + 1.613817 -0.150939 1.372768 + 0.246000 1.277000 2.204000 + 0.700574 2.113638 1.673433 + -0.833890 1.418606 2.247444 + 0.805000 1.209000 3.616000 + 0.348841 0.362765 4.129716 + 1.882927 1.058793 3.555904 + 0.514000 2.486000 4.387000 + 0.967229 3.319979 3.851124 + -0.566581 2.623729 4.425408 + 1.057000 2.433000 5.773000 + 0.844001 3.296709 6.251266 + 0.636837 1.660542 6.269861 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K20.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K20.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K20" 1 22 1 "p" 0 +!entry.K20.unit.residuesPdbSequenceNumber array int + 1 +!entry.K20.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K20.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K21.off b/share/off/LYN/K21.off new file mode 100644 index 0000000..2290e8e --- /dev/null +++ b/share/off/LYN/K21.off @@ -0,0 +1,159 @@ +!!index array str + "K21" +!entry.K21.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K21.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K21.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K21.unit.childsequence single int + 2 +!entry.K21.unit.connect array int + 1 + 20 +!entry.K21.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K21.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K21.unit.name single str + "" +!entry.K21.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.079326 -0.845949 1.946730 + 1.613817 -0.150939 1.372768 + 0.246000 1.277000 2.204000 + 0.700574 2.113638 1.673433 + -0.833890 1.418606 2.247444 + 0.805000 1.209000 3.616000 + 0.348841 0.362765 4.129716 + 1.882927 1.058793 3.555904 + 0.514000 2.486000 4.387000 + -0.562206 2.658015 4.369884 + 0.842725 2.346089 5.416788 + 1.214000 3.662000 3.798000 + 0.996002 4.488075 4.336681 + 2.211274 3.502992 3.814156 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K21.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K21.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K21" 1 22 1 "p" 0 +!entry.K21.unit.residuesPdbSequenceNumber array int + 1 +!entry.K21.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K21.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K22.off b/share/off/LYN/K22.off new file mode 100644 index 0000000..0afa3e6 --- /dev/null +++ b/share/off/LYN/K22.off @@ -0,0 +1,159 @@ +!!index array str + "K22" +!entry.K22.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K22.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K22.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K22.unit.childsequence single int + 2 +!entry.K22.unit.connect array int + 1 + 20 +!entry.K22.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K22.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K22.unit.name single str + "" +!entry.K22.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.079326 -0.845949 1.946730 + 1.613817 -0.150939 1.372768 + 0.246000 1.277000 2.204000 + 0.700574 2.113638 1.673433 + -0.833890 1.418606 2.247444 + 0.805000 1.209000 3.616000 + 0.348841 0.362765 4.129716 + 1.882927 1.058793 3.555904 + 0.514000 2.486000 4.387000 + 1.020836 2.426417 5.350155 + 0.912547 3.326390 3.818666 + -0.946000 2.683000 4.606000 + -1.096804 3.539323 5.119876 + -1.415775 2.738665 3.713637 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K22.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K22.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K22" 1 22 1 "p" 0 +!entry.K22.unit.residuesPdbSequenceNumber array int + 1 +!entry.K22.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K22.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K23.off b/share/off/LYN/K23.off new file mode 100644 index 0000000..6581ccc --- /dev/null +++ b/share/off/LYN/K23.off @@ -0,0 +1,159 @@ +!!index array str + "K23" +!entry.K23.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K23.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K23.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K23.unit.childsequence single int + 2 +!entry.K23.unit.connect array int + 1 + 20 +!entry.K23.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K23.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K23.unit.name single str + "" +!entry.K23.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.079326 -0.845949 1.946730 + 1.613817 -0.150939 1.372768 + 0.246000 1.277000 2.204000 + 0.700574 2.113638 1.673433 + -0.833890 1.418606 2.247444 + 0.805000 1.209000 3.616000 + 1.858778 0.936037 3.559942 + 0.708968 2.192661 4.075661 + 0.060000 0.183000 4.455000 + -0.991656 0.467605 4.488479 + 0.157554 -0.789240 3.971956 + 0.597000 0.104000 5.842000 + 0.077456 -0.586131 6.365349 + 1.571366 -0.160125 5.811221 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K23.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K23.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K23" 1 22 1 "p" 0 +!entry.K23.unit.residuesPdbSequenceNumber array int + 1 +!entry.K23.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K23.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K24.off b/share/off/LYN/K24.off new file mode 100644 index 0000000..4399127 --- /dev/null +++ b/share/off/LYN/K24.off @@ -0,0 +1,159 @@ +!!index array str + "K24" +!entry.K24.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K24.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K24.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K24.unit.childsequence single int + 2 +!entry.K24.unit.connect array int + 1 + 20 +!entry.K24.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K24.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K24.unit.name single str + "" +!entry.K24.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.079326 -0.845949 1.946730 + 1.613817 -0.150939 1.372768 + 0.246000 1.277000 2.204000 + 0.700574 2.113638 1.673433 + -0.833890 1.418606 2.247444 + 0.805000 1.209000 3.616000 + 1.858778 0.936037 3.559942 + 0.708968 2.192661 4.075661 + 0.060000 0.183000 4.455000 + 0.103926 -0.776526 3.939751 + 0.562007 0.100484 5.418991 + -1.363000 0.567000 4.668000 + -1.821654 -0.137564 5.227755 + -1.403923 1.455888 5.145809 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K24.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K24.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K24" 1 22 1 "p" 0 +!entry.K24.unit.residuesPdbSequenceNumber array int + 1 +!entry.K24.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K24.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K25.off b/share/off/LYN/K25.off new file mode 100644 index 0000000..a3540d9 --- /dev/null +++ b/share/off/LYN/K25.off @@ -0,0 +1,159 @@ +!!index array str + "K25" +!entry.K25.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K25.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K25.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K25.unit.childsequence single int + 2 +!entry.K25.unit.connect array int + 1 + 20 +!entry.K25.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K25.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K25.unit.name single str + "" +!entry.K25.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.079326 -0.845949 1.946730 + 1.613817 -0.150939 1.372768 + 0.246000 1.277000 2.204000 + 0.700574 2.113638 1.673433 + -0.833890 1.418606 2.247444 + 0.805000 1.209000 3.616000 + 0.444847 2.073109 4.174305 + 0.444398 0.295516 4.088877 + 2.325000 1.209000 3.608000 + 2.663942 0.345857 3.035109 + 2.664396 2.123408 3.121413 + 2.887000 1.142000 4.985000 + 3.895872 1.144058 4.937321 + 2.573395 1.941942 5.515890 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K25.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K25.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K25" 1 22 1 "p" 0 +!entry.K25.unit.residuesPdbSequenceNumber array int + 1 +!entry.K25.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K25.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K26.off b/share/off/LYN/K26.off new file mode 100644 index 0000000..0163a36 --- /dev/null +++ b/share/off/LYN/K26.off @@ -0,0 +1,159 @@ +!!index array str + "K26" +!entry.K26.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K26.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K26.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K26.unit.childsequence single int + 2 +!entry.K26.unit.connect array int + 1 + 20 +!entry.K26.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K26.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K26.unit.name single str + "" +!entry.K26.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.079326 -0.845949 1.946730 + 1.613817 -0.150939 1.372768 + 0.246000 1.277000 2.204000 + 0.700574 2.113638 1.673433 + -0.833890 1.418606 2.247444 + 0.805000 1.209000 3.616000 + 0.444847 2.073109 4.174305 + 0.444398 0.295516 4.088877 + 2.325000 1.209000 3.608000 + 2.672488 1.056417 4.629798 + 2.663817 0.383190 2.982428 + 2.877000 2.489000 3.082000 + 3.886191 2.450003 3.092624 + 2.555476 2.630366 2.135038 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K26.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K26.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K26" 1 22 1 "p" 0 +!entry.K26.unit.residuesPdbSequenceNumber array int + 1 +!entry.K26.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K26.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K27.off b/share/off/LYN/K27.off new file mode 100644 index 0000000..504218e --- /dev/null +++ b/share/off/LYN/K27.off @@ -0,0 +1,159 @@ +!!index array str + "K27" +!entry.K27.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K27.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K27.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K27.unit.childsequence single int + 2 +!entry.K27.unit.connect array int + 1 + 20 +!entry.K27.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K27.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K27.unit.name single str + "" +!entry.K27.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.150839 -0.895759 1.920202 + 1.622502 -0.060095 1.369741 + 0.143000 1.225000 2.242000 + -0.938675 1.346744 2.184913 + 0.435806 1.064739 3.279633 + 0.822000 2.477000 1.712000 + 1.901488 2.336386 1.767066 + 0.527098 2.618284 0.672206 + 0.429000 3.703000 2.521000 + -0.653383 3.817825 2.463020 + 0.721119 3.536037 3.557769 + 1.087000 4.939000 2.013000 + 0.801069 5.727935 2.575072 + 2.089964 4.832973 2.067039 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K27.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K27.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K27" 1 22 1 "p" 0 +!entry.K27.unit.residuesPdbSequenceNumber array int + 1 +!entry.K27.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K27.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K28.off b/share/off/LYN/K28.off new file mode 100644 index 0000000..3a69aa9 --- /dev/null +++ b/share/off/LYN/K28.off @@ -0,0 +1,159 @@ +!!index array str + "K28" +!entry.K28.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K28.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K28.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K28.unit.childsequence single int + 2 +!entry.K28.unit.connect array int + 1 + 20 +!entry.K28.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K28.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K28.unit.name single str + "" +!entry.K28.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.150839 -0.895759 1.920202 + 1.622502 -0.060095 1.369741 + 0.143000 1.225000 2.242000 + -0.938675 1.346744 2.184913 + 0.435806 1.064739 3.279633 + 0.822000 2.477000 1.712000 + 1.901488 2.336386 1.767066 + 0.527098 2.618284 0.672206 + 0.429000 3.703000 2.521000 + 0.663781 3.511090 3.567971 + 1.017404 4.549269 2.166447 + -1.021000 4.016000 2.387000 + -1.241117 4.833833 2.937270 + -1.238677 4.194280 1.416984 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K28.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K28.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K28" 1 22 1 "p" 0 +!entry.K28.unit.residuesPdbSequenceNumber array int + 1 +!entry.K28.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K28.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K29.off b/share/off/LYN/K29.off new file mode 100644 index 0000000..7484ebb --- /dev/null +++ b/share/off/LYN/K29.off @@ -0,0 +1,159 @@ +!!index array str + "K29" +!entry.K29.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K29.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K29.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K29.unit.childsequence single int + 2 +!entry.K29.unit.connect array int + 1 + 20 +!entry.K29.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K29.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K29.unit.name single str + "" +!entry.K29.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.150839 -0.895759 1.920202 + 1.622502 -0.060095 1.369741 + 0.143000 1.225000 2.242000 + -0.938675 1.346744 2.184913 + 0.435806 1.064739 3.279633 + 0.822000 2.477000 1.712000 + 0.626729 2.551415 0.642219 + 0.397605 3.343333 2.219401 + 2.322000 2.435000 1.951000 + 2.494909 2.348344 3.023704 + 2.724026 1.556361 1.446553 + 3.001000 3.657000 1.436000 + 3.993112 3.590894 1.613321 + 2.841259 3.737254 0.441947 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K29.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K29.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K29" 1 22 1 "p" 0 +!entry.K29.unit.residuesPdbSequenceNumber array int + 1 +!entry.K29.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K29.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K30.off b/share/off/LYN/K30.off new file mode 100644 index 0000000..5356036 --- /dev/null +++ b/share/off/LYN/K30.off @@ -0,0 +1,159 @@ +!!index array str + "K30" +!entry.K30.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K30.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K30.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K30.unit.childsequence single int + 2 +!entry.K30.unit.connect array int + 1 + 20 +!entry.K30.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K30.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K30.unit.name single str + "" +!entry.K30.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.098218 0.860097 1.939635 + 0.185931 -0.917082 1.906828 + 2.051000 0.073000 1.529000 + 2.473785 -0.787594 1.010607 + 2.386068 0.989583 1.043504 + 2.513000 0.069000 2.977000 + 2.076169 0.929511 3.483752 + 2.162613 -0.847735 3.451262 + 4.029000 0.141000 3.072000 + 4.445726 -0.720241 2.549789 + 4.359290 1.057009 2.582168 + 4.497000 0.138000 4.486000 + 5.505610 0.186675 4.506886 + 4.111308 0.936202 4.969957 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K30.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K30.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K30" 1 22 1 "p" 0 +!entry.K30.unit.residuesPdbSequenceNumber array int + 1 +!entry.K30.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K30.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K31.off b/share/off/LYN/K31.off new file mode 100644 index 0000000..59efece --- /dev/null +++ b/share/off/LYN/K31.off @@ -0,0 +1,159 @@ +!!index array str + "K31" +!entry.K31.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K31.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K31.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K31.unit.childsequence single int + 2 +!entry.K31.unit.connect array int + 1 + 20 +!entry.K31.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K31.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K31.unit.name single str + "" +!entry.K31.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.098218 0.860097 1.939635 + 0.185931 -0.917082 1.906828 + 2.051000 0.073000 1.529000 + 2.473785 -0.787594 1.010607 + 2.386068 0.989583 1.043504 + 2.513000 0.069000 2.977000 + 2.076169 0.929511 3.483752 + 2.162613 -0.847735 3.451262 + 4.029000 0.141000 3.072000 + 4.363706 1.023991 2.527575 + 4.301054 0.238036 4.123033 + 4.680000 -1.070000 2.501000 + 5.682930 -0.983397 2.583047 + 4.370316 -1.888267 3.005613 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K31.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K31.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K31" 1 22 1 "p" 0 +!entry.K31.unit.residuesPdbSequenceNumber array int + 1 +!entry.K31.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K31.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K32.off b/share/off/LYN/K32.off new file mode 100644 index 0000000..01282f8 --- /dev/null +++ b/share/off/LYN/K32.off @@ -0,0 +1,159 @@ +!!index array str + "K32" +!entry.K32.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K32.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K32.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K32.unit.childsequence single int + 2 +!entry.K32.unit.connect array int + 1 + 20 +!entry.K32.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K32.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K32.unit.name single str + "" +!entry.K32.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.098218 0.860097 1.939635 + 0.185931 -0.917082 1.906828 + 2.051000 0.073000 1.529000 + 2.473785 -0.787594 1.010607 + 2.386068 0.989583 1.043504 + 2.513000 0.069000 2.977000 + 2.076169 0.929511 3.483752 + 2.162613 -0.847735 3.451262 + 4.029000 0.141000 3.072000 + 4.311693 0.032196 4.119066 + 4.447446 -0.684082 2.495596 + 4.557000 1.431000 2.547000 + 5.563775 1.440230 2.627112 + 4.295524 1.531817 1.576657 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K32.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K32.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K32" 1 22 1 "p" 0 +!entry.K32.unit.residuesPdbSequenceNumber array int + 1 +!entry.K32.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K32.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K33.off b/share/off/LYN/K33.off new file mode 100644 index 0000000..d5d44ac --- /dev/null +++ b/share/off/LYN/K33.off @@ -0,0 +1,159 @@ +!!index array str + "K33" +!entry.K33.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K33.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K33.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K33.unit.childsequence single int + 2 +!entry.K33.unit.connect array int + 1 + 20 +!entry.K33.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K33.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K33.unit.name single str + "" +!entry.K33.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.098218 0.860097 1.939635 + 0.185931 -0.917082 1.906828 + 2.051000 0.073000 1.529000 + 2.473785 -0.787594 1.010607 + 2.386068 0.989583 1.043504 + 2.513000 0.069000 2.977000 + 2.060670 -0.783455 3.483771 + 3.598155 -0.032013 2.995296 + 2.112000 1.351000 3.687000 + 2.563825 2.190198 3.158132 + 1.026296 1.438789 3.646523 + 2.558000 1.362000 5.108000 + 2.273280 2.227658 5.543511 + 2.139103 0.584705 5.598343 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K33.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K33.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K33" 1 22 1 "p" 0 +!entry.K33.unit.residuesPdbSequenceNumber array int + 1 +!entry.K33.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K33.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K34.off b/share/off/LYN/K34.off new file mode 100644 index 0000000..cf292e6 --- /dev/null +++ b/share/off/LYN/K34.off @@ -0,0 +1,159 @@ +!!index array str + "K34" +!entry.K34.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K34.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K34.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K34.unit.childsequence single int + 2 +!entry.K34.unit.connect array int + 1 + 20 +!entry.K34.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K34.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K34.unit.name single str + "" +!entry.K34.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.098218 0.860097 1.939635 + 0.185931 -0.917082 1.906828 + 2.051000 0.073000 1.529000 + 2.473785 -0.787594 1.010607 + 2.386068 0.989583 1.043504 + 2.513000 0.069000 2.977000 + 3.583025 0.275332 3.000919 + 1.980092 0.853725 3.513950 + 2.241000 -1.272000 3.639000 + 1.169137 -1.464635 3.593151 + 2.772358 -2.042780 3.080739 + 2.688000 -1.291000 5.059000 + 2.490524 -2.195809 5.462018 + 3.681264 -1.112944 5.101676 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K34.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K34.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K34" 1 22 1 "p" 0 +!entry.K34.unit.residuesPdbSequenceNumber array int + 1 +!entry.K34.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K34.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K35.off b/share/off/LYN/K35.off new file mode 100644 index 0000000..d6802b4 --- /dev/null +++ b/share/off/LYN/K35.off @@ -0,0 +1,159 @@ +!!index array str + "K35" +!entry.K35.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K35.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K35.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K35.unit.childsequence single int + 2 +!entry.K35.unit.connect array int + 1 + 20 +!entry.K35.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K35.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K35.unit.name single str + "" +!entry.K35.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.098218 0.860097 1.939635 + 0.185931 -0.917082 1.906828 + 2.051000 0.073000 1.529000 + 2.341084 -0.085099 2.567729 + 2.476586 -0.716269 0.909295 + 2.570000 1.422000 1.058000 + 2.264402 1.569526 0.022169 + 2.129318 2.200564 1.680686 + 4.085000 1.494000 1.154000 + 4.369890 1.331808 2.193534 + 4.504961 0.701329 0.534803 + 4.608000 2.811000 0.696000 + 5.614883 2.819245 0.774856 + 4.344488 2.961295 -0.267365 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K35.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K35.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K35" 1 22 1 "p" 0 +!entry.K35.unit.residuesPdbSequenceNumber array int + 1 +!entry.K35.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K35.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K36.off b/share/off/LYN/K36.off new file mode 100644 index 0000000..590d100 --- /dev/null +++ b/share/off/LYN/K36.off @@ -0,0 +1,159 @@ +!!index array str + "K36" +!entry.K36.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K36.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K36.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K36.unit.childsequence single int + 2 +!entry.K36.unit.connect array int + 1 + 20 +!entry.K36.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K36.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K36.unit.name single str + "" +!entry.K36.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 0.098218 0.860097 1.939635 + 0.185931 -0.917082 1.906828 + 2.051000 0.073000 1.529000 + 2.341084 -0.085099 2.567729 + 2.476586 -0.716269 0.909295 + 2.570000 1.422000 1.058000 + 2.264402 1.569526 0.022169 + 2.129318 2.200564 1.680686 + 4.085000 1.494000 1.154000 + 4.395155 2.508799 0.904826 + 4.373264 1.268286 2.180672 + 4.747000 0.532000 0.230000 + 5.749551 0.610739 0.323761 + 4.460069 -0.408431 0.460995 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K36.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K36.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K36" 1 22 1 "p" 0 +!entry.K36.unit.residuesPdbSequenceNumber array int + 1 +!entry.K36.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K36.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K37.off b/share/off/LYN/K37.off new file mode 100644 index 0000000..ae900d2 --- /dev/null +++ b/share/off/LYN/K37.off @@ -0,0 +1,159 @@ +!!index array str + "K37" +!entry.K37.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K37.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K37.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K37.unit.childsequence single int + 2 +!entry.K37.unit.connect array int + 1 + 20 +!entry.K37.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K37.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K37.unit.name single str + "" +!entry.K37.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 1.622502 0.060096 1.369741 + 0.150838 0.895759 1.920203 + 0.143000 -1.225000 2.242000 + -0.944782 -1.276407 2.288770 + 0.526816 -2.112118 1.738205 + 0.708000 -1.159000 3.652000 + 1.794500 -1.098945 3.588677 + 0.322902 -0.263235 4.139242 + 0.315000 -2.384000 4.461000 + -0.773177 -2.431940 4.501904 + 0.698188 -3.267819 3.950970 + 0.862000 -2.334000 5.846000 + 0.579731 -3.162767 6.349556 + 1.870337 -2.290005 5.808329 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K37.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K37.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K37" 1 22 1 "p" 0 +!entry.K37.unit.residuesPdbSequenceNumber array int + 1 +!entry.K37.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K37.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYN/K38.off b/share/off/LYN/K38.off new file mode 100644 index 0000000..0cf6655 --- /dev/null +++ b/share/off/LYN/K38.off @@ -0,0 +1,159 @@ +!!index array str + "K38" +!entry.K38.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131072 1 7 -0.415700 + "H" "H" 0 1 131072 2 1 0.271900 + "CA" "CX" 0 1 131072 3 -1 -0.072060 + "HA" "H1" 0 1 131072 4 1 0.099400 + "CB" "CT" 0 1 131072 5 6 -0.048450 + "HB2" "HC" 0 1 131072 6 1 0.034000 + "HB3" "HC" 0 1 131072 7 1 0.034000 + "CG" "CT" 0 1 131072 8 6 0.066120 + "HG2" "HC" 0 1 131072 9 1 0.010410 + "HG3" "HC" 0 1 131072 10 1 0.010410 + "CD" "CT" 0 1 131072 11 6 -0.037680 + "HD2" "HC" 0 1 131072 12 1 0.011550 + "HD3" "HC" 0 1 131072 13 1 0.011550 + "CE" "CT" 0 1 131072 14 6 0.326040 + "HE2" "HP" 0 1 131072 15 1 -0.033580 + "HE3" "HP" 0 1 131072 16 1 -0.033580 + "NZ" "N3" 0 1 131072 17 7 -1.035810 + "HZ2" "H" 0 1 131072 18 1 0.386040 + "HZ3" "H" 0 1 131072 19 1 0.386040 + "C" "C" 0 1 131072 20 6 0.597300 + "O" "O" 0 1 131072 21 8 -0.567900 +!entry.K38.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K38.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K38.unit.childsequence single int + 2 +!entry.K38.unit.connect array int + 1 + 20 +!entry.K38.unit.connectivity table int atom1x int atom2x int flags + 20 21 1 + 17 18 1 + 17 19 1 + 14 15 1 + 14 16 1 + 14 17 1 + 11 12 1 + 11 13 1 + 11 14 1 + 8 9 1 + 8 10 1 + 8 11 1 + 5 6 1 + 5 7 1 + 5 8 1 + 3 4 1 + 3 5 1 + 3 20 1 + 1 2 1 + 1 3 1 +!entry.K38.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K38.unit.name single str + "" +!entry.K38.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.936827 -0.770142 -0.444640 + 0.0 0.0 0.0 + 0.369140 0.889824 -0.509949 + 0.536000 0.0 1.433000 + 1.622502 0.060096 1.369741 + 0.150838 0.895759 1.920203 + 0.143000 -1.225000 2.242000 + -0.944782 -1.276407 2.288770 + 0.526816 -2.112118 1.738205 + 0.708000 -1.159000 3.652000 + 1.794500 -1.098945 3.588677 + 0.322902 -0.263235 4.139242 + 0.315000 -2.384000 4.461000 + 0.655386 -2.239944 5.486420 + -0.771679 -2.467995 4.447856 + 0.916000 -3.631000 3.909000 + 0.631965 -4.419635 4.472453 + 0.600379 -3.764897 2.958972 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K38.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 1 20 0 0 0 0 +!entry.K38.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K38" 1 22 1 "p" 0 +!entry.K38.unit.residuesPdbSequenceNumber array int + 1 +!entry.K38.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K38.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K01.off b/share/off/LYS/K01.off new file mode 100644 index 0000000..149b172 --- /dev/null +++ b/share/off/LYS/K01.off @@ -0,0 +1,165 @@ +!!index array str + "K01" +!entry.K01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K01.unit.childsequence single int + 2 +!entry.K01.unit.connect array int + 1 + 21 +!entry.K01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 21 17 + 3 5 17 + 5 7 17 + 5 6 17 + 5 8 17 + 8 10 17 + 8 9 17 + 8 11 17 + 11 12 17 + 11 13 17 + 11 14 17 + 14 15 17 + 14 16 17 + 14 17 17 + 17 18 17 + 17 20 17 + 17 19 17 + 21 22 17 +!entry.K01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 + "R" 1 "A" 20 + "R" 1 "A" 21 + "R" 1 "A" 22 +!entry.K01.unit.name single str + "" +!entry.K01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.349000 0.363000 4.130000 + 1.883000 1.059000 3.556000 + 0.514000 2.486000 4.387000 + 0.967000 3.320000 3.851000 + -0.567000 2.624000 4.425000 + 1.057000 2.433000 5.773000 + 2.058000 2.306000 5.738000 + 0.844000 3.297000 6.251000 + 0.637000 1.661000 6.270000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K01" 1 23 1 "?" 0 +!entry.K01.unit.residuesPdbSequenceNumber array int + 1 +!entry.K01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K02.off b/share/off/LYS/K02.off new file mode 100644 index 0000000..c6af608 --- /dev/null +++ b/share/off/LYS/K02.off @@ -0,0 +1,328 @@ +!!index array str + "K02" +!entry.K02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K02.unit.childsequence single int + 2 +!entry.K02.unit.connect array int + 1 + 21 +!entry.K02.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K02.unit.name single str + "" +!entry.K02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.349000 0.363000 4.130000 + 1.883000 1.059000 3.556000 + 0.514000 2.486000 4.387000 + -0.562213 2.657877 4.370105 + 0.842439 2.345832 5.417306 + 1.214000 3.662000 3.798000 + 0.909442 3.792400 2.844273 + 0.995636 4.488036 4.336823 + 2.210984 3.503404 3.814200 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K02" 1 23 1 "?" 0 +!entry.K02.unit.residuesPdbSequenceNumber array int + 1 +!entry.K02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 +!entry.K02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K02.unit.childsequence single int + 2 +!entry.K02.unit.connect array int + 0 + 0 +!entry.K02.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K02.unit.name single str + "" +!entry.K02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.349000 0.363000 4.130000 + 1.883000 1.059000 3.556000 + 0.514000 2.486000 4.387000 + 1.021037 2.426533 5.350036 + 0.913132 3.326659 3.818639 + -0.946000 2.683000 4.606000 + -1.315581 1.905093 5.132903 + -1.096498 3.539378 5.120117 + -1.415854 2.738879 3.714087 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K02" 1 23 1 "?" 0 +!entry.K02.unit.residuesPdbSequenceNumber array int + 1 +!entry.K02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K03.off b/share/off/LYS/K03.off new file mode 100644 index 0000000..f3324b2 --- /dev/null +++ b/share/off/LYS/K03.off @@ -0,0 +1,165 @@ +!!index array str + "K03" +!entry.K03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K03.unit.childsequence single int + 2 +!entry.K03.unit.connect array int + 1 + 21 +!entry.K03.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K03.unit.name single str + "" +!entry.K03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.349000 0.363000 4.130000 + 1.883000 1.059000 3.556000 + 0.514000 2.486000 4.387000 + 1.021037 2.426533 5.350036 + 0.913132 3.326659 3.818639 + -0.946000 2.683000 4.606000 + -1.315581 1.905093 5.132903 + -1.096498 3.539378 5.120117 + -1.415854 2.738879 3.714087 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K03" 1 23 1 "?" 0 +!entry.K03.unit.residuesPdbSequenceNumber array int + 1 +!entry.K03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K04.off b/share/off/LYS/K04.off new file mode 100644 index 0000000..5cfaa86 --- /dev/null +++ b/share/off/LYS/K04.off @@ -0,0 +1,165 @@ +!!index array str + "K04" +!entry.K04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K04.unit.childsequence single int + 2 +!entry.K04.unit.connect array int + 1 + 21 +!entry.K04.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K04.unit.name single str + "" +!entry.K04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 1.858661 0.935969 3.560320 + 0.708812 2.192607 4.075835 + 0.060000 0.183000 4.455000 + -0.991684 0.467455 4.488267 + 0.157219 -0.789529 3.971488 + 0.597000 0.104000 5.842000 + 0.506360 1.004190 6.290105 + 0.077086 -0.586134 6.365215 + 1.570990 -0.160214 5.811547 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K04" 1 23 1 "?" 0 +!entry.K04.unit.residuesPdbSequenceNumber array int + 1 +!entry.K04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K05.off b/share/off/LYS/K05.off new file mode 100644 index 0000000..e8754ed --- /dev/null +++ b/share/off/LYS/K05.off @@ -0,0 +1,165 @@ +!!index array str + "K05" +!entry.K05.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K05.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K05.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K05.unit.childsequence single int + 2 +!entry.K05.unit.connect array int + 1 + 21 +!entry.K05.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K05.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K05.unit.name single str + "" +!entry.K05.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 1.858661 0.935969 3.560320 + 0.708812 2.192607 4.075835 + 0.060000 0.183000 4.455000 + 0.104143 -0.776569 3.939888 + 0.562510 0.100134 5.419192 + -1.363000 0.567000 4.668000 + -1.828634 0.643020 3.775385 + -1.821490 -0.137913 5.227673 + -1.404214 1.455475 5.145814 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K05.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K05.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K05" 1 23 1 "?" 0 +!entry.K05.unit.residuesPdbSequenceNumber array int + 1 +!entry.K05.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K05.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K06.off b/share/off/LYS/K06.off new file mode 100644 index 0000000..a7820b2 --- /dev/null +++ b/share/off/LYS/K06.off @@ -0,0 +1,165 @@ +!!index array str + "K06" +!entry.K06.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K06.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K06.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K06.unit.childsequence single int + 2 +!entry.K06.unit.connect array int + 1 + 21 +!entry.K06.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K06.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K06.unit.name single str + "" +!entry.K06.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.445160 2.072962 4.174510 + 0.444607 0.295402 4.088905 + 2.325000 1.209000 3.608000 + 2.663939 0.346016 3.034903 + 2.664494 2.123563 3.120795 + 2.887000 1.142000 4.985000 + 2.573387 0.294880 5.435987 + 3.895980 1.143876 4.936989 + 2.573819 1.941667 5.515890 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K06.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K06.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K06" 1 23 1 "?" 0 +!entry.K06.unit.residuesPdbSequenceNumber array int + 1 +!entry.K06.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K06.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K07.off b/share/off/LYS/K07.off new file mode 100644 index 0000000..668b707 --- /dev/null +++ b/share/off/LYS/K07.off @@ -0,0 +1,165 @@ +!!index array str + "K07" +!entry.K07.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K07.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K07.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K07.unit.childsequence single int + 2 +!entry.K07.unit.connect array int + 1 + 21 +!entry.K07.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K07.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K07.unit.name single str + "" +!entry.K07.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079000 -0.846000 1.947000 + 1.614000 -0.151000 1.373000 + 0.246000 1.277000 2.204000 + 0.701000 2.114000 1.673000 + -0.834000 1.419000 2.247000 + 0.805000 1.209000 3.616000 + 0.445160 2.072962 4.174510 + 0.444607 0.295402 4.088905 + 2.325000 1.209000 3.608000 + 2.672486 1.056162 4.629741 + 2.663919 0.382565 2.982549 + 2.877000 2.489000 3.082000 + 2.563921 3.254233 3.661444 + 3.886302 2.449780 3.092929 + 2.555901 2.630484 2.135284 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K07.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K07.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K07" 1 23 1 "?" 0 +!entry.K07.unit.residuesPdbSequenceNumber array int + 1 +!entry.K07.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K07.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K08.off b/share/off/LYS/K08.off new file mode 100644 index 0000000..c9f93ea --- /dev/null +++ b/share/off/LYS/K08.off @@ -0,0 +1,165 @@ +!!index array str + "K08" +!entry.K08.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K08.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K08.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K08.unit.childsequence single int + 2 +!entry.K08.unit.connect array int + 1 + 21 +!entry.K08.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K08.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K08.unit.name single str + "" +!entry.K08.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.150519 -0.895845 1.920470 + 1.622690 -0.060148 1.369971 + 0.143000 1.225000 2.242000 + -0.939341 1.346689 2.184680 + 0.435295 1.064558 3.279899 + 0.822000 2.477000 1.712000 + 1.901425 2.336780 1.767024 + 0.526976 2.618489 0.672228 + 0.429000 3.703000 2.521000 + -0.653392 3.817678 2.463235 + 0.720826 3.535742 3.558261 + 1.087000 4.939000 2.013000 + 0.816299 5.094445 1.052837 + 0.800701 5.727871 2.575195 + 2.089651 4.833367 2.067087 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K08.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K08.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K08" 1 23 1 "?" 0 +!entry.K08.unit.residuesPdbSequenceNumber array int + 1 +!entry.K08.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K08.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K09.off b/share/off/LYS/K09.off new file mode 100644 index 0000000..e56569b --- /dev/null +++ b/share/off/LYS/K09.off @@ -0,0 +1,165 @@ +!!index array str + "K09" +!entry.K09.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K09.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K09.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K09.unit.childsequence single int + 2 +!entry.K09.unit.connect array int + 1 + 21 +!entry.K09.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K09.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K09.unit.name single str + "" +!entry.K09.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.150519 -0.895845 1.920470 + 1.622690 -0.060148 1.369971 + 0.143000 1.225000 2.242000 + -0.939341 1.346689 2.184680 + 0.435295 1.064558 3.279899 + 0.822000 2.477000 1.712000 + 1.901425 2.336780 1.767024 + 0.526976 2.618489 0.672228 + 0.429000 3.703000 2.521000 + 0.664013 3.511196 3.567920 + 1.017993 4.549483 2.166597 + -1.021000 4.016000 2.387000 + -1.566511 3.232641 2.715818 + -1.240880 4.833838 2.937585 + -1.238856 4.194460 1.417421 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K09.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K09.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K09" 1 23 1 "?" 0 +!entry.K09.unit.residuesPdbSequenceNumber array int + 1 +!entry.K09.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K09.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K10.off b/share/off/LYS/K10.off new file mode 100644 index 0000000..e3880ce --- /dev/null +++ b/share/off/LYS/K10.off @@ -0,0 +1,165 @@ +!!index array str + "K10" +!entry.K10.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K10.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K10.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K10.unit.childsequence single int + 2 +!entry.K10.unit.connect array int + 1 + 21 +!entry.K10.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K10.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K10.unit.name single str + "" +!entry.K10.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.150519 -0.895845 1.920470 + 1.622690 -0.060148 1.369971 + 0.143000 1.225000 2.242000 + -0.939341 1.346689 2.184680 + 0.435295 1.064558 3.279899 + 0.822000 2.477000 1.712000 + 0.627039 2.551658 0.642297 + 0.397800 3.343408 2.219519 + 2.322000 2.435000 1.951000 + 2.494906 2.348086 3.023665 + 2.724083 1.555744 1.446731 + 3.001000 3.657000 1.436000 + 2.629375 4.471145 1.903352 + 3.993165 3.590691 1.613655 + 2.841644 3.737378 0.442251 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K10.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K10.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K10" 1 23 1 "?" 0 +!entry.K10.unit.residuesPdbSequenceNumber array int + 1 +!entry.K10.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K10.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K11.off b/share/off/LYS/K11.off new file mode 100644 index 0000000..a212c7e --- /dev/null +++ b/share/off/LYS/K11.off @@ -0,0 +1,165 @@ +!!index array str + "K11" +!entry.K11.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K11.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K11.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K11.unit.childsequence single int + 2 +!entry.K11.unit.connect array int + 1 + 21 +!entry.K11.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K11.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K11.unit.name single str + "" +!entry.K11.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 2.076473 0.929385 3.483982 + 2.162824 -0.847839 3.451307 + 4.029000 0.141000 3.072000 + 4.445731 -0.720088 2.549578 + 4.359423 1.057151 2.581554 + 4.497000 0.138000 4.486000 + 4.191806 -0.710559 4.940048 + 5.505749 0.186488 4.506568 + 4.111743 0.935948 4.969993 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K11.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K11.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K11" 1 23 1 "?" 0 +!entry.K11.unit.residuesPdbSequenceNumber array int + 1 +!entry.K11.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K11.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K12.off b/share/off/LYS/K12.off new file mode 100644 index 0000000..4bd6deb --- /dev/null +++ b/share/off/LYS/K12.off @@ -0,0 +1,165 @@ +!!index array str + "K12" +!entry.K12.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K12.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K12.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K12.unit.childsequence single int + 2 +!entry.K12.unit.connect array int + 1 + 21 +!entry.K12.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K12.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K12.unit.name single str + "" +!entry.K12.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 2.076473 0.929385 3.483982 + 2.162824 -0.847839 3.451307 + 4.029000 0.141000 3.072000 + 4.363684 1.024118 2.527802 + 4.301106 0.238545 4.123424 + 4.680000 -1.070000 2.501000 + 4.428784 -1.160050 1.527277 + 5.683023 -0.983016 2.583018 + 4.370750 -1.888139 3.005387 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K12.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K12.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K12" 1 23 1 "?" 0 +!entry.K12.unit.residuesPdbSequenceNumber array int + 1 +!entry.K12.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K12.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K13.off b/share/off/LYS/K13.off new file mode 100644 index 0000000..b812f6e --- /dev/null +++ b/share/off/LYS/K13.off @@ -0,0 +1,165 @@ +!!index array str + "K13" +!entry.K13.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K13.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K13.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K13.unit.childsequence single int + 2 +!entry.K13.unit.connect array int + 1 + 21 +!entry.K13.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K13.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K13.unit.name single str + "" +!entry.K13.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 2.076473 0.929385 3.483982 + 2.162824 -0.847839 3.451307 + 4.029000 0.141000 3.072000 + 4.311707 0.031940 4.119017 + 4.447568 -0.684698 2.495742 + 4.557000 1.431000 2.547000 + 4.170147 2.195594 3.080943 + 5.563876 1.440020 2.627430 + 4.295926 1.531962 1.576928 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K13.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K13.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K13" 1 23 1 "?" 0 +!entry.K13.unit.residuesPdbSequenceNumber array int + 1 +!entry.K13.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K13.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K14.off b/share/off/LYS/K14.off new file mode 100644 index 0000000..ef39d5f --- /dev/null +++ b/share/off/LYS/K14.off @@ -0,0 +1,165 @@ +!!index array str + "K14" +!entry.K14.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K14.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K14.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K14.unit.childsequence single int + 2 +!entry.K14.unit.connect array int + 1 + 21 +!entry.K14.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K14.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K14.unit.name single str + "" +!entry.K14.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 2.060797 -0.783205 3.484058 + 3.598212 -0.031800 2.995391 + 2.112000 1.351000 3.687000 + 2.563605 2.190205 3.157992 + 1.025894 1.439029 3.646079 + 2.558000 1.362000 5.108000 + 3.563679 1.281277 5.146055 + 2.273284 2.227941 5.543238 + 2.139234 0.585174 5.598479 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K14.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K14.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K14" 1 23 1 "?" 0 +!entry.K14.unit.residuesPdbSequenceNumber array int + 1 +!entry.K14.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K14.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K15.off b/share/off/LYS/K15.off new file mode 100644 index 0000000..3ee11df --- /dev/null +++ b/share/off/LYS/K15.off @@ -0,0 +1,165 @@ +!!index array str + "K15" +!entry.K15.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K15.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K15.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K15.unit.childsequence single int + 2 +!entry.K15.unit.connect array int + 1 + 21 +!entry.K15.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K15.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K15.unit.name single str + "" +!entry.K15.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.473838 -0.788236 1.010314 + 2.386240 0.989399 1.042955 + 2.513000 0.069000 2.977000 + 3.582930 0.275175 3.001276 + 1.979966 0.853589 3.514103 + 2.241000 -1.272000 3.639000 + 1.169187 -1.464755 3.592925 + 2.772205 -2.043122 3.080215 + 2.688000 -1.291000 5.059000 + 2.195691 -0.577582 5.576708 + 2.490198 -2.195951 5.461849 + 3.680947 -1.113224 5.101953 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K15.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K15.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K15" 1 23 1 "?" 0 +!entry.K15.unit.residuesPdbSequenceNumber array int + 1 +!entry.K15.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K15.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K16.off b/share/off/LYS/K16.off new file mode 100644 index 0000000..58007ed --- /dev/null +++ b/share/off/LYS/K16.off @@ -0,0 +1,165 @@ +!!index array str + "K16" +!entry.K16.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K16.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K16.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K16.unit.childsequence single int + 2 +!entry.K16.unit.connect array int + 1 + 21 +!entry.K16.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K16.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K16.unit.name single str + "" +!entry.K16.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.341044 -0.085132 2.568434 + 2.476710 -0.716708 0.909690 + 2.570000 1.422000 1.058000 + 2.264698 1.569788 0.022241 + 2.129517 2.200645 1.680792 + 4.085000 1.494000 1.154000 + 4.369905 1.331555 2.193472 + 4.505085 0.700707 0.534917 + 4.608000 2.811000 0.696000 + 4.219742 3.545572 1.269598 + 5.614985 2.819020 0.775162 + 4.344890 2.961427 -0.267088 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K16.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K16.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K16" 1 23 1 "?" 0 +!entry.K16.unit.residuesPdbSequenceNumber array int + 1 +!entry.K16.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K16.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K17.off b/share/off/LYS/K17.off new file mode 100644 index 0000000..34a92ed --- /dev/null +++ b/share/off/LYS/K17.off @@ -0,0 +1,165 @@ +!!index array str + "K17" +!entry.K17.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K17.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K17.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K17.unit.childsequence single int + 2 +!entry.K17.unit.connect array int + 1 + 21 +!entry.K17.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K17.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K17.unit.name single str + "" +!entry.K17.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.098350 0.860490 1.939735 + 0.185947 -0.917146 1.907122 + 2.051000 0.073000 1.529000 + 2.341044 -0.085132 2.568434 + 2.476710 -0.716708 0.909690 + 2.570000 1.422000 1.058000 + 2.264698 1.569788 0.022241 + 2.129517 2.200645 1.680792 + 4.085000 1.494000 1.154000 + 4.395134 2.508848 0.905081 + 4.373314 1.268651 2.181201 + 4.747000 0.532000 0.230000 + 4.480769 0.740985 -0.721210 + 5.749638 0.611113 0.323850 + 4.460496 -0.408230 0.460814 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K17.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K17.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K17" 1 23 1 "?" 0 +!entry.K17.unit.residuesPdbSequenceNumber array int + 1 +!entry.K17.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K17.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K18.off b/share/off/LYS/K18.off new file mode 100644 index 0000000..b123c8c --- /dev/null +++ b/share/off/LYS/K18.off @@ -0,0 +1,165 @@ +!!index array str + "K18" +!entry.K18.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K18.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K18.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K18.unit.childsequence single int + 2 +!entry.K18.unit.connect array int + 1 + 21 +!entry.K18.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K18.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.K18.unit.name single str + "" +!entry.K18.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.622823 0.059818 1.369769 + 0.150928 0.895867 1.920470 + 0.143000 -1.225000 2.242000 + -0.945461 -1.276207 2.288750 + 0.526339 -2.112325 1.737899 + 0.708000 -1.159000 3.652000 + 1.794413 -1.099055 3.589053 + 0.322772 -0.263338 4.139415 + 0.315000 -2.384000 4.461000 + -0.773160 -2.432086 4.501688 + 0.697953 -3.268183 3.950494 + 0.862000 -2.334000 5.846000 + 0.506915 -1.515798 6.319090 + 0.579378 -3.162878 6.349422 + 1.870008 -2.290213 5.808652 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K18.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K18.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K18" 1 23 1 "?" 0 +!entry.K18.unit.residuesPdbSequenceNumber array int + 1 +!entry.K18.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K18.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/LYS/K19.off b/share/off/LYS/K19.off new file mode 100644 index 0000000..e366797 --- /dev/null +++ b/share/off/LYS/K19.off @@ -0,0 +1,165 @@ +!!index array str + "K19" +!entry.K19.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.347900 + "H" "H" 0 1 131075 2 1 0.274700 + "CA" "CX" 0 1 131075 3 20 -0.240000 + "HA" "H1" 0 1 131075 4 1 0.142600 + "CB" "CT" 0 1 131075 5 6 -0.009400 + "HB2" "HC" 0 1 131075 6 1 0.036200 + "HB3" "HC" 0 1 131075 7 1 0.036200 + "CG" "CT" 0 1 131075 8 6 0.018700 + "HG2" "HC" 0 1 131075 9 1 0.010300 + "HG3" "HC" 0 1 131075 10 1 0.010300 + "CD" "CT" 0 1 131075 11 6 -0.047900 + "HD2" "HC" 0 1 131075 12 1 0.062100 + "HD3" "HC" 0 1 131075 13 1 0.062100 + "CE" "CT" 0 1 131075 14 6 -0.014300 + "HE2" "HP" 0 1 131075 15 1 0.113500 + "HE3" "HP" 0 1 131075 16 1 0.113500 + "NZ" "N3" 0 1 131075 17 7 -0.385400 + "HZ1" "H" 0 1 131075 18 1 0.340000 + "HZ2" "H" 0 1 131075 19 1 0.340000 + "HZ3" "H" 0 1 131075 20 1 0.340000 + "C" "C" 0 1 131075 21 6 0.734100 + "O" "O" 0 1 131075 22 8 -0.589400 +!entry.K19.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "HC" 0 -1 0.0 + "HG3" "HC" 0 -1 0.0 + "CD" "CT" 0 -1 0.0 + "HD2" "HC" 0 -1 0.0 + "HD3" "HC" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE2" "HP" 0 -1 0.0 + "HE3" "HP" 0 -1 0.0 + "NZ" "N3" 0 -1 0.0 + "HZ1" "H" 0 -1 0.0 + "HZ2" "H" 0 -1 0.0 + "HZ3" "H" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.K19.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K19.unit.childsequence single int + 2 +!entry.K19.unit.connect array int + 1 + 21 +!entry.K19.unit.connectivity table int atom1x int atom2x int flags + 21 22 17 + 17 18 17 + 17 20 17 + 17 19 17 + 14 15 17 + 14 16 17 + 14 17 17 + 11 12 17 + 11 13 17 + 11 14 17 + 8 10 17 + 8 9 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 21 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.K19.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 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-1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.K19.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.K19.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "K19" 1 23 1 "?" 0 +!entry.K19.unit.residuesPdbSequenceNumber array int + 1 +!entry.K19.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.K19.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M01.off b/share/off/MET/M01.off new file mode 100644 index 0000000..5998f26 --- /dev/null +++ b/share/off/MET/M01.off @@ -0,0 +1,135 @@ +!!index array str + "M01" +!entry.M01.unit.atoms table str name str 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0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M01.unit.childsequence single int + 2 +!entry.M01.unit.connect array int + 1 + 16 +!entry.M01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 16 17 + 3 5 17 + 5 7 17 + 5 6 17 + 5 8 17 + 8 9 17 + 8 10 17 + 8 11 17 + 11 12 17 + 12 13 17 + 12 15 17 + 12 14 17 + 16 17 17 +!entry.M01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 +!entry.M01.unit.name single str + "" +!entry.M01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.107000 -0.866000 1.937000 + 1.618000 -0.115000 1.371000 + 0.205000 1.258000 2.219000 + -0.877000 1.392000 2.204000 + 0.539000 1.113000 3.247000 + 0.993000 2.730000 1.543000 + 2.708000 2.414000 1.952000 + 3.031000 1.489000 1.475000 + 3.325000 3.240000 1.597000 + 2.813000 2.321000 3.033000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M01" 1 18 1 "?" 0 +!entry.M01.unit.residuesPdbSequenceNumber array int + 1 +!entry.M01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M02.off b/share/off/MET/M02.off new file mode 100644 index 0000000..f437351 --- /dev/null +++ b/share/off/MET/M02.off @@ -0,0 +1,135 @@ +!!index array str + "M02" +!entry.M02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M02.unit.childsequence single int + 2 +!entry.M02.unit.connect array int + 1 + 16 +!entry.M02.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M02.unit.name single str + "" +!entry.M02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.107000 -0.866000 1.937000 + 1.618000 -0.115000 1.371000 + 0.205000 1.258000 2.219000 + -0.877000 1.392000 2.204000 + 0.539000 1.113000 3.247000 + 0.993000 2.730000 1.543000 + 0.403000 3.983000 2.679000 + 0.729291 3.739841 3.689886 + 0.806528 4.954253 2.391210 + -0.686027 4.018671 2.647658 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M02" 1 18 1 "?" 0 +!entry.M02.unit.residuesPdbSequenceNumber array int + 1 +!entry.M02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M03.off b/share/off/MET/M03.off new file mode 100644 index 0000000..31e8ec7 --- /dev/null +++ b/share/off/MET/M03.off @@ -0,0 +1,135 @@ +!!index array str + "M03" +!entry.M03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M03.unit.childsequence single int + 2 +!entry.M03.unit.connect array int + 1 + 16 +!entry.M03.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M03.unit.name single str + "" +!entry.M03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.107000 -0.866000 1.937000 + 1.618000 -0.115000 1.371000 + 0.205000 1.258000 2.219000 + -0.877000 1.392000 2.204000 + 0.539000 1.113000 3.247000 + 0.993000 2.730000 1.543000 + -0.387000 3.495000 0.695000 + -1.177604 3.714839 1.412007 + -0.056531 4.421207 0.223916 + -0.767226 2.815392 -0.067756 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M03" 1 18 1 "?" 0 +!entry.M03.unit.residuesPdbSequenceNumber array int + 1 +!entry.M03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M04.off b/share/off/MET/M04.off new file mode 100644 index 0000000..dbd226e --- /dev/null +++ b/share/off/MET/M04.off @@ -0,0 +1,135 @@ +!!index array str + "M04" +!entry.M04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M04.unit.childsequence single int + 2 +!entry.M04.unit.connect array int + 1 + 16 +!entry.M04.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M04.unit.name single str + "" +!entry.M04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079262 -0.845486 1.947351 + 1.613690 -0.150753 1.372587 + 0.246000 1.278000 2.204000 + 0.700324 2.109942 1.665142 + -0.835344 1.415147 2.239362 + 0.893000 1.238000 3.886000 + -0.288000 0.149000 4.678000 + -0.275569 -0.821993 4.183529 + -0.021430 0.024936 5.728018 + -1.286328 0.580650 4.605514 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M04" 1 18 1 "?" 0 +!entry.M04.unit.residuesPdbSequenceNumber array int + 1 +!entry.M04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M05.off b/share/off/MET/M05.off new file mode 100644 index 0000000..ef853f7 --- /dev/null +++ b/share/off/MET/M05.off @@ -0,0 +1,135 @@ +!!index array str + "M05" +!entry.M05.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M05.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M05.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M05.unit.childsequence single int + 2 +!entry.M05.unit.connect array int + 1 + 16 +!entry.M05.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M05.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M05.unit.name single str + "" +!entry.M05.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079262 -0.845486 1.947351 + 1.613690 -0.150753 1.372587 + 0.246000 1.278000 2.204000 + 0.700324 2.109942 1.665142 + -0.835344 1.415147 2.239362 + 0.893000 1.238000 3.886000 + 0.387000 2.850000 4.481000 + -0.698688 2.930687 4.433524 + 0.715498 2.976640 5.513008 + 0.836218 3.624660 3.859437 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M05.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M05.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M05" 1 18 1 "?" 0 +!entry.M05.unit.residuesPdbSequenceNumber array int + 1 +!entry.M05.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M05.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M06.off b/share/off/MET/M06.off new file mode 100644 index 0000000..c49e9ee --- /dev/null +++ b/share/off/MET/M06.off @@ -0,0 +1,135 @@ +!!index array str + "M06" +!entry.M06.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M06.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M06.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M06.unit.childsequence single int + 2 +!entry.M06.unit.connect array int + 1 + 16 +!entry.M06.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M06.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M06.unit.name single str + "" +!entry.M06.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.079262 -0.845486 1.947351 + 1.613690 -0.150753 1.372587 + 0.246000 1.278000 2.204000 + 0.700324 2.109942 1.665142 + -0.835344 1.415147 2.239362 + 0.893000 1.238000 3.886000 + 2.643000 1.475000 3.580000 + 2.798021 2.428562 3.075845 + 3.181680 1.473990 4.528058 + 3.014938 0.666657 2.950334 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M06.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M06.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M06" 1 18 1 "?" 0 +!entry.M06.unit.residuesPdbSequenceNumber array int + 1 +!entry.M06.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M06.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M07.off b/share/off/MET/M07.off new file mode 100644 index 0000000..8773d6c --- /dev/null +++ b/share/off/MET/M07.off @@ -0,0 +1,135 @@ +!!index array str + "M07" +!entry.M07.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M07.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M07.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M07.unit.childsequence single int + 2 +!entry.M07.unit.connect array int + 1 + 16 +!entry.M07.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M07.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M07.unit.name single str + "" +!entry.M07.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.099136 0.860453 1.939738 + 0.185532 -0.916881 1.906598 + 2.051000 0.072000 1.529000 + 2.465036 -0.789443 1.004219 + 2.378497 0.988801 1.037484 + 2.643000 0.069000 3.231000 + 2.242000 1.742000 3.731000 + 1.167313 1.899807 3.643661 + 2.548414 1.895859 4.766098 + 2.766291 2.449307 3.088294 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M07.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M07.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M07" 1 18 1 "?" 0 +!entry.M07.unit.residuesPdbSequenceNumber array int + 1 +!entry.M07.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M07.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M08.off b/share/off/MET/M08.off new file mode 100644 index 0000000..a18350c --- /dev/null +++ b/share/off/MET/M08.off @@ -0,0 +1,135 @@ +!!index array str + "M08" +!entry.M08.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M08.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M08.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M08.unit.childsequence single int + 2 +!entry.M08.unit.connect array int + 1 + 16 +!entry.M08.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M08.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M08.unit.name single str + "" +!entry.M08.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.099136 0.860453 1.939738 + 0.185532 -0.916881 1.906598 + 2.051000 0.072000 1.529000 + 2.465036 -0.789443 1.004219 + 2.378497 0.988801 1.037484 + 2.643000 0.069000 3.231000 + 4.413000 0.160000 2.975000 + 4.655242 1.072894 2.431469 + 4.920471 0.166800 3.940099 + 4.742018 -0.704312 2.397984 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M08.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M08.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M08" 1 18 1 "?" 0 +!entry.M08.unit.residuesPdbSequenceNumber array int + 1 +!entry.M08.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 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131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M09.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M09.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M09.unit.childsequence single int + 2 +!entry.M09.unit.connect array int + 1 + 16 +!entry.M09.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M09.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M09.unit.name single str + "" +!entry.M09.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.099136 0.860453 1.939738 + 0.185532 -0.916881 1.906598 + 2.051000 0.072000 1.529000 + 2.465036 -0.789443 1.004219 + 2.378497 0.988801 1.037484 + 2.643000 0.069000 3.231000 + 2.406000 -1.652000 3.669000 + 2.994696 -2.281276 3.001968 + 2.728028 -1.813316 4.698206 + 1.351059 -1.909562 3.574154 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M09.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M09.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M09" 1 18 1 "?" 0 +!entry.M09.unit.residuesPdbSequenceNumber array int + 1 +!entry.M09.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M09.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M10.off b/share/off/MET/M10.off new file mode 100644 index 0000000..c4e6b3c --- /dev/null +++ b/share/off/MET/M10.off @@ -0,0 +1,135 @@ +!!index array str + "M10" +!entry.M10.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M10.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M10.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M10.unit.childsequence single int + 2 +!entry.M10.unit.connect array int + 1 + 16 +!entry.M10.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M10.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M10.unit.name single str + "" +!entry.M10.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.099136 0.860453 1.939738 + 0.185532 -0.916881 1.906598 + 2.051000 0.072000 1.529000 + 2.330036 -0.038097 2.577295 + 2.467116 -0.755545 0.953342 + 2.716000 1.625000 0.899000 + 4.470000 1.372000 1.159000 + 4.798366 0.497759 0.597429 + 5.018970 2.249989 0.817302 + 4.661426 1.214646 2.220523 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M10.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M10.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M10" 1 18 1 "?" 0 +!entry.M10.unit.residuesPdbSequenceNumber array int + 1 +!entry.M10.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M10.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M11.off b/share/off/MET/M11.off new file mode 100644 index 0000000..df18ac5 --- /dev/null +++ b/share/off/MET/M11.off @@ -0,0 +1,135 @@ +!!index array str + "M11" +!entry.M11.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M11.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M11.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M11.unit.childsequence single int + 2 +!entry.M11.unit.connect array int + 1 + 16 +!entry.M11.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M11.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M11.unit.name single str + "" +!entry.M11.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.099136 0.860453 1.939738 + 0.185532 -0.916881 1.906598 + 2.051000 0.072000 1.529000 + 2.330036 -0.038097 2.577295 + 2.467116 -0.755545 0.953342 + 2.716000 1.625000 0.899000 + 2.288000 2.741000 2.233000 + 2.763118 2.405254 3.154423 + 2.634241 3.746420 1.991673 + 1.206055 2.751707 2.365349 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M11.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M11.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M11" 1 18 1 "?" 0 +!entry.M11.unit.residuesPdbSequenceNumber array int + 1 +!entry.M11.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M11.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M12.off b/share/off/MET/M12.off new file mode 100644 index 0000000..a4fbfbe --- /dev/null +++ b/share/off/MET/M12.off @@ -0,0 +1,135 @@ +!!index array str + "M12" +!entry.M12.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M12.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M12.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M12.unit.childsequence single int + 2 +!entry.M12.unit.connect array int + 1 + 16 +!entry.M12.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M12.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M12.unit.name single str + "" +!entry.M12.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.622484 0.059867 1.369902 + 0.150575 0.895785 1.919631 + 0.143000 -1.225000 2.243000 + -0.945728 -1.271545 2.280554 + 0.527011 -2.107787 1.730567 + 0.792000 -1.187000 3.923000 + 2.516000 -1.577000 3.629000 + 2.953241 -0.822115 2.975967 + 3.052966 -1.590945 4.577927 + 2.591841 -2.555490 3.154615 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M12.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M12.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M12" 1 18 1 "?" 0 +!entry.M12.unit.residuesPdbSequenceNumber array int + 1 +!entry.M12.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M12.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/MET/M13.off b/share/off/MET/M13.off new file mode 100644 index 0000000..9bb0917 --- /dev/null +++ b/share/off/MET/M13.off @@ -0,0 +1,135 @@ +!!index array str + "M13" +!entry.M13.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.023700 + "HA" "H1" 0 1 131075 4 1 0.088000 + "CB" "CT" 0 1 131075 5 6 0.034200 + "HB2" "HC" 0 1 131075 6 1 0.024100 + "HB3" "HC" 0 1 131075 7 1 0.024100 + "CG" "CT" 0 1 131075 8 6 0.001800 + "HG2" "H1" 0 1 131075 9 1 0.044000 + "HG3" "H1" 0 1 131075 10 1 0.044000 + "SD" "S" 0 1 131075 11 16 -0.273700 + "CE" "CT" 0 1 131075 12 6 -0.053600 + "HE1" "H1" 0 1 131075 13 1 0.068400 + "HE2" "H1" 0 1 131075 14 1 0.068400 + "HE3" "H1" 0 1 131075 15 1 0.068400 + "C" "C" 0 1 131075 16 6 0.597300 + "O" "O" 0 1 131075 17 8 -0.567900 +!entry.M13.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CT" 0 -1 0.0 + "HG2" "H1" 0 -1 0.0 + "HG3" "H1" 0 -1 0.0 + "SD" "S" 0 -1 0.0 + "CE" "CT" 0 -1 0.0 + "HE1" "H1" 0 -1 0.0 + "HE2" "H1" 0 -1 0.0 + "HE3" "H1" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.M13.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M13.unit.childsequence single int + 2 +!entry.M13.unit.connect array int + 1 + 16 +!entry.M13.unit.connectivity table int atom1x int atom2x int flags + 16 17 17 + 12 13 17 + 12 15 17 + 12 14 17 + 11 12 17 + 8 9 17 + 8 10 17 + 8 11 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 16 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.M13.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.M13.unit.name single str + "" +!entry.M13.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.622484 0.059867 1.369902 + 0.150575 0.895785 1.919631 + 0.143000 -1.225000 2.243000 + -0.945728 -1.271545 2.280554 + 0.527011 -2.107787 1.730567 + 0.792000 -1.187000 3.923000 + -0.294000 0.021000 4.679000 + -1.324483 -0.328111 4.618101 + -0.017411 0.154737 5.725233 + -0.201243 0.972124 4.154601 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.M13.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.M13.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "M13" 1 18 1 "?" 0 +!entry.M13.unit.residuesPdbSequenceNumber array int + 1 +!entry.M13.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.M13.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/PHE/P01.off b/share/off/PHE/P01.off new file mode 100644 index 0000000..3bfdceb --- /dev/null +++ b/share/off/PHE/P01.off @@ -0,0 +1,154 @@ +!!index array str + "P01" +!entry.P01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.002400 + "HA" "H1" 0 1 131075 4 1 0.097800 + "CB" "CT" 0 1 131075 5 6 -0.034300 + "HB2" "HC" 0 1 131075 6 1 0.029500 + "HB3" "HC" 0 1 131075 7 1 0.029500 + "CG" "CA" 0 1 131075 8 6 0.011800 + "CD1" "CA" 0 1 131075 9 6 -0.125600 + "HD1" "HA" 0 1 131075 10 1 0.133000 + "CE1" "CA" 0 1 131075 11 6 -0.170400 + "HE1" "HA" 0 1 131075 12 1 0.143000 + "CZ" "CA" 0 1 131075 13 6 -0.107200 + "HZ" "HA" 0 1 131075 14 1 0.129700 + "CE2" "CA" 0 1 131075 15 6 -0.170400 + "HE2" "HA" 0 1 131075 16 1 0.143000 + "CD2" "CA" 0 1 131075 17 6 -0.125600 + "HD2" "HA" 0 1 131075 18 1 0.133000 + "C" "C" 0 1 131075 19 6 0.597300 + "O" "O" 0 1 131075 20 8 -0.567900 +!entry.P01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CA" 0 -1 0.0 + "CD1" "CA" 0 -1 0.0 + "HD1" "HA" 0 -1 0.0 + "CE1" "CA" 0 -1 0.0 + "HE1" "HA" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "HZ" "HA" 0 -1 0.0 + "CE2" "CA" 0 -1 0.0 + "HE2" "HA" 0 -1 0.0 + "CD2" "CA" 0 -1 0.0 + "HD2" "HA" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.P01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.P01.unit.childsequence single int + 2 +!entry.P01.unit.connect array int + 1 + 19 +!entry.P01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 19 17 + 3 5 17 + 5 7 17 + 5 6 17 + 5 8 17 + 8 17 17 + 8 9 17 + 9 10 17 + 9 11 17 + 11 12 17 + 11 13 17 + 13 14 17 + 13 15 17 + 15 16 17 + 15 17 17 + 17 18 17 + 19 20 17 +!entry.P01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 + "R" 1 "A" 20 +!entry.P01.unit.name single str + "" +!entry.P01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.114000 -0.835000 1.993000 + 1.623000 -0.081000 1.424000 + 0.205000 1.245000 2.204000 + 1.005000 2.371000 2.107000 + 1.884000 2.347000 1.462000 + 0.700000 3.517000 2.816000 + 1.340000 4.395000 2.729000 + -0.410000 3.551000 3.631000 + -0.652000 4.454000 4.192000 + -1.215000 2.438000 3.736000 + -2.094000 2.460000 4.380000 + -0.908000 1.294000 3.025000 + -1.546000 0.414000 3.106000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.P01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.P01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "P01" 1 21 1 "?" 0 +!entry.P01.unit.residuesPdbSequenceNumber array int + 1 +!entry.P01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.P01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/PHE/P02.off b/share/off/PHE/P02.off new file mode 100644 index 0000000..8a421cc --- /dev/null +++ b/share/off/PHE/P02.off @@ -0,0 +1,154 @@ +!!index array str + "P02" +!entry.P02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.002400 + "HA" "H1" 0 1 131075 4 1 0.097800 + "CB" "CT" 0 1 131075 5 6 -0.034300 + "HB2" "HC" 0 1 131075 6 1 0.029500 + "HB3" "HC" 0 1 131075 7 1 0.029500 + "CG" "CA" 0 1 131075 8 6 0.011800 + "CD1" "CA" 0 1 131075 9 6 -0.125600 + "HD1" "HA" 0 1 131075 10 1 0.133000 + "CE1" "CA" 0 1 131075 11 6 -0.170400 + "HE1" "HA" 0 1 131075 12 1 0.143000 + "CZ" "CA" 0 1 131075 13 6 -0.107200 + "HZ" "HA" 0 1 131075 14 1 0.129700 + "CE2" "CA" 0 1 131075 15 6 -0.170400 + "HE2" "HA" 0 1 131075 16 1 0.143000 + "CD2" "CA" 0 1 131075 17 6 -0.125600 + "HD2" "HA" 0 1 131075 18 1 0.133000 + "C" "C" 0 1 131075 19 6 0.597300 + "O" "O" 0 1 131075 20 8 -0.567900 +!entry.P02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CA" 0 -1 0.0 + "CD1" "CA" 0 -1 0.0 + "HD1" "HA" 0 -1 0.0 + "CE1" "CA" 0 -1 0.0 + "HE1" "HA" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "HZ" "HA" 0 -1 0.0 + "CE2" "CA" 0 -1 0.0 + "HE2" "HA" 0 -1 0.0 + "CD2" "CA" 0 -1 0.0 + "HD2" "HA" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.P02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.P02.unit.childsequence single int + 2 +!entry.P02.unit.connect array int + 1 + 19 +!entry.P02.unit.connectivity table int atom1x int atom2x int flags + 19 20 17 + 17 18 17 + 15 16 17 + 15 17 17 + 13 14 17 + 13 15 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 17 17 + 8 9 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 19 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.P02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.P02.unit.name single str + "" +!entry.P02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.114792 -0.835082 1.993473 + 1.623030 -0.080507 1.423217 + 0.205000 1.245000 2.204000 + 0.058000 2.460000 1.556000 + 0.185310 2.506350 0.473925 + -0.247000 3.606000 2.265000 + -0.358614 4.554687 1.740035 + -0.410000 3.551000 3.632000 + -0.651448 4.453893 4.193410 + -0.266000 2.349000 4.289000 + -0.391796 2.300946 5.370539 + 0.038000 1.204000 3.577000 + 0.149022 0.252253 4.096477 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.P02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.P02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "P02" 1 21 1 "?" 0 +!entry.P02.unit.residuesPdbSequenceNumber array int + 1 +!entry.P02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.P02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/PHE/P03.off b/share/off/PHE/P03.off new file mode 100644 index 0000000..7c33a9b --- /dev/null +++ b/share/off/PHE/P03.off @@ -0,0 +1,154 @@ +!!index array str + "P03" +!entry.P03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.002400 + "HA" "H1" 0 1 131075 4 1 0.097800 + "CB" "CT" 0 1 131075 5 6 -0.034300 + "HB2" "HC" 0 1 131075 6 1 0.029500 + "HB3" "HC" 0 1 131075 7 1 0.029500 + "CG" "CA" 0 1 131075 8 6 0.011800 + "CD1" "CA" 0 1 131075 9 6 -0.125600 + "HD1" "HA" 0 1 131075 10 1 0.133000 + "CE1" "CA" 0 1 131075 11 6 -0.170400 + "HE1" "HA" 0 1 131075 12 1 0.143000 + "CZ" "CA" 0 1 131075 13 6 -0.107200 + "HZ" "HA" 0 1 131075 14 1 0.129700 + "CE2" "CA" 0 1 131075 15 6 -0.170400 + "HE2" "HA" 0 1 131075 16 1 0.143000 + "CD2" "CA" 0 1 131075 17 6 -0.125600 + "HD2" "HA" 0 1 131075 18 1 0.133000 + "C" "C" 0 1 131075 19 6 0.597300 + "O" "O" 0 1 131075 20 8 -0.567900 +!entry.P03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CA" 0 -1 0.0 + "CD1" "CA" 0 -1 0.0 + "HD1" "HA" 0 -1 0.0 + "CE1" "CA" 0 -1 0.0 + "HE1" "HA" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "HZ" "HA" 0 -1 0.0 + "CE2" "CA" 0 -1 0.0 + "HE2" "HA" 0 -1 0.0 + "CD2" "CA" 0 -1 0.0 + "HD2" "HA" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.P03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.P03.unit.childsequence single int + 2 +!entry.P03.unit.connect array int + 1 + 19 +!entry.P03.unit.connectivity table int atom1x int atom2x int flags + 19 20 17 + 17 18 17 + 15 16 17 + 15 17 17 + 13 14 17 + 13 15 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 17 17 + 8 9 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 19 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.P03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.P03.unit.name single str + "" +!entry.P03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.150069 0.859487 1.981861 + 0.238382 -0.918090 1.939700 + 2.033000 0.072000 1.520000 + 2.693000 1.280000 1.376000 + 2.112813 2.186015 1.197780 + 4.071000 1.347000 1.456000 + 4.576000 2.306063 1.340993 + 4.806000 0.203000 1.681000 + 5.893301 0.252368 1.744507 + 4.162000 -1.005000 1.825000 + 4.739819 -1.912122 2.001395 + 2.784000 -1.068000 1.746000 + 2.274329 -2.024389 1.862453 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.P03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.P03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "P03" 1 21 1 "?" 0 +!entry.P03.unit.residuesPdbSequenceNumber array int + 1 +!entry.P03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.P03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/PHE/P04.off b/share/off/PHE/P04.off new file mode 100644 index 0000000..edd99f1 --- /dev/null +++ b/share/off/PHE/P04.off @@ -0,0 +1,154 @@ +!!index array str + "P04" +!entry.P04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.002400 + "HA" "H1" 0 1 131075 4 1 0.097800 + "CB" "CT" 0 1 131075 5 6 -0.034300 + "HB2" "HC" 0 1 131075 6 1 0.029500 + "HB3" "HC" 0 1 131075 7 1 0.029500 + "CG" "CA" 0 1 131075 8 6 0.011800 + "CD1" "CA" 0 1 131075 9 6 -0.125600 + "HD1" "HA" 0 1 131075 10 1 0.133000 + "CE1" "CA" 0 1 131075 11 6 -0.170400 + "HE1" "HA" 0 1 131075 12 1 0.143000 + "CZ" "CA" 0 1 131075 13 6 -0.107200 + "HZ" "HA" 0 1 131075 14 1 0.129700 + "CE2" "CA" 0 1 131075 15 6 -0.170400 + "HE2" "HA" 0 1 131075 16 1 0.143000 + "CD2" "CA" 0 1 131075 17 6 -0.125600 + "HD2" "HA" 0 1 131075 18 1 0.133000 + "C" "C" 0 1 131075 19 6 0.597300 + "O" "O" 0 1 131075 20 8 -0.567900 +!entry.P04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CA" 0 -1 0.0 + "CD1" "CA" 0 -1 0.0 + "HD1" "HA" 0 -1 0.0 + "CE1" "CA" 0 -1 0.0 + "HE1" "HA" 0 -1 0.0 + "CZ" "CA" 0 -1 0.0 + "HZ" "HA" 0 -1 0.0 + "CE2" "CA" 0 -1 0.0 + "HE2" "HA" 0 -1 0.0 + "CD2" "CA" 0 -1 0.0 + "HD2" "HA" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.P04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.P04.unit.childsequence single int + 2 +!entry.P04.unit.connect array int + 1 + 19 +!entry.P04.unit.connectivity table int atom1x int atom2x int flags + 19 20 17 + 17 18 17 + 15 16 17 + 15 17 17 + 13 14 17 + 13 15 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 17 17 + 8 9 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 19 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.P04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.P04.unit.name single str + "" +!entry.P04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.625919 0.031157 1.429121 + 0.149789 0.863940 1.973981 + 0.144000 -1.213000 2.226000 + 0.944000 -2.343000 2.232000 + 1.867640 -2.346685 1.652243 + 0.583000 -3.459000 2.963000 + 1.223658 -4.340810 2.958309 + -0.583000 -3.458000 3.696000 + -0.869384 -4.338194 4.272140 + -1.388000 -2.341000 3.699000 + -2.311771 -2.335793 4.277343 + -1.024000 -1.226000 2.968000 + -1.659808 -0.340706 2.970865 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.P04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.P04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "P04" 1 21 1 "?" 0 +!entry.P04.unit.residuesPdbSequenceNumber array int + 1 +!entry.P04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.P04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/SER/S01.off b/share/off/SER/S01.off new file mode 100644 index 0000000..b6b4a23 --- /dev/null +++ b/share/off/SER/S01.off @@ -0,0 +1,99 @@ +!!index array str + "S01" +!entry.S01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.024900 + "HA" "H1" 0 1 131075 4 1 0.084300 + "CB" "CT" 0 1 131075 5 6 0.211700 + "HB2" "H1" 0 1 131075 6 1 0.035200 + "HB3" "H1" 0 1 131075 7 1 0.035200 + "OG" "OH" 0 1 131075 8 8 -0.654600 + "HG" "HO" 0 1 131075 9 1 0.427500 + "C" "C" 0 1 131075 10 6 0.597300 + "O" "O" 0 1 131075 11 8 -0.567900 +!entry.S01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "H1" 0 -1 0.0 + "HB3" "H1" 0 -1 0.0 + "OG" "OH" 0 -1 0.0 + "HG" "HO" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.S01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.S01.unit.childsequence single int + 2 +!entry.S01.unit.connect array int + 1 + 10 +!entry.S01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 10 17 + 3 5 17 + 5 7 17 + 5 6 17 + 5 8 17 + 8 9 17 + 10 11 17 +!entry.S01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 +!entry.S01.unit.name single str + "" +!entry.S01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.625000 0.044000 1.399000 + 0.153000 0.880000 1.949000 + 0.133000 -1.167000 2.128000 + 0.481000 -1.143000 3.022000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.S01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.S01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "S01" 1 12 1 "?" 0 +!entry.S01.unit.residuesPdbSequenceNumber array int + 1 +!entry.S01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.S01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/SER/S02.off b/share/off/SER/S02.off new file mode 100644 index 0000000..e43ddc3 --- /dev/null +++ b/share/off/SER/S02.off @@ -0,0 +1,99 @@ +!!index array str + "S02" +!entry.S02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.024900 + "HA" "H1" 0 1 131075 4 1 0.084300 + "CB" "CT" 0 1 131075 5 6 0.211700 + "HB2" "H1" 0 1 131075 6 1 0.035200 + "HB3" "H1" 0 1 131075 7 1 0.035200 + "OG" "OH" 0 1 131075 8 8 -0.654600 + "HG" "HO" 0 1 131075 9 1 0.427500 + "C" "C" 0 1 131075 10 6 0.597300 + "O" "O" 0 1 131075 11 8 -0.567900 +!entry.S02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "H1" 0 -1 0.0 + "HB3" "H1" 0 -1 0.0 + "OG" "OH" 0 -1 0.0 + "HG" "HO" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.S02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.S02.unit.childsequence single int + 2 +!entry.S02.unit.connect array int + 1 + 10 +!entry.S02.unit.connectivity table int atom1x int atom2x int flags + 10 11 17 + 8 9 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 10 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.S02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.S02.unit.name single str + "" +!entry.S02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.125261 0.861757 1.959955 + 0.212185 -0.915750 1.926854 + 1.951000 0.069000 1.448000 + 2.261633 0.067559 2.355976 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.S02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.S02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "S02" 1 12 1 "?" 0 +!entry.S02.unit.residuesPdbSequenceNumber array int + 1 +!entry.S02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.S02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/SER/S03.off b/share/off/SER/S03.off new file mode 100644 index 0000000..15ff77d --- /dev/null +++ b/share/off/SER/S03.off @@ -0,0 +1,99 @@ +!!index array str + "S03" +!entry.S03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.024900 + "HA" "H1" 0 1 131075 4 1 0.084300 + "CB" "CT" 0 1 131075 5 6 0.211700 + "HB2" "H1" 0 1 131075 6 1 0.035200 + "HB3" "H1" 0 1 131075 7 1 0.035200 + "OG" "OH" 0 1 131075 8 8 -0.654600 + "HG" "HO" 0 1 131075 9 1 0.427500 + "C" "C" 0 1 131075 10 6 0.597300 + "O" "O" 0 1 131075 11 8 -0.567900 +!entry.S03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "H1" 0 -1 0.0 + "HB3" "H1" 0 -1 0.0 + "OG" "OH" 0 -1 0.0 + "HG" "HO" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.S03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.S03.unit.childsequence single int + 2 +!entry.S03.unit.connect array int + 1 + 10 +!entry.S03.unit.connectivity table int atom1x int atom2x int flags + 10 11 17 + 8 9 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 10 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.S03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.S03.unit.name single str + "" +!entry.S03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.109627 -0.850535 1.965738 + 1.620650 -0.098941 1.399967 + 0.192000 1.198000 2.106000 + 0.538875 1.173262 3.000417 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.S03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.S03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "S03" 1 12 1 "?" 0 +!entry.S03.unit.residuesPdbSequenceNumber array int + 1 +!entry.S03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.S03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/THR/T01.off b/share/off/THR/T01.off new file mode 100644 index 0000000..b8747b2 --- /dev/null +++ b/share/off/THR/T01.off @@ -0,0 +1,117 @@ +!!index array str + "T01" +!entry.T01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.038900 + "HA" "H1" 0 1 131075 4 1 0.100700 + "CB" "CT" 0 1 131075 5 6 0.365400 + "HB" "H1" 0 1 131075 6 1 0.004300 + "CG2" "CT" 0 1 131075 7 6 -0.243800 + "HG21" "HC" 0 1 131075 8 80 0.064200 + "HG22" "HC" 0 1 131075 9 80 0.064200 + "HG23" "HC" 0 1 131075 10 80 0.064200 + "OG1" "OH" 0 1 131075 11 8 -0.676100 + "HG1" "HO" 0 1 131075 12 1 0.410200 + "C" "C" 0 1 131075 13 6 0.597300 + "O" "O" 0 1 131075 14 8 -0.567900 +!entry.T01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB" "H1" 0 -1 0.0 + "CG2" "CT" 0 -1 0.0 + "HG21" "HC" 0 -1 0.0 + "HG22" "HC" 0 -1 0.0 + "HG23" "HC" 0 -1 0.0 + "OG1" "OH" 0 -1 0.0 + "HG1" "HO" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.T01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.T01.unit.childsequence single int + 2 +!entry.T01.unit.connect array int + 1 + 13 +!entry.T01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 13 17 + 3 5 17 + 5 6 17 + 5 11 17 + 5 7 17 + 7 10 17 + 7 8 17 + 7 9 17 + 11 12 17 + 13 14 17 +!entry.T01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 +!entry.T01.unit.name single str + "" +!entry.T01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.765000 -0.453000 + 0.0 0.0 0.0 + 0.360000 0.895000 -0.507000 + 0.564000 -0.015000 1.433000 + 1.652000 0.020000 1.379000 + 0.057000 1.185000 2.218000 + -1.031000 1.151000 2.273000 + 0.472000 1.162000 3.226000 + 0.367000 2.103000 1.719000 + 0.150000 -1.214000 2.100000 + 0.515000 -1.229000 2.988000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.T01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.T01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "T01" 1 15 1 "?" 0 +!entry.T01.unit.residuesPdbSequenceNumber array int + 1 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"C" "C" 0 1 131075 13 6 0.597300 + "O" "O" 0 1 131075 14 8 -0.567900 +!entry.T03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB" "H1" 0 -1 0.0 + "CG2" "CT" 0 -1 0.0 + "HG21" "HC" 0 -1 0.0 + "HG22" "HC" 0 -1 0.0 + "HG23" "HC" 0 -1 0.0 + "OG1" "OH" 0 -1 0.0 + "HG1" "HO" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.T03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.T03.unit.childsequence single int + 2 +!entry.T03.unit.connect array int + 1 + 13 +!entry.T03.unit.connectivity table int atom1x int atom2x int flags + 13 14 17 + 11 12 17 + 7 10 17 + 7 8 17 + 7 9 17 + 5 6 17 + 5 11 17 + 5 7 17 + 3 4 17 + 3 13 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.T03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 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+ "HZ2" "HA" 0 1 131075 15 1 0.157200 + "CH2" "CA" 0 1 131075 16 6 -0.113400 + "HH2" "HA" 0 1 131075 17 1 0.141700 + "CZ3" "CA" 0 1 131075 18 6 -0.197200 + "HZ3" "HA" 0 1 131075 19 1 0.144700 + "CE3" "CA" 0 1 131075 20 6 -0.238700 + "HE3" "HA" 0 1 131075 21 1 0.170000 + "CD2" "CB" 0 1 131075 22 6 0.124300 + "C" "C" 0 1 131075 23 6 0.597300 + "O" "O" 0 1 131075 24 8 -0.567900 +!entry.W01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C*" 0 -1 0.0 + "CD1" "CW" 0 -1 0.0 + "HD1" "H4" 0 -1 0.0 + "NE1" "NA" 0 -1 0.0 + "HE1" "H" 0 -1 0.0 + "CE2" "CN" 0 -1 0.0 + "CZ2" "CA" 0 -1 0.0 + "HZ2" "HA" 0 -1 0.0 + "CH2" "CA" 0 -1 0.0 + "HH2" "HA" 0 -1 0.0 + "CZ3" "CA" 0 -1 0.0 + "HZ3" "HA" 0 -1 0.0 + "CE3" "CA" 0 -1 0.0 + "HE3" "HA" 0 -1 0.0 + "CD2" "CB" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.W01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W01.unit.childsequence single int + 2 +!entry.W01.unit.connect array int + 1 + 23 +!entry.W01.unit.connectivity table int atom1x int atom2x int flags + 23 24 17 + 20 21 17 + 20 22 17 + 18 19 17 + 18 20 17 + 16 17 17 + 16 18 17 + 14 15 17 + 14 16 17 + 13 14 17 + 13 22 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 9 17 + 8 22 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 23 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.W01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 24 + "R" 1 "A" 23 + "R" 1 "A" 22 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.W01.unit.name single str + "" +!entry.W01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.944517 -0.032842 0.888984 + 0.0 0.0 0.0 + 0.354282 0.892018 -0.515769 + 0.536000 0.0 1.433000 + 0.133769 -0.844825 1.991106 + 1.619981 -0.108378 1.446684 + 0.203000 1.244000 2.198000 + -0.857000 1.430000 3.038000 + -1.611795 0.679632 3.252795 + -0.833000 2.702000 3.557000 + -1.505851 3.096123 4.205577 + 0.261000 3.364000 3.052000 + 0.706000 4.665000 3.282000 + 0.184344 5.340650 3.945365 + 1.845000 5.067000 2.635000 + 2.211904 6.072700 2.803005 + 2.536000 4.200000 1.771000 + 3.429322 4.561678 1.280575 + 2.095000 2.910000 1.544000 + 2.613692 2.234702 0.880991 + 0.936000 2.475000 2.192000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.W01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.W01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "W01" 1 25 1 "?" 0 +!entry.W01.unit.residuesPdbSequenceNumber array int + 1 +!entry.W01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/TRP/W02.off b/share/off/TRP/W02.off new file mode 100644 index 0000000..3775296 --- /dev/null +++ b/share/off/TRP/W02.off @@ -0,0 +1,179 @@ +!!index array str + "W02" +!entry.W02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.027500 + "HA" "H1" 0 1 131075 4 1 0.112300 + "CB" "CT" 0 1 131075 5 6 -0.005000 + "HB2" "HC" 0 1 131075 6 1 0.033900 + "HB3" "HC" 0 1 131075 7 1 0.033900 + "CG" "C*" 0 1 131075 8 6 -0.141500 + "CD1" "CW" 0 1 131075 9 6 -0.163800 + "HD1" "H4" 0 1 131075 10 1 0.206200 + "NE1" "NA" 0 1 131075 11 7 -0.341800 + "HE1" "H" 0 1 131075 12 1 0.341200 + "CE2" "CN" 0 1 131075 13 6 0.138000 + "CZ2" "CA" 0 1 131075 14 6 -0.260100 + "HZ2" "HA" 0 1 131075 15 1 0.157200 + "CH2" "CA" 0 1 131075 16 6 -0.113400 + "HH2" "HA" 0 1 131075 17 1 0.141700 + "CZ3" "CA" 0 1 131075 18 6 -0.197200 + "HZ3" "HA" 0 1 131075 19 1 0.144700 + "CE3" "CA" 0 1 131075 20 6 -0.238700 + "HE3" "HA" 0 1 131075 21 1 0.170000 + "CD2" "CB" 0 1 131075 22 6 0.124300 + "C" "C" 0 1 131075 23 6 0.597300 + "O" "O" 0 1 131075 24 8 -0.567900 +!entry.W02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C*" 0 -1 0.0 + "CD1" "CW" 0 -1 0.0 + "HD1" "H4" 0 -1 0.0 + "NE1" "NA" 0 -1 0.0 + "HE1" "H" 0 -1 0.0 + "CE2" "CN" 0 -1 0.0 + "CZ2" "CA" 0 -1 0.0 + "HZ2" "HA" 0 -1 0.0 + "CH2" "CA" 0 -1 0.0 + "HH2" "HA" 0 -1 0.0 + "CZ3" "CA" 0 -1 0.0 + "HZ3" "HA" 0 -1 0.0 + "CE3" "CA" 0 -1 0.0 + "HE3" "HA" 0 -1 0.0 + "CD2" "CB" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.W02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W02.unit.childsequence single int + 2 +!entry.W02.unit.connect array int + 1 + 23 +!entry.W02.unit.connectivity table int atom1x int atom2x int flags + 2 1 17 + 3 1 17 + 4 3 17 + 5 3 17 + 6 5 17 + 7 5 17 + 8 5 17 + 9 8 17 + 10 9 17 + 11 9 17 + 12 11 17 + 13 11 17 + 14 13 17 + 15 14 17 + 16 14 17 + 17 16 17 + 18 16 17 + 19 18 17 + 20 18 17 + 21 20 17 + 22 20 17 + 22 13 17 + 22 8 17 + 23 3 17 + 24 23 17 +!entry.W02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 + "R" 1 "A" 20 + "R" 1 "A" 21 + "R" 1 "A" 22 + "R" 1 "A" 23 + "R" 1 "A" 24 +!entry.W02.unit.name single str + "" +!entry.W02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.944517 -0.032842 0.888984 + 0.0 0.0 0.0 + 0.354282 0.892018 -0.515769 + 0.536000 0.0 1.433000 + 0.133769 -0.844825 1.991106 + 1.619981 -0.108378 1.446684 + 0.203000 1.244000 2.198000 + -0.438000 2.352000 1.722000 + -0.784662 2.471652 0.700035 + -0.565000 3.290000 2.717000 + -1.001762 4.201050 2.627890 + 0.0 2.793000 3.867000 + 0.114000 3.369000 5.131000 + -0.268653 4.356551 5.347798 + 0.734000 2.635000 6.107000 + 0.830881 3.062820 7.097889 + 1.235000 1.349000 5.842000 + 1.717070 0.806100 6.643386 + 1.121000 0.777000 4.589000 + 1.505143 -0.207599 4.370714 + 0.493000 1.506000 3.577000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.W02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.W02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "W02" 1 25 1 "?" 0 +!entry.W02.unit.residuesPdbSequenceNumber array int + 1 +!entry.W02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/TRP/W03.off b/share/off/TRP/W03.off new file mode 100644 index 0000000..81797c5 --- /dev/null +++ b/share/off/TRP/W03.off @@ -0,0 +1,179 @@ +!!index array str + "W03" +!entry.W03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.027500 + "HA" "H1" 0 1 131075 4 1 0.112300 + "CB" "CT" 0 1 131075 5 6 -0.005000 + "HB2" "HC" 0 1 131075 6 1 0.033900 + "HB3" "HC" 0 1 131075 7 1 0.033900 + "CG" "C*" 0 1 131075 8 6 -0.141500 + "CD1" "CW" 0 1 131075 9 6 -0.163800 + "HD1" "H4" 0 1 131075 10 1 0.206200 + "NE1" "NA" 0 1 131075 11 7 -0.341800 + "HE1" "H" 0 1 131075 12 1 0.341200 + "CE2" "CN" 0 1 131075 13 6 0.138000 + "CZ2" "CA" 0 1 131075 14 6 -0.260100 + "HZ2" "HA" 0 1 131075 15 1 0.157200 + "CH2" "CA" 0 1 131075 16 6 -0.113400 + "HH2" "HA" 0 1 131075 17 1 0.141700 + "CZ3" "CA" 0 1 131075 18 6 -0.197200 + "HZ3" "HA" 0 1 131075 19 1 0.144700 + "CE3" "CA" 0 1 131075 20 6 -0.238700 + "HE3" "HA" 0 1 131075 21 1 0.170000 + "CD2" "CB" 0 1 131075 22 6 0.124300 + "C" "C" 0 1 131075 23 6 0.597300 + "O" "O" 0 1 131075 24 8 -0.567900 +!entry.W03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C*" 0 -1 0.0 + "CD1" "CW" 0 -1 0.0 + "HD1" "H4" 0 -1 0.0 + "NE1" "NA" 0 -1 0.0 + "HE1" "H" 0 -1 0.0 + "CE2" "CN" 0 -1 0.0 + "CZ2" "CA" 0 -1 0.0 + "HZ2" "HA" 0 -1 0.0 + "CH2" "CA" 0 -1 0.0 + "HH2" "HA" 0 -1 0.0 + "CZ3" "CA" 0 -1 0.0 + "HZ3" "HA" 0 -1 0.0 + "CE3" "CA" 0 -1 0.0 + "HE3" "HA" 0 -1 0.0 + "CD2" "CB" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.W03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W03.unit.childsequence single int + 2 +!entry.W03.unit.connect array int + 1 + 23 +!entry.W03.unit.connectivity table int atom1x int atom2x int flags + 2 1 17 + 3 1 17 + 4 3 17 + 5 3 17 + 6 5 17 + 7 5 17 + 8 5 17 + 9 8 17 + 10 9 17 + 11 9 17 + 12 11 17 + 13 11 17 + 14 13 17 + 15 14 17 + 16 14 17 + 17 16 17 + 18 16 17 + 19 18 17 + 20 18 17 + 21 20 17 + 22 20 17 + 22 13 17 + 22 8 17 + 23 3 17 + 24 23 17 +!entry.W03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 + "R" 1 "A" 20 + "R" 1 "A" 21 + "R" 1 "A" 22 + "R" 1 "A" 23 + "R" 1 "A" 24 +!entry.W03.unit.name single str + "" +!entry.W03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.944517 -0.032842 0.888984 + 0.0 0.0 0.0 + 0.354282 0.892018 -0.515769 + 0.536000 0.0 1.433000 + 0.133769 -0.844825 1.991106 + 1.619981 -0.108378 1.446684 + 0.203000 1.244000 2.198000 + 0.947000 2.386000 2.269000 + 1.902611 2.530364 1.774155 + 0.318000 3.313000 3.066000 + 0.657564 4.243724 3.283168 + -0.858000 2.772000 3.527000 + -1.832000 3.322000 4.360000 + -1.745387 4.322190 4.760998 + -2.920000 2.545000 4.659000 + -3.691512 2.954110 5.300619 + -3.048000 1.243000 4.147000 + -3.923467 0.666326 4.412248 + -2.083000 0.698000 3.320000 + -2.166433 -0.301717 2.922187 + -0.964000 1.470000 2.999000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.W03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.W03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "W03" 1 25 1 "?" 0 +!entry.W03.unit.residuesPdbSequenceNumber array int + 1 +!entry.W03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/TRP/W04.off b/share/off/TRP/W04.off new file mode 100644 index 0000000..a2736bd --- /dev/null +++ b/share/off/TRP/W04.off @@ -0,0 +1,179 @@ +!!index array str + "W04" +!entry.W04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.027500 + "HA" "H1" 0 1 131075 4 1 0.112300 + "CB" "CT" 0 1 131075 5 6 -0.005000 + "HB2" "HC" 0 1 131075 6 1 0.033900 + "HB3" "HC" 0 1 131075 7 1 0.033900 + "CG" "C*" 0 1 131075 8 6 -0.141500 + "CD1" "CW" 0 1 131075 9 6 -0.163800 + "HD1" "H4" 0 1 131075 10 1 0.206200 + "NE1" "NA" 0 1 131075 11 7 -0.341800 + "HE1" "H" 0 1 131075 12 1 0.341200 + "CE2" "CN" 0 1 131075 13 6 0.138000 + "CZ2" "CA" 0 1 131075 14 6 -0.260100 + "HZ2" "HA" 0 1 131075 15 1 0.157200 + "CH2" "CA" 0 1 131075 16 6 -0.113400 + "HH2" "HA" 0 1 131075 17 1 0.141700 + "CZ3" "CA" 0 1 131075 18 6 -0.197200 + "HZ3" "HA" 0 1 131075 19 1 0.144700 + "CE3" "CA" 0 1 131075 20 6 -0.238700 + "HE3" "HA" 0 1 131075 21 1 0.170000 + "CD2" "CB" 0 1 131075 22 6 0.124300 + "C" "C" 0 1 131075 23 6 0.597300 + "O" "O" 0 1 131075 24 8 -0.567900 +!entry.W04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C*" 0 -1 0.0 + "CD1" "CW" 0 -1 0.0 + "HD1" "H4" 0 -1 0.0 + "NE1" "NA" 0 -1 0.0 + "HE1" "H" 0 -1 0.0 + "CE2" "CN" 0 -1 0.0 + "CZ2" "CA" 0 -1 0.0 + "HZ2" "HA" 0 -1 0.0 + "CH2" "CA" 0 -1 0.0 + "HH2" "HA" 0 -1 0.0 + "CZ3" "CA" 0 -1 0.0 + "HZ3" "HA" 0 -1 0.0 + "CE3" "CA" 0 -1 0.0 + "HE3" "HA" 0 -1 0.0 + "CD2" "CB" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.W04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W04.unit.childsequence single int + 2 +!entry.W04.unit.connect array int + 1 + 23 +!entry.W04.unit.connectivity table int atom1x int atom2x int flags + 2 1 17 + 3 1 17 + 4 3 17 + 5 3 17 + 6 5 17 + 7 5 17 + 8 5 17 + 9 8 17 + 10 9 17 + 11 9 17 + 12 11 17 + 13 11 17 + 14 13 17 + 15 14 17 + 16 14 17 + 17 16 17 + 18 16 17 + 19 18 17 + 20 18 17 + 21 20 17 + 22 20 17 + 22 13 17 + 22 8 17 + 23 3 17 + 24 23 17 +!entry.W04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 + "R" 1 "A" 20 + "R" 1 "A" 21 + "R" 1 "A" 22 + "R" 1 "A" 23 + "R" 1 "A" 24 +!entry.W04.unit.name single str + "" +!entry.W04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.944517 -0.032842 0.888984 + 0.0 0.0 0.0 + 0.354282 0.892018 -0.515769 + 0.536000 0.0 1.433000 + 0.136703 0.846938 1.990009 + 0.225064 -0.896421 1.968440 + 2.030000 0.072000 1.514000 + 2.794000 1.201000 1.579000 + 2.400011 2.212731 1.570187 + 4.126000 0.870000 1.643000 + 4.902032 1.520759 1.697773 + 4.241000 -0.499000 1.621000 + 5.379000 -1.304000 1.665000 + 6.374254 -0.886977 1.730135 + 5.196000 -2.661000 1.627000 + 6.066665 -3.305082 1.664116 + 3.909000 -3.219000 1.546000 + 3.812568 -4.295688 1.517788 + 2.781000 -2.422000 1.503000 + 1.787177 -2.837454 1.436950 + 2.940000 -1.035000 1.540000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.W04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.W04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "W04" 1 25 1 "?" 0 +!entry.W04.unit.residuesPdbSequenceNumber array int + 1 +!entry.W04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/TRP/W05.off b/share/off/TRP/W05.off new file mode 100644 index 0000000..16556e5 --- /dev/null +++ b/share/off/TRP/W05.off @@ -0,0 +1,179 @@ +!!index array str + "W05" +!entry.W05.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.027500 + "HA" "H1" 0 1 131075 4 1 0.112300 + "CB" "CT" 0 1 131075 5 6 -0.005000 + "HB2" "HC" 0 1 131075 6 1 0.033900 + "HB3" "HC" 0 1 131075 7 1 0.033900 + "CG" "C*" 0 1 131075 8 6 -0.141500 + "CD1" "CW" 0 1 131075 9 6 -0.163800 + "HD1" "H4" 0 1 131075 10 1 0.206200 + "NE1" "NA" 0 1 131075 11 7 -0.341800 + "HE1" "H" 0 1 131075 12 1 0.341200 + "CE2" "CN" 0 1 131075 13 6 0.138000 + "CZ2" "CA" 0 1 131075 14 6 -0.260100 + "HZ2" "HA" 0 1 131075 15 1 0.157200 + "CH2" "CA" 0 1 131075 16 6 -0.113400 + "HH2" "HA" 0 1 131075 17 1 0.141700 + "CZ3" "CA" 0 1 131075 18 6 -0.197200 + "HZ3" "HA" 0 1 131075 19 1 0.144700 + "CE3" "CA" 0 1 131075 20 6 -0.238700 + "HE3" "HA" 0 1 131075 21 1 0.170000 + "CD2" "CB" 0 1 131075 22 6 0.124300 + "C" "C" 0 1 131075 23 6 0.597300 + "O" "O" 0 1 131075 24 8 -0.567900 +!entry.W05.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C*" 0 -1 0.0 + "CD1" "CW" 0 -1 0.0 + "HD1" "H4" 0 -1 0.0 + "NE1" "NA" 0 -1 0.0 + "HE1" "H" 0 -1 0.0 + "CE2" "CN" 0 -1 0.0 + "CZ2" "CA" 0 -1 0.0 + "HZ2" "HA" 0 -1 0.0 + "CH2" "CA" 0 -1 0.0 + "HH2" "HA" 0 -1 0.0 + "CZ3" "CA" 0 -1 0.0 + "HZ3" "HA" 0 -1 0.0 + "CE3" "CA" 0 -1 0.0 + "HE3" "HA" 0 -1 0.0 + "CD2" "CB" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.W05.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W05.unit.childsequence single int + 2 +!entry.W05.unit.connect array int + 1 + 23 +!entry.W05.unit.connectivity table int atom1x int atom2x int flags + 2 1 17 + 3 1 17 + 4 3 17 + 5 3 17 + 6 5 17 + 7 5 17 + 8 5 17 + 9 8 17 + 10 9 17 + 11 9 17 + 12 11 17 + 13 11 17 + 14 13 17 + 15 14 17 + 16 14 17 + 17 16 17 + 18 16 17 + 19 18 17 + 20 18 17 + 21 20 17 + 22 20 17 + 22 13 17 + 22 8 17 + 23 3 17 + 24 23 17 +!entry.W05.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 + "R" 1 "A" 20 + "R" 1 "A" 21 + "R" 1 "A" 22 + "R" 1 "A" 23 + "R" 1 "A" 24 +!entry.W05.unit.name single str + "" +!entry.W05.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.944517 -0.032842 0.888984 + 0.0 0.0 0.0 + 0.354282 0.892018 -0.515769 + 0.536000 0.0 1.433000 + 0.136703 0.846938 1.990009 + 0.225064 -0.896421 1.968440 + 2.030000 0.072000 1.514000 + 2.884000 -0.948000 1.821000 + 2.573494 -1.960878 2.058840 + 4.183000 -0.502000 1.797000 + 5.009760 -1.057642 1.987900 + 4.185000 0.833000 1.469000 + 5.252000 1.718000 1.322000 + 6.277854 1.408132 1.464431 + 4.958000 3.013000 0.983000 + 5.772820 3.716392 0.858158 + 3.630000 3.431000 0.794000 + 3.444958 4.463036 0.529399 + 2.572000 2.554000 0.939000 + 1.547406 2.863129 0.800088 + 2.846000 1.228000 1.283000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.W05.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.W05.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "W05" 1 25 1 "?" 0 +!entry.W05.unit.residuesPdbSequenceNumber array int + 1 +!entry.W05.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W05.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/TRP/W06.off b/share/off/TRP/W06.off new file mode 100644 index 0000000..89a3943 --- /dev/null +++ b/share/off/TRP/W06.off @@ -0,0 +1,179 @@ +!!index array str + "W06" +!entry.W06.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.027500 + "HA" "H1" 0 1 131075 4 1 0.112300 + "CB" "CT" 0 1 131075 5 6 -0.005000 + "HB2" "HC" 0 1 131075 6 1 0.033900 + "HB3" "HC" 0 1 131075 7 1 0.033900 + "CG" "C*" 0 1 131075 8 6 -0.141500 + "CD1" "CW" 0 1 131075 9 6 -0.163800 + "HD1" "H4" 0 1 131075 10 1 0.206200 + "NE1" "NA" 0 1 131075 11 7 -0.341800 + "HE1" "H" 0 1 131075 12 1 0.341200 + "CE2" "CN" 0 1 131075 13 6 0.138000 + "CZ2" "CA" 0 1 131075 14 6 -0.260100 + "HZ2" "HA" 0 1 131075 15 1 0.157200 + "CH2" "CA" 0 1 131075 16 6 -0.113400 + "HH2" "HA" 0 1 131075 17 1 0.141700 + "CZ3" "CA" 0 1 131075 18 6 -0.197200 + "HZ3" "HA" 0 1 131075 19 1 0.144700 + "CE3" "CA" 0 1 131075 20 6 -0.238700 + "HE3" "HA" 0 1 131075 21 1 0.170000 + "CD2" "CB" 0 1 131075 22 6 0.124300 + "C" "C" 0 1 131075 23 6 0.597300 + "O" "O" 0 1 131075 24 8 -0.567900 +!entry.W06.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C*" 0 -1 0.0 + "CD1" "CW" 0 -1 0.0 + "HD1" "H4" 0 -1 0.0 + "NE1" "NA" 0 -1 0.0 + "HE1" "H" 0 -1 0.0 + "CE2" "CN" 0 -1 0.0 + "CZ2" "CA" 0 -1 0.0 + "HZ2" "HA" 0 -1 0.0 + "CH2" "CA" 0 -1 0.0 + "HH2" "HA" 0 -1 0.0 + "CZ3" "CA" 0 -1 0.0 + "HZ3" "HA" 0 -1 0.0 + "CE3" "CA" 0 -1 0.0 + "HE3" "HA" 0 -1 0.0 + "CD2" "CB" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.W06.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W06.unit.childsequence single int + 2 +!entry.W06.unit.connect array int + 1 + 23 +!entry.W06.unit.connectivity table int atom1x int atom2x int flags + 2 1 17 + 3 1 17 + 4 3 17 + 5 3 17 + 6 5 17 + 7 5 17 + 8 5 17 + 9 8 17 + 10 9 17 + 11 9 17 + 12 11 17 + 13 11 17 + 14 13 17 + 15 14 17 + 16 14 17 + 17 16 17 + 18 16 17 + 19 18 17 + 20 18 17 + 21 20 17 + 22 20 17 + 22 13 17 + 22 8 17 + 23 3 17 + 24 23 17 +!entry.W06.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 + "R" 1 "A" 20 + "R" 1 "A" 21 + "R" 1 "A" 22 + "R" 1 "A" 23 + "R" 1 "A" 24 +!entry.W06.unit.name single str + "" +!entry.W06.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.944517 -0.032842 0.888984 + 0.0 0.0 0.0 + 0.354282 0.892018 -0.515769 + 0.536000 0.0 1.433000 + 1.624286 0.051318 1.433592 + 0.185079 0.872277 1.983395 + 0.142000 -1.212000 2.220000 + 0.830000 -2.387000 2.313000 + 1.767359 -2.593779 1.805551 + 0.158000 -3.267000 3.127000 + 0.452891 -4.208456 3.362402 + -0.991000 -2.661000 3.577000 + -1.989000 -3.147000 4.421000 + -1.949592 -4.141842 4.842210 + -3.037000 -2.312000 4.706000 + -3.822511 -2.667602 5.362351 + -3.102000 -1.016000 4.168000 + -3.948691 -0.392611 4.420690 + -2.113000 -0.534000 3.333000 + -2.152718 0.457836 2.909522 + -1.033000 -1.365000 3.026000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.W06.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.W06.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "W06" 1 25 1 "?" 0 +!entry.W06.unit.residuesPdbSequenceNumber array int + 1 +!entry.W06.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W06.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/TRP/W07.off b/share/off/TRP/W07.off new file mode 100644 index 0000000..b605b53 --- /dev/null +++ b/share/off/TRP/W07.off @@ -0,0 +1,179 @@ +!!index array str + "W07" +!entry.W07.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 6 -0.027500 + "HA" "H1" 0 1 131075 4 1 0.112300 + "CB" "CT" 0 1 131075 5 6 -0.005000 + "HB2" "HC" 0 1 131075 6 1 0.033900 + "HB3" "HC" 0 1 131075 7 1 0.033900 + "CG" "C*" 0 1 131075 8 6 -0.141500 + "CD1" "CW" 0 1 131075 9 6 -0.163800 + "HD1" "H4" 0 1 131075 10 1 0.206200 + "NE1" "NA" 0 1 131075 11 7 -0.341800 + "HE1" "H" 0 1 131075 12 1 0.341200 + "CE2" "CN" 0 1 131075 13 6 0.138000 + "CZ2" "CA" 0 1 131075 14 6 -0.260100 + "HZ2" "HA" 0 1 131075 15 1 0.157200 + "CH2" "CA" 0 1 131075 16 6 -0.113400 + "HH2" "HA" 0 1 131075 17 1 0.141700 + "CZ3" "CA" 0 1 131075 18 6 -0.197200 + "HZ3" "HA" 0 1 131075 19 1 0.144700 + "CE3" "CA" 0 1 131075 20 6 -0.238700 + "HE3" "HA" 0 1 131075 21 1 0.170000 + "CD2" "CB" 0 1 131075 22 6 0.124300 + "C" "C" 0 1 131075 23 6 0.597300 + "O" "O" 0 1 131075 24 8 -0.567900 +!entry.W07.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "C*" 0 -1 0.0 + "CD1" "CW" 0 -1 0.0 + "HD1" "H4" 0 -1 0.0 + "NE1" "NA" 0 -1 0.0 + "HE1" "H" 0 -1 0.0 + "CE2" "CN" 0 -1 0.0 + "CZ2" "CA" 0 -1 0.0 + "HZ2" "HA" 0 -1 0.0 + "CH2" "CA" 0 -1 0.0 + "HH2" "HA" 0 -1 0.0 + "CZ3" "CA" 0 -1 0.0 + "HZ3" "HA" 0 -1 0.0 + "CE3" "CA" 0 -1 0.0 + "HE3" "HA" 0 -1 0.0 + "CD2" "CB" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.W07.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W07.unit.childsequence single int + 2 +!entry.W07.unit.connect array int + 1 + 23 +!entry.W07.unit.connectivity table int atom1x int atom2x int flags + 2 1 17 + 3 1 17 + 4 3 17 + 5 3 17 + 6 5 17 + 7 5 17 + 8 5 17 + 9 8 17 + 10 9 17 + 11 9 17 + 12 11 17 + 13 11 17 + 14 13 17 + 15 14 17 + 16 14 17 + 17 16 17 + 18 16 17 + 19 18 17 + 20 18 17 + 21 20 17 + 22 20 17 + 22 13 17 + 22 8 17 + 23 3 17 + 24 23 17 +!entry.W07.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 + "R" 1 "A" 20 + "R" 1 "A" 21 + "R" 1 "A" 22 + "R" 1 "A" 23 + "R" 1 "A" 24 +!entry.W07.unit.name single str + "" +!entry.W07.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.944517 -0.032842 0.888984 + 0.0 0.0 0.0 + 0.354282 0.892018 -0.515769 + 0.536000 0.0 1.433000 + 1.624286 0.051318 1.433592 + 0.185079 0.872277 1.983395 + 0.142000 -1.212000 2.220000 + -0.976000 -1.363000 2.988000 + -1.732458 -0.597518 3.131917 + -0.995000 -2.613000 3.557000 + -1.714162 -2.979782 4.170995 + 0.128000 -3.297000 3.158000 + 0.549000 -4.589000 3.469000 + -0.024088 -5.238853 4.115485 + 1.728000 -5.019000 2.921000 + 2.072214 -6.021379 3.146896 + 2.484000 -4.188000 2.077000 + 3.408699 -4.570449 1.667103 + 2.067000 -2.907000 1.768000 + 2.640127 -2.256440 1.125391 + 0.868000 -2.445000 2.314000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.W07.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.W07.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "W07" 1 25 1 "?" 0 +!entry.W07.unit.residuesPdbSequenceNumber array int + 1 +!entry.W07.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.W07.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/TYR/Y01.off b/share/off/TYR/Y01.off new file mode 100644 index 0000000..3a53616 --- /dev/null +++ b/share/off/TYR/Y01.off @@ -0,0 +1,160 @@ +!!index array str + "Y01" +!entry.Y01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.001400 + "HA" "H1" 0 1 131075 4 1 0.087600 + "CB" "CT" 0 1 131075 5 6 -0.015200 + "HB2" "HC" 0 1 131075 6 1 0.029500 + "HB3" "HC" 0 1 131075 7 1 0.029500 + "CG" "CA" 0 1 131075 8 6 -0.001100 + "CD1" "CA" 0 1 131075 9 6 -0.190600 + "HD1" "HA" 0 1 131075 10 1 0.169900 + "CE1" "CA" 0 1 131075 11 6 -0.234100 + "HE1" "HA" 0 1 131075 12 1 0.165600 + "CZ" "C" 0 1 131075 13 6 0.322600 + "OH" "OH" 0 1 131075 14 8 -0.557900 + "HH" "HO" 0 1 131075 15 1 0.399200 + "CE2" "CA" 0 1 131075 16 6 -0.234100 + "HE2" "HA" 0 1 131075 17 1 0.165600 + "CD2" "CA" 0 1 131075 18 6 -0.190600 + "HD2" "HA" 0 1 131075 19 1 0.169900 + "C" "C" 0 1 131075 20 6 0.597300 + "O" "O" 0 1 131075 21 8 -0.567900 +!entry.Y01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CA" 0 -1 0.0 + "CD1" "CA" 0 -1 0.0 + "HD1" "HA" 0 -1 0.0 + "CE1" "CA" 0 -1 0.0 + "HE1" "HA" 0 -1 0.0 + "CZ" "C" 0 -1 0.0 + "OH" "OH" 0 -1 0.0 + "HH" "HO" 0 -1 0.0 + "CE2" "CA" 0 -1 0.0 + "HE2" "HA" 0 -1 0.0 + "CD2" "CA" 0 -1 0.0 + "HD2" "HA" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.Y01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Y01.unit.childsequence single int + 2 +!entry.Y01.unit.connect array int + 1 + 20 +!entry.Y01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 20 17 + 3 5 17 + 5 7 17 + 5 6 17 + 5 8 17 + 8 18 17 + 8 9 17 + 9 10 17 + 9 11 17 + 11 12 17 + 11 13 17 + 13 14 17 + 13 16 17 + 14 15 17 + 16 17 17 + 16 18 17 + 18 19 17 + 20 21 17 +!entry.Y01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 + "R" 1 "A" 17 + "R" 1 "A" 18 + "R" 1 "A" 19 + "R" 1 "A" 20 + "R" 1 "A" 21 +!entry.Y01.unit.name single str + "" +!entry.Y01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.108000 -0.866000 1.938000 + 1.618000 -0.113000 1.373000 + 0.203000 1.253000 2.212000 + 1.005000 2.383000 2.118000 + 1.882000 2.353000 1.471000 + 0.708000 3.531000 2.826000 + 1.343000 4.413000 2.746000 + -0.414000 3.555000 3.646000 + -0.716000 4.695000 4.354000 + -0.088000 5.406000 4.206000 + -1.225000 2.441000 3.754000 + -2.105000 2.456000 4.397000 + -0.912000 1.301000 3.038000 + -1.546000 0.417000 3.116000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.Y01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.Y01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "Y01" 1 22 1 "?" 0 +!entry.Y01.unit.residuesPdbSequenceNumber array int + 1 +!entry.Y01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Y01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/TYR/Y02.off b/share/off/TYR/Y02.off new file mode 100644 index 0000000..bf81307 --- /dev/null +++ b/share/off/TYR/Y02.off @@ -0,0 +1,160 @@ +!!index array str + "Y02" +!entry.Y02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.001400 + "HA" "H1" 0 1 131075 4 1 0.087600 + "CB" "CT" 0 1 131075 5 6 -0.015200 + "HB2" "HC" 0 1 131075 6 1 0.029500 + "HB3" "HC" 0 1 131075 7 1 0.029500 + "CG" "CA" 0 1 131075 8 6 -0.001100 + "CD1" "CA" 0 1 131075 9 6 -0.190600 + "HD1" "HA" 0 1 131075 10 1 0.169900 + "CE1" "CA" 0 1 131075 11 6 -0.234100 + "HE1" "HA" 0 1 131075 12 1 0.165600 + "CZ" "C" 0 1 131075 13 6 0.322600 + "OH" "OH" 0 1 131075 14 8 -0.557900 + "HH" "HO" 0 1 131075 15 1 0.399200 + "CE2" "CA" 0 1 131075 16 6 -0.234100 + "HE2" "HA" 0 1 131075 17 1 0.165600 + "CD2" "CA" 0 1 131075 18 6 -0.190600 + "HD2" "HA" 0 1 131075 19 1 0.169900 + "C" "C" 0 1 131075 20 6 0.597300 + "O" "O" 0 1 131075 21 8 -0.567900 +!entry.Y02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CA" 0 -1 0.0 + "CD1" "CA" 0 -1 0.0 + "HD1" "HA" 0 -1 0.0 + "CE1" "CA" 0 -1 0.0 + "HE1" "HA" 0 -1 0.0 + "CZ" "C" 0 -1 0.0 + "OH" "OH" 0 -1 0.0 + "HH" "HO" 0 -1 0.0 + "CE2" "CA" 0 -1 0.0 + "HE2" "HA" 0 -1 0.0 + "CD2" "CA" 0 -1 0.0 + "HD2" "HA" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.Y02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Y02.unit.childsequence single int + 2 +!entry.Y02.unit.connect array int + 1 + 20 +!entry.Y02.unit.connectivity table int atom1x int atom2x int flags + 20 21 17 + 18 19 17 + 16 17 17 + 16 18 17 + 14 15 17 + 13 14 17 + 13 16 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 18 17 + 8 9 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 20 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.Y02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.Y02.unit.name single str + "" +!entry.Y02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.108194 -0.866024 1.938122 + 1.618002 -0.112878 1.372805 + 0.203000 1.253000 2.212000 + 0.056000 2.474000 1.566000 + 0.184641 2.515399 0.484161 + -0.248000 3.623000 2.270000 + -0.362256 4.576350 1.754619 + -0.410000 3.555000 3.649000 + -0.712000 4.694000 4.357000 + -0.787052 5.472820 3.800569 + -0.267000 2.349000 4.310000 + -0.392210 2.292731 5.391310 + 0.037000 1.210000 3.590000 + 0.150826 0.254591 4.103550 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.Y02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.Y02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "Y02" 1 22 1 "?" 0 +!entry.Y02.unit.residuesPdbSequenceNumber array int + 1 +!entry.Y02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Y02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/TYR/Y03.off b/share/off/TYR/Y03.off new file mode 100644 index 0000000..39f6dfd --- /dev/null +++ b/share/off/TYR/Y03.off @@ -0,0 +1,160 @@ +!!index array str + "Y03" +!entry.Y03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.001400 + "HA" "H1" 0 1 131075 4 1 0.087600 + "CB" "CT" 0 1 131075 5 6 -0.015200 + "HB2" "HC" 0 1 131075 6 1 0.029500 + "HB3" "HC" 0 1 131075 7 1 0.029500 + "CG" "CA" 0 1 131075 8 6 -0.001100 + "CD1" "CA" 0 1 131075 9 6 -0.190600 + "HD1" "HA" 0 1 131075 10 1 0.169900 + "CE1" "CA" 0 1 131075 11 6 -0.234100 + "HE1" "HA" 0 1 131075 12 1 0.165600 + "CZ" "C" 0 1 131075 13 6 0.322600 + "OH" "OH" 0 1 131075 14 8 -0.557900 + "HH" "HO" 0 1 131075 15 1 0.399200 + "CE2" "CA" 0 1 131075 16 6 -0.234100 + "HE2" "HA" 0 1 131075 17 1 0.165600 + "CD2" "CA" 0 1 131075 18 6 -0.190600 + "HD2" "HA" 0 1 131075 19 1 0.169900 + "C" "C" 0 1 131075 20 6 0.597300 + "O" "O" 0 1 131075 21 8 -0.567900 +!entry.Y03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CA" 0 -1 0.0 + "CD1" "CA" 0 -1 0.0 + "HD1" "HA" 0 -1 0.0 + "CE1" "CA" 0 -1 0.0 + "HE1" "HA" 0 -1 0.0 + "CZ" "C" 0 -1 0.0 + "OH" "OH" 0 -1 0.0 + "HH" "HO" 0 -1 0.0 + "CE2" "CA" 0 -1 0.0 + "HE2" "HA" 0 -1 0.0 + "CD2" "CA" 0 -1 0.0 + "HD2" "HA" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.Y03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Y03.unit.childsequence single int + 2 +!entry.Y03.unit.connect array int + 1 + 20 +!entry.Y03.unit.connectivity table int atom1x int atom2x int flags + 20 21 17 + 18 19 17 + 16 17 17 + 16 18 17 + 14 15 17 + 13 14 17 + 13 16 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 18 17 + 8 9 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 20 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.Y03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.Y03.unit.name single str + "" +!entry.Y03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 0.099897 0.860422 1.940596 + 0.188191 -0.916517 1.908520 + 2.044000 0.073000 1.523000 + 2.708000 1.284000 1.381000 + 2.122197 2.186212 1.203557 + 4.084000 1.359000 1.461000 + 4.595625 2.314358 1.346637 + 4.818000 0.201000 1.690000 + 6.189000 0.267000 1.772000 + 6.529313 1.157395 1.657138 + 4.176000 -1.015000 1.835000 + 4.748310 -1.925168 2.014248 + 2.799000 -1.071000 1.751000 + 2.284299 -2.025854 1.864284 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.Y03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.Y03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "Y03" 1 22 1 "?" 0 +!entry.Y03.unit.residuesPdbSequenceNumber array int + 1 +!entry.Y03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Y03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/TYR/Y04.off b/share/off/TYR/Y04.off new file mode 100644 index 0000000..6b69ddb --- /dev/null +++ b/share/off/TYR/Y04.off @@ -0,0 +1,160 @@ +!!index array str + "Y04" +!entry.Y04.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.001400 + "HA" "H1" 0 1 131075 4 1 0.087600 + "CB" "CT" 0 1 131075 5 6 -0.015200 + "HB2" "HC" 0 1 131075 6 1 0.029500 + "HB3" "HC" 0 1 131075 7 1 0.029500 + "CG" "CA" 0 1 131075 8 6 -0.001100 + "CD1" "CA" 0 1 131075 9 6 -0.190600 + "HD1" "HA" 0 1 131075 10 1 0.169900 + "CE1" "CA" 0 1 131075 11 6 -0.234100 + "HE1" "HA" 0 1 131075 12 1 0.165600 + "CZ" "C" 0 1 131075 13 6 0.322600 + "OH" "OH" 0 1 131075 14 8 -0.557900 + "HH" "HO" 0 1 131075 15 1 0.399200 + "CE2" "CA" 0 1 131075 16 6 -0.234100 + "HE2" "HA" 0 1 131075 17 1 0.165600 + "CD2" "CA" 0 1 131075 18 6 -0.190600 + "HD2" "HA" 0 1 131075 19 1 0.169900 + "C" "C" 0 1 131075 20 6 0.597300 + "O" "O" 0 1 131075 21 8 -0.567900 +!entry.Y04.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB2" "HC" 0 -1 0.0 + "HB3" "HC" 0 -1 0.0 + "CG" "CA" 0 -1 0.0 + "CD1" "CA" 0 -1 0.0 + "HD1" "HA" 0 -1 0.0 + "CE1" "CA" 0 -1 0.0 + "HE1" "HA" 0 -1 0.0 + "CZ" "C" 0 -1 0.0 + "OH" "OH" 0 -1 0.0 + "HH" "HO" 0 -1 0.0 + "CE2" "CA" 0 -1 0.0 + "HE2" "HA" 0 -1 0.0 + "CD2" "CA" 0 -1 0.0 + "HD2" "HA" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.Y04.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Y04.unit.childsequence single int + 2 +!entry.Y04.unit.connect array int + 1 + 20 +!entry.Y04.unit.connectivity table int atom1x int atom2x int flags + 20 21 17 + 18 19 17 + 16 17 17 + 16 18 17 + 14 15 17 + 13 14 17 + 13 16 17 + 11 12 17 + 11 13 17 + 9 10 17 + 9 11 17 + 8 18 17 + 8 9 17 + 5 7 17 + 5 6 17 + 5 8 17 + 3 4 17 + 3 20 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.Y04.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 21 + "R" 1 "A" 20 + "R" 1 "A" 19 + "R" 1 "A" 18 + "R" 1 "A" 17 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.Y04.unit.name single str + "" +!entry.Y04.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.770000 -0.445000 + 0.0 0.0 0.0 + 0.369000 0.890000 -0.510000 + 0.536000 0.0 1.433000 + 1.622667 0.059777 1.371790 + 0.150362 0.894082 1.921870 + 0.143000 -1.221000 2.234000 + 0.944000 -2.355000 2.242000 + 1.865041 -2.351141 1.658642 + 0.593000 -3.474000 2.971000 + 1.229178 -4.358775 2.972066 + -0.584000 -3.464000 3.710000 + -0.942000 -4.574000 4.438000 + -0.308978 -5.291977 4.363163 + -1.397000 -2.345000 3.715000 + -2.321465 -2.334093 4.292338 + -1.029000 -1.235000 2.980000 + -1.663036 -0.347593 2.978252 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.Y04.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.Y04.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "Y04" 1 22 1 "?" 0 +!entry.Y04.unit.residuesPdbSequenceNumber array int + 1 +!entry.Y04.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.Y04.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/VAL/V01.off b/share/off/VAL/V01.off new file mode 100644 index 0000000..8292e5a --- /dev/null +++ b/share/off/VAL/V01.off @@ -0,0 +1,129 @@ +!!index array str + "V01" +!entry.V01.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.087500 + "HA" "H1" 0 1 131075 4 1 0.096900 + "CB" "CT" 0 1 131075 5 6 0.298500 + "HB" "HC" 0 1 131075 6 1 -0.029700 + "CG1" "CT" 0 1 131075 7 6 -0.319200 + "HG11" "HC" 0 1 131075 8 80 0.079100 + "HG12" "HC" 0 1 131075 9 80 0.079100 + "HG13" "HC" 0 1 131075 10 80 0.079100 + "CG2" "CT" 0 1 131075 11 6 -0.319200 + "HG21" "HC" 0 1 131075 12 80 0.079100 + "HG22" "HC" 0 1 131075 13 80 0.079100 + "HG23" "HC" 0 1 131075 14 80 0.079100 + "C" "C" 0 1 131075 15 6 0.597300 + "O" "O" 0 1 131075 16 8 -0.567900 +!entry.V01.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB" "HC" 0 -1 0.0 + "CG1" "CT" 0 -1 0.0 + "HG11" "HC" 0 -1 0.0 + "HG12" "HC" 0 -1 0.0 + "HG13" "HC" 0 -1 0.0 + "CG2" "CT" 0 -1 0.0 + "HG21" "HC" 0 -1 0.0 + "HG22" "HC" 0 -1 0.0 + "HG23" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.V01.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.V01.unit.childsequence single int + 2 +!entry.V01.unit.connect array int + 1 + 15 +!entry.V01.unit.connectivity table int atom1x int atom2x int flags + 1 2 17 + 1 3 17 + 3 4 17 + 3 15 17 + 3 5 17 + 5 6 17 + 5 11 17 + 5 7 17 + 7 9 17 + 7 10 17 + 7 8 17 + 11 12 17 + 11 13 17 + 11 14 17 + 15 16 17 +!entry.V01.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 1 + "R" 1 "A" 2 + "R" 1 "A" 3 + "R" 1 "A" 4 + "R" 1 "A" 5 + "R" 1 "A" 6 + "R" 1 "A" 7 + "R" 1 "A" 8 + "R" 1 "A" 9 + "R" 1 "A" 10 + "R" 1 "A" 11 + "R" 1 "A" 12 + "R" 1 "A" 13 + "R" 1 "A" 14 + "R" 1 "A" 15 + "R" 1 "A" 16 +!entry.V01.unit.name single str + "" +!entry.V01.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.765000 -0.453000 + 0.0 0.0 0.0 + 0.360000 0.895000 -0.507000 + 0.564000 -0.015000 1.433000 + 0.138000 -0.873000 1.953000 + 2.080000 -0.139000 1.408000 + 2.507000 0.719000 0.888000 + 2.459000 -0.170000 2.429000 + 2.362000 -1.055000 0.889000 + 0.199000 1.269000 2.162000 + -0.885000 1.376000 2.190000 + 0.587000 1.232000 3.180000 + 0.634000 2.121000 1.639000 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.V01.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.V01.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "V01" 1 17 1 "?" 0 +!entry.V01.unit.residuesPdbSequenceNumber array int + 1 +!entry.V01.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.V01.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/VAL/V02.off b/share/off/VAL/V02.off new file mode 100644 index 0000000..ed0d49c --- /dev/null +++ b/share/off/VAL/V02.off @@ -0,0 +1,129 @@ +!!index array str + "V02" +!entry.V02.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.087500 + "HA" "H1" 0 1 131075 4 1 0.096900 + "CB" "CT" 0 1 131075 5 6 0.298500 + "HB" "HC" 0 1 131075 6 1 -0.029700 + "CG1" "CT" 0 1 131075 7 6 -0.319200 + "HG11" "HC" 0 1 131075 8 80 0.079100 + "HG12" "HC" 0 1 131075 9 80 0.079100 + "HG13" "HC" 0 1 131075 10 80 0.079100 + "CG2" "CT" 0 1 131075 11 6 -0.319200 + "HG21" "HC" 0 1 131075 12 80 0.079100 + "HG22" "HC" 0 1 131075 13 80 0.079100 + "HG23" "HC" 0 1 131075 14 80 0.079100 + "C" "C" 0 1 131075 15 6 0.597300 + "O" "O" 0 1 131075 16 8 -0.567900 +!entry.V02.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB" "HC" 0 -1 0.0 + "CG1" "CT" 0 -1 0.0 + "HG11" "HC" 0 -1 0.0 + "HG12" "HC" 0 -1 0.0 + "HG13" "HC" 0 -1 0.0 + "CG2" "CT" 0 -1 0.0 + "HG21" "HC" 0 -1 0.0 + "HG22" "HC" 0 -1 0.0 + "HG23" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.V02.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.V02.unit.childsequence single int + 2 +!entry.V02.unit.connect array int + 1 + 15 +!entry.V02.unit.connectivity table int atom1x int atom2x int flags + 15 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 7 9 17 + 7 10 17 + 7 8 17 + 5 6 17 + 5 11 17 + 5 7 17 + 3 4 17 + 3 15 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.V02.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.V02.unit.name single str + "" +!entry.V02.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.765000 -0.453000 + 0.0 0.0 0.0 + 0.360000 0.895000 -0.507000 + 0.564000 -0.015000 1.433000 + 0.138101 -0.010172 0.429692 + 0.096000 -1.257000 2.176000 + 0.521581 -1.262771 3.179863 + -0.991450 -1.252322 2.242881 + 0.422006 -2.147406 1.638562 + 0.096000 1.211000 2.203000 + 0.422746 2.112433 1.685365 + -0.991965 1.204647 2.270292 + 0.521383 1.194967 3.206718 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.V02.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.V02.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "V02" 1 17 1 "?" 0 +!entry.V02.unit.residuesPdbSequenceNumber array int + 1 +!entry.V02.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.V02.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/share/off/VAL/V03.off b/share/off/VAL/V03.off new file mode 100644 index 0000000..8ce4b22 --- /dev/null +++ b/share/off/VAL/V03.off @@ -0,0 +1,129 @@ +!!index array str + "V03" +!entry.V03.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg + "N" "N" 0 1 131075 1 7 -0.415700 + "H" "H" 0 1 131075 2 1 0.271900 + "CA" "CX" 0 1 131075 3 20 -0.087500 + "HA" "H1" 0 1 131075 4 1 0.096900 + "CB" "CT" 0 1 131075 5 6 0.298500 + "HB" "HC" 0 1 131075 6 1 -0.029700 + "CG1" "CT" 0 1 131075 7 6 -0.319200 + "HG11" "HC" 0 1 131075 8 80 0.079100 + "HG12" "HC" 0 1 131075 9 80 0.079100 + "HG13" "HC" 0 1 131075 10 80 0.079100 + "CG2" "CT" 0 1 131075 11 6 -0.319200 + "HG21" "HC" 0 1 131075 12 80 0.079100 + "HG22" "HC" 0 1 131075 13 80 0.079100 + "HG23" "HC" 0 1 131075 14 80 0.079100 + "C" "C" 0 1 131075 15 6 0.597300 + "O" "O" 0 1 131075 16 8 -0.567900 +!entry.V03.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg + "N" "N" 0 -1 0.0 + "H" "H" 0 -1 0.0 + "CA" "CX" 0 -1 0.0 + "HA" "H1" 0 -1 0.0 + "CB" "CT" 0 -1 0.0 + "HB" "HC" 0 -1 0.0 + "CG1" "CT" 0 -1 0.0 + "HG11" "HC" 0 -1 0.0 + "HG12" "HC" 0 -1 0.0 + "HG13" "HC" 0 -1 0.0 + "CG2" "CT" 0 -1 0.0 + "HG21" "HC" 0 -1 0.0 + "HG22" "HC" 0 -1 0.0 + "HG23" "HC" 0 -1 0.0 + "C" "C" 0 -1 0.0 + "O" "O" 0 -1 0.0 +!entry.V03.unit.boundbox array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.V03.unit.childsequence single int + 2 +!entry.V03.unit.connect array int + 1 + 15 +!entry.V03.unit.connectivity table int atom1x int atom2x int flags + 15 16 17 + 11 12 17 + 11 13 17 + 11 14 17 + 7 9 17 + 7 10 17 + 7 8 17 + 5 6 17 + 5 11 17 + 5 7 17 + 3 4 17 + 3 15 17 + 3 5 17 + 1 2 17 + 1 3 17 +!entry.V03.unit.hierarchy table str abovetype int abovex str belowtype int belowx + "U" 0 "R" 1 + "R" 1 "A" 16 + "R" 1 "A" 15 + "R" 1 "A" 14 + "R" 1 "A" 13 + "R" 1 "A" 12 + "R" 1 "A" 11 + "R" 1 "A" 10 + "R" 1 "A" 9 + "R" 1 "A" 8 + "R" 1 "A" 7 + "R" 1 "A" 6 + "R" 1 "A" 5 + "R" 1 "A" 4 + "R" 1 "A" 3 + "R" 1 "A" 2 + "R" 1 "A" 1 +!entry.V03.unit.name single str + "" +!entry.V03.unit.positions table dbl x dbl y dbl z + -1.458000 0.0 0.0 + -1.937000 -0.765000 -0.453000 + 0.0 0.0 0.0 + 0.360000 0.895000 -0.507000 + 0.564000 -0.015000 1.433000 + 0.184366 -0.025155 0.411327 + 2.083000 0.060000 1.408000 + 2.463926 0.070351 2.429607 + 2.481041 -0.806560 0.881046 + 2.394338 0.970097 0.895425 + 0.157000 -1.292000 2.152000 + -0.929940 -1.363099 2.180212 + 0.563943 -2.153194 1.621926 + 0.545829 -1.276277 3.170441 + 0.551000 -1.198000 -0.766000 + 0.024000 -2.306000 -0.667000 +!entry.V03.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x + 0 0 0 0 0 0 +!entry.V03.unit.residues table str name int seq int childseq int startatomx str restype int imagingx + "V03" 1 17 1 "?" 0 +!entry.V03.unit.residuesPdbSequenceNumber array int + 1 +!entry.V03.unit.solventcap array dbl + -1.000000 + 0.0 + 0.0 + 0.0 + 0.0 +!entry.V03.unit.velocities table dbl x dbl y dbl z + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 + 0.0 0.0 0.0 diff --git a/src/JobConfig.py b/src/JobConfig.py index aa01870..70e39ab 100755 --- a/src/JobConfig.py +++ b/src/JobConfig.py @@ -1,7 +1,8 @@ ''' -Created on Oct 5, 2016 +JobConfig reads the input file and sets up the settings object used for the computation -@author: nbrownin +.. codeauthor:: Nicholas Browning +.. codeauthor:: Simon Duerr dev@simonduerr.eu ''' from __future__ import print_function from __future__ import absolute_import @@ -15,17 +16,25 @@ import ConfigParser except: import configparser -from .gaapi import operator_types +from src.gaapi import operator_types import sys -import openbabel +import os +from openbabel import openbabel import collections from src import constants as cnts class Settings(object): ''' - classdocs + Holds settings for one EVOLVE job read from the config file. + This is called in the main function with the input file as argument (see :func:`src.JobConfig.Settings.__init__`). + + The default options are set below. ''' + + # ToDO Use all these options as default values in the configparser + # This is only supported in Python 3 + composition_optimization = False composition_residue_indexes = None composition_lower_bounds = None @@ -33,6 +42,7 @@ class Settings(object): composition_library = None allowed_residue_types = None + convergence_cycles=15 backbone_dihedral_optimization = False dihedral_residue_indexes = None @@ -46,47 +56,111 @@ class Settings(object): population_file_path = None unbiased_protein_composition_generator = False - + swissprot_composition_generator = False + population_size = 0 max_iteration = 0 initial_energy = 0.0 helical_dielectric = 0 - + gpu_openmm=False + simAnneal=False initial_molecule = None + + multi_individual = False + no_frames =1 + use_compute_cluster=False + compute_cluster_cores=16 + + originalResidues=None + + no_evaluators=1 + update_files=False + + use_res_type=False + curr_iteration=0 + + generator="" def __init__(self, configFilePath): + ''' + + uses `ConfigParser` to read input file and input molecule(s) + + Parameters + ---------- + configFilePath : str + path to inputfile + ''' self.configFilePath = configFilePath - # config parser module is small caps in Py3 and capitals in Py2 if sys.version_info[0] < 3: self.config = ConfigParser.ConfigParser() else: self.config = configparser.ConfigParser() self.config.read(configFilePath) - + # PARSE [GA_MULTIINDI] + if (self.config.has_section('GA_MULTIMMPBSA')): + self.multi_individual = self.config.getboolean('GA_MULTIMMPBSA', 'multi_individual') + self.molecule_dir = self.config.get('GA_MULTIMMPBSA', 'molecule_dir') + self.no_frames = int(self.config.get('GA_MULTIMMPBSA', 'no_frames')) + self.use_compute_cluster=self.config.getboolean('GA_MULTIMMPBSA', 'use_compute_cluster') + if (self.use_compute_cluster==True): + self.compute_cluster_nodes=int(self.config.get('GA_MULTIMMPBSA', 'compute_cluster_nodes')) + self.compute_cluster_ntasks=int(self.config.get('GA_MULTIMMPBSA', 'compute_cluster_ntasks')) + self.compute_cluster_queuename=self.config.get('GA_MULTIMMPBSA', 'compute_cluster_queuename') + self.energy_calculator=self.config.get('GA_MULTIMMPBSA', 'energy_calculator') + # PARSE [MOLECULE] - self.initial_molecule_path = str(self.config.get('MOLECULE', 'initial_molecule').strip('\'')) - # openbabel parse - obConversion = openbabel.OBConversion() - if (not obConversion.SetInFormat(self.initial_molecule_path.split(".")[1])): - print("Problem reading ", self.initial_molecule_path, " filetype: ", self.initial_molecule_path.split(".")[1]) - sys.exit(0) - print("Succesfully set molecule filetype:", self.initial_molecule_path.split(".")[1]) - - self.initial_molecule = openbabel.OBMol() - - if (not obConversion.ReadFile(self.initial_molecule, self.initial_molecule_path)): - print("Problem reading ", self.initial_molecule_path) - sys.exit(0) - print("Succesfully read molecule:", self.initial_molecule_path) - + if (self.multi_individual): + print("MULTI INDIVIDUAL SETTING: \n reading multiple molecules.") + input_frames_list = os.listdir(self.molecule_dir) # can only contain pdb files, nothing else. Should implement valueError + print(input_frames_list) + if (len(input_frames_list) != self.no_frames): + print("Number of frames does not match number of found pdb files in input dir") + sys.exit(0) + self.initial_molecule = [] + for i, x in enumerate(input_frames_list): + molecule_path = self.molecule_dir + x + if molecule_path[0:2]=='./': + molecule_path = molecule_path[2:] #prevent ./ paths + + print(molecule_path) + obConversion = openbabel.OBConversion() + if (not obConversion.SetInFormat(molecule_path.split(".")[1])): + print("Problem reading Molecule", molecule_path) + sys.exit(0) + print("Succesfully set molecule filetype:", molecule_path.split(".")[1]) + self.initial_molecule.append(openbabel.OBMol()) + if (not obConversion.ReadFile(self.initial_molecule[i], molecule_path)): + print("Problem reading ", molecule_path) + sys.exit(0) + print("Succesfully read molecule:", molecule_path) + pass + pass + else: + self.initial_molecule_path = str(self.config.get('MOLECULE', 'initial_molecule').strip('\'')) + # openbabel parse + obConversion = openbabel.OBConversion() + if (not obConversion.SetInFormat(self.initial_molecule_path.split(".")[1])): + print("Problem reading ", self.initial_molecule_path, " filetype: ", self.initial_molecule_path.split(".")[1]) + sys.exit(0) + print("Succesfully set molecule filetype:", self.initial_molecule_path.split(".")[1]) + + self.initial_molecule = openbabel.OBMol() + + if (not obConversion.ReadFile(self.initial_molecule, self.initial_molecule_path)): + print("Problem reading ", self.initial_molecule_path) + sys.exit(0) + print("Succesfully read molecule:", self.initial_molecule_path) + pass # PARSE [OPTIMIZATION] if self.config.has_option('OPTIMIZATION', 'composition_optimization'): self.composition_optimization = self.config.getboolean('OPTIMIZATION', 'composition_optimization') + self.convergence_cycles = self.config.getint('OPTIMIZATION', 'convergence_cycles', fallback=15) if (self.composition_optimization): self.composition_residue_indexes = [int(v) for v in self.config.get('OPTIMIZATION', 'composition_residue_indexes').split()] @@ -120,12 +194,20 @@ def __init__(self, configFilePath): self.sidechain_dihedral_optimisation = self.config.getboolean('OPTIMIZATION', 'sidechain_dihedral_optimisation') else: self.sidechain_dihedral_optimisation = False + + if self.config.has_option('MOLECULE', 'use_res_type'): + self.use_res_type = self.config.getboolean('MOLECULE', 'use_res_type') # PARSE [GA GLOBAL] if (self.config.has_option('GA_GLOBAL', 'seed_population')): self.seed_population = self.config.getboolean('GA_GLOBAL', 'seed_population') self.population_file_path = self.config.get('GA_GLOBAL', 'population_file_path') self.population_size = int(self.config.get('GA_GLOBAL', 'population_size')) + + if self.population_size%2!=0: + print('The size of the population must be even.') + sys.exit(0) + self.max_iteration = int(self.config.get('GA_GLOBAL', 'max_iteration')) # PARSE [GA_SELECTION] @@ -171,7 +253,9 @@ def __init__(self, configFilePath): self.num_mc_steps = int(self.config.get('MC_GENERATE', 'num_mc_steps')) if (self.config.has_section('GENERATOR')): - self.unbiased_protein_composition_generator = self.config.getboolean('GENERATOR', 'unbiased_protein_composition_generator') + #self.unbiased_protein_composition_generator = self.config.getboolean('GENERATOR', 'unbiased_protein_composition_generator') + #self.swissprot_composition_generator = self.config.getboolean('GENERATOR','swissprot_composition_generator') # deprecated + self.generator = self.config.get('GENERATOR','generator') # PARSE EVALUATORS if (self.config.has_section('EVALUATOR')): @@ -179,15 +263,38 @@ def __init__(self, configFilePath): if "turbomole_scf_energy" in self.evaluators: # parse turbomole specifics self.turbomole_template = self.config.get('EVALUATOR', 'turbomole_template') - if "amber" in self.evaluators: + if "amber" or "mmpbsa_multi" in self.evaluators: self.tleap_template = self.config.get('EVALUATOR', 'tleap_template') self.amber_params = self.config.get('EVALUATOR', 'amber_params') self.mpi_procs = int(self.config.get('EVALUATOR', 'mpi_processors')) + if "mmpbsa_multi" in self.evaluators: + self.mmpbsa_params = self.config.get('EVALUATOR', 'mmpbsa_params') + self.update_files = True + if "stability_multi" in self.evaluators or 'helical_stability' in self.evaluators: + self.initial_fitness_computation = True + self.write_energies = self.config.getboolean('EVALUATOR', 'write_energies', fallback=False) if "helical_stability" in self.evaluators: self.tleap_template = self.config.get('EVALUATOR', 'tleap_template') self.amber_params = self.config.get('EVALUATOR', 'amber_params') self.mpi_procs = int(self.config.get('EVALUATOR', 'mpi_processors')) self.helical_dielectric = int(float(self.config.get('EVALUATOR', 'dielectric'))) + self.gpu_openmm = self.config.getboolean('EVALUATOR', 'gpu_openmm', fallback=False) + self.md = self.config.getboolean('EVALUATOR', 'md', fallback=False) + self.replicas = self.config.get('EVALUATOR', 'replicas', fallback=1) + self.gpudeviceindex = self.config.get('EVALUATOR', 'gpudeviceindex', fallback=0) + self.simAnneal = self.config.getboolean('EVALUATOR', 'simAnneal', fallback=False) + + self.write_energies = self.config.getboolean('EVALUATOR', 'write_energies', fallback=False) + + self.entropy_correction = self.config.get('EVALUATOR', 'entropy_correction', fallback=None) + + if (self.entropy_correction == 'PicketSternberg'): + self.entropy_correction = 0 + elif (self.entropy_correction == "AbagyanTotrov"): + self.entropy_correction = 1 + elif (self.entropy_correction == "KoehlDelarue"): + self.entropy_correction = 2 + if (self.helical_dielectric == 80): self.helical_dielectric = 2 elif (self.helical_dielectric == 50): @@ -207,6 +314,11 @@ def __init__(self, configFilePath): def printSettings(self): + ''' + + prints settings as ordered dictionary + + ''' ordered_dict = collections.OrderedDict(self.__dict__) # No change since self.__dict__ already disordered..., could be removed for attribute, value in list(ordered_dict.items()): print('{} : {}'.format(attribute, value)) diff --git a/src/MoleculeCreator.py b/src/MoleculeCreator.py index 01c9b7b..3b6290f 100755 --- a/src/MoleculeCreator.py +++ b/src/MoleculeCreator.py @@ -3,7 +3,7 @@ Contains a few key functions for performing mutations specifically on proteins. Extensions to more general molecules should be straightforward to implement based on the code here. -@author: Nicholas Browning +.. codeauthor:: Nicholas Browning ''' from __future__ import division from __future__ import print_function @@ -11,12 +11,19 @@ from builtins import range from past.utils import old_div -import openbabel -from openbabel import OBResidue -from openbabel import OBAtom -from openbabel import OBMol -from openbabel import OBAtomTyper +# import openbabel +# from openbabel import OBResidue +# from openbabel import OBAtom +# from openbabel import OBMol +# from openbabel import OBAtomTyper +from openbabel import openbabel +from openbabel.openbabel import OBResidue +from openbabel.openbabel import OBAtom +from openbabel.openbabel import OBMol +from openbabel.openbabel import OBAtomTyper import numpy as np +import os + from . import MoleculeInfo as mi @@ -111,30 +118,32 @@ def add_fragment(mol, fragment, id_start): new_atom.SetId(id) new_atom.SetVector(frag_atom.GetVector()) new_atom.SetAtomicNum(frag_atom.GetAtomicNum()) - new_atom.SetType(frag_atom.GetType()) new_atom.SetSpinMultiplicity(frag_atom.GetSpinMultiplicity()) new_atom.SetFormalCharge(frag_atom.GetFormalCharge()) - new_atom.SetImplicitValence(frag_atom.GetImplicitValence()) + + #new_atom.SetImplicitValence(frag_atom.GetImplicitValence()) + new_atom.SetImplicitHCount(frag_atom.GetImplicitHCount()) new_atom.SetPartialCharge(frag_atom.GetPartialCharge()) - + for data in frag_atom.GetData(): new_atom.SetData(data) id += 1 + #print(debugAtom(new_atom)) for obbond in openbabel.OBMolBondIter(fragment): begin_atom = obbond.GetBeginAtom() end_atom = obbond.GetEndAtom() - mol.AddBond(obbond.GetBeginAtomIdx() + prevAtoms, obbond.GetEndAtomIdx() + prevAtoms, obbond.GetBO(), obbond.GetFlags()) + mol.AddBond(obbond.GetBeginAtomIdx() + prevAtoms, obbond.GetEndAtomIdx() + prevAtoms, obbond.GetBondOrder(), obbond.GetFlags()) def debugAtom(obatom): - return "AN:", obatom.GetAtomicNum(), "T:", obatom.GetType(), "idx:", obatom.GetIdx(), "id:", obatom.GetId(), "BO(1):", obatom.CountBondsOfOrder(1) + return "AN:", obatom.GetAtomicNum(), "T:", obatom.GetType(), obatom.GetResidue().GetName(), "idx:", obatom.GetIdx(), "id:", obatom.GetId(), "BO(1):", obatom.CountBondsOfOrder(1) def debugBond(obbond): - return "begin_idx:", obbond.GetBeginAtomIdx(), "end_idx:", obbond.GetEndAtomIdx(), "norm:", obbond.GetLength(), "BO:", obbond.GetBO() + return "begin_idx:", obbond.GetBeginAtomIdx(), "end_idx:", obbond.GetEndAtomIdx(), "norm:", obbond.GetLength(), "BO:", obbond.GetBondOrder() def getAtomByID(mol, atom_id): @@ -143,7 +152,7 @@ def getAtomByID(mol, atom_id): return mol.GetAtom(i) -def swapsidechain (mol, res_index, aa_mol): +def swapsidechain(settings, mol, res_index, aa_mol): """ Mutates a certain residue in a protein to another amino acid. @@ -163,30 +172,50 @@ def swapsidechain (mol, res_index, aa_mol): """ mol.BeginModify() - + aa_mol.BeginModify() + + #mol.SetChainsPerceived(False) + + curr = mol.GetResidue(res_index) - + new = aa_mol.GetResidue(0) - mol_CA = mi.getAlphaCarbon(curr) mol_CB = mi.getBetaAtom(curr) mol_N = mi.getBBNitrogen(curr) - + mol_NplusOne = mi.getPlus1BBNitrogen(curr) + mol_C = mi.getBBCarboxyl(curr) + aa_CA = mi.getAlphaCarbon(new) aa_CB = mi.getBetaAtom(new) aa_bb_nitrogen = mi.getBBNitrogen(new) aa_gamma_atom = mi.getChi1DihedralAtom(new) + aa_bb_oxygen = mi.getBBCarboxyl(new) + - frag_res = aa_CB.GetResidue() + frag_res = new frag_name = frag_res.GetName() + + + res_name =mi.getResType(curr) aa_tor = 0 + aa_tor2 = 0 if (aa_gamma_atom is not None): aa_tor = aa_mol.GetTorsion(aa_gamma_atom, aa_CA, aa_CB, aa_bb_nitrogen) + - mol_cb_vec = np.asarray([mol_CB.GetX(), mol_CB.GetY(), mol_CB.GetZ()]) - mol_ca_vec = np.asarray([mol_CA.GetX(), mol_CA.GetY(), mol_CA.GetZ()]) + psi_tor = mol.GetTorsion(mol_N, mol_CA, mol_C, mol_NplusOne) + + + try: + mol_cb_vec = np.asarray([mol_CB.GetX(), mol_CB.GetY(), mol_CB.GetZ()]) + mol_ca_vec = np.asarray([mol_CA.GetX(), mol_CA.GetY(), mol_CA.GetZ()]) + except: + print('could not get coordinates from the molecule. EVOLVE needs a protonated structure') + exit() + frag_cb_vec = np.asarray([aa_CB.GetX(), aa_CB.GetY(), aa_CB.GetZ()]) frag_ca_vec = np.asarray([aa_CA.GetX(), aa_CA.GetY(), aa_CA.GetZ()]) @@ -224,6 +253,7 @@ def swapsidechain (mol, res_index, aa_mol): frag_atom_ids_del = [aa_mol.GetAtom(i).GetId() for i in frag_atoms_del] frag_atom_ids_del.append(aa_CA.GetId()) + # delete unnecessary atoms for i in range (0, len(frag_atom_ids_del)): @@ -235,7 +265,7 @@ def swapsidechain (mol, res_index, aa_mol): res.RemoveAtom(atom) aa_mol.DeleteAtom(atom) - + for i in range (0, len(mol_atom_ids_del)): atom = getAtomByID(mol, mol_atom_ids_del[i]) @@ -250,8 +280,8 @@ def swapsidechain (mol, res_index, aa_mol): # add fragment to the protein add_fragment(mol, aa_mol, orig_num_atoms) - - mol.EndModify() + + #mol.EndModify() renum_atoms = openbabel.vectorInt(prev_atoms + aa_mol.NumAtoms()) @@ -274,54 +304,112 @@ def swapsidechain (mol, res_index, aa_mol): if (atom.GetId() == aa_CB.GetId()): corr_frag_cb = atom + mol.AddBond(mol_CA.GetIdx(), corr_frag_cb.GetIdx(), 1) frag_res_type = mi.getResType(frag_res) - curr.SetName(frag_name) - + if settings.use_res_type == True: + curr.SetName(frag_res_type) + pass + else: + curr.SetName(frag_name) + for obatom in openbabel.OBResidueAtomIter(frag_res): frag_atom = getAtomByID(mol, obatom.GetId()) curr.AddAtom(frag_atom) - curr.SetAtomID(frag_atom, frag_res.GetAtomID(obatom)) - alpha_carbon = mi.getAlphaCarbon(curr) - bb_nitrogen = mi.getBBNitrogen(curr) - beta_atom = mi.getBetaAtom(curr) - chi_atom = mi.getChi1DihedralAtom(curr) - - if (chi_atom is not None and aa_gamma_atom is not None): - mol.SetTorsion(bb_nitrogen, alpha_carbon, beta_atom, chi_atom, aa_tor * (old_div(np.pi, 180.0))) - # need to renumber IDs now to be consecutive mol.RenumberAtoms(renum_atoms) for i in range (1, mol.NumAtoms() + 1) : - mol.GetAtom(i).SetId(i - 1) - - -if __name__ == '__main__': - print("Starting") + mol.GetAtom(i).SetId(i - 1) + aa_mol.EndModify() + + + # For several residues in order for the amber settings to work, one needs to rename a few hydrogens which is done here. + # if old resname = glycine we need to rename the remaining H to HA, the other has been replaced by the sidechain + if res_name=="GLY": + for obatom in openbabel.OBResidueAtomIter(curr): + if curr.GetAtomID(obatom) in ["HA2", "HA3", " HA2", " HA2 "]: + curr.SetAtomID(obatom, "HA") + + if frag_res_type=="GLY" and settings.use_res_type: + for obatom in openbabel.OBResidueAtomIter(curr): + #print("."+curr.GetAtomID(obatom)+".") + if curr.GetAtomID(obatom) in ["HA", " HA", " HA "] : + curr.SetAtomID(obatom, "HA2") + + if frag_res_type=="HID" and settings.use_res_type: + for obatom in openbabel.OBResidueAtomIter(curr): + if curr.GetAtomID(obatom)in ["HD3", "HD4", "HD5", "HD6", "HD7", "HD8"]: + curr.SetAtomID(obatom, "HD1") + + if frag_res_type=="HID" and frag_name=="HD2" and settings.use_res_type: + for obatom in openbabel.OBResidueAtomIter(curr): + if curr.GetAtomID(obatom)=="HD2": + curr.SetAtomID(obatom, "HD1") + if curr.GetAtomID(obatom)=="H1": + curr.SetAtomID(obatom, "HD2") + + if frag_name=="HE2" and settings.use_res_type: + for obatom in openbabel.OBResidueAtomIter(curr): + if curr.GetAtomID(obatom)=="HE2": + curr.SetAtomID(obatom, "HE1") + for obatom in openbabel.OBResidueAtomIter(curr): + if curr.GetAtomID(obatom)=="H1": + curr.SetAtomID(obatom, "HE2") + + if frag_res_type=="HIE" and frag_name!="HE2" and settings.use_res_type: + for obatom in openbabel.OBResidueAtomIter(curr): + if curr.GetAtomID(obatom) in ["HE3", "HE4", "HE5", "HE6", "HE7", "HE8"]: + curr.SetAtomID(obatom, "HE1") + + mol.SetAromaticPerceived(False) + # Fix to get around openbabel screwing up the structure when calling EndModify() + # This is necessary because we need to set the Chi1 dihedral correctly obConversion = openbabel.OBConversion() - obConversion.SetInAndOutFormats("pdb", "pdb") + obConversion.SetInAndOutFormats("pdb", "pdb") + obConversion.WriteFile(mol, "temp.pdb") + obConversion = openbabel.OBConversion() + obConversion.SetInAndOutFormats("pdb", "pdb") + obConversion.ReadFile(mol, "temp.pdb") + # os.remove('temp.pdb') - mol = openbabel.OBMol() - - obtype = openbabel.OBAtomTyper() - obConversion.ReadFile(mol, "gpgg.pdb") - - frag2 = openbabel.OBMol() - obConversion.SetInAndOutFormats("mol2", "pdb") - obConversion.ReadFile(frag2, "/lcbcdata/nbrownin/Rotamers_mol2/HID/HD3.mol2") + + + # preparation for setting the chi1 dihedral + curr = mol.GetResidue(res_index) + + alpha_carbon = mi.getAlphaCarbon(curr) + bb_nitrogen = mi.getBBNitrogen(curr) + beta_atom = mi.getBetaAtom(curr) + chi_atom = mi.getChi1DihedralAtom(curr) + bb_carbonyl = mi.getBBCarboxyl(curr) + bb_nitrogenPlusOne = mi.getPlus1BBNitrogen(curr) - print("first swap") + psi_tor_before = mol.GetTorsion(bb_nitrogen, alpha_carbon, bb_carbonyl, bb_nitrogenPlusOne) + # print('BB oxygen', aa_mol.GetTorsion(aa_gamma_atom, aa_CA, aa_CB, aa_bb_oxygen)) + + + ## Here the correct dihedral needs to be set! + if (chi_atom is not None and aa_gamma_atom is not None ): + # mol.SetTorsion(bb_carbonyl, alpha_carbon, beta_atom, chi_atom, aa_tor2 * np.pi/180.0) + mol.SetTorsion(bb_nitrogen, alpha_carbon, beta_atom, chi_atom, aa_tor * np.pi/180.0) + # mol.SetTorsion(bb_nitrogen, alpha_carbon, bb_carbonyl, bb_nitrogenPlusOne, psi_tor*-180* np.pi/180.0) + psi_tor_after = mol.GetTorsion(bb_nitrogen, alpha_carbon, bb_carbonyl, bb_nitrogenPlusOne) + + if psi_tor_before != psi_tor_after: + print('something went wrong for this individual') + - swapsidechain(mol, 1, frag) + + + + - print("second swap") - swapsidechain(mol, 3, frag2) - print("WRITING OUT") - obConversion.WriteFile(mol, "test2.pdb") +if __name__ == '__main__': + pass diff --git a/src/MoleculeInfo.py b/src/MoleculeInfo.py index 74c887b..9b13339 100755 --- a/src/MoleculeInfo.py +++ b/src/MoleculeInfo.py @@ -3,7 +3,7 @@ Contains helper functions for finding + identifying certain atoms in proteins. -@author: Nicholas Browning +.. codeauthor:: Nicholas Browning ''' from __future__ import division from __future__ import print_function @@ -12,9 +12,12 @@ from builtins import str from builtins import range from past.utils import old_div -import openbabel -from openbabel import OBResidue -from openbabel import OBAtom +# import openbabel +# from openbabel import OBResidue +# from openbabel import OBAtom +from openbabel import openbabel +from openbabel.openbabel import OBResidue +from openbabel.openbabel import OBAtom import numpy as np from . import constants @@ -83,13 +86,14 @@ def getResType(obres): Query residue """ res = obres.GetName() - + # check richardson rotamers and return rotamer_type for i in range (0, len(constants.rotamers)): if (constants.rotamers[i] == res): return constants.rotamer_types[i] # seems to be a standard AA, search 3-letter code list + # DUPLICATE for i in range (0, len(constants.rotamer_types)): if (constants.rotamer_types[i] == res): return constants.rotamer_types[i] @@ -110,17 +114,14 @@ def getAlphaCarbon(obres): Query residue """ res = obres.GetName() - for obatom in openbabel.OBResidueAtomIter(obres): - - if (obatom.IsCarbon()): + + if (obatom.GetAtomicNum()==6): carboxl_carbon = getConnectedCarboxylCarbon(obatom) - # identify carboxyl carbon in peptide if (carboxl_carbon is not None): # now also find the nitrogen amide_nitro = getConnectedAmideNitrogen(obatom) - if (amide_nitro is not None): return obatom return None @@ -141,14 +142,14 @@ def getConnectedAmideNitrogen(calpha_atom): # --> assume that atom is the alpha_carbon if (obres.GetName() == "PRO"): for obatom in openbabel.OBAtomAtomIter(calpha_atom): - if (obatom.IsNitrogen()): + if (obatom.GetAtomicNum()==7): return obatom else: for obatom in openbabel.OBAtomAtomIter(calpha_atom): - if (obatom.IsNitrogen()): + if (obatom.GetAtomicNum()==7): for obatom2 in openbabel.OBAtomAtomIter(obatom): - if (obatom2.IsHydrogen()): + if (obatom2.GetAtomicNum()==1): return obatom return None @@ -165,7 +166,7 @@ def getConnectedCarboxylCarbon(atom): obres = atom.GetResidue() for obatom in openbabel.OBAtomAtomIter(atom): - if (obatom.IsCarbon()): + if (obatom.GetAtomicNum()==6): for obbond in openbabel.OBAtomBondIter(obatom): if (countBonds(obbond.GetNbrAtom(obatom)) == 1 and obbond.GetNbrAtom(obatom).GetAtomicNum() == 8): @@ -183,13 +184,13 @@ def getBetaAtom(obres): obres : OBResidue Query residue """ - + alpha_carbon = getAlphaCarbon(obres) bbcarboxyl = getBBCarboxyl(obres) bbnitrogen = getBBNitrogen(obres) - + if alpha_carbon is None: return None @@ -204,13 +205,12 @@ def getBetaAtom(obres): carboxyl_vec = np.asarray([bbcarboxyl.GetX(), bbcarboxyl.GetY(), bbcarboxyl.GetZ()]) res = getResType(obres) - for obatom in openbabel.OBAtomAtomIter(alpha_carbon): if (res == "GLY"): if (obatom.GetType() == 'H'): # want to find the L-enantiomer of the two GLY hydrogens on CA ob_vec = np.asarray([obatom.GetX(), obatom.GetY(), obatom.GetZ()]) - + RH = ob_vec - alpha_vec RC = carboxyl_vec - alpha_vec RN = nitro_vec - alpha_vec @@ -220,7 +220,7 @@ def getBetaAtom(obres): return obatom else: - if (bbcarboxyl is not None and obatom.IsCarbon() and obatom.GetIdx() != bbcarboxyl.GetIdx()): + if (bbcarboxyl is not None and obatom.GetAtomicNum()==6 and obatom.GetIdx() != bbcarboxyl.GetIdx()): return obatom return None @@ -241,7 +241,7 @@ def getBBNitrogen(obres): return None for obatom in openbabel.OBAtomAtomIter(alpha_carbon): - if (obatom.IsNitrogen()): + if (obatom.GetAtomicNum()==7): return obatom return None @@ -266,7 +266,7 @@ def getNeg1BBCarboxyl(obres): if (obatom == ca): continue - if (obatom.IsHydrogen()): + if (obatom.GetAtomicNum()==1): continue for obbond in openbabel.OBAtomBondIter(obatom): @@ -292,7 +292,7 @@ def getBBCarboxyl(obres): for obatom in openbabel.OBAtomAtomIter(ca_atom): - if (not obatom.IsCarbon()): + if (not obatom.GetAtomicNum()==6): continue for obbond in openbabel.OBAtomBondIter(obatom): @@ -318,7 +318,7 @@ def getPlus1BBNitrogen(obres): for obatom in openbabel.OBAtomAtomIter(bb_n): - if (obatom.IsNitrogen()): + if (obatom.GetAtomicNum()==7): return obatom return None @@ -403,8 +403,8 @@ def getChiDihedralAtomIndexes(mol, residue_indexes): chi_atoms.append(res_chi_atoms) return np.asarray(chi_atoms) - - + + def getPhiPsiDihedralByAtomIndex(mol, dihedral_atom_indexes): """ Returns a list of [phi, psi] dihedrals for the backbone dihedrals given by dihedral_atom_indexes @@ -602,6 +602,7 @@ def getChi1DihedralAtom(obres): beta_atom = getBetaAtom(obres) gamma_atom = None + if beta_atom is None: return None @@ -612,13 +613,13 @@ def getChi1DihedralAtom(obres): if (obatom.GetIdx() == alpha_carbon.GetIdx()): continue - if ((res == "SER" or res == "THR") and obatom.IsOxygen()): + if ((res == "SER" or res == "THR") and obatom.GetAtomicNum()==8): return obatom - elif (res == "CYS" and obatom.IsSulfur()): + elif (res == "CYS" and obatom.GetAtomicNum()==16): return obatom - elif (res == "ALA" and obatom.IsHydrogen()): + elif (res == "ALA" and obatom.GetAtomicNum()==1): return obatom - elif((res != "SER" and res != "THR" and res != "CYS" and res != "ALA") and obatom.IsCarbon()): + elif((res != "SER" and res != "THR" and res != "CYS" and res != "ALA") and obatom.GetAtomicNum()==6): return obatom return None diff --git a/src/constants.py b/src/constants.py index 0b171f0..b418b30 100755 --- a/src/constants.py +++ b/src/constants.py @@ -1,9 +1,12 @@ ''' -main.py +constants file + +.. codeauthor:: Nicholas Browning +.. codeauthor:: Simon Duerr dev@simonduerr.eu -@author: Nicholas Browning ''' import numpy as np +import pygmo as pg element2mass = {'Ru': 101.904348, 'Re': 186.955744, 'Rf': 261.10869, 'Ra': 226.025403, 'Rb': 84.9118, 'Rn': 222.017571, 'Rh': 102.905503, 'Be': 9.012183, @@ -56,7 +59,7 @@ 'M01', 'M02', 'M03', 'M04', 'M05', 'M06', 'M07', 'M08', 'M09', 'M10', \ 'M11', 'M12', 'M13', 'P01', 'P02', 'P03', 'P04', 'S01', 'S02', 'S03', \ 'T01', 'T02', 'T03', 'W01', 'W02', 'W03', 'W04', 'W05', 'W06', 'W07', \ - 'Y01', 'Y02', 'Y03', 'Y04', 'V01', 'V02', 'V03' + 'Y01', 'Y02', 'Y03', 'Y04', 'V01', 'V02', 'V03', 'HIN' ] selected_rotamers = rotamers @@ -79,19 +82,34 @@ 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', 'MET', \ 'MET', 'MET', 'MET', 'PHE', 'PHE', 'PHE', 'PHE', 'SER', 'SER', 'SER', \ 'THR', 'THR', 'THR', 'TRP', 'TRP', 'TRP', 'TRP', 'TRP', 'TRP', 'TRP', \ - 'TYR', 'TYR', 'TYR', 'TYR', 'VAL', 'VAL', 'VAL' + 'TYR', 'TYR', 'TYR', 'TYR', 'VAL', 'VAL', 'VAL', 'HIN' ] selected_rotamer_types = rotamer_types -allowed_residue_types = ['GLY', 'ALA', 'ARG', 'ASP', 'ASH', 'ASN', 'CYS', 'GLU', 'GLH', 'GLN', 'HID', 'HIE', 'HIP', 'ILE', 'LEU', 'LYS', 'LYN', 'MET', 'PHE', 'SER', 'THR', 'TRP', 'TYR', 'VAL'] +allowed_residue_types = ['GLY', 'ALA', 'ARG', 'ASP', 'ASH', 'ASN', 'CYS', 'GLU', 'GLH', 'GLN', 'HID', 'HIE', 'HIP', 'ILE', 'LEU', 'LYS', 'LYN', 'MET', 'PHE', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'HIN'] + +# Vacic et al, BMC Bioinformatics 211(8), 2007, https://doi.org/10.1186/1471-2105-8-211 +swissprot_probabilities = {'ALA': 0.0789, 'ARG': 0.054, 'ASH': 0.02675, 'ASP': 0.02675, 'ASN': 0.0413, \ + 'CYS': 0.015, 'GLH': 0.0335, 'GLU': 0.0335, 'GLN': 0.0395, 'GLY': 0.0696, \ + 'HID': 0.00763, 'HIE': 0.00763, 'HIP': 0.00763, 'ILE': 0.059, 'LEU': 0.0965, \ + 'LYN': 0.0296, 'LYS': 0.0296, 'MET': 0.0238, 'PHE': 0.0396, 'SER': 0.0683, \ + 'THR': 0.0541, 'TRP': 0.0113, 'TYR': 0.0303, 'VAL': 0.0673, 'PRO': 0.0483} + # 10, 50, 80 energies = {'ALA': (13.03, 12.14 , 12.06), 'ARG': (-170.77, -176.22 , -176.73), 'ASH': (-43.74, -45.64, -45.82), 'ASP': (-52.27, -58.92, -59.55), 'ASN': (-72.72, -74.29, -74.44), \ 'CYS': (13.55, 12.58, 12.49), 'GLH': (-36.86, -38.93, -39.13), 'GLU': (-47.00, -53.61, -54.30), 'GLN': (-56.93, -58.79, -58.97), 'GLY':(7.11, 6.15, 6.06), \ - 'HID': (12.43, 10.83, 10.68), 'HIE':(8.74, 7.22, 7.08), 'HIP': (22.66, 17.17, 16.62), 'ILE': (10.74, 9.93, 9.85), 'LEU': (-10.04, -10.88, -10.96), \ + 'HIN': (12.43, 10.83, 10.68), 'HID': (12.43, 10.83, 10.68), 'HIE':(8.74, 7.22, 7.08), 'HIP': (22.66, 17.17, 16.62), 'ILE': (10.74, 9.93, 9.85), 'LEU': (-10.04, -10.88, -10.96), \ 'LYN': (-4.36, -5.73, -5.85), 'LYS': (-9.60, -15.72, -16.29), 'MET': (8.36, 7.47, 7.29), 'PHE': (11.05, 10.04, 9.95), 'SER': (-0.71, -2.32, -2.47), \ 'THR': (-19.37, -20.45, -20.59), 'TRP':(14.43, 13.07, 12.94), 'TYR': (-13.28, -14.89, -15.05), 'VAL':(-7.58, -8.41, -8.49) } +# PicketSternberg, AbagyanTotrov, KoehlDelarue +entropy_corrections={'ALA':(0,0,0), 'ARG':(-2.03,-2.13,-1.21), 'ASN':(-1.57,-0.81,-0.75), 'ASP':(-1.25,-0.61,-0.65), 'CYS':(-0.55,-1.14,-0.63),\ + 'GLN':(-2.11,-2.02,-1.29), 'GLU':(-1.81,-1.65,-1.31), 'GLY':(0,0,0), 'HIS':(-0.96,-0.99,-0.92), 'ILE':(-0.89,-0.75,-0.94),\ + 'LEU':(-0.78,-0.75,-0.94), 'LYS':(-1.94,-2.21,-1.63), 'MET':(-1.61,-1.53,-1.24), 'PHE':(-0.58,-0.58,-0.65), 'PRO':(0,0,-0.3),\ + 'SER':(-1.71,-1.19,-0.43), 'THR':(-1.63,-1.12,-0.57), 'TRP':(-0.97,-0.97,-1.14), 'TYR':(-0.98,-0.99,-1.07),\ + 'VAL':(-0.51,-0.5,-0.62), 'HIN': (-0.96,-0.99,-0.92),'HID':(-0.96,-0.99,-0.92),'HIP':(-0.96,-0.99,-0.92),'HIE':(-0.96,-0.99,-0.92),\ + 'ASH':(-1.25,-0.61,-0.65),'LYN':(-1.94,-2.21,-1.63),'GLH':(-1.81,-1.65,-1.31),} def subselect_rotamers(type_list): indices = [i for i, x in enumerate(rotamer_types) if (x in type_list)] return [rotamers[i] for i in indices] @@ -107,3 +125,18 @@ def subselect_rotamer_energy_dict(type_list): new_dict[i] = energies[i] return new_dict + +def sort_population_ndsa(settings,population): + #this sorts population according to non dominated sorting and crowding distance for all of the objectives + #determine length of fitnesses + no_objectives=len(population[0].fitnesses) + #sort based on fitness values + fitness_values=[] + for individual in population: + fitness_values.append([individual.fitnesses[i] for i in xrange(0,no_objectives)]) + pass + sorted_population_idx=pg.sort_population_mo(points = fitness_values) + sorted_population=[] + for i in sorted_population_idx: + sorted_population.append(population[i]) + return sorted_population diff --git a/src/gaapi/Individual.py b/src/gaapi/Individual.py index 3dc6ee1..55ee559 100755 --- a/src/gaapi/Individual.py +++ b/src/gaapi/Individual.py @@ -1,7 +1,10 @@ ''' -main.py +Individual sets up the Invidiuals for EVOLVE computation -@author: Nicholas Browning +Depending on context the individual is deepcopied or initalised. + +.. codeauthor:: Nicholas Browning +.. codeauthor:: Simon Duerr dev@simonduerr.eu ''' from __future__ import print_function from builtins import str @@ -10,21 +13,44 @@ from src import MoleculeInfo as mi from src import MoleculeCreator as mcr import copy -import openbabel +from openbabel import openbabel import numpy as np +import pygmo as pg class Individual(object): - def __init__(self, settings, orig=None, initial_mol=False): + def __init__(self, settings, orig=None): if orig is None: self.initialise_constructor(settings) else: self.copy_constructor(settings, orig) def initialise_constructor(self, settings): + ''' + + Initalises the Individual from the read in PDB file and initializes all variables. + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + + Returns + ------- + + ''' - self.mol = openbabel.OBMol(settings.initial_molecule) - + if (settings.multi_individual): + self.mol=[None]*settings.no_frames + for i,x in enumerate(settings.initial_molecule): + self.mol[i]=openbabel.OBMol(x) + pass + pass + else: + self.mol = openbabel.OBMol(settings.initial_molecule) + pass + + self.stability = 0 # print self.mol, settings.initial_molecule self.dihedral_residue_indexes = None self.phi_dihedrals = None @@ -36,6 +62,8 @@ def initialise_constructor(self, settings): self.chi_angles = None self.chi_atoms = None + self.energies = {"wt":None, "wt_corr":None, "mut":None, "mut_corr":None} + if (settings.backbone_dihedral_optimization): @@ -60,7 +88,16 @@ def initialise_constructor(self, settings): # doing this to get around PySwigObject's inability to be deepcopied def copy_constructor(self, settings, orig): import copy - self.mol = openbabel.OBMol(orig.mol) + + if (settings.multi_individual): + self.mol=[None]*settings.no_frames + for i,x in enumerate(orig.mol): + self.mol[i]=openbabel.OBMol(x) + pass + pass + else: + self.mol = openbabel.OBMol(orig.mol) + pass # print self.mol, orig.mol self.dihedral_residue_indexes = copy.deepcopy(orig.dihedral_residue_indexes) @@ -86,14 +123,33 @@ def copy_constructor(self, settings, orig): self.fitnesses = copy.deepcopy(orig.fitnesses) + self.energies = orig.energies def saveMol(self, file_path): + ''' + saves molecule as file specified by the path that was passed + + Parameters + ---------- + file_path: str + path to the file including ending to retrieve format. Must be compatible to openbabel output + + ''' obconv = openbabel.OBConversion() obconv.SetOutFormat(file_path.split('.')[1]) obconv.WriteFile(self.mol, file_path) def collectChiAtomPointers(self): + ''' + + #TODO + Nick + + Returns + ------- + + ''' chi_atoms = [] # OBAtom references are now different -need to refind corresponding atoms @@ -126,8 +182,52 @@ def collectChiAtomPointers(self): chi_atoms.append(res_chi_atoms) return chi_atoms + + def setStability(self,value): + ''' + + Set stability to defined values + + Parameters + ---------- + value + + Returns + ------- + + ''' + self.stability=value + + def setEnergies(self,wt, wt_corr, mut, mut_corr): + ''' + + Set energies + + Parameters + ---------- + value + + Returns + ------- + + ''' + self.energies.update({"wt":wt, "wt_corr":wt_corr, "mut":mut, "mut_corr":mut_corr}) + def updatePhiPsiDihedrals(self, settings): + ''' + + #TODO + Nick + + Parameters + ---------- + settings + + Returns + ------- + + ''' phi_psi_dihedrals = self.getPhiPsiDihedrals(settings) for j in range (0, len(self.dihedral_residue_indexes)): @@ -135,6 +235,18 @@ def updatePhiPsiDihedrals(self, settings): self.psi_dihedrals[j] = phi_psi_dihedrals[j][1] def getPhiPsiDihedrals(self, settings): + ''' + + #TODO Nick + + Parameters + ---------- + settings + + Returns + ------- + + ''' '''returns (phi, psi) tuple''' if (self.dihedral_residue_indexes == None): return None @@ -142,6 +254,9 @@ def getPhiPsiDihedrals(self, settings): return mi.getPhiPsiDihedralByAtomIndex(self.mol, settings.backbone_dihedral_atom_idxs) def applyPhiPsiDihedrals(self, settings): + ''' + #TODO Nick + ''' if (self.phi_dihedrals is None): return @@ -171,27 +286,75 @@ def applyPhiPsiDihedrals(self, settings): def applyComposition(self, settings): + ''' + + selects rotamer for all positions to mutate based on input file + for this takes the mol2 file of the residue to mutate and uses the swapsidechain method to exchange sidechains + + run for every iteration of the ga after mutate and crossover publications + + Parameters + ---------- + settings: + + + + ''' from src import constants - + if (self.composition_residue_indexes == None): return - + print(self.composition_residue_indexes) cmp = [] + if (settings.verbose): + print("Created Individual:") for i in range(0, len(self.composition_residue_indexes)): - frag = openbabel.OBMol() - obConversion = openbabel.OBConversion() - obConversion.SetInFormat("mol2") - - rotamer_type = constants.selected_rotamers[self.composition[i]] - cmp.append(rotamer_type) - obConversion.ReadFile(frag, settings.composition_library + "/" + rotamer_type + ".mol2") - mcr.swapsidechain(self.mol, self.composition_residue_indexes[i], frag) - print("Created Individual:", cmp) + if (settings.multi_individual): + for x in range(0, settings.no_frames): + # Need to include frag inside the loop, because the open babel objects get modified inside swapsidechain + frag = openbabel.OBMol() + obConversion = openbabel.OBConversion() + obConversion.SetInFormat("mol2") + + rotamer_type = constants.rotamers[self.composition[i]] + + obConversion.ReadFile(frag, settings.composition_library + "/" + rotamer_type + ".mol2") + try: + mcr.swapsidechain(settings, self.mol[x], self.composition_residue_indexes[i], frag) + except AttributeError as e: + print(f"{i} went wrong, ignore it") + pass + cmp.append(rotamer_type) # append only after loop because all individuals are identical + else: + frag = openbabel.OBMol() + obConversion = openbabel.OBConversion() + obConversion.SetInFormat("mol2") + + rotamer_type = constants.selected_rotamers[self.composition[i]] + cmp.append(rotamer_type) + if (settings.verbose): + print(cmp) + obConversion.ReadFile(frag, settings.composition_library + "/" + rotamer_type + ".mol2") + mcr.swapsidechain(settings, self.mol, self.composition_residue_indexes[i], frag) + + def applyChiDihedrals(self, settings): + ''' + + set dihedrals for dihedral optimization + + Parameters + ---------- + settings + + Returns + ------- + + ''' if (self.chi_angles is None or len(self.chi_angles) == 0): return @@ -215,8 +378,24 @@ def updateChiAngles(self, settings): def dominates(self, individual): + ''' + + to compare individuals. For one fitness the minimal value is used. + For multiple fitnesses non_domination rank is used as implemented in the pygmo library. + + Parameters + ---------- + individual : object + see :class:`src.gaapi.Individual` + + Returns + ------- + domination : bool + individual 1 dominates individual 2 + ''' if (len(self.fitnesses) > 1) : - # TODO + print("Dominance:", self.fitnesses, individual.fitnesses, pg.pareto_dominance(obj1=self.fitnesses, obj2=individual.fitnesses)) + return pg.pareto_dominance(obj1 = self.fitnesses,obj2=individual.fitnesses) pass else: return (self.fitnesses[0] < individual.fitnesses[0]) @@ -228,13 +407,47 @@ def getFitness(self, index): return self.fitnesses[index] def __lt__(self, other): + ''' + use dominate function for comparisons as the individual can have multiple fitnesses + Parameters + ---------- + other: object + see :class:`src.gaapi.Individual` + + + Returns + ------- + dominiation: bool + 1 if self < other is true, 0 if self <0 false + + ''' return self.dominates(other) def __gt__(self, other): + ''' + use dominate function for comparisons as the individual can have multiple fitnesses + Parameters + ---------- + other: object + see :class:`src.gaapi.Individual` + + + Returns + ------- + dominiation: bool + 1 if self > other is true, 0 if self >0 false + + ''' return other.dominates(self) class PSOIndividual(Individual): - + ''' + + #TODO + NIck, perhaps can be deleted + + + ''' def __init__(self, settings, orig=None): if orig is None: self.initialise_constructor(settings) diff --git a/src/gaapi/crossovers.py b/src/gaapi/crossovers.py index eed9cce..570b9c9 100755 --- a/src/gaapi/crossovers.py +++ b/src/gaapi/crossovers.py @@ -1,8 +1,9 @@ ''' -crossovers.py +Crossover operatons -@author: Nicholas Browning +.. codeauthor:: Nicholas Browning ''' + from __future__ import division from __future__ import print_function from __future__ import absolute_import @@ -11,13 +12,33 @@ import copy import numpy as np from . import Individual + def crossover(settings, individuals, crossover_op, **args): + ''' + + General wrapper function for each crossover, that is executed for each crossover and calls crossover_op() as defined by the input file. + + + If you implement a new type of optimization other than dihedral or composition optimization you need to define the crossver operation here. + + Parameters + ---------- + settings: object + see :class:`src.JobConfig.Settings` + individuals + crossover_op + args + + Returns + ------- + new_population : list + list of individuals where crossover has occured + ''' print("CROSSOVER {}".format(settings.crossover)) new_population = [] for i in range (0, settings.population_size, 2): - if np.random.random() < settings.mating_probability: if (settings.verbose): print("CROSS Individuals: ", i, i + 1) @@ -31,6 +52,28 @@ def crossover(settings, individuals, crossover_op, **args): return new_population def uniform_crossover(settings, mom, dad, **kargs): + ''' + + this swaps the composition or dihedrals randomly if random number is lower than the genewise_crossover_probability set in the input file + + Parameters + ---------- + settings: object + see :class:`src.JobConfig.Settings` + mom : object + individual 1 from current generation + dad : object + individual 2 from current generation + kargs + + Returns + ------- + sis : object + new individual 1 for next generation where crossover has occurred + bro : object + new individual 2 for next generation where crossover has occurred + + ''' bro = Individual.Individual(settings, dad) sis = Individual.Individual(settings, mom) @@ -78,6 +121,25 @@ def uniform_crossover(settings, mom, dad, **kargs): def sim_b(m, d, di, lb, ub): + ''' + + helper function for simulated binary crossover + + Parameters + ---------- + m + d + di + lb + ub + + Returns + ------- + sis_val : int + todo + bro_val : int + todo + ''' m = float(m) d = float(d) @@ -107,6 +169,38 @@ def sim_b(m, d, di, lb, ub): return sis_val, bro_val def simulated_binary_crossover(settings, mom, dad, **kargs): + ''' + + This performs simulated binary crossover. + + In the input file the following section needs to be set. + + .. code-block:: python + + [GA_CROSSOVER] + crossover = sbx + sbx_distribution_index = 7.0 + mating_probability = 0.7 + genewise_crossover_probability = 0.4 + + + Parameters + ---------- + settings: object + see :class:`src.JobConfig.Settings` + mom : object + individual 1 from current generation + dad : object + individual 2 from current generation + kargs + + Returns + ------- + sis : object + new individual 1 for next generation where crossover has occurred + bro : object + new individual 2 for next generation where crossover has occurred + ''' from src import constants di = settings.sbx_distribution_index diff --git a/src/gaapi/generators.py b/src/gaapi/generators.py index b5c26f4..14bf6d7 100755 --- a/src/gaapi/generators.py +++ b/src/gaapi/generators.py @@ -1,7 +1,8 @@ ''' -generators.py +The generator populates the first generation with a set of rotamers based on the selection in the input file -@author: Nicholas Browning +.. codeauthor:: Nicholas Browning +.. codeauthor:: Simon Duerr dev@simonduerr.eu ''' from __future__ import print_function from __future__ import absolute_import @@ -13,11 +14,24 @@ import numpy as np from src import MoleculeInfo as mi -import openbabel +from openbabel import openbabel -# Initialisation of the first population def initialisePopulation(settings): + ''' + + Initialisation of the first population + + Parameters + ---------- + settings: object + see :class:`src.JobConfig.Settings` + + Returns + ------- + individuals: list + a list containing objects holding each one individual with its properties and the associated molfile as OBMolec + ''' individuals = [] @@ -28,9 +42,50 @@ def initialisePopulation(settings): return individuals +def generate(settings, population, generator_op, **args): + ''' + + Generator operation that selects the coressponding generator operation function from the setting object + + Select one of the three options in the input file as follows. + + Only needed if you use composition optimization + + .. code-block:: python + + [GENERATOR] + generator=swissprot|uniform|random + + + Parameters + ---------- + settings: object + see :class:`src.JobConfig.Settings` + population: list + list of :class:`src.gaapi.Individual` + + Returns + ------- + generator_op : function + selected replacer + + ''' + return generator_op(settings, population, **args) -# Generate dihedrals with uniform distribution def UniformDihedralGenerator(settings, individuals): + ''' + + Generate dihedrals with uniform distribution. + Parameters + ---------- + settings : object + see :class:`src.JobConfig` + individuals : object + see :class:`src.gaapi.Individual` + + + + ''' num_phipsi = len(settings.dihedral_residue_indexes) @@ -41,9 +96,86 @@ def UniformDihedralGenerator(settings, individuals): indiv.phi_dihedrals[j] = initial_solution[j][0] indiv.psi_dihedrals[j] = initial_solution[j][1] indiv.applyPhiPsiDihedrals(settings) - + + +def swissprot_composition_generator(settings, individuals): + ''' + + Generates a composition distribution from the probabilities present in swissprot + + Parameters + ---------- + settings + individuals + + Returns + ------- + + ''' + def swissprot_to_index(min, max, selected_rotamers, selected_rotamer_types, swissprot): + rot_count_dict = {} + + for i in range(min, max): + rot_type = selected_rotamer_types[i] + if rot_type in rot_count_dict.keys(): + rot_count_dict[rot_type] = rot_count_dict[rot_type] + 1 + else: + rot_count_dict[rot_type] = 0 + + rotamer_counts = rot_count_dict.values() + + rot_types = list(rot_count_dict.keys()) + # todo potentially both unbiased and swissprot should be unified + # same code as below only that we don"t use randint but use a normalized probability + probabilities = [] + for key in rot_types: + probabilities.append(swissprot[key]) + pass + # normalize probabilities to 1 + sum_probabilities = sum(probabilities) + norm_probabilities = [float(i) / sum_probabilities for i in probabilities] + which_type = np.random.choice(len(rot_types), p=norm_probabilities) + + chosen_rot = rot_types[which_type] + + allowed_indexes = [] + for i in range(min, max): + rot_type = selected_rotamer_types[i] + + if (rot_type == chosen_rot): + allowed_indexes.append(i) + + allowed_indexes = np.asarray(allowed_indexes) + + rel_index = np.random.randint(0, len(allowed_indexes)) + + return allowed_indexes[rel_index] + + for i in range(0, settings.population_size): + indiv = individuals[i] + + for j in range(0, len(settings.composition_residue_indexes)): + indiv.composition[j] = swissprot_to_index(settings.composition_lower_bounds[j], + settings.composition_upper_bounds[j], cnts.selected_rotamers, + cnts.selected_rotamer_types, cnts.swissprot_probabilities) + + print(indiv.composition) + indiv.applyComposition(settings) def UniformCompositionGenerator(settings, individuals): + ''' + + This will randomly sample all the selected rotamers and thus will oversample amino acids with many rotamers (e.g Lys) compared to alanine. + + + Parameters + ---------- + settings : object + see :class:`src.JobConfig` + individuals : object + see :class:`src.gaapi.Individual` + + ''' for i in range (0, settings.population_size): indiv = individuals[i] @@ -54,9 +186,42 @@ def UniformCompositionGenerator(settings, individuals): def unbiased_protein_composition_generator(settings, individuals): - - # Generates an unbiased sample across all rotamers (ie weights each rotamer type equally for initial sampling) - def get_ubia_index(min, max, selected_rotamers, selected_rotamer_types): + ''' + + Generates an unbiased sample across all rotamers (ie weights each rotamer type equally for initial sampling) + All amino acids have probability of :math:`\\frac{ 1 }{n(selected amino acid types}` to be selected. + + Parameters + ---------- + settings : object + see :class:`src.JobConfig` + individuals : object + see :class:`src.gaapi.Individual` + + Returns + ------- + + ''' + + def get_ubia_index(min, max, selected_rotamer_types): + ''' + + defines the indexes of allowed rotamers + + Parameters + ---------- + min : int + lower bound of allowed rotamers for this site + max : int + upper bound of allowed rotamers for this site + selected_rotamer_types: + list of rotamer types that are alllowed according to input file + + Returns + ------- + allowed_indexes[rel_index]: int + random index within bounds of this rotamer + ''' rot_count_dict = {} for i in range(min, max): @@ -91,22 +256,40 @@ def get_ubia_index(min, max, selected_rotamers, selected_rotamer_types): indiv = individuals[i] for j in range (0, len(settings.composition_residue_indexes)): - indiv.composition[j] = get_ubia_index(settings.composition_lower_bounds[j], settings.composition_upper_bounds[j], cnts.selected_rotamers, cnts.selected_rotamer_types) + indiv.composition[j] = get_ubia_index(settings.composition_lower_bounds[j], settings.composition_upper_bounds[j], cnts.selected_rotamers) print(indiv.composition) indiv.applyComposition(settings) - -# Generate dihedrals by Monte Carlo + def MonteCarloDihedralGenerator(settings, individuals, prob_pointers=None): - -# [MC_GENERATE] -# mc_generate_dihedrals = True -# distribution_path = 's' -# mcmove_lbound = -45.0 -# mcmove_ubound = 45.0 -# num_mc_steps = 1000 -# dihedral_probability_pointers = 1 2 3 1 + ''' + + Generate dihedrals by Monte Carlo simulation + + to use this option in the inputfile use + + [MC_GENERATE] + mc_generate_dihedrals = True + distribution_path = 's' + mcmove_lbound = -45.0 + mcmove_ubound = 45.0 + num_mc_steps = 1000 + dihedral_probability_pointers = 1 2 3 1 + + Parameters + ---------- + settings : object + see :class:`src.JobConfig` + individuals : object + see :class:`src.gaapi.Individual` + prob_pointers + + Returns + ------- + + ''' + from deprecated.montecarlo import dihedral_opt as mcopt @@ -141,11 +324,24 @@ def MonteCarloDihedralGenerator(settings, individuals, prob_pointers=None): indiv.psi_dihedrals[j] = dihedrals[i * num_phipsi + j][1] -# Generate dihedrals with BASILISK by trained DBN that interpolates continuous distribution and gives side-chain angles chis + def BasiliskSideChainDihedralsGenerator(settings, individuals): + ''' + + Generate dihedrals with BASILISK by trained DBN that interpolates continuous distribution and gives side-chain angles chis + MC dihedrals generation like in upper function + MonteCarloDihedralGenerator(settings, individuals) + + Parameters + ---------- + settings + individuals + + Returns + ------- + + ''' - # MC dihedrals generation like in upper function - # MonteCarloDihedralGenerator(settings, individuals) print("BASILISK_OPT BACKBONE & SIDE CHAIN DIHEDRALS ARE GENERATED") @@ -197,6 +393,18 @@ def BasiliskSideChainDihedralsGenerator(settings, individuals): def getBasiliskSample(obmol): + ''' + + #TODO Nick + + Parameters + ---------- + obmol + + Returns + ------- + + ''' from deprecated.basilisk.basilisk_lib import basilisk_dbn res_name, res_index = getResidueIndexes(obmol) @@ -218,6 +426,18 @@ def getBasiliskSample(obmol): def getResidueIndexes(obmol): + ''' + + #TODO Nick + + Parameters + ---------- + obmol + + Returns + ------- + + ''' from deprecated.basilisk.basilisk_lib import basilisk_utils from src import MoleculeInfo as mi res_index = [] @@ -231,7 +451,8 @@ def getResidueIndexes(obmol): def getMCProbPinters(obmol): - + + # TODO Nick pointers = [] for i in range(obmol.NumResidues()): @@ -252,6 +473,10 @@ def getMCProbPinters(obmol): if __name__ == "__main__": + ''' + Test for standalone run for the basilisk test case. + Should be moved to a test #TODO + ''' import openbabel import sys from math import degrees, radians diff --git a/src/gaapi/generators.py~ b/src/gaapi/generators.py~ deleted file mode 100755 index c5db097..0000000 --- a/src/gaapi/generators.py~ +++ /dev/null @@ -1,94 +0,0 @@ -''' -crossovers.py - -@author: Nicholas Browning -''' -import Individual -import constants -import numpy as np - -def initialisePopulation(settings): - - individuals = [] - - for i in xrange (0, settings.population_size): - indiv = Individual.Individual(settings) - - individuals.append(indiv) - - return individuals - -def defaultGenerator(settings): - pass - -def MonteCarloDihedralGenerator(settings, individuals): - -# [MC_GENERATE] -# mc_generate_dihedrals = True -# distribution_path = 's' -# mcmove_lbound = -45.0 -# mcmove_ubound = 45.0 -# num_mc_steps = 1000 -# dihedral_probability_pointers = 1 2 3 1 - - from src.montecarlo import dihedral_opt as mcopt - - probs = mcopt.loadDefaultProbabilityDistributions() - - num_phipsi = len(settings.dihedral_residue_indexes) - - initial_solution = np.random.uniform(low=-180, high=180, size=(num_phipsi * settings.population_size, 2)) - - print "INITIAL DIHEDRALS" - - for i in xrange (settings.population_size): - print initial_solution[i * num_phipsi: (i + 1) * num_phipsi] - move_lows = [settings.mcmove_lbound] * num_phipsi * settings.population_size - move_highs = [settings.mcmove_ubound] * num_phipsi * settings.population_size - - # TODO do this once with N*M array or per individual? - # Can pack intial solution as an N*M array without problems...probably easiest - need to also create temp prob_pointer array of same size - - pointers = [] - - for i in xrange (0, settings.population_size): - for j in xrange (0, len (settings.dihedral_probability_pointers)): - pointers.append(settings.dihedral_probability_pointers[j]) - - dihedrals = mcopt.optimisePsiPhi(probs, pointers, initial_solution, settings.num_mc_steps, move_lows, move_highs) - print "MC_OPT DIHEDRALS" - - for i in xrange (settings.population_size): - print dihedrals[i * num_phipsi: (i + 1) * num_phipsi] - - for i in xrange (0, settings.population_size): - indiv = individuals[i] - for j in xrange (0, len(indiv.phi_dihedrals)): - indiv.phi_dihedrals[j] = dihedrals[i * num_phipsi + j][0] - indiv.psi_dihedrals[j] = dihedrals[i * num_phipsi + j][1] - -def UniformDihedralGenerator(settings, individuals): - - num_phipsi = len(settings.dihedral_residue_indexes) - - initial_solution = np.random.uniform(low=-180, high=180, size=(num_phipsi, 2)) - - for i in xrange (0, settings.population_size): - indiv = individuals[i] - for j in xrange (0, len(indiv.phi_psi_dihedrals)): - indiv.phi_psi_dihedrals[j] = (dihedrals[j][0], dihedrals[j][1]) - indiv.applyPhiPsiDihedrals() - - -def UniformCompositionGenerator(settings, individuals): - - for i in xrange (0, settings.population_size): - indiv = individuals[i] - for j in xrange (0, len(settings.composition_residue_indexes)): - indiv.composition[j] = np.random.randint(low=settings.composition_lower_bounds[j], high=settings.composition_upper_bounds[j]) - - - - - - diff --git a/src/gaapi/mutators.py b/src/gaapi/mutators.py index 0994553..6d7ff35 100755 --- a/src/gaapi/mutators.py +++ b/src/gaapi/mutators.py @@ -95,6 +95,26 @@ def poly(indiv_i, xl, xu, eta): return x def polynomial_mutation(settings, individual, **args): + ''' + + .. code-block:: python + + [GA_MUTATION] + mutator = polynomial_mutation + mutation_probability = 0.3 + genewise__mutation_probability = 0.15 + poly_eta = 7.0 + + Parameters + ---------- + settings + individual + args + + Returns + ------- + + ''' eta = settings.poly_eta mut_rate = settings.genewise_mutation_probability diff --git a/src/gaapi/operator_types.py b/src/gaapi/operator_types.py index 929e305..d510ed6 100755 --- a/src/gaapi/operator_types.py +++ b/src/gaapi/operator_types.py @@ -2,7 +2,7 @@ @author: Nicholas Browning ''' # #SUPPORTED OPERATOR TYPES# - +import evaluators as evals # terrible version of Enum struct as python 2.7 doesn't have it # crossover types @@ -16,7 +16,18 @@ # replacer types SWAP = 'swap' ELITIST = 'elitism' +NSGA2 = 'nsga2' + +# generators +UNIFORM= 'uniform' +UNBIASED= 'random' +SWISSPROT= 'swissprot' # selector ty[es TOURNAMENT_WOR = 'tournament_wor' +availableEvaluators = {"helical_stability": evals.helical_stability, + "mmpbsa_multi": evals.mmpbsa_multi, + "stability_multi": evals.stability_multi, + "pmemd": evals.amber_energy_simplified} + diff --git a/src/gaapi/replacers.py b/src/gaapi/replacers.py index d711cb2..5482326 100755 --- a/src/gaapi/replacers.py +++ b/src/gaapi/replacers.py @@ -1,29 +1,102 @@ ''' -replacers.py +Replacers are used to modify a population after crossover and mutation have occured -@author: Nicholas Browning +.. codeauthor:: Nicholas Browning ''' + from __future__ import print_function from __future__ import absolute_import from builtins import range import numpy as np from . import Individual +import pygmo as pg +from src import outprocesses as op def replace(settings, parents, children, replace_op, **args): + ''' + + Replace operation that selects the coressponding replacer function from the setting object + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + parents: list + list of :class:`src.gaapi.Individual.Individual` + children: list + list of :class:`src.gaapi.Individual.Individual` + replace_op: function + the chosen replacer function in the :func:`main.initalise_ga` + args + + Returns + ------- + replace_op : function + return values of the selected replacer + + ''' return replace_op(settings, parents, children, **args) def swap_replace(settings, parents, children, **args): + ''' + + Only returns the children + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + parents: list + list of see :class:`src.gaapi.Individual.Individual` + children: list + list of see :class:`src.gaapi.Individual.Individual` + args + + Returns + ------- + + ''' return children def elitist_replace(settings, parents, children, **args): + ''' + + Does an elitist replacement to improve GA convergence. + According to the `elitist_factor` set a percentage of the most fit parents is retained. + + This is used only in single objective runs. The nsga2 algorithm is already elitist + + Use in the input file like so: + + .. code-block:: python + + [GA_REPLACER] + replacer = elitism + elitist_factor = 0.25 + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + parents: list + list of see :class:`src.gaapi.Individual.Individual` + children: list + list of see :class:`src.gaapi.Individual.Individual` + args + + Returns + ------- + elitst_population: list + list of :class:`src.gaapi.Individual.Individual` containing a population with elist parents chosen according to elistim_factor and the rest being children + ''' elitist_factor = settings.elitist_factor num_elites = int(elitist_factor * settings.population_size) print("ELITIST REPLACER with {} elite parents".format(num_elites)) - parent_indexes = np.arange(settings.population_size) - child_indexes = np.arange(settings.population_size) + #parent_indexes = np.arange(settings.population_size) + #child_indexes = np.arange(settings.population_size) #deprecated sorted_parent_indexes = np.argsort(parents) sorted_child_indexes = np.argsort(children) @@ -45,5 +118,93 @@ def elitist_replace(settings, parents, children, **args): return elitist_population + + +def non_dominated_sorting(settings, parents, children, **args): + ''' + + fast non dominated sorting (NDSA-II) by Deb et. al. to sort individuals. + Automatically used if more than one evaluator is used. + + .. code-block:: python + + [GA_REPLACER] + replacer = nsga2 + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + parents: list + list of see :class:`src.gaapi.Individual.Individual` + children: list + list of see :class:`src.gaapi.Individual.Individual` + args + + Returns + ------- + new_population: list + list containing the individuals for the next generation chosen according to non-domination rank and crowding distance sorting + ''' + print("Using fast non dominated sorting (NDSA-II) by Deb et. al. to sort individuals") + # make fitness array containing whole family + familyFitnesses = [[0, 0]] * settings.population_size * 2 # TODO only two fitnesses currently. Need to make this general! + for i in range(0, settings.population_size): + familyFitnesses[i] = [parents[i].fitnesses[0], parents[i].fitnesses[1]] + childi = i + settings.population_size + familyFitnesses[childi] = [children[i].fitnesses[0], children[i].fitnesses[1]] + pass + if settings.verbose: + print("Family Fitnesses", familyFitnesses) + pass + # sort using non dominated sorting and then select based on non-domination ranks and crowding distance, this returns the N best individuals that make up the next parent population + new_population_idx = pg.select_best_N_mo(points=familyFitnesses, N=settings.population_size) + ndf, dl, dc, ndr = pg.fast_non_dominated_sorting(points=familyFitnesses) + new_population = [] + if settings.verbose: + print('id <', settings.population_size, '= parent population,', 'id >', settings.population_size, '= child population') + print('nsga-II fittest individuals', new_population_idx) + print('first front from nsga-II:') + first_front = [] + ff_str = '' + for x in ndf[0]: + first_front.append(familyFitnesses[x]) + ff_str += str(familyFitnesses[x]) + if settings.store_intermediate_mol: + if x > settings.population_size - 1: + child_idx = x - settings.population_size + molfile = children[int(child_idx)].mol[0] + pass + else: + molfile = parents[int(x)].mol[0] + pass + indFitness = ' ' + for k in familyFitnesses[x]: + indFitness += str(k) + ' ' + pass + op.writeFrontFile(path=settings.output_path, file=molfile, fitness=indFitness, + iteration=settings.curr_iteration, frontid=x) + pass + pass + + pass + if settings.verbose: + print(ff_str) + pass + + op.writeFrontLog(path=settings.output_path, front=first_front, iteration=settings.curr_iteration) + pass + + # Loop through all individuals and include them in the new_population + for i in new_population_idx: + # because of the elitism we sort both the parents and children, we then have to add from the correct subpopulation (children or parents) + if i > settings.population_size - 1: + child_idx = i - settings.population_size + new_population.append(children[int(child_idx)]) + pass + else: + new_population.append(parents[int(i)]) + + return new_population diff --git a/src/gaapi/selectors.py b/src/gaapi/selectors.py index 676b7d6..0120e22 100755 --- a/src/gaapi/selectors.py +++ b/src/gaapi/selectors.py @@ -1,7 +1,7 @@ ''' -selectrors.py +This contains the selectors used for selecting the individuals allowed to mate -@author: Nicholas Browning +.. codeauthor:: Nicholas Browning ''' from __future__ import print_function @@ -9,11 +9,54 @@ import numpy as np def selector(settings, individuals, selector_op, **args): + ''' + + Prints the selector used to the output and run the selector + + Parameters + ---------- + settings: object + see :class:`src.JobConfig.Settings` + individuals: list + list of individuals of this generation + selector_op : str + defined by JobInput + args + + Returns + ------- + selector_op : func + selected selctor function + + ''' print("SELECTORS {}".format(settings.selector)) return selector_op(settings, individuals, **args) def tournamentSelectionWOR(settings, individuals, **kargs): + ''' + + Tournament selection where two individuals fight a tournament and the stronger one is allowed to mate + + .. code-block:: python + + [GA_SELECTION] + selector = tournament_wor + tournament_size = 2 + + Parameters + ---------- + settings : object + see :class:`src.JobConfig.Settings` + individuals + kargs + + Returns + ------- + indeces: np.array + indeces of selected individuals + + ''' tournament_size = settings.tournament_size indexes = np.arange(settings.population_size) @@ -22,10 +65,24 @@ def tournamentSelectionWOR(settings, individuals, **kargs): for _ in range(0, settings.population_size): np.random.shuffle(indexes) - min_idx = np.argmin([individuals[i] for i in indexes[:tournament_size]]) #J: NOT individuals[i].fitness? random selection? + min_idx = np.argmin([individuals[i] for i in indexes[:tournament_size]]) result.append(indexes[:tournament_size][min_idx]) return np.asarray(result) def roulette_wheel(settings, individuals, **kargs): + ''' + + not implemented + + Parameters + ---------- + settings + individuals + kargs + + Returns + ------- + + ''' pass diff --git a/src/methods.py b/src/methods.py index 37e7760..6041d6d 100755 --- a/src/methods.py +++ b/src/methods.py @@ -1,7 +1,8 @@ ''' -Created on Nov 4, 2015 +contains methods used in varipus components + +.. codeauthor:: Nicholas Browning -@author: roethlisbergergroup ''' from __future__ import division diff --git a/src/outprocesses.py b/src/outprocesses.py index 231450c..4b46820 100644 --- a/src/outprocesses.py +++ b/src/outprocesses.py @@ -1,10 +1,11 @@ ''' -Created on Jan 10, 2018 +All processes that operate outside of the EVOLVE main code like simulation codes should be included in this. -@author: Nicholas Browning & Justin Villard - -All functions used to run softwares out of the GA code +.. codeauthor:: Nicholas Browning +.. codeauthor:: Simon Duerr dev@simonduerr.eu +.. codeauthor:: Justin Villard ''' + from __future__ import division from __future__ import print_function @@ -16,26 +17,56 @@ import os import subprocess import numpy as np +from openbabel import openbabel +import time -def runtleap(work_dir="", mol_file="mol.pdb", tleaptemp="tleap_template.in", tleapin="leap.in", inpcrd_out="mol.inpcrd", prmtop_out="mol.prmtop"): - # TODO - """ +def runtleap(work_dir="", mol_file="mol_amber.pdb", tleaptemp="tleap_template.in", tleapin="leap.in", inpcrd_out="mol.inpcrd", prmtop_out="mol.prmtop"): + ''' + + runs tleap to process a pdb file into a valid amber prmtop file. + This procedure needs to be verified before runinng evolve such that the topology building process does not fail. + If the setting for the resname is not set the mol files need to be reloaded. + Parameters ---------- + work_dir : string working directory mol_file : string - + path to PDB file tleaptemp - - """ + tleapin + inpcrd_out + prmtop_out + + Returns + ------- + + ''' if (os.path.exists(work_dir + inpcrd_out)): os.remove(work_dir + inpcrd_out) if (os.path.exists(work_dir + prmtop_out)): os.remove(work_dir + prmtop_out) - + + try: + f = open(work_dir+mol_file, "w") + FNULL = open(os.devnull, 'w') + pPDB4Amber = subprocess.Popen(["pdb4amber", work_dir+'mol.pdb', ], universal_newlines=True, stdout=f, + stderr=FNULL) + pPDB4Amber.wait() + print('running pdb4amber') + FNULL.close() + f.close() + except IOError as e: + sys.exit("I/O error on '%s': %s" % (e.filename, e.strerror)) + except subprocess.CalledProcessError as e: + sys.exit("pdb4amber failed processing mutated.pdb, returned code %d " % (e.returncode)) + except OSError as e: + sys.exit("failed to execute pdb4amber: %s" % (str(e))) + pass + f = open(tleaptemp, "r") g = f.readlines() filename = (work_dir + mol_file).split('.')[0] @@ -54,6 +85,7 @@ def runtleap(work_dir="", mol_file="mol.pdb", tleaptemp="tleap_template.in", tle for line in g: ff.write(line) ff.close() + f.close() # proc = subprocess.Popen([tleap_path+"/bin/tleap", "-f", work_dir+tleapin], stdout=subprocess.PIPE) # out, err = proc.communicate() @@ -73,15 +105,449 @@ def runtleap(work_dir="", mol_file="mol.pdb", tleaptemp="tleap_template.in", tle except OSError as e: sys.exit("failed to execute tleap: %s" % (str(e))) - + +def runtleapMultiInd(work_dir="", leap_inputfile="tleap_template.in", n_frames=10): + ''' + + Takes the pdb file written to disk after openbabel mutation, + then uses pdb4amber to process it and add TER statements for tleap. + Then tleap is run on all frames of the individual. + + If the option `use_res_type=True` is not used, then you need to include all necessary *.off files for the a99SB forcefield in the share directory + If you want to track which rotamer was placed this might be an option. If you use a forcefield different than a99SB you have to use `use_res_type=True` + + Parameters + ---------- + work_dir: str + working directory + leap_inputfile: str + path to inputfile in config file + n_frames: int + number of frames + + ''' + logfile = open(work_dir + "/evaluator_mmpbsa_multi.log", "a") + logfile.write("1. Running parameter generation for " + str(n_frames) + " frames\n") + logfile.write("1.1 Converting files from openbabel to amber format\n") + processes = [] + try: + for frame in range(0, n_frames): + os.chdir(work_dir + "/frame" + str(frame)) + f = open('mutated_ter.pdb', "w") + FNULL = open(os.devnull, 'w') + pPDB4Amber = subprocess.Popen(["pdb4amber", "mutated.pdb", "--nohyd"], universal_newlines=True, stdout=f, + stderr=FNULL) + processes.append((pPDB4Amber, f, FNULL)) + # f.close() # In order to avoid I/O errrors with low ulimit it might be necessary to use subprocess call. Then files should be immediateluy closed + # FNULL.close() + os.chdir("../../") + pass + for p, f, FNULL in processes: + p.wait() + FNULL.close() + f.close() + pass + except IOError as e: + sys.exit("I/O error on '%s': %s" % (e.filename, e.strerror)) + except subprocess.CalledProcessError as e: + sys.exit("pdb4amber failed processing mutated.pdb, returned code %d " % (e.returncode)) + except OSError as e: + sys.exit("failed to execute pdb4amber: %s" % (str(e))) + pass + # then run leap in every directory, this will generate all the necessary parameter files + logfile.write("1.2 Running tleap\n") + processes = [] + try: + for frame in range(0, n_frames): + os.chdir(work_dir + "/frame" + str(frame)) + foutanderr = open('leap.log', 'w') + pLeap = subprocess.Popen(["tleap", "-f", leap_inputfile], stdout=foutanderr, stderr=subprocess.STDOUT) + processes.append((pLeap, foutanderr)) + os.chdir("../../") + pass + for p, f in processes: + p.wait() + f.close() + pass + except IOError as e: + sys.exit("I/O error on '%s': %s" % (e.filename, e.strerror)) + except subprocess.CalledProcessError as e: + sys.exit("tleap failed, returned code %d (check '" + work_dir + "/leap.log')" % (e.returncode)) + except OSError as e: + sys.exit("failed to execute tleap: %s" % (str(e))) + pass + logfile.close() + + +def runPMEMDMultiInd(work_dir="", np=20, amberin='', n_frames=10, compute_cluster=False, ntasks=60, nodes=6, queuename="debug"): + ''' + + minimization of multiple frames in parallel for mmpbsa_multi evuluator + All files are put in work_dir/frame* folders + We're using the multipmemd version of pmemd.MPI. For this we generate a groupfile in the work dir and then call pmemd + Cannot use pmemd.cuda because of GPU precision model. With unreasonable geometry (atoms very close together which can be the case if swapping a large sidechain for a small sidechain with the GA) forces can be truncated or, in the worst case, overflow the fixed precision presentation. + + In order to maximize the performance the multipmemd module is used. + + #ToDO + Gromacs should be possible here as well using parmed + + Parameters + ---------- + work_dir: str + working directory + np: int + number of processor cores + amberin: : str + /path/to/amberinput file + n_frames: int + number of frames + compute_cluster: bool + Determines whether a submit script shall be created and submitted using sbatch + ntasks: int + number of tasks for slurm + nodes: int + number of nodes for slumr + queuename: str + name of the queue + + ''' + + logfile = open(work_dir + "/evaluator_mmpbsa_multi.log", "a") + logfile.write("Ran minimization using following command: ") + f = open(work_dir + "/groupfile", "w") + f.write('') + f.close() + f = open(work_dir + "/groupfile", "a") + for frame in range(0, n_frames): + path = work_dir + "/frame" + str(frame) + "/" + f.write( + '-O -i ' + amberin + ' -o ' + path + 'min.out -p ' + path + 'GB1AZI_solv.prmtop -c ' + path + 'GB1AZI_solv.inpcrd -r ' + path + 'min.rst -suffix frame' + str( + frame) + ' -l ' + path + 'logfile -inf ' + path + 'mdinfo \n') + # f.write('-O -i '+amberin+' -o '+path+'min.out -p '+path+'GB1AZI_solv.prmtop -c '+path+'GB1AZI_solv.inpcrd -r '+path+'min.rst -suffix frame'+str(frame)+"\n") #for use in sander + pass + f.close() + individualStart = time.time() + # If we calculate on a compute cluster make runscript and run command + # potentially it should be changed from sbatch to srun to have the complete GA in a slurm script to not block one core on the login node + if (compute_cluster): + if (os.path.isfile('./run_pmemd.sh') == False): + pmemdscript = "#!/bin/bash\n#SBATCH -J GA-min\n#SBATCH --partition={}\n#SBATCH --time=00:05:00\n#SBATCH --nodes={}\n#SBATCH --ntasks-per-node={}\n#SBATCH --mem=10000\n#SBATCH --output=slurm/job.out\n#SBATCH --error=slurm/error.err\n### Load Modules ###\nmodule load amber/16/intel-17.0.4\nsrun pmemd.MPI -ng {} -groupfile {} \n".format( + str(queuename), str(nodes), str(ntasks), str(n_frames), work_dir + "/groupfile") + pmemdscript_f = open("run_pmemd.sh", "w") + pmemdscript_f.write(pmemdscript) + pmemdscript_f.close() + pass + # execute with sbatch and wait for command to finish + pMin = subprocess.Popen('sbatch -W run_pmemd.sh', stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True) + output, error = pMin.communicate() + pMin.wait() + if (pMin.returncode != 0 and pMin.returncode != 174): + sys.exit("failed to execute sbatch and pmemd.MPI. Only slurm is supported\n: %d, %s, %s" % ( + pMin.returncode, output, error)) + if pMin.returncode == 174: + print("Segmentation fault occured, skipping this individual") + return 0 + pass + pass + else: + logfile.write('mpirun -np ' + str(np) + ' pmemd.MPI -ng ' + str(n_frames) + ' -groupfile ' + work_dir + '/groupfile\n') + pMin = subprocess.Popen('mpirun -np ' + str(np) + ' pmemd.MPI -ng ' + str(n_frames) + ' -groupfile ' + work_dir + '/groupfile',stdout=logfile, shell=True) + output, error = pMin.communicate() + pMin.wait() + if (pMin.returncode != 0 and pMin.returncode != 174): + sys.exit("failed to execute sbatch and pmemd.MPI. Only slurm is supported\n: %d, %s, %s" % ( + pMin.returncode, output, error)) + if pMin.returncode == 174: + print("Segmentation fault occured, skipping this individual") + return 0 + pass + individualEnd = time.time() + logfile.write("Runtime of pmemd " + str(individualEnd - individualStart) + "sec." + "\n") + # after pmemd has finished we convert the rst file to a pdb file + logfile.write("Converting rst files to pdb format\n") + processes = [] + try: + for frame in range(0, n_frames): + path = work_dir + '/frame' + str(frame) + '/' + f = open(path + 'min.pdb', "w") + pPDBConv = subprocess.Popen(['ambpdb', '-p', path + 'GB1AZI_solv.prmtop', '-c', path + 'min.rst.frame' + str(frame)],universal_newlines=True, stdout=f) + processes.append((pPDBConv, f)) + pass + for p, f in processes: + p.wait() + f.seek(0) + f.close() + pass + except IOError as e: + sys.exit("I/O error on '%s': %s" % (e.filename, e.strerror)) + except subprocess.CalledProcessError as e: + sys.exit("ambpdb failed, returned code %d" % (e.returncode)) + except OSError as e: + sys.exit("failed to execute ambpdb: %s" % (str(e))) + pass + # then we remove the solvent waters from the minimization, This is necessary as the different frames can have different amounts of solvent and therefore the prmtop files are different, which cannot be the case for the MMPBSA calculation. + logfile.write("Desolvating complex using pdb4amber -d and removing counter ions\n") + processes = [] + individualStart = time.time() + try: + for frame in range(0, n_frames): + os.chdir(work_dir + "/frame" + str(frame)) + f = open("min_nosolv.pdb", "w") + FNULL = open(os.devnull, 'w') + pSolvStrip = subprocess.Popen(["pdb4amber", "-s", ":Cl-,Na+", "-d", "min.pdb"], universal_newlines=True,stdout=f, stderr=FNULL) + # f.close() # In order to avoid I/O errrors use subprocess call. + # FNULL.close() + processes.append((pSolvStrip, f, FNULL)) + os.chdir("../../") + pass + + for p, f, fnull in processes: + p.wait() + f.close() + fnull.close() + pass + except IOError as e: + sys.exit("I/O error on '%s': %s" % (e.filename, e.strerror)) + except subprocess.CalledProcessError as e: + sys.exit("pdb4amber -d failed, returned code %d " % (e.returncode)) + except OSError as e: + sys.exit("failed to execute pdb4amber -d: %s" % (str(e))) + + individualEnd = time.time() + logfile.write("Runtime of Desolvation: " + str(individualEnd - individualStart) + " sec." + "\n") + logfile.close() + return 1 + pass + + +def runMMPBSAMultiInd(work_dir="", mmpbsa_inputfile="mmpbsa.in", n_frames=10, compute_cluster=False, ntasks=60, nodes=6,queuename="debug", energy_evaluator="gb"): + ''' + + MMPBSA calculation with mmpbsa_multi evaluator. Takes all minimized files for the frames of the Individual and runs an MMPBSA calclation using MMPBSA.py.MPI + Extracts the MMPBSA energy and returns it. + Stores the energy from the implicit solvent calculation in the `work_dir/evaluators_stability_multi.log` + + Parameters + ---------- + work_dir: str + working directory + mmpbsa_inputfile: str + /path/to/mmpbsa input file + n_frames: int + number of frames + compute_cluster: bool + Determines whether a submit script shall be created and submitted using sbatch + ntasks: int + number of tasks for slurm + nodes: int + number of nodes for slumr + queuename: str + name of the queue + + Returns + ------- + binding_affinity: float + value extracted from MMPBSA.log file + ''' + framesstring = "" + logfile = open(work_dir + "/evaluator_mmpbsa_multi.log", "a") + # construct framestring with paths to all frames + for frame in range(0, n_frames): + framesstring += "./frame" + str(frame) + "/min_nosolv.pdb " + pass + # If we calculate on a compute cluster make runscript and run command + # potentially it should be changed from sbatch to srun to have the complete GA in a slurm script to not block one core on the login node + os.chdir(work_dir) + if (compute_cluster): + if (os.path.isfile('./run_mmpbsa.sh') == False): + mmpbsascript = """#!/bin/bash +#SBATCH -J GA-MMPBSA +#SBATCH --partition=%s +#SBATCH --time=00:05:00 +#SBATCH --nodes=%s +#SBATCH --ntasks-per-node=%s +#SBATCH --mem=10000 +#SBATCH --output=slurm/job.out +#SBATCH --error=slurm/error.err +module load amber/16/intel-17.0.4 +srun -n %s MMPBSA.py.MPI -O -i inp/mmpbsa.in -o work_dir/mmpbsa.log -cp work_dir/frame0/dry_complex.prmtop -rp work_dir/frame0/receptor.prmtop -lp work_dir/frame0/ligand.prmtop -y %s""" % ( + str(queuename), str(nodes), str(ntasks), str(n_frames), framesstring) + mmpbsascript_f = open("run_mmpbsa.sh", "w") + mmpbsascript_f.write(mmpbsascript) + mmpbsascript_f.close() + pass + logfile.write("Submitting batch job and wait for it to finish\n") + pMMPBSA = subprocess.Popen("sbatch -W run_mmpbsa.sh", stdout=subprocess.PIPE, stderr=subprocess.PIPE, + shell=True) + output, error = pMMPBSA.communicate() + pMMPBSA.wait() + if pMMPBSA.returncode != 0: + sys.exit("failed to execute sbatch and run MMPBSA calculation.\n: %d, %s, %s" % ( + pMMPBSA.returncode, output, error)) + pass + pass + else: + logfile.write("mpirun -np " + str( + n_frames) + " MMPBSA.py.MPI -O -i " + mmpbsa_inputfile + " -o /mmpbsa.log -cp ./frame0/dry_complex.prmtop -rp ./frame0/receptor.prmtop -lp ./frame0/ligand.prmtop -y " + framesstring + "\n\n") + logfile.close() # need to open and reclose to have correct order of writing + logfile = open("./evaluator_mmpbsa_multi.log", "a") + pMMPBSA = subprocess.Popen("mpirun -np " + str( + n_frames) + " MMPBSA.py.MPI -O -i " + mmpbsa_inputfile + " -o ./mmpbsa.log -cp ./frame0/dry_complex.prmtop -rp ./frame0/receptor.prmtop -lp ./frame0/ligand.prmtop -y " + framesstring, + stdin=None, stdout=logfile, stderr=None, shell=True) + output, error = pMMPBSA.communicate() + pMMPBSA.wait() + if pMMPBSA.returncode != 0: + sys.exit("failed to execute MMPBSA.MPI : %d, %s, %s" % (pMMPBSA.returncode, output, error)) + pass + os.chdir("../") + # Grab output from mmpbsa calculation + fp = open(work_dir + "/mmpbsa.log") + if energy_evaluator == "gb": + linenumber = 87 + n_frames # GB + pass + else: + linenumber = 150 + n_frames # GB+PB calculation line number + pass + for i, line in enumerate(fp): + if i == int(linenumber): # set to 96 for gb or 159 to pb calculation + binding_affinity_GB = line[25:36] + break + fp.close() + logfile.close() + return float(binding_affinity_GB) + pass + + +def writeFrontLog(path="", front='', iteration=0): + ''' + + write front log as semicolon seperated values with fitnesses seperated by comma + + Parameters + ---------- + path: str + path to the current working directory, not work_dir/ + front: int + id of the front + iteration: int + iteration counter of the GA + ''' + filename = path + '/first_fronts.log' + + print("Writing first front to", filename) + + if iteration > 0: + append_write = 'a' # append if already exists + else: + append_write = 'w' # make a new file if not + string = '' + for item in front: + string += str(item[0]) + ',' + str(item[1]) + ';' + frontsfile = open(filename, append_write) + frontsfile.write(string + '\n') + frontsfile.close() + pass + + +def writeEnergyLog(path="", energies=None, iteration=0): + ''' + + write log of energies for all min_mols as comma seperated values + + The format is energy wt, correction wt, energy_mut, correction_mut + + Parameters + ---------- + path: str + path to the current working directory, not work_dir/ + energies: list + (energy wt, correction wt, energy_mut, correction_mut) + iteration: int + iteration counter of the GA + ''' + filename = path + '/energy.log' + + print("Writing energies", filename) + + if iteration > 0: + append_write = 'a' # append if already exists + else: + append_write = 'w' # make a new file if not + string = '' + for item in energies.keys(): + string += str(energies[item]) + ',' + frontsfile = open(filename, append_write) + frontsfile.write(string + '\n') + frontsfile.close() + pass + + +def writeFrontFile(path="", file='', fitness='', iteration=0, frontid=0): + ''' + + write pdb files for each molecule in the first pareto front + + Parameters + ---------- + path: str + path to the current working directory, not work_dir/ + file: Object + OBMol to write to disk + fitness: list + list of fitness values + iteration: int + iteration counter of the GA + frontid: int + id of the individual in the front to write to disk + ''' + if not os.path.exists(path + "/intermediate_molecules"): + os.makedirs(path + "/intermediate_molecules") + obConversion = openbabel.OBConversion() + obConversion.SetOutFormat("pdb") + file.SetTitle("fitness:" + fitness) + obConversion.WriteFile(file, path + '/intermediate_molecules/' + "min_iter_" + str(iteration + 1) + "_front_" + str( + frontid) + ".pdb") + + pass + + def runAmberMPI(work_dir="", np=16, amberin="amber_minimization.in", prmtop="mol.prmtop", inpcrd="mol.inpcrd", amberout="amber.out", restart="amber.rst"): + ''' + + Amber MPI documentation - ''' Actually already made by amber with flag -O - if (os.path.exists(work_dir + amberout)): - os.remove(work_dir + amberout) - if (os.path.exists(work_dir + restart)): - os.remove(work_dir + restart) - ''' + %TODO + Why is this there? Should go into one block with pmemd + + Parameters + ---------- + work_dir: str + path to calculations where amber was run + np: int + number of cores, set in the input file + amberin: str + file to amber input + prmtop: str + name of the amber parameter file + inpcrd: str + name of the input coordinates + amberout: str + name of amber out put file + restart: str + name of restart file + + Returns + ------- + + ''' + + # Actually already made by amber with flag -O + #if (os.path.exists(work_dir + amberout)): + # os.remove(work_dir + amberout) + #if (os.path.exists(work_dir + restart)): + # os.remove(work_dir + restart) + # # proc = subprocess.Popen(["mpirun", "-np", str(np), "sander.MPI", "-O", "-i", amberin, "-o", work_dir+amberout, "-c", work_dir+inpcrd, "-p", work_dir+prmtop, "-r", work_dir+restart], stdout=subprocess.PIPE) # can use pmemd if not in vaccum, more efficient parallelization but apparently doesn't work in vaccum # out, err = proc.communicate() @@ -107,6 +573,36 @@ def runAmberMPI(work_dir="", np=16, amberin="amber_minimization.in", prmtop="mol def runPMEMD(work_dir="", np=20, amberin="amber_minimization.in", prmtop="mol.prmtop", inpcrd="mol.inpcrd", amberout="amber.out", restart="amber.rst", use_cuda=False): + ''' + + run PMED using the specified number of cores . + use cuda should be set to false for all minimizations/ early heating! + Otherwise forces might be truncated + + + Parameters + ---------- + work_dir: str + path to calculations where amber was run + np: int + number of cores, set in the input file + amberin: str + file to amber input + prmtop: str + name of the amber parameter file + inpcrd: str + name of the input coordinates + amberout: str + name of amber out put file + restart: str + name of restart file + use_cuda: boolean + determine if cuda should be used + + Returns + ------- + nothing, exits if amber has problems + ''' if (work_dir == ""): foutanderr = open('amber.log', 'w') @@ -132,6 +628,33 @@ def runPMEMD(work_dir="", np=20, amberin="amber_minimization.in", prmtop="mol.pr def runMMPBSA(work_dir="", mmpbsa_in="mmpbsa.in", prmtop="mol.prmtop", inpcrd="mol.inpcrd", final_results="mmpbsa.dat", decomp_results="mmpbsa_decomp.dat"): + ''' + + runs a mmpbsa calculation using the files in the workdir. + File names are defined in the input file + Runs a decomposition analysis too. + + Used with evaluator decomp + + Parameters + ---------- + work_dir: str + path to calculations where amber was run + mmpbsa_in: str + name of the mmpbsa file + prmtop: str + name of the amber parameter file + inpcrd: str + name of the input coordinates + final_results:str + name of the mmpbsa dat file + decomp_results: str + name of the file for the decompositon output + + Returns + ------- + nothing + ''' if (work_dir == ""): foutanderr = open('mmpbsa.log', 'w') @@ -151,6 +674,19 @@ def runMMPBSA(work_dir="", mmpbsa_in="mmpbsa.in", prmtop="mol.prmtop", inpcrd="m def parseMMPBSA(mmpbsa_file_path): + ''' + + read MMPBSA energy + + + Parameters + ---------- + mmpbsa_file_path + + Returns + ------- + + ''' import os if not os.path.isfile(mmpbsa_file_path): @@ -177,9 +713,26 @@ def parseMMPBSA(mmpbsa_file_path): def parseMMBPSA_total_decomp(mmpbsa_file_path, num_res): + ''' + + parse MMPBSA total decompostion + + #TODO + Nick + + Parameters + ---------- + mmpbsa_file_path + num_res + + Returns + ------- + + ''' import os if not os.path.isfile(mmpbsa_file_path): + return None mmpbsa_file = open(mmpbsa_file_path, 'r') @@ -225,6 +778,21 @@ def parseMMBPSA_total_decomp(mmpbsa_file_path, num_res): def parseMMBPSA_backbone_decomp(mmpbsa_file_path, num_res): + ''' + + parse MMPBSA backbone decomposition + #TODO + Nick + + Parameters + ---------- + mmpbsa_file_path + num_res + + Returns + ------- + + ''' import os @@ -275,7 +843,22 @@ def parseMMBPSA_backbone_decomp(mmpbsa_file_path, num_res): def parseMMBPSA_sidechain_decomp(mmpbsa_file_path, num_res): - + ''' + + parse MMPBSA energies from sidechain decomposition + + #TODO + Nick + + Parameters + ---------- + mmpbsa_file_path + num_res + + Returns + ------- + + ''' import os if not os.path.isfile(mmpbsa_file_path): @@ -325,6 +908,20 @@ def parseMMBPSA_sidechain_decomp(mmpbsa_file_path, num_res): def parseMMPBSA_pairwise_total(mmpbsa_file_path, num_res): + ''' + + parse MMPBSA pairwise decomposition for all residues + TODO + + Parameters + ---------- + mmpbsa_file_path + num_res + + Returns + ------- + + ''' import os @@ -377,32 +974,49 @@ def parseMMPBSA_pairwise_total(mmpbsa_file_path, num_res): def parseAmberEnergy(amber_file): - # FINAL RESULTS - # - # - # - # NSTEP ENERGY RMS GMAX NAME NUMBER - # 100 -2.0167E+03 4.7684E-01 4.3950E+00 C 853 - # - # BOND = 30.0701 ANGLE = 77.6956 DIHED = 484.1676 - # VDWAALS = -404.1386 EEL = -4577.1353 EGB = -877.2771 - # 1-4 VDW = 169.7472 1-4 EEL = 3080.1239 RESTRAINT = 0.0000 - # - # -------------------------------------------------------------------------------- - # 5. TIMINGS - # -------------------------------------------------------------------------------- - # + ''' + + parses an amber energy file (shown below) + + .. code-block:: none + + # FINAL RESULTS + # + # + # + # NSTEP ENERGY RMS GMAX NAME NUMBER + # 100 -2.0167E+03 4.7684E-01 4.3950E+00 C 853 + # + # BOND = 30.0701 ANGLE = 77.6956 DIHED = 484.1676 + # VDWAALS = -404.1386 EEL = -4577.1353 EGB = -877.2771 + # 1-4 VDW = 169.7472 1-4 EEL = 3080.1239 RESTRAINT = 0.0000 + # + + + + Parameters + ---------- + amber_file: str + path to amber.out file. + + Returns + ------- + final_energy:int + 999 if file not found and exits programm + finaly energy from amber file + ''' + + if (not os.path.exists(amber_file)): print("Amber output file not found") return "Error" amberout = open(amber_file, 'r') lines = amberout.readlines() - + amberout.close() for i, line in enumerate(lines): if ("FINAL RESULTS" in line): data = lines[i + 5].split() - if 'data' in locals(): if ('NaN' in data[1]): return 999 @@ -411,10 +1025,62 @@ def parseAmberEnergy(amber_file): else: print("Not able to find Amber energy in output file") sys.exit() + return 999 + +def parseGBEnergy(amber_file): + """ + parses GB energy output file based on the ff: line containing the total energy of the system from the GB calculation + + .. code-block:: none + + File: _MMPBSA_complex_gb.mdout.X (x=[0,no_frames]) + + ff: 0 -1899.89 788.43 -214.15 -1413.76 0.00 -1060.41 4.75e+00 + BOND = 35.2852 ANGLE = 156.4010 DIHED = 596.7431 + VDWAALS = -378.8097 EEL = -4714.2131 EGB = -1060.4105 + 1-4 VDW = 164.6609 1-4 EEL = 3300.4508 RESTRAINT = 0.0000 + ESURF = 0.0000 + + Parameters + ---------- + amber_file: str + /path/to/MMPBSAoutput file + + Returns + ------- + energy: float + energy value extracted from MMPBSA file or 999 if not found + + """ + + + if (not os.path.exists(amber_file)): + print("Amber output file not found") + return 999 + + amberout = open(amber_file, 'r') + lines = amberout.readlines() + + for i, line in enumerate(lines): + if ("ff:" in line): + data = lines[i].split() + + if 'data' in locals(): + if ('NaN' in data[2]): + return 999 + else: + return float(data[2]) + else: + print("Not able to find Amber energy in output file") + # sys.exit() # commented because sometimes a segfault occurs with pmemd and then this individual is only skipped based on the exit code + return 999 if __name__ == "__main__": + ''' + Standalone run with first sys argument as the path to the pdb file and test minimization with amber. + ''' import sys runtleap(mol_file=sys.argv[1]) runAmberMPI() diff --git a/src/outprocesses.py~ b/src/outprocesses.py~ deleted file mode 100644 index 4e7edd1..0000000 --- a/src/outprocesses.py~ +++ /dev/null @@ -1,99 +0,0 @@ -''' -Created on Jan 10, 2018 - -@author: Nicholas Browning & Justin Villard - -All functions used to run softwares out of the GA code -''' - - -import os -import subprocess - -def runtleap(work_dir="", mol_file="temp_in_molecule.pdb", tleaptemp="leap_template.in", tleapin="leap.in", inpcrd_out="leap_temp_mol.inpcrd", prmtop_out="leap_temp_mol.prmtop"): - # TODO - if (os.path.exists(work_dir + inpcrd_out)): - os.remove(work_dir + inpcrd_out) - if (os.path.exists(work_dir + prmtop_out)): - os.remove(work_dir + prmtop_out) - - f = open(tleaptemp, "r") - g = f.readlines() - filename = (work_dir+mol_file).split('.')[0] - - for i, line in enumerate(g): - if ("mol" and "=") in line and ("mol2" in mol_file): - g[i] = "mol = loadmol2 " + work_dir+mol_file + "\n" - elif ("mol" and "=") in line and ("pdb" in mol_file): - g[i] = "mol = loadpdb " + work_dir+mol_file + "\n" - elif ("saveoff") in line: - g[i] = "saveoff mol " + filename + ".lib\n" - elif "saveamberparm" in line: - g[i] = "saveamberparm mol " + work_dir+prmtop_out + " " + work_dir+inpcrd_out + "\n" - - i = open(work_dir+tleapin, 'w') - for line in g: - i.write(line) - i.close() - - #proc = subprocess.Popen([tleap_path+"/bin/tleap", "-f", work_dir+tleapin], stdout=subprocess.PIPE) - #out, err = proc.communicate() - - foutanderr = open(work_dir+'/leap.log','w') - try: - proc = subprocess.Popen(["tleap", "-f", work_dir+tleapin], stdout=foutanderr, stderr=subprocess.STDOUT) - proc.wait() - foutanderr.close() - except IOError as e: - sys.exit("I/O error on '%s': %s" % (e.filename, e.strerror)) - except subprocess.CalledProcessError as e: - sys.exit("tleap failed, returned code %d (check '"+work_dir+"/leap.log')" % (e.returncode)) - except OSError as e: - sys.exit("failed to execute tleap: %s" % (str(e))) - - -def runAmberMPI(work_dir="", np=2, amberin="amber_minimization.in", prmtop="leap_temp_mol.prmtop", inpcrd="leap_temp_mol.inpcrd", amberout="amber.out", restart="amber.rst"): - - ''' Actually already made by amber with flag -O - if (os.path.exists(work_dir + amberout)): - os.remove(work_dir + amberout) - if (os.path.exists(work_dir + restart)): - os.remove(work_dir + restart) - ''' - proc = subprocess.Popen(["mpirun", "-np", str(np), "sander.MPI", "-O", "-i", amberin, "-o", work_dir+amberout, "-c", work_dir+inpcrd, "-p", work_dir+prmtop, "-r", work_dir+restart], stdout=subprocess.PIPE) - # can use pmemd if not in vaccum, more efficient parallelization but apparently doesn't work in vaccum - out, err = proc.communicate() - - -def parseAmberEnergy(amber_file): - # FINAL RESULTS - # - # - # - # NSTEP ENERGY RMS GMAX NAME NUMBER - # 100 -2.0167E+03 4.7684E-01 4.3950E+00 C 853 - # - # BOND = 30.0701 ANGLE = 77.6956 DIHED = 484.1676 - # VDWAALS = -404.1386 EEL = -4577.1353 EGB = -877.2771 - # 1-4 VDW = 169.7472 1-4 EEL = 3080.1239 RESTRAINT = 0.0000 - # - # -------------------------------------------------------------------------------- - # 5. TIMINGS - # -------------------------------------------------------------------------------- - # - if (not os.path.exists(amber_file)): - print("Amber output file not found") - return "Error" - - amberout = open(amber_file, 'r') - lines = amberout.readlines() - - for i, line in enumerate(lines): - if ("FINAL RESULTS" in line): - data = lines[i + 5].split() - - if 'data' in locals(): - return float(data[1]) - else: - print("Not able to find Amber energy in output file") - raise EOFError diff --git a/src/tools/mutate_protein.py b/src/tools/mutate_protein.py index e7208ac..b03daab 100755 --- a/src/tools/mutate_protein.py +++ b/src/tools/mutate_protein.py @@ -58,7 +58,7 @@ sys.exit() print("Swapping Side Chain") - mc.swapsidechain(mol, args.res_index, frag) + mc.swapsidechain(settings, mol, args.res_index, frag) print("Writing File:", args.out_molecule) obConversion.WriteFile(mol, args.out_molecule) diff --git a/tests/nick_tests/helical_stability/amber_run/leap.in 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../../../share/off/LYN/K35.off +loadOff ../../../share/off/LYN/K36.off +loadOff ../../../share/off/LYN/K37.off +loadOff ../../../share/off/LYN/K38.off mol = loadpdb ./amber_run/mol.pdb diff --git a/tests/nick_tests/helical_stability/final.pdb b/tests/nick_tests/helical_stability/final.pdb new file mode 100644 index 0000000..81411f4 --- /dev/null +++ b/tests/nick_tests/helical_stability/final.pdb @@ -0,0 +1,720 @@ +COMPND ./amber_run/min_struct.pdb +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +ATOM 1 H1 ACE 1 -2.913 -4.219 2.709 1.00 0.00 H +ATOM 2 CH3 ACE 1 -1.874 -4.413 2.446 1.00 0.00 C +ATOM 3 H2 ACE 1 -1.786 -5.416 2.031 1.00 0.00 H +ATOM 4 H3 ACE 1 -1.253 -4.332 3.338 1.00 0.00 H +ATOM 5 C ACE 1 -1.423 -3.396 1.422 1.00 0.00 C +ATOM 6 O ACE 1 -1.057 -3.761 0.308 1.00 0.00 O +ATOM 7 N K25 2 -1.427 -2.118 1.812 1.00 0.00 N +ATOM 8 H K25 2 -1.757 -1.923 2.747 1.00 0.00 H +ATOM 9 CA K25 2 -1.101 -0.972 0.940 1.00 0.00 C +ATOM 10 HA K25 2 -1.719 -1.061 0.044 1.00 0.00 H +ATOM 11 CB K25 2 -1.510 0.338 1.642 1.00 0.00 C +ATOM 12 HB2 K25 2 -1.401 1.160 0.933 1.00 0.00 H +ATOM 13 HB3 K25 2 -2.566 0.269 1.907 1.00 0.00 H +ATOM 14 CG K25 2 -0.682 0.661 2.901 1.00 0.00 C +ATOM 15 HG2 K25 2 -0.789 -0.142 3.632 1.00 0.00 H +ATOM 16 HG3 K25 2 0.371 0.732 2.627 1.00 0.00 H +ATOM 17 CD K25 2 -1.091 1.987 3.560 1.00 0.00 C +ATOM 18 HD2 K25 2 -0.393 2.196 4.373 1.00 0.00 H +ATOM 19 HD3 K25 2 -1.022 2.791 2.826 1.00 0.00 H +ATOM 20 CE K25 2 -2.513 1.928 4.130 1.00 0.00 C +ATOM 21 HE2 K25 2 -3.221 1.750 3.321 1.00 0.00 H +ATOM 22 HE3 K25 2 -2.577 1.107 4.844 1.00 0.00 H +ATOM 23 NZ K25 2 -2.887 3.177 4.818 1.00 0.00 N +ATOM 24 HZ2 K25 2 -3.815 3.046 5.211 1.00 0.00 H +ATOM 25 HZ3 K25 2 -2.260 3.293 5.608 1.00 0.00 H +ATOM 26 C K25 2 0.359 -0.921 0.443 1.00 0.00 C +ATOM 27 O K25 2 0.678 -0.144 -0.459 1.00 0.00 O +ATOM 28 N W03 3 1.247 -1.764 0.984 1.00 0.00 N +ATOM 29 H W03 3 0.930 -2.381 1.716 1.00 0.00 H +ATOM 30 CA W03 3 2.652 -1.849 0.563 1.00 0.00 C +ATOM 31 HA W03 3 3.119 -0.879 0.735 1.00 0.00 H +ATOM 32 CB W03 3 3.388 -2.883 1.429 1.00 0.00 C +ATOM 33 HB2 W03 3 4.458 -2.768 1.249 1.00 0.00 H +ATOM 34 HB3 W03 3 3.218 -2.651 2.481 1.00 0.00 H +ATOM 35 CG W03 3 3.043 -4.324 1.182 1.00 0.00 C +ATOM 36 CD1 W03 3 2.165 -5.061 1.900 1.00 0.00 C +ATOM 37 HD1 W03 3 1.610 -4.705 2.762 1.00 0.00 H +ATOM 38 NE1 W03 3 2.082 -6.335 1.369 1.00 0.00 N +ATOM 39 HE1 W03 3 1.484 -7.061 1.752 1.00 0.00 H +ATOM 40 CE2 W03 3 2.913 -6.486 0.279 1.00 0.00 C +ATOM 41 CZ2 W03 3 3.180 -7.563 -0.580 1.00 0.00 C +ATOM 42 HZ2 W03 3 2.676 -8.510 -0.440 1.00 0.00 H +ATOM 43 CH2 W03 3 4.108 -7.394 -1.623 1.00 0.00 C +ATOM 44 HH2 W03 3 4.325 -8.214 -2.296 1.00 0.00 H +ATOM 45 CZ3 W03 3 4.757 -6.156 -1.788 1.00 0.00 C +ATOM 46 HZ3 W03 3 5.474 -6.030 -2.590 1.00 0.00 H +ATOM 47 CE3 W03 3 4.485 -5.084 -0.916 1.00 0.00 C +ATOM 48 HE3 W03 3 4.999 -4.142 -1.051 1.00 0.00 H +ATOM 49 CD2 W03 3 3.550 -5.216 0.137 1.00 0.00 C +ATOM 50 C W03 3 2.803 -2.170 -0.934 1.00 0.00 C +ATOM 51 O W03 3 3.751 -1.697 -1.557 1.00 0.00 O +ATOM 52 N T03 4 1.856 -2.903 -1.535 1.00 0.00 N +ATOM 53 H T03 4 1.088 -3.248 -0.972 1.00 0.00 H +ATOM 54 CA T03 4 1.853 -3.246 -2.972 1.00 0.00 C +ATOM 55 HA T03 4 2.778 -3.771 -3.208 1.00 0.00 H +ATOM 56 CB T03 4 0.686 -4.185 -3.321 1.00 0.00 C +ATOM 57 HB T03 4 0.702 -4.379 -4.395 1.00 0.00 H +ATOM 58 CG2 T03 4 0.784 -5.523 -2.587 1.00 0.00 C +ATOM 59 HG21 T03 4 0.701 -5.377 -1.510 1.00 0.00 H +ATOM 60 HG22 T03 4 -0.014 -6.186 -2.920 1.00 0.00 H +ATOM 61 HG23 T03 4 1.742 -5.992 -2.812 1.00 0.00 H +ATOM 62 OG1 T03 4 -0.546 -3.581 -2.977 1.00 0.00 O +ATOM 63 HG1 T03 4 -1.269 -4.179 -3.245 1.00 0.00 H +ATOM 64 C T03 4 1.777 -2.004 -3.868 1.00 0.00 C +ATOM 65 O T03 4 2.474 -1.925 -4.881 1.00 0.00 O +ATOM 66 N HP4 5 0.986 -1.001 -3.465 1.00 0.00 N +ATOM 67 H HP4 5 0.422 -1.171 -2.641 1.00 0.00 H +ATOM 68 CA HP4 5 0.948 0.337 -4.071 1.00 0.00 C +ATOM 69 HA HP4 5 0.900 0.242 -5.158 1.00 0.00 H +ATOM 70 CB HP4 5 -0.331 1.057 -3.592 1.00 0.00 C +ATOM 71 HB2 HP4 5 -1.198 0.577 -4.051 1.00 0.00 H +ATOM 72 HB3 HP4 5 -0.437 0.939 -2.513 1.00 0.00 H +ATOM 73 CG HP4 5 -0.381 2.538 -3.886 1.00 0.00 C +ATOM 74 ND1 HP4 5 0.101 3.553 -3.075 1.00 0.00 N +ATOM 75 HD1 HP4 5 0.556 3.442 -2.157 1.00 0.00 H +ATOM 76 CE1 HP4 5 -0.172 4.730 -3.674 1.00 0.00 C +ATOM 77 HE1 HP4 5 0.049 5.712 -3.264 1.00 0.00 H +ATOM 78 NE2 HP4 5 -0.792 4.488 -4.849 1.00 0.00 N +ATOM 79 HE2 HP4 5 -1.130 5.194 -5.500 1.00 0.00 H +ATOM 80 CD2 HP4 5 -0.931 3.118 -4.997 1.00 0.00 C +ATOM 81 HD2 HP4 5 -1.404 2.600 -5.825 1.00 0.00 H +ATOM 82 C HP4 5 2.219 1.130 -3.753 1.00 0.00 C +ATOM 83 O HP4 5 2.851 1.682 -4.651 1.00 0.00 O +ATOM 84 N D05 6 2.611 1.180 -2.480 1.00 0.00 N +ATOM 85 H D05 6 2.043 0.702 -1.789 1.00 0.00 H +ATOM 86 CA D05 6 3.661 2.094 -2.009 1.00 0.00 C +ATOM 87 HA D05 6 3.450 3.092 -2.398 1.00 0.00 H +ATOM 88 CB D05 6 3.620 2.182 -0.476 1.00 0.00 C +ATOM 89 HB2 D05 6 3.693 1.176 -0.061 1.00 0.00 H +ATOM 90 HB3 D05 6 4.496 2.742 -0.145 1.00 0.00 H +ATOM 91 CG D05 6 2.363 2.887 0.081 1.00 0.00 C +ATOM 92 OD1 D05 6 1.529 3.406 -0.704 1.00 0.00 O +ATOM 93 OD2 D05 6 2.229 2.948 1.327 1.00 0.00 O +ATOM 94 C D05 6 5.069 1.727 -2.514 1.00 0.00 C +ATOM 95 O D05 6 5.817 2.622 -2.911 1.00 0.00 O +ATOM 96 N Y02 7 5.429 0.437 -2.583 1.00 0.00 N +ATOM 97 H Y02 7 4.795 -0.275 -2.230 1.00 0.00 H +ATOM 98 CA Y02 7 6.725 0.021 -3.145 1.00 0.00 C +ATOM 99 HA Y02 7 7.494 0.636 -2.675 1.00 0.00 H +ATOM 100 CB Y02 7 7.048 -1.447 -2.791 1.00 0.00 C +ATOM 101 HB2 Y02 7 8.091 -1.483 -2.475 1.00 0.00 H +ATOM 102 HB3 Y02 7 6.460 -1.762 -1.928 1.00 0.00 H +ATOM 103 CG Y02 7 6.879 -2.456 -3.916 1.00 0.00 C +ATOM 104 CD1 Y02 7 5.642 -3.098 -4.113 1.00 0.00 C +ATOM 105 HD1 Y02 7 4.821 -2.888 -3.447 1.00 0.00 H +ATOM 106 CE1 Y02 7 5.471 -4.007 -5.175 1.00 0.00 C +ATOM 107 HE1 Y02 7 4.517 -4.494 -5.323 1.00 0.00 H +ATOM 108 CZ Y02 7 6.546 -4.276 -6.052 1.00 0.00 C +ATOM 109 OH Y02 7 6.397 -5.152 -7.086 1.00 0.00 O +ATOM 110 HH Y02 7 5.520 -5.576 -7.099 1.00 0.00 H +ATOM 111 CE2 Y02 7 7.787 -3.633 -5.854 1.00 0.00 C +ATOM 112 HE2 Y02 7 8.607 -3.841 -6.528 1.00 0.00 H +ATOM 113 CD2 Y02 7 7.953 -2.727 -4.788 1.00 0.00 C +ATOM 114 HD2 Y02 7 8.905 -2.231 -4.647 1.00 0.00 H +ATOM 115 C Y02 7 6.798 0.295 -4.659 1.00 0.00 C +ATOM 116 O Y02 7 7.835 0.741 -5.153 1.00 0.00 O +ATOM 117 N K14 8 5.689 0.103 -5.392 1.00 0.00 N +ATOM 118 H K14 8 4.880 -0.287 -4.925 1.00 0.00 H +ATOM 119 CA K14 8 5.586 0.412 -6.828 1.00 0.00 C +ATOM 120 HA K14 8 6.426 -0.060 -7.341 1.00 0.00 H +ATOM 121 CB K14 8 4.283 -0.198 -7.378 1.00 0.00 C +ATOM 122 HB2 K14 8 4.255 -1.251 -7.092 1.00 0.00 H +ATOM 123 HB3 K14 8 3.423 0.304 -6.933 1.00 0.00 H +ATOM 124 CG K14 8 4.196 -0.095 -8.911 1.00 0.00 C +ATOM 125 HG2 K14 8 4.203 0.958 -9.198 1.00 0.00 H +ATOM 126 HG3 K14 8 5.070 -0.574 -9.355 1.00 0.00 H +ATOM 127 CD K14 8 2.923 -0.734 -9.491 1.00 0.00 C +ATOM 128 HD2 K14 8 2.047 -0.278 -9.024 1.00 0.00 H +ATOM 129 HD3 K14 8 2.893 -0.514 -10.560 1.00 0.00 H +ATOM 130 CE K14 8 2.885 -2.258 -9.291 1.00 0.00 C +ATOM 131 HE2 K14 8 3.807 -2.688 -9.699 1.00 0.00 H +ATOM 132 HE3 K14 8 2.862 -2.477 -8.218 1.00 0.00 H +ATOM 133 NZ K14 8 1.702 -2.871 -9.960 1.00 0.00 N +ATOM 134 HZ1 K14 8 1.711 -2.704 -10.960 1.00 0.00 H +ATOM 135 HZ2 K14 8 1.685 -3.875 -9.826 1.00 0.00 H +ATOM 136 HZ3 K14 8 0.832 -2.503 -9.594 1.00 0.00 H +ATOM 137 C K14 8 5.694 1.919 -7.090 1.00 0.00 C +ATOM 138 O K14 8 6.419 2.329 -7.996 1.00 0.00 O +ATOM 139 N L04 9 5.053 2.743 -6.255 1.00 0.00 N +ATOM 140 H L04 9 4.436 2.323 -5.566 1.00 0.00 H +ATOM 141 CA L04 9 5.176 4.206 -6.274 1.00 0.00 C +ATOM 142 HA L04 9 4.885 4.557 -7.265 1.00 0.00 H +ATOM 143 CB L04 9 4.176 4.797 -5.259 1.00 0.00 C +ATOM 144 HB2 L04 9 3.201 4.365 -5.490 1.00 0.00 H +ATOM 145 HB3 L04 9 4.440 4.482 -4.249 1.00 0.00 H +ATOM 146 CG L04 9 4.035 6.335 -5.291 1.00 0.00 C +ATOM 147 HG L04 9 4.059 6.682 -6.324 1.00 0.00 H +ATOM 148 CD1 L04 9 2.687 6.730 -4.685 1.00 0.00 C +ATOM 149 HD11 L04 9 2.626 6.387 -3.651 1.00 0.00 H +ATOM 150 HD12 L04 9 2.569 7.814 -4.713 1.00 0.00 H +ATOM 151 HD13 L04 9 1.879 6.285 -5.267 1.00 0.00 H +ATOM 152 CD2 L04 9 5.112 7.068 -4.484 1.00 0.00 C +ATOM 153 HD21 L04 9 6.089 6.954 -4.947 1.00 0.00 H +ATOM 154 HD22 L04 9 4.888 8.135 -4.454 1.00 0.00 H +ATOM 155 HD23 L04 9 5.147 6.684 -3.464 1.00 0.00 H +ATOM 156 C L04 9 6.631 4.644 -6.034 1.00 0.00 C +ATOM 157 O L04 9 7.161 5.448 -6.799 1.00 0.00 O +ATOM 158 N K30 10 7.308 4.074 -5.031 1.00 0.00 N +ATOM 159 H K30 10 6.809 3.448 -4.404 1.00 0.00 H +ATOM 160 CA K30 10 8.728 4.341 -4.764 1.00 0.00 C +ATOM 161 HA K30 10 8.852 5.416 -4.623 1.00 0.00 H +ATOM 162 CB K30 10 9.125 3.638 -3.454 1.00 0.00 C +ATOM 163 HB2 K30 10 8.426 3.937 -2.671 1.00 0.00 H +ATOM 164 HB3 K30 10 9.056 2.557 -3.581 1.00 0.00 H +ATOM 165 CG K30 10 10.548 4.001 -3.001 1.00 0.00 C +ATOM 166 HG2 K30 10 11.268 3.665 -3.748 1.00 0.00 H +ATOM 167 HG3 K30 10 10.627 5.084 -2.895 1.00 0.00 H +ATOM 168 CD K30 10 10.879 3.338 -1.659 1.00 0.00 C +ATOM 169 HD2 K30 10 10.169 3.675 -0.902 1.00 0.00 H +ATOM 170 HD3 K30 10 10.808 2.254 -1.763 1.00 0.00 H +ATOM 171 CE K30 10 12.300 3.718 -1.229 1.00 0.00 C +ATOM 172 HE2 K30 10 13.005 3.386 -1.990 1.00 0.00 H +ATOM 173 HE3 K30 10 12.366 4.802 -1.133 1.00 0.00 H +ATOM 174 NZ K30 10 12.669 3.108 0.061 1.00 0.00 N +ATOM 175 HZ2 K30 10 13.598 3.439 0.303 1.00 0.00 H +ATOM 176 HZ3 K30 10 12.043 3.478 0.769 1.00 0.00 H +ATOM 177 C K30 10 9.623 3.923 -5.946 1.00 0.00 C +ATOM 178 O K30 10 10.498 4.689 -6.351 1.00 0.00 O +ATOM 179 N A01 11 9.375 2.755 -6.546 1.00 0.00 N +ATOM 180 H A01 11 8.669 2.148 -6.143 1.00 0.00 H +ATOM 181 CA A01 11 10.131 2.251 -7.693 1.00 0.00 C +ATOM 182 HA A01 11 11.189 2.227 -7.422 1.00 0.00 H +ATOM 183 CB A01 11 9.688 0.811 -7.984 1.00 0.00 C +ATOM 184 HB1 A01 11 9.844 0.189 -7.101 1.00 0.00 H +ATOM 185 HB2 A01 11 8.634 0.785 -8.260 1.00 0.00 H +ATOM 186 HB3 A01 11 10.279 0.405 -8.807 1.00 0.00 H +ATOM 187 C A01 11 9.999 3.153 -8.936 1.00 0.00 C +ATOM 188 O A01 11 11.014 3.518 -9.532 1.00 0.00 O +ATOM 189 N K23 12 8.781 3.575 -9.310 1.00 0.00 N +ATOM 190 H K23 12 7.967 3.222 -8.812 1.00 0.00 H +ATOM 191 CA K23 12 8.589 4.493 -10.446 1.00 0.00 C +ATOM 192 HA K23 12 9.203 4.119 -11.267 1.00 0.00 H +ATOM 193 CB K23 12 7.134 4.453 -10.955 1.00 0.00 C +ATOM 194 HB2 K23 12 7.105 4.945 -11.928 1.00 0.00 H +ATOM 195 HB3 K23 12 6.851 3.409 -11.103 1.00 0.00 H +ATOM 196 CG K23 12 6.105 5.125 -10.033 1.00 0.00 C +ATOM 197 HG2 K23 12 6.212 4.708 -9.038 1.00 0.00 H +ATOM 198 HG3 K23 12 6.300 6.197 -9.980 1.00 0.00 H +ATOM 199 CD K23 12 4.655 4.903 -10.483 1.00 0.00 C +ATOM 200 HD2 K23 12 4.456 3.832 -10.542 1.00 0.00 H +ATOM 201 HD3 K23 12 3.992 5.338 -9.733 1.00 0.00 H +ATOM 202 CE K23 12 4.372 5.557 -11.841 1.00 0.00 C +ATOM 203 HE2 K23 12 4.594 6.622 -11.779 1.00 0.00 H +ATOM 204 HE3 K23 12 5.010 5.104 -12.599 1.00 0.00 H +ATOM 205 NZ K23 12 2.968 5.388 -12.253 1.00 0.00 N +ATOM 206 HZ2 K23 12 2.865 5.809 -13.172 1.00 0.00 H +ATOM 207 HZ3 K23 12 2.799 4.395 -12.376 1.00 0.00 H +ATOM 208 C K23 12 9.096 5.916 -10.150 1.00 0.00 C +ATOM 209 O K23 12 9.643 6.561 -11.043 1.00 0.00 O +ATOM 210 N D07 13 9.004 6.384 -8.898 1.00 0.00 N +ATOM 211 H D07 13 8.504 5.829 -8.209 1.00 0.00 H +ATOM 212 CA D07 13 9.587 7.664 -8.467 1.00 0.00 C +ATOM 213 HA D07 13 9.213 8.451 -9.125 1.00 0.00 H +ATOM 214 CB D07 13 9.120 7.984 -7.039 1.00 0.00 C +ATOM 215 HB2 D07 13 8.030 8.019 -7.013 1.00 0.00 H +ATOM 216 HB3 D07 13 9.452 7.201 -6.357 1.00 0.00 H +ATOM 217 CG D07 13 9.650 9.333 -6.554 1.00 0.00 C +ATOM 218 OD1 D07 13 9.240 10.422 -6.948 1.00 0.00 O +ATOM 219 OD2 D07 13 10.650 9.244 -5.641 1.00 0.00 O +ATOM 220 HD2 D07 13 10.934 10.140 -5.364 1.00 0.00 H +ATOM 221 C D07 13 11.126 7.659 -8.567 1.00 0.00 C +ATOM 222 O D07 13 11.717 8.631 -9.040 1.00 0.00 O +ATOM 223 N Y03 14 11.778 6.548 -8.201 1.00 0.00 N +ATOM 224 H Y03 14 11.255 5.801 -7.755 1.00 0.00 H +ATOM 225 CA Y03 14 13.214 6.343 -8.422 1.00 0.00 C +ATOM 226 HA Y03 14 13.761 7.181 -7.988 1.00 0.00 H +ATOM 227 CB Y03 14 13.657 5.061 -7.697 1.00 0.00 C +ATOM 228 HB2 Y03 14 13.441 5.171 -6.633 1.00 0.00 H +ATOM 229 HB3 Y03 14 13.068 4.218 -8.058 1.00 0.00 H +ATOM 230 CG Y03 14 15.128 4.720 -7.862 1.00 0.00 C +ATOM 231 CD1 Y03 14 16.067 5.182 -6.918 1.00 0.00 C +ATOM 232 HD1 Y03 14 15.740 5.777 -6.075 1.00 0.00 H +ATOM 233 CE1 Y03 14 17.434 4.874 -7.070 1.00 0.00 C +ATOM 234 HE1 Y03 14 18.152 5.234 -6.347 1.00 0.00 H +ATOM 235 CZ Y03 14 17.867 4.108 -8.176 1.00 0.00 C +ATOM 236 OH Y03 14 19.187 3.808 -8.338 1.00 0.00 O +ATOM 237 HH Y03 14 19.747 4.179 -7.633 1.00 0.00 H +ATOM 238 CE2 Y03 14 16.924 3.641 -9.117 1.00 0.00 C +ATOM 239 HE2 Y03 14 17.259 3.049 -9.957 1.00 0.00 H +ATOM 240 CD2 Y03 14 15.557 3.941 -8.956 1.00 0.00 C +ATOM 241 HD2 Y03 14 14.839 3.572 -9.677 1.00 0.00 H +ATOM 242 C Y03 14 13.550 6.301 -9.923 1.00 0.00 C +ATOM 243 O Y03 14 14.415 7.045 -10.385 1.00 0.00 O +ATOM 244 N A01 15 12.833 5.490 -10.710 1.00 0.00 N +ATOM 245 H A01 15 12.140 4.884 -10.280 1.00 0.00 H +ATOM 246 CA A01 15 13.097 5.323 -12.141 1.00 0.00 C +ATOM 247 HA A01 15 14.130 4.991 -12.262 1.00 0.00 H +ATOM 248 CB A01 15 12.178 4.221 -12.683 1.00 0.00 C +ATOM 249 HB1 A01 15 12.340 3.295 -12.128 1.00 0.00 H +ATOM 250 HB2 A01 15 11.133 4.518 -12.589 1.00 0.00 H +ATOM 251 HB3 A01 15 12.402 4.042 -13.735 1.00 0.00 H +ATOM 252 C A01 15 12.942 6.634 -12.937 1.00 0.00 C +ATOM 253 O A01 15 13.825 6.982 -13.720 1.00 0.00 O +ATOM 254 N T02 16 11.867 7.401 -12.710 1.00 0.00 N +ATOM 255 H T02 16 11.158 7.064 -12.063 1.00 0.00 H +ATOM 256 CA T02 16 11.626 8.670 -13.427 1.00 0.00 C +ATOM 257 HA T02 16 11.737 8.459 -14.488 1.00 0.00 H +ATOM 258 CB T02 16 10.178 9.156 -13.228 1.00 0.00 C +ATOM 259 HB T02 16 9.517 8.291 -13.302 1.00 0.00 H +ATOM 260 CG2 T02 16 9.919 9.853 -11.892 1.00 0.00 C +ATOM 261 HG21 T02 16 10.459 10.799 -11.839 1.00 0.00 H +ATOM 262 HG22 T02 16 8.852 10.045 -11.779 1.00 0.00 H +ATOM 263 HG23 T02 16 10.242 9.210 -11.079 1.00 0.00 H +ATOM 264 OG1 T02 16 9.835 10.057 -14.260 1.00 0.00 O +ATOM 265 HG1 T02 16 8.880 10.252 -14.196 1.00 0.00 H +ATOM 266 C T02 16 12.661 9.758 -13.090 1.00 0.00 C +ATOM 267 O T02 16 12.957 10.615 -13.925 1.00 0.00 O +ATOM 268 N M08 17 13.280 9.693 -11.901 1.00 0.00 N +ATOM 269 H M08 17 12.988 8.978 -11.248 1.00 0.00 H +ATOM 270 CA M08 17 14.442 10.511 -11.540 1.00 0.00 C +ATOM 271 HA M08 17 14.268 11.537 -11.872 1.00 0.00 H +ATOM 272 CB M08 17 14.592 10.537 -10.008 1.00 0.00 C +ATOM 273 HB2 M08 17 13.693 10.980 -9.577 1.00 0.00 H +ATOM 274 HB3 M08 17 14.687 9.521 -9.626 1.00 0.00 H +ATOM 275 CG M08 17 15.807 11.344 -9.538 1.00 0.00 C +ATOM 276 HG2 M08 17 16.714 10.870 -9.914 1.00 0.00 H +ATOM 277 HG3 M08 17 15.746 12.351 -9.952 1.00 0.00 H +ATOM 278 SD M08 17 15.939 11.464 -7.734 1.00 0.00 S +ATOM 279 CE M08 17 17.536 12.312 -7.603 1.00 0.00 C +ATOM 280 HE1 M08 17 17.483 13.279 -8.106 1.00 0.00 H +ATOM 281 HE2 M08 17 17.783 12.467 -6.553 1.00 0.00 H +ATOM 282 HE3 M08 17 18.314 11.705 -8.067 1.00 0.00 H +ATOM 283 C M08 17 15.718 10.015 -12.243 1.00 0.00 C +ATOM 284 O M08 17 16.315 10.744 -13.036 1.00 0.00 O +ATOM 285 N P04 18 16.147 8.777 -11.984 1.00 0.00 N +ATOM 286 H P04 18 15.600 8.191 -11.361 1.00 0.00 H +ATOM 287 CA P04 18 17.466 8.288 -12.410 1.00 0.00 C +ATOM 288 HA P04 18 18.169 9.111 -12.279 1.00 0.00 H +ATOM 289 CB P04 18 17.934 7.174 -11.463 1.00 0.00 C +ATOM 290 HB2 P04 18 17.141 6.434 -11.338 1.00 0.00 H +ATOM 291 HB3 P04 18 18.793 6.665 -11.903 1.00 0.00 H +ATOM 292 CG P04 18 18.360 7.723 -10.111 1.00 0.00 C +ATOM 293 CD1 P04 18 17.494 7.672 -9.003 1.00 0.00 C +ATOM 294 HD1 P04 18 16.531 7.194 -9.090 1.00 0.00 H +ATOM 295 CE1 P04 18 17.880 8.238 -7.775 1.00 0.00 C +ATOM 296 HE1 P04 18 17.209 8.198 -6.929 1.00 0.00 H +ATOM 297 CZ P04 18 19.137 8.855 -7.647 1.00 0.00 C +ATOM 298 HZ P04 18 19.433 9.290 -6.701 1.00 0.00 H +ATOM 299 CE2 P04 18 20.007 8.906 -8.749 1.00 0.00 C +ATOM 300 HE2 P04 18 20.974 9.382 -8.653 1.00 0.00 H +ATOM 301 CD2 P04 18 19.619 8.343 -9.978 1.00 0.00 C +ATOM 302 HD2 P04 18 20.289 8.393 -10.826 1.00 0.00 H +ATOM 303 C P04 18 17.586 7.926 -13.904 1.00 0.00 C +ATOM 304 O P04 18 18.707 7.743 -14.386 1.00 0.00 O +ATOM 305 N K22 19 16.484 7.902 -14.669 1.00 0.00 N +ATOM 306 H K22 19 15.576 7.936 -14.219 1.00 0.00 H +ATOM 307 CA K22 19 16.540 7.913 -16.142 1.00 0.00 C +ATOM 308 HA K22 19 17.311 7.205 -16.452 1.00 0.00 H +ATOM 309 CB K22 19 15.209 7.406 -16.734 1.00 0.00 C +ATOM 310 HB2 K22 19 15.386 7.125 -17.773 1.00 0.00 H +ATOM 311 HB3 K22 19 14.902 6.506 -16.200 1.00 0.00 H +ATOM 312 CG K22 19 14.067 8.438 -16.709 1.00 0.00 C +ATOM 313 HG2 K22 19 13.929 8.805 -15.694 1.00 0.00 H +ATOM 314 HG3 K22 19 14.330 9.278 -17.352 1.00 0.00 H +ATOM 315 CD K22 19 12.756 7.814 -17.207 1.00 0.00 C +ATOM 316 HD2 K22 19 12.906 7.367 -18.192 1.00 0.00 H +ATOM 317 HD3 K22 19 12.460 7.025 -16.515 1.00 0.00 H +ATOM 318 CE K22 19 11.618 8.840 -17.284 1.00 0.00 C +ATOM 319 HE2 K22 19 10.680 8.310 -17.447 1.00 0.00 H +ATOM 320 HE3 K22 19 11.558 9.380 -16.340 1.00 0.00 H +ATOM 321 NZ K22 19 11.796 9.811 -18.379 1.00 0.00 N +ATOM 322 HZ2 K22 19 11.010 10.453 -18.350 1.00 0.00 H +ATOM 323 HZ3 K22 19 12.621 10.362 -18.174 1.00 0.00 H +ATOM 324 C K22 19 16.938 9.287 -16.729 1.00 0.00 C +ATOM 325 O K22 19 17.364 9.356 -17.884 1.00 0.00 O +ATOM 326 N D02 20 16.795 10.372 -15.956 1.00 0.00 N +ATOM 327 H D02 20 16.458 10.239 -15.012 1.00 0.00 H +ATOM 328 CA D02 20 17.050 11.758 -16.381 1.00 0.00 C +ATOM 329 HA D02 20 17.242 11.780 -17.455 1.00 0.00 H +ATOM 330 CB D02 20 15.786 12.589 -16.124 1.00 0.00 C +ATOM 331 HB2 D02 20 14.936 12.105 -16.610 1.00 0.00 H +ATOM 332 HB3 D02 20 15.585 12.619 -15.050 1.00 0.00 H +ATOM 333 CG D02 20 15.927 14.019 -16.673 1.00 0.00 C +ATOM 334 OD1 D02 20 15.907 14.193 -17.916 1.00 0.00 O +ATOM 335 OD2 D02 20 16.038 14.977 -15.870 1.00 0.00 O +ATOM 336 C D02 20 18.276 12.392 -15.690 1.00 0.00 C +ATOM 337 O D02 20 19.031 13.135 -16.324 1.00 0.00 O +ATOM 338 N E07 21 18.512 12.076 -14.412 1.00 0.00 N +ATOM 339 H E07 21 17.829 11.501 -13.934 1.00 0.00 H +ATOM 340 CA E07 21 19.717 12.475 -13.670 1.00 0.00 C +ATOM 341 HA E07 21 19.836 13.555 -13.763 1.00 0.00 H +ATOM 342 CB E07 21 19.567 12.126 -12.177 1.00 0.00 C +ATOM 343 HB2 E07 21 19.274 11.080 -12.084 1.00 0.00 H +ATOM 344 HB3 E07 21 20.534 12.233 -11.686 1.00 0.00 H +ATOM 345 CG E07 21 18.543 12.995 -11.429 1.00 0.00 C +ATOM 346 HG2 E07 21 17.558 12.849 -11.877 1.00 0.00 H +ATOM 347 HG3 E07 21 18.491 12.639 -10.399 1.00 0.00 H +ATOM 348 CD E07 21 18.900 14.499 -11.418 1.00 0.00 C +ATOM 349 OE1 E07 21 20.103 14.857 -11.365 1.00 0.00 O +ATOM 350 OE2 E07 21 17.972 15.344 -11.444 1.00 0.00 O +ATOM 351 C E07 21 21.008 11.832 -14.224 1.00 0.00 C +ATOM 352 O E07 21 21.002 10.707 -14.739 1.00 0.00 O +ATOM 353 N NME 22 22.137 12.543 -14.086 1.00 0.00 N +ATOM 354 H NME 22 22.073 13.448 -13.638 1.00 0.00 H +ATOM 355 CH3 NME 22 23.456 12.103 -14.540 1.00 0.00 C +ATOM 356 HH31 NME 22 23.443 11.935 -15.619 1.00 0.00 H +ATOM 357 HH32 NME 22 24.205 12.864 -14.312 1.00 0.00 H +ATOM 358 HH33 NME 22 23.733 11.173 -14.041 1.00 0.00 H +CONECT 1 2 +CONECT 2 5 3 1 4 +CONECT 3 2 +CONECT 4 2 +CONECT 5 6 7 2 +CONECT 6 5 +CONECT 7 9 5 8 +CONECT 8 7 +CONECT 9 10 26 11 7 +CONECT 10 9 +CONECT 11 12 9 13 14 +CONECT 12 11 +CONECT 13 11 +CONECT 14 11 16 17 15 +CONECT 15 14 +CONECT 16 14 +CONECT 17 19 14 20 18 +CONECT 18 17 +CONECT 19 17 +CONECT 20 21 17 23 22 +CONECT 21 20 +CONECT 22 20 +CONECT 23 20 24 25 +CONECT 24 23 +CONECT 25 23 +CONECT 26 27 9 28 +CONECT 27 26 +CONECT 28 26 30 29 +CONECT 29 28 +CONECT 30 50 31 28 32 +CONECT 31 30 +CONECT 32 30 35 33 34 +CONECT 33 32 +CONECT 34 32 +CONECT 35 49 32 36 +CONECT 36 35 38 37 +CONECT 37 36 +CONECT 38 40 39 36 +CONECT 39 38 +CONECT 40 41 49 38 +CONECT 41 43 42 40 +CONECT 42 41 +CONECT 43 44 45 41 +CONECT 44 43 +CONECT 45 46 43 47 +CONECT 46 45 +CONECT 47 45 48 49 +CONECT 48 47 +CONECT 49 47 40 35 +CONECT 50 51 52 30 +CONECT 51 50 +CONECT 52 54 53 50 +CONECT 53 52 +CONECT 54 64 56 55 52 +CONECT 55 54 +CONECT 56 57 62 54 58 +CONECT 57 56 +CONECT 58 56 60 61 59 +CONECT 59 58 +CONECT 60 58 +CONECT 61 58 +CONECT 62 56 63 +CONECT 63 62 +CONECT 64 65 66 54 +CONECT 65 64 +CONECT 66 68 64 67 +CONECT 67 66 +CONECT 68 69 82 70 66 +CONECT 69 68 +CONECT 70 68 71 73 72 +CONECT 71 70 +CONECT 72 70 +CONECT 73 80 70 74 +CONECT 74 73 76 75 +CONECT 75 74 +CONECT 76 78 77 74 +CONECT 77 76 +CONECT 78 79 80 76 +CONECT 79 78 +CONECT 80 81 78 73 +CONECT 81 80 +CONECT 82 83 68 84 +CONECT 83 82 +CONECT 84 82 86 85 +CONECT 85 84 +CONECT 86 94 84 87 88 +CONECT 87 86 +CONECT 88 86 90 89 91 +CONECT 89 88 +CONECT 90 88 +CONECT 91 92 88 93 +CONECT 92 91 +CONECT 93 91 +CONECT 94 95 96 86 +CONECT 95 94 +CONECT 96 98 94 97 +CONECT 97 96 +CONECT 98 115 100 99 96 +CONECT 99 98 +CONECT 100 103 98 101 102 +CONECT 101 100 +CONECT 102 100 +CONECT 103 113 104 100 +CONECT 104 106 103 105 +CONECT 105 104 +CONECT 106 108 107 104 +CONECT 107 106 +CONECT 108 109 111 106 +CONECT 109 110 108 +CONECT 110 109 +CONECT 111 112 108 113 +CONECT 112 111 +CONECT 113 111 114 103 +CONECT 114 113 +CONECT 115 117 116 98 +CONECT 116 115 +CONECT 117 119 118 115 +CONECT 118 117 +CONECT 119 121 120 137 117 +CONECT 120 119 +CONECT 121 124 122 123 119 +CONECT 122 121 +CONECT 123 121 +CONECT 124 127 126 125 121 +CONECT 125 124 +CONECT 126 124 +CONECT 127 129 130 128 124 +CONECT 128 127 +CONECT 129 127 +CONECT 130 133 131 127 132 +CONECT 131 130 +CONECT 132 130 +CONECT 133 134 135 136 130 +CONECT 134 133 +CONECT 135 133 +CONECT 136 133 +CONECT 137 138 119 139 +CONECT 138 137 +CONECT 139 137 141 140 +CONECT 140 139 +CONECT 141 142 139 156 143 +CONECT 142 141 +CONECT 143 141 144 146 145 +CONECT 144 143 +CONECT 145 143 +CONECT 146 147 143 148 152 +CONECT 147 146 +CONECT 148 146 151 150 149 +CONECT 149 148 +CONECT 150 148 +CONECT 151 148 +CONECT 152 146 153 154 155 +CONECT 153 152 +CONECT 154 152 +CONECT 155 152 +CONECT 156 157 141 158 +CONECT 157 156 +CONECT 158 156 160 159 +CONECT 159 158 +CONECT 160 177 158 161 162 +CONECT 161 160 +CONECT 162 160 164 165 163 +CONECT 163 162 +CONECT 164 162 +CONECT 165 166 162 167 168 +CONECT 166 165 +CONECT 167 165 +CONECT 168 165 170 171 169 +CONECT 169 168 +CONECT 170 168 +CONECT 171 172 168 173 174 +CONECT 172 171 +CONECT 173 171 +CONECT 174 171 175 176 +CONECT 175 174 +CONECT 176 174 +CONECT 177 179 178 160 +CONECT 178 177 +CONECT 179 181 180 177 +CONECT 180 179 +CONECT 181 187 183 182 179 +CONECT 182 181 +CONECT 183 186 185 181 184 +CONECT 184 183 +CONECT 185 183 +CONECT 186 183 +CONECT 187 188 189 181 +CONECT 188 187 +CONECT 189 191 187 190 +CONECT 190 189 +CONECT 191 192 193 208 189 +CONECT 192 191 +CONECT 193 194 195 191 196 +CONECT 194 193 +CONECT 195 193 +CONECT 196 193 199 198 197 +CONECT 197 196 +CONECT 198 196 +CONECT 199 202 200 196 201 +CONECT 200 199 +CONECT 201 199 +CONECT 202 204 205 203 199 +CONECT 203 202 +CONECT 204 202 +CONECT 205 206 207 202 +CONECT 206 205 +CONECT 207 205 +CONECT 208 209 191 210 +CONECT 209 208 +CONECT 210 208 212 211 +CONECT 211 210 +CONECT 212 213 210 221 214 +CONECT 213 212 +CONECT 214 212 215 217 216 +CONECT 215 214 +CONECT 216 214 +CONECT 217 214 218 219 +CONECT 218 217 +CONECT 219 217 220 +CONECT 220 219 +CONECT 221 222 212 223 +CONECT 222 221 +CONECT 223 221 225 224 +CONECT 224 223 +CONECT 225 242 223 226 227 +CONECT 226 225 +CONECT 227 225 229 230 228 +CONECT 228 227 +CONECT 229 227 +CONECT 230 240 227 231 +CONECT 231 230 233 232 +CONECT 232 231 +CONECT 233 235 231 234 +CONECT 234 233 +CONECT 235 238 236 233 +CONECT 236 235 237 +CONECT 237 236 +CONECT 238 239 240 235 +CONECT 239 238 +CONECT 240 241 238 230 +CONECT 241 240 +CONECT 242 244 243 225 +CONECT 243 242 +CONECT 244 246 245 242 +CONECT 245 244 +CONECT 246 252 248 247 244 +CONECT 247 246 +CONECT 248 251 250 246 249 +CONECT 249 248 +CONECT 250 248 +CONECT 251 248 +CONECT 252 253 254 246 +CONECT 253 252 +CONECT 254 256 252 255 +CONECT 255 254 +CONECT 256 257 258 266 254 +CONECT 257 256 +CONECT 258 264 256 259 260 +CONECT 259 258 +CONECT 260 258 261 262 263 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 265 258 +CONECT 265 264 +CONECT 266 267 256 268 +CONECT 267 266 +CONECT 268 266 270 269 +CONECT 269 268 +CONECT 270 283 268 271 272 +CONECT 271 270 +CONECT 272 270 274 273 275 +CONECT 273 272 +CONECT 274 272 +CONECT 275 272 277 276 278 +CONECT 276 275 +CONECT 277 275 +CONECT 278 275 279 +CONECT 279 280 282 278 281 +CONECT 280 279 +CONECT 281 279 +CONECT 282 279 +CONECT 283 284 285 270 +CONECT 284 283 +CONECT 285 287 283 286 +CONECT 286 285 +CONECT 287 303 288 285 289 +CONECT 288 287 +CONECT 289 287 291 290 292 +CONECT 290 289 +CONECT 291 289 +CONECT 292 289 301 293 +CONECT 293 292 294 295 +CONECT 294 293 +CONECT 295 293 297 296 +CONECT 296 295 +CONECT 297 299 295 298 +CONECT 298 297 +CONECT 299 301 300 297 +CONECT 300 299 +CONECT 301 302 292 299 +CONECT 302 301 +CONECT 303 305 304 287 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 309 324 308 305 +CONECT 308 307 +CONECT 309 310 312 311 307 +CONECT 310 309 +CONECT 311 309 +CONECT 312 314 315 309 313 +CONECT 313 312 +CONECT 314 312 +CONECT 315 316 318 312 317 +CONECT 316 315 +CONECT 317 315 +CONECT 318 321 319 315 320 +CONECT 319 318 +CONECT 320 318 +CONECT 321 322 323 318 +CONECT 322 321 +CONECT 323 321 +CONECT 324 325 307 326 +CONECT 325 324 +CONECT 326 324 328 327 +CONECT 327 326 +CONECT 328 329 330 326 336 +CONECT 329 328 +CONECT 330 333 331 328 332 +CONECT 331 330 +CONECT 332 330 +CONECT 333 334 330 335 +CONECT 334 333 +CONECT 335 333 +CONECT 336 328 337 338 +CONECT 337 336 +CONECT 338 336 339 340 +CONECT 339 338 +CONECT 340 338 351 341 342 +CONECT 341 340 +CONECT 342 340 343 344 345 +CONECT 343 342 +CONECT 344 342 +CONECT 345 342 346 348 347 +CONECT 346 345 +CONECT 347 345 +CONECT 348 350 345 349 +CONECT 349 348 +CONECT 350 348 +CONECT 351 352 353 340 +CONECT 352 351 +CONECT 353 355 351 354 +CONECT 354 353 +CONECT 355 356 357 353 358 +CONECT 356 355 +CONECT 357 355 +CONECT 358 355 +MASTER 0 0 0 0 0 0 0 0 358 0 358 0 +END diff --git a/tests/nick_tests/helical_stability/ga_input.in b/tests/nick_tests/helical_stability/ga_input.in index d5fa516..b9d9395 100644 --- a/tests/nick_tests/helical_stability/ga_input.in +++ b/tests/nick_tests/helical_stability/ga_input.in @@ -4,11 +4,11 @@ composition_optimization = True composition_residue_indexes = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 composition_lower_bounds = 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 composition_upper_bounds = 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 -composition_library = /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library_Flat +composition_library = ../../../share/flat/ min_fitness = -500.0 [MOLECULE] -initial_molecule = /share/lcbcsrv5/lcbcdata/nbrownin/EVOLVE_A20/ALA20.pdb +initial_molecule = ALA20.pdb [IO] store_intermediate_mol = True @@ -48,5 +48,8 @@ poly_eta = 7.0 replacer = elitism elitist_factor = 0.25 +[GENERATOR] +generator = random + [DEBUG] verbose = True diff --git a/tests/nick_tests/helical_stability/initial_fitness.dat b/tests/nick_tests/helical_stability/initial_fitness.dat index d4af323..043f389 100644 --- a/tests/nick_tests/helical_stability/initial_fitness.dat +++ b/tests/nick_tests/helical_stability/initial_fitness.dat @@ -1 +1 @@ --64.173 \ No newline at end of file +"[-64.173]" \ No newline at end of file diff --git a/tests/nick_tests/helical_stability/run_example.sh b/tests/nick_tests/helical_stability/run_example.sh new file mode 100755 index 0000000..b15a1cf --- /dev/null +++ b/tests/nick_tests/helical_stability/run_example.sh @@ -0,0 +1 @@ +python -u ../../../main.py -input_file ga_input.in diff --git a/tests/nick_tests/helical_stability/tleap_template.in b/tests/nick_tests/helical_stability/tleap_template.in index e64a795..0108648 100644 --- a/tests/nick_tests/helical_stability/tleap_template.in +++ b/tests/nick_tests/helical_stability/tleap_template.in @@ -2,183 +2,183 @@ source leaprc.protein.ff14SB #source /software/amber/18/intel-17.0.4/dat/leap/cmd/oldff/leaprc.ff99SB #source /software/amber/14/amber14-intelmpi/dat/leap/cmd/leaprc.ff12SB -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ALA/A01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R05.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R06.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R07.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R08.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R09.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R10.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R11.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R12.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R13.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R14.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R15.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R16.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R17.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R18.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R19.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R20.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R21.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R22.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R23.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R24.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R25.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R26.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R27.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ARG/R28.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASP/D01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASP/D02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASP/D03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASP/D04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASP/D05.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASH/D06.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASH/D07.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASH/D08.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASH/D09.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASH/D10.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASN/N01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASN/N02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASN/N03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASN/N04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASN/N05.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASN/N06.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ASN/N07.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/CYS/C01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/CYS/C02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/CYS/C03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLU/E01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLU/E02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLU/E03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLU/E04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLU/E05.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLU/E06.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLU/E07.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLH/E08.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLH/E09.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLH/E10.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLH/E11.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLH/E12.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLH/E13.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLH/E14.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLN/Q01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLN/Q02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLN/Q03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLN/Q04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLN/Q05.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/GLY/G01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HID/HD1.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HID/HD2.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HID/HD3.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HID/HD4.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HID/HD5.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HID/HD6.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HID/HD7.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HID/HD8.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIE/HE1.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIE/HE2.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIE/HE3.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIE/HE4.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIE/HE5.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIE/HE6.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIE/HE7.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIE/HE8.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIP/HP1.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIP/HP2.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIP/HP3.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIP/HP4.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIP/HP5.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIP/HP6.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIP/HP7.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/HIP/HP8.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ILE/I01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ILE/I02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ILE/I03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ILE/I04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/ILE/I05.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LEU/L01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LEU/L02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LEU/L03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LEU/L04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M05.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M06.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M07.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M08.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M09.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M10.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M11.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M12.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/MET/M13.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/PHE/P01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/PHE/P02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/PHE/P03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/PHE/P04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/SER/S01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/SER/S02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/SER/S03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/THR/T01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/THR/T02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/THR/T03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TRP/W01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TRP/W02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TRP/W03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TRP/W04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TRP/W05.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TRP/W06.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TRP/W07.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TYR/Y01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TYR/Y02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TYR/Y03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/TYR/Y04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/VAL/V01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/VAL/V02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/VAL/V03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K01.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K02.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K03.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K04.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K05.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K06.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K07.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K08.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K09.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K10.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K11.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K12.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K13.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K14.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K15.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K16.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K17.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K18.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYS/K19.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K20.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K21.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K22.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K23.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K24.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K25.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K26.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K27.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K28.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K29.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K30.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K31.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K32.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K33.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K34.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K35.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K36.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K37.off -loadOff /share/lcbcsrv5/lcbcdata/nbrownin/Rotamer_Library/LYN/K38.off +loadOff ../../../share/off/ALA/A01.off +loadOff ../../../share/off/ARG/R01.off +loadOff ../../../share/off/ARG/R02.off +loadOff ../../../share/off/ARG/R03.off +loadOff ../../../share/off/ARG/R04.off +loadOff ../../../share/off/ARG/R05.off +loadOff ../../../share/off/ARG/R06.off +loadOff ../../../share/off/ARG/R07.off +loadOff ../../../share/off/ARG/R08.off +loadOff ../../../share/off/ARG/R09.off +loadOff ../../../share/off/ARG/R10.off +loadOff ../../../share/off/ARG/R11.off +loadOff ../../../share/off/ARG/R12.off +loadOff ../../../share/off/ARG/R13.off +loadOff ../../../share/off/ARG/R14.off +loadOff ../../../share/off/ARG/R15.off +loadOff ../../../share/off/ARG/R16.off +loadOff ../../../share/off/ARG/R17.off +loadOff ../../../share/off/ARG/R18.off +loadOff ../../../share/off/ARG/R19.off +loadOff ../../../share/off/ARG/R20.off +loadOff ../../../share/off/ARG/R21.off +loadOff ../../../share/off/ARG/R22.off +loadOff ../../../share/off/ARG/R23.off +loadOff ../../../share/off/ARG/R24.off +loadOff ../../../share/off/ARG/R25.off +loadOff ../../../share/off/ARG/R26.off +loadOff ../../../share/off/ARG/R27.off +loadOff ../../../share/off/ARG/R28.off +loadOff ../../../share/off/ASP/D01.off +loadOff ../../../share/off/ASP/D02.off +loadOff ../../../share/off/ASP/D03.off +loadOff ../../../share/off/ASP/D04.off +loadOff ../../../share/off/ASP/D05.off +loadOff ../../../share/off/ASH/D06.off +loadOff ../../../share/off/ASH/D07.off +loadOff ../../../share/off/ASH/D08.off +loadOff ../../../share/off/ASH/D09.off +loadOff ../../../share/off/ASH/D10.off +loadOff ../../../share/off/ASN/N01.off +loadOff ../../../share/off/ASN/N02.off +loadOff ../../../share/off/ASN/N03.off +loadOff ../../../share/off/ASN/N04.off +loadOff ../../../share/off/ASN/N05.off +loadOff ../../../share/off/ASN/N06.off +loadOff ../../../share/off/ASN/N07.off +loadOff ../../../share/off/CYS/C01.off +loadOff ../../../share/off/CYS/C02.off +loadOff ../../../share/off/CYS/C03.off +loadOff ../../../share/off/GLU/E01.off +loadOff ../../../share/off/GLU/E02.off +loadOff ../../../share/off/GLU/E03.off +loadOff ../../../share/off/GLU/E04.off +loadOff ../../../share/off/GLU/E05.off +loadOff ../../../share/off/GLU/E06.off +loadOff ../../../share/off/GLU/E07.off +loadOff ../../../share/off/GLH/E08.off +loadOff ../../../share/off/GLH/E09.off +loadOff ../../../share/off/GLH/E10.off +loadOff ../../../share/off/GLH/E11.off +loadOff ../../../share/off/GLH/E12.off +loadOff ../../../share/off/GLH/E13.off +loadOff ../../../share/off/GLH/E14.off +loadOff ../../../share/off/GLN/Q01.off +loadOff ../../../share/off/GLN/Q02.off +loadOff ../../../share/off/GLN/Q03.off +loadOff ../../../share/off/GLN/Q04.off +loadOff ../../../share/off/GLN/Q05.off +loadOff ../../../share/off/GLY/G01.off +loadOff ../../../share/off/HID/HD1.off +loadOff ../../../share/off/HID/HD2.off +loadOff ../../../share/off/HID/HD3.off +loadOff ../../../share/off/HID/HD4.off +loadOff ../../../share/off/HID/HD5.off +loadOff ../../../share/off/HID/HD6.off +loadOff ../../../share/off/HID/HD7.off +loadOff ../../../share/off/HID/HD8.off +loadOff ../../../share/off/HIE/HE1.off +loadOff ../../../share/off/HIE/HE2.off +loadOff ../../../share/off/HIE/HE3.off +loadOff ../../../share/off/HIE/HE4.off +loadOff ../../../share/off/HIE/HE5.off +loadOff ../../../share/off/HIE/HE6.off +loadOff ../../../share/off/HIE/HE7.off +loadOff ../../../share/off/HIE/HE8.off +loadOff ../../../share/off/HIP/HP1.off +loadOff ../../../share/off/HIP/HP2.off +loadOff ../../../share/off/HIP/HP3.off +loadOff ../../../share/off/HIP/HP4.off +loadOff ../../../share/off/HIP/HP5.off +loadOff ../../../share/off/HIP/HP6.off +loadOff ../../../share/off/HIP/HP7.off +loadOff ../../../share/off/HIP/HP8.off +loadOff ../../../share/off/ILE/I01.off +loadOff ../../../share/off/ILE/I02.off +loadOff ../../../share/off/ILE/I03.off +loadOff ../../../share/off/ILE/I04.off +loadOff ../../../share/off/ILE/I05.off +loadOff ../../../share/off/LEU/L01.off +loadOff ../../../share/off/LEU/L02.off +loadOff ../../../share/off/LEU/L03.off +loadOff ../../../share/off/LEU/L04.off +loadOff ../../../share/off/MET/M01.off +loadOff ../../../share/off/MET/M02.off +loadOff ../../../share/off/MET/M03.off +loadOff ../../../share/off/MET/M04.off +loadOff ../../../share/off/MET/M05.off +loadOff ../../../share/off/MET/M06.off +loadOff ../../../share/off/MET/M07.off +loadOff ../../../share/off/MET/M08.off +loadOff ../../../share/off/MET/M09.off +loadOff ../../../share/off/MET/M10.off +loadOff ../../../share/off/MET/M11.off +loadOff ../../../share/off/MET/M12.off +loadOff ../../../share/off/MET/M13.off +loadOff ../../../share/off/PHE/P01.off +loadOff ../../../share/off/PHE/P02.off +loadOff ../../../share/off/PHE/P03.off +loadOff ../../../share/off/PHE/P04.off +loadOff ../../../share/off/SER/S01.off +loadOff ../../../share/off/SER/S02.off +loadOff ../../../share/off/SER/S03.off +loadOff ../../../share/off/THR/T01.off +loadOff ../../../share/off/THR/T02.off +loadOff ../../../share/off/THR/T03.off +loadOff ../../../share/off/TRP/W01.off +loadOff ../../../share/off/TRP/W02.off +loadOff ../../../share/off/TRP/W03.off +loadOff ../../../share/off/TRP/W04.off +loadOff ../../../share/off/TRP/W05.off +loadOff ../../../share/off/TRP/W06.off +loadOff ../../../share/off/TRP/W07.off +loadOff ../../../share/off/TYR/Y01.off +loadOff ../../../share/off/TYR/Y02.off +loadOff ../../../share/off/TYR/Y03.off +loadOff ../../../share/off/TYR/Y04.off +loadOff ../../../share/off/VAL/V01.off +loadOff ../../../share/off/VAL/V02.off +loadOff ../../../share/off/VAL/V03.off +loadOff ../../../share/off/LYS/K01.off +loadOff ../../../share/off/LYS/K02.off +loadOff ../../../share/off/LYS/K03.off +loadOff ../../../share/off/LYS/K04.off +loadOff ../../../share/off/LYS/K05.off +loadOff ../../../share/off/LYS/K06.off +loadOff ../../../share/off/LYS/K07.off +loadOff ../../../share/off/LYS/K08.off +loadOff ../../../share/off/LYS/K09.off +loadOff ../../../share/off/LYS/K10.off +loadOff ../../../share/off/LYS/K11.off +loadOff ../../../share/off/LYS/K12.off +loadOff ../../../share/off/LYS/K13.off +loadOff ../../../share/off/LYS/K14.off +loadOff ../../../share/off/LYS/K15.off +loadOff ../../../share/off/LYS/K16.off +loadOff ../../../share/off/LYS/K17.off +loadOff ../../../share/off/LYS/K18.off +loadOff ../../../share/off/LYS/K19.off +loadOff ../../../share/off/LYN/K20.off +loadOff ../../../share/off/LYN/K21.off +loadOff ../../../share/off/LYN/K22.off +loadOff ../../../share/off/LYN/K23.off +loadOff ../../../share/off/LYN/K24.off +loadOff ../../../share/off/LYN/K25.off +loadOff ../../../share/off/LYN/K26.off +loadOff ../../../share/off/LYN/K27.off +loadOff ../../../share/off/LYN/K28.off +loadOff ../../../share/off/LYN/K29.off +loadOff ../../../share/off/LYN/K30.off +loadOff ../../../share/off/LYN/K31.off +loadOff ../../../share/off/LYN/K32.off +loadOff ../../../share/off/LYN/K33.off +loadOff ../../../share/off/LYN/K34.off +loadOff ../../../share/off/LYN/K35.off +loadOff ../../../share/off/LYN/K36.off +loadOff ../../../share/off/LYN/K37.off +loadOff ../../../share/off/LYN/K38.off mol = loadpdb "ALA20_mut.pdb" diff --git a/tests/nsga2/.gitignore b/tests/nsga2/.gitignore new file mode 100644 index 0000000..df0dbbd --- /dev/null +++ b/tests/nsga2/.gitignore @@ -0,0 +1 @@ +work_dir diff --git a/tests/nsga2/final.pdb b/tests/nsga2/final.pdb new file mode 100644 index 0000000..925b319 --- /dev/null +++ b/tests/nsga2/final.pdb @@ -0,0 +1,1785 @@ +COMPND fitness: -6.2188 90.21749999999975 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 P1 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HX1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HX1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HX1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HX1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HX1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HX1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HX1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HX1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N ARG 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H ARG 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA ARG 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 CB ARG 8 32.132 -93.836 -4.510 1.00 0.00 C +ATOM 136 HB2 ARG 8 33.183 -94.106 -4.615 1.00 0.00 H +ATOM 137 HB3 ARG 8 31.914 -92.975 -5.142 1.00 0.00 H +ATOM 138 CG ARG 8 31.841 -93.485 -3.060 1.00 0.00 C +ATOM 139 HG2 ARG 8 31.934 -94.390 -2.458 1.00 0.00 H +ATOM 140 HG3 ARG 8 32.574 -92.751 -2.726 1.00 0.00 H +ATOM 141 CD ARG 8 30.442 -92.914 -2.901 1.00 0.00 C +ATOM 142 HD2 ARG 8 29.722 -93.620 -3.312 1.00 0.00 H +ATOM 143 HD3 ARG 8 30.238 -92.765 -1.841 1.00 0.00 H +ATOM 144 NE ARG 8 30.290 -91.636 -3.591 1.00 0.00 N +ATOM 145 HE ARG 8 29.906 -91.657 -4.525 1.00 0.00 H +ATOM 146 CZ ARG 8 30.622 -90.461 -3.067 1.00 0.00 C +ATOM 147 NH1 ARG 8 30.448 -89.350 -3.770 1.00 0.00 N +ATOM 148 HH11 ARG 8 30.063 -89.401 -4.703 1.00 0.00 H +ATOM 149 HH12 ARG 8 30.702 -88.457 -3.370 1.00 0.00 H +ATOM 150 NH2 ARG 8 31.126 -90.399 -1.843 1.00 0.00 N +ATOM 151 HH21 ARG 8 31.255 -91.247 -1.310 1.00 0.00 H +ATOM 152 HH22 ARG 8 31.377 -89.503 -1.447 1.00 0.00 H +ATOM 153 HA ARG 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 154 C ARG 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 155 O ARG 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 156 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 157 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 158 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 161 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 162 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 163 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 164 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 165 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 166 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 167 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 168 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 169 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 170 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 171 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 172 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 173 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 174 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 175 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 176 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 177 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 178 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 179 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 180 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 181 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 182 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 183 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 184 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 185 N SER 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 186 H SER 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 187 CA SER 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 188 CB SER 11 32.207-101.574 0.711 1.00 0.00 C +ATOM 189 HB2 SER 11 32.416-100.511 0.583 1.00 0.00 H +ATOM 190 HB3 SER 11 31.863-101.756 1.728 1.00 0.00 H +ATOM 191 OG SER 11 33.389-102.318 0.472 1.00 0.00 O +ATOM 192 HG SER 11 34.068-102.048 1.093 1.00 0.00 H +ATOM 193 HA SER 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 194 C SER 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 195 O SER 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 196 N CYS 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 197 H CYS 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 198 CA CYS 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 199 CB CYS 12 28.130 -98.237 -0.161 1.00 0.00 C +ATOM 200 HB2 CYS 12 28.781 -97.808 -0.923 1.00 0.00 H +ATOM 201 HB3 CYS 12 27.157 -97.746 -0.196 1.00 0.00 H +ATOM 202 SG CYS 12 28.866 -97.786 1.444 1.00 0.00 S +ATOM 203 HG CYS 12 28.829 -96.471 1.249 1.00 0.00 H +ATOM 204 HA CYS 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 205 C CYS 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 206 O CYS 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 207 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 208 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 209 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 210 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 211 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 212 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 213 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 214 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 215 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 216 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 217 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 218 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 219 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 220 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 221 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 222 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 223 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 224 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 225 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 226 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 227 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 228 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 229 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 230 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 231 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 232 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 233 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 234 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 235 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 236 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 237 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 238 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 239 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 240 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 241 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 242 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 243 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 244 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 245 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 246 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 247 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 248 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 249 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 250 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 251 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 252 N HY1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 253 CA HY1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 254 C HY1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 255 O HY1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 256 CB HY1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 257 CG HY1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 258 CD2 HY1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 259 ND1 HY1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 260 CE1 HY1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 261 NE2 HY1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 262 H HY1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 263 HA HY1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 264 HB2 HY1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 265 HB3 HY1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 266 HD1 HY1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 267 HD2 HY1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 268 HE1 HY1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 269 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 270 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 271 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 272 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 273 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 274 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 275 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 276 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 277 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 278 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 279 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 280 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 281 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 282 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 283 N HY2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 284 CA HY2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 285 C HY2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 286 O HY2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 287 CB HY2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 288 CG HY2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 289 CD2 HY2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 290 ND1 HY2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 291 CE1 HY2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 292 NE2 HY2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 293 H HY2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 294 HA HY2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 295 HB2 HY2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 296 HB3 HY2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 297 HD1 HY2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 298 HD2 HY2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 299 HE1 HY2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 300 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 301 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 302 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 303 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 304 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 305 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 306 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 307 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 308 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 309 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 310 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 311 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 312 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 313 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 314 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 315 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 316 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 317 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 318 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 319 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 320 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 321 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 322 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 323 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 324 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 325 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 326 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 327 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 328 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 329 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 330 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 331 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 332 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 333 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 334 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 335 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 336 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 337 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 338 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 339 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 340 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 341 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 342 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 343 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 344 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 345 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 346 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 347 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 348 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 349 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 350 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 351 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 352 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 353 N TRP 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 354 H TRP 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 355 CA TRP 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 356 CB TRP 23 21.411 -85.256 -16.822 1.00 0.00 C +ATOM 357 HB2 TRP 23 20.471 -85.768 -16.621 1.00 0.00 H +ATOM 358 HB3 TRP 23 21.494 -85.175 -17.905 1.00 0.00 H +ATOM 359 CG TRP 23 22.519 -86.148 -16.354 1.00 0.00 C +ATOM 360 CD1 TRP 23 23.651 -86.478 -17.042 1.00 0.00 C +ATOM 361 HD1 TRP 23 23.887 -86.129 -18.044 1.00 0.00 H +ATOM 362 NE1 TRP 23 24.435 -87.319 -16.290 1.00 0.00 N +ATOM 363 HE1 TRP 23 25.328 -87.711 -16.568 1.00 0.00 H +ATOM 364 CE2 TRP 23 23.809 -87.548 -15.088 1.00 0.00 C +ATOM 365 CZ2 TRP 23 24.208 -88.327 -14.004 1.00 0.00 C +ATOM 366 HZ2 TRP 23 25.139 -88.878 -14.005 1.00 0.00 H +ATOM 367 CH2 TRP 23 23.375 -88.374 -12.917 1.00 0.00 C +ATOM 368 HH2 TRP 23 23.669 -88.969 -12.061 1.00 0.00 H +ATOM 369 CZ3 TRP 23 22.163 -87.664 -12.899 1.00 0.00 C +ATOM 370 HZ3 TRP 23 21.536 -87.731 -12.021 1.00 0.00 H +ATOM 371 CE3 TRP 23 21.767 -86.890 -13.974 1.00 0.00 C +ATOM 372 HE3 TRP 23 20.836 -86.342 -13.975 1.00 0.00 H +ATOM 373 CD2 TRP 23 22.599 -86.826 -15.093 1.00 0.00 C +ATOM 374 HA TRP 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 375 C TRP 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 376 O TRP 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 377 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 378 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 379 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 380 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 381 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 382 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 383 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 384 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 385 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 386 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 387 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 388 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 389 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 390 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 391 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 392 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 393 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 394 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 395 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 396 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 397 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 398 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 399 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 400 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 401 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 402 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 403 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 404 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 405 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 406 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 407 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 408 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 409 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 410 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 411 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 412 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 413 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 414 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 415 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 416 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 417 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 418 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 419 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 420 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 421 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 422 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 423 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 424 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 425 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 426 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 427 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 428 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 429 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 430 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 431 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 432 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 433 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 434 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 435 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 436 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 437 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 438 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 439 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 440 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 441 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 442 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 443 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 444 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 445 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 446 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 447 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 448 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 449 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 450 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 451 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 452 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 453 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 454 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 455 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 456 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 457 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 458 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 459 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 460 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 461 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 462 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 463 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 464 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 465 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 466 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 467 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 468 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 469 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 470 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 471 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 472 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 473 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 474 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 475 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 476 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 477 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 478 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 479 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 480 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 481 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 482 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 483 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 484 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 485 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 486 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 487 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 488 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 489 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 490 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 491 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 492 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 493 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 494 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 495 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 496 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 497 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 498 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 499 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 500 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 501 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 502 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 503 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 504 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 505 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 506 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 507 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 508 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 509 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 510 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 511 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 512 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 513 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 514 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 515 N LYN 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 516 H LYN 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 517 CA LYN 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 518 CB LYN 33 27.315 -82.525 -3.272 1.00 0.00 C +ATOM 519 HB2 LYN 33 26.398 -81.939 -3.213 1.00 0.00 H +ATOM 520 HB3 LYN 33 27.388 -82.987 -4.256 1.00 0.00 H +ATOM 521 CG LYN 33 27.295 -83.606 -2.204 1.00 0.00 C +ATOM 522 HG2 LYN 33 28.222 -84.177 -2.270 1.00 0.00 H +ATOM 523 HG3 LYN 33 27.231 -83.128 -1.227 1.00 0.00 H +ATOM 524 CD LYN 33 26.111 -84.541 -2.388 1.00 0.00 C +ATOM 525 HD2 LYN 33 26.114 -84.908 -3.414 1.00 0.00 H +ATOM 526 HD3 LYN 33 26.222 -85.381 -1.702 1.00 0.00 H +ATOM 527 CE LYN 33 24.798 -83.829 -2.109 1.00 0.00 C +ATOM 528 HE2 LYN 33 24.821 -83.460 -1.084 1.00 0.00 H +ATOM 529 HE3 LYN 33 24.713 -82.987 -2.797 1.00 0.00 H +ATOM 530 NZ LYN 33 23.628 -84.733 -2.286 1.00 0.00 N +ATOM 531 HZ2 LYN 33 22.777 -84.224 -2.092 1.00 0.00 H +ATOM 532 HZ3 LYN 33 23.607 -85.075 -3.236 1.00 0.00 H +ATOM 533 HA LYN 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 534 C LYN 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 535 O LYN 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 536 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 537 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 538 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 539 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 540 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 541 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 542 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 543 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 544 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 545 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 546 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 547 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 548 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 549 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 550 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 551 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 552 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 553 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 554 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 555 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 556 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 557 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 558 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 559 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 560 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 561 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 562 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 563 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 564 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 565 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 566 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 567 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 568 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 569 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 570 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 571 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 572 N LYS 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 573 H LYS 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 574 CA LYS 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 575 CB LYS 37 33.048 -83.879 0.496 1.00 0.00 C +ATOM 576 HB2 LYS 37 33.471 -84.650 1.141 1.00 0.00 H +ATOM 577 HB3 LYS 37 31.965 -83.860 0.615 1.00 0.00 H +ATOM 578 CG LYS 37 33.393 -84.185 -0.952 1.00 0.00 C +ATOM 579 HG2 LYS 37 32.972 -83.401 -1.582 1.00 0.00 H +ATOM 580 HG3 LYS 37 34.478 -84.192 -1.057 1.00 0.00 H +ATOM 581 CD LYS 37 32.834 -85.533 -1.380 1.00 0.00 C +ATOM 582 HD2 LYS 37 33.256 -86.304 -0.735 1.00 0.00 H +ATOM 583 HD3 LYS 37 31.751 -85.513 -1.262 1.00 0.00 H +ATOM 584 CE LYS 37 33.180 -85.839 -2.828 1.00 0.00 C +ATOM 585 HE2 LYS 37 34.262 -85.779 -2.941 1.00 0.00 H +ATOM 586 HE3 LYS 37 32.849 -86.853 -3.051 1.00 0.00 H +ATOM 587 NZ LYS 37 32.529 -84.884 -3.768 1.00 0.00 N1+ +ATOM 588 HZ1 LYS 37 32.837 -83.945 -3.561 1.00 0.00 H +ATOM 589 HZ2 LYS 37 32.782 -85.121 -4.717 1.00 0.00 H +ATOM 590 HZ3 LYS 37 31.526 -84.940 -3.663 1.00 0.00 H +ATOM 591 HA LYS 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 592 C LYS 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 593 O LYS 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 594 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 595 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 596 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 597 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 598 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 599 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 600 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 601 N ARG 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 602 H ARG 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 603 CA ARG 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 604 CB ARG 39 38.868 -82.517 -4.462 1.00 0.00 C +ATOM 605 HB2 ARG 39 39.200 -82.458 -5.498 1.00 0.00 H +ATOM 606 HB3 ARG 39 39.426 -81.798 -3.861 1.00 0.00 H +ATOM 607 CG ARG 39 39.115 -83.920 -3.930 1.00 0.00 C +ATOM 608 HG2 ARG 39 38.452 -84.611 -4.452 1.00 0.00 H +ATOM 609 HG3 ARG 39 40.151 -84.191 -4.132 1.00 0.00 H +ATOM 610 CD ARG 39 38.853 -83.997 -2.436 1.00 0.00 C +ATOM 611 HD2 ARG 39 39.516 -83.301 -1.923 1.00 0.00 H +ATOM 612 HD3 ARG 39 37.817 -83.720 -2.242 1.00 0.00 H +ATOM 613 NE ARG 39 39.085 -85.339 -1.908 1.00 0.00 N +ATOM 614 HE ARG 39 39.993 -85.527 -1.508 1.00 0.00 H +ATOM 615 CZ ARG 39 38.183 -86.314 -1.923 1.00 0.00 C +ATOM 616 NH1 ARG 39 36.981 -86.099 -2.440 1.00 0.00 N +ATOM 617 HH11 ARG 39 36.755 -85.192 -2.822 1.00 0.00 H +ATOM 618 HH12 ARG 39 36.298 -86.842 -2.450 1.00 0.00 H +ATOM 619 NH2 ARG 39 38.485 -87.503 -1.419 1.00 0.00 N +ATOM 620 HH21 ARG 39 39.402 -87.663 -1.025 1.00 0.00 H +ATOM 621 HH22 ARG 39 37.797 -88.243 -1.432 1.00 0.00 H +ATOM 622 HA ARG 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 623 C ARG 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 624 O ARG 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 625 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 626 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 627 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 628 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 629 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 630 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 631 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 632 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 633 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 634 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 635 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 636 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 637 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 638 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 639 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 640 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 641 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 642 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 643 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 644 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 645 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 646 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 647 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 648 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 649 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 650 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 651 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 652 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 653 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 654 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 655 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 656 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 657 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 658 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 659 N ARG 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 660 H ARG 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 661 CA ARG 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 662 CB ARG 43 29.884 -89.033 -12.452 1.00 0.00 C +ATOM 663 HB2 ARG 43 29.195 -89.866 -12.312 1.00 0.00 H +ATOM 664 HB3 ARG 43 30.406 -88.833 -11.516 1.00 0.00 H +ATOM 665 CG ARG 43 29.106 -87.797 -12.871 1.00 0.00 C +ATOM 666 HG2 ARG 43 29.809 -86.976 -13.016 1.00 0.00 H +ATOM 667 HG3 ARG 43 28.598 -88.009 -13.812 1.00 0.00 H +ATOM 668 CD ARG 43 28.081 -87.406 -11.819 1.00 0.00 C +ATOM 669 HD2 ARG 43 27.386 -88.233 -11.676 1.00 0.00 H +ATOM 670 HD3 ARG 43 28.596 -87.199 -10.881 1.00 0.00 H +ATOM 671 NE ARG 43 27.323 -86.221 -12.207 1.00 0.00 N +ATOM 672 HE ARG 43 26.435 -86.368 -12.663 1.00 0.00 H +ATOM 673 CZ ARG 43 27.730 -84.973 -11.997 1.00 0.00 C +ATOM 674 NH1 ARG 43 28.892 -84.745 -11.401 1.00 0.00 N +ATOM 675 HH11 ARG 43 29.466 -85.523 -11.108 1.00 0.00 H +ATOM 676 HH12 ARG 43 29.198 -83.796 -11.243 1.00 0.00 H +ATOM 677 NH2 ARG 43 26.972 -83.955 -12.384 1.00 0.00 N +ATOM 678 HH21 ARG 43 26.087 -84.131 -12.838 1.00 0.00 H +ATOM 679 HH22 ARG 43 27.284 -83.008 -12.223 1.00 0.00 H +ATOM 680 HA ARG 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 681 C ARG 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 682 O ARG 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 683 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 684 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 685 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 686 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 687 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 688 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 689 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 690 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 691 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 692 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 693 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 694 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 695 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 696 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 697 N ILE 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 698 H ILE 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 699 CA ILE 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 700 CB ILE 45 25.264 -89.243 -17.471 1.00 0.00 C +ATOM 701 HB ILE 45 24.177 -89.166 -17.456 1.00 0.00 H +ATOM 702 CG2 ILE 45 25.843 -88.467 -16.298 1.00 0.00 C +ATOM 703 HG21 ILE 45 26.931 -88.545 -16.312 1.00 0.00 H +ATOM 704 HG22 ILE 45 25.553 -87.420 -16.375 1.00 0.00 H +ATOM 705 HG23 ILE 45 25.464 -88.881 -15.364 1.00 0.00 H +ATOM 706 CG1 ILE 45 25.812 -88.644 -18.767 1.00 0.00 C +ATOM 707 HG12 ILE 45 25.634 -87.570 -18.727 1.00 0.00 H +ATOM 708 HG13 ILE 45 26.886 -88.835 -18.784 1.00 0.00 H +ATOM 709 CD1 ILE 45 25.179 -89.214 -20.018 1.00 0.00 C +ATOM 710 HD11 ILE 45 24.105 -89.024 -20.003 1.00 0.00 H +ATOM 711 HD12 ILE 45 25.619 -88.741 -20.896 1.00 0.00 H +ATOM 712 HD13 ILE 45 25.357 -90.289 -20.058 1.00 0.00 H +ATOM 713 HA ILE 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 714 C ILE 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 715 O ILE 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 716 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 717 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 718 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 719 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 720 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 721 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 722 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 723 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 724 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 725 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 726 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 727 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 728 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 729 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 730 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 731 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 732 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 733 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 734 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 735 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 736 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 737 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 738 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 739 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 740 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 741 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 742 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 743 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 744 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 745 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 746 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 747 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 748 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 749 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 750 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 751 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 752 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 753 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 754 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 755 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 756 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 757 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 758 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 759 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 760 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 761 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 762 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 763 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 764 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 765 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 766 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 767 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 768 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 769 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 770 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 771 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 772 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 773 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 774 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 775 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 776 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 777 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 778 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 779 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 780 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 781 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 782 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 783 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 784 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 785 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 786 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 787 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 788 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 789 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 790 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 791 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 792 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 793 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 794 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 795 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 796 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 797 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 798 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 799 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 800 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 801 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 802 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 803 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 804 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 805 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 806 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 807 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 808 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 809 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 810 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 811 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 812 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 813 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 814 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 815 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 816 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 817 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 818 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 819 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 820 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 821 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 822 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 823 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 824 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 825 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 826 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 827 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 828 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 829 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 830 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 831 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 832 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 833 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 834 N THR 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 835 H THR 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 836 CA THR 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 837 CB THR 54 32.307 -94.492 -10.190 1.00 0.00 C +ATOM 838 HB THR 54 31.944 -95.343 -9.615 1.00 0.00 H +ATOM 839 CG2 THR 54 33.789 -94.670 -10.479 1.00 0.00 C +ATOM 840 HG21 THR 54 34.153 -93.819 -11.054 1.00 0.00 H +ATOM 841 HG22 THR 54 34.338 -94.734 -9.539 1.00 0.00 H +ATOM 842 HG23 THR 54 33.941 -95.586 -11.051 1.00 0.00 H +ATOM 843 OG1 THR 54 32.122 -93.285 -9.439 1.00 0.00 O +ATOM 844 HG1 THR 54 32.609 -93.345 -8.613 1.00 0.00 H +ATOM 845 HA THR 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 846 C THR 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 847 O THR 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 848 N GLN 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 849 H GLN 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 850 CA GLN 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 851 CB GLN 55 34.660 -96.376 -14.407 1.00 0.00 C +ATOM 852 HB2 GLN 55 34.997 -97.154 -15.093 1.00 0.00 H +ATOM 853 HB3 GLN 55 34.127 -95.606 -14.966 1.00 0.00 H +ATOM 854 CG GLN 55 35.862 -95.756 -13.713 1.00 0.00 C +ATOM 855 HG2 GLN 55 35.513 -94.985 -13.026 1.00 0.00 H +ATOM 856 HG3 GLN 55 36.382 -96.534 -13.153 1.00 0.00 H +ATOM 857 CD GLN 55 36.837 -95.128 -14.689 1.00 0.00 C +ATOM 858 OE1 GLN 55 36.898 -95.513 -15.856 1.00 0.00 O +ATOM 859 NE2 GLN 55 37.605 -94.154 -14.211 1.00 0.00 N +ATOM 860 HE21 GLN 55 38.274 -93.699 -14.816 1.00 0.00 H +ATOM 861 HE22 GLN 55 37.517 -93.873 -13.245 1.00 0.00 H +ATOM 862 HA GLN 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 863 C GLN 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 864 O GLN 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 865 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 866 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 867 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 868 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 869 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 870 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 871 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 872 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 873 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 874 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 875 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 876 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 877 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 878 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 879 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 880 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 881 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 Zn +ATOM 882 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 883 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 884 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 885 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 886 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 887 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +ATOM 888 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 889 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 890 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 17 15 13 16 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 65 60 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 68 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 65 69 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 881 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 104 106 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 111 112 113 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 153 132 154 135 +CONECT 135 136 137 138 134 +CONECT 136 135 +CONECT 137 135 +CONECT 138 135 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 142 143 144 +CONECT 142 141 +CONECT 143 141 +CONECT 144 141 145 146 +CONECT 145 144 +CONECT 146 144 147 150 +CONECT 147 146 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 146 151 152 +CONECT 151 150 +CONECT 152 150 +CONECT 153 134 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 165 169 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 170 175 +CONECT 174 173 +CONECT 175 173 +CONECT 176 178 179 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 182 181 176 180 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 193 194 188 +CONECT 188 189 190 191 187 +CONECT 189 188 +CONECT 190 188 +CONECT 191 188 192 +CONECT 192 191 +CONECT 193 187 +CONECT 194 196 187 195 +CONECT 195 194 +CONECT 196 197 198 194 +CONECT 197 196 +CONECT 198 205 196 204 199 +CONECT 199 200 201 202 198 +CONECT 200 199 +CONECT 201 199 +CONECT 202 199 203 +CONECT 203 202 +CONECT 204 198 +CONECT 205 206 207 198 +CONECT 206 205 +CONECT 207 209 205 208 +CONECT 208 207 +CONECT 209 210 211 227 207 +CONECT 210 209 +CONECT 211 214 209 212 213 +CONECT 212 211 +CONECT 213 211 +CONECT 214 216 215 217 211 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 214 220 219 +CONECT 218 217 +CONECT 219 217 +CONECT 220 222 217 223 221 +CONECT 221 220 +CONECT 222 220 +CONECT 223 226 220 224 225 +CONECT 224 223 +CONECT 225 223 +CONECT 226 223 +CONECT 227 228 209 229 +CONECT 228 227 +CONECT 229 227 231 230 +CONECT 230 229 +CONECT 231 234 229 232 233 +CONECT 232 231 +CONECT 233 231 +CONECT 234 235 236 231 +CONECT 235 234 +CONECT 236 238 234 237 +CONECT 237 236 +CONECT 238 240 239 250 236 +CONECT 239 238 +CONECT 240 246 241 242 238 +CONECT 241 240 +CONECT 242 240 245 244 243 +CONECT 243 242 +CONECT 244 242 +CONECT 245 242 +CONECT 246 248 249 247 240 +CONECT 247 246 +CONECT 248 246 +CONECT 249 246 +CONECT 250 252 238 251 +CONECT 251 250 +CONECT 252 262 253 250 +CONECT 253 254 252 263 256 +CONECT 254 255 269 253 +CONECT 255 254 +CONECT 256 253 257 264 265 +CONECT 257 258 259 256 +CONECT 258 261 267 257 +CONECT 259 260 257 266 +CONECT 260 261 268 259 +CONECT 261 881 260 258 +CONECT 262 252 +CONECT 263 253 +CONECT 264 256 +CONECT 265 256 +CONECT 266 259 +CONECT 267 258 +CONECT 268 260 +CONECT 269 271 254 270 +CONECT 270 269 +CONECT 271 272 273 281 269 +CONECT 272 271 +CONECT 273 274 275 271 279 +CONECT 274 273 +CONECT 275 276 277 273 278 +CONECT 276 275 +CONECT 277 275 +CONECT 278 275 +CONECT 279 273 280 +CONECT 280 279 +CONECT 281 283 271 282 +CONECT 282 281 +CONECT 283 293 284 281 +CONECT 284 285 287 283 294 +CONECT 285 286 300 284 +CONECT 286 285 +CONECT 287 295 296 284 288 +CONECT 288 287 289 290 +CONECT 289 298 288 292 +CONECT 290 288 297 291 +CONECT 291 292 290 299 +CONECT 292 289 291 881 +CONECT 293 283 +CONECT 294 284 +CONECT 295 287 +CONECT 296 287 +CONECT 297 290 +CONECT 298 289 +CONECT 299 291 +CONECT 300 302 285 301 +CONECT 301 300 +CONECT 302 313 303 300 304 +CONECT 303 302 +CONECT 304 302 307 306 305 +CONECT 305 304 +CONECT 306 304 +CONECT 307 309 310 304 308 +CONECT 308 307 +CONECT 309 307 +CONECT 310 311 307 312 +CONECT 311 310 +CONECT 312 310 +CONECT 313 315 314 302 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 323 319 318 315 +CONECT 318 317 +CONECT 319 322 321 317 320 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 325 324 317 +CONECT 324 323 +CONECT 325 327 326 323 +CONECT 326 325 +CONECT 327 339 329 328 325 +CONECT 328 327 +CONECT 329 330 335 327 331 +CONECT 330 329 +CONECT 331 329 332 334 333 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 338 337 329 336 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 340 341 327 +CONECT 340 339 +CONECT 341 343 339 342 +CONECT 342 341 +CONECT 343 345 344 351 341 +CONECT 344 343 +CONECT 345 348 346 347 343 +CONECT 346 345 +CONECT 347 345 +CONECT 348 349 350 345 +CONECT 349 348 +CONECT 350 348 +CONECT 351 343 353 352 +CONECT 352 351 +CONECT 353 354 351 355 +CONECT 354 353 +CONECT 355 353 375 374 356 +CONECT 356 357 358 359 355 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 360 373 +CONECT 360 359 361 362 +CONECT 361 360 +CONECT 362 360 363 364 +CONECT 363 362 +CONECT 364 362 365 373 +CONECT 365 364 366 367 +CONECT 366 365 +CONECT 367 365 368 369 +CONECT 368 367 +CONECT 369 367 370 371 +CONECT 370 369 +CONECT 371 369 372 373 +CONECT 372 371 +CONECT 373 359 364 371 +CONECT 374 355 +CONECT 375 377 355 376 +CONECT 376 375 +CONECT 377 378 379 375 +CONECT 378 377 +CONECT 379 381 377 380 385 +CONECT 380 379 +CONECT 381 383 382 384 379 +CONECT 382 381 +CONECT 383 381 +CONECT 384 381 +CONECT 385 379 386 387 +CONECT 386 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 391 390 400 +CONECT 390 389 +CONECT 391 394 389 392 393 +CONECT 392 391 +CONECT 393 391 +CONECT 394 395 397 396 391 +CONECT 395 394 +CONECT 396 394 +CONECT 397 399 394 398 +CONECT 398 397 +CONECT 399 397 +CONECT 400 389 402 401 +CONECT 401 400 +CONECT 402 403 400 404 +CONECT 403 402 +CONECT 404 402 406 410 405 +CONECT 405 404 +CONECT 406 407 408 404 409 +CONECT 407 406 +CONECT 408 406 +CONECT 409 406 +CONECT 410 412 404 411 +CONECT 411 410 +CONECT 412 413 414 410 +CONECT 413 412 +CONECT 414 416 412 415 425 +CONECT 415 414 +CONECT 416 417 418 419 414 +CONECT 417 416 +CONECT 418 416 +CONECT 419 422 416 421 420 +CONECT 420 419 +CONECT 421 419 +CONECT 422 423 424 419 +CONECT 423 422 +CONECT 424 422 +CONECT 425 414 427 426 +CONECT 426 425 +CONECT 427 428 425 429 +CONECT 428 427 +CONECT 429 427 431 430 447 +CONECT 430 429 +CONECT 431 434 432 433 429 +CONECT 432 431 +CONECT 433 431 +CONECT 434 437 436 435 431 +CONECT 435 434 +CONECT 436 434 +CONECT 437 440 438 434 439 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 442 441 437 +CONECT 441 440 +CONECT 442 440 +CONECT 443 446 445 444 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 +CONECT 447 429 449 448 +CONECT 448 447 +CONECT 449 450 447 451 +CONECT 450 449 +CONECT 451 449 453 452 467 +CONECT 452 451 +CONECT 453 456 454 451 455 +CONECT 454 453 +CONECT 455 453 +CONECT 456 457 465 453 +CONECT 457 459 458 456 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 462 459 463 +CONECT 462 461 +CONECT 463 461 464 465 +CONECT 464 463 +CONECT 465 463 456 466 +CONECT 466 465 +CONECT 467 451 469 468 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 473 469 481 472 +CONECT 472 471 +CONECT 473 474 479 475 471 +CONECT 474 473 +CONECT 475 476 473 477 478 +CONECT 476 475 +CONECT 477 475 +CONECT 478 475 +CONECT 479 480 473 +CONECT 480 479 +CONECT 481 483 471 482 +CONECT 482 481 +CONECT 483 484 485 481 +CONECT 484 483 +CONECT 485 487 483 486 503 +CONECT 486 485 +CONECT 487 490 488 489 485 +CONECT 488 487 +CONECT 489 487 +CONECT 490 493 492 491 487 +CONECT 491 490 +CONECT 492 490 +CONECT 493 496 494 495 490 +CONECT 494 493 +CONECT 495 493 +CONECT 496 498 499 497 493 +CONECT 497 496 +CONECT 498 496 +CONECT 499 501 496 500 502 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 485 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 508 513 +CONECT 508 507 +CONECT 509 511 512 507 510 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 507 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 534 533 518 +CONECT 518 519 520 521 517 +CONECT 519 518 +CONECT 520 518 +CONECT 521 518 522 523 524 +CONECT 522 521 +CONECT 523 521 +CONECT 524 521 525 526 527 +CONECT 525 524 +CONECT 526 524 +CONECT 527 524 528 529 530 +CONECT 528 527 +CONECT 529 527 +CONECT 530 527 531 532 +CONECT 531 530 +CONECT 532 530 +CONECT 533 517 +CONECT 534 536 517 535 +CONECT 535 534 +CONECT 536 537 538 534 +CONECT 537 536 +CONECT 538 540 536 544 539 +CONECT 539 538 +CONECT 540 541 542 543 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 +CONECT 544 546 538 545 +CONECT 545 544 +CONECT 546 547 548 544 +CONECT 547 546 +CONECT 548 550 546 549 558 +CONECT 549 548 +CONECT 550 553 551 552 548 +CONECT 551 550 +CONECT 552 550 +CONECT 553 555 554 550 +CONECT 554 553 +CONECT 555 557 556 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 548 560 559 +CONECT 559 558 +CONECT 560 561 558 562 +CONECT 561 560 +CONECT 562 560 563 564 570 +CONECT 563 562 +CONECT 564 565 562 567 566 +CONECT 565 564 +CONECT 566 564 +CONECT 567 568 569 564 +CONECT 568 567 +CONECT 569 567 +CONECT 570 562 572 571 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 592 591 575 +CONECT 575 576 577 578 574 +CONECT 576 575 +CONECT 577 575 +CONECT 578 575 579 580 581 +CONECT 579 578 +CONECT 580 578 +CONECT 581 578 582 583 584 +CONECT 582 581 +CONECT 583 581 +CONECT 584 581 585 586 587 +CONECT 585 584 +CONECT 586 584 +CONECT 587 584 588 589 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 574 +CONECT 592 594 574 593 +CONECT 593 592 +CONECT 594 595 596 592 +CONECT 595 594 +CONECT 596 599 598 594 597 +CONECT 597 596 +CONECT 598 596 +CONECT 599 601 600 596 +CONECT 600 599 +CONECT 601 603 602 599 +CONECT 602 601 +CONECT 603 623 622 601 604 +CONECT 604 605 606 607 603 +CONECT 605 604 +CONECT 606 604 +CONECT 607 604 608 609 610 +CONECT 608 607 +CONECT 609 607 +CONECT 610 607 611 612 613 +CONECT 611 610 +CONECT 612 610 +CONECT 613 610 614 615 +CONECT 614 613 +CONECT 615 613 616 619 +CONECT 616 615 617 618 +CONECT 617 616 +CONECT 618 616 +CONECT 619 615 620 621 +CONECT 620 619 +CONECT 621 619 +CONECT 622 603 +CONECT 623 625 624 603 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 629 635 628 625 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 632 +CONECT 635 636 637 627 +CONECT 636 635 +CONECT 637 639 635 638 +CONECT 638 637 +CONECT 639 642 640 641 637 +CONECT 640 639 +CONECT 641 639 +CONECT 642 644 643 639 +CONECT 643 642 +CONECT 644 646 645 642 +CONECT 645 644 +CONECT 646 648 647 657 644 +CONECT 647 646 +CONECT 648 650 651 649 646 +CONECT 649 648 +CONECT 650 648 +CONECT 651 653 654 648 652 +CONECT 652 651 +CONECT 653 651 +CONECT 654 655 651 656 +CONECT 655 654 +CONECT 656 654 +CONECT 657 659 646 658 +CONECT 658 657 +CONECT 659 660 661 657 +CONECT 660 659 +CONECT 661 681 659 680 662 +CONECT 662 663 664 665 661 +CONECT 663 662 +CONECT 664 662 +CONECT 665 662 666 667 668 +CONECT 666 665 +CONECT 667 665 +CONECT 668 665 669 670 671 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 672 673 +CONECT 672 671 +CONECT 673 671 674 677 +CONECT 674 673 675 676 +CONECT 675 674 +CONECT 676 674 +CONECT 677 673 678 679 +CONECT 678 677 +CONECT 679 677 +CONECT 680 661 +CONECT 681 682 683 661 +CONECT 682 681 +CONECT 683 685 681 684 +CONECT 684 683 +CONECT 685 686 687 695 683 +CONECT 686 685 +CONECT 687 689 693 685 688 +CONECT 688 687 +CONECT 689 692 691 690 687 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 +CONECT 693 687 694 +CONECT 694 693 +CONECT 695 697 685 696 +CONECT 696 695 +CONECT 697 698 699 695 +CONECT 698 697 +CONECT 699 714 697 713 700 +CONECT 700 701 702 706 699 +CONECT 701 700 +CONECT 702 700 703 704 705 +CONECT 703 702 +CONECT 704 702 +CONECT 705 702 +CONECT 706 700 707 708 709 +CONECT 707 706 +CONECT 708 706 +CONECT 709 706 710 711 712 +CONECT 710 709 +CONECT 711 709 +CONECT 712 709 +CONECT 713 699 +CONECT 714 715 716 699 +CONECT 715 714 +CONECT 716 718 714 717 +CONECT 717 716 +CONECT 718 719 726 720 716 +CONECT 719 718 +CONECT 720 723 718 721 722 +CONECT 721 720 +CONECT 722 720 +CONECT 723 725 724 720 +CONECT 724 723 +CONECT 725 723 +CONECT 726 728 718 727 +CONECT 727 726 +CONECT 728 729 730 726 +CONECT 729 728 +CONECT 730 732 728 738 731 +CONECT 731 730 +CONECT 732 734 735 733 730 +CONECT 733 732 +CONECT 734 732 +CONECT 735 736 732 737 +CONECT 736 735 +CONECT 737 735 +CONECT 738 740 730 739 +CONECT 739 738 +CONECT 740 741 742 738 +CONECT 741 740 +CONECT 742 744 743 740 748 +CONECT 743 742 +CONECT 744 747 745 746 742 +CONECT 745 744 +CONECT 746 744 +CONECT 747 744 +CONECT 748 742 749 750 +CONECT 749 748 +CONECT 750 748 751 752 +CONECT 751 750 +CONECT 752 750 753 754 762 +CONECT 753 752 +CONECT 754 756 752 760 755 +CONECT 755 754 +CONECT 756 758 759 757 754 +CONECT 757 756 +CONECT 758 756 +CONECT 759 756 +CONECT 760 761 754 +CONECT 761 760 +CONECT 762 752 764 763 +CONECT 763 762 +CONECT 764 765 766 762 +CONECT 765 764 +CONECT 766 767 764 768 784 +CONECT 767 766 +CONECT 768 771 766 770 769 +CONECT 769 768 +CONECT 770 768 +CONECT 771 774 772 773 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 777 776 775 771 +CONECT 775 774 +CONECT 776 774 +CONECT 777 780 779 778 774 +CONECT 778 777 +CONECT 779 777 +CONECT 780 782 781 783 777 +CONECT 781 780 +CONECT 782 780 +CONECT 783 780 +CONECT 784 766 786 785 +CONECT 785 784 +CONECT 786 787 784 788 +CONECT 787 786 +CONECT 788 786 798 790 789 +CONECT 789 788 +CONECT 790 791 788 796 792 +CONECT 791 790 +CONECT 792 790 793 794 795 +CONECT 793 792 +CONECT 794 792 +CONECT 795 792 +CONECT 796 797 790 +CONECT 797 796 +CONECT 798 799 788 800 +CONECT 799 798 +CONECT 800 798 802 801 +CONECT 801 800 +CONECT 802 803 800 804 818 +CONECT 803 802 +CONECT 804 807 802 806 805 +CONECT 805 804 +CONECT 806 804 +CONECT 807 816 808 804 +CONECT 808 810 807 809 +CONECT 809 808 +CONECT 810 812 811 808 +CONECT 811 810 +CONECT 812 813 814 810 +CONECT 813 812 +CONECT 814 815 812 816 +CONECT 815 814 +CONECT 816 814 817 807 +CONECT 817 816 +CONECT 818 802 820 819 +CONECT 819 818 +CONECT 820 821 818 822 +CONECT 821 820 +CONECT 822 820 824 832 823 +CONECT 823 822 +CONECT 824 830 826 825 822 +CONECT 825 824 +CONECT 826 827 829 824 828 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 +CONECT 830 831 824 +CONECT 831 830 +CONECT 832 833 822 834 +CONECT 833 832 +CONECT 834 832 836 835 +CONECT 835 834 +CONECT 836 846 845 834 837 +CONECT 837 838 839 843 836 +CONECT 838 837 +CONECT 839 837 840 841 842 +CONECT 840 839 +CONECT 841 839 +CONECT 842 839 +CONECT 843 837 844 +CONECT 844 843 +CONECT 845 836 +CONECT 846 848 847 836 +CONECT 847 846 +CONECT 848 850 849 846 +CONECT 849 848 +CONECT 850 862 848 863 851 +CONECT 851 852 853 854 850 +CONECT 852 851 +CONECT 853 851 +CONECT 854 851 855 856 857 +CONECT 855 854 +CONECT 856 854 +CONECT 857 854 858 859 +CONECT 858 857 +CONECT 859 857 860 861 +CONECT 860 859 +CONECT 861 859 +CONECT 862 850 +CONECT 863 850 865 864 +CONECT 864 863 +CONECT 865 866 863 867 +CONECT 866 865 +CONECT 867 869 865 878 868 +CONECT 868 867 +CONECT 869 871 870 872 867 +CONECT 870 869 +CONECT 871 869 +CONECT 872 873 869 874 875 +CONECT 873 872 +CONECT 874 872 +CONECT 875 872 876 877 +CONECT 876 875 +CONECT 877 875 +CONECT 878 880 867 879 +CONECT 879 878 +CONECT 880 878 +CONECT 881 87 292 882 261 +CONECT 882 881 884 +CONECT 883 886 884 887 885 +CONECT 884 882 883 +CONECT 885 883 +CONECT 886 883 +CONECT 887 883 +CONECT 888 889 +CONECT 889 888 890 +CONECT 890 889 +MASTER 0 0 0 0 0 0 0 0 890 0 890 0 +END diff --git a/tests/nsga2/first_fronts.log b/tests/nsga2/first_fronts.log new file mode 100644 index 0000000..03fe739 --- /dev/null +++ b/tests/nsga2/first_fronts.log @@ -0,0 +1,5 @@ +-0.2933,51.061666666666724;-1.2907,59.98833333333391;-0.3891,51.34500000000048;-2.8894,84.35416666666652;-1.2907,59.98833333333391;-1.2907,59.98833333333391; +-0.3475,49.977499999999736;-2.8894,84.35416666666652;-1.2907,59.98833333333391;-1.2907,59.98833333333391;-0.3475,49.977499999999736;-3.7512,86.6599999999994; +-0.331,51.38249999999948;-0.331,51.38249999999948;-3.7512,86.6599999999994;-2.8843,83.41749999999979;-2.8843,83.41749999999979;-0.331,51.38249999999948;-6.2239,90.03083333333325; +-0.331,51.38249999999948;-0.331,51.38249999999948;-6.2239,90.03083333333325;-3.1818,51.504999999999654; +-0.304,51.40416666666647;-0.304,51.40416666666647;-6.2188,90.21749999999975;-3.1818,51.504999999999654;-6.2188,90.21749999999975;-6.2188,90.21749999999975;-0.304,51.40416666666647;-0.304,51.40416666666647; diff --git a/tests/nsga2/fitnesses.dat b/tests/nsga2/fitnesses.dat new file mode 100644 index 0000000..5cdf9e5 --- /dev/null +++ b/tests/nsga2/fitnesses.dat @@ -0,0 +1 @@ +1.3332 87.05750000000012 diff --git a/tests/nsga2/ga_input.in b/tests/nsga2/ga_input.in new file mode 100644 index 0000000..7d3b7b1 --- /dev/null +++ b/tests/nsga2/ga_input.in @@ -0,0 +1,68 @@ +[OPTIMIZATION] +dihedral_optimization = False +composition_optimization = True +composition_residue_indexes = 7 10 11 32 36 38 53 54 22 42 44 +composition_lower_bounds = 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +composition_upper_bounds = 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 177 +composition_library = ../../share/flat + + +[MOLECULE] +use_res_type=True + +[IO] +store_intermediate_mol = True +output_path = . +output_file = final.pdb + +[GA_GLOBAL] +seed_population = False +population_file_path = None +population_size = 4 +max_iteration = 5 + + +[EVALUATOR] +evaluators = mmpbsa_multi stability_multi +tleap_template =/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/tests/nsga2/inp/leap.in +amber_params =/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/tests/nsga2/inp/min.in +mmpbsa_params=/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/tests/nsga2/inp/mmpbsa.in +mpi_processors =24 +dielectric = 80.0 + +[GA_MULTIMMPBSA] +multi_individual = True +no_frames =12 +molecule_dir=./pdbs_rename/ +use_compute_cluster=False +compute_cluster_nodes=6 +compute_cluster_ntasks=10 +compute_cluster_queuename=nccr-short +energy_calculator=pb + +[GA_SELECTION] +selector = tournament_wor +tournament_size = 2 + +[GA_CROSSOVER] +crossover = sbx +sbx_distribution_index = 7.0 +mating_probability = 0.7 +genewise_crossover_probability = 0.4 + +[GA_MUTATION] +mutator = polynomial_mutation +mutation_probability = 0.3 +genewise__mutation_probability = 0.15 +poly_eta = 7.0 + +[GA_REPLACER] +replacer = nsga2 + +[GENERATOR] +unbiased_protein_composition_generator=False +swissprot_composition_generator=True +generator=swissprot + +[DEBUG] +verbose = True diff --git a/tests/nsga2/initial_fitness.dat b/tests/nsga2/initial_fitness.dat new file mode 100644 index 0000000..5a70a59 --- /dev/null +++ b/tests/nsga2/initial_fitness.dat @@ -0,0 +1 @@ +"[ 9.04000000e-01 -1.90197583e+03]" \ No newline at end of file diff --git a/tests/nsga2/inp/ACN.frcmod b/tests/nsga2/inp/ACN.frcmod new file mode 100644 index 0000000..c60366e --- /dev/null +++ b/tests/nsga2/inp/ACN.frcmod @@ -0,0 +1,15 @@ 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off + + +#parameters from MCPB.py for Acetonitrile (resname AN1) to Zinc with Zinc Amber Force Field +addAtomTypes { + { "M1" "Zn" "sp3" } + { "Y1" "N" "sp3" } + { "Y2" "N" "sp3" } + { "Y3" "N" "sp3" } + { "Y4" "N" "sp3" } +} + +#HX episilon protonated his +#HY delta protonated +#had to be renamed because of naming conflict with rotamer library +HX1 = loadmol2 ../../inp/HX1.mol2 +HY1 = loadmol2 ../../inp/HY1.mol2 +HY2 = loadmol2 ../../inp/HY2.mol2 +ZN1 = loadmol2 ../../inp/ZN1.mol2 +AN1 = loadmol2 ../../inp/AN1.mol2 +AZI = loadmol2 ../../inp/AZI.mol2 +loadamberparams ../../inp/AZI.frcmod +loadamberparams ../../inp/ACN.frcmod +loadamberparams frcmod.ions1lm_126_tip3p +loadamberparams ../../inp/GB1AZI_mcpbpy.frcmod + +#necessary for igb8 +set default PBRadii mbondi3 + +# load pdb twice, in one we have to delete the ligand to make the right parameter file for MMPBSA +mol = loadpdb mutated_ter.pdb +receptor = loadpdb mutated_ter.pdb +remove receptor receptor.59 + +# bond statements as required by ZAFF because of unusual residues +bond mol.5.ND1 mol.57.ZN +bond mol.16.NE2 mol.57.ZN +bond mol.18.NE2 mol.57.ZN +bond mol.57.ZN mol.58.N +bond mol.4.C mol.5.N +bond mol.5.C mol.6.N +bond mol.15.C mol.16.N +bond mol.16.C mol.17.N +bond mol.17.C mol.18.N +bond mol.18.C mol.19.N + + +bond receptor.5.ND1 receptor.57.ZN +bond receptor.16.NE2 receptor.57.ZN +bond receptor.18.NE2 receptor.57.ZN +bond receptor.57.ZN receptor.58.N +bond receptor.4.C receptor.5.N +bond receptor.5.C receptor.6.N +bond receptor.15.C receptor.16.N +bond receptor.16.C receptor.17.N +bond receptor.17.C receptor.18.N +bond receptor.18.C receptor.19.N + + +#save dry files and dry parameter files for MMPBSA +savepdb mol GB1AZI_dry.pdb +saveamberparm mol dry_complex.prmtop dry_complex.inpcrd +saveAmberParm receptor receptor.prmtop receptor.crd +saveAmberParm AZI ligand.prmtop ligand.crd + + +# solvate and neutralize for minimization +solvatebox mol TIP3PBOX 10.0 +addions mol Na+ 0 +addions mol Cl- 0 +savepdb mol GB1AZI_solv.pdb +saveamberparm mol GB1AZI_solv.prmtop GB1AZI_solv.inpcrd +quit + diff --git a/tests/nsga2/inp/min.in b/tests/nsga2/inp/min.in new file mode 100644 index 0000000..a58e619 --- /dev/null +++ b/tests/nsga2/inp/min.in @@ -0,0 +1,9 @@ +initial minimization whole system + &cntrl + imin = 1, + maxcyc = 500, + ncyc = 250, + ntb = 1, + ntr = 0, + cut = 12.0 + / diff --git a/tests/nsga2/inp/mmpbsa.in b/tests/nsga2/inp/mmpbsa.in new file mode 100644 index 0000000..b533d14 --- /dev/null +++ b/tests/nsga2/inp/mmpbsa.in @@ -0,0 +1,11 @@ +mm_pbsa_input +&general + keep_files=1, +/ +&gb + igb=8, + saltcon=0.150, +/ +&pb +radiopt=0, +/ diff --git a/tests/nsga2/inp/pdbs/cluster.c0.pdb b/tests/nsga2/inp/pdbs/cluster.c0.pdb new file mode 100644 index 0000000..ab82d88 --- /dev/null +++ b/tests/nsga2/inp/pdbs/cluster.c0.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.003 -82.385 -13.374 1.00 0.00 N +ATOM 2 H1 MET 1 14.002 -82.237 -13.397 1.00 0.00 H +ATOM 3 H2 MET 1 12.617 -82.051 -12.503 1.00 0.00 H +ATOM 4 H3 MET 1 12.504 -81.958 -14.141 1.00 0.00 H +ATOM 5 CA MET 1 12.817 -83.815 -13.490 1.00 0.00 C +ATOM 6 HA MET 1 11.778 -84.048 -13.256 1.00 0.00 H +ATOM 7 CB MET 1 13.115 -84.298 -14.885 1.00 0.00 C +ATOM 8 HB2 MET 1 12.606 -83.694 -15.637 1.00 0.00 H +ATOM 9 HB3 MET 1 14.200 -84.279 -14.995 1.00 0.00 H +ATOM 10 CG MET 1 12.731 -85.746 -15.065 1.00 0.00 C +ATOM 11 HG2 MET 1 13.407 -86.338 -14.449 1.00 0.00 H +ATOM 12 HG3 MET 1 11.721 -85.895 -14.683 1.00 0.00 H +ATOM 13 SD MET 1 12.823 -86.418 -16.750 1.00 0.00 S +ATOM 14 CE MET 1 14.431 -85.904 -17.273 1.00 0.00 C +ATOM 15 HE1 MET 1 14.505 -84.817 -17.243 1.00 0.00 H +ATOM 16 HE2 MET 1 14.645 -86.267 -18.278 1.00 0.00 H +ATOM 17 HE3 MET 1 15.153 -86.228 -16.522 1.00 0.00 H +ATOM 18 C MET 1 13.793 -84.410 -12.415 1.00 0.00 C +ATOM 19 O MET 1 14.945 -84.014 -12.426 1.00 0.00 O +ATOM 20 N GLN 2 13.498 -85.513 -11.769 1.00 0.00 N +ATOM 21 H GLN 2 12.549 -85.852 -11.842 1.00 0.00 H +ATOM 22 CA GLN 2 14.392 -86.212 -10.788 1.00 0.00 C +ATOM 23 HA GLN 2 15.109 -85.500 -10.379 1.00 0.00 H +ATOM 24 CB GLN 2 13.532 -86.703 -9.584 1.00 0.00 C +ATOM 25 HB2 GLN 2 12.804 -87.367 -10.050 1.00 0.00 H +ATOM 26 HB3 GLN 2 14.174 -87.312 -8.948 1.00 0.00 H +ATOM 27 CG GLN 2 12.872 -85.678 -8.664 1.00 0.00 C +ATOM 28 HG2 GLN 2 12.717 -84.745 -9.207 1.00 0.00 H +ATOM 29 HG3 GLN 2 11.843 -86.032 -8.594 1.00 0.00 H +ATOM 30 CD GLN 2 13.455 -85.553 -7.230 1.00 0.00 C +ATOM 31 OE1 GLN 2 14.595 -85.887 -6.905 1.00 0.00 O +ATOM 32 NE2 GLN 2 12.745 -84.855 -6.361 1.00 0.00 N +ATOM 33 HE21 GLN 2 13.149 -84.584 -5.476 1.00 0.00 H +ATOM 34 HE22 GLN 2 11.825 -84.541 -6.635 1.00 0.00 H +ATOM 35 C GLN 2 15.364 -87.269 -11.360 1.00 0.00 C +ATOM 36 O GLN 2 15.084 -88.492 -11.421 1.00 0.00 O +ATOM 37 N TYR 3 16.524 -86.790 -11.746 1.00 0.00 N +ATOM 38 H TYR 3 16.697 -85.805 -11.600 1.00 0.00 H +ATOM 39 CA TYR 3 17.652 -87.622 -12.295 1.00 0.00 C +ATOM 40 HA TYR 3 17.346 -88.300 -13.092 1.00 0.00 H +ATOM 41 CB TYR 3 18.732 -86.723 -12.825 1.00 0.00 C +ATOM 42 HB2 TYR 3 18.930 -85.993 -12.040 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.577 -87.393 -12.988 1.00 0.00 H +ATOM 44 CG TYR 3 18.239 -85.944 -14.076 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.512 -86.427 -15.374 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.989 -87.392 -15.466 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.208 -85.626 -16.456 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.401 -85.981 -17.457 1.00 0.00 H +ATOM 49 CZ TYR 3 17.537 -84.430 -16.197 1.00 0.00 C +ATOM 50 OH TYR 3 17.251 -83.606 -17.273 1.00 0.00 O +ATOM 51 HH TYR 3 17.750 -83.947 -18.018 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.080 -83.989 -14.937 1.00 0.00 C +ATOM 53 HE2 TYR 3 16.489 -83.091 -14.826 1.00 0.00 H +ATOM 54 CD2 TYR 3 17.557 -84.744 -13.876 1.00 0.00 C +ATOM 55 HD2 TYR 3 17.250 -84.430 -12.890 1.00 0.00 H +ATOM 56 C TYR 3 18.233 -88.485 -11.236 1.00 0.00 C +ATOM 57 O TYR 3 18.255 -88.097 -10.086 1.00 0.00 O +ATOM 58 N LYS 4 18.815 -89.665 -11.571 1.00 0.00 N +ATOM 59 H LYS 4 18.746 -89.897 -12.552 1.00 0.00 H +ATOM 60 CA LYS 4 19.306 -90.687 -10.646 1.00 0.00 C +ATOM 61 HA LYS 4 18.862 -90.648 -9.652 1.00 0.00 H +ATOM 62 CB LYS 4 18.907 -92.011 -11.231 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.018 -92.083 -12.313 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.503 -92.764 -10.715 1.00 0.00 H +ATOM 65 CG LYS 4 17.494 -92.443 -10.928 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.555 -93.455 -11.326 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.327 -92.579 -9.859 1.00 0.00 H +ATOM 68 CD LYS 4 16.367 -91.656 -11.615 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.479 -90.608 -11.336 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.460 -91.723 -12.699 1.00 0.00 H +ATOM 71 CE LYS 4 15.044 -92.119 -11.098 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.905 -93.136 -11.464 1.00 0.00 H +ATOM 73 HE3 LYS 4 14.909 -92.215 -10.021 1.00 0.00 H +ATOM 74 NZ LYS 4 13.859 -91.347 -11.574 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.011 -91.799 -11.263 1.00 0.00 H +ATOM 76 HZ2 LYS 4 13.927 -91.300 -12.580 1.00 0.00 H +ATOM 77 HZ3 LYS 4 13.863 -90.405 -11.208 1.00 0.00 H +ATOM 78 C LYS 4 20.764 -90.556 -10.378 1.00 0.00 C +ATOM 79 O LYS 4 21.451 -89.991 -11.198 1.00 0.00 O +ATOM 80 N HE1 5 21.236 -90.868 -9.176 1.00 0.00 N +ATOM 81 CA HE1 5 22.633 -90.844 -8.790 1.00 0.00 C +ATOM 82 C HE1 5 22.860 -91.880 -7.748 1.00 0.00 C +ATOM 83 O HE1 5 22.130 -91.930 -6.740 1.00 0.00 O +ATOM 84 CB HE1 5 23.000 -89.454 -8.200 1.00 0.00 C +ATOM 85 CG HE1 5 24.375 -89.185 -7.655 1.00 0.00 C +ATOM 86 CD2 HE1 5 25.595 -89.645 -8.102 1.00 0.00 C +ATOM 87 ND1 HE1 5 24.610 -88.515 -6.436 1.00 0.00 N +ATOM 88 CE1 HE1 5 25.927 -88.544 -6.216 1.00 0.00 C +ATOM 89 NE2 HE1 5 26.563 -89.214 -7.195 1.00 0.00 N +ATOM 90 H HE1 5 20.551 -91.052 -8.456 1.00 0.00 H +ATOM 91 HA HE1 5 23.202 -90.939 -9.715 1.00 0.00 H +ATOM 92 HB2 HE1 5 22.281 -89.349 -7.387 1.00 0.00 H +ATOM 93 HB3 HE1 5 22.813 -88.724 -8.987 1.00 0.00 H +ATOM 94 HD2 HE1 5 25.748 -90.244 -8.988 1.00 0.00 H +ATOM 95 HE1 HE1 5 26.353 -88.113 -5.321 1.00 0.00 H +ATOM 96 HE2 HE1 5 27.558 -89.358 -7.283 1.00 0.00 H +ATOM 97 N ILE 6 23.793 -92.766 -8.096 1.00 0.00 N +ATOM 98 H ILE 6 24.340 -92.519 -8.908 1.00 0.00 H +ATOM 99 CA ILE 6 24.284 -93.842 -7.256 1.00 0.00 C +ATOM 100 HA ILE 6 23.487 -94.109 -6.561 1.00 0.00 H +ATOM 101 CB ILE 6 24.784 -95.053 -8.041 1.00 0.00 C +ATOM 102 HB ILE 6 25.551 -94.655 -8.705 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.653 -96.002 -7.134 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.787 -97.003 -7.544 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.091 -96.213 -6.224 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.668 -95.658 -6.934 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.708 -95.750 -8.838 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.000 -96.203 -8.144 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.233 -94.940 -9.390 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.159 -96.794 -9.808 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.643 -97.733 -9.607 1.00 0.00 H +ATOM 112 HD12 ILE 6 25.244 -96.801 -9.916 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.832 -96.454 -10.790 1.00 0.00 H +ATOM 114 C ILE 6 25.375 -93.259 -6.384 1.00 0.00 C +ATOM 115 O ILE 6 26.051 -92.352 -6.818 1.00 0.00 O +ATOM 116 N VAL 7 25.483 -93.673 -5.108 1.00 0.00 N +ATOM 117 H VAL 7 24.735 -94.223 -4.710 1.00 0.00 H +ATOM 118 CA VAL 7 26.464 -93.171 -4.144 1.00 0.00 C +ATOM 119 HA VAL 7 26.160 -92.151 -3.909 1.00 0.00 H +ATOM 120 CB VAL 7 26.371 -94.134 -2.892 1.00 0.00 C +ATOM 121 HB VAL 7 25.315 -94.325 -2.706 1.00 0.00 H +ATOM 122 CG1 VAL 7 26.987 -95.528 -3.080 1.00 0.00 C +ATOM 123 HG11 VAL 7 26.815 -96.170 -2.216 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.551 -96.054 -3.929 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.075 -95.496 -3.137 1.00 0.00 H +ATOM 126 CG2 VAL 7 26.863 -93.468 -1.556 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.944 -93.325 -1.522 1.00 0.00 H +ATOM 128 HG22 VAL 7 26.444 -92.465 -1.623 1.00 0.00 H +ATOM 129 HG23 VAL 7 26.450 -93.911 -0.650 1.00 0.00 H +ATOM 130 C VAL 7 27.920 -93.106 -4.626 1.00 0.00 C +ATOM 131 O VAL 7 28.384 -94.132 -5.137 1.00 0.00 O +ATOM 132 N ASN 8 28.705 -91.990 -4.436 1.00 0.00 N +ATOM 133 H ASN 8 28.205 -91.186 -4.084 1.00 0.00 H +ATOM 134 CA ASN 8 30.076 -91.774 -4.932 1.00 0.00 C +ATOM 135 HA ASN 8 30.106 -92.084 -5.977 1.00 0.00 H +ATOM 136 CB ASN 8 30.499 -90.318 -4.922 1.00 0.00 C +ATOM 137 HB2 ASN 8 30.667 -89.870 -3.943 1.00 0.00 H +ATOM 138 HB3 ASN 8 31.421 -90.273 -5.501 1.00 0.00 H +ATOM 139 CG ASN 8 29.611 -89.516 -5.873 1.00 0.00 C +ATOM 140 OD1 ASN 8 29.312 -89.960 -6.946 1.00 0.00 O +ATOM 141 ND2 ASN 8 29.325 -88.294 -5.555 1.00 0.00 N +ATOM 142 HD21 ASN 8 29.622 -87.946 -4.655 1.00 0.00 H +ATOM 143 HD22 ASN 8 28.724 -87.755 -6.162 1.00 0.00 H +ATOM 144 C ASN 8 31.162 -92.680 -4.209 1.00 0.00 C +ATOM 145 O ASN 8 32.221 -93.053 -4.794 1.00 0.00 O +ATOM 146 N GLY 9 31.065 -92.866 -2.886 1.00 0.00 N +ATOM 147 H GLY 9 30.240 -92.520 -2.416 1.00 0.00 H +ATOM 148 CA GLY 9 32.126 -93.588 -2.175 1.00 0.00 C +ATOM 149 HA2 GLY 9 33.081 -93.109 -2.393 1.00 0.00 H +ATOM 150 HA3 GLY 9 31.883 -93.412 -1.127 1.00 0.00 H +ATOM 151 C GLY 9 32.181 -95.107 -2.483 1.00 0.00 C +ATOM 152 O GLY 9 31.118 -95.718 -2.522 1.00 0.00 O +ATOM 153 N LYS 10 33.396 -95.646 -2.719 1.00 0.00 N +ATOM 154 H LYS 10 34.226 -95.072 -2.755 1.00 0.00 H +ATOM 155 CA LYS 10 33.694 -97.050 -3.089 1.00 0.00 C +ATOM 156 HA LYS 10 33.113 -97.278 -3.982 1.00 0.00 H +ATOM 157 CB LYS 10 35.170 -97.299 -3.292 1.00 0.00 C +ATOM 158 HB2 LYS 10 35.542 -96.397 -3.778 1.00 0.00 H +ATOM 159 HB3 LYS 10 35.747 -97.466 -2.382 1.00 0.00 H +ATOM 160 CG LYS 10 35.547 -98.488 -4.193 1.00 0.00 C +ATOM 161 HG2 LYS 10 36.578 -98.814 -4.058 1.00 0.00 H +ATOM 162 HG3 LYS 10 34.990 -99.341 -3.806 1.00 0.00 H +ATOM 163 CD LYS 10 35.244 -98.240 -5.663 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.165 -98.319 -5.796 1.00 0.00 H +ATOM 165 HD3 LYS 10 35.592 -97.241 -5.925 1.00 0.00 H +ATOM 166 CE LYS 10 36.083 -99.280 -6.461 1.00 0.00 C +ATOM 167 HE2 LYS 10 36.916 -98.665 -6.803 1.00 0.00 H +ATOM 168 HE3 LYS 10 36.334-100.150 -5.854 1.00 0.00 H +ATOM 169 NZ LYS 10 35.389 -99.738 -7.669 1.00 0.00 N +ATOM 170 HZ1 LYS 10 36.005-100.420 -8.089 1.00 0.00 H +ATOM 171 HZ2 LYS 10 35.281 -99.070 -8.420 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.510-100.213 -7.521 1.00 0.00 H +ATOM 173 C LYS 10 33.207 -97.944 -2.011 1.00 0.00 C +ATOM 174 O LYS 10 32.723 -99.071 -2.275 1.00 0.00 O +ATOM 175 N THR 11 33.314 -97.513 -0.694 1.00 0.00 N +ATOM 176 H THR 11 33.703 -96.599 -0.508 1.00 0.00 H +ATOM 177 CA THR 11 32.898 -98.349 0.466 1.00 0.00 C +ATOM 178 HA THR 11 33.208 -99.375 0.272 1.00 0.00 H +ATOM 179 CB THR 11 33.655 -97.924 1.744 1.00 0.00 C +ATOM 180 HB THR 11 33.382 -96.901 2.001 1.00 0.00 H +ATOM 181 CG2 THR 11 33.385 -98.912 2.893 1.00 0.00 C +ATOM 182 HG21 THR 11 33.667 -99.910 2.556 1.00 0.00 H +ATOM 183 HG22 THR 11 32.352 -98.822 3.228 1.00 0.00 H +ATOM 184 HG23 THR 11 33.848 -98.545 3.809 1.00 0.00 H +ATOM 185 OG1 THR 11 34.980 -97.861 1.431 1.00 0.00 O +ATOM 186 HG1 THR 11 35.242 -97.154 2.024 1.00 0.00 H +ATOM 187 C THR 11 31.353 -98.380 0.721 1.00 0.00 C +ATOM 188 O THR 11 30.780 -99.420 1.019 1.00 0.00 O +ATOM 189 N LEU 12 30.675 -97.257 0.441 1.00 0.00 N +ATOM 190 H LEU 12 31.225 -96.475 0.115 1.00 0.00 H +ATOM 191 CA LEU 12 29.285 -97.049 0.680 1.00 0.00 C +ATOM 192 HA LEU 12 29.101 -97.412 1.691 1.00 0.00 H +ATOM 193 CB LEU 12 28.963 -95.525 0.513 1.00 0.00 C +ATOM 194 HB2 LEU 12 29.250 -95.173 -0.478 1.00 0.00 H +ATOM 195 HB3 LEU 12 27.893 -95.317 0.507 1.00 0.00 H +ATOM 196 CG LEU 12 29.583 -94.518 1.481 1.00 0.00 C +ATOM 197 HG LEU 12 30.652 -94.444 1.284 1.00 0.00 H +ATOM 198 CD1 LEU 12 29.129 -93.101 1.110 1.00 0.00 C +ATOM 199 HD11 LEU 12 29.552 -92.878 0.130 1.00 0.00 H +ATOM 200 HD12 LEU 12 29.562 -92.324 1.740 1.00 0.00 H +ATOM 201 HD13 LEU 12 28.040 -93.111 1.066 1.00 0.00 H +ATOM 202 CD2 LEU 12 29.367 -94.965 2.920 1.00 0.00 C +ATOM 203 HD21 LEU 12 28.315 -94.824 3.168 1.00 0.00 H +ATOM 204 HD22 LEU 12 29.944 -94.271 3.532 1.00 0.00 H +ATOM 205 HD23 LEU 12 29.799 -95.902 3.270 1.00 0.00 H +ATOM 206 C LEU 12 28.295 -97.900 -0.191 1.00 0.00 C +ATOM 207 O LEU 12 28.691 -98.433 -1.246 1.00 0.00 O +ATOM 208 N LYS 13 27.025 -97.994 0.162 1.00 0.00 N +ATOM 209 H LYS 13 26.862 -97.638 1.094 1.00 0.00 H +ATOM 210 CA LYS 13 25.924 -98.405 -0.769 1.00 0.00 C +ATOM 211 HA LYS 13 26.326 -98.434 -1.781 1.00 0.00 H +ATOM 212 CB LYS 13 25.310 -99.722 -0.435 1.00 0.00 C +ATOM 213 HB2 LYS 13 26.035-100.303 0.135 1.00 0.00 H +ATOM 214 HB3 LYS 13 24.446 -99.623 0.222 1.00 0.00 H +ATOM 215 CG LYS 13 24.919-100.548 -1.680 1.00 0.00 C +ATOM 216 HG2 LYS 13 24.240-100.011 -2.343 1.00 0.00 H +ATOM 217 HG3 LYS 13 25.826-100.676 -2.271 1.00 0.00 H +ATOM 218 CD LYS 13 24.390-102.004 -1.364 1.00 0.00 C +ATOM 219 HD2 LYS 13 25.125-102.576 -0.797 1.00 0.00 H +ATOM 220 HD3 LYS 13 23.508-101.938 -0.728 1.00 0.00 H +ATOM 221 CE LYS 13 24.059-102.705 -2.632 1.00 0.00 C +ATOM 222 HE2 LYS 13 23.166-102.224 -3.031 1.00 0.00 H +ATOM 223 HE3 LYS 13 24.895-102.557 -3.316 1.00 0.00 H +ATOM 224 NZ LYS 13 23.906-104.154 -2.391 1.00 0.00 N +ATOM 225 HZ1 LYS 13 23.756-104.732 -3.206 1.00 0.00 H +ATOM 226 HZ2 LYS 13 23.095-104.467 -1.877 1.00 0.00 H +ATOM 227 HZ3 LYS 13 24.791-104.463 -2.013 1.00 0.00 H +ATOM 228 C LYS 13 24.865 -97.255 -0.794 1.00 0.00 C +ATOM 229 O LYS 13 24.654 -96.482 0.149 1.00 0.00 O +ATOM 230 N GLY 14 24.127 -97.175 -1.987 1.00 0.00 N +ATOM 231 H GLY 14 24.487 -97.719 -2.759 1.00 0.00 H +ATOM 232 CA GLY 14 22.835 -96.591 -2.119 1.00 0.00 C +ATOM 233 HA2 GLY 14 22.083 -97.380 -2.118 1.00 0.00 H +ATOM 234 HA3 GLY 14 22.598 -95.895 -1.314 1.00 0.00 H +ATOM 235 C GLY 14 22.633 -95.846 -3.437 1.00 0.00 C +ATOM 236 O GLY 14 23.468 -95.809 -4.331 1.00 0.00 O +ATOM 237 N VAL 15 21.367 -95.348 -3.615 1.00 0.00 N +ATOM 238 H VAL 15 20.730 -95.486 -2.843 1.00 0.00 H +ATOM 239 CA VAL 15 20.878 -94.707 -4.872 1.00 0.00 C +ATOM 240 HA VAL 15 21.671 -94.016 -5.156 1.00 0.00 H +ATOM 241 CB VAL 15 20.427 -95.687 -6.008 1.00 0.00 C +ATOM 242 HB VAL 15 21.280 -96.162 -6.493 1.00 0.00 H +ATOM 243 CG1 VAL 15 19.523 -96.806 -5.380 1.00 0.00 C +ATOM 244 HG11 VAL 15 20.028 -97.324 -4.565 1.00 0.00 H +ATOM 245 HG12 VAL 15 18.753 -96.250 -4.846 1.00 0.00 H +ATOM 246 HG13 VAL 15 19.151 -97.440 -6.185 1.00 0.00 H +ATOM 247 CG2 VAL 15 19.564 -95.065 -7.114 1.00 0.00 C +ATOM 248 HG21 VAL 15 18.561 -94.833 -6.757 1.00 0.00 H +ATOM 249 HG22 VAL 15 19.947 -94.090 -7.415 1.00 0.00 H +ATOM 250 HG23 VAL 15 19.540 -95.683 -8.012 1.00 0.00 H +ATOM 251 C VAL 15 19.774 -93.788 -4.383 1.00 0.00 C +ATOM 252 O VAL 15 18.964 -94.140 -3.529 1.00 0.00 O +ATOM 253 N HD1 16 19.776 -92.607 -4.950 1.00 0.00 N +ATOM 254 CA HD1 16 18.705 -91.571 -4.726 1.00 0.00 C +ATOM 255 C HD1 16 18.539 -90.671 -5.984 1.00 0.00 C +ATOM 256 O HD1 16 19.152 -90.970 -6.975 1.00 0.00 O +ATOM 257 CB HD1 16 18.923 -90.757 -3.425 1.00 0.00 C +ATOM 258 CG HD1 16 20.327 -90.259 -3.395 1.00 0.00 C +ATOM 259 CD2 HD1 16 20.818 -89.181 -4.103 1.00 0.00 C +ATOM 260 ND1 HD1 16 21.461 -90.840 -2.819 1.00 0.00 N +ATOM 261 CE1 HD1 16 22.547 -90.140 -3.210 1.00 0.00 C +ATOM 262 NE2 HD1 16 22.189 -89.185 -4.079 1.00 0.00 N +ATOM 263 H HD1 16 20.277 -92.551 -5.825 1.00 0.00 H +ATOM 264 HA HD1 16 17.775 -92.127 -4.611 1.00 0.00 H +ATOM 265 HB2 HD1 16 18.177 -89.985 -3.233 1.00 0.00 H +ATOM 266 HB3 HD1 16 18.929 -91.458 -2.591 1.00 0.00 H +ATOM 267 HD1 HD1 16 21.402 -91.458 -2.023 1.00 0.00 H +ATOM 268 HD2 HD1 16 20.307 -88.536 -4.803 1.00 0.00 H +ATOM 269 HE1 HD1 16 23.556 -90.472 -3.017 1.00 0.00 H +ATOM 270 N THR 17 17.803 -89.554 -5.942 1.00 0.00 N +ATOM 271 H THR 17 17.407 -89.228 -5.072 1.00 0.00 H +ATOM 272 CA THR 17 17.554 -88.605 -7.052 1.00 0.00 C +ATOM 273 HA THR 17 18.405 -88.789 -7.708 1.00 0.00 H +ATOM 274 CB THR 17 16.200 -88.825 -7.683 1.00 0.00 C +ATOM 275 HB THR 17 16.109 -88.094 -8.486 1.00 0.00 H +ATOM 276 CG2 THR 17 15.863 -90.180 -8.250 1.00 0.00 C +ATOM 277 HG21 THR 17 14.884 -90.078 -8.718 1.00 0.00 H +ATOM 278 HG22 THR 17 15.887 -90.930 -7.459 1.00 0.00 H +ATOM 279 HG23 THR 17 16.699 -90.433 -8.901 1.00 0.00 H +ATOM 280 OG1 THR 17 15.228 -88.538 -6.755 1.00 0.00 O +ATOM 281 HG1 THR 17 15.314 -87.586 -6.667 1.00 0.00 H +ATOM 282 C THR 17 17.702 -87.154 -6.642 1.00 0.00 C +ATOM 283 O THR 17 17.601 -86.727 -5.469 1.00 0.00 O +ATOM 284 N HD2 18 18.069 -86.402 -7.655 1.00 0.00 N +ATOM 285 CA HD2 18 18.252 -84.946 -7.689 1.00 0.00 C +ATOM 286 C HD2 18 17.313 -84.220 -8.672 1.00 0.00 C +ATOM 287 O HD2 18 17.365 -84.402 -9.885 1.00 0.00 O +ATOM 288 CB HD2 18 19.705 -84.616 -8.062 1.00 0.00 C +ATOM 289 CG HD2 18 20.667 -85.115 -6.967 1.00 0.00 C +ATOM 290 CD2 HD2 18 21.429 -86.246 -7.020 1.00 0.00 C +ATOM 291 ND1 HD2 18 20.822 -84.630 -5.709 1.00 0.00 N +ATOM 292 CE1 HD2 18 21.768 -85.352 -5.134 1.00 0.00 C +ATOM 293 NE2 HD2 18 22.197 -86.357 -5.891 1.00 0.00 N +ATOM 294 H HD2 18 18.099 -86.919 -8.522 1.00 0.00 H +ATOM 295 HA HD2 18 18.136 -84.590 -6.665 1.00 0.00 H +ATOM 296 HB2 HD2 18 19.966 -84.994 -9.050 1.00 0.00 H +ATOM 297 HB3 HD2 18 19.844 -83.535 -8.091 1.00 0.00 H +ATOM 298 HD1 HD2 18 20.305 -83.884 -5.265 1.00 0.00 H +ATOM 299 HD2 HD2 18 21.492 -86.986 -7.804 1.00 0.00 H +ATOM 300 HE1 HD2 18 22.098 -85.277 -4.108 1.00 0.00 H +ATOM 301 N GLU 19 16.425 -83.470 -8.041 1.00 0.00 N +ATOM 302 H GLU 19 16.326 -83.468 -7.036 1.00 0.00 H +ATOM 303 CA GLU 19 15.612 -82.532 -8.833 1.00 0.00 C +ATOM 304 HA GLU 19 15.308 -83.097 -9.714 1.00 0.00 H +ATOM 305 CB GLU 19 14.413 -82.083 -7.946 1.00 0.00 C +ATOM 306 HB2 GLU 19 13.737 -82.892 -7.669 1.00 0.00 H +ATOM 307 HB3 GLU 19 14.683 -81.729 -6.951 1.00 0.00 H +ATOM 308 CG GLU 19 13.594 -80.995 -8.686 1.00 0.00 C +ATOM 309 HG2 GLU 19 12.624 -81.040 -8.192 1.00 0.00 H +ATOM 310 HG3 GLU 19 14.051 -80.030 -8.470 1.00 0.00 H +ATOM 311 CD GLU 19 13.315 -81.269 -10.163 1.00 0.00 C +ATOM 312 OE1 GLU 19 13.381 -80.373 -11.030 1.00 0.00 O +ATOM 313 OE2 GLU 19 13.083 -82.420 -10.513 1.00 0.00 O +ATOM 314 C GLU 19 16.449 -81.390 -9.456 1.00 0.00 C +ATOM 315 O GLU 19 17.164 -80.695 -8.743 1.00 0.00 O +ATOM 316 N ALA 20 16.420 -81.418 -10.836 1.00 0.00 N +ATOM 317 H ALA 20 15.655 -81.905 -11.281 1.00 0.00 H +ATOM 318 CA ALA 20 17.282 -80.691 -11.785 1.00 0.00 C +ATOM 319 HA ALA 20 17.631 -79.732 -11.401 1.00 0.00 H +ATOM 320 CB ALA 20 18.579 -81.539 -11.940 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.182 -81.429 -11.038 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.115 -81.118 -12.790 1.00 0.00 H +ATOM 323 HB3 ALA 20 18.303 -82.574 -12.140 1.00 0.00 H +ATOM 324 C ALA 20 16.456 -80.252 -13.046 1.00 0.00 C +ATOM 325 O ALA 20 15.700 -81.034 -13.624 1.00 0.00 O +ATOM 326 N VAL 21 16.724 -79.046 -13.503 1.00 0.00 N +ATOM 327 H VAL 21 17.183 -78.470 -12.812 1.00 0.00 H +ATOM 328 CA VAL 21 16.105 -78.400 -14.665 1.00 0.00 C +ATOM 329 HA VAL 21 15.042 -78.628 -14.747 1.00 0.00 H +ATOM 330 CB VAL 21 16.256 -76.900 -14.405 1.00 0.00 C +ATOM 331 HB VAL 21 15.945 -76.700 -13.380 1.00 0.00 H +ATOM 332 CG1 VAL 21 17.738 -76.329 -14.474 1.00 0.00 C +ATOM 333 HG11 VAL 21 18.385 -76.866 -13.781 1.00 0.00 H +ATOM 334 HG12 VAL 21 17.594 -75.302 -14.138 1.00 0.00 H +ATOM 335 HG13 VAL 21 18.235 -76.274 -15.443 1.00 0.00 H +ATOM 336 CG2 VAL 21 15.316 -76.103 -15.267 1.00 0.00 C +ATOM 337 HG21 VAL 21 14.297 -76.277 -14.922 1.00 0.00 H +ATOM 338 HG22 VAL 21 15.450 -76.334 -16.324 1.00 0.00 H +ATOM 339 HG23 VAL 21 15.624 -75.066 -15.135 1.00 0.00 H +ATOM 340 C VAL 21 16.767 -78.909 -15.951 1.00 0.00 C +ATOM 341 O VAL 21 16.074 -78.833 -16.983 1.00 0.00 O +ATOM 342 N ASP 22 17.887 -79.606 -15.953 1.00 0.00 N +ATOM 343 H ASP 22 18.542 -79.463 -15.198 1.00 0.00 H +ATOM 344 CA ASP 22 18.521 -80.345 -17.055 1.00 0.00 C +ATOM 345 HA ASP 22 17.806 -81.057 -17.467 1.00 0.00 H +ATOM 346 CB ASP 22 18.888 -79.364 -18.181 1.00 0.00 C +ATOM 347 HB2 ASP 22 17.970 -78.837 -18.443 1.00 0.00 H +ATOM 348 HB3 ASP 22 19.726 -78.735 -17.882 1.00 0.00 H +ATOM 349 CG ASP 22 19.322 -80.039 -19.504 1.00 0.00 C +ATOM 350 OD1 ASP 22 19.088 -81.229 -19.805 1.00 0.00 O +ATOM 351 OD2 ASP 22 19.862 -79.356 -20.406 1.00 0.00 O +ATOM 352 C ASP 22 19.768 -81.124 -16.601 1.00 0.00 C +ATOM 353 O ASP 22 20.262 -80.957 -15.494 1.00 0.00 O +ATOM 354 N ALA 23 20.315 -82.021 -17.433 1.00 0.00 N +ATOM 355 H ALA 23 20.053 -82.073 -18.407 1.00 0.00 H +ATOM 356 CA ALA 23 21.369 -82.966 -17.042 1.00 0.00 C +ATOM 357 HA ALA 23 21.146 -83.639 -16.214 1.00 0.00 H +ATOM 358 CB ALA 23 21.749 -83.931 -18.250 1.00 0.00 C +ATOM 359 HB1 ALA 23 21.277 -84.913 -18.230 1.00 0.00 H +ATOM 360 HB2 ALA 23 22.812 -84.172 -18.275 1.00 0.00 H +ATOM 361 HB3 ALA 23 21.400 -83.469 -19.174 1.00 0.00 H +ATOM 362 C ALA 23 22.657 -82.173 -16.647 1.00 0.00 C +ATOM 363 O ALA 23 23.513 -82.680 -15.914 1.00 0.00 O +ATOM 364 N ALA 24 22.923 -81.031 -17.224 1.00 0.00 N +ATOM 365 H ALA 24 22.510 -80.847 -18.127 1.00 0.00 H +ATOM 366 CA ALA 24 24.006 -80.199 -16.705 1.00 0.00 C +ATOM 367 HA ALA 24 24.983 -80.631 -16.918 1.00 0.00 H +ATOM 368 CB ALA 24 23.858 -78.891 -17.419 1.00 0.00 C +ATOM 369 HB1 ALA 24 24.709 -78.243 -17.207 1.00 0.00 H +ATOM 370 HB2 ALA 24 22.978 -78.368 -17.046 1.00 0.00 H +ATOM 371 HB3 ALA 24 23.710 -79.094 -18.479 1.00 0.00 H +ATOM 372 C ALA 24 23.897 -80.018 -15.236 1.00 0.00 C +ATOM 373 O ALA 24 24.856 -80.180 -14.468 1.00 0.00 O +ATOM 374 N GLU 25 22.679 -79.672 -14.732 1.00 0.00 N +ATOM 375 H GLU 25 21.900 -79.746 -15.371 1.00 0.00 H +ATOM 376 CA GLU 25 22.427 -79.307 -13.339 1.00 0.00 C +ATOM 377 HA GLU 25 23.289 -78.739 -12.990 1.00 0.00 H +ATOM 378 CB GLU 25 21.163 -78.514 -13.289 1.00 0.00 C +ATOM 379 HB2 GLU 25 21.171 -77.708 -14.022 1.00 0.00 H +ATOM 380 HB3 GLU 25 20.298 -79.120 -13.557 1.00 0.00 H +ATOM 381 CG GLU 25 20.850 -77.842 -11.942 1.00 0.00 C +ATOM 382 HG2 GLU 25 19.841 -77.431 -11.912 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.827 -78.581 -11.141 1.00 0.00 H +ATOM 384 CD GLU 25 21.895 -76.813 -11.415 1.00 0.00 C +ATOM 385 OE1 GLU 25 22.995 -76.660 -12.007 1.00 0.00 O +ATOM 386 OE2 GLU 25 21.546 -76.123 -10.467 1.00 0.00 O +ATOM 387 C GLU 25 22.456 -80.563 -12.368 1.00 0.00 C +ATOM 388 O GLU 25 22.920 -80.544 -11.204 1.00 0.00 O +ATOM 389 N ALA 26 22.038 -81.730 -12.815 1.00 0.00 N +ATOM 390 H ALA 26 21.868 -81.727 -13.810 1.00 0.00 H +ATOM 391 CA ALA 26 22.154 -83.037 -12.252 1.00 0.00 C +ATOM 392 HA ALA 26 21.780 -82.944 -11.232 1.00 0.00 H +ATOM 393 CB ALA 26 21.242 -84.009 -13.103 1.00 0.00 C +ATOM 394 HB1 ALA 26 20.272 -83.545 -13.283 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.043 -84.922 -12.542 1.00 0.00 H +ATOM 396 HB3 ALA 26 21.625 -84.101 -14.119 1.00 0.00 H +ATOM 397 C ALA 26 23.616 -83.574 -12.104 1.00 0.00 C +ATOM 398 O ALA 26 24.058 -84.137 -11.121 1.00 0.00 O +ATOM 399 N GLU 27 24.428 -83.275 -13.081 1.00 0.00 N +ATOM 400 H GLU 27 24.082 -82.964 -13.977 1.00 0.00 H +ATOM 401 CA GLU 27 25.873 -83.634 -13.013 1.00 0.00 C +ATOM 402 HA GLU 27 25.991 -84.679 -12.728 1.00 0.00 H +ATOM 403 CB GLU 27 26.535 -83.623 -14.373 1.00 0.00 C +ATOM 404 HB2 GLU 27 25.873 -84.118 -15.083 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.644 -82.611 -14.762 1.00 0.00 H +ATOM 406 CG GLU 27 27.879 -84.361 -14.545 1.00 0.00 C +ATOM 407 HG2 GLU 27 28.554 -83.741 -13.954 1.00 0.00 H +ATOM 408 HG3 GLU 27 27.867 -85.323 -14.033 1.00 0.00 H +ATOM 409 CD GLU 27 28.477 -84.565 -15.977 1.00 0.00 C +ATOM 410 OE1 GLU 27 28.276 -83.726 -16.873 1.00 0.00 O +ATOM 411 OE2 GLU 27 29.291 -85.484 -16.225 1.00 0.00 O +ATOM 412 C GLU 27 26.675 -82.855 -12.004 1.00 0.00 C +ATOM 413 O GLU 27 27.556 -83.410 -11.359 1.00 0.00 O +ATOM 414 N LYS 28 26.219 -81.598 -11.784 1.00 0.00 N +ATOM 415 H LYS 28 25.359 -81.401 -12.276 1.00 0.00 H +ATOM 416 CA LYS 28 26.609 -80.705 -10.709 1.00 0.00 C +ATOM 417 HA LYS 28 27.695 -80.743 -10.621 1.00 0.00 H +ATOM 418 CB LYS 28 26.048 -79.324 -10.868 1.00 0.00 C +ATOM 419 HB2 LYS 28 26.059 -79.063 -11.926 1.00 0.00 H +ATOM 420 HB3 LYS 28 25.026 -79.221 -10.504 1.00 0.00 H +ATOM 421 CG LYS 28 26.803 -78.262 -10.161 1.00 0.00 C +ATOM 422 HG2 LYS 28 26.999 -78.589 -9.140 1.00 0.00 H +ATOM 423 HG3 LYS 28 27.745 -78.196 -10.705 1.00 0.00 H +ATOM 424 CD LYS 28 26.015 -76.937 -10.142 1.00 0.00 C +ATOM 425 HD2 LYS 28 26.713 -76.148 -9.863 1.00 0.00 H +ATOM 426 HD3 LYS 28 25.617 -76.634 -11.111 1.00 0.00 H +ATOM 427 CE LYS 28 24.938 -76.779 -9.092 1.00 0.00 C +ATOM 428 HE2 LYS 28 24.247 -77.623 -9.094 1.00 0.00 H +ATOM 429 HE3 LYS 28 25.423 -76.791 -8.116 1.00 0.00 H +ATOM 430 NZ LYS 28 24.217 -75.465 -9.203 1.00 0.00 N +ATOM 431 HZ1 LYS 28 23.775 -75.543 -10.108 1.00 0.00 H +ATOM 432 HZ2 LYS 28 24.853 -74.683 -9.253 1.00 0.00 H +ATOM 433 HZ3 LYS 28 23.419 -75.295 -8.607 1.00 0.00 H +ATOM 434 C LYS 28 26.151 -81.335 -9.350 1.00 0.00 C +ATOM 435 O LYS 28 27.015 -81.743 -8.567 1.00 0.00 O +ATOM 436 N PHE 29 24.865 -81.528 -9.052 1.00 0.00 N +ATOM 437 H PHE 29 24.172 -81.229 -9.724 1.00 0.00 H +ATOM 438 CA PHE 29 24.394 -82.219 -7.841 1.00 0.00 C +ATOM 439 HA PHE 29 24.837 -81.639 -7.031 1.00 0.00 H +ATOM 440 CB PHE 29 22.863 -82.138 -7.771 1.00 0.00 C +ATOM 441 HB2 PHE 29 22.511 -82.718 -8.624 1.00 0.00 H +ATOM 442 HB3 PHE 29 22.567 -82.429 -6.763 1.00 0.00 H +ATOM 443 CG PHE 29 22.136 -80.856 -8.074 1.00 0.00 C +ATOM 444 CD1 PHE 29 20.965 -80.784 -8.796 1.00 0.00 C +ATOM 445 HD1 PHE 29 20.436 -81.637 -9.197 1.00 0.00 H +ATOM 446 CE1 PHE 29 20.202 -79.595 -8.777 1.00 0.00 C +ATOM 447 HE1 PHE 29 19.240 -79.727 -9.248 1.00 0.00 H +ATOM 448 CZ PHE 29 20.640 -78.463 -8.121 1.00 0.00 C +ATOM 449 HZ PHE 29 20.036 -77.570 -8.196 1.00 0.00 H +ATOM 450 CE2 PHE 29 21.842 -78.499 -7.464 1.00 0.00 C +ATOM 451 HE2 PHE 29 22.213 -77.633 -6.936 1.00 0.00 H +ATOM 452 CD2 PHE 29 22.629 -79.719 -7.460 1.00 0.00 C +ATOM 453 HD2 PHE 29 23.546 -79.666 -6.893 1.00 0.00 H +ATOM 454 C PHE 29 24.873 -83.687 -7.674 1.00 0.00 C +ATOM 455 O PHE 29 24.630 -84.308 -6.684 1.00 0.00 O +ATOM 456 N THR 30 25.432 -84.263 -8.734 1.00 0.00 N +ATOM 457 H THR 30 25.332 -83.795 -9.624 1.00 0.00 H +ATOM 458 CA THR 30 26.236 -85.502 -8.605 1.00 0.00 C +ATOM 459 HA THR 30 25.623 -86.189 -8.020 1.00 0.00 H +ATOM 460 CB THR 30 26.361 -86.163 -9.978 1.00 0.00 C +ATOM 461 HB THR 30 26.457 -85.494 -10.834 1.00 0.00 H +ATOM 462 CG2 THR 30 27.407 -87.240 -10.150 1.00 0.00 C +ATOM 463 HG21 THR 30 28.338 -86.672 -10.176 1.00 0.00 H +ATOM 464 HG22 THR 30 27.446 -87.999 -9.368 1.00 0.00 H +ATOM 465 HG23 THR 30 27.222 -87.776 -11.080 1.00 0.00 H +ATOM 466 OG1 THR 30 25.104 -86.750 -10.174 1.00 0.00 O +ATOM 467 HG1 THR 30 24.513 -85.995 -10.223 1.00 0.00 H +ATOM 468 C THR 30 27.581 -85.401 -7.877 1.00 0.00 C +ATOM 469 O THR 30 27.843 -86.348 -7.161 1.00 0.00 O +ATOM 470 N LYS 31 28.327 -84.376 -8.073 1.00 0.00 N +ATOM 471 H LYS 31 27.861 -83.647 -8.594 1.00 0.00 H +ATOM 472 CA LYS 31 29.754 -84.265 -7.656 1.00 0.00 C +ATOM 473 HA LYS 31 30.064 -85.101 -7.030 1.00 0.00 H +ATOM 474 CB LYS 31 30.635 -84.242 -8.939 1.00 0.00 C +ATOM 475 HB2 LYS 31 31.634 -84.493 -8.580 1.00 0.00 H +ATOM 476 HB3 LYS 31 30.252 -84.971 -9.653 1.00 0.00 H +ATOM 477 CG LYS 31 30.724 -82.881 -9.608 1.00 0.00 C +ATOM 478 HG2 LYS 31 29.700 -82.549 -9.783 1.00 0.00 H +ATOM 479 HG3 LYS 31 31.178 -82.106 -8.991 1.00 0.00 H +ATOM 480 CD LYS 31 31.531 -83.075 -10.901 1.00 0.00 C +ATOM 481 HD2 LYS 31 32.588 -82.904 -10.694 1.00 0.00 H +ATOM 482 HD3 LYS 31 31.500 -84.047 -11.393 1.00 0.00 H +ATOM 483 CE LYS 31 31.132 -81.948 -11.907 1.00 0.00 C +ATOM 484 HE2 LYS 31 30.043 -81.976 -11.950 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.238 -80.940 -11.506 1.00 0.00 H +ATOM 486 NZ LYS 31 31.945 -82.152 -13.105 1.00 0.00 N +ATOM 487 HZ1 LYS 31 32.905 -82.148 -12.792 1.00 0.00 H +ATOM 488 HZ2 LYS 31 31.750 -81.454 -13.809 1.00 0.00 H +ATOM 489 HZ3 LYS 31 31.845 -83.057 -13.542 1.00 0.00 H +ATOM 490 C LYS 31 30.051 -83.074 -6.793 1.00 0.00 C +ATOM 491 O LYS 31 31.191 -82.892 -6.386 1.00 0.00 O +ATOM 492 N ALA 32 29.097 -82.244 -6.391 1.00 0.00 N +ATOM 493 H ALA 32 28.125 -82.371 -6.633 1.00 0.00 H +ATOM 494 CA ALA 32 29.379 -81.000 -5.661 1.00 0.00 C +ATOM 495 HA ALA 32 30.133 -80.404 -6.176 1.00 0.00 H +ATOM 496 CB ALA 32 28.237 -80.054 -5.840 1.00 0.00 C +ATOM 497 HB1 ALA 32 28.276 -79.645 -6.850 1.00 0.00 H +ATOM 498 HB2 ALA 32 27.284 -80.540 -5.631 1.00 0.00 H +ATOM 499 HB3 ALA 32 28.407 -79.138 -5.275 1.00 0.00 H +ATOM 500 C ALA 32 29.818 -81.217 -4.150 1.00 0.00 C +ATOM 501 O ALA 32 30.452 -80.343 -3.589 1.00 0.00 O +ATOM 502 N ASP 33 29.490 -82.287 -3.511 1.00 0.00 N +ATOM 503 H ASP 33 29.135 -83.042 -4.080 1.00 0.00 H +ATOM 504 CA ASP 33 30.077 -82.624 -2.211 1.00 0.00 C +ATOM 505 HA ASP 33 30.322 -81.705 -1.679 1.00 0.00 H +ATOM 506 CB ASP 33 28.995 -83.209 -1.253 1.00 0.00 C +ATOM 507 HB2 ASP 33 29.416 -83.447 -0.276 1.00 0.00 H +ATOM 508 HB3 ASP 33 28.120 -82.560 -1.208 1.00 0.00 H +ATOM 509 CG ASP 33 28.479 -84.568 -1.759 1.00 0.00 C +ATOM 510 OD1 ASP 33 28.863 -85.631 -1.283 1.00 0.00 O +ATOM 511 OD2 ASP 33 27.665 -84.598 -2.711 1.00 0.00 O +ATOM 512 C ASP 33 31.307 -83.534 -2.268 1.00 0.00 C +ATOM 513 O ASP 33 32.078 -83.638 -1.313 1.00 0.00 O +ATOM 514 N ALA 34 31.496 -84.201 -3.424 1.00 0.00 N +ATOM 515 H ALA 34 30.779 -84.243 -4.134 1.00 0.00 H +ATOM 516 CA ALA 34 32.733 -84.860 -3.774 1.00 0.00 C +ATOM 517 HA ALA 34 32.951 -85.596 -3.000 1.00 0.00 H +ATOM 518 CB ALA 34 32.310 -85.804 -4.929 1.00 0.00 C +ATOM 519 HB1 ALA 34 33.114 -86.440 -5.299 1.00 0.00 H +ATOM 520 HB2 ALA 34 31.950 -85.307 -5.830 1.00 0.00 H +ATOM 521 HB3 ALA 34 31.480 -86.385 -4.526 1.00 0.00 H +ATOM 522 C ALA 34 33.831 -83.836 -4.032 1.00 0.00 C +ATOM 523 O ALA 34 34.984 -84.065 -3.594 1.00 0.00 O +ATOM 524 N ASN 35 33.603 -82.701 -4.642 1.00 0.00 N +ATOM 525 H ASN 35 32.709 -82.536 -5.082 1.00 0.00 H +ATOM 526 CA ASN 35 34.538 -81.623 -4.774 1.00 0.00 C +ATOM 527 HA ASN 35 35.429 -82.022 -5.259 1.00 0.00 H +ATOM 528 CB ASN 35 33.786 -80.524 -5.542 1.00 0.00 C +ATOM 529 HB2 ASN 35 33.242 -80.826 -6.437 1.00 0.00 H +ATOM 530 HB3 ASN 35 33.030 -80.056 -4.911 1.00 0.00 H +ATOM 531 CG ASN 35 34.593 -79.341 -5.873 1.00 0.00 C +ATOM 532 OD1 ASN 35 35.286 -78.723 -5.085 1.00 0.00 O +ATOM 533 ND2 ASN 35 34.514 -78.885 -7.060 1.00 0.00 N +ATOM 534 HD21 ASN 35 33.911 -79.383 -7.699 1.00 0.00 H +ATOM 535 HD22 ASN 35 35.186 -78.189 -7.349 1.00 0.00 H +ATOM 536 C ASN 35 35.101 -81.198 -3.375 1.00 0.00 C +ATOM 537 O ASN 35 36.273 -80.925 -3.302 1.00 0.00 O +ATOM 538 N ASP 36 34.215 -81.026 -2.349 1.00 0.00 N +ATOM 539 H ASP 36 33.242 -81.266 -2.467 1.00 0.00 H +ATOM 540 CA ASP 36 34.549 -80.676 -0.967 1.00 0.00 C +ATOM 541 HA ASP 36 35.275 -79.874 -1.096 1.00 0.00 H +ATOM 542 CB ASP 36 33.265 -80.255 -0.251 1.00 0.00 C +ATOM 543 HB2 ASP 36 32.621 -81.094 0.014 1.00 0.00 H +ATOM 544 HB3 ASP 36 33.587 -79.987 0.755 1.00 0.00 H +ATOM 545 CG ASP 36 32.370 -79.110 -0.745 1.00 0.00 C +ATOM 546 OD1 ASP 36 31.173 -79.106 -0.339 1.00 0.00 O +ATOM 547 OD2 ASP 36 32.744 -78.041 -1.298 1.00 0.00 O +ATOM 548 C ASP 36 35.327 -81.810 -0.260 1.00 0.00 C +ATOM 549 O ASP 36 36.251 -81.454 0.485 1.00 0.00 O +ATOM 550 N LYS 37 34.986 -83.081 -0.445 1.00 0.00 N +ATOM 551 H LYS 37 34.105 -83.272 -0.901 1.00 0.00 H +ATOM 552 CA LYS 37 35.806 -84.166 0.129 1.00 0.00 C +ATOM 553 HA LYS 37 35.848 -84.121 1.217 1.00 0.00 H +ATOM 554 CB LYS 37 34.988 -85.458 -0.215 1.00 0.00 C +ATOM 555 HB2 LYS 37 35.531 -86.397 -0.110 1.00 0.00 H +ATOM 556 HB3 LYS 37 34.731 -85.421 -1.274 1.00 0.00 H +ATOM 557 CG LYS 37 33.690 -85.554 0.636 1.00 0.00 C +ATOM 558 HG2 LYS 37 33.068 -84.667 0.517 1.00 0.00 H +ATOM 559 HG3 LYS 37 33.958 -85.623 1.690 1.00 0.00 H +ATOM 560 CD LYS 37 32.932 -86.857 0.214 1.00 0.00 C +ATOM 561 HD2 LYS 37 32.683 -86.751 -0.842 1.00 0.00 H +ATOM 562 HD3 LYS 37 33.392 -87.797 0.521 1.00 0.00 H +ATOM 563 CE LYS 37 31.625 -87.061 0.863 1.00 0.00 C +ATOM 564 HE2 LYS 37 31.172 -88.005 0.561 1.00 0.00 H +ATOM 565 HE3 LYS 37 31.761 -87.114 1.943 1.00 0.00 H +ATOM 566 NZ LYS 37 30.636 -85.996 0.646 1.00 0.00 N +ATOM 567 HZ1 LYS 37 30.326 -85.814 -0.298 1.00 0.00 H +ATOM 568 HZ2 LYS 37 29.928 -85.893 1.360 1.00 0.00 H +ATOM 569 HZ3 LYS 37 31.143 -85.142 0.828 1.00 0.00 H +ATOM 570 C LYS 37 37.250 -84.222 -0.304 1.00 0.00 C +ATOM 571 O LYS 37 38.032 -84.825 0.368 1.00 0.00 O +ATOM 572 N GLY 38 37.482 -83.648 -1.463 1.00 0.00 N +ATOM 573 H GLY 38 36.686 -83.455 -2.055 1.00 0.00 H +ATOM 574 CA GLY 38 38.757 -83.610 -2.168 1.00 0.00 C +ATOM 575 HA2 GLY 38 38.890 -82.650 -2.668 1.00 0.00 H +ATOM 576 HA3 GLY 38 39.533 -83.657 -1.405 1.00 0.00 H +ATOM 577 C GLY 38 38.999 -84.774 -3.167 1.00 0.00 C +ATOM 578 O GLY 38 40.067 -85.317 -3.239 1.00 0.00 O +ATOM 579 N VAL 39 37.958 -85.187 -3.923 1.00 0.00 N +ATOM 580 H VAL 39 37.062 -84.728 -3.843 1.00 0.00 H +ATOM 581 CA VAL 39 37.854 -86.391 -4.709 1.00 0.00 C +ATOM 582 HA VAL 39 38.222 -87.200 -4.078 1.00 0.00 H +ATOM 583 CB VAL 39 36.369 -86.696 -4.990 1.00 0.00 C +ATOM 584 HB VAL 39 35.786 -85.835 -5.319 1.00 0.00 H +ATOM 585 CG1 VAL 39 36.025 -87.642 -6.120 1.00 0.00 C +ATOM 586 HG11 VAL 39 35.008 -88.027 -6.199 1.00 0.00 H +ATOM 587 HG12 VAL 39 36.457 -88.591 -5.803 1.00 0.00 H +ATOM 588 HG13 VAL 39 36.427 -87.348 -7.089 1.00 0.00 H +ATOM 589 CG2 VAL 39 35.680 -87.237 -3.699 1.00 0.00 C +ATOM 590 HG21 VAL 39 35.878 -86.487 -2.932 1.00 0.00 H +ATOM 591 HG22 VAL 39 36.176 -88.171 -3.438 1.00 0.00 H +ATOM 592 HG23 VAL 39 34.660 -87.575 -3.879 1.00 0.00 H +ATOM 593 C VAL 39 38.570 -86.375 -6.056 1.00 0.00 C +ATOM 594 O VAL 39 38.425 -85.421 -6.883 1.00 0.00 O +ATOM 595 N ASP 40 39.301 -87.453 -6.333 1.00 0.00 N +ATOM 596 H ASP 40 39.311 -88.161 -5.612 1.00 0.00 H +ATOM 597 CA ASP 40 40.034 -87.651 -7.597 1.00 0.00 C +ATOM 598 HA ASP 40 40.339 -86.707 -8.048 1.00 0.00 H +ATOM 599 CB ASP 40 41.261 -88.624 -7.423 1.00 0.00 C +ATOM 600 HB2 ASP 40 40.792 -89.496 -6.968 1.00 0.00 H +ATOM 601 HB3 ASP 40 41.783 -88.890 -8.342 1.00 0.00 H +ATOM 602 CG ASP 40 42.342 -88.174 -6.419 1.00 0.00 C +ATOM 603 OD1 ASP 40 43.030 -87.181 -6.650 1.00 0.00 O +ATOM 604 OD2 ASP 40 42.498 -88.814 -5.360 1.00 0.00 O +ATOM 605 C ASP 40 39.157 -88.306 -8.722 1.00 0.00 C +ATOM 606 O ASP 40 39.552 -88.251 -9.906 1.00 0.00 O +ATOM 607 N GLY 41 37.899 -88.745 -8.480 1.00 0.00 N +ATOM 608 H GLY 41 37.464 -88.448 -7.618 1.00 0.00 H +ATOM 609 CA GLY 41 37.042 -89.393 -9.497 1.00 0.00 C +ATOM 610 HA2 GLY 41 37.684 -90.199 -9.853 1.00 0.00 H +ATOM 611 HA3 GLY 41 36.127 -89.730 -9.009 1.00 0.00 H +ATOM 612 C GLY 41 36.520 -88.496 -10.645 1.00 0.00 C +ATOM 613 O GLY 41 36.667 -87.320 -10.633 1.00 0.00 O +ATOM 614 N GLU 42 35.863 -89.181 -11.596 1.00 0.00 N +ATOM 615 H GLU 42 35.775 -90.185 -11.661 1.00 0.00 H +ATOM 616 CA GLU 42 35.126 -88.499 -12.729 1.00 0.00 C +ATOM 617 HA GLU 42 34.832 -87.535 -12.314 1.00 0.00 H +ATOM 618 CB GLU 42 36.042 -88.184 -13.965 1.00 0.00 C +ATOM 619 HB2 GLU 42 36.883 -87.600 -13.591 1.00 0.00 H +ATOM 620 HB3 GLU 42 36.450 -89.155 -14.245 1.00 0.00 H +ATOM 621 CG GLU 42 35.404 -87.462 -15.172 1.00 0.00 C +ATOM 622 HG2 GLU 42 36.198 -87.317 -15.906 1.00 0.00 H +ATOM 623 HG3 GLU 42 34.653 -88.015 -15.737 1.00 0.00 H +ATOM 624 CD GLU 42 34.676 -86.147 -14.809 1.00 0.00 C +ATOM 625 OE1 GLU 42 35.224 -85.424 -13.906 1.00 0.00 O +ATOM 626 OE2 GLU 42 33.549 -85.907 -15.236 1.00 0.00 O +ATOM 627 C GLU 42 33.885 -89.317 -13.141 1.00 0.00 C +ATOM 628 O GLU 42 33.835 -90.577 -13.093 1.00 0.00 O +ATOM 629 N TRP 43 32.845 -88.586 -13.568 1.00 0.00 N +ATOM 630 H TRP 43 32.952 -87.643 -13.915 1.00 0.00 H +ATOM 631 CA TRP 43 31.447 -89.085 -13.794 1.00 0.00 C +ATOM 632 HA TRP 43 31.244 -89.982 -13.208 1.00 0.00 H +ATOM 633 CB TRP 43 30.463 -88.012 -13.160 1.00 0.00 C +ATOM 634 HB2 TRP 43 30.633 -87.037 -13.617 1.00 0.00 H +ATOM 635 HB3 TRP 43 29.414 -88.219 -13.371 1.00 0.00 H +ATOM 636 CG TRP 43 30.598 -88.075 -11.685 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.833 -88.833 -10.840 1.00 0.00 C +ATOM 638 HD1 TRP 43 29.017 -89.506 -11.059 1.00 0.00 H +ATOM 639 NE1 TRP 43 30.301 -88.753 -9.543 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.965 -89.332 -8.788 1.00 0.00 H +ATOM 641 CE2 TRP 43 31.346 -87.881 -9.472 1.00 0.00 C +ATOM 642 CZ2 TRP 43 32.159 -87.436 -8.393 1.00 0.00 C +ATOM 643 HZ2 TRP 43 31.895 -87.734 -7.389 1.00 0.00 H +ATOM 644 CH2 TRP 43 33.237 -86.576 -8.663 1.00 0.00 C +ATOM 645 HH2 TRP 43 33.781 -86.166 -7.824 1.00 0.00 H +ATOM 646 CZ3 TRP 43 33.507 -86.168 -9.972 1.00 0.00 C +ATOM 647 HZ3 TRP 43 34.249 -85.408 -10.170 1.00 0.00 H +ATOM 648 CE3 TRP 43 32.671 -86.599 -11.051 1.00 0.00 C +ATOM 649 HE3 TRP 43 32.888 -86.229 -12.042 1.00 0.00 H +ATOM 650 CD2 TRP 43 31.652 -87.536 -10.834 1.00 0.00 C +ATOM 651 C TRP 43 30.984 -89.476 -15.202 1.00 0.00 C +ATOM 652 O TRP 43 31.747 -89.252 -16.157 1.00 0.00 O +ATOM 653 N THR 44 29.855 -90.233 -15.354 1.00 0.00 N +ATOM 654 H THR 44 29.460 -90.605 -14.502 1.00 0.00 H +ATOM 655 CA THR 44 29.200 -90.637 -16.640 1.00 0.00 C +ATOM 656 HA THR 44 29.474 -90.012 -17.489 1.00 0.00 H +ATOM 657 CB THR 44 29.687 -92.079 -17.003 1.00 0.00 C +ATOM 658 HB THR 44 30.776 -92.032 -17.016 1.00 0.00 H +ATOM 659 CG2 THR 44 29.196 -93.158 -16.047 1.00 0.00 C +ATOM 660 HG21 THR 44 29.864 -94.000 -16.232 1.00 0.00 H +ATOM 661 HG22 THR 44 28.160 -93.428 -16.248 1.00 0.00 H +ATOM 662 HG23 THR 44 29.319 -92.873 -15.002 1.00 0.00 H +ATOM 663 OG1 THR 44 29.410 -92.542 -18.304 1.00 0.00 O +ATOM 664 HG1 THR 44 30.140 -92.182 -18.813 1.00 0.00 H +ATOM 665 C THR 44 27.685 -90.558 -16.584 1.00 0.00 C +ATOM 666 O THR 44 27.135 -90.735 -15.466 1.00 0.00 O +ATOM 667 N TYR 45 27.014 -90.422 -17.682 1.00 0.00 N +ATOM 668 H TYR 45 27.499 -90.330 -18.563 1.00 0.00 H +ATOM 669 CA TYR 45 25.599 -90.288 -17.748 1.00 0.00 C +ATOM 670 HA TYR 45 25.193 -90.409 -16.744 1.00 0.00 H +ATOM 671 CB TYR 45 25.219 -88.871 -18.135 1.00 0.00 C +ATOM 672 HB2 TYR 45 25.501 -88.214 -17.313 1.00 0.00 H +ATOM 673 HB3 TYR 45 25.703 -88.608 -19.076 1.00 0.00 H +ATOM 674 CG TYR 45 23.741 -88.648 -18.345 1.00 0.00 C +ATOM 675 CD1 TYR 45 22.812 -88.913 -17.276 1.00 0.00 C +ATOM 676 HD1 TYR 45 23.153 -89.162 -16.282 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.440 -88.568 -17.468 1.00 0.00 C +ATOM 678 HE1 TYR 45 20.762 -88.662 -16.634 1.00 0.00 H +ATOM 679 CZ TYR 45 20.993 -88.058 -18.675 1.00 0.00 C +ATOM 680 OH TYR 45 19.690 -87.783 -18.858 1.00 0.00 O +ATOM 681 HH TYR 45 19.596 -87.383 -19.725 1.00 0.00 H +ATOM 682 CE2 TYR 45 21.871 -87.924 -19.790 1.00 0.00 C +ATOM 683 HE2 TYR 45 21.528 -87.638 -20.773 1.00 0.00 H +ATOM 684 CD2 TYR 45 23.283 -88.190 -19.560 1.00 0.00 C +ATOM 685 HD2 TYR 45 23.968 -88.058 -20.384 1.00 0.00 H +ATOM 686 C TYR 45 25.056 -91.453 -18.571 1.00 0.00 C +ATOM 687 O TYR 45 25.503 -91.719 -19.687 1.00 0.00 O +ATOM 688 N ASP 46 23.955 -92.072 -18.193 1.00 0.00 N +ATOM 689 H ASP 46 23.602 -91.794 -17.289 1.00 0.00 H +ATOM 690 CA ASP 46 23.118 -92.872 -19.108 1.00 0.00 C +ATOM 691 HA ASP 46 23.589 -92.879 -20.091 1.00 0.00 H +ATOM 692 CB ASP 46 22.876 -94.314 -18.595 1.00 0.00 C +ATOM 693 HB2 ASP 46 23.895 -94.642 -18.392 1.00 0.00 H +ATOM 694 HB3 ASP 46 22.338 -94.307 -17.647 1.00 0.00 H +ATOM 695 CG ASP 46 22.177 -95.214 -19.623 1.00 0.00 C +ATOM 696 OD1 ASP 46 21.265 -95.928 -19.224 1.00 0.00 O +ATOM 697 OD2 ASP 46 22.486 -95.098 -20.850 1.00 0.00 O +ATOM 698 C ASP 46 21.771 -92.131 -19.370 1.00 0.00 C +ATOM 699 O ASP 46 20.816 -92.037 -18.539 1.00 0.00 O +ATOM 700 N ASP 47 21.603 -91.517 -20.509 1.00 0.00 N +ATOM 701 H ASP 47 22.253 -91.634 -21.274 1.00 0.00 H +ATOM 702 CA ASP 47 20.325 -90.875 -20.896 1.00 0.00 C +ATOM 703 HA ASP 47 20.150 -90.144 -20.107 1.00 0.00 H +ATOM 704 CB ASP 47 20.583 -90.030 -22.187 1.00 0.00 C +ATOM 705 HB2 ASP 47 21.477 -89.447 -21.967 1.00 0.00 H +ATOM 706 HB3 ASP 47 20.893 -90.578 -23.077 1.00 0.00 H +ATOM 707 CG ASP 47 19.410 -89.180 -22.489 1.00 0.00 C +ATOM 708 OD1 ASP 47 19.177 -88.398 -21.550 1.00 0.00 O +ATOM 709 OD2 ASP 47 18.837 -89.223 -23.605 1.00 0.00 O +ATOM 710 C ASP 47 19.128 -91.784 -21.032 1.00 0.00 C +ATOM 711 O ASP 47 17.952 -91.393 -20.821 1.00 0.00 O +ATOM 712 N ALA 48 19.382 -93.059 -21.356 1.00 0.00 N +ATOM 713 H ALA 48 20.329 -93.204 -21.674 1.00 0.00 H +ATOM 714 CA ALA 48 18.312 -94.149 -21.383 1.00 0.00 C +ATOM 715 HA ALA 48 17.506 -93.766 -22.010 1.00 0.00 H +ATOM 716 CB ALA 48 18.907 -95.437 -21.922 1.00 0.00 C +ATOM 717 HB1 ALA 48 18.084 -96.059 -22.273 1.00 0.00 H +ATOM 718 HB2 ALA 48 19.340 -95.984 -21.084 1.00 0.00 H +ATOM 719 HB3 ALA 48 19.484 -95.299 -22.836 1.00 0.00 H +ATOM 720 C ALA 48 17.673 -94.398 -19.978 1.00 0.00 C +ATOM 721 O ALA 48 16.549 -94.828 -19.875 1.00 0.00 O +ATOM 722 N THR 49 18.364 -94.098 -18.894 1.00 0.00 N +ATOM 723 H THR 49 19.232 -93.634 -19.120 1.00 0.00 H +ATOM 724 CA THR 49 17.893 -94.471 -17.507 1.00 0.00 C +ATOM 725 HA THR 49 16.824 -94.674 -17.557 1.00 0.00 H +ATOM 726 CB THR 49 18.686 -95.654 -16.840 1.00 0.00 C +ATOM 727 HB THR 49 18.397 -95.584 -15.791 1.00 0.00 H +ATOM 728 CG2 THR 49 18.424 -97.120 -17.344 1.00 0.00 C +ATOM 729 HG21 THR 49 17.356 -97.320 -17.254 1.00 0.00 H +ATOM 730 HG22 THR 49 19.025 -97.802 -16.743 1.00 0.00 H +ATOM 731 HG23 THR 49 18.693 -97.144 -18.400 1.00 0.00 H +ATOM 732 OG1 THR 49 20.039 -95.427 -16.944 1.00 0.00 O +ATOM 733 HG1 THR 49 20.311 -95.518 -17.860 1.00 0.00 H +ATOM 734 C THR 49 18.027 -93.258 -16.601 1.00 0.00 C +ATOM 735 O THR 49 17.858 -93.336 -15.385 1.00 0.00 O +ATOM 736 N LYS 50 18.394 -92.109 -17.113 1.00 0.00 N +ATOM 737 H LYS 50 18.607 -92.060 -18.099 1.00 0.00 H +ATOM 738 CA LYS 50 18.641 -90.839 -16.493 1.00 0.00 C +ATOM 739 HA LYS 50 19.172 -90.262 -17.250 1.00 0.00 H +ATOM 740 CB LYS 50 17.275 -90.257 -16.156 1.00 0.00 C +ATOM 741 HB2 LYS 50 16.783 -90.842 -15.379 1.00 0.00 H +ATOM 742 HB3 LYS 50 17.373 -89.297 -15.649 1.00 0.00 H +ATOM 743 CG LYS 50 16.260 -90.142 -17.325 1.00 0.00 C +ATOM 744 HG2 LYS 50 16.045 -91.138 -17.711 1.00 0.00 H +ATOM 745 HG3 LYS 50 15.348 -89.732 -16.892 1.00 0.00 H +ATOM 746 CD LYS 50 16.666 -89.169 -18.397 1.00 0.00 C +ATOM 747 HD2 LYS 50 16.516 -88.190 -17.942 1.00 0.00 H +ATOM 748 HD3 LYS 50 17.734 -89.198 -18.610 1.00 0.00 H +ATOM 749 CE LYS 50 15.787 -89.250 -19.626 1.00 0.00 C +ATOM 750 HE2 LYS 50 15.380 -90.235 -19.852 1.00 0.00 H +ATOM 751 HE3 LYS 50 14.855 -88.690 -19.543 1.00 0.00 H +ATOM 752 NZ LYS 50 16.454 -88.757 -20.820 1.00 0.00 N +ATOM 753 HZ1 LYS 50 16.322 -87.761 -20.916 1.00 0.00 H +ATOM 754 HZ2 LYS 50 16.006 -88.999 -21.692 1.00 0.00 H +ATOM 755 HZ3 LYS 50 17.437 -88.978 -20.893 1.00 0.00 H +ATOM 756 C LYS 50 19.563 -90.789 -15.316 1.00 0.00 C +ATOM 757 O LYS 50 19.460 -89.987 -14.409 1.00 0.00 O +ATOM 758 N THR 51 20.589 -91.709 -15.350 1.00 0.00 N +ATOM 759 H THR 51 20.749 -92.297 -16.156 1.00 0.00 H +ATOM 760 CA THR 51 21.429 -91.967 -14.222 1.00 0.00 C +ATOM 761 HA THR 51 20.984 -91.579 -13.305 1.00 0.00 H +ATOM 762 CB THR 51 21.480 -93.477 -13.900 1.00 0.00 C +ATOM 763 HB THR 51 21.853 -94.030 -14.762 1.00 0.00 H +ATOM 764 CG2 THR 51 22.289 -93.792 -12.642 1.00 0.00 C +ATOM 765 HG21 THR 51 22.050 -94.813 -12.344 1.00 0.00 H +ATOM 766 HG22 THR 51 22.063 -93.060 -11.866 1.00 0.00 H +ATOM 767 HG23 THR 51 23.355 -93.687 -12.844 1.00 0.00 H +ATOM 768 OG1 THR 51 20.206 -93.986 -13.526 1.00 0.00 O +ATOM 769 HG1 THR 51 19.630 -93.641 -14.212 1.00 0.00 H +ATOM 770 C THR 51 22.800 -91.398 -14.407 1.00 0.00 C +ATOM 771 O THR 51 23.462 -91.734 -15.365 1.00 0.00 O +ATOM 772 N PHE 52 23.282 -90.751 -13.357 1.00 0.00 N +ATOM 773 H PHE 52 22.695 -90.583 -12.552 1.00 0.00 H +ATOM 774 CA PHE 52 24.653 -90.434 -13.150 1.00 0.00 C +ATOM 775 HA PHE 52 25.175 -90.499 -14.105 1.00 0.00 H +ATOM 776 CB PHE 52 24.779 -89.010 -12.592 1.00 0.00 C +ATOM 777 HB2 PHE 52 24.272 -88.864 -11.638 1.00 0.00 H +ATOM 778 HB3 PHE 52 25.842 -88.851 -12.408 1.00 0.00 H +ATOM 779 CG PHE 52 24.291 -87.940 -13.639 1.00 0.00 C +ATOM 780 CD1 PHE 52 22.920 -87.601 -13.642 1.00 0.00 C +ATOM 781 HD1 PHE 52 22.347 -87.916 -12.782 1.00 0.00 H +ATOM 782 CE1 PHE 52 22.366 -86.778 -14.618 1.00 0.00 C +ATOM 783 HE1 PHE 52 21.298 -86.619 -14.635 1.00 0.00 H +ATOM 784 CZ PHE 52 23.251 -86.274 -15.639 1.00 0.00 C +ATOM 785 HZ PHE 52 22.790 -85.720 -16.444 1.00 0.00 H +ATOM 786 CE2 PHE 52 24.617 -86.554 -15.603 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.211 -86.099 -16.381 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.175 -87.332 -14.560 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.238 -87.521 -14.548 1.00 0.00 H +ATOM 790 C PHE 52 25.333 -91.434 -12.262 1.00 0.00 C +ATOM 791 O PHE 52 24.888 -91.679 -11.080 1.00 0.00 O +ATOM 792 N THR 53 26.500 -91.876 -12.634 1.00 0.00 N +ATOM 793 H THR 53 26.839 -91.611 -13.548 1.00 0.00 H +ATOM 794 CA THR 53 27.460 -92.652 -11.790 1.00 0.00 C +ATOM 795 HA THR 53 27.198 -92.509 -10.742 1.00 0.00 H +ATOM 796 CB THR 53 27.461 -94.153 -12.356 1.00 0.00 C +ATOM 797 HB THR 53 28.140 -94.831 -11.838 1.00 0.00 H +ATOM 798 CG2 THR 53 26.066 -94.762 -12.190 1.00 0.00 C +ATOM 799 HG21 THR 53 26.147 -95.816 -12.457 1.00 0.00 H +ATOM 800 HG22 THR 53 25.367 -94.257 -12.856 1.00 0.00 H +ATOM 801 HG23 THR 53 25.660 -94.632 -11.186 1.00 0.00 H +ATOM 802 OG1 THR 53 27.763 -94.344 -13.714 1.00 0.00 O +ATOM 803 HG1 THR 53 28.317 -95.111 -13.876 1.00 0.00 H +ATOM 804 C THR 53 28.861 -92.044 -11.808 1.00 0.00 C +ATOM 805 O THR 53 29.178 -91.322 -12.747 1.00 0.00 O +ATOM 806 N VAL 54 29.662 -92.315 -10.726 1.00 0.00 N +ATOM 807 H VAL 54 29.360 -92.813 -9.901 1.00 0.00 H +ATOM 808 CA VAL 54 31.118 -92.047 -10.754 1.00 0.00 C +ATOM 809 HA VAL 54 31.227 -91.087 -11.258 1.00 0.00 H +ATOM 810 CB VAL 54 31.756 -91.933 -9.347 1.00 0.00 C +ATOM 811 HB VAL 54 31.186 -91.265 -8.701 1.00 0.00 H +ATOM 812 CG1 VAL 54 31.875 -93.166 -8.570 1.00 0.00 C +ATOM 813 HG11 VAL 54 32.467 -93.877 -9.146 1.00 0.00 H +ATOM 814 HG12 VAL 54 30.910 -93.563 -8.254 1.00 0.00 H +ATOM 815 HG13 VAL 54 32.445 -92.965 -7.663 1.00 0.00 H +ATOM 816 CG2 VAL 54 33.141 -91.318 -9.447 1.00 0.00 C +ATOM 817 HG21 VAL 54 33.027 -90.549 -10.212 1.00 0.00 H +ATOM 818 HG22 VAL 54 33.855 -92.047 -9.831 1.00 0.00 H +ATOM 819 HG23 VAL 54 33.570 -91.017 -8.491 1.00 0.00 H +ATOM 820 C VAL 54 31.747 -93.236 -11.489 1.00 0.00 C +ATOM 821 O VAL 54 31.154 -94.302 -11.502 1.00 0.00 O +ATOM 822 N THR 55 32.825 -93.071 -12.225 1.00 0.00 N +ATOM 823 H THR 55 33.222 -92.143 -12.267 1.00 0.00 H +ATOM 824 CA THR 55 33.448 -94.137 -12.971 1.00 0.00 C +ATOM 825 HA THR 55 32.819 -94.901 -13.427 1.00 0.00 H +ATOM 826 CB THR 55 34.250 -93.589 -14.144 1.00 0.00 C +ATOM 827 HB THR 55 34.813 -94.469 -14.453 1.00 0.00 H +ATOM 828 CG2 THR 55 33.274 -93.104 -15.236 1.00 0.00 C +ATOM 829 HG21 THR 55 33.841 -93.067 -16.167 1.00 0.00 H +ATOM 830 HG22 THR 55 32.881 -92.184 -14.806 1.00 0.00 H +ATOM 831 HG23 THR 55 32.420 -93.781 -15.227 1.00 0.00 H +ATOM 832 OG1 THR 55 35.179 -92.569 -13.759 1.00 0.00 O +ATOM 833 HG1 THR 55 34.698 -91.752 -13.610 1.00 0.00 H +ATOM 834 C THR 55 34.333 -95.037 -12.158 1.00 0.00 C +ATOM 835 O THR 55 34.939 -95.972 -12.713 1.00 0.00 O +ATOM 836 N GLU 56 34.624 -94.752 -10.883 1.00 0.00 N +ATOM 837 H GLU 56 34.153 -93.950 -10.487 1.00 0.00 H +ATOM 838 CA GLU 56 35.479 -95.643 -10.031 1.00 0.00 C +ATOM 839 HA GLU 56 36.244 -96.128 -10.637 1.00 0.00 H +ATOM 840 CB GLU 56 36.171 -94.743 -8.949 1.00 0.00 C +ATOM 841 HB2 GLU 56 36.595 -93.841 -9.390 1.00 0.00 H +ATOM 842 HB3 GLU 56 35.423 -94.372 -8.248 1.00 0.00 H +ATOM 843 CG GLU 56 37.240 -95.427 -8.121 1.00 0.00 C +ATOM 844 HG2 GLU 56 36.764 -96.258 -7.601 1.00 0.00 H +ATOM 845 HG3 GLU 56 38.020 -95.859 -8.748 1.00 0.00 H +ATOM 846 CD GLU 56 37.882 -94.614 -6.927 1.00 0.00 C +ATOM 847 OE1 GLU 56 37.631 -93.416 -6.824 1.00 0.00 O +ATOM 848 OE2 GLU 56 38.755 -95.207 -6.239 1.00 0.00 O +ATOM 849 C GLU 56 34.611 -96.753 -9.416 1.00 0.00 C +ATOM 850 O GLU 56 33.525 -96.464 -8.904 1.00 0.00 O +ATOM 851 OXT GLU 56 34.987 -97.898 -9.681 1.00 0.00 O +ATOM 852 ZN ZN1 57 23.286 -87.843 -5.235 1.00 0.00 ZN +ATOM 853 N AN1 58 24.247 -86.891 -3.605 1.00 0.00 N +ATOM 854 C AN1 58 25.528 -86.334 -1.430 1.00 0.00 C +ATOM 855 C1 AN1 58 24.831 -86.692 -2.639 1.00 0.00 C +ATOM 856 H AN1 58 24.954 -86.539 -0.519 1.00 0.00 H +ATOM 857 H1 AN1 58 25.675 -85.271 -1.204 1.00 0.00 H +ATOM 858 H2 AN1 58 26.505 -86.827 -1.353 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 25.354 -89.992 -1.364 1.00 0.00 N +ATOM 860 N2 AZI 59 26.182 -89.857 -2.203 1.00 0.00 N +ATOM 861 N3 AZI 59 27.156 -89.740 -3.029 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/inp/pdbs/cluster.c1.pdb b/tests/nsga2/inp/pdbs/cluster.c1.pdb new file mode 100644 index 0000000..f34443e --- /dev/null +++ b/tests/nsga2/inp/pdbs/cluster.c1.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.307 -83.210 -13.471 1.00 0.00 N +ATOM 2 H1 MET 1 12.755 -82.814 -14.218 1.00 0.00 H +ATOM 3 H2 MET 1 14.229 -82.830 -13.632 1.00 0.00 H +ATOM 4 H3 MET 1 13.128 -82.821 -12.556 1.00 0.00 H +ATOM 5 CA MET 1 13.250 -84.693 -13.515 1.00 0.00 C +ATOM 6 HA MET 1 12.199 -84.955 -13.391 1.00 0.00 H +ATOM 7 CB MET 1 13.665 -85.311 -14.832 1.00 0.00 C +ATOM 8 HB2 MET 1 12.976 -84.978 -15.608 1.00 0.00 H +ATOM 9 HB3 MET 1 14.690 -85.001 -15.037 1.00 0.00 H +ATOM 10 CG MET 1 13.508 -86.910 -14.922 1.00 0.00 C +ATOM 11 HG2 MET 1 12.725 -87.228 -14.234 1.00 0.00 H +ATOM 12 HG3 MET 1 13.200 -87.271 -15.903 1.00 0.00 H +ATOM 13 SD MET 1 14.945 -87.895 -14.430 1.00 0.00 S +ATOM 14 CE MET 1 15.996 -87.471 -15.838 1.00 0.00 C +ATOM 15 HE1 MET 1 16.279 -86.419 -15.867 1.00 0.00 H +ATOM 16 HE2 MET 1 15.483 -87.808 -16.739 1.00 0.00 H +ATOM 17 HE3 MET 1 16.908 -88.067 -15.835 1.00 0.00 H +ATOM 18 C MET 1 13.977 -85.230 -12.322 1.00 0.00 C +ATOM 19 O MET 1 15.086 -84.776 -11.988 1.00 0.00 O +ATOM 20 N GLN 2 13.374 -86.082 -11.462 1.00 0.00 N +ATOM 21 H GLN 2 12.431 -86.320 -11.733 1.00 0.00 H +ATOM 22 CA GLN 2 14.013 -86.803 -10.298 1.00 0.00 C +ATOM 23 HA GLN 2 14.494 -86.096 -9.623 1.00 0.00 H +ATOM 24 CB GLN 2 12.749 -87.393 -9.506 1.00 0.00 C +ATOM 25 HB2 GLN 2 11.987 -87.668 -10.236 1.00 0.00 H +ATOM 26 HB3 GLN 2 13.076 -88.211 -8.865 1.00 0.00 H +ATOM 27 CG GLN 2 12.194 -86.252 -8.651 1.00 0.00 C +ATOM 28 HG2 GLN 2 12.351 -85.276 -9.110 1.00 0.00 H +ATOM 29 HG3 GLN 2 11.109 -86.356 -8.676 1.00 0.00 H +ATOM 30 CD GLN 2 12.690 -86.197 -7.235 1.00 0.00 C +ATOM 31 OE1 GLN 2 13.611 -86.918 -6.965 1.00 0.00 O +ATOM 32 NE2 GLN 2 12.016 -85.444 -6.434 1.00 0.00 N +ATOM 33 HE21 GLN 2 12.688 -85.006 -5.821 1.00 0.00 H +ATOM 34 HE22 GLN 2 11.200 -84.926 -6.726 1.00 0.00 H +ATOM 35 C GLN 2 15.100 -87.823 -10.749 1.00 0.00 C +ATOM 36 O GLN 2 14.786 -89.034 -10.914 1.00 0.00 O +ATOM 37 N TYR 3 16.311 -87.371 -10.964 1.00 0.00 N +ATOM 38 H TYR 3 16.498 -86.382 -10.883 1.00 0.00 H +ATOM 39 CA TYR 3 17.489 -88.228 -11.130 1.00 0.00 C +ATOM 40 HA TYR 3 17.315 -88.873 -11.991 1.00 0.00 H +ATOM 41 CB TYR 3 18.740 -87.334 -11.389 1.00 0.00 C +ATOM 42 HB2 TYR 3 18.937 -86.710 -10.516 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.613 -87.987 -11.403 1.00 0.00 H +ATOM 44 CG TYR 3 18.811 -86.630 -12.687 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.384 -87.291 -13.776 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.959 -88.184 -13.578 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.427 -86.574 -14.948 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.931 -86.909 -15.843 1.00 0.00 H +ATOM 49 CZ TYR 3 18.784 -85.314 -15.051 1.00 0.00 C +ATOM 50 OH TYR 3 18.752 -84.646 -16.213 1.00 0.00 O +ATOM 51 HH TYR 3 18.759 -85.247 -16.961 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.193 -84.719 -13.929 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.727 -83.751 -14.039 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.256 -85.356 -12.686 1.00 0.00 C +ATOM 55 HD2 TYR 3 17.818 -84.939 -11.791 1.00 0.00 H +ATOM 56 C TYR 3 17.741 -89.165 -9.918 1.00 0.00 C +ATOM 57 O TYR 3 17.507 -88.691 -8.807 1.00 0.00 O +ATOM 58 N LYS 4 18.091 -90.413 -10.142 1.00 0.00 N +ATOM 59 H LYS 4 18.353 -90.774 -11.048 1.00 0.00 H +ATOM 60 CA LYS 4 18.480 -91.338 -8.995 1.00 0.00 C +ATOM 61 HA LYS 4 17.838 -91.135 -8.137 1.00 0.00 H +ATOM 62 CB LYS 4 18.431 -92.766 -9.505 1.00 0.00 C +ATOM 63 HB2 LYS 4 17.583 -92.913 -10.174 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.244 -92.943 -10.209 1.00 0.00 H +ATOM 65 CG LYS 4 18.216 -93.805 -8.416 1.00 0.00 C +ATOM 66 HG2 LYS 4 19.179 -93.858 -7.908 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.534 -93.380 -7.680 1.00 0.00 H +ATOM 68 CD LYS 4 17.560 -95.106 -8.900 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.337 -95.636 -7.974 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.738 -94.927 -9.594 1.00 0.00 H +ATOM 71 CE LYS 4 18.582 -95.930 -9.689 1.00 0.00 C +ATOM 72 HE2 LYS 4 18.856 -95.439 -10.622 1.00 0.00 H +ATOM 73 HE3 LYS 4 19.462 -95.972 -9.046 1.00 0.00 H +ATOM 74 NZ LYS 4 17.978 -97.260 -10.002 1.00 0.00 N +ATOM 75 HZ1 LYS 4 18.671 -97.760 -10.541 1.00 0.00 H +ATOM 76 HZ2 LYS 4 17.130 -97.126 -10.533 1.00 0.00 H +ATOM 77 HZ3 LYS 4 17.736 -97.821 -9.197 1.00 0.00 H +ATOM 78 C LYS 4 19.942 -91.086 -8.487 1.00 0.00 C +ATOM 79 O LYS 4 20.814 -90.618 -9.269 1.00 0.00 O +ATOM 80 N HE1 5 20.221 -91.270 -7.216 1.00 0.00 N +ATOM 81 CA HE1 5 21.478 -90.986 -6.479 1.00 0.00 C +ATOM 82 C HE1 5 21.702 -91.838 -5.250 1.00 0.00 C +ATOM 83 O HE1 5 20.727 -92.159 -4.650 1.00 0.00 O +ATOM 84 CB HE1 5 21.383 -89.521 -6.042 1.00 0.00 C +ATOM 85 CG HE1 5 22.724 -89.117 -5.388 1.00 0.00 C +ATOM 86 CD2 HE1 5 23.928 -89.227 -5.981 1.00 0.00 C +ATOM 87 ND1 HE1 5 22.884 -88.527 -4.130 1.00 0.00 N +ATOM 88 CE1 HE1 5 24.158 -88.313 -3.933 1.00 0.00 C +ATOM 89 NE2 HE1 5 24.830 -88.696 -5.063 1.00 0.00 N +ATOM 90 H HE1 5 19.495 -91.570 -6.581 1.00 0.00 H +ATOM 91 HA HE1 5 22.277 -90.957 -7.220 1.00 0.00 H +ATOM 92 HB2 HE1 5 20.583 -89.455 -5.304 1.00 0.00 H +ATOM 93 HB3 HE1 5 21.033 -88.820 -6.799 1.00 0.00 H +ATOM 94 HD2 HE1 5 24.201 -89.625 -6.948 1.00 0.00 H +ATOM 95 HE1 HE1 5 24.702 -87.941 -3.077 1.00 0.00 H +ATOM 96 HE2 HE1 5 25.829 -88.713 -5.206 1.00 0.00 H +ATOM 97 N ILE 6 22.944 -92.098 -4.842 1.00 0.00 N +ATOM 98 H ILE 6 23.684 -91.689 -5.395 1.00 0.00 H +ATOM 99 CA ILE 6 23.307 -93.005 -3.758 1.00 0.00 C +ATOM 100 HA ILE 6 22.714 -93.917 -3.816 1.00 0.00 H +ATOM 101 CB ILE 6 24.792 -93.351 -3.986 1.00 0.00 C +ATOM 102 HB ILE 6 25.177 -93.816 -3.079 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.947 -94.521 -4.972 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.972 -94.861 -4.821 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.690 -94.340 -6.015 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.271 -95.335 -4.711 1.00 0.00 H +ATOM 107 CG1 ILE 6 25.628 -92.043 -4.153 1.00 0.00 C +ATOM 108 HG12 ILE 6 25.420 -91.776 -5.190 1.00 0.00 H +ATOM 109 HG13 ILE 6 25.265 -91.196 -3.571 1.00 0.00 H +ATOM 110 CD1 ILE 6 27.125 -92.316 -3.918 1.00 0.00 C +ATOM 111 HD11 ILE 6 27.641 -91.369 -4.078 1.00 0.00 H +ATOM 112 HD12 ILE 6 27.382 -93.089 -4.642 1.00 0.00 H +ATOM 113 HD13 ILE 6 27.424 -92.635 -2.919 1.00 0.00 H +ATOM 114 C ILE 6 23.209 -92.407 -2.299 1.00 0.00 C +ATOM 115 O ILE 6 23.128 -91.143 -2.086 1.00 0.00 O +ATOM 116 N VAL 7 23.133 -93.350 -1.329 1.00 0.00 N +ATOM 117 H VAL 7 22.899 -94.293 -1.606 1.00 0.00 H +ATOM 118 CA VAL 7 23.552 -93.089 0.006 1.00 0.00 C +ATOM 119 HA VAL 7 24.275 -92.273 -0.017 1.00 0.00 H +ATOM 120 CB VAL 7 22.332 -92.538 0.871 1.00 0.00 C +ATOM 121 HB VAL 7 22.006 -91.606 0.410 1.00 0.00 H +ATOM 122 CG1 VAL 7 21.152 -93.561 0.790 1.00 0.00 C +ATOM 123 HG11 VAL 7 20.749 -93.426 -0.214 1.00 0.00 H +ATOM 124 HG12 VAL 7 21.578 -94.537 1.024 1.00 0.00 H +ATOM 125 HG13 VAL 7 20.426 -93.363 1.578 1.00 0.00 H +ATOM 126 CG2 VAL 7 22.782 -92.274 2.314 1.00 0.00 C +ATOM 127 HG21 VAL 7 21.964 -91.697 2.744 1.00 0.00 H +ATOM 128 HG22 VAL 7 22.962 -93.233 2.800 1.00 0.00 H +ATOM 129 HG23 VAL 7 23.635 -91.599 2.380 1.00 0.00 H +ATOM 130 C VAL 7 24.338 -94.185 0.587 1.00 0.00 C +ATOM 131 O VAL 7 24.097 -95.382 0.407 1.00 0.00 O +ATOM 132 N ASN 8 25.312 -93.826 1.476 1.00 0.00 N +ATOM 133 H ASN 8 25.459 -92.852 1.696 1.00 0.00 H +ATOM 134 CA ASN 8 25.965 -94.795 2.302 1.00 0.00 C +ATOM 135 HA ASN 8 25.282 -95.641 2.391 1.00 0.00 H +ATOM 136 CB ASN 8 27.285 -95.264 1.665 1.00 0.00 C +ATOM 137 HB2 ASN 8 27.973 -94.419 1.632 1.00 0.00 H +ATOM 138 HB3 ASN 8 27.732 -95.991 2.342 1.00 0.00 H +ATOM 139 CG ASN 8 27.219 -95.832 0.308 1.00 0.00 C +ATOM 140 OD1 ASN 8 26.981 -97.019 0.270 1.00 0.00 O +ATOM 141 ND2 ASN 8 27.663 -95.154 -0.682 1.00 0.00 N +ATOM 142 HD21 ASN 8 27.858 -94.170 -0.574 1.00 0.00 H +ATOM 143 HD22 ASN 8 27.680 -95.585 -1.595 1.00 0.00 H +ATOM 144 C ASN 8 26.201 -94.343 3.679 1.00 0.00 C +ATOM 145 O ASN 8 26.289 -93.158 3.892 1.00 0.00 O +ATOM 146 N GLY 9 26.367 -95.244 4.646 1.00 0.00 N +ATOM 147 H GLY 9 26.237 -96.228 4.456 1.00 0.00 H +ATOM 148 CA GLY 9 26.885 -94.809 6.008 1.00 0.00 C +ATOM 149 HA2 GLY 9 27.506 -93.914 5.972 1.00 0.00 H +ATOM 150 HA3 GLY 9 26.014 -94.528 6.600 1.00 0.00 H +ATOM 151 C GLY 9 27.720 -95.891 6.611 1.00 0.00 C +ATOM 152 O GLY 9 28.431 -96.662 5.954 1.00 0.00 O +ATOM 153 N LYS 10 27.765 -95.979 7.936 1.00 0.00 N +ATOM 154 H LYS 10 27.109 -95.407 8.448 1.00 0.00 H +ATOM 155 CA LYS 10 28.616 -96.863 8.737 1.00 0.00 C +ATOM 156 HA LYS 10 29.664 -96.584 8.625 1.00 0.00 H +ATOM 157 CB LYS 10 28.280 -96.575 10.272 1.00 0.00 C +ATOM 158 HB2 LYS 10 28.414 -95.522 10.521 1.00 0.00 H +ATOM 159 HB3 LYS 10 27.243 -96.887 10.392 1.00 0.00 H +ATOM 160 CG LYS 10 29.161 -97.346 11.252 1.00 0.00 C +ATOM 161 HG2 LYS 10 28.937 -97.015 12.266 1.00 0.00 H +ATOM 162 HG3 LYS 10 29.042 -98.427 11.189 1.00 0.00 H +ATOM 163 CD LYS 10 30.608 -96.873 11.148 1.00 0.00 C +ATOM 164 HD2 LYS 10 31.055 -97.141 10.191 1.00 0.00 H +ATOM 165 HD3 LYS 10 30.698 -95.787 11.134 1.00 0.00 H +ATOM 166 CE LYS 10 31.398 -97.334 12.351 1.00 0.00 C +ATOM 167 HE2 LYS 10 31.024 -96.837 13.246 1.00 0.00 H +ATOM 168 HE3 LYS 10 31.193 -98.379 12.583 1.00 0.00 H +ATOM 169 NZ LYS 10 32.808 -97.015 12.107 1.00 0.00 N +ATOM 170 HZ1 LYS 10 33.071 -97.423 11.221 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.346 -97.315 12.908 1.00 0.00 H +ATOM 172 HZ3 LYS 10 32.862 -96.006 12.116 1.00 0.00 H +ATOM 173 C LYS 10 28.409 -98.358 8.476 1.00 0.00 C +ATOM 174 O LYS 10 29.432 -99.020 8.321 1.00 0.00 O +ATOM 175 N THR 11 27.086 -98.726 8.186 1.00 0.00 N +ATOM 176 H THR 11 26.453 -98.113 8.679 1.00 0.00 H +ATOM 177 CA THR 11 26.638-100.043 7.558 1.00 0.00 C +ATOM 178 HA THR 11 27.456-100.300 6.885 1.00 0.00 H +ATOM 179 CB THR 11 26.400-101.167 8.557 1.00 0.00 C +ATOM 180 HB THR 11 26.349-102.135 8.058 1.00 0.00 H +ATOM 181 CG2 THR 11 27.591-101.465 9.500 1.00 0.00 C +ATOM 182 HG21 THR 11 27.727-100.558 10.090 1.00 0.00 H +ATOM 183 HG22 THR 11 28.509-101.419 8.915 1.00 0.00 H +ATOM 184 HG23 THR 11 27.537-102.381 10.089 1.00 0.00 H +ATOM 185 OG1 THR 11 25.171-101.019 9.262 1.00 0.00 O +ATOM 186 HG1 THR 11 24.492-101.345 8.667 1.00 0.00 H +ATOM 187 C THR 11 25.502 -99.866 6.587 1.00 0.00 C +ATOM 188 O THR 11 25.511-100.514 5.566 1.00 0.00 O +ATOM 189 N LEU 12 24.532 -98.964 6.929 1.00 0.00 N +ATOM 190 H LEU 12 24.535 -98.476 7.814 1.00 0.00 H +ATOM 191 CA LEU 12 23.451 -98.542 5.991 1.00 0.00 C +ATOM 192 HA LEU 12 22.737 -99.362 5.908 1.00 0.00 H +ATOM 193 CB LEU 12 22.667 -97.349 6.647 1.00 0.00 C +ATOM 194 HB2 LEU 12 22.297 -97.700 7.609 1.00 0.00 H +ATOM 195 HB3 LEU 12 23.406 -96.560 6.790 1.00 0.00 H +ATOM 196 CG LEU 12 21.481 -96.831 5.846 1.00 0.00 C +ATOM 197 HG LEU 12 21.135 -97.707 5.297 1.00 0.00 H +ATOM 198 CD1 LEU 12 20.204 -96.226 6.507 1.00 0.00 C +ATOM 199 HD11 LEU 12 19.640 -95.641 5.781 1.00 0.00 H +ATOM 200 HD12 LEU 12 20.399 -95.691 7.437 1.00 0.00 H +ATOM 201 HD13 LEU 12 19.596 -97.108 6.709 1.00 0.00 H +ATOM 202 CD2 LEU 12 21.988 -95.724 4.963 1.00 0.00 C +ATOM 203 HD21 LEU 12 21.126 -95.505 4.334 1.00 0.00 H +ATOM 204 HD22 LEU 12 22.794 -95.974 4.273 1.00 0.00 H +ATOM 205 HD23 LEU 12 22.321 -94.841 5.508 1.00 0.00 H +ATOM 206 C LEU 12 24.041 -98.216 4.582 1.00 0.00 C +ATOM 207 O LEU 12 24.984 -97.475 4.521 1.00 0.00 O +ATOM 208 N LYS 13 23.329 -98.630 3.492 1.00 0.00 N +ATOM 209 H LYS 13 22.563 -99.253 3.705 1.00 0.00 H +ATOM 210 CA LYS 13 23.622 -98.330 2.046 1.00 0.00 C +ATOM 211 HA LYS 13 23.942 -97.288 2.031 1.00 0.00 H +ATOM 212 CB LYS 13 24.840 -99.271 1.671 1.00 0.00 C +ATOM 213 HB2 LYS 13 24.932 -99.201 0.587 1.00 0.00 H +ATOM 214 HB3 LYS 13 25.761 -98.921 2.139 1.00 0.00 H +ATOM 215 CG LYS 13 24.583-100.816 1.953 1.00 0.00 C +ATOM 216 HG2 LYS 13 24.377-101.036 3.000 1.00 0.00 H +ATOM 217 HG3 LYS 13 23.720-101.151 1.377 1.00 0.00 H +ATOM 218 CD LYS 13 25.725-101.669 1.468 1.00 0.00 C +ATOM 219 HD2 LYS 13 25.473-102.729 1.446 1.00 0.00 H +ATOM 220 HD3 LYS 13 25.866-101.378 0.427 1.00 0.00 H +ATOM 221 CE LYS 13 27.042-101.397 2.197 1.00 0.00 C +ATOM 222 HE2 LYS 13 27.872-101.499 1.498 1.00 0.00 H +ATOM 223 HE3 LYS 13 26.977-100.438 2.712 1.00 0.00 H +ATOM 224 NZ LYS 13 27.235-102.346 3.357 1.00 0.00 N +ATOM 225 HZ1 LYS 13 27.935-101.977 3.985 1.00 0.00 H +ATOM 226 HZ2 LYS 13 27.561-103.245 3.034 1.00 0.00 H +ATOM 227 HZ3 LYS 13 26.337-102.446 3.808 1.00 0.00 H +ATOM 228 C LYS 13 22.349 -98.445 1.200 1.00 0.00 C +ATOM 229 O LYS 13 21.435 -99.150 1.648 1.00 0.00 O +ATOM 230 N GLY 14 22.192 -97.569 0.255 1.00 0.00 N +ATOM 231 H GLY 14 22.884 -96.869 0.030 1.00 0.00 H +ATOM 232 CA GLY 14 20.889 -97.417 -0.390 1.00 0.00 C +ATOM 233 HA2 GLY 14 20.389 -98.332 -0.706 1.00 0.00 H +ATOM 234 HA3 GLY 14 20.266 -96.897 0.338 1.00 0.00 H +ATOM 235 C GLY 14 20.995 -96.360 -1.495 1.00 0.00 C +ATOM 236 O GLY 14 22.092 -95.855 -1.799 1.00 0.00 O +ATOM 237 N VAL 15 19.810 -95.933 -1.961 1.00 0.00 N +ATOM 238 H VAL 15 18.949 -96.385 -1.688 1.00 0.00 H +ATOM 239 CA VAL 15 19.597 -95.113 -3.118 1.00 0.00 C +ATOM 240 HA VAL 15 20.405 -94.381 -3.119 1.00 0.00 H +ATOM 241 CB VAL 15 19.693 -95.997 -4.394 1.00 0.00 C +ATOM 242 HB VAL 15 20.736 -96.133 -4.680 1.00 0.00 H +ATOM 243 CG1 VAL 15 19.095 -97.418 -4.175 1.00 0.00 C +ATOM 244 HG11 VAL 15 18.908 -97.824 -5.169 1.00 0.00 H +ATOM 245 HG12 VAL 15 19.724 -98.082 -3.582 1.00 0.00 H +ATOM 246 HG13 VAL 15 18.104 -97.431 -3.719 1.00 0.00 H +ATOM 247 CG2 VAL 15 19.036 -95.409 -5.654 1.00 0.00 C +ATOM 248 HG21 VAL 15 19.265 -94.347 -5.742 1.00 0.00 H +ATOM 249 HG22 VAL 15 19.427 -96.011 -6.474 1.00 0.00 H +ATOM 250 HG23 VAL 15 17.969 -95.588 -5.519 1.00 0.00 H +ATOM 251 C VAL 15 18.262 -94.322 -2.975 1.00 0.00 C +ATOM 252 O VAL 15 17.345 -94.774 -2.322 1.00 0.00 O +ATOM 253 N HD1 16 18.224 -93.078 -3.453 1.00 0.00 N +ATOM 254 CA HD1 16 17.159 -92.137 -3.518 1.00 0.00 C +ATOM 255 C HD1 16 17.199 -91.314 -4.829 1.00 0.00 C +ATOM 256 O HD1 16 18.013 -91.586 -5.721 1.00 0.00 O +ATOM 257 CB HD1 16 17.179 -91.338 -2.175 1.00 0.00 C +ATOM 258 CG HD1 16 18.474 -90.732 -1.807 1.00 0.00 C +ATOM 259 CD2 HD1 16 19.192 -89.994 -2.685 1.00 0.00 C +ATOM 260 ND1 HD1 16 19.036 -90.449 -0.539 1.00 0.00 N +ATOM 261 CE1 HD1 16 20.205 -89.792 -0.701 1.00 0.00 C +ATOM 262 NE2 HD1 16 20.332 -89.426 -2.010 1.00 0.00 N +ATOM 263 H HD1 16 19.114 -92.865 -3.880 1.00 0.00 H +ATOM 264 HA HD1 16 16.247 -92.732 -3.571 1.00 0.00 H +ATOM 265 HB2 HD1 16 16.396 -90.580 -2.180 1.00 0.00 H +ATOM 266 HB3 HD1 16 17.066 -92.053 -1.360 1.00 0.00 H +ATOM 267 HD1 HD1 16 18.587 -90.536 0.362 1.00 0.00 H +ATOM 268 HD2 HD1 16 18.995 -89.833 -3.735 1.00 0.00 H +ATOM 269 HE1 HD1 16 20.863 -89.346 0.030 1.00 0.00 H +ATOM 270 N THR 17 16.356 -90.237 -4.912 1.00 0.00 N +ATOM 271 H THR 17 15.634 -90.131 -4.214 1.00 0.00 H +ATOM 272 CA THR 17 16.164 -89.387 -6.031 1.00 0.00 C +ATOM 273 HA THR 17 16.937 -89.448 -6.797 1.00 0.00 H +ATOM 274 CB THR 17 14.861 -89.726 -6.783 1.00 0.00 C +ATOM 275 HB THR 17 14.987 -89.024 -7.607 1.00 0.00 H +ATOM 276 CG2 THR 17 14.766 -91.189 -7.273 1.00 0.00 C +ATOM 277 HG21 THR 17 14.048 -91.308 -8.084 1.00 0.00 H +ATOM 278 HG22 THR 17 14.656 -91.885 -6.442 1.00 0.00 H +ATOM 279 HG23 THR 17 15.664 -91.545 -7.777 1.00 0.00 H +ATOM 280 OG1 THR 17 13.624 -89.520 -6.050 1.00 0.00 O +ATOM 281 HG1 THR 17 13.443 -88.586 -6.179 1.00 0.00 H +ATOM 282 C THR 17 16.351 -87.917 -5.606 1.00 0.00 C +ATOM 283 O THR 17 16.132 -87.477 -4.456 1.00 0.00 O +ATOM 284 N HD2 18 16.654 -87.127 -6.642 1.00 0.00 N +ATOM 285 CA HD2 18 16.903 -85.627 -6.579 1.00 0.00 C +ATOM 286 C HD2 18 16.401 -84.906 -7.816 1.00 0.00 C +ATOM 287 O HD2 18 17.038 -84.931 -8.913 1.00 0.00 O +ATOM 288 CB HD2 18 18.402 -85.301 -6.451 1.00 0.00 C +ATOM 289 CG HD2 18 18.964 -85.653 -5.103 1.00 0.00 C +ATOM 290 CD2 HD2 18 19.996 -86.597 -4.943 1.00 0.00 C +ATOM 291 ND1 HD2 18 18.703 -85.106 -3.871 1.00 0.00 N +ATOM 292 CE1 HD2 18 19.583 -85.715 -3.020 1.00 0.00 C +ATOM 293 NE2 HD2 18 20.296 -86.731 -3.629 1.00 0.00 N +ATOM 294 H HD2 18 16.787 -87.498 -7.572 1.00 0.00 H +ATOM 295 HA HD2 18 16.414 -85.189 -5.709 1.00 0.00 H +ATOM 296 HB2 HD2 18 18.888 -85.906 -7.216 1.00 0.00 H +ATOM 297 HB3 HD2 18 18.549 -84.244 -6.677 1.00 0.00 H +ATOM 298 HD1 HD2 18 18.009 -84.419 -3.613 1.00 0.00 H +ATOM 299 HD2 HD2 18 20.294 -87.203 -5.786 1.00 0.00 H +ATOM 300 HE1 HD2 18 19.730 -85.575 -1.959 1.00 0.00 H +ATOM 301 N GLU 19 15.298 -84.119 -7.691 1.00 0.00 N +ATOM 302 H GLU 19 14.958 -84.011 -6.747 1.00 0.00 H +ATOM 303 CA GLU 19 14.712 -83.330 -8.768 1.00 0.00 C +ATOM 304 HA GLU 19 14.437 -83.964 -9.611 1.00 0.00 H +ATOM 305 CB GLU 19 13.421 -82.616 -8.252 1.00 0.00 C +ATOM 306 HB2 GLU 19 12.647 -83.347 -8.017 1.00 0.00 H +ATOM 307 HB3 GLU 19 13.573 -82.226 -7.246 1.00 0.00 H +ATOM 308 CG GLU 19 12.736 -81.540 -9.087 1.00 0.00 C +ATOM 309 HG2 GLU 19 11.760 -81.331 -8.650 1.00 0.00 H +ATOM 310 HG3 GLU 19 13.314 -80.617 -9.124 1.00 0.00 H +ATOM 311 CD GLU 19 12.543 -81.927 -10.534 1.00 0.00 C +ATOM 312 OE1 GLU 19 13.036 -81.240 -11.472 1.00 0.00 O +ATOM 313 OE2 GLU 19 11.880 -82.920 -10.839 1.00 0.00 O +ATOM 314 C GLU 19 15.701 -82.249 -9.282 1.00 0.00 C +ATOM 315 O GLU 19 16.202 -81.486 -8.450 1.00 0.00 O +ATOM 316 N ALA 20 15.876 -82.153 -10.583 1.00 0.00 N +ATOM 317 H ALA 20 15.626 -82.950 -11.150 1.00 0.00 H +ATOM 318 CA ALA 20 16.717 -81.142 -11.248 1.00 0.00 C +ATOM 319 HA ALA 20 16.551 -80.212 -10.704 1.00 0.00 H +ATOM 320 CB ALA 20 18.160 -81.669 -11.237 1.00 0.00 C +ATOM 321 HB1 ALA 20 18.489 -82.014 -10.257 1.00 0.00 H +ATOM 322 HB2 ALA 20 18.808 -80.811 -11.417 1.00 0.00 H +ATOM 323 HB3 ALA 20 18.253 -82.456 -11.985 1.00 0.00 H +ATOM 324 C ALA 20 16.174 -80.906 -12.690 1.00 0.00 C +ATOM 325 O ALA 20 15.848 -81.876 -13.388 1.00 0.00 O +ATOM 326 N VAL 21 16.131 -79.689 -13.197 1.00 0.00 N +ATOM 327 H VAL 21 16.335 -78.918 -12.578 1.00 0.00 H +ATOM 328 CA VAL 21 15.501 -79.300 -14.500 1.00 0.00 C +ATOM 329 HA VAL 21 14.507 -79.717 -14.340 1.00 0.00 H +ATOM 330 CB VAL 21 15.502 -77.697 -14.595 1.00 0.00 C +ATOM 331 HB VAL 21 15.092 -77.304 -13.664 1.00 0.00 H +ATOM 332 CG1 VAL 21 16.936 -77.139 -14.670 1.00 0.00 C +ATOM 333 HG11 VAL 21 17.524 -77.502 -15.512 1.00 0.00 H +ATOM 334 HG12 VAL 21 17.397 -77.534 -13.765 1.00 0.00 H +ATOM 335 HG13 VAL 21 16.952 -76.049 -14.660 1.00 0.00 H +ATOM 336 CG2 VAL 21 14.631 -77.179 -15.735 1.00 0.00 C +ATOM 337 HG21 VAL 21 13.580 -77.456 -15.648 1.00 0.00 H +ATOM 338 HG22 VAL 21 14.883 -77.512 -16.742 1.00 0.00 H +ATOM 339 HG23 VAL 21 14.768 -76.098 -15.711 1.00 0.00 H +ATOM 340 C VAL 21 16.197 -79.991 -15.695 1.00 0.00 C +ATOM 341 O VAL 21 15.511 -80.347 -16.671 1.00 0.00 O +ATOM 342 N ASP 22 17.549 -80.198 -15.644 1.00 0.00 N +ATOM 343 H ASP 22 18.006 -79.924 -14.787 1.00 0.00 H +ATOM 344 CA ASP 22 18.329 -80.812 -16.703 1.00 0.00 C +ATOM 345 HA ASP 22 17.763 -81.611 -17.182 1.00 0.00 H +ATOM 346 CB ASP 22 18.530 -79.754 -17.881 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.723 -80.386 -18.747 1.00 0.00 H +ATOM 348 HB3 ASP 22 17.614 -79.186 -18.047 1.00 0.00 H +ATOM 349 CG ASP 22 19.718 -78.823 -17.761 1.00 0.00 C +ATOM 350 OD1 ASP 22 19.956 -78.190 -18.805 1.00 0.00 O +ATOM 351 OD2 ASP 22 20.407 -78.802 -16.756 1.00 0.00 O +ATOM 352 C ASP 22 19.676 -81.428 -16.233 1.00 0.00 C +ATOM 353 O ASP 22 20.217 -81.129 -15.119 1.00 0.00 O +ATOM 354 N ALA 23 20.272 -82.224 -17.140 1.00 0.00 N +ATOM 355 H ALA 23 19.944 -82.210 -18.095 1.00 0.00 H +ATOM 356 CA ALA 23 21.582 -82.812 -16.965 1.00 0.00 C +ATOM 357 HA ALA 23 21.483 -83.440 -16.079 1.00 0.00 H +ATOM 358 CB ALA 23 21.995 -83.708 -18.140 1.00 0.00 C +ATOM 359 HB1 ALA 23 22.486 -83.224 -18.984 1.00 0.00 H +ATOM 360 HB2 ALA 23 21.075 -84.221 -18.420 1.00 0.00 H +ATOM 361 HB3 ALA 23 22.720 -84.415 -17.739 1.00 0.00 H +ATOM 362 C ALA 23 22.799 -81.813 -16.691 1.00 0.00 C +ATOM 363 O ALA 23 23.835 -82.256 -16.230 1.00 0.00 O +ATOM 364 N ALA 24 22.670 -80.526 -16.989 1.00 0.00 N +ATOM 365 H ALA 24 21.820 -80.211 -17.434 1.00 0.00 H +ATOM 366 CA ALA 24 23.732 -79.628 -16.519 1.00 0.00 C +ATOM 367 HA ALA 24 24.706 -80.047 -16.772 1.00 0.00 H +ATOM 368 CB ALA 24 23.524 -78.343 -17.439 1.00 0.00 C +ATOM 369 HB1 ALA 24 23.488 -78.613 -18.494 1.00 0.00 H +ATOM 370 HB2 ALA 24 24.351 -77.634 -17.481 1.00 0.00 H +ATOM 371 HB3 ALA 24 22.573 -77.837 -17.275 1.00 0.00 H +ATOM 372 C ALA 24 23.684 -79.301 -15.018 1.00 0.00 C +ATOM 373 O ALA 24 24.768 -79.355 -14.435 1.00 0.00 O +ATOM 374 N GLU 25 22.515 -79.074 -14.496 1.00 0.00 N +ATOM 375 H GLU 25 21.706 -79.249 -15.074 1.00 0.00 H +ATOM 376 CA GLU 25 22.216 -78.730 -13.028 1.00 0.00 C +ATOM 377 HA GLU 25 22.888 -77.938 -12.699 1.00 0.00 H +ATOM 378 CB GLU 25 20.698 -78.160 -13.013 1.00 0.00 C +ATOM 379 HB2 GLU 25 20.584 -77.316 -13.693 1.00 0.00 H +ATOM 380 HB3 GLU 25 20.022 -78.908 -13.428 1.00 0.00 H +ATOM 381 CG GLU 25 20.290 -77.760 -11.577 1.00 0.00 C +ATOM 382 HG2 GLU 25 19.299 -77.308 -11.514 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.322 -78.666 -10.973 1.00 0.00 H +ATOM 384 CD GLU 25 21.285 -76.683 -10.935 1.00 0.00 C +ATOM 385 OE1 GLU 25 21.763 -75.806 -11.706 1.00 0.00 O +ATOM 386 OE2 GLU 25 21.662 -76.825 -9.747 1.00 0.00 O +ATOM 387 C GLU 25 22.398 -80.014 -12.169 1.00 0.00 C +ATOM 388 O GLU 25 22.851 -79.999 -11.059 1.00 0.00 O +ATOM 389 N ALA 26 22.145 -81.204 -12.702 1.00 0.00 N +ATOM 390 H ALA 26 21.714 -81.232 -13.615 1.00 0.00 H +ATOM 391 CA ALA 26 22.212 -82.466 -12.048 1.00 0.00 C +ATOM 392 HA ALA 26 21.733 -82.504 -11.069 1.00 0.00 H +ATOM 393 CB ALA 26 21.327 -83.453 -12.823 1.00 0.00 C +ATOM 394 HB1 ALA 26 21.466 -84.413 -12.326 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.494 -83.438 -13.900 1.00 0.00 H +ATOM 396 HB3 ALA 26 20.270 -83.205 -12.732 1.00 0.00 H +ATOM 397 C ALA 26 23.618 -83.059 -12.015 1.00 0.00 C +ATOM 398 O ALA 26 23.893 -83.895 -11.162 1.00 0.00 O +ATOM 399 N GLU 27 24.504 -82.656 -12.962 1.00 0.00 N +ATOM 400 H GLU 27 24.222 -82.178 -13.806 1.00 0.00 H +ATOM 401 CA GLU 27 25.946 -83.100 -12.939 1.00 0.00 C +ATOM 402 HA GLU 27 25.868 -84.177 -13.087 1.00 0.00 H +ATOM 403 CB GLU 27 26.747 -82.312 -13.980 1.00 0.00 C +ATOM 404 HB2 GLU 27 26.285 -82.384 -14.965 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.954 -81.275 -13.716 1.00 0.00 H +ATOM 406 CG GLU 27 28.184 -82.775 -14.113 1.00 0.00 C +ATOM 407 HG2 GLU 27 28.881 -82.550 -13.306 1.00 0.00 H +ATOM 408 HG3 GLU 27 28.184 -83.865 -14.105 1.00 0.00 H +ATOM 409 CD GLU 27 28.808 -82.278 -15.370 1.00 0.00 C +ATOM 410 OE1 GLU 27 29.879 -81.578 -15.332 1.00 0.00 O +ATOM 411 OE2 GLU 27 28.314 -82.568 -16.526 1.00 0.00 O +ATOM 412 C GLU 27 26.625 -82.908 -11.587 1.00 0.00 C +ATOM 413 O GLU 27 27.451 -83.655 -11.087 1.00 0.00 O +ATOM 414 N LYS 28 26.139 -81.880 -10.843 1.00 0.00 N +ATOM 415 H LYS 28 25.452 -81.270 -11.261 1.00 0.00 H +ATOM 416 CA LYS 28 26.627 -81.399 -9.503 1.00 0.00 C +ATOM 417 HA LYS 28 27.671 -81.084 -9.496 1.00 0.00 H +ATOM 418 CB LYS 28 25.978 -80.043 -9.187 1.00 0.00 C +ATOM 419 HB2 LYS 28 24.913 -80.275 -9.151 1.00 0.00 H +ATOM 420 HB3 LYS 28 26.241 -79.832 -8.150 1.00 0.00 H +ATOM 421 CG LYS 28 26.073 -78.888 -10.104 1.00 0.00 C +ATOM 422 HG2 LYS 28 27.078 -78.508 -10.286 1.00 0.00 H +ATOM 423 HG3 LYS 28 25.536 -79.176 -11.007 1.00 0.00 H +ATOM 424 CD LYS 28 25.189 -77.725 -9.572 1.00 0.00 C +ATOM 425 HD2 LYS 28 24.165 -78.073 -9.706 1.00 0.00 H +ATOM 426 HD3 LYS 28 25.403 -77.472 -8.534 1.00 0.00 H +ATOM 427 CE LYS 28 25.291 -76.481 -10.441 1.00 0.00 C +ATOM 428 HE2 LYS 28 26.316 -76.116 -10.373 1.00 0.00 H +ATOM 429 HE3 LYS 28 25.184 -76.808 -11.475 1.00 0.00 H +ATOM 430 NZ LYS 28 24.229 -75.492 -10.153 1.00 0.00 N +ATOM 431 HZ1 LYS 28 24.098 -75.291 -9.172 1.00 0.00 H +ATOM 432 HZ2 LYS 28 23.325 -75.696 -10.555 1.00 0.00 H +ATOM 433 HZ3 LYS 28 24.600 -74.623 -10.509 1.00 0.00 H +ATOM 434 C LYS 28 26.487 -82.368 -8.278 1.00 0.00 C +ATOM 435 O LYS 28 27.270 -82.355 -7.316 1.00 0.00 O +ATOM 436 N PHE 29 25.475 -83.237 -8.417 1.00 0.00 N +ATOM 437 H PHE 29 24.983 -83.179 -9.298 1.00 0.00 H +ATOM 438 CA PHE 29 25.319 -84.341 -7.395 1.00 0.00 C +ATOM 439 HA PHE 29 25.229 -84.000 -6.364 1.00 0.00 H +ATOM 440 CB PHE 29 23.998 -85.137 -7.681 1.00 0.00 C +ATOM 441 HB2 PHE 29 24.091 -85.638 -8.644 1.00 0.00 H +ATOM 442 HB3 PHE 29 23.894 -85.901 -6.910 1.00 0.00 H +ATOM 443 CG PHE 29 22.676 -84.327 -7.783 1.00 0.00 C +ATOM 444 CD1 PHE 29 21.670 -84.634 -8.688 1.00 0.00 C +ATOM 445 HD1 PHE 29 21.781 -85.539 -9.267 1.00 0.00 H +ATOM 446 CE1 PHE 29 20.459 -83.923 -8.881 1.00 0.00 C +ATOM 447 HE1 PHE 29 19.685 -84.087 -9.616 1.00 0.00 H +ATOM 448 CZ PHE 29 20.326 -82.818 -8.035 1.00 0.00 C +ATOM 449 HZ PHE 29 19.430 -82.233 -8.180 1.00 0.00 H +ATOM 450 CE2 PHE 29 21.294 -82.421 -7.078 1.00 0.00 C +ATOM 451 HE2 PHE 29 21.128 -81.436 -6.669 1.00 0.00 H +ATOM 452 CD2 PHE 29 22.463 -83.145 -7.087 1.00 0.00 C +ATOM 453 HD2 PHE 29 23.239 -82.678 -6.499 1.00 0.00 H +ATOM 454 C PHE 29 26.579 -85.264 -7.416 1.00 0.00 C +ATOM 455 O PHE 29 27.251 -85.519 -6.376 1.00 0.00 O +ATOM 456 N THR 30 26.924 -85.734 -8.592 1.00 0.00 N +ATOM 457 H THR 30 26.250 -85.671 -9.343 1.00 0.00 H +ATOM 458 CA THR 30 28.124 -86.506 -8.806 1.00 0.00 C +ATOM 459 HA THR 30 28.057 -87.315 -8.079 1.00 0.00 H +ATOM 460 CB THR 30 28.070 -87.174 -10.185 1.00 0.00 C +ATOM 461 HB THR 30 27.976 -86.343 -10.884 1.00 0.00 H +ATOM 462 CG2 THR 30 29.144 -88.121 -10.618 1.00 0.00 C +ATOM 463 HG21 THR 30 28.857 -88.564 -11.571 1.00 0.00 H +ATOM 464 HG22 THR 30 30.064 -87.586 -10.853 1.00 0.00 H +ATOM 465 HG23 THR 30 29.225 -88.877 -9.837 1.00 0.00 H +ATOM 466 OG1 THR 30 26.866 -87.953 -10.222 1.00 0.00 O +ATOM 467 HG1 THR 30 26.148 -87.317 -10.166 1.00 0.00 H +ATOM 468 C THR 30 29.400 -85.750 -8.520 1.00 0.00 C +ATOM 469 O THR 30 30.349 -86.333 -7.995 1.00 0.00 O +ATOM 470 N LYS 31 29.530 -84.396 -8.736 1.00 0.00 N +ATOM 471 H LYS 31 28.761 -83.906 -9.170 1.00 0.00 H +ATOM 472 CA LYS 31 30.774 -83.632 -8.600 1.00 0.00 C +ATOM 473 HA LYS 31 31.553 -84.147 -9.162 1.00 0.00 H +ATOM 474 CB LYS 31 30.579 -82.176 -9.076 1.00 0.00 C +ATOM 475 HB2 LYS 31 29.707 -81.717 -8.610 1.00 0.00 H +ATOM 476 HB3 LYS 31 31.423 -81.629 -8.654 1.00 0.00 H +ATOM 477 CG LYS 31 30.484 -82.148 -10.610 1.00 0.00 C +ATOM 478 HG2 LYS 31 29.891 -82.998 -10.947 1.00 0.00 H +ATOM 479 HG3 LYS 31 30.108 -81.177 -10.934 1.00 0.00 H +ATOM 480 CD LYS 31 31.839 -82.424 -11.230 1.00 0.00 C +ATOM 481 HD2 LYS 31 32.434 -83.229 -10.799 1.00 0.00 H +ATOM 482 HD3 LYS 31 31.714 -82.700 -12.277 1.00 0.00 H +ATOM 483 CE LYS 31 32.600 -81.123 -11.208 1.00 0.00 C +ATOM 484 HE2 LYS 31 32.027 -80.351 -11.724 1.00 0.00 H +ATOM 485 HE3 LYS 31 32.635 -80.817 -10.162 1.00 0.00 H +ATOM 486 NZ LYS 31 33.975 -81.326 -11.759 1.00 0.00 N +ATOM 487 HZ1 LYS 31 33.986 -81.622 -12.724 1.00 0.00 H +ATOM 488 HZ2 LYS 31 34.482 -82.003 -11.206 1.00 0.00 H +ATOM 489 HZ3 LYS 31 34.520 -80.477 -11.784 1.00 0.00 H +ATOM 490 C LYS 31 31.141 -83.558 -7.137 1.00 0.00 C +ATOM 491 O LYS 31 32.271 -83.561 -6.692 1.00 0.00 O +ATOM 492 N ALA 32 30.111 -83.338 -6.299 1.00 0.00 N +ATOM 493 H ALA 32 29.249 -82.951 -6.655 1.00 0.00 H +ATOM 494 CA ALA 32 30.279 -83.181 -4.811 1.00 0.00 C +ATOM 495 HA ALA 32 31.012 -82.404 -4.597 1.00 0.00 H +ATOM 496 CB ALA 32 28.870 -82.791 -4.212 1.00 0.00 C +ATOM 497 HB1 ALA 32 28.954 -82.670 -3.132 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.393 -81.901 -4.624 1.00 0.00 H +ATOM 499 HB3 ALA 32 28.213 -83.645 -4.382 1.00 0.00 H +ATOM 500 C ALA 32 30.816 -84.413 -4.216 1.00 0.00 C +ATOM 501 O ALA 32 31.909 -84.315 -3.590 1.00 0.00 O +ATOM 502 N ASP 33 30.319 -85.594 -4.565 1.00 0.00 N +ATOM 503 H ASP 33 29.463 -85.593 -5.100 1.00 0.00 H +ATOM 504 CA ASP 33 30.803 -86.895 -4.201 1.00 0.00 C +ATOM 505 HA ASP 33 30.909 -86.851 -3.117 1.00 0.00 H +ATOM 506 CB ASP 33 29.924 -88.092 -4.562 1.00 0.00 C +ATOM 507 HB2 ASP 33 29.777 -88.293 -5.623 1.00 0.00 H +ATOM 508 HB3 ASP 33 30.543 -88.899 -4.170 1.00 0.00 H +ATOM 509 CG ASP 33 28.542 -88.214 -3.871 1.00 0.00 C +ATOM 510 OD1 ASP 33 27.580 -88.403 -4.603 1.00 0.00 O +ATOM 511 OD2 ASP 33 28.424 -87.983 -2.699 1.00 0.00 O +ATOM 512 C ASP 33 32.221 -87.122 -4.704 1.00 0.00 C +ATOM 513 O ASP 33 33.043 -87.699 -4.065 1.00 0.00 O +ATOM 514 N ALA 34 32.528 -86.707 -5.972 1.00 0.00 N +ATOM 515 H ALA 34 31.879 -86.133 -6.490 1.00 0.00 H +ATOM 516 CA ALA 34 33.886 -86.723 -6.596 1.00 0.00 C +ATOM 517 HA ALA 34 34.272 -87.743 -6.592 1.00 0.00 H +ATOM 518 CB ALA 34 33.813 -86.257 -8.029 1.00 0.00 C +ATOM 519 HB1 ALA 34 33.834 -85.176 -8.168 1.00 0.00 H +ATOM 520 HB2 ALA 34 33.080 -86.760 -8.658 1.00 0.00 H +ATOM 521 HB3 ALA 34 34.809 -86.398 -8.450 1.00 0.00 H +ATOM 522 C ALA 34 34.835 -85.888 -5.854 1.00 0.00 C +ATOM 523 O ALA 34 36.008 -86.255 -5.796 1.00 0.00 O +ATOM 524 N ASN 35 34.377 -84.739 -5.347 1.00 0.00 N +ATOM 525 H ASN 35 33.447 -84.379 -5.508 1.00 0.00 H +ATOM 526 CA ASN 35 35.197 -83.948 -4.412 1.00 0.00 C +ATOM 527 HA ASN 35 36.154 -83.767 -4.900 1.00 0.00 H +ATOM 528 CB ASN 35 34.568 -82.484 -4.181 1.00 0.00 C +ATOM 529 HB2 ASN 35 34.466 -81.979 -5.142 1.00 0.00 H +ATOM 530 HB3 ASN 35 33.530 -82.586 -3.863 1.00 0.00 H +ATOM 531 CG ASN 35 35.406 -81.677 -3.292 1.00 0.00 C +ATOM 532 OD1 ASN 35 35.241 -81.710 -2.097 1.00 0.00 O +ATOM 533 ND2 ASN 35 36.486 -81.103 -3.759 1.00 0.00 N +ATOM 534 HD21 ASN 35 36.616 -81.048 -4.759 1.00 0.00 H +ATOM 535 HD22 ASN 35 37.178 -80.692 -3.149 1.00 0.00 H +ATOM 536 C ASN 35 35.421 -84.676 -3.150 1.00 0.00 C +ATOM 537 O ASN 35 36.549 -84.783 -2.710 1.00 0.00 O +ATOM 538 N ASP 36 34.389 -85.308 -2.572 1.00 0.00 N +ATOM 539 H ASP 36 33.505 -85.018 -2.966 1.00 0.00 H +ATOM 540 CA ASP 36 34.435 -85.991 -1.250 1.00 0.00 C +ATOM 541 HA ASP 36 34.790 -85.314 -0.473 1.00 0.00 H +ATOM 542 CB ASP 36 32.996 -86.380 -0.739 1.00 0.00 C +ATOM 543 HB2 ASP 36 32.502 -86.976 -1.506 1.00 0.00 H +ATOM 544 HB3 ASP 36 33.118 -86.916 0.202 1.00 0.00 H +ATOM 545 CG ASP 36 31.983 -85.222 -0.444 1.00 0.00 C +ATOM 546 OD1 ASP 36 32.470 -84.124 -0.195 1.00 0.00 O +ATOM 547 OD2 ASP 36 30.774 -85.486 -0.357 1.00 0.00 O +ATOM 548 C ASP 36 35.447 -87.184 -1.364 1.00 0.00 C +ATOM 549 O ASP 36 36.051 -87.490 -0.385 1.00 0.00 O +ATOM 550 N LYS 37 35.632 -87.758 -2.556 1.00 0.00 N +ATOM 551 H LYS 37 35.091 -87.410 -3.335 1.00 0.00 H +ATOM 552 CA LYS 37 36.637 -88.807 -2.801 1.00 0.00 C +ATOM 553 HA LYS 37 36.720 -89.335 -1.852 1.00 0.00 H +ATOM 554 CB LYS 37 35.912 -89.819 -3.752 1.00 0.00 C +ATOM 555 HB2 LYS 37 35.841 -89.331 -4.724 1.00 0.00 H +ATOM 556 HB3 LYS 37 34.913 -89.998 -3.355 1.00 0.00 H +ATOM 557 CG LYS 37 36.610 -91.205 -3.865 1.00 0.00 C +ATOM 558 HG2 LYS 37 36.905 -91.489 -2.855 1.00 0.00 H +ATOM 559 HG3 LYS 37 37.469 -91.069 -4.522 1.00 0.00 H +ATOM 560 CD LYS 37 35.695 -92.281 -4.504 1.00 0.00 C +ATOM 561 HD2 LYS 37 34.746 -92.378 -3.978 1.00 0.00 H +ATOM 562 HD3 LYS 37 35.427 -91.990 -5.519 1.00 0.00 H +ATOM 563 CE LYS 37 36.239 -93.681 -4.702 1.00 0.00 C +ATOM 564 HE2 LYS 37 36.690 -94.057 -3.784 1.00 0.00 H +ATOM 565 HE3 LYS 37 35.363 -94.291 -4.925 1.00 0.00 H +ATOM 566 NZ LYS 37 37.309 -93.787 -5.747 1.00 0.00 N +ATOM 567 HZ1 LYS 37 37.521 -94.733 -6.028 1.00 0.00 H +ATOM 568 HZ2 LYS 37 36.972 -93.361 -6.599 1.00 0.00 H +ATOM 569 HZ3 LYS 37 38.165 -93.384 -5.391 1.00 0.00 H +ATOM 570 C LYS 37 38.018 -88.391 -3.344 1.00 0.00 C +ATOM 571 O LYS 37 38.886 -89.241 -3.440 1.00 0.00 O +ATOM 572 N GLY 38 38.183 -87.177 -3.872 1.00 0.00 N +ATOM 573 H GLY 38 37.396 -86.546 -3.809 1.00 0.00 H +ATOM 574 CA GLY 38 39.387 -86.583 -4.443 1.00 0.00 C +ATOM 575 HA2 GLY 38 39.325 -85.496 -4.475 1.00 0.00 H +ATOM 576 HA3 GLY 38 40.181 -86.993 -3.819 1.00 0.00 H +ATOM 577 C GLY 38 39.729 -86.970 -5.886 1.00 0.00 C +ATOM 578 O GLY 38 40.905 -87.248 -6.153 1.00 0.00 O +ATOM 579 N VAL 39 38.763 -86.968 -6.797 1.00 0.00 N +ATOM 580 H VAL 39 37.855 -86.659 -6.481 1.00 0.00 H +ATOM 581 CA VAL 39 38.776 -87.337 -8.259 1.00 0.00 C +ATOM 582 HA VAL 39 39.698 -87.892 -8.433 1.00 0.00 H +ATOM 583 CB VAL 39 37.732 -88.315 -8.798 1.00 0.00 C +ATOM 584 HB VAL 39 36.777 -87.792 -8.853 1.00 0.00 H +ATOM 585 CG1 VAL 39 38.140 -88.854 -10.182 1.00 0.00 C +ATOM 586 HG11 VAL 39 38.209 -88.147 -11.008 1.00 0.00 H +ATOM 587 HG12 VAL 39 37.394 -89.588 -10.487 1.00 0.00 H +ATOM 588 HG13 VAL 39 39.097 -89.363 -10.072 1.00 0.00 H +ATOM 589 CG2 VAL 39 37.533 -89.463 -7.772 1.00 0.00 C +ATOM 590 HG21 VAL 39 38.434 -89.957 -7.409 1.00 0.00 H +ATOM 591 HG22 VAL 39 36.823 -90.178 -8.188 1.00 0.00 H +ATOM 592 HG23 VAL 39 37.126 -89.043 -6.852 1.00 0.00 H +ATOM 593 C VAL 39 38.673 -86.043 -9.126 1.00 0.00 C +ATOM 594 O VAL 39 37.655 -85.377 -9.199 1.00 0.00 O +ATOM 595 N ASP 40 39.713 -85.808 -9.910 1.00 0.00 N +ATOM 596 H ASP 40 40.545 -86.371 -9.810 1.00 0.00 H +ATOM 597 CA ASP 40 39.725 -84.690 -10.868 1.00 0.00 C +ATOM 598 HA ASP 40 39.063 -83.924 -10.463 1.00 0.00 H +ATOM 599 CB ASP 40 41.116 -84.074 -10.999 1.00 0.00 C +ATOM 600 HB2 ASP 40 41.810 -84.703 -11.557 1.00 0.00 H +ATOM 601 HB3 ASP 40 40.955 -83.137 -11.532 1.00 0.00 H +ATOM 602 CG ASP 40 41.688 -83.626 -9.688 1.00 0.00 C +ATOM 603 OD1 ASP 40 40.863 -83.257 -8.826 1.00 0.00 O +ATOM 604 OD2 ASP 40 42.977 -83.521 -9.492 1.00 0.00 O +ATOM 605 C ASP 40 39.035 -85.025 -12.228 1.00 0.00 C +ATOM 606 O ASP 40 39.299 -86.121 -12.712 1.00 0.00 O +ATOM 607 N GLY 41 38.341 -84.046 -12.815 1.00 0.00 N +ATOM 608 H GLY 41 38.159 -83.162 -12.363 1.00 0.00 H +ATOM 609 CA GLY 41 37.627 -84.356 -14.051 1.00 0.00 C +ATOM 610 HA2 GLY 41 38.347 -84.587 -14.837 1.00 0.00 H +ATOM 611 HA3 GLY 41 36.993 -85.224 -13.870 1.00 0.00 H +ATOM 612 C GLY 41 36.814 -83.190 -14.606 1.00 0.00 C +ATOM 613 O GLY 41 36.357 -82.335 -13.824 1.00 0.00 O +ATOM 614 N GLU 42 36.256 -83.413 -15.811 1.00 0.00 N +ATOM 615 H GLU 42 36.690 -84.035 -16.478 1.00 0.00 H +ATOM 616 CA GLU 42 35.136 -82.684 -16.376 1.00 0.00 C +ATOM 617 HA GLU 42 34.719 -82.134 -15.532 1.00 0.00 H +ATOM 618 CB GLU 42 35.667 -81.765 -17.515 1.00 0.00 C +ATOM 619 HB2 GLU 42 36.239 -80.986 -17.011 1.00 0.00 H +ATOM 620 HB3 GLU 42 36.396 -82.250 -18.164 1.00 0.00 H +ATOM 621 CG GLU 42 34.421 -81.159 -18.321 1.00 0.00 C +ATOM 622 HG2 GLU 42 34.940 -80.512 -19.028 1.00 0.00 H +ATOM 623 HG3 GLU 42 33.992 -82.022 -18.829 1.00 0.00 H +ATOM 624 CD GLU 42 33.328 -80.389 -17.479 1.00 0.00 C +ATOM 625 OE1 GLU 42 32.349 -80.046 -18.165 1.00 0.00 O +ATOM 626 OE2 GLU 42 33.376 -80.130 -16.286 1.00 0.00 O +ATOM 627 C GLU 42 34.153 -83.831 -16.808 1.00 0.00 C +ATOM 628 O GLU 42 34.510 -84.852 -17.399 1.00 0.00 O +ATOM 629 N TRP 43 32.909 -83.660 -16.469 1.00 0.00 N +ATOM 630 H TRP 43 32.580 -82.798 -16.057 1.00 0.00 H +ATOM 631 CA TRP 43 31.904 -84.707 -16.522 1.00 0.00 C +ATOM 632 HA TRP 43 32.381 -85.677 -16.662 1.00 0.00 H +ATOM 633 CB TRP 43 31.152 -84.882 -15.206 1.00 0.00 C +ATOM 634 HB2 TRP 43 31.202 -83.973 -14.606 1.00 0.00 H +ATOM 635 HB3 TRP 43 30.147 -85.269 -15.374 1.00 0.00 H +ATOM 636 CG TRP 43 31.638 -86.040 -14.355 1.00 0.00 C +ATOM 637 CD1 TRP 43 31.152 -87.325 -14.279 1.00 0.00 C +ATOM 638 HD1 TRP 43 30.400 -87.654 -14.980 1.00 0.00 H +ATOM 639 NE1 TRP 43 31.802 -88.042 -13.283 1.00 0.00 N +ATOM 640 HE1 TRP 43 31.606 -89.018 -13.113 1.00 0.00 H +ATOM 641 CE2 TRP 43 32.827 -87.308 -12.726 1.00 0.00 C +ATOM 642 CZ2 TRP 43 33.713 -87.617 -11.666 1.00 0.00 C +ATOM 643 HZ2 TRP 43 33.768 -88.588 -11.197 1.00 0.00 H +ATOM 644 CH2 TRP 43 34.715 -86.699 -11.333 1.00 0.00 C +ATOM 645 HH2 TRP 43 35.352 -86.915 -10.487 1.00 0.00 H +ATOM 646 CZ3 TRP 43 34.654 -85.434 -11.952 1.00 0.00 C +ATOM 647 HZ3 TRP 43 35.322 -84.703 -11.520 1.00 0.00 H +ATOM 648 CE3 TRP 43 33.728 -85.090 -12.945 1.00 0.00 C +ATOM 649 HE3 TRP 43 33.697 -84.101 -13.378 1.00 0.00 H +ATOM 650 CD2 TRP 43 32.749 -85.998 -13.377 1.00 0.00 C +ATOM 651 C TRP 43 30.958 -84.478 -17.662 1.00 0.00 C +ATOM 652 O TRP 43 30.811 -83.383 -18.258 1.00 0.00 O +ATOM 653 N THR 44 30.253 -85.596 -18.020 1.00 0.00 N +ATOM 654 H THR 44 30.453 -86.484 -17.582 1.00 0.00 H +ATOM 655 CA THR 44 29.242 -85.712 -19.096 1.00 0.00 C +ATOM 656 HA THR 44 28.844 -84.697 -19.110 1.00 0.00 H +ATOM 657 CB THR 44 29.963 -85.967 -20.451 1.00 0.00 C +ATOM 658 HB THR 44 30.743 -85.232 -20.647 1.00 0.00 H +ATOM 659 CG2 THR 44 30.620 -87.315 -20.489 1.00 0.00 C +ATOM 660 HG21 THR 44 31.028 -87.582 -21.464 1.00 0.00 H +ATOM 661 HG22 THR 44 29.834 -88.010 -20.190 1.00 0.00 H +ATOM 662 HG23 THR 44 31.328 -87.311 -19.660 1.00 0.00 H +ATOM 663 OG1 THR 44 29.062 -85.818 -21.539 1.00 0.00 O +ATOM 664 HG1 THR 44 29.356 -85.042 -22.021 1.00 0.00 H +ATOM 665 C THR 44 28.135 -86.694 -18.781 1.00 0.00 C +ATOM 666 O THR 44 28.328 -87.733 -18.125 1.00 0.00 O +ATOM 667 N TYR 45 26.921 -86.432 -19.182 1.00 0.00 N +ATOM 668 H TYR 45 26.850 -85.639 -19.804 1.00 0.00 H +ATOM 669 CA TYR 45 25.803 -87.330 -19.107 1.00 0.00 C +ATOM 670 HA TYR 45 25.927 -87.936 -18.209 1.00 0.00 H +ATOM 671 CB TYR 45 24.405 -86.625 -18.783 1.00 0.00 C +ATOM 672 HB2 TYR 45 24.577 -85.998 -17.908 1.00 0.00 H +ATOM 673 HB3 TYR 45 24.174 -86.103 -19.712 1.00 0.00 H +ATOM 674 CG TYR 45 23.267 -87.515 -18.451 1.00 0.00 C +ATOM 675 CD1 TYR 45 23.331 -88.279 -17.278 1.00 0.00 C +ATOM 676 HD1 TYR 45 24.208 -88.231 -16.649 1.00 0.00 H +ATOM 677 CE1 TYR 45 22.166 -89.049 -16.968 1.00 0.00 C +ATOM 678 HE1 TYR 45 22.186 -89.711 -16.115 1.00 0.00 H +ATOM 679 CZ TYR 45 21.046 -89.089 -17.811 1.00 0.00 C +ATOM 680 OH TYR 45 19.831 -89.530 -17.448 1.00 0.00 O +ATOM 681 HH TYR 45 19.191 -89.675 -18.148 1.00 0.00 H +ATOM 682 CE2 TYR 45 21.085 -88.339 -19.044 1.00 0.00 C +ATOM 683 HE2 TYR 45 20.279 -88.346 -19.763 1.00 0.00 H +ATOM 684 CD2 TYR 45 22.220 -87.642 -19.384 1.00 0.00 C +ATOM 685 HD2 TYR 45 22.147 -87.041 -20.278 1.00 0.00 H +ATOM 686 C TYR 45 25.752 -88.246 -20.329 1.00 0.00 C +ATOM 687 O TYR 45 25.715 -87.885 -21.482 1.00 0.00 O +ATOM 688 N ASP 46 25.642 -89.546 -20.060 1.00 0.00 N +ATOM 689 H ASP 46 25.697 -89.787 -19.081 1.00 0.00 H +ATOM 690 CA ASP 46 25.394 -90.600 -21.096 1.00 0.00 C +ATOM 691 HA ASP 46 25.387 -90.178 -22.101 1.00 0.00 H +ATOM 692 CB ASP 46 26.518 -91.607 -21.129 1.00 0.00 C +ATOM 693 HB2 ASP 46 27.492 -91.246 -21.459 1.00 0.00 H +ATOM 694 HB3 ASP 46 26.677 -91.785 -20.065 1.00 0.00 H +ATOM 695 CG ASP 46 26.100 -92.845 -21.865 1.00 0.00 C +ATOM 696 OD1 ASP 46 26.500 -93.957 -21.405 1.00 0.00 O +ATOM 697 OD2 ASP 46 25.554 -92.813 -22.968 1.00 0.00 O +ATOM 698 C ASP 46 23.998 -91.197 -20.907 1.00 0.00 C +ATOM 699 O ASP 46 23.692 -91.990 -20.025 1.00 0.00 O +ATOM 700 N ASP 47 23.080 -90.726 -21.724 1.00 0.00 N +ATOM 701 H ASP 47 23.374 -90.232 -22.555 1.00 0.00 H +ATOM 702 CA ASP 47 21.676 -90.943 -21.422 1.00 0.00 C +ATOM 703 HA ASP 47 21.298 -90.838 -20.405 1.00 0.00 H +ATOM 704 CB ASP 47 20.921 -89.905 -22.098 1.00 0.00 C +ATOM 705 HB2 ASP 47 19.851 -89.948 -21.893 1.00 0.00 H +ATOM 706 HB3 ASP 47 21.275 -88.935 -21.750 1.00 0.00 H +ATOM 707 CG ASP 47 21.109 -89.759 -23.633 1.00 0.00 C +ATOM 708 OD1 ASP 47 22.264 -89.586 -24.089 1.00 0.00 O +ATOM 709 OD2 ASP 47 20.143 -89.788 -24.424 1.00 0.00 O +ATOM 710 C ASP 47 21.268 -92.423 -21.874 1.00 0.00 C +ATOM 711 O ASP 47 20.135 -92.848 -21.526 1.00 0.00 O +ATOM 712 N ALA 48 22.070 -93.145 -22.665 1.00 0.00 N +ATOM 713 H ALA 48 22.864 -92.666 -23.064 1.00 0.00 H +ATOM 714 CA ALA 48 21.717 -94.463 -22.988 1.00 0.00 C +ATOM 715 HA ALA 48 20.674 -94.633 -23.258 1.00 0.00 H +ATOM 716 CB ALA 48 22.489 -94.831 -24.202 1.00 0.00 C +ATOM 717 HB1 ALA 48 22.079 -95.729 -24.665 1.00 0.00 H +ATOM 718 HB2 ALA 48 23.547 -94.912 -23.950 1.00 0.00 H +ATOM 719 HB3 ALA 48 22.244 -94.086 -24.959 1.00 0.00 H +ATOM 720 C ALA 48 22.033 -95.416 -21.814 1.00 0.00 C +ATOM 721 O ALA 48 21.594 -96.543 -21.915 1.00 0.00 O +ATOM 722 N THR 49 22.790 -95.016 -20.753 1.00 0.00 N +ATOM 723 H THR 49 23.217 -94.100 -20.748 1.00 0.00 H +ATOM 724 CA THR 49 22.948 -95.793 -19.461 1.00 0.00 C +ATOM 725 HA THR 49 22.422 -96.742 -19.571 1.00 0.00 H +ATOM 726 CB THR 49 24.402 -96.064 -19.190 1.00 0.00 C +ATOM 727 HB THR 49 24.476 -96.577 -18.231 1.00 0.00 H +ATOM 728 CG2 THR 49 25.031 -97.005 -20.258 1.00 0.00 C +ATOM 729 HG21 THR 49 24.620 -97.994 -20.054 1.00 0.00 H +ATOM 730 HG22 THR 49 26.117 -96.983 -20.167 1.00 0.00 H +ATOM 731 HG23 THR 49 24.747 -96.723 -21.272 1.00 0.00 H +ATOM 732 OG1 THR 49 25.108 -94.811 -19.180 1.00 0.00 O +ATOM 733 HG1 THR 49 25.496 -94.601 -20.033 1.00 0.00 H +ATOM 734 C THR 49 22.272 -95.075 -18.270 1.00 0.00 C +ATOM 735 O THR 49 22.425 -95.440 -17.119 1.00 0.00 O +ATOM 736 N LYS 50 21.680 -93.912 -18.567 1.00 0.00 N +ATOM 737 H LYS 50 21.373 -93.708 -19.507 1.00 0.00 H +ATOM 738 CA LYS 50 21.112 -92.940 -17.544 1.00 0.00 C +ATOM 739 HA LYS 50 20.925 -92.001 -18.065 1.00 0.00 H +ATOM 740 CB LYS 50 19.799 -93.432 -16.891 1.00 0.00 C +ATOM 741 HB2 LYS 50 19.886 -94.410 -16.417 1.00 0.00 H +ATOM 742 HB3 LYS 50 19.478 -92.615 -16.245 1.00 0.00 H +ATOM 743 CG LYS 50 18.729 -93.696 -17.970 1.00 0.00 C +ATOM 744 HG2 LYS 50 18.611 -92.932 -18.738 1.00 0.00 H +ATOM 745 HG3 LYS 50 19.073 -94.496 -18.626 1.00 0.00 H +ATOM 746 CD LYS 50 17.369 -94.097 -17.406 1.00 0.00 C +ATOM 747 HD2 LYS 50 17.665 -94.764 -16.596 1.00 0.00 H +ATOM 748 HD3 LYS 50 16.837 -93.229 -17.017 1.00 0.00 H +ATOM 749 CE LYS 50 16.566 -94.818 -18.463 1.00 0.00 C +ATOM 750 HE2 LYS 50 16.672 -94.318 -19.426 1.00 0.00 H +ATOM 751 HE3 LYS 50 16.981 -95.809 -18.644 1.00 0.00 H +ATOM 752 NZ LYS 50 15.152 -94.979 -18.013 1.00 0.00 N +ATOM 753 HZ1 LYS 50 15.105 -95.295 -17.055 1.00 0.00 H +ATOM 754 HZ2 LYS 50 14.641 -95.652 -18.566 1.00 0.00 H +ATOM 755 HZ3 LYS 50 14.685 -94.090 -18.125 1.00 0.00 H +ATOM 756 C LYS 50 22.205 -92.610 -16.482 1.00 0.00 C +ATOM 757 O LYS 50 21.873 -92.533 -15.304 1.00 0.00 O +ATOM 758 N THR 51 23.426 -92.224 -16.883 1.00 0.00 N +ATOM 759 H THR 51 23.558 -92.110 -17.877 1.00 0.00 H +ATOM 760 CA THR 51 24.510 -92.137 -15.846 1.00 0.00 C +ATOM 761 HA THR 51 24.096 -91.872 -14.873 1.00 0.00 H +ATOM 762 CB THR 51 25.363 -93.350 -15.536 1.00 0.00 C +ATOM 763 HB THR 51 26.279 -93.050 -15.027 1.00 0.00 H +ATOM 764 CG2 THR 51 24.555 -94.278 -14.710 1.00 0.00 C +ATOM 765 HG21 THR 51 24.129 -93.731 -13.869 1.00 0.00 H +ATOM 766 HG22 THR 51 25.250 -95.018 -14.312 1.00 0.00 H +ATOM 767 HG23 THR 51 23.897 -94.971 -15.234 1.00 0.00 H +ATOM 768 OG1 THR 51 25.813 -94.002 -16.682 1.00 0.00 O +ATOM 769 HG1 THR 51 25.146 -93.968 -17.371 1.00 0.00 H +ATOM 770 C THR 51 25.464 -90.950 -16.139 1.00 0.00 C +ATOM 771 O THR 51 25.817 -90.691 -17.330 1.00 0.00 O +ATOM 772 N PHE 52 25.991 -90.258 -15.068 1.00 0.00 N +ATOM 773 H PHE 52 25.652 -90.490 -14.146 1.00 0.00 H +ATOM 774 CA PHE 52 27.008 -89.208 -15.149 1.00 0.00 C +ATOM 775 HA PHE 52 26.966 -88.668 -16.095 1.00 0.00 H +ATOM 776 CB PHE 52 26.839 -88.209 -14.061 1.00 0.00 C +ATOM 777 HB2 PHE 52 27.018 -88.688 -13.098 1.00 0.00 H +ATOM 778 HB3 PHE 52 27.590 -87.425 -14.165 1.00 0.00 H +ATOM 779 CG PHE 52 25.435 -87.498 -14.050 1.00 0.00 C +ATOM 780 CD1 PHE 52 24.500 -87.958 -13.044 1.00 0.00 C +ATOM 781 HD1 PHE 52 24.847 -88.676 -12.316 1.00 0.00 H +ATOM 782 CE1 PHE 52 23.273 -87.371 -12.941 1.00 0.00 C +ATOM 783 HE1 PHE 52 22.662 -87.630 -12.089 1.00 0.00 H +ATOM 784 CZ PHE 52 22.751 -86.486 -13.889 1.00 0.00 C +ATOM 785 HZ PHE 52 21.758 -86.091 -13.738 1.00 0.00 H +ATOM 786 CE2 PHE 52 23.674 -86.059 -14.872 1.00 0.00 C +ATOM 787 HE2 PHE 52 23.323 -85.473 -15.708 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.043 -86.506 -14.944 1.00 0.00 C +ATOM 789 HD2 PHE 52 25.692 -86.207 -15.755 1.00 0.00 H +ATOM 790 C PHE 52 28.419 -89.910 -15.127 1.00 0.00 C +ATOM 791 O PHE 52 28.726 -90.648 -14.178 1.00 0.00 O +ATOM 792 N THR 53 29.319 -89.573 -16.062 1.00 0.00 N +ATOM 793 H THR 53 29.058 -88.952 -16.815 1.00 0.00 H +ATOM 794 CA THR 53 30.630 -90.228 -16.391 1.00 0.00 C +ATOM 795 HA THR 53 31.195 -90.535 -15.511 1.00 0.00 H +ATOM 796 CB THR 53 30.394 -91.529 -17.243 1.00 0.00 C +ATOM 797 HB THR 53 29.698 -92.201 -16.741 1.00 0.00 H +ATOM 798 CG2 THR 53 29.760 -91.275 -18.609 1.00 0.00 C +ATOM 799 HG21 THR 53 28.820 -90.745 -18.454 1.00 0.00 H +ATOM 800 HG22 THR 53 29.563 -92.185 -19.176 1.00 0.00 H +ATOM 801 HG23 THR 53 30.404 -90.573 -19.139 1.00 0.00 H +ATOM 802 OG1 THR 53 31.494 -92.244 -17.703 1.00 0.00 O +ATOM 803 HG1 THR 53 32.035 -92.468 -16.942 1.00 0.00 H +ATOM 804 C THR 53 31.564 -89.194 -17.122 1.00 0.00 C +ATOM 805 O THR 53 31.197 -88.073 -17.343 1.00 0.00 O +ATOM 806 N VAL 54 32.809 -89.577 -17.244 1.00 0.00 N +ATOM 807 H VAL 54 32.934 -90.563 -17.065 1.00 0.00 H +ATOM 808 CA VAL 54 33.934 -88.724 -17.617 1.00 0.00 C +ATOM 809 HA VAL 54 33.703 -87.695 -17.343 1.00 0.00 H +ATOM 810 CB VAL 54 35.266 -89.172 -16.913 1.00 0.00 C +ATOM 811 HB VAL 54 36.016 -88.407 -17.114 1.00 0.00 H +ATOM 812 CG1 VAL 54 35.147 -89.283 -15.377 1.00 0.00 C +ATOM 813 HG11 VAL 54 36.060 -89.633 -14.898 1.00 0.00 H +ATOM 814 HG12 VAL 54 34.395 -90.038 -15.145 1.00 0.00 H +ATOM 815 HG13 VAL 54 34.937 -88.259 -15.070 1.00 0.00 H +ATOM 816 CG2 VAL 54 35.680 -90.569 -17.450 1.00 0.00 C +ATOM 817 HG21 VAL 54 35.919 -90.483 -18.509 1.00 0.00 H +ATOM 818 HG22 VAL 54 34.916 -91.335 -17.316 1.00 0.00 H +ATOM 819 HG23 VAL 54 36.591 -90.747 -16.878 1.00 0.00 H +ATOM 820 C VAL 54 34.177 -88.429 -19.142 1.00 0.00 C +ATOM 821 O VAL 54 33.704 -89.206 -20.025 1.00 0.00 O +ATOM 822 N THR 55 34.950 -87.350 -19.319 1.00 0.00 N +ATOM 823 H THR 55 35.271 -86.843 -18.506 1.00 0.00 H +ATOM 824 CA THR 55 35.362 -86.802 -20.646 1.00 0.00 C +ATOM 825 HA THR 55 34.697 -87.065 -21.468 1.00 0.00 H +ATOM 826 CB THR 55 35.490 -85.224 -20.627 1.00 0.00 C +ATOM 827 HB THR 55 35.950 -84.981 -21.585 1.00 0.00 H +ATOM 828 CG2 THR 55 34.155 -84.501 -20.705 1.00 0.00 C +ATOM 829 HG21 THR 55 33.559 -84.515 -19.792 1.00 0.00 H +ATOM 830 HG22 THR 55 33.580 -85.008 -21.480 1.00 0.00 H +ATOM 831 HG23 THR 55 34.248 -83.463 -21.024 1.00 0.00 H +ATOM 832 OG1 THR 55 36.306 -84.631 -19.639 1.00 0.00 O +ATOM 833 HG1 THR 55 35.841 -84.699 -18.802 1.00 0.00 H +ATOM 834 C THR 55 36.758 -87.380 -20.971 1.00 0.00 C +ATOM 835 O THR 55 37.680 -87.454 -20.153 1.00 0.00 O +ATOM 836 N GLU 56 36.886 -87.802 -22.232 1.00 0.00 N +ATOM 837 H GLU 56 36.066 -87.681 -22.809 1.00 0.00 H +ATOM 838 CA GLU 56 38.177 -88.427 -22.791 1.00 0.00 C +ATOM 839 HA GLU 56 38.846 -88.716 -21.980 1.00 0.00 H +ATOM 840 CB GLU 56 37.772 -89.791 -23.386 1.00 0.00 C +ATOM 841 HB2 GLU 56 38.729 -90.262 -23.612 1.00 0.00 H +ATOM 842 HB3 GLU 56 37.243 -90.368 -22.628 1.00 0.00 H +ATOM 843 CG GLU 56 36.789 -89.704 -24.566 1.00 0.00 C +ATOM 844 HG2 GLU 56 35.812 -89.489 -24.135 1.00 0.00 H +ATOM 845 HG3 GLU 56 37.087 -88.847 -25.171 1.00 0.00 H +ATOM 846 CD GLU 56 36.779 -90.995 -25.442 1.00 0.00 C +ATOM 847 OE1 GLU 56 36.669 -92.141 -24.939 1.00 0.00 O +ATOM 848 OE2 GLU 56 36.904 -90.944 -26.682 1.00 0.00 O +ATOM 849 C GLU 56 38.945 -87.485 -23.665 1.00 0.00 C +ATOM 850 O GLU 56 38.334 -86.500 -24.122 1.00 0.00 O +ATOM 851 OXT GLU 56 40.126 -87.842 -23.843 1.00 0.00 O +ATOM 852 ZN ZN1 57 21.506 -88.083 -2.842 1.00 0.00 ZN +ATOM 853 N AN1 58 22.451 -87.153 -1.550 1.00 0.00 N +ATOM 854 C AN1 58 23.653 -85.378 -0.040 1.00 0.00 C +ATOM 855 C1 AN1 58 23.049 -86.384 -0.899 1.00 0.00 C +ATOM 856 H AN1 58 23.964 -85.837 0.907 1.00 0.00 H +ATOM 857 H1 AN1 58 22.868 -84.634 0.139 1.00 0.00 H +ATOM 858 H2 AN1 58 24.483 -84.914 -0.586 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 21.306 -87.464 1.883 1.00 0.00 N +ATOM 860 N2 AZI 59 22.381 -88.022 1.919 1.00 0.00 N +ATOM 861 N3 AZI 59 23.533 -88.509 2.037 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/inp/pdbs/cluster.c2.pdb b/tests/nsga2/inp/pdbs/cluster.c2.pdb new file mode 100644 index 0000000..caa2f2f --- /dev/null +++ b/tests/nsga2/inp/pdbs/cluster.c2.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 14.644 -84.188 -13.280 1.00 0.00 N +ATOM 2 H1 MET 1 13.995 -83.838 -13.970 1.00 0.00 H +ATOM 3 H2 MET 1 15.569 -83.790 -13.356 1.00 0.00 H +ATOM 4 H3 MET 1 14.221 -83.982 -12.386 1.00 0.00 H +ATOM 5 CA MET 1 14.776 -85.661 -13.392 1.00 0.00 C +ATOM 6 HA MET 1 13.799 -86.144 -13.396 1.00 0.00 H +ATOM 7 CB MET 1 15.585 -85.864 -14.654 1.00 0.00 C +ATOM 8 HB2 MET 1 15.568 -85.080 -15.411 1.00 0.00 H +ATOM 9 HB3 MET 1 16.612 -85.945 -14.299 1.00 0.00 H +ATOM 10 CG MET 1 15.207 -87.153 -15.328 1.00 0.00 C +ATOM 11 HG2 MET 1 14.207 -86.961 -15.715 1.00 0.00 H +ATOM 12 HG3 MET 1 15.874 -87.271 -16.182 1.00 0.00 H +ATOM 13 SD MET 1 15.213 -88.683 -14.433 1.00 0.00 S +ATOM 14 CE MET 1 16.991 -88.964 -14.447 1.00 0.00 C +ATOM 15 HE1 MET 1 17.445 -88.228 -13.783 1.00 0.00 H +ATOM 16 HE2 MET 1 17.521 -88.745 -15.374 1.00 0.00 H +ATOM 17 HE3 MET 1 17.261 -90.002 -14.251 1.00 0.00 H +ATOM 18 C MET 1 15.543 -86.234 -12.172 1.00 0.00 C +ATOM 19 O MET 1 16.468 -85.556 -11.698 1.00 0.00 O +ATOM 20 N GLN 2 15.244 -87.442 -11.754 1.00 0.00 N +ATOM 21 H GLN 2 14.458 -87.835 -12.251 1.00 0.00 H +ATOM 22 CA GLN 2 15.728 -88.164 -10.614 1.00 0.00 C +ATOM 23 HA GLN 2 16.135 -87.486 -9.863 1.00 0.00 H +ATOM 24 CB GLN 2 14.434 -88.877 -10.039 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.987 -89.350 -10.914 1.00 0.00 H +ATOM 26 HB3 GLN 2 14.638 -89.695 -9.347 1.00 0.00 H +ATOM 27 CG GLN 2 13.580 -87.814 -9.266 1.00 0.00 C +ATOM 28 HG2 GLN 2 13.762 -86.811 -9.653 1.00 0.00 H +ATOM 29 HG3 GLN 2 12.514 -87.915 -9.467 1.00 0.00 H +ATOM 30 CD GLN 2 13.729 -87.942 -7.781 1.00 0.00 C +ATOM 31 OE1 GLN 2 14.732 -88.437 -7.267 1.00 0.00 O +ATOM 32 NE2 GLN 2 12.726 -87.582 -7.013 1.00 0.00 N +ATOM 33 HE21 GLN 2 12.732 -87.748 -6.017 1.00 0.00 H +ATOM 34 HE22 GLN 2 11.880 -87.107 -7.292 1.00 0.00 H +ATOM 35 C GLN 2 16.927 -89.099 -11.014 1.00 0.00 C +ATOM 36 O GLN 2 16.820 -90.305 -11.119 1.00 0.00 O +ATOM 37 N TYR 3 18.078 -88.464 -11.178 1.00 0.00 N +ATOM 38 H TYR 3 18.106 -87.460 -11.077 1.00 0.00 H +ATOM 39 CA TYR 3 19.262 -89.207 -11.586 1.00 0.00 C +ATOM 40 HA TYR 3 19.066 -89.799 -12.481 1.00 0.00 H +ATOM 41 CB TYR 3 20.314 -88.154 -11.981 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.548 -87.605 -11.069 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.214 -88.737 -12.177 1.00 0.00 H +ATOM 44 CG TYR 3 19.971 -87.292 -13.131 1.00 0.00 C +ATOM 45 CD1 TYR 3 20.204 -87.730 -14.449 1.00 0.00 C +ATOM 46 HD1 TYR 3 20.551 -88.707 -14.751 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.961 -86.845 -15.526 1.00 0.00 C +ATOM 48 HE1 TYR 3 20.181 -87.204 -16.521 1.00 0.00 H +ATOM 49 CZ TYR 3 19.504 -85.552 -15.331 1.00 0.00 C +ATOM 50 OH TYR 3 19.355 -84.765 -16.422 1.00 0.00 O +ATOM 51 HH TYR 3 18.837 -83.999 -16.163 1.00 0.00 H +ATOM 52 CE2 TYR 3 19.193 -85.127 -14.025 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.867 -84.111 -13.856 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.336 -86.043 -12.974 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.125 -85.774 -11.950 1.00 0.00 H +ATOM 56 C TYR 3 19.827 -90.196 -10.512 1.00 0.00 C +ATOM 57 O TYR 3 19.845 -89.875 -9.355 1.00 0.00 O +ATOM 58 N LYS 4 20.338 -91.337 -10.947 1.00 0.00 N +ATOM 59 H LYS 4 20.344 -91.606 -11.920 1.00 0.00 H +ATOM 60 CA LYS 4 20.759 -92.415 -10.026 1.00 0.00 C +ATOM 61 HA LYS 4 20.102 -92.362 -9.157 1.00 0.00 H +ATOM 62 CB LYS 4 20.695 -93.819 -10.608 1.00 0.00 C +ATOM 63 HB2 LYS 4 21.251 -93.889 -11.544 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.217 -94.542 -9.981 1.00 0.00 H +ATOM 65 CG LYS 4 19.290 -94.437 -10.877 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.671 -94.221 -10.007 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.912 -93.806 -11.682 1.00 0.00 H +ATOM 68 CD LYS 4 19.325 -95.910 -11.258 1.00 0.00 C +ATOM 69 HD2 LYS 4 19.993 -95.954 -12.119 1.00 0.00 H +ATOM 70 HD3 LYS 4 19.755 -96.560 -10.495 1.00 0.00 H +ATOM 71 CE LYS 4 17.806 -96.277 -11.334 1.00 0.00 C +ATOM 72 HE2 LYS 4 17.774 -97.364 -11.410 1.00 0.00 H +ATOM 73 HE3 LYS 4 17.371 -96.089 -10.353 1.00 0.00 H +ATOM 74 NZ LYS 4 17.095 -95.545 -12.370 1.00 0.00 N +ATOM 75 HZ1 LYS 4 17.087 -94.545 -12.229 1.00 0.00 H +ATOM 76 HZ2 LYS 4 16.135 -95.854 -12.323 1.00 0.00 H +ATOM 77 HZ3 LYS 4 17.392 -95.799 -13.301 1.00 0.00 H +ATOM 78 C LYS 4 22.104 -92.076 -9.407 1.00 0.00 C +ATOM 79 O LYS 4 22.849 -91.469 -10.218 1.00 0.00 O +ATOM 80 N HE1 5 22.387 -92.402 -8.117 1.00 0.00 N +ATOM 81 CA HE1 5 23.642 -92.000 -7.524 1.00 0.00 C +ATOM 82 C HE1 5 23.875 -93.008 -6.356 1.00 0.00 C +ATOM 83 O HE1 5 22.861 -93.385 -5.692 1.00 0.00 O +ATOM 84 CB HE1 5 23.498 -90.597 -6.918 1.00 0.00 C +ATOM 85 CG HE1 5 24.771 -90.113 -6.288 1.00 0.00 C +ATOM 86 CD2 HE1 5 26.003 -90.088 -6.908 1.00 0.00 C +ATOM 87 ND1 HE1 5 24.991 -89.891 -4.904 1.00 0.00 N +ATOM 88 CE1 HE1 5 26.307 -89.626 -4.778 1.00 0.00 C +ATOM 89 NE2 HE1 5 26.953 -89.792 -5.956 1.00 0.00 N +ATOM 90 H HE1 5 21.757 -92.951 -7.550 1.00 0.00 H +ATOM 91 HA HE1 5 24.450 -92.097 -8.250 1.00 0.00 H +ATOM 92 HB2 HE1 5 22.687 -90.650 -6.191 1.00 0.00 H +ATOM 93 HB3 HE1 5 23.175 -89.870 -7.663 1.00 0.00 H +ATOM 94 HD2 HE1 5 26.147 -90.248 -7.966 1.00 0.00 H +ATOM 95 HE1 HE1 5 26.775 -89.224 -3.892 1.00 0.00 H +ATOM 96 HE2 HE1 5 27.947 -89.643 -6.062 1.00 0.00 H +ATOM 97 N ILE 6 25.097 -93.539 -6.146 1.00 0.00 N +ATOM 98 H ILE 6 25.755 -93.297 -6.873 1.00 0.00 H +ATOM 99 CA ILE 6 25.449 -94.641 -5.236 1.00 0.00 C +ATOM 100 HA ILE 6 24.683 -95.417 -5.251 1.00 0.00 H +ATOM 101 CB ILE 6 26.754 -95.298 -5.777 1.00 0.00 C +ATOM 102 HB ILE 6 27.443 -94.482 -5.992 1.00 0.00 H +ATOM 103 CG2 ILE 6 27.463 -96.200 -4.720 1.00 0.00 C +ATOM 104 HG21 ILE 6 27.641 -95.697 -3.769 1.00 0.00 H +ATOM 105 HG22 ILE 6 28.492 -96.470 -4.957 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.771 -97.015 -4.505 1.00 0.00 H +ATOM 107 CG1 ILE 6 26.440 -96.114 -7.085 1.00 0.00 C +ATOM 108 HG12 ILE 6 25.722 -96.843 -6.709 1.00 0.00 H +ATOM 109 HG13 ILE 6 26.043 -95.402 -7.809 1.00 0.00 H +ATOM 110 CD1 ILE 6 27.554 -96.745 -7.790 1.00 0.00 C +ATOM 111 HD11 ILE 6 28.105 -95.948 -8.290 1.00 0.00 H +ATOM 112 HD12 ILE 6 27.092 -97.288 -8.614 1.00 0.00 H +ATOM 113 HD13 ILE 6 28.255 -97.302 -7.169 1.00 0.00 H +ATOM 114 C ILE 6 25.577 -94.080 -3.796 1.00 0.00 C +ATOM 115 O ILE 6 26.129 -92.959 -3.650 1.00 0.00 O +ATOM 116 N VAL 7 24.862 -94.797 -2.910 1.00 0.00 N +ATOM 117 H VAL 7 24.457 -95.642 -3.285 1.00 0.00 H +ATOM 118 CA VAL 7 24.848 -94.482 -1.467 1.00 0.00 C +ATOM 119 HA VAL 7 24.443 -93.475 -1.365 1.00 0.00 H +ATOM 120 CB VAL 7 23.872 -95.252 -0.649 1.00 0.00 C +ATOM 121 HB VAL 7 23.805 -94.824 0.352 1.00 0.00 H +ATOM 122 CG1 VAL 7 22.473 -95.078 -1.290 1.00 0.00 C +ATOM 123 HG11 VAL 7 21.642 -95.607 -0.824 1.00 0.00 H +ATOM 124 HG12 VAL 7 22.136 -94.042 -1.334 1.00 0.00 H +ATOM 125 HG13 VAL 7 22.540 -95.419 -2.324 1.00 0.00 H +ATOM 126 CG2 VAL 7 24.339 -96.707 -0.392 1.00 0.00 C +ATOM 127 HG21 VAL 7 23.658 -97.192 0.307 1.00 0.00 H +ATOM 128 HG22 VAL 7 24.153 -97.311 -1.280 1.00 0.00 H +ATOM 129 HG23 VAL 7 25.331 -96.756 0.058 1.00 0.00 H +ATOM 130 C VAL 7 26.210 -94.455 -0.757 1.00 0.00 C +ATOM 131 O VAL 7 27.170 -95.164 -1.119 1.00 0.00 O +ATOM 132 N ASN 8 26.276 -93.796 0.362 1.00 0.00 N +ATOM 133 H ASN 8 25.558 -93.112 0.552 1.00 0.00 H +ATOM 134 CA ASN 8 27.469 -93.705 1.298 1.00 0.00 C +ATOM 135 HA ASN 8 28.197 -94.491 1.092 1.00 0.00 H +ATOM 136 CB ASN 8 28.235 -92.402 0.966 1.00 0.00 C +ATOM 137 HB2 ASN 8 28.587 -92.508 -0.060 1.00 0.00 H +ATOM 138 HB3 ASN 8 27.608 -91.515 1.068 1.00 0.00 H +ATOM 139 CG ASN 8 29.572 -92.299 1.633 1.00 0.00 C +ATOM 140 OD1 ASN 8 30.351 -93.212 1.648 1.00 0.00 O +ATOM 141 ND2 ASN 8 29.857 -91.254 2.280 1.00 0.00 N +ATOM 142 HD21 ASN 8 29.152 -90.531 2.322 1.00 0.00 H +ATOM 143 HD22 ASN 8 30.727 -91.174 2.786 1.00 0.00 H +ATOM 144 C ASN 8 26.936 -93.755 2.743 1.00 0.00 C +ATOM 145 O ASN 8 27.509 -94.458 3.557 1.00 0.00 O +ATOM 146 N GLY 9 25.817 -93.047 2.959 1.00 0.00 N +ATOM 147 H GLY 9 25.482 -92.493 2.184 1.00 0.00 H +ATOM 148 CA GLY 9 24.977 -93.111 4.174 1.00 0.00 C +ATOM 149 HA2 GLY 9 25.529 -92.458 4.850 1.00 0.00 H +ATOM 150 HA3 GLY 9 23.983 -92.689 4.024 1.00 0.00 H +ATOM 151 C GLY 9 24.926 -94.576 4.677 1.00 0.00 C +ATOM 152 O GLY 9 24.439 -95.554 4.059 1.00 0.00 O +ATOM 153 N LYS 10 25.413 -94.723 5.942 1.00 0.00 N +ATOM 154 H LYS 10 25.708 -93.853 6.362 1.00 0.00 H +ATOM 155 CA LYS 10 25.570 -95.910 6.760 1.00 0.00 C +ATOM 156 HA LYS 10 26.393 -96.441 6.282 1.00 0.00 H +ATOM 157 CB LYS 10 26.265 -95.637 8.097 1.00 0.00 C +ATOM 158 HB2 LYS 10 26.475 -96.600 8.564 1.00 0.00 H +ATOM 159 HB3 LYS 10 27.242 -95.168 7.980 1.00 0.00 H +ATOM 160 CG LYS 10 25.404 -94.784 9.009 1.00 0.00 C +ATOM 161 HG2 LYS 10 25.009 -93.913 8.486 1.00 0.00 H +ATOM 162 HG3 LYS 10 24.537 -95.361 9.330 1.00 0.00 H +ATOM 163 CD LYS 10 26.235 -94.163 10.160 1.00 0.00 C +ATOM 164 HD2 LYS 10 26.626 -94.921 10.839 1.00 0.00 H +ATOM 165 HD3 LYS 10 26.958 -93.457 9.751 1.00 0.00 H +ATOM 166 CE LYS 10 25.281 -93.322 10.991 1.00 0.00 C +ATOM 167 HE2 LYS 10 25.077 -92.334 10.579 1.00 0.00 H +ATOM 168 HE3 LYS 10 24.288 -93.760 11.092 1.00 0.00 H +ATOM 169 NZ LYS 10 25.845 -93.216 12.364 1.00 0.00 N +ATOM 170 HZ1 LYS 10 26.696 -92.675 12.430 1.00 0.00 H +ATOM 171 HZ2 LYS 10 26.036 -94.128 12.754 1.00 0.00 H +ATOM 172 HZ3 LYS 10 25.186 -92.774 12.989 1.00 0.00 H +ATOM 173 C LYS 10 24.344 -96.755 6.831 1.00 0.00 C +ATOM 174 O LYS 10 24.459 -98.012 6.839 1.00 0.00 O +ATOM 175 N THR 11 23.108 -96.201 6.847 1.00 0.00 N +ATOM 176 H THR 11 23.062 -95.220 7.084 1.00 0.00 H +ATOM 177 CA THR 11 21.808 -96.830 6.895 1.00 0.00 C +ATOM 178 HA THR 11 21.729 -97.631 7.630 1.00 0.00 H +ATOM 179 CB THR 11 20.720 -95.779 7.244 1.00 0.00 C +ATOM 180 HB THR 11 19.696 -96.084 7.028 1.00 0.00 H +ATOM 181 CG2 THR 11 20.750 -95.421 8.698 1.00 0.00 C +ATOM 182 HG21 THR 11 21.759 -95.288 9.088 1.00 0.00 H +ATOM 183 HG22 THR 11 20.227 -96.208 9.240 1.00 0.00 H +ATOM 184 HG23 THR 11 20.138 -94.546 8.917 1.00 0.00 H +ATOM 185 OG1 THR 11 21.042 -94.581 6.608 1.00 0.00 O +ATOM 186 HG1 THR 11 20.208 -94.135 6.444 1.00 0.00 H +ATOM 187 C THR 11 21.507 -97.506 5.578 1.00 0.00 C +ATOM 188 O THR 11 20.617 -98.357 5.513 1.00 0.00 O +ATOM 189 N LEU 12 22.178 -97.046 4.459 1.00 0.00 N +ATOM 190 H LEU 12 22.998 -96.456 4.492 1.00 0.00 H +ATOM 191 CA LEU 12 21.740 -97.426 3.110 1.00 0.00 C +ATOM 192 HA LEU 12 20.708 -97.772 3.168 1.00 0.00 H +ATOM 193 CB LEU 12 21.790 -96.046 2.342 1.00 0.00 C +ATOM 194 HB2 LEU 12 22.828 -95.784 2.138 1.00 0.00 H +ATOM 195 HB3 LEU 12 21.240 -96.185 1.412 1.00 0.00 H +ATOM 196 CG LEU 12 21.230 -94.809 3.078 1.00 0.00 C +ATOM 197 HG LEU 12 21.910 -94.677 3.920 1.00 0.00 H +ATOM 198 CD1 LEU 12 21.508 -93.623 2.221 1.00 0.00 C +ATOM 199 HD11 LEU 12 21.323 -92.727 2.814 1.00 0.00 H +ATOM 200 HD12 LEU 12 20.881 -93.555 1.332 1.00 0.00 H +ATOM 201 HD13 LEU 12 22.504 -93.497 1.797 1.00 0.00 H +ATOM 202 CD2 LEU 12 19.778 -94.901 3.517 1.00 0.00 C +ATOM 203 HD21 LEU 12 19.560 -95.723 4.199 1.00 0.00 H +ATOM 204 HD22 LEU 12 19.219 -95.026 2.590 1.00 0.00 H +ATOM 205 HD23 LEU 12 19.430 -94.001 4.024 1.00 0.00 H +ATOM 206 C LEU 12 22.643 -98.548 2.448 1.00 0.00 C +ATOM 207 O LEU 12 23.674 -98.897 3.017 1.00 0.00 O +ATOM 208 N LYS 13 22.115 -99.138 1.375 1.00 0.00 N +ATOM 209 H LYS 13 21.195 -98.875 1.051 1.00 0.00 H +ATOM 210 CA LYS 13 22.797-100.114 0.473 1.00 0.00 C +ATOM 211 HA LYS 13 23.886-100.061 0.458 1.00 0.00 H +ATOM 212 CB LYS 13 22.389-101.485 0.927 1.00 0.00 C +ATOM 213 HB2 LYS 13 22.922-101.722 1.848 1.00 0.00 H +ATOM 214 HB3 LYS 13 21.318-101.551 1.120 1.00 0.00 H +ATOM 215 CG LYS 13 22.856-102.627 -0.035 1.00 0.00 C +ATOM 216 HG2 LYS 13 22.226-102.463 -0.910 1.00 0.00 H +ATOM 217 HG3 LYS 13 23.918-102.434 -0.182 1.00 0.00 H +ATOM 218 CD LYS 13 22.603-103.978 0.606 1.00 0.00 C +ATOM 219 HD2 LYS 13 23.200-104.125 1.507 1.00 0.00 H +ATOM 220 HD3 LYS 13 21.580-104.078 0.968 1.00 0.00 H +ATOM 221 CE LYS 13 22.999-105.222 -0.343 1.00 0.00 C +ATOM 222 HE2 LYS 13 22.046-105.629 -0.681 1.00 0.00 H +ATOM 223 HE3 LYS 13 23.510-104.879 -1.243 1.00 0.00 H +ATOM 224 NZ LYS 13 23.824-106.239 0.417 1.00 0.00 N +ATOM 225 HZ1 LYS 13 24.695-105.847 0.744 1.00 0.00 H +ATOM 226 HZ2 LYS 13 23.953-107.092 -0.109 1.00 0.00 H +ATOM 227 HZ3 LYS 13 23.280-106.565 1.203 1.00 0.00 H +ATOM 228 C LYS 13 22.276 -99.819 -0.928 1.00 0.00 C +ATOM 229 O LYS 13 21.071 -99.612 -1.097 1.00 0.00 O +ATOM 230 N GLY 14 23.198 -99.853 -1.949 1.00 0.00 N +ATOM 231 H GLY 14 24.191 -99.960 -1.794 1.00 0.00 H +ATOM 232 CA GLY 14 22.869 -99.753 -3.371 1.00 0.00 C +ATOM 233 HA2 GLY 14 23.599-100.310 -3.958 1.00 0.00 H +ATOM 234 HA3 GLY 14 21.909-100.231 -3.567 1.00 0.00 H +ATOM 235 C GLY 14 22.874 -98.257 -3.853 1.00 0.00 C +ATOM 236 O GLY 14 23.878 -97.537 -3.807 1.00 0.00 O +ATOM 237 N VAL 15 21.685 -97.811 -4.294 1.00 0.00 N +ATOM 238 H VAL 15 20.938 -98.477 -4.433 1.00 0.00 H +ATOM 239 CA VAL 15 21.540 -96.490 -4.955 1.00 0.00 C +ATOM 240 HA VAL 15 22.395 -95.824 -4.834 1.00 0.00 H +ATOM 241 CB VAL 15 21.356 -96.646 -6.484 1.00 0.00 C +ATOM 242 HB VAL 15 20.967 -95.707 -6.877 1.00 0.00 H +ATOM 243 CG1 VAL 15 22.736 -96.775 -7.107 1.00 0.00 C +ATOM 244 HG11 VAL 15 23.441 -96.060 -6.681 1.00 0.00 H +ATOM 245 HG12 VAL 15 23.168 -97.766 -6.967 1.00 0.00 H +ATOM 246 HG13 VAL 15 22.748 -96.706 -8.194 1.00 0.00 H +ATOM 247 CG2 VAL 15 20.428 -97.762 -6.891 1.00 0.00 C +ATOM 248 HG21 VAL 15 20.017 -97.618 -7.890 1.00 0.00 H +ATOM 249 HG22 VAL 15 20.959 -98.712 -6.826 1.00 0.00 H +ATOM 250 HG23 VAL 15 19.555 -97.840 -6.243 1.00 0.00 H +ATOM 251 C VAL 15 20.362 -95.690 -4.352 1.00 0.00 C +ATOM 252 O VAL 15 19.360 -96.281 -3.816 1.00 0.00 O +ATOM 253 N HD1 16 20.408 -94.382 -4.424 1.00 0.00 N +ATOM 254 CA HD1 16 19.290 -93.446 -4.406 1.00 0.00 C +ATOM 255 C HD1 16 19.271 -92.622 -5.652 1.00 0.00 C +ATOM 256 O HD1 16 20.101 -92.706 -6.504 1.00 0.00 O +ATOM 257 CB HD1 16 19.171 -92.642 -3.048 1.00 0.00 C +ATOM 258 CG HD1 16 20.428 -91.874 -2.658 1.00 0.00 C +ATOM 259 CD2 HD1 16 21.414 -91.460 -3.481 1.00 0.00 C +ATOM 260 ND1 HD1 16 20.844 -91.580 -1.366 1.00 0.00 N +ATOM 261 CE1 HD1 16 21.947 -90.935 -1.497 1.00 0.00 C +ATOM 262 NE2 HD1 16 22.376 -90.823 -2.759 1.00 0.00 N +ATOM 263 H HD1 16 21.221 -93.943 -4.832 1.00 0.00 H +ATOM 264 HA HD1 16 18.364 -94.020 -4.451 1.00 0.00 H +ATOM 265 HB2 HD1 16 18.236 -92.093 -2.941 1.00 0.00 H +ATOM 266 HB3 HD1 16 18.985 -93.449 -2.340 1.00 0.00 H +ATOM 267 HD1 HD1 16 20.246 -91.516 -0.554 1.00 0.00 H +ATOM 268 HD2 HD1 16 21.505 -91.687 -4.533 1.00 0.00 H +ATOM 269 HE1 HD1 16 22.486 -90.417 -0.718 1.00 0.00 H +ATOM 270 N THR 17 18.244 -91.739 -5.753 1.00 0.00 N +ATOM 271 H THR 17 17.608 -91.623 -4.977 1.00 0.00 H +ATOM 272 CA THR 17 18.067 -90.669 -6.751 1.00 0.00 C +ATOM 273 HA THR 17 18.937 -90.791 -7.397 1.00 0.00 H +ATOM 274 CB THR 17 16.845 -90.789 -7.592 1.00 0.00 C +ATOM 275 HB THR 17 16.787 -89.944 -8.278 1.00 0.00 H +ATOM 276 CG2 THR 17 16.796 -92.127 -8.402 1.00 0.00 C +ATOM 277 HG21 THR 17 16.535 -92.927 -7.709 1.00 0.00 H +ATOM 278 HG22 THR 17 17.708 -92.446 -8.907 1.00 0.00 H +ATOM 279 HG23 THR 17 15.960 -92.052 -9.097 1.00 0.00 H +ATOM 280 OG1 THR 17 15.684 -90.807 -6.747 1.00 0.00 O +ATOM 281 HG1 THR 17 15.383 -89.896 -6.765 1.00 0.00 H +ATOM 282 C THR 17 18.145 -89.192 -6.215 1.00 0.00 C +ATOM 283 O THR 17 17.628 -88.985 -5.127 1.00 0.00 O +ATOM 284 N HD2 18 18.739 -88.294 -7.027 1.00 0.00 N +ATOM 285 CA HD2 18 18.626 -86.821 -6.706 1.00 0.00 C +ATOM 286 C HD2 18 18.022 -86.120 -7.917 1.00 0.00 C +ATOM 287 O HD2 18 18.595 -86.137 -9.019 1.00 0.00 O +ATOM 288 CB HD2 18 20.020 -86.288 -6.415 1.00 0.00 C +ATOM 289 CG HD2 18 20.743 -86.923 -5.271 1.00 0.00 C +ATOM 290 CD2 HD2 18 21.887 -87.628 -5.384 1.00 0.00 C +ATOM 291 ND1 HD2 18 20.426 -86.842 -3.922 1.00 0.00 N +ATOM 292 CE1 HD2 18 21.445 -87.420 -3.288 1.00 0.00 C +ATOM 293 NE2 HD2 18 22.405 -87.777 -4.116 1.00 0.00 N +ATOM 294 H HD2 18 18.926 -88.605 -7.970 1.00 0.00 H +ATOM 295 HA HD2 18 18.133 -86.556 -5.771 1.00 0.00 H +ATOM 296 HB2 HD2 18 20.615 -86.429 -7.317 1.00 0.00 H +ATOM 297 HB3 HD2 18 19.885 -85.229 -6.193 1.00 0.00 H +ATOM 298 HD1 HD2 18 19.615 -86.351 -3.571 1.00 0.00 H +ATOM 299 HD2 HD2 18 22.262 -87.956 -6.342 1.00 0.00 H +ATOM 300 HE1 HD2 18 21.433 -87.598 -2.223 1.00 0.00 H +ATOM 301 N GLU 19 16.889 -85.426 -7.645 1.00 0.00 N +ATOM 302 H GLU 19 16.506 -85.473 -6.711 1.00 0.00 H +ATOM 303 CA GLU 19 16.183 -84.530 -8.551 1.00 0.00 C +ATOM 304 HA GLU 19 15.832 -85.077 -9.426 1.00 0.00 H +ATOM 305 CB GLU 19 14.925 -84.034 -7.824 1.00 0.00 C +ATOM 306 HB2 GLU 19 14.310 -84.913 -7.630 1.00 0.00 H +ATOM 307 HB3 GLU 19 15.308 -83.734 -6.848 1.00 0.00 H +ATOM 308 CG GLU 19 14.027 -82.817 -8.308 1.00 0.00 C +ATOM 309 HG2 GLU 19 13.276 -82.587 -7.553 1.00 0.00 H +ATOM 310 HG3 GLU 19 14.634 -81.914 -8.370 1.00 0.00 H +ATOM 311 CD GLU 19 13.386 -83.101 -9.719 1.00 0.00 C +ATOM 312 OE1 GLU 19 14.052 -83.547 -10.635 1.00 0.00 O +ATOM 313 OE2 GLU 19 12.214 -82.826 -10.035 1.00 0.00 O +ATOM 314 C GLU 19 17.042 -83.393 -9.080 1.00 0.00 C +ATOM 315 O GLU 19 17.878 -82.872 -8.311 1.00 0.00 O +ATOM 316 N ALA 20 16.870 -82.873 -10.319 1.00 0.00 N +ATOM 317 H ALA 20 16.115 -83.313 -10.826 1.00 0.00 H +ATOM 318 CA ALA 20 17.505 -81.658 -10.831 1.00 0.00 C +ATOM 319 HA ALA 20 17.618 -80.922 -10.035 1.00 0.00 H +ATOM 320 CB ALA 20 18.867 -81.981 -11.392 1.00 0.00 C +ATOM 321 HB1 ALA 20 18.777 -82.747 -12.161 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.597 -82.208 -10.615 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.257 -81.086 -11.877 1.00 0.00 H +ATOM 324 C ALA 20 16.684 -81.026 -11.960 1.00 0.00 C +ATOM 325 O ALA 20 16.171 -81.790 -12.788 1.00 0.00 O +ATOM 326 N VAL 21 16.618 -79.698 -12.043 1.00 0.00 N +ATOM 327 H VAL 21 16.971 -79.107 -11.304 1.00 0.00 H +ATOM 328 CA VAL 21 15.849 -79.129 -13.155 1.00 0.00 C +ATOM 329 HA VAL 21 14.863 -79.585 -13.064 1.00 0.00 H +ATOM 330 CB VAL 21 15.617 -77.598 -12.962 1.00 0.00 C +ATOM 331 HB VAL 21 15.042 -77.257 -13.824 1.00 0.00 H +ATOM 332 CG1 VAL 21 14.709 -77.404 -11.800 1.00 0.00 C +ATOM 333 HG11 VAL 21 15.303 -77.750 -10.953 1.00 0.00 H +ATOM 334 HG12 VAL 21 13.753 -77.901 -11.961 1.00 0.00 H +ATOM 335 HG13 VAL 21 14.388 -76.365 -11.859 1.00 0.00 H +ATOM 336 CG2 VAL 21 16.884 -76.758 -12.835 1.00 0.00 C +ATOM 337 HG21 VAL 21 17.564 -77.100 -13.615 1.00 0.00 H +ATOM 338 HG22 VAL 21 17.371 -76.876 -11.867 1.00 0.00 H +ATOM 339 HG23 VAL 21 16.669 -75.692 -12.897 1.00 0.00 H +ATOM 340 C VAL 21 16.464 -79.359 -14.536 1.00 0.00 C +ATOM 341 O VAL 21 15.759 -79.126 -15.505 1.00 0.00 O +ATOM 342 N ASP 22 17.718 -79.792 -14.715 1.00 0.00 N +ATOM 343 H ASP 22 18.192 -79.984 -13.844 1.00 0.00 H +ATOM 344 CA ASP 22 18.577 -79.688 -15.880 1.00 0.00 C +ATOM 345 HA ASP 22 18.068 -80.201 -16.696 1.00 0.00 H +ATOM 346 CB ASP 22 18.824 -78.161 -16.128 1.00 0.00 C +ATOM 347 HB2 ASP 22 17.862 -77.661 -16.237 1.00 0.00 H +ATOM 348 HB3 ASP 22 19.200 -77.676 -15.227 1.00 0.00 H +ATOM 349 CG ASP 22 19.644 -77.868 -17.450 1.00 0.00 C +ATOM 350 OD1 ASP 22 20.125 -76.688 -17.595 1.00 0.00 O +ATOM 351 OD2 ASP 22 19.642 -78.802 -18.260 1.00 0.00 O +ATOM 352 C ASP 22 19.902 -80.449 -15.637 1.00 0.00 C +ATOM 353 O ASP 22 20.430 -80.349 -14.513 1.00 0.00 O +ATOM 354 N ALA 23 20.448 -81.036 -16.698 1.00 0.00 N +ATOM 355 H ALA 23 19.991 -80.916 -17.591 1.00 0.00 H +ATOM 356 CA ALA 23 21.619 -81.954 -16.570 1.00 0.00 C +ATOM 357 HA ALA 23 21.382 -82.786 -15.908 1.00 0.00 H +ATOM 358 CB ALA 23 21.835 -82.515 -17.986 1.00 0.00 C +ATOM 359 HB1 ALA 23 22.822 -82.978 -17.987 1.00 0.00 H +ATOM 360 HB2 ALA 23 21.677 -81.785 -18.780 1.00 0.00 H +ATOM 361 HB3 ALA 23 21.044 -83.245 -18.156 1.00 0.00 H +ATOM 362 C ALA 23 22.860 -81.202 -15.985 1.00 0.00 C +ATOM 363 O ALA 23 23.721 -81.780 -15.342 1.00 0.00 O +ATOM 364 N ALA 24 22.977 -79.903 -16.258 1.00 0.00 N +ATOM 365 H ALA 24 22.392 -79.492 -16.971 1.00 0.00 H +ATOM 366 CA ALA 24 24.023 -78.989 -15.782 1.00 0.00 C +ATOM 367 HA ALA 24 24.990 -79.376 -16.106 1.00 0.00 H +ATOM 368 CB ALA 24 23.828 -77.626 -16.487 1.00 0.00 C +ATOM 369 HB1 ALA 24 24.070 -77.590 -17.549 1.00 0.00 H +ATOM 370 HB2 ALA 24 24.358 -76.767 -16.078 1.00 0.00 H +ATOM 371 HB3 ALA 24 22.753 -77.462 -16.411 1.00 0.00 H +ATOM 372 C ALA 24 24.014 -78.807 -14.276 1.00 0.00 C +ATOM 373 O ALA 24 24.989 -78.582 -13.578 1.00 0.00 O +ATOM 374 N GLU 25 22.800 -78.848 -13.722 1.00 0.00 N +ATOM 375 H GLU 25 21.948 -78.894 -14.263 1.00 0.00 H +ATOM 376 CA GLU 25 22.626 -78.751 -12.248 1.00 0.00 C +ATOM 377 HA GLU 25 23.223 -77.989 -11.747 1.00 0.00 H +ATOM 378 CB GLU 25 21.219 -78.157 -12.051 1.00 0.00 C +ATOM 379 HB2 GLU 25 20.567 -78.858 -12.571 1.00 0.00 H +ATOM 380 HB3 GLU 25 20.915 -78.277 -11.011 1.00 0.00 H +ATOM 381 CG GLU 25 21.083 -76.688 -12.437 1.00 0.00 C +ATOM 382 HG2 GLU 25 21.253 -76.659 -13.513 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.051 -76.401 -12.238 1.00 0.00 H +ATOM 384 CD GLU 25 22.048 -75.847 -11.578 1.00 0.00 C +ATOM 385 OE1 GLU 25 23.271 -75.829 -11.816 1.00 0.00 O +ATOM 386 OE2 GLU 25 21.598 -75.315 -10.573 1.00 0.00 O +ATOM 387 C GLU 25 22.876 -80.053 -11.521 1.00 0.00 C +ATOM 388 O GLU 25 23.495 -80.085 -10.441 1.00 0.00 O +ATOM 389 N ALA 26 22.395 -81.150 -12.106 1.00 0.00 N +ATOM 390 H ALA 26 21.829 -80.975 -12.925 1.00 0.00 H +ATOM 391 CA ALA 26 22.811 -82.559 -11.784 1.00 0.00 C +ATOM 392 HA ALA 26 22.571 -82.782 -10.744 1.00 0.00 H +ATOM 393 CB ALA 26 22.133 -83.558 -12.701 1.00 0.00 C +ATOM 394 HB1 ALA 26 21.067 -83.573 -12.474 1.00 0.00 H +ATOM 395 HB2 ALA 26 22.516 -84.573 -12.594 1.00 0.00 H +ATOM 396 HB3 ALA 26 22.109 -83.170 -13.719 1.00 0.00 H +ATOM 397 C ALA 26 24.379 -82.670 -11.863 1.00 0.00 C +ATOM 398 O ALA 26 25.003 -83.276 -11.052 1.00 0.00 O +ATOM 399 N GLU 27 25.034 -82.023 -12.846 1.00 0.00 N +ATOM 400 H GLU 27 24.490 -81.546 -13.550 1.00 0.00 H +ATOM 401 CA GLU 27 26.475 -82.138 -13.131 1.00 0.00 C +ATOM 402 HA GLU 27 26.602 -83.216 -13.026 1.00 0.00 H +ATOM 403 CB GLU 27 26.820 -81.791 -14.605 1.00 0.00 C +ATOM 404 HB2 GLU 27 26.329 -82.498 -15.273 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.428 -80.803 -14.843 1.00 0.00 H +ATOM 406 CG GLU 27 28.259 -81.867 -15.030 1.00 0.00 C +ATOM 407 HG2 GLU 27 28.911 -81.742 -14.166 1.00 0.00 H +ATOM 408 HG3 GLU 27 28.328 -82.904 -15.359 1.00 0.00 H +ATOM 409 CD GLU 27 28.512 -81.002 -16.232 1.00 0.00 C +ATOM 410 OE1 GLU 27 29.628 -80.360 -16.189 1.00 0.00 O +ATOM 411 OE2 GLU 27 27.824 -81.052 -17.270 1.00 0.00 O +ATOM 412 C GLU 27 27.210 -81.345 -12.080 1.00 0.00 C +ATOM 413 O GLU 27 28.243 -81.769 -11.602 1.00 0.00 O +ATOM 414 N LYS 28 26.754 -80.098 -11.808 1.00 0.00 N +ATOM 415 H LYS 28 25.983 -79.760 -12.366 1.00 0.00 H +ATOM 416 CA LYS 28 27.204 -79.290 -10.660 1.00 0.00 C +ATOM 417 HA LYS 28 28.257 -79.136 -10.895 1.00 0.00 H +ATOM 418 CB LYS 28 26.469 -77.927 -10.585 1.00 0.00 C +ATOM 419 HB2 LYS 28 26.393 -77.510 -11.589 1.00 0.00 H +ATOM 420 HB3 LYS 28 25.415 -78.137 -10.405 1.00 0.00 H +ATOM 421 CG LYS 28 27.101 -77.055 -9.465 1.00 0.00 C +ATOM 422 HG2 LYS 28 26.891 -77.460 -8.475 1.00 0.00 H +ATOM 423 HG3 LYS 28 28.152 -77.062 -9.754 1.00 0.00 H +ATOM 424 CD LYS 28 26.439 -75.688 -9.466 1.00 0.00 C +ATOM 425 HD2 LYS 28 26.872 -74.933 -8.811 1.00 0.00 H +ATOM 426 HD3 LYS 28 26.458 -75.218 -10.449 1.00 0.00 H +ATOM 427 CE LYS 28 24.992 -75.836 -9.059 1.00 0.00 C +ATOM 428 HE2 LYS 28 24.560 -76.767 -9.427 1.00 0.00 H +ATOM 429 HE3 LYS 28 25.016 -75.940 -7.975 1.00 0.00 H +ATOM 430 NZ LYS 28 24.201 -74.638 -9.394 1.00 0.00 N +ATOM 431 HZ1 LYS 28 24.650 -73.743 -9.261 1.00 0.00 H +ATOM 432 HZ2 LYS 28 23.476 -74.553 -8.696 1.00 0.00 H +ATOM 433 HZ3 LYS 28 23.868 -74.675 -10.347 1.00 0.00 H +ATOM 434 C LYS 28 27.138 -80.046 -9.341 1.00 0.00 C +ATOM 435 O LYS 28 28.076 -79.986 -8.539 1.00 0.00 O +ATOM 436 N PHE 29 26.070 -80.854 -9.032 1.00 0.00 N +ATOM 437 H PHE 29 25.273 -80.871 -9.652 1.00 0.00 H +ATOM 438 CA PHE 29 26.111 -81.833 -7.947 1.00 0.00 C +ATOM 439 HA PHE 29 26.313 -81.431 -6.955 1.00 0.00 H +ATOM 440 CB PHE 29 24.715 -82.376 -7.795 1.00 0.00 C +ATOM 441 HB2 PHE 29 24.158 -81.663 -7.188 1.00 0.00 H +ATOM 442 HB3 PHE 29 24.190 -82.453 -8.747 1.00 0.00 H +ATOM 443 CG PHE 29 24.690 -83.748 -7.057 1.00 0.00 C +ATOM 444 CD1 PHE 29 24.632 -83.818 -5.720 1.00 0.00 C +ATOM 445 HD1 PHE 29 24.464 -82.901 -5.175 1.00 0.00 H +ATOM 446 CE1 PHE 29 24.687 -84.993 -4.940 1.00 0.00 C +ATOM 447 HE1 PHE 29 24.402 -85.034 -3.899 1.00 0.00 H +ATOM 448 CZ PHE 29 25.044 -86.210 -5.552 1.00 0.00 C +ATOM 449 HZ PHE 29 25.113 -87.118 -4.972 1.00 0.00 H +ATOM 450 CE2 PHE 29 25.213 -86.204 -6.995 1.00 0.00 C +ATOM 451 HE2 PHE 29 25.467 -87.092 -7.555 1.00 0.00 H +ATOM 452 CD2 PHE 29 24.979 -84.980 -7.698 1.00 0.00 C +ATOM 453 HD2 PHE 29 24.908 -85.038 -8.774 1.00 0.00 H +ATOM 454 C PHE 29 27.171 -82.970 -8.099 1.00 0.00 C +ATOM 455 O PHE 29 27.898 -83.351 -7.133 1.00 0.00 O +ATOM 456 N THR 30 27.406 -83.521 -9.268 1.00 0.00 N +ATOM 457 H THR 30 26.865 -83.231 -10.071 1.00 0.00 H +ATOM 458 CA THR 30 28.307 -84.642 -9.476 1.00 0.00 C +ATOM 459 HA THR 30 28.115 -85.445 -8.765 1.00 0.00 H +ATOM 460 CB THR 30 28.189 -85.214 -10.872 1.00 0.00 C +ATOM 461 HB THR 30 28.425 -84.398 -11.555 1.00 0.00 H +ATOM 462 CG2 THR 30 29.177 -86.376 -11.260 1.00 0.00 C +ATOM 463 HG21 THR 30 28.957 -87.298 -10.720 1.00 0.00 H +ATOM 464 HG22 THR 30 28.940 -86.646 -12.289 1.00 0.00 H +ATOM 465 HG23 THR 30 30.245 -86.206 -11.125 1.00 0.00 H +ATOM 466 OG1 THR 30 26.900 -85.726 -11.083 1.00 0.00 O +ATOM 467 HG1 THR 30 26.295 -84.989 -10.980 1.00 0.00 H +ATOM 468 C THR 30 29.703 -84.100 -9.203 1.00 0.00 C +ATOM 469 O THR 30 30.408 -84.825 -8.518 1.00 0.00 O +ATOM 470 N LYS 31 30.015 -82.849 -9.732 1.00 0.00 N +ATOM 471 H LYS 31 29.343 -82.390 -10.330 1.00 0.00 H +ATOM 472 CA LYS 31 31.266 -82.229 -9.430 1.00 0.00 C +ATOM 473 HA LYS 31 32.005 -82.929 -9.819 1.00 0.00 H +ATOM 474 CB LYS 31 31.414 -80.900 -10.213 1.00 0.00 C +ATOM 475 HB2 LYS 31 30.472 -80.363 -10.099 1.00 0.00 H +ATOM 476 HB3 LYS 31 32.220 -80.329 -9.754 1.00 0.00 H +ATOM 477 CG LYS 31 31.759 -81.122 -11.677 1.00 0.00 C +ATOM 478 HG2 LYS 31 32.799 -81.437 -11.763 1.00 0.00 H +ATOM 479 HG3 LYS 31 31.120 -81.939 -12.013 1.00 0.00 H +ATOM 480 CD LYS 31 31.443 -79.857 -12.553 1.00 0.00 C +ATOM 481 HD2 LYS 31 30.371 -79.667 -12.602 1.00 0.00 H +ATOM 482 HD3 LYS 31 31.911 -78.959 -12.150 1.00 0.00 H +ATOM 483 CE LYS 31 31.961 -79.968 -13.995 1.00 0.00 C +ATOM 484 HE2 LYS 31 31.610 -80.882 -14.474 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.688 -79.011 -14.438 1.00 0.00 H +ATOM 486 NZ LYS 31 33.489 -79.967 -14.034 1.00 0.00 N +ATOM 487 HZ1 LYS 31 33.955 -79.103 -13.797 1.00 0.00 H +ATOM 488 HZ2 LYS 31 33.914 -80.141 -14.934 1.00 0.00 H +ATOM 489 HZ3 LYS 31 33.924 -80.695 -13.485 1.00 0.00 H +ATOM 490 C LYS 31 31.506 -81.964 -7.939 1.00 0.00 C +ATOM 491 O LYS 31 32.669 -82.073 -7.455 1.00 0.00 O +ATOM 492 N ALA 32 30.485 -81.647 -7.171 1.00 0.00 N +ATOM 493 H ALA 32 29.531 -81.658 -7.502 1.00 0.00 H +ATOM 494 CA ALA 32 30.544 -81.364 -5.698 1.00 0.00 C +ATOM 495 HA ALA 32 31.495 -80.858 -5.533 1.00 0.00 H +ATOM 496 CB ALA 32 29.395 -80.414 -5.413 1.00 0.00 C +ATOM 497 HB1 ALA 32 29.418 -79.599 -6.136 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.492 -80.990 -5.612 1.00 0.00 H +ATOM 499 HB3 ALA 32 29.416 -80.155 -4.354 1.00 0.00 H +ATOM 500 C ALA 32 30.631 -82.603 -4.870 1.00 0.00 C +ATOM 501 O ALA 32 31.400 -82.655 -3.902 1.00 0.00 O +ATOM 502 N ASP 33 30.050 -83.703 -5.328 1.00 0.00 N +ATOM 503 H ASP 33 29.432 -83.558 -6.113 1.00 0.00 H +ATOM 504 CA ASP 33 30.133 -85.083 -4.801 1.00 0.00 C +ATOM 505 HA ASP 33 29.992 -85.064 -3.721 1.00 0.00 H +ATOM 506 CB ASP 33 28.998 -85.863 -5.493 1.00 0.00 C +ATOM 507 HB2 ASP 33 28.059 -85.381 -5.222 1.00 0.00 H +ATOM 508 HB3 ASP 33 29.060 -85.771 -6.577 1.00 0.00 H +ATOM 509 CG ASP 33 28.920 -87.290 -5.011 1.00 0.00 C +ATOM 510 OD1 ASP 33 29.402 -88.237 -5.661 1.00 0.00 O +ATOM 511 OD2 ASP 33 28.458 -87.434 -3.866 1.00 0.00 O +ATOM 512 C ASP 33 31.495 -85.693 -5.033 1.00 0.00 C +ATOM 513 O ASP 33 31.986 -86.309 -4.124 1.00 0.00 O +ATOM 514 N ALA 34 32.074 -85.395 -6.146 1.00 0.00 N +ATOM 515 H ALA 34 31.496 -85.157 -6.939 1.00 0.00 H +ATOM 516 CA ALA 34 33.409 -85.682 -6.431 1.00 0.00 C +ATOM 517 HA ALA 34 33.620 -86.749 -6.364 1.00 0.00 H +ATOM 518 CB ALA 34 33.701 -85.344 -7.944 1.00 0.00 C +ATOM 519 HB1 ALA 34 34.697 -85.730 -8.161 1.00 0.00 H +ATOM 520 HB2 ALA 34 33.683 -84.273 -8.144 1.00 0.00 H +ATOM 521 HB3 ALA 34 33.108 -85.978 -8.603 1.00 0.00 H +ATOM 522 C ALA 34 34.362 -84.980 -5.489 1.00 0.00 C +ATOM 523 O ALA 34 35.233 -85.571 -4.874 1.00 0.00 O +ATOM 524 N ASN 35 34.160 -83.660 -5.409 1.00 0.00 N +ATOM 525 H ASN 35 33.240 -83.299 -5.620 1.00 0.00 H +ATOM 526 CA ASN 35 35.115 -82.848 -4.583 1.00 0.00 C +ATOM 527 HA ASN 35 36.125 -82.832 -4.991 1.00 0.00 H +ATOM 528 CB ASN 35 34.752 -81.329 -4.662 1.00 0.00 C +ATOM 529 HB2 ASN 35 34.804 -81.175 -5.740 1.00 0.00 H +ATOM 530 HB3 ASN 35 33.747 -81.205 -4.258 1.00 0.00 H +ATOM 531 CG ASN 35 35.773 -80.453 -4.007 1.00 0.00 C +ATOM 532 OD1 ASN 35 35.781 -80.404 -2.827 1.00 0.00 O +ATOM 533 ND2 ASN 35 36.659 -79.779 -4.693 1.00 0.00 N +ATOM 534 HD21 ASN 35 36.759 -79.908 -5.690 1.00 0.00 H +ATOM 535 HD22 ASN 35 37.414 -79.325 -4.200 1.00 0.00 H +ATOM 536 C ASN 35 35.269 -83.320 -3.101 1.00 0.00 C +ATOM 537 O ASN 35 36.403 -83.362 -2.654 1.00 0.00 O +ATOM 538 N ASP 36 34.159 -83.692 -2.485 1.00 0.00 N +ATOM 539 H ASP 36 33.269 -83.436 -2.886 1.00 0.00 H +ATOM 540 CA ASP 36 34.046 -84.246 -1.122 1.00 0.00 C +ATOM 541 HA ASP 36 34.638 -83.651 -0.427 1.00 0.00 H +ATOM 542 CB ASP 36 32.610 -84.149 -0.655 1.00 0.00 C +ATOM 543 HB2 ASP 36 32.021 -84.743 -1.354 1.00 0.00 H +ATOM 544 HB3 ASP 36 32.590 -84.548 0.359 1.00 0.00 H +ATOM 545 CG ASP 36 31.851 -82.798 -0.668 1.00 0.00 C +ATOM 546 OD1 ASP 36 32.399 -81.666 -0.835 1.00 0.00 O +ATOM 547 OD2 ASP 36 30.629 -82.858 -0.465 1.00 0.00 O +ATOM 548 C ASP 36 34.557 -85.685 -0.920 1.00 0.00 C +ATOM 549 O ASP 36 34.931 -86.147 0.174 1.00 0.00 O +ATOM 550 N LYS 37 34.649 -86.403 -2.034 1.00 0.00 N +ATOM 551 H LYS 37 34.161 -85.989 -2.815 1.00 0.00 H +ATOM 552 CA LYS 37 35.524 -87.586 -2.081 1.00 0.00 C +ATOM 553 HA LYS 37 35.630 -87.982 -1.071 1.00 0.00 H +ATOM 554 CB LYS 37 34.874 -88.637 -3.070 1.00 0.00 C +ATOM 555 HB2 LYS 37 35.698 -89.215 -3.489 1.00 0.00 H +ATOM 556 HB3 LYS 37 34.377 -88.057 -3.848 1.00 0.00 H +ATOM 557 CG LYS 37 33.883 -89.596 -2.388 1.00 0.00 C +ATOM 558 HG2 LYS 37 33.005 -89.097 -1.978 1.00 0.00 H +ATOM 559 HG3 LYS 37 34.332 -90.077 -1.519 1.00 0.00 H +ATOM 560 CD LYS 37 33.350 -90.625 -3.381 1.00 0.00 C +ATOM 561 HD2 LYS 37 34.217 -91.178 -3.743 1.00 0.00 H +ATOM 562 HD3 LYS 37 32.734 -91.344 -2.840 1.00 0.00 H +ATOM 563 CE LYS 37 32.501 -90.147 -4.543 1.00 0.00 C +ATOM 564 HE2 LYS 37 33.148 -89.667 -5.278 1.00 0.00 H +ATOM 565 HE3 LYS 37 32.107 -90.945 -5.172 1.00 0.00 H +ATOM 566 NZ LYS 37 31.447 -89.208 -4.072 1.00 0.00 N +ATOM 567 HZ1 LYS 37 31.761 -88.261 -3.914 1.00 0.00 H +ATOM 568 HZ2 LYS 37 30.785 -89.006 -4.807 1.00 0.00 H +ATOM 569 HZ3 LYS 37 30.869 -89.577 -3.330 1.00 0.00 H +ATOM 570 C LYS 37 37.000 -87.287 -2.439 1.00 0.00 C +ATOM 571 O LYS 37 37.828 -88.204 -2.443 1.00 0.00 O +ATOM 572 N GLY 38 37.337 -86.014 -2.599 1.00 0.00 N +ATOM 573 H GLY 38 36.664 -85.263 -2.538 1.00 0.00 H +ATOM 574 CA GLY 38 38.666 -85.547 -2.972 1.00 0.00 C +ATOM 575 HA2 GLY 38 38.698 -84.470 -2.810 1.00 0.00 H +ATOM 576 HA3 GLY 38 39.330 -86.007 -2.240 1.00 0.00 H +ATOM 577 C GLY 38 39.097 -85.908 -4.399 1.00 0.00 C +ATOM 578 O GLY 38 40.261 -86.356 -4.603 1.00 0.00 O +ATOM 579 N VAL 39 38.204 -85.716 -5.305 1.00 0.00 N +ATOM 580 H VAL 39 37.314 -85.445 -4.912 1.00 0.00 H +ATOM 581 CA VAL 39 38.219 -86.074 -6.778 1.00 0.00 C +ATOM 582 HA VAL 39 39.236 -86.361 -7.046 1.00 0.00 H +ATOM 583 CB VAL 39 37.261 -87.227 -6.951 1.00 0.00 C +ATOM 584 HB VAL 39 36.255 -86.946 -6.640 1.00 0.00 H +ATOM 585 CG1 VAL 39 37.194 -87.665 -8.474 1.00 0.00 C +ATOM 586 HG11 VAL 39 38.167 -87.789 -8.950 1.00 0.00 H +ATOM 587 HG12 VAL 39 36.685 -86.981 -9.154 1.00 0.00 H +ATOM 588 HG13 VAL 39 36.601 -88.579 -8.481 1.00 0.00 H +ATOM 589 CG2 VAL 39 37.671 -88.613 -6.289 1.00 0.00 C +ATOM 590 HG21 VAL 39 37.793 -88.478 -5.214 1.00 0.00 H +ATOM 591 HG22 VAL 39 38.532 -89.100 -6.747 1.00 0.00 H +ATOM 592 HG23 VAL 39 36.904 -89.386 -6.350 1.00 0.00 H +ATOM 593 C VAL 39 37.761 -84.775 -7.616 1.00 0.00 C +ATOM 594 O VAL 39 37.040 -83.865 -7.138 1.00 0.00 O +ATOM 595 N ASP 40 38.176 -84.637 -8.874 1.00 0.00 N +ATOM 596 H ASP 40 38.625 -85.451 -9.269 1.00 0.00 H +ATOM 597 CA ASP 40 37.920 -83.461 -9.740 1.00 0.00 C +ATOM 598 HA ASP 40 36.917 -83.065 -9.585 1.00 0.00 H +ATOM 599 CB ASP 40 38.961 -82.315 -9.491 1.00 0.00 C +ATOM 600 HB2 ASP 40 38.790 -82.056 -8.446 1.00 0.00 H +ATOM 601 HB3 ASP 40 39.920 -82.749 -9.774 1.00 0.00 H +ATOM 602 CG ASP 40 38.560 -81.077 -10.327 1.00 0.00 C +ATOM 603 OD1 ASP 40 39.483 -80.315 -10.650 1.00 0.00 O +ATOM 604 OD2 ASP 40 37.415 -80.807 -10.736 1.00 0.00 O +ATOM 605 C ASP 40 37.866 -83.978 -11.223 1.00 0.00 C +ATOM 606 O ASP 40 38.243 -85.148 -11.429 1.00 0.00 O +ATOM 607 N GLY 41 37.302 -83.188 -12.156 1.00 0.00 N +ATOM 608 H GLY 41 37.020 -82.249 -11.914 1.00 0.00 H +ATOM 609 CA GLY 41 37.061 -83.745 -13.444 1.00 0.00 C +ATOM 610 HA2 GLY 41 37.980 -83.767 -14.030 1.00 0.00 H +ATOM 611 HA3 GLY 41 36.720 -84.776 -13.351 1.00 0.00 H +ATOM 612 C GLY 41 35.948 -83.074 -14.206 1.00 0.00 C +ATOM 613 O GLY 41 35.381 -82.072 -13.779 1.00 0.00 O +ATOM 614 N GLU 42 35.525 -83.760 -15.288 1.00 0.00 N +ATOM 615 H GLU 42 36.023 -84.606 -15.523 1.00 0.00 H +ATOM 616 CA GLU 42 34.475 -83.295 -16.249 1.00 0.00 C +ATOM 617 HA GLU 42 33.903 -82.495 -15.778 1.00 0.00 H +ATOM 618 CB GLU 42 35.091 -82.819 -17.528 1.00 0.00 C +ATOM 619 HB2 GLU 42 35.733 -83.633 -17.866 1.00 0.00 H +ATOM 620 HB3 GLU 42 34.357 -82.549 -18.288 1.00 0.00 H +ATOM 621 CG GLU 42 36.018 -81.625 -17.487 1.00 0.00 C +ATOM 622 HG2 GLU 42 36.924 -81.901 -16.947 1.00 0.00 H +ATOM 623 HG3 GLU 42 36.368 -81.389 -18.492 1.00 0.00 H +ATOM 624 CD GLU 42 35.403 -80.371 -16.802 1.00 0.00 C +ATOM 625 OE1 GLU 42 34.127 -80.120 -16.843 1.00 0.00 O +ATOM 626 OE2 GLU 42 36.194 -79.649 -16.213 1.00 0.00 O +ATOM 627 C GLU 42 33.610 -84.491 -16.607 1.00 0.00 C +ATOM 628 O GLU 42 34.204 -85.526 -16.946 1.00 0.00 O +ATOM 629 N TRP 43 32.319 -84.401 -16.354 1.00 0.00 N +ATOM 630 H TRP 43 31.865 -83.522 -16.150 1.00 0.00 H +ATOM 631 CA TRP 43 31.454 -85.592 -16.395 1.00 0.00 C +ATOM 632 HA TRP 43 31.974 -86.498 -16.707 1.00 0.00 H +ATOM 633 CB TRP 43 30.759 -85.899 -15.035 1.00 0.00 C +ATOM 634 HB2 TRP 43 30.357 -84.955 -14.666 1.00 0.00 H +ATOM 635 HB3 TRP 43 29.962 -86.614 -15.239 1.00 0.00 H +ATOM 636 CG TRP 43 31.630 -86.501 -13.955 1.00 0.00 C +ATOM 637 CD1 TRP 43 31.612 -87.780 -13.595 1.00 0.00 C +ATOM 638 HD1 TRP 43 30.918 -88.494 -14.013 1.00 0.00 H +ATOM 639 NE1 TRP 43 32.581 -87.984 -12.639 1.00 0.00 N +ATOM 640 HE1 TRP 43 32.697 -88.872 -12.172 1.00 0.00 H +ATOM 641 CE2 TRP 43 33.294 -86.866 -12.252 1.00 0.00 C +ATOM 642 CZ2 TRP 43 34.351 -86.613 -11.357 1.00 0.00 C +ATOM 643 HZ2 TRP 43 34.767 -87.378 -10.717 1.00 0.00 H +ATOM 644 CH2 TRP 43 34.631 -85.275 -11.099 1.00 0.00 C +ATOM 645 HH2 TRP 43 35.467 -85.023 -10.464 1.00 0.00 H +ATOM 646 CZ3 TRP 43 34.047 -84.271 -11.878 1.00 0.00 C +ATOM 647 HZ3 TRP 43 34.413 -83.291 -11.609 1.00 0.00 H +ATOM 648 CE3 TRP 43 33.166 -84.568 -12.942 1.00 0.00 C +ATOM 649 HE3 TRP 43 32.775 -83.745 -13.521 1.00 0.00 H +ATOM 650 CD2 TRP 43 32.657 -85.836 -13.074 1.00 0.00 C +ATOM 651 C TRP 43 30.398 -85.390 -17.510 1.00 0.00 C +ATOM 652 O TRP 43 30.190 -84.327 -18.036 1.00 0.00 O +ATOM 653 N THR 44 29.813 -86.491 -17.931 1.00 0.00 N +ATOM 654 H THR 44 29.907 -87.225 -17.243 1.00 0.00 H +ATOM 655 CA THR 44 28.868 -86.641 -19.063 1.00 0.00 C +ATOM 656 HA THR 44 28.374 -85.670 -19.097 1.00 0.00 H +ATOM 657 CB THR 44 29.553 -86.818 -20.413 1.00 0.00 C +ATOM 658 HB THR 44 30.505 -86.293 -20.489 1.00 0.00 H +ATOM 659 CG2 THR 44 29.958 -88.297 -20.710 1.00 0.00 C +ATOM 660 HG21 THR 44 30.274 -88.473 -21.738 1.00 0.00 H +ATOM 661 HG22 THR 44 29.098 -88.965 -20.667 1.00 0.00 H +ATOM 662 HG23 THR 44 30.734 -88.620 -20.016 1.00 0.00 H +ATOM 663 OG1 THR 44 28.618 -86.543 -21.424 1.00 0.00 O +ATOM 664 HG1 THR 44 28.708 -85.596 -21.551 1.00 0.00 H +ATOM 665 C THR 44 27.828 -87.701 -18.708 1.00 0.00 C +ATOM 666 O THR 44 28.069 -88.510 -17.866 1.00 0.00 O +ATOM 667 N TYR 45 26.675 -87.637 -19.445 1.00 0.00 N +ATOM 668 H TYR 45 26.617 -87.192 -20.350 1.00 0.00 H +ATOM 669 CA TYR 45 25.537 -88.486 -19.120 1.00 0.00 C +ATOM 670 HA TYR 45 25.516 -88.725 -18.057 1.00 0.00 H +ATOM 671 CB TYR 45 24.307 -87.589 -19.389 1.00 0.00 C +ATOM 672 HB2 TYR 45 24.506 -86.675 -18.829 1.00 0.00 H +ATOM 673 HB3 TYR 45 24.395 -87.321 -20.441 1.00 0.00 H +ATOM 674 CG TYR 45 22.943 -88.227 -19.186 1.00 0.00 C +ATOM 675 CD1 TYR 45 22.592 -88.636 -17.906 1.00 0.00 C +ATOM 676 HD1 TYR 45 23.189 -88.330 -17.060 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.331 -89.263 -17.658 1.00 0.00 C +ATOM 678 HE1 TYR 45 21.075 -89.656 -16.685 1.00 0.00 H +ATOM 679 CZ TYR 45 20.451 -89.434 -18.732 1.00 0.00 C +ATOM 680 OH TYR 45 19.196 -90.037 -18.522 1.00 0.00 O +ATOM 681 HH TYR 45 18.895 -90.410 -19.354 1.00 0.00 H +ATOM 682 CE2 TYR 45 20.791 -88.965 -20.028 1.00 0.00 C +ATOM 683 HE2 TYR 45 20.008 -89.076 -20.763 1.00 0.00 H +ATOM 684 CD2 TYR 45 22.067 -88.374 -20.347 1.00 0.00 C +ATOM 685 HD2 TYR 45 22.449 -88.103 -21.319 1.00 0.00 H +ATOM 686 C TYR 45 25.371 -89.890 -19.856 1.00 0.00 C +ATOM 687 O TYR 45 25.698 -90.116 -20.975 1.00 0.00 O +ATOM 688 N ASP 46 24.925 -90.843 -19.040 1.00 0.00 N +ATOM 689 H ASP 46 24.615 -90.500 -18.141 1.00 0.00 H +ATOM 690 CA ASP 46 24.561 -92.200 -19.416 1.00 0.00 C +ATOM 691 HA ASP 46 24.735 -92.364 -20.479 1.00 0.00 H +ATOM 692 CB ASP 46 25.534 -93.221 -18.712 1.00 0.00 C +ATOM 693 HB2 ASP 46 26.516 -92.907 -19.066 1.00 0.00 H +ATOM 694 HB3 ASP 46 25.405 -93.156 -17.631 1.00 0.00 H +ATOM 695 CG ASP 46 25.342 -94.724 -19.148 1.00 0.00 C +ATOM 696 OD1 ASP 46 25.661 -95.664 -18.374 1.00 0.00 O +ATOM 697 OD2 ASP 46 24.995 -94.896 -20.335 1.00 0.00 O +ATOM 698 C ASP 46 23.069 -92.460 -19.223 1.00 0.00 C +ATOM 699 O ASP 46 22.645 -92.839 -18.083 1.00 0.00 O +ATOM 700 N ASP 47 22.299 -92.322 -20.317 1.00 0.00 N +ATOM 701 H ASP 47 22.713 -92.092 -21.209 1.00 0.00 H +ATOM 702 CA ASP 47 20.826 -92.534 -20.366 1.00 0.00 C +ATOM 703 HA ASP 47 20.358 -91.944 -19.578 1.00 0.00 H +ATOM 704 CB ASP 47 20.273 -92.102 -21.727 1.00 0.00 C +ATOM 705 HB2 ASP 47 20.880 -91.241 -22.004 1.00 0.00 H +ATOM 706 HB3 ASP 47 20.486 -92.865 -22.476 1.00 0.00 H +ATOM 707 CG ASP 47 18.757 -91.754 -21.653 1.00 0.00 C +ATOM 708 OD1 ASP 47 18.183 -91.281 -20.616 1.00 0.00 O +ATOM 709 OD2 ASP 47 18.022 -92.067 -22.613 1.00 0.00 O +ATOM 710 C ASP 47 20.394 -93.965 -20.092 1.00 0.00 C +ATOM 711 O ASP 47 19.500 -94.255 -19.371 1.00 0.00 O +ATOM 712 N ALA 48 21.243 -94.915 -20.508 1.00 0.00 N +ATOM 713 H ALA 48 21.975 -94.528 -21.086 1.00 0.00 H +ATOM 714 CA ALA 48 21.138 -96.344 -20.342 1.00 0.00 C +ATOM 715 HA ALA 48 20.175 -96.682 -20.722 1.00 0.00 H +ATOM 716 CB ALA 48 22.100 -97.013 -21.296 1.00 0.00 C +ATOM 717 HB1 ALA 48 22.022 -98.098 -21.244 1.00 0.00 H +ATOM 718 HB2 ALA 48 23.095 -96.658 -21.027 1.00 0.00 H +ATOM 719 HB3 ALA 48 21.983 -96.741 -22.345 1.00 0.00 H +ATOM 720 C ALA 48 21.227 -96.831 -18.893 1.00 0.00 C +ATOM 721 O ALA 48 20.815 -97.981 -18.595 1.00 0.00 O +ATOM 722 N THR 49 21.844 -96.065 -18.003 1.00 0.00 N +ATOM 723 H THR 49 22.322 -95.216 -18.268 1.00 0.00 H +ATOM 724 CA THR 49 21.724 -96.295 -16.529 1.00 0.00 C +ATOM 725 HA THR 49 20.821 -96.860 -16.295 1.00 0.00 H +ATOM 726 CB THR 49 22.969 -96.974 -16.001 1.00 0.00 C +ATOM 727 HB THR 49 22.826 -96.976 -14.920 1.00 0.00 H +ATOM 728 CG2 THR 49 23.314 -98.364 -16.549 1.00 0.00 C +ATOM 729 HG21 THR 49 22.505 -98.991 -16.175 1.00 0.00 H +ATOM 730 HG22 THR 49 24.250 -98.710 -16.109 1.00 0.00 H +ATOM 731 HG23 THR 49 23.353 -98.387 -17.638 1.00 0.00 H +ATOM 732 OG1 THR 49 24.036 -96.104 -16.153 1.00 0.00 O +ATOM 733 HG1 THR 49 24.348 -96.113 -17.060 1.00 0.00 H +ATOM 734 C THR 49 21.282 -95.047 -15.721 1.00 0.00 C +ATOM 735 O THR 49 21.234 -95.058 -14.482 1.00 0.00 O +ATOM 736 N LYS 50 20.777 -93.998 -16.360 1.00 0.00 N +ATOM 737 H LYS 50 21.112 -93.950 -17.311 1.00 0.00 H +ATOM 738 CA LYS 50 20.296 -92.725 -15.796 1.00 0.00 C +ATOM 739 HA LYS 50 20.235 -91.942 -16.553 1.00 0.00 H +ATOM 740 CB LYS 50 18.861 -92.873 -15.196 1.00 0.00 C +ATOM 741 HB2 LYS 50 18.998 -93.470 -14.295 1.00 0.00 H +ATOM 742 HB3 LYS 50 18.479 -91.918 -14.836 1.00 0.00 H +ATOM 743 CG LYS 50 17.781 -93.436 -16.101 1.00 0.00 C +ATOM 744 HG2 LYS 50 18.041 -94.436 -16.447 1.00 0.00 H +ATOM 745 HG3 LYS 50 16.878 -93.560 -15.503 1.00 0.00 H +ATOM 746 CD LYS 50 17.456 -92.476 -17.239 1.00 0.00 C +ATOM 747 HD2 LYS 50 17.091 -91.521 -16.862 1.00 0.00 H +ATOM 748 HD3 LYS 50 18.269 -92.335 -17.952 1.00 0.00 H +ATOM 749 CE LYS 50 16.307 -93.100 -17.945 1.00 0.00 C +ATOM 750 HE2 LYS 50 16.565 -94.074 -18.360 1.00 0.00 H +ATOM 751 HE3 LYS 50 15.475 -93.147 -17.244 1.00 0.00 H +ATOM 752 NZ LYS 50 15.991 -92.218 -19.073 1.00 0.00 N +ATOM 753 HZ1 LYS 50 15.313 -92.609 -19.712 1.00 0.00 H +ATOM 754 HZ2 LYS 50 16.833 -92.082 -19.614 1.00 0.00 H +ATOM 755 HZ3 LYS 50 15.695 -91.306 -18.757 1.00 0.00 H +ATOM 756 C LYS 50 21.227 -92.123 -14.789 1.00 0.00 C +ATOM 757 O LYS 50 20.801 -91.552 -13.762 1.00 0.00 O +ATOM 758 N THR 51 22.521 -92.075 -15.140 1.00 0.00 N +ATOM 759 H THR 51 22.755 -92.464 -16.043 1.00 0.00 H +ATOM 760 CA THR 51 23.532 -91.425 -14.332 1.00 0.00 C +ATOM 761 HA THR 51 23.014 -90.665 -13.747 1.00 0.00 H +ATOM 762 CB THR 51 24.273 -92.414 -13.354 1.00 0.00 C +ATOM 763 HB THR 51 23.590 -93.203 -13.036 1.00 0.00 H +ATOM 764 CG2 THR 51 25.291 -93.290 -14.175 1.00 0.00 C +ATOM 765 HG21 THR 51 25.789 -94.003 -13.518 1.00 0.00 H +ATOM 766 HG22 THR 51 25.990 -92.753 -14.817 1.00 0.00 H +ATOM 767 HG23 THR 51 24.653 -93.978 -14.728 1.00 0.00 H +ATOM 768 OG1 THR 51 24.864 -91.905 -12.190 1.00 0.00 O +ATOM 769 HG1 THR 51 24.241 -92.004 -11.466 1.00 0.00 H +ATOM 770 C THR 51 24.543 -90.598 -15.096 1.00 0.00 C +ATOM 771 O THR 51 24.543 -90.457 -16.307 1.00 0.00 O +ATOM 772 N PHE 52 25.463 -89.984 -14.345 1.00 0.00 N +ATOM 773 H PHE 52 25.385 -90.117 -13.347 1.00 0.00 H +ATOM 774 CA PHE 52 26.681 -89.345 -14.773 1.00 0.00 C +ATOM 775 HA PHE 52 26.567 -89.174 -15.843 1.00 0.00 H +ATOM 776 CB PHE 52 26.901 -88.075 -13.989 1.00 0.00 C +ATOM 777 HB2 PHE 52 26.753 -88.236 -12.921 1.00 0.00 H +ATOM 778 HB3 PHE 52 27.898 -87.643 -14.084 1.00 0.00 H +ATOM 779 CG PHE 52 25.958 -87.001 -14.361 1.00 0.00 C +ATOM 780 CD1 PHE 52 24.699 -86.937 -13.873 1.00 0.00 C +ATOM 781 HD1 PHE 52 24.499 -87.665 -13.101 1.00 0.00 H +ATOM 782 CE1 PHE 52 23.760 -85.980 -14.309 1.00 0.00 C +ATOM 783 HE1 PHE 52 22.735 -86.003 -13.970 1.00 0.00 H +ATOM 784 CZ PHE 52 24.112 -85.087 -15.329 1.00 0.00 C +ATOM 785 HZ PHE 52 23.375 -84.361 -15.639 1.00 0.00 H +ATOM 786 CE2 PHE 52 25.403 -85.149 -15.889 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.688 -84.505 -16.708 1.00 0.00 H +ATOM 788 CD2 PHE 52 26.267 -86.081 -15.387 1.00 0.00 C +ATOM 789 HD2 PHE 52 27.245 -86.098 -15.844 1.00 0.00 H +ATOM 790 C PHE 52 27.955 -90.212 -14.764 1.00 0.00 C +ATOM 791 O PHE 52 28.091 -91.004 -13.846 1.00 0.00 O +ATOM 792 N THR 53 28.962 -89.941 -15.583 1.00 0.00 N +ATOM 793 H THR 53 28.844 -89.141 -16.188 1.00 0.00 H +ATOM 794 CA THR 53 30.185 -90.713 -15.830 1.00 0.00 C +ATOM 795 HA THR 53 30.587 -91.078 -14.885 1.00 0.00 H +ATOM 796 CB THR 53 29.923 -91.935 -16.823 1.00 0.00 C +ATOM 797 HB THR 53 29.009 -92.453 -16.534 1.00 0.00 H +ATOM 798 CG2 THR 53 29.892 -91.518 -18.283 1.00 0.00 C +ATOM 799 HG21 THR 53 30.905 -91.201 -18.532 1.00 0.00 H +ATOM 800 HG22 THR 53 29.280 -90.667 -18.580 1.00 0.00 H +ATOM 801 HG23 THR 53 29.647 -92.392 -18.887 1.00 0.00 H +ATOM 802 OG1 THR 53 30.953 -92.839 -16.708 1.00 0.00 O +ATOM 803 HG1 THR 53 30.430 -93.635 -16.828 1.00 0.00 H +ATOM 804 C THR 53 31.296 -89.791 -16.269 1.00 0.00 C +ATOM 805 O THR 53 31.029 -88.717 -16.790 1.00 0.00 O +ATOM 806 N VAL 54 32.533 -90.112 -16.010 1.00 0.00 N +ATOM 807 H VAL 54 32.751 -91.080 -15.820 1.00 0.00 H +ATOM 808 CA VAL 54 33.586 -89.330 -16.542 1.00 0.00 C +ATOM 809 HA VAL 54 33.379 -88.317 -16.197 1.00 0.00 H +ATOM 810 CB VAL 54 34.971 -89.768 -15.986 1.00 0.00 C +ATOM 811 HB VAL 54 35.044 -90.855 -15.989 1.00 0.00 H +ATOM 812 CG1 VAL 54 36.115 -89.127 -16.706 1.00 0.00 C +ATOM 813 HG11 VAL 54 37.037 -89.364 -16.174 1.00 0.00 H +ATOM 814 HG12 VAL 54 36.046 -88.044 -16.599 1.00 0.00 H +ATOM 815 HG13 VAL 54 36.203 -89.565 -17.701 1.00 0.00 H +ATOM 816 CG2 VAL 54 35.128 -89.308 -14.583 1.00 0.00 C +ATOM 817 HG21 VAL 54 35.853 -89.954 -14.088 1.00 0.00 H +ATOM 818 HG22 VAL 54 34.209 -89.527 -14.040 1.00 0.00 H +ATOM 819 HG23 VAL 54 35.337 -88.245 -14.468 1.00 0.00 H +ATOM 820 C VAL 54 33.698 -89.368 -18.152 1.00 0.00 C +ATOM 821 O VAL 54 33.572 -90.360 -18.797 1.00 0.00 O +ATOM 822 N THR 55 34.028 -88.213 -18.761 1.00 0.00 N +ATOM 823 H THR 55 34.134 -87.454 -18.104 1.00 0.00 H +ATOM 824 CA THR 55 34.157 -87.876 -20.203 1.00 0.00 C +ATOM 825 HA THR 55 33.313 -88.379 -20.677 1.00 0.00 H +ATOM 826 CB THR 55 33.990 -86.296 -20.420 1.00 0.00 C +ATOM 827 HB THR 55 34.953 -85.789 -20.376 1.00 0.00 H +ATOM 828 CG2 THR 55 33.326 -86.028 -21.790 1.00 0.00 C +ATOM 829 HG21 THR 55 32.927 -85.016 -21.867 1.00 0.00 H +ATOM 830 HG22 THR 55 32.561 -86.788 -21.955 1.00 0.00 H +ATOM 831 HG23 THR 55 34.105 -86.121 -22.547 1.00 0.00 H +ATOM 832 OG1 THR 55 33.116 -85.722 -19.507 1.00 0.00 O +ATOM 833 HG1 THR 55 33.625 -85.598 -18.702 1.00 0.00 H +ATOM 834 C THR 55 35.454 -88.498 -20.880 1.00 0.00 C +ATOM 835 O THR 55 36.189 -87.835 -21.567 1.00 0.00 O +ATOM 836 N GLU 56 35.579 -89.796 -20.790 1.00 0.00 N +ATOM 837 H GLU 56 34.877 -90.350 -20.319 1.00 0.00 H +ATOM 838 CA GLU 56 36.751 -90.567 -21.295 1.00 0.00 C +ATOM 839 HA GLU 56 37.378 -89.932 -21.919 1.00 0.00 H +ATOM 840 CB GLU 56 37.704 -91.025 -20.193 1.00 0.00 C +ATOM 841 HB2 GLU 56 37.062 -91.522 -19.465 1.00 0.00 H +ATOM 842 HB3 GLU 56 38.400 -91.775 -20.567 1.00 0.00 H +ATOM 843 CG GLU 56 38.397 -89.882 -19.349 1.00 0.00 C +ATOM 844 HG2 GLU 56 37.727 -89.023 -19.303 1.00 0.00 H +ATOM 845 HG3 GLU 56 38.456 -90.203 -18.309 1.00 0.00 H +ATOM 846 CD GLU 56 39.811 -89.583 -19.899 1.00 0.00 C +ATOM 847 OE1 GLU 56 40.732 -89.432 -19.071 1.00 0.00 O +ATOM 848 OE2 GLU 56 39.992 -89.318 -21.122 1.00 0.00 O +ATOM 849 C GLU 56 36.334 -91.704 -22.203 1.00 0.00 C +ATOM 850 O GLU 56 35.617 -92.679 -21.855 1.00 0.00 O +ATOM 851 OXT GLU 56 36.693 -91.563 -23.411 1.00 0.00 O +ATOM 852 ZN ZN1 57 23.494 -89.371 -3.603 1.00 0.00 ZN +ATOM 853 N AN1 58 24.379 -88.712 -2.072 1.00 0.00 N +ATOM 854 C AN1 58 26.023 -87.693 -0.337 1.00 0.00 C +ATOM 855 C1 AN1 58 25.009 -88.219 -1.300 1.00 0.00 C +ATOM 856 H AN1 58 26.760 -87.140 -0.931 1.00 0.00 H +ATOM 857 H1 AN1 58 26.524 -88.573 0.085 1.00 0.00 H +ATOM 858 H2 AN1 58 25.557 -87.173 0.509 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 24.358 -89.961 2.072 1.00 0.00 N +ATOM 860 N2 AZI 59 24.824 -90.520 1.075 1.00 0.00 N +ATOM 861 N3 AZI 59 25.265 -91.148 0.059 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/inp/pdbs/cluster.c3.pdb b/tests/nsga2/inp/pdbs/cluster.c3.pdb new file mode 100644 index 0000000..8806817 --- /dev/null +++ b/tests/nsga2/inp/pdbs/cluster.c3.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.249 -81.839 -12.770 1.00 0.00 N +ATOM 2 H1 MET 1 12.938 -81.497 -13.668 1.00 0.00 H +ATOM 3 H2 MET 1 14.206 -81.525 -12.691 1.00 0.00 H +ATOM 4 H3 MET 1 12.748 -81.392 -12.015 1.00 0.00 H +ATOM 5 CA MET 1 13.129 -83.292 -12.725 1.00 0.00 C +ATOM 6 HA MET 1 12.070 -83.548 -12.729 1.00 0.00 H +ATOM 7 CB MET 1 13.687 -83.982 -13.923 1.00 0.00 C +ATOM 8 HB2 MET 1 13.129 -83.614 -14.784 1.00 0.00 H +ATOM 9 HB3 MET 1 14.727 -83.683 -14.053 1.00 0.00 H +ATOM 10 CG MET 1 13.817 -85.521 -13.913 1.00 0.00 C +ATOM 11 HG2 MET 1 14.214 -85.839 -14.877 1.00 0.00 H +ATOM 12 HG3 MET 1 14.565 -85.837 -13.186 1.00 0.00 H +ATOM 13 SD MET 1 12.337 -86.491 -13.680 1.00 0.00 S +ATOM 14 CE MET 1 12.967 -88.072 -14.025 1.00 0.00 C +ATOM 15 HE1 MET 1 12.293 -88.864 -13.699 1.00 0.00 H +ATOM 16 HE2 MET 1 13.920 -88.182 -13.507 1.00 0.00 H +ATOM 17 HE3 MET 1 13.087 -88.225 -15.098 1.00 0.00 H +ATOM 18 C MET 1 13.718 -83.864 -11.418 1.00 0.00 C +ATOM 19 O MET 1 14.814 -83.488 -11.035 1.00 0.00 O +ATOM 20 N GLN 2 13.100 -84.814 -10.771 1.00 0.00 N +ATOM 21 H GLN 2 12.204 -85.139 -11.104 1.00 0.00 H +ATOM 22 CA GLN 2 13.593 -85.557 -9.617 1.00 0.00 C +ATOM 23 HA GLN 2 14.242 -84.925 -9.012 1.00 0.00 H +ATOM 24 CB GLN 2 12.424 -86.031 -8.682 1.00 0.00 C +ATOM 25 HB2 GLN 2 11.499 -86.094 -9.256 1.00 0.00 H +ATOM 26 HB3 GLN 2 12.685 -87.008 -8.278 1.00 0.00 H +ATOM 27 CG GLN 2 12.171 -85.044 -7.565 1.00 0.00 C +ATOM 28 HG2 GLN 2 11.963 -84.059 -7.983 1.00 0.00 H +ATOM 29 HG3 GLN 2 11.311 -85.419 -7.010 1.00 0.00 H +ATOM 30 CD GLN 2 13.298 -84.982 -6.484 1.00 0.00 C +ATOM 31 OE1 GLN 2 14.293 -85.694 -6.452 1.00 0.00 O +ATOM 32 NE2 GLN 2 13.245 -84.062 -5.536 1.00 0.00 N +ATOM 33 HE21 GLN 2 13.971 -84.025 -4.835 1.00 0.00 H +ATOM 34 HE22 GLN 2 12.518 -83.362 -5.577 1.00 0.00 H +ATOM 35 C GLN 2 14.474 -86.754 -10.101 1.00 0.00 C +ATOM 36 O GLN 2 13.959 -87.867 -10.292 1.00 0.00 O +ATOM 37 N TYR 3 15.756 -86.468 -10.276 1.00 0.00 N +ATOM 38 H TYR 3 16.132 -85.592 -9.944 1.00 0.00 H +ATOM 39 CA TYR 3 16.683 -87.422 -10.839 1.00 0.00 C +ATOM 40 HA TYR 3 16.209 -87.976 -11.649 1.00 0.00 H +ATOM 41 CB TYR 3 17.838 -86.659 -11.515 1.00 0.00 C +ATOM 42 HB2 TYR 3 18.237 -85.943 -10.795 1.00 0.00 H +ATOM 43 HB3 TYR 3 18.636 -87.385 -11.669 1.00 0.00 H +ATOM 44 CG TYR 3 17.548 -85.917 -12.814 1.00 0.00 C +ATOM 45 CD1 TYR 3 17.429 -86.636 -14.014 1.00 0.00 C +ATOM 46 HD1 TYR 3 17.604 -87.701 -14.002 1.00 0.00 H +ATOM 47 CE1 TYR 3 17.367 -86.013 -15.274 1.00 0.00 C +ATOM 48 HE1 TYR 3 17.367 -86.607 -16.176 1.00 0.00 H +ATOM 49 CZ TYR 3 17.244 -84.598 -15.320 1.00 0.00 C +ATOM 50 OH TYR 3 17.062 -84.041 -16.497 1.00 0.00 O +ATOM 51 HH TYR 3 17.066 -84.652 -17.238 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.422 -83.922 -14.132 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.314 -82.850 -14.205 1.00 0.00 H +ATOM 54 CD2 TYR 3 17.611 -84.519 -12.907 1.00 0.00 C +ATOM 55 HD2 TYR 3 17.791 -83.961 -12.000 1.00 0.00 H +ATOM 56 C TYR 3 17.277 -88.415 -9.798 1.00 0.00 C +ATOM 57 O TYR 3 17.631 -88.011 -8.650 1.00 0.00 O +ATOM 58 N LYS 4 17.553 -89.721 -10.195 1.00 0.00 N +ATOM 59 H LYS 4 17.254 -90.053 -11.101 1.00 0.00 H +ATOM 60 CA LYS 4 18.237 -90.638 -9.317 1.00 0.00 C +ATOM 61 HA LYS 4 17.700 -90.657 -8.369 1.00 0.00 H +ATOM 62 CB LYS 4 18.087 -92.018 -9.967 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.275 -91.948 -11.038 1.00 0.00 H +ATOM 64 HB3 LYS 4 18.775 -92.761 -9.563 1.00 0.00 H +ATOM 65 CG LYS 4 16.655 -92.560 -9.842 1.00 0.00 C +ATOM 66 HG2 LYS 4 16.367 -92.763 -8.811 1.00 0.00 H +ATOM 67 HG3 LYS 4 15.987 -91.860 -10.343 1.00 0.00 H +ATOM 68 CD LYS 4 16.528 -93.874 -10.517 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.017 -93.776 -11.486 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.961 -94.691 -9.940 1.00 0.00 H +ATOM 71 CE LYS 4 15.104 -94.395 -10.618 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.173 -95.452 -10.873 1.00 0.00 H +ATOM 73 HE3 LYS 4 14.681 -94.226 -9.628 1.00 0.00 H +ATOM 74 NZ LYS 4 14.300 -93.605 -11.539 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.912 -92.827 -11.025 1.00 0.00 H +ATOM 76 HZ2 LYS 4 13.578 -94.215 -11.895 1.00 0.00 H +ATOM 77 HZ3 LYS 4 14.716 -93.320 -12.414 1.00 0.00 H +ATOM 78 C LYS 4 19.732 -90.437 -9.064 1.00 0.00 C +ATOM 79 O LYS 4 20.570 -90.018 -9.893 1.00 0.00 O +ATOM 80 N HE1 5 20.090 -90.562 -7.782 1.00 0.00 N +ATOM 81 CA HE1 5 21.471 -90.521 -7.340 1.00 0.00 C +ATOM 82 C HE1 5 21.879 -91.487 -6.290 1.00 0.00 C +ATOM 83 O HE1 5 21.098 -91.684 -5.402 1.00 0.00 O +ATOM 84 CB HE1 5 21.823 -89.077 -6.859 1.00 0.00 C +ATOM 85 CG HE1 5 23.173 -88.974 -6.188 1.00 0.00 C +ATOM 86 CD2 HE1 5 24.369 -89.278 -6.775 1.00 0.00 C +ATOM 87 ND1 HE1 5 23.432 -88.329 -4.943 1.00 0.00 N +ATOM 88 CE1 HE1 5 24.767 -88.311 -4.905 1.00 0.00 C +ATOM 89 NE2 HE1 5 25.391 -88.877 -5.948 1.00 0.00 N +ATOM 90 H HE1 5 19.445 -90.946 -7.107 1.00 0.00 H +ATOM 91 HA HE1 5 22.055 -90.625 -8.255 1.00 0.00 H +ATOM 92 HB2 HE1 5 21.033 -88.642 -6.247 1.00 0.00 H +ATOM 93 HB3 HE1 5 21.829 -88.369 -7.689 1.00 0.00 H +ATOM 94 HD2 HE1 5 24.530 -89.757 -7.730 1.00 0.00 H +ATOM 95 HE1 HE1 5 25.362 -88.111 -4.026 1.00 0.00 H +ATOM 96 HE2 HE1 5 26.377 -89.090 -5.983 1.00 0.00 H +ATOM 97 N ILE 6 23.111 -92.019 -6.413 1.00 0.00 N +ATOM 98 H ILE 6 23.729 -91.884 -7.200 1.00 0.00 H +ATOM 99 CA ILE 6 23.511 -92.995 -5.437 1.00 0.00 C +ATOM 100 HA ILE 6 22.682 -93.634 -5.135 1.00 0.00 H +ATOM 101 CB ILE 6 24.514 -93.915 -6.128 1.00 0.00 C +ATOM 102 HB ILE 6 24.106 -94.063 -7.128 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.881 -93.283 -6.292 1.00 0.00 C +ATOM 104 HG21 ILE 6 26.475 -93.883 -6.981 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.382 -93.185 -5.328 1.00 0.00 H +ATOM 106 HG23 ILE 6 25.629 -92.270 -6.603 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.639 -95.318 -5.405 1.00 0.00 C +ATOM 108 HG12 ILE 6 25.305 -95.251 -4.545 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.648 -95.641 -5.087 1.00 0.00 H +ATOM 110 CD1 ILE 6 25.077 -96.369 -6.432 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.285 -96.627 -7.134 1.00 0.00 H +ATOM 112 HD12 ILE 6 25.125 -97.388 -6.048 1.00 0.00 H +ATOM 113 HD13 ILE 6 25.915 -96.193 -7.107 1.00 0.00 H +ATOM 114 C ILE 6 24.059 -92.425 -4.058 1.00 0.00 C +ATOM 115 O ILE 6 24.418 -91.291 -3.942 1.00 0.00 O +ATOM 116 N VAL 7 24.082 -93.325 -3.079 1.00 0.00 N +ATOM 117 H VAL 7 23.589 -94.189 -3.252 1.00 0.00 H +ATOM 118 CA VAL 7 24.306 -92.959 -1.684 1.00 0.00 C +ATOM 119 HA VAL 7 25.114 -92.235 -1.784 1.00 0.00 H +ATOM 120 CB VAL 7 23.062 -92.261 -1.104 1.00 0.00 C +ATOM 121 HB VAL 7 22.679 -91.601 -1.882 1.00 0.00 H +ATOM 122 CG1 VAL 7 21.881 -93.285 -0.828 1.00 0.00 C +ATOM 123 HG11 VAL 7 22.170 -94.101 -0.166 1.00 0.00 H +ATOM 124 HG12 VAL 7 21.053 -92.894 -0.237 1.00 0.00 H +ATOM 125 HG13 VAL 7 21.512 -93.613 -1.800 1.00 0.00 H +ATOM 126 CG2 VAL 7 23.389 -91.461 0.150 1.00 0.00 C +ATOM 127 HG21 VAL 7 24.249 -90.823 -0.053 1.00 0.00 H +ATOM 128 HG22 VAL 7 22.585 -90.801 0.477 1.00 0.00 H +ATOM 129 HG23 VAL 7 23.654 -92.169 0.936 1.00 0.00 H +ATOM 130 C VAL 7 24.853 -94.101 -0.907 1.00 0.00 C +ATOM 131 O VAL 7 24.466 -95.229 -1.029 1.00 0.00 O +ATOM 132 N ASN 8 25.835 -93.786 -0.002 1.00 0.00 N +ATOM 133 H ASN 8 26.044 -92.812 0.164 1.00 0.00 H +ATOM 134 CA ASN 8 26.622 -94.709 0.845 1.00 0.00 C +ATOM 135 HA ASN 8 26.358 -95.744 0.628 1.00 0.00 H +ATOM 136 CB ASN 8 28.047 -94.687 0.314 1.00 0.00 C +ATOM 137 HB2 ASN 8 28.004 -94.867 -0.760 1.00 0.00 H +ATOM 138 HB3 ASN 8 28.452 -93.699 0.533 1.00 0.00 H +ATOM 139 CG ASN 8 29.047 -95.822 0.785 1.00 0.00 C +ATOM 140 OD1 ASN 8 28.782 -96.957 1.129 1.00 0.00 O +ATOM 141 ND2 ASN 8 30.288 -95.436 0.722 1.00 0.00 N +ATOM 142 HD21 ASN 8 30.563 -94.548 0.330 1.00 0.00 H +ATOM 143 HD22 ASN 8 30.955 -96.188 0.815 1.00 0.00 H +ATOM 144 C ASN 8 26.425 -94.446 2.340 1.00 0.00 C +ATOM 145 O ASN 8 26.524 -93.276 2.769 1.00 0.00 O +ATOM 146 N GLY 9 26.240 -95.437 3.189 1.00 0.00 N +ATOM 147 H GLY 9 26.278 -96.353 2.766 1.00 0.00 H +ATOM 148 CA GLY 9 26.076 -95.307 4.605 1.00 0.00 C +ATOM 149 HA2 GLY 9 26.318 -94.290 4.913 1.00 0.00 H +ATOM 150 HA3 GLY 9 25.041 -95.556 4.843 1.00 0.00 H +ATOM 151 C GLY 9 27.076 -96.088 5.445 1.00 0.00 C +ATOM 152 O GLY 9 28.240 -96.314 4.969 1.00 0.00 O +ATOM 153 N LYS 10 26.648 -96.427 6.645 1.00 0.00 N +ATOM 154 H LYS 10 25.737 -96.071 6.897 1.00 0.00 H +ATOM 155 CA LYS 10 27.178 -97.443 7.553 1.00 0.00 C +ATOM 156 HA LYS 10 28.215 -97.123 7.662 1.00 0.00 H +ATOM 157 CB LYS 10 26.381 -97.349 8.982 1.00 0.00 C +ATOM 158 HB2 LYS 10 26.176 -96.288 9.125 1.00 0.00 H +ATOM 159 HB3 LYS 10 25.397 -97.798 8.851 1.00 0.00 H +ATOM 160 CG LYS 10 27.137 -98.073 10.143 1.00 0.00 C +ATOM 161 HG2 LYS 10 27.348 -99.069 9.752 1.00 0.00 H +ATOM 162 HG3 LYS 10 28.090 -97.549 10.217 1.00 0.00 H +ATOM 163 CD LYS 10 26.518 -98.075 11.535 1.00 0.00 C +ATOM 164 HD2 LYS 10 25.496 -98.426 11.392 1.00 0.00 H +ATOM 165 HD3 LYS 10 26.973 -98.868 12.128 1.00 0.00 H +ATOM 166 CE LYS 10 26.494 -96.638 12.087 1.00 0.00 C +ATOM 167 HE2 LYS 10 27.512 -96.323 12.315 1.00 0.00 H +ATOM 168 HE3 LYS 10 25.907 -96.002 11.424 1.00 0.00 H +ATOM 169 NZ LYS 10 25.891 -96.600 13.422 1.00 0.00 N +ATOM 170 HZ1 LYS 10 26.309 -95.858 13.964 1.00 0.00 H +ATOM 171 HZ2 LYS 10 26.062 -97.471 13.905 1.00 0.00 H +ATOM 172 HZ3 LYS 10 24.902 -96.399 13.371 1.00 0.00 H +ATOM 173 C LYS 10 27.292 -98.929 7.176 1.00 0.00 C +ATOM 174 O LYS 10 28.204 -99.597 7.626 1.00 0.00 O +ATOM 175 N THR 11 26.477 -99.440 6.305 1.00 0.00 N +ATOM 176 H THR 11 25.648 -98.921 6.050 1.00 0.00 H +ATOM 177 CA THR 11 26.673-100.778 5.654 1.00 0.00 C +ATOM 178 HA THR 11 27.701-101.073 5.443 1.00 0.00 H +ATOM 179 CB THR 11 26.121-101.856 6.592 1.00 0.00 C +ATOM 180 HB THR 11 26.815-101.799 7.430 1.00 0.00 H +ATOM 181 CG2 THR 11 24.751-101.591 7.217 1.00 0.00 C +ATOM 182 HG21 THR 11 24.718-101.125 8.202 1.00 0.00 H +ATOM 183 HG22 THR 11 24.161-102.507 7.178 1.00 0.00 H +ATOM 184 HG23 THR 11 24.327-100.848 6.541 1.00 0.00 H +ATOM 185 OG1 THR 11 26.188-103.087 5.892 1.00 0.00 O +ATOM 186 HG1 THR 11 27.086-103.400 6.024 1.00 0.00 H +ATOM 187 C THR 11 25.934-100.809 4.266 1.00 0.00 C +ATOM 188 O THR 11 26.355-101.540 3.337 1.00 0.00 O +ATOM 189 N LEU 12 24.794-100.179 4.127 1.00 0.00 N +ATOM 190 H LEU 12 24.497 -99.605 4.903 1.00 0.00 H +ATOM 191 CA LEU 12 24.034-100.163 2.862 1.00 0.00 C +ATOM 192 HA LEU 12 24.001-101.171 2.448 1.00 0.00 H +ATOM 193 CB LEU 12 22.534 -99.965 3.207 1.00 0.00 C +ATOM 194 HB2 LEU 12 22.142-100.755 3.847 1.00 0.00 H +ATOM 195 HB3 LEU 12 22.463 -99.004 3.717 1.00 0.00 H +ATOM 196 CG LEU 12 21.593 -99.990 2.003 1.00 0.00 C +ATOM 197 HG LEU 12 22.022 -99.429 1.173 1.00 0.00 H +ATOM 198 CD1 LEU 12 21.411-101.347 1.408 1.00 0.00 C +ATOM 199 HD11 LEU 12 20.617-101.879 1.932 1.00 0.00 H +ATOM 200 HD12 LEU 12 22.279-101.971 1.623 1.00 0.00 H +ATOM 201 HD13 LEU 12 21.006-101.363 0.396 1.00 0.00 H +ATOM 202 CD2 LEU 12 20.191 -99.285 2.167 1.00 0.00 C +ATOM 203 HD21 LEU 12 20.377 -98.220 2.300 1.00 0.00 H +ATOM 204 HD22 LEU 12 19.700 -99.743 3.026 1.00 0.00 H +ATOM 205 HD23 LEU 12 19.536 -99.384 1.301 1.00 0.00 H +ATOM 206 C LEU 12 24.544 -99.096 1.863 1.00 0.00 C +ATOM 207 O LEU 12 24.639 -97.935 2.218 1.00 0.00 O +ATOM 208 N LYS 13 24.776 -99.523 0.613 1.00 0.00 N +ATOM 209 H LYS 13 24.694-100.515 0.441 1.00 0.00 H +ATOM 210 CA LYS 13 24.757 -98.620 -0.636 1.00 0.00 C +ATOM 211 HA LYS 13 24.859 -97.597 -0.274 1.00 0.00 H +ATOM 212 CB LYS 13 25.854 -99.014 -1.595 1.00 0.00 C +ATOM 213 HB2 LYS 13 26.769 -99.134 -1.014 1.00 0.00 H +ATOM 214 HB3 LYS 13 25.553 -99.947 -2.072 1.00 0.00 H +ATOM 215 CG LYS 13 26.428 -97.994 -2.513 1.00 0.00 C +ATOM 216 HG2 LYS 13 25.598 -97.709 -3.158 1.00 0.00 H +ATOM 217 HG3 LYS 13 26.795 -97.163 -1.910 1.00 0.00 H +ATOM 218 CD LYS 13 27.584 -98.526 -3.395 1.00 0.00 C +ATOM 219 HD2 LYS 13 28.200 -97.699 -3.747 1.00 0.00 H +ATOM 220 HD3 LYS 13 28.126 -99.265 -2.804 1.00 0.00 H +ATOM 221 CE LYS 13 26.880 -99.265 -4.553 1.00 0.00 C +ATOM 222 HE2 LYS 13 26.249-100.128 -4.339 1.00 0.00 H +ATOM 223 HE3 LYS 13 26.312 -98.458 -5.015 1.00 0.00 H +ATOM 224 NZ LYS 13 27.766 -99.819 -5.682 1.00 0.00 N +ATOM 225 HZ1 LYS 13 28.450 -99.157 -6.021 1.00 0.00 H +ATOM 226 HZ2 LYS 13 27.325 -99.966 -6.579 1.00 0.00 H +ATOM 227 HZ3 LYS 13 28.238-100.681 -5.450 1.00 0.00 H +ATOM 228 C LYS 13 23.437 -98.712 -1.252 1.00 0.00 C +ATOM 229 O LYS 13 22.935 -99.815 -1.519 1.00 0.00 O +ATOM 230 N GLY 14 22.866 -97.590 -1.608 1.00 0.00 N +ATOM 231 H GLY 14 23.403 -96.740 -1.506 1.00 0.00 H +ATOM 232 CA GLY 14 21.539 -97.490 -2.150 1.00 0.00 C +ATOM 233 HA2 GLY 14 21.299 -98.339 -2.791 1.00 0.00 H +ATOM 234 HA3 GLY 14 20.797 -97.607 -1.361 1.00 0.00 H +ATOM 235 C GLY 14 21.286 -96.210 -3.006 1.00 0.00 C +ATOM 236 O GLY 14 22.258 -95.425 -3.236 1.00 0.00 O +ATOM 237 N VAL 15 20.034 -96.113 -3.452 1.00 0.00 N +ATOM 238 H VAL 15 19.449 -96.913 -3.257 1.00 0.00 H +ATOM 239 CA VAL 15 19.677 -95.003 -4.395 1.00 0.00 C +ATOM 240 HA VAL 15 20.491 -94.319 -4.636 1.00 0.00 H +ATOM 241 CB VAL 15 19.317 -95.537 -5.815 1.00 0.00 C +ATOM 242 HB VAL 15 18.415 -96.148 -5.776 1.00 0.00 H +ATOM 243 CG1 VAL 15 19.023 -94.374 -6.831 1.00 0.00 C +ATOM 244 HG11 VAL 15 19.861 -93.686 -6.722 1.00 0.00 H +ATOM 245 HG12 VAL 15 18.926 -94.788 -7.835 1.00 0.00 H +ATOM 246 HG13 VAL 15 18.054 -93.919 -6.628 1.00 0.00 H +ATOM 247 CG2 VAL 15 20.487 -96.427 -6.302 1.00 0.00 C +ATOM 248 HG21 VAL 15 21.366 -95.821 -6.080 1.00 0.00 H +ATOM 249 HG22 VAL 15 20.577 -97.391 -5.801 1.00 0.00 H +ATOM 250 HG23 VAL 15 20.370 -96.655 -7.361 1.00 0.00 H +ATOM 251 C VAL 15 18.523 -94.154 -3.814 1.00 0.00 C +ATOM 252 O VAL 15 17.531 -94.593 -3.256 1.00 0.00 O +ATOM 253 N HD1 16 18.587 -92.911 -4.150 1.00 0.00 N +ATOM 254 CA HD1 16 17.608 -91.912 -3.759 1.00 0.00 C +ATOM 255 C HD1 16 17.470 -90.916 -4.882 1.00 0.00 C +ATOM 256 O HD1 16 18.050 -91.132 -5.964 1.00 0.00 O +ATOM 257 CB HD1 16 17.922 -91.348 -2.336 1.00 0.00 C +ATOM 258 CG HD1 16 19.254 -90.714 -2.213 1.00 0.00 C +ATOM 259 CD2 HD1 16 20.038 -90.069 -3.135 1.00 0.00 C +ATOM 260 ND1 HD1 16 19.772 -90.388 -1.006 1.00 0.00 N +ATOM 261 CE1 HD1 16 20.859 -89.618 -1.180 1.00 0.00 C +ATOM 262 NE2 HD1 16 21.055 -89.303 -2.517 1.00 0.00 N +ATOM 263 H HD1 16 19.382 -92.624 -4.703 1.00 0.00 H +ATOM 264 HA HD1 16 16.689 -92.495 -3.692 1.00 0.00 H +ATOM 265 HB2 HD1 16 17.097 -90.666 -2.134 1.00 0.00 H +ATOM 266 HB3 HD1 16 17.948 -92.176 -1.627 1.00 0.00 H +ATOM 267 HD1 HD1 16 19.407 -90.625 -0.094 1.00 0.00 H +ATOM 268 HD2 HD1 16 19.911 -89.975 -4.203 1.00 0.00 H +ATOM 269 HE1 HD1 16 21.404 -89.269 -0.316 1.00 0.00 H +ATOM 270 N THR 17 16.679 -89.861 -4.762 1.00 0.00 N +ATOM 271 H THR 17 16.218 -89.584 -3.907 1.00 0.00 H +ATOM 272 CA THR 17 16.556 -88.891 -5.889 1.00 0.00 C +ATOM 273 HA THR 17 17.336 -89.051 -6.633 1.00 0.00 H +ATOM 274 CB THR 17 15.286 -88.855 -6.641 1.00 0.00 C +ATOM 275 HB THR 17 15.439 -88.257 -7.539 1.00 0.00 H +ATOM 276 CG2 THR 17 14.873 -90.235 -7.127 1.00 0.00 C +ATOM 277 HG21 THR 17 14.454 -90.835 -6.319 1.00 0.00 H +ATOM 278 HG22 THR 17 15.790 -90.736 -7.438 1.00 0.00 H +ATOM 279 HG23 THR 17 14.159 -90.066 -7.933 1.00 0.00 H +ATOM 280 OG1 THR 17 14.153 -88.380 -6.000 1.00 0.00 O +ATOM 281 HG1 THR 17 14.095 -87.442 -6.192 1.00 0.00 H +ATOM 282 C THR 17 16.918 -87.454 -5.440 1.00 0.00 C +ATOM 283 O THR 17 16.935 -87.135 -4.255 1.00 0.00 O +ATOM 284 N HD2 18 17.166 -86.589 -6.435 1.00 0.00 N +ATOM 285 CA HD2 18 17.376 -85.135 -6.167 1.00 0.00 C +ATOM 286 C HD2 18 16.838 -84.378 -7.357 1.00 0.00 C +ATOM 287 O HD2 18 16.831 -84.794 -8.522 1.00 0.00 O +ATOM 288 CB HD2 18 18.831 -84.753 -5.909 1.00 0.00 C +ATOM 289 CG HD2 18 19.493 -85.348 -4.693 1.00 0.00 C +ATOM 290 CD2 HD2 18 20.763 -85.952 -4.766 1.00 0.00 C +ATOM 291 ND1 HD2 18 19.083 -85.364 -3.359 1.00 0.00 N +ATOM 292 CE1 HD2 18 20.119 -86.003 -2.681 1.00 0.00 C +ATOM 293 NE2 HD2 18 21.106 -86.420 -3.553 1.00 0.00 N +ATOM 294 H HD2 18 17.086 -86.944 -7.377 1.00 0.00 H +ATOM 295 HA HD2 18 16.733 -84.784 -5.360 1.00 0.00 H +ATOM 296 HB2 HD2 18 19.400 -85.024 -6.798 1.00 0.00 H +ATOM 297 HB3 HD2 18 18.832 -83.664 -5.870 1.00 0.00 H +ATOM 298 HD1 HD2 18 18.183 -85.090 -2.991 1.00 0.00 H +ATOM 299 HD2 HD2 18 21.348 -86.038 -5.670 1.00 0.00 H +ATOM 300 HE1 HD2 18 19.986 -86.268 -1.642 1.00 0.00 H +ATOM 301 N GLU 19 16.208 -83.232 -7.018 1.00 0.00 N +ATOM 302 H GLU 19 16.374 -82.863 -6.093 1.00 0.00 H +ATOM 303 CA GLU 19 15.685 -82.359 -8.078 1.00 0.00 C +ATOM 304 HA GLU 19 15.143 -82.979 -8.792 1.00 0.00 H +ATOM 305 CB GLU 19 14.600 -81.450 -7.567 1.00 0.00 C +ATOM 306 HB2 GLU 19 13.681 -82.011 -7.391 1.00 0.00 H +ATOM 307 HB3 GLU 19 14.891 -81.085 -6.582 1.00 0.00 H +ATOM 308 CG GLU 19 14.199 -80.163 -8.374 1.00 0.00 C +ATOM 309 HG2 GLU 19 13.386 -79.776 -7.760 1.00 0.00 H +ATOM 310 HG3 GLU 19 14.995 -79.422 -8.448 1.00 0.00 H +ATOM 311 CD GLU 19 13.655 -80.522 -9.754 1.00 0.00 C +ATOM 312 OE1 GLU 19 12.772 -81.410 -9.951 1.00 0.00 O +ATOM 313 OE2 GLU 19 14.046 -79.883 -10.714 1.00 0.00 O +ATOM 314 C GLU 19 16.764 -81.502 -8.794 1.00 0.00 C +ATOM 315 O GLU 19 17.439 -80.747 -8.064 1.00 0.00 O +ATOM 316 N ALA 20 16.810 -81.413 -10.082 1.00 0.00 N +ATOM 317 H ALA 20 16.322 -82.117 -10.617 1.00 0.00 H +ATOM 318 CA ALA 20 17.442 -80.360 -10.838 1.00 0.00 C +ATOM 319 HA ALA 20 17.214 -79.441 -10.298 1.00 0.00 H +ATOM 320 CB ALA 20 18.996 -80.689 -10.830 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.505 -79.964 -11.464 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.176 -81.650 -11.312 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.513 -80.826 -9.880 1.00 0.00 H +ATOM 324 C ALA 20 16.766 -80.187 -12.247 1.00 0.00 C +ATOM 325 O ALA 20 16.148 -81.077 -12.795 1.00 0.00 O +ATOM 326 N VAL 21 16.800 -78.968 -12.789 1.00 0.00 N +ATOM 327 H VAL 21 17.287 -78.239 -12.286 1.00 0.00 H +ATOM 328 CA VAL 21 15.991 -78.605 -13.958 1.00 0.00 C +ATOM 329 HA VAL 21 15.049 -79.147 -13.880 1.00 0.00 H +ATOM 330 CB VAL 21 15.833 -77.087 -13.926 1.00 0.00 C +ATOM 331 HB VAL 21 15.819 -76.848 -12.863 1.00 0.00 H +ATOM 332 CG1 VAL 21 16.863 -76.319 -14.649 1.00 0.00 C +ATOM 333 HG11 VAL 21 17.823 -76.692 -14.293 1.00 0.00 H +ATOM 334 HG12 VAL 21 16.893 -75.260 -14.393 1.00 0.00 H +ATOM 335 HG13 VAL 21 16.765 -76.475 -15.723 1.00 0.00 H +ATOM 336 CG2 VAL 21 14.391 -76.751 -14.414 1.00 0.00 C +ATOM 337 HG21 VAL 21 14.188 -75.745 -14.047 1.00 0.00 H +ATOM 338 HG22 VAL 21 13.659 -77.436 -13.986 1.00 0.00 H +ATOM 339 HG23 VAL 21 14.284 -76.850 -15.494 1.00 0.00 H +ATOM 340 C VAL 21 16.520 -79.169 -15.286 1.00 0.00 C +ATOM 341 O VAL 21 15.832 -79.207 -16.259 1.00 0.00 O +ATOM 342 N ASP 22 17.764 -79.653 -15.258 1.00 0.00 N +ATOM 343 H ASP 22 18.362 -79.494 -14.459 1.00 0.00 H +ATOM 344 CA ASP 22 18.500 -80.306 -16.358 1.00 0.00 C +ATOM 345 HA ASP 22 17.804 -80.945 -16.901 1.00 0.00 H +ATOM 346 CB ASP 22 19.034 -79.192 -17.207 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.313 -78.379 -17.285 1.00 0.00 H +ATOM 348 HB3 ASP 22 19.898 -78.724 -16.734 1.00 0.00 H +ATOM 349 CG ASP 22 19.508 -79.486 -18.629 1.00 0.00 C +ATOM 350 OD1 ASP 22 19.441 -78.567 -19.470 1.00 0.00 O +ATOM 351 OD2 ASP 22 20.183 -80.487 -18.890 1.00 0.00 O +ATOM 352 C ASP 22 19.530 -81.215 -15.850 1.00 0.00 C +ATOM 353 O ASP 22 20.216 -80.803 -14.855 1.00 0.00 O +ATOM 354 N ALA 23 19.887 -82.265 -16.574 1.00 0.00 N +ATOM 355 H ALA 23 19.287 -82.664 -17.282 1.00 0.00 H +ATOM 356 CA ALA 23 21.022 -83.095 -16.330 1.00 0.00 C +ATOM 357 HA ALA 23 20.808 -83.448 -15.321 1.00 0.00 H +ATOM 358 CB ALA 23 21.103 -84.328 -17.259 1.00 0.00 C +ATOM 359 HB1 ALA 23 21.837 -85.049 -16.900 1.00 0.00 H +ATOM 360 HB2 ALA 23 21.431 -84.040 -18.257 1.00 0.00 H +ATOM 361 HB3 ALA 23 20.101 -84.758 -17.248 1.00 0.00 H +ATOM 362 C ALA 23 22.376 -82.323 -16.319 1.00 0.00 C +ATOM 363 O ALA 23 23.234 -82.627 -15.520 1.00 0.00 O +ATOM 364 N ALA 24 22.512 -81.228 -17.039 1.00 0.00 N +ATOM 365 H ALA 24 21.710 -80.873 -17.540 1.00 0.00 H +ATOM 366 CA ALA 24 23.616 -80.232 -16.806 1.00 0.00 C +ATOM 367 HA ALA 24 24.594 -80.629 -17.077 1.00 0.00 H +ATOM 368 CB ALA 24 23.301 -78.994 -17.693 1.00 0.00 C +ATOM 369 HB1 ALA 24 22.323 -78.615 -17.398 1.00 0.00 H +ATOM 370 HB2 ALA 24 23.575 -79.210 -18.726 1.00 0.00 H +ATOM 371 HB3 ALA 24 24.043 -78.255 -17.392 1.00 0.00 H +ATOM 372 C ALA 24 23.824 -79.790 -15.348 1.00 0.00 C +ATOM 373 O ALA 24 24.904 -79.621 -14.796 1.00 0.00 O +ATOM 374 N GLU 25 22.695 -79.523 -14.770 1.00 0.00 N +ATOM 375 H GLU 25 21.849 -79.654 -15.306 1.00 0.00 H +ATOM 376 CA GLU 25 22.599 -79.083 -13.374 1.00 0.00 C +ATOM 377 HA GLU 25 23.531 -78.594 -13.089 1.00 0.00 H +ATOM 378 CB GLU 25 21.340 -78.169 -13.189 1.00 0.00 C +ATOM 379 HB2 GLU 25 20.450 -78.794 -13.258 1.00 0.00 H +ATOM 380 HB3 GLU 25 21.254 -77.894 -12.137 1.00 0.00 H +ATOM 381 CG GLU 25 21.357 -76.967 -14.124 1.00 0.00 C +ATOM 382 HG2 GLU 25 21.217 -77.352 -15.134 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.472 -76.381 -13.876 1.00 0.00 H +ATOM 384 CD GLU 25 22.687 -76.201 -14.041 1.00 0.00 C +ATOM 385 OE1 GLU 25 23.194 -76.064 -12.860 1.00 0.00 O +ATOM 386 OE2 GLU 25 23.186 -75.655 -15.060 1.00 0.00 O +ATOM 387 C GLU 25 22.549 -80.351 -12.395 1.00 0.00 C +ATOM 388 O GLU 25 23.253 -80.366 -11.394 1.00 0.00 O +ATOM 389 N ALA 26 21.824 -81.421 -12.730 1.00 0.00 N +ATOM 390 H ALA 26 21.233 -81.317 -13.542 1.00 0.00 H +ATOM 391 CA ALA 26 21.849 -82.650 -11.870 1.00 0.00 C +ATOM 392 HA ALA 26 21.529 -82.277 -10.897 1.00 0.00 H +ATOM 393 CB ALA 26 20.813 -83.568 -12.481 1.00 0.00 C +ATOM 394 HB1 ALA 26 20.621 -84.357 -11.753 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.203 -84.030 -13.388 1.00 0.00 H +ATOM 396 HB3 ALA 26 19.893 -83.019 -12.680 1.00 0.00 H +ATOM 397 C ALA 26 23.235 -83.380 -11.689 1.00 0.00 C +ATOM 398 O ALA 26 23.407 -84.135 -10.717 1.00 0.00 O +ATOM 399 N GLU 27 24.133 -83.095 -12.605 1.00 0.00 N +ATOM 400 H GLU 27 23.866 -82.484 -13.363 1.00 0.00 H +ATOM 401 CA GLU 27 25.548 -83.485 -12.592 1.00 0.00 C +ATOM 402 HA GLU 27 25.573 -84.566 -12.729 1.00 0.00 H +ATOM 403 CB GLU 27 26.170 -82.805 -13.849 1.00 0.00 C +ATOM 404 HB2 GLU 27 25.642 -83.036 -14.774 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.186 -81.720 -13.751 1.00 0.00 H +ATOM 406 CG GLU 27 27.625 -83.195 -14.123 1.00 0.00 C +ATOM 407 HG2 GLU 27 28.132 -83.404 -13.181 1.00 0.00 H +ATOM 408 HG3 GLU 27 27.575 -84.108 -14.716 1.00 0.00 H +ATOM 409 CD GLU 27 28.419 -82.182 -14.992 1.00 0.00 C +ATOM 410 OE1 GLU 27 28.220 -82.008 -16.202 1.00 0.00 O +ATOM 411 OE2 GLU 27 28.967 -81.273 -14.360 1.00 0.00 O +ATOM 412 C GLU 27 26.299 -83.116 -11.339 1.00 0.00 C +ATOM 413 O GLU 27 27.086 -83.910 -10.801 1.00 0.00 O +ATOM 414 N LYS 28 25.835 -82.009 -10.737 1.00 0.00 N +ATOM 415 H LYS 28 25.059 -81.552 -11.194 1.00 0.00 H +ATOM 416 CA LYS 28 26.357 -81.482 -9.497 1.00 0.00 C +ATOM 417 HA LYS 28 27.364 -81.130 -9.718 1.00 0.00 H +ATOM 418 CB LYS 28 25.694 -80.144 -9.067 1.00 0.00 C +ATOM 419 HB2 LYS 28 25.581 -79.516 -9.951 1.00 0.00 H +ATOM 420 HB3 LYS 28 24.654 -80.217 -8.751 1.00 0.00 H +ATOM 421 CG LYS 28 26.375 -79.258 -7.917 1.00 0.00 C +ATOM 422 HG2 LYS 28 26.404 -79.905 -7.040 1.00 0.00 H +ATOM 423 HG3 LYS 28 27.367 -79.042 -8.313 1.00 0.00 H +ATOM 424 CD LYS 28 25.648 -77.972 -7.582 1.00 0.00 C +ATOM 425 HD2 LYS 28 25.839 -77.270 -8.394 1.00 0.00 H +ATOM 426 HD3 LYS 28 24.571 -78.129 -7.536 1.00 0.00 H +ATOM 427 CE LYS 28 26.314 -77.483 -6.290 1.00 0.00 C +ATOM 428 HE2 LYS 28 25.763 -76.653 -5.846 1.00 0.00 H +ATOM 429 HE3 LYS 28 26.301 -78.317 -5.589 1.00 0.00 H +ATOM 430 NZ LYS 28 27.696 -76.918 -6.442 1.00 0.00 N +ATOM 431 HZ1 LYS 28 27.767 -76.382 -7.295 1.00 0.00 H +ATOM 432 HZ2 LYS 28 28.406 -77.625 -6.568 1.00 0.00 H +ATOM 433 HZ3 LYS 28 27.957 -76.424 -5.601 1.00 0.00 H +ATOM 434 C LYS 28 26.328 -82.549 -8.348 1.00 0.00 C +ATOM 435 O LYS 28 27.352 -82.637 -7.694 1.00 0.00 O +ATOM 436 N PHE 29 25.282 -83.347 -8.039 1.00 0.00 N +ATOM 437 H PHE 29 24.514 -83.324 -8.695 1.00 0.00 H +ATOM 438 CA PHE 29 25.273 -84.345 -6.919 1.00 0.00 C +ATOM 439 HA PHE 29 25.532 -83.867 -5.974 1.00 0.00 H +ATOM 440 CB PHE 29 23.802 -84.890 -6.809 1.00 0.00 C +ATOM 441 HB2 PHE 29 23.707 -85.702 -7.530 1.00 0.00 H +ATOM 442 HB3 PHE 29 23.665 -85.405 -5.858 1.00 0.00 H +ATOM 443 CG PHE 29 22.655 -83.900 -6.983 1.00 0.00 C +ATOM 444 CD1 PHE 29 22.540 -82.858 -6.095 1.00 0.00 C +ATOM 445 HD1 PHE 29 23.194 -82.707 -5.249 1.00 0.00 H +ATOM 446 CE1 PHE 29 21.544 -81.867 -6.265 1.00 0.00 C +ATOM 447 HE1 PHE 29 21.440 -81.043 -5.574 1.00 0.00 H +ATOM 448 CZ PHE 29 20.580 -82.037 -7.278 1.00 0.00 C +ATOM 449 HZ PHE 29 19.777 -81.315 -7.275 1.00 0.00 H +ATOM 450 CE2 PHE 29 20.619 -83.073 -8.226 1.00 0.00 C +ATOM 451 HE2 PHE 29 19.894 -83.255 -9.006 1.00 0.00 H +ATOM 452 CD2 PHE 29 21.666 -84.036 -8.052 1.00 0.00 C +ATOM 453 HD2 PHE 29 21.707 -84.820 -8.794 1.00 0.00 H +ATOM 454 C PHE 29 26.260 -85.532 -7.120 1.00 0.00 C +ATOM 455 O PHE 29 26.896 -85.969 -6.157 1.00 0.00 O +ATOM 456 N THR 30 26.568 -85.994 -8.303 1.00 0.00 N +ATOM 457 H THR 30 26.214 -85.534 -9.130 1.00 0.00 H +ATOM 458 CA THR 30 27.720 -86.953 -8.655 1.00 0.00 C +ATOM 459 HA THR 30 27.731 -87.734 -7.894 1.00 0.00 H +ATOM 460 CB THR 30 27.677 -87.542 -10.058 1.00 0.00 C +ATOM 461 HB THR 30 27.474 -86.712 -10.734 1.00 0.00 H +ATOM 462 CG2 THR 30 28.868 -88.482 -10.484 1.00 0.00 C +ATOM 463 HG21 THR 30 29.210 -89.157 -9.699 1.00 0.00 H +ATOM 464 HG22 THR 30 28.649 -89.107 -11.349 1.00 0.00 H +ATOM 465 HG23 THR 30 29.728 -87.882 -10.783 1.00 0.00 H +ATOM 466 OG1 THR 30 26.530 -88.343 -10.163 1.00 0.00 O +ATOM 467 HG1 THR 30 25.755 -87.828 -10.398 1.00 0.00 H +ATOM 468 C THR 30 29.039 -86.178 -8.583 1.00 0.00 C +ATOM 469 O THR 30 29.940 -86.650 -7.973 1.00 0.00 O +ATOM 470 N LYS 31 29.078 -84.929 -9.053 1.00 0.00 N +ATOM 471 H LYS 31 28.313 -84.478 -9.534 1.00 0.00 H +ATOM 472 CA LYS 31 30.265 -84.093 -8.947 1.00 0.00 C +ATOM 473 HA LYS 31 31.135 -84.617 -9.341 1.00 0.00 H +ATOM 474 CB LYS 31 30.110 -82.812 -9.831 1.00 0.00 C +ATOM 475 HB2 LYS 31 30.100 -83.105 -10.880 1.00 0.00 H +ATOM 476 HB3 LYS 31 29.158 -82.370 -9.537 1.00 0.00 H +ATOM 477 CG LYS 31 31.078 -81.644 -9.608 1.00 0.00 C +ATOM 478 HG2 LYS 31 30.681 -80.755 -10.099 1.00 0.00 H +ATOM 479 HG3 LYS 31 31.104 -81.348 -8.559 1.00 0.00 H +ATOM 480 CD LYS 31 32.520 -81.846 -9.978 1.00 0.00 C +ATOM 481 HD2 LYS 31 33.140 -81.568 -9.125 1.00 0.00 H +ATOM 482 HD3 LYS 31 32.672 -82.917 -10.109 1.00 0.00 H +ATOM 483 CE LYS 31 32.836 -80.977 -11.240 1.00 0.00 C +ATOM 484 HE2 LYS 31 32.437 -81.420 -12.151 1.00 0.00 H +ATOM 485 HE3 LYS 31 32.412 -79.979 -11.128 1.00 0.00 H +ATOM 486 NZ LYS 31 34.314 -80.918 -11.522 1.00 0.00 N +ATOM 487 HZ1 LYS 31 34.557 -81.898 -11.553 1.00 0.00 H +ATOM 488 HZ2 LYS 31 34.937 -80.575 -10.804 1.00 0.00 H +ATOM 489 HZ3 LYS 31 34.516 -80.533 -12.434 1.00 0.00 H +ATOM 490 C LYS 31 30.750 -83.676 -7.488 1.00 0.00 C +ATOM 491 O LYS 31 32.000 -83.554 -7.221 1.00 0.00 O +ATOM 492 N ALA 32 29.792 -83.554 -6.606 1.00 0.00 N +ATOM 493 H ALA 32 28.839 -83.565 -6.939 1.00 0.00 H +ATOM 494 CA ALA 32 30.051 -83.253 -5.189 1.00 0.00 C +ATOM 495 HA ALA 32 30.741 -82.411 -5.150 1.00 0.00 H +ATOM 496 CB ALA 32 28.722 -82.868 -4.484 1.00 0.00 C +ATOM 497 HB1 ALA 32 28.241 -82.061 -5.037 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.143 -83.791 -4.475 1.00 0.00 H +ATOM 499 HB3 ALA 32 29.005 -82.530 -3.487 1.00 0.00 H +ATOM 500 C ALA 32 30.685 -84.514 -4.421 1.00 0.00 C +ATOM 501 O ALA 32 31.547 -84.294 -3.599 1.00 0.00 O +ATOM 502 N ASP 33 30.317 -85.727 -4.808 1.00 0.00 N +ATOM 503 H ASP 33 29.675 -85.732 -5.587 1.00 0.00 H +ATOM 504 CA ASP 33 31.099 -86.941 -4.397 1.00 0.00 C +ATOM 505 HA ASP 33 31.146 -86.865 -3.311 1.00 0.00 H +ATOM 506 CB ASP 33 30.259 -88.177 -4.775 1.00 0.00 C +ATOM 507 HB2 ASP 33 30.236 -88.098 -5.862 1.00 0.00 H +ATOM 508 HB3 ASP 33 30.785 -89.100 -4.535 1.00 0.00 H +ATOM 509 CG ASP 33 28.864 -88.254 -4.222 1.00 0.00 C +ATOM 510 OD1 ASP 33 28.470 -87.531 -3.234 1.00 0.00 O +ATOM 511 OD2 ASP 33 28.053 -89.021 -4.796 1.00 0.00 O +ATOM 512 C ASP 33 32.496 -87.088 -4.872 1.00 0.00 C +ATOM 513 O ASP 33 33.287 -87.765 -4.230 1.00 0.00 O +ATOM 514 N ALA 34 32.771 -86.590 -6.076 1.00 0.00 N +ATOM 515 H ALA 34 32.015 -86.491 -6.738 1.00 0.00 H +ATOM 516 CA ALA 34 34.130 -86.599 -6.577 1.00 0.00 C +ATOM 517 HA ALA 34 34.692 -87.491 -6.301 1.00 0.00 H +ATOM 518 CB ALA 34 34.183 -86.370 -8.076 1.00 0.00 C +ATOM 519 HB1 ALA 34 33.706 -87.227 -8.551 1.00 0.00 H +ATOM 520 HB2 ALA 34 35.162 -86.007 -8.388 1.00 0.00 H +ATOM 521 HB3 ALA 34 33.497 -85.564 -8.337 1.00 0.00 H +ATOM 522 C ALA 34 34.931 -85.470 -5.815 1.00 0.00 C +ATOM 523 O ALA 34 36.153 -85.665 -5.584 1.00 0.00 O +ATOM 524 N ASN 35 34.243 -84.334 -5.512 1.00 0.00 N +ATOM 525 H ASN 35 33.310 -84.274 -5.894 1.00 0.00 H +ATOM 526 CA ASN 35 34.883 -83.188 -4.782 1.00 0.00 C +ATOM 527 HA ASN 35 35.797 -83.022 -5.353 1.00 0.00 H +ATOM 528 CB ASN 35 33.968 -81.968 -4.646 1.00 0.00 C +ATOM 529 HB2 ASN 35 33.035 -82.281 -4.179 1.00 0.00 H +ATOM 530 HB3 ASN 35 34.485 -81.346 -3.915 1.00 0.00 H +ATOM 531 CG ASN 35 33.699 -81.200 -5.925 1.00 0.00 C +ATOM 532 OD1 ASN 35 34.498 -81.215 -6.836 1.00 0.00 O +ATOM 533 ND2 ASN 35 32.619 -80.445 -5.917 1.00 0.00 N +ATOM 534 HD21 ASN 35 32.072 -80.448 -5.068 1.00 0.00 H +ATOM 535 HD22 ASN 35 32.644 -79.711 -6.610 1.00 0.00 H +ATOM 536 C ASN 35 35.241 -83.673 -3.378 1.00 0.00 C +ATOM 537 O ASN 35 36.305 -83.328 -2.871 1.00 0.00 O +ATOM 538 N ASP 36 34.624 -84.670 -2.728 1.00 0.00 N +ATOM 539 H ASP 36 33.639 -84.770 -2.929 1.00 0.00 H +ATOM 540 CA ASP 36 35.062 -85.271 -1.402 1.00 0.00 C +ATOM 541 HA ASP 36 35.371 -84.506 -0.690 1.00 0.00 H +ATOM 542 CB ASP 36 33.859 -86.145 -0.992 1.00 0.00 C +ATOM 543 HB2 ASP 36 32.924 -85.681 -1.307 1.00 0.00 H +ATOM 544 HB3 ASP 36 34.054 -87.099 -1.483 1.00 0.00 H +ATOM 545 CG ASP 36 33.640 -86.187 0.521 1.00 0.00 C +ATOM 546 OD1 ASP 36 32.659 -86.821 0.996 1.00 0.00 O +ATOM 547 OD2 ASP 36 34.437 -85.521 1.241 1.00 0.00 O +ATOM 548 C ASP 36 36.305 -86.239 -1.606 1.00 0.00 C +ATOM 549 O ASP 36 37.105 -86.472 -0.700 1.00 0.00 O +ATOM 550 N LYS 37 36.478 -86.769 -2.808 1.00 0.00 N +ATOM 551 H LYS 37 35.743 -86.515 -3.452 1.00 0.00 H +ATOM 552 CA LYS 37 37.546 -87.679 -3.265 1.00 0.00 C +ATOM 553 HA LYS 37 37.940 -88.130 -2.354 1.00 0.00 H +ATOM 554 CB LYS 37 36.974 -88.825 -4.204 1.00 0.00 C +ATOM 555 HB2 LYS 37 37.760 -89.300 -4.792 1.00 0.00 H +ATOM 556 HB3 LYS 37 36.354 -88.360 -4.971 1.00 0.00 H +ATOM 557 CG LYS 37 36.052 -89.765 -3.444 1.00 0.00 C +ATOM 558 HG2 LYS 37 35.154 -89.232 -3.132 1.00 0.00 H +ATOM 559 HG3 LYS 37 36.635 -90.186 -2.624 1.00 0.00 H +ATOM 560 CD LYS 37 35.650 -90.919 -4.295 1.00 0.00 C +ATOM 561 HD2 LYS 37 36.611 -91.335 -4.597 1.00 0.00 H +ATOM 562 HD3 LYS 37 35.052 -91.580 -3.667 1.00 0.00 H +ATOM 563 CE LYS 37 34.876 -90.655 -5.639 1.00 0.00 C +ATOM 564 HE2 LYS 37 35.290 -89.758 -6.099 1.00 0.00 H +ATOM 565 HE3 LYS 37 34.954 -91.522 -6.295 1.00 0.00 H +ATOM 566 NZ LYS 37 33.477 -90.342 -5.129 1.00 0.00 N +ATOM 567 HZ1 LYS 37 32.928 -89.997 -5.903 1.00 0.00 H +ATOM 568 HZ2 LYS 37 32.989 -91.206 -4.941 1.00 0.00 H +ATOM 569 HZ3 LYS 37 33.400 -89.748 -4.316 1.00 0.00 H +ATOM 570 C LYS 37 38.735 -86.967 -3.941 1.00 0.00 C +ATOM 571 O LYS 37 39.704 -87.565 -4.438 1.00 0.00 O +ATOM 572 N GLY 38 38.633 -85.631 -3.794 1.00 0.00 N +ATOM 573 H GLY 38 37.818 -85.242 -3.343 1.00 0.00 H +ATOM 574 CA GLY 38 39.672 -84.680 -4.187 1.00 0.00 C +ATOM 575 HA2 GLY 38 39.167 -83.729 -4.019 1.00 0.00 H +ATOM 576 HA3 GLY 38 40.564 -84.680 -3.561 1.00 0.00 H +ATOM 577 C GLY 38 40.029 -84.651 -5.701 1.00 0.00 C +ATOM 578 O GLY 38 41.132 -84.214 -6.030 1.00 0.00 O +ATOM 579 N VAL 39 39.039 -84.904 -6.587 1.00 0.00 N +ATOM 580 H VAL 39 38.120 -85.105 -6.220 1.00 0.00 H +ATOM 581 CA VAL 39 39.308 -84.823 -8.044 1.00 0.00 C +ATOM 582 HA VAL 39 40.348 -84.954 -8.341 1.00 0.00 H +ATOM 583 CB VAL 39 38.639 -86.029 -8.760 1.00 0.00 C +ATOM 584 HB VAL 39 37.565 -86.020 -8.575 1.00 0.00 H +ATOM 585 CG1 VAL 39 38.829 -85.925 -10.351 1.00 0.00 C +ATOM 586 HG11 VAL 39 39.882 -85.834 -10.617 1.00 0.00 H +ATOM 587 HG12 VAL 39 38.278 -85.061 -10.723 1.00 0.00 H +ATOM 588 HG13 VAL 39 38.538 -86.850 -10.849 1.00 0.00 H +ATOM 589 CG2 VAL 39 39.202 -87.302 -8.230 1.00 0.00 C +ATOM 590 HG21 VAL 39 40.290 -87.270 -8.278 1.00 0.00 H +ATOM 591 HG22 VAL 39 38.807 -88.118 -8.836 1.00 0.00 H +ATOM 592 HG23 VAL 39 38.956 -87.427 -7.176 1.00 0.00 H +ATOM 593 C VAL 39 38.762 -83.491 -8.644 1.00 0.00 C +ATOM 594 O VAL 39 37.723 -83.035 -8.222 1.00 0.00 O +ATOM 595 N ASP 40 39.525 -82.873 -9.521 1.00 0.00 N +ATOM 596 H ASP 40 40.501 -83.133 -9.525 1.00 0.00 H +ATOM 597 CA ASP 40 39.120 -81.536 -10.078 1.00 0.00 C +ATOM 598 HA ASP 40 38.254 -81.192 -9.512 1.00 0.00 H +ATOM 599 CB ASP 40 40.273 -80.479 -10.189 1.00 0.00 C +ATOM 600 HB2 ASP 40 41.099 -80.945 -10.726 1.00 0.00 H +ATOM 601 HB3 ASP 40 39.917 -79.604 -10.734 1.00 0.00 H +ATOM 602 CG ASP 40 40.868 -80.216 -8.842 1.00 0.00 C +ATOM 603 OD1 ASP 40 40.263 -80.534 -7.752 1.00 0.00 O +ATOM 604 OD2 ASP 40 41.970 -79.636 -8.862 1.00 0.00 O +ATOM 605 C ASP 40 38.489 -81.653 -11.530 1.00 0.00 C +ATOM 606 O ASP 40 37.742 -80.765 -11.904 1.00 0.00 O +ATOM 607 N GLY 41 38.640 -82.868 -12.190 1.00 0.00 N +ATOM 608 H GLY 41 39.198 -83.606 -11.785 1.00 0.00 H +ATOM 609 CA GLY 41 37.920 -83.266 -13.452 1.00 0.00 C +ATOM 610 HA2 GLY 41 38.262 -82.519 -14.168 1.00 0.00 H +ATOM 611 HA3 GLY 41 38.245 -84.286 -13.660 1.00 0.00 H +ATOM 612 C GLY 41 36.368 -83.317 -13.374 1.00 0.00 C +ATOM 613 O GLY 41 35.813 -82.997 -12.329 1.00 0.00 O +ATOM 614 N GLU 42 35.794 -83.687 -14.525 1.00 0.00 N +ATOM 615 H GLU 42 36.373 -84.063 -15.263 1.00 0.00 H +ATOM 616 CA GLU 42 34.321 -83.568 -14.896 1.00 0.00 C +ATOM 617 HA GLU 42 33.845 -83.080 -14.045 1.00 0.00 H +ATOM 618 CB GLU 42 34.206 -82.664 -16.160 1.00 0.00 C +ATOM 619 HB2 GLU 42 34.883 -83.053 -16.920 1.00 0.00 H +ATOM 620 HB3 GLU 42 33.167 -82.760 -16.476 1.00 0.00 H +ATOM 621 CG GLU 42 34.624 -81.183 -16.032 1.00 0.00 C +ATOM 622 HG2 GLU 42 35.702 -81.220 -15.872 1.00 0.00 H +ATOM 623 HG3 GLU 42 34.352 -80.681 -16.960 1.00 0.00 H +ATOM 624 CD GLU 42 34.062 -80.445 -14.799 1.00 0.00 C +ATOM 625 OE1 GLU 42 34.806 -79.703 -14.135 1.00 0.00 O +ATOM 626 OE2 GLU 42 32.856 -80.666 -14.520 1.00 0.00 O +ATOM 627 C GLU 42 33.723 -84.893 -15.217 1.00 0.00 C +ATOM 628 O GLU 42 34.229 -85.711 -16.008 1.00 0.00 O +ATOM 629 N TRP 43 32.472 -85.099 -14.864 1.00 0.00 N +ATOM 630 H TRP 43 32.004 -84.362 -14.354 1.00 0.00 H +ATOM 631 CA TRP 43 31.559 -86.149 -15.266 1.00 0.00 C +ATOM 632 HA TRP 43 32.122 -87.059 -15.475 1.00 0.00 H +ATOM 633 CB TRP 43 30.773 -86.399 -13.993 1.00 0.00 C +ATOM 634 HB2 TRP 43 30.445 -85.442 -13.590 1.00 0.00 H +ATOM 635 HB3 TRP 43 29.902 -86.912 -14.400 1.00 0.00 H +ATOM 636 CG TRP 43 31.344 -87.366 -13.025 1.00 0.00 C +ATOM 637 CD1 TRP 43 30.977 -88.654 -12.958 1.00 0.00 C +ATOM 638 HD1 TRP 43 30.140 -89.145 -13.431 1.00 0.00 H +ATOM 639 NE1 TRP 43 31.855 -89.340 -12.098 1.00 0.00 N +ATOM 640 HE1 TRP 43 31.778 -90.336 -11.949 1.00 0.00 H +ATOM 641 CE2 TRP 43 32.922 -88.547 -11.757 1.00 0.00 C +ATOM 642 CZ2 TRP 43 34.166 -88.846 -11.149 1.00 0.00 C +ATOM 643 HZ2 TRP 43 34.397 -89.836 -10.784 1.00 0.00 H +ATOM 644 CH2 TRP 43 35.047 -87.784 -10.958 1.00 0.00 C +ATOM 645 HH2 TRP 43 35.979 -87.838 -10.414 1.00 0.00 H +ATOM 646 CZ3 TRP 43 34.743 -86.520 -11.397 1.00 0.00 C +ATOM 647 HZ3 TRP 43 35.454 -85.709 -11.339 1.00 0.00 H +ATOM 648 CE3 TRP 43 33.535 -86.262 -12.048 1.00 0.00 C +ATOM 649 HE3 TRP 43 33.353 -85.274 -12.444 1.00 0.00 H +ATOM 650 CD2 TRP 43 32.590 -87.304 -12.240 1.00 0.00 C +ATOM 651 C TRP 43 30.625 -85.872 -16.551 1.00 0.00 C +ATOM 652 O TRP 43 30.358 -84.719 -16.878 1.00 0.00 O +ATOM 653 N THR 44 29.980 -86.921 -17.068 1.00 0.00 N +ATOM 654 H THR 44 30.065 -87.857 -16.700 1.00 0.00 H +ATOM 655 CA THR 44 29.064 -86.818 -18.209 1.00 0.00 C +ATOM 656 HA THR 44 28.508 -85.882 -18.159 1.00 0.00 H +ATOM 657 CB THR 44 29.919 -86.740 -19.518 1.00 0.00 C +ATOM 658 HB THR 44 30.459 -85.794 -19.466 1.00 0.00 H +ATOM 659 CG2 THR 44 30.771 -87.948 -19.790 1.00 0.00 C +ATOM 660 HG21 THR 44 30.120 -88.766 -20.098 1.00 0.00 H +ATOM 661 HG22 THR 44 31.437 -88.184 -18.959 1.00 0.00 H +ATOM 662 HG23 THR 44 31.463 -87.787 -20.617 1.00 0.00 H +ATOM 663 OG1 THR 44 29.068 -86.560 -20.594 1.00 0.00 O +ATOM 664 HG1 THR 44 28.808 -85.641 -20.503 1.00 0.00 H +ATOM 665 C THR 44 28.048 -88.016 -18.230 1.00 0.00 C +ATOM 666 O THR 44 28.355 -89.058 -17.645 1.00 0.00 O +ATOM 667 N TYR 45 26.831 -87.836 -18.764 1.00 0.00 N +ATOM 668 H TYR 45 26.689 -86.985 -19.288 1.00 0.00 H +ATOM 669 CA TYR 45 25.726 -88.735 -18.635 1.00 0.00 C +ATOM 670 HA TYR 45 25.852 -89.280 -17.699 1.00 0.00 H +ATOM 671 CB TYR 45 24.438 -87.884 -18.588 1.00 0.00 C +ATOM 672 HB2 TYR 45 24.628 -86.944 -18.069 1.00 0.00 H +ATOM 673 HB3 TYR 45 24.221 -87.408 -19.544 1.00 0.00 H +ATOM 674 CG TYR 45 23.094 -88.484 -18.038 1.00 0.00 C +ATOM 675 CD1 TYR 45 23.160 -89.362 -16.969 1.00 0.00 C +ATOM 676 HD1 TYR 45 24.082 -89.540 -16.435 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.976 -89.791 -16.403 1.00 0.00 C +ATOM 678 HE1 TYR 45 21.959 -90.263 -15.432 1.00 0.00 H +ATOM 679 CZ TYR 45 20.714 -89.447 -16.978 1.00 0.00 C +ATOM 680 OH TYR 45 19.557 -89.983 -16.504 1.00 0.00 O +ATOM 681 HH TYR 45 18.831 -89.831 -17.115 1.00 0.00 H +ATOM 682 CE2 TYR 45 20.730 -88.726 -18.198 1.00 0.00 C +ATOM 683 HE2 TYR 45 19.820 -88.479 -18.725 1.00 0.00 H +ATOM 684 CD2 TYR 45 21.901 -88.246 -18.761 1.00 0.00 C +ATOM 685 HD2 TYR 45 21.916 -87.641 -19.656 1.00 0.00 H +ATOM 686 C TYR 45 25.543 -89.778 -19.711 1.00 0.00 C +ATOM 687 O TYR 45 25.315 -89.493 -20.928 1.00 0.00 O +ATOM 688 N ASP 46 25.566 -91.056 -19.274 1.00 0.00 N +ATOM 689 H ASP 46 25.646 -91.252 -18.287 1.00 0.00 H +ATOM 690 CA ASP 46 25.399 -92.238 -20.057 1.00 0.00 C +ATOM 691 HA ASP 46 25.861 -92.128 -21.039 1.00 0.00 H +ATOM 692 CB ASP 46 26.144 -93.411 -19.409 1.00 0.00 C +ATOM 693 HB2 ASP 46 27.146 -93.143 -19.074 1.00 0.00 H +ATOM 694 HB3 ASP 46 25.629 -93.609 -18.469 1.00 0.00 H +ATOM 695 CG ASP 46 26.175 -94.707 -20.228 1.00 0.00 C +ATOM 696 OD1 ASP 46 26.716 -95.697 -19.631 1.00 0.00 O +ATOM 697 OD2 ASP 46 25.503 -94.820 -21.261 1.00 0.00 O +ATOM 698 C ASP 46 23.932 -92.492 -20.333 1.00 0.00 C +ATOM 699 O ASP 46 23.138 -92.910 -19.496 1.00 0.00 O +ATOM 700 N ASP 47 23.631 -92.314 -21.599 1.00 0.00 N +ATOM 701 H ASP 47 24.346 -91.959 -22.218 1.00 0.00 H +ATOM 702 CA ASP 47 22.340 -92.617 -22.117 1.00 0.00 C +ATOM 703 HA ASP 47 21.652 -92.020 -21.518 1.00 0.00 H +ATOM 704 CB ASP 47 22.249 -92.036 -23.584 1.00 0.00 C +ATOM 705 HB2 ASP 47 22.490 -90.976 -23.510 1.00 0.00 H +ATOM 706 HB3 ASP 47 22.971 -92.574 -24.198 1.00 0.00 H +ATOM 707 CG ASP 47 20.879 -91.996 -24.168 1.00 0.00 C +ATOM 708 OD1 ASP 47 19.892 -91.899 -23.412 1.00 0.00 O +ATOM 709 OD2 ASP 47 20.824 -92.104 -25.414 1.00 0.00 O +ATOM 710 C ASP 47 21.936 -94.144 -22.003 1.00 0.00 C +ATOM 711 O ASP 47 20.755 -94.463 -21.884 1.00 0.00 O +ATOM 712 N ALA 48 22.940 -95.063 -22.092 1.00 0.00 N +ATOM 713 H ALA 48 23.912 -94.808 -22.191 1.00 0.00 H +ATOM 714 CA ALA 48 22.723 -96.503 -22.055 1.00 0.00 C +ATOM 715 HA ALA 48 21.840 -96.771 -22.634 1.00 0.00 H +ATOM 716 CB ALA 48 23.902 -97.234 -22.668 1.00 0.00 C +ATOM 717 HB1 ALA 48 23.801 -98.319 -22.628 1.00 0.00 H +ATOM 718 HB2 ALA 48 24.876 -96.899 -22.313 1.00 0.00 H +ATOM 719 HB3 ALA 48 23.866 -96.947 -23.719 1.00 0.00 H +ATOM 720 C ALA 48 22.432 -96.954 -20.675 1.00 0.00 C +ATOM 721 O ALA 48 21.804 -97.992 -20.494 1.00 0.00 O +ATOM 722 N THR 49 22.936 -96.316 -19.626 1.00 0.00 N +ATOM 723 H THR 49 23.607 -95.586 -19.819 1.00 0.00 H +ATOM 724 CA THR 49 22.668 -96.635 -18.204 1.00 0.00 C +ATOM 725 HA THR 49 22.144 -97.591 -18.195 1.00 0.00 H +ATOM 726 CB THR 49 23.990 -96.903 -17.431 1.00 0.00 C +ATOM 727 HB THR 49 23.713 -96.979 -16.379 1.00 0.00 H +ATOM 728 CG2 THR 49 24.580 -98.189 -18.022 1.00 0.00 C +ATOM 729 HG21 THR 49 25.479 -98.427 -17.454 1.00 0.00 H +ATOM 730 HG22 THR 49 24.820 -98.119 -19.083 1.00 0.00 H +ATOM 731 HG23 THR 49 23.956 -99.082 -17.977 1.00 0.00 H +ATOM 732 OG1 THR 49 24.925 -95.846 -17.530 1.00 0.00 O +ATOM 733 HG1 THR 49 25.597 -96.189 -18.124 1.00 0.00 H +ATOM 734 C THR 49 21.792 -95.719 -17.372 1.00 0.00 C +ATOM 735 O THR 49 21.460 -95.962 -16.260 1.00 0.00 O +ATOM 736 N LYS 50 21.407 -94.555 -17.972 1.00 0.00 N +ATOM 737 H LYS 50 21.601 -94.438 -18.956 1.00 0.00 H +ATOM 738 CA LYS 50 20.772 -93.387 -17.329 1.00 0.00 C +ATOM 739 HA LYS 50 20.953 -92.491 -17.924 1.00 0.00 H +ATOM 740 CB LYS 50 19.258 -93.688 -17.342 1.00 0.00 C +ATOM 741 HB2 LYS 50 19.086 -94.618 -16.800 1.00 0.00 H +ATOM 742 HB3 LYS 50 18.652 -92.949 -16.819 1.00 0.00 H +ATOM 743 CG LYS 50 18.626 -93.829 -18.718 1.00 0.00 C +ATOM 744 HG2 LYS 50 19.285 -94.531 -19.230 1.00 0.00 H +ATOM 745 HG3 LYS 50 17.671 -94.345 -18.618 1.00 0.00 H +ATOM 746 CD LYS 50 18.402 -92.511 -19.488 1.00 0.00 C +ATOM 747 HD2 LYS 50 17.940 -91.814 -18.789 1.00 0.00 H +ATOM 748 HD3 LYS 50 19.367 -92.070 -19.737 1.00 0.00 H +ATOM 749 CE LYS 50 17.486 -92.637 -20.642 1.00 0.00 C +ATOM 750 HE2 LYS 50 16.592 -93.163 -20.308 1.00 0.00 H +ATOM 751 HE3 LYS 50 17.306 -91.667 -21.107 1.00 0.00 H +ATOM 752 NZ LYS 50 18.140 -93.448 -21.747 1.00 0.00 N +ATOM 753 HZ1 LYS 50 17.477 -93.526 -22.504 1.00 0.00 H +ATOM 754 HZ2 LYS 50 18.381 -94.373 -21.421 1.00 0.00 H +ATOM 755 HZ3 LYS 50 18.992 -93.029 -22.094 1.00 0.00 H +ATOM 756 C LYS 50 21.413 -93.123 -16.008 1.00 0.00 C +ATOM 757 O LYS 50 20.838 -93.178 -14.906 1.00 0.00 O +ATOM 758 N THR 51 22.695 -92.826 -16.097 1.00 0.00 N +ATOM 759 H THR 51 23.108 -93.049 -16.991 1.00 0.00 H +ATOM 760 CA THR 51 23.584 -92.669 -15.001 1.00 0.00 C +ATOM 761 HA THR 51 23.200 -92.137 -14.131 1.00 0.00 H +ATOM 762 CB THR 51 23.988 -94.106 -14.535 1.00 0.00 C +ATOM 763 HB THR 51 24.276 -94.733 -15.379 1.00 0.00 H +ATOM 764 CG2 THR 51 25.137 -94.185 -13.556 1.00 0.00 C +ATOM 765 HG21 THR 51 26.090 -94.015 -14.057 1.00 0.00 H +ATOM 766 HG22 THR 51 25.367 -95.214 -13.280 1.00 0.00 H +ATOM 767 HG23 THR 51 25.090 -93.557 -12.666 1.00 0.00 H +ATOM 768 OG1 THR 51 22.956 -94.823 -13.884 1.00 0.00 O +ATOM 769 HG1 THR 51 22.210 -94.765 -14.485 1.00 0.00 H +ATOM 770 C THR 51 24.986 -91.856 -15.325 1.00 0.00 C +ATOM 771 O THR 51 25.532 -91.912 -16.457 1.00 0.00 O +ATOM 772 N PHE 52 25.452 -91.009 -14.397 1.00 0.00 N +ATOM 773 H PHE 52 24.998 -91.085 -13.498 1.00 0.00 H +ATOM 774 CA PHE 52 26.634 -90.197 -14.611 1.00 0.00 C +ATOM 775 HA PHE 52 26.723 -89.758 -15.605 1.00 0.00 H +ATOM 776 CB PHE 52 26.737 -89.040 -13.599 1.00 0.00 C +ATOM 777 HB2 PHE 52 26.498 -89.421 -12.606 1.00 0.00 H +ATOM 778 HB3 PHE 52 27.776 -88.712 -13.576 1.00 0.00 H +ATOM 779 CG PHE 52 26.066 -87.793 -14.020 1.00 0.00 C +ATOM 780 CD1 PHE 52 24.757 -87.518 -13.510 1.00 0.00 C +ATOM 781 HD1 PHE 52 24.500 -88.314 -12.827 1.00 0.00 H +ATOM 782 CE1 PHE 52 23.954 -86.437 -13.968 1.00 0.00 C +ATOM 783 HE1 PHE 52 23.054 -86.157 -13.442 1.00 0.00 H +ATOM 784 CZ PHE 52 24.453 -85.668 -15.035 1.00 0.00 C +ATOM 785 HZ PHE 52 23.875 -84.802 -15.324 1.00 0.00 H +ATOM 786 CE2 PHE 52 25.713 -85.919 -15.624 1.00 0.00 C +ATOM 787 HE2 PHE 52 26.070 -85.218 -16.364 1.00 0.00 H +ATOM 788 CD2 PHE 52 26.522 -87.035 -15.084 1.00 0.00 C +ATOM 789 HD2 PHE 52 27.507 -87.184 -15.502 1.00 0.00 H +ATOM 790 C PHE 52 27.872 -91.135 -14.568 1.00 0.00 C +ATOM 791 O PHE 52 27.771 -92.151 -13.817 1.00 0.00 O +ATOM 792 N THR 53 28.937 -90.753 -15.319 1.00 0.00 N +ATOM 793 H THR 53 28.732 -89.994 -15.952 1.00 0.00 H +ATOM 794 CA THR 53 30.323 -91.326 -15.443 1.00 0.00 C +ATOM 795 HA THR 53 30.729 -91.801 -14.550 1.00 0.00 H +ATOM 796 CB THR 53 30.314 -92.412 -16.571 1.00 0.00 C +ATOM 797 HB THR 53 29.572 -93.189 -16.386 1.00 0.00 H +ATOM 798 CG2 THR 53 29.816 -91.935 -17.943 1.00 0.00 C +ATOM 799 HG21 THR 53 28.727 -91.938 -17.997 1.00 0.00 H +ATOM 800 HG22 THR 53 30.182 -92.634 -18.694 1.00 0.00 H +ATOM 801 HG23 THR 53 30.206 -90.948 -18.194 1.00 0.00 H +ATOM 802 OG1 THR 53 31.579 -93.063 -16.762 1.00 0.00 O +ATOM 803 HG1 THR 53 31.700 -93.638 -16.003 1.00 0.00 H +ATOM 804 C THR 53 31.436 -90.308 -15.786 1.00 0.00 C +ATOM 805 O THR 53 31.127 -89.220 -16.213 1.00 0.00 O +ATOM 806 N VAL 54 32.724 -90.493 -15.347 1.00 0.00 N +ATOM 807 H VAL 54 33.037 -91.300 -14.827 1.00 0.00 H +ATOM 808 CA VAL 54 33.809 -89.447 -15.585 1.00 0.00 C +ATOM 809 HA VAL 54 33.440 -88.465 -15.289 1.00 0.00 H +ATOM 810 CB VAL 54 34.877 -89.781 -14.548 1.00 0.00 C +ATOM 811 HB VAL 54 34.427 -90.048 -13.591 1.00 0.00 H +ATOM 812 CG1 VAL 54 35.775 -90.937 -14.935 1.00 0.00 C +ATOM 813 HG11 VAL 54 36.527 -91.118 -14.167 1.00 0.00 H +ATOM 814 HG12 VAL 54 36.219 -90.855 -15.928 1.00 0.00 H +ATOM 815 HG13 VAL 54 35.210 -91.866 -15.005 1.00 0.00 H +ATOM 816 CG2 VAL 54 35.879 -88.639 -14.351 1.00 0.00 C +ATOM 817 HG21 VAL 54 36.267 -88.238 -15.287 1.00 0.00 H +ATOM 818 HG22 VAL 54 36.604 -88.972 -13.608 1.00 0.00 H +ATOM 819 HG23 VAL 54 35.290 -87.809 -13.961 1.00 0.00 H +ATOM 820 C VAL 54 34.264 -89.371 -17.038 1.00 0.00 C +ATOM 821 O VAL 54 34.258 -90.336 -17.795 1.00 0.00 O +ATOM 822 N THR 55 34.593 -88.162 -17.472 1.00 0.00 N +ATOM 823 H THR 55 34.735 -87.423 -16.798 1.00 0.00 H +ATOM 824 CA THR 55 35.062 -87.902 -18.893 1.00 0.00 C +ATOM 825 HA THR 55 34.295 -88.337 -19.534 1.00 0.00 H +ATOM 826 CB THR 55 35.253 -86.382 -19.172 1.00 0.00 C +ATOM 827 HB THR 55 35.884 -86.294 -20.057 1.00 0.00 H +ATOM 828 CG2 THR 55 34.001 -85.612 -19.507 1.00 0.00 C +ATOM 829 HG21 THR 55 34.281 -84.662 -19.962 1.00 0.00 H +ATOM 830 HG22 THR 55 33.433 -85.343 -18.617 1.00 0.00 H +ATOM 831 HG23 THR 55 33.309 -86.122 -20.177 1.00 0.00 H +ATOM 832 OG1 THR 55 35.935 -85.729 -18.179 1.00 0.00 O +ATOM 833 HG1 THR 55 35.328 -85.646 -17.439 1.00 0.00 H +ATOM 834 C THR 55 36.425 -88.631 -19.042 1.00 0.00 C +ATOM 835 O THR 55 37.213 -88.762 -18.168 1.00 0.00 O +ATOM 836 N GLU 56 36.719 -89.110 -20.215 1.00 0.00 N +ATOM 837 H GLU 56 35.963 -89.006 -20.877 1.00 0.00 H +ATOM 838 CA GLU 56 37.988 -89.782 -20.621 1.00 0.00 C +ATOM 839 HA GLU 56 38.494 -90.090 -19.706 1.00 0.00 H +ATOM 840 CB GLU 56 37.657 -91.122 -21.386 1.00 0.00 C +ATOM 841 HB2 GLU 56 37.142 -91.690 -20.611 1.00 0.00 H +ATOM 842 HB3 GLU 56 37.034 -90.962 -22.265 1.00 0.00 H +ATOM 843 CG GLU 56 38.937 -91.923 -21.686 1.00 0.00 C +ATOM 844 HG2 GLU 56 38.704 -92.607 -22.502 1.00 0.00 H +ATOM 845 HG3 GLU 56 39.736 -91.416 -22.228 1.00 0.00 H +ATOM 846 CD GLU 56 39.546 -92.723 -20.552 1.00 0.00 C +ATOM 847 OE1 GLU 56 40.036 -93.818 -20.817 1.00 0.00 O +ATOM 848 OE2 GLU 56 39.680 -92.135 -19.460 1.00 0.00 O +ATOM 849 C GLU 56 38.931 -88.951 -21.540 1.00 0.00 C +ATOM 850 O GLU 56 40.168 -88.756 -21.205 1.00 0.00 O +ATOM 851 OXT GLU 56 38.464 -88.535 -22.646 1.00 0.00 O +ATOM 852 ZN ZN1 57 22.220 -88.032 -3.317 1.00 0.00 ZN +ATOM 853 N AN1 58 23.432 -87.519 -1.943 1.00 0.00 N +ATOM 854 C AN1 58 25.191 -86.425 -0.472 1.00 0.00 C +ATOM 855 C1 AN1 58 24.251 -87.028 -1.312 1.00 0.00 C +ATOM 856 H AN1 58 25.048 -85.338 -0.427 1.00 0.00 H +ATOM 857 H1 AN1 58 26.209 -86.643 -0.818 1.00 0.00 H +ATOM 858 H2 AN1 58 25.105 -86.893 0.516 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 21.617 -86.776 0.744 1.00 0.00 N +ATOM 860 N2 AZI 59 22.082 -87.644 1.440 1.00 0.00 N +ATOM 861 N3 AZI 59 22.580 -88.500 2.217 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/inp/pdbs/cluster.c4.pdb b/tests/nsga2/inp/pdbs/cluster.c4.pdb new file mode 100644 index 0000000..54c2a31 --- /dev/null +++ b/tests/nsga2/inp/pdbs/cluster.c4.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.742 -82.001 -13.195 1.00 0.00 N +ATOM 2 H1 MET 1 14.660 -81.584 -13.256 1.00 0.00 H +ATOM 3 H2 MET 1 13.346 -81.921 -12.270 1.00 0.00 H +ATOM 4 H3 MET 1 13.166 -81.464 -13.828 1.00 0.00 H +ATOM 5 CA MET 1 13.695 -83.453 -13.524 1.00 0.00 C +ATOM 6 HA MET 1 12.662 -83.726 -13.307 1.00 0.00 H +ATOM 7 CB MET 1 14.014 -83.690 -14.987 1.00 0.00 C +ATOM 8 HB2 MET 1 13.118 -83.478 -15.570 1.00 0.00 H +ATOM 9 HB3 MET 1 14.799 -83.000 -15.296 1.00 0.00 H +ATOM 10 CG MET 1 14.468 -85.152 -15.240 1.00 0.00 C +ATOM 11 HG2 MET 1 15.527 -85.171 -14.983 1.00 0.00 H +ATOM 12 HG3 MET 1 13.937 -85.890 -14.638 1.00 0.00 H +ATOM 13 SD MET 1 14.500 -85.601 -17.012 1.00 0.00 S +ATOM 14 CE MET 1 12.831 -86.320 -17.251 1.00 0.00 C +ATOM 15 HE1 MET 1 12.127 -85.605 -16.825 1.00 0.00 H +ATOM 16 HE2 MET 1 12.743 -87.163 -16.565 1.00 0.00 H +ATOM 17 HE3 MET 1 12.742 -86.570 -18.308 1.00 0.00 H +ATOM 18 C MET 1 14.563 -84.116 -12.464 1.00 0.00 C +ATOM 19 O MET 1 15.647 -83.580 -12.064 1.00 0.00 O +ATOM 20 N GLN 2 14.131 -85.285 -11.892 1.00 0.00 N +ATOM 21 H GLN 2 13.228 -85.659 -12.144 1.00 0.00 H +ATOM 22 CA GLN 2 14.816 -86.157 -10.835 1.00 0.00 C +ATOM 23 HA GLN 2 15.168 -85.566 -9.990 1.00 0.00 H +ATOM 24 CB GLN 2 13.794 -87.177 -10.135 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.219 -87.751 -10.861 1.00 0.00 H +ATOM 26 HB3 GLN 2 14.411 -87.822 -9.508 1.00 0.00 H +ATOM 27 CG GLN 2 12.863 -86.628 -9.037 1.00 0.00 C +ATOM 28 HG2 GLN 2 12.372 -87.465 -8.541 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.457 -86.064 -8.318 1.00 0.00 H +ATOM 30 CD GLN 2 11.784 -85.668 -9.486 1.00 0.00 C +ATOM 31 OE1 GLN 2 11.368 -85.631 -10.637 1.00 0.00 O +ATOM 32 NE2 GLN 2 11.201 -84.845 -8.633 1.00 0.00 N +ATOM 33 HE21 GLN 2 10.492 -84.248 -9.036 1.00 0.00 H +ATOM 34 HE22 GLN 2 11.466 -84.899 -7.660 1.00 0.00 H +ATOM 35 C GLN 2 16.072 -86.794 -11.472 1.00 0.00 C +ATOM 36 O GLN 2 15.915 -87.264 -12.585 1.00 0.00 O +ATOM 37 N TYR 3 17.136 -87.099 -10.748 1.00 0.00 N +ATOM 38 H TYR 3 17.085 -86.687 -9.828 1.00 0.00 H +ATOM 39 CA TYR 3 18.311 -87.773 -11.218 1.00 0.00 C +ATOM 40 HA TYR 3 18.021 -88.415 -12.049 1.00 0.00 H +ATOM 41 CB TYR 3 19.328 -86.679 -11.689 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.468 -86.079 -10.790 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.306 -87.093 -11.932 1.00 0.00 H +ATOM 44 CG TYR 3 18.992 -85.864 -12.904 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.033 -86.517 -14.161 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.485 -87.497 -14.197 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.569 -85.804 -15.280 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.609 -86.256 -16.260 1.00 0.00 H +ATOM 49 CZ TYR 3 18.009 -84.521 -15.132 1.00 0.00 C +ATOM 50 OH TYR 3 17.745 -83.828 -16.286 1.00 0.00 O +ATOM 51 HH TYR 3 17.637 -84.335 -17.094 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.836 -83.937 -13.881 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.336 -82.980 -13.880 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.360 -84.615 -12.779 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.204 -84.203 -11.793 1.00 0.00 H +ATOM 56 C TYR 3 18.893 -88.680 -10.144 1.00 0.00 C +ATOM 57 O TYR 3 19.111 -88.180 -8.985 1.00 0.00 O +ATOM 58 N LYS 4 19.086 -89.936 -10.371 1.00 0.00 N +ATOM 59 H LYS 4 18.893 -90.251 -11.311 1.00 0.00 H +ATOM 60 CA LYS 4 19.763 -90.830 -9.402 1.00 0.00 C +ATOM 61 HA LYS 4 19.378 -90.752 -8.385 1.00 0.00 H +ATOM 62 CB LYS 4 19.295 -92.266 -9.777 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.210 -92.396 -10.856 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.030 -92.979 -9.404 1.00 0.00 H +ATOM 65 CG LYS 4 17.907 -92.713 -9.185 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.963 -92.741 -8.097 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.128 -91.986 -9.417 1.00 0.00 H +ATOM 68 CD LYS 4 17.517 -94.086 -9.732 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.544 -94.068 -10.822 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.218 -94.812 -9.321 1.00 0.00 H +ATOM 71 CE LYS 4 16.067 -94.410 -9.298 1.00 0.00 C +ATOM 72 HE2 LYS 4 16.040 -94.204 -8.228 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.341 -93.735 -9.751 1.00 0.00 H +ATOM 74 NZ LYS 4 15.751 -95.839 -9.542 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.521 -96.423 -9.249 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.416 -96.087 -10.462 1.00 0.00 H +ATOM 77 HZ3 LYS 4 14.946 -96.157 -9.022 1.00 0.00 H +ATOM 78 C LYS 4 21.231 -90.770 -9.415 1.00 0.00 C +ATOM 79 O LYS 4 21.788 -90.265 -10.396 1.00 0.00 O +ATOM 80 N HE1 5 21.892 -91.064 -8.290 1.00 0.00 N +ATOM 81 CA HE1 5 23.319 -90.865 -8.075 1.00 0.00 C +ATOM 82 C HE1 5 23.721 -91.955 -7.054 1.00 0.00 C +ATOM 83 O HE1 5 23.072 -92.224 -6.040 1.00 0.00 O +ATOM 84 CB HE1 5 23.563 -89.478 -7.425 1.00 0.00 C +ATOM 85 CG HE1 5 25.073 -89.214 -7.110 1.00 0.00 C +ATOM 86 CD2 HE1 5 26.197 -89.643 -7.785 1.00 0.00 C +ATOM 87 ND1 HE1 5 25.391 -88.177 -6.228 1.00 0.00 N +ATOM 88 CE1 HE1 5 26.719 -88.065 -6.337 1.00 0.00 C +ATOM 89 NE2 HE1 5 27.203 -88.919 -7.256 1.00 0.00 N +ATOM 90 H HE1 5 21.298 -91.289 -7.505 1.00 0.00 H +ATOM 91 HA HE1 5 23.925 -90.922 -8.980 1.00 0.00 H +ATOM 92 HB2 HE1 5 22.879 -89.370 -6.583 1.00 0.00 H +ATOM 93 HB3 HE1 5 23.283 -88.622 -8.040 1.00 0.00 H +ATOM 94 HD2 HE1 5 26.243 -90.348 -8.602 1.00 0.00 H +ATOM 95 HE1 HE1 5 27.336 -87.573 -5.600 1.00 0.00 H +ATOM 96 HE2 HE1 5 28.168 -88.972 -7.550 1.00 0.00 H +ATOM 97 N ILE 6 24.801 -92.645 -7.359 1.00 0.00 N +ATOM 98 H ILE 6 25.257 -92.573 -8.258 1.00 0.00 H +ATOM 99 CA ILE 6 25.255 -93.700 -6.469 1.00 0.00 C +ATOM 100 HA ILE 6 24.438 -94.314 -6.091 1.00 0.00 H +ATOM 101 CB ILE 6 26.171 -94.739 -7.178 1.00 0.00 C +ATOM 102 HB ILE 6 26.431 -95.510 -6.452 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.455 -95.481 -8.281 1.00 0.00 C +ATOM 104 HG21 ILE 6 26.095 -96.301 -8.606 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.274 -94.846 -9.149 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.485 -95.780 -7.886 1.00 0.00 H +ATOM 107 CG1 ILE 6 27.397 -94.028 -7.797 1.00 0.00 C +ATOM 108 HG12 ILE 6 27.184 -93.252 -8.532 1.00 0.00 H +ATOM 109 HG13 ILE 6 27.935 -93.515 -6.999 1.00 0.00 H +ATOM 110 CD1 ILE 6 28.400 -95.011 -8.486 1.00 0.00 C +ATOM 111 HD11 ILE 6 28.127 -94.955 -9.540 1.00 0.00 H +ATOM 112 HD12 ILE 6 28.315 -96.032 -8.114 1.00 0.00 H +ATOM 113 HD13 ILE 6 29.419 -94.633 -8.407 1.00 0.00 H +ATOM 114 C ILE 6 25.835 -93.186 -5.149 1.00 0.00 C +ATOM 115 O ILE 6 26.258 -92.057 -5.123 1.00 0.00 O +ATOM 116 N VAL 7 25.777 -93.934 -4.084 1.00 0.00 N +ATOM 117 H VAL 7 25.343 -94.842 -4.001 1.00 0.00 H +ATOM 118 CA VAL 7 26.569 -93.682 -2.865 1.00 0.00 C +ATOM 119 HA VAL 7 26.357 -92.658 -2.558 1.00 0.00 H +ATOM 120 CB VAL 7 26.167 -94.775 -1.836 1.00 0.00 C +ATOM 121 HB VAL 7 25.082 -94.862 -1.783 1.00 0.00 H +ATOM 122 CG1 VAL 7 26.828 -96.070 -2.330 1.00 0.00 C +ATOM 123 HG11 VAL 7 26.423 -96.820 -1.651 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.577 -96.232 -3.379 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.909 -96.038 -2.200 1.00 0.00 H +ATOM 126 CG2 VAL 7 26.738 -94.543 -0.394 1.00 0.00 C +ATOM 127 HG21 VAL 7 26.223 -93.715 0.093 1.00 0.00 H +ATOM 128 HG22 VAL 7 26.607 -95.363 0.312 1.00 0.00 H +ATOM 129 HG23 VAL 7 27.808 -94.378 -0.521 1.00 0.00 H +ATOM 130 C VAL 7 28.097 -93.659 -3.164 1.00 0.00 C +ATOM 131 O VAL 7 28.471 -94.184 -4.223 1.00 0.00 O +ATOM 132 N ASN 8 28.913 -92.962 -2.355 1.00 0.00 N +ATOM 133 H ASN 8 28.503 -92.549 -1.529 1.00 0.00 H +ATOM 134 CA ASN 8 30.299 -92.908 -2.810 1.00 0.00 C +ATOM 135 HA ASN 8 30.317 -92.731 -3.885 1.00 0.00 H +ATOM 136 CB ASN 8 30.983 -91.676 -2.189 1.00 0.00 C +ATOM 137 HB2 ASN 8 30.285 -90.839 -2.146 1.00 0.00 H +ATOM 138 HB3 ASN 8 31.190 -91.820 -1.129 1.00 0.00 H +ATOM 139 CG ASN 8 32.266 -91.262 -2.831 1.00 0.00 C +ATOM 140 OD1 ASN 8 33.317 -91.616 -2.417 1.00 0.00 O +ATOM 141 ND2 ASN 8 32.208 -90.346 -3.823 1.00 0.00 N +ATOM 142 HD21 ASN 8 31.269 -90.021 -4.002 1.00 0.00 H +ATOM 143 HD22 ASN 8 33.045 -89.866 -4.121 1.00 0.00 H +ATOM 144 C ASN 8 31.131 -94.221 -2.587 1.00 0.00 C +ATOM 145 O ASN 8 31.942 -94.568 -3.467 1.00 0.00 O +ATOM 146 N GLY 9 30.928 -95.098 -1.597 1.00 0.00 N +ATOM 147 H GLY 9 30.142 -94.866 -1.007 1.00 0.00 H +ATOM 148 CA GLY 9 31.767 -96.306 -1.329 1.00 0.00 C +ATOM 149 HA2 GLY 9 32.836 -96.096 -1.334 1.00 0.00 H +ATOM 150 HA3 GLY 9 31.530 -96.685 -0.335 1.00 0.00 H +ATOM 151 C GLY 9 31.508 -97.421 -2.362 1.00 0.00 C +ATOM 152 O GLY 9 30.364 -97.687 -2.711 1.00 0.00 O +ATOM 153 N LYS 10 32.536 -97.943 -3.016 1.00 0.00 N +ATOM 154 H LYS 10 33.443 -97.542 -2.822 1.00 0.00 H +ATOM 155 CA LYS 10 32.372 -98.827 -4.213 1.00 0.00 C +ATOM 156 HA LYS 10 31.504 -98.467 -4.766 1.00 0.00 H +ATOM 157 CB LYS 10 33.584 -98.722 -5.069 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.406 -99.161 -4.505 1.00 0.00 H +ATOM 159 HB3 LYS 10 33.476 -99.309 -5.980 1.00 0.00 H +ATOM 160 CG LYS 10 34.050 -97.302 -5.538 1.00 0.00 C +ATOM 161 HG2 LYS 10 34.411 -96.683 -4.717 1.00 0.00 H +ATOM 162 HG3 LYS 10 34.990 -97.422 -6.077 1.00 0.00 H +ATOM 163 CD LYS 10 33.057 -96.484 -6.378 1.00 0.00 C +ATOM 164 HD2 LYS 10 32.772 -97.176 -7.170 1.00 0.00 H +ATOM 165 HD3 LYS 10 32.097 -96.342 -5.881 1.00 0.00 H +ATOM 166 CE LYS 10 33.486 -95.098 -6.779 1.00 0.00 C +ATOM 167 HE2 LYS 10 34.424 -95.265 -7.308 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.836 -94.676 -7.545 1.00 0.00 H +ATOM 169 NZ LYS 10 33.717 -94.146 -5.658 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.019 -93.265 -6.051 1.00 0.00 H +ATOM 171 HZ2 LYS 10 34.446 -94.545 -5.085 1.00 0.00 H +ATOM 172 HZ3 LYS 10 32.940 -93.947 -5.045 1.00 0.00 H +ATOM 173 C LYS 10 31.994-100.261 -3.878 1.00 0.00 C +ATOM 174 O LYS 10 31.485-101.031 -4.675 1.00 0.00 O +ATOM 175 N THR 11 32.122-100.685 -2.602 1.00 0.00 N +ATOM 176 H THR 11 32.544 -99.963 -2.037 1.00 0.00 H +ATOM 177 CA THR 11 31.408-101.825 -1.972 1.00 0.00 C +ATOM 178 HA THR 11 31.347-102.602 -2.735 1.00 0.00 H +ATOM 179 CB THR 11 32.268-102.429 -0.847 1.00 0.00 C +ATOM 180 HB THR 11 32.226-101.779 0.027 1.00 0.00 H +ATOM 181 CG2 THR 11 31.711-103.770 -0.331 1.00 0.00 C +ATOM 182 HG21 THR 11 32.416-104.189 0.387 1.00 0.00 H +ATOM 183 HG22 THR 11 31.501-104.526 -1.088 1.00 0.00 H +ATOM 184 HG23 THR 11 30.764-103.681 0.201 1.00 0.00 H +ATOM 185 OG1 THR 11 33.481-102.789 -1.332 1.00 0.00 O +ATOM 186 HG1 THR 11 33.962-101.958 -1.333 1.00 0.00 H +ATOM 187 C THR 11 29.920-101.519 -1.603 1.00 0.00 C +ATOM 188 O THR 11 29.125-102.425 -1.678 1.00 0.00 O +ATOM 189 N LEU 12 29.600-100.298 -1.142 1.00 0.00 N +ATOM 190 H LEU 12 30.315 -99.584 -1.145 1.00 0.00 H +ATOM 191 CA LEU 12 28.324-100.009 -0.485 1.00 0.00 C +ATOM 192 HA LEU 12 28.116-100.724 0.311 1.00 0.00 H +ATOM 193 CB LEU 12 28.313 -98.628 0.150 1.00 0.00 C +ATOM 194 HB2 LEU 12 28.802 -98.005 -0.599 1.00 0.00 H +ATOM 195 HB3 LEU 12 27.315 -98.200 0.248 1.00 0.00 H +ATOM 196 CG LEU 12 29.162 -98.539 1.397 1.00 0.00 C +ATOM 197 HG LEU 12 30.199 -98.827 1.228 1.00 0.00 H +ATOM 198 CD1 LEU 12 29.111 -97.086 1.900 1.00 0.00 C +ATOM 199 HD11 LEU 12 29.699 -96.427 1.262 1.00 0.00 H +ATOM 200 HD12 LEU 12 29.685 -97.039 2.825 1.00 0.00 H +ATOM 201 HD13 LEU 12 28.052 -96.834 1.958 1.00 0.00 H +ATOM 202 CD2 LEU 12 28.546 -99.424 2.518 1.00 0.00 C +ATOM 203 HD21 LEU 12 28.935 -99.146 3.498 1.00 0.00 H +ATOM 204 HD22 LEU 12 28.712-100.497 2.421 1.00 0.00 H +ATOM 205 HD23 LEU 12 27.470 -99.336 2.669 1.00 0.00 H +ATOM 206 C LEU 12 27.112-100.093 -1.506 1.00 0.00 C +ATOM 207 O LEU 12 26.055-100.674 -1.211 1.00 0.00 O +ATOM 208 N LYS 13 27.289 -99.702 -2.743 1.00 0.00 N +ATOM 209 H LYS 13 28.239 -99.425 -2.945 1.00 0.00 H +ATOM 210 CA LYS 13 26.341 -99.834 -3.955 1.00 0.00 C +ATOM 211 HA LYS 13 26.836 -99.343 -4.792 1.00 0.00 H +ATOM 212 CB LYS 13 26.306-101.332 -4.279 1.00 0.00 C +ATOM 213 HB2 LYS 13 26.029-101.894 -3.386 1.00 0.00 H +ATOM 214 HB3 LYS 13 25.534-101.491 -5.032 1.00 0.00 H +ATOM 215 CG LYS 13 27.642-101.923 -4.771 1.00 0.00 C +ATOM 216 HG2 LYS 13 28.095-101.301 -5.542 1.00 0.00 H +ATOM 217 HG3 LYS 13 28.453-101.944 -4.043 1.00 0.00 H +ATOM 218 CD LYS 13 27.341-103.304 -5.332 1.00 0.00 C +ATOM 219 HD2 LYS 13 26.575-103.228 -6.103 1.00 0.00 H +ATOM 220 HD3 LYS 13 28.285-103.605 -5.788 1.00 0.00 H +ATOM 221 CE LYS 13 26.970-104.363 -4.267 1.00 0.00 C +ATOM 222 HE2 LYS 13 25.962-104.211 -3.881 1.00 0.00 H +ATOM 223 HE3 LYS 13 26.925-105.261 -4.884 1.00 0.00 H +ATOM 224 NZ LYS 13 27.950-104.519 -3.205 1.00 0.00 N +ATOM 225 HZ1 LYS 13 28.839-104.834 -3.565 1.00 0.00 H +ATOM 226 HZ2 LYS 13 27.672-105.193 -2.506 1.00 0.00 H +ATOM 227 HZ3 LYS 13 28.180-103.670 -2.708 1.00 0.00 H +ATOM 228 C LYS 13 24.936 -99.184 -3.798 1.00 0.00 C +ATOM 229 O LYS 13 24.202 -99.164 -4.740 1.00 0.00 O +ATOM 230 N GLY 14 24.586 -98.668 -2.652 1.00 0.00 N +ATOM 231 H GLY 14 25.267 -98.781 -1.915 1.00 0.00 H +ATOM 232 CA GLY 14 23.301 -97.988 -2.482 1.00 0.00 C +ATOM 233 HA2 GLY 14 22.550 -98.746 -2.704 1.00 0.00 H +ATOM 234 HA3 GLY 14 23.052 -97.814 -1.435 1.00 0.00 H +ATOM 235 C GLY 14 23.056 -96.736 -3.405 1.00 0.00 C +ATOM 236 O GLY 14 24.023 -96.090 -3.888 1.00 0.00 O +ATOM 237 N VAL 15 21.770 -96.334 -3.572 1.00 0.00 N +ATOM 238 H VAL 15 21.014 -96.794 -3.085 1.00 0.00 H +ATOM 239 CA VAL 15 21.434 -95.170 -4.425 1.00 0.00 C +ATOM 240 HA VAL 15 22.293 -94.527 -4.616 1.00 0.00 H +ATOM 241 CB VAL 15 20.641 -95.679 -5.780 1.00 0.00 C +ATOM 242 HB VAL 15 19.817 -96.354 -5.547 1.00 0.00 H +ATOM 243 CG1 VAL 15 20.293 -94.603 -6.769 1.00 0.00 C +ATOM 244 HG11 VAL 15 21.145 -93.958 -6.985 1.00 0.00 H +ATOM 245 HG12 VAL 15 19.889 -95.003 -7.698 1.00 0.00 H +ATOM 246 HG13 VAL 15 19.463 -94.041 -6.341 1.00 0.00 H +ATOM 247 CG2 VAL 15 21.662 -96.600 -6.523 1.00 0.00 C +ATOM 248 HG21 VAL 15 21.681 -97.553 -5.994 1.00 0.00 H +ATOM 249 HG22 VAL 15 21.350 -96.743 -7.558 1.00 0.00 H +ATOM 250 HG23 VAL 15 22.705 -96.299 -6.428 1.00 0.00 H +ATOM 251 C VAL 15 20.483 -94.208 -3.693 1.00 0.00 C +ATOM 252 O VAL 15 19.622 -94.538 -2.872 1.00 0.00 O +ATOM 253 N HD1 16 20.563 -92.988 -4.195 1.00 0.00 N +ATOM 254 CA HD1 16 19.755 -91.836 -3.717 1.00 0.00 C +ATOM 255 C HD1 16 19.546 -90.904 -5.011 1.00 0.00 C +ATOM 256 O HD1 16 20.203 -91.106 -6.041 1.00 0.00 O +ATOM 257 CB HD1 16 20.449 -90.956 -2.572 1.00 0.00 C +ATOM 258 CG HD1 16 21.810 -90.503 -2.958 1.00 0.00 C +ATOM 259 CD2 HD1 16 22.277 -89.202 -3.152 1.00 0.00 C +ATOM 260 ND1 HD1 16 22.927 -91.297 -3.056 1.00 0.00 N +ATOM 261 CE1 HD1 16 23.957 -90.518 -3.401 1.00 0.00 C +ATOM 262 NE2 HD1 16 23.642 -89.198 -3.526 1.00 0.00 N +ATOM 263 H HD1 16 21.265 -92.733 -4.874 1.00 0.00 H +ATOM 264 HA HD1 16 18.847 -92.360 -3.420 1.00 0.00 H +ATOM 265 HB2 HD1 16 19.807 -90.106 -2.340 1.00 0.00 H +ATOM 266 HB3 HD1 16 20.502 -91.541 -1.654 1.00 0.00 H +ATOM 267 HD1 HD1 16 22.905 -92.260 -2.754 1.00 0.00 H +ATOM 268 HD2 HD1 16 21.702 -88.288 -3.182 1.00 0.00 H +ATOM 269 HE1 HD1 16 24.975 -90.881 -3.412 1.00 0.00 H +ATOM 270 N THR 17 18.624 -89.926 -4.910 1.00 0.00 N +ATOM 271 H THR 17 18.265 -89.873 -3.968 1.00 0.00 H +ATOM 272 CA THR 17 18.106 -88.927 -5.887 1.00 0.00 C +ATOM 273 HA THR 17 18.662 -89.089 -6.810 1.00 0.00 H +ATOM 274 CB THR 17 16.679 -89.423 -6.244 1.00 0.00 C +ATOM 275 HB THR 17 16.169 -89.567 -5.292 1.00 0.00 H +ATOM 276 CG2 THR 17 15.809 -88.605 -7.113 1.00 0.00 C +ATOM 277 HG21 THR 17 14.763 -88.879 -6.971 1.00 0.00 H +ATOM 278 HG22 THR 17 16.162 -88.596 -8.144 1.00 0.00 H +ATOM 279 HG23 THR 17 15.898 -87.545 -6.875 1.00 0.00 H +ATOM 280 OG1 THR 17 16.616 -90.622 -6.811 1.00 0.00 O +ATOM 281 HG1 THR 17 16.850 -91.292 -6.164 1.00 0.00 H +ATOM 282 C THR 17 18.174 -87.450 -5.640 1.00 0.00 C +ATOM 283 O THR 17 17.535 -86.924 -4.717 1.00 0.00 O +ATOM 284 N HD2 18 18.759 -86.697 -6.598 1.00 0.00 N +ATOM 285 CA HD2 18 18.803 -85.191 -6.773 1.00 0.00 C +ATOM 286 C HD2 18 17.761 -84.715 -7.873 1.00 0.00 C +ATOM 287 O HD2 18 16.980 -85.461 -8.438 1.00 0.00 O +ATOM 288 CB HD2 18 20.236 -84.798 -7.164 1.00 0.00 C +ATOM 289 CG HD2 18 21.266 -85.243 -6.241 1.00 0.00 C +ATOM 290 CD2 HD2 18 22.048 -86.344 -6.304 1.00 0.00 C +ATOM 291 ND1 HD2 18 21.564 -84.690 -4.987 1.00 0.00 N +ATOM 292 CE1 HD2 18 22.443 -85.437 -4.323 1.00 0.00 C +ATOM 293 NE2 HD2 18 22.705 -86.474 -5.098 1.00 0.00 N +ATOM 294 H HD2 18 19.086 -87.189 -7.417 1.00 0.00 H +ATOM 295 HA HD2 18 18.572 -84.773 -5.793 1.00 0.00 H +ATOM 296 HB2 HD2 18 20.398 -85.331 -8.101 1.00 0.00 H +ATOM 297 HB3 HD2 18 20.265 -83.755 -7.480 1.00 0.00 H +ATOM 298 HD1 HD2 18 21.111 -83.882 -4.585 1.00 0.00 H +ATOM 299 HD2 HD2 18 22.097 -86.971 -7.181 1.00 0.00 H +ATOM 300 HE1 HD2 18 22.755 -85.273 -3.302 1.00 0.00 H +ATOM 301 N GLU 19 17.620 -83.412 -8.072 1.00 0.00 N +ATOM 302 H GLU 19 17.909 -82.838 -7.293 1.00 0.00 H +ATOM 303 CA GLU 19 16.617 -82.815 -9.051 1.00 0.00 C +ATOM 304 HA GLU 19 16.452 -83.509 -9.876 1.00 0.00 H +ATOM 305 CB GLU 19 15.291 -82.627 -8.277 1.00 0.00 C +ATOM 306 HB2 GLU 19 15.233 -83.569 -7.731 1.00 0.00 H +ATOM 307 HB3 GLU 19 15.356 -81.749 -7.634 1.00 0.00 H +ATOM 308 CG GLU 19 14.001 -82.410 -9.133 1.00 0.00 C +ATOM 309 HG2 GLU 19 14.032 -83.056 -10.011 1.00 0.00 H +ATOM 310 HG3 GLU 19 13.058 -82.660 -8.646 1.00 0.00 H +ATOM 311 CD GLU 19 13.982 -80.932 -9.619 1.00 0.00 C +ATOM 312 OE1 GLU 19 13.836 -80.678 -10.827 1.00 0.00 O +ATOM 313 OE2 GLU 19 14.122 -79.979 -8.804 1.00 0.00 O +ATOM 314 C GLU 19 17.332 -81.605 -9.695 1.00 0.00 C +ATOM 315 O GLU 19 17.887 -80.742 -8.944 1.00 0.00 O +ATOM 316 N ALA 20 17.270 -81.314 -11.015 1.00 0.00 N +ATOM 317 H ALA 20 16.686 -81.887 -11.607 1.00 0.00 H +ATOM 318 CA ALA 20 17.722 -80.133 -11.780 1.00 0.00 C +ATOM 319 HA ALA 20 17.617 -79.235 -11.171 1.00 0.00 H +ATOM 320 CB ALA 20 19.244 -80.152 -12.150 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.711 -80.193 -11.167 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.553 -79.270 -12.711 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.517 -81.070 -12.672 1.00 0.00 H +ATOM 324 C ALA 20 16.793 -79.923 -13.019 1.00 0.00 C +ATOM 325 O ALA 20 16.205 -80.873 -13.482 1.00 0.00 O +ATOM 326 N VAL 21 16.780 -78.802 -13.622 1.00 0.00 N +ATOM 327 H VAL 21 17.330 -78.066 -13.204 1.00 0.00 H +ATOM 328 CA VAL 21 16.167 -78.638 -14.960 1.00 0.00 C +ATOM 329 HA VAL 21 15.153 -79.020 -14.843 1.00 0.00 H +ATOM 330 CB VAL 21 16.189 -77.213 -15.402 1.00 0.00 C +ATOM 331 HB VAL 21 15.661 -76.531 -14.736 1.00 0.00 H +ATOM 332 CG1 VAL 21 17.686 -76.670 -15.361 1.00 0.00 C +ATOM 333 HG11 VAL 21 18.417 -77.210 -14.760 1.00 0.00 H +ATOM 334 HG12 VAL 21 17.676 -75.641 -15.003 1.00 0.00 H +ATOM 335 HG13 VAL 21 18.150 -76.702 -16.347 1.00 0.00 H +ATOM 336 CG2 VAL 21 15.525 -77.006 -16.731 1.00 0.00 C +ATOM 337 HG21 VAL 21 14.486 -77.337 -16.711 1.00 0.00 H +ATOM 338 HG22 VAL 21 16.141 -77.451 -17.513 1.00 0.00 H +ATOM 339 HG23 VAL 21 15.550 -75.929 -16.891 1.00 0.00 H +ATOM 340 C VAL 21 16.844 -79.554 -16.010 1.00 0.00 C +ATOM 341 O VAL 21 16.171 -79.894 -16.982 1.00 0.00 O +ATOM 342 N ASP 22 18.133 -79.936 -15.925 1.00 0.00 N +ATOM 343 H ASP 22 18.678 -79.621 -15.136 1.00 0.00 H +ATOM 344 CA ASP 22 18.932 -80.377 -17.057 1.00 0.00 C +ATOM 345 HA ASP 22 18.311 -80.935 -17.758 1.00 0.00 H +ATOM 346 CB ASP 22 19.491 -79.060 -17.707 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.655 -78.364 -17.786 1.00 0.00 H +ATOM 348 HB3 ASP 22 20.245 -78.649 -17.037 1.00 0.00 H +ATOM 349 CG ASP 22 20.190 -79.219 -19.079 1.00 0.00 C +ATOM 350 OD1 ASP 22 20.835 -80.258 -19.333 1.00 0.00 O +ATOM 351 OD2 ASP 22 20.167 -78.287 -19.875 1.00 0.00 O +ATOM 352 C ASP 22 20.068 -81.342 -16.546 1.00 0.00 C +ATOM 353 O ASP 22 20.686 -80.974 -15.529 1.00 0.00 O +ATOM 354 N ALA 23 20.418 -82.450 -17.253 1.00 0.00 N +ATOM 355 H ALA 23 19.805 -82.600 -18.041 1.00 0.00 H +ATOM 356 CA ALA 23 21.569 -83.267 -17.004 1.00 0.00 C +ATOM 357 HA ALA 23 21.438 -83.669 -15.999 1.00 0.00 H +ATOM 358 CB ALA 23 21.633 -84.343 -18.118 1.00 0.00 C +ATOM 359 HB1 ALA 23 20.838 -85.083 -18.026 1.00 0.00 H +ATOM 360 HB2 ALA 23 22.588 -84.864 -18.050 1.00 0.00 H +ATOM 361 HB3 ALA 23 21.541 -83.910 -19.114 1.00 0.00 H +ATOM 362 C ALA 23 22.923 -82.321 -16.998 1.00 0.00 C +ATOM 363 O ALA 23 23.927 -82.653 -16.384 1.00 0.00 O +ATOM 364 N ALA 24 22.925 -81.181 -17.657 1.00 0.00 N +ATOM 365 H ALA 24 22.173 -80.961 -18.295 1.00 0.00 H +ATOM 366 CA ALA 24 24.095 -80.307 -17.800 1.00 0.00 C +ATOM 367 HA ALA 24 24.952 -80.979 -17.764 1.00 0.00 H +ATOM 368 CB ALA 24 23.920 -79.460 -19.054 1.00 0.00 C +ATOM 369 HB1 ALA 24 24.781 -78.817 -19.235 1.00 0.00 H +ATOM 370 HB2 ALA 24 22.995 -78.885 -19.009 1.00 0.00 H +ATOM 371 HB3 ALA 24 23.707 -80.030 -19.958 1.00 0.00 H +ATOM 372 C ALA 24 24.228 -79.358 -16.511 1.00 0.00 C +ATOM 373 O ALA 24 25.308 -79.004 -16.070 1.00 0.00 O +ATOM 374 N GLU 25 23.101 -79.141 -15.883 1.00 0.00 N +ATOM 375 H GLU 25 22.264 -79.529 -16.294 1.00 0.00 H +ATOM 376 CA GLU 25 23.138 -78.485 -14.564 1.00 0.00 C +ATOM 377 HA GLU 25 23.921 -77.735 -14.678 1.00 0.00 H +ATOM 378 CB GLU 25 21.773 -77.926 -14.231 1.00 0.00 C +ATOM 379 HB2 GLU 25 20.973 -78.644 -14.411 1.00 0.00 H +ATOM 380 HB3 GLU 25 21.760 -77.733 -13.158 1.00 0.00 H +ATOM 381 CG GLU 25 21.459 -76.578 -14.949 1.00 0.00 C +ATOM 382 HG2 GLU 25 21.322 -76.730 -16.020 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.596 -76.097 -14.489 1.00 0.00 H +ATOM 384 CD GLU 25 22.567 -75.544 -14.820 1.00 0.00 C +ATOM 385 OE1 GLU 25 23.326 -75.512 -13.800 1.00 0.00 O +ATOM 386 OE2 GLU 25 22.908 -74.913 -15.824 1.00 0.00 O +ATOM 387 C GLU 25 23.572 -79.485 -13.501 1.00 0.00 C +ATOM 388 O GLU 25 24.475 -79.255 -12.660 1.00 0.00 O +ATOM 389 N ALA 26 23.047 -80.709 -13.557 1.00 0.00 N +ATOM 390 H ALA 26 22.397 -80.907 -14.304 1.00 0.00 H +ATOM 391 CA ALA 26 23.261 -81.814 -12.679 1.00 0.00 C +ATOM 392 HA ALA 26 23.121 -81.591 -11.622 1.00 0.00 H +ATOM 393 CB ALA 26 22.203 -82.819 -13.179 1.00 0.00 C +ATOM 394 HB1 ALA 26 22.451 -83.186 -14.175 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.263 -82.268 -13.219 1.00 0.00 H +ATOM 396 HB3 ALA 26 22.118 -83.590 -12.413 1.00 0.00 H +ATOM 397 C ALA 26 24.681 -82.371 -12.822 1.00 0.00 C +ATOM 398 O ALA 26 25.192 -82.998 -11.887 1.00 0.00 O +ATOM 399 N GLU 27 25.438 -82.098 -13.914 1.00 0.00 N +ATOM 400 H GLU 27 24.963 -81.828 -14.764 1.00 0.00 H +ATOM 401 CA GLU 27 26.839 -82.385 -14.000 1.00 0.00 C +ATOM 402 HA GLU 27 27.068 -83.361 -13.572 1.00 0.00 H +ATOM 403 CB GLU 27 27.124 -82.428 -15.491 1.00 0.00 C +ATOM 404 HB2 GLU 27 26.577 -83.300 -15.850 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.682 -81.513 -15.886 1.00 0.00 H +ATOM 406 CG GLU 27 28.623 -82.540 -15.868 1.00 0.00 C +ATOM 407 HG2 GLU 27 29.186 -81.784 -15.321 1.00 0.00 H +ATOM 408 HG3 GLU 27 29.128 -83.379 -15.390 1.00 0.00 H +ATOM 409 CD GLU 27 28.974 -82.413 -17.386 1.00 0.00 C +ATOM 410 OE1 GLU 27 28.663 -83.350 -18.204 1.00 0.00 O +ATOM 411 OE2 GLU 27 29.475 -81.343 -17.812 1.00 0.00 O +ATOM 412 C GLU 27 27.719 -81.366 -13.222 1.00 0.00 C +ATOM 413 O GLU 27 28.583 -81.709 -12.430 1.00 0.00 O +ATOM 414 N LYS 28 27.352 -80.136 -13.403 1.00 0.00 N +ATOM 415 H LYS 28 26.676 -79.933 -14.125 1.00 0.00 H +ATOM 416 CA LYS 28 28.037 -78.942 -12.746 1.00 0.00 C +ATOM 417 HA LYS 28 29.107 -79.073 -12.909 1.00 0.00 H +ATOM 418 CB LYS 28 27.543 -77.626 -13.441 1.00 0.00 C +ATOM 419 HB2 LYS 28 26.454 -77.572 -13.421 1.00 0.00 H +ATOM 420 HB3 LYS 28 27.704 -76.719 -12.858 1.00 0.00 H +ATOM 421 CG LYS 28 28.194 -77.303 -14.799 1.00 0.00 C +ATOM 422 HG2 LYS 28 29.270 -77.133 -14.754 1.00 0.00 H +ATOM 423 HG3 LYS 28 28.051 -78.089 -15.541 1.00 0.00 H +ATOM 424 CD LYS 28 27.652 -76.060 -15.405 1.00 0.00 C +ATOM 425 HD2 LYS 28 27.989 -75.238 -14.773 1.00 0.00 H +ATOM 426 HD3 LYS 28 28.142 -75.989 -16.376 1.00 0.00 H +ATOM 427 CE LYS 28 26.127 -76.053 -15.800 1.00 0.00 C +ATOM 428 HE2 LYS 28 25.930 -76.784 -16.584 1.00 0.00 H +ATOM 429 HE3 LYS 28 25.567 -76.445 -14.951 1.00 0.00 H +ATOM 430 NZ LYS 28 25.683 -74.739 -16.287 1.00 0.00 N +ATOM 431 HZ1 LYS 28 26.057 -74.531 -17.202 1.00 0.00 H +ATOM 432 HZ2 LYS 28 25.994 -74.014 -15.656 1.00 0.00 H +ATOM 433 HZ3 LYS 28 24.684 -74.615 -16.210 1.00 0.00 H +ATOM 434 C LYS 28 27.814 -79.048 -11.191 1.00 0.00 C +ATOM 435 O LYS 28 28.737 -78.802 -10.422 1.00 0.00 O +ATOM 436 N PHE 29 26.655 -79.461 -10.761 1.00 0.00 N +ATOM 437 H PHE 29 25.903 -79.580 -11.425 1.00 0.00 H +ATOM 438 CA PHE 29 26.347 -79.554 -9.316 1.00 0.00 C +ATOM 439 HA PHE 29 26.818 -78.719 -8.797 1.00 0.00 H +ATOM 440 CB PHE 29 24.820 -79.546 -9.123 1.00 0.00 C +ATOM 441 HB2 PHE 29 24.295 -80.387 -9.576 1.00 0.00 H +ATOM 442 HB3 PHE 29 24.584 -79.678 -8.067 1.00 0.00 H +ATOM 443 CG PHE 29 24.027 -78.297 -9.438 1.00 0.00 C +ATOM 444 CD1 PHE 29 24.575 -77.089 -9.013 1.00 0.00 C +ATOM 445 HD1 PHE 29 25.313 -77.097 -8.224 1.00 0.00 H +ATOM 446 CE1 PHE 29 23.943 -75.869 -9.324 1.00 0.00 C +ATOM 447 HE1 PHE 29 24.297 -74.891 -9.034 1.00 0.00 H +ATOM 448 CZ PHE 29 22.720 -75.863 -10.020 1.00 0.00 C +ATOM 449 HZ PHE 29 22.135 -74.976 -10.212 1.00 0.00 H +ATOM 450 CE2 PHE 29 22.151 -77.096 -10.396 1.00 0.00 C +ATOM 451 HE2 PHE 29 21.151 -77.104 -10.804 1.00 0.00 H +ATOM 452 CD2 PHE 29 22.801 -78.323 -10.114 1.00 0.00 C +ATOM 453 HD2 PHE 29 22.417 -79.274 -10.454 1.00 0.00 H +ATOM 454 C PHE 29 26.924 -80.834 -8.678 1.00 0.00 C +ATOM 455 O PHE 29 27.403 -80.777 -7.586 1.00 0.00 O +ATOM 456 N THR 30 26.921 -81.901 -9.421 1.00 0.00 N +ATOM 457 H THR 30 26.589 -81.849 -10.374 1.00 0.00 H +ATOM 458 CA THR 30 27.516 -83.208 -8.955 1.00 0.00 C +ATOM 459 HA THR 30 27.046 -83.516 -8.021 1.00 0.00 H +ATOM 460 CB THR 30 27.284 -84.230 -10.031 1.00 0.00 C +ATOM 461 HB THR 30 27.678 -83.824 -10.962 1.00 0.00 H +ATOM 462 CG2 THR 30 28.046 -85.638 -9.719 1.00 0.00 C +ATOM 463 HG21 THR 30 28.143 -85.872 -8.659 1.00 0.00 H +ATOM 464 HG22 THR 30 27.690 -86.417 -10.393 1.00 0.00 H +ATOM 465 HG23 THR 30 29.070 -85.597 -10.090 1.00 0.00 H +ATOM 466 OG1 THR 30 25.905 -84.509 -10.173 1.00 0.00 O +ATOM 467 HG1 THR 30 25.456 -84.055 -10.890 1.00 0.00 H +ATOM 468 C THR 30 29.030 -83.045 -8.703 1.00 0.00 C +ATOM 469 O THR 30 29.579 -83.387 -7.646 1.00 0.00 O +ATOM 470 N LYS 31 29.738 -82.356 -9.547 1.00 0.00 N +ATOM 471 H LYS 31 29.317 -82.227 -10.456 1.00 0.00 H +ATOM 472 CA LYS 31 31.180 -81.947 -9.307 1.00 0.00 C +ATOM 473 HA LYS 31 31.801 -82.816 -9.090 1.00 0.00 H +ATOM 474 CB LYS 31 31.721 -81.356 -10.638 1.00 0.00 C +ATOM 475 HB2 LYS 31 30.931 -80.720 -11.036 1.00 0.00 H +ATOM 476 HB3 LYS 31 32.724 -80.948 -10.515 1.00 0.00 H +ATOM 477 CG LYS 31 31.813 -82.530 -11.653 1.00 0.00 C +ATOM 478 HG2 LYS 31 32.647 -83.219 -11.517 1.00 0.00 H +ATOM 479 HG3 LYS 31 30.929 -83.164 -11.593 1.00 0.00 H +ATOM 480 CD LYS 31 32.112 -82.036 -13.148 1.00 0.00 C +ATOM 481 HD2 LYS 31 31.525 -81.119 -13.204 1.00 0.00 H +ATOM 482 HD3 LYS 31 33.200 -82.013 -13.204 1.00 0.00 H +ATOM 483 CE LYS 31 31.616 -83.017 -14.212 1.00 0.00 C +ATOM 484 HE2 LYS 31 30.555 -83.223 -14.071 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.605 -82.644 -15.236 1.00 0.00 H +ATOM 486 NZ LYS 31 32.390 -84.321 -14.251 1.00 0.00 N +ATOM 487 HZ1 LYS 31 33.389 -84.208 -14.348 1.00 0.00 H +ATOM 488 HZ2 LYS 31 32.108 -84.897 -15.031 1.00 0.00 H +ATOM 489 HZ3 LYS 31 32.256 -84.800 -13.373 1.00 0.00 H +ATOM 490 C LYS 31 31.396 -80.848 -8.206 1.00 0.00 C +ATOM 491 O LYS 31 32.371 -80.940 -7.495 1.00 0.00 O +ATOM 492 N ALA 32 30.384 -80.065 -7.962 1.00 0.00 N +ATOM 493 H ALA 32 29.657 -80.058 -8.662 1.00 0.00 H +ATOM 494 CA ALA 32 30.432 -78.974 -7.003 1.00 0.00 C +ATOM 495 HA ALA 32 31.459 -78.611 -6.970 1.00 0.00 H +ATOM 496 CB ALA 32 29.390 -77.889 -7.301 1.00 0.00 C +ATOM 497 HB1 ALA 32 29.341 -77.626 -8.357 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.430 -78.233 -6.915 1.00 0.00 H +ATOM 499 HB3 ALA 32 29.596 -77.024 -6.670 1.00 0.00 H +ATOM 500 C ALA 32 30.301 -79.588 -5.585 1.00 0.00 C +ATOM 501 O ALA 32 30.914 -79.110 -4.636 1.00 0.00 O +ATOM 502 N ASP 33 29.480 -80.590 -5.385 1.00 0.00 N +ATOM 503 H ASP 33 28.933 -81.013 -6.121 1.00 0.00 H +ATOM 504 CA ASP 33 29.354 -81.209 -4.042 1.00 0.00 C +ATOM 505 HA ASP 33 29.290 -80.371 -3.348 1.00 0.00 H +ATOM 506 CB ASP 33 28.085 -82.035 -3.903 1.00 0.00 C +ATOM 507 HB2 ASP 33 28.001 -82.713 -4.752 1.00 0.00 H +ATOM 508 HB3 ASP 33 28.272 -82.659 -3.029 1.00 0.00 H +ATOM 509 CG ASP 33 26.805 -81.212 -3.806 1.00 0.00 C +ATOM 510 OD1 ASP 33 26.832 -79.971 -3.607 1.00 0.00 O +ATOM 511 OD2 ASP 33 25.698 -81.796 -3.801 1.00 0.00 O +ATOM 512 C ASP 33 30.593 -81.992 -3.683 1.00 0.00 C +ATOM 513 O ASP 33 31.024 -81.932 -2.510 1.00 0.00 O +ATOM 514 N ALA 34 31.174 -82.728 -4.664 1.00 0.00 N +ATOM 515 H ALA 34 30.691 -82.802 -5.548 1.00 0.00 H +ATOM 516 CA ALA 34 32.464 -83.379 -4.446 1.00 0.00 C +ATOM 517 HA ALA 34 32.430 -84.077 -3.609 1.00 0.00 H +ATOM 518 CB ALA 34 32.933 -84.108 -5.688 1.00 0.00 C +ATOM 519 HB1 ALA 34 32.505 -85.110 -5.667 1.00 0.00 H +ATOM 520 HB2 ALA 34 33.998 -84.331 -5.626 1.00 0.00 H +ATOM 521 HB3 ALA 34 32.613 -83.671 -6.634 1.00 0.00 H +ATOM 522 C ALA 34 33.442 -82.363 -3.965 1.00 0.00 C +ATOM 523 O ALA 34 34.204 -82.594 -2.970 1.00 0.00 O +ATOM 524 N ASN 35 33.472 -81.171 -4.570 1.00 0.00 N +ATOM 525 H ASN 35 32.668 -80.895 -5.115 1.00 0.00 H +ATOM 526 CA ASN 35 34.434 -80.124 -4.211 1.00 0.00 C +ATOM 527 HA ASN 35 35.457 -80.496 -4.155 1.00 0.00 H +ATOM 528 CB ASN 35 34.437 -79.041 -5.301 1.00 0.00 C +ATOM 529 HB2 ASN 35 34.769 -79.393 -6.278 1.00 0.00 H +ATOM 530 HB3 ASN 35 33.505 -78.479 -5.248 1.00 0.00 H +ATOM 531 CG ASN 35 35.554 -78.147 -4.865 1.00 0.00 C +ATOM 532 OD1 ASN 35 36.708 -78.466 -4.769 1.00 0.00 O +ATOM 533 ND2 ASN 35 35.274 -76.837 -4.638 1.00 0.00 N +ATOM 534 HD21 ASN 35 34.364 -76.437 -4.815 1.00 0.00 H +ATOM 535 HD22 ASN 35 35.970 -76.226 -4.236 1.00 0.00 H +ATOM 536 C ASN 35 34.098 -79.475 -2.887 1.00 0.00 C +ATOM 537 O ASN 35 35.068 -79.199 -2.198 1.00 0.00 O +ATOM 538 N ASP 36 32.793 -79.365 -2.410 1.00 0.00 N +ATOM 539 H ASP 36 32.145 -79.625 -3.140 1.00 0.00 H +ATOM 540 CA ASP 36 32.380 -79.060 -1.026 1.00 0.00 C +ATOM 541 HA ASP 36 32.931 -78.130 -0.883 1.00 0.00 H +ATOM 542 CB ASP 36 30.912 -78.764 -0.955 1.00 0.00 C +ATOM 543 HB2 ASP 36 30.374 -79.640 -1.317 1.00 0.00 H +ATOM 544 HB3 ASP 36 30.701 -78.542 0.091 1.00 0.00 H +ATOM 545 CG ASP 36 30.367 -77.502 -1.713 1.00 0.00 C +ATOM 546 OD1 ASP 36 31.149 -76.538 -2.030 1.00 0.00 O +ATOM 547 OD2 ASP 36 29.126 -77.390 -1.707 1.00 0.00 O +ATOM 548 C ASP 36 32.745 -80.087 0.014 1.00 0.00 C +ATOM 549 O ASP 36 32.970 -79.681 1.147 1.00 0.00 O +ATOM 550 N LYS 37 33.013 -81.315 -0.431 1.00 0.00 N +ATOM 551 H LYS 37 32.716 -81.562 -1.364 1.00 0.00 H +ATOM 552 CA LYS 37 33.636 -82.348 0.414 1.00 0.00 C +ATOM 553 HA LYS 37 33.413 -82.198 1.471 1.00 0.00 H +ATOM 554 CB LYS 37 32.951 -83.658 0.080 1.00 0.00 C +ATOM 555 HB2 LYS 37 33.074 -83.872 -0.982 1.00 0.00 H +ATOM 556 HB3 LYS 37 31.893 -83.654 0.341 1.00 0.00 H +ATOM 557 CG LYS 37 33.432 -84.988 0.712 1.00 0.00 C +ATOM 558 HG2 LYS 37 34.402 -85.228 0.277 1.00 0.00 H +ATOM 559 HG3 LYS 37 32.639 -85.678 0.423 1.00 0.00 H +ATOM 560 CD LYS 37 33.367 -85.139 2.227 1.00 0.00 C +ATOM 561 HD2 LYS 37 34.014 -84.429 2.743 1.00 0.00 H +ATOM 562 HD3 LYS 37 32.342 -84.995 2.567 1.00 0.00 H +ATOM 563 CE LYS 37 33.815 -86.561 2.578 1.00 0.00 C +ATOM 564 HE2 LYS 37 32.918 -87.135 2.344 1.00 0.00 H +ATOM 565 HE3 LYS 37 34.642 -86.919 1.967 1.00 0.00 H +ATOM 566 NZ LYS 37 34.100 -86.642 4.016 1.00 0.00 N +ATOM 567 HZ1 LYS 37 34.719 -85.869 4.214 1.00 0.00 H +ATOM 568 HZ2 LYS 37 33.307 -86.487 4.621 1.00 0.00 H +ATOM 569 HZ3 LYS 37 34.526 -87.522 4.268 1.00 0.00 H +ATOM 570 C LYS 37 35.160 -82.343 0.320 1.00 0.00 C +ATOM 571 O LYS 37 35.771 -82.832 1.269 1.00 0.00 O +ATOM 572 N GLY 38 35.674 -81.629 -0.662 1.00 0.00 N +ATOM 573 H GLY 38 35.087 -81.182 -1.351 1.00 0.00 H +ATOM 574 CA GLY 38 37.113 -81.501 -0.748 1.00 0.00 C +ATOM 575 HA2 GLY 38 37.379 -80.701 -1.439 1.00 0.00 H +ATOM 576 HA3 GLY 38 37.628 -81.308 0.193 1.00 0.00 H +ATOM 577 C GLY 38 37.665 -82.842 -1.267 1.00 0.00 C +ATOM 578 O GLY 38 38.794 -83.245 -0.990 1.00 0.00 O +ATOM 579 N VAL 39 36.835 -83.667 -1.948 1.00 0.00 N +ATOM 580 H VAL 39 35.914 -83.312 -2.162 1.00 0.00 H +ATOM 581 CA VAL 39 37.266 -84.992 -2.463 1.00 0.00 C +ATOM 582 HA VAL 39 38.353 -85.076 -2.472 1.00 0.00 H +ATOM 583 CB VAL 39 36.854 -86.198 -1.547 1.00 0.00 C +ATOM 584 HB VAL 39 35.765 -86.143 -1.545 1.00 0.00 H +ATOM 585 CG1 VAL 39 37.208 -87.635 -2.051 1.00 0.00 C +ATOM 586 HG11 VAL 39 37.024 -88.395 -1.292 1.00 0.00 H +ATOM 587 HG12 VAL 39 38.247 -87.550 -2.370 1.00 0.00 H +ATOM 588 HG13 VAL 39 36.569 -87.913 -2.889 1.00 0.00 H +ATOM 589 CG2 VAL 39 37.485 -86.049 -0.153 1.00 0.00 C +ATOM 590 HG21 VAL 39 37.291 -86.889 0.516 1.00 0.00 H +ATOM 591 HG22 VAL 39 36.905 -85.267 0.336 1.00 0.00 H +ATOM 592 HG23 VAL 39 38.548 -85.831 -0.248 1.00 0.00 H +ATOM 593 C VAL 39 36.779 -85.337 -3.926 1.00 0.00 C +ATOM 594 O VAL 39 35.598 -85.638 -4.138 1.00 0.00 O +ATOM 595 N ASP 40 37.673 -85.271 -4.894 1.00 0.00 N +ATOM 596 H ASP 40 38.591 -84.924 -4.653 1.00 0.00 H +ATOM 597 CA ASP 40 37.337 -85.499 -6.251 1.00 0.00 C +ATOM 598 HA ASP 40 36.570 -84.756 -6.472 1.00 0.00 H +ATOM 599 CB ASP 40 38.561 -85.175 -7.159 1.00 0.00 C +ATOM 600 HB2 ASP 40 38.994 -84.204 -6.920 1.00 0.00 H +ATOM 601 HB3 ASP 40 39.365 -85.830 -6.822 1.00 0.00 H +ATOM 602 CG ASP 40 38.317 -85.086 -8.650 1.00 0.00 C +ATOM 603 OD1 ASP 40 37.114 -85.063 -9.080 1.00 0.00 O +ATOM 604 OD2 ASP 40 39.324 -85.048 -9.413 1.00 0.00 O +ATOM 605 C ASP 40 36.796 -86.875 -6.626 1.00 0.00 C +ATOM 606 O ASP 40 37.214 -87.903 -6.100 1.00 0.00 O +ATOM 607 N GLY 41 35.855 -86.878 -7.560 1.00 0.00 N +ATOM 608 H GLY 41 35.937 -86.077 -8.170 1.00 0.00 H +ATOM 609 CA GLY 41 35.094 -87.999 -8.141 1.00 0.00 C +ATOM 610 HA2 GLY 41 35.731 -88.839 -8.420 1.00 0.00 H +ATOM 611 HA3 GLY 41 34.272 -88.377 -7.533 1.00 0.00 H +ATOM 612 C GLY 41 34.381 -87.525 -9.408 1.00 0.00 C +ATOM 613 O GLY 41 34.362 -86.404 -9.824 1.00 0.00 O +ATOM 614 N GLU 42 33.788 -88.603 -10.007 1.00 0.00 N +ATOM 615 H GLU 42 33.596 -89.414 -9.436 1.00 0.00 H +ATOM 616 CA GLU 42 33.365 -88.715 -11.465 1.00 0.00 C +ATOM 617 HA GLU 42 32.810 -87.821 -11.751 1.00 0.00 H +ATOM 618 CB GLU 42 34.449 -88.929 -12.532 1.00 0.00 C +ATOM 619 HB2 GLU 42 33.912 -88.915 -13.480 1.00 0.00 H +ATOM 620 HB3 GLU 42 35.156 -88.106 -12.424 1.00 0.00 H +ATOM 621 CG GLU 42 35.290 -90.205 -12.356 1.00 0.00 C +ATOM 622 HG2 GLU 42 34.631 -91.069 -12.269 1.00 0.00 H +ATOM 623 HG3 GLU 42 35.773 -90.386 -13.316 1.00 0.00 H +ATOM 624 CD GLU 42 36.275 -90.282 -11.236 1.00 0.00 C +ATOM 625 OE1 GLU 42 36.232 -91.255 -10.473 1.00 0.00 O +ATOM 626 OE2 GLU 42 37.059 -89.291 -11.092 1.00 0.00 O +ATOM 627 C GLU 42 32.328 -89.925 -11.589 1.00 0.00 C +ATOM 628 O GLU 42 32.322 -90.781 -10.667 1.00 0.00 O +ATOM 629 N TRP 43 31.494 -89.889 -12.661 1.00 0.00 N +ATOM 630 H TRP 43 31.684 -89.055 -13.198 1.00 0.00 H +ATOM 631 CA TRP 43 30.263 -90.591 -12.828 1.00 0.00 C +ATOM 632 HA TRP 43 30.294 -91.606 -12.431 1.00 0.00 H +ATOM 633 CB TRP 43 29.061 -89.988 -12.128 1.00 0.00 C +ATOM 634 HB2 TRP 43 29.013 -88.955 -12.473 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.084 -90.387 -12.400 1.00 0.00 H +ATOM 636 CG TRP 43 29.228 -90.038 -10.630 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.011 -91.169 -9.938 1.00 0.00 C +ATOM 638 HD1 TRP 43 28.689 -92.120 -10.336 1.00 0.00 H +ATOM 639 NE1 TRP 43 29.370 -90.960 -8.622 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.200 -91.660 -7.915 1.00 0.00 H +ATOM 641 CE2 TRP 43 29.906 -89.706 -8.453 1.00 0.00 C +ATOM 642 CZ2 TRP 43 30.379 -89.110 -7.292 1.00 0.00 C +ATOM 643 HZ2 TRP 43 30.133 -89.541 -6.333 1.00 0.00 H +ATOM 644 CH2 TRP 43 30.959 -87.853 -7.435 1.00 0.00 C +ATOM 645 HH2 TRP 43 31.348 -87.404 -6.532 1.00 0.00 H +ATOM 646 CZ3 TRP 43 30.958 -87.154 -8.600 1.00 0.00 C +ATOM 647 HZ3 TRP 43 31.304 -86.131 -8.624 1.00 0.00 H +ATOM 648 CE3 TRP 43 30.454 -87.794 -9.778 1.00 0.00 C +ATOM 649 HE3 TRP 43 30.495 -87.211 -10.686 1.00 0.00 H +ATOM 650 CD2 TRP 43 29.862 -89.110 -9.715 1.00 0.00 C +ATOM 651 C TRP 43 30.043 -90.680 -14.341 1.00 0.00 C +ATOM 652 O TRP 43 30.186 -89.681 -15.115 1.00 0.00 O +ATOM 653 N THR 44 29.711 -91.860 -14.795 1.00 0.00 N +ATOM 654 H THR 44 29.473 -92.576 -14.124 1.00 0.00 H +ATOM 655 CA THR 44 29.059 -92.060 -16.020 1.00 0.00 C +ATOM 656 HA THR 44 29.593 -91.695 -16.897 1.00 0.00 H +ATOM 657 CB THR 44 28.991 -93.575 -16.240 1.00 0.00 C +ATOM 658 HB THR 44 28.438 -94.137 -15.487 1.00 0.00 H +ATOM 659 CG2 THR 44 28.340 -93.904 -17.570 1.00 0.00 C +ATOM 660 HG21 THR 44 27.398 -93.356 -17.544 1.00 0.00 H +ATOM 661 HG22 THR 44 28.183 -94.980 -17.645 1.00 0.00 H +ATOM 662 HG23 THR 44 28.856 -93.608 -18.484 1.00 0.00 H +ATOM 663 OG1 THR 44 30.225 -94.180 -16.279 1.00 0.00 O +ATOM 664 HG1 THR 44 30.246 -94.831 -15.574 1.00 0.00 H +ATOM 665 C THR 44 27.680 -91.437 -15.944 1.00 0.00 C +ATOM 666 O THR 44 27.121 -91.386 -14.813 1.00 0.00 O +ATOM 667 N TYR 45 27.179 -90.839 -17.003 1.00 0.00 N +ATOM 668 H TYR 45 27.673 -90.716 -17.876 1.00 0.00 H +ATOM 669 CA TYR 45 25.709 -90.507 -17.155 1.00 0.00 C +ATOM 670 HA TYR 45 25.280 -90.574 -16.155 1.00 0.00 H +ATOM 671 CB TYR 45 25.538 -89.088 -17.672 1.00 0.00 C +ATOM 672 HB2 TYR 45 26.120 -88.381 -17.080 1.00 0.00 H +ATOM 673 HB3 TYR 45 25.979 -89.153 -18.667 1.00 0.00 H +ATOM 674 CG TYR 45 24.026 -88.715 -17.750 1.00 0.00 C +ATOM 675 CD1 TYR 45 23.160 -88.474 -16.613 1.00 0.00 C +ATOM 676 HD1 TYR 45 23.544 -88.432 -15.605 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.846 -88.256 -16.927 1.00 0.00 C +ATOM 678 HE1 TYR 45 21.165 -88.235 -16.088 1.00 0.00 H +ATOM 679 CZ TYR 45 21.278 -88.131 -18.222 1.00 0.00 C +ATOM 680 OH TYR 45 19.938 -87.846 -18.352 1.00 0.00 O +ATOM 681 HH TYR 45 19.562 -87.976 -19.226 1.00 0.00 H +ATOM 682 CE2 TYR 45 22.133 -88.380 -19.311 1.00 0.00 C +ATOM 683 HE2 TYR 45 21.730 -88.417 -20.312 1.00 0.00 H +ATOM 684 CD2 TYR 45 23.514 -88.717 -19.106 1.00 0.00 C +ATOM 685 HD2 TYR 45 24.205 -88.919 -19.911 1.00 0.00 H +ATOM 686 C TYR 45 24.975 -91.572 -17.968 1.00 0.00 C +ATOM 687 O TYR 45 25.273 -91.791 -19.146 1.00 0.00 O +ATOM 688 N ASP 46 23.921 -92.180 -17.374 1.00 0.00 N +ATOM 689 H ASP 46 23.677 -91.884 -16.440 1.00 0.00 H +ATOM 690 CA ASP 46 23.041 -93.149 -17.940 1.00 0.00 C +ATOM 691 HA ASP 46 23.513 -93.575 -18.826 1.00 0.00 H +ATOM 692 CB ASP 46 22.922 -94.353 -17.065 1.00 0.00 C +ATOM 693 HB2 ASP 46 23.924 -94.741 -16.881 1.00 0.00 H +ATOM 694 HB3 ASP 46 22.454 -94.075 -16.120 1.00 0.00 H +ATOM 695 CG ASP 46 22.035 -95.459 -17.645 1.00 0.00 C +ATOM 696 OD1 ASP 46 22.224 -95.853 -18.809 1.00 0.00 O +ATOM 697 OD2 ASP 46 21.113 -95.995 -16.967 1.00 0.00 O +ATOM 698 C ASP 46 21.650 -92.653 -18.312 1.00 0.00 C +ATOM 699 O ASP 46 20.692 -92.658 -17.500 1.00 0.00 O +ATOM 700 N ASP 47 21.420 -92.211 -19.550 1.00 0.00 N +ATOM 701 H ASP 47 22.040 -92.334 -20.338 1.00 0.00 H +ATOM 702 CA ASP 47 20.166 -91.504 -19.928 1.00 0.00 C +ATOM 703 HA ASP 47 20.096 -90.741 -19.152 1.00 0.00 H +ATOM 704 CB ASP 47 20.279 -90.710 -21.195 1.00 0.00 C +ATOM 705 HB2 ASP 47 21.244 -90.205 -21.221 1.00 0.00 H +ATOM 706 HB3 ASP 47 20.335 -91.301 -22.110 1.00 0.00 H +ATOM 707 CG ASP 47 19.152 -89.717 -21.405 1.00 0.00 C +ATOM 708 OD1 ASP 47 18.161 -90.018 -22.131 1.00 0.00 O +ATOM 709 OD2 ASP 47 19.101 -88.751 -20.621 1.00 0.00 O +ATOM 710 C ASP 47 18.973 -92.463 -19.912 1.00 0.00 C +ATOM 711 O ASP 47 17.855 -91.957 -19.869 1.00 0.00 O +ATOM 712 N ALA 48 19.233 -93.770 -20.015 1.00 0.00 N +ATOM 713 H ALA 48 20.179 -94.124 -20.036 1.00 0.00 H +ATOM 714 CA ALA 48 18.179 -94.779 -19.994 1.00 0.00 C +ATOM 715 HA ALA 48 17.395 -94.450 -20.676 1.00 0.00 H +ATOM 716 CB ALA 48 18.823 -96.100 -20.402 1.00 0.00 C +ATOM 717 HB1 ALA 48 18.043 -96.836 -20.596 1.00 0.00 H +ATOM 718 HB2 ALA 48 19.482 -96.538 -19.652 1.00 0.00 H +ATOM 719 HB3 ALA 48 19.399 -95.927 -21.312 1.00 0.00 H +ATOM 720 C ALA 48 17.535 -94.930 -18.593 1.00 0.00 C +ATOM 721 O ALA 48 16.617 -95.711 -18.427 1.00 0.00 O +ATOM 722 N THR 49 18.049 -94.226 -17.545 1.00 0.00 N +ATOM 723 H THR 49 18.971 -93.829 -17.658 1.00 0.00 H +ATOM 724 CA THR 49 17.521 -94.114 -16.203 1.00 0.00 C +ATOM 725 HA THR 49 16.451 -94.290 -16.313 1.00 0.00 H +ATOM 726 CB THR 49 18.134 -95.227 -15.229 1.00 0.00 C +ATOM 727 HB THR 49 17.592 -95.055 -14.300 1.00 0.00 H +ATOM 728 CG2 THR 49 17.946 -96.697 -15.694 1.00 0.00 C +ATOM 729 HG21 THR 49 18.666 -97.248 -15.089 1.00 0.00 H +ATOM 730 HG22 THR 49 18.116 -96.906 -16.750 1.00 0.00 H +ATOM 731 HG23 THR 49 16.946 -97.051 -15.446 1.00 0.00 H +ATOM 732 OG1 THR 49 19.566 -94.976 -15.157 1.00 0.00 O +ATOM 733 HG1 THR 49 19.846 -95.298 -16.016 1.00 0.00 H +ATOM 734 C THR 49 17.754 -92.747 -15.553 1.00 0.00 C +ATOM 735 O THR 49 17.460 -92.657 -14.332 1.00 0.00 O +ATOM 736 N LYS 50 18.327 -91.678 -16.184 1.00 0.00 N +ATOM 737 H LYS 50 18.549 -91.847 -17.154 1.00 0.00 H +ATOM 738 CA LYS 50 18.583 -90.384 -15.623 1.00 0.00 C +ATOM 739 HA LYS 50 19.260 -89.881 -16.314 1.00 0.00 H +ATOM 740 CB LYS 50 17.279 -89.704 -15.491 1.00 0.00 C +ATOM 741 HB2 LYS 50 16.671 -90.134 -14.695 1.00 0.00 H +ATOM 742 HB3 LYS 50 17.475 -88.727 -15.050 1.00 0.00 H +ATOM 743 CG LYS 50 16.318 -89.510 -16.735 1.00 0.00 C +ATOM 744 HG2 LYS 50 15.854 -90.449 -17.037 1.00 0.00 H +ATOM 745 HG3 LYS 50 15.465 -88.934 -16.376 1.00 0.00 H +ATOM 746 CD LYS 50 16.952 -88.926 -18.020 1.00 0.00 C +ATOM 747 HD2 LYS 50 17.243 -87.900 -17.795 1.00 0.00 H +ATOM 748 HD3 LYS 50 17.753 -89.597 -18.328 1.00 0.00 H +ATOM 749 CE LYS 50 15.978 -88.915 -19.250 1.00 0.00 C +ATOM 750 HE2 LYS 50 15.848 -89.966 -19.510 1.00 0.00 H +ATOM 751 HE3 LYS 50 15.047 -88.400 -19.016 1.00 0.00 H +ATOM 752 NZ LYS 50 16.523 -88.240 -20.405 1.00 0.00 N +ATOM 753 HZ1 LYS 50 17.483 -88.514 -20.558 1.00 0.00 H +ATOM 754 HZ2 LYS 50 16.524 -87.236 -20.303 1.00 0.00 H +ATOM 755 HZ3 LYS 50 16.015 -88.377 -21.268 1.00 0.00 H +ATOM 756 C LYS 50 19.504 -90.479 -14.377 1.00 0.00 C +ATOM 757 O LYS 50 19.151 -90.057 -13.299 1.00 0.00 O +ATOM 758 N THR 51 20.618 -91.263 -14.509 1.00 0.00 N +ATOM 759 H THR 51 20.740 -91.704 -15.409 1.00 0.00 H +ATOM 760 CA THR 51 21.520 -91.696 -13.384 1.00 0.00 C +ATOM 761 HA THR 51 21.218 -91.175 -12.476 1.00 0.00 H +ATOM 762 CB THR 51 21.388 -93.254 -13.098 1.00 0.00 C +ATOM 763 HB THR 51 21.838 -93.893 -13.858 1.00 0.00 H +ATOM 764 CG2 THR 51 22.157 -93.724 -11.804 1.00 0.00 C +ATOM 765 HG21 THR 51 21.567 -93.672 -10.889 1.00 0.00 H +ATOM 766 HG22 THR 51 23.145 -93.289 -11.657 1.00 0.00 H +ATOM 767 HG23 THR 51 22.374 -94.781 -11.959 1.00 0.00 H +ATOM 768 OG1 THR 51 20.085 -93.726 -12.775 1.00 0.00 O +ATOM 769 HG1 THR 51 19.560 -93.816 -13.573 1.00 0.00 H +ATOM 770 C THR 51 22.956 -91.301 -13.584 1.00 0.00 C +ATOM 771 O THR 51 23.551 -91.549 -14.698 1.00 0.00 O +ATOM 772 N PHE 52 23.576 -90.694 -12.576 1.00 0.00 N +ATOM 773 H PHE 52 22.986 -90.307 -11.853 1.00 0.00 H +ATOM 774 CA PHE 52 25.013 -90.566 -12.354 1.00 0.00 C +ATOM 775 HA PHE 52 25.510 -90.453 -13.317 1.00 0.00 H +ATOM 776 CB PHE 52 25.155 -89.223 -11.541 1.00 0.00 C +ATOM 777 HB2 PHE 52 24.597 -89.203 -10.605 1.00 0.00 H +ATOM 778 HB3 PHE 52 26.205 -89.077 -11.290 1.00 0.00 H +ATOM 779 CG PHE 52 24.761 -88.029 -12.410 1.00 0.00 C +ATOM 780 CD1 PHE 52 23.515 -87.448 -12.335 1.00 0.00 C +ATOM 781 HD1 PHE 52 22.977 -87.760 -11.452 1.00 0.00 H +ATOM 782 CE1 PHE 52 23.148 -86.369 -13.118 1.00 0.00 C +ATOM 783 HE1 PHE 52 22.157 -85.940 -13.089 1.00 0.00 H +ATOM 784 CZ PHE 52 23.994 -85.955 -14.139 1.00 0.00 C +ATOM 785 HZ PHE 52 23.702 -85.130 -14.772 1.00 0.00 H +ATOM 786 CE2 PHE 52 25.278 -86.585 -14.341 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.927 -86.455 -15.195 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.656 -87.587 -13.416 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.525 -88.226 -13.485 1.00 0.00 H +ATOM 790 C PHE 52 25.600 -91.781 -11.594 1.00 0.00 C +ATOM 791 O PHE 52 25.349 -91.980 -10.374 1.00 0.00 O +ATOM 792 N THR 53 26.281 -92.585 -12.373 1.00 0.00 N +ATOM 793 H THR 53 26.430 -92.282 -13.325 1.00 0.00 H +ATOM 794 CA THR 53 26.632 -94.021 -12.076 1.00 0.00 C +ATOM 795 HA THR 53 26.473 -94.151 -11.005 1.00 0.00 H +ATOM 796 CB THR 53 25.661 -94.950 -12.790 1.00 0.00 C +ATOM 797 HB THR 53 24.626 -94.799 -12.484 1.00 0.00 H +ATOM 798 CG2 THR 53 25.785 -95.196 -14.345 1.00 0.00 C +ATOM 799 HG21 THR 53 24.951 -95.830 -14.647 1.00 0.00 H +ATOM 800 HG22 THR 53 26.721 -95.690 -14.610 1.00 0.00 H +ATOM 801 HG23 THR 53 25.559 -94.302 -14.926 1.00 0.00 H +ATOM 802 OG1 THR 53 25.883 -96.177 -12.138 1.00 0.00 O +ATOM 803 HG1 THR 53 25.068 -96.683 -12.166 1.00 0.00 H +ATOM 804 C THR 53 28.049 -94.430 -12.344 1.00 0.00 C +ATOM 805 O THR 53 28.883 -93.497 -12.552 1.00 0.00 O +ATOM 806 N VAL 54 28.387 -95.692 -12.146 1.00 0.00 N +ATOM 807 H VAL 54 27.708 -96.438 -12.094 1.00 0.00 H +ATOM 808 CA VAL 54 29.809 -96.129 -11.985 1.00 0.00 C +ATOM 809 HA VAL 54 30.282 -95.580 -11.170 1.00 0.00 H +ATOM 810 CB VAL 54 29.835 -97.652 -11.706 1.00 0.00 C +ATOM 811 HB VAL 54 30.838 -98.068 -11.801 1.00 0.00 H +ATOM 812 CG1 VAL 54 29.289 -98.055 -10.305 1.00 0.00 C +ATOM 813 HG11 VAL 54 29.365 -99.137 -10.196 1.00 0.00 H +ATOM 814 HG12 VAL 54 28.226 -97.827 -10.225 1.00 0.00 H +ATOM 815 HG13 VAL 54 29.882 -97.635 -9.492 1.00 0.00 H +ATOM 816 CG2 VAL 54 29.058 -98.412 -12.706 1.00 0.00 C +ATOM 817 HG21 VAL 54 28.019 -98.107 -12.838 1.00 0.00 H +ATOM 818 HG22 VAL 54 29.032 -99.467 -12.431 1.00 0.00 H +ATOM 819 HG23 VAL 54 29.464 -98.371 -13.717 1.00 0.00 H +ATOM 820 C VAL 54 30.662 -95.830 -13.249 1.00 0.00 C +ATOM 821 O VAL 54 30.105 -95.946 -14.354 1.00 0.00 O +ATOM 822 N THR 55 31.988 -95.572 -12.966 1.00 0.00 N +ATOM 823 H THR 55 32.271 -95.408 -12.011 1.00 0.00 H +ATOM 824 CA THR 55 33.055 -95.396 -13.974 1.00 0.00 C +ATOM 825 HA THR 55 32.527 -95.075 -14.872 1.00 0.00 H +ATOM 826 CB THR 55 34.036 -94.276 -13.664 1.00 0.00 C +ATOM 827 HB THR 55 34.842 -94.538 -12.979 1.00 0.00 H +ATOM 828 CG2 THR 55 34.681 -93.748 -14.963 1.00 0.00 C +ATOM 829 HG21 THR 55 35.128 -92.763 -14.823 1.00 0.00 H +ATOM 830 HG22 THR 55 33.961 -93.678 -15.778 1.00 0.00 H +ATOM 831 HG23 THR 55 35.238 -94.559 -15.431 1.00 0.00 H +ATOM 832 OG1 THR 55 33.328 -93.015 -13.204 1.00 0.00 O +ATOM 833 HG1 THR 55 33.385 -92.970 -12.246 1.00 0.00 H +ATOM 834 C THR 55 33.905 -96.698 -14.166 1.00 0.00 C +ATOM 835 O THR 55 34.494 -97.170 -13.205 1.00 0.00 O +ATOM 836 N GLU 56 33.979 -97.251 -15.366 1.00 0.00 N +ATOM 837 H GLU 56 33.397 -96.793 -16.052 1.00 0.00 H +ATOM 838 CA GLU 56 34.666 -98.532 -15.761 1.00 0.00 C +ATOM 839 HA GLU 56 35.495 -98.715 -15.077 1.00 0.00 H +ATOM 840 CB GLU 56 33.668 -99.641 -15.638 1.00 0.00 C +ATOM 841 HB2 GLU 56 33.244 -99.711 -14.637 1.00 0.00 H +ATOM 842 HB3 GLU 56 32.773 -99.356 -16.191 1.00 0.00 H +ATOM 843 CG GLU 56 34.130-101.051 -16.059 1.00 0.00 C +ATOM 844 HG2 GLU 56 33.347-101.808 -16.007 1.00 0.00 H +ATOM 845 HG3 GLU 56 34.375-101.110 -17.119 1.00 0.00 H +ATOM 846 CD GLU 56 35.319-101.546 -15.251 1.00 0.00 C +ATOM 847 OE1 GLU 56 36.026-102.428 -15.760 1.00 0.00 O +ATOM 848 OE2 GLU 56 35.559-101.093 -14.114 1.00 0.00 O +ATOM 849 C GLU 56 35.318 -98.483 -17.157 1.00 0.00 C +ATOM 850 O GLU 56 34.579 -98.206 -18.083 1.00 0.00 O +ATOM 851 OXT GLU 56 36.550 -98.638 -17.194 1.00 0.00 O +ATOM 852 ZN ZN1 57 24.315 -87.683 -4.676 1.00 0.00 ZN +ATOM 853 N AN1 58 25.477 -86.586 -3.491 1.00 0.00 N +ATOM 854 C AN1 58 26.619 -85.064 -1.671 1.00 0.00 C +ATOM 855 C1 AN1 58 26.057 -85.997 -2.692 1.00 0.00 C +ATOM 856 H AN1 58 26.186 -84.057 -1.706 1.00 0.00 H +ATOM 857 H1 AN1 58 27.710 -85.052 -1.552 1.00 0.00 H +ATOM 858 H2 AN1 58 26.410 -85.529 -0.700 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 27.178 -90.340 -1.361 1.00 0.00 N +ATOM 860 N2 AZI 59 26.182 -89.679 -1.087 1.00 0.00 N +ATOM 861 N3 AZI 59 25.129 -89.015 -0.745 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/inp/pdbs/cluster.c5.pdb b/tests/nsga2/inp/pdbs/cluster.c5.pdb new file mode 100644 index 0000000..fb7fc40 --- /dev/null +++ b/tests/nsga2/inp/pdbs/cluster.c5.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.496 -81.728 -12.696 1.00 0.00 N +ATOM 2 H1 MET 1 13.556 -81.576 -11.699 1.00 0.00 H +ATOM 3 H2 MET 1 12.638 -81.373 -13.092 1.00 0.00 H +ATOM 4 H3 MET 1 14.282 -81.277 -13.143 1.00 0.00 H +ATOM 5 CA MET 1 13.482 -83.157 -12.927 1.00 0.00 C +ATOM 6 HA MET 1 12.450 -83.445 -12.729 1.00 0.00 H +ATOM 7 CB MET 1 13.834 -83.502 -14.365 1.00 0.00 C +ATOM 8 HB2 MET 1 13.142 -83.178 -15.143 1.00 0.00 H +ATOM 9 HB3 MET 1 14.846 -83.170 -14.598 1.00 0.00 H +ATOM 10 CG MET 1 13.848 -85.010 -14.759 1.00 0.00 C +ATOM 11 HG2 MET 1 13.928 -85.235 -15.823 1.00 0.00 H +ATOM 12 HG3 MET 1 14.673 -85.452 -14.199 1.00 0.00 H +ATOM 13 SD MET 1 12.244 -85.835 -14.186 1.00 0.00 S +ATOM 14 CE MET 1 11.389 -86.092 -15.741 1.00 0.00 C +ATOM 15 HE1 MET 1 10.530 -86.700 -15.457 1.00 0.00 H +ATOM 16 HE2 MET 1 11.947 -86.651 -16.493 1.00 0.00 H +ATOM 17 HE3 MET 1 11.027 -85.155 -16.163 1.00 0.00 H +ATOM 18 C MET 1 14.448 -83.743 -11.931 1.00 0.00 C +ATOM 19 O MET 1 15.580 -83.304 -11.808 1.00 0.00 O +ATOM 20 N GLN 2 14.102 -84.883 -11.292 1.00 0.00 N +ATOM 21 H GLN 2 13.242 -85.379 -11.480 1.00 0.00 H +ATOM 22 CA GLN 2 14.980 -85.564 -10.283 1.00 0.00 C +ATOM 23 HA GLN 2 15.645 -84.890 -9.743 1.00 0.00 H +ATOM 24 CB GLN 2 14.106 -86.197 -9.177 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.416 -86.878 -9.674 1.00 0.00 H +ATOM 26 HB3 GLN 2 14.782 -86.744 -8.519 1.00 0.00 H +ATOM 27 CG GLN 2 13.388 -85.156 -8.321 1.00 0.00 C +ATOM 28 HG2 GLN 2 13.941 -84.219 -8.384 1.00 0.00 H +ATOM 29 HG3 GLN 2 12.415 -84.978 -8.778 1.00 0.00 H +ATOM 30 CD GLN 2 13.154 -85.564 -6.877 1.00 0.00 C +ATOM 31 OE1 GLN 2 13.238 -84.800 -5.998 1.00 0.00 O +ATOM 32 NE2 GLN 2 12.974 -86.850 -6.553 1.00 0.00 N +ATOM 33 HE21 GLN 2 12.712 -87.099 -5.609 1.00 0.00 H +ATOM 34 HE22 GLN 2 12.843 -87.545 -7.274 1.00 0.00 H +ATOM 35 C GLN 2 15.802 -86.534 -11.048 1.00 0.00 C +ATOM 36 O GLN 2 15.178 -87.435 -11.566 1.00 0.00 O +ATOM 37 N TYR 3 17.175 -86.285 -11.113 1.00 0.00 N +ATOM 38 H TYR 3 17.528 -85.437 -10.694 1.00 0.00 H +ATOM 39 CA TYR 3 18.151 -87.144 -11.678 1.00 0.00 C +ATOM 40 HA TYR 3 17.666 -87.810 -12.393 1.00 0.00 H +ATOM 41 CB TYR 3 19.108 -86.320 -12.493 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.809 -85.661 -11.979 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.824 -86.993 -12.965 1.00 0.00 H +ATOM 44 CG TYR 3 18.418 -85.580 -13.622 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.292 -86.212 -14.861 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.565 -87.247 -15.006 1.00 0.00 H +ATOM 47 CE1 TYR 3 17.517 -85.644 -15.933 1.00 0.00 C +ATOM 48 HE1 TYR 3 17.357 -86.155 -16.871 1.00 0.00 H +ATOM 49 CZ TYR 3 17.108 -84.295 -15.917 1.00 0.00 C +ATOM 50 OH TYR 3 16.498 -83.774 -16.977 1.00 0.00 O +ATOM 51 HH TYR 3 16.630 -84.315 -17.759 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.417 -83.638 -14.719 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.132 -82.622 -14.493 1.00 0.00 H +ATOM 54 CD2 TYR 3 17.984 -84.269 -13.625 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.074 -83.780 -12.666 1.00 0.00 H +ATOM 56 C TYR 3 18.897 -87.913 -10.590 1.00 0.00 C +ATOM 57 O TYR 3 19.688 -87.289 -9.857 1.00 0.00 O +ATOM 58 N LYS 4 18.590 -89.212 -10.539 1.00 0.00 N +ATOM 59 H LYS 4 18.001 -89.567 -11.279 1.00 0.00 H +ATOM 60 CA LYS 4 19.174 -90.200 -9.595 1.00 0.00 C +ATOM 61 HA LYS 4 18.905 -89.884 -8.587 1.00 0.00 H +ATOM 62 CB LYS 4 18.501 -91.551 -9.898 1.00 0.00 C +ATOM 63 HB2 LYS 4 17.428 -91.372 -9.965 1.00 0.00 H +ATOM 64 HB3 LYS 4 18.853 -91.987 -10.833 1.00 0.00 H +ATOM 65 CG LYS 4 18.730 -92.615 -8.785 1.00 0.00 C +ATOM 66 HG2 LYS 4 19.729 -93.026 -8.929 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.736 -92.147 -7.800 1.00 0.00 H +ATOM 68 CD LYS 4 17.684 -93.717 -8.921 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.640 -94.238 -7.964 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.675 -93.306 -8.948 1.00 0.00 H +ATOM 71 CE LYS 4 17.867 -94.846 -10.017 1.00 0.00 C +ATOM 72 HE2 LYS 4 18.895 -95.204 -10.078 1.00 0.00 H +ATOM 73 HE3 LYS 4 17.105 -95.591 -9.787 1.00 0.00 H +ATOM 74 NZ LYS 4 17.539 -94.478 -11.368 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.617 -94.068 -11.406 1.00 0.00 H +ATOM 76 HZ2 LYS 4 17.594 -95.225 -12.045 1.00 0.00 H +ATOM 77 HZ3 LYS 4 18.214 -93.844 -11.770 1.00 0.00 H +ATOM 78 C LYS 4 20.655 -90.227 -9.687 1.00 0.00 C +ATOM 79 O LYS 4 21.247 -90.000 -10.756 1.00 0.00 O +ATOM 80 N HE1 5 21.407 -90.504 -8.598 1.00 0.00 N +ATOM 81 CA HE1 5 22.875 -90.774 -8.664 1.00 0.00 C +ATOM 82 C HE1 5 23.193 -91.849 -7.672 1.00 0.00 C +ATOM 83 O HE1 5 22.731 -91.777 -6.536 1.00 0.00 O +ATOM 84 CB HE1 5 23.666 -89.504 -8.446 1.00 0.00 C +ATOM 85 CG HE1 5 25.153 -89.475 -8.445 1.00 0.00 C +ATOM 86 CD2 HE1 5 25.950 -90.520 -8.740 1.00 0.00 C +ATOM 87 ND1 HE1 5 25.849 -88.360 -8.003 1.00 0.00 N +ATOM 88 CE1 HE1 5 27.103 -88.846 -7.953 1.00 0.00 C +ATOM 89 NE2 HE1 5 27.196 -90.164 -8.356 1.00 0.00 N +ATOM 90 H HE1 5 20.862 -90.604 -7.754 1.00 0.00 H +ATOM 91 HA HE1 5 23.126 -91.209 -9.631 1.00 0.00 H +ATOM 92 HB2 HE1 5 23.410 -89.259 -7.415 1.00 0.00 H +ATOM 93 HB3 HE1 5 23.193 -88.740 -9.063 1.00 0.00 H +ATOM 94 HD2 HE1 5 25.686 -91.493 -9.129 1.00 0.00 H +ATOM 95 HE1 HE1 5 27.996 -88.347 -7.605 1.00 0.00 H +ATOM 96 HE2 HE1 5 28.012 -90.756 -8.310 1.00 0.00 H +ATOM 97 N ILE 6 23.559 -93.009 -8.215 1.00 0.00 N +ATOM 98 H ILE 6 23.771 -93.078 -9.200 1.00 0.00 H +ATOM 99 CA ILE 6 23.856 -94.192 -7.518 1.00 0.00 C +ATOM 100 HA ILE 6 23.198 -94.208 -6.649 1.00 0.00 H +ATOM 101 CB ILE 6 23.494 -95.464 -8.398 1.00 0.00 C +ATOM 102 HB ILE 6 23.463 -96.279 -7.675 1.00 0.00 H +ATOM 103 CG2 ILE 6 22.012 -95.437 -8.831 1.00 0.00 C +ATOM 104 HG21 ILE 6 21.315 -95.038 -8.094 1.00 0.00 H +ATOM 105 HG22 ILE 6 21.701 -96.446 -9.100 1.00 0.00 H +ATOM 106 HG23 ILE 6 21.974 -94.785 -9.704 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.493 -95.641 -9.517 1.00 0.00 C +ATOM 108 HG12 ILE 6 24.396 -94.861 -10.273 1.00 0.00 H +ATOM 109 HG13 ILE 6 25.518 -95.701 -9.151 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.272 -96.967 -10.314 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.348 -97.778 -9.590 1.00 0.00 H +ATOM 112 HD12 ILE 6 25.134 -96.987 -10.980 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.313 -96.997 -10.833 1.00 0.00 H +ATOM 114 C ILE 6 25.295 -94.090 -7.054 1.00 0.00 C +ATOM 115 O ILE 6 26.057 -93.397 -7.704 1.00 0.00 O +ATOM 116 N VAL 7 25.540 -94.665 -5.897 1.00 0.00 N +ATOM 117 H VAL 7 24.818 -95.241 -5.488 1.00 0.00 H +ATOM 118 CA VAL 7 26.853 -94.510 -5.182 1.00 0.00 C +ATOM 119 HA VAL 7 27.533 -93.893 -5.771 1.00 0.00 H +ATOM 120 CB VAL 7 26.589 -93.792 -3.840 1.00 0.00 C +ATOM 121 HB VAL 7 25.924 -94.453 -3.285 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.837 -93.387 -3.099 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.524 -92.860 -3.761 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.511 -92.732 -2.292 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.384 -94.228 -2.672 1.00 0.00 H +ATOM 126 CG2 VAL 7 25.777 -92.507 -4.081 1.00 0.00 C +ATOM 127 HG21 VAL 7 25.813 -91.912 -3.169 1.00 0.00 H +ATOM 128 HG22 VAL 7 26.122 -91.986 -4.974 1.00 0.00 H +ATOM 129 HG23 VAL 7 24.749 -92.728 -4.368 1.00 0.00 H +ATOM 130 C VAL 7 27.468 -95.866 -5.088 1.00 0.00 C +ATOM 131 O VAL 7 26.833 -96.930 -5.164 1.00 0.00 O +ATOM 132 N ASN 8 28.828 -95.756 -4.910 1.00 0.00 N +ATOM 133 H ASN 8 29.269 -94.856 -4.786 1.00 0.00 H +ATOM 134 CA ASN 8 29.845 -96.798 -4.856 1.00 0.00 C +ATOM 135 HA ASN 8 29.422 -97.787 -5.028 1.00 0.00 H +ATOM 136 CB ASN 8 30.714 -96.561 -6.052 1.00 0.00 C +ATOM 137 HB2 ASN 8 29.989 -96.662 -6.860 1.00 0.00 H +ATOM 138 HB3 ASN 8 31.115 -95.560 -5.891 1.00 0.00 H +ATOM 139 CG ASN 8 31.870 -97.542 -6.260 1.00 0.00 C +ATOM 140 OD1 ASN 8 32.993 -97.449 -5.775 1.00 0.00 O +ATOM 141 ND2 ASN 8 31.619 -98.508 -7.112 1.00 0.00 N +ATOM 142 HD21 ASN 8 30.701 -98.489 -7.531 1.00 0.00 H +ATOM 143 HD22 ASN 8 32.354 -99.170 -7.320 1.00 0.00 H +ATOM 144 C ASN 8 30.464 -96.897 -3.413 1.00 0.00 C +ATOM 145 O ASN 8 30.860 -95.889 -2.773 1.00 0.00 O +ATOM 146 N GLY 9 30.693 -98.117 -2.974 1.00 0.00 N +ATOM 147 H GLY 9 30.316 -98.880 -3.518 1.00 0.00 H +ATOM 148 CA GLY 9 31.159 -98.375 -1.614 1.00 0.00 C +ATOM 149 HA2 GLY 9 31.848 -97.547 -1.448 1.00 0.00 H +ATOM 150 HA3 GLY 9 30.317 -98.421 -0.924 1.00 0.00 H +ATOM 151 C GLY 9 31.897 -99.697 -1.502 1.00 0.00 C +ATOM 152 O GLY 9 31.832-100.563 -2.330 1.00 0.00 O +ATOM 153 N LYS 10 32.696 -99.914 -0.459 1.00 0.00 N +ATOM 154 H LYS 10 32.711 -99.148 0.200 1.00 0.00 H +ATOM 155 CA LYS 10 33.611-101.070 -0.193 1.00 0.00 C +ATOM 156 HA LYS 10 34.260-101.177 -1.062 1.00 0.00 H +ATOM 157 CB LYS 10 34.479-100.809 1.069 1.00 0.00 C +ATOM 158 HB2 LYS 10 33.824-100.381 1.828 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.788-101.825 1.318 1.00 0.00 H +ATOM 160 CG LYS 10 35.676 -99.869 0.750 1.00 0.00 C +ATOM 161 HG2 LYS 10 36.200-100.395 -0.048 1.00 0.00 H +ATOM 162 HG3 LYS 10 35.329 -98.888 0.424 1.00 0.00 H +ATOM 163 CD LYS 10 36.691 -99.652 1.917 1.00 0.00 C +ATOM 164 HD2 LYS 10 37.273 -98.746 1.749 1.00 0.00 H +ATOM 165 HD3 LYS 10 36.048 -99.415 2.764 1.00 0.00 H +ATOM 166 CE LYS 10 37.621-100.790 2.356 1.00 0.00 C +ATOM 167 HE2 LYS 10 38.124-100.424 3.251 1.00 0.00 H +ATOM 168 HE3 LYS 10 37.020-101.665 2.605 1.00 0.00 H +ATOM 169 NZ LYS 10 38.592-101.087 1.244 1.00 0.00 N +ATOM 170 HZ1 LYS 10 38.919-100.220 0.843 1.00 0.00 H +ATOM 171 HZ2 LYS 10 38.154-101.569 0.471 1.00 0.00 H +ATOM 172 HZ3 LYS 10 39.430-101.488 1.641 1.00 0.00 H +ATOM 173 C LYS 10 32.831-102.328 -0.104 1.00 0.00 C +ATOM 174 O LYS 10 33.182-103.323 -0.773 1.00 0.00 O +ATOM 175 N THR 11 31.585-102.251 0.460 1.00 0.00 N +ATOM 176 H THR 11 31.343-101.448 1.022 1.00 0.00 H +ATOM 177 CA THR 11 30.586-103.321 0.661 1.00 0.00 C +ATOM 178 HA THR 11 30.854-104.065 -0.090 1.00 0.00 H +ATOM 179 CB THR 11 30.642-103.858 2.066 1.00 0.00 C +ATOM 180 HB THR 11 29.823-104.577 2.052 1.00 0.00 H +ATOM 181 CG2 THR 11 31.906-104.658 2.306 1.00 0.00 C +ATOM 182 HG21 THR 11 32.045-105.549 1.694 1.00 0.00 H +ATOM 183 HG22 THR 11 31.894-105.111 3.297 1.00 0.00 H +ATOM 184 HG23 THR 11 32.841-104.131 2.120 1.00 0.00 H +ATOM 185 OG1 THR 11 30.402-102.936 3.145 1.00 0.00 O +ATOM 186 HG1 THR 11 29.496-103.157 3.371 1.00 0.00 H +ATOM 187 C THR 11 29.108-102.885 0.459 1.00 0.00 C +ATOM 188 O THR 11 28.272-103.787 0.443 1.00 0.00 O +ATOM 189 N LEU 12 28.843-101.597 0.246 1.00 0.00 N +ATOM 190 H LEU 12 29.602-100.943 0.116 1.00 0.00 H +ATOM 191 CA LEU 12 27.573-100.899 0.158 1.00 0.00 C +ATOM 192 HA LEU 12 26.745-101.607 0.202 1.00 0.00 H +ATOM 193 CB LEU 12 27.402 -99.851 1.265 1.00 0.00 C +ATOM 194 HB2 LEU 12 28.184 -99.098 1.169 1.00 0.00 H +ATOM 195 HB3 LEU 12 26.493 -99.280 1.071 1.00 0.00 H +ATOM 196 CG LEU 12 27.435-100.459 2.701 1.00 0.00 C +ATOM 197 HG LEU 12 28.218-101.210 2.813 1.00 0.00 H +ATOM 198 CD1 LEU 12 27.680 -99.317 3.736 1.00 0.00 C +ATOM 199 HD11 LEU 12 28.721 -99.052 3.549 1.00 0.00 H +ATOM 200 HD12 LEU 12 27.549 -99.733 4.735 1.00 0.00 H +ATOM 201 HD13 LEU 12 27.041 -98.443 3.610 1.00 0.00 H +ATOM 202 CD2 LEU 12 26.095-101.055 3.201 1.00 0.00 C +ATOM 203 HD21 LEU 12 25.729-101.810 2.506 1.00 0.00 H +ATOM 204 HD22 LEU 12 25.328-100.295 3.345 1.00 0.00 H +ATOM 205 HD23 LEU 12 26.396-101.612 4.089 1.00 0.00 H +ATOM 206 C LEU 12 27.442-100.233 -1.244 1.00 0.00 C +ATOM 207 O LEU 12 28.476 -99.823 -1.833 1.00 0.00 O +ATOM 208 N LYS 13 26.209-100.166 -1.794 1.00 0.00 N +ATOM 209 H LYS 13 25.424-100.564 -1.299 1.00 0.00 H +ATOM 210 CA LYS 13 25.936 -99.329 -2.980 1.00 0.00 C +ATOM 211 HA LYS 13 26.800 -98.701 -3.200 1.00 0.00 H +ATOM 212 CB LYS 13 25.688-100.285 -4.158 1.00 0.00 C +ATOM 213 HB2 LYS 13 24.957-101.023 -3.829 1.00 0.00 H +ATOM 214 HB3 LYS 13 25.237 -99.618 -4.893 1.00 0.00 H +ATOM 215 CG LYS 13 26.920-101.016 -4.720 1.00 0.00 C +ATOM 216 HG2 LYS 13 27.748-100.312 -4.792 1.00 0.00 H +ATOM 217 HG3 LYS 13 27.317-101.717 -3.987 1.00 0.00 H +ATOM 218 CD LYS 13 26.639-101.804 -6.018 1.00 0.00 C +ATOM 219 HD2 LYS 13 26.191-101.146 -6.763 1.00 0.00 H +ATOM 220 HD3 LYS 13 27.543-102.228 -6.455 1.00 0.00 H +ATOM 221 CE LYS 13 25.684-102.980 -5.646 1.00 0.00 C +ATOM 222 HE2 LYS 13 26.336-103.723 -5.187 1.00 0.00 H +ATOM 223 HE3 LYS 13 24.932-102.754 -4.890 1.00 0.00 H +ATOM 224 NZ LYS 13 25.118-103.480 -6.926 1.00 0.00 N +ATOM 225 HZ1 LYS 13 24.563-102.731 -7.317 1.00 0.00 H +ATOM 226 HZ2 LYS 13 24.512-104.270 -6.758 1.00 0.00 H +ATOM 227 HZ3 LYS 13 25.863-103.717 -7.565 1.00 0.00 H +ATOM 228 C LYS 13 24.749 -98.447 -2.760 1.00 0.00 C +ATOM 229 O LYS 13 23.618 -98.742 -3.084 1.00 0.00 O +ATOM 230 N GLY 14 25.011 -97.328 -2.064 1.00 0.00 N +ATOM 231 H GLY 14 25.838 -97.357 -1.486 1.00 0.00 H +ATOM 232 CA GLY 14 24.016 -96.337 -1.718 1.00 0.00 C +ATOM 233 HA2 GLY 14 23.232 -96.881 -1.192 1.00 0.00 H +ATOM 234 HA3 GLY 14 24.437 -95.588 -1.048 1.00 0.00 H +ATOM 235 C GLY 14 23.449 -95.609 -2.945 1.00 0.00 C +ATOM 236 O GLY 14 23.906 -95.840 -4.089 1.00 0.00 O +ATOM 237 N VAL 15 22.401 -94.801 -2.776 1.00 0.00 N +ATOM 238 H VAL 15 22.186 -94.669 -1.798 1.00 0.00 H +ATOM 239 CA VAL 15 21.716 -93.947 -3.847 1.00 0.00 C +ATOM 240 HA VAL 15 22.528 -93.680 -4.523 1.00 0.00 H +ATOM 241 CB VAL 15 20.813 -94.806 -4.675 1.00 0.00 C +ATOM 242 HB VAL 15 21.377 -95.655 -5.061 1.00 0.00 H +ATOM 243 CG1 VAL 15 19.706 -95.422 -3.883 1.00 0.00 C +ATOM 244 HG11 VAL 15 19.235 -96.129 -4.566 1.00 0.00 H +ATOM 245 HG12 VAL 15 20.100 -95.919 -2.997 1.00 0.00 H +ATOM 246 HG13 VAL 15 19.041 -94.651 -3.492 1.00 0.00 H +ATOM 247 CG2 VAL 15 20.208 -94.056 -5.884 1.00 0.00 C +ATOM 248 HG21 VAL 15 19.698 -94.710 -6.591 1.00 0.00 H +ATOM 249 HG22 VAL 15 19.484 -93.319 -5.538 1.00 0.00 H +ATOM 250 HG23 VAL 15 20.965 -93.518 -6.454 1.00 0.00 H +ATOM 251 C VAL 15 21.150 -92.634 -3.263 1.00 0.00 C +ATOM 252 O VAL 15 20.576 -92.554 -2.177 1.00 0.00 O +ATOM 253 N HD1 16 21.181 -91.594 -4.087 1.00 0.00 N +ATOM 254 CA HD1 16 20.470 -90.352 -3.858 1.00 0.00 C +ATOM 255 C HD1 16 20.036 -89.734 -5.241 1.00 0.00 C +ATOM 256 O HD1 16 19.864 -90.400 -6.259 1.00 0.00 O +ATOM 257 CB HD1 16 21.334 -89.332 -3.032 1.00 0.00 C +ATOM 258 CG HD1 16 22.639 -88.999 -3.709 1.00 0.00 C +ATOM 259 CD2 HD1 16 22.857 -88.044 -4.670 1.00 0.00 C +ATOM 260 ND1 HD1 16 23.833 -89.615 -3.476 1.00 0.00 N +ATOM 261 CE1 HD1 16 24.716 -89.037 -4.305 1.00 0.00 C +ATOM 262 NE2 HD1 16 24.211 -88.008 -4.995 1.00 0.00 N +ATOM 263 H HD1 16 21.689 -91.693 -4.954 1.00 0.00 H +ATOM 264 HA HD1 16 19.518 -90.634 -3.409 1.00 0.00 H +ATOM 265 HB2 HD1 16 20.848 -88.415 -2.697 1.00 0.00 H +ATOM 266 HB3 HD1 16 21.596 -89.764 -2.066 1.00 0.00 H +ATOM 267 HD1 HD1 16 23.965 -90.470 -2.956 1.00 0.00 H +ATOM 268 HD2 HD1 16 22.075 -87.472 -5.145 1.00 0.00 H +ATOM 269 HE1 HD1 16 25.752 -89.334 -4.240 1.00 0.00 H +ATOM 270 N THR 17 19.739 -88.454 -5.222 1.00 0.00 N +ATOM 271 H THR 17 19.691 -87.926 -4.363 1.00 0.00 H +ATOM 272 CA THR 17 19.223 -87.730 -6.408 1.00 0.00 C +ATOM 273 HA THR 17 19.623 -88.215 -7.298 1.00 0.00 H +ATOM 274 CB THR 17 17.684 -87.801 -6.403 1.00 0.00 C +ATOM 275 HB THR 17 17.323 -88.820 -6.267 1.00 0.00 H +ATOM 276 CG2 THR 17 16.969 -86.795 -5.465 1.00 0.00 C +ATOM 277 HG21 THR 17 16.850 -85.787 -5.864 1.00 0.00 H +ATOM 278 HG22 THR 17 17.501 -86.713 -4.517 1.00 0.00 H +ATOM 279 HG23 THR 17 15.941 -87.130 -5.331 1.00 0.00 H +ATOM 280 OG1 THR 17 17.250 -87.539 -7.705 1.00 0.00 O +ATOM 281 HG1 THR 17 16.565 -88.123 -8.039 1.00 0.00 H +ATOM 282 C THR 17 19.581 -86.260 -6.472 1.00 0.00 C +ATOM 283 O THR 17 20.256 -85.743 -5.627 1.00 0.00 O +ATOM 284 N HD2 18 19.253 -85.633 -7.542 1.00 0.00 N +ATOM 285 CA HD2 18 19.599 -84.225 -7.918 1.00 0.00 C +ATOM 286 C HD2 18 18.494 -83.616 -8.790 1.00 0.00 C +ATOM 287 O HD2 18 18.308 -83.942 -9.978 1.00 0.00 O +ATOM 288 CB HD2 18 20.928 -84.131 -8.622 1.00 0.00 C +ATOM 289 CG HD2 18 22.152 -84.443 -7.768 1.00 0.00 C +ATOM 290 CD2 HD2 18 23.030 -85.439 -8.016 1.00 0.00 C +ATOM 291 ND1 HD2 18 22.497 -83.902 -6.522 1.00 0.00 N +ATOM 292 CE1 HD2 18 23.728 -84.419 -6.226 1.00 0.00 C +ATOM 293 NE2 HD2 18 24.021 -85.473 -7.031 1.00 0.00 N +ATOM 294 H HD2 18 18.784 -86.288 -8.152 1.00 0.00 H +ATOM 295 HA HD2 18 19.604 -83.604 -7.022 1.00 0.00 H +ATOM 296 HB2 HD2 18 20.879 -84.853 -9.437 1.00 0.00 H +ATOM 297 HB3 HD2 18 21.043 -83.100 -8.958 1.00 0.00 H +ATOM 298 HD1 HD2 18 22.140 -83.079 -6.059 1.00 0.00 H +ATOM 299 HD2 HD2 18 23.009 -86.090 -8.878 1.00 0.00 H +ATOM 300 HE1 HD2 18 24.302 -84.255 -5.326 1.00 0.00 H +ATOM 301 N GLU 19 17.821 -82.566 -8.312 1.00 0.00 N +ATOM 302 H GLU 19 17.981 -82.379 -7.332 1.00 0.00 H +ATOM 303 CA GLU 19 16.706 -81.915 -8.975 1.00 0.00 C +ATOM 304 HA GLU 19 16.181 -82.674 -9.555 1.00 0.00 H +ATOM 305 CB GLU 19 15.859 -81.325 -7.850 1.00 0.00 C +ATOM 306 HB2 GLU 19 15.274 -82.089 -7.338 1.00 0.00 H +ATOM 307 HB3 GLU 19 16.475 -80.898 -7.059 1.00 0.00 H +ATOM 308 CG GLU 19 14.756 -80.287 -8.300 1.00 0.00 C +ATOM 309 HG2 GLU 19 14.086 -80.009 -7.486 1.00 0.00 H +ATOM 310 HG3 GLU 19 15.414 -79.456 -8.550 1.00 0.00 H +ATOM 311 CD GLU 19 13.967 -80.701 -9.549 1.00 0.00 C +ATOM 312 OE1 GLU 19 13.764 -79.872 -10.472 1.00 0.00 O +ATOM 313 OE2 GLU 19 13.489 -81.831 -9.722 1.00 0.00 O +ATOM 314 C GLU 19 17.341 -80.872 -9.837 1.00 0.00 C +ATOM 315 O GLU 19 17.910 -79.933 -9.343 1.00 0.00 O +ATOM 316 N ALA 20 17.177 -80.955 -11.171 1.00 0.00 N +ATOM 317 H ALA 20 16.921 -81.880 -11.485 1.00 0.00 H +ATOM 318 CA ALA 20 17.572 -79.889 -12.061 1.00 0.00 C +ATOM 319 HA ALA 20 17.557 -79.009 -11.418 1.00 0.00 H +ATOM 320 CB ALA 20 19.050 -80.056 -12.524 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.309 -79.222 -13.175 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.164 -81.071 -12.904 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.561 -79.949 -11.567 1.00 0.00 H +ATOM 324 C ALA 20 16.728 -79.637 -13.278 1.00 0.00 C +ATOM 325 O ALA 20 15.906 -80.452 -13.569 1.00 0.00 O +ATOM 326 N VAL 21 16.942 -78.471 -14.018 1.00 0.00 N +ATOM 327 H VAL 21 17.427 -77.727 -13.538 1.00 0.00 H +ATOM 328 CA VAL 21 16.254 -78.217 -15.245 1.00 0.00 C +ATOM 329 HA VAL 21 15.230 -78.549 -15.072 1.00 0.00 H +ATOM 330 CB VAL 21 16.213 -76.648 -15.533 1.00 0.00 C +ATOM 331 HB VAL 21 15.838 -76.548 -16.552 1.00 0.00 H +ATOM 332 CG1 VAL 21 15.388 -75.930 -14.471 1.00 0.00 C +ATOM 333 HG11 VAL 21 15.829 -75.832 -13.479 1.00 0.00 H +ATOM 334 HG12 VAL 21 14.474 -76.516 -14.370 1.00 0.00 H +ATOM 335 HG13 VAL 21 15.092 -74.945 -14.834 1.00 0.00 H +ATOM 336 CG2 VAL 21 17.625 -76.035 -15.568 1.00 0.00 C +ATOM 337 HG21 VAL 21 18.227 -76.418 -16.392 1.00 0.00 H +ATOM 338 HG22 VAL 21 18.001 -76.169 -14.554 1.00 0.00 H +ATOM 339 HG23 VAL 21 17.634 -74.969 -15.795 1.00 0.00 H +ATOM 340 C VAL 21 16.845 -79.023 -16.417 1.00 0.00 C +ATOM 341 O VAL 21 16.236 -79.191 -17.475 1.00 0.00 O +ATOM 342 N ASP 22 18.068 -79.561 -16.299 1.00 0.00 N +ATOM 343 H ASP 22 18.530 -79.493 -15.403 1.00 0.00 H +ATOM 344 CA ASP 22 18.668 -80.469 -17.297 1.00 0.00 C +ATOM 345 HA ASP 22 17.880 -81.008 -17.822 1.00 0.00 H +ATOM 346 CB ASP 22 19.248 -79.554 -18.504 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.518 -78.818 -18.842 1.00 0.00 H +ATOM 348 HB3 ASP 22 19.944 -78.824 -18.090 1.00 0.00 H +ATOM 349 CG ASP 22 19.804 -80.314 -19.648 1.00 0.00 C +ATOM 350 OD1 ASP 22 20.716 -79.751 -20.389 1.00 0.00 O +ATOM 351 OD2 ASP 22 19.308 -81.459 -19.881 1.00 0.00 O +ATOM 352 C ASP 22 19.749 -81.343 -16.703 1.00 0.00 C +ATOM 353 O ASP 22 20.332 -80.965 -15.621 1.00 0.00 O +ATOM 354 N ALA 23 20.109 -82.459 -17.321 1.00 0.00 N +ATOM 355 H ALA 23 19.537 -82.802 -18.079 1.00 0.00 H +ATOM 356 CA ALA 23 21.034 -83.372 -16.600 1.00 0.00 C +ATOM 357 HA ALA 23 20.687 -83.474 -15.572 1.00 0.00 H +ATOM 358 CB ALA 23 20.861 -84.826 -17.253 1.00 0.00 C +ATOM 359 HB1 ALA 23 19.813 -85.125 -17.280 1.00 0.00 H +ATOM 360 HB2 ALA 23 21.406 -85.576 -16.679 1.00 0.00 H +ATOM 361 HB3 ALA 23 21.234 -84.897 -18.275 1.00 0.00 H +ATOM 362 C ALA 23 22.482 -82.792 -16.501 1.00 0.00 C +ATOM 363 O ALA 23 23.161 -83.031 -15.514 1.00 0.00 O +ATOM 364 N ALA 24 22.945 -81.990 -17.499 1.00 0.00 N +ATOM 365 H ALA 24 22.450 -81.867 -18.371 1.00 0.00 H +ATOM 366 CA ALA 24 24.213 -81.288 -17.323 1.00 0.00 C +ATOM 367 HA ALA 24 25.012 -82.002 -17.123 1.00 0.00 H +ATOM 368 CB ALA 24 24.586 -80.547 -18.665 1.00 0.00 C +ATOM 369 HB1 ALA 24 23.764 -79.883 -18.933 1.00 0.00 H +ATOM 370 HB2 ALA 24 24.633 -81.240 -19.505 1.00 0.00 H +ATOM 371 HB3 ALA 24 25.520 -79.988 -18.613 1.00 0.00 H +ATOM 372 C ALA 24 24.288 -80.304 -16.207 1.00 0.00 C +ATOM 373 O ALA 24 25.385 -79.967 -15.808 1.00 0.00 O +ATOM 374 N GLU 25 23.221 -79.844 -15.649 1.00 0.00 N +ATOM 375 H GLU 25 22.366 -80.152 -16.090 1.00 0.00 H +ATOM 376 CA GLU 25 23.107 -79.040 -14.421 1.00 0.00 C +ATOM 377 HA GLU 25 24.023 -78.456 -14.330 1.00 0.00 H +ATOM 378 CB GLU 25 21.870 -78.152 -14.483 1.00 0.00 C +ATOM 379 HB2 GLU 25 20.925 -78.693 -14.423 1.00 0.00 H +ATOM 380 HB3 GLU 25 21.876 -77.499 -13.610 1.00 0.00 H +ATOM 381 CG GLU 25 21.929 -77.100 -15.662 1.00 0.00 C +ATOM 382 HG2 GLU 25 22.111 -77.599 -16.613 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.947 -76.639 -15.550 1.00 0.00 H +ATOM 384 CD GLU 25 22.967 -75.926 -15.575 1.00 0.00 C +ATOM 385 OE1 GLU 25 23.817 -75.854 -16.479 1.00 0.00 O +ATOM 386 OE2 GLU 25 22.922 -75.185 -14.567 1.00 0.00 O +ATOM 387 C GLU 25 22.880 -79.952 -13.128 1.00 0.00 C +ATOM 388 O GLU 25 23.545 -79.611 -12.122 1.00 0.00 O +ATOM 389 N ALA 26 22.248 -81.127 -13.212 1.00 0.00 N +ATOM 390 H ALA 26 21.838 -81.445 -14.079 1.00 0.00 H +ATOM 391 CA ALA 26 22.394 -82.095 -12.107 1.00 0.00 C +ATOM 392 HA ALA 26 22.021 -81.630 -11.194 1.00 0.00 H +ATOM 393 CB ALA 26 21.390 -83.290 -12.252 1.00 0.00 C +ATOM 394 HB1 ALA 26 21.817 -84.159 -11.752 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.298 -83.504 -13.317 1.00 0.00 H +ATOM 396 HB3 ALA 26 20.462 -82.921 -11.814 1.00 0.00 H +ATOM 397 C ALA 26 23.805 -82.591 -11.887 1.00 0.00 C +ATOM 398 O ALA 26 24.120 -82.926 -10.743 1.00 0.00 O +ATOM 399 N GLU 27 24.522 -82.693 -13.007 1.00 0.00 N +ATOM 400 H GLU 27 24.082 -82.517 -13.899 1.00 0.00 H +ATOM 401 CA GLU 27 25.933 -83.107 -13.055 1.00 0.00 C +ATOM 402 HA GLU 27 26.151 -84.105 -12.674 1.00 0.00 H +ATOM 403 CB GLU 27 26.341 -83.131 -14.490 1.00 0.00 C +ATOM 404 HB2 GLU 27 25.722 -83.898 -14.955 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.201 -82.147 -14.938 1.00 0.00 H +ATOM 406 CG GLU 27 27.852 -83.532 -14.601 1.00 0.00 C +ATOM 407 HG2 GLU 27 28.468 -83.237 -13.751 1.00 0.00 H +ATOM 408 HG3 GLU 27 27.878 -84.619 -14.683 1.00 0.00 H +ATOM 409 CD GLU 27 28.486 -82.940 -15.830 1.00 0.00 C +ATOM 410 OE1 GLU 27 27.826 -82.335 -16.720 1.00 0.00 O +ATOM 411 OE2 GLU 27 29.682 -83.191 -16.031 1.00 0.00 O +ATOM 412 C GLU 27 26.735 -82.073 -12.257 1.00 0.00 C +ATOM 413 O GLU 27 27.583 -82.465 -11.425 1.00 0.00 O +ATOM 414 N LYS 28 26.560 -80.714 -12.454 1.00 0.00 N +ATOM 415 H LYS 28 25.776 -80.562 -13.072 1.00 0.00 H +ATOM 416 CA LYS 28 27.187 -79.640 -11.682 1.00 0.00 C +ATOM 417 HA LYS 28 28.267 -79.704 -11.818 1.00 0.00 H +ATOM 418 CB LYS 28 26.884 -78.253 -12.235 1.00 0.00 C +ATOM 419 HB2 LYS 28 25.806 -78.090 -12.207 1.00 0.00 H +ATOM 420 HB3 LYS 28 27.331 -77.510 -11.575 1.00 0.00 H +ATOM 421 CG LYS 28 27.338 -78.021 -13.724 1.00 0.00 C +ATOM 422 HG2 LYS 28 28.426 -78.076 -13.767 1.00 0.00 H +ATOM 423 HG3 LYS 28 26.929 -78.850 -14.302 1.00 0.00 H +ATOM 424 CD LYS 28 26.968 -76.720 -14.340 1.00 0.00 C +ATOM 425 HD2 LYS 28 25.887 -76.680 -14.212 1.00 0.00 H +ATOM 426 HD3 LYS 28 27.542 -75.873 -13.963 1.00 0.00 H +ATOM 427 CE LYS 28 27.260 -76.778 -15.826 1.00 0.00 C +ATOM 428 HE2 LYS 28 28.334 -76.947 -15.914 1.00 0.00 H +ATOM 429 HE3 LYS 28 26.750 -77.647 -16.239 1.00 0.00 H +ATOM 430 NZ LYS 28 26.761 -75.474 -16.439 1.00 0.00 N +ATOM 431 HZ1 LYS 28 27.189 -74.637 -16.070 1.00 0.00 H +ATOM 432 HZ2 LYS 28 25.756 -75.419 -16.347 1.00 0.00 H +ATOM 433 HZ3 LYS 28 26.965 -75.658 -17.411 1.00 0.00 H +ATOM 434 C LYS 28 26.876 -79.718 -10.220 1.00 0.00 C +ATOM 435 O LYS 28 27.782 -79.740 -9.373 1.00 0.00 O +ATOM 436 N PHE 29 25.622 -79.980 -9.846 1.00 0.00 N +ATOM 437 H PHE 29 25.002 -80.146 -10.626 1.00 0.00 H +ATOM 438 CA PHE 29 25.245 -80.297 -8.470 1.00 0.00 C +ATOM 439 HA PHE 29 25.648 -79.501 -7.843 1.00 0.00 H +ATOM 440 CB PHE 29 23.687 -80.381 -8.283 1.00 0.00 C +ATOM 441 HB2 PHE 29 23.307 -81.072 -9.035 1.00 0.00 H +ATOM 442 HB3 PHE 29 23.392 -80.720 -7.290 1.00 0.00 H +ATOM 443 CG PHE 29 22.948 -79.118 -8.484 1.00 0.00 C +ATOM 444 CD1 PHE 29 21.808 -79.072 -9.276 1.00 0.00 C +ATOM 445 HD1 PHE 29 21.467 -79.981 -9.749 1.00 0.00 H +ATOM 446 CE1 PHE 29 21.001 -77.890 -9.305 1.00 0.00 C +ATOM 447 HE1 PHE 29 20.176 -77.857 -10.001 1.00 0.00 H +ATOM 448 CZ PHE 29 21.433 -76.732 -8.687 1.00 0.00 C +ATOM 449 HZ PHE 29 20.889 -75.799 -8.721 1.00 0.00 H +ATOM 450 CE2 PHE 29 22.578 -76.704 -7.896 1.00 0.00 C +ATOM 451 HE2 PHE 29 22.822 -75.769 -7.414 1.00 0.00 H +ATOM 452 CD2 PHE 29 23.358 -77.925 -7.815 1.00 0.00 C +ATOM 453 HD2 PHE 29 24.271 -77.910 -7.238 1.00 0.00 H +ATOM 454 C PHE 29 25.972 -81.600 -7.896 1.00 0.00 C +ATOM 455 O PHE 29 26.456 -81.595 -6.742 1.00 0.00 O +ATOM 456 N THR 30 26.142 -82.591 -8.718 1.00 0.00 N +ATOM 457 H THR 30 25.568 -82.582 -9.549 1.00 0.00 H +ATOM 458 CA THR 30 26.857 -83.834 -8.415 1.00 0.00 C +ATOM 459 HA THR 30 26.483 -84.328 -7.518 1.00 0.00 H +ATOM 460 CB THR 30 26.893 -84.886 -9.525 1.00 0.00 C +ATOM 461 HB THR 30 26.855 -84.570 -10.568 1.00 0.00 H +ATOM 462 CG2 THR 30 28.139 -85.872 -9.503 1.00 0.00 C +ATOM 463 HG21 THR 30 28.530 -86.018 -8.496 1.00 0.00 H +ATOM 464 HG22 THR 30 27.768 -86.813 -9.911 1.00 0.00 H +ATOM 465 HG23 THR 30 28.930 -85.505 -10.157 1.00 0.00 H +ATOM 466 OG1 THR 30 25.723 -85.602 -9.308 1.00 0.00 O +ATOM 467 HG1 THR 30 24.935 -85.054 -9.285 1.00 0.00 H +ATOM 468 C THR 30 28.342 -83.488 -8.072 1.00 0.00 C +ATOM 469 O THR 30 28.838 -83.864 -7.018 1.00 0.00 O +ATOM 470 N LYS 31 29.058 -82.692 -8.924 1.00 0.00 N +ATOM 471 H LYS 31 28.525 -82.366 -9.718 1.00 0.00 H +ATOM 472 CA LYS 31 30.458 -82.190 -8.755 1.00 0.00 C +ATOM 473 HA LYS 31 31.129 -83.024 -8.547 1.00 0.00 H +ATOM 474 CB LYS 31 30.941 -81.586 -10.123 1.00 0.00 C +ATOM 475 HB2 LYS 31 30.087 -81.032 -10.513 1.00 0.00 H +ATOM 476 HB3 LYS 31 31.803 -80.932 -9.991 1.00 0.00 H +ATOM 477 CG LYS 31 31.253 -82.699 -11.156 1.00 0.00 C +ATOM 478 HG2 LYS 31 32.178 -83.209 -10.885 1.00 0.00 H +ATOM 479 HG3 LYS 31 30.416 -83.378 -11.320 1.00 0.00 H +ATOM 480 CD LYS 31 31.445 -82.169 -12.569 1.00 0.00 C +ATOM 481 HD2 LYS 31 30.515 -81.698 -12.889 1.00 0.00 H +ATOM 482 HD3 LYS 31 32.212 -81.398 -12.647 1.00 0.00 H +ATOM 483 CE LYS 31 31.802 -83.408 -13.371 1.00 0.00 C +ATOM 484 HE2 LYS 31 32.576 -83.897 -12.779 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.033 -84.171 -13.251 1.00 0.00 H +ATOM 486 NZ LYS 31 32.199 -83.177 -14.747 1.00 0.00 N +ATOM 487 HZ1 LYS 31 32.945 -82.496 -14.751 1.00 0.00 H +ATOM 488 HZ2 LYS 31 31.424 -82.829 -15.293 1.00 0.00 H +ATOM 489 HZ3 LYS 31 32.443 -84.057 -15.179 1.00 0.00 H +ATOM 490 C LYS 31 30.562 -81.202 -7.557 1.00 0.00 C +ATOM 491 O LYS 31 31.665 -80.941 -6.960 1.00 0.00 O +ATOM 492 N ALA 32 29.473 -80.496 -7.147 1.00 0.00 N +ATOM 493 H ALA 32 28.584 -80.627 -7.608 1.00 0.00 H +ATOM 494 CA ALA 32 29.512 -79.488 -6.130 1.00 0.00 C +ATOM 495 HA ALA 32 30.427 -78.897 -6.178 1.00 0.00 H +ATOM 496 CB ALA 32 28.384 -78.506 -6.431 1.00 0.00 C +ATOM 497 HB1 ALA 32 27.470 -79.101 -6.449 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.367 -77.712 -5.684 1.00 0.00 H +ATOM 499 HB3 ALA 32 28.452 -77.914 -7.344 1.00 0.00 H +ATOM 500 C ALA 32 29.614 -80.096 -4.704 1.00 0.00 C +ATOM 501 O ALA 32 30.437 -79.745 -3.936 1.00 0.00 O +ATOM 502 N ASP 33 28.779 -81.100 -4.452 1.00 0.00 N +ATOM 503 H ASP 33 28.017 -81.220 -5.104 1.00 0.00 H +ATOM 504 CA ASP 33 28.804 -81.948 -3.239 1.00 0.00 C +ATOM 505 HA ASP 33 28.730 -81.228 -2.424 1.00 0.00 H +ATOM 506 CB ASP 33 27.624 -82.915 -3.175 1.00 0.00 C +ATOM 507 HB2 ASP 33 27.611 -83.534 -4.072 1.00 0.00 H +ATOM 508 HB3 ASP 33 27.812 -83.565 -2.321 1.00 0.00 H +ATOM 509 CG ASP 33 26.255 -82.245 -3.046 1.00 0.00 C +ATOM 510 OD1 ASP 33 25.282 -83.010 -3.137 1.00 0.00 O +ATOM 511 OD2 ASP 33 26.136 -81.060 -2.905 1.00 0.00 O +ATOM 512 C ASP 33 30.071 -82.818 -3.068 1.00 0.00 C +ATOM 513 O ASP 33 30.568 -83.002 -1.930 1.00 0.00 O +ATOM 514 N ALA 34 30.690 -83.107 -4.169 1.00 0.00 N +ATOM 515 H ALA 34 30.160 -82.993 -5.021 1.00 0.00 H +ATOM 516 CA ALA 34 32.075 -83.675 -4.340 1.00 0.00 C +ATOM 517 HA ALA 34 32.227 -84.435 -3.573 1.00 0.00 H +ATOM 518 CB ALA 34 32.051 -84.354 -5.774 1.00 0.00 C +ATOM 519 HB1 ALA 34 33.067 -84.729 -5.895 1.00 0.00 H +ATOM 520 HB2 ALA 34 31.840 -83.647 -6.576 1.00 0.00 H +ATOM 521 HB3 ALA 34 31.485 -85.279 -5.886 1.00 0.00 H +ATOM 522 C ALA 34 33.166 -82.697 -4.118 1.00 0.00 C +ATOM 523 O ALA 34 34.180 -83.040 -3.436 1.00 0.00 O +ATOM 524 N ASN 35 33.022 -81.436 -4.608 1.00 0.00 N +ATOM 525 H ASN 35 32.207 -81.169 -5.142 1.00 0.00 H +ATOM 526 CA ASN 35 34.016 -80.421 -4.337 1.00 0.00 C +ATOM 527 HA ASN 35 34.999 -80.794 -4.626 1.00 0.00 H +ATOM 528 CB ASN 35 33.792 -79.128 -5.187 1.00 0.00 C +ATOM 529 HB2 ASN 35 33.602 -79.293 -6.247 1.00 0.00 H +ATOM 530 HB3 ASN 35 32.826 -78.797 -4.806 1.00 0.00 H +ATOM 531 CG ASN 35 34.751 -78.052 -5.039 1.00 0.00 C +ATOM 532 OD1 ASN 35 35.959 -78.247 -4.969 1.00 0.00 O +ATOM 533 ND2 ASN 35 34.256 -76.869 -4.938 1.00 0.00 N +ATOM 534 HD21 ASN 35 33.259 -76.783 -4.798 1.00 0.00 H +ATOM 535 HD22 ASN 35 34.956 -76.150 -4.826 1.00 0.00 H +ATOM 536 C ASN 35 34.090 -80.187 -2.777 1.00 0.00 C +ATOM 537 O ASN 35 35.232 -80.163 -2.262 1.00 0.00 O +ATOM 538 N ASP 36 32.913 -80.091 -2.124 1.00 0.00 N +ATOM 539 H ASP 36 32.062 -79.999 -2.659 1.00 0.00 H +ATOM 540 CA ASP 36 32.903 -80.039 -0.672 1.00 0.00 C +ATOM 541 HA ASP 36 33.285 -79.088 -0.299 1.00 0.00 H +ATOM 542 CB ASP 36 31.424 -80.109 -0.256 1.00 0.00 C +ATOM 543 HB2 ASP 36 30.862 -80.974 -0.607 1.00 0.00 H +ATOM 544 HB3 ASP 36 31.478 -80.108 0.833 1.00 0.00 H +ATOM 545 CG ASP 36 30.585 -78.928 -0.786 1.00 0.00 C +ATOM 546 OD1 ASP 36 29.346 -79.042 -1.011 1.00 0.00 O +ATOM 547 OD2 ASP 36 31.090 -77.787 -1.059 1.00 0.00 O +ATOM 548 C ASP 36 33.613 -81.176 0.078 1.00 0.00 C +ATOM 549 O ASP 36 33.971 -81.039 1.250 1.00 0.00 O +ATOM 550 N LYS 37 33.576 -82.386 -0.425 1.00 0.00 N +ATOM 551 H LYS 37 33.143 -82.490 -1.331 1.00 0.00 H +ATOM 552 CA LYS 37 34.163 -83.569 0.235 1.00 0.00 C +ATOM 553 HA LYS 37 34.176 -83.470 1.320 1.00 0.00 H +ATOM 554 CB LYS 37 33.309 -84.788 -0.120 1.00 0.00 C +ATOM 555 HB2 LYS 37 33.743 -85.750 0.155 1.00 0.00 H +ATOM 556 HB3 LYS 37 33.098 -84.775 -1.189 1.00 0.00 H +ATOM 557 CG LYS 37 31.961 -84.898 0.670 1.00 0.00 C +ATOM 558 HG2 LYS 37 31.411 -83.958 0.716 1.00 0.00 H +ATOM 559 HG3 LYS 37 32.094 -85.309 1.671 1.00 0.00 H +ATOM 560 CD LYS 37 31.040 -85.850 -0.065 1.00 0.00 C +ATOM 561 HD2 LYS 37 30.665 -85.485 -1.021 1.00 0.00 H +ATOM 562 HD3 LYS 37 31.539 -86.807 -0.216 1.00 0.00 H +ATOM 563 CE LYS 37 29.762 -86.143 0.685 1.00 0.00 C +ATOM 564 HE2 LYS 37 29.999 -86.532 1.675 1.00 0.00 H +ATOM 565 HE3 LYS 37 29.245 -85.188 0.771 1.00 0.00 H +ATOM 566 NZ LYS 37 28.844 -87.037 -0.139 1.00 0.00 N +ATOM 567 HZ1 LYS 37 28.448 -86.547 -0.928 1.00 0.00 H +ATOM 568 HZ2 LYS 37 29.378 -87.782 -0.563 1.00 0.00 H +ATOM 569 HZ3 LYS 37 28.203 -87.641 0.356 1.00 0.00 H +ATOM 570 C LYS 37 35.566 -83.821 -0.267 1.00 0.00 C +ATOM 571 O LYS 37 36.233 -84.609 0.398 1.00 0.00 O +ATOM 572 N GLY 38 35.980 -83.165 -1.348 1.00 0.00 N +ATOM 573 H GLY 38 35.370 -82.446 -1.710 1.00 0.00 H +ATOM 574 CA GLY 38 37.338 -83.427 -1.939 1.00 0.00 C +ATOM 575 HA2 GLY 38 37.740 -82.582 -2.497 1.00 0.00 H +ATOM 576 HA3 GLY 38 38.050 -83.561 -1.124 1.00 0.00 H +ATOM 577 C GLY 38 37.472 -84.638 -2.824 1.00 0.00 C +ATOM 578 O GLY 38 38.592 -85.106 -2.991 1.00 0.00 O +ATOM 579 N VAL 39 36.387 -85.059 -3.515 1.00 0.00 N +ATOM 580 H VAL 39 35.528 -84.538 -3.406 1.00 0.00 H +ATOM 581 CA VAL 39 36.374 -86.144 -4.544 1.00 0.00 C +ATOM 582 HA VAL 39 37.206 -86.799 -4.284 1.00 0.00 H +ATOM 583 CB VAL 39 35.023 -86.770 -4.491 1.00 0.00 C +ATOM 584 HB VAL 39 34.390 -85.972 -4.878 1.00 0.00 H +ATOM 585 CG1 VAL 39 34.953 -88.058 -5.460 1.00 0.00 C +ATOM 586 HG11 VAL 39 33.938 -88.442 -5.563 1.00 0.00 H +ATOM 587 HG12 VAL 39 35.685 -88.787 -5.112 1.00 0.00 H +ATOM 588 HG13 VAL 39 35.279 -87.767 -6.458 1.00 0.00 H +ATOM 589 CG2 VAL 39 34.662 -87.223 -3.041 1.00 0.00 C +ATOM 590 HG21 VAL 39 34.416 -86.395 -2.376 1.00 0.00 H +ATOM 591 HG22 VAL 39 35.426 -87.744 -2.464 1.00 0.00 H +ATOM 592 HG23 VAL 39 33.761 -87.836 -3.027 1.00 0.00 H +ATOM 593 C VAL 39 36.699 -85.670 -5.965 1.00 0.00 C +ATOM 594 O VAL 39 35.867 -84.944 -6.562 1.00 0.00 O +ATOM 595 N ASP 40 37.822 -86.089 -6.581 1.00 0.00 N +ATOM 596 H ASP 40 38.331 -86.755 -6.018 1.00 0.00 H +ATOM 597 CA ASP 40 38.367 -85.753 -7.913 1.00 0.00 C +ATOM 598 HA ASP 40 37.885 -84.816 -8.190 1.00 0.00 H +ATOM 599 CB ASP 40 39.876 -85.597 -7.897 1.00 0.00 C +ATOM 600 HB2 ASP 40 40.263 -85.200 -8.836 1.00 0.00 H +ATOM 601 HB3 ASP 40 40.110 -84.790 -7.203 1.00 0.00 H +ATOM 602 CG ASP 40 40.739 -86.788 -7.433 1.00 0.00 C +ATOM 603 OD1 ASP 40 41.981 -86.815 -7.557 1.00 0.00 O +ATOM 604 OD2 ASP 40 40.178 -87.637 -6.708 1.00 0.00 O +ATOM 605 C ASP 40 37.929 -86.724 -9.078 1.00 0.00 C +ATOM 606 O ASP 40 38.610 -86.810 -10.053 1.00 0.00 O +ATOM 607 N GLY 41 36.961 -87.573 -8.845 1.00 0.00 N +ATOM 608 H GLY 41 36.719 -87.739 -7.878 1.00 0.00 H +ATOM 609 CA GLY 41 36.333 -88.573 -9.785 1.00 0.00 C +ATOM 610 HA2 GLY 41 37.003 -89.361 -10.130 1.00 0.00 H +ATOM 611 HA3 GLY 41 35.439 -88.946 -9.286 1.00 0.00 H +ATOM 612 C GLY 41 35.779 -87.786 -11.057 1.00 0.00 C +ATOM 613 O GLY 41 35.797 -86.560 -11.146 1.00 0.00 O +ATOM 614 N GLU 42 35.168 -88.527 -11.976 1.00 0.00 N +ATOM 615 H GLU 42 35.388 -89.512 -12.019 1.00 0.00 H +ATOM 616 CA GLU 42 34.254 -88.015 -13.053 1.00 0.00 C +ATOM 617 HA GLU 42 34.091 -86.947 -12.908 1.00 0.00 H +ATOM 618 CB GLU 42 34.997 -87.972 -14.404 1.00 0.00 C +ATOM 619 HB2 GLU 42 35.946 -87.468 -14.220 1.00 0.00 H +ATOM 620 HB3 GLU 42 35.368 -88.979 -14.599 1.00 0.00 H +ATOM 621 CG GLU 42 34.365 -87.413 -15.715 1.00 0.00 C +ATOM 622 HG2 GLU 42 35.153 -87.328 -16.462 1.00 0.00 H +ATOM 623 HG3 GLU 42 33.608 -88.113 -16.070 1.00 0.00 H +ATOM 624 CD GLU 42 33.727 -86.054 -15.502 1.00 0.00 C +ATOM 625 OE1 GLU 42 34.416 -85.047 -15.764 1.00 0.00 O +ATOM 626 OE2 GLU 42 32.543 -85.969 -15.170 1.00 0.00 O +ATOM 627 C GLU 42 32.910 -88.730 -12.994 1.00 0.00 C +ATOM 628 O GLU 42 32.817 -89.826 -12.438 1.00 0.00 O +ATOM 629 N TRP 43 31.841 -88.173 -13.602 1.00 0.00 N +ATOM 630 H TRP 43 31.980 -87.296 -14.084 1.00 0.00 H +ATOM 631 CA TRP 43 30.439 -88.639 -13.453 1.00 0.00 C +ATOM 632 HA TRP 43 30.534 -89.617 -12.982 1.00 0.00 H +ATOM 633 CB TRP 43 29.707 -87.763 -12.495 1.00 0.00 C +ATOM 634 HB2 TRP 43 29.945 -86.747 -12.807 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.639 -87.944 -12.614 1.00 0.00 H +ATOM 636 CG TRP 43 30.071 -87.943 -11.045 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.746 -89.024 -10.335 1.00 0.00 C +ATOM 638 HD1 TRP 43 29.201 -89.901 -10.649 1.00 0.00 H +ATOM 639 NE1 TRP 43 30.329 -88.881 -9.092 1.00 0.00 N +ATOM 640 HE1 TRP 43 30.242 -89.550 -8.340 1.00 0.00 H +ATOM 641 CE2 TRP 43 31.225 -87.863 -9.035 1.00 0.00 C +ATOM 642 CZ2 TRP 43 32.161 -87.481 -8.071 1.00 0.00 C +ATOM 643 HZ2 TRP 43 32.236 -87.997 -7.126 1.00 0.00 H +ATOM 644 CH2 TRP 43 32.938 -86.419 -8.392 1.00 0.00 C +ATOM 645 HH2 TRP 43 33.617 -86.102 -7.615 1.00 0.00 H +ATOM 646 CZ3 TRP 43 32.931 -85.783 -9.643 1.00 0.00 C +ATOM 647 HZ3 TRP 43 33.694 -85.038 -9.816 1.00 0.00 H +ATOM 648 CE3 TRP 43 32.033 -86.207 -10.630 1.00 0.00 C +ATOM 649 HE3 TRP 43 32.044 -85.730 -11.599 1.00 0.00 H +ATOM 650 CD2 TRP 43 31.130 -87.228 -10.316 1.00 0.00 C +ATOM 651 C TRP 43 29.791 -88.846 -14.841 1.00 0.00 C +ATOM 652 O TRP 43 29.446 -87.858 -15.495 1.00 0.00 O +ATOM 653 N THR 44 29.650 -90.123 -15.157 1.00 0.00 N +ATOM 654 H THR 44 29.754 -90.799 -14.414 1.00 0.00 H +ATOM 655 CA THR 44 28.887 -90.553 -16.344 1.00 0.00 C +ATOM 656 HA THR 44 29.088 -89.850 -17.152 1.00 0.00 H +ATOM 657 CB THR 44 29.276 -91.946 -16.752 1.00 0.00 C +ATOM 658 HB THR 44 30.342 -91.919 -16.976 1.00 0.00 H +ATOM 659 CG2 THR 44 29.281 -93.006 -15.636 1.00 0.00 C +ATOM 660 HG21 THR 44 30.111 -92.844 -14.948 1.00 0.00 H +ATOM 661 HG22 THR 44 29.348 -93.964 -16.149 1.00 0.00 H +ATOM 662 HG23 THR 44 28.328 -92.975 -15.106 1.00 0.00 H +ATOM 663 OG1 THR 44 28.457 -92.517 -17.770 1.00 0.00 O +ATOM 664 HG1 THR 44 28.668 -92.057 -18.586 1.00 0.00 H +ATOM 665 C THR 44 27.355 -90.550 -16.066 1.00 0.00 C +ATOM 666 O THR 44 26.888 -90.639 -14.957 1.00 0.00 O +ATOM 667 N TYR 45 26.642 -90.403 -17.162 1.00 0.00 N +ATOM 668 H TYR 45 27.169 -90.436 -18.023 1.00 0.00 H +ATOM 669 CA TYR 45 25.204 -90.270 -17.251 1.00 0.00 C +ATOM 670 HA TYR 45 24.753 -90.423 -16.270 1.00 0.00 H +ATOM 671 CB TYR 45 24.801 -88.850 -17.600 1.00 0.00 C +ATOM 672 HB2 TYR 45 25.235 -88.176 -16.861 1.00 0.00 H +ATOM 673 HB3 TYR 45 25.322 -88.593 -18.523 1.00 0.00 H +ATOM 674 CG TYR 45 23.303 -88.530 -17.635 1.00 0.00 C +ATOM 675 CD1 TYR 45 22.503 -88.741 -16.501 1.00 0.00 C +ATOM 676 HD1 TYR 45 22.982 -89.030 -15.577 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.072 -88.681 -16.562 1.00 0.00 C +ATOM 678 HE1 TYR 45 20.508 -88.877 -15.662 1.00 0.00 H +ATOM 679 CZ TYR 45 20.451 -88.219 -17.748 1.00 0.00 C +ATOM 680 OH TYR 45 19.066 -88.077 -17.738 1.00 0.00 O +ATOM 681 HH TYR 45 18.789 -87.577 -18.510 1.00 0.00 H +ATOM 682 CE2 TYR 45 21.237 -87.951 -18.898 1.00 0.00 C +ATOM 683 HE2 TYR 45 20.813 -87.750 -19.871 1.00 0.00 H +ATOM 684 CD2 TYR 45 22.652 -88.108 -18.773 1.00 0.00 C +ATOM 685 HD2 TYR 45 23.325 -87.990 -19.609 1.00 0.00 H +ATOM 686 C TYR 45 24.527 -91.391 -18.105 1.00 0.00 C +ATOM 687 O TYR 45 24.962 -91.667 -19.253 1.00 0.00 O +ATOM 688 N ASP 46 23.422 -91.931 -17.658 1.00 0.00 N +ATOM 689 H ASP 46 22.985 -91.617 -16.803 1.00 0.00 H +ATOM 690 CA ASP 46 22.600 -92.924 -18.380 1.00 0.00 C +ATOM 691 HA ASP 46 22.919 -92.979 -19.421 1.00 0.00 H +ATOM 692 CB ASP 46 22.596 -94.331 -17.804 1.00 0.00 C +ATOM 693 HB2 ASP 46 23.638 -94.649 -17.847 1.00 0.00 H +ATOM 694 HB3 ASP 46 22.288 -94.306 -16.759 1.00 0.00 H +ATOM 695 CG ASP 46 21.683 -95.290 -18.566 1.00 0.00 C +ATOM 696 OD1 ASP 46 21.097 -96.220 -17.917 1.00 0.00 O +ATOM 697 OD2 ASP 46 21.400 -95.011 -19.805 1.00 0.00 O +ATOM 698 C ASP 46 21.126 -92.334 -18.442 1.00 0.00 C +ATOM 699 O ASP 46 20.309 -92.481 -17.555 1.00 0.00 O +ATOM 700 N ASP 47 20.786 -91.808 -19.634 1.00 0.00 N +ATOM 701 H ASP 47 21.408 -91.987 -20.410 1.00 0.00 H +ATOM 702 CA ASP 47 19.528 -91.210 -19.974 1.00 0.00 C +ATOM 703 HA ASP 47 19.270 -90.405 -19.287 1.00 0.00 H +ATOM 704 CB ASP 47 19.787 -90.507 -21.374 1.00 0.00 C +ATOM 705 HB2 ASP 47 20.622 -89.816 -21.265 1.00 0.00 H +ATOM 706 HB3 ASP 47 20.040 -91.279 -22.101 1.00 0.00 H +ATOM 707 CG ASP 47 18.615 -89.643 -21.876 1.00 0.00 C +ATOM 708 OD1 ASP 47 17.620 -89.446 -21.158 1.00 0.00 O +ATOM 709 OD2 ASP 47 18.794 -89.093 -23.003 1.00 0.00 O +ATOM 710 C ASP 47 18.390 -92.228 -19.926 1.00 0.00 C +ATOM 711 O ASP 47 17.228 -92.011 -19.469 1.00 0.00 O +ATOM 712 N ALA 48 18.646 -93.476 -20.387 1.00 0.00 N +ATOM 713 H ALA 48 19.548 -93.543 -20.836 1.00 0.00 H +ATOM 714 CA ALA 48 17.613 -94.569 -20.428 1.00 0.00 C +ATOM 715 HA ALA 48 16.780 -94.154 -20.995 1.00 0.00 H +ATOM 716 CB ALA 48 18.243 -95.791 -21.114 1.00 0.00 C +ATOM 717 HB1 ALA 48 19.150 -96.080 -20.584 1.00 0.00 H +ATOM 718 HB2 ALA 48 18.516 -95.451 -22.113 1.00 0.00 H +ATOM 719 HB3 ALA 48 17.541 -96.623 -21.064 1.00 0.00 H +ATOM 720 C ALA 48 17.132 -94.818 -18.993 1.00 0.00 C +ATOM 721 O ALA 48 15.907 -95.015 -18.819 1.00 0.00 O +ATOM 722 N THR 49 17.922 -94.755 -17.922 1.00 0.00 N +ATOM 723 H THR 49 18.893 -94.693 -18.193 1.00 0.00 H +ATOM 724 CA THR 49 17.426 -94.861 -16.502 1.00 0.00 C +ATOM 725 HA THR 49 16.431 -95.305 -16.536 1.00 0.00 H +ATOM 726 CB THR 49 18.217 -95.924 -15.679 1.00 0.00 C +ATOM 727 HB THR 49 17.994 -95.904 -14.613 1.00 0.00 H +ATOM 728 CG2 THR 49 18.418 -97.345 -16.170 1.00 0.00 C +ATOM 729 HG21 THR 49 18.841 -97.440 -17.170 1.00 0.00 H +ATOM 730 HG22 THR 49 17.405 -97.715 -16.331 1.00 0.00 H +ATOM 731 HG23 THR 49 19.021 -98.014 -15.557 1.00 0.00 H +ATOM 732 OG1 THR 49 19.552 -95.468 -15.810 1.00 0.00 O +ATOM 733 HG1 THR 49 19.923 -95.812 -16.626 1.00 0.00 H +ATOM 734 C THR 49 17.421 -93.573 -15.671 1.00 0.00 C +ATOM 735 O THR 49 17.174 -93.600 -14.452 1.00 0.00 O +ATOM 736 N LYS 50 17.782 -92.422 -16.316 1.00 0.00 N +ATOM 737 H LYS 50 18.132 -92.635 -17.239 1.00 0.00 H +ATOM 738 CA LYS 50 17.876 -91.084 -15.709 1.00 0.00 C +ATOM 739 HA LYS 50 18.433 -90.477 -16.423 1.00 0.00 H +ATOM 740 CB LYS 50 16.542 -90.484 -15.317 1.00 0.00 C +ATOM 741 HB2 LYS 50 16.115 -91.046 -14.486 1.00 0.00 H +ATOM 742 HB3 LYS 50 16.644 -89.457 -14.966 1.00 0.00 H +ATOM 743 CG LYS 50 15.587 -90.483 -16.482 1.00 0.00 C +ATOM 744 HG2 LYS 50 15.415 -91.502 -16.829 1.00 0.00 H +ATOM 745 HG3 LYS 50 14.645 -90.031 -16.173 1.00 0.00 H +ATOM 746 CD LYS 50 16.058 -89.536 -17.616 1.00 0.00 C +ATOM 747 HD2 LYS 50 16.273 -88.554 -17.196 1.00 0.00 H +ATOM 748 HD3 LYS 50 16.958 -89.948 -18.073 1.00 0.00 H +ATOM 749 CE LYS 50 14.977 -89.328 -18.637 1.00 0.00 C +ATOM 750 HE2 LYS 50 14.718 -90.244 -19.168 1.00 0.00 H +ATOM 751 HE3 LYS 50 14.095 -88.969 -18.107 1.00 0.00 H +ATOM 752 NZ LYS 50 15.515 -88.431 -19.696 1.00 0.00 N +ATOM 753 HZ1 LYS 50 16.033 -87.612 -19.411 1.00 0.00 H +ATOM 754 HZ2 LYS 50 14.765 -88.073 -20.269 1.00 0.00 H +ATOM 755 HZ3 LYS 50 16.199 -88.930 -20.248 1.00 0.00 H +ATOM 756 C LYS 50 18.888 -90.991 -14.559 1.00 0.00 C +ATOM 757 O LYS 50 18.547 -90.562 -13.462 1.00 0.00 O +ATOM 758 N THR 51 20.022 -91.601 -14.770 1.00 0.00 N +ATOM 759 H THR 51 20.095 -91.955 -15.713 1.00 0.00 H +ATOM 760 CA THR 51 20.996 -91.998 -13.672 1.00 0.00 C +ATOM 761 HA THR 51 20.639 -91.552 -12.743 1.00 0.00 H +ATOM 762 CB THR 51 20.958 -93.521 -13.437 1.00 0.00 C +ATOM 763 HB THR 51 21.435 -94.080 -14.242 1.00 0.00 H +ATOM 764 CG2 THR 51 21.669 -93.919 -12.122 1.00 0.00 C +ATOM 765 HG21 THR 51 21.319 -93.311 -11.287 1.00 0.00 H +ATOM 766 HG22 THR 51 22.706 -93.636 -12.305 1.00 0.00 H +ATOM 767 HG23 THR 51 21.564 -94.989 -11.943 1.00 0.00 H +ATOM 768 OG1 THR 51 19.675 -94.077 -13.258 1.00 0.00 O +ATOM 769 HG1 THR 51 19.357 -94.048 -14.164 1.00 0.00 H +ATOM 770 C THR 51 22.464 -91.653 -13.897 1.00 0.00 C +ATOM 771 O THR 51 23.052 -91.885 -14.942 1.00 0.00 O +ATOM 772 N PHE 52 23.010 -90.969 -12.900 1.00 0.00 N +ATOM 773 H PHE 52 22.385 -90.847 -12.116 1.00 0.00 H +ATOM 774 CA PHE 52 24.443 -90.694 -12.851 1.00 0.00 C +ATOM 775 HA PHE 52 24.870 -90.599 -13.849 1.00 0.00 H +ATOM 776 CB PHE 52 24.650 -89.364 -12.073 1.00 0.00 C +ATOM 777 HB2 PHE 52 23.967 -89.291 -11.227 1.00 0.00 H +ATOM 778 HB3 PHE 52 25.651 -89.206 -11.673 1.00 0.00 H +ATOM 779 CG PHE 52 24.362 -88.248 -13.050 1.00 0.00 C +ATOM 780 CD1 PHE 52 23.031 -87.758 -13.200 1.00 0.00 C +ATOM 781 HD1 PHE 52 22.227 -88.112 -12.572 1.00 0.00 H +ATOM 782 CE1 PHE 52 22.776 -86.696 -14.080 1.00 0.00 C +ATOM 783 HE1 PHE 52 21.802 -86.242 -14.185 1.00 0.00 H +ATOM 784 CZ PHE 52 23.794 -86.192 -14.870 1.00 0.00 C +ATOM 785 HZ PHE 52 23.596 -85.505 -15.679 1.00 0.00 H +ATOM 786 CE2 PHE 52 25.082 -86.608 -14.670 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.831 -86.099 -15.259 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.423 -87.631 -13.732 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.432 -88.011 -13.675 1.00 0.00 H +ATOM 790 C PHE 52 25.239 -91.768 -12.039 1.00 0.00 C +ATOM 791 O PHE 52 24.699 -92.411 -11.113 1.00 0.00 O +ATOM 792 N THR 53 26.512 -91.952 -12.414 1.00 0.00 N +ATOM 793 H THR 53 26.798 -91.257 -13.088 1.00 0.00 H +ATOM 794 CA THR 53 27.486 -92.947 -11.870 1.00 0.00 C +ATOM 795 HA THR 53 27.202 -93.228 -10.856 1.00 0.00 H +ATOM 796 CB THR 53 27.348 -94.303 -12.631 1.00 0.00 C +ATOM 797 HB THR 53 27.978 -94.251 -13.519 1.00 0.00 H +ATOM 798 CG2 THR 53 27.875 -95.508 -11.840 1.00 0.00 C +ATOM 799 HG21 THR 53 27.505 -96.437 -12.273 1.00 0.00 H +ATOM 800 HG22 THR 53 27.590 -95.398 -10.794 1.00 0.00 H +ATOM 801 HG23 THR 53 28.964 -95.478 -11.826 1.00 0.00 H +ATOM 802 OG1 THR 53 25.999 -94.654 -12.964 1.00 0.00 O +ATOM 803 HG1 THR 53 25.829 -94.330 -13.852 1.00 0.00 H +ATOM 804 C THR 53 28.969 -92.484 -11.831 1.00 0.00 C +ATOM 805 O THR 53 29.362 -91.697 -12.697 1.00 0.00 O +ATOM 806 N VAL 54 29.726 -92.738 -10.762 1.00 0.00 N +ATOM 807 H VAL 54 29.409 -93.303 -9.988 1.00 0.00 H +ATOM 808 CA VAL 54 31.163 -92.409 -10.710 1.00 0.00 C +ATOM 809 HA VAL 54 31.230 -91.414 -11.148 1.00 0.00 H +ATOM 810 CB VAL 54 31.657 -92.418 -9.199 1.00 0.00 C +ATOM 811 HB VAL 54 31.019 -91.742 -8.630 1.00 0.00 H +ATOM 812 CG1 VAL 54 31.640 -93.855 -8.735 1.00 0.00 C +ATOM 813 HG11 VAL 54 32.516 -94.328 -9.178 1.00 0.00 H +ATOM 814 HG12 VAL 54 30.709 -94.344 -9.021 1.00 0.00 H +ATOM 815 HG13 VAL 54 31.687 -93.885 -7.646 1.00 0.00 H +ATOM 816 CG2 VAL 54 33.070 -91.832 -9.069 1.00 0.00 C +ATOM 817 HG21 VAL 54 33.239 -91.745 -7.996 1.00 0.00 H +ATOM 818 HG22 VAL 54 33.172 -90.865 -9.561 1.00 0.00 H +ATOM 819 HG23 VAL 54 33.829 -92.477 -9.511 1.00 0.00 H +ATOM 820 C VAL 54 31.980 -93.258 -11.627 1.00 0.00 C +ATOM 821 O VAL 54 31.733 -94.412 -11.869 1.00 0.00 O +ATOM 822 N THR 55 32.994 -92.622 -12.226 1.00 0.00 N +ATOM 823 H THR 55 33.091 -91.620 -12.307 1.00 0.00 H +ATOM 824 CA THR 55 34.078 -93.319 -12.841 1.00 0.00 C +ATOM 825 HA THR 55 34.062 -94.365 -12.533 1.00 0.00 H +ATOM 826 CB THR 55 33.877 -93.370 -14.348 1.00 0.00 C +ATOM 827 HB THR 55 32.924 -93.884 -14.475 1.00 0.00 H +ATOM 828 CG2 THR 55 33.894 -92.120 -15.172 1.00 0.00 C +ATOM 829 HG21 THR 55 34.894 -91.740 -15.377 1.00 0.00 H +ATOM 830 HG22 THR 55 33.327 -91.391 -14.593 1.00 0.00 H +ATOM 831 HG23 THR 55 33.416 -92.254 -16.143 1.00 0.00 H +ATOM 832 OG1 THR 55 34.949 -94.141 -14.881 1.00 0.00 O +ATOM 833 HG1 THR 55 34.589 -94.612 -15.636 1.00 0.00 H +ATOM 834 C THR 55 35.385 -92.656 -12.519 1.00 0.00 C +ATOM 835 O THR 55 35.544 -91.459 -12.379 1.00 0.00 O +ATOM 836 N GLU 56 36.379 -93.530 -12.262 1.00 0.00 N +ATOM 837 H GLU 56 36.062 -94.470 -12.448 1.00 0.00 H +ATOM 838 CA GLU 56 37.616 -93.250 -11.595 1.00 0.00 C +ATOM 839 HA GLU 56 37.604 -92.240 -11.184 1.00 0.00 H +ATOM 840 CB GLU 56 37.866 -94.143 -10.385 1.00 0.00 C +ATOM 841 HB2 GLU 56 37.899 -95.206 -10.622 1.00 0.00 H +ATOM 842 HB3 GLU 56 38.762 -93.842 -9.843 1.00 0.00 H +ATOM 843 CG GLU 56 36.670 -93.986 -9.445 1.00 0.00 C +ATOM 844 HG2 GLU 56 36.396 -92.932 -9.391 1.00 0.00 H +ATOM 845 HG3 GLU 56 35.834 -94.624 -9.732 1.00 0.00 H +ATOM 846 CD GLU 56 37.068 -94.292 -7.961 1.00 0.00 C +ATOM 847 OE1 GLU 56 37.875 -93.586 -7.298 1.00 0.00 O +ATOM 848 OE2 GLU 56 36.524 -95.253 -7.436 1.00 0.00 O +ATOM 849 C GLU 56 38.740 -93.284 -12.623 1.00 0.00 C +ATOM 850 O GLU 56 39.000 -92.299 -13.292 1.00 0.00 O +ATOM 851 OXT GLU 56 39.381 -94.364 -12.719 1.00 0.00 O +ATOM 852 ZN ZN1 57 25.100 -87.152 -6.560 1.00 0.00 ZN +ATOM 853 N AN1 58 26.967 -86.664 -5.694 1.00 0.00 N +ATOM 854 C AN1 58 29.314 -86.682 -4.687 1.00 0.00 C +ATOM 855 C1 AN1 58 27.986 -86.551 -5.171 1.00 0.00 C +ATOM 856 H AN1 58 29.917 -86.607 -5.600 1.00 0.00 H +ATOM 857 H1 AN1 58 29.495 -87.631 -4.167 1.00 0.00 H +ATOM 858 H2 AN1 58 29.640 -85.822 -4.090 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 29.727 -90.743 -6.412 1.00 0.00 N +ATOM 860 N2 AZI 59 29.040 -90.347 -5.478 1.00 0.00 N +ATOM 861 N3 AZI 59 28.347 -89.841 -4.556 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/inp/pdbs/cluster.c6.pdb b/tests/nsga2/inp/pdbs/cluster.c6.pdb new file mode 100644 index 0000000..5a511d2 --- /dev/null +++ b/tests/nsga2/inp/pdbs/cluster.c6.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HE1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HE1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HE1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HE1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HE1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HE1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HE1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HE1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HE1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HE1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HE1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HE1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HE1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HE1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HE1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HE1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HE1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N ASN 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H ASN 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA ASN 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 HA ASN 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 136 CB ASN 8 32.146 -93.816 -4.501 1.00 0.00 C +ATOM 137 HB2 ASN 8 31.899 -92.888 -5.015 1.00 0.00 H +ATOM 138 HB3 ASN 8 31.764 -93.743 -3.483 1.00 0.00 H +ATOM 139 CG ASN 8 33.605 -94.026 -4.560 1.00 0.00 C +ATOM 140 OD1 ASN 8 34.120 -94.429 -5.587 1.00 0.00 O +ATOM 141 ND2 ASN 8 34.230 -93.804 -3.459 1.00 0.00 N +ATOM 142 HD21 ASN 8 33.763 -93.677 -2.573 1.00 0.00 H +ATOM 143 HD22 ASN 8 35.231 -93.787 -3.589 1.00 0.00 H +ATOM 144 C ASN 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 145 O ASN 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 146 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 147 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 148 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 149 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 150 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 151 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 152 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 153 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 154 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 155 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 156 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 157 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 158 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 159 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 160 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 161 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 162 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 163 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 164 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 165 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 166 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 167 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 168 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 169 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 170 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 171 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 172 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 173 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 174 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 175 N THR 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 176 H THR 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 177 CA THR 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 178 HA THR 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 179 CB THR 11 32.204-101.575 0.708 1.00 0.00 C +ATOM 180 HB THR 11 32.357-100.511 0.524 1.00 0.00 H +ATOM 181 CG2 THR 11 31.844-101.737 2.186 1.00 0.00 C +ATOM 182 HG21 THR 11 31.939-102.768 2.527 1.00 0.00 H +ATOM 183 HG22 THR 11 30.866-101.287 2.359 1.00 0.00 H +ATOM 184 HG23 THR 11 32.641-101.220 2.720 1.00 0.00 H +ATOM 185 OG1 THR 11 33.395-102.365 0.540 1.00 0.00 O +ATOM 186 HG1 THR 11 33.889-101.797 -0.056 1.00 0.00 H +ATOM 187 C THR 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 188 O THR 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 189 N LEU 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 190 H LEU 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 191 CA LEU 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 192 HA LEU 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 193 CB LEU 12 28.128 -98.251 -0.163 1.00 0.00 C +ATOM 194 HB2 LEU 12 28.747 -97.809 -0.944 1.00 0.00 H +ATOM 195 HB3 LEU 12 27.159 -97.765 -0.285 1.00 0.00 H +ATOM 196 CG LEU 12 28.691 -97.864 1.224 1.00 0.00 C +ATOM 197 HG LEU 12 29.731 -98.167 1.352 1.00 0.00 H +ATOM 198 CD1 LEU 12 28.636 -96.332 1.379 1.00 0.00 C +ATOM 199 HD11 LEU 12 27.594 -96.036 1.503 1.00 0.00 H +ATOM 200 HD12 LEU 12 28.995 -95.783 0.508 1.00 0.00 H +ATOM 201 HD13 LEU 12 29.219 -95.938 2.212 1.00 0.00 H +ATOM 202 CD2 LEU 12 27.939 -98.536 2.321 1.00 0.00 C +ATOM 203 HD21 LEU 12 26.858 -98.614 2.209 1.00 0.00 H +ATOM 204 HD22 LEU 12 28.012 -97.961 3.244 1.00 0.00 H +ATOM 205 HD23 LEU 12 28.324 -99.549 2.439 1.00 0.00 H +ATOM 206 C LEU 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 207 O LEU 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 208 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 209 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 210 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 211 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 212 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 213 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 214 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 215 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 216 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 217 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 218 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 219 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 220 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 221 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 222 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 223 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 224 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 225 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 226 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 227 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 228 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 229 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 230 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 231 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 232 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 233 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 234 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 235 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 236 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 237 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 238 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 239 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 240 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 241 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 242 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 243 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 244 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 245 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 246 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 247 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 248 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 249 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 250 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 251 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 252 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 253 N HD1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 254 CA HD1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 255 C HD1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 256 O HD1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 257 CB HD1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 258 CG HD1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 259 CD2 HD1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 260 ND1 HD1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 261 CE1 HD1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 262 NE2 HD1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 263 H HD1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 264 HA HD1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 265 HB2 HD1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 266 HB3 HD1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 267 HD1 HD1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 268 HD2 HD1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 269 HE1 HD1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 270 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 271 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 272 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 273 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 274 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 275 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 276 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 277 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 278 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 279 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 280 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 281 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 282 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 283 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 284 N HD2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 285 CA HD2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 286 C HD2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 287 O HD2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 288 CB HD2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 289 CG HD2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 290 CD2 HD2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 291 ND1 HD2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 292 CE1 HD2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 293 NE2 HD2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 294 H HD2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 295 HA HD2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 296 HB2 HD2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 297 HB3 HD2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 298 HD1 HD2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 299 HD2 HD2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 300 HE1 HD2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 301 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 302 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 303 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 304 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 305 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 306 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 307 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 308 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 309 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 310 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 311 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 312 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 313 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 314 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 315 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 316 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 317 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 318 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 319 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 320 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 324 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 325 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 326 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 327 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 328 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 329 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 330 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 331 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 332 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 333 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 334 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 335 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 336 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 337 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 338 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 339 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 340 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 341 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 342 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 343 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 344 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 345 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 346 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 348 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 349 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 350 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 351 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 352 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 353 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 354 N ALA 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 355 H ALA 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 356 CA ALA 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 357 HA ALA 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 358 CB ALA 23 21.411 -85.209 -16.800 1.00 0.00 C +ATOM 359 HB1 ALA 23 20.431 -85.678 -16.716 1.00 0.00 H +ATOM 360 HB2 ALA 23 22.276 -85.746 -16.411 1.00 0.00 H +ATOM 361 HB3 ALA 23 21.537 -85.216 -17.883 1.00 0.00 H +ATOM 362 C ALA 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 363 O ALA 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 364 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 365 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 366 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 367 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 368 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 369 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 370 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 371 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 372 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 373 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 374 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 375 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 376 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 377 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 378 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 379 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 380 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 381 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 382 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 383 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 384 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 385 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 386 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 387 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 388 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 389 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 390 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 391 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 392 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 393 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 394 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 395 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 396 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 397 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 398 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 399 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 400 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 401 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 402 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 403 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 404 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 405 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 406 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 407 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 408 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 409 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 410 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 411 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 412 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 413 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 414 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 415 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 416 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 417 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 418 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 419 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 420 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 421 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 422 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 423 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 424 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 425 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 426 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 427 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 428 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 429 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 430 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 431 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 432 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 433 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 434 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 435 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 436 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 437 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 438 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 439 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 440 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 441 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 442 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 443 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 444 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 445 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 446 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 447 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 448 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 449 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 450 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 451 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 452 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 453 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 454 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 455 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 456 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 457 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 458 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 459 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 460 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 461 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 462 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 463 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 464 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 465 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 466 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 467 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 468 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 469 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 470 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 471 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 472 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 473 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 474 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 475 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 476 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 477 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 478 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 479 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 480 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 481 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 482 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 483 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 484 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 485 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 486 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 487 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 488 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 489 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 490 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 491 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 492 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 493 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 494 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 495 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 496 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 497 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 499 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 500 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 501 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 502 N ASP 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 503 H ASP 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 504 CA ASP 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 505 HA ASP 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 506 CB ASP 33 27.285 -82.550 -3.275 1.00 0.00 C +ATOM 507 HB2 ASP 33 27.070 -82.631 -4.341 1.00 0.00 H +ATOM 508 HB3 ASP 33 27.480 -83.490 -2.758 1.00 0.00 H +ATOM 509 CG ASP 33 26.062 -81.973 -2.556 1.00 0.00 C +ATOM 510 OD1 ASP 33 26.059 -81.149 -1.590 1.00 0.00 O +ATOM 511 OD2 ASP 33 24.981 -82.468 -2.893 1.00 0.00 O +ATOM 512 C ASP 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 513 O ASP 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 514 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 515 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 516 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 517 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 518 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 519 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 520 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 521 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 522 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 523 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 524 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 525 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 526 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 527 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 528 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 529 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 530 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 531 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 532 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 533 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 534 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 535 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 536 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 537 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 538 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 539 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 540 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 541 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 542 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 543 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 544 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 545 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 546 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 547 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 548 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 549 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 550 N LYS 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 551 H LYS 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 552 CA LYS 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 553 HA LYS 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 554 CB LYS 37 33.044 -83.890 0.492 1.00 0.00 C +ATOM 555 HB2 LYS 37 33.704 -84.182 -0.324 1.00 0.00 H +ATOM 556 HB3 LYS 37 32.044 -83.685 0.109 1.00 0.00 H +ATOM 557 CG LYS 37 33.023 -85.092 1.498 1.00 0.00 C +ATOM 558 HG2 LYS 37 34.055 -85.316 1.771 1.00 0.00 H +ATOM 559 HG3 LYS 37 32.588 -86.026 1.143 1.00 0.00 H +ATOM 560 CD LYS 37 32.368 -84.647 2.798 1.00 0.00 C +ATOM 561 HD2 LYS 37 33.041 -83.989 3.348 1.00 0.00 H +ATOM 562 HD3 LYS 37 31.481 -84.078 2.521 1.00 0.00 H +ATOM 563 CE LYS 37 31.843 -85.740 3.758 1.00 0.00 C +ATOM 564 HE2 LYS 37 31.269 -86.486 3.209 1.00 0.00 H +ATOM 565 HE3 LYS 37 32.782 -86.119 4.162 1.00 0.00 H +ATOM 566 NZ LYS 37 30.964 -85.188 4.782 1.00 0.00 N +ATOM 567 HZ1 LYS 37 30.663 -85.862 5.471 1.00 0.00 H +ATOM 568 HZ2 LYS 37 31.341 -84.446 5.354 1.00 0.00 H +ATOM 569 HZ3 LYS 37 30.082 -84.950 4.352 1.00 0.00 H +ATOM 570 C LYS 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 571 O LYS 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 572 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 573 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 574 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 575 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 576 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 577 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 578 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 579 N VAL 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 580 H VAL 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 581 CA VAL 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 582 HA VAL 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 583 CB VAL 39 38.891 -82.524 -4.462 1.00 0.00 C +ATOM 584 HB VAL 39 39.317 -81.884 -3.689 1.00 0.00 H +ATOM 585 CG1 VAL 39 39.045 -84.024 -4.046 1.00 0.00 C +ATOM 586 HG11 VAL 39 38.540 -84.751 -4.683 1.00 0.00 H +ATOM 587 HG12 VAL 39 38.662 -84.168 -3.035 1.00 0.00 H +ATOM 588 HG13 VAL 39 40.112 -84.247 -4.020 1.00 0.00 H +ATOM 589 CG2 VAL 39 39.643 -82.296 -5.727 1.00 0.00 C +ATOM 590 HG21 VAL 39 39.691 -81.242 -5.998 1.00 0.00 H +ATOM 591 HG22 VAL 39 39.506 -83.026 -6.525 1.00 0.00 H +ATOM 592 HG23 VAL 39 40.685 -82.416 -5.433 1.00 0.00 H +ATOM 593 C VAL 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 594 O VAL 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 595 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 596 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 597 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 598 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 599 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 600 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 601 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 602 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 603 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 604 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 605 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 606 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 607 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 608 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 609 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 610 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 611 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 612 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 613 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 614 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 615 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 616 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 617 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 618 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 619 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 620 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 621 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 622 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 623 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 624 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 625 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 626 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 627 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 628 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 629 N TRP 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 630 H TRP 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 631 CA TRP 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 632 HA TRP 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 633 CB TRP 43 29.876 -89.029 -12.444 1.00 0.00 C +ATOM 634 HB2 TRP 43 29.503 -88.069 -12.801 1.00 0.00 H +ATOM 635 HB3 TRP 43 29.062 -89.753 -12.459 1.00 0.00 H +ATOM 636 CG TRP 43 30.277 -88.851 -10.984 1.00 0.00 C +ATOM 637 CD1 TRP 43 30.211 -89.826 -10.086 1.00 0.00 C +ATOM 638 HD1 TRP 43 29.901 -90.849 -10.237 1.00 0.00 H +ATOM 639 NE1 TRP 43 30.313 -89.311 -8.803 1.00 0.00 N +ATOM 640 HE1 TRP 43 30.143 -89.896 -7.998 1.00 0.00 H +ATOM 641 CE2 TRP 43 30.850 -88.041 -8.852 1.00 0.00 C +ATOM 642 CZ2 TRP 43 31.574 -87.297 -7.879 1.00 0.00 C +ATOM 643 HZ2 TRP 43 31.872 -87.675 -6.913 1.00 0.00 H +ATOM 644 CH2 TRP 43 32.072 -86.069 -8.368 1.00 0.00 C +ATOM 645 HH2 TRP 43 32.606 -85.462 -7.652 1.00 0.00 H +ATOM 646 CZ3 TRP 43 31.842 -85.605 -9.645 1.00 0.00 C +ATOM 647 HZ3 TRP 43 32.178 -84.591 -9.804 1.00 0.00 H +ATOM 648 CE3 TRP 43 31.196 -86.439 -10.563 1.00 0.00 C +ATOM 649 HE3 TRP 43 31.112 -86.096 -11.583 1.00 0.00 H +ATOM 650 CD2 TRP 43 30.704 -87.685 -10.223 1.00 0.00 C +ATOM 651 C TRP 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 652 O TRP 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 653 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 654 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 655 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 656 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 657 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 658 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 659 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 660 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 661 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 662 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 663 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 664 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 665 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 666 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 667 N TYR 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 668 H TYR 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 669 CA TYR 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 670 HA TYR 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 671 CB TYR 45 25.262 -89.237 -17.471 1.00 0.00 C +ATOM 672 HB2 TYR 45 25.896 -88.648 -16.809 1.00 0.00 H +ATOM 673 HB3 TYR 45 25.626 -88.921 -18.449 1.00 0.00 H +ATOM 674 CG TYR 45 23.793 -88.837 -17.410 1.00 0.00 C +ATOM 675 CD1 TYR 45 23.124 -88.997 -16.190 1.00 0.00 C +ATOM 676 HD1 TYR 45 23.701 -89.314 -15.334 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.732 -88.954 -16.201 1.00 0.00 C +ATOM 678 HE1 TYR 45 21.212 -89.071 -15.262 1.00 0.00 H +ATOM 679 CZ TYR 45 21.040 -88.543 -17.373 1.00 0.00 C +ATOM 680 OH TYR 45 19.674 -88.445 -17.471 1.00 0.00 O +ATOM 681 HH TYR 45 19.332 -87.944 -18.215 1.00 0.00 H +ATOM 682 CE2 TYR 45 21.775 -88.308 -18.512 1.00 0.00 C +ATOM 683 HE2 TYR 45 21.234 -88.095 -19.423 1.00 0.00 H +ATOM 684 CD2 TYR 45 23.183 -88.420 -18.594 1.00 0.00 C +ATOM 685 HD2 TYR 45 23.697 -88.354 -19.542 1.00 0.00 H +ATOM 686 C TYR 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 687 O TYR 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 688 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 689 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 690 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 691 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 692 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 693 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 694 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 695 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 696 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 697 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 698 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 699 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 700 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 701 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 702 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 703 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 704 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 705 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 706 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 707 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 708 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 709 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 710 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 711 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 712 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 713 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 714 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 715 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 716 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 717 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 718 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 719 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 720 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 721 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 722 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 723 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 724 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 725 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 726 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 727 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 728 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 729 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 730 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 731 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 732 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 733 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 734 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 735 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 736 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 737 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 738 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 739 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 740 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 741 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 742 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 743 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 744 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 745 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 746 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 747 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 748 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 749 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 750 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 751 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 752 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 753 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 754 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 755 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 756 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 757 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 758 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 759 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 760 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 761 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 762 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 763 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 764 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 765 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 766 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 767 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 768 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 769 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 770 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 771 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 772 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 773 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 774 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 775 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 776 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 777 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 778 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 779 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 780 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 781 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 782 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 783 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 784 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 785 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 786 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 787 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 788 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 789 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 790 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 791 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 792 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 793 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 794 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 795 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 796 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 797 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 798 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 799 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 800 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 801 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 802 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 803 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 804 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 805 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 806 N VAL 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 807 H VAL 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 808 CA VAL 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 809 HA VAL 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 810 CB VAL 54 32.330 -94.494 -10.152 1.00 0.00 C +ATOM 811 HB VAL 54 33.344 -94.863 -10.307 1.00 0.00 H +ATOM 812 CG1 VAL 54 32.412 -93.108 -9.426 1.00 0.00 C +ATOM 813 HG11 VAL 54 31.413 -92.672 -9.392 1.00 0.00 H +ATOM 814 HG12 VAL 54 32.793 -92.426 -10.185 1.00 0.00 H +ATOM 815 HG13 VAL 54 32.996 -93.249 -8.517 1.00 0.00 H +ATOM 816 CG2 VAL 54 31.697 -95.463 -9.131 1.00 0.00 C +ATOM 817 HG21 VAL 54 31.735 -96.514 -9.416 1.00 0.00 H +ATOM 818 HG22 VAL 54 30.696 -95.192 -8.795 1.00 0.00 H +ATOM 819 HG23 VAL 54 32.270 -95.399 -8.206 1.00 0.00 H +ATOM 820 C VAL 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 821 O VAL 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 822 N THR 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 823 H THR 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 824 CA THR 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 825 HA THR 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 826 CB THR 55 34.669 -96.370 -14.416 1.00 0.00 C +ATOM 827 HB THR 55 35.283 -97.152 -14.861 1.00 0.00 H +ATOM 828 CG2 THR 55 34.047 -95.619 -15.548 1.00 0.00 C +ATOM 829 HG21 THR 55 33.407 -96.285 -16.127 1.00 0.00 H +ATOM 830 HG22 THR 55 34.741 -95.280 -16.318 1.00 0.00 H +ATOM 831 HG23 THR 55 33.461 -94.791 -15.149 1.00 0.00 H +ATOM 832 OG1 THR 55 35.654 -95.595 -13.719 1.00 0.00 O +ATOM 833 HG1 THR 55 36.236 -96.212 -13.269 1.00 0.00 H +ATOM 834 C THR 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 835 O THR 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 836 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 837 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 838 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 839 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 840 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 841 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 842 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 843 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 844 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 845 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 846 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 847 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 848 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 849 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 850 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 851 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 852 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 ZN +ATOM 853 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 854 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 855 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 856 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 857 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 858 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 860 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 861 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/inp/pdbs/cluster.c7.pdb b/tests/nsga2/inp/pdbs/cluster.c7.pdb new file mode 100644 index 0000000..f15b519 --- /dev/null +++ b/tests/nsga2/inp/pdbs/cluster.c7.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.461 -82.980 -13.332 1.00 0.00 N +ATOM 2 H1 MET 1 13.005 -82.539 -14.118 1.00 0.00 H +ATOM 3 H2 MET 1 14.450 -82.775 -13.314 1.00 0.00 H +ATOM 4 H3 MET 1 13.086 -82.628 -12.463 1.00 0.00 H +ATOM 5 CA MET 1 13.261 -84.417 -13.314 1.00 0.00 C +ATOM 6 HA MET 1 12.207 -84.603 -13.104 1.00 0.00 H +ATOM 7 CB MET 1 13.428 -84.992 -14.787 1.00 0.00 C +ATOM 8 HB2 MET 1 12.713 -84.691 -15.553 1.00 0.00 H +ATOM 9 HB3 MET 1 14.346 -84.468 -15.052 1.00 0.00 H +ATOM 10 CG MET 1 13.944 -86.436 -14.946 1.00 0.00 C +ATOM 11 HG2 MET 1 14.882 -86.425 -14.390 1.00 0.00 H +ATOM 12 HG3 MET 1 13.260 -87.136 -14.467 1.00 0.00 H +ATOM 13 SD MET 1 14.341 -86.923 -16.648 1.00 0.00 S +ATOM 14 CE MET 1 14.090 -88.696 -16.414 1.00 0.00 C +ATOM 15 HE1 MET 1 13.025 -88.925 -16.402 1.00 0.00 H +ATOM 16 HE2 MET 1 14.514 -88.966 -15.446 1.00 0.00 H +ATOM 17 HE3 MET 1 14.637 -89.232 -17.190 1.00 0.00 H +ATOM 18 C MET 1 14.093 -84.977 -12.210 1.00 0.00 C +ATOM 19 O MET 1 15.134 -84.349 -11.887 1.00 0.00 O +ATOM 20 N GLN 2 13.849 -86.175 -11.649 1.00 0.00 N +ATOM 21 H GLN 2 12.993 -86.606 -11.968 1.00 0.00 H +ATOM 22 CA GLN 2 14.627 -86.837 -10.606 1.00 0.00 C +ATOM 23 HA GLN 2 15.041 -86.112 -9.906 1.00 0.00 H +ATOM 24 CB GLN 2 13.676 -87.775 -9.832 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.237 -88.376 -10.628 1.00 0.00 H +ATOM 26 HB3 GLN 2 14.300 -88.499 -9.307 1.00 0.00 H +ATOM 27 CG GLN 2 12.663 -87.103 -8.890 1.00 0.00 C +ATOM 28 HG2 GLN 2 12.185 -86.316 -9.473 1.00 0.00 H +ATOM 29 HG3 GLN 2 11.885 -87.823 -8.633 1.00 0.00 H +ATOM 30 CD GLN 2 13.435 -86.697 -7.576 1.00 0.00 C +ATOM 31 OE1 GLN 2 14.554 -87.081 -7.320 1.00 0.00 O +ATOM 32 NE2 GLN 2 12.854 -85.907 -6.764 1.00 0.00 N +ATOM 33 HE21 GLN 2 13.394 -85.432 -6.054 1.00 0.00 H +ATOM 34 HE22 GLN 2 11.925 -85.548 -6.929 1.00 0.00 H +ATOM 35 C GLN 2 15.709 -87.659 -11.205 1.00 0.00 C +ATOM 36 O GLN 2 15.572 -88.229 -12.322 1.00 0.00 O +ATOM 37 N TYR 3 16.837 -87.721 -10.515 1.00 0.00 N +ATOM 38 H TYR 3 16.915 -87.105 -9.719 1.00 0.00 H +ATOM 39 CA TYR 3 18.111 -88.415 -10.854 1.00 0.00 C +ATOM 40 HA TYR 3 17.976 -89.107 -11.686 1.00 0.00 H +ATOM 41 CB TYR 3 19.063 -87.407 -11.343 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.061 -86.652 -10.556 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.107 -87.722 -11.374 1.00 0.00 H +ATOM 44 CG TYR 3 18.655 -86.624 -12.614 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.126 -87.079 -13.904 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.690 -87.994 -14.005 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.742 -86.398 -15.120 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.017 -86.733 -16.109 1.00 0.00 H +ATOM 49 CZ TYR 3 17.901 -85.285 -14.991 1.00 0.00 C +ATOM 50 OH TYR 3 17.459 -84.558 -16.079 1.00 0.00 O +ATOM 51 HH TYR 3 17.416 -85.123 -16.855 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.484 -84.756 -13.758 1.00 0.00 C +ATOM 53 HE2 TYR 3 16.836 -83.896 -13.676 1.00 0.00 H +ATOM 54 CD2 TYR 3 17.770 -85.544 -12.590 1.00 0.00 C +ATOM 55 HD2 TYR 3 17.263 -85.326 -11.662 1.00 0.00 H +ATOM 56 C TYR 3 18.799 -89.221 -9.696 1.00 0.00 C +ATOM 57 O TYR 3 18.782 -88.754 -8.575 1.00 0.00 O +ATOM 58 N LYS 4 19.461 -90.388 -9.973 1.00 0.00 N +ATOM 59 H LYS 4 19.468 -90.729 -10.923 1.00 0.00 H +ATOM 60 CA LYS 4 20.120 -91.307 -9.010 1.00 0.00 C +ATOM 61 HA LYS 4 19.318 -91.600 -8.334 1.00 0.00 H +ATOM 62 CB LYS 4 20.543 -92.622 -9.739 1.00 0.00 C +ATOM 63 HB2 LYS 4 21.269 -92.425 -10.527 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.051 -93.284 -9.038 1.00 0.00 H +ATOM 65 CG LYS 4 19.364 -93.507 -10.294 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.689 -93.616 -9.445 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.957 -92.968 -11.149 1.00 0.00 H +ATOM 68 CD LYS 4 19.629 -94.939 -10.766 1.00 0.00 C +ATOM 69 HD2 LYS 4 20.250 -94.907 -11.661 1.00 0.00 H +ATOM 70 HD3 LYS 4 20.235 -95.409 -9.991 1.00 0.00 H +ATOM 71 CE LYS 4 18.298 -95.741 -10.896 1.00 0.00 C +ATOM 72 HE2 LYS 4 17.746 -95.453 -10.001 1.00 0.00 H +ATOM 73 HE3 LYS 4 17.741 -95.314 -11.730 1.00 0.00 H +ATOM 74 NZ LYS 4 18.403 -97.179 -11.000 1.00 0.00 N +ATOM 75 HZ1 LYS 4 17.466 -97.482 -11.224 1.00 0.00 H +ATOM 76 HZ2 LYS 4 18.751 -97.655 -10.179 1.00 0.00 H +ATOM 77 HZ3 LYS 4 18.945 -97.518 -11.782 1.00 0.00 H +ATOM 78 C LYS 4 21.316 -90.668 -8.253 1.00 0.00 C +ATOM 79 O LYS 4 22.084 -89.938 -8.841 1.00 0.00 O +ATOM 80 N HE1 5 21.389 -91.042 -6.959 1.00 0.00 N +ATOM 81 CA HE1 5 22.478 -90.650 -6.009 1.00 0.00 C +ATOM 82 C HE1 5 22.591 -91.660 -4.828 1.00 0.00 C +ATOM 83 O HE1 5 21.633 -92.342 -4.422 1.00 0.00 O +ATOM 84 CB HE1 5 22.336 -89.265 -5.534 1.00 0.00 C +ATOM 85 CG HE1 5 23.520 -88.794 -4.766 1.00 0.00 C +ATOM 86 CD2 HE1 5 24.831 -88.707 -5.217 1.00 0.00 C +ATOM 87 ND1 HE1 5 23.549 -88.589 -3.392 1.00 0.00 N +ATOM 88 CE1 HE1 5 24.834 -88.483 -3.035 1.00 0.00 C +ATOM 89 NE2 HE1 5 25.654 -88.475 -4.106 1.00 0.00 N +ATOM 90 H HE1 5 20.688 -91.682 -6.616 1.00 0.00 H +ATOM 91 HA HE1 5 23.419 -90.652 -6.559 1.00 0.00 H +ATOM 92 HB2 HE1 5 21.417 -89.238 -4.949 1.00 0.00 H +ATOM 93 HB3 HE1 5 22.187 -88.626 -6.405 1.00 0.00 H +ATOM 94 HD2 HE1 5 25.203 -88.780 -6.228 1.00 0.00 H +ATOM 95 HE1 HE1 5 25.254 -88.285 -2.060 1.00 0.00 H +ATOM 96 HE2 HE1 5 26.661 -88.451 -4.170 1.00 0.00 H +ATOM 97 N ILE 6 23.799 -91.740 -4.230 1.00 0.00 N +ATOM 98 H ILE 6 24.620 -91.346 -4.668 1.00 0.00 H +ATOM 99 CA ILE 6 24.040 -92.671 -3.200 1.00 0.00 C +ATOM 100 HA ILE 6 23.387 -93.527 -3.374 1.00 0.00 H +ATOM 101 CB ILE 6 25.546 -93.115 -3.108 1.00 0.00 C +ATOM 102 HB ILE 6 25.653 -93.725 -2.211 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.880 -94.044 -4.261 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.762 -93.628 -5.262 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.192 -94.888 -4.273 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.900 -94.427 -4.223 1.00 0.00 H +ATOM 107 CG1 ILE 6 26.548 -91.956 -2.935 1.00 0.00 C +ATOM 108 HG12 ILE 6 26.474 -91.363 -3.846 1.00 0.00 H +ATOM 109 HG13 ILE 6 26.273 -91.302 -2.107 1.00 0.00 H +ATOM 110 CD1 ILE 6 28.014 -92.405 -2.706 1.00 0.00 C +ATOM 111 HD11 ILE 6 28.525 -91.443 -2.696 1.00 0.00 H +ATOM 112 HD12 ILE 6 28.471 -92.976 -3.514 1.00 0.00 H +ATOM 113 HD13 ILE 6 28.271 -92.875 -1.757 1.00 0.00 H +ATOM 114 C ILE 6 23.514 -92.270 -1.866 1.00 0.00 C +ATOM 115 O ILE 6 23.636 -91.131 -1.403 1.00 0.00 O +ATOM 116 N VAL 7 23.252 -93.278 -1.049 1.00 0.00 N +ATOM 117 H VAL 7 23.149 -94.178 -1.496 1.00 0.00 H +ATOM 118 CA VAL 7 23.083 -93.275 0.459 1.00 0.00 C +ATOM 119 HA VAL 7 22.983 -92.225 0.732 1.00 0.00 H +ATOM 120 CB VAL 7 21.844 -93.993 0.907 1.00 0.00 C +ATOM 121 HB VAL 7 21.979 -94.930 0.366 1.00 0.00 H +ATOM 122 CG1 VAL 7 21.622 -94.167 2.383 1.00 0.00 C +ATOM 123 HG11 VAL 7 20.705 -94.750 2.463 1.00 0.00 H +ATOM 124 HG12 VAL 7 22.441 -94.621 2.941 1.00 0.00 H +ATOM 125 HG13 VAL 7 21.442 -93.204 2.862 1.00 0.00 H +ATOM 126 CG2 VAL 7 20.470 -93.333 0.389 1.00 0.00 C +ATOM 127 HG21 VAL 7 19.593 -93.769 0.866 1.00 0.00 H +ATOM 128 HG22 VAL 7 20.558 -92.326 0.799 1.00 0.00 H +ATOM 129 HG23 VAL 7 20.458 -93.436 -0.696 1.00 0.00 H +ATOM 130 C VAL 7 24.356 -93.650 1.103 1.00 0.00 C +ATOM 131 O VAL 7 24.685 -94.869 1.091 1.00 0.00 O +ATOM 132 N ASN 8 25.128 -92.661 1.539 1.00 0.00 N +ATOM 133 H ASN 8 24.823 -91.705 1.419 1.00 0.00 H +ATOM 134 CA ASN 8 26.429 -92.834 2.276 1.00 0.00 C +ATOM 135 HA ASN 8 26.816 -93.783 1.903 1.00 0.00 H +ATOM 136 CB ASN 8 27.410 -91.759 1.736 1.00 0.00 C +ATOM 137 HB2 ASN 8 27.536 -91.957 0.672 1.00 0.00 H +ATOM 138 HB3 ASN 8 27.077 -90.739 1.929 1.00 0.00 H +ATOM 139 CG ASN 8 28.811 -91.955 2.248 1.00 0.00 C +ATOM 140 OD1 ASN 8 29.146 -93.068 2.566 1.00 0.00 O +ATOM 141 ND2 ASN 8 29.663 -90.996 2.386 1.00 0.00 N +ATOM 142 HD21 ASN 8 29.311 -90.050 2.407 1.00 0.00 H +ATOM 143 HD22 ASN 8 30.557 -91.278 2.763 1.00 0.00 H +ATOM 144 C ASN 8 26.299 -92.845 3.836 1.00 0.00 C +ATOM 145 O ASN 8 25.744 -91.906 4.375 1.00 0.00 O +ATOM 146 N GLY 9 26.864 -93.885 4.452 1.00 0.00 N +ATOM 147 H GLY 9 27.500 -94.457 3.915 1.00 0.00 H +ATOM 148 CA GLY 9 26.793 -94.338 5.884 1.00 0.00 C +ATOM 149 HA2 GLY 9 26.786 -93.508 6.590 1.00 0.00 H +ATOM 150 HA3 GLY 9 25.852 -94.825 6.139 1.00 0.00 H +ATOM 151 C GLY 9 27.824 -95.421 6.286 1.00 0.00 C +ATOM 152 O GLY 9 28.497 -96.011 5.476 1.00 0.00 O +ATOM 153 N LYS 10 28.057 -95.550 7.574 1.00 0.00 N +ATOM 154 H LYS 10 27.648 -94.807 8.121 1.00 0.00 H +ATOM 155 CA LYS 10 28.977 -96.501 8.275 1.00 0.00 C +ATOM 156 HA LYS 10 29.922 -96.479 7.732 1.00 0.00 H +ATOM 157 CB LYS 10 29.211 -96.129 9.754 1.00 0.00 C +ATOM 158 HB2 LYS 10 28.254 -95.985 10.257 1.00 0.00 H +ATOM 159 HB3 LYS 10 29.681 -96.938 10.313 1.00 0.00 H +ATOM 160 CG LYS 10 30.047 -94.830 9.820 1.00 0.00 C +ATOM 161 HG2 LYS 10 31.040 -95.023 9.415 1.00 0.00 H +ATOM 162 HG3 LYS 10 29.575 -94.054 9.218 1.00 0.00 H +ATOM 163 CD LYS 10 30.072 -94.267 11.250 1.00 0.00 C +ATOM 164 HD2 LYS 10 30.381 -93.222 11.262 1.00 0.00 H +ATOM 165 HD3 LYS 10 29.026 -94.339 11.549 1.00 0.00 H +ATOM 166 CE LYS 10 30.884 -95.130 12.094 1.00 0.00 C +ATOM 167 HE2 LYS 10 30.582 -96.177 12.064 1.00 0.00 H +ATOM 168 HE3 LYS 10 31.871 -95.143 11.631 1.00 0.00 H +ATOM 169 NZ LYS 10 30.971 -94.755 13.544 1.00 0.00 N +ATOM 170 HZ1 LYS 10 31.193 -95.552 14.123 1.00 0.00 H +ATOM 171 HZ2 LYS 10 30.131 -94.270 13.829 1.00 0.00 H +ATOM 172 HZ3 LYS 10 31.758 -94.150 13.729 1.00 0.00 H +ATOM 173 C LYS 10 28.362 -97.856 8.179 1.00 0.00 C +ATOM 174 O LYS 10 29.133 -98.742 7.831 1.00 0.00 O +ATOM 175 N THR 11 27.080 -97.958 8.339 1.00 0.00 N +ATOM 176 H THR 11 26.744 -97.073 8.689 1.00 0.00 H +ATOM 177 CA THR 11 26.277 -99.210 8.217 1.00 0.00 C +ATOM 178 HA THR 11 27.024-100.004 8.245 1.00 0.00 H +ATOM 179 CB THR 11 25.306 -99.418 9.458 1.00 0.00 C +ATOM 180 HB THR 11 24.743-100.334 9.281 1.00 0.00 H +ATOM 181 CG2 THR 11 25.974 -99.490 10.860 1.00 0.00 C +ATOM 182 HG21 THR 11 26.471 -98.570 11.168 1.00 0.00 H +ATOM 183 HG22 THR 11 26.627-100.362 10.859 1.00 0.00 H +ATOM 184 HG23 THR 11 25.209 -99.677 11.613 1.00 0.00 H +ATOM 185 OG1 THR 11 24.469 -98.330 9.570 1.00 0.00 O +ATOM 186 HG1 THR 11 23.748 -98.597 10.146 1.00 0.00 H +ATOM 187 C THR 11 25.589 -99.277 6.891 1.00 0.00 C +ATOM 188 O THR 11 25.799-100.149 6.061 1.00 0.00 O +ATOM 189 N LEU 12 24.646 -98.354 6.724 1.00 0.00 N +ATOM 190 H LEU 12 24.558 -97.649 7.442 1.00 0.00 H +ATOM 191 CA LEU 12 23.800 -98.387 5.574 1.00 0.00 C +ATOM 192 HA LEU 12 23.460 -99.423 5.585 1.00 0.00 H +ATOM 193 CB LEU 12 22.578 -97.493 5.645 1.00 0.00 C +ATOM 194 HB2 LEU 12 22.915 -96.479 5.429 1.00 0.00 H +ATOM 195 HB3 LEU 12 21.864 -97.707 4.849 1.00 0.00 H +ATOM 196 CG LEU 12 21.864 -97.440 7.053 1.00 0.00 C +ATOM 197 HG LEU 12 22.391 -96.749 7.712 1.00 0.00 H +ATOM 198 CD1 LEU 12 20.511 -96.745 6.777 1.00 0.00 C +ATOM 199 HD11 LEU 12 19.870 -97.472 6.280 1.00 0.00 H +ATOM 200 HD12 LEU 12 20.638 -95.866 6.145 1.00 0.00 H +ATOM 201 HD13 LEU 12 20.045 -96.312 7.662 1.00 0.00 H +ATOM 202 CD2 LEU 12 21.739 -98.613 7.873 1.00 0.00 C +ATOM 203 HD21 LEU 12 21.111 -99.340 7.357 1.00 0.00 H +ATOM 204 HD22 LEU 12 21.149 -98.339 8.747 1.00 0.00 H +ATOM 205 HD23 LEU 12 22.718 -99.035 8.102 1.00 0.00 H +ATOM 206 C LEU 12 24.474 -98.059 4.265 1.00 0.00 C +ATOM 207 O LEU 12 25.493 -97.419 4.196 1.00 0.00 O +ATOM 208 N LYS 13 23.820 -98.484 3.190 1.00 0.00 N +ATOM 209 H LYS 13 22.957 -98.991 3.324 1.00 0.00 H +ATOM 210 CA LYS 13 24.211 -98.329 1.816 1.00 0.00 C +ATOM 211 HA LYS 13 24.635 -97.341 1.636 1.00 0.00 H +ATOM 212 CB LYS 13 25.340 -99.311 1.471 1.00 0.00 C +ATOM 213 HB2 LYS 13 26.201 -99.167 2.124 1.00 0.00 H +ATOM 214 HB3 LYS 13 25.032-100.333 1.690 1.00 0.00 H +ATOM 215 CG LYS 13 25.920 -99.154 0.074 1.00 0.00 C +ATOM 216 HG2 LYS 13 25.146 -99.422 -0.644 1.00 0.00 H +ATOM 217 HG3 LYS 13 26.301 -98.157 -0.147 1.00 0.00 H +ATOM 218 CD LYS 13 27.049-100.234 -0.229 1.00 0.00 C +ATOM 219 HD2 LYS 13 27.756-100.182 0.599 1.00 0.00 H +ATOM 220 HD3 LYS 13 26.685-101.257 -0.138 1.00 0.00 H +ATOM 221 CE LYS 13 27.543-100.095 -1.651 1.00 0.00 C +ATOM 222 HE2 LYS 13 26.655 -99.936 -2.263 1.00 0.00 H +ATOM 223 HE3 LYS 13 28.156 -99.194 -1.645 1.00 0.00 H +ATOM 224 NZ LYS 13 28.176-101.370 -2.123 1.00 0.00 N +ATOM 225 HZ1 LYS 13 28.343-101.353 -3.119 1.00 0.00 H +ATOM 226 HZ2 LYS 13 27.493-102.107 -2.018 1.00 0.00 H +ATOM 227 HZ3 LYS 13 28.974-101.635 -1.564 1.00 0.00 H +ATOM 228 C LYS 13 23.041 -98.462 0.848 1.00 0.00 C +ATOM 229 O LYS 13 22.237 -99.391 0.928 1.00 0.00 O +ATOM 230 N GLY 14 23.029 -97.608 -0.193 1.00 0.00 N +ATOM 231 H GLY 14 23.786 -96.948 -0.299 1.00 0.00 H +ATOM 232 CA GLY 14 22.095 -97.830 -1.346 1.00 0.00 C +ATOM 233 HA2 GLY 14 22.395 -98.709 -1.916 1.00 0.00 H +ATOM 234 HA3 GLY 14 21.122 -98.204 -1.028 1.00 0.00 H +ATOM 235 C GLY 14 21.989 -96.594 -2.225 1.00 0.00 C +ATOM 236 O GLY 14 22.905 -95.819 -2.469 1.00 0.00 O +ATOM 237 N VAL 15 20.778 -96.407 -2.789 1.00 0.00 N +ATOM 238 H VAL 15 20.011 -96.937 -2.400 1.00 0.00 H +ATOM 239 CA VAL 15 20.408 -95.320 -3.703 1.00 0.00 C +ATOM 240 HA VAL 15 21.160 -94.531 -3.704 1.00 0.00 H +ATOM 241 CB VAL 15 20.463 -95.842 -5.170 1.00 0.00 C +ATOM 242 HB VAL 15 19.711 -96.590 -5.420 1.00 0.00 H +ATOM 243 CG1 VAL 15 20.052 -94.733 -6.222 1.00 0.00 C +ATOM 244 HG11 VAL 15 20.626 -93.809 -6.154 1.00 0.00 H +ATOM 245 HG12 VAL 15 20.192 -95.124 -7.230 1.00 0.00 H +ATOM 246 HG13 VAL 15 18.974 -94.596 -6.148 1.00 0.00 H +ATOM 247 CG2 VAL 15 21.797 -96.352 -5.685 1.00 0.00 C +ATOM 248 HG21 VAL 15 22.582 -95.639 -5.433 1.00 0.00 H +ATOM 249 HG22 VAL 15 22.022 -97.299 -5.193 1.00 0.00 H +ATOM 250 HG23 VAL 15 21.712 -96.511 -6.760 1.00 0.00 H +ATOM 251 C VAL 15 19.103 -94.619 -3.305 1.00 0.00 C +ATOM 252 O VAL 15 18.155 -95.272 -2.908 1.00 0.00 O +ATOM 253 N HD1 16 19.047 -93.298 -3.326 1.00 0.00 N +ATOM 254 CA HD1 16 17.896 -92.339 -3.450 1.00 0.00 C +ATOM 255 C HD1 16 18.075 -91.445 -4.762 1.00 0.00 C +ATOM 256 O HD1 16 19.222 -91.358 -5.298 1.00 0.00 O +ATOM 257 CB HD1 16 17.703 -91.433 -2.210 1.00 0.00 C +ATOM 258 CG HD1 16 18.873 -90.707 -1.697 1.00 0.00 C +ATOM 259 CD2 HD1 16 19.964 -90.317 -2.404 1.00 0.00 C +ATOM 260 ND1 HD1 16 19.009 -90.341 -0.381 1.00 0.00 N +ATOM 261 CE1 HD1 16 20.208 -89.683 -0.315 1.00 0.00 C +ATOM 262 NE2 HD1 16 20.744 -89.577 -1.556 1.00 0.00 N +ATOM 263 H HD1 16 19.836 -93.039 -3.899 1.00 0.00 H +ATOM 264 HA HD1 16 16.973 -92.905 -3.577 1.00 0.00 H +ATOM 265 HB2 HD1 16 16.947 -90.674 -2.415 1.00 0.00 H +ATOM 266 HB3 HD1 16 17.350 -92.077 -1.405 1.00 0.00 H +ATOM 267 HD1 HD1 16 18.365 -90.444 0.390 1.00 0.00 H +ATOM 268 HD2 HD1 16 20.198 -90.460 -3.448 1.00 0.00 H +ATOM 269 HE1 HD1 16 20.579 -89.236 0.595 1.00 0.00 H +ATOM 270 N THR 17 17.010 -90.833 -5.201 1.00 0.00 N +ATOM 271 H THR 17 16.105 -91.071 -4.822 1.00 0.00 H +ATOM 272 CA THR 17 17.170 -89.815 -6.250 1.00 0.00 C +ATOM 273 HA THR 17 18.083 -89.951 -6.829 1.00 0.00 H +ATOM 274 CB THR 17 16.030 -89.936 -7.271 1.00 0.00 C +ATOM 275 HB THR 17 16.177 -89.114 -7.972 1.00 0.00 H +ATOM 276 CG2 THR 17 16.034 -91.222 -7.990 1.00 0.00 C +ATOM 277 HG21 THR 17 17.077 -91.514 -8.110 1.00 0.00 H +ATOM 278 HG22 THR 17 15.547 -91.205 -8.965 1.00 0.00 H +ATOM 279 HG23 THR 17 15.368 -91.872 -7.422 1.00 0.00 H +ATOM 280 OG1 THR 17 14.764 -89.893 -6.644 1.00 0.00 O +ATOM 281 HG1 THR 17 14.527 -88.979 -6.472 1.00 0.00 H +ATOM 282 C THR 17 17.159 -88.409 -5.686 1.00 0.00 C +ATOM 283 O THR 17 16.726 -88.243 -4.501 1.00 0.00 O +ATOM 284 N HD2 18 17.616 -87.438 -6.449 1.00 0.00 N +ATOM 285 CA HD2 18 17.417 -85.963 -6.201 1.00 0.00 C +ATOM 286 C HD2 18 16.829 -85.181 -7.410 1.00 0.00 C +ATOM 287 O HD2 18 17.272 -85.357 -8.560 1.00 0.00 O +ATOM 288 CB HD2 18 18.777 -85.366 -5.857 1.00 0.00 C +ATOM 289 CG HD2 18 19.399 -85.956 -4.617 1.00 0.00 C +ATOM 290 CD2 HD2 18 20.723 -86.287 -4.431 1.00 0.00 C +ATOM 291 ND1 HD2 18 18.723 -86.081 -3.413 1.00 0.00 N +ATOM 292 CE1 HD2 18 19.586 -86.556 -2.542 1.00 0.00 C +ATOM 293 NE2 HD2 18 20.775 -86.754 -3.104 1.00 0.00 N +ATOM 294 H HD2 18 18.021 -87.783 -7.308 1.00 0.00 H +ATOM 295 HA HD2 18 16.756 -85.806 -5.349 1.00 0.00 H +ATOM 296 HB2 HD2 18 19.488 -85.671 -6.625 1.00 0.00 H +ATOM 297 HB3 HD2 18 18.756 -84.300 -5.632 1.00 0.00 H +ATOM 298 HD1 HD2 18 17.876 -85.571 -3.208 1.00 0.00 H +ATOM 299 HD2 HD2 18 21.492 -86.279 -5.189 1.00 0.00 H +ATOM 300 HE1 HD2 18 19.392 -86.671 -1.486 1.00 0.00 H +ATOM 301 N GLU 19 15.886 -84.287 -7.245 1.00 0.00 N +ATOM 302 H GLU 19 15.403 -84.184 -6.364 1.00 0.00 H +ATOM 303 CA GLU 19 15.405 -83.467 -8.351 1.00 0.00 C +ATOM 304 HA GLU 19 14.994 -84.078 -9.154 1.00 0.00 H +ATOM 305 CB GLU 19 14.315 -82.501 -7.793 1.00 0.00 C +ATOM 306 HB2 GLU 19 13.591 -83.069 -7.208 1.00 0.00 H +ATOM 307 HB3 GLU 19 14.769 -81.909 -6.998 1.00 0.00 H +ATOM 308 CG GLU 19 13.654 -81.516 -8.745 1.00 0.00 C +ATOM 309 HG2 GLU 19 12.789 -81.035 -8.289 1.00 0.00 H +ATOM 310 HG3 GLU 19 14.319 -80.659 -8.848 1.00 0.00 H +ATOM 311 CD GLU 19 13.172 -82.035 -10.102 1.00 0.00 C +ATOM 312 OE1 GLU 19 13.138 -81.231 -11.129 1.00 0.00 O +ATOM 313 OE2 GLU 19 12.774 -83.224 -10.330 1.00 0.00 O +ATOM 314 C GLU 19 16.479 -82.497 -8.888 1.00 0.00 C +ATOM 315 O GLU 19 17.181 -81.940 -8.015 1.00 0.00 O +ATOM 316 N ALA 20 16.593 -82.297 -10.196 1.00 0.00 N +ATOM 317 H ALA 20 16.328 -83.004 -10.867 1.00 0.00 H +ATOM 318 CA ALA 20 17.098 -80.999 -10.639 1.00 0.00 C +ATOM 319 HA ALA 20 16.702 -80.156 -10.073 1.00 0.00 H +ATOM 320 CB ALA 20 18.635 -81.066 -10.522 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.017 -81.724 -11.303 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.041 -81.355 -9.553 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.064 -80.105 -10.805 1.00 0.00 H +ATOM 324 C ALA 20 16.649 -80.677 -12.081 1.00 0.00 C +ATOM 325 O ALA 20 16.104 -81.467 -12.826 1.00 0.00 O +ATOM 326 N VAL 21 16.765 -79.383 -12.424 1.00 0.00 N +ATOM 327 H VAL 21 17.265 -78.778 -11.789 1.00 0.00 H +ATOM 328 CA VAL 21 16.042 -78.839 -13.587 1.00 0.00 C +ATOM 329 HA VAL 21 14.978 -78.919 -13.363 1.00 0.00 H +ATOM 330 CB VAL 21 16.191 -77.271 -13.652 1.00 0.00 C +ATOM 331 HB VAL 21 15.846 -76.869 -12.699 1.00 0.00 H +ATOM 332 CG1 VAL 21 17.693 -76.938 -13.724 1.00 0.00 C +ATOM 333 HG11 VAL 21 18.114 -77.374 -14.630 1.00 0.00 H +ATOM 334 HG12 VAL 21 18.211 -77.249 -12.817 1.00 0.00 H +ATOM 335 HG13 VAL 21 17.818 -75.855 -13.755 1.00 0.00 H +ATOM 336 CG2 VAL 21 15.437 -76.548 -14.727 1.00 0.00 C +ATOM 337 HG21 VAL 21 15.717 -76.867 -15.731 1.00 0.00 H +ATOM 338 HG22 VAL 21 15.538 -75.464 -14.788 1.00 0.00 H +ATOM 339 HG23 VAL 21 14.379 -76.744 -14.555 1.00 0.00 H +ATOM 340 C VAL 21 16.315 -79.531 -14.935 1.00 0.00 C +ATOM 341 O VAL 21 15.443 -79.618 -15.771 1.00 0.00 O +ATOM 342 N ASP 22 17.478 -80.094 -15.143 1.00 0.00 N +ATOM 343 H ASP 22 18.172 -80.059 -14.410 1.00 0.00 H +ATOM 344 CA ASP 22 17.850 -80.943 -16.225 1.00 0.00 C +ATOM 345 HA ASP 22 17.039 -81.638 -16.445 1.00 0.00 H +ATOM 346 CB ASP 22 18.066 -80.102 -17.474 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.025 -80.764 -18.339 1.00 0.00 H +ATOM 348 HB3 ASP 22 17.209 -79.432 -17.544 1.00 0.00 H +ATOM 349 CG ASP 22 19.343 -79.282 -17.619 1.00 0.00 C +ATOM 350 OD1 ASP 22 19.912 -78.955 -16.551 1.00 0.00 O +ATOM 351 OD2 ASP 22 19.604 -78.944 -18.775 1.00 0.00 O +ATOM 352 C ASP 22 19.076 -81.675 -15.744 1.00 0.00 C +ATOM 353 O ASP 22 19.597 -81.518 -14.646 1.00 0.00 O +ATOM 354 N ALA 23 19.579 -82.485 -16.642 1.00 0.00 N +ATOM 355 H ALA 23 19.016 -82.641 -17.466 1.00 0.00 H +ATOM 356 CA ALA 23 20.742 -83.411 -16.354 1.00 0.00 C +ATOM 357 HA ALA 23 20.502 -83.984 -15.459 1.00 0.00 H +ATOM 358 CB ALA 23 20.911 -84.281 -17.626 1.00 0.00 C +ATOM 359 HB1 ALA 23 20.828 -83.677 -18.529 1.00 0.00 H +ATOM 360 HB2 ALA 23 20.155 -85.056 -17.755 1.00 0.00 H +ATOM 361 HB3 ALA 23 21.880 -84.778 -17.572 1.00 0.00 H +ATOM 362 C ALA 23 22.047 -82.535 -16.115 1.00 0.00 C +ATOM 363 O ALA 23 22.991 -83.021 -15.425 1.00 0.00 O +ATOM 364 N ALA 24 22.101 -81.298 -16.654 1.00 0.00 N +ATOM 365 H ALA 24 21.328 -80.879 -17.151 1.00 0.00 H +ATOM 366 CA ALA 24 23.225 -80.380 -16.549 1.00 0.00 C +ATOM 367 HA ALA 24 24.101 -81.020 -16.656 1.00 0.00 H +ATOM 368 CB ALA 24 23.210 -79.284 -17.586 1.00 0.00 C +ATOM 369 HB1 ALA 24 23.112 -79.843 -18.517 1.00 0.00 H +ATOM 370 HB2 ALA 24 24.217 -78.878 -17.682 1.00 0.00 H +ATOM 371 HB3 ALA 24 22.426 -78.539 -17.445 1.00 0.00 H +ATOM 372 C ALA 24 23.204 -79.751 -15.162 1.00 0.00 C +ATOM 373 O ALA 24 24.195 -79.332 -14.573 1.00 0.00 O +ATOM 374 N GLU 25 22.036 -79.583 -14.433 1.00 0.00 N +ATOM 375 H GLU 25 21.173 -79.525 -14.955 1.00 0.00 H +ATOM 376 CA GLU 25 22.036 -79.316 -12.999 1.00 0.00 C +ATOM 377 HA GLU 25 22.922 -78.737 -12.739 1.00 0.00 H +ATOM 378 CB GLU 25 20.824 -78.373 -12.685 1.00 0.00 C +ATOM 379 HB2 GLU 25 20.744 -77.680 -13.523 1.00 0.00 H +ATOM 380 HB3 GLU 25 19.968 -79.039 -12.795 1.00 0.00 H +ATOM 381 CG GLU 25 20.729 -77.612 -11.352 1.00 0.00 C +ATOM 382 HG2 GLU 25 19.760 -77.118 -11.420 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.681 -78.274 -10.487 1.00 0.00 H +ATOM 384 CD GLU 25 21.947 -76.714 -11.121 1.00 0.00 C +ATOM 385 OE1 GLU 25 22.374 -76.013 -12.050 1.00 0.00 O +ATOM 386 OE2 GLU 25 22.441 -76.631 -9.985 1.00 0.00 O +ATOM 387 C GLU 25 22.021 -80.601 -12.094 1.00 0.00 C +ATOM 388 O GLU 25 22.424 -80.601 -10.899 1.00 0.00 O +ATOM 389 N ALA 26 21.598 -81.775 -12.586 1.00 0.00 N +ATOM 390 H ALA 26 21.250 -81.888 -13.527 1.00 0.00 H +ATOM 391 CA ALA 26 21.771 -83.032 -11.857 1.00 0.00 C +ATOM 392 HA ALA 26 21.573 -82.945 -10.788 1.00 0.00 H +ATOM 393 CB ALA 26 20.811 -84.060 -12.331 1.00 0.00 C +ATOM 394 HB1 ALA 26 20.848 -84.934 -11.682 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.156 -84.370 -13.317 1.00 0.00 H +ATOM 396 HB3 ALA 26 19.813 -83.623 -12.376 1.00 0.00 H +ATOM 397 C ALA 26 23.203 -83.579 -11.933 1.00 0.00 C +ATOM 398 O ALA 26 23.600 -84.254 -11.031 1.00 0.00 O +ATOM 399 N GLU 27 24.062 -83.359 -12.935 1.00 0.00 N +ATOM 400 H GLU 27 23.715 -82.927 -13.779 1.00 0.00 H +ATOM 401 CA GLU 27 25.440 -83.887 -12.979 1.00 0.00 C +ATOM 402 HA GLU 27 25.511 -84.965 -12.833 1.00 0.00 H +ATOM 403 CB GLU 27 26.072 -83.463 -14.344 1.00 0.00 C +ATOM 404 HB2 GLU 27 26.949 -84.109 -14.297 1.00 0.00 H +ATOM 405 HB3 GLU 27 25.444 -83.679 -15.209 1.00 0.00 H +ATOM 406 CG GLU 27 26.394 -82.024 -14.508 1.00 0.00 C +ATOM 407 HG2 GLU 27 25.496 -81.410 -14.449 1.00 0.00 H +ATOM 408 HG3 GLU 27 26.913 -81.668 -13.618 1.00 0.00 H +ATOM 409 CD GLU 27 27.201 -81.794 -15.783 1.00 0.00 C +ATOM 410 OE1 GLU 27 28.060 -80.864 -15.878 1.00 0.00 O +ATOM 411 OE2 GLU 27 26.969 -82.473 -16.781 1.00 0.00 O +ATOM 412 C GLU 27 26.338 -83.409 -11.872 1.00 0.00 C +ATOM 413 O GLU 27 27.441 -83.910 -11.588 1.00 0.00 O +ATOM 414 N LYS 28 25.870 -82.402 -11.147 1.00 0.00 N +ATOM 415 H LYS 28 24.968 -82.045 -11.428 1.00 0.00 H +ATOM 416 CA LYS 28 26.382 -81.831 -9.928 1.00 0.00 C +ATOM 417 HA LYS 28 27.458 -81.699 -10.040 1.00 0.00 H +ATOM 418 CB LYS 28 25.767 -80.464 -9.766 1.00 0.00 C +ATOM 419 HB2 LYS 28 24.732 -80.671 -9.494 1.00 0.00 H +ATOM 420 HB3 LYS 28 26.204 -79.989 -8.888 1.00 0.00 H +ATOM 421 CG LYS 28 25.855 -79.505 -10.913 1.00 0.00 C +ATOM 422 HG2 LYS 28 26.912 -79.456 -11.175 1.00 0.00 H +ATOM 423 HG3 LYS 28 25.321 -79.931 -11.762 1.00 0.00 H +ATOM 424 CD LYS 28 25.275 -78.102 -10.638 1.00 0.00 C +ATOM 425 HD2 LYS 28 24.195 -78.189 -10.522 1.00 0.00 H +ATOM 426 HD3 LYS 28 25.679 -77.782 -9.677 1.00 0.00 H +ATOM 427 CE LYS 28 25.754 -77.037 -11.633 1.00 0.00 C +ATOM 428 HE2 LYS 28 26.841 -77.053 -11.551 1.00 0.00 H +ATOM 429 HE3 LYS 28 25.306 -77.440 -12.541 1.00 0.00 H +ATOM 430 NZ LYS 28 25.119 -75.731 -11.294 1.00 0.00 N +ATOM 431 HZ1 LYS 28 24.126 -75.903 -11.352 1.00 0.00 H +ATOM 432 HZ2 LYS 28 25.374 -74.970 -11.908 1.00 0.00 H +ATOM 433 HZ3 LYS 28 25.319 -75.470 -10.339 1.00 0.00 H +ATOM 434 C LYS 28 26.273 -82.784 -8.712 1.00 0.00 C +ATOM 435 O LYS 28 27.136 -82.639 -7.829 1.00 0.00 O +ATOM 436 N PHE 29 25.500 -83.875 -8.676 1.00 0.00 N +ATOM 437 H PHE 29 24.814 -83.991 -9.408 1.00 0.00 H +ATOM 438 CA PHE 29 25.567 -84.947 -7.692 1.00 0.00 C +ATOM 439 HA PHE 29 25.581 -84.491 -6.702 1.00 0.00 H +ATOM 440 CB PHE 29 24.188 -85.700 -7.669 1.00 0.00 C +ATOM 441 HB2 PHE 29 24.149 -86.404 -8.500 1.00 0.00 H +ATOM 442 HB3 PHE 29 24.188 -86.271 -6.740 1.00 0.00 H +ATOM 443 CG PHE 29 22.902 -84.849 -7.621 1.00 0.00 C +ATOM 444 CD1 PHE 29 21.935 -84.940 -8.631 1.00 0.00 C +ATOM 445 HD1 PHE 29 22.120 -85.658 -9.415 1.00 0.00 H +ATOM 446 CE1 PHE 29 20.714 -84.233 -8.546 1.00 0.00 C +ATOM 447 HE1 PHE 29 19.983 -84.212 -9.340 1.00 0.00 H +ATOM 448 CZ PHE 29 20.605 -83.254 -7.536 1.00 0.00 C +ATOM 449 HZ PHE 29 19.694 -82.688 -7.412 1.00 0.00 H +ATOM 450 CE2 PHE 29 21.661 -83.086 -6.603 1.00 0.00 C +ATOM 451 HE2 PHE 29 21.669 -82.215 -5.964 1.00 0.00 H +ATOM 452 CD2 PHE 29 22.761 -83.885 -6.608 1.00 0.00 C +ATOM 453 HD2 PHE 29 23.624 -83.719 -5.982 1.00 0.00 H +ATOM 454 C PHE 29 26.717 -85.957 -7.763 1.00 0.00 C +ATOM 455 O PHE 29 27.405 -86.297 -6.817 1.00 0.00 O +ATOM 456 N THR 30 27.121 -86.211 -9.010 1.00 0.00 N +ATOM 457 H THR 30 26.604 -85.860 -9.803 1.00 0.00 H +ATOM 458 CA THR 30 28.308 -86.999 -9.275 1.00 0.00 C +ATOM 459 HA THR 30 28.272 -87.816 -8.554 1.00 0.00 H +ATOM 460 CB THR 30 28.440 -87.566 -10.688 1.00 0.00 C +ATOM 461 HB THR 30 28.600 -86.780 -11.425 1.00 0.00 H +ATOM 462 CG2 THR 30 29.632 -88.518 -10.792 1.00 0.00 C +ATOM 463 HG21 THR 30 30.562 -87.954 -10.720 1.00 0.00 H +ATOM 464 HG22 THR 30 29.618 -89.217 -9.955 1.00 0.00 H +ATOM 465 HG23 THR 30 29.510 -88.992 -11.766 1.00 0.00 H +ATOM 466 OG1 THR 30 27.344 -88.335 -11.109 1.00 0.00 O +ATOM 467 HG1 THR 30 26.648 -87.698 -11.288 1.00 0.00 H +ATOM 468 C THR 30 29.596 -86.151 -9.081 1.00 0.00 C +ATOM 469 O THR 30 30.568 -86.626 -8.566 1.00 0.00 O +ATOM 470 N LYS 31 29.600 -84.889 -9.497 1.00 0.00 N +ATOM 471 H LYS 31 28.784 -84.557 -9.991 1.00 0.00 H +ATOM 472 CA LYS 31 30.767 -83.966 -9.298 1.00 0.00 C +ATOM 473 HA LYS 31 31.647 -84.418 -9.756 1.00 0.00 H +ATOM 474 CB LYS 31 30.479 -82.663 -10.011 1.00 0.00 C +ATOM 475 HB2 LYS 31 29.505 -82.202 -9.844 1.00 0.00 H +ATOM 476 HB3 LYS 31 31.290 -81.966 -9.803 1.00 0.00 H +ATOM 477 CG LYS 31 30.535 -82.961 -11.531 1.00 0.00 C +ATOM 478 HG2 LYS 31 31.526 -83.231 -11.895 1.00 0.00 H +ATOM 479 HG3 LYS 31 29.909 -83.813 -11.796 1.00 0.00 H +ATOM 480 CD LYS 31 30.141 -81.677 -12.291 1.00 0.00 C +ATOM 481 HD2 LYS 31 29.104 -81.401 -12.097 1.00 0.00 H +ATOM 482 HD3 LYS 31 30.703 -80.851 -11.856 1.00 0.00 H +ATOM 483 CE LYS 31 30.400 -81.789 -13.869 1.00 0.00 C +ATOM 484 HE2 LYS 31 31.315 -82.381 -13.900 1.00 0.00 H +ATOM 485 HE3 LYS 31 29.665 -82.336 -14.460 1.00 0.00 H +ATOM 486 NZ LYS 31 30.566 -80.451 -14.557 1.00 0.00 N +ATOM 487 HZ1 LYS 31 30.897 -79.752 -13.907 1.00 0.00 H +ATOM 488 HZ2 LYS 31 29.697 -80.172 -14.989 1.00 0.00 H +ATOM 489 HZ3 LYS 31 31.312 -80.533 -15.233 1.00 0.00 H +ATOM 490 C LYS 31 31.055 -83.705 -7.815 1.00 0.00 C +ATOM 491 O LYS 31 32.225 -83.821 -7.426 1.00 0.00 O +ATOM 492 N ALA 32 30.046 -83.609 -6.948 1.00 0.00 N +ATOM 493 H ALA 32 29.115 -83.459 -7.310 1.00 0.00 H +ATOM 494 CA ALA 32 30.212 -83.561 -5.477 1.00 0.00 C +ATOM 495 HA ALA 32 30.920 -82.749 -5.308 1.00 0.00 H +ATOM 496 CB ALA 32 28.819 -83.237 -4.982 1.00 0.00 C +ATOM 497 HB1 ALA 32 28.694 -82.157 -5.056 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.022 -83.759 -5.511 1.00 0.00 H +ATOM 499 HB3 ALA 32 28.740 -83.582 -3.951 1.00 0.00 H +ATOM 500 C ALA 32 30.829 -84.880 -4.953 1.00 0.00 C +ATOM 501 O ALA 32 31.756 -84.949 -4.147 1.00 0.00 O +ATOM 502 N ASP 33 30.298 -86.075 -5.448 1.00 0.00 N +ATOM 503 H ASP 33 29.552 -86.002 -6.125 1.00 0.00 H +ATOM 504 CA ASP 33 30.919 -87.373 -5.182 1.00 0.00 C +ATOM 505 HA ASP 33 30.887 -87.556 -4.108 1.00 0.00 H +ATOM 506 CB ASP 33 30.027 -88.482 -5.900 1.00 0.00 C +ATOM 507 HB2 ASP 33 29.955 -88.240 -6.960 1.00 0.00 H +ATOM 508 HB3 ASP 33 30.596 -89.412 -5.885 1.00 0.00 H +ATOM 509 CG ASP 33 28.680 -88.784 -5.221 1.00 0.00 C +ATOM 510 OD1 ASP 33 27.980 -89.658 -5.717 1.00 0.00 O +ATOM 511 OD2 ASP 33 28.262 -88.103 -4.341 1.00 0.00 O +ATOM 512 C ASP 33 32.374 -87.550 -5.549 1.00 0.00 C +ATOM 513 O ASP 33 33.158 -88.189 -4.853 1.00 0.00 O +ATOM 514 N ALA 34 32.827 -87.072 -6.711 1.00 0.00 N +ATOM 515 H ALA 34 32.238 -86.506 -7.305 1.00 0.00 H +ATOM 516 CA ALA 34 34.270 -86.984 -7.036 1.00 0.00 C +ATOM 517 HA ALA 34 34.619 -88.015 -6.988 1.00 0.00 H +ATOM 518 CB ALA 34 34.622 -86.493 -8.457 1.00 0.00 C +ATOM 519 HB1 ALA 34 35.646 -86.131 -8.550 1.00 0.00 H +ATOM 520 HB2 ALA 34 33.983 -85.631 -8.648 1.00 0.00 H +ATOM 521 HB3 ALA 34 34.327 -87.103 -9.311 1.00 0.00 H +ATOM 522 C ALA 34 34.995 -86.121 -6.011 1.00 0.00 C +ATOM 523 O ALA 34 36.060 -86.412 -5.614 1.00 0.00 O +ATOM 524 N ASN 35 34.418 -84.945 -5.629 1.00 0.00 N +ATOM 525 H ASN 35 33.492 -84.812 -6.009 1.00 0.00 H +ATOM 526 CA ASN 35 34.891 -83.965 -4.674 1.00 0.00 C +ATOM 527 HA ASN 35 35.915 -83.724 -4.957 1.00 0.00 H +ATOM 528 CB ASN 35 33.953 -82.751 -4.746 1.00 0.00 C +ATOM 529 HB2 ASN 35 33.863 -82.558 -5.815 1.00 0.00 H +ATOM 530 HB3 ASN 35 33.014 -83.089 -4.308 1.00 0.00 H +ATOM 531 CG ASN 35 34.433 -81.513 -3.999 1.00 0.00 C +ATOM 532 OD1 ASN 35 35.391 -80.894 -4.439 1.00 0.00 O +ATOM 533 ND2 ASN 35 33.672 -81.072 -2.990 1.00 0.00 N +ATOM 534 HD21 ASN 35 32.854 -81.609 -2.739 1.00 0.00 H +ATOM 535 HD22 ASN 35 33.981 -80.289 -2.433 1.00 0.00 H +ATOM 536 C ASN 35 34.997 -84.495 -3.211 1.00 0.00 C +ATOM 537 O ASN 35 35.883 -84.221 -2.459 1.00 0.00 O +ATOM 538 N ASP 36 34.065 -85.292 -2.765 1.00 0.00 N +ATOM 539 H ASP 36 33.285 -85.368 -3.401 1.00 0.00 H +ATOM 540 CA ASP 36 34.025 -86.145 -1.540 1.00 0.00 C +ATOM 541 HA ASP 36 34.219 -85.517 -0.670 1.00 0.00 H +ATOM 542 CB ASP 36 32.689 -86.809 -1.436 1.00 0.00 C +ATOM 543 HB2 ASP 36 31.951 -86.029 -1.247 1.00 0.00 H +ATOM 544 HB3 ASP 36 32.486 -87.274 -2.400 1.00 0.00 H +ATOM 545 CG ASP 36 32.472 -87.797 -0.404 1.00 0.00 C +ATOM 546 OD1 ASP 36 32.584 -87.451 0.756 1.00 0.00 O +ATOM 547 OD2 ASP 36 31.810 -88.828 -0.753 1.00 0.00 O +ATOM 548 C ASP 36 35.147 -87.220 -1.475 1.00 0.00 C +ATOM 549 O ASP 36 35.530 -87.698 -0.402 1.00 0.00 O +ATOM 550 N LYS 37 35.707 -87.576 -2.642 1.00 0.00 N +ATOM 551 H LYS 37 35.304 -87.200 -3.489 1.00 0.00 H +ATOM 552 CA LYS 37 36.850 -88.523 -2.847 1.00 0.00 C +ATOM 553 HA LYS 37 36.931 -88.851 -1.810 1.00 0.00 H +ATOM 554 CB LYS 37 36.363 -89.773 -3.648 1.00 0.00 C +ATOM 555 HB2 LYS 37 37.183 -90.462 -3.852 1.00 0.00 H +ATOM 556 HB3 LYS 37 35.988 -89.443 -4.617 1.00 0.00 H +ATOM 557 CG LYS 37 35.289 -90.598 -3.009 1.00 0.00 C +ATOM 558 HG2 LYS 37 34.465 -89.967 -2.675 1.00 0.00 H +ATOM 559 HG3 LYS 37 35.746 -90.927 -2.076 1.00 0.00 H +ATOM 560 CD LYS 37 34.971 -91.854 -3.769 1.00 0.00 C +ATOM 561 HD2 LYS 37 35.846 -92.487 -3.911 1.00 0.00 H +ATOM 562 HD3 LYS 37 34.255 -92.401 -3.156 1.00 0.00 H +ATOM 563 CE LYS 37 34.533 -91.569 -5.222 1.00 0.00 C +ATOM 564 HE2 LYS 37 35.118 -90.758 -5.657 1.00 0.00 H +ATOM 565 HE3 LYS 37 34.666 -92.494 -5.783 1.00 0.00 H +ATOM 566 NZ LYS 37 33.146 -91.058 -5.337 1.00 0.00 N +ATOM 567 HZ1 LYS 37 33.021 -90.129 -4.962 1.00 0.00 H +ATOM 568 HZ2 LYS 37 32.893 -91.220 -6.301 1.00 0.00 H +ATOM 569 HZ3 LYS 37 32.575 -91.729 -4.842 1.00 0.00 H +ATOM 570 C LYS 37 38.168 -87.870 -3.302 1.00 0.00 C +ATOM 571 O LYS 37 39.257 -88.460 -3.371 1.00 0.00 O +ATOM 572 N GLY 38 38.088 -86.513 -3.532 1.00 0.00 N +ATOM 573 H GLY 38 37.156 -86.134 -3.452 1.00 0.00 H +ATOM 574 CA GLY 38 39.201 -85.694 -3.998 1.00 0.00 C +ATOM 575 HA2 GLY 38 38.836 -84.670 -3.919 1.00 0.00 H +ATOM 576 HA3 GLY 38 40.033 -85.786 -3.300 1.00 0.00 H +ATOM 577 C GLY 38 39.710 -85.968 -5.448 1.00 0.00 C +ATOM 578 O GLY 38 40.834 -85.772 -5.801 1.00 0.00 O +ATOM 579 N VAL 39 38.790 -86.495 -6.298 1.00 0.00 N +ATOM 580 H VAL 39 37.849 -86.593 -5.945 1.00 0.00 H +ATOM 581 CA VAL 39 39.160 -87.178 -7.582 1.00 0.00 C +ATOM 582 HA VAL 39 40.135 -87.612 -7.359 1.00 0.00 H +ATOM 583 CB VAL 39 38.121 -88.231 -7.918 1.00 0.00 C +ATOM 584 HB VAL 39 37.185 -87.743 -8.190 1.00 0.00 H +ATOM 585 CG1 VAL 39 38.555 -88.968 -9.205 1.00 0.00 C +ATOM 586 HG11 VAL 39 37.792 -89.699 -9.468 1.00 0.00 H +ATOM 587 HG12 VAL 39 39.512 -89.474 -9.081 1.00 0.00 H +ATOM 588 HG13 VAL 39 38.588 -88.271 -10.042 1.00 0.00 H +ATOM 589 CG2 VAL 39 37.861 -89.264 -6.840 1.00 0.00 C +ATOM 590 HG21 VAL 39 38.746 -89.893 -6.741 1.00 0.00 H +ATOM 591 HG22 VAL 39 37.000 -89.886 -7.084 1.00 0.00 H +ATOM 592 HG23 VAL 39 37.749 -88.779 -5.870 1.00 0.00 H +ATOM 593 C VAL 39 39.236 -86.091 -8.702 1.00 0.00 C +ATOM 594 O VAL 39 38.414 -85.143 -8.758 1.00 0.00 O +ATOM 595 N ASP 40 40.249 -86.215 -9.620 1.00 0.00 N +ATOM 596 H ASP 40 40.765 -87.069 -9.462 1.00 0.00 H +ATOM 597 CA ASP 40 40.539 -85.324 -10.722 1.00 0.00 C +ATOM 598 HA ASP 40 39.991 -84.383 -10.663 1.00 0.00 H +ATOM 599 CB ASP 40 42.003 -85.060 -10.920 1.00 0.00 C +ATOM 600 HB2 ASP 40 42.457 -86.028 -11.133 1.00 0.00 H +ATOM 601 HB3 ASP 40 42.162 -84.493 -11.837 1.00 0.00 H +ATOM 602 CG ASP 40 42.626 -84.234 -9.797 1.00 0.00 C +ATOM 603 OD1 ASP 40 43.519 -84.691 -8.991 1.00 0.00 O +ATOM 604 OD2 ASP 40 42.125 -83.088 -9.626 1.00 0.00 O +ATOM 605 C ASP 40 39.951 -85.901 -11.956 1.00 0.00 C +ATOM 606 O ASP 40 39.943 -87.174 -12.162 1.00 0.00 O +ATOM 607 N GLY 41 39.505 -85.051 -12.913 1.00 0.00 N +ATOM 608 H GLY 41 39.701 -84.072 -12.764 1.00 0.00 H +ATOM 609 CA GLY 41 38.740 -85.447 -14.133 1.00 0.00 C +ATOM 610 HA2 GLY 41 39.296 -85.197 -15.037 1.00 0.00 H +ATOM 611 HA3 GLY 41 38.581 -86.525 -14.150 1.00 0.00 H +ATOM 612 C GLY 41 37.468 -84.620 -14.236 1.00 0.00 C +ATOM 613 O GLY 41 37.282 -83.600 -13.521 1.00 0.00 O +ATOM 614 N GLU 42 36.592 -84.884 -15.171 1.00 0.00 N +ATOM 615 H GLU 42 36.778 -85.646 -15.807 1.00 0.00 H +ATOM 616 CA GLU 42 35.315 -84.076 -15.434 1.00 0.00 C +ATOM 617 HA GLU 42 35.051 -83.592 -14.493 1.00 0.00 H +ATOM 618 CB GLU 42 35.577 -82.991 -16.403 1.00 0.00 C +ATOM 619 HB2 GLU 42 36.227 -82.248 -15.941 1.00 0.00 H +ATOM 620 HB3 GLU 42 36.159 -83.462 -17.194 1.00 0.00 H +ATOM 621 CG GLU 42 34.380 -82.151 -17.021 1.00 0.00 C +ATOM 622 HG2 GLU 42 34.813 -81.352 -17.622 1.00 0.00 H +ATOM 623 HG3 GLU 42 33.875 -82.910 -17.619 1.00 0.00 H +ATOM 624 CD GLU 42 33.318 -81.531 -16.127 1.00 0.00 C +ATOM 625 OE1 GLU 42 33.371 -81.836 -14.916 1.00 0.00 O +ATOM 626 OE2 GLU 42 32.672 -80.520 -16.529 1.00 0.00 O +ATOM 627 C GLU 42 34.235 -84.964 -15.946 1.00 0.00 C +ATOM 628 O GLU 42 34.496 -85.838 -16.758 1.00 0.00 O +ATOM 629 N TRP 43 33.001 -84.717 -15.547 1.00 0.00 N +ATOM 630 H TRP 43 32.917 -83.834 -15.064 1.00 0.00 H +ATOM 631 CA TRP 43 31.835 -85.607 -15.578 1.00 0.00 C +ATOM 632 HA TRP 43 32.281 -86.463 -16.084 1.00 0.00 H +ATOM 633 CB TRP 43 31.528 -86.078 -14.181 1.00 0.00 C +ATOM 634 HB2 TRP 43 31.373 -85.210 -13.541 1.00 0.00 H +ATOM 635 HB3 TRP 43 30.695 -86.776 -14.263 1.00 0.00 H +ATOM 636 CG TRP 43 32.565 -86.947 -13.579 1.00 0.00 C +ATOM 637 CD1 TRP 43 32.547 -88.297 -13.643 1.00 0.00 C +ATOM 638 HD1 TRP 43 31.734 -88.887 -14.039 1.00 0.00 H +ATOM 639 NE1 TRP 43 33.659 -88.772 -13.030 1.00 0.00 N +ATOM 640 HE1 TRP 43 33.797 -89.768 -12.928 1.00 0.00 H +ATOM 641 CE2 TRP 43 34.540 -87.814 -12.570 1.00 0.00 C +ATOM 642 CZ2 TRP 43 35.796 -87.795 -11.988 1.00 0.00 C +ATOM 643 HZ2 TRP 43 36.281 -88.747 -11.831 1.00 0.00 H +ATOM 644 CH2 TRP 43 36.237 -86.621 -11.419 1.00 0.00 C +ATOM 645 HH2 TRP 43 37.216 -86.598 -10.963 1.00 0.00 H +ATOM 646 CZ3 TRP 43 35.505 -85.396 -11.586 1.00 0.00 C +ATOM 647 HZ3 TRP 43 35.839 -84.491 -11.101 1.00 0.00 H +ATOM 648 CE3 TRP 43 34.281 -85.413 -12.306 1.00 0.00 C +ATOM 649 HE3 TRP 43 33.660 -84.532 -12.375 1.00 0.00 H +ATOM 650 CD2 TRP 43 33.773 -86.618 -12.786 1.00 0.00 C +ATOM 651 C TRP 43 30.557 -85.070 -16.296 1.00 0.00 C +ATOM 652 O TRP 43 30.474 -83.862 -16.384 1.00 0.00 O +ATOM 653 N THR 44 29.573 -85.922 -16.689 1.00 0.00 N +ATOM 654 H THR 44 29.650 -86.894 -16.429 1.00 0.00 H +ATOM 655 CA THR 44 28.339 -85.429 -17.294 1.00 0.00 C +ATOM 656 HA THR 44 27.956 -84.661 -16.622 1.00 0.00 H +ATOM 657 CB THR 44 28.644 -84.842 -18.697 1.00 0.00 C +ATOM 658 HB THR 44 29.567 -84.264 -18.647 1.00 0.00 H +ATOM 659 CG2 THR 44 28.836 -85.892 -19.778 1.00 0.00 C +ATOM 660 HG21 THR 44 29.071 -85.407 -20.726 1.00 0.00 H +ATOM 661 HG22 THR 44 27.840 -86.321 -19.887 1.00 0.00 H +ATOM 662 HG23 THR 44 29.522 -86.662 -19.423 1.00 0.00 H +ATOM 663 OG1 THR 44 27.487 -84.020 -18.950 1.00 0.00 O +ATOM 664 HG1 THR 44 27.543 -83.336 -18.279 1.00 0.00 H +ATOM 665 C THR 44 27.259 -86.572 -17.373 1.00 0.00 C +ATOM 666 O THR 44 27.605 -87.713 -17.110 1.00 0.00 O +ATOM 667 N TYR 45 26.026 -86.291 -17.842 1.00 0.00 N +ATOM 668 H TYR 45 25.916 -85.335 -18.151 1.00 0.00 H +ATOM 669 CA TYR 45 24.962 -87.343 -18.117 1.00 0.00 C +ATOM 670 HA TYR 45 25.140 -88.154 -17.410 1.00 0.00 H +ATOM 671 CB TYR 45 23.554 -86.704 -17.779 1.00 0.00 C +ATOM 672 HB2 TYR 45 23.687 -86.233 -16.805 1.00 0.00 H +ATOM 673 HB3 TYR 45 23.260 -85.984 -18.542 1.00 0.00 H +ATOM 674 CG TYR 45 22.358 -87.689 -17.686 1.00 0.00 C +ATOM 675 CD1 TYR 45 22.152 -88.556 -16.624 1.00 0.00 C +ATOM 676 HD1 TYR 45 22.738 -88.633 -15.720 1.00 0.00 H +ATOM 677 CE1 TYR 45 20.967 -89.368 -16.652 1.00 0.00 C +ATOM 678 HE1 TYR 45 20.752 -89.945 -15.766 1.00 0.00 H +ATOM 679 CZ TYR 45 20.085 -89.317 -17.749 1.00 0.00 C +ATOM 680 OH TYR 45 19.011 -90.211 -17.750 1.00 0.00 O +ATOM 681 HH TYR 45 18.776 -90.576 -16.894 1.00 0.00 H +ATOM 682 CE2 TYR 45 20.313 -88.500 -18.865 1.00 0.00 C +ATOM 683 HE2 TYR 45 19.683 -88.503 -19.742 1.00 0.00 H +ATOM 684 CD2 TYR 45 21.489 -87.708 -18.789 1.00 0.00 C +ATOM 685 HD2 TYR 45 21.606 -87.063 -19.647 1.00 0.00 H +ATOM 686 C TYR 45 25.031 -87.842 -19.550 1.00 0.00 C +ATOM 687 O TYR 45 25.676 -87.197 -20.442 1.00 0.00 O +ATOM 688 N ASP 46 24.377 -88.931 -19.753 1.00 0.00 N +ATOM 689 H ASP 46 24.171 -89.415 -18.891 1.00 0.00 H +ATOM 690 CA ASP 46 24.209 -89.678 -21.034 1.00 0.00 C +ATOM 691 HA ASP 46 24.381 -88.969 -21.844 1.00 0.00 H +ATOM 692 CB ASP 46 25.265 -90.738 -21.157 1.00 0.00 C +ATOM 693 HB2 ASP 46 26.246 -90.266 -21.202 1.00 0.00 H +ATOM 694 HB3 ASP 46 25.185 -91.390 -20.286 1.00 0.00 H +ATOM 695 CG ASP 46 25.139 -91.618 -22.399 1.00 0.00 C +ATOM 696 OD1 ASP 46 24.367 -91.266 -23.319 1.00 0.00 O +ATOM 697 OD2 ASP 46 25.544 -92.803 -22.315 1.00 0.00 O +ATOM 698 C ASP 46 22.784 -90.366 -21.154 1.00 0.00 C +ATOM 699 O ASP 46 22.512 -91.442 -20.629 1.00 0.00 O +ATOM 700 N ASP 47 21.831 -89.674 -21.787 1.00 0.00 N +ATOM 701 H ASP 47 22.132 -88.795 -22.182 1.00 0.00 H +ATOM 702 CA ASP 47 20.400 -90.065 -21.898 1.00 0.00 C +ATOM 703 HA ASP 47 20.000 -90.241 -20.899 1.00 0.00 H +ATOM 704 CB ASP 47 19.704 -88.776 -22.500 1.00 0.00 C +ATOM 705 HB2 ASP 47 20.159 -87.873 -22.091 1.00 0.00 H +ATOM 706 HB3 ASP 47 19.943 -88.798 -23.563 1.00 0.00 H +ATOM 707 CG ASP 47 18.169 -88.731 -22.353 1.00 0.00 C +ATOM 708 OD1 ASP 47 17.489 -88.164 -23.282 1.00 0.00 O +ATOM 709 OD2 ASP 47 17.662 -89.335 -21.356 1.00 0.00 O +ATOM 710 C ASP 47 20.223 -91.328 -22.841 1.00 0.00 C +ATOM 711 O ASP 47 19.052 -91.766 -23.018 1.00 0.00 O +ATOM 712 N ALA 48 21.228 -91.859 -23.521 1.00 0.00 N +ATOM 713 H ALA 48 22.149 -91.448 -23.473 1.00 0.00 H +ATOM 714 CA ALA 48 21.062 -93.088 -24.282 1.00 0.00 C +ATOM 715 HA ALA 48 20.037 -92.998 -24.643 1.00 0.00 H +ATOM 716 CB ALA 48 22.070 -93.057 -25.415 1.00 0.00 C +ATOM 717 HB1 ALA 48 21.878 -93.965 -25.988 1.00 0.00 H +ATOM 718 HB2 ALA 48 23.070 -93.161 -24.995 1.00 0.00 H +ATOM 719 HB3 ALA 48 21.923 -92.173 -26.036 1.00 0.00 H +ATOM 720 C ALA 48 21.302 -94.338 -23.426 1.00 0.00 C +ATOM 721 O ALA 48 20.989 -95.419 -23.816 1.00 0.00 O +ATOM 722 N THR 49 21.886 -94.142 -22.271 1.00 0.00 N +ATOM 723 H THR 49 22.110 -93.204 -21.972 1.00 0.00 H +ATOM 724 CA THR 49 22.288 -95.160 -21.255 1.00 0.00 C +ATOM 725 HA THR 49 21.811 -96.080 -21.590 1.00 0.00 H +ATOM 726 CB THR 49 23.796 -95.524 -21.271 1.00 0.00 C +ATOM 727 HB THR 49 23.816 -96.431 -20.667 1.00 0.00 H +ATOM 728 CG2 THR 49 24.525 -95.849 -22.621 1.00 0.00 C +ATOM 729 HG21 THR 49 24.059 -96.784 -22.932 1.00 0.00 H +ATOM 730 HG22 THR 49 25.580 -96.014 -22.401 1.00 0.00 H +ATOM 731 HG23 THR 49 24.386 -94.992 -23.280 1.00 0.00 H +ATOM 732 OG1 THR 49 24.572 -94.603 -20.555 1.00 0.00 O +ATOM 733 HG1 THR 49 24.749 -93.823 -21.086 1.00 0.00 H +ATOM 734 C THR 49 21.789 -94.758 -19.884 1.00 0.00 C +ATOM 735 O THR 49 22.105 -95.498 -18.993 1.00 0.00 O +ATOM 736 N LYS 50 21.000 -93.695 -19.760 1.00 0.00 N +ATOM 737 H LYS 50 20.836 -93.146 -20.592 1.00 0.00 H +ATOM 738 CA LYS 50 20.376 -93.344 -18.491 1.00 0.00 C +ATOM 739 HA LYS 50 20.137 -92.305 -18.716 1.00 0.00 H +ATOM 740 CB LYS 50 19.090 -94.271 -18.171 1.00 0.00 C +ATOM 741 HB2 LYS 50 19.433 -95.276 -17.923 1.00 0.00 H +ATOM 742 HB3 LYS 50 18.515 -93.869 -17.336 1.00 0.00 H +ATOM 743 CG LYS 50 18.104 -94.384 -19.380 1.00 0.00 C +ATOM 744 HG2 LYS 50 18.635 -94.957 -20.141 1.00 0.00 H +ATOM 745 HG3 LYS 50 17.305 -95.067 -19.090 1.00 0.00 H +ATOM 746 CD LYS 50 17.556 -92.985 -19.842 1.00 0.00 C +ATOM 747 HD2 LYS 50 17.034 -92.507 -19.013 1.00 0.00 H +ATOM 748 HD3 LYS 50 18.332 -92.309 -20.201 1.00 0.00 H +ATOM 749 CE LYS 50 16.550 -93.210 -20.941 1.00 0.00 C +ATOM 750 HE2 LYS 50 16.973 -93.854 -21.712 1.00 0.00 H +ATOM 751 HE3 LYS 50 15.623 -93.672 -20.601 1.00 0.00 H +ATOM 752 NZ LYS 50 16.215 -91.847 -21.543 1.00 0.00 N +ATOM 753 HZ1 LYS 50 16.935 -91.148 -21.434 1.00 0.00 H +ATOM 754 HZ2 LYS 50 15.419 -91.368 -21.146 1.00 0.00 H +ATOM 755 HZ3 LYS 50 16.020 -91.910 -22.532 1.00 0.00 H +ATOM 756 C LYS 50 21.330 -93.187 -17.264 1.00 0.00 C +ATOM 757 O LYS 50 21.003 -93.476 -16.144 1.00 0.00 O +ATOM 758 N THR 51 22.598 -92.776 -17.534 1.00 0.00 N +ATOM 759 H THR 51 22.842 -92.492 -18.472 1.00 0.00 H +ATOM 760 CA THR 51 23.638 -92.842 -16.463 1.00 0.00 C +ATOM 761 HA THR 51 23.188 -92.783 -15.472 1.00 0.00 H +ATOM 762 CB THR 51 24.388 -94.205 -16.522 1.00 0.00 C +ATOM 763 HB THR 51 25.103 -94.182 -17.345 1.00 0.00 H +ATOM 764 CG2 THR 51 25.325 -94.415 -15.296 1.00 0.00 C +ATOM 765 HG21 THR 51 25.792 -95.397 -15.361 1.00 0.00 H +ATOM 766 HG22 THR 51 24.803 -94.349 -14.341 1.00 0.00 H +ATOM 767 HG23 THR 51 26.069 -93.624 -15.198 1.00 0.00 H +ATOM 768 OG1 THR 51 23.468 -95.322 -16.695 1.00 0.00 O +ATOM 769 HG1 THR 51 23.225 -95.290 -17.623 1.00 0.00 H +ATOM 770 C THR 51 24.630 -91.657 -16.542 1.00 0.00 C +ATOM 771 O THR 51 24.915 -91.107 -17.590 1.00 0.00 O +ATOM 772 N PHE 52 25.120 -91.218 -15.369 1.00 0.00 N +ATOM 773 H PHE 52 24.982 -91.817 -14.568 1.00 0.00 H +ATOM 774 CA PHE 52 26.182 -90.262 -15.217 1.00 0.00 C +ATOM 775 HA PHE 52 26.010 -89.512 -15.989 1.00 0.00 H +ATOM 776 CB PHE 52 26.165 -89.494 -13.922 1.00 0.00 C +ATOM 777 HB2 PHE 52 26.456 -90.189 -13.135 1.00 0.00 H +ATOM 778 HB3 PHE 52 26.945 -88.739 -14.022 1.00 0.00 H +ATOM 779 CG PHE 52 24.973 -88.690 -13.526 1.00 0.00 C +ATOM 780 CD1 PHE 52 24.083 -89.098 -12.503 1.00 0.00 C +ATOM 781 HD1 PHE 52 24.190 -90.041 -11.987 1.00 0.00 H +ATOM 782 CE1 PHE 52 22.941 -88.347 -12.187 1.00 0.00 C +ATOM 783 HE1 PHE 52 22.268 -88.720 -11.429 1.00 0.00 H +ATOM 784 CZ PHE 52 22.660 -87.155 -12.870 1.00 0.00 C +ATOM 785 HZ PHE 52 21.734 -86.641 -12.655 1.00 0.00 H +ATOM 786 CE2 PHE 52 23.558 -86.738 -13.911 1.00 0.00 C +ATOM 787 HE2 PHE 52 23.380 -85.812 -14.437 1.00 0.00 H +ATOM 788 CD2 PHE 52 24.732 -87.464 -14.167 1.00 0.00 C +ATOM 789 HD2 PHE 52 25.372 -87.140 -14.975 1.00 0.00 H +ATOM 790 C PHE 52 27.562 -90.907 -15.378 1.00 0.00 C +ATOM 791 O PHE 52 27.789 -92.049 -15.079 1.00 0.00 O +ATOM 792 N THR 53 28.489 -90.147 -15.994 1.00 0.00 N +ATOM 793 H THR 53 28.319 -89.163 -16.151 1.00 0.00 H +ATOM 794 CA THR 53 29.656 -90.725 -16.629 1.00 0.00 C +ATOM 795 HA THR 53 30.070 -91.489 -15.971 1.00 0.00 H +ATOM 796 CB THR 53 29.352 -91.338 -17.965 1.00 0.00 C +ATOM 797 HB THR 53 28.405 -91.871 -17.878 1.00 0.00 H +ATOM 798 CG2 THR 53 29.032 -90.319 -19.039 1.00 0.00 C +ATOM 799 HG21 THR 53 28.484 -89.469 -18.631 1.00 0.00 H +ATOM 800 HG22 THR 53 28.404 -90.718 -19.836 1.00 0.00 H +ATOM 801 HG23 THR 53 29.929 -89.794 -19.366 1.00 0.00 H +ATOM 802 OG1 THR 53 30.276 -92.225 -18.418 1.00 0.00 O +ATOM 803 HG1 THR 53 30.013 -93.064 -18.032 1.00 0.00 H +ATOM 804 C THR 53 30.801 -89.763 -16.780 1.00 0.00 C +ATOM 805 O THR 53 30.601 -88.566 -16.590 1.00 0.00 O +ATOM 806 N VAL 54 32.002 -90.237 -16.994 1.00 0.00 N +ATOM 807 H VAL 54 32.018 -91.210 -17.265 1.00 0.00 H +ATOM 808 CA VAL 54 33.282 -89.480 -17.248 1.00 0.00 C +ATOM 809 HA VAL 54 33.167 -88.589 -16.630 1.00 0.00 H +ATOM 810 CB VAL 54 34.466 -90.216 -16.569 1.00 0.00 C +ATOM 811 HB VAL 54 34.100 -90.517 -15.588 1.00 0.00 H +ATOM 812 CG1 VAL 54 35.142 -91.441 -17.237 1.00 0.00 C +ATOM 813 HG11 VAL 54 35.547 -91.155 -18.208 1.00 0.00 H +ATOM 814 HG12 VAL 54 34.337 -92.158 -17.396 1.00 0.00 H +ATOM 815 HG13 VAL 54 35.901 -91.847 -16.568 1.00 0.00 H +ATOM 816 CG2 VAL 54 35.662 -89.332 -16.235 1.00 0.00 C +ATOM 817 HG21 VAL 54 36.311 -89.990 -15.657 1.00 0.00 H +ATOM 818 HG22 VAL 54 35.448 -88.566 -15.490 1.00 0.00 H +ATOM 819 HG23 VAL 54 36.167 -88.869 -17.083 1.00 0.00 H +ATOM 820 C VAL 54 33.456 -89.029 -18.715 1.00 0.00 C +ATOM 821 O VAL 54 33.289 -89.849 -19.635 1.00 0.00 O +ATOM 822 N THR 55 33.907 -87.840 -18.852 1.00 0.00 N +ATOM 823 H THR 55 34.175 -87.369 -18.000 1.00 0.00 H +ATOM 824 CA THR 55 34.379 -87.242 -20.074 1.00 0.00 C +ATOM 825 HA THR 55 34.137 -87.838 -20.954 1.00 0.00 H +ATOM 826 CB THR 55 33.840 -85.771 -20.284 1.00 0.00 C +ATOM 827 HB THR 55 34.004 -85.439 -21.309 1.00 0.00 H +ATOM 828 CG2 THR 55 32.393 -85.518 -19.941 1.00 0.00 C +ATOM 829 HG21 THR 55 32.203 -85.087 -18.958 1.00 0.00 H +ATOM 830 HG22 THR 55 31.875 -86.476 -19.901 1.00 0.00 H +ATOM 831 HG23 THR 55 32.023 -84.836 -20.706 1.00 0.00 H +ATOM 832 OG1 THR 55 34.631 -84.912 -19.386 1.00 0.00 O +ATOM 833 HG1 THR 55 34.576 -85.266 -18.495 1.00 0.00 H +ATOM 834 C THR 55 35.916 -87.206 -20.226 1.00 0.00 C +ATOM 835 O THR 55 36.747 -87.461 -19.336 1.00 0.00 O +ATOM 836 N GLU 56 36.334 -86.937 -21.491 1.00 0.00 N +ATOM 837 H GLU 56 35.566 -86.824 -22.136 1.00 0.00 H +ATOM 838 CA GLU 56 37.733 -87.018 -21.993 1.00 0.00 C +ATOM 839 HA GLU 56 38.235 -87.804 -21.430 1.00 0.00 H +ATOM 840 CB GLU 56 37.672 -87.571 -23.372 1.00 0.00 C +ATOM 841 HB2 GLU 56 37.366 -86.830 -24.110 1.00 0.00 H +ATOM 842 HB3 GLU 56 38.719 -87.762 -23.605 1.00 0.00 H +ATOM 843 CG GLU 56 36.987 -88.927 -23.472 1.00 0.00 C +ATOM 844 HG2 GLU 56 37.383 -89.352 -24.394 1.00 0.00 H +ATOM 845 HG3 GLU 56 37.337 -89.588 -22.679 1.00 0.00 H +ATOM 846 CD GLU 56 35.503 -88.940 -23.558 1.00 0.00 C +ATOM 847 OE1 GLU 56 34.797 -87.919 -23.793 1.00 0.00 O +ATOM 848 OE2 GLU 56 34.918 -90.059 -23.481 1.00 0.00 O +ATOM 849 C GLU 56 38.551 -85.722 -21.989 1.00 0.00 C +ATOM 850 O GLU 56 39.755 -85.756 -21.550 1.00 0.00 O +ATOM 851 OXT GLU 56 38.066 -84.621 -22.399 1.00 0.00 O +ATOM 852 ZN ZN1 57 21.962 -88.030 -2.252 1.00 0.00 ZN +ATOM 853 N AN1 58 22.684 -87.248 -0.507 1.00 0.00 N +ATOM 854 C AN1 58 23.156 -86.839 2.059 1.00 0.00 C +ATOM 855 C1 AN1 58 22.978 -87.033 0.582 1.00 0.00 C +ATOM 856 H AN1 58 22.277 -86.213 2.255 1.00 0.00 H +ATOM 857 H1 AN1 58 24.043 -86.218 2.233 1.00 0.00 H +ATOM 858 H2 AN1 58 23.120 -87.755 2.662 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 17.408 -87.122 1.579 1.00 0.00 N +ATOM 860 N2 AZI 59 18.634 -86.921 1.420 1.00 0.00 N +ATOM 861 N3 AZI 59 19.841 -86.739 1.211 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/inp/pdbs/cluster.c8.pdb b/tests/nsga2/inp/pdbs/cluster.c8.pdb new file mode 100644 index 0000000..1fc916a --- /dev/null +++ b/tests/nsga2/inp/pdbs/cluster.c8.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.921 -81.871 -14.343 1.00 0.00 N +ATOM 2 H1 MET 1 14.869 -81.579 -14.148 1.00 0.00 H +ATOM 3 H2 MET 1 13.368 -81.557 -13.558 1.00 0.00 H +ATOM 4 H3 MET 1 13.637 -81.522 -15.247 1.00 0.00 H +ATOM 5 CA MET 1 13.777 -83.340 -14.319 1.00 0.00 C +ATOM 6 HA MET 1 12.694 -83.452 -14.273 1.00 0.00 H +ATOM 7 CB MET 1 14.417 -84.024 -15.635 1.00 0.00 C +ATOM 8 HB2 MET 1 13.739 -83.941 -16.484 1.00 0.00 H +ATOM 9 HB3 MET 1 15.258 -83.374 -15.880 1.00 0.00 H +ATOM 10 CG MET 1 14.914 -85.464 -15.548 1.00 0.00 C +ATOM 11 HG2 MET 1 15.491 -85.619 -16.460 1.00 0.00 H +ATOM 12 HG3 MET 1 15.641 -85.592 -14.746 1.00 0.00 H +ATOM 13 SD MET 1 13.694 -86.744 -15.342 1.00 0.00 S +ATOM 14 CE MET 1 12.844 -86.818 -16.891 1.00 0.00 C +ATOM 15 HE1 MET 1 12.441 -85.860 -17.221 1.00 0.00 H +ATOM 16 HE2 MET 1 12.022 -87.532 -16.842 1.00 0.00 H +ATOM 17 HE3 MET 1 13.515 -87.136 -17.689 1.00 0.00 H +ATOM 18 C MET 1 14.458 -83.816 -12.991 1.00 0.00 C +ATOM 19 O MET 1 15.523 -83.346 -12.558 1.00 0.00 O +ATOM 20 N GLN 2 13.897 -84.833 -12.374 1.00 0.00 N +ATOM 21 H GLN 2 13.021 -85.111 -12.794 1.00 0.00 H +ATOM 22 CA GLN 2 14.474 -85.680 -11.226 1.00 0.00 C +ATOM 23 HA GLN 2 14.952 -85.062 -10.466 1.00 0.00 H +ATOM 24 CB GLN 2 13.208 -86.271 -10.447 1.00 0.00 C +ATOM 25 HB2 GLN 2 12.499 -85.469 -10.247 1.00 0.00 H +ATOM 26 HB3 GLN 2 12.744 -86.972 -11.141 1.00 0.00 H +ATOM 27 CG GLN 2 13.497 -87.166 -9.295 1.00 0.00 C +ATOM 28 HG2 GLN 2 13.957 -88.104 -9.607 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.251 -86.595 -8.755 1.00 0.00 H +ATOM 30 CD GLN 2 12.285 -87.400 -8.519 1.00 0.00 C +ATOM 31 OE1 GLN 2 11.637 -88.433 -8.636 1.00 0.00 O +ATOM 32 NE2 GLN 2 11.927 -86.490 -7.713 1.00 0.00 N +ATOM 33 HE21 GLN 2 11.202 -86.742 -7.057 1.00 0.00 H +ATOM 34 HE22 GLN 2 12.491 -85.656 -7.798 1.00 0.00 H +ATOM 35 C GLN 2 15.466 -86.837 -11.631 1.00 0.00 C +ATOM 36 O GLN 2 15.053 -87.916 -11.986 1.00 0.00 O +ATOM 37 N TYR 3 16.775 -86.584 -11.551 1.00 0.00 N +ATOM 38 H TYR 3 17.123 -85.735 -11.128 1.00 0.00 H +ATOM 39 CA TYR 3 17.771 -87.564 -11.964 1.00 0.00 C +ATOM 40 HA TYR 3 17.313 -88.271 -12.655 1.00 0.00 H +ATOM 41 CB TYR 3 19.006 -86.895 -12.646 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.499 -86.219 -11.948 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.700 -87.727 -12.765 1.00 0.00 H +ATOM 44 CG TYR 3 18.698 -86.159 -13.977 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.565 -86.788 -15.198 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.901 -87.810 -15.289 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.148 -86.073 -16.345 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.141 -86.534 -17.322 1.00 0.00 H +ATOM 49 CZ TYR 3 17.953 -84.718 -16.219 1.00 0.00 C +ATOM 50 OH TYR 3 17.604 -83.917 -17.277 1.00 0.00 O +ATOM 51 HH TYR 3 17.237 -84.416 -18.010 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.135 -84.079 -14.926 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.941 -83.018 -14.881 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.646 -84.781 -13.840 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.734 -84.358 -12.850 1.00 0.00 H +ATOM 56 C TYR 3 18.256 -88.359 -10.791 1.00 0.00 C +ATOM 57 O TYR 3 18.335 -87.830 -9.636 1.00 0.00 O +ATOM 58 N LYS 4 18.596 -89.686 -11.012 1.00 0.00 N +ATOM 59 H LYS 4 18.517 -90.039 -11.955 1.00 0.00 H +ATOM 60 CA LYS 4 19.183 -90.476 -9.960 1.00 0.00 C +ATOM 61 HA LYS 4 18.711 -90.181 -9.023 1.00 0.00 H +ATOM 62 CB LYS 4 18.806 -91.973 -10.205 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.541 -92.429 -10.868 1.00 0.00 H +ATOM 64 HB3 LYS 4 18.979 -92.557 -9.302 1.00 0.00 H +ATOM 65 CG LYS 4 17.382 -92.249 -10.829 1.00 0.00 C +ATOM 66 HG2 LYS 4 16.591 -91.848 -10.196 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.198 -91.854 -11.828 1.00 0.00 H +ATOM 68 CD LYS 4 17.218 -93.746 -10.995 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.874 -94.090 -11.795 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.436 -94.320 -10.095 1.00 0.00 H +ATOM 71 CE LYS 4 15.773 -94.099 -11.464 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.705 -95.150 -11.747 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.144 -93.913 -10.593 1.00 0.00 H +ATOM 74 NZ LYS 4 15.360 -93.359 -12.729 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.844 -93.595 -13.583 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.370 -92.362 -12.569 1.00 0.00 H +ATOM 77 HZ3 LYS 4 14.403 -93.601 -12.942 1.00 0.00 H +ATOM 78 C LYS 4 20.712 -90.246 -9.868 1.00 0.00 C +ATOM 79 O LYS 4 21.339 -89.932 -10.899 1.00 0.00 O +ATOM 80 N HE1 5 21.157 -90.323 -8.628 1.00 0.00 N +ATOM 81 CA HE1 5 22.577 -90.254 -8.143 1.00 0.00 C +ATOM 82 C HE1 5 22.780 -91.510 -7.279 1.00 0.00 C +ATOM 83 O HE1 5 22.059 -91.731 -6.321 1.00 0.00 O +ATOM 84 CB HE1 5 22.905 -88.931 -7.404 1.00 0.00 C +ATOM 85 CG HE1 5 24.252 -88.842 -6.710 1.00 0.00 C +ATOM 86 CD2 HE1 5 25.467 -89.141 -7.300 1.00 0.00 C +ATOM 87 ND1 HE1 5 24.596 -88.111 -5.538 1.00 0.00 N +ATOM 88 CE1 HE1 5 25.920 -88.240 -5.320 1.00 0.00 C +ATOM 89 NE2 HE1 5 26.478 -88.827 -6.408 1.00 0.00 N +ATOM 90 H HE1 5 20.392 -90.395 -7.973 1.00 0.00 H +ATOM 91 HA HE1 5 23.185 -90.265 -9.047 1.00 0.00 H +ATOM 92 HB2 HE1 5 22.120 -88.862 -6.651 1.00 0.00 H +ATOM 93 HB3 HE1 5 22.809 -88.113 -8.118 1.00 0.00 H +ATOM 94 HD2 HE1 5 25.623 -89.543 -8.290 1.00 0.00 H +ATOM 95 HE1 HE1 5 26.409 -87.659 -4.553 1.00 0.00 H +ATOM 96 HE2 HE1 5 27.470 -88.968 -6.531 1.00 0.00 H +ATOM 97 N ILE 6 23.686 -92.419 -7.665 1.00 0.00 N +ATOM 98 H ILE 6 24.055 -92.315 -8.599 1.00 0.00 H +ATOM 99 CA ILE 6 24.259 -93.424 -6.761 1.00 0.00 C +ATOM 100 HA ILE 6 23.527 -93.868 -6.086 1.00 0.00 H +ATOM 101 CB ILE 6 24.667 -94.566 -7.730 1.00 0.00 C +ATOM 102 HB ILE 6 25.222 -94.162 -8.577 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.588 -95.590 -6.983 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.118 -96.116 -6.152 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.458 -95.135 -6.509 1.00 0.00 H +ATOM 106 HG23 ILE 6 25.907 -96.388 -7.653 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.424 -95.232 -8.324 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.313 -96.194 -7.823 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.537 -94.610 -8.203 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.597 -95.481 -9.893 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.651 -95.808 -10.325 1.00 0.00 H +ATOM 112 HD12 ILE 6 24.342 -96.244 -10.118 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.806 -94.521 -10.364 1.00 0.00 H +ATOM 114 C ILE 6 25.408 -92.835 -5.912 1.00 0.00 C +ATOM 115 O ILE 6 26.116 -91.966 -6.403 1.00 0.00 O +ATOM 116 N VAL 7 25.544 -93.263 -4.634 1.00 0.00 N +ATOM 117 H VAL 7 24.933 -94.015 -4.349 1.00 0.00 H +ATOM 118 CA VAL 7 26.579 -92.879 -3.647 1.00 0.00 C +ATOM 119 HA VAL 7 26.341 -91.871 -3.309 1.00 0.00 H +ATOM 120 CB VAL 7 26.574 -93.814 -2.429 1.00 0.00 C +ATOM 121 HB VAL 7 25.567 -93.830 -2.012 1.00 0.00 H +ATOM 122 CG1 VAL 7 26.979 -95.288 -2.559 1.00 0.00 C +ATOM 123 HG11 VAL 7 26.730 -95.829 -1.646 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.303 -95.723 -3.295 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.990 -95.588 -2.832 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.414 -93.280 -1.275 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.284 -93.772 -0.310 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.461 -93.320 -1.574 1.00 0.00 H +ATOM 129 HG23 VAL 7 27.125 -92.244 -1.098 1.00 0.00 H +ATOM 130 C VAL 7 28.064 -92.846 -4.191 1.00 0.00 C +ATOM 131 O VAL 7 28.405 -93.773 -4.954 1.00 0.00 O +ATOM 132 N ASN 8 28.799 -91.743 -3.961 1.00 0.00 N +ATOM 133 H ASN 8 28.494 -91.123 -3.224 1.00 0.00 H +ATOM 134 CA ASN 8 30.121 -91.631 -4.588 1.00 0.00 C +ATOM 135 HA ASN 8 30.116 -91.790 -5.666 1.00 0.00 H +ATOM 136 CB ASN 8 30.647 -90.195 -4.473 1.00 0.00 C +ATOM 137 HB2 ASN 8 30.543 -89.818 -3.455 1.00 0.00 H +ATOM 138 HB3 ASN 8 31.688 -90.200 -4.795 1.00 0.00 H +ATOM 139 CG ASN 8 29.933 -89.153 -5.311 1.00 0.00 C +ATOM 140 OD1 ASN 8 29.276 -89.495 -6.263 1.00 0.00 O +ATOM 141 ND2 ASN 8 29.961 -87.921 -4.910 1.00 0.00 N +ATOM 142 HD21 ASN 8 30.463 -87.646 -4.078 1.00 0.00 H +ATOM 143 HD22 ASN 8 29.417 -87.296 -5.488 1.00 0.00 H +ATOM 144 C ASN 8 31.165 -92.621 -3.962 1.00 0.00 C +ATOM 145 O ASN 8 31.866 -93.301 -4.695 1.00 0.00 O +ATOM 146 N GLY 9 31.266 -92.786 -2.627 1.00 0.00 N +ATOM 147 H GLY 9 30.597 -92.292 -2.054 1.00 0.00 H +ATOM 148 CA GLY 9 32.249 -93.661 -1.943 1.00 0.00 C +ATOM 149 HA2 GLY 9 33.280 -93.368 -2.143 1.00 0.00 H +ATOM 150 HA3 GLY 9 31.995 -93.643 -0.883 1.00 0.00 H +ATOM 151 C GLY 9 32.090 -95.108 -2.410 1.00 0.00 C +ATOM 152 O GLY 9 31.000 -95.693 -2.186 1.00 0.00 O +ATOM 153 N LYS 10 33.168 -95.675 -3.033 1.00 0.00 N +ATOM 154 H LYS 10 33.978 -95.072 -3.069 1.00 0.00 H +ATOM 155 CA LYS 10 33.069 -96.908 -3.785 1.00 0.00 C +ATOM 156 HA LYS 10 32.144 -96.896 -4.363 1.00 0.00 H +ATOM 157 CB LYS 10 34.112 -97.117 -4.909 1.00 0.00 C +ATOM 158 HB2 LYS 10 33.720 -98.014 -5.388 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.131 -96.272 -5.598 1.00 0.00 H +ATOM 160 CG LYS 10 35.580 -97.413 -4.444 1.00 0.00 C +ATOM 161 HG2 LYS 10 35.943 -96.564 -3.865 1.00 0.00 H +ATOM 162 HG3 LYS 10 35.500 -98.288 -3.798 1.00 0.00 H +ATOM 163 CD LYS 10 36.768 -97.611 -5.413 1.00 0.00 C +ATOM 164 HD2 LYS 10 37.088 -96.611 -5.706 1.00 0.00 H +ATOM 165 HD3 LYS 10 37.629 -97.979 -4.856 1.00 0.00 H +ATOM 166 CE LYS 10 36.329 -98.512 -6.559 1.00 0.00 C +ATOM 167 HE2 LYS 10 35.814 -99.424 -6.258 1.00 0.00 H +ATOM 168 HE3 LYS 10 35.439 -98.090 -7.027 1.00 0.00 H +ATOM 169 NZ LYS 10 37.445 -98.857 -7.492 1.00 0.00 N +ATOM 170 HZ1 LYS 10 38.162 -99.326 -6.958 1.00 0.00 H +ATOM 171 HZ2 LYS 10 37.801 -98.084 -8.036 1.00 0.00 H +ATOM 172 HZ3 LYS 10 37.118 -99.469 -8.226 1.00 0.00 H +ATOM 173 C LYS 10 32.801 -98.179 -2.897 1.00 0.00 C +ATOM 174 O LYS 10 32.119 -99.096 -3.387 1.00 0.00 O +ATOM 175 N THR 11 33.207 -98.208 -1.641 1.00 0.00 N +ATOM 176 H THR 11 33.675 -97.388 -1.283 1.00 0.00 H +ATOM 177 CA THR 11 32.964 -99.347 -0.712 1.00 0.00 C +ATOM 178 HA THR 11 33.320-100.265 -1.179 1.00 0.00 H +ATOM 179 CB THR 11 33.737 -99.151 0.596 1.00 0.00 C +ATOM 180 HB THR 11 33.536-100.053 1.174 1.00 0.00 H +ATOM 181 CG2 THR 11 35.257 -99.083 0.399 1.00 0.00 C +ATOM 182 HG21 THR 11 35.564 -98.047 0.257 1.00 0.00 H +ATOM 183 HG22 THR 11 35.617 -99.803 -0.336 1.00 0.00 H +ATOM 184 HG23 THR 11 35.778 -99.396 1.303 1.00 0.00 H +ATOM 185 OG1 THR 11 33.319 -97.995 1.241 1.00 0.00 O +ATOM 186 HG1 THR 11 33.495 -98.200 2.162 1.00 0.00 H +ATOM 187 C THR 11 31.462 -99.528 -0.357 1.00 0.00 C +ATOM 188 O THR 11 31.008-100.485 0.337 1.00 0.00 O +ATOM 189 N LEU 12 30.633 -98.557 -0.740 1.00 0.00 N +ATOM 190 H LEU 12 31.044 -97.800 -1.268 1.00 0.00 H +ATOM 191 CA LEU 12 29.196 -98.436 -0.445 1.00 0.00 C +ATOM 192 HA LEU 12 28.849 -99.121 0.328 1.00 0.00 H +ATOM 193 CB LEU 12 28.957 -96.994 0.112 1.00 0.00 C +ATOM 194 HB2 LEU 12 29.365 -96.233 -0.552 1.00 0.00 H +ATOM 195 HB3 LEU 12 27.908 -96.797 0.333 1.00 0.00 H +ATOM 196 CG LEU 12 29.680 -96.617 1.447 1.00 0.00 C +ATOM 197 HG LEU 12 30.761 -96.664 1.313 1.00 0.00 H +ATOM 198 CD1 LEU 12 29.426 -95.151 1.753 1.00 0.00 C +ATOM 199 HD11 LEU 12 28.413 -94.909 2.078 1.00 0.00 H +ATOM 200 HD12 LEU 12 29.531 -94.591 0.824 1.00 0.00 H +ATOM 201 HD13 LEU 12 30.150 -94.710 2.438 1.00 0.00 H +ATOM 202 CD2 LEU 12 29.257 -97.424 2.695 1.00 0.00 C +ATOM 203 HD21 LEU 12 29.403 -98.503 2.637 1.00 0.00 H +ATOM 204 HD22 LEU 12 28.170 -97.373 2.755 1.00 0.00 H +ATOM 205 HD23 LEU 12 29.683 -97.057 3.628 1.00 0.00 H +ATOM 206 C LEU 12 28.286 -98.702 -1.659 1.00 0.00 C +ATOM 207 O LEU 12 28.762 -99.045 -2.707 1.00 0.00 O +ATOM 208 N LYS 13 26.971 -98.583 -1.456 1.00 0.00 N +ATOM 209 H LYS 13 26.774 -98.325 -0.500 1.00 0.00 H +ATOM 210 CA LYS 13 25.918 -98.732 -2.454 1.00 0.00 C +ATOM 211 HA LYS 13 26.291 -98.287 -3.377 1.00 0.00 H +ATOM 212 CB LYS 13 25.618-100.260 -2.728 1.00 0.00 C +ATOM 213 HB2 LYS 13 24.868-100.451 -3.496 1.00 0.00 H +ATOM 214 HB3 LYS 13 26.550-100.673 -3.113 1.00 0.00 H +ATOM 215 CG LYS 13 25.280-101.101 -1.442 1.00 0.00 C +ATOM 216 HG2 LYS 13 26.064-100.830 -0.735 1.00 0.00 H +ATOM 217 HG3 LYS 13 24.342-100.814 -0.968 1.00 0.00 H +ATOM 218 CD LYS 13 25.301-102.684 -1.590 1.00 0.00 C +ATOM 219 HD2 LYS 13 26.121-102.974 -2.246 1.00 0.00 H +ATOM 220 HD3 LYS 13 25.590-103.065 -0.610 1.00 0.00 H +ATOM 221 CE LYS 13 24.044-103.271 -2.255 1.00 0.00 C +ATOM 222 HE2 LYS 13 23.150-103.059 -1.668 1.00 0.00 H +ATOM 223 HE3 LYS 13 23.947-102.956 -3.294 1.00 0.00 H +ATOM 224 NZ LYS 13 24.118-104.768 -2.401 1.00 0.00 N +ATOM 225 HZ1 LYS 13 24.887-105.073 -2.980 1.00 0.00 H +ATOM 226 HZ2 LYS 13 23.284-105.112 -2.854 1.00 0.00 H +ATOM 227 HZ3 LYS 13 24.143-105.035 -1.427 1.00 0.00 H +ATOM 228 C LYS 13 24.659 -97.941 -2.025 1.00 0.00 C +ATOM 229 O LYS 13 24.605 -97.583 -0.845 1.00 0.00 O +ATOM 230 N GLY 14 23.662 -97.861 -2.933 1.00 0.00 N +ATOM 231 H GLY 14 23.797 -98.259 -3.851 1.00 0.00 H +ATOM 232 CA GLY 14 22.353 -97.258 -2.744 1.00 0.00 C +ATOM 233 HA2 GLY 14 21.608 -97.996 -3.042 1.00 0.00 H +ATOM 234 HA3 GLY 14 22.145 -97.029 -1.699 1.00 0.00 H +ATOM 235 C GLY 14 22.203 -96.077 -3.688 1.00 0.00 C +ATOM 236 O GLY 14 23.147 -95.354 -4.093 1.00 0.00 O +ATOM 237 N VAL 15 20.975 -95.917 -4.184 1.00 0.00 N +ATOM 238 H VAL 15 20.270 -96.291 -3.565 1.00 0.00 H +ATOM 239 CA VAL 15 20.564 -94.974 -5.240 1.00 0.00 C +ATOM 240 HA VAL 15 21.453 -94.473 -5.622 1.00 0.00 H +ATOM 241 CB VAL 15 20.112 -95.859 -6.464 1.00 0.00 C +ATOM 242 HB VAL 15 21.003 -96.342 -6.865 1.00 0.00 H +ATOM 243 CG1 VAL 15 18.995 -96.907 -6.067 1.00 0.00 C +ATOM 244 HG11 VAL 15 19.327 -97.466 -5.192 1.00 0.00 H +ATOM 245 HG12 VAL 15 18.045 -96.408 -5.877 1.00 0.00 H +ATOM 246 HG13 VAL 15 18.940 -97.571 -6.930 1.00 0.00 H +ATOM 247 CG2 VAL 15 19.538 -94.960 -7.667 1.00 0.00 C +ATOM 248 HG21 VAL 15 19.744 -95.404 -8.641 1.00 0.00 H +ATOM 249 HG22 VAL 15 18.474 -94.759 -7.544 1.00 0.00 H +ATOM 250 HG23 VAL 15 20.022 -93.985 -7.719 1.00 0.00 H +ATOM 251 C VAL 15 19.535 -93.971 -4.667 1.00 0.00 C +ATOM 252 O VAL 15 18.567 -94.484 -4.115 1.00 0.00 O +ATOM 253 N HD1 16 19.769 -92.696 -4.718 1.00 0.00 N +ATOM 254 CA HD1 16 18.792 -91.687 -4.399 1.00 0.00 C +ATOM 255 C HD1 16 18.591 -90.676 -5.515 1.00 0.00 C +ATOM 256 O HD1 16 19.446 -90.538 -6.375 1.00 0.00 O +ATOM 257 CB HD1 16 19.207 -90.885 -3.171 1.00 0.00 C +ATOM 258 CG HD1 16 20.522 -90.141 -3.148 1.00 0.00 C +ATOM 259 CD2 HD1 16 20.748 -88.870 -3.613 1.00 0.00 C +ATOM 260 ND1 HD1 16 21.730 -90.654 -2.604 1.00 0.00 N +ATOM 261 CE1 HD1 16 22.645 -89.755 -2.832 1.00 0.00 C +ATOM 262 NE2 HD1 16 22.152 -88.677 -3.472 1.00 0.00 N +ATOM 263 H HD1 16 20.656 -92.381 -5.084 1.00 0.00 H +ATOM 264 HA HD1 16 17.822 -92.144 -4.199 1.00 0.00 H +ATOM 265 HB2 HD1 16 18.534 -90.046 -2.996 1.00 0.00 H +ATOM 266 HB3 HD1 16 19.084 -91.604 -2.361 1.00 0.00 H +ATOM 267 HD1 HD1 16 21.958 -91.542 -2.182 1.00 0.00 H +ATOM 268 HD2 HD1 16 20.033 -88.220 -4.093 1.00 0.00 H +ATOM 269 HE1 HD1 16 23.717 -89.892 -2.820 1.00 0.00 H +ATOM 270 N THR 17 17.492 -89.870 -5.494 1.00 0.00 N +ATOM 271 H THR 17 16.877 -89.984 -4.701 1.00 0.00 H +ATOM 272 CA THR 17 17.430 -88.725 -6.504 1.00 0.00 C +ATOM 273 HA THR 17 17.898 -89.164 -7.384 1.00 0.00 H +ATOM 274 CB THR 17 16.005 -88.657 -6.901 1.00 0.00 C +ATOM 275 HB THR 17 15.940 -87.958 -7.735 1.00 0.00 H +ATOM 276 CG2 THR 17 15.470 -89.991 -7.446 1.00 0.00 C +ATOM 277 HG21 THR 17 14.380 -89.982 -7.422 1.00 0.00 H +ATOM 278 HG22 THR 17 15.776 -90.843 -6.840 1.00 0.00 H +ATOM 279 HG23 THR 17 15.820 -89.982 -8.478 1.00 0.00 H +ATOM 280 OG1 THR 17 15.115 -88.381 -5.845 1.00 0.00 O +ATOM 281 HG1 THR 17 15.198 -87.429 -5.751 1.00 0.00 H +ATOM 282 C THR 17 17.998 -87.343 -6.187 1.00 0.00 C +ATOM 283 O THR 17 18.177 -86.981 -5.051 1.00 0.00 O +ATOM 284 N HD2 18 18.113 -86.460 -7.175 1.00 0.00 N +ATOM 285 CA HD2 18 18.195 -85.026 -7.115 1.00 0.00 C +ATOM 286 C HD2 18 17.526 -84.339 -8.322 1.00 0.00 C +ATOM 287 O HD2 18 17.780 -84.833 -9.450 1.00 0.00 O +ATOM 288 CB HD2 18 19.633 -84.463 -7.142 1.00 0.00 C +ATOM 289 CG HD2 18 20.472 -84.863 -5.995 1.00 0.00 C +ATOM 290 CD2 HD2 18 21.612 -85.662 -6.088 1.00 0.00 C +ATOM 291 ND1 HD2 18 20.478 -84.473 -4.702 1.00 0.00 N +ATOM 292 CE1 HD2 18 21.506 -84.974 -4.051 1.00 0.00 C +ATOM 293 NE2 HD2 18 22.258 -85.733 -4.821 1.00 0.00 N +ATOM 294 H HD2 18 18.033 -86.861 -8.098 1.00 0.00 H +ATOM 295 HA HD2 18 17.655 -84.729 -6.216 1.00 0.00 H +ATOM 296 HB2 HD2 18 20.133 -84.724 -8.074 1.00 0.00 H +ATOM 297 HB3 HD2 18 19.495 -83.382 -7.119 1.00 0.00 H +ATOM 298 HD1 HD2 18 19.686 -84.065 -4.227 1.00 0.00 H +ATOM 299 HD2 HD2 18 21.945 -86.132 -7.002 1.00 0.00 H +ATOM 300 HE1 HD2 18 21.618 -84.976 -2.977 1.00 0.00 H +ATOM 301 N GLU 19 16.791 -83.316 -8.196 1.00 0.00 N +ATOM 302 H GLU 19 16.619 -82.947 -7.271 1.00 0.00 H +ATOM 303 CA GLU 19 16.189 -82.534 -9.335 1.00 0.00 C +ATOM 304 HA GLU 19 15.717 -83.199 -10.058 1.00 0.00 H +ATOM 305 CB GLU 19 15.137 -81.529 -8.866 1.00 0.00 C +ATOM 306 HB2 GLU 19 15.489 -80.967 -8.001 1.00 0.00 H +ATOM 307 HB3 GLU 19 14.979 -80.849 -9.703 1.00 0.00 H +ATOM 308 CG GLU 19 13.832 -82.232 -8.509 1.00 0.00 C +ATOM 309 HG2 GLU 19 13.133 -81.449 -8.216 1.00 0.00 H +ATOM 310 HG3 GLU 19 13.498 -82.698 -9.436 1.00 0.00 H +ATOM 311 CD GLU 19 13.874 -83.145 -7.309 1.00 0.00 C +ATOM 312 OE1 GLU 19 13.277 -84.235 -7.458 1.00 0.00 O +ATOM 313 OE2 GLU 19 14.458 -82.709 -6.268 1.00 0.00 O +ATOM 314 C GLU 19 17.251 -81.733 -10.058 1.00 0.00 C +ATOM 315 O GLU 19 18.268 -81.319 -9.500 1.00 0.00 O +ATOM 316 N ALA 20 17.028 -81.355 -11.340 1.00 0.00 N +ATOM 317 H ALA 20 16.280 -81.854 -11.799 1.00 0.00 H +ATOM 318 CA ALA 20 17.832 -80.409 -12.050 1.00 0.00 C +ATOM 319 HA ALA 20 18.005 -79.573 -11.373 1.00 0.00 H +ATOM 320 CB ALA 20 19.230 -80.954 -12.548 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.834 -80.087 -12.815 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.052 -81.464 -13.494 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.619 -81.606 -11.766 1.00 0.00 H +ATOM 324 C ALA 20 17.056 -79.787 -13.172 1.00 0.00 C +ATOM 325 O ALA 20 16.181 -80.408 -13.715 1.00 0.00 O +ATOM 326 N VAL 21 17.289 -78.553 -13.518 1.00 0.00 N +ATOM 327 H VAL 21 17.746 -78.039 -12.778 1.00 0.00 H +ATOM 328 CA VAL 21 16.732 -77.990 -14.750 1.00 0.00 C +ATOM 329 HA VAL 21 15.652 -78.087 -14.636 1.00 0.00 H +ATOM 330 CB VAL 21 17.136 -76.481 -14.780 1.00 0.00 C +ATOM 331 HB VAL 21 16.756 -76.067 -13.846 1.00 0.00 H +ATOM 332 CG1 VAL 21 18.619 -76.064 -15.092 1.00 0.00 C +ATOM 333 HG11 VAL 21 19.278 -76.406 -14.294 1.00 0.00 H +ATOM 334 HG12 VAL 21 18.706 -74.978 -15.116 1.00 0.00 H +ATOM 335 HG13 VAL 21 19.016 -76.460 -16.026 1.00 0.00 H +ATOM 336 CG2 VAL 21 16.276 -75.791 -15.898 1.00 0.00 C +ATOM 337 HG21 VAL 21 16.118 -74.740 -15.657 1.00 0.00 H +ATOM 338 HG22 VAL 21 15.270 -76.210 -15.925 1.00 0.00 H +ATOM 339 HG23 VAL 21 16.648 -75.920 -16.914 1.00 0.00 H +ATOM 340 C VAL 21 17.256 -78.738 -15.996 1.00 0.00 C +ATOM 341 O VAL 21 16.475 -78.765 -16.944 1.00 0.00 O +ATOM 342 N ASP 22 18.437 -79.309 -15.891 1.00 0.00 N +ATOM 343 H ASP 22 18.977 -79.325 -15.037 1.00 0.00 H +ATOM 344 CA ASP 22 19.048 -79.929 -17.085 1.00 0.00 C +ATOM 345 HA ASP 22 18.319 -80.415 -17.733 1.00 0.00 H +ATOM 346 CB ASP 22 19.542 -78.764 -17.995 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.678 -78.140 -18.226 1.00 0.00 H +ATOM 348 HB3 ASP 22 20.326 -78.249 -17.441 1.00 0.00 H +ATOM 349 CG ASP 22 20.203 -79.111 -19.319 1.00 0.00 C +ATOM 350 OD1 ASP 22 20.289 -80.263 -19.789 1.00 0.00 O +ATOM 351 OD2 ASP 22 20.450 -78.160 -20.067 1.00 0.00 O +ATOM 352 C ASP 22 20.148 -80.929 -16.699 1.00 0.00 C +ATOM 353 O ASP 22 20.667 -80.878 -15.622 1.00 0.00 O +ATOM 354 N ALA 23 20.544 -81.877 -17.574 1.00 0.00 N +ATOM 355 H ALA 23 20.146 -81.753 -18.494 1.00 0.00 H +ATOM 356 CA ALA 23 21.479 -82.989 -17.380 1.00 0.00 C +ATOM 357 HA ALA 23 21.100 -83.658 -16.607 1.00 0.00 H +ATOM 358 CB ALA 23 21.628 -83.905 -18.579 1.00 0.00 C +ATOM 359 HB1 ALA 23 21.706 -83.265 -19.458 1.00 0.00 H +ATOM 360 HB2 ALA 23 20.749 -84.537 -18.708 1.00 0.00 H +ATOM 361 HB3 ALA 23 22.414 -84.651 -18.460 1.00 0.00 H +ATOM 362 C ALA 23 22.935 -82.526 -17.010 1.00 0.00 C +ATOM 363 O ALA 23 23.566 -83.061 -16.124 1.00 0.00 O +ATOM 364 N ALA 24 23.292 -81.350 -17.606 1.00 0.00 N +ATOM 365 H ALA 24 22.582 -80.982 -18.222 1.00 0.00 H +ATOM 366 CA ALA 24 24.481 -80.518 -17.307 1.00 0.00 C +ATOM 367 HA ALA 24 25.415 -81.069 -17.415 1.00 0.00 H +ATOM 368 CB ALA 24 24.690 -79.490 -18.349 1.00 0.00 C +ATOM 369 HB1 ALA 24 23.905 -78.739 -18.443 1.00 0.00 H +ATOM 370 HB2 ALA 24 24.836 -79.975 -19.314 1.00 0.00 H +ATOM 371 HB3 ALA 24 25.669 -79.069 -18.120 1.00 0.00 H +ATOM 372 C ALA 24 24.539 -79.932 -15.873 1.00 0.00 C +ATOM 373 O ALA 24 25.628 -79.664 -15.344 1.00 0.00 O +ATOM 374 N GLU 25 23.340 -79.686 -15.282 1.00 0.00 N +ATOM 375 H GLU 25 22.546 -79.727 -15.904 1.00 0.00 H +ATOM 376 CA GLU 25 23.192 -79.129 -13.938 1.00 0.00 C +ATOM 377 HA GLU 25 24.072 -78.636 -13.526 1.00 0.00 H +ATOM 378 CB GLU 25 22.015 -78.222 -14.035 1.00 0.00 C +ATOM 379 HB2 GLU 25 21.125 -78.805 -14.273 1.00 0.00 H +ATOM 380 HB3 GLU 25 22.004 -77.839 -13.015 1.00 0.00 H +ATOM 381 CG GLU 25 22.298 -76.987 -14.939 1.00 0.00 C +ATOM 382 HG2 GLU 25 22.107 -77.306 -15.963 1.00 0.00 H +ATOM 383 HG3 GLU 25 21.545 -76.229 -14.724 1.00 0.00 H +ATOM 384 CD GLU 25 23.723 -76.353 -14.820 1.00 0.00 C +ATOM 385 OE1 GLU 25 24.466 -76.418 -15.814 1.00 0.00 O +ATOM 386 OE2 GLU 25 24.034 -75.970 -13.669 1.00 0.00 O +ATOM 387 C GLU 25 22.970 -80.238 -12.865 1.00 0.00 C +ATOM 388 O GLU 25 23.317 -80.099 -11.679 1.00 0.00 O +ATOM 389 N ALA 26 22.554 -81.399 -13.289 1.00 0.00 N +ATOM 390 H ALA 26 22.148 -81.395 -14.214 1.00 0.00 H +ATOM 391 CA ALA 26 22.491 -82.596 -12.463 1.00 0.00 C +ATOM 392 HA ALA 26 21.949 -82.408 -11.536 1.00 0.00 H +ATOM 393 CB ALA 26 21.698 -83.718 -13.106 1.00 0.00 C +ATOM 394 HB1 ALA 26 20.714 -83.328 -13.363 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.634 -84.614 -12.488 1.00 0.00 H +ATOM 396 HB3 ALA 26 22.203 -83.878 -14.059 1.00 0.00 H +ATOM 397 C ALA 26 23.873 -83.149 -12.105 1.00 0.00 C +ATOM 398 O ALA 26 24.127 -83.578 -10.974 1.00 0.00 O +ATOM 399 N GLU 27 24.793 -83.012 -13.038 1.00 0.00 N +ATOM 400 H GLU 27 24.481 -82.831 -13.981 1.00 0.00 H +ATOM 401 CA GLU 27 26.205 -83.450 -12.914 1.00 0.00 C +ATOM 402 HA GLU 27 26.268 -84.444 -12.471 1.00 0.00 H +ATOM 403 CB GLU 27 26.839 -83.500 -14.345 1.00 0.00 C +ATOM 404 HB2 GLU 27 26.255 -84.179 -14.966 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.734 -82.499 -14.764 1.00 0.00 H +ATOM 406 CG GLU 27 28.309 -83.938 -14.422 1.00 0.00 C +ATOM 407 HG2 GLU 27 28.522 -84.622 -13.600 1.00 0.00 H +ATOM 408 HG3 GLU 27 28.399 -84.453 -15.378 1.00 0.00 H +ATOM 409 CD GLU 27 29.426 -82.861 -14.512 1.00 0.00 C +ATOM 410 OE1 GLU 27 29.105 -81.716 -14.269 1.00 0.00 O +ATOM 411 OE2 GLU 27 30.585 -83.181 -14.753 1.00 0.00 O +ATOM 412 C GLU 27 26.897 -82.570 -11.818 1.00 0.00 C +ATOM 413 O GLU 27 27.492 -83.045 -10.876 1.00 0.00 O +ATOM 414 N LYS 28 26.649 -81.261 -11.833 1.00 0.00 N +ATOM 415 H LYS 28 25.898 -80.921 -12.417 1.00 0.00 H +ATOM 416 CA LYS 28 27.274 -80.280 -10.874 1.00 0.00 C +ATOM 417 HA LYS 28 28.358 -80.348 -10.777 1.00 0.00 H +ATOM 418 CB LYS 28 26.935 -78.903 -11.308 1.00 0.00 C +ATOM 419 HB2 LYS 28 25.846 -78.891 -11.331 1.00 0.00 H +ATOM 420 HB3 LYS 28 27.195 -78.109 -10.609 1.00 0.00 H +ATOM 421 CG LYS 28 27.520 -78.527 -12.699 1.00 0.00 C +ATOM 422 HG2 LYS 28 28.603 -78.628 -12.774 1.00 0.00 H +ATOM 423 HG3 LYS 28 27.174 -79.341 -13.336 1.00 0.00 H +ATOM 424 CD LYS 28 26.985 -77.201 -13.188 1.00 0.00 C +ATOM 425 HD2 LYS 28 25.922 -77.246 -13.427 1.00 0.00 H +ATOM 426 HD3 LYS 28 27.253 -76.433 -12.463 1.00 0.00 H +ATOM 427 CE LYS 28 27.690 -77.097 -14.546 1.00 0.00 C +ATOM 428 HE2 LYS 28 28.744 -76.998 -14.287 1.00 0.00 H +ATOM 429 HE3 LYS 28 27.493 -78.004 -15.118 1.00 0.00 H +ATOM 430 NZ LYS 28 27.257 -75.915 -15.329 1.00 0.00 N +ATOM 431 HZ1 LYS 28 27.358 -75.085 -14.762 1.00 0.00 H +ATOM 432 HZ2 LYS 28 26.256 -75.987 -15.441 1.00 0.00 H +ATOM 433 HZ3 LYS 28 27.714 -75.830 -16.225 1.00 0.00 H +ATOM 434 C LYS 28 26.786 -80.567 -9.464 1.00 0.00 C +ATOM 435 O LYS 28 27.544 -80.630 -8.518 1.00 0.00 O +ATOM 436 N PHE 29 25.505 -80.925 -9.299 1.00 0.00 N +ATOM 437 H PHE 29 24.835 -81.027 -10.048 1.00 0.00 H +ATOM 438 CA PHE 29 25.024 -81.260 -7.936 1.00 0.00 C +ATOM 439 HA PHE 29 25.531 -80.616 -7.217 1.00 0.00 H +ATOM 440 CB PHE 29 23.540 -81.082 -8.057 1.00 0.00 C +ATOM 441 HB2 PHE 29 23.281 -80.301 -8.772 1.00 0.00 H +ATOM 442 HB3 PHE 29 23.063 -82.034 -8.292 1.00 0.00 H +ATOM 443 CG PHE 29 22.903 -80.812 -6.686 1.00 0.00 C +ATOM 444 CD1 PHE 29 22.689 -79.462 -6.341 1.00 0.00 C +ATOM 445 HD1 PHE 29 23.000 -78.722 -7.063 1.00 0.00 H +ATOM 446 CE1 PHE 29 22.284 -79.160 -5.046 1.00 0.00 C +ATOM 447 HE1 PHE 29 22.198 -78.104 -4.836 1.00 0.00 H +ATOM 448 CZ PHE 29 21.989 -80.123 -4.104 1.00 0.00 C +ATOM 449 HZ PHE 29 21.600 -79.922 -3.117 1.00 0.00 H +ATOM 450 CE2 PHE 29 22.179 -81.449 -4.449 1.00 0.00 C +ATOM 451 HE2 PHE 29 22.033 -82.279 -3.773 1.00 0.00 H +ATOM 452 CD2 PHE 29 22.631 -81.806 -5.742 1.00 0.00 C +ATOM 453 HD2 PHE 29 22.898 -82.828 -5.966 1.00 0.00 H +ATOM 454 C PHE 29 25.461 -82.712 -7.409 1.00 0.00 C +ATOM 455 O PHE 29 25.697 -82.856 -6.236 1.00 0.00 O +ATOM 456 N THR 30 25.707 -83.621 -8.357 1.00 0.00 N +ATOM 457 H THR 30 25.635 -83.332 -9.322 1.00 0.00 H +ATOM 458 CA THR 30 26.208 -84.965 -8.066 1.00 0.00 C +ATOM 459 HA THR 30 25.608 -85.378 -7.256 1.00 0.00 H +ATOM 460 CB THR 30 26.084 -85.875 -9.308 1.00 0.00 C +ATOM 461 HB THR 30 25.874 -85.221 -10.155 1.00 0.00 H +ATOM 462 CG2 THR 30 27.196 -86.736 -9.852 1.00 0.00 C +ATOM 463 HG21 THR 30 28.153 -86.218 -9.917 1.00 0.00 H +ATOM 464 HG22 THR 30 27.390 -87.486 -9.084 1.00 0.00 H +ATOM 465 HG23 THR 30 26.874 -87.347 -10.695 1.00 0.00 H +ATOM 466 OG1 THR 30 24.959 -86.743 -9.151 1.00 0.00 O +ATOM 467 HG1 THR 30 24.150 -86.233 -9.064 1.00 0.00 H +ATOM 468 C THR 30 27.602 -84.834 -7.458 1.00 0.00 C +ATOM 469 O THR 30 27.982 -85.567 -6.536 1.00 0.00 O +ATOM 470 N LYS 31 28.389 -83.964 -8.060 1.00 0.00 N +ATOM 471 H LYS 31 28.029 -83.476 -8.867 1.00 0.00 H +ATOM 472 CA LYS 31 29.845 -83.879 -7.769 1.00 0.00 C +ATOM 473 HA LYS 31 30.125 -84.833 -7.324 1.00 0.00 H +ATOM 474 CB LYS 31 30.553 -83.808 -9.172 1.00 0.00 C +ATOM 475 HB2 LYS 31 31.586 -84.075 -8.949 1.00 0.00 H +ATOM 476 HB3 LYS 31 30.155 -84.572 -9.839 1.00 0.00 H +ATOM 477 CG LYS 31 30.439 -82.427 -9.831 1.00 0.00 C +ATOM 478 HG2 LYS 31 29.402 -82.121 -9.692 1.00 0.00 H +ATOM 479 HG3 LYS 31 31.149 -81.853 -9.235 1.00 0.00 H +ATOM 480 CD LYS 31 30.933 -82.291 -11.280 1.00 0.00 C +ATOM 481 HD2 LYS 31 30.109 -82.589 -11.929 1.00 0.00 H +ATOM 482 HD3 LYS 31 31.131 -81.238 -11.477 1.00 0.00 H +ATOM 483 CE LYS 31 32.205 -83.101 -11.598 1.00 0.00 C +ATOM 484 HE2 LYS 31 33.016 -82.806 -10.932 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.988 -84.169 -11.568 1.00 0.00 H +ATOM 486 NZ LYS 31 32.655 -82.994 -12.990 1.00 0.00 N +ATOM 487 HZ1 LYS 31 33.350 -83.694 -13.207 1.00 0.00 H +ATOM 488 HZ2 LYS 31 33.001 -82.091 -13.280 1.00 0.00 H +ATOM 489 HZ3 LYS 31 31.986 -83.157 -13.728 1.00 0.00 H +ATOM 490 C LYS 31 30.218 -82.787 -6.714 1.00 0.00 C +ATOM 491 O LYS 31 31.284 -82.775 -6.216 1.00 0.00 O +ATOM 492 N ALA 32 29.240 -81.928 -6.355 1.00 0.00 N +ATOM 493 H ALA 32 28.307 -82.010 -6.734 1.00 0.00 H +ATOM 494 CA ALA 32 29.552 -80.929 -5.322 1.00 0.00 C +ATOM 495 HA ALA 32 30.411 -80.348 -5.658 1.00 0.00 H +ATOM 496 CB ALA 32 28.294 -80.071 -5.100 1.00 0.00 C +ATOM 497 HB1 ALA 32 28.514 -79.164 -4.538 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.069 -79.802 -6.132 1.00 0.00 H +ATOM 499 HB3 ALA 32 27.427 -80.647 -4.776 1.00 0.00 H +ATOM 500 C ALA 32 29.971 -81.485 -3.943 1.00 0.00 C +ATOM 501 O ALA 32 30.808 -80.916 -3.287 1.00 0.00 O +ATOM 502 N ASP 33 29.339 -82.599 -3.492 1.00 0.00 N +ATOM 503 H ASP 33 28.670 -83.085 -4.072 1.00 0.00 H +ATOM 504 CA ASP 33 29.868 -83.300 -2.330 1.00 0.00 C +ATOM 505 HA ASP 33 29.951 -82.528 -1.565 1.00 0.00 H +ATOM 506 CB ASP 33 28.813 -84.281 -1.797 1.00 0.00 C +ATOM 507 HB2 ASP 33 27.812 -83.860 -1.901 1.00 0.00 H +ATOM 508 HB3 ASP 33 28.811 -85.254 -2.288 1.00 0.00 H +ATOM 509 CG ASP 33 29.079 -84.654 -0.308 1.00 0.00 C +ATOM 510 OD1 ASP 33 28.610 -83.976 0.635 1.00 0.00 O +ATOM 511 OD2 ASP 33 29.658 -85.775 -0.187 1.00 0.00 O +ATOM 512 C ASP 33 31.261 -83.814 -2.522 1.00 0.00 C +ATOM 513 O ASP 33 32.025 -83.626 -1.546 1.00 0.00 O +ATOM 514 N ALA 34 31.686 -84.490 -3.542 1.00 0.00 N +ATOM 515 H ALA 34 30.943 -84.854 -4.121 1.00 0.00 H +ATOM 516 CA ALA 34 33.057 -84.764 -3.839 1.00 0.00 C +ATOM 517 HA ALA 34 33.458 -85.537 -3.184 1.00 0.00 H +ATOM 518 CB ALA 34 33.054 -85.408 -5.260 1.00 0.00 C +ATOM 519 HB1 ALA 34 34.060 -85.508 -5.665 1.00 0.00 H +ATOM 520 HB2 ALA 34 32.445 -84.921 -6.022 1.00 0.00 H +ATOM 521 HB3 ALA 34 32.640 -86.416 -5.279 1.00 0.00 H +ATOM 522 C ALA 34 33.945 -83.501 -3.824 1.00 0.00 C +ATOM 523 O ALA 34 35.023 -83.475 -3.188 1.00 0.00 O +ATOM 524 N ASN 35 33.497 -82.349 -4.398 1.00 0.00 N +ATOM 525 H ASN 35 32.637 -82.408 -4.923 1.00 0.00 H +ATOM 526 CA ASN 35 34.198 -81.062 -4.400 1.00 0.00 C +ATOM 527 HA ASN 35 35.192 -81.057 -4.849 1.00 0.00 H +ATOM 528 CB ASN 35 33.383 -79.949 -5.124 1.00 0.00 C +ATOM 529 HB2 ASN 35 32.376 -79.876 -4.714 1.00 0.00 H +ATOM 530 HB3 ASN 35 33.798 -78.963 -4.912 1.00 0.00 H +ATOM 531 CG ASN 35 33.231 -80.132 -6.645 1.00 0.00 C +ATOM 532 OD1 ASN 35 33.733 -81.003 -7.339 1.00 0.00 O +ATOM 533 ND2 ASN 35 32.636 -79.160 -7.299 1.00 0.00 N +ATOM 534 HD21 ASN 35 32.218 -78.407 -6.771 1.00 0.00 H +ATOM 535 HD22 ASN 35 32.609 -79.207 -8.307 1.00 0.00 H +ATOM 536 C ASN 35 34.368 -80.609 -2.923 1.00 0.00 C +ATOM 537 O ASN 35 35.388 -80.028 -2.585 1.00 0.00 O +ATOM 538 N ASP 36 33.411 -80.804 -2.035 1.00 0.00 N +ATOM 539 H ASP 36 32.502 -81.181 -2.264 1.00 0.00 H +ATOM 540 CA ASP 36 33.585 -80.452 -0.603 1.00 0.00 C +ATOM 541 HA ASP 36 33.977 -79.443 -0.479 1.00 0.00 H +ATOM 542 CB ASP 36 32.232 -80.439 0.038 1.00 0.00 C +ATOM 543 HB2 ASP 36 31.519 -79.752 -0.417 1.00 0.00 H +ATOM 544 HB3 ASP 36 31.933 -81.485 -0.036 1.00 0.00 H +ATOM 545 CG ASP 36 32.258 -80.149 1.514 1.00 0.00 C +ATOM 546 OD1 ASP 36 32.252 -81.070 2.340 1.00 0.00 O +ATOM 547 OD2 ASP 36 32.184 -78.917 1.947 1.00 0.00 O +ATOM 548 C ASP 36 34.537 -81.384 0.175 1.00 0.00 C +ATOM 549 O ASP 36 35.181 -80.968 1.120 1.00 0.00 O +ATOM 550 N LYS 37 34.569 -82.699 -0.251 1.00 0.00 N +ATOM 551 H LYS 37 33.911 -83.034 -0.940 1.00 0.00 H +ATOM 552 CA LYS 37 35.464 -83.677 0.391 1.00 0.00 C +ATOM 553 HA LYS 37 35.607 -83.403 1.436 1.00 0.00 H +ATOM 554 CB LYS 37 34.774 -85.079 0.415 1.00 0.00 C +ATOM 555 HB2 LYS 37 35.620 -85.688 0.095 1.00 0.00 H +ATOM 556 HB3 LYS 37 34.036 -85.016 -0.384 1.00 0.00 H +ATOM 557 CG LYS 37 34.332 -85.624 1.766 1.00 0.00 C +ATOM 558 HG2 LYS 37 35.217 -85.724 2.395 1.00 0.00 H +ATOM 559 HG3 LYS 37 34.044 -86.671 1.664 1.00 0.00 H +ATOM 560 CD LYS 37 33.217 -84.913 2.555 1.00 0.00 C +ATOM 561 HD2 LYS 37 32.903 -85.596 3.345 1.00 0.00 H +ATOM 562 HD3 LYS 37 33.553 -83.992 3.030 1.00 0.00 H +ATOM 563 CE LYS 37 31.972 -84.545 1.721 1.00 0.00 C +ATOM 564 HE2 LYS 37 32.338 -84.198 0.754 1.00 0.00 H +ATOM 565 HE3 LYS 37 31.457 -85.491 1.554 1.00 0.00 H +ATOM 566 NZ LYS 37 31.002 -83.633 2.403 1.00 0.00 N +ATOM 567 HZ1 LYS 37 30.261 -83.468 1.736 1.00 0.00 H +ATOM 568 HZ2 LYS 37 30.564 -84.135 3.162 1.00 0.00 H +ATOM 569 HZ3 LYS 37 31.460 -82.752 2.587 1.00 0.00 H +ATOM 570 C LYS 37 36.949 -83.669 -0.145 1.00 0.00 C +ATOM 571 O LYS 37 37.795 -84.418 0.346 1.00 0.00 O +ATOM 572 N GLY 38 37.248 -82.834 -1.113 1.00 0.00 N +ATOM 573 H GLY 38 36.498 -82.311 -1.542 1.00 0.00 H +ATOM 574 CA GLY 38 38.544 -82.741 -1.826 1.00 0.00 C +ATOM 575 HA2 GLY 38 38.697 -81.767 -2.293 1.00 0.00 H +ATOM 576 HA3 GLY 38 39.307 -82.805 -1.050 1.00 0.00 H +ATOM 577 C GLY 38 38.778 -83.829 -2.883 1.00 0.00 C +ATOM 578 O GLY 38 39.903 -84.018 -3.344 1.00 0.00 O +ATOM 579 N VAL 39 37.767 -84.595 -3.250 1.00 0.00 N +ATOM 580 H VAL 39 36.873 -84.366 -2.839 1.00 0.00 H +ATOM 581 CA VAL 39 37.951 -85.830 -4.016 1.00 0.00 C +ATOM 582 HA VAL 39 38.972 -86.165 -3.834 1.00 0.00 H +ATOM 583 CB VAL 39 36.925 -86.856 -3.405 1.00 0.00 C +ATOM 584 HB VAL 39 35.939 -86.452 -3.174 1.00 0.00 H +ATOM 585 CG1 VAL 39 36.793 -88.060 -4.383 1.00 0.00 C +ATOM 586 HG11 VAL 39 36.589 -87.687 -5.387 1.00 0.00 H +ATOM 587 HG12 VAL 39 35.921 -88.679 -4.171 1.00 0.00 H +ATOM 588 HG13 VAL 39 37.728 -88.601 -4.532 1.00 0.00 H +ATOM 589 CG2 VAL 39 37.474 -87.474 -2.145 1.00 0.00 C +ATOM 590 HG21 VAL 39 37.629 -86.699 -1.395 1.00 0.00 H +ATOM 591 HG22 VAL 39 38.441 -87.937 -2.346 1.00 0.00 H +ATOM 592 HG23 VAL 39 36.903 -88.296 -1.713 1.00 0.00 H +ATOM 593 C VAL 39 37.793 -85.484 -5.477 1.00 0.00 C +ATOM 594 O VAL 39 36.948 -84.788 -5.914 1.00 0.00 O +ATOM 595 N ASP 40 38.660 -86.095 -6.297 1.00 0.00 N +ATOM 596 H ASP 40 39.302 -86.727 -5.842 1.00 0.00 H +ATOM 597 CA ASP 40 38.614 -86.098 -7.802 1.00 0.00 C +ATOM 598 HA ASP 40 38.055 -85.216 -8.116 1.00 0.00 H +ATOM 599 CB ASP 40 39.959 -85.723 -8.445 1.00 0.00 C +ATOM 600 HB2 ASP 40 40.688 -86.527 -8.350 1.00 0.00 H +ATOM 601 HB3 ASP 40 39.865 -85.590 -9.523 1.00 0.00 H +ATOM 602 CG ASP 40 40.738 -84.520 -7.974 1.00 0.00 C +ATOM 603 OD1 ASP 40 40.132 -83.482 -7.635 1.00 0.00 O +ATOM 604 OD2 ASP 40 42.001 -84.583 -7.978 1.00 0.00 O +ATOM 605 C ASP 40 38.051 -87.384 -8.330 1.00 0.00 C +ATOM 606 O ASP 40 37.810 -88.380 -7.599 1.00 0.00 O +ATOM 607 N GLY 41 37.746 -87.408 -9.589 1.00 0.00 N +ATOM 608 H GLY 41 37.693 -86.579 -10.165 1.00 0.00 H +ATOM 609 CA GLY 41 37.288 -88.662 -10.236 1.00 0.00 C +ATOM 610 HA2 GLY 41 38.136 -89.129 -10.738 1.00 0.00 H +ATOM 611 HA3 GLY 41 36.791 -89.302 -9.506 1.00 0.00 H +ATOM 612 C GLY 41 36.272 -88.205 -11.372 1.00 0.00 C +ATOM 613 O GLY 41 36.097 -87.040 -11.673 1.00 0.00 O +ATOM 614 N GLU 42 35.594 -89.212 -11.877 1.00 0.00 N +ATOM 615 H GLU 42 35.767 -90.173 -11.620 1.00 0.00 H +ATOM 616 CA GLU 42 34.585 -88.979 -12.986 1.00 0.00 C +ATOM 617 HA GLU 42 34.450 -87.908 -13.139 1.00 0.00 H +ATOM 618 CB GLU 42 35.192 -89.345 -14.354 1.00 0.00 C +ATOM 619 HB2 GLU 42 35.174 -90.429 -14.467 1.00 0.00 H +ATOM 620 HB3 GLU 42 34.444 -89.025 -15.078 1.00 0.00 H +ATOM 621 CG GLU 42 36.573 -88.781 -14.748 1.00 0.00 C +ATOM 622 HG2 GLU 42 37.249 -89.266 -14.044 1.00 0.00 H +ATOM 623 HG3 GLU 42 36.864 -89.095 -15.750 1.00 0.00 H +ATOM 624 CD GLU 42 36.733 -87.282 -14.599 1.00 0.00 C +ATOM 625 OE1 GLU 42 35.757 -86.554 -14.853 1.00 0.00 O +ATOM 626 OE2 GLU 42 37.842 -86.853 -14.141 1.00 0.00 O +ATOM 627 C GLU 42 33.205 -89.633 -12.764 1.00 0.00 C +ATOM 628 O GLU 42 33.040 -90.563 -11.989 1.00 0.00 O +ATOM 629 N TRP 43 32.264 -89.154 -13.569 1.00 0.00 N +ATOM 630 H TRP 43 32.530 -88.646 -14.400 1.00 0.00 H +ATOM 631 CA TRP 43 30.851 -89.664 -13.515 1.00 0.00 C +ATOM 632 HA TRP 43 30.875 -90.525 -12.847 1.00 0.00 H +ATOM 633 CB TRP 43 29.864 -88.757 -12.810 1.00 0.00 C +ATOM 634 HB2 TRP 43 29.823 -87.792 -13.316 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.888 -89.238 -12.873 1.00 0.00 H +ATOM 636 CG TRP 43 30.136 -88.638 -11.352 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.390 -89.256 -10.408 1.00 0.00 C +ATOM 638 HD1 TRP 43 28.534 -89.905 -10.525 1.00 0.00 H +ATOM 639 NE1 TRP 43 29.978 -88.943 -9.164 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.668 -89.383 -8.309 1.00 0.00 H +ATOM 641 CE2 TRP 43 31.000 -88.042 -9.255 1.00 0.00 C +ATOM 642 CZ2 TRP 43 31.822 -87.436 -8.285 1.00 0.00 C +ATOM 643 HZ2 TRP 43 31.657 -87.621 -7.234 1.00 0.00 H +ATOM 644 CH2 TRP 43 32.777 -86.516 -8.704 1.00 0.00 C +ATOM 645 HH2 TRP 43 33.208 -85.869 -7.954 1.00 0.00 H +ATOM 646 CZ3 TRP 43 32.952 -86.274 -10.052 1.00 0.00 C +ATOM 647 HZ3 TRP 43 33.627 -85.504 -10.393 1.00 0.00 H +ATOM 648 CE3 TRP 43 32.181 -87.031 -10.988 1.00 0.00 C +ATOM 649 HE3 TRP 43 32.359 -86.839 -12.036 1.00 0.00 H +ATOM 650 CD2 TRP 43 31.172 -87.904 -10.661 1.00 0.00 C +ATOM 651 C TRP 43 30.379 -90.170 -14.869 1.00 0.00 C +ATOM 652 O TRP 43 30.540 -89.486 -15.895 1.00 0.00 O +ATOM 653 N THR 44 29.748 -91.335 -14.901 1.00 0.00 N +ATOM 654 H THR 44 29.573 -91.922 -14.098 1.00 0.00 H +ATOM 655 CA THR 44 29.056 -91.745 -16.059 1.00 0.00 C +ATOM 656 HA THR 44 29.475 -91.187 -16.896 1.00 0.00 H +ATOM 657 CB THR 44 29.360 -93.227 -16.425 1.00 0.00 C +ATOM 658 HB THR 44 29.019 -93.873 -15.616 1.00 0.00 H +ATOM 659 CG2 THR 44 28.609 -93.574 -17.724 1.00 0.00 C +ATOM 660 HG21 THR 44 28.817 -92.791 -18.453 1.00 0.00 H +ATOM 661 HG22 THR 44 27.559 -93.580 -17.432 1.00 0.00 H +ATOM 662 HG23 THR 44 29.008 -94.532 -18.055 1.00 0.00 H +ATOM 663 OG1 THR 44 30.732 -93.303 -16.610 1.00 0.00 O +ATOM 664 HG1 THR 44 31.128 -92.656 -16.021 1.00 0.00 H +ATOM 665 C THR 44 27.586 -91.475 -15.914 1.00 0.00 C +ATOM 666 O THR 44 26.928 -92.049 -14.997 1.00 0.00 O +ATOM 667 N TYR 45 27.019 -90.745 -16.838 1.00 0.00 N +ATOM 668 H TYR 45 27.577 -90.435 -17.621 1.00 0.00 H +ATOM 669 CA TYR 45 25.584 -90.597 -17.069 1.00 0.00 C +ATOM 670 HA TYR 45 25.015 -90.540 -16.141 1.00 0.00 H +ATOM 671 CB TYR 45 25.353 -89.363 -17.984 1.00 0.00 C +ATOM 672 HB2 TYR 45 25.812 -88.487 -17.524 1.00 0.00 H +ATOM 673 HB3 TYR 45 25.828 -89.603 -18.935 1.00 0.00 H +ATOM 674 CG TYR 45 23.929 -88.931 -18.219 1.00 0.00 C +ATOM 675 CD1 TYR 45 22.997 -88.793 -17.110 1.00 0.00 C +ATOM 676 HD1 TYR 45 23.347 -88.941 -16.099 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.675 -88.391 -17.238 1.00 0.00 C +ATOM 678 HE1 TYR 45 20.996 -88.271 -16.407 1.00 0.00 H +ATOM 679 CZ TYR 45 21.159 -88.187 -18.552 1.00 0.00 C +ATOM 680 OH TYR 45 19.883 -87.833 -18.762 1.00 0.00 O +ATOM 681 HH TYR 45 19.722 -87.560 -19.668 1.00 0.00 H +ATOM 682 CE2 TYR 45 22.022 -88.295 -19.702 1.00 0.00 C +ATOM 683 HE2 TYR 45 21.530 -88.249 -20.662 1.00 0.00 H +ATOM 684 CD2 TYR 45 23.361 -88.767 -19.499 1.00 0.00 C +ATOM 685 HD2 TYR 45 24.017 -89.028 -20.316 1.00 0.00 H +ATOM 686 C TYR 45 25.097 -91.845 -17.849 1.00 0.00 C +ATOM 687 O TYR 45 25.804 -92.409 -18.736 1.00 0.00 O +ATOM 688 N ASP 46 23.866 -92.261 -17.604 1.00 0.00 N +ATOM 689 H ASP 46 23.517 -91.761 -16.800 1.00 0.00 H +ATOM 690 CA ASP 46 23.070 -93.160 -18.445 1.00 0.00 C +ATOM 691 HA ASP 46 23.597 -93.270 -19.392 1.00 0.00 H +ATOM 692 CB ASP 46 22.904 -94.482 -17.759 1.00 0.00 C +ATOM 693 HB2 ASP 46 23.911 -94.816 -17.512 1.00 0.00 H +ATOM 694 HB3 ASP 46 22.328 -94.494 -16.834 1.00 0.00 H +ATOM 695 CG ASP 46 22.157 -95.431 -18.762 1.00 0.00 C +ATOM 696 OD1 ASP 46 22.305 -95.201 -20.007 1.00 0.00 O +ATOM 697 OD2 ASP 46 21.591 -96.457 -18.370 1.00 0.00 O +ATOM 698 C ASP 46 21.640 -92.567 -18.691 1.00 0.00 C +ATOM 699 O ASP 46 20.848 -92.558 -17.703 1.00 0.00 O +ATOM 700 N ASP 47 21.310 -92.092 -19.880 1.00 0.00 N +ATOM 701 H ASP 47 22.100 -92.132 -20.508 1.00 0.00 H +ATOM 702 CA ASP 47 20.001 -91.513 -20.211 1.00 0.00 C +ATOM 703 HA ASP 47 19.785 -90.831 -19.388 1.00 0.00 H +ATOM 704 CB ASP 47 20.015 -90.786 -21.504 1.00 0.00 C +ATOM 705 HB2 ASP 47 20.898 -90.189 -21.733 1.00 0.00 H +ATOM 706 HB3 ASP 47 19.978 -91.486 -22.339 1.00 0.00 H +ATOM 707 CG ASP 47 18.890 -89.782 -21.654 1.00 0.00 C +ATOM 708 OD1 ASP 47 19.113 -88.568 -21.359 1.00 0.00 O +ATOM 709 OD2 ASP 47 17.780 -90.019 -22.080 1.00 0.00 O +ATOM 710 C ASP 47 18.824 -92.538 -20.186 1.00 0.00 C +ATOM 711 O ASP 47 17.704 -92.178 -19.801 1.00 0.00 O +ATOM 712 N ALA 48 19.030 -93.804 -20.526 1.00 0.00 N +ATOM 713 H ALA 48 19.859 -94.129 -21.002 1.00 0.00 H +ATOM 714 CA ALA 48 17.937 -94.753 -20.384 1.00 0.00 C +ATOM 715 HA ALA 48 17.033 -94.333 -20.825 1.00 0.00 H +ATOM 716 CB ALA 48 18.356 -96.064 -21.130 1.00 0.00 C +ATOM 717 HB1 ALA 48 17.441 -96.576 -21.427 1.00 0.00 H +ATOM 718 HB2 ALA 48 19.012 -96.578 -20.428 1.00 0.00 H +ATOM 719 HB3 ALA 48 18.960 -95.759 -21.985 1.00 0.00 H +ATOM 720 C ALA 48 17.508 -95.055 -18.935 1.00 0.00 C +ATOM 721 O ALA 48 16.413 -95.569 -18.817 1.00 0.00 O +ATOM 722 N THR 49 18.370 -94.747 -17.949 1.00 0.00 N +ATOM 723 H THR 49 19.286 -94.386 -18.175 1.00 0.00 H +ATOM 724 CA THR 49 17.944 -94.868 -16.529 1.00 0.00 C +ATOM 725 HA THR 49 16.930 -95.268 -16.551 1.00 0.00 H +ATOM 726 CB THR 49 18.782 -95.814 -15.696 1.00 0.00 C +ATOM 727 HB THR 49 18.595 -95.644 -14.636 1.00 0.00 H +ATOM 728 CG2 THR 49 18.422 -97.262 -15.972 1.00 0.00 C +ATOM 729 HG21 THR 49 18.583 -97.550 -17.011 1.00 0.00 H +ATOM 730 HG22 THR 49 17.407 -97.421 -15.609 1.00 0.00 H +ATOM 731 HG23 THR 49 18.945 -97.878 -15.241 1.00 0.00 H +ATOM 732 OG1 THR 49 20.202 -95.676 -15.988 1.00 0.00 O +ATOM 733 HG1 THR 49 20.403 -96.024 -16.860 1.00 0.00 H +ATOM 734 C THR 49 17.812 -93.509 -15.858 1.00 0.00 C +ATOM 735 O THR 49 17.586 -93.484 -14.653 1.00 0.00 O +ATOM 736 N LYS 50 18.108 -92.417 -16.556 1.00 0.00 N +ATOM 737 H LYS 50 18.502 -92.505 -17.482 1.00 0.00 H +ATOM 738 CA LYS 50 18.235 -91.024 -16.096 1.00 0.00 C +ATOM 739 HA LYS 50 18.742 -90.497 -16.904 1.00 0.00 H +ATOM 740 CB LYS 50 16.821 -90.400 -15.922 1.00 0.00 C +ATOM 741 HB2 LYS 50 16.297 -91.050 -15.222 1.00 0.00 H +ATOM 742 HB3 LYS 50 16.899 -89.383 -15.537 1.00 0.00 H +ATOM 743 CG LYS 50 16.032 -90.240 -17.238 1.00 0.00 C +ATOM 744 HG2 LYS 50 16.129 -91.151 -17.828 1.00 0.00 H +ATOM 745 HG3 LYS 50 14.969 -90.181 -17.002 1.00 0.00 H +ATOM 746 CD LYS 50 16.316 -89.061 -18.183 1.00 0.00 C +ATOM 747 HD2 LYS 50 16.073 -88.089 -17.754 1.00 0.00 H +ATOM 748 HD3 LYS 50 17.369 -89.075 -18.463 1.00 0.00 H +ATOM 749 CE LYS 50 15.510 -89.075 -19.445 1.00 0.00 C +ATOM 750 HE2 LYS 50 14.443 -89.042 -19.223 1.00 0.00 H +ATOM 751 HE3 LYS 50 15.681 -88.168 -20.024 1.00 0.00 H +ATOM 752 NZ LYS 50 15.806 -90.167 -20.366 1.00 0.00 N +ATOM 753 HZ1 LYS 50 16.800 -90.191 -20.543 1.00 0.00 H +ATOM 754 HZ2 LYS 50 15.379 -90.063 -21.275 1.00 0.00 H +ATOM 755 HZ3 LYS 50 15.575 -91.101 -20.058 1.00 0.00 H +ATOM 756 C LYS 50 19.323 -90.871 -14.900 1.00 0.00 C +ATOM 757 O LYS 50 19.033 -90.121 -13.978 1.00 0.00 O +ATOM 758 N THR 51 20.459 -91.637 -14.893 1.00 0.00 N +ATOM 759 H THR 51 20.643 -92.098 -15.773 1.00 0.00 H +ATOM 760 CA THR 51 21.294 -91.877 -13.686 1.00 0.00 C +ATOM 761 HA THR 51 20.831 -91.465 -12.790 1.00 0.00 H +ATOM 762 CB THR 51 21.310 -93.349 -13.465 1.00 0.00 C +ATOM 763 HB THR 51 21.674 -93.860 -14.356 1.00 0.00 H +ATOM 764 CG2 THR 51 22.110 -93.824 -12.205 1.00 0.00 C +ATOM 765 HG21 THR 51 21.706 -93.261 -11.363 1.00 0.00 H +ATOM 766 HG22 THR 51 23.175 -93.655 -12.362 1.00 0.00 H +ATOM 767 HG23 THR 51 21.787 -94.862 -12.133 1.00 0.00 H +ATOM 768 OG1 THR 51 20.062 -93.784 -13.211 1.00 0.00 O +ATOM 769 HG1 THR 51 19.684 -93.593 -14.072 1.00 0.00 H +ATOM 770 C THR 51 22.732 -91.238 -13.783 1.00 0.00 C +ATOM 771 O THR 51 23.367 -91.328 -14.826 1.00 0.00 O +ATOM 772 N PHE 52 23.278 -90.790 -12.684 1.00 0.00 N +ATOM 773 H PHE 52 22.674 -90.536 -11.915 1.00 0.00 H +ATOM 774 CA PHE 52 24.671 -90.588 -12.494 1.00 0.00 C +ATOM 775 HA PHE 52 25.135 -90.684 -13.476 1.00 0.00 H +ATOM 776 CB PHE 52 24.952 -89.137 -12.086 1.00 0.00 C +ATOM 777 HB2 PHE 52 24.410 -88.900 -11.170 1.00 0.00 H +ATOM 778 HB3 PHE 52 26.030 -89.093 -11.924 1.00 0.00 H +ATOM 779 CG PHE 52 24.513 -88.071 -13.105 1.00 0.00 C +ATOM 780 CD1 PHE 52 23.240 -87.513 -13.024 1.00 0.00 C +ATOM 781 HD1 PHE 52 22.561 -87.809 -12.238 1.00 0.00 H +ATOM 782 CE1 PHE 52 22.972 -86.665 -14.121 1.00 0.00 C +ATOM 783 HE1 PHE 52 21.945 -86.337 -14.190 1.00 0.00 H +ATOM 784 CZ PHE 52 23.885 -86.384 -15.139 1.00 0.00 C +ATOM 785 HZ PHE 52 23.585 -85.653 -15.875 1.00 0.00 H +ATOM 786 CE2 PHE 52 25.213 -86.823 -15.093 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.913 -86.342 -15.759 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.517 -87.753 -14.074 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.515 -88.133 -13.913 1.00 0.00 H +ATOM 790 C PHE 52 25.177 -91.611 -11.414 1.00 0.00 C +ATOM 791 O PHE 52 24.600 -91.858 -10.361 1.00 0.00 O +ATOM 792 N THR 53 26.311 -92.259 -11.890 1.00 0.00 N +ATOM 793 H THR 53 26.752 -91.953 -12.745 1.00 0.00 H +ATOM 794 CA THR 53 27.250 -93.154 -11.086 1.00 0.00 C +ATOM 795 HA THR 53 27.045 -93.145 -10.015 1.00 0.00 H +ATOM 796 CB THR 53 27.065 -94.658 -11.382 1.00 0.00 C +ATOM 797 HB THR 53 26.004 -94.906 -11.409 1.00 0.00 H +ATOM 798 CG2 THR 53 27.631 -95.088 -12.739 1.00 0.00 C +ATOM 799 HG21 THR 53 28.718 -95.168 -12.701 1.00 0.00 H +ATOM 800 HG22 THR 53 27.186 -94.456 -13.507 1.00 0.00 H +ATOM 801 HG23 THR 53 27.220 -96.082 -12.918 1.00 0.00 H +ATOM 802 OG1 THR 53 27.690 -95.537 -10.496 1.00 0.00 O +ATOM 803 HG1 THR 53 27.876 -96.366 -10.943 1.00 0.00 H +ATOM 804 C THR 53 28.655 -92.694 -11.337 1.00 0.00 C +ATOM 805 O THR 53 28.916 -91.947 -12.272 1.00 0.00 O +ATOM 806 N VAL 54 29.650 -93.087 -10.500 1.00 0.00 N +ATOM 807 H VAL 54 29.428 -93.703 -9.731 1.00 0.00 H +ATOM 808 CA VAL 54 31.065 -92.912 -10.720 1.00 0.00 C +ATOM 809 HA VAL 54 31.143 -91.840 -10.903 1.00 0.00 H +ATOM 810 CB VAL 54 31.832 -93.244 -9.401 1.00 0.00 C +ATOM 811 HB VAL 54 31.583 -94.248 -9.056 1.00 0.00 H +ATOM 812 CG1 VAL 54 33.337 -93.202 -9.568 1.00 0.00 C +ATOM 813 HG11 VAL 54 33.625 -94.052 -10.187 1.00 0.00 H +ATOM 814 HG12 VAL 54 33.747 -93.175 -8.559 1.00 0.00 H +ATOM 815 HG13 VAL 54 33.663 -92.273 -10.036 1.00 0.00 H +ATOM 816 CG2 VAL 54 31.483 -92.378 -8.230 1.00 0.00 C +ATOM 817 HG21 VAL 54 30.420 -92.530 -8.044 1.00 0.00 H +ATOM 818 HG22 VAL 54 31.842 -91.361 -8.387 1.00 0.00 H +ATOM 819 HG23 VAL 54 31.924 -92.766 -7.312 1.00 0.00 H +ATOM 820 C VAL 54 31.630 -93.801 -11.880 1.00 0.00 C +ATOM 821 O VAL 54 31.344 -94.997 -11.945 1.00 0.00 O +ATOM 822 N THR 55 32.463 -93.199 -12.733 1.00 0.00 N +ATOM 823 H THR 55 32.651 -92.208 -12.672 1.00 0.00 H +ATOM 824 CA THR 55 33.209 -93.945 -13.745 1.00 0.00 C +ATOM 825 HA THR 55 32.517 -94.438 -14.429 1.00 0.00 H +ATOM 826 CB THR 55 33.920 -92.938 -14.622 1.00 0.00 C +ATOM 827 HB THR 55 34.554 -92.281 -14.027 1.00 0.00 H +ATOM 828 CG2 THR 55 34.836 -93.628 -15.624 1.00 0.00 C +ATOM 829 HG21 THR 55 34.335 -94.462 -16.116 1.00 0.00 H +ATOM 830 HG22 THR 55 35.706 -94.059 -15.129 1.00 0.00 H +ATOM 831 HG23 THR 55 35.210 -92.892 -16.336 1.00 0.00 H +ATOM 832 OG1 THR 55 32.944 -92.076 -15.191 1.00 0.00 O +ATOM 833 HG1 THR 55 33.500 -91.599 -15.812 1.00 0.00 H +ATOM 834 C THR 55 34.203 -95.018 -13.310 1.00 0.00 C +ATOM 835 O THR 55 35.162 -94.900 -12.548 1.00 0.00 O +ATOM 836 N GLU 56 33.853 -96.191 -13.831 1.00 0.00 N +ATOM 837 H GLU 56 32.973 -96.122 -14.321 1.00 0.00 H +ATOM 838 CA GLU 56 34.429 -97.504 -13.580 1.00 0.00 C +ATOM 839 HA GLU 56 35.479 -97.522 -13.288 1.00 0.00 H +ATOM 840 CB GLU 56 33.623 -98.059 -12.330 1.00 0.00 C +ATOM 841 HB2 GLU 56 32.582 -97.738 -12.349 1.00 0.00 H +ATOM 842 HB3 GLU 56 33.651 -99.149 -12.350 1.00 0.00 H +ATOM 843 CG GLU 56 34.341 -97.719 -10.990 1.00 0.00 C +ATOM 844 HG2 GLU 56 34.303 -96.636 -10.866 1.00 0.00 H +ATOM 845 HG3 GLU 56 33.704 -98.213 -10.256 1.00 0.00 H +ATOM 846 CD GLU 56 35.803 -98.221 -10.845 1.00 0.00 C +ATOM 847 OE1 GLU 56 36.177 -99.118 -11.643 1.00 0.00 O +ATOM 848 OE2 GLU 56 36.611 -97.623 -10.110 1.00 0.00 O +ATOM 849 C GLU 56 34.334 -98.394 -14.839 1.00 0.00 C +ATOM 850 O GLU 56 35.068 -98.144 -15.793 1.00 0.00 O +ATOM 851 OXT GLU 56 33.499 -99.353 -14.852 1.00 0.00 O +ATOM 852 ZN ZN1 57 23.231 -87.325 -4.270 1.00 0.00 ZN +ATOM 853 N AN1 58 24.369 -86.764 -2.736 1.00 0.00 N +ATOM 854 C AN1 58 25.300 -85.919 -0.432 1.00 0.00 C +ATOM 855 C1 AN1 58 24.825 -86.465 -1.714 1.00 0.00 C +ATOM 856 H AN1 58 25.084 -84.844 -0.408 1.00 0.00 H +ATOM 857 H1 AN1 58 26.382 -86.066 -0.325 1.00 0.00 H +ATOM 858 H2 AN1 58 24.826 -86.472 0.388 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 26.075 -89.271 -2.458 1.00 0.00 N +ATOM 860 N2 AZI 59 27.232 -89.395 -2.126 1.00 0.00 N +ATOM 861 N3 AZI 59 28.453 -89.281 -1.850 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/inp/pdbs/cluster.c9.pdb b/tests/nsga2/inp/pdbs/cluster.c9.pdb new file mode 100644 index 0000000..ef3e34e --- /dev/null +++ b/tests/nsga2/inp/pdbs/cluster.c9.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.280 -82.161 -12.986 1.00 0.00 N +ATOM 2 H1 MET 1 13.609 -81.951 -12.055 1.00 0.00 H +ATOM 3 H2 MET 1 12.273 -82.082 -12.973 1.00 0.00 H +ATOM 4 H3 MET 1 13.702 -81.520 -13.643 1.00 0.00 H +ATOM 5 CA MET 1 13.613 -83.553 -13.412 1.00 0.00 C +ATOM 6 HA MET 1 12.647 -84.000 -13.646 1.00 0.00 H +ATOM 7 CB MET 1 14.287 -83.532 -14.781 1.00 0.00 C +ATOM 8 HB2 MET 1 13.707 -83.147 -15.620 1.00 0.00 H +ATOM 9 HB3 MET 1 15.224 -82.983 -14.685 1.00 0.00 H +ATOM 10 CG MET 1 14.666 -84.916 -15.344 1.00 0.00 C +ATOM 11 HG2 MET 1 14.976 -84.674 -16.361 1.00 0.00 H +ATOM 12 HG3 MET 1 15.533 -85.369 -14.863 1.00 0.00 H +ATOM 13 SD MET 1 13.339 -86.079 -15.367 1.00 0.00 S +ATOM 14 CE MET 1 12.132 -85.391 -16.645 1.00 0.00 C +ATOM 15 HE1 MET 1 11.702 -86.232 -17.190 1.00 0.00 H +ATOM 16 HE2 MET 1 12.624 -84.768 -17.392 1.00 0.00 H +ATOM 17 HE3 MET 1 11.272 -84.800 -16.330 1.00 0.00 H +ATOM 18 C MET 1 14.386 -84.382 -12.397 1.00 0.00 C +ATOM 19 O MET 1 15.427 -83.891 -12.010 1.00 0.00 O +ATOM 20 N GLN 2 13.874 -85.466 -11.878 1.00 0.00 N +ATOM 21 H GLN 2 12.939 -85.745 -12.139 1.00 0.00 H +ATOM 22 CA GLN 2 14.517 -86.329 -10.818 1.00 0.00 C +ATOM 23 HA GLN 2 15.001 -85.655 -10.110 1.00 0.00 H +ATOM 24 CB GLN 2 13.301 -86.996 -10.112 1.00 0.00 C +ATOM 25 HB2 GLN 2 12.672 -87.652 -10.714 1.00 0.00 H +ATOM 26 HB3 GLN 2 13.772 -87.695 -9.422 1.00 0.00 H +ATOM 27 CG GLN 2 12.443 -86.012 -9.259 1.00 0.00 C +ATOM 28 HG2 GLN 2 12.439 -85.019 -9.708 1.00 0.00 H +ATOM 29 HG3 GLN 2 11.468 -86.479 -9.403 1.00 0.00 H +ATOM 30 CD GLN 2 12.798 -85.981 -7.801 1.00 0.00 C +ATOM 31 OE1 GLN 2 13.900 -86.364 -7.373 1.00 0.00 O +ATOM 32 NE2 GLN 2 11.960 -85.457 -6.990 1.00 0.00 N +ATOM 33 HE21 GLN 2 12.178 -85.347 -6.010 1.00 0.00 H +ATOM 34 HE22 GLN 2 11.037 -85.203 -7.313 1.00 0.00 H +ATOM 35 C GLN 2 15.507 -87.318 -11.384 1.00 0.00 C +ATOM 36 O GLN 2 15.106 -88.486 -11.649 1.00 0.00 O +ATOM 37 N TYR 3 16.816 -86.922 -11.415 1.00 0.00 N +ATOM 38 H TYR 3 16.987 -86.018 -11.000 1.00 0.00 H +ATOM 39 CA TYR 3 17.931 -87.713 -11.945 1.00 0.00 C +ATOM 40 HA TYR 3 17.565 -88.189 -12.855 1.00 0.00 H +ATOM 41 CB TYR 3 19.018 -86.768 -12.354 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.281 -86.101 -11.533 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.872 -87.353 -12.696 1.00 0.00 H +ATOM 44 CG TYR 3 18.638 -85.866 -13.508 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.709 -86.358 -14.789 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.109 -87.347 -14.962 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.400 -85.460 -15.869 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.468 -85.801 -16.891 1.00 0.00 H +ATOM 49 CZ TYR 3 18.010 -84.125 -15.640 1.00 0.00 C +ATOM 50 OH TYR 3 17.704 -83.356 -16.746 1.00 0.00 O +ATOM 51 HH TYR 3 17.903 -83.815 -17.565 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.009 -83.621 -14.344 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.641 -82.650 -14.046 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.331 -84.501 -13.314 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.211 -84.196 -12.285 1.00 0.00 H +ATOM 56 C TYR 3 18.408 -88.706 -10.876 1.00 0.00 C +ATOM 57 O TYR 3 18.959 -88.281 -9.848 1.00 0.00 O +ATOM 58 N LYS 4 18.304 -90.012 -11.226 1.00 0.00 N +ATOM 59 H LYS 4 17.878 -90.302 -12.094 1.00 0.00 H +ATOM 60 CA LYS 4 18.872 -91.028 -10.312 1.00 0.00 C +ATOM 61 HA LYS 4 18.513 -90.818 -9.305 1.00 0.00 H +ATOM 62 CB LYS 4 18.346 -92.448 -10.688 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.415 -92.619 -11.762 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.046 -93.132 -10.208 1.00 0.00 H +ATOM 65 CG LYS 4 16.840 -92.565 -10.324 1.00 0.00 C +ATOM 66 HG2 LYS 4 16.631 -92.411 -9.265 1.00 0.00 H +ATOM 67 HG3 LYS 4 16.338 -91.775 -10.883 1.00 0.00 H +ATOM 68 CD LYS 4 16.235 -93.931 -10.724 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.789 -94.741 -10.250 1.00 0.00 H +ATOM 70 HD3 LYS 4 15.213 -93.903 -10.345 1.00 0.00 H +ATOM 71 CE LYS 4 16.172 -94.172 -12.279 1.00 0.00 C +ATOM 72 HE2 LYS 4 17.100 -93.687 -12.580 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.124 -95.240 -12.490 1.00 0.00 H +ATOM 74 NZ LYS 4 15.011 -93.445 -12.896 1.00 0.00 N +ATOM 75 HZ1 LYS 4 14.185 -94.026 -12.916 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.289 -93.203 -13.836 1.00 0.00 H +ATOM 77 HZ3 LYS 4 14.880 -92.590 -12.374 1.00 0.00 H +ATOM 78 C LYS 4 20.384 -91.034 -10.263 1.00 0.00 C +ATOM 79 O LYS 4 20.986 -90.909 -11.348 1.00 0.00 O +ATOM 80 N HE1 5 20.976 -91.370 -9.106 1.00 0.00 N +ATOM 81 CA HE1 5 22.495 -91.359 -9.024 1.00 0.00 C +ATOM 82 C HE1 5 22.886 -92.646 -8.370 1.00 0.00 C +ATOM 83 O HE1 5 22.744 -92.705 -7.205 1.00 0.00 O +ATOM 84 CB HE1 5 23.020 -90.042 -8.530 1.00 0.00 C +ATOM 85 CG HE1 5 24.517 -89.811 -8.453 1.00 0.00 C +ATOM 86 CD2 HE1 5 25.467 -90.486 -9.137 1.00 0.00 C +ATOM 87 ND1 HE1 5 25.067 -88.841 -7.672 1.00 0.00 N +ATOM 88 CE1 HE1 5 26.367 -88.860 -7.972 1.00 0.00 C +ATOM 89 NE2 HE1 5 26.660 -89.875 -8.843 1.00 0.00 N +ATOM 90 H HE1 5 20.383 -91.469 -8.294 1.00 0.00 H +ATOM 91 HA HE1 5 22.820 -91.463 -10.059 1.00 0.00 H +ATOM 92 HB2 HE1 5 22.516 -89.922 -7.571 1.00 0.00 H +ATOM 93 HB3 HE1 5 22.663 -89.279 -9.221 1.00 0.00 H +ATOM 94 HD2 HE1 5 25.319 -91.319 -9.808 1.00 0.00 H +ATOM 95 HE1 HE1 5 27.072 -88.252 -7.424 1.00 0.00 H +ATOM 96 HE2 HE1 5 27.456 -89.907 -9.464 1.00 0.00 H +ATOM 97 N ILE 6 23.417 -93.632 -9.027 1.00 0.00 N +ATOM 98 H ILE 6 23.598 -93.338 -9.976 1.00 0.00 H +ATOM 99 CA ILE 6 24.011 -94.880 -8.558 1.00 0.00 C +ATOM 100 HA ILE 6 23.464 -95.183 -7.665 1.00 0.00 H +ATOM 101 CB ILE 6 23.901 -96.015 -9.728 1.00 0.00 C +ATOM 102 HB ILE 6 24.488 -95.668 -10.578 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.555 -97.324 -9.271 1.00 0.00 C +ATOM 104 HG21 ILE 6 24.575 -97.996 -10.129 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.019 -97.810 -8.456 1.00 0.00 H +ATOM 106 HG23 ILE 6 25.584 -97.043 -9.045 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.406 -96.213 -10.136 1.00 0.00 C +ATOM 108 HG12 ILE 6 21.833 -96.416 -9.231 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.016 -95.296 -10.578 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.167 -97.381 -11.104 1.00 0.00 C +ATOM 111 HD11 ILE 6 21.221 -97.352 -11.644 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.316 -98.379 -10.691 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.964 -97.281 -11.841 1.00 0.00 H +ATOM 114 C ILE 6 25.528 -94.678 -8.186 1.00 0.00 C +ATOM 115 O ILE 6 26.351 -94.413 -9.066 1.00 0.00 O +ATOM 116 N VAL 7 25.869 -94.750 -6.932 1.00 0.00 N +ATOM 117 H VAL 7 25.200 -95.198 -6.322 1.00 0.00 H +ATOM 118 CA VAL 7 27.215 -94.505 -6.320 1.00 0.00 C +ATOM 119 HA VAL 7 27.865 -94.141 -7.115 1.00 0.00 H +ATOM 120 CB VAL 7 27.074 -93.343 -5.221 1.00 0.00 C +ATOM 121 HB VAL 7 28.026 -93.097 -4.750 1.00 0.00 H +ATOM 122 CG1 VAL 7 26.504 -92.114 -6.048 1.00 0.00 C +ATOM 123 HG11 VAL 7 27.197 -91.879 -6.856 1.00 0.00 H +ATOM 124 HG12 VAL 7 25.556 -92.355 -6.530 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.385 -91.250 -5.394 1.00 0.00 H +ATOM 126 CG2 VAL 7 26.138 -93.692 -4.077 1.00 0.00 C +ATOM 127 HG21 VAL 7 26.045 -92.769 -3.505 1.00 0.00 H +ATOM 128 HG22 VAL 7 25.186 -94.130 -4.377 1.00 0.00 H +ATOM 129 HG23 VAL 7 26.736 -94.352 -3.449 1.00 0.00 H +ATOM 130 C VAL 7 27.868 -95.661 -5.702 1.00 0.00 C +ATOM 131 O VAL 7 27.178 -96.548 -5.152 1.00 0.00 O +ATOM 132 N ASN 8 29.211 -95.887 -5.940 1.00 0.00 N +ATOM 133 H ASN 8 29.709 -95.225 -6.518 1.00 0.00 H +ATOM 134 CA ASN 8 29.922 -97.142 -5.443 1.00 0.00 C +ATOM 135 HA ASN 8 29.470 -97.454 -4.502 1.00 0.00 H +ATOM 136 CB ASN 8 29.723 -98.233 -6.526 1.00 0.00 C +ATOM 137 HB2 ASN 8 28.838 -98.082 -7.144 1.00 0.00 H +ATOM 138 HB3 ASN 8 30.502 -98.119 -7.280 1.00 0.00 H +ATOM 139 CG ASN 8 29.898 -99.574 -5.953 1.00 0.00 C +ATOM 140 OD1 ASN 8 30.464 -99.833 -4.899 1.00 0.00 O +ATOM 141 ND2 ASN 8 29.250-100.550 -6.631 1.00 0.00 N +ATOM 142 HD21 ASN 8 28.585-100.384 -7.372 1.00 0.00 H +ATOM 143 HD22 ASN 8 29.344-101.499 -6.298 1.00 0.00 H +ATOM 144 C ASN 8 31.368 -96.798 -5.165 1.00 0.00 C +ATOM 145 O ASN 8 32.076 -96.165 -5.902 1.00 0.00 O +ATOM 146 N GLY 9 31.859 -97.405 -4.109 1.00 0.00 N +ATOM 147 H GLY 9 31.225 -97.834 -3.449 1.00 0.00 H +ATOM 148 CA GLY 9 33.247 -97.319 -3.620 1.00 0.00 C +ATOM 149 HA2 GLY 9 33.838 -97.797 -4.402 1.00 0.00 H +ATOM 150 HA3 GLY 9 33.471 -96.252 -3.643 1.00 0.00 H +ATOM 151 C GLY 9 33.539 -98.115 -2.286 1.00 0.00 C +ATOM 152 O GLY 9 32.966 -99.139 -1.989 1.00 0.00 O +ATOM 153 N LYS 10 34.487 -97.630 -1.532 1.00 0.00 N +ATOM 154 H LYS 10 34.883 -96.748 -1.822 1.00 0.00 H +ATOM 155 CA LYS 10 35.001 -98.212 -0.236 1.00 0.00 C +ATOM 156 HA LYS 10 34.601 -99.223 -0.166 1.00 0.00 H +ATOM 157 CB LYS 10 36.526 -98.105 -0.325 1.00 0.00 C +ATOM 158 HB2 LYS 10 36.803 -97.057 -0.209 1.00 0.00 H +ATOM 159 HB3 LYS 10 36.925 -98.626 0.545 1.00 0.00 H +ATOM 160 CG LYS 10 37.012 -98.798 -1.622 1.00 0.00 C +ATOM 161 HG2 LYS 10 36.541 -99.765 -1.798 1.00 0.00 H +ATOM 162 HG3 LYS 10 36.751 -98.195 -2.491 1.00 0.00 H +ATOM 163 CD LYS 10 38.474 -99.000 -1.787 1.00 0.00 C +ATOM 164 HD2 LYS 10 38.721 -99.746 -1.031 1.00 0.00 H +ATOM 165 HD3 LYS 10 38.745 -99.356 -2.781 1.00 0.00 H +ATOM 166 CE LYS 10 39.284 -97.744 -1.380 1.00 0.00 C +ATOM 167 HE2 LYS 10 38.963 -96.900 -1.990 1.00 0.00 H +ATOM 168 HE3 LYS 10 39.095 -97.521 -0.330 1.00 0.00 H +ATOM 169 NZ LYS 10 40.728 -97.939 -1.468 1.00 0.00 N +ATOM 170 HZ1 LYS 10 41.137 -98.810 -1.163 1.00 0.00 H +ATOM 171 HZ2 LYS 10 41.247 -97.182 -1.046 1.00 0.00 H +ATOM 172 HZ3 LYS 10 41.041 -98.039 -2.423 1.00 0.00 H +ATOM 173 C LYS 10 34.364 -97.545 1.003 1.00 0.00 C +ATOM 174 O LYS 10 34.689 -98.018 2.102 1.00 0.00 O +ATOM 175 N THR 11 33.483 -96.567 0.814 1.00 0.00 N +ATOM 176 H THR 11 33.278 -96.427 -0.165 1.00 0.00 H +ATOM 177 CA THR 11 32.757 -95.950 1.952 1.00 0.00 C +ATOM 178 HA THR 11 32.788 -96.637 2.798 1.00 0.00 H +ATOM 179 CB THR 11 33.510 -94.718 2.474 1.00 0.00 C +ATOM 180 HB THR 11 33.754 -94.086 1.620 1.00 0.00 H +ATOM 181 CG2 THR 11 32.699 -93.853 3.374 1.00 0.00 C +ATOM 182 HG21 THR 11 32.495 -94.501 4.226 1.00 0.00 H +ATOM 183 HG22 THR 11 31.736 -93.569 2.951 1.00 0.00 H +ATOM 184 HG23 THR 11 33.276 -92.948 3.564 1.00 0.00 H +ATOM 185 OG1 THR 11 34.693 -95.118 3.129 1.00 0.00 O +ATOM 186 HG1 THR 11 34.364 -95.834 3.677 1.00 0.00 H +ATOM 187 C THR 11 31.302 -95.696 1.471 1.00 0.00 C +ATOM 188 O THR 11 30.365 -96.152 2.190 1.00 0.00 O +ATOM 189 N LEU 12 31.046 -95.044 0.310 1.00 0.00 N +ATOM 190 H LEU 12 31.815 -94.778 -0.289 1.00 0.00 H +ATOM 191 CA LEU 12 29.809 -94.867 -0.343 1.00 0.00 C +ATOM 192 HA LEU 12 29.023 -94.555 0.345 1.00 0.00 H +ATOM 193 CB LEU 12 29.934 -93.718 -1.389 1.00 0.00 C +ATOM 194 HB2 LEU 12 30.829 -93.916 -1.979 1.00 0.00 H +ATOM 195 HB3 LEU 12 29.095 -93.783 -2.081 1.00 0.00 H +ATOM 196 CG LEU 12 30.159 -92.204 -0.851 1.00 0.00 C +ATOM 197 HG LEU 12 31.084 -91.900 -0.360 1.00 0.00 H +ATOM 198 CD1 LEU 12 30.239 -91.267 -2.104 1.00 0.00 C +ATOM 199 HD11 LEU 12 31.101 -91.470 -2.740 1.00 0.00 H +ATOM 200 HD12 LEU 12 30.487 -90.241 -1.833 1.00 0.00 H +ATOM 201 HD13 LEU 12 29.279 -91.291 -2.619 1.00 0.00 H +ATOM 202 CD2 LEU 12 28.919 -91.800 -0.017 1.00 0.00 C +ATOM 203 HD21 LEU 12 28.092 -92.241 -0.573 1.00 0.00 H +ATOM 204 HD22 LEU 12 28.883 -90.713 -0.088 1.00 0.00 H +ATOM 205 HD23 LEU 12 28.975 -92.176 1.004 1.00 0.00 H +ATOM 206 C LEU 12 29.316 -96.081 -1.133 1.00 0.00 C +ATOM 207 O LEU 12 30.070 -96.628 -1.949 1.00 0.00 O +ATOM 208 N LYS 13 28.119 -96.581 -0.957 1.00 0.00 N +ATOM 209 H LYS 13 27.378 -96.113 -0.456 1.00 0.00 H +ATOM 210 CA LYS 13 27.651 -97.695 -1.808 1.00 0.00 C +ATOM 211 HA LYS 13 28.049 -97.513 -2.807 1.00 0.00 H +ATOM 212 CB LYS 13 28.272 -99.042 -1.379 1.00 0.00 C +ATOM 213 HB2 LYS 13 29.320 -99.070 -1.676 1.00 0.00 H +ATOM 214 HB3 LYS 13 28.141 -99.166 -0.304 1.00 0.00 H +ATOM 215 CG LYS 13 27.718-100.347 -2.084 1.00 0.00 C +ATOM 216 HG2 LYS 13 26.651-100.396 -1.871 1.00 0.00 H +ATOM 217 HG3 LYS 13 27.805-100.229 -3.164 1.00 0.00 H +ATOM 218 CD LYS 13 28.391-101.622 -1.661 1.00 0.00 C +ATOM 219 HD2 LYS 13 27.935-102.112 -0.801 1.00 0.00 H +ATOM 220 HD3 LYS 13 28.123-102.354 -2.423 1.00 0.00 H +ATOM 221 CE LYS 13 29.845-101.549 -1.662 1.00 0.00 C +ATOM 222 HE2 LYS 13 30.236-101.480 -2.677 1.00 0.00 H +ATOM 223 HE3 LYS 13 30.183-100.681 -1.096 1.00 0.00 H +ATOM 224 NZ LYS 13 30.357-102.712 -0.941 1.00 0.00 N +ATOM 225 HZ1 LYS 13 29.899-102.839 -0.049 1.00 0.00 H +ATOM 226 HZ2 LYS 13 31.307-102.614 -0.614 1.00 0.00 H +ATOM 227 HZ3 LYS 13 30.195-103.604 -1.387 1.00 0.00 H +ATOM 228 C LYS 13 26.128 -97.752 -1.904 1.00 0.00 C +ATOM 229 O LYS 13 25.519 -97.910 -0.832 1.00 0.00 O +ATOM 230 N GLY 14 25.488 -97.698 -3.083 1.00 0.00 N +ATOM 231 H GLY 14 25.998 -97.649 -3.954 1.00 0.00 H +ATOM 232 CA GLY 14 24.020 -97.691 -3.253 1.00 0.00 C +ATOM 233 HA2 GLY 14 23.786 -98.721 -3.522 1.00 0.00 H +ATOM 234 HA3 GLY 14 23.537 -97.600 -2.280 1.00 0.00 H +ATOM 235 C GLY 14 23.451 -96.682 -4.231 1.00 0.00 C +ATOM 236 O GLY 14 24.222 -96.336 -5.150 1.00 0.00 O +ATOM 237 N VAL 15 22.180 -96.208 -4.024 1.00 0.00 N +ATOM 238 H VAL 15 21.584 -96.411 -3.233 1.00 0.00 H +ATOM 239 CA VAL 15 21.604 -95.283 -4.991 1.00 0.00 C +ATOM 240 HA VAL 15 22.413 -94.920 -5.623 1.00 0.00 H +ATOM 241 CB VAL 15 20.792 -96.208 -5.936 1.00 0.00 C +ATOM 242 HB VAL 15 21.510 -96.839 -6.459 1.00 0.00 H +ATOM 243 CG1 VAL 15 19.681 -97.074 -5.438 1.00 0.00 C +ATOM 244 HG11 VAL 15 19.049 -96.601 -4.687 1.00 0.00 H +ATOM 245 HG12 VAL 15 18.991 -97.311 -6.248 1.00 0.00 H +ATOM 246 HG13 VAL 15 20.057 -97.993 -4.989 1.00 0.00 H +ATOM 247 CG2 VAL 15 20.249 -95.423 -7.131 1.00 0.00 C +ATOM 248 HG21 VAL 15 19.425 -94.810 -6.765 1.00 0.00 H +ATOM 249 HG22 VAL 15 21.020 -94.808 -7.594 1.00 0.00 H +ATOM 250 HG23 VAL 15 19.914 -96.222 -7.791 1.00 0.00 H +ATOM 251 C VAL 15 20.844 -94.134 -4.327 1.00 0.00 C +ATOM 252 O VAL 15 20.251 -94.318 -3.237 1.00 0.00 O +ATOM 253 N HD1 16 20.886 -92.953 -4.884 1.00 0.00 N +ATOM 254 CA HD1 16 20.006 -91.858 -4.473 1.00 0.00 C +ATOM 255 C HD1 16 19.569 -90.957 -5.644 1.00 0.00 C +ATOM 256 O HD1 16 19.819 -91.387 -6.740 1.00 0.00 O +ATOM 257 CB HD1 16 20.563 -90.960 -3.317 1.00 0.00 C +ATOM 258 CG HD1 16 21.874 -90.319 -3.617 1.00 0.00 C +ATOM 259 CD2 HD1 16 22.061 -89.268 -4.389 1.00 0.00 C +ATOM 260 ND1 HD1 16 23.131 -90.680 -3.120 1.00 0.00 N +ATOM 261 CE1 HD1 16 24.002 -89.851 -3.717 1.00 0.00 C +ATOM 262 NE2 HD1 16 23.438 -88.993 -4.553 1.00 0.00 N +ATOM 263 H HD1 16 21.469 -92.776 -5.689 1.00 0.00 H +ATOM 264 HA HD1 16 19.047 -92.248 -4.132 1.00 0.00 H +ATOM 265 HB2 HD1 16 19.849 -90.190 -3.025 1.00 0.00 H +ATOM 266 HB3 HD1 16 20.745 -91.570 -2.432 1.00 0.00 H +ATOM 267 HD1 HD1 16 23.372 -91.286 -2.348 1.00 0.00 H +ATOM 268 HD2 HD1 16 21.331 -88.694 -4.939 1.00 0.00 H +ATOM 269 HE1 HD1 16 25.060 -89.728 -3.536 1.00 0.00 H +ATOM 270 N THR 17 18.889 -89.801 -5.488 1.00 0.00 N +ATOM 271 H THR 17 18.701 -89.546 -4.529 1.00 0.00 H +ATOM 272 CA THR 17 18.294 -88.983 -6.625 1.00 0.00 C +ATOM 273 HA THR 17 18.823 -89.219 -7.548 1.00 0.00 H +ATOM 274 CB THR 17 16.825 -89.385 -6.837 1.00 0.00 C +ATOM 275 HB THR 17 16.243 -89.363 -5.915 1.00 0.00 H +ATOM 276 CG2 THR 17 16.108 -88.680 -7.994 1.00 0.00 C +ATOM 277 HG21 THR 17 15.070 -89.010 -8.043 1.00 0.00 H +ATOM 278 HG22 THR 17 16.656 -88.900 -8.910 1.00 0.00 H +ATOM 279 HG23 THR 17 16.002 -87.613 -7.797 1.00 0.00 H +ATOM 280 OG1 THR 17 16.932 -90.709 -7.118 1.00 0.00 O +ATOM 281 HG1 THR 17 16.141 -91.184 -6.853 1.00 0.00 H +ATOM 282 C THR 17 18.435 -87.505 -6.446 1.00 0.00 C +ATOM 283 O THR 17 18.361 -87.028 -5.321 1.00 0.00 O +ATOM 284 N HD2 18 18.704 -86.766 -7.500 1.00 0.00 N +ATOM 285 CA HD2 18 18.873 -85.326 -7.560 1.00 0.00 C +ATOM 286 C HD2 18 17.744 -84.793 -8.466 1.00 0.00 C +ATOM 287 O HD2 18 17.736 -85.086 -9.678 1.00 0.00 O +ATOM 288 CB HD2 18 20.257 -84.856 -8.107 1.00 0.00 C +ATOM 289 CG HD2 18 21.408 -85.206 -7.198 1.00 0.00 C +ATOM 290 CD2 HD2 18 22.271 -86.281 -7.407 1.00 0.00 C +ATOM 291 ND1 HD2 18 21.651 -84.741 -5.930 1.00 0.00 N +ATOM 292 CE1 HD2 18 22.567 -85.525 -5.343 1.00 0.00 C +ATOM 293 NE2 HD2 18 23.020 -86.415 -6.231 1.00 0.00 N +ATOM 294 H HD2 18 18.703 -87.307 -8.353 1.00 0.00 H +ATOM 295 HA HD2 18 18.677 -84.988 -6.542 1.00 0.00 H +ATOM 296 HB2 HD2 18 20.434 -85.313 -9.080 1.00 0.00 H +ATOM 297 HB3 HD2 18 20.307 -83.777 -8.249 1.00 0.00 H +ATOM 298 HD1 HD2 18 21.081 -84.054 -5.457 1.00 0.00 H +ATOM 299 HD2 HD2 18 22.172 -87.106 -8.096 1.00 0.00 H +ATOM 300 HE1 HD2 18 22.998 -85.359 -4.367 1.00 0.00 H +ATOM 301 N GLU 19 16.802 -84.018 -7.938 1.00 0.00 N +ATOM 302 H GLU 19 16.750 -83.908 -6.935 1.00 0.00 H +ATOM 303 CA GLU 19 15.959 -82.946 -8.677 1.00 0.00 C +ATOM 304 HA GLU 19 15.427 -83.440 -9.490 1.00 0.00 H +ATOM 305 CB GLU 19 14.805 -82.399 -7.821 1.00 0.00 C +ATOM 306 HB2 GLU 19 14.035 -83.168 -7.747 1.00 0.00 H +ATOM 307 HB3 GLU 19 15.181 -82.202 -6.817 1.00 0.00 H +ATOM 308 CG GLU 19 14.360 -80.991 -8.178 1.00 0.00 C +ATOM 309 HG2 GLU 19 13.821 -80.584 -7.323 1.00 0.00 H +ATOM 310 HG3 GLU 19 15.130 -80.221 -8.214 1.00 0.00 H +ATOM 311 CD GLU 19 13.389 -81.042 -9.346 1.00 0.00 C +ATOM 312 OE1 GLU 19 12.148 -81.250 -9.209 1.00 0.00 O +ATOM 313 OE2 GLU 19 13.926 -81.049 -10.520 1.00 0.00 O +ATOM 314 C GLU 19 16.941 -81.844 -9.307 1.00 0.00 C +ATOM 315 O GLU 19 17.639 -81.132 -8.606 1.00 0.00 O +ATOM 316 N ALA 20 16.883 -81.734 -10.640 1.00 0.00 N +ATOM 317 H ALA 20 16.443 -82.457 -11.191 1.00 0.00 H +ATOM 318 CA ALA 20 17.545 -80.700 -11.413 1.00 0.00 C +ATOM 319 HA ALA 20 17.513 -79.924 -10.648 1.00 0.00 H +ATOM 320 CB ALA 20 18.975 -81.049 -11.784 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.024 -81.969 -12.366 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.581 -81.187 -10.889 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.396 -80.299 -12.453 1.00 0.00 H +ATOM 324 C ALA 20 16.749 -80.283 -12.607 1.00 0.00 C +ATOM 325 O ALA 20 15.927 -81.106 -13.099 1.00 0.00 O +ATOM 326 N VAL 21 16.980 -79.095 -13.144 1.00 0.00 N +ATOM 327 H VAL 21 17.528 -78.396 -12.664 1.00 0.00 H +ATOM 328 CA VAL 21 16.330 -78.653 -14.380 1.00 0.00 C +ATOM 329 HA VAL 21 15.283 -78.926 -14.244 1.00 0.00 H +ATOM 330 CB VAL 21 16.391 -77.090 -14.565 1.00 0.00 C +ATOM 331 HB VAL 21 15.900 -76.619 -13.714 1.00 0.00 H +ATOM 332 CG1 VAL 21 17.855 -76.573 -14.659 1.00 0.00 C +ATOM 333 HG11 VAL 21 18.511 -76.828 -13.827 1.00 0.00 H +ATOM 334 HG12 VAL 21 17.805 -75.485 -14.640 1.00 0.00 H +ATOM 335 HG13 VAL 21 18.387 -76.796 -15.584 1.00 0.00 H +ATOM 336 CG2 VAL 21 15.685 -76.614 -15.876 1.00 0.00 C +ATOM 337 HG21 VAL 21 15.754 -75.540 -16.047 1.00 0.00 H +ATOM 338 HG22 VAL 21 14.638 -76.919 -15.872 1.00 0.00 H +ATOM 339 HG23 VAL 21 16.147 -77.200 -16.670 1.00 0.00 H +ATOM 340 C VAL 21 16.980 -79.463 -15.556 1.00 0.00 C +ATOM 341 O VAL 21 16.261 -79.888 -16.436 1.00 0.00 O +ATOM 342 N ASP 22 18.240 -79.826 -15.445 1.00 0.00 N +ATOM 343 H ASP 22 18.772 -79.382 -14.710 1.00 0.00 H +ATOM 344 CA ASP 22 19.129 -80.351 -16.531 1.00 0.00 C +ATOM 345 HA ASP 22 18.516 -80.927 -17.225 1.00 0.00 H +ATOM 346 CB ASP 22 19.747 -79.213 -17.316 1.00 0.00 C +ATOM 347 HB2 ASP 22 19.004 -78.526 -17.721 1.00 0.00 H +ATOM 348 HB3 ASP 22 20.392 -78.653 -16.639 1.00 0.00 H +ATOM 349 CG ASP 22 20.504 -79.537 -18.635 1.00 0.00 C +ATOM 350 OD1 ASP 22 20.241 -80.640 -19.198 1.00 0.00 O +ATOM 351 OD2 ASP 22 21.423 -78.793 -19.096 1.00 0.00 O +ATOM 352 C ASP 22 20.159 -81.318 -15.891 1.00 0.00 C +ATOM 353 O ASP 22 20.608 -81.062 -14.771 1.00 0.00 O +ATOM 354 N ALA 23 20.550 -82.323 -16.664 1.00 0.00 N +ATOM 355 H ALA 23 20.098 -82.486 -17.552 1.00 0.00 H +ATOM 356 CA ALA 23 21.692 -83.131 -16.246 1.00 0.00 C +ATOM 357 HA ALA 23 21.547 -83.553 -15.252 1.00 0.00 H +ATOM 358 CB ALA 23 21.845 -84.374 -17.178 1.00 0.00 C +ATOM 359 HB1 ALA 23 20.869 -84.859 -17.165 1.00 0.00 H +ATOM 360 HB2 ALA 23 22.675 -84.961 -16.783 1.00 0.00 H +ATOM 361 HB3 ALA 23 22.254 -84.179 -18.169 1.00 0.00 H +ATOM 362 C ALA 23 22.972 -82.381 -16.150 1.00 0.00 C +ATOM 363 O ALA 23 23.769 -82.750 -15.286 1.00 0.00 O +ATOM 364 N ALA 24 23.191 -81.259 -16.772 1.00 0.00 N +ATOM 365 H ALA 24 22.437 -80.843 -17.299 1.00 0.00 H +ATOM 366 CA ALA 24 24.437 -80.511 -16.616 1.00 0.00 C +ATOM 367 HA ALA 24 25.291 -81.184 -16.538 1.00 0.00 H +ATOM 368 CB ALA 24 24.680 -79.688 -17.851 1.00 0.00 C +ATOM 369 HB1 ALA 24 24.779 -80.355 -18.707 1.00 0.00 H +ATOM 370 HB2 ALA 24 25.649 -79.201 -17.742 1.00 0.00 H +ATOM 371 HB3 ALA 24 23.833 -79.018 -17.997 1.00 0.00 H +ATOM 372 C ALA 24 24.495 -79.774 -15.281 1.00 0.00 C +ATOM 373 O ALA 24 25.551 -79.682 -14.655 1.00 0.00 O +ATOM 374 N GLU 25 23.340 -79.344 -14.766 1.00 0.00 N +ATOM 375 H GLU 25 22.505 -79.535 -15.302 1.00 0.00 H +ATOM 376 CA GLU 25 23.258 -78.703 -13.501 1.00 0.00 C +ATOM 377 HA GLU 25 24.101 -78.013 -13.472 1.00 0.00 H +ATOM 378 CB GLU 25 21.922 -77.882 -13.373 1.00 0.00 C +ATOM 379 HB2 GLU 25 21.103 -78.494 -13.751 1.00 0.00 H +ATOM 380 HB3 GLU 25 21.882 -77.511 -12.349 1.00 0.00 H +ATOM 381 CG GLU 25 21.896 -76.565 -14.228 1.00 0.00 C +ATOM 382 HG2 GLU 25 21.871 -76.764 -15.300 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.976 -76.040 -13.971 1.00 0.00 H +ATOM 384 CD GLU 25 23.139 -75.688 -13.901 1.00 0.00 C +ATOM 385 OE1 GLU 25 23.566 -75.704 -12.718 1.00 0.00 O +ATOM 386 OE2 GLU 25 23.735 -75.004 -14.838 1.00 0.00 O +ATOM 387 C GLU 25 23.466 -79.680 -12.350 1.00 0.00 C +ATOM 388 O GLU 25 24.169 -79.349 -11.398 1.00 0.00 O +ATOM 389 N ALA 26 22.999 -80.945 -12.388 1.00 0.00 N +ATOM 390 H ALA 26 22.549 -81.236 -13.244 1.00 0.00 H +ATOM 391 CA ALA 26 23.369 -81.993 -11.454 1.00 0.00 C +ATOM 392 HA ALA 26 22.993 -81.611 -10.505 1.00 0.00 H +ATOM 393 CB ALA 26 22.442 -83.198 -11.750 1.00 0.00 C +ATOM 394 HB1 ALA 26 21.443 -83.009 -11.356 1.00 0.00 H +ATOM 395 HB2 ALA 26 22.856 -84.055 -11.217 1.00 0.00 H +ATOM 396 HB3 ALA 26 22.364 -83.489 -12.798 1.00 0.00 H +ATOM 397 C ALA 26 24.902 -82.220 -11.583 1.00 0.00 C +ATOM 398 O ALA 26 25.628 -82.263 -10.597 1.00 0.00 O +ATOM 399 N GLU 27 25.422 -82.506 -12.784 1.00 0.00 N +ATOM 400 H GLU 27 24.737 -82.674 -13.507 1.00 0.00 H +ATOM 401 CA GLU 27 26.794 -82.950 -12.894 1.00 0.00 C +ATOM 402 HA GLU 27 26.864 -83.799 -12.214 1.00 0.00 H +ATOM 403 CB GLU 27 27.161 -83.515 -14.294 1.00 0.00 C +ATOM 404 HB2 GLU 27 27.850 -84.358 -14.333 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.265 -83.924 -14.761 1.00 0.00 H +ATOM 406 CG GLU 27 27.615 -82.481 -15.199 1.00 0.00 C +ATOM 407 HG2 GLU 27 26.866 -81.690 -15.215 1.00 0.00 H +ATOM 408 HG3 GLU 27 28.512 -82.044 -14.760 1.00 0.00 H +ATOM 409 CD GLU 27 28.088 -82.922 -16.619 1.00 0.00 C +ATOM 410 OE1 GLU 27 28.851 -82.181 -17.298 1.00 0.00 O +ATOM 411 OE2 GLU 27 27.604 -84.019 -17.102 1.00 0.00 O +ATOM 412 C GLU 27 27.773 -81.847 -12.404 1.00 0.00 C +ATOM 413 O GLU 27 28.899 -82.076 -11.851 1.00 0.00 O +ATOM 414 N LYS 28 27.377 -80.569 -12.540 1.00 0.00 N +ATOM 415 H LYS 28 26.459 -80.474 -12.948 1.00 0.00 H +ATOM 416 CA LYS 28 28.021 -79.366 -12.053 1.00 0.00 C +ATOM 417 HA LYS 28 29.087 -79.517 -12.223 1.00 0.00 H +ATOM 418 CB LYS 28 27.510 -78.082 -12.812 1.00 0.00 C +ATOM 419 HB2 LYS 28 26.422 -78.121 -12.871 1.00 0.00 H +ATOM 420 HB3 LYS 28 27.705 -77.135 -12.308 1.00 0.00 H +ATOM 421 CG LYS 28 28.050 -77.938 -14.231 1.00 0.00 C +ATOM 422 HG2 LYS 28 29.131 -77.794 -14.213 1.00 0.00 H +ATOM 423 HG3 LYS 28 27.853 -78.861 -14.775 1.00 0.00 H +ATOM 424 CD LYS 28 27.405 -76.836 -15.041 1.00 0.00 C +ATOM 425 HD2 LYS 28 26.342 -77.055 -15.137 1.00 0.00 H +ATOM 426 HD3 LYS 28 27.517 -75.878 -14.534 1.00 0.00 H +ATOM 427 CE LYS 28 27.971 -76.773 -16.474 1.00 0.00 C +ATOM 428 HE2 LYS 28 29.005 -76.429 -16.440 1.00 0.00 H +ATOM 429 HE3 LYS 28 27.690 -77.658 -17.045 1.00 0.00 H +ATOM 430 NZ LYS 28 27.215 -75.776 -17.241 1.00 0.00 N +ATOM 431 HZ1 LYS 28 27.329 -74.885 -16.780 1.00 0.00 H +ATOM 432 HZ2 LYS 28 26.222 -75.940 -17.326 1.00 0.00 H +ATOM 433 HZ3 LYS 28 27.655 -75.685 -18.146 1.00 0.00 H +ATOM 434 C LYS 28 27.876 -79.178 -10.592 1.00 0.00 C +ATOM 435 O LYS 28 28.936 -79.038 -9.884 1.00 0.00 O +ATOM 436 N PHE 29 26.728 -79.475 -9.962 1.00 0.00 N +ATOM 437 H PHE 29 25.896 -79.739 -10.471 1.00 0.00 H +ATOM 438 CA PHE 29 26.505 -79.489 -8.523 1.00 0.00 C +ATOM 439 HA PHE 29 26.786 -78.478 -8.228 1.00 0.00 H +ATOM 440 CB PHE 29 25.017 -79.610 -8.304 1.00 0.00 C +ATOM 441 HB2 PHE 29 24.474 -78.740 -8.674 1.00 0.00 H +ATOM 442 HB3 PHE 29 24.593 -80.361 -8.970 1.00 0.00 H +ATOM 443 CG PHE 29 24.626 -79.880 -6.913 1.00 0.00 C +ATOM 444 CD1 PHE 29 24.848 -78.913 -5.887 1.00 0.00 C +ATOM 445 HD1 PHE 29 25.418 -78.016 -6.079 1.00 0.00 H +ATOM 446 CE1 PHE 29 24.350 -79.136 -4.606 1.00 0.00 C +ATOM 447 HE1 PHE 29 24.655 -78.439 -3.839 1.00 0.00 H +ATOM 448 CZ PHE 29 23.662 -80.373 -4.272 1.00 0.00 C +ATOM 449 HZ PHE 29 23.362 -80.528 -3.246 1.00 0.00 H +ATOM 450 CE2 PHE 29 23.592 -81.348 -5.256 1.00 0.00 C +ATOM 451 HE2 PHE 29 23.131 -82.249 -4.879 1.00 0.00 H +ATOM 452 CD2 PHE 29 23.995 -81.122 -6.578 1.00 0.00 C +ATOM 453 HD2 PHE 29 23.802 -81.863 -7.340 1.00 0.00 H +ATOM 454 C PHE 29 27.242 -80.681 -7.726 1.00 0.00 C +ATOM 455 O PHE 29 27.886 -80.422 -6.744 1.00 0.00 O +ATOM 456 N THR 30 27.255 -81.817 -8.361 1.00 0.00 N +ATOM 457 H THR 30 26.820 -81.805 -9.273 1.00 0.00 H +ATOM 458 CA THR 30 27.894 -83.032 -7.824 1.00 0.00 C +ATOM 459 HA THR 30 27.366 -83.384 -6.938 1.00 0.00 H +ATOM 460 CB THR 30 27.670 -84.175 -8.786 1.00 0.00 C +ATOM 461 HB THR 30 28.138 -83.943 -9.743 1.00 0.00 H +ATOM 462 CG2 THR 30 28.401 -85.404 -8.336 1.00 0.00 C +ATOM 463 HG21 THR 30 29.480 -85.417 -8.488 1.00 0.00 H +ATOM 464 HG22 THR 30 28.284 -85.551 -7.262 1.00 0.00 H +ATOM 465 HG23 THR 30 27.978 -86.254 -8.872 1.00 0.00 H +ATOM 466 OG1 THR 30 26.289 -84.359 -8.931 1.00 0.00 O +ATOM 467 HG1 THR 30 25.994 -83.736 -9.600 1.00 0.00 H +ATOM 468 C THR 30 29.334 -82.835 -7.619 1.00 0.00 C +ATOM 469 O THR 30 29.825 -83.145 -6.500 1.00 0.00 O +ATOM 470 N LYS 31 30.083 -82.429 -8.564 1.00 0.00 N +ATOM 471 H LYS 31 29.681 -82.228 -9.468 1.00 0.00 H +ATOM 472 CA LYS 31 31.529 -82.102 -8.388 1.00 0.00 C +ATOM 473 HA LYS 31 31.957 -82.940 -7.838 1.00 0.00 H +ATOM 474 CB LYS 31 32.179 -82.008 -9.752 1.00 0.00 C +ATOM 475 HB2 LYS 31 31.769 -81.134 -10.258 1.00 0.00 H +ATOM 476 HB3 LYS 31 33.268 -81.963 -9.749 1.00 0.00 H +ATOM 477 CG LYS 31 31.961 -83.319 -10.485 1.00 0.00 C +ATOM 478 HG2 LYS 31 32.251 -84.196 -9.907 1.00 0.00 H +ATOM 479 HG3 LYS 31 30.895 -83.456 -10.668 1.00 0.00 H +ATOM 480 CD LYS 31 32.721 -83.390 -11.821 1.00 0.00 C +ATOM 481 HD2 LYS 31 32.289 -82.623 -12.464 1.00 0.00 H +ATOM 482 HD3 LYS 31 33.802 -83.259 -11.785 1.00 0.00 H +ATOM 483 CE LYS 31 32.488 -84.760 -12.550 1.00 0.00 C +ATOM 484 HE2 LYS 31 33.033 -85.586 -12.093 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.446 -85.080 -12.517 1.00 0.00 H +ATOM 486 NZ LYS 31 32.807 -84.619 -14.015 1.00 0.00 N +ATOM 487 HZ1 LYS 31 33.664 -84.092 -14.103 1.00 0.00 H +ATOM 488 HZ2 LYS 31 32.006 -84.203 -14.468 1.00 0.00 H +ATOM 489 HZ3 LYS 31 33.057 -85.528 -14.375 1.00 0.00 H +ATOM 490 C LYS 31 31.882 -80.990 -7.447 1.00 0.00 C +ATOM 491 O LYS 31 32.906 -81.080 -6.846 1.00 0.00 O +ATOM 492 N ALA 32 31.013 -79.969 -7.410 1.00 0.00 N +ATOM 493 H ALA 32 30.121 -80.051 -7.877 1.00 0.00 H +ATOM 494 CA ALA 32 31.130 -78.841 -6.512 1.00 0.00 C +ATOM 495 HA ALA 32 32.119 -78.431 -6.717 1.00 0.00 H +ATOM 496 CB ALA 32 30.123 -77.705 -6.786 1.00 0.00 C +ATOM 497 HB1 ALA 32 30.226 -76.930 -6.026 1.00 0.00 H +ATOM 498 HB2 ALA 32 30.349 -77.281 -7.764 1.00 0.00 H +ATOM 499 HB3 ALA 32 29.150 -78.176 -6.928 1.00 0.00 H +ATOM 500 C ALA 32 30.843 -79.262 -5.059 1.00 0.00 C +ATOM 501 O ALA 32 31.645 -78.908 -4.226 1.00 0.00 O +ATOM 502 N ASP 33 29.905 -80.165 -4.788 1.00 0.00 N +ATOM 503 H ASP 33 29.336 -80.490 -5.557 1.00 0.00 H +ATOM 504 CA ASP 33 29.484 -80.583 -3.453 1.00 0.00 C +ATOM 505 HA ASP 33 29.310 -79.630 -2.952 1.00 0.00 H +ATOM 506 CB ASP 33 28.118 -81.275 -3.504 1.00 0.00 C +ATOM 507 HB2 ASP 33 27.490 -80.628 -4.116 1.00 0.00 H +ATOM 508 HB3 ASP 33 28.239 -82.208 -4.056 1.00 0.00 H +ATOM 509 CG ASP 33 27.496 -81.465 -2.095 1.00 0.00 C +ATOM 510 OD1 ASP 33 27.114 -82.637 -1.769 1.00 0.00 O +ATOM 511 OD2 ASP 33 27.502 -80.521 -1.257 1.00 0.00 O +ATOM 512 C ASP 33 30.653 -81.498 -2.896 1.00 0.00 C +ATOM 513 O ASP 33 31.077 -81.360 -1.774 1.00 0.00 O +ATOM 514 N ALA 34 31.136 -82.388 -3.774 1.00 0.00 N +ATOM 515 H ALA 34 30.710 -82.374 -4.690 1.00 0.00 H +ATOM 516 CA ALA 34 32.220 -83.316 -3.531 1.00 0.00 C +ATOM 517 HA ALA 34 32.016 -83.947 -2.666 1.00 0.00 H +ATOM 518 CB ALA 34 32.248 -84.281 -4.703 1.00 0.00 C +ATOM 519 HB1 ALA 34 31.414 -84.978 -4.622 1.00 0.00 H +ATOM 520 HB2 ALA 34 33.093 -84.969 -4.721 1.00 0.00 H +ATOM 521 HB3 ALA 34 32.312 -83.793 -5.675 1.00 0.00 H +ATOM 522 C ALA 34 33.481 -82.532 -3.312 1.00 0.00 C +ATOM 523 O ALA 34 34.071 -82.651 -2.223 1.00 0.00 O +ATOM 524 N ASN 35 33.890 -81.556 -4.112 1.00 0.00 N +ATOM 525 H ASN 35 33.434 -81.286 -4.971 1.00 0.00 H +ATOM 526 CA ASN 35 35.086 -80.786 -3.732 1.00 0.00 C +ATOM 527 HA ASN 35 35.895 -81.469 -3.471 1.00 0.00 H +ATOM 528 CB ASN 35 35.410 -79.939 -4.942 1.00 0.00 C +ATOM 529 HB2 ASN 35 35.345 -80.584 -5.818 1.00 0.00 H +ATOM 530 HB3 ASN 35 34.731 -79.086 -4.974 1.00 0.00 H +ATOM 531 CG ASN 35 36.853 -79.391 -4.872 1.00 0.00 C +ATOM 532 OD1 ASN 35 37.683 -79.612 -4.017 1.00 0.00 O +ATOM 533 ND2 ASN 35 37.058 -78.405 -5.722 1.00 0.00 N +ATOM 534 HD21 ASN 35 36.408 -78.202 -6.468 1.00 0.00 H +ATOM 535 HD22 ASN 35 37.924 -77.892 -5.643 1.00 0.00 H +ATOM 536 C ASN 35 34.851 -79.989 -2.394 1.00 0.00 C +ATOM 537 O ASN 35 35.818 -79.827 -1.600 1.00 0.00 O +ATOM 538 N ASP 36 33.653 -79.568 -1.999 1.00 0.00 N +ATOM 539 H ASP 36 32.931 -79.786 -2.671 1.00 0.00 H +ATOM 540 CA ASP 36 33.397 -78.972 -0.714 1.00 0.00 C +ATOM 541 HA ASP 36 34.195 -78.240 -0.590 1.00 0.00 H +ATOM 542 CB ASP 36 32.038 -78.343 -0.586 1.00 0.00 C +ATOM 543 HB2 ASP 36 32.006 -77.586 -1.370 1.00 0.00 H +ATOM 544 HB3 ASP 36 31.314 -79.117 -0.842 1.00 0.00 H +ATOM 545 CG ASP 36 31.623 -77.869 0.830 1.00 0.00 C +ATOM 546 OD1 ASP 36 32.422 -77.450 1.691 1.00 0.00 O +ATOM 547 OD2 ASP 36 30.421 -77.974 1.049 1.00 0.00 O +ATOM 548 C ASP 36 33.542 -80.037 0.448 1.00 0.00 C +ATOM 549 O ASP 36 34.196 -79.739 1.468 1.00 0.00 O +ATOM 550 N LYS 37 33.061 -81.289 0.249 1.00 0.00 N +ATOM 551 H LYS 37 32.646 -81.497 -0.648 1.00 0.00 H +ATOM 552 CA LYS 37 33.261 -82.468 1.091 1.00 0.00 C +ATOM 553 HA LYS 37 33.239 -82.167 2.138 1.00 0.00 H +ATOM 554 CB LYS 37 32.188 -83.515 0.813 1.00 0.00 C +ATOM 555 HB2 LYS 37 32.396 -84.383 1.438 1.00 0.00 H +ATOM 556 HB3 LYS 37 32.206 -83.854 -0.223 1.00 0.00 H +ATOM 557 CG LYS 37 30.818 -82.900 1.296 1.00 0.00 C +ATOM 558 HG2 LYS 37 30.636 -81.925 0.844 1.00 0.00 H +ATOM 559 HG3 LYS 37 30.923 -82.753 2.371 1.00 0.00 H +ATOM 560 CD LYS 37 29.516 -83.646 0.959 1.00 0.00 C +ATOM 561 HD2 LYS 37 29.478 -83.610 -0.130 1.00 0.00 H +ATOM 562 HD3 LYS 37 29.630 -84.709 1.172 1.00 0.00 H +ATOM 563 CE LYS 37 28.256 -83.089 1.636 1.00 0.00 C +ATOM 564 HE2 LYS 37 27.385 -83.616 1.247 1.00 0.00 H +ATOM 565 HE3 LYS 37 28.292 -83.184 2.722 1.00 0.00 H +ATOM 566 NZ LYS 37 27.982 -81.660 1.292 1.00 0.00 N +ATOM 567 HZ1 LYS 37 27.686 -81.530 0.335 1.00 0.00 H +ATOM 568 HZ2 LYS 37 27.277 -81.201 1.851 1.00 0.00 H +ATOM 569 HZ3 LYS 37 28.780 -81.054 1.423 1.00 0.00 H +ATOM 570 C LYS 37 34.681 -83.025 0.972 1.00 0.00 C +ATOM 571 O LYS 37 34.960 -84.026 1.622 1.00 0.00 O +ATOM 572 N GLY 38 35.609 -82.396 0.235 1.00 0.00 N +ATOM 573 H GLY 38 35.365 -81.526 -0.218 1.00 0.00 H +ATOM 574 CA GLY 38 37.010 -82.827 0.163 1.00 0.00 C +ATOM 575 HA2 GLY 38 37.613 -81.932 0.010 1.00 0.00 H +ATOM 576 HA3 GLY 38 37.298 -83.323 1.090 1.00 0.00 H +ATOM 577 C GLY 38 37.366 -83.924 -0.890 1.00 0.00 C +ATOM 578 O GLY 38 38.539 -84.224 -1.043 1.00 0.00 O +ATOM 579 N VAL 39 36.436 -84.450 -1.687 1.00 0.00 N +ATOM 580 H VAL 39 35.507 -84.064 -1.777 1.00 0.00 H +ATOM 581 CA VAL 39 36.647 -85.776 -2.369 1.00 0.00 C +ATOM 582 HA VAL 39 37.714 -85.992 -2.314 1.00 0.00 H +ATOM 583 CB VAL 39 35.922 -86.925 -1.707 1.00 0.00 C +ATOM 584 HB VAL 39 36.223 -87.876 -2.145 1.00 0.00 H +ATOM 585 CG1 VAL 39 36.288 -86.964 -0.252 1.00 0.00 C +ATOM 586 HG11 VAL 39 35.738 -87.795 0.189 1.00 0.00 H +ATOM 587 HG12 VAL 39 35.856 -86.134 0.307 1.00 0.00 H +ATOM 588 HG13 VAL 39 37.360 -87.146 -0.172 1.00 0.00 H +ATOM 589 CG2 VAL 39 34.387 -86.851 -1.724 1.00 0.00 C +ATOM 590 HG21 VAL 39 34.095 -86.785 -2.772 1.00 0.00 H +ATOM 591 HG22 VAL 39 34.114 -85.879 -1.313 1.00 0.00 H +ATOM 592 HG23 VAL 39 33.857 -87.654 -1.213 1.00 0.00 H +ATOM 593 C VAL 39 36.382 -85.670 -3.905 1.00 0.00 C +ATOM 594 O VAL 39 36.043 -84.594 -4.364 1.00 0.00 O +ATOM 595 N ASP 40 36.651 -86.709 -4.703 1.00 0.00 N +ATOM 596 H ASP 40 36.766 -87.591 -4.225 1.00 0.00 H +ATOM 597 CA ASP 40 36.673 -86.682 -6.172 1.00 0.00 C +ATOM 598 HA ASP 40 36.060 -85.940 -6.683 1.00 0.00 H +ATOM 599 CB ASP 40 38.187 -86.377 -6.533 1.00 0.00 C +ATOM 600 HB2 ASP 40 38.723 -85.687 -5.881 1.00 0.00 H +ATOM 601 HB3 ASP 40 38.813 -87.270 -6.509 1.00 0.00 H +ATOM 602 CG ASP 40 38.287 -85.701 -7.923 1.00 0.00 C +ATOM 603 OD1 ASP 40 39.331 -85.074 -8.135 1.00 0.00 O +ATOM 604 OD2 ASP 40 37.386 -85.931 -8.790 1.00 0.00 O +ATOM 605 C ASP 40 36.222 -88.108 -6.755 1.00 0.00 C +ATOM 606 O ASP 40 36.269 -89.127 -6.049 1.00 0.00 O +ATOM 607 N GLY 41 35.905 -88.165 -8.058 1.00 0.00 N +ATOM 608 H GLY 41 36.029 -87.320 -8.597 1.00 0.00 H +ATOM 609 CA GLY 41 35.637 -89.310 -8.896 1.00 0.00 C +ATOM 610 HA2 GLY 41 36.551 -89.885 -9.042 1.00 0.00 H +ATOM 611 HA3 GLY 41 34.825 -89.919 -8.500 1.00 0.00 H +ATOM 612 C GLY 41 35.124 -88.899 -10.323 1.00 0.00 C +ATOM 613 O GLY 41 35.372 -87.786 -10.795 1.00 0.00 O +ATOM 614 N GLU 42 34.342 -89.831 -10.990 1.00 0.00 N +ATOM 615 H GLU 42 34.022 -90.611 -10.433 1.00 0.00 H +ATOM 616 CA GLU 42 33.690 -89.564 -12.266 1.00 0.00 C +ATOM 617 HA GLU 42 33.420 -88.510 -12.322 1.00 0.00 H +ATOM 618 CB GLU 42 34.709 -89.754 -13.445 1.00 0.00 C +ATOM 619 HB2 GLU 42 35.604 -89.173 -13.225 1.00 0.00 H +ATOM 620 HB3 GLU 42 34.920 -90.814 -13.587 1.00 0.00 H +ATOM 621 CG GLU 42 34.144 -89.306 -14.826 1.00 0.00 C +ATOM 622 HG2 GLU 42 35.078 -89.298 -15.388 1.00 0.00 H +ATOM 623 HG3 GLU 42 33.327 -89.907 -15.226 1.00 0.00 H +ATOM 624 CD GLU 42 33.725 -87.861 -14.857 1.00 0.00 C +ATOM 625 OE1 GLU 42 32.684 -87.597 -14.358 1.00 0.00 O +ATOM 626 OE2 GLU 42 34.490 -86.929 -15.164 1.00 0.00 O +ATOM 627 C GLU 42 32.486 -90.478 -12.518 1.00 0.00 C +ATOM 628 O GLU 42 32.495 -91.665 -12.220 1.00 0.00 O +ATOM 629 N TRP 43 31.528 -89.889 -13.229 1.00 0.00 N +ATOM 630 H TRP 43 31.678 -88.919 -13.467 1.00 0.00 H +ATOM 631 CA TRP 43 30.219 -90.509 -13.500 1.00 0.00 C +ATOM 632 HA TRP 43 30.182 -91.547 -13.170 1.00 0.00 H +ATOM 633 CB TRP 43 29.093 -89.971 -12.607 1.00 0.00 C +ATOM 634 HB2 TRP 43 28.703 -88.979 -12.833 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.228 -90.617 -12.758 1.00 0.00 H +ATOM 636 CG TRP 43 29.393 -90.055 -11.161 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.156 -91.183 -10.373 1.00 0.00 C +ATOM 638 HD1 TRP 43 28.724 -92.093 -10.761 1.00 0.00 H +ATOM 639 NE1 TRP 43 29.479 -91.025 -9.040 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.448 -91.702 -8.291 1.00 0.00 H +ATOM 641 CE2 TRP 43 30.262 -89.887 -8.965 1.00 0.00 C +ATOM 642 CZ2 TRP 43 30.928 -89.297 -7.897 1.00 0.00 C +ATOM 643 HZ2 TRP 43 30.982 -89.842 -6.966 1.00 0.00 H +ATOM 644 CH2 TRP 43 31.636 -88.091 -8.018 1.00 0.00 C +ATOM 645 HH2 TRP 43 32.210 -87.709 -7.187 1.00 0.00 H +ATOM 646 CZ3 TRP 43 31.756 -87.507 -9.250 1.00 0.00 C +ATOM 647 HZ3 TRP 43 32.411 -86.650 -9.311 1.00 0.00 H +ATOM 648 CE3 TRP 43 31.006 -88.024 -10.330 1.00 0.00 C +ATOM 649 HE3 TRP 43 30.987 -87.534 -11.292 1.00 0.00 H +ATOM 650 CD2 TRP 43 30.240 -89.249 -10.241 1.00 0.00 C +ATOM 651 C TRP 43 29.827 -90.472 -15.002 1.00 0.00 C +ATOM 652 O TRP 43 30.334 -89.551 -15.662 1.00 0.00 O +ATOM 653 N THR 44 28.979 -91.338 -15.535 1.00 0.00 N +ATOM 654 H THR 44 28.545 -91.981 -14.888 1.00 0.00 H +ATOM 655 CA THR 44 28.411 -91.245 -16.845 1.00 0.00 C +ATOM 656 HA THR 44 28.581 -90.238 -17.225 1.00 0.00 H +ATOM 657 CB THR 44 29.099 -92.286 -17.720 1.00 0.00 C +ATOM 658 HB THR 44 30.128 -91.930 -17.776 1.00 0.00 H +ATOM 659 CG2 THR 44 29.095 -93.729 -17.318 1.00 0.00 C +ATOM 660 HG21 THR 44 29.848 -94.308 -17.854 1.00 0.00 H +ATOM 661 HG22 THR 44 28.147 -94.199 -17.580 1.00 0.00 H +ATOM 662 HG23 THR 44 29.293 -93.723 -16.246 1.00 0.00 H +ATOM 663 OG1 THR 44 28.684 -92.321 -19.078 1.00 0.00 O +ATOM 664 HG1 THR 44 28.881 -91.492 -19.521 1.00 0.00 H +ATOM 665 C THR 44 26.877 -91.380 -16.794 1.00 0.00 C +ATOM 666 O THR 44 26.285 -92.166 -15.992 1.00 0.00 O +ATOM 667 N TYR 45 26.141 -90.623 -17.624 1.00 0.00 N +ATOM 668 H TYR 45 26.651 -90.057 -18.288 1.00 0.00 H +ATOM 669 CA TYR 45 24.661 -90.390 -17.675 1.00 0.00 C +ATOM 670 HA TYR 45 24.239 -90.467 -16.673 1.00 0.00 H +ATOM 671 CB TYR 45 24.453 -88.934 -17.941 1.00 0.00 C +ATOM 672 HB2 TYR 45 25.059 -88.424 -17.192 1.00 0.00 H +ATOM 673 HB3 TYR 45 24.894 -88.675 -18.904 1.00 0.00 H +ATOM 674 CG TYR 45 23.063 -88.453 -17.902 1.00 0.00 C +ATOM 675 CD1 TYR 45 22.231 -88.765 -16.752 1.00 0.00 C +ATOM 676 HD1 TYR 45 22.669 -88.978 -15.788 1.00 0.00 H +ATOM 677 CE1 TYR 45 20.827 -88.516 -16.805 1.00 0.00 C +ATOM 678 HE1 TYR 45 20.214 -88.832 -15.974 1.00 0.00 H +ATOM 679 CZ TYR 45 20.218 -88.001 -17.971 1.00 0.00 C +ATOM 680 OH TYR 45 18.899 -87.821 -18.108 1.00 0.00 O +ATOM 681 HH TYR 45 18.702 -87.629 -19.028 1.00 0.00 H +ATOM 682 CE2 TYR 45 21.027 -87.737 -19.087 1.00 0.00 C +ATOM 683 HE2 TYR 45 20.647 -87.280 -19.989 1.00 0.00 H +ATOM 684 CD2 TYR 45 22.413 -87.941 -19.032 1.00 0.00 C +ATOM 685 HD2 TYR 45 23.000 -87.624 -19.881 1.00 0.00 H +ATOM 686 C TYR 45 23.947 -91.452 -18.650 1.00 0.00 C +ATOM 687 O TYR 45 24.444 -91.850 -19.711 1.00 0.00 O +ATOM 688 N ASP 46 22.707 -91.796 -18.343 1.00 0.00 N +ATOM 689 H ASP 46 22.336 -91.401 -17.490 1.00 0.00 H +ATOM 690 CA ASP 46 21.712 -92.586 -19.152 1.00 0.00 C +ATOM 691 HA ASP 46 22.182 -92.798 -20.112 1.00 0.00 H +ATOM 692 CB ASP 46 21.514 -93.914 -18.490 1.00 0.00 C +ATOM 693 HB2 ASP 46 22.440 -94.489 -18.484 1.00 0.00 H +ATOM 694 HB3 ASP 46 21.095 -93.770 -17.494 1.00 0.00 H +ATOM 695 CG ASP 46 20.430 -94.728 -19.296 1.00 0.00 C +ATOM 696 OD1 ASP 46 19.747 -95.645 -18.741 1.00 0.00 O +ATOM 697 OD2 ASP 46 20.358 -94.604 -20.518 1.00 0.00 O +ATOM 698 C ASP 46 20.357 -91.779 -19.356 1.00 0.00 C +ATOM 699 O ASP 46 19.587 -91.778 -18.400 1.00 0.00 O +ATOM 700 N ASP 47 20.075 -91.074 -20.472 1.00 0.00 N +ATOM 701 H ASP 47 20.830 -91.031 -21.141 1.00 0.00 H +ATOM 702 CA ASP 47 18.878 -90.271 -20.775 1.00 0.00 C +ATOM 703 HA ASP 47 18.749 -89.740 -19.831 1.00 0.00 H +ATOM 704 CB ASP 47 19.250 -89.309 -21.899 1.00 0.00 C +ATOM 705 HB2 ASP 47 20.263 -89.013 -21.628 1.00 0.00 H +ATOM 706 HB3 ASP 47 19.423 -89.752 -22.880 1.00 0.00 H +ATOM 707 CG ASP 47 18.363 -88.080 -21.762 1.00 0.00 C +ATOM 708 OD1 ASP 47 18.028 -87.593 -20.647 1.00 0.00 O +ATOM 709 OD2 ASP 47 18.041 -87.575 -22.877 1.00 0.00 O +ATOM 710 C ASP 47 17.584 -91.076 -20.998 1.00 0.00 C +ATOM 711 O ASP 47 16.484 -90.560 -21.011 1.00 0.00 O +ATOM 712 N ALA 48 17.764 -92.373 -21.164 1.00 0.00 N +ATOM 713 H ALA 48 18.698 -92.718 -21.336 1.00 0.00 H +ATOM 714 CA ALA 48 16.696 -93.333 -21.310 1.00 0.00 C +ATOM 715 HA ALA 48 15.944 -92.943 -21.995 1.00 0.00 H +ATOM 716 CB ALA 48 17.298 -94.557 -22.044 1.00 0.00 C +ATOM 717 HB1 ALA 48 17.995 -95.038 -21.358 1.00 0.00 H +ATOM 718 HB2 ALA 48 17.826 -94.129 -22.897 1.00 0.00 H +ATOM 719 HB3 ALA 48 16.499 -95.248 -22.312 1.00 0.00 H +ATOM 720 C ALA 48 16.080 -93.541 -19.924 1.00 0.00 C +ATOM 721 O ALA 48 14.924 -93.143 -19.728 1.00 0.00 O +ATOM 722 N THR 49 16.863 -93.976 -18.918 1.00 0.00 N +ATOM 723 H THR 49 17.798 -94.327 -19.070 1.00 0.00 H +ATOM 724 CA THR 49 16.362 -94.202 -17.562 1.00 0.00 C +ATOM 725 HA THR 49 15.294 -94.404 -17.642 1.00 0.00 H +ATOM 726 CB THR 49 17.103 -95.252 -16.710 1.00 0.00 C +ATOM 727 HB THR 49 16.747 -95.229 -15.681 1.00 0.00 H +ATOM 728 CG2 THR 49 16.977 -96.709 -17.206 1.00 0.00 C +ATOM 729 HG21 THR 49 17.914 -97.265 -17.206 1.00 0.00 H +ATOM 730 HG22 THR 49 16.660 -96.800 -18.245 1.00 0.00 H +ATOM 731 HG23 THR 49 16.179 -97.115 -16.583 1.00 0.00 H +ATOM 732 OG1 THR 49 18.426 -95.017 -16.532 1.00 0.00 O +ATOM 733 HG1 THR 49 18.856 -95.306 -17.340 1.00 0.00 H +ATOM 734 C THR 49 16.410 -92.922 -16.659 1.00 0.00 C +ATOM 735 O THR 49 15.827 -92.962 -15.581 1.00 0.00 O +ATOM 736 N LYS 50 17.123 -91.860 -17.063 1.00 0.00 N +ATOM 737 H LYS 50 17.699 -91.951 -17.888 1.00 0.00 H +ATOM 738 CA LYS 50 17.547 -90.734 -16.307 1.00 0.00 C +ATOM 739 HA LYS 50 18.097 -90.129 -17.027 1.00 0.00 H +ATOM 740 CB LYS 50 16.282 -89.938 -15.872 1.00 0.00 C +ATOM 741 HB2 LYS 50 15.666 -90.475 -15.151 1.00 0.00 H +ATOM 742 HB3 LYS 50 16.507 -89.033 -15.306 1.00 0.00 H +ATOM 743 CG LYS 50 15.263 -89.616 -16.975 1.00 0.00 C +ATOM 744 HG2 LYS 50 14.962 -90.559 -17.431 1.00 0.00 H +ATOM 745 HG3 LYS 50 14.439 -89.051 -16.537 1.00 0.00 H +ATOM 746 CD LYS 50 15.737 -88.656 -18.078 1.00 0.00 C +ATOM 747 HD2 LYS 50 15.842 -87.655 -17.658 1.00 0.00 H +ATOM 748 HD3 LYS 50 16.714 -89.006 -18.411 1.00 0.00 H +ATOM 749 CE LYS 50 14.807 -88.585 -19.270 1.00 0.00 C +ATOM 750 HE2 LYS 50 14.863 -89.469 -19.906 1.00 0.00 H +ATOM 751 HE3 LYS 50 13.811 -88.509 -18.834 1.00 0.00 H +ATOM 752 NZ LYS 50 15.069 -87.325 -19.942 1.00 0.00 N +ATOM 753 HZ1 LYS 50 14.950 -86.477 -19.405 1.00 0.00 H +ATOM 754 HZ2 LYS 50 14.484 -87.184 -20.753 1.00 0.00 H +ATOM 755 HZ3 LYS 50 16.009 -87.316 -20.311 1.00 0.00 H +ATOM 756 C LYS 50 18.534 -91.002 -15.206 1.00 0.00 C +ATOM 757 O LYS 50 18.233 -90.612 -14.098 1.00 0.00 O +ATOM 758 N THR 51 19.676 -91.665 -15.380 1.00 0.00 N +ATOM 759 H THR 51 20.035 -91.797 -16.315 1.00 0.00 H +ATOM 760 CA THR 51 20.500 -92.209 -14.276 1.00 0.00 C +ATOM 761 HA THR 51 20.178 -91.888 -13.285 1.00 0.00 H +ATOM 762 CB THR 51 20.264 -93.739 -14.213 1.00 0.00 C +ATOM 763 HB THR 51 20.565 -94.192 -15.158 1.00 0.00 H +ATOM 764 CG2 THR 51 20.965 -94.370 -12.972 1.00 0.00 C +ATOM 765 HG21 THR 51 20.704 -93.888 -12.030 1.00 0.00 H +ATOM 766 HG22 THR 51 22.050 -94.331 -13.072 1.00 0.00 H +ATOM 767 HG23 THR 51 20.708 -95.422 -12.843 1.00 0.00 H +ATOM 768 OG1 THR 51 18.966 -94.007 -14.002 1.00 0.00 O +ATOM 769 HG1 THR 51 18.734 -94.463 -14.814 1.00 0.00 H +ATOM 770 C THR 51 22.049 -91.917 -14.464 1.00 0.00 C +ATOM 771 O THR 51 22.594 -92.119 -15.565 1.00 0.00 O +ATOM 772 N PHE 52 22.666 -91.429 -13.388 1.00 0.00 N +ATOM 773 H PHE 52 22.142 -91.400 -12.526 1.00 0.00 H +ATOM 774 CA PHE 52 24.140 -91.318 -13.353 1.00 0.00 C +ATOM 775 HA PHE 52 24.514 -91.192 -14.369 1.00 0.00 H +ATOM 776 CB PHE 52 24.442 -90.043 -12.551 1.00 0.00 C +ATOM 777 HB2 PHE 52 23.910 -89.975 -11.603 1.00 0.00 H +ATOM 778 HB3 PHE 52 25.492 -90.086 -12.261 1.00 0.00 H +ATOM 779 CG PHE 52 24.238 -88.694 -13.231 1.00 0.00 C +ATOM 780 CD1 PHE 52 22.995 -87.965 -13.129 1.00 0.00 C +ATOM 781 HD1 PHE 52 22.221 -88.445 -12.548 1.00 0.00 H +ATOM 782 CE1 PHE 52 22.803 -86.730 -13.818 1.00 0.00 C +ATOM 783 HE1 PHE 52 21.864 -86.197 -13.769 1.00 0.00 H +ATOM 784 CZ PHE 52 23.891 -86.168 -14.518 1.00 0.00 C +ATOM 785 HZ PHE 52 23.745 -85.162 -14.883 1.00 0.00 H +ATOM 786 CE2 PHE 52 25.094 -86.894 -14.670 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.932 -86.532 -15.248 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.275 -88.092 -13.913 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.201 -88.635 -14.034 1.00 0.00 H +ATOM 790 C PHE 52 24.674 -92.647 -12.729 1.00 0.00 C +ATOM 791 O PHE 52 24.358 -92.883 -11.542 1.00 0.00 O +ATOM 792 N THR 53 25.689 -93.234 -13.338 1.00 0.00 N +ATOM 793 H THR 53 25.922 -92.885 -14.256 1.00 0.00 H +ATOM 794 CA THR 53 26.454 -94.409 -12.892 1.00 0.00 C +ATOM 795 HA THR 53 26.055 -94.679 -11.914 1.00 0.00 H +ATOM 796 CB THR 53 26.177 -95.740 -13.674 1.00 0.00 C +ATOM 797 HB THR 53 26.623 -95.583 -14.656 1.00 0.00 H +ATOM 798 CG2 THR 53 26.860 -96.974 -13.095 1.00 0.00 C +ATOM 799 HG21 THR 53 26.487 -97.872 -13.588 1.00 0.00 H +ATOM 800 HG22 THR 53 26.545 -97.220 -12.081 1.00 0.00 H +ATOM 801 HG23 THR 53 27.926 -96.923 -13.316 1.00 0.00 H +ATOM 802 OG1 THR 53 24.882 -96.001 -13.827 1.00 0.00 O +ATOM 803 HG1 THR 53 24.559 -95.359 -14.463 1.00 0.00 H +ATOM 804 C THR 53 27.875 -94.080 -12.719 1.00 0.00 C +ATOM 805 O THR 53 28.439 -93.470 -13.607 1.00 0.00 O +ATOM 806 N VAL 54 28.467 -94.481 -11.568 1.00 0.00 N +ATOM 807 H VAL 54 27.950 -94.786 -10.755 1.00 0.00 H +ATOM 808 CA VAL 54 29.899 -94.341 -11.486 1.00 0.00 C +ATOM 809 HA VAL 54 30.049 -93.286 -11.717 1.00 0.00 H +ATOM 810 CB VAL 54 30.381 -94.643 -10.034 1.00 0.00 C +ATOM 811 HB VAL 54 29.691 -94.179 -9.330 1.00 0.00 H +ATOM 812 CG1 VAL 54 30.430 -96.109 -9.587 1.00 0.00 C +ATOM 813 HG11 VAL 54 30.752 -96.085 -8.546 1.00 0.00 H +ATOM 814 HG12 VAL 54 31.242 -96.629 -10.096 1.00 0.00 H +ATOM 815 HG13 VAL 54 29.464 -96.613 -9.587 1.00 0.00 H +ATOM 816 CG2 VAL 54 31.651 -93.871 -9.757 1.00 0.00 C +ATOM 817 HG21 VAL 54 32.512 -94.179 -10.350 1.00 0.00 H +ATOM 818 HG22 VAL 54 31.900 -93.996 -8.704 1.00 0.00 H +ATOM 819 HG23 VAL 54 31.597 -92.794 -9.915 1.00 0.00 H +ATOM 820 C VAL 54 30.695 -95.048 -12.558 1.00 0.00 C +ATOM 821 O VAL 54 30.354 -96.187 -12.866 1.00 0.00 O +ATOM 822 N THR 55 31.698 -94.425 -13.200 1.00 0.00 N +ATOM 823 H THR 55 31.831 -93.445 -12.993 1.00 0.00 H +ATOM 824 CA THR 55 32.628 -95.087 -14.124 1.00 0.00 C +ATOM 825 HA THR 55 32.096 -95.618 -14.913 1.00 0.00 H +ATOM 826 CB THR 55 33.498 -94.104 -14.896 1.00 0.00 C +ATOM 827 HB THR 55 34.112 -94.637 -15.622 1.00 0.00 H +ATOM 828 CG2 THR 55 32.532 -93.094 -15.604 1.00 0.00 C +ATOM 829 HG21 THR 55 31.859 -93.605 -16.293 1.00 0.00 H +ATOM 830 HG22 THR 55 33.239 -92.519 -16.202 1.00 0.00 H +ATOM 831 HG23 THR 55 32.010 -92.428 -14.916 1.00 0.00 H +ATOM 832 OG1 THR 55 34.408 -93.395 -14.089 1.00 0.00 O +ATOM 833 HG1 THR 55 33.804 -92.942 -13.496 1.00 0.00 H +ATOM 834 C THR 55 33.497 -95.981 -13.302 1.00 0.00 C +ATOM 835 O THR 55 33.890 -95.598 -12.188 1.00 0.00 O +ATOM 836 N GLU 56 33.755 -97.176 -13.767 1.00 0.00 N +ATOM 837 H GLU 56 33.343 -97.456 -14.645 1.00 0.00 H +ATOM 838 CA GLU 56 34.621 -98.221 -13.079 1.00 0.00 C +ATOM 839 HA GLU 56 35.316 -97.832 -12.335 1.00 0.00 H +ATOM 840 CB GLU 56 33.719 -99.263 -12.420 1.00 0.00 C +ATOM 841 HB2 GLU 56 33.113 -98.713 -11.701 1.00 0.00 H +ATOM 842 HB3 GLU 56 33.048 -99.783 -13.103 1.00 0.00 H +ATOM 843 CG GLU 56 34.533-100.266 -11.656 1.00 0.00 C +ATOM 844 HG2 GLU 56 33.914-101.059 -11.236 1.00 0.00 H +ATOM 845 HG3 GLU 56 35.187-100.829 -12.322 1.00 0.00 H +ATOM 846 CD GLU 56 35.410 -99.685 -10.463 1.00 0.00 C +ATOM 847 OE1 GLU 56 34.806 -98.970 -9.573 1.00 0.00 O +ATOM 848 OE2 GLU 56 36.645 -99.943 -10.491 1.00 0.00 O +ATOM 849 C GLU 56 35.461 -98.765 -14.136 1.00 0.00 C +ATOM 850 O GLU 56 34.871 -99.177 -15.187 1.00 0.00 O +ATOM 851 OXT GLU 56 36.719 -98.821 -14.039 1.00 0.00 O +ATOM 852 ZN ZN1 57 24.217 -87.896 -5.966 1.00 0.00 ZN +ATOM 853 N AN1 58 25.801 -86.974 -4.960 1.00 0.00 N +ATOM 854 C AN1 58 28.059 -85.994 -4.192 1.00 0.00 C +ATOM 855 C1 AN1 58 26.802 -86.540 -4.575 1.00 0.00 C +ATOM 856 H AN1 58 28.871 -86.419 -4.794 1.00 0.00 H +ATOM 857 H1 AN1 58 28.363 -86.440 -3.237 1.00 0.00 H +ATOM 858 H2 AN1 58 28.180 -84.904 -4.221 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 20.392 -87.396 -1.895 1.00 0.00 N +ATOM 860 N2 AZI 59 21.476 -86.802 -1.843 1.00 0.00 N +ATOM 861 N3 AZI 59 22.557 -86.184 -1.654 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/inp/readme.rst b/tests/nsga2/inp/readme.rst new file mode 100644 index 0000000..e2956be --- /dev/null +++ b/tests/nsga2/inp/readme.rst @@ -0,0 +1,23 @@ +| **Creation date:** 2019-03-15 +| **Metadata type:** Calculation +| **Subject:** Biochemistry +| **Project title:** Gb1 +| **Author:** Simon Duerr +| **Email:** simon.durr@epfl.ch # configuration file for create_metadata.py + + +GENERAL DESCRIPTION +=================== + +The rotamer library uses the same residue names as the residues from the MCPB + +I changed my parameters from HE1, HD1, HD2 to HX1, HY1, HY2 + +The following files were changed: +All mol2 files + + +the input pdb files + +the leap.in file (Bond commands!!) + diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_1.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_1.pdb new file mode 100644 index 0000000..323a1dd --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_1.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.2933 51.061666666666724 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.971 23.610 1.00 0.00 N +ATOM 2 H1 MET 1 15.141 38.355 24.553 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.345 23.090 1.00 0.00 H +ATOM 4 H3 MET 1 16.014 38.281 23.181 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.500 23.668 1.00 0.00 C +ATOM 6 HA MET 1 14.171 36.197 24.096 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.872 22.269 1.00 0.00 C +ATOM 8 HB2 MET 1 14.392 36.151 21.668 1.00 0.00 H +ATOM 9 HB3 MET 1 16.153 36.270 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.371 34.332 22.296 1.00 0.00 C +ATOM 11 HG2 MET 1 16.259 34.062 22.867 1.00 0.00 H +ATOM 12 HG3 MET 1 14.494 33.923 22.804 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.525 20.666 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.569 20.066 1.00 0.00 C +ATOM 15 HE1 MET 1 13.461 34.598 20.015 1.00 0.00 H +ATOM 16 HE2 MET 1 13.777 33.132 19.069 1.00 0.00 H +ATOM 17 HE3 MET 1 13.174 32.990 20.731 1.00 0.00 H +ATOM 18 C MET 1 16.221 36.029 24.598 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.397 24.423 1.00 0.00 O +ATOM 20 N GLN 2 15.881 35.189 25.579 1.00 0.00 N +ATOM 21 H GLN 2 14.910 34.997 25.765 1.00 0.00 H +ATOM 22 CA GLN 2 16.846 34.478 26.432 1.00 0.00 C +ATOM 23 HA GLN 2 17.652 35.157 26.726 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.071 27.724 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.138 33.651 27.491 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.661 33.315 28.273 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.253 28.685 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.470 36.090 28.162 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.203 34.972 29.417 1.00 0.00 H +ATOM 30 CD GLN 2 17.129 35.580 29.526 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.165 34.936 29.493 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.030 36.469 30.482 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.772 36.536 31.098 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.109 36.733 30.768 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.304 25.672 1.00 0.00 C +ATOM 36 O GLN 2 17.100 32.148 25.833 1.00 0.00 O +ATOM 37 N TYR 3 18.476 33.620 24.822 1.00 0.00 N +ATOM 38 H TYR 3 18.753 34.594 24.753 1.00 0.00 H +ATOM 39 CA TYR 3 19.257 32.618 24.101 1.00 0.00 C +ATOM 40 HA TYR 3 18.571 31.963 23.563 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.286 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.865 33.945 23.646 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.482 22.671 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.069 21.936 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.528 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.821 32.423 20.552 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.146 34.202 19.540 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.115 33.734 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.845 35.572 19.674 1.00 0.00 C +ATOM 50 OH TYR 3 18.515 36.305 18.581 1.00 0.00 O +ATOM 51 HH TYR 3 18.774 35.870 17.765 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.190 20.937 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.729 37.250 21.020 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.323 35.442 22.065 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.447 35.936 23.020 1.00 0.00 H +ATOM 56 C TYR 3 20.090 31.765 25.077 1.00 0.00 C +ATOM 57 O TYR 3 20.462 32.246 26.149 1.00 0.00 O +ATOM 58 N LYS 4 20.401 30.506 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.251 30.222 23.770 1.00 0.00 H +ATOM 60 CA LYS 4 21.012 29.502 25.631 1.00 0.00 C +ATOM 61 HA LYS 4 20.728 29.716 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.477 28.101 25.270 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.521 27.983 24.189 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.144 27.345 25.695 1.00 0.00 H +ATOM 65 CG LYS 4 19.051 27.747 25.735 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.886 26.697 25.494 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.996 27.852 26.817 1.00 0.00 H +ATOM 68 CD LYS 4 17.924 28.566 25.082 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.889 29.561 25.522 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.146 28.677 24.019 1.00 0.00 H +ATOM 71 CE LYS 4 16.545 27.894 25.197 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.511 24.666 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.594 26.934 24.678 1.00 0.00 H +ATOM 74 NZ LYS 4 16.096 27.673 26.597 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.986 28.550 27.087 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.208 27.171 26.603 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.759 27.086 27.088 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.617 1.00 0.00 C +ATOM 79 O LYS 4 23.197 29.888 24.646 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.028 26.694 1.00 0.00 N +HETATM 81 CA HX1 5 24.626 28.831 26.818 1.00 0.00 C +HETATM 82 C HX1 5 24.900 27.673 27.781 1.00 0.00 C +HETATM 83 O HX1 5 24.403 27.682 28.908 1.00 0.00 O +HETATM 84 CB HX1 5 25.263 30.145 27.305 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.390 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.070 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.386 27.859 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.096 27.752 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.937 29.837 27.334 1.00 0.00 N +HETATM 90 H HX1 5 22.597 28.839 27.518 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.840 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.382 28.291 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.939 30.946 26.638 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.281 26.698 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.530 31.749 28.082 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.838 29.357 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.635 26.658 27.325 1.00 0.00 N +ATOM 98 H ILE 6 26.017 26.713 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.005 25.472 28.115 1.00 0.00 C +ATOM 100 HA ILE 6 25.305 25.371 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.849 24.199 27.245 1.00 0.00 C +ATOM 102 HB ILE 6 26.399 24.347 26.315 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.407 22.939 27.933 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.891 22.758 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.284 22.071 27.286 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.479 23.047 28.114 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.343 24.015 26.915 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.790 23.879 27.844 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.966 24.918 26.434 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.005 22.849 25.979 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.173 21.896 26.480 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.950 22.908 25.704 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.610 22.906 25.075 1.00 0.00 H +ATOM 114 C ILE 6 27.394 25.667 28.753 1.00 0.00 C +ATOM 115 O ILE 6 28.229 26.397 28.221 1.00 0.00 O +ATOM 116 N VAL 7 27.601 25.080 29.936 1.00 0.00 N +ATOM 117 H VAL 7 26.870 24.477 30.295 1.00 0.00 H +ATOM 118 CA VAL 7 28.779 25.286 30.801 1.00 0.00 C +ATOM 119 HA VAL 7 28.879 26.361 30.956 1.00 0.00 H +ATOM 120 CB VAL 7 28.501 24.640 32.176 1.00 0.00 C +ATOM 121 HB VAL 7 27.502 24.948 32.483 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.525 23.106 32.131 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.535 22.744 31.923 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.192 22.714 33.086 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.858 22.745 31.347 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.450 25.110 33.283 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.290 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.078 24.777 34.249 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.448 24.701 33.140 1.00 0.00 H +ATOM 130 C VAL 7 30.113 24.804 30.200 1.00 0.00 C +ATOM 131 O VAL 7 30.155 23.918 29.349 1.00 0.00 O +ATOM 132 N THR 8 31.216 25.379 30.688 1.00 0.00 N +ATOM 133 H THR 8 31.111 26.090 31.396 1.00 0.00 H +ATOM 134 CA THR 8 32.599 24.973 30.394 1.00 0.00 C +ATOM 135 HA THR 8 32.693 24.829 29.317 1.00 0.00 H +ATOM 136 CB THR 8 33.573 26.088 30.820 1.00 0.00 C +ATOM 137 HB THR 8 34.598 25.756 30.643 1.00 0.00 H +ATOM 138 CG2 THR 8 33.360 27.395 30.062 1.00 0.00 C +ATOM 139 HG21 THR 8 32.387 27.825 30.304 1.00 0.00 H +ATOM 140 HG22 THR 8 34.136 28.111 30.331 1.00 0.00 H +ATOM 141 HG23 THR 8 33.406 27.215 28.989 1.00 0.00 H +ATOM 142 OG1 THR 8 33.423 26.394 32.187 1.00 0.00 O +ATOM 143 HG1 THR 8 33.805 27.264 32.325 1.00 0.00 H +ATOM 144 C THR 8 33.011 23.656 31.078 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.249 32.104 1.00 0.00 O +ATOM 146 N GLY 9 34.050 23.008 30.534 1.00 0.00 N +ATOM 147 H GLY 9 34.405 23.337 29.651 1.00 0.00 H +ATOM 148 CA GLY 9 34.626 21.773 31.078 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.617 21.618 30.655 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.880 32.158 1.00 0.00 H +ATOM 151 C GLY 9 33.783 20.523 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.022 20.484 29.825 1.00 0.00 O +ATOM 153 N LYS 10 33.951 19.480 31.615 1.00 0.00 N +ATOM 154 H LYS 10 34.670 19.560 32.316 1.00 0.00 H +ATOM 155 CA LYS 10 33.230 18.191 31.479 1.00 0.00 C +ATOM 156 HA LYS 10 32.289 18.403 30.967 1.00 0.00 H +ATOM 157 CB LYS 10 34.057 17.246 30.577 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.677 17.847 29.907 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.724 16.640 31.194 1.00 0.00 H +ATOM 160 CG LYS 10 33.192 16.330 29.692 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.593 15.666 30.314 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.519 16.953 29.100 1.00 0.00 H +ATOM 163 CD LYS 10 34.058 15.492 28.736 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.721 16.156 28.179 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.661 14.791 29.314 1.00 0.00 H +ATOM 166 CE LYS 10 33.179 14.718 27.746 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.965 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.471 15.413 27.288 1.00 0.00 H +ATOM 169 NZ LYS 10 33.977 14.072 26.676 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.736 13.512 27.043 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.382 13.524 26.065 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.427 14.774 26.073 1.00 0.00 H +ATOM 173 C LYS 10 32.821 17.544 32.814 1.00 0.00 C +ATOM 174 O LYS 10 32.336 16.416 32.832 1.00 0.00 O +ATOM 175 N SER 11 33.037 18.243 33.935 1.00 0.00 N +ATOM 176 H SER 11 33.494 19.132 33.842 1.00 0.00 H +ATOM 177 CA SER 11 32.566 17.848 35.280 1.00 0.00 C +ATOM 178 HA SER 11 32.499 16.758 35.340 1.00 0.00 H +ATOM 179 CB SER 11 33.553 18.325 36.353 1.00 0.00 C +ATOM 180 HB2 SER 11 33.585 19.415 36.355 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.980 37.332 1.00 0.00 H +ATOM 182 OG SER 11 34.850 17.821 36.094 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.425 36.456 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.420 35.589 1.00 0.00 C +ATOM 185 O SER 11 30.351 17.750 36.199 1.00 0.00 O +ATOM 186 N CYS 12 30.919 19.655 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.630 20.134 34.627 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.270 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.870 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.351 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.324 22.215 34.523 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.251 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.149 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.145 23.412 37.057 1.00 0.00 H +ATOM 195 C CYS 12 28.853 19.936 33.838 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.667 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.513 19.990 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.060 20.142 34.736 1.00 0.00 H +ATOM 199 CA LYS 13 26.667 19.722 32.662 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.862 31.773 1.00 0.00 H +ATOM 201 CB LYS 13 26.223 18.247 32.706 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.032 17.655 33.143 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.346 18.144 33.358 1.00 0.00 H +ATOM 204 CG LYS 13 25.915 17.636 31.324 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.036 18.108 30.884 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.767 17.822 30.669 1.00 0.00 H +ATOM 207 CD LYS 13 25.684 16.116 31.406 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.690 15.716 30.391 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.518 15.663 31.947 1.00 0.00 H +ATOM 210 CE LYS 13 24.346 15.744 32.064 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.166 16.386 32.929 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.553 15.951 31.340 1.00 0.00 H +ATOM 213 NZ LYS 13 24.304 14.308 32.452 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.875 14.098 33.271 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.357 13.998 32.643 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.687 13.729 31.706 1.00 0.00 H +ATOM 217 C LYS 13 25.488 20.707 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.584 20.487 31.712 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.787 33.298 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.945 33.874 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.754 33.376 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.445 22.193 33.447 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.483 23.331 34.294 1.00 0.00 H +ATOM 224 C GLY 14 24.286 23.716 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.214 23.892 31.407 1.00 0.00 O +ATOM 226 N VAL 15 23.145 24.398 32.111 1.00 0.00 N +ATOM 227 H VAL 15 22.435 24.245 32.812 1.00 0.00 H +ATOM 228 CA VAL 15 22.778 25.387 31.071 1.00 0.00 C +ATOM 229 HA VAL 15 23.675 25.626 30.492 1.00 0.00 H +ATOM 230 CB VAL 15 21.760 24.737 30.089 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.856 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.450 24.318 30.766 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.937 25.178 31.211 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.793 23.856 30.028 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.579 31.548 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.416 25.668 28.927 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.331 26.008 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.820 25.120 28.196 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.841 26.533 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.282 26.686 31.729 1.00 0.00 C +ATOM 241 O VAL 15 21.713 26.632 32.818 1.00 0.00 O +HETATM 242 N HY1 16 22.496 27.830 31.091 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.109 31.451 1.00 0.00 C +HETATM 244 C HY1 16 21.616 29.887 30.135 1.00 0.00 C +HETATM 245 O HY1 16 21.779 29.351 29.023 1.00 0.00 O +HETATM 246 CB HY1 16 22.864 29.868 32.413 1.00 0.00 C +HETATM 247 CG HY1 16 24.211 30.223 31.813 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.549 31.404 31.207 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.321 29.396 31.740 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.303 30.091 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.880 31.315 30.788 1.00 0.00 N +HETATM 252 H HY1 16 22.998 27.783 30.210 1.00 0.00 H +HETATM 253 HA HY1 16 20.968 28.987 31.945 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.396 30.793 32.772 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.026 29.255 33.296 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.399 28.458 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.907 32.258 31.095 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.728 30.996 1.00 0.00 H +ATOM 259 N THR 17 21.166 31.142 30.265 1.00 0.00 N +ATOM 260 H THR 17 21.050 31.474 31.217 1.00 0.00 H +ATOM 261 CA THR 17 20.736 32.025 29.172 1.00 0.00 C +ATOM 262 HA THR 17 21.119 31.633 28.284 1.00 0.00 H +ATOM 263 CB THR 17 19.152 32.017 29.049 1.00 0.00 C +ATOM 264 HB THR 17 18.936 32.610 28.167 1.00 0.00 H +ATOM 265 CG2 THR 17 18.596 30.674 28.723 1.00 0.00 C +ATOM 266 HG21 THR 17 18.786 29.901 29.421 1.00 0.00 H +ATOM 267 HG22 THR 17 17.506 30.691 28.630 1.00 0.00 H +ATOM 268 HG23 THR 17 18.926 30.322 27.779 1.00 0.00 H +ATOM 269 OG1 THR 17 18.480 32.472 30.205 1.00 0.00 O +ATOM 270 HG1 THR 17 18.568 33.453 30.220 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.457 29.234 1.00 0.00 C +ATOM 272 O THR 17 21.702 33.916 30.266 1.00 0.00 O +HETATM 273 N HY2 18 21.139 34.162 28.101 1.00 0.00 N +HETATM 274 CA HY2 18 21.450 35.620 27.971 1.00 0.00 C +HETATM 275 C HY2 18 20.329 36.290 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.985 35.837 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.774 35.820 27.259 1.00 0.00 C +HETATM 278 CG HY2 18 24.005 35.327 28.003 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.420 34.030 28.155 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.943 36.119 28.644 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.315 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.706 27.237 1.00 0.00 H +HETATM 284 HA HY2 18 21.503 36.046 29.013 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.748 35.297 26.297 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.910 36.879 27.057 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.955 37.127 28.681 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.926 33.165 27.774 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.761 35.647 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.807 37.387 27.748 1.00 0.00 N +ATOM 291 H GLU 19 20.141 37.684 28.643 1.00 0.00 H +ATOM 292 CA GLU 19 18.799 38.219 27.101 1.00 0.00 C +ATOM 293 HA GLU 19 18.058 37.555 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.065 39.080 28.156 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.754 38.431 28.967 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.775 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.833 39.852 27.657 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.550 28.422 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.089 40.412 26.764 1.00 0.00 H +ATOM 300 CD GLU 19 15.654 38.901 27.366 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.588 38.373 26.223 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.813 38.691 28.275 1.00 0.00 O +ATOM 303 C GLU 19 19.405 39.113 25.992 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.857 26.273 1.00 0.00 O +ATOM 305 N ALA 20 18.878 39.052 24.761 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.354 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.961 23.686 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.963 24.094 1.00 0.00 H +ATOM 309 CB ALA 20 20.592 39.489 23.094 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.465 38.517 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.951 40.206 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.350 39.401 23.870 1.00 0.00 H +ATOM 313 C ALA 20 18.191 40.036 22.579 1.00 0.00 C +ATOM 314 O ALA 20 17.360 39.133 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.087 21.745 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.824 21.920 1.00 0.00 H +ATOM 317 CA VAL 21 17.460 41.147 20.465 1.00 0.00 C +ATOM 318 HA VAL 21 16.472 40.723 20.625 1.00 0.00 H +ATOM 319 CB VAL 21 17.274 42.597 19.972 1.00 0.00 C +ATOM 320 HB VAL 21 16.616 42.570 19.108 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.597 43.470 21.033 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.255 43.626 21.888 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.349 44.439 20.598 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.674 42.997 21.365 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.583 43.276 19.536 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.004 42.764 18.670 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.380 44.306 19.239 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.316 43.278 20.344 1.00 0.00 H +ATOM 329 C VAL 21 18.121 40.329 19.353 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.986 18.375 1.00 0.00 O +ATOM 331 N ASP 22 19.414 40.050 19.506 1.00 0.00 N +ATOM 332 H ASP 22 19.863 40.329 20.361 1.00 0.00 H +ATOM 333 CA ASP 22 20.295 39.463 18.502 1.00 0.00 C +ATOM 334 HA ASP 22 19.714 38.825 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.941 40.588 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.174 41.079 17.075 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.377 41.324 18.356 1.00 0.00 H +ATOM 338 CG ASP 22 22.025 40.044 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.147 40.586 16.800 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.763 39.018 16.087 1.00 0.00 O +ATOM 341 C ASP 22 21.366 38.597 19.178 1.00 0.00 C +ATOM 342 O ASP 22 21.825 38.880 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.789 37.545 18.492 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.489 17.520 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.608 18.984 1.00 0.00 C +ATOM 346 HA TRP 23 22.545 36.357 20.016 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.348 18.138 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.974 18.216 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.840 35.604 17.094 1.00 0.00 H +ATOM 350 CG TRP 23 23.573 34.243 18.531 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.517 33.704 17.734 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.739 34.020 16.723 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.129 32.678 18.412 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.903 32.155 18.035 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.589 32.475 19.659 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.825 31.536 20.665 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.540 30.741 20.523 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.682 21.888 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.012 22.701 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.765 22.099 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.900 23.082 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.005 33.658 21.055 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.310 34.465 21.213 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.637 33.527 19.797 1.00 0.00 C +ATOM 365 C TRP 23 24.210 37.185 18.982 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.925 1.00 0.00 O +ATOM 367 N ALA 24 24.557 38.022 17.997 1.00 0.00 N +ATOM 368 H ALA 24 23.880 38.261 17.279 1.00 0.00 H +ATOM 369 CA ALA 24 25.846 38.717 17.976 1.00 0.00 C +ATOM 370 HA ALA 24 26.618 38.001 18.267 1.00 0.00 H +ATOM 371 CB ALA 24 26.158 39.140 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.443 39.882 16.189 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.160 39.562 16.482 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.110 38.273 15.877 1.00 0.00 H +ATOM 375 C ALA 24 25.929 39.882 18.994 1.00 0.00 C +ATOM 376 O ALA 24 27.022 40.384 19.270 1.00 0.00 O +ATOM 377 N GLU 25 24.812 40.285 19.610 1.00 0.00 N +ATOM 378 H GLU 25 23.932 39.945 19.243 1.00 0.00 H +ATOM 379 CA GLU 25 24.791 41.075 20.852 1.00 0.00 C +ATOM 380 HA GLU 25 25.642 41.755 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.512 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.646 41.279 20.820 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.451 42.386 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.432 43.037 19.875 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.632 42.630 18.885 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.410 43.424 19.863 1.00 0.00 H +ATOM 387 CD GLU 25 24.380 44.197 20.185 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.918 45.196 20.744 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.601 44.048 19.836 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.102 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.517 23.016 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.005 22.132 1.00 0.00 N +ATOM 393 H ALA 26 23.666 38.775 21.367 1.00 0.00 H +ATOM 394 CA ALA 26 24.460 38.029 23.217 1.00 0.00 C +ATOM 395 HA ALA 26 24.199 38.524 24.148 1.00 0.00 H +ATOM 396 CB ALA 26 23.491 36.862 23.015 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.772 36.287 22.133 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.204 23.883 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.231 22.894 1.00 0.00 H +ATOM 400 C ALA 26 25.918 37.533 23.365 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.227 24.482 1.00 0.00 O +ATOM 402 N GLU 27 26.710 37.510 22.283 1.00 0.00 N +ATOM 403 H GLU 27 26.268 37.638 21.376 1.00 0.00 H +ATOM 404 CA GLU 27 28.167 37.303 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.369 36.351 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.763 37.247 20.913 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.152 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.735 38.251 20.486 1.00 0.00 H +ATOM 409 CG GLU 27 30.208 36.724 20.921 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.145 21.771 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.190 35.641 21.055 1.00 0.00 H +ATOM 412 CD GLU 27 30.982 37.089 19.641 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.725 38.106 19.696 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.343 18.641 1.00 0.00 O +ATOM 415 C GLU 27 28.849 38.396 23.183 1.00 0.00 C +ATOM 416 O GLU 27 29.572 38.094 24.134 1.00 0.00 O +ATOM 417 N LYS 28 28.548 39.673 22.914 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.853 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.817 23.666 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.667 1.00 0.00 H +ATOM 421 CB LYS 28 28.699 42.145 22.993 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.278 23.048 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.170 42.962 23.542 1.00 0.00 H +ATOM 424 CG LYS 28 29.137 42.221 21.519 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.207 42.027 21.443 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.604 41.462 20.949 1.00 0.00 H +ATOM 427 CD LYS 28 28.837 43.604 20.920 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.819 43.907 21.172 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.521 44.332 21.364 1.00 0.00 H +ATOM 430 CE LYS 28 29.006 43.629 19.396 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.103 44.670 19.084 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.926 43.113 19.127 1.00 0.00 H +ATOM 433 NZ LYS 28 27.842 43.021 18.708 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.981 43.489 19.017 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.904 43.103 17.704 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.722 42.040 18.958 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.782 25.132 1.00 0.00 C +ATOM 438 O LYS 28 29.482 40.969 26.019 1.00 0.00 O +ATOM 439 N PHE 29 27.393 40.452 25.417 1.00 0.00 N +ATOM 440 H PHE 29 26.740 40.365 24.642 1.00 0.00 H +ATOM 441 CA PHE 29 26.903 40.286 26.793 1.00 0.00 C +ATOM 442 HA PHE 29 27.228 41.146 27.379 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.264 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.038 39.343 26.310 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.022 40.230 27.832 1.00 0.00 H +ATOM 446 CG PHE 29 24.678 41.443 26.116 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.465 41.235 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.015 40.254 25.407 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.830 42.300 24.767 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.907 42.126 24.234 1.00 0.00 H +ATOM 451 CZ PHE 29 23.399 43.584 24.790 1.00 0.00 C +ATOM 452 HZ PHE 29 22.919 44.396 24.265 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.591 43.806 25.498 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.027 44.796 25.527 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.226 42.742 26.165 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.139 42.936 26.704 1.00 0.00 H +ATOM 457 C PHE 29 27.484 39.050 27.507 1.00 0.00 C +ATOM 458 O PHE 29 27.589 39.038 28.735 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.768 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.042 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.683 36.892 27.316 1.00 0.00 C +ATOM 462 HA THR 30 28.208 36.545 28.227 1.00 0.00 H +ATOM 463 CB THR 30 28.692 35.717 26.333 1.00 0.00 C +ATOM 464 HB THR 30 29.073 36.025 25.357 1.00 0.00 H +ATOM 465 CG2 THR 30 29.496 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.137 34.212 27.801 1.00 0.00 H +ATOM 467 HG22 THR 30 29.369 33.689 26.123 1.00 0.00 H +ATOM 468 HG23 THR 30 30.559 34.746 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.365 35.280 26.188 1.00 0.00 O +ATOM 470 HG1 THR 30 26.960 35.883 25.542 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.982 28.769 1.00 0.00 O +ATOM 473 N LYS 31 30.746 38.122 26.832 1.00 0.00 N +ATOM 474 H LYS 31 30.287 38.320 25.947 1.00 0.00 H +ATOM 475 CA LYS 31 32.078 38.702 27.069 1.00 0.00 C +ATOM 476 HA LYS 31 32.749 37.905 27.376 1.00 0.00 H +ATOM 477 CB LYS 31 32.616 39.317 25.766 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.011 25.348 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.529 39.865 25.987 1.00 0.00 H +ATOM 480 CG LYS 31 32.930 38.210 24.744 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.684 37.553 25.176 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.045 37.629 24.525 1.00 0.00 H +ATOM 483 CD LYS 31 33.459 38.817 23.435 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.384 22.952 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.299 39.497 23.642 1.00 0.00 H +ATOM 486 CE LYS 31 33.923 37.725 22.466 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.107 37.055 22.246 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.216 38.195 21.540 1.00 0.00 H +ATOM 489 NZ LYS 31 35.077 36.976 23.015 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.822 36.247 23.679 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.553 36.469 22.265 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.760 37.567 23.503 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.188 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.780 28.917 1.00 0.00 O +ATOM 495 N ALA 32 31.031 40.509 28.373 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.873 41.412 29.515 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.138 29.505 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.375 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.495 29.375 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.875 30.215 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.557 42.757 28.446 1.00 0.00 H +ATOM 503 C ALA 32 30.963 40.638 30.838 1.00 0.00 C +ATOM 504 O ALA 32 31.881 40.886 31.616 1.00 0.00 O +ATOM 505 N LYN 33 30.117 39.613 31.030 1.00 0.00 N +ATOM 506 H LYN 33 29.390 39.457 30.346 1.00 0.00 H +ATOM 507 CA LYN 33 30.156 38.755 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.022 39.383 33.110 1.00 0.00 H +ATOM 509 CB LYN 33 29.008 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.061 37.156 31.262 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.141 37.038 33.024 1.00 0.00 H +ATOM 512 CG LYN 33 27.610 38.358 32.315 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.564 38.982 33.207 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.412 38.981 31.444 1.00 0.00 H +ATOM 515 CD LYN 33 26.535 37.267 32.412 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.691 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.632 36.748 33.365 1.00 0.00 H +ATOM 518 CE LYN 33 25.122 37.835 32.288 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.934 38.514 33.114 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.035 38.378 31.349 1.00 0.00 H +ATOM 521 NZ LYN 33 24.115 36.761 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.184 37.154 32.261 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.253 36.113 31.547 1.00 0.00 H +ATOM 524 C LYN 33 31.510 38.042 32.391 1.00 0.00 C +ATOM 525 O LYN 33 32.007 37.921 33.505 1.00 0.00 O +ATOM 526 N ALA 34 32.143 37.585 31.305 1.00 0.00 N +ATOM 527 H ALA 34 31.696 37.677 30.400 1.00 0.00 H +ATOM 528 CA ALA 34 33.470 36.966 31.389 1.00 0.00 C +ATOM 529 HA ALA 34 33.428 36.160 32.125 1.00 0.00 H +ATOM 530 CB ALA 34 33.816 36.355 30.029 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.962 37.145 29.294 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.776 30.132 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.693 29.698 1.00 0.00 H +ATOM 534 C ALA 34 34.572 37.946 31.865 1.00 0.00 C +ATOM 535 O ALA 34 35.469 37.540 32.604 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.224 31.488 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.504 30.885 1.00 0.00 H +ATOM 538 CA ASN 35 35.368 40.286 32.000 1.00 0.00 C +ATOM 539 HA ASN 35 36.366 39.870 32.113 1.00 0.00 H +ATOM 540 CB ASN 35 35.476 41.416 30.969 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.486 41.702 30.624 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.287 31.449 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.031 29.800 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.581 41.002 29.898 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.705 28.668 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.448 27.895 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.600 28.628 1.00 0.00 H +ATOM 548 C ASN 35 34.981 40.786 33.404 1.00 0.00 C +ATOM 549 O ASN 35 35.867 41.207 34.150 1.00 0.00 O +ATOM 550 N ASP 36 33.718 40.635 33.831 1.00 0.00 N +ATOM 551 H ASP 36 32.984 40.413 33.166 1.00 0.00 H +ATOM 552 CA ASP 36 33.339 40.772 35.249 1.00 0.00 C +ATOM 553 HA ASP 36 33.668 41.747 35.602 1.00 0.00 H +ATOM 554 CB ASP 36 31.819 40.767 35.440 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.448 39.783 35.229 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.607 40.876 36.498 1.00 0.00 H +ATOM 557 CG ASP 36 30.981 41.783 34.657 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.512 42.876 34.366 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.778 41.515 34.402 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.708 36.125 1.00 0.00 C +ATOM 561 O ASP 36 34.482 40.004 37.236 1.00 0.00 O +ATOM 562 N PHE 37 34.227 38.480 35.608 1.00 0.00 N +ATOM 563 H PHE 37 33.752 38.279 34.737 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.459 36.179 1.00 0.00 C +ATOM 565 HA PHE 37 35.118 37.611 37.257 1.00 0.00 H +ATOM 566 CB PHE 37 34.574 36.041 35.932 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.663 35.825 34.870 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.334 36.446 1.00 0.00 H +ATOM 569 CG PHE 37 33.150 35.763 36.385 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.139 35.558 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.374 35.619 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.312 35.833 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.039 35.198 35.094 1.00 0.00 H +ATOM 574 CZ PHE 37 30.507 35.235 37.199 1.00 0.00 C +ATOM 575 HZ PHE 37 29.492 35.053 37.510 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.515 35.403 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.270 35.352 39.211 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.833 35.668 37.752 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.601 35.814 38.491 1.00 0.00 H +ATOM 580 C PHE 37 36.607 37.580 35.742 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.679 36.016 1.00 0.00 O +ATOM 582 N GLY 38 36.998 38.676 35.079 1.00 0.00 N +ATOM 583 H GLY 38 36.291 39.378 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.389 39.091 34.839 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.499 40.111 35.207 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.054 38.469 35.438 1.00 0.00 H +ATOM 587 C GLY 38 38.925 39.060 33.393 1.00 0.00 C +ATOM 588 O GLY 38 39.874 39.792 33.112 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.227 32.486 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.727 32.761 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.052 31.091 1.00 0.00 C +ATOM 592 HA ARG 39 38.944 39.045 30.646 1.00 0.00 H +ATOM 593 CB ARG 39 40.304 37.440 31.075 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.635 37.431 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.987 38.106 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.522 36.013 31.628 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.039 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.753 31.461 1.00 0.00 H +ATOM 599 CD ARG 39 40.222 35.826 33.132 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.861 36.507 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.182 36.080 33.342 1.00 0.00 H +ATOM 602 NE ARG 39 40.446 34.443 33.599 1.00 0.00 N +ATOM 603 HE ARG 39 41.205 34.297 34.244 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.303 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.469 32.494 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.429 34.360 32.093 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.296 32.621 32.084 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.954 32.226 33.819 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.694 32.095 34.491 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.336 31.450 33.602 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.225 30.193 1.00 0.00 C +ATOM 612 O ARG 39 37.522 36.137 30.605 1.00 0.00 O +ATOM 613 N ASP 40 37.650 37.678 28.959 1.00 0.00 N +ATOM 614 H ASP 40 38.029 38.573 28.674 1.00 0.00 H +ATOM 615 CA ASP 40 36.889 36.892 27.966 1.00 0.00 C +ATOM 616 HA ASP 40 36.166 36.309 28.530 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.733 26.970 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.444 37.038 26.402 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.369 38.350 27.538 1.00 0.00 H +ATOM 620 CG ASP 40 36.824 38.628 25.969 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.257 39.725 26.392 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.837 38.322 24.743 1.00 0.00 O +ATOM 623 C ASP 40 37.720 35.861 27.181 1.00 0.00 C +ATOM 624 O ASP 40 38.885 36.078 26.862 1.00 0.00 O +ATOM 625 N GLY 41 37.056 34.759 26.814 1.00 0.00 N +ATOM 626 H GLY 41 36.099 34.682 27.117 1.00 0.00 H +ATOM 627 CA GLY 41 37.471 33.828 25.758 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.459 34.099 25.383 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.531 32.823 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.482 33.818 24.581 1.00 0.00 C +ATOM 631 O GLY 41 35.578 34.655 24.504 1.00 0.00 O +ATOM 632 N GLU 42 36.638 32.853 23.674 1.00 0.00 N +ATOM 633 H GLU 42 37.348 32.156 23.829 1.00 0.00 H +ATOM 634 CA GLU 42 35.799 32.668 22.476 1.00 0.00 C +ATOM 635 HA GLU 42 35.112 33.509 22.376 1.00 0.00 H +ATOM 636 CB GLU 42 36.683 32.629 21.214 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.158 31.650 21.167 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.035 32.711 20.341 1.00 0.00 H +ATOM 639 CG GLU 42 37.803 33.693 21.111 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.575 33.457 21.850 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.277 33.620 20.129 1.00 0.00 H +ATOM 642 CD GLU 42 37.343 35.144 21.318 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.154 35.459 21.111 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.167 36.006 21.711 1.00 0.00 O +ATOM 645 C GLU 42 34.948 31.386 22.578 1.00 0.00 C +ATOM 646 O GLU 42 35.393 30.398 23.170 1.00 0.00 O +ATOM 647 N ALA 43 33.745 31.391 21.989 1.00 0.00 N +ATOM 648 H ALA 43 33.480 32.196 21.440 1.00 0.00 H +ATOM 649 CA ALA 43 32.756 30.306 22.060 1.00 0.00 C +ATOM 650 HA ALA 43 33.248 29.388 22.388 1.00 0.00 H +ATOM 651 CB ALA 43 31.692 30.672 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.181 31.592 22.812 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.958 29.866 23.177 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.164 30.811 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.110 30.017 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.882 30.932 19.898 1.00 0.00 O +ATOM 657 N THR 44 31.798 28.746 20.423 1.00 0.00 N +ATOM 658 H THR 44 31.919 28.067 21.167 1.00 0.00 H +ATOM 659 CA THR 44 31.131 28.283 19.194 1.00 0.00 C +ATOM 660 HA THR 44 31.425 28.947 18.381 1.00 0.00 H +ATOM 661 CB THR 44 31.610 26.868 18.823 1.00 0.00 C +ATOM 662 HB THR 44 31.430 26.188 19.656 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.281 17.554 1.00 0.00 C +ATOM 664 HG21 THR 44 31.071 26.990 16.727 1.00 0.00 H +ATOM 665 HG22 THR 44 31.502 25.358 17.280 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.037 17.727 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.927 18.561 1.00 0.00 O +ATOM 668 HG1 THR 44 33.234 26.124 18.092 1.00 0.00 H +ATOM 669 C THR 44 29.605 28.381 19.326 1.00 0.00 C +ATOM 670 O THR 44 29.072 28.429 20.436 1.00 0.00 O +ATOM 671 N ILE 45 28.899 28.459 18.193 1.00 0.00 N +ATOM 672 H ILE 45 29.373 28.324 17.314 1.00 0.00 H +ATOM 673 CA ILE 45 27.479 28.840 18.123 1.00 0.00 C +ATOM 674 HA ILE 45 27.060 28.756 19.126 1.00 0.00 H +ATOM 675 CB ILE 45 27.332 30.316 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.271 30.529 17.778 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.069 31.232 18.677 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.151 31.108 18.586 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.833 32.282 18.499 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.768 30.969 19.687 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.758 30.692 16.252 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.018 31.752 16.233 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.657 30.140 15.968 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.506 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.730 30.935 15.529 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.975 31.017 14.269 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.530 29.452 14.955 1.00 0.00 H +ATOM 688 C ILE 45 26.629 27.925 17.243 1.00 0.00 C +ATOM 689 O ILE 45 27.122 27.344 16.276 1.00 0.00 O +ATOM 690 N ASP 46 25.329 27.880 17.545 1.00 0.00 N +ATOM 691 H ASP 46 25.032 28.297 18.421 1.00 0.00 H +ATOM 692 CA ASP 46 24.280 27.260 16.735 1.00 0.00 C +ATOM 693 HA ASP 46 24.584 27.262 15.684 1.00 0.00 H +ATOM 694 CB ASP 46 24.077 25.807 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.221 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.955 25.788 18.267 1.00 0.00 H +ATOM 697 CG ASP 46 22.841 25.170 16.544 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.475 17.281 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.561 25.439 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.957 28.050 16.850 1.00 0.00 C +ATOM 701 O ASP 46 22.507 28.363 17.955 1.00 0.00 O +ATOM 702 N ASP 47 22.309 28.333 15.716 1.00 0.00 N +ATOM 703 H ASP 47 22.678 27.944 14.861 1.00 0.00 H +ATOM 704 CA ASP 47 20.969 28.925 15.674 1.00 0.00 C +ATOM 705 HA ASP 47 20.875 29.653 16.485 1.00 0.00 H +ATOM 706 CB ASP 47 20.776 29.673 14.345 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.520 30.467 14.253 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.912 28.978 13.514 1.00 0.00 H +ATOM 709 CG ASP 47 19.366 30.275 14.271 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.485 29.674 13.614 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.064 31.235 15.016 1.00 0.00 O +ATOM 712 C ASP 47 19.852 27.876 15.878 1.00 0.00 C +ATOM 713 O ASP 47 18.842 28.184 16.513 1.00 0.00 O +ATOM 714 N ALA 48 20.002 26.636 15.396 1.00 0.00 N +ATOM 715 H ALA 48 20.917 26.342 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.934 25.626 15.412 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.054 14.931 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.425 14.583 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.276 23.967 15.053 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.686 14.514 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.674 24.756 13.580 1.00 0.00 H +ATOM 722 C ALA 48 18.524 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.929 17.099 1.00 0.00 O +ATOM 724 N THR 49 19.475 25.245 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.436 25.295 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.265 25.120 19.229 1.00 0.00 C +ATOM 727 HA THR 49 18.215 24.872 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.099 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.818 23.859 20.868 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.628 19.137 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.666 18.098 1.00 0.00 H +ATOM 732 HG22 THR 49 20.434 21.857 19.654 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.165 1.00 0.00 H +ATOM 734 OG1 THR 49 21.477 24.245 19.774 1.00 0.00 O +ATOM 735 HG1 THR 49 21.730 24.270 18.816 1.00 0.00 H +ATOM 736 C THR 49 19.505 26.429 19.997 1.00 0.00 C +ATOM 737 O THR 49 19.426 26.431 21.226 1.00 0.00 O +ATOM 738 N LYS 50 19.766 27.551 19.307 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.297 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.906 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.354 29.538 19.086 1.00 0.00 H +ATOM 742 CB LYS 50 18.564 29.472 20.292 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.160 28.830 21.074 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.700 30.459 20.736 1.00 0.00 H +ATOM 745 CG LYS 50 17.492 29.593 19.188 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.426 28.657 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.740 19.683 1.00 0.00 H +ATOM 748 CD LYS 50 17.704 30.775 18.223 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.703 31.695 18.813 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.688 17.723 1.00 0.00 H +ATOM 751 CE LYS 50 16.571 30.869 17.187 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.603 17.664 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.507 31.899 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.997 16.018 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.231 29.102 16.282 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.013 29.838 15.434 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.544 30.418 15.421 1.00 0.00 H +ATOM 758 C LYS 50 20.986 28.948 21.020 1.00 0.00 C +ATOM 759 O LYS 50 20.693 29.519 22.082 1.00 0.00 O +ATOM 760 N THR 51 22.146 28.292 20.857 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.962 19.926 1.00 0.00 H +ATOM 762 CA THR 51 23.055 27.904 21.959 1.00 0.00 C +ATOM 763 HA THR 51 22.763 28.429 22.858 1.00 0.00 H +ATOM 764 CB THR 51 22.885 26.404 22.277 1.00 0.00 C +ATOM 765 HB THR 51 22.979 25.813 21.354 1.00 0.00 H +ATOM 766 CG2 THR 51 23.850 25.861 23.317 1.00 0.00 C +ATOM 767 HG21 THR 51 23.812 26.474 24.218 1.00 0.00 H +ATOM 768 HG22 THR 51 23.577 24.840 23.588 1.00 0.00 H +ATOM 769 HG23 THR 51 24.876 25.835 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.633 26.168 22.875 1.00 0.00 O +ATOM 771 HG1 THR 51 20.953 26.250 22.182 1.00 0.00 H +ATOM 772 C THR 51 24.556 28.224 21.725 1.00 0.00 C +ATOM 773 O THR 51 25.085 28.000 20.641 1.00 0.00 O +ATOM 774 N PHE 52 25.248 28.694 22.772 1.00 0.00 N +ATOM 775 H PHE 52 24.712 28.952 23.592 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.779 22.880 1.00 0.00 C +ATOM 777 HA PHE 52 27.145 28.937 21.899 1.00 0.00 H +ATOM 778 CB PHE 52 27.149 29.952 23.821 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.476 29.958 24.659 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.735 24.193 1.00 0.00 H +ATOM 781 CG PHE 52 27.217 31.347 23.228 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.428 32.382 23.752 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.751 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.443 33.652 23.161 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.777 34.431 23.515 1.00 0.00 H +ATOM 786 CZ PHE 52 27.281 33.893 22.066 1.00 0.00 C +ATOM 787 HZ PHE 52 27.244 34.837 21.559 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.160 32.902 21.616 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.836 33.108 20.791 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.628 22.199 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.778 30.857 21.828 1.00 0.00 H +ATOM 792 C PHE 52 27.331 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.809 27.010 24.505 1.00 0.00 O +ATOM 794 N THR 53 28.487 27.066 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.851 27.522 22.146 1.00 0.00 H +ATOM 796 CA THR 53 29.281 25.929 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.048 25.798 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.936 24.611 22.782 1.00 0.00 C +ATOM 799 HB THR 53 29.512 23.804 23.241 1.00 0.00 H +ATOM 800 CG2 THR 53 27.461 24.225 22.862 1.00 0.00 C +ATOM 801 HG21 THR 53 26.865 24.906 22.255 1.00 0.00 H +ATOM 802 HG22 THR 53 27.326 23.209 22.494 1.00 0.00 H +ATOM 803 HG23 THR 53 27.124 24.271 23.898 1.00 0.00 H +ATOM 804 OG1 THR 53 29.273 24.680 21.420 1.00 0.00 O +ATOM 805 HG1 THR 53 28.756 24.016 20.955 1.00 0.00 H +ATOM 806 C THR 53 30.804 26.149 23.413 1.00 0.00 C +ATOM 807 O THR 53 31.287 27.022 22.688 1.00 0.00 O +ATOM 808 N THR 54 31.571 25.328 24.145 1.00 0.00 N +ATOM 809 H THR 54 31.111 24.655 24.737 1.00 0.00 H +ATOM 810 CA THR 54 33.043 25.241 24.080 1.00 0.00 C +ATOM 811 HA THR 54 33.416 26.036 23.436 1.00 0.00 H +ATOM 812 CB THR 54 33.668 25.452 25.473 1.00 0.00 C +ATOM 813 HB THR 54 33.373 24.632 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.195 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.517 26.335 24.770 1.00 0.00 H +ATOM 816 HG22 THR 54 35.553 25.813 26.470 1.00 0.00 H +ATOM 817 HG23 THR 54 35.642 24.609 25.193 1.00 0.00 H +ATOM 818 OG1 THR 54 33.203 26.662 26.026 1.00 0.00 O +ATOM 819 HG1 THR 54 33.876 26.992 26.625 1.00 0.00 H +ATOM 820 C THR 54 33.479 23.896 23.474 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.895 23.605 1.00 0.00 O +ATOM 822 N GLN 55 34.635 23.879 22.803 1.00 0.00 N +ATOM 823 H GLN 55 35.157 24.739 22.761 1.00 0.00 H +ATOM 824 CA GLN 55 35.264 22.693 22.195 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.165 21.639 1.00 0.00 H +ATOM 826 CB GLN 55 36.319 23.163 21.173 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.730 22.295 20.657 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.804 23.775 20.430 1.00 0.00 H +ATOM 829 CG GLN 55 37.482 23.993 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.096 24.713 22.482 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.177 23.334 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.249 24.773 20.686 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.326 24.397 19.523 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.831 25.902 21.034 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.408 26.355 20.331 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.724 26.275 21.962 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.680 23.225 1.00 0.00 C +ATOM 838 O GLN 55 36.112 22.047 24.363 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.413 22.804 1.00 0.00 N +ATOM 840 H GLU 56 35.794 20.234 21.832 1.00 0.00 H +ATOM 841 CA GLU 56 36.491 19.249 23.573 1.00 0.00 C +ATOM 842 HA GLU 56 36.152 19.337 24.602 1.00 0.00 H +ATOM 843 CB GLU 56 35.885 17.954 22.967 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.804 17.985 23.074 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.993 21.896 1.00 0.00 H +ATOM 846 CG GLU 56 36.403 16.582 23.463 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.458 15.931 22.591 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.423 16.669 23.812 1.00 0.00 H +ATOM 849 CD GLU 56 35.548 15.855 24.520 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.094 15.347 25.534 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.325 15.660 24.312 1.00 0.00 O +ATOM 852 C GLU 56 38.030 19.202 23.644 1.00 0.00 C +ATOM 853 O GLU 56 38.535 19.186 24.796 1.00 0.00 O +ATOM 854 OXT GLU 56 38.680 19.141 22.579 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.717 32.457 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.341 33.248 30.282 1.00 0.00 N +HETATM 857 C AN1 58 30.690 33.885 31.200 1.00 0.00 C +HETATM 858 C1 AN1 58 29.363 33.529 30.704 1.00 0.00 C +HETATM 859 H AN1 58 30.622 34.282 32.217 1.00 0.00 H +HETATM 860 H1 AN1 58 31.134 34.634 30.540 1.00 0.00 H +HETATM 861 H2 AN1 58 31.317 32.983 31.203 1.00 0.00 H +HETATM 862 N1 AZI 59 31.272 30.355 29.425 1.00 0.00 N +HETATM 863 N2 AZI 59 30.474 30.251 30.345 1.00 0.00 N +HETATM 864 N3 AZI 59 29.631 30.165 31.291 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 144 148 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 643 639 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_2.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_2.pdb new file mode 100644 index 0000000..7a0c97e --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_2.pdb @@ -0,0 +1,1753 @@ +COMPND fitness: -1.2907 59.98833333333391 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 55.366 58.077 52.044 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.215 37.914 23.523 1.00 0.00 N +ATOM 2 H1 MET 1 15.201 38.296 24.464 1.00 0.00 H +ATOM 3 H2 MET 1 14.443 38.284 22.998 1.00 0.00 H +ATOM 4 H3 MET 1 16.084 38.206 23.097 1.00 0.00 H +ATOM 5 CA MET 1 15.167 36.444 23.594 1.00 0.00 C +ATOM 6 HA MET 1 14.223 36.155 24.051 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.794 22.200 1.00 0.00 C +ATOM 8 HB2 MET 1 14.404 36.123 21.604 1.00 0.00 H +ATOM 9 HB3 MET 1 16.168 36.123 21.701 1.00 0.00 H +ATOM 10 CG MET 1 15.256 34.254 22.251 1.00 0.00 C +ATOM 11 HG2 MET 1 16.133 33.929 22.814 1.00 0.00 H +ATOM 12 HG3 MET 1 14.367 33.916 22.786 1.00 0.00 H +ATOM 13 SD MET 1 15.317 33.393 20.646 1.00 0.00 S +ATOM 14 CE MET 1 13.636 33.641 20.008 1.00 0.00 C +ATOM 15 HE1 MET 1 13.415 34.705 19.929 1.00 0.00 H +ATOM 16 HE2 MET 1 13.557 33.192 19.017 1.00 0.00 H +ATOM 17 HE3 MET 1 12.912 33.164 20.670 1.00 0.00 H +ATOM 18 C MET 1 16.285 35.966 24.511 1.00 0.00 C +ATOM 19 O MET 1 17.429 36.370 24.340 1.00 0.00 O +ATOM 20 N GLN 2 15.963 35.099 25.473 1.00 0.00 N +ATOM 21 H GLN 2 14.992 34.874 25.632 1.00 0.00 H +ATOM 22 CA GLN 2 16.928 34.438 26.358 1.00 0.00 C +ATOM 23 HA GLN 2 17.697 35.150 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 16.177 34.003 27.636 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.213 33.562 27.357 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.744 33.245 28.172 1.00 0.00 H +ATOM 27 CG GLN 2 15.930 35.169 28.587 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.504 36.019 28.045 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.177 34.846 29.297 1.00 0.00 H +ATOM 30 CD GLN 2 17.140 35.548 29.441 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.211 34.972 29.368 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.976 36.450 30.363 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.748 36.615 30.982 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.068 36.818 30.542 1.00 0.00 H +ATOM 35 C GLN 2 17.653 33.291 25.623 1.00 0.00 C +ATOM 36 O GLN 2 17.281 32.121 25.734 1.00 0.00 O +ATOM 37 N TYR 3 18.675 33.646 24.841 1.00 0.00 N +ATOM 38 H TYR 3 18.926 34.635 24.813 1.00 0.00 H +ATOM 39 CA TYR 3 19.508 32.709 24.085 1.00 0.00 C +ATOM 40 HA TYR 3 18.854 32.101 23.459 1.00 0.00 H +ATOM 41 CB TYR 3 20.458 33.508 23.197 1.00 0.00 C +ATOM 42 HB2 TYR 3 21.071 34.153 23.827 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.125 32.817 22.690 1.00 0.00 H +ATOM 44 CG TYR 3 19.760 34.349 22.152 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.102 33.711 21.087 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.079 32.633 21.039 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.519 34.465 20.054 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.049 33.973 19.217 1.00 0.00 H +ATOM 49 CZ TYR 3 18.571 35.872 20.103 1.00 0.00 C +ATOM 50 OH TYR 3 18.027 36.608 19.103 1.00 0.00 O +ATOM 51 HH TYR 3 18.041 36.130 18.273 1.00 0.00 H +ATOM 52 CE2 TYR 3 19.176 36.515 21.200 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.196 37.592 21.223 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.774 35.755 22.224 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.247 36.252 23.059 1.00 0.00 H +ATOM 56 C TYR 3 20.295 31.786 25.023 1.00 0.00 C +ATOM 57 O TYR 3 20.806 32.243 26.044 1.00 0.00 O +ATOM 58 N LYS 4 20.410 30.492 24.696 1.00 0.00 N +ATOM 59 H LYS 4 20.118 30.201 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 21.014 29.461 25.566 1.00 0.00 C +ATOM 61 HA LYS 4 20.744 29.654 26.602 1.00 0.00 H +ATOM 62 CB LYS 4 20.480 28.067 25.177 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.496 27.976 24.094 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.160 27.307 25.570 1.00 0.00 H +ATOM 65 CG LYS 4 19.070 27.701 25.676 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.897 26.669 25.374 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.060 27.742 26.766 1.00 0.00 H +ATOM 68 CD LYS 4 17.920 28.560 25.120 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.927 29.535 25.607 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.090 28.713 24.052 1.00 0.00 H +ATOM 71 CE LYS 4 16.533 27.909 25.279 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.777 28.600 24.894 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.509 27.012 24.654 1.00 0.00 H +ATOM 74 NZ LYS 4 16.205 27.518 26.673 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.269 28.291 27.318 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.276 27.107 26.716 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.829 26.763 26.958 1.00 0.00 H +ATOM 78 C LYS 4 22.547 29.475 25.513 1.00 0.00 C +ATOM 79 O LYS 4 23.144 29.819 24.501 1.00 0.00 O +HETATM 80 N HX1 5 23.203 29.039 26.584 1.00 0.00 N +HETATM 81 CA HX1 5 24.662 28.868 26.669 1.00 0.00 C +HETATM 82 C HX1 5 24.985 27.668 27.567 1.00 0.00 C +HETATM 83 O HX1 5 24.522 27.612 28.710 1.00 0.00 O +HETATM 84 CB HX1 5 25.294 30.185 27.169 1.00 0.00 C +HETATM 85 CG HX1 5 26.807 30.275 27.239 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.721 29.336 26.838 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.483 31.361 27.814 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.782 31.031 27.730 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.957 29.808 27.202 1.00 0.00 N +HETATM 90 H HX1 5 22.658 28.869 27.426 1.00 0.00 H +HETATM 91 HA HX1 5 25.052 28.661 25.672 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.899 30.401 28.163 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.958 30.992 26.516 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.539 28.374 26.378 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.578 31.603 28.187 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.812 29.251 27.293 1.00 0.00 H +ATOM 97 N ILE 6 25.726 26.695 27.028 1.00 0.00 N +ATOM 98 H ILE 6 26.046 26.815 26.070 1.00 0.00 H +ATOM 99 CA ILE 6 26.199 25.479 27.709 1.00 0.00 C +ATOM 100 HA ILE 6 25.697 25.404 28.676 1.00 0.00 H +ATOM 101 CB ILE 6 25.811 24.216 26.902 1.00 0.00 C +ATOM 102 HB ILE 6 26.234 24.306 25.901 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.373 22.929 27.541 1.00 0.00 C +ATOM 104 HG21 ILE 6 26.002 22.820 28.562 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.078 22.054 26.963 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.464 22.944 27.545 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.270 24.130 26.784 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.842 24.047 27.783 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.891 25.046 26.331 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.745 22.969 25.931 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.890 22.021 26.449 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.678 23.107 25.758 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.263 22.948 24.971 1.00 0.00 H +ATOM 114 C ILE 6 27.708 25.597 28.003 1.00 0.00 C +ATOM 115 O ILE 6 28.447 26.273 27.288 1.00 0.00 O +ATOM 116 N VAL 7 28.126 24.994 29.115 1.00 0.00 N +ATOM 117 H VAL 7 27.488 24.344 29.551 1.00 0.00 H +ATOM 118 CA VAL 7 29.238 25.447 29.963 1.00 0.00 C +ATOM 119 HA VAL 7 29.296 26.533 29.871 1.00 0.00 H +ATOM 120 CB VAL 7 28.813 25.143 31.416 1.00 0.00 C +ATOM 121 HB VAL 7 27.762 25.424 31.517 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.895 23.654 31.773 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.924 23.309 31.694 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.538 23.499 32.790 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.276 23.071 31.090 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.567 25.988 32.435 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.358 27.041 32.248 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.232 25.736 33.441 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.636 25.813 32.353 1.00 0.00 H +ATOM 130 C VAL 7 30.639 24.901 29.585 1.00 0.00 C +ATOM 131 O VAL 7 30.785 23.764 29.143 1.00 0.00 O +ATOM 132 N GLU 8 31.685 25.707 29.802 1.00 0.00 N +ATOM 133 H GLU 8 31.473 26.676 30.027 1.00 0.00 H +ATOM 134 CA GLU 8 33.119 25.383 29.624 1.00 0.00 C +ATOM 135 HA GLU 8 33.310 25.152 28.575 1.00 0.00 H +ATOM 136 CB GLU 8 33.917 26.667 29.977 1.00 0.00 C +ATOM 137 HB2 GLU 8 33.712 27.426 29.223 1.00 0.00 H +ATOM 138 HB3 GLU 8 33.497 27.048 30.911 1.00 0.00 H +ATOM 139 CG GLU 8 35.447 26.584 30.222 1.00 0.00 C +ATOM 140 HG2 GLU 8 35.729 27.498 30.753 1.00 0.00 H +ATOM 141 HG3 GLU 8 35.683 25.765 30.900 1.00 0.00 H +ATOM 142 CD GLU 8 36.359 26.500 28.992 1.00 0.00 C +ATOM 143 OE1 GLU 8 36.012 27.041 27.916 1.00 0.00 O +ATOM 144 OE2 GLU 8 37.521 26.054 29.135 1.00 0.00 O +ATOM 145 C GLU 8 33.570 24.164 30.464 1.00 0.00 C +ATOM 146 O GLU 8 33.840 24.286 31.658 1.00 0.00 O +ATOM 147 N GLY 9 33.696 22.982 29.849 1.00 0.00 N +ATOM 148 H GLY 9 33.287 22.892 28.929 1.00 0.00 H +ATOM 149 CA GLY 9 34.345 21.797 30.438 1.00 0.00 C +ATOM 150 HA2 GLY 9 35.247 21.575 29.868 1.00 0.00 H +ATOM 151 HA3 GLY 9 34.650 22.011 31.462 1.00 0.00 H +ATOM 152 C GLY 9 33.492 20.522 30.448 1.00 0.00 C +ATOM 153 O GLY 9 32.620 20.332 29.602 1.00 0.00 O +ATOM 154 N LYS 10 33.792 19.600 31.384 1.00 0.00 N +ATOM 155 H LYS 10 34.546 19.810 32.024 1.00 0.00 H +ATOM 156 CA LYS 10 33.231 18.228 31.369 1.00 0.00 C +ATOM 157 HA LYS 10 32.207 18.313 30.994 1.00 0.00 H +ATOM 158 CB LYS 10 34.029 17.371 30.353 1.00 0.00 C +ATOM 159 HB2 LYS 10 34.519 18.019 29.622 1.00 0.00 H +ATOM 160 HB3 LYS 10 34.809 16.806 30.866 1.00 0.00 H +ATOM 161 CG LYS 10 33.125 16.407 29.565 1.00 0.00 C +ATOM 162 HG2 LYS 10 32.575 15.759 30.248 1.00 0.00 H +ATOM 163 HG3 LYS 10 32.406 16.996 28.991 1.00 0.00 H +ATOM 164 CD LYS 10 33.941 15.541 28.595 1.00 0.00 C +ATOM 165 HD2 LYS 10 34.578 16.183 27.985 1.00 0.00 H +ATOM 166 HD3 LYS 10 34.568 14.847 29.158 1.00 0.00 H +ATOM 167 CE LYS 10 32.994 14.759 27.678 1.00 0.00 C +ATOM 168 HE2 LYS 10 32.438 14.025 28.267 1.00 0.00 H +ATOM 169 HE3 LYS 10 32.275 15.460 27.247 1.00 0.00 H +ATOM 170 NZ LYS 10 33.721 14.092 26.575 1.00 0.00 N +ATOM 171 HZ1 LYS 10 34.417 13.448 26.913 1.00 0.00 H +ATOM 172 HZ2 LYS 10 33.061 13.594 25.979 1.00 0.00 H +ATOM 173 HZ3 LYS 10 34.203 14.795 26.004 1.00 0.00 H +ATOM 174 C LYS 10 33.089 17.528 32.737 1.00 0.00 C +ATOM 175 O LYS 10 33.156 16.303 32.800 1.00 0.00 O +ATOM 176 N ARG 11 32.949 18.273 33.841 1.00 0.00 N +ATOM 177 H ARG 11 32.915 19.267 33.709 1.00 0.00 H +ATOM 178 CA ARG 11 32.662 17.722 35.194 1.00 0.00 C +ATOM 179 HA ARG 11 32.758 16.632 35.161 1.00 0.00 H +ATOM 180 CB ARG 11 33.685 18.237 36.231 1.00 0.00 C +ATOM 181 HB2 ARG 11 33.709 19.326 36.208 1.00 0.00 H +ATOM 182 HB3 ARG 11 33.355 17.924 37.222 1.00 0.00 H +ATOM 183 CG ARG 11 35.099 17.680 35.989 1.00 0.00 C +ATOM 184 HG2 ARG 11 35.055 16.589 35.999 1.00 0.00 H +ATOM 185 HG3 ARG 11 35.449 18.007 35.010 1.00 0.00 H +ATOM 186 CD ARG 11 36.103 18.142 37.058 1.00 0.00 C +ATOM 187 HD2 ARG 11 36.071 19.228 37.118 1.00 0.00 H +ATOM 188 HD3 ARG 11 35.803 17.740 38.029 1.00 0.00 H +ATOM 189 NE ARG 11 37.479 17.692 36.740 1.00 0.00 N +ATOM 190 HE ARG 11 37.569 16.946 36.073 1.00 0.00 H +ATOM 191 CZ ARG 11 38.615 18.198 37.201 1.00 0.00 C +ATOM 192 NH1 ARG 11 38.667 19.233 37.987 1.00 0.00 N +ATOM 193 HH11 ARG 11 37.829 19.772 38.112 1.00 0.00 H +ATOM 194 HH12 ARG 11 39.560 19.686 38.132 1.00 0.00 H +ATOM 195 NH2 ARG 11 39.749 17.650 36.875 1.00 0.00 N +ATOM 196 HH21 ARG 11 39.795 16.894 36.219 1.00 0.00 H +ATOM 197 HH22 ARG 11 40.609 18.031 37.266 1.00 0.00 H +ATOM 198 C ARG 11 31.206 17.954 35.609 1.00 0.00 C +ATOM 199 O ARG 11 30.490 17.005 35.900 1.00 0.00 O +ATOM 200 N TYR 12 30.762 19.208 35.566 1.00 0.00 N +ATOM 201 H TYR 12 31.434 19.929 35.379 1.00 0.00 H +ATOM 202 CA TYR 12 29.346 19.607 35.531 1.00 0.00 C +ATOM 203 HA TYR 12 28.789 18.986 36.247 1.00 0.00 H +ATOM 204 CB TYR 12 29.234 21.066 36.001 1.00 0.00 C +ATOM 205 HB2 TYR 12 28.187 21.379 35.945 1.00 0.00 H +ATOM 206 HB3 TYR 12 29.493 21.077 37.062 1.00 0.00 H +ATOM 207 CG TYR 12 30.105 22.126 35.333 1.00 0.00 C +ATOM 208 CD1 TYR 12 30.870 21.891 34.171 1.00 0.00 C +ATOM 209 HD1 TYR 12 30.824 20.950 33.636 1.00 0.00 H +ATOM 210 CE1 TYR 12 31.738 22.879 33.670 1.00 0.00 C +ATOM 211 HE1 TYR 12 32.313 22.692 32.776 1.00 0.00 H +ATOM 212 CZ TYR 12 31.833 24.123 34.322 1.00 0.00 C +ATOM 213 OH TYR 12 32.699 25.074 33.898 1.00 0.00 O +ATOM 214 HH TYR 12 33.108 24.847 33.030 1.00 0.00 H +ATOM 215 CE2 TYR 12 30.999 24.398 35.419 1.00 0.00 C +ATOM 216 HE2 TYR 12 31.006 25.385 35.861 1.00 0.00 H +ATOM 217 CD2 TYR 12 30.158 23.394 35.933 1.00 0.00 C +ATOM 218 HD2 TYR 12 29.558 23.604 36.815 1.00 0.00 H +ATOM 219 C TYR 12 28.690 19.397 34.145 1.00 0.00 C +ATOM 220 O TYR 12 29.368 19.005 33.196 1.00 0.00 O +ATOM 221 N LYS 13 27.382 19.683 34.028 1.00 0.00 N +ATOM 222 H LYS 13 26.894 19.964 34.865 1.00 0.00 H +ATOM 223 CA LYS 13 26.590 19.509 32.789 1.00 0.00 C +ATOM 224 HA LYS 13 27.257 19.685 31.944 1.00 0.00 H +ATOM 225 CB LYS 13 26.113 18.042 32.728 1.00 0.00 C +ATOM 226 HB2 LYS 13 26.870 17.413 33.196 1.00 0.00 H +ATOM 227 HB3 LYS 13 25.191 17.936 33.302 1.00 0.00 H +ATOM 228 CG LYS 13 25.912 17.515 31.295 1.00 0.00 C +ATOM 229 HG2 LYS 13 25.056 18.000 30.825 1.00 0.00 H +ATOM 230 HG3 LYS 13 26.803 17.746 30.711 1.00 0.00 H +ATOM 231 CD LYS 13 25.715 15.990 31.282 1.00 0.00 C +ATOM 232 HD2 LYS 13 25.753 15.643 30.248 1.00 0.00 H +ATOM 233 HD3 LYS 13 26.543 15.525 31.821 1.00 0.00 H +ATOM 234 CE LYS 13 24.376 15.549 31.892 1.00 0.00 C +ATOM 235 HE2 LYS 13 24.136 16.182 32.751 1.00 0.00 H +ATOM 236 HE3 LYS 13 23.603 15.708 31.133 1.00 0.00 H +ATOM 237 NZ LYS 13 24.406 14.121 32.306 1.00 0.00 N +ATOM 238 HZ1 LYS 13 24.934 13.975 33.159 1.00 0.00 H +ATOM 239 HZ2 LYS 13 23.466 13.759 32.451 1.00 0.00 H +ATOM 240 HZ3 LYS 13 24.860 13.553 31.592 1.00 0.00 H +ATOM 241 C LYS 13 25.440 20.533 32.632 1.00 0.00 C +ATOM 242 O LYS 13 24.397 20.233 32.051 1.00 0.00 O +ATOM 243 N GLY 14 25.597 21.720 33.227 1.00 0.00 N +ATOM 244 H GLY 14 26.491 21.921 33.646 1.00 0.00 H +ATOM 245 CA GLY 14 24.547 22.749 33.314 1.00 0.00 C +ATOM 246 HA2 GLY 14 23.595 22.255 33.508 1.00 0.00 H +ATOM 247 HA3 GLY 14 24.753 23.393 34.169 1.00 0.00 H +ATOM 248 C GLY 14 24.384 23.636 32.065 1.00 0.00 C +ATOM 249 O GLY 14 25.241 23.673 31.182 1.00 0.00 O +ATOM 250 N VAL 15 23.283 24.395 32.031 1.00 0.00 N +ATOM 251 H VAL 15 22.640 24.337 32.808 1.00 0.00 H +ATOM 252 CA VAL 15 22.902 25.355 30.981 1.00 0.00 C +ATOM 253 HA VAL 15 23.781 25.595 30.382 1.00 0.00 H +ATOM 254 CB VAL 15 21.857 24.717 30.034 1.00 0.00 C +ATOM 255 HB VAL 15 22.299 23.817 29.609 1.00 0.00 H +ATOM 256 CG1 VAL 15 20.551 24.300 30.731 1.00 0.00 C +ATOM 257 HG11 VAL 15 20.049 25.165 31.169 1.00 0.00 H +ATOM 258 HG12 VAL 15 19.882 23.832 30.007 1.00 0.00 H +ATOM 259 HG13 VAL 15 20.757 23.573 31.519 1.00 0.00 H +ATOM 260 CG2 VAL 15 21.481 25.640 28.867 1.00 0.00 C +ATOM 261 HG21 VAL 15 22.382 25.990 28.366 1.00 0.00 H +ATOM 262 HG22 VAL 15 20.879 25.084 28.146 1.00 0.00 H +ATOM 263 HG23 VAL 15 20.901 26.492 29.221 1.00 0.00 H +ATOM 264 C VAL 15 22.399 26.651 31.633 1.00 0.00 C +ATOM 265 O VAL 15 21.845 26.618 32.728 1.00 0.00 O +HETATM 266 N HY1 16 22.593 27.795 30.980 1.00 0.00 N +HETATM 267 CA HY1 16 22.005 29.092 31.344 1.00 0.00 C +HETATM 268 C HY1 16 21.694 29.890 30.062 1.00 0.00 C +HETATM 269 O HY1 16 21.860 29.375 28.949 1.00 0.00 O +HETATM 270 CB HY1 16 22.928 29.838 32.334 1.00 0.00 C +HETATM 271 CG HY1 16 24.278 30.202 31.763 1.00 0.00 C +HETATM 272 CD2 HY1 16 24.599 31.380 31.142 1.00 0.00 C +HETATM 273 ND1 HY1 16 25.407 29.412 31.750 1.00 0.00 N +HETATM 274 CE1 HY1 16 26.387 30.121 31.164 1.00 0.00 C +HETATM 275 NE2 HY1 16 25.942 31.324 30.761 1.00 0.00 N +HETATM 276 H HY1 16 23.089 27.760 30.095 1.00 0.00 H +HETATM 277 HA HY1 16 21.042 28.937 31.836 1.00 0.00 H +HETATM 278 HB2 HY1 16 22.448 30.747 32.701 1.00 0.00 H +HETATM 279 HB3 HY1 16 23.076 29.209 33.217 1.00 0.00 H +HETATM 280 HD1 HY1 16 25.502 28.501 32.177 1.00 0.00 H +HETATM 281 HD2 HY1 16 23.933 32.219 30.992 1.00 0.00 H +HETATM 282 HE1 HY1 16 27.419 29.794 31.067 1.00 0.00 H +ATOM 283 N THR 17 21.213 31.125 30.221 1.00 0.00 N +ATOM 284 H THR 17 21.084 31.439 31.169 1.00 0.00 H +ATOM 285 CA THR 17 20.771 32.009 29.122 1.00 0.00 C +ATOM 286 HA THR 17 21.190 31.603 28.215 1.00 0.00 H +ATOM 287 CB THR 17 19.244 32.008 28.942 1.00 0.00 C +ATOM 288 HB THR 17 19.023 32.578 28.042 1.00 0.00 H +ATOM 289 CG2 THR 17 18.642 30.640 28.642 1.00 0.00 C +ATOM 290 HG21 THR 17 18.864 29.923 29.430 1.00 0.00 H +ATOM 291 HG22 THR 17 17.562 30.744 28.553 1.00 0.00 H +ATOM 292 HG23 THR 17 19.034 30.311 27.693 1.00 0.00 H +ATOM 293 OG1 THR 17 18.523 32.465 30.065 1.00 0.00 O +ATOM 294 HG1 THR 17 18.606 33.430 30.107 1.00 0.00 H +ATOM 295 C THR 17 21.279 33.458 29.181 1.00 0.00 C +ATOM 296 O THR 17 21.726 33.926 30.226 1.00 0.00 O +HETATM 297 N HY2 18 21.213 34.175 28.055 1.00 0.00 N +HETATM 298 CA HY2 18 21.495 35.612 27.957 1.00 0.00 C +HETATM 299 C HY2 18 20.395 36.305 27.153 1.00 0.00 C +HETATM 300 O HY2 18 20.079 35.863 26.049 1.00 0.00 O +HETATM 301 CB HY2 18 22.848 35.842 27.247 1.00 0.00 C +HETATM 302 CG HY2 18 24.050 35.344 28.020 1.00 0.00 C +HETATM 303 CD2 HY2 18 24.548 34.066 28.017 1.00 0.00 C +HETATM 304 ND1 HY2 18 24.828 36.083 28.888 1.00 0.00 N +HETATM 305 CE1 HY2 18 25.770 35.264 29.383 1.00 0.00 C +HETATM 306 NE2 HY2 18 25.640 34.024 28.889 1.00 0.00 N +HETATM 307 H HY2 18 20.908 33.715 27.202 1.00 0.00 H +HETATM 308 HA HY2 18 21.529 36.051 28.954 1.00 0.00 H +HETATM 309 HB2 HY2 18 22.822 35.342 26.280 1.00 0.00 H +HETATM 310 HB3 HY2 18 22.973 36.910 27.064 1.00 0.00 H +HETATM 311 HD1 HY2 18 24.725 37.067 29.105 1.00 0.00 H +HETATM 312 HD2 HY2 18 24.156 33.232 27.450 1.00 0.00 H +HETATM 313 HE1 HY2 18 26.531 35.559 30.091 1.00 0.00 H +ATOM 314 N GLU 19 19.822 37.382 27.687 1.00 0.00 N +ATOM 315 H GLU 19 20.120 37.688 28.599 1.00 0.00 H +ATOM 316 CA GLU 19 18.828 38.211 26.992 1.00 0.00 C +ATOM 317 HA GLU 19 18.106 37.555 26.510 1.00 0.00 H +ATOM 318 CB GLU 19 18.086 39.074 28.032 1.00 0.00 C +ATOM 319 HB2 GLU 19 17.783 38.444 28.864 1.00 0.00 H +ATOM 320 HB3 GLU 19 18.779 39.814 28.429 1.00 0.00 H +ATOM 321 CG GLU 19 16.839 39.798 27.502 1.00 0.00 C +ATOM 322 HG2 GLU 19 16.549 40.555 28.233 1.00 0.00 H +ATOM 323 HG3 GLU 19 17.073 40.313 26.569 1.00 0.00 H +ATOM 324 CD GLU 19 15.667 38.828 27.300 1.00 0.00 C +ATOM 325 OE1 GLU 19 15.544 38.285 26.172 1.00 0.00 O +ATOM 326 OE2 GLU 19 14.908 38.603 28.271 1.00 0.00 O +ATOM 327 C GLU 19 19.483 39.095 25.913 1.00 0.00 C +ATOM 328 O GLU 19 20.430 39.823 26.208 1.00 0.00 O +ATOM 329 N ALA 20 18.977 39.059 24.676 1.00 0.00 N +ATOM 330 H ALA 20 18.268 38.367 24.467 1.00 0.00 H +ATOM 331 CA ALA 20 19.340 40.004 23.612 1.00 0.00 C +ATOM 332 HA ALA 20 19.410 41.004 24.042 1.00 0.00 H +ATOM 333 CB ALA 20 20.714 39.620 23.042 1.00 0.00 C +ATOM 334 HB1 ALA 20 20.657 38.642 22.573 1.00 0.00 H +ATOM 335 HB2 ALA 20 21.036 40.351 22.302 1.00 0.00 H +ATOM 336 HB3 ALA 20 21.459 39.585 23.834 1.00 0.00 H +ATOM 337 C ALA 20 18.286 40.039 22.486 1.00 0.00 C +ATOM 338 O ALA 20 17.384 39.200 22.439 1.00 0.00 O +ATOM 339 N VAL 21 18.416 40.981 21.545 1.00 0.00 N +ATOM 340 H VAL 21 19.145 41.670 21.653 1.00 0.00 H +ATOM 341 CA VAL 21 17.672 40.975 20.262 1.00 0.00 C +ATOM 342 HA VAL 21 16.689 40.537 20.427 1.00 0.00 H +ATOM 343 CB VAL 21 17.448 42.410 19.731 1.00 0.00 C +ATOM 344 HB VAL 21 16.804 42.345 18.853 1.00 0.00 H +ATOM 345 CG1 VAL 21 16.721 43.284 20.761 1.00 0.00 C +ATOM 346 HG11 VAL 21 17.357 43.476 21.625 1.00 0.00 H +ATOM 347 HG12 VAL 21 16.455 44.237 20.303 1.00 0.00 H +ATOM 348 HG13 VAL 21 15.806 42.790 21.088 1.00 0.00 H +ATOM 349 CG2 VAL 21 18.744 43.117 19.309 1.00 0.00 C +ATOM 350 HG21 VAL 21 19.218 42.578 18.489 1.00 0.00 H +ATOM 351 HG22 VAL 21 18.510 44.121 18.954 1.00 0.00 H +ATOM 352 HG23 VAL 21 19.441 43.191 20.143 1.00 0.00 H +ATOM 353 C VAL 21 18.344 40.117 19.176 1.00 0.00 C +ATOM 354 O VAL 21 17.744 39.875 18.133 1.00 0.00 O +ATOM 355 N ASP 22 19.590 39.693 19.410 1.00 0.00 N +ATOM 356 H ASP 22 20.003 39.905 20.303 1.00 0.00 H +ATOM 357 CA ASP 22 20.496 39.093 18.428 1.00 0.00 C +ATOM 358 HA ASP 22 19.939 38.443 17.752 1.00 0.00 H +ATOM 359 CB ASP 22 21.118 40.245 17.617 1.00 0.00 C +ATOM 360 HB2 ASP 22 20.331 40.741 17.046 1.00 0.00 H +ATOM 361 HB3 ASP 22 21.537 40.973 18.314 1.00 0.00 H +ATOM 362 CG ASP 22 22.212 39.808 16.646 1.00 0.00 C +ATOM 363 OD1 ASP 22 23.135 40.614 16.431 1.00 0.00 O +ATOM 364 OD2 ASP 22 22.150 38.658 16.158 1.00 0.00 O +ATOM 365 C ASP 22 21.589 38.257 19.129 1.00 0.00 C +ATOM 366 O ASP 22 22.026 38.601 20.232 1.00 0.00 O +ATOM 367 N PHE 23 22.075 37.194 18.482 1.00 0.00 N +ATOM 368 H PHE 23 21.801 37.088 17.511 1.00 0.00 H +ATOM 369 CA PHE 23 23.223 36.413 18.957 1.00 0.00 C +ATOM 370 HA PHE 23 23.033 36.100 19.983 1.00 0.00 H +ATOM 371 CB PHE 23 23.435 35.163 18.098 1.00 0.00 C +ATOM 372 HB2 PHE 23 23.449 35.439 17.042 1.00 0.00 H +ATOM 373 HB3 PHE 23 24.415 34.748 18.336 1.00 0.00 H +ATOM 374 CG PHE 23 22.418 34.075 18.332 1.00 0.00 C +ATOM 375 CD1 PHE 23 21.326 33.930 17.460 1.00 0.00 C +ATOM 376 HD1 PHE 23 21.215 34.591 16.613 1.00 0.00 H +ATOM 377 CE1 PHE 23 20.387 32.912 17.686 1.00 0.00 C +ATOM 378 HE1 PHE 23 19.553 32.789 17.010 1.00 0.00 H +ATOM 379 CZ PHE 23 20.545 32.053 18.784 1.00 0.00 C +ATOM 380 HZ PHE 23 19.804 31.307 18.977 1.00 0.00 H +ATOM 381 CE2 PHE 23 21.642 32.183 19.650 1.00 0.00 C +ATOM 382 HE2 PHE 23 21.763 31.512 20.488 1.00 0.00 H +ATOM 383 CD2 PHE 23 22.581 33.199 19.421 1.00 0.00 C +ATOM 384 HD2 PHE 23 23.433 33.303 20.076 1.00 0.00 H +ATOM 385 C PHE 23 24.522 37.216 18.948 1.00 0.00 C +ATOM 386 O PHE 23 25.288 37.123 19.906 1.00 0.00 O +ATOM 387 N ALA 24 24.777 38.032 17.920 1.00 0.00 N +ATOM 388 H ALA 24 24.098 38.127 17.167 1.00 0.00 H +ATOM 389 CA ALA 24 26.004 38.826 17.863 1.00 0.00 C +ATOM 390 HA ALA 24 26.836 38.166 18.118 1.00 0.00 H +ATOM 391 CB ALA 24 26.244 39.297 16.423 1.00 0.00 C +ATOM 392 HB1 ALA 24 25.486 40.016 16.122 1.00 0.00 H +ATOM 393 HB2 ALA 24 27.226 39.763 16.347 1.00 0.00 H +ATOM 394 HB3 ALA 24 26.209 38.442 15.744 1.00 0.00 H +ATOM 395 C ALA 24 26.024 39.969 18.904 1.00 0.00 C +ATOM 396 O ALA 24 27.084 40.536 19.172 1.00 0.00 O +ATOM 397 N GLU 25 24.892 40.281 19.545 1.00 0.00 N +ATOM 398 H GLU 25 24.041 39.856 19.205 1.00 0.00 H +ATOM 399 CA GLU 25 24.819 41.085 20.776 1.00 0.00 C +ATOM 400 HA GLU 25 25.636 41.806 20.796 1.00 0.00 H +ATOM 401 CB GLU 25 23.498 41.871 20.814 1.00 0.00 C +ATOM 402 HB2 GLU 25 22.673 41.163 20.774 1.00 0.00 H +ATOM 403 HB3 GLU 25 23.429 42.408 21.760 1.00 0.00 H +ATOM 404 CG GLU 25 23.310 42.881 19.671 1.00 0.00 C +ATOM 405 HG2 GLU 25 23.577 42.429 18.714 1.00 0.00 H +ATOM 406 HG3 GLU 25 22.247 43.135 19.624 1.00 0.00 H +ATOM 407 CD GLU 25 24.114 44.170 19.880 1.00 0.00 C +ATOM 408 OE1 GLU 25 23.462 45.220 20.101 1.00 0.00 O +ATOM 409 OE2 GLU 25 25.371 44.098 19.811 1.00 0.00 O +ATOM 410 C GLU 25 24.959 40.215 22.041 1.00 0.00 C +ATOM 411 O GLU 25 25.732 40.553 22.938 1.00 0.00 O +ATOM 412 N ALA 26 24.299 39.050 22.103 1.00 0.00 N +ATOM 413 H ALA 26 23.662 38.814 21.352 1.00 0.00 H +ATOM 414 CA ALA 26 24.423 38.100 23.218 1.00 0.00 C +ATOM 415 HA ALA 26 24.130 38.609 24.131 1.00 0.00 H +ATOM 416 CB ALA 26 23.471 36.923 22.993 1.00 0.00 C +ATOM 417 HB1 ALA 26 23.770 36.368 22.108 1.00 0.00 H +ATOM 418 HB2 ALA 26 23.499 36.260 23.854 1.00 0.00 H +ATOM 419 HB3 ALA 26 22.460 37.285 22.860 1.00 0.00 H +ATOM 420 C ALA 26 25.868 37.595 23.424 1.00 0.00 C +ATOM 421 O ALA 26 26.292 37.316 24.550 1.00 0.00 O +ATOM 422 N GLU 27 26.659 37.515 22.348 1.00 0.00 N +ATOM 423 H GLU 27 26.221 37.663 21.441 1.00 0.00 H +ATOM 424 CA GLU 27 28.109 37.261 22.347 1.00 0.00 C +ATOM 425 HA GLU 27 28.316 36.315 22.855 1.00 0.00 H +ATOM 426 CB GLU 27 28.586 37.117 20.887 1.00 0.00 C +ATOM 427 HB2 GLU 27 28.014 36.303 20.438 1.00 0.00 H +ATOM 428 HB3 GLU 27 28.354 38.028 20.337 1.00 0.00 H +ATOM 429 CG GLU 27 30.079 36.836 20.757 1.00 0.00 C +ATOM 430 HG2 GLU 27 30.614 37.779 20.882 1.00 0.00 H +ATOM 431 HG3 GLU 27 30.401 36.162 21.554 1.00 0.00 H +ATOM 432 CD GLU 27 30.366 36.227 19.390 1.00 0.00 C +ATOM 433 OE1 GLU 27 30.986 36.917 18.564 1.00 0.00 O +ATOM 434 OE2 GLU 27 29.944 35.073 19.158 1.00 0.00 O +ATOM 435 C GLU 27 28.855 38.375 23.112 1.00 0.00 C +ATOM 436 O GLU 27 29.633 38.083 24.023 1.00 0.00 O +ATOM 437 N LYS 28 28.553 39.656 22.836 1.00 0.00 N +ATOM 438 H LYS 28 27.822 39.830 22.156 1.00 0.00 H +ATOM 439 CA LYS 28 29.116 40.802 23.576 1.00 0.00 C +ATOM 440 HA LYS 28 30.202 40.719 23.569 1.00 0.00 H +ATOM 441 CB LYS 28 28.725 42.140 22.919 1.00 0.00 C +ATOM 442 HB2 LYS 28 27.648 42.281 22.995 1.00 0.00 H +ATOM 443 HB3 LYS 28 29.205 42.945 23.473 1.00 0.00 H +ATOM 444 CG LYS 28 29.135 42.250 21.442 1.00 0.00 C +ATOM 445 HG2 LYS 28 30.206 42.069 21.341 1.00 0.00 H +ATOM 446 HG3 LYS 28 28.602 41.496 20.871 1.00 0.00 H +ATOM 447 CD LYS 28 28.806 43.646 20.888 1.00 0.00 C +ATOM 448 HD2 LYS 28 27.796 43.939 21.184 1.00 0.00 H +ATOM 449 HD3 LYS 28 29.505 44.362 21.322 1.00 0.00 H +ATOM 450 CE LYS 28 28.917 43.732 19.359 1.00 0.00 C +ATOM 451 HE2 LYS 28 29.049 44.784 19.086 1.00 0.00 H +ATOM 452 HE3 LYS 28 29.802 43.181 19.025 1.00 0.00 H +ATOM 453 NZ LYS 28 27.696 43.214 18.694 1.00 0.00 N +ATOM 454 HZ1 LYS 28 26.858 43.680 19.063 1.00 0.00 H +ATOM 455 HZ2 LYS 28 27.718 43.355 17.696 1.00 0.00 H +ATOM 456 HZ3 LYS 28 27.563 42.223 18.882 1.00 0.00 H +ATOM 457 C LYS 28 28.694 40.774 25.048 1.00 0.00 C +ATOM 458 O LYS 28 29.531 40.971 25.922 1.00 0.00 O +ATOM 459 N PHE 29 27.433 40.461 25.351 1.00 0.00 N +ATOM 460 H PHE 29 26.770 40.367 24.587 1.00 0.00 H +ATOM 461 CA PHE 29 26.956 40.324 26.737 1.00 0.00 C +ATOM 462 HA PHE 29 27.288 41.196 27.301 1.00 0.00 H +ATOM 463 CB PHE 29 25.418 40.308 26.753 1.00 0.00 C +ATOM 464 HB2 PHE 29 25.082 39.379 26.290 1.00 0.00 H +ATOM 465 HB3 PHE 29 25.083 40.298 27.791 1.00 0.00 H +ATOM 466 CG PHE 29 24.734 41.474 26.050 1.00 0.00 C +ATOM 467 CD1 PHE 29 23.512 41.261 25.382 1.00 0.00 C +ATOM 468 HD1 PHE 29 23.048 40.287 25.399 1.00 0.00 H +ATOM 469 CE1 PHE 29 22.881 42.313 24.694 1.00 0.00 C +ATOM 470 HE1 PHE 29 21.946 42.138 24.183 1.00 0.00 H +ATOM 471 CZ PHE 29 23.462 43.592 24.675 1.00 0.00 C +ATOM 472 HZ PHE 29 22.980 44.397 24.138 1.00 0.00 H +ATOM 473 CE2 PHE 29 24.664 43.823 25.367 1.00 0.00 C +ATOM 474 HE2 PHE 29 25.105 44.809 25.369 1.00 0.00 H +ATOM 475 CD2 PHE 29 25.293 42.771 26.056 1.00 0.00 C +ATOM 476 HD2 PHE 29 26.211 42.971 26.586 1.00 0.00 H +ATOM 477 C PHE 29 27.555 39.107 27.465 1.00 0.00 C +ATOM 478 O PHE 29 27.773 39.150 28.677 1.00 0.00 O +ATOM 479 N THR 30 27.896 38.038 26.741 1.00 0.00 N +ATOM 480 H THR 30 27.619 38.016 25.764 1.00 0.00 H +ATOM 481 CA THR 30 28.673 36.905 27.271 1.00 0.00 C +ATOM 482 HA THR 30 28.197 36.550 28.185 1.00 0.00 H +ATOM 483 CB THR 30 28.682 35.736 26.276 1.00 0.00 C +ATOM 484 HB THR 30 29.041 36.062 25.302 1.00 0.00 H +ATOM 485 CG2 THR 30 29.498 34.534 26.746 1.00 0.00 C +ATOM 486 HG21 THR 30 29.142 34.220 27.721 1.00 0.00 H +ATOM 487 HG22 THR 30 29.367 33.720 26.036 1.00 0.00 H +ATOM 488 HG23 THR 30 30.560 34.772 26.807 1.00 0.00 H +ATOM 489 OG1 THR 30 27.360 35.286 26.150 1.00 0.00 O +ATOM 490 HG1 THR 30 26.921 35.901 25.540 1.00 0.00 H +ATOM 491 C THR 30 30.096 37.329 27.627 1.00 0.00 C +ATOM 492 O THR 30 30.588 36.990 28.705 1.00 0.00 O +ATOM 493 N LYS 31 30.738 38.118 26.757 1.00 0.00 N +ATOM 494 H LYS 31 30.278 38.309 25.872 1.00 0.00 H +ATOM 495 CA LYS 31 32.079 38.688 26.976 1.00 0.00 C +ATOM 496 HA LYS 31 32.743 37.884 27.300 1.00 0.00 H +ATOM 497 CB LYS 31 32.621 39.274 25.671 1.00 0.00 C +ATOM 498 HB2 LYS 31 31.903 39.978 25.246 1.00 0.00 H +ATOM 499 HB3 LYS 31 33.541 39.820 25.894 1.00 0.00 H +ATOM 500 CG LYS 31 32.944 38.173 24.651 1.00 0.00 C +ATOM 501 HG2 LYS 31 33.671 37.499 25.091 1.00 0.00 H +ATOM 502 HG3 LYS 31 32.056 37.589 24.426 1.00 0.00 H +ATOM 503 CD LYS 31 33.506 38.765 23.356 1.00 0.00 C +ATOM 504 HD2 LYS 31 32.713 39.327 22.866 1.00 0.00 H +ATOM 505 HD3 LYS 31 34.316 39.458 23.597 1.00 0.00 H +ATOM 506 CE LYS 31 34.009 37.678 22.410 1.00 0.00 C +ATOM 507 HE2 LYS 31 33.210 36.951 22.212 1.00 0.00 H +ATOM 508 HE3 LYS 31 34.294 38.148 21.459 1.00 0.00 H +ATOM 509 NZ LYS 31 35.192 36.994 22.980 1.00 0.00 N +ATOM 510 HZ1 LYS 31 34.970 36.242 23.631 1.00 0.00 H +ATOM 511 HZ2 LYS 31 35.696 36.535 22.223 1.00 0.00 H +ATOM 512 HZ3 LYS 31 35.853 37.636 23.423 1.00 0.00 H +ATOM 513 C LYS 31 32.124 39.737 28.088 1.00 0.00 C +ATOM 514 O LYS 31 33.110 39.767 28.820 1.00 0.00 O +ATOM 515 N ALA 32 31.066 40.529 28.271 1.00 0.00 N +ATOM 516 H ALA 32 30.350 40.537 27.557 1.00 0.00 H +ATOM 517 CA ALA 32 30.916 41.417 29.424 1.00 0.00 C +ATOM 518 HA ALA 32 31.761 42.109 29.453 1.00 0.00 H +ATOM 519 CB ALA 32 29.630 42.243 29.272 1.00 0.00 C +ATOM 520 HB1 ALA 32 28.757 41.591 29.251 1.00 0.00 H +ATOM 521 HB2 ALA 32 29.539 42.927 30.118 1.00 0.00 H +ATOM 522 HB3 ALA 32 29.672 42.826 28.351 1.00 0.00 H +ATOM 523 C ALA 32 30.942 40.605 30.729 1.00 0.00 C +ATOM 524 O ALA 32 31.851 40.784 31.532 1.00 0.00 O +ATOM 525 N GLH 33 30.050 39.611 30.870 1.00 0.00 N +ATOM 526 H GLH 33 29.333 39.496 30.165 1.00 0.00 H +ATOM 527 CA GLH 33 30.047 38.725 32.041 1.00 0.00 C +ATOM 528 HA GLH 33 29.911 39.335 32.935 1.00 0.00 H +ATOM 529 CB GLH 33 28.891 37.715 31.963 1.00 0.00 C +ATOM 530 HB2 GLH 33 28.942 37.165 31.022 1.00 0.00 H +ATOM 531 HB3 GLH 33 29.025 37.002 32.778 1.00 0.00 H +ATOM 532 CG GLH 33 27.500 38.357 32.108 1.00 0.00 C +ATOM 533 HG2 GLH 33 27.504 39.042 32.957 1.00 0.00 H +ATOM 534 HG3 GLH 33 27.261 38.931 31.214 1.00 0.00 H +ATOM 535 CD GLH 33 26.406 37.318 32.358 1.00 0.00 C +ATOM 536 OE1 GLH 33 26.558 36.242 32.918 1.00 0.00 O +ATOM 537 OE2 GLH 33 25.174 37.633 31.910 1.00 0.00 O +ATOM 538 HE2 GLH 33 24.616 36.913 32.215 1.00 0.00 H +ATOM 539 C GLH 33 31.373 37.970 32.231 1.00 0.00 C +ATOM 540 O GLH 33 31.760 37.707 33.362 1.00 0.00 O +ATOM 541 N ALA 34 32.084 37.609 31.158 1.00 0.00 N +ATOM 542 H ALA 34 31.708 37.793 30.237 1.00 0.00 H +ATOM 543 CA ALA 34 33.402 36.984 31.269 1.00 0.00 C +ATOM 544 HA ALA 34 33.329 36.147 31.965 1.00 0.00 H +ATOM 545 CB ALA 34 33.799 36.424 29.900 1.00 0.00 C +ATOM 546 HB1 ALA 34 34.021 37.239 29.214 1.00 0.00 H +ATOM 547 HB2 ALA 34 34.684 35.801 30.018 1.00 0.00 H +ATOM 548 HB3 ALA 34 32.997 35.812 29.491 1.00 0.00 H +ATOM 549 C ALA 34 34.464 37.950 31.840 1.00 0.00 C +ATOM 550 O ALA 34 35.200 37.571 32.750 1.00 0.00 O +ATOM 551 N ASN 35 34.500 39.207 31.376 1.00 0.00 N +ATOM 552 H ASN 35 33.842 39.482 30.658 1.00 0.00 H +ATOM 553 CA ASN 35 35.384 40.242 31.928 1.00 0.00 C +ATOM 554 HA ASN 35 36.374 39.806 32.012 1.00 0.00 H +ATOM 555 CB ASN 35 35.506 41.432 30.957 1.00 0.00 C +ATOM 556 HB2 ASN 35 34.515 41.759 30.649 1.00 0.00 H +ATOM 557 HB3 ASN 35 35.980 42.260 31.484 1.00 0.00 H +ATOM 558 CG ASN 35 36.370 41.137 29.738 1.00 0.00 C +ATOM 559 OD1 ASN 35 37.587 41.194 29.762 1.00 0.00 O +ATOM 560 ND2 ASN 35 35.776 40.836 28.613 1.00 0.00 N +ATOM 561 HD21 ASN 35 36.375 40.628 27.819 1.00 0.00 H +ATOM 562 HD22 ASN 35 34.782 40.669 28.608 1.00 0.00 H +ATOM 563 C ASN 35 34.989 40.686 33.358 1.00 0.00 C +ATOM 564 O ASN 35 35.858 41.125 34.108 1.00 0.00 O +ATOM 565 N ASP 36 33.730 40.502 33.781 1.00 0.00 N +ATOM 566 H ASP 36 33.014 40.300 33.091 1.00 0.00 H +ATOM 567 CA ASP 36 33.323 40.680 35.189 1.00 0.00 C +ATOM 568 HA ASP 36 33.626 41.677 35.506 1.00 0.00 H +ATOM 569 CB ASP 36 31.790 40.605 35.367 1.00 0.00 C +ATOM 570 HB2 ASP 36 31.453 39.608 35.113 1.00 0.00 H +ATOM 571 HB3 ASP 36 31.583 40.721 36.432 1.00 0.00 H +ATOM 572 CG ASP 36 30.936 41.606 34.560 1.00 0.00 C +ATOM 573 OD1 ASP 36 31.454 42.673 34.150 1.00 0.00 O +ATOM 574 OD2 ASP 36 29.729 41.321 34.369 1.00 0.00 O +ATOM 575 C ASP 36 34.022 39.677 36.139 1.00 0.00 C +ATOM 576 O ASP 36 34.366 40.036 37.265 1.00 0.00 O +ATOM 577 N TYR 37 34.279 38.436 35.693 1.00 0.00 N +ATOM 578 H TYR 37 33.929 38.187 34.778 1.00 0.00 H +ATOM 579 CA TYR 37 35.150 37.478 36.405 1.00 0.00 C +ATOM 580 HA TYR 37 35.031 37.637 37.477 1.00 0.00 H +ATOM 581 CB TYR 37 34.728 36.029 36.102 1.00 0.00 C +ATOM 582 HB2 TYR 37 34.894 35.833 35.042 1.00 0.00 H +ATOM 583 HB3 TYR 37 35.387 35.360 36.657 1.00 0.00 H +ATOM 584 CG TYR 37 33.295 35.659 36.456 1.00 0.00 C +ATOM 585 CD1 TYR 37 32.330 35.550 35.437 1.00 0.00 C +ATOM 586 HD1 TYR 37 32.623 35.735 34.416 1.00 0.00 H +ATOM 587 CE1 TYR 37 30.995 35.227 35.746 1.00 0.00 C +ATOM 588 HE1 TYR 37 30.257 35.181 34.963 1.00 0.00 H +ATOM 589 CZ TYR 37 30.630 34.968 37.084 1.00 0.00 C +ATOM 590 OH TYR 37 29.350 34.633 37.395 1.00 0.00 O +ATOM 591 HH TYR 37 28.718 35.000 36.775 1.00 0.00 H +ATOM 592 CE2 TYR 37 31.601 35.043 38.103 1.00 0.00 C +ATOM 593 HE2 TYR 37 31.310 34.844 39.122 1.00 0.00 H +ATOM 594 CD2 TYR 37 32.930 35.393 37.791 1.00 0.00 C +ATOM 595 HD2 TYR 37 33.670 35.453 38.575 1.00 0.00 H +ATOM 596 C TYR 37 36.653 37.661 36.084 1.00 0.00 C +ATOM 597 O TYR 37 37.509 37.230 36.866 1.00 0.00 O +ATOM 598 N GLY 38 36.981 38.278 34.941 1.00 0.00 N +ATOM 599 H GLY 38 36.217 38.563 34.340 1.00 0.00 H +ATOM 600 CA GLY 38 38.332 38.695 34.549 1.00 0.00 C +ATOM 601 HA2 GLY 38 38.510 39.692 34.952 1.00 0.00 H +ATOM 602 HA3 GLY 38 39.067 38.019 34.987 1.00 0.00 H +ATOM 603 C GLY 38 38.572 38.753 33.033 1.00 0.00 C +ATOM 604 O GLY 38 38.680 39.832 32.466 1.00 0.00 O +ATOM 605 N VAL 39 38.769 37.587 32.407 1.00 0.00 N +ATOM 606 H VAL 39 38.528 36.772 32.947 1.00 0.00 H +ATOM 607 CA VAL 39 39.120 37.334 30.982 1.00 0.00 C +ATOM 608 HA VAL 39 39.589 36.353 31.045 1.00 0.00 H +ATOM 609 CB VAL 39 40.278 38.199 30.408 1.00 0.00 C +ATOM 610 HB VAL 39 39.887 39.155 30.060 1.00 0.00 H +ATOM 611 CG1 VAL 39 41.410 38.442 31.429 1.00 0.00 C +ATOM 612 HG11 VAL 39 41.633 37.519 31.969 1.00 0.00 H +ATOM 613 HG12 VAL 39 42.308 38.801 30.921 1.00 0.00 H +ATOM 614 HG13 VAL 39 41.103 39.214 32.136 1.00 0.00 H +ATOM 615 CG2 VAL 39 40.949 37.487 29.219 1.00 0.00 C +ATOM 616 HG21 VAL 39 41.725 38.123 28.799 1.00 0.00 H +ATOM 617 HG22 VAL 39 41.401 36.553 29.543 1.00 0.00 H +ATOM 618 HG23 VAL 39 40.242 37.276 28.424 1.00 0.00 H +ATOM 619 C VAL 39 37.923 37.009 30.055 1.00 0.00 C +ATOM 620 O VAL 39 37.209 36.068 30.396 1.00 0.00 O +ATOM 621 N ASP 40 37.721 37.611 28.865 1.00 0.00 N +ATOM 622 H ASP 40 38.260 38.435 28.629 1.00 0.00 H +ATOM 623 CA ASP 40 36.920 36.948 27.802 1.00 0.00 C +ATOM 624 HA ASP 40 36.182 36.330 28.311 1.00 0.00 H +ATOM 625 CB ASP 40 36.053 37.904 26.947 1.00 0.00 C +ATOM 626 HB2 ASP 40 35.316 37.280 26.435 1.00 0.00 H +ATOM 627 HB3 ASP 40 35.494 38.546 27.614 1.00 0.00 H +ATOM 628 CG ASP 40 36.769 38.774 25.899 1.00 0.00 C +ATOM 629 OD1 ASP 40 37.171 39.908 26.230 1.00 0.00 O +ATOM 630 OD2 ASP 40 36.863 38.346 24.717 1.00 0.00 O +ATOM 631 C ASP 40 37.719 35.999 26.893 1.00 0.00 C +ATOM 632 O ASP 40 38.616 36.413 26.153 1.00 0.00 O +ATOM 633 N GLY 41 37.291 34.734 26.866 1.00 0.00 N +ATOM 634 H GLY 41 36.626 34.447 27.571 1.00 0.00 H +ATOM 635 CA GLY 41 37.610 33.768 25.816 1.00 0.00 C +ATOM 636 HA2 GLY 41 38.623 33.946 25.456 1.00 0.00 H +ATOM 637 HA3 GLY 41 37.580 32.771 26.242 1.00 0.00 H +ATOM 638 C GLY 41 36.655 33.826 24.612 1.00 0.00 C +ATOM 639 O GLY 41 35.774 34.683 24.510 1.00 0.00 O +ATOM 640 N GLU 42 36.792 32.855 23.705 1.00 0.00 N +ATOM 641 H GLU 42 37.487 32.129 23.865 1.00 0.00 H +ATOM 642 CA GLU 42 36.009 32.689 22.461 1.00 0.00 C +ATOM 643 HA GLU 42 35.334 33.540 22.334 1.00 0.00 H +ATOM 644 CB GLU 42 36.923 32.654 21.234 1.00 0.00 C +ATOM 645 HB2 GLU 42 37.390 31.662 21.199 1.00 0.00 H +ATOM 646 HB3 GLU 42 36.257 32.698 20.374 1.00 0.00 H +ATOM 647 CG GLU 42 37.926 33.780 21.144 1.00 0.00 C +ATOM 648 HG2 GLU 42 38.767 33.538 21.797 1.00 0.00 H +ATOM 649 HG3 GLU 42 38.362 33.796 20.165 1.00 0.00 H +ATOM 650 CD GLU 42 37.448 35.144 21.511 1.00 0.00 C +ATOM 651 OE1 GLU 42 36.392 35.531 21.013 1.00 0.00 O +ATOM 652 OE2 GLU 42 38.019 35.817 22.405 1.00 0.00 O +ATOM 653 C GLU 42 35.098 31.428 22.559 1.00 0.00 C +ATOM 654 O GLU 42 35.470 30.440 23.214 1.00 0.00 O +ATOM 655 N ILE 43 33.966 31.444 21.825 1.00 0.00 N +ATOM 656 H ILE 43 33.809 32.250 21.208 1.00 0.00 H +ATOM 657 CA ILE 43 32.887 30.421 21.861 1.00 0.00 C +ATOM 658 HA ILE 43 33.331 29.490 22.218 1.00 0.00 H +ATOM 659 CB ILE 43 31.749 30.833 22.843 1.00 0.00 C +ATOM 660 HB ILE 43 30.876 30.251 22.570 1.00 0.00 H +ATOM 661 CG2 ILE 43 32.120 30.445 24.279 1.00 0.00 C +ATOM 662 HG21 ILE 43 32.995 30.995 24.605 1.00 0.00 H +ATOM 663 HG22 ILE 43 31.282 30.667 24.932 1.00 0.00 H +ATOM 664 HG23 ILE 43 32.325 29.379 24.324 1.00 0.00 H +ATOM 665 CG1 ILE 43 31.340 32.325 22.832 1.00 0.00 C +ATOM 666 HG12 ILE 43 30.451 32.421 23.459 1.00 0.00 H +ATOM 667 HG13 ILE 43 32.122 32.931 23.275 1.00 0.00 H +ATOM 668 CD1 ILE 43 30.995 32.906 21.457 1.00 0.00 C +ATOM 669 HD11 ILE 43 30.366 32.224 20.891 1.00 0.00 H +ATOM 670 HD12 ILE 43 30.466 33.847 21.588 1.00 0.00 H +ATOM 671 HD13 ILE 43 31.907 33.103 20.890 1.00 0.00 H +ATOM 672 C ILE 43 32.351 30.121 20.452 1.00 0.00 C +ATOM 673 O ILE 43 32.559 30.895 19.514 1.00 0.00 O +ATOM 674 N THR 44 31.619 29.018 20.340 1.00 0.00 N +ATOM 675 H THR 44 31.486 28.447 21.169 1.00 0.00 H +ATOM 676 CA THR 44 30.903 28.600 19.128 1.00 0.00 C +ATOM 677 HA THR 44 31.230 29.213 18.290 1.00 0.00 H +ATOM 678 CB THR 44 31.269 27.144 18.781 1.00 0.00 C +ATOM 679 HB THR 44 31.001 26.477 19.600 1.00 0.00 H +ATOM 680 CG2 THR 44 30.624 26.613 17.495 1.00 0.00 C +ATOM 681 HG21 THR 44 30.802 27.305 16.665 1.00 0.00 H +ATOM 682 HG22 THR 44 31.041 25.628 17.235 1.00 0.00 H +ATOM 683 HG23 THR 44 29.544 26.485 17.639 1.00 0.00 H +ATOM 684 OG1 THR 44 32.661 27.056 18.558 1.00 0.00 O +ATOM 685 HG1 THR 44 32.846 26.251 18.066 1.00 0.00 H +ATOM 686 C THR 44 29.392 28.779 19.281 1.00 0.00 C +ATOM 687 O THR 44 28.876 28.725 20.395 1.00 0.00 O +ATOM 688 N GLN 45 28.679 29.026 18.178 1.00 0.00 N +ATOM 689 H GLN 45 29.149 29.020 17.288 1.00 0.00 H +ATOM 690 CA GLN 45 27.222 29.231 18.139 1.00 0.00 C +ATOM 691 HA GLN 45 26.819 29.205 19.153 1.00 0.00 H +ATOM 692 CB GLN 45 26.897 30.607 17.518 1.00 0.00 C +ATOM 693 HB2 GLN 45 27.284 30.625 16.500 1.00 0.00 H +ATOM 694 HB3 GLN 45 25.809 30.696 17.459 1.00 0.00 H +ATOM 695 CG GLN 45 27.454 31.826 18.281 1.00 0.00 C +ATOM 696 HG2 GLN 45 27.104 31.768 19.310 1.00 0.00 H +ATOM 697 HG3 GLN 45 28.542 31.780 18.287 1.00 0.00 H +ATOM 698 CD GLN 45 27.016 33.162 17.659 1.00 0.00 C +ATOM 699 OE1 GLN 45 26.064 33.244 16.898 1.00 0.00 O +ATOM 700 NE2 GLN 45 27.679 34.270 17.903 1.00 0.00 N +ATOM 701 HE21 GLN 45 27.355 35.101 17.453 1.00 0.00 H +ATOM 702 HE22 GLN 45 28.552 34.317 18.441 1.00 0.00 H +ATOM 703 C GLN 45 26.480 28.159 17.312 1.00 0.00 C +ATOM 704 O GLN 45 27.046 27.601 16.370 1.00 0.00 O +ATOM 705 N ASP 46 25.191 27.966 17.604 1.00 0.00 N +ATOM 706 H ASP 46 24.838 28.365 18.468 1.00 0.00 H +ATOM 707 CA ASP 46 24.203 27.294 16.751 1.00 0.00 C +ATOM 708 HA ASP 46 24.528 27.356 15.711 1.00 0.00 H +ATOM 709 CB ASP 46 24.079 25.812 17.147 1.00 0.00 C +ATOM 710 HB2 ASP 46 24.979 25.272 16.851 1.00 0.00 H +ATOM 711 HB3 ASP 46 23.981 25.747 18.230 1.00 0.00 H +ATOM 712 CG ASP 46 22.852 25.158 16.507 1.00 0.00 C +ATOM 713 OD1 ASP 46 22.104 24.474 17.241 1.00 0.00 O +ATOM 714 OD2 ASP 46 22.584 25.407 15.313 1.00 0.00 O +ATOM 715 C ASP 46 22.831 27.991 16.868 1.00 0.00 C +ATOM 716 O ASP 46 22.288 28.138 17.964 1.00 0.00 O +ATOM 717 N ASP 47 22.230 28.373 15.739 1.00 0.00 N +ATOM 718 H ASP 47 22.690 28.167 14.865 1.00 0.00 H +ATOM 719 CA ASP 47 20.867 28.919 15.690 1.00 0.00 C +ATOM 720 HA ASP 47 20.729 29.593 16.537 1.00 0.00 H +ATOM 721 CB ASP 47 20.693 29.766 14.416 1.00 0.00 C +ATOM 722 HB2 ASP 47 21.415 30.585 14.422 1.00 0.00 H +ATOM 723 HB3 ASP 47 20.882 29.148 13.536 1.00 0.00 H +ATOM 724 CG ASP 47 19.278 30.347 14.340 1.00 0.00 C +ATOM 725 OD1 ASP 47 18.430 29.775 13.625 1.00 0.00 O +ATOM 726 OD2 ASP 47 18.941 31.266 15.120 1.00 0.00 O +ATOM 727 C ASP 47 19.773 27.830 15.792 1.00 0.00 C +ATOM 728 O ASP 47 18.707 28.086 16.356 1.00 0.00 O +ATOM 729 N ALA 48 20.006 26.600 15.319 1.00 0.00 N +ATOM 730 H ALA 48 20.951 26.350 15.024 1.00 0.00 H +ATOM 731 CA ALA 48 18.970 25.560 15.236 1.00 0.00 C +ATOM 732 HA ALA 48 18.105 25.984 14.723 1.00 0.00 H +ATOM 733 CB ALA 48 19.510 24.405 14.386 1.00 0.00 C +ATOM 734 HB1 ALA 48 20.362 23.940 14.885 1.00 0.00 H +ATOM 735 HB2 ALA 48 18.729 23.659 14.239 1.00 0.00 H +ATOM 736 HB3 ALA 48 19.832 24.783 13.415 1.00 0.00 H +ATOM 737 C ALA 48 18.489 25.071 16.618 1.00 0.00 C +ATOM 738 O ALA 48 17.304 24.774 16.796 1.00 0.00 O +ATOM 739 N THR 49 19.392 25.037 17.602 1.00 0.00 N +ATOM 740 H THR 49 20.372 25.112 17.325 1.00 0.00 H +ATOM 741 CA THR 49 19.113 24.869 19.043 1.00 0.00 C +ATOM 742 HA THR 49 18.084 24.531 19.159 1.00 0.00 H +ATOM 743 CB THR 49 20.020 23.800 19.672 1.00 0.00 C +ATOM 744 HB THR 49 19.698 23.651 20.702 1.00 0.00 H +ATOM 745 CG2 THR 49 19.958 22.443 18.975 1.00 0.00 C +ATOM 746 HG21 THR 49 20.321 22.522 17.950 1.00 0.00 H +ATOM 747 HG22 THR 49 20.590 21.745 19.521 1.00 0.00 H +ATOM 748 HG23 THR 49 18.931 22.081 18.973 1.00 0.00 H +ATOM 749 OG1 THR 49 21.361 24.217 19.698 1.00 0.00 O +ATOM 750 HG1 THR 49 21.679 24.247 18.761 1.00 0.00 H +ATOM 751 C THR 49 19.231 26.177 19.841 1.00 0.00 C +ATOM 752 O THR 49 19.101 26.167 21.068 1.00 0.00 O +ATOM 753 N LYS 50 19.468 27.312 19.167 1.00 0.00 N +ATOM 754 H LYS 50 19.560 27.226 18.161 1.00 0.00 H +ATOM 755 CA LYS 50 19.589 28.671 19.731 1.00 0.00 C +ATOM 756 HA LYS 50 20.008 29.273 18.928 1.00 0.00 H +ATOM 757 CB LYS 50 18.185 29.226 20.094 1.00 0.00 C +ATOM 758 HB2 LYS 50 17.768 28.587 20.874 1.00 0.00 H +ATOM 759 HB3 LYS 50 18.294 30.221 20.527 1.00 0.00 H +ATOM 760 CG LYS 50 17.144 29.315 18.956 1.00 0.00 C +ATOM 761 HG2 LYS 50 17.135 28.389 18.385 1.00 0.00 H +ATOM 762 HG3 LYS 50 16.161 29.418 19.417 1.00 0.00 H +ATOM 763 CD LYS 50 17.338 30.517 18.014 1.00 0.00 C +ATOM 764 HD2 LYS 50 17.289 31.432 18.604 1.00 0.00 H +ATOM 765 HD3 LYS 50 18.319 30.466 17.544 1.00 0.00 H +ATOM 766 CE LYS 50 16.255 30.586 16.925 1.00 0.00 C +ATOM 767 HE2 LYS 50 15.311 30.225 17.334 1.00 0.00 H +ATOM 768 HE3 LYS 50 16.117 31.628 16.628 1.00 0.00 H +ATOM 769 NZ LYS 50 16.628 29.801 15.728 1.00 0.00 N +ATOM 770 HZ1 LYS 50 17.134 28.955 15.975 1.00 0.00 H +ATOM 771 HZ2 LYS 50 15.839 29.559 15.145 1.00 0.00 H +ATOM 772 HZ3 LYS 50 17.313 30.309 15.154 1.00 0.00 H +ATOM 773 C LYS 50 20.608 28.778 20.892 1.00 0.00 C +ATOM 774 O LYS 50 20.304 29.382 21.927 1.00 0.00 O +ATOM 775 N THR 51 21.791 28.170 20.745 1.00 0.00 N +ATOM 776 H THR 51 22.017 27.827 19.813 1.00 0.00 H +ATOM 777 CA THR 51 22.737 27.843 21.835 1.00 0.00 C +ATOM 778 HA THR 51 22.433 28.389 22.721 1.00 0.00 H +ATOM 779 CB THR 51 22.629 26.341 22.176 1.00 0.00 C +ATOM 780 HB THR 51 22.792 25.755 21.272 1.00 0.00 H +ATOM 781 CG2 THR 51 23.614 25.869 23.247 1.00 0.00 C +ATOM 782 HG21 THR 51 23.549 26.508 24.126 1.00 0.00 H +ATOM 783 HG22 THR 51 23.377 24.843 23.525 1.00 0.00 H +ATOM 784 HG23 THR 51 24.627 25.883 22.852 1.00 0.00 H +ATOM 785 OG1 THR 51 21.358 26.039 22.712 1.00 0.00 O +ATOM 786 HG1 THR 51 20.709 26.084 21.991 1.00 0.00 H +ATOM 787 C THR 51 24.207 28.217 21.545 1.00 0.00 C +ATOM 788 O THR 51 24.716 27.973 20.456 1.00 0.00 O +ATOM 789 N PHE 52 24.918 28.749 22.550 1.00 0.00 N +ATOM 790 H PHE 52 24.402 29.020 23.376 1.00 0.00 H +ATOM 791 CA PHE 52 26.389 28.875 22.610 1.00 0.00 C +ATOM 792 HA PHE 52 26.783 28.971 21.598 1.00 0.00 H +ATOM 793 CB PHE 52 26.774 30.130 23.412 1.00 0.00 C +ATOM 794 HB2 PHE 52 26.267 30.101 24.374 1.00 0.00 H +ATOM 795 HB3 PHE 52 27.845 30.085 23.622 1.00 0.00 H +ATOM 796 CG PHE 52 26.494 31.471 22.766 1.00 0.00 C +ATOM 797 CD1 PHE 52 25.266 32.130 22.966 1.00 0.00 C +ATOM 798 HD1 PHE 52 24.487 31.661 23.545 1.00 0.00 H +ATOM 799 CE1 PHE 52 25.047 33.404 22.412 1.00 0.00 C +ATOM 800 HE1 PHE 52 24.099 33.900 22.556 1.00 0.00 H +ATOM 801 CZ PHE 52 26.060 34.026 21.662 1.00 0.00 C +ATOM 802 HZ PHE 52 25.893 34.995 21.218 1.00 0.00 H +ATOM 803 CE2 PHE 52 27.293 33.379 21.473 1.00 0.00 C +ATOM 804 HE2 PHE 52 28.070 33.856 20.889 1.00 0.00 H +ATOM 805 CD2 PHE 52 27.503 32.100 22.017 1.00 0.00 C +ATOM 806 HD2 PHE 52 28.441 31.592 21.854 1.00 0.00 H +ATOM 807 C PHE 52 27.066 27.661 23.288 1.00 0.00 C +ATOM 808 O PHE 52 26.544 27.156 24.288 1.00 0.00 O +ATOM 809 N THR 53 28.266 27.263 22.839 1.00 0.00 N +ATOM 810 H THR 53 28.641 27.723 22.012 1.00 0.00 H +ATOM 811 CA THR 53 29.074 26.151 23.403 1.00 0.00 C +ATOM 812 HA THR 53 28.798 26.016 24.449 1.00 0.00 H +ATOM 813 CB THR 53 28.800 24.819 22.672 1.00 0.00 C +ATOM 814 HB THR 53 29.387 24.035 23.153 1.00 0.00 H +ATOM 815 CG2 THR 53 27.341 24.373 22.695 1.00 0.00 C +ATOM 816 HG21 THR 53 26.734 25.036 22.079 1.00 0.00 H +ATOM 817 HG22 THR 53 27.264 23.356 22.311 1.00 0.00 H +ATOM 818 HG23 THR 53 26.972 24.389 23.719 1.00 0.00 H +ATOM 819 OG1 THR 53 29.192 24.898 21.323 1.00 0.00 O +ATOM 820 HG1 THR 53 28.756 24.184 20.851 1.00 0.00 H +ATOM 821 C THR 53 30.594 26.406 23.377 1.00 0.00 C +ATOM 822 O THR 53 31.083 27.326 22.718 1.00 0.00 O +ATOM 823 N ALA 54 31.348 25.564 24.100 1.00 0.00 N +ATOM 824 H ALA 54 30.876 24.846 24.626 1.00 0.00 H +ATOM 825 CA ALA 54 32.812 25.456 24.054 1.00 0.00 C +ATOM 826 HA ALA 54 33.210 26.268 23.442 1.00 0.00 H +ATOM 827 CB ALA 54 33.366 25.629 25.475 1.00 0.00 C +ATOM 828 HB1 ALA 54 33.015 24.817 26.113 1.00 0.00 H +ATOM 829 HB2 ALA 54 34.457 25.616 25.456 1.00 0.00 H +ATOM 830 HB3 ALA 54 33.038 26.583 25.891 1.00 0.00 H +ATOM 831 C ALA 54 33.278 24.123 23.415 1.00 0.00 C +ATOM 832 O ALA 54 32.505 23.167 23.298 1.00 0.00 O +ATOM 833 N GLH 55 34.548 24.067 22.999 1.00 0.00 N +ATOM 834 H GLH 55 35.146 24.849 23.215 1.00 0.00 H +ATOM 835 CA GLH 55 35.168 22.922 22.308 1.00 0.00 C +ATOM 836 HA GLH 55 34.398 22.426 21.716 1.00 0.00 H +ATOM 837 CB GLH 55 36.234 23.451 21.327 1.00 0.00 C +ATOM 838 HB2 GLH 55 36.972 24.031 21.884 1.00 0.00 H +ATOM 839 HB3 GLH 55 36.743 22.608 20.858 1.00 0.00 H +ATOM 840 CG GLH 55 35.617 24.327 20.216 1.00 0.00 C +ATOM 841 HG2 GLH 55 34.958 23.714 19.601 1.00 0.00 H +ATOM 842 HG3 GLH 55 35.020 25.129 20.650 1.00 0.00 H +ATOM 843 CD GLH 55 36.655 24.987 19.312 1.00 0.00 C +ATOM 844 OE1 GLH 55 37.842 25.121 19.573 1.00 0.00 O +ATOM 845 OE2 GLH 55 36.155 25.451 18.149 1.00 0.00 O +ATOM 846 HE2 GLH 55 36.883 25.858 17.675 1.00 0.00 H +ATOM 847 C GLH 55 35.736 21.856 23.279 1.00 0.00 C +ATOM 848 O GLH 55 36.043 22.164 24.428 1.00 0.00 O +ATOM 849 N GLU 56 35.854 20.603 22.810 1.00 0.00 N +ATOM 850 H GLU 56 35.627 20.451 21.842 1.00 0.00 H +ATOM 851 CA GLU 56 36.225 19.391 23.580 1.00 0.00 C +ATOM 852 HA GLU 56 35.760 19.455 24.564 1.00 0.00 H +ATOM 853 CB GLU 56 35.617 18.165 22.855 1.00 0.00 C +ATOM 854 HB2 GLU 56 34.541 18.196 23.027 1.00 0.00 H +ATOM 855 HB3 GLU 56 35.768 18.297 21.782 1.00 0.00 H +ATOM 856 CG GLU 56 36.111 16.739 23.193 1.00 0.00 C +ATOM 857 HG2 GLU 56 35.454 16.031 22.680 1.00 0.00 H +ATOM 858 HG3 GLU 56 37.100 16.595 22.754 1.00 0.00 H +ATOM 859 CD GLU 56 36.165 16.375 24.688 1.00 0.00 C +ATOM 860 OE1 GLU 56 37.290 16.354 25.251 1.00 0.00 O +ATOM 861 OE2 GLU 56 35.109 16.022 25.266 1.00 0.00 O +ATOM 862 C GLU 56 37.723 19.244 23.888 1.00 0.00 C +ATOM 863 O GLU 56 38.090 19.361 25.078 1.00 0.00 O +ATOM 864 OXT GLU 56 38.506 18.730 23.060 1.00 0.00 O +HETATM 865 ZN ZN1 57 26.762 32.444 29.336 1.00 0.00 Zn +HETATM 866 N AN1 58 28.364 33.308 30.222 1.00 0.00 N +HETATM 867 C AN1 58 30.678 34.028 31.184 1.00 0.00 C +HETATM 868 C1 AN1 58 29.379 33.629 30.674 1.00 0.00 C +HETATM 869 H AN1 58 30.582 34.423 32.200 1.00 0.00 H +HETATM 870 H1 AN1 58 31.113 34.795 30.535 1.00 0.00 H +HETATM 871 H2 AN1 58 31.336 33.149 31.202 1.00 0.00 H +HETATM 872 N1 AZI 59 30.830 28.620 29.341 1.00 0.00 N +HETATM 873 N2 AZI 59 30.309 29.481 30.054 1.00 0.00 N +HETATM 874 N3 AZI 59 29.759 30.371 30.755 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 73 72 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 865 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 121 122 126 +CONECT 121 120 +CONECT 122 125 120 123 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 127 129 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 145 +CONECT 135 134 +CONECT 136 137 134 139 138 +CONECT 137 136 +CONECT 138 136 +CONECT 139 142 136 140 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 144 139 +CONECT 143 142 +CONECT 144 142 +CONECT 145 134 147 146 +CONECT 146 145 +CONECT 147 148 149 145 +CONECT 148 147 +CONECT 149 147 150 152 151 +CONECT 150 149 +CONECT 151 149 +CONECT 152 153 149 154 +CONECT 153 152 +CONECT 154 152 156 155 +CONECT 155 154 +CONECT 156 158 157 154 174 +CONECT 157 156 +CONECT 158 161 159 160 156 +CONECT 159 158 +CONECT 160 158 +CONECT 161 164 163 162 158 +CONECT 162 161 +CONECT 163 161 +CONECT 164 167 165 166 161 +CONECT 165 164 +CONECT 166 164 +CONECT 167 170 169 168 164 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 170 +CONECT 174 156 175 176 +CONECT 175 174 +CONECT 176 174 177 178 +CONECT 177 176 +CONECT 178 176 179 198 180 +CONECT 179 178 +CONECT 180 178 183 181 182 +CONECT 181 180 +CONECT 182 180 +CONECT 183 185 184 180 186 +CONECT 184 183 +CONECT 185 183 +CONECT 186 183 189 187 188 +CONECT 187 186 +CONECT 188 186 +CONECT 189 190 186 191 +CONECT 190 189 +CONECT 191 189 195 192 +CONECT 192 191 193 194 +CONECT 193 192 +CONECT 194 192 +CONECT 195 196 191 197 +CONECT 196 195 +CONECT 197 195 +CONECT 198 178 200 199 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 219 200 204 203 +CONECT 203 202 +CONECT 204 207 202 205 206 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 217 204 +CONECT 208 209 210 207 +CONECT 209 208 +CONECT 210 211 208 212 +CONECT 211 210 +CONECT 212 210 213 215 +CONECT 213 214 212 +CONECT 214 213 +CONECT 215 212 216 217 +CONECT 216 215 +CONECT 217 207 215 218 +CONECT 218 217 +CONECT 219 220 221 202 +CONECT 220 219 +CONECT 221 223 219 222 +CONECT 222 221 +CONECT 223 224 241 225 221 +CONECT 224 223 +CONECT 225 228 223 226 227 +CONECT 226 225 +CONECT 227 225 +CONECT 228 230 229 231 225 +CONECT 229 228 +CONECT 230 228 +CONECT 231 232 228 233 234 +CONECT 232 231 +CONECT 233 231 +CONECT 234 236 231 237 235 +CONECT 235 234 +CONECT 236 234 +CONECT 237 240 234 239 238 +CONECT 238 237 +CONECT 239 237 +CONECT 240 237 +CONECT 241 242 223 243 +CONECT 242 241 +CONECT 243 241 245 244 +CONECT 244 243 +CONECT 245 248 243 246 247 +CONECT 246 245 +CONECT 247 245 +CONECT 248 249 250 245 +CONECT 249 248 +CONECT 250 252 248 251 +CONECT 251 250 +CONECT 252 254 253 264 250 +CONECT 253 252 +CONECT 254 260 255 256 252 +CONECT 255 254 +CONECT 256 258 254 257 259 +CONECT 257 256 +CONECT 258 256 +CONECT 259 256 +CONECT 260 262 261 263 254 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 252 265 +CONECT 265 264 +CONECT 266 276 267 264 +CONECT 267 268 266 277 270 +CONECT 268 269 283 267 +CONECT 269 268 +CONECT 270 267 271 278 279 +CONECT 271 272 273 270 +CONECT 272 275 281 271 +CONECT 273 274 271 280 +CONECT 274 275 282 273 +CONECT 275 865 272 274 +CONECT 276 266 +CONECT 277 267 +CONECT 278 270 +CONECT 279 270 +CONECT 280 273 +CONECT 281 272 +CONECT 282 274 +CONECT 283 285 268 284 +CONECT 284 283 +CONECT 285 286 287 295 283 +CONECT 286 285 +CONECT 287 288 289 285 293 +CONECT 288 287 +CONECT 289 292 291 287 290 +CONECT 290 289 +CONECT 291 289 +CONECT 292 289 +CONECT 293 287 294 +CONECT 294 293 +CONECT 295 297 285 296 +CONECT 296 295 +CONECT 297 307 298 295 +CONECT 298 299 301 297 308 +CONECT 299 300 314 298 +CONECT 300 299 +CONECT 301 309 310 298 302 +CONECT 302 301 303 304 +CONECT 303 312 302 306 +CONECT 304 302 311 305 +CONECT 305 304 306 313 +CONECT 306 303 865 305 +CONECT 307 297 +CONECT 308 298 +CONECT 309 301 +CONECT 310 301 +CONECT 311 304 +CONECT 312 303 +CONECT 313 305 +CONECT 314 316 299 315 +CONECT 315 314 +CONECT 316 327 317 314 318 +CONECT 317 316 +CONECT 318 316 321 320 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 323 324 318 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 325 321 326 +CONECT 325 324 +CONECT 326 324 +CONECT 327 329 328 316 +CONECT 328 327 +CONECT 329 331 330 327 +CONECT 330 329 +CONECT 331 337 333 332 329 +CONECT 332 331 +CONECT 333 335 334 331 336 +CONECT 334 333 +CONECT 335 333 +CONECT 336 333 +CONECT 337 339 338 331 +CONECT 338 337 +CONECT 339 341 340 337 +CONECT 340 339 +CONECT 341 353 343 342 339 +CONECT 342 341 +CONECT 343 344 349 341 345 +CONECT 344 343 +CONECT 345 343 347 348 346 +CONECT 346 345 +CONECT 347 345 +CONECT 348 345 +CONECT 349 350 351 343 352 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 341 +CONECT 354 353 +CONECT 355 357 353 356 +CONECT 356 355 +CONECT 357 359 358 365 355 +CONECT 358 357 +CONECT 359 362 360 361 357 +CONECT 360 359 +CONECT 361 359 +CONECT 362 364 363 359 +CONECT 363 362 +CONECT 364 362 +CONECT 365 357 367 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 385 370 +CONECT 370 369 +CONECT 371 372 374 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 375 371 383 +CONECT 375 376 377 374 +CONECT 376 375 +CONECT 377 378 375 379 +CONECT 378 377 +CONECT 379 377 380 381 +CONECT 380 379 +CONECT 381 379 383 382 +CONECT 382 381 +CONECT 383 374 381 384 +CONECT 384 383 +CONECT 385 387 369 386 +CONECT 386 385 +CONECT 387 388 389 385 +CONECT 388 387 +CONECT 389 391 387 390 395 +CONECT 390 389 +CONECT 391 394 392 393 389 +CONECT 392 391 +CONECT 393 391 +CONECT 394 391 +CONECT 395 389 396 397 +CONECT 396 395 +CONECT 397 395 398 399 +CONECT 398 397 +CONECT 399 397 400 401 410 +CONECT 400 399 +CONECT 401 404 402 399 403 +CONECT 402 401 +CONECT 403 401 +CONECT 404 405 406 407 401 +CONECT 405 404 +CONECT 406 404 +CONECT 407 404 409 408 +CONECT 408 407 +CONECT 409 407 +CONECT 410 399 412 411 +CONECT 411 410 +CONECT 412 413 410 414 +CONECT 413 412 +CONECT 414 412 416 420 415 +CONECT 415 414 +CONECT 416 417 419 414 418 +CONECT 417 416 +CONECT 418 416 +CONECT 419 416 +CONECT 420 422 414 421 +CONECT 421 420 +CONECT 422 423 424 420 +CONECT 423 422 +CONECT 424 426 422 425 435 +CONECT 425 424 +CONECT 426 428 427 429 424 +CONECT 427 426 +CONECT 428 426 +CONECT 429 432 430 426 431 +CONECT 430 429 +CONECT 431 429 +CONECT 432 433 434 429 +CONECT 433 432 +CONECT 434 432 +CONECT 435 424 437 436 +CONECT 436 435 +CONECT 437 438 435 439 +CONECT 438 437 +CONECT 439 437 441 440 457 +CONECT 440 439 +CONECT 441 444 442 443 439 +CONECT 442 441 +CONECT 443 441 +CONECT 444 446 447 445 441 +CONECT 445 444 +CONECT 446 444 +CONECT 447 450 448 449 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 452 451 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 455 456 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 453 +CONECT 457 439 459 458 +CONECT 458 457 +CONECT 459 460 457 461 +CONECT 460 459 +CONECT 461 459 463 462 477 +CONECT 462 461 +CONECT 463 466 464 461 465 +CONECT 464 463 +CONECT 465 463 +CONECT 466 467 475 463 +CONECT 467 469 468 466 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 472 469 473 +CONECT 472 471 +CONECT 473 471 474 475 +CONECT 474 473 +CONECT 475 473 466 476 +CONECT 476 475 +CONECT 477 461 479 478 +CONECT 478 477 +CONECT 479 480 481 477 +CONECT 480 479 +CONECT 481 483 479 491 482 +CONECT 482 481 +CONECT 483 484 489 485 481 +CONECT 484 483 +CONECT 485 487 483 488 486 +CONECT 486 485 +CONECT 487 485 +CONECT 488 485 +CONECT 489 490 483 +CONECT 490 489 +CONECT 491 493 481 492 +CONECT 492 491 +CONECT 493 494 495 491 +CONECT 494 493 +CONECT 495 497 493 496 513 +CONECT 496 495 +CONECT 497 500 498 499 495 +CONECT 498 497 +CONECT 499 497 +CONECT 500 503 502 501 497 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 504 505 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 508 507 509 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 506 512 510 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 495 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 518 523 +CONECT 518 517 +CONECT 519 522 520 517 521 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 +CONECT 523 517 525 524 +CONECT 524 523 +CONECT 525 526 523 527 +CONECT 526 525 +CONECT 527 525 529 539 528 +CONECT 528 527 +CONECT 529 530 527 532 531 +CONECT 530 529 +CONECT 531 529 +CONECT 532 534 529 535 533 +CONECT 533 532 +CONECT 534 532 +CONECT 535 537 532 536 +CONECT 536 535 +CONECT 537 538 535 +CONECT 538 537 +CONECT 539 541 527 540 +CONECT 540 539 +CONECT 541 542 543 539 +CONECT 542 541 +CONECT 543 545 541 549 544 +CONECT 544 543 +CONECT 545 546 548 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 545 +CONECT 549 543 551 550 +CONECT 550 549 +CONECT 551 552 549 553 +CONECT 552 551 +CONECT 553 555 551 554 563 +CONECT 554 553 +CONECT 555 558 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 560 559 555 +CONECT 559 558 +CONECT 560 561 562 558 +CONECT 561 560 +CONECT 562 560 +CONECT 563 553 565 564 +CONECT 564 563 +CONECT 565 566 563 567 +CONECT 566 565 +CONECT 567 565 569 568 575 +CONECT 568 567 +CONECT 569 572 570 567 571 +CONECT 570 569 +CONECT 571 569 +CONECT 572 573 574 569 +CONECT 573 572 +CONECT 574 572 +CONECT 575 567 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 596 581 580 +CONECT 580 579 +CONECT 581 582 579 584 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 585 581 594 +CONECT 585 586 587 584 +CONECT 586 585 +CONECT 587 588 585 589 +CONECT 588 587 +CONECT 589 587 590 592 +CONECT 590 591 589 +CONECT 591 590 +CONECT 592 589 594 593 +CONECT 593 592 +CONECT 594 584 592 595 +CONECT 595 594 +CONECT 596 598 579 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 598 601 602 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 619 609 608 605 +CONECT 608 607 +CONECT 609 615 610 607 611 +CONECT 610 609 +CONECT 611 609 613 612 614 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 +CONECT 615 618 616 617 609 +CONECT 616 615 +CONECT 617 615 +CONECT 618 615 +CONECT 619 621 620 607 +CONECT 620 619 +CONECT 621 623 622 619 +CONECT 622 621 +CONECT 623 631 625 624 621 +CONECT 624 623 +CONECT 625 628 626 627 623 +CONECT 626 625 +CONECT 627 625 +CONECT 628 630 629 625 +CONECT 629 628 +CONECT 630 628 +CONECT 631 632 633 623 +CONECT 632 631 +CONECT 633 635 631 634 +CONECT 634 633 +CONECT 635 638 636 637 633 +CONECT 636 635 +CONECT 637 635 +CONECT 638 640 639 635 +CONECT 639 638 +CONECT 640 642 641 638 +CONECT 641 640 +CONECT 642 644 643 653 640 +CONECT 643 642 +CONECT 644 646 647 645 642 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 644 650 648 +CONECT 648 647 +CONECT 649 647 +CONECT 650 651 647 652 +CONECT 651 650 +CONECT 652 650 +CONECT 653 655 642 654 +CONECT 654 653 +CONECT 655 656 657 653 +CONECT 656 655 +CONECT 657 672 655 658 659 +CONECT 658 657 +CONECT 659 657 660 665 661 +CONECT 660 659 +CONECT 661 659 664 662 663 +CONECT 662 661 +CONECT 663 661 +CONECT 664 661 +CONECT 665 668 659 667 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 671 669 670 665 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 +CONECT 672 673 674 657 +CONECT 673 672 +CONECT 674 676 672 675 +CONECT 675 674 +CONECT 676 677 678 686 674 +CONECT 677 676 +CONECT 678 680 684 676 679 +CONECT 679 678 +CONECT 680 681 682 683 678 +CONECT 681 680 +CONECT 682 680 +CONECT 683 680 +CONECT 684 685 678 +CONECT 685 684 +CONECT 686 688 676 687 +CONECT 687 686 +CONECT 688 689 690 686 +CONECT 689 688 +CONECT 690 703 692 688 691 +CONECT 691 690 +CONECT 692 693 694 690 695 +CONECT 693 692 +CONECT 694 692 +CONECT 695 692 698 697 696 +CONECT 696 695 +CONECT 697 695 +CONECT 698 699 700 695 +CONECT 699 698 +CONECT 700 701 698 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 704 705 690 +CONECT 704 703 +CONECT 705 707 703 706 +CONECT 706 705 +CONECT 707 708 715 709 705 +CONECT 708 707 +CONECT 709 712 707 710 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 709 713 +CONECT 713 712 +CONECT 714 712 +CONECT 715 717 707 716 +CONECT 716 715 +CONECT 717 718 719 715 +CONECT 718 717 +CONECT 719 721 717 727 720 +CONECT 720 719 +CONECT 721 723 724 722 719 +CONECT 722 721 +CONECT 723 721 +CONECT 724 725 721 726 +CONECT 725 724 +CONECT 726 724 +CONECT 727 729 719 728 +CONECT 728 727 +CONECT 729 730 731 727 +CONECT 730 729 +CONECT 731 733 732 729 737 +CONECT 732 731 +CONECT 733 736 735 734 731 +CONECT 734 733 +CONECT 735 733 +CONECT 736 733 +CONECT 737 731 738 739 +CONECT 738 737 +CONECT 739 737 740 741 +CONECT 740 739 +CONECT 741 739 742 743 751 +CONECT 742 741 +CONECT 743 745 741 749 744 +CONECT 744 743 +CONECT 745 746 748 747 743 +CONECT 746 745 +CONECT 747 745 +CONECT 748 745 +CONECT 749 750 743 +CONECT 750 749 +CONECT 751 741 753 752 +CONECT 752 751 +CONECT 753 754 755 751 +CONECT 754 753 +CONECT 755 756 753 757 773 +CONECT 756 755 +CONECT 757 760 755 759 758 +CONECT 758 757 +CONECT 759 757 +CONECT 760 763 761 762 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 766 765 764 760 +CONECT 764 763 +CONECT 765 763 +CONECT 766 769 768 767 763 +CONECT 767 766 +CONECT 768 766 +CONECT 769 771 772 770 766 +CONECT 770 769 +CONECT 771 769 +CONECT 772 769 +CONECT 773 755 775 774 +CONECT 774 773 +CONECT 775 776 773 777 +CONECT 776 775 +CONECT 777 775 787 779 778 +CONECT 778 777 +CONECT 779 780 777 785 781 +CONECT 780 779 +CONECT 781 779 784 783 782 +CONECT 782 781 +CONECT 783 781 +CONECT 784 781 +CONECT 785 786 779 +CONECT 786 785 +CONECT 787 788 777 789 +CONECT 788 787 +CONECT 789 787 791 790 +CONECT 790 789 +CONECT 791 792 789 807 793 +CONECT 792 791 +CONECT 793 791 796 795 794 +CONECT 794 793 +CONECT 795 793 +CONECT 796 805 797 793 +CONECT 797 799 796 798 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 804 801 805 +CONECT 804 803 +CONECT 805 803 806 796 +CONECT 806 805 +CONECT 807 791 809 808 +CONECT 808 807 +CONECT 809 810 807 811 +CONECT 810 809 +CONECT 811 813 809 821 812 +CONECT 812 811 +CONECT 813 819 815 814 811 +CONECT 814 813 +CONECT 815 816 817 813 818 +CONECT 816 815 +CONECT 817 815 +CONECT 818 815 +CONECT 819 820 813 +CONECT 820 819 +CONECT 821 822 811 823 +CONECT 822 821 +CONECT 823 821 825 824 +CONECT 824 823 +CONECT 825 831 826 823 827 +CONECT 826 825 +CONECT 827 825 829 830 828 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 833 832 825 +CONECT 832 831 +CONECT 833 835 834 831 +CONECT 834 833 +CONECT 835 837 836 833 847 +CONECT 836 835 +CONECT 837 840 839 838 835 +CONECT 838 837 +CONECT 839 837 +CONECT 840 843 841 842 837 +CONECT 841 840 +CONECT 842 840 +CONECT 843 845 844 840 +CONECT 844 843 +CONECT 845 846 843 +CONECT 846 845 +CONECT 847 835 849 848 +CONECT 848 847 +CONECT 849 850 847 851 +CONECT 850 849 +CONECT 851 849 853 862 852 +CONECT 852 851 +CONECT 853 855 854 856 851 +CONECT 854 853 +CONECT 855 853 +CONECT 856 857 858 853 859 +CONECT 857 856 +CONECT 858 856 +CONECT 859 856 860 861 +CONECT 860 859 +CONECT 861 859 +CONECT 862 864 851 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 87 306 866 275 +CONECT 866 865 868 +CONECT 867 870 868 871 869 +CONECT 868 866 867 +CONECT 869 867 +CONECT 870 867 +CONECT 871 867 +CONECT 872 873 +CONECT 873 872 874 +CONECT 874 873 +MASTER 0 0 0 0 0 0 0 0 874 0 874 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_20.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_20.pdb new file mode 100644 index 0000000..79b4370 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_20.pdb @@ -0,0 +1,1751 @@ +COMPND fitness: 0.2006 34.955833333333885 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 53.760 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.706 37.886 23.581 1.00 0.00 N +ATOM 2 H1 MET 1 14.749 38.238 24.533 1.00 0.00 H +ATOM 3 H2 MET 1 13.829 38.169 23.176 1.00 0.00 H +ATOM 4 H3 MET 1 15.478 38.310 23.086 1.00 0.00 H +ATOM 5 CA MET 1 14.851 36.420 23.597 1.00 0.00 C +ATOM 6 HA MET 1 13.953 36.014 24.063 1.00 0.00 H +ATOM 7 CB MET 1 14.969 35.842 22.177 1.00 0.00 C +ATOM 8 HB2 MET 1 14.064 36.081 21.614 1.00 0.00 H +ATOM 9 HB3 MET 1 15.823 36.297 21.666 1.00 0.00 H +ATOM 10 CG MET 1 15.165 34.310 22.176 1.00 0.00 C +ATOM 11 HG2 MET 1 16.090 34.079 22.710 1.00 0.00 H +ATOM 12 HG3 MET 1 14.334 33.844 22.717 1.00 0.00 H +ATOM 13 SD MET 1 15.286 33.532 20.532 1.00 0.00 S +ATOM 14 CE MET 1 13.549 33.554 20.000 1.00 0.00 C +ATOM 15 HE1 MET 1 13.179 34.578 19.964 1.00 0.00 H +ATOM 16 HE2 MET 1 13.475 33.117 19.005 1.00 0.00 H +ATOM 17 HE3 MET 1 12.940 32.969 20.690 1.00 0.00 H +ATOM 18 C MET 1 16.032 36.004 24.465 1.00 0.00 C +ATOM 19 O MET 1 17.174 36.338 24.175 1.00 0.00 O +ATOM 20 N GLN 2 15.766 35.226 25.515 1.00 0.00 N +ATOM 21 H GLN 2 14.800 35.161 25.819 1.00 0.00 H +ATOM 22 CA GLN 2 16.765 34.525 26.328 1.00 0.00 C +ATOM 23 HA GLN 2 17.538 35.224 26.644 1.00 0.00 H +ATOM 24 CB GLN 2 16.051 34.015 27.602 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.088 33.573 27.326 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.637 33.246 28.099 1.00 0.00 H +ATOM 27 CG GLN 2 15.805 35.140 28.632 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.365 36.001 28.132 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.053 34.786 29.319 1.00 0.00 H +ATOM 30 CD GLN 2 16.973 35.488 29.493 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.071 34.945 29.413 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.833 36.321 30.508 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.613 36.439 31.078 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.891 36.574 30.769 1.00 0.00 H +ATOM 35 C GLN 2 17.477 33.392 25.541 1.00 0.00 C +ATOM 36 O GLN 2 17.096 32.222 25.636 1.00 0.00 O +ATOM 37 N TYR 3 18.510 33.742 24.771 1.00 0.00 N +ATOM 38 H TYR 3 18.754 34.726 24.744 1.00 0.00 H +ATOM 39 CA TYR 3 19.380 32.793 24.062 1.00 0.00 C +ATOM 40 HA TYR 3 18.761 32.171 23.418 1.00 0.00 H +ATOM 41 CB TYR 3 20.392 33.554 23.202 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.886 34.309 23.814 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.161 32.854 22.874 1.00 0.00 H +ATOM 44 CG TYR 3 19.813 34.221 21.968 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.748 33.507 20.755 1.00 0.00 C +ATOM 46 HD1 TYR 3 20.107 32.486 20.709 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.237 34.123 19.596 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.202 33.578 18.664 1.00 0.00 H +ATOM 49 CZ TYR 3 18.782 35.457 19.652 1.00 0.00 C +ATOM 50 OH TYR 3 18.300 36.062 18.536 1.00 0.00 O +ATOM 51 HH TYR 3 18.492 35.558 17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.842 36.171 20.866 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.493 37.193 20.900 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.365 35.555 22.019 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.422 36.111 22.948 1.00 0.00 H +ATOM 56 C TYR 3 20.120 31.884 25.048 1.00 0.00 C +ATOM 57 O TYR 3 20.505 32.333 26.128 1.00 0.00 O +ATOM 58 N LYS 4 20.323 30.607 24.705 1.00 0.00 N +ATOM 59 H LYS 4 20.126 30.331 23.745 1.00 0.00 H +ATOM 60 CA LYS 4 20.911 29.575 25.585 1.00 0.00 C +ATOM 61 HA LYS 4 20.630 29.781 26.614 1.00 0.00 H +ATOM 62 CB LYS 4 20.369 28.183 25.194 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.399 28.094 24.112 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.038 27.418 25.594 1.00 0.00 H +ATOM 65 CG LYS 4 18.947 27.829 25.665 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.779 26.781 25.421 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.891 27.930 26.749 1.00 0.00 H +ATOM 68 CD LYS 4 17.828 28.654 25.008 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.829 29.667 25.407 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.024 28.715 23.936 1.00 0.00 H +ATOM 71 CE LYS 4 16.438 28.028 25.194 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.709 28.642 24.658 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.443 27.043 24.720 1.00 0.00 H +ATOM 74 NZ LYS 4 16.042 27.893 26.618 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.058 28.789 27.085 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.115 27.490 26.685 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.661 27.244 27.088 1.00 0.00 H +ATOM 78 C LYS 4 22.447 29.579 25.565 1.00 0.00 C +ATOM 79 O LYS 4 23.079 29.932 24.574 1.00 0.00 O +HETATM 80 N HX1 5 23.060 29.115 26.652 1.00 0.00 N +HETATM 81 CA HX1 5 24.511 28.919 26.790 1.00 0.00 C +HETATM 82 C HX1 5 24.767 27.744 27.738 1.00 0.00 C +HETATM 83 O HX1 5 24.226 27.725 28.848 1.00 0.00 O +HETATM 84 CB HX1 5 25.134 30.227 27.312 1.00 0.00 C +HETATM 85 CG HX1 5 26.642 30.356 27.313 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.559 29.544 26.698 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.306 31.439 27.902 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.606 31.235 27.624 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.793 30.127 26.890 1.00 0.00 N +HETATM 90 H HX1 5 22.486 28.938 27.475 1.00 0.00 H +HETATM 91 HA HX1 5 24.940 28.687 25.814 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.784 30.402 28.329 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.755 31.051 26.703 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.379 28.640 26.135 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.407 31.896 27.922 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.693 29.846 26.462 1.00 0.00 H +ATOM 97 N ILE 6 25.523 26.740 27.292 1.00 0.00 N +ATOM 98 H ILE 6 25.940 26.814 26.368 1.00 0.00 H +ATOM 99 CA ILE 6 25.853 25.534 28.075 1.00 0.00 C +ATOM 100 HA ILE 6 25.153 25.454 28.905 1.00 0.00 H +ATOM 101 CB ILE 6 25.652 24.264 27.210 1.00 0.00 C +ATOM 102 HB ILE 6 26.197 24.394 26.276 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.186 22.990 27.896 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.669 22.819 28.842 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.043 22.125 27.249 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.260 23.074 28.076 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.141 24.115 26.898 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.594 24.001 27.833 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.783 25.024 26.414 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.763 22.946 25.979 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.912 21.994 26.489 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.709 23.027 25.712 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.363 22.976 25.069 1.00 0.00 H +ATOM 114 C ILE 6 27.246 25.681 28.711 1.00 0.00 C +ATOM 115 O ILE 6 28.113 26.347 28.158 1.00 0.00 O +ATOM 116 N VAL 7 27.419 25.119 29.912 1.00 0.00 N +ATOM 117 H VAL 7 26.656 24.539 30.262 1.00 0.00 H +ATOM 118 CA VAL 7 28.561 25.342 30.817 1.00 0.00 C +ATOM 119 HA VAL 7 28.673 26.427 30.917 1.00 0.00 H +ATOM 120 CB VAL 7 28.213 24.772 32.208 1.00 0.00 C +ATOM 121 HB VAL 7 27.200 25.097 32.454 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.231 23.235 32.243 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.247 22.862 32.100 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.857 22.890 33.199 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.602 22.836 31.446 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.120 25.292 33.331 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.158 26.382 33.292 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.717 24.983 34.293 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.127 24.891 33.221 1.00 0.00 H +ATOM 130 C VAL 7 29.910 24.818 30.311 1.00 0.00 C +ATOM 131 O VAL 7 29.989 23.801 29.618 1.00 0.00 O +ATOM 132 N ARG 8 30.995 25.487 30.732 1.00 0.00 N +ATOM 133 H ARG 8 30.824 26.376 31.173 1.00 0.00 H +ATOM 134 CA ARG 8 32.396 25.025 30.620 1.00 0.00 C +ATOM 135 HA ARG 8 32.562 24.823 29.552 1.00 0.00 H +ATOM 136 CB ARG 8 33.329 26.144 31.051 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.353 25.892 30.783 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.088 27.021 30.485 1.00 0.00 H +ATOM 139 CG ARG 8 33.262 26.481 32.584 1.00 0.00 C +ATOM 140 HG2 ARG 8 32.210 26.612 32.829 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.620 25.636 33.137 1.00 0.00 H +ATOM 142 CD ARG 8 34.077 27.718 32.990 1.00 0.00 C +ATOM 143 HD2 ARG 8 33.868 27.880 34.087 1.00 0.00 H +ATOM 144 HD3 ARG 8 35.158 27.518 32.742 1.00 0.00 H +ATOM 145 NE ARG 8 33.586 28.878 32.219 1.00 0.00 N +ATOM 146 HE ARG 8 32.681 28.860 31.740 1.00 0.00 H +ATOM 147 CZ ARG 8 34.373 29.923 32.016 1.00 0.00 C +ATOM 148 NH1 ARG 8 34.136 30.778 31.068 1.00 0.00 N +ATOM 149 HH11 ARG 8 33.523 30.453 30.342 1.00 0.00 H +ATOM 150 HH12 ARG 8 34.858 31.452 30.878 1.00 0.00 H +ATOM 151 NH2 ARG 8 35.460 30.180 32.723 1.00 0.00 N +ATOM 152 HH21 ARG 8 35.716 29.659 33.526 1.00 0.00 H +ATOM 153 HH22 ARG 8 36.015 30.965 32.458 1.00 0.00 H +ATOM 154 C ARG 8 32.704 23.728 31.380 1.00 0.00 C +ATOM 155 O ARG 8 32.120 23.425 32.414 1.00 0.00 O +ATOM 156 N GLY 9 33.751 23.041 30.932 1.00 0.00 N +ATOM 157 H GLY 9 34.105 23.316 30.032 1.00 0.00 H +ATOM 158 CA GLY 9 34.266 21.801 31.519 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.321 21.684 31.265 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.181 21.865 32.609 1.00 0.00 H +ATOM 161 C GLY 9 33.502 20.560 31.039 1.00 0.00 C +ATOM 162 O GLY 9 32.728 20.622 30.091 1.00 0.00 O +ATOM 163 N LYS 10 33.730 19.425 31.710 1.00 0.00 N +ATOM 164 H LYS 10 34.499 19.421 32.360 1.00 0.00 H +ATOM 165 CA LYS 10 32.964 18.174 31.519 1.00 0.00 C +ATOM 166 HA LYS 10 32.053 18.429 30.973 1.00 0.00 H +ATOM 167 CB LYS 10 33.790 17.215 30.636 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.419 17.808 29.970 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.447 16.616 31.267 1.00 0.00 H +ATOM 170 CG LYS 10 32.931 16.295 29.751 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.361 15.606 30.375 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.232 16.909 29.181 1.00 0.00 H +ATOM 173 CD LYS 10 33.813 15.504 28.768 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.424 16.206 28.195 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.470 14.835 29.325 1.00 0.00 H +ATOM 176 CE LYS 10 32.968 14.681 27.788 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.459 13.886 28.340 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.207 15.337 27.355 1.00 0.00 H +ATOM 179 NZ LYS 10 33.802 14.113 26.697 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.604 13.594 27.048 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.268 13.526 26.075 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.202 14.859 26.115 1.00 0.00 H +ATOM 183 C LYS 10 32.484 17.550 32.842 1.00 0.00 C +ATOM 184 O LYS 10 31.827 16.515 32.848 1.00 0.00 O +ATOM 185 N ILE 11 32.828 18.188 33.969 1.00 0.00 N +ATOM 186 H ILE 11 33.389 19.014 33.869 1.00 0.00 H +ATOM 187 CA ILE 11 32.370 17.844 35.327 1.00 0.00 C +ATOM 188 HA ILE 11 32.263 16.760 35.400 1.00 0.00 H +ATOM 189 CB ILE 11 33.419 18.291 36.379 1.00 0.00 C +ATOM 190 HB ILE 11 32.995 18.091 37.366 1.00 0.00 H +ATOM 191 CG2 ILE 11 34.680 17.420 36.238 1.00 0.00 C +ATOM 192 HG21 ILE 11 35.200 17.644 35.306 1.00 0.00 H +ATOM 193 HG22 ILE 11 35.362 17.597 37.069 1.00 0.00 H +ATOM 194 HG23 ILE 11 34.408 16.365 36.245 1.00 0.00 H +ATOM 195 CG1 ILE 11 33.757 19.803 36.308 1.00 0.00 C +ATOM 196 HG12 ILE 11 34.236 20.032 35.355 1.00 0.00 H +ATOM 197 HG13 ILE 11 32.838 20.382 36.372 1.00 0.00 H +ATOM 198 CD1 ILE 11 34.672 20.301 37.434 1.00 0.00 C +ATOM 199 HD11 ILE 11 35.660 19.850 37.355 1.00 0.00 H +ATOM 200 HD12 ILE 11 34.780 21.384 37.354 1.00 0.00 H +ATOM 201 HD13 ILE 11 34.232 20.061 38.403 1.00 0.00 H +ATOM 202 C ILE 11 30.982 18.429 35.640 1.00 0.00 C +ATOM 203 O ILE 11 30.193 17.790 36.330 1.00 0.00 O +ATOM 204 N ASN 12 30.674 19.612 35.098 1.00 0.00 N +ATOM 205 H ASN 12 31.344 20.030 34.476 1.00 0.00 H +ATOM 206 CA ASN 12 29.351 20.232 35.143 1.00 0.00 C +ATOM 207 HA ASN 12 28.775 19.792 35.961 1.00 0.00 H +ATOM 208 CB ASN 12 29.494 21.747 35.401 1.00 0.00 C +ATOM 209 HB2 ASN 12 30.094 22.190 34.604 1.00 0.00 H +ATOM 210 HB3 ASN 12 28.508 22.207 35.377 1.00 0.00 H +ATOM 211 CG ASN 12 30.119 22.119 36.739 1.00 0.00 C +ATOM 212 OD1 ASN 12 30.304 21.320 37.639 1.00 0.00 O +ATOM 213 ND2 ASN 12 30.444 23.376 36.921 1.00 0.00 N +ATOM 214 HD21 ASN 12 30.796 23.622 37.831 1.00 0.00 H +ATOM 215 HD22 ASN 12 30.293 24.059 36.202 1.00 0.00 H +ATOM 216 C ASN 12 28.609 19.953 33.824 1.00 0.00 C +ATOM 217 O ASN 12 29.242 19.747 32.791 1.00 0.00 O +ATOM 218 N LYS 13 27.271 19.984 33.850 1.00 0.00 N +ATOM 219 H LYS 13 26.825 20.098 34.748 1.00 0.00 H +ATOM 220 CA LYS 13 26.410 19.721 32.673 1.00 0.00 C +ATOM 221 HA LYS 13 27.010 19.891 31.775 1.00 0.00 H +ATOM 222 CB LYS 13 26.002 18.233 32.699 1.00 0.00 C +ATOM 223 HB2 LYS 13 26.824 17.654 33.127 1.00 0.00 H +ATOM 224 HB3 LYS 13 25.134 18.119 33.351 1.00 0.00 H +ATOM 225 CG LYS 13 25.710 17.643 31.306 1.00 0.00 C +ATOM 226 HG2 LYS 13 24.871 18.161 30.837 1.00 0.00 H +ATOM 227 HG3 LYS 13 26.593 17.781 30.678 1.00 0.00 H +ATOM 228 CD LYS 13 25.406 16.136 31.388 1.00 0.00 C +ATOM 229 HD2 LYS 13 25.415 15.720 30.379 1.00 0.00 H +ATOM 230 HD3 LYS 13 26.186 15.643 31.973 1.00 0.00 H +ATOM 231 CE LYS 13 24.033 15.865 32.015 1.00 0.00 C +ATOM 232 HE2 LYS 13 23.897 16.512 32.882 1.00 0.00 H +ATOM 233 HE3 LYS 13 23.264 16.134 31.281 1.00 0.00 H +ATOM 234 NZ LYS 13 23.881 14.452 32.441 1.00 0.00 N +ATOM 235 HZ1 LYS 13 24.460 14.227 33.248 1.00 0.00 H +ATOM 236 HZ2 LYS 13 22.914 14.270 32.694 1.00 0.00 H +ATOM 237 HZ3 LYS 13 24.176 13.806 31.712 1.00 0.00 H +ATOM 238 C LYS 13 25.214 20.682 32.560 1.00 0.00 C +ATOM 239 O LYS 13 24.236 20.403 31.876 1.00 0.00 O +ATOM 240 N GLY 14 25.268 21.801 33.287 1.00 0.00 N +ATOM 241 H GLY 14 26.125 21.994 33.773 1.00 0.00 H +ATOM 242 CA GLY 14 24.187 22.782 33.378 1.00 0.00 C +ATOM 243 HA2 GLY 14 23.239 22.249 33.482 1.00 0.00 H +ATOM 244 HA3 GLY 14 24.322 23.384 34.277 1.00 0.00 H +ATOM 245 C GLY 14 24.077 23.727 32.175 1.00 0.00 C +ATOM 246 O GLY 14 25.000 23.873 31.369 1.00 0.00 O +ATOM 247 N VAL 15 22.942 24.423 32.093 1.00 0.00 N +ATOM 248 H VAL 15 22.251 24.288 32.818 1.00 0.00 H +ATOM 249 CA VAL 15 22.587 25.389 31.048 1.00 0.00 C +ATOM 250 HA VAL 15 23.475 25.623 30.465 1.00 0.00 H +ATOM 251 CB VAL 15 21.554 24.757 30.083 1.00 0.00 C +ATOM 252 HB VAL 15 22.007 23.858 29.665 1.00 0.00 H +ATOM 253 CG1 VAL 15 20.245 24.335 30.772 1.00 0.00 C +ATOM 254 HG11 VAL 15 19.745 25.195 31.217 1.00 0.00 H +ATOM 255 HG12 VAL 15 19.580 23.874 30.039 1.00 0.00 H +ATOM 256 HG13 VAL 15 20.448 23.596 31.549 1.00 0.00 H +ATOM 257 CG2 VAL 15 21.200 25.681 28.913 1.00 0.00 C +ATOM 258 HG21 VAL 15 22.111 26.022 28.420 1.00 0.00 H +ATOM 259 HG22 VAL 15 20.603 25.126 28.186 1.00 0.00 H +ATOM 260 HG23 VAL 15 20.624 26.538 29.259 1.00 0.00 H +ATOM 261 C VAL 15 22.103 26.695 31.699 1.00 0.00 C +ATOM 262 O VAL 15 21.551 26.665 32.792 1.00 0.00 O +HETATM 263 N HY1 16 22.327 27.828 31.047 1.00 0.00 N +HETATM 264 CA HY1 16 21.760 29.135 31.406 1.00 0.00 C +HETATM 265 C HY1 16 21.467 29.928 30.107 1.00 0.00 C +HETATM 266 O HY1 16 21.630 29.412 28.998 1.00 0.00 O +HETATM 267 CB HY1 16 22.707 29.865 32.385 1.00 0.00 C +HETATM 268 CG HY1 16 24.062 30.211 31.816 1.00 0.00 C +HETATM 269 CD2 HY1 16 24.437 31.418 31.284 1.00 0.00 C +HETATM 270 ND1 HY1 16 25.153 29.370 31.721 1.00 0.00 N +HETATM 271 CE1 HY1 16 26.164 30.075 31.178 1.00 0.00 C +HETATM 272 NE2 HY1 16 25.773 31.329 30.877 1.00 0.00 N +HETATM 273 H HY1 16 22.816 27.783 30.157 1.00 0.00 H +HETATM 274 HA HY1 16 20.806 28.987 31.919 1.00 0.00 H +HETATM 275 HB2 HY1 16 22.233 30.789 32.740 1.00 0.00 H +HETATM 276 HB3 HY1 16 22.852 29.241 33.271 1.00 0.00 H +HETATM 277 HD1 HY1 16 25.200 28.407 32.032 1.00 0.00 H +HETATM 278 HD2 HY1 16 23.805 32.295 31.200 1.00 0.00 H +HETATM 279 HE1 HY1 16 27.172 29.696 31.002 1.00 0.00 H +ATOM 280 N THR 17 21.015 31.171 30.260 1.00 0.00 N +ATOM 281 H THR 17 20.875 31.518 31.199 1.00 0.00 H +ATOM 282 CA THR 17 20.587 32.073 29.175 1.00 0.00 C +ATOM 283 HA THR 17 21.035 31.700 28.277 1.00 0.00 H +ATOM 284 CB THR 17 19.030 32.023 28.984 1.00 0.00 C +ATOM 285 HB THR 17 18.795 32.654 28.110 1.00 0.00 H +ATOM 286 CG2 THR 17 18.468 30.674 28.637 1.00 0.00 C +ATOM 287 HG21 THR 17 18.675 29.919 29.385 1.00 0.00 H +ATOM 288 HG22 THR 17 17.383 30.707 28.533 1.00 0.00 H +ATOM 289 HG23 THR 17 18.843 30.327 27.701 1.00 0.00 H +ATOM 290 OG1 THR 17 18.369 32.477 30.133 1.00 0.00 O +ATOM 291 HG1 THR 17 18.429 33.453 30.103 1.00 0.00 H +ATOM 292 C THR 17 21.072 33.504 29.274 1.00 0.00 C +ATOM 293 O THR 17 21.476 33.947 30.344 1.00 0.00 O +HETATM 294 N HY2 18 21.016 34.231 28.150 1.00 0.00 N +HETATM 295 CA HY2 18 21.307 35.662 28.069 1.00 0.00 C +HETATM 296 C HY2 18 20.202 36.364 27.265 1.00 0.00 C +HETATM 297 O HY2 18 19.903 35.947 26.153 1.00 0.00 O +HETATM 298 CB HY2 18 22.659 35.892 27.400 1.00 0.00 C +HETATM 299 CG HY2 18 23.839 35.381 28.197 1.00 0.00 C +HETATM 300 CD2 HY2 18 24.427 34.143 28.107 1.00 0.00 C +HETATM 301 ND1 HY2 18 24.472 36.042 29.236 1.00 0.00 N +HETATM 302 CE1 HY2 18 25.414 35.225 29.735 1.00 0.00 C +HETATM 303 NE2 HY2 18 25.427 34.050 29.082 1.00 0.00 N +HETATM 304 H HY2 18 20.711 33.758 27.286 1.00 0.00 H +HETATM 305 HA HY2 18 21.320 36.093 29.094 1.00 0.00 H +HETATM 306 HB2 HY2 18 22.678 35.393 26.415 1.00 0.00 H +HETATM 307 HB3 HY2 18 22.805 36.962 27.231 1.00 0.00 H +HETATM 308 HD1 HY2 18 24.267 36.972 29.578 1.00 0.00 H +HETATM 309 HD2 HY2 18 24.151 33.366 27.414 1.00 0.00 H +HETATM 310 HE1 HY2 18 26.061 35.470 30.573 1.00 0.00 H +ATOM 311 N GLU 19 19.617 37.424 27.817 1.00 0.00 N +ATOM 312 H GLU 19 19.912 37.708 28.733 1.00 0.00 H +ATOM 313 CA GLU 19 18.554 38.214 27.171 1.00 0.00 C +ATOM 314 HA GLU 19 17.873 37.510 26.695 1.00 0.00 H +ATOM 315 CB GLU 19 17.794 39.010 28.252 1.00 0.00 C +ATOM 316 HB2 GLU 19 17.498 38.319 29.033 1.00 0.00 H +ATOM 317 HB3 GLU 19 18.484 39.722 28.706 1.00 0.00 H +ATOM 318 CG GLU 19 16.528 39.764 27.806 1.00 0.00 C +ATOM 319 HG2 GLU 19 16.081 40.241 28.677 1.00 0.00 H +ATOM 320 HG3 GLU 19 16.822 40.551 27.111 1.00 0.00 H +ATOM 321 CD GLU 19 15.527 38.847 27.112 1.00 0.00 C +ATOM 322 OE1 GLU 19 15.723 38.525 25.933 1.00 0.00 O +ATOM 323 OE2 GLU 19 14.522 38.407 27.744 1.00 0.00 O +ATOM 324 C GLU 19 19.119 39.137 26.073 1.00 0.00 C +ATOM 325 O GLU 19 20.037 39.915 26.345 1.00 0.00 O +ATOM 326 N ALA 20 18.576 39.061 24.852 1.00 0.00 N +ATOM 327 H ALA 20 17.822 38.399 24.697 1.00 0.00 H +ATOM 328 CA ALA 20 18.963 39.927 23.730 1.00 0.00 C +ATOM 329 HA ALA 20 19.104 40.942 24.107 1.00 0.00 H +ATOM 330 CB ALA 20 20.302 39.432 23.164 1.00 0.00 C +ATOM 331 HB1 ALA 20 20.175 38.451 22.709 1.00 0.00 H +ATOM 332 HB2 ALA 20 20.672 40.127 22.412 1.00 0.00 H +ATOM 333 HB3 ALA 20 21.049 39.362 23.953 1.00 0.00 H +ATOM 334 C ALA 20 17.900 39.976 22.615 1.00 0.00 C +ATOM 335 O ALA 20 17.000 39.132 22.532 1.00 0.00 O +ATOM 336 N VAL 21 18.032 40.951 21.705 1.00 0.00 N +ATOM 337 H VAL 21 18.763 41.634 21.843 1.00 0.00 H +ATOM 338 CA VAL 21 17.310 40.985 20.411 1.00 0.00 C +ATOM 339 HA VAL 21 16.313 40.565 20.548 1.00 0.00 H +ATOM 340 CB VAL 21 17.133 42.431 19.895 1.00 0.00 C +ATOM 341 HB VAL 21 16.495 42.396 19.010 1.00 0.00 H +ATOM 342 CG1 VAL 21 16.424 43.316 20.929 1.00 0.00 C +ATOM 343 HG11 VAL 21 17.057 43.473 21.801 1.00 0.00 H +ATOM 344 HG12 VAL 21 16.196 44.284 20.481 1.00 0.00 H +ATOM 345 HG13 VAL 21 15.489 42.849 21.233 1.00 0.00 H +ATOM 346 CG2 VAL 21 18.452 43.110 19.492 1.00 0.00 C +ATOM 347 HG21 VAL 21 18.909 42.579 18.656 1.00 0.00 H +ATOM 348 HG22 VAL 21 18.255 44.131 19.164 1.00 0.00 H +ATOM 349 HG23 VAL 21 19.151 43.135 20.328 1.00 0.00 H +ATOM 350 C VAL 21 17.993 40.142 19.324 1.00 0.00 C +ATOM 351 O VAL 21 17.386 39.859 18.296 1.00 0.00 O +ATOM 352 N ASP 22 19.256 39.773 19.542 1.00 0.00 N +ATOM 353 H ASP 22 19.668 40.001 20.431 1.00 0.00 H +ATOM 354 CA ASP 22 20.168 39.176 18.565 1.00 0.00 C +ATOM 355 HA ASP 22 19.614 38.516 17.894 1.00 0.00 H +ATOM 356 CB ASP 22 20.805 40.313 17.742 1.00 0.00 C +ATOM 357 HB2 ASP 22 20.014 40.829 17.193 1.00 0.00 H +ATOM 358 HB3 ASP 22 21.263 41.030 18.429 1.00 0.00 H +ATOM 359 CG ASP 22 21.865 39.863 16.732 1.00 0.00 C +ATOM 360 OD1 ASP 22 22.666 40.720 16.329 1.00 0.00 O +ATOM 361 OD2 ASP 22 21.892 38.654 16.390 1.00 0.00 O +ATOM 362 C ASP 22 21.241 38.346 19.297 1.00 0.00 C +ATOM 363 O ASP 22 21.709 38.726 20.374 1.00 0.00 O +ATOM 364 N TRP 23 21.661 37.231 18.707 1.00 0.00 N +ATOM 365 H TRP 23 21.420 37.116 17.729 1.00 0.00 H +ATOM 366 CA TRP 23 22.741 36.405 19.237 1.00 0.00 C +ATOM 367 HA TRP 23 22.527 36.186 20.282 1.00 0.00 H +ATOM 368 CB TRP 23 22.787 35.085 18.467 1.00 0.00 C +ATOM 369 HB2 TRP 23 23.528 34.450 18.949 1.00 0.00 H +ATOM 370 HB3 TRP 23 21.823 34.584 18.561 1.00 0.00 H +ATOM 371 CG TRP 23 23.151 35.197 17.019 1.00 0.00 C +ATOM 372 CD1 TRP 23 22.272 35.285 15.994 1.00 0.00 C +ATOM 373 HD1 TRP 23 21.192 35.280 16.095 1.00 0.00 H +ATOM 374 NE1 TRP 23 22.956 35.432 14.810 1.00 0.00 N +ATOM 375 HE1 TRP 23 22.487 35.597 13.928 1.00 0.00 H +ATOM 376 CE2 TRP 23 24.325 35.434 14.999 1.00 0.00 C +ATOM 377 CZ2 TRP 23 25.420 35.534 14.128 1.00 0.00 C +ATOM 378 HZ2 TRP 23 25.265 35.630 13.065 1.00 0.00 H +ATOM 379 CH2 TRP 23 26.723 35.510 14.657 1.00 0.00 C +ATOM 380 HH2 TRP 23 27.580 35.586 14.002 1.00 0.00 H +ATOM 381 CZ3 TRP 23 26.918 35.406 16.041 1.00 0.00 C +ATOM 382 HZ3 TRP 23 27.922 35.416 16.451 1.00 0.00 H +ATOM 383 CE3 TRP 23 25.810 35.302 16.908 1.00 0.00 C +ATOM 384 HE3 TRP 23 25.987 35.226 17.970 1.00 0.00 H +ATOM 385 CD2 TRP 23 24.486 35.302 16.412 1.00 0.00 C +ATOM 386 C TRP 23 24.096 37.119 19.168 1.00 0.00 C +ATOM 387 O TRP 23 24.916 36.927 20.062 1.00 0.00 O +ATOM 388 N ALA 24 24.337 37.978 18.168 1.00 0.00 N +ATOM 389 H ALA 24 23.637 38.105 17.439 1.00 0.00 H +ATOM 390 CA ALA 24 25.596 38.722 18.063 1.00 0.00 C +ATOM 391 HA ALA 24 26.415 38.041 18.302 1.00 0.00 H +ATOM 392 CB ALA 24 25.796 39.160 16.609 1.00 0.00 C +ATOM 393 HB1 ALA 24 25.037 39.883 16.321 1.00 0.00 H +ATOM 394 HB2 ALA 24 26.781 39.611 16.491 1.00 0.00 H +ATOM 395 HB3 ALA 24 25.729 38.293 15.953 1.00 0.00 H +ATOM 396 C ALA 24 25.688 39.892 19.069 1.00 0.00 C +ATOM 397 O ALA 24 26.775 40.419 19.314 1.00 0.00 O +ATOM 398 N GLU 25 24.575 40.272 19.707 1.00 0.00 N +ATOM 399 H GLU 25 23.703 39.860 19.406 1.00 0.00 H +ATOM 400 CA GLU 25 24.564 41.070 20.942 1.00 0.00 C +ATOM 401 HA GLU 25 25.413 41.753 20.944 1.00 0.00 H +ATOM 402 CB GLU 25 23.279 41.913 21.016 1.00 0.00 C +ATOM 403 HB2 GLU 25 22.416 41.265 20.876 1.00 0.00 H +ATOM 404 HB3 GLU 25 23.199 42.351 22.009 1.00 0.00 H +ATOM 405 CG GLU 25 23.224 43.049 19.985 1.00 0.00 C +ATOM 406 HG2 GLU 25 23.370 42.641 18.983 1.00 0.00 H +ATOM 407 HG3 GLU 25 22.231 43.500 20.006 1.00 0.00 H +ATOM 408 CD GLU 25 24.281 44.118 20.274 1.00 0.00 C +ATOM 409 OE1 GLU 25 23.971 45.033 21.095 1.00 0.00 O +ATOM 410 OE2 GLU 25 25.383 44.012 19.712 1.00 0.00 O +ATOM 411 C GLU 25 24.720 40.180 22.190 1.00 0.00 C +ATOM 412 O GLU 25 25.493 40.513 23.087 1.00 0.00 O +ATOM 413 N ALA 26 24.078 39.005 22.230 1.00 0.00 N +ATOM 414 H ALA 26 23.434 38.775 21.481 1.00 0.00 H +ATOM 415 CA ALA 26 24.262 38.030 23.314 1.00 0.00 C +ATOM 416 HA ALA 26 24.018 38.530 24.248 1.00 0.00 H +ATOM 417 CB ALA 26 23.286 36.867 23.126 1.00 0.00 C +ATOM 418 HB1 ALA 26 23.576 36.275 22.262 1.00 0.00 H +ATOM 419 HB2 ALA 26 23.306 36.229 24.009 1.00 0.00 H +ATOM 420 HB3 ALA 26 22.273 37.244 22.985 1.00 0.00 H +ATOM 421 C ALA 26 25.722 37.528 23.441 1.00 0.00 C +ATOM 422 O ALA 26 26.162 37.235 24.556 1.00 0.00 O +ATOM 423 N GLU 27 26.493 37.491 22.347 1.00 0.00 N +ATOM 424 H GLU 27 26.033 37.603 21.449 1.00 0.00 H +ATOM 425 CA GLU 27 27.951 37.284 22.354 1.00 0.00 C +ATOM 426 HA GLU 27 28.171 36.313 22.795 1.00 0.00 H +ATOM 427 CB GLU 27 28.487 37.285 20.891 1.00 0.00 C +ATOM 428 HB2 GLU 27 27.911 36.567 20.306 1.00 0.00 H +ATOM 429 HB3 GLU 27 28.312 38.276 20.472 1.00 0.00 H +ATOM 430 CG GLU 27 29.985 36.945 20.779 1.00 0.00 C +ATOM 431 HG2 GLU 27 30.513 37.333 21.654 1.00 0.00 H +ATOM 432 HG3 GLU 27 30.092 35.855 20.804 1.00 0.00 H +ATOM 433 CD GLU 27 30.650 37.506 19.513 1.00 0.00 C +ATOM 434 OE1 GLU 27 31.627 38.300 19.663 1.00 0.00 O +ATOM 435 OE2 GLU 27 30.222 37.150 18.388 1.00 0.00 O +ATOM 436 C GLU 27 28.647 38.367 23.205 1.00 0.00 C +ATOM 437 O GLU 27 29.390 38.056 24.135 1.00 0.00 O +ATOM 438 N LYS 28 28.339 39.647 22.961 1.00 0.00 N +ATOM 439 H LYS 28 27.645 39.833 22.247 1.00 0.00 H +ATOM 440 CA LYS 28 28.898 40.786 23.711 1.00 0.00 C +ATOM 441 HA LYS 28 29.985 40.703 23.701 1.00 0.00 H +ATOM 442 CB LYS 28 28.505 42.117 23.042 1.00 0.00 C +ATOM 443 HB2 LYS 28 27.425 42.257 23.111 1.00 0.00 H +ATOM 444 HB3 LYS 28 28.986 42.930 23.587 1.00 0.00 H +ATOM 445 CG LYS 28 28.924 42.198 21.562 1.00 0.00 C +ATOM 446 HG2 LYS 28 29.999 42.025 21.478 1.00 0.00 H +ATOM 447 HG3 LYS 28 28.402 41.429 20.995 1.00 0.00 H +ATOM 448 CD LYS 28 28.588 43.576 20.968 1.00 0.00 C +ATOM 449 HD2 LYS 28 27.551 43.834 21.189 1.00 0.00 H +ATOM 450 HD3 LYS 28 29.226 44.324 21.445 1.00 0.00 H +ATOM 451 CE LYS 28 28.804 43.629 19.447 1.00 0.00 C +ATOM 452 HE2 LYS 28 28.895 44.677 19.150 1.00 0.00 H +ATOM 453 HE3 LYS 28 29.747 43.139 19.207 1.00 0.00 H +ATOM 454 NZ LYS 28 27.683 42.995 18.707 1.00 0.00 N +ATOM 455 HZ1 LYS 28 26.803 43.454 18.966 1.00 0.00 H +ATOM 456 HZ2 LYS 28 27.784 43.061 17.704 1.00 0.00 H +ATOM 457 HZ3 LYS 28 27.557 42.020 18.973 1.00 0.00 H +ATOM 458 C LYS 28 28.476 40.762 25.184 1.00 0.00 C +ATOM 459 O LYS 28 29.307 40.984 26.063 1.00 0.00 O +ATOM 460 N PHE 29 27.217 40.429 25.479 1.00 0.00 N +ATOM 461 H PHE 29 26.564 40.322 24.708 1.00 0.00 H +ATOM 462 CA PHE 29 26.729 40.281 26.860 1.00 0.00 C +ATOM 463 HA PHE 29 27.042 41.157 27.431 1.00 0.00 H +ATOM 464 CB PHE 29 25.191 40.242 26.862 1.00 0.00 C +ATOM 465 HB2 PHE 29 24.876 39.313 26.383 1.00 0.00 H +ATOM 466 HB3 PHE 29 24.850 40.209 27.898 1.00 0.00 H +ATOM 467 CG PHE 29 24.488 41.408 26.175 1.00 0.00 C +ATOM 468 CD1 PHE 29 23.267 41.187 25.508 1.00 0.00 C +ATOM 469 HD1 PHE 29 22.819 40.206 25.500 1.00 0.00 H +ATOM 470 CE1 PHE 29 22.623 42.240 24.836 1.00 0.00 C +ATOM 471 HE1 PHE 29 21.695 42.058 24.314 1.00 0.00 H +ATOM 472 CZ PHE 29 23.192 43.525 24.828 1.00 0.00 C +ATOM 473 HZ PHE 29 22.711 44.329 24.289 1.00 0.00 H +ATOM 474 CE2 PHE 29 24.392 43.761 25.519 1.00 0.00 C +ATOM 475 HE2 PHE 29 24.829 44.750 25.522 1.00 0.00 H +ATOM 476 CD2 PHE 29 25.034 42.709 26.196 1.00 0.00 C +ATOM 477 HD2 PHE 29 25.955 42.914 26.717 1.00 0.00 H +ATOM 478 C PHE 29 27.331 39.064 27.587 1.00 0.00 C +ATOM 479 O PHE 29 27.564 39.116 28.794 1.00 0.00 O +ATOM 480 N THR 30 27.664 37.988 26.864 1.00 0.00 N +ATOM 481 H THR 30 27.404 37.969 25.881 1.00 0.00 H +ATOM 482 CA THR 30 28.438 36.848 27.390 1.00 0.00 C +ATOM 483 HA THR 30 27.962 36.492 28.308 1.00 0.00 H +ATOM 484 CB THR 30 28.452 35.694 26.382 1.00 0.00 C +ATOM 485 HB THR 30 28.838 36.036 25.423 1.00 0.00 H +ATOM 486 CG2 THR 30 29.298 34.499 26.835 1.00 0.00 C +ATOM 487 HG21 THR 30 28.966 34.175 27.816 1.00 0.00 H +ATOM 488 HG22 THR 30 29.194 33.683 26.125 1.00 0.00 H +ATOM 489 HG23 THR 30 30.351 34.770 26.881 1.00 0.00 H +ATOM 490 OG1 THR 30 27.135 35.224 26.192 1.00 0.00 O +ATOM 491 HG1 THR 30 26.693 35.860 25.604 1.00 0.00 H +ATOM 492 C THR 30 29.862 37.280 27.757 1.00 0.00 C +ATOM 493 O THR 30 30.350 36.958 28.845 1.00 0.00 O +ATOM 494 N LYS 31 30.509 38.072 26.891 1.00 0.00 N +ATOM 495 H LYS 31 30.056 38.263 26.002 1.00 0.00 H +ATOM 496 CA LYS 31 31.842 38.645 27.130 1.00 0.00 C +ATOM 497 HA LYS 31 32.517 37.843 27.424 1.00 0.00 H +ATOM 498 CB LYS 31 32.377 39.269 25.832 1.00 0.00 C +ATOM 499 HB2 LYS 31 31.651 39.978 25.435 1.00 0.00 H +ATOM 500 HB3 LYS 31 33.299 39.811 26.045 1.00 0.00 H +ATOM 501 CG LYS 31 32.673 38.184 24.783 1.00 0.00 C +ATOM 502 HG2 LYS 31 33.439 37.518 25.183 1.00 0.00 H +ATOM 503 HG3 LYS 31 31.781 37.591 24.586 1.00 0.00 H +ATOM 504 CD LYS 31 33.164 38.817 23.475 1.00 0.00 C +ATOM 505 HD2 LYS 31 32.356 39.423 23.041 1.00 0.00 H +ATOM 506 HD3 LYS 31 34.032 39.451 23.670 1.00 0.00 H +ATOM 507 CE LYS 31 33.562 37.733 22.467 1.00 0.00 C +ATOM 508 HE2 LYS 31 32.714 37.078 22.267 1.00 0.00 H +ATOM 509 HE3 LYS 31 33.801 38.225 21.526 1.00 0.00 H +ATOM 510 NZ LYS 31 34.727 36.943 22.929 1.00 0.00 N +ATOM 511 HZ1 LYS 31 34.487 36.218 23.592 1.00 0.00 H +ATOM 512 HZ2 LYS 31 35.176 36.453 22.151 1.00 0.00 H +ATOM 513 HZ3 LYS 31 35.421 37.509 23.406 1.00 0.00 H +ATOM 514 C LYS 31 31.876 39.661 28.271 1.00 0.00 C +ATOM 515 O LYS 31 32.884 39.717 28.969 1.00 0.00 O +ATOM 516 N ALA 32 30.792 40.398 28.519 1.00 0.00 N +ATOM 517 H ALA 32 30.037 40.383 27.847 1.00 0.00 H +ATOM 518 CA ALA 32 30.658 41.236 29.714 1.00 0.00 C +ATOM 519 HA ALA 32 31.497 41.935 29.749 1.00 0.00 H +ATOM 520 CB ALA 32 29.365 42.057 29.627 1.00 0.00 C +ATOM 521 HB1 ALA 32 28.494 41.401 29.610 1.00 0.00 H +ATOM 522 HB2 ALA 32 29.291 42.710 30.500 1.00 0.00 H +ATOM 523 HB3 ALA 32 29.373 42.670 28.724 1.00 0.00 H +ATOM 524 C ALA 32 30.729 40.385 30.992 1.00 0.00 C +ATOM 525 O ALA 32 31.641 40.567 31.790 1.00 0.00 O +ATOM 526 N MET 33 29.874 39.359 31.121 1.00 0.00 N +ATOM 527 H MET 33 29.154 39.250 30.419 1.00 0.00 H +ATOM 528 CA MET 33 29.881 38.434 32.268 1.00 0.00 C +ATOM 529 HA MET 33 29.719 39.019 33.178 1.00 0.00 H +ATOM 530 CB MET 33 28.697 37.460 32.101 1.00 0.00 C +ATOM 531 HB2 MET 33 27.776 38.036 32.003 1.00 0.00 H +ATOM 532 HB3 MET 33 28.838 36.897 31.178 1.00 0.00 H +ATOM 533 CG MET 33 28.515 36.455 33.248 1.00 0.00 C +ATOM 534 HG2 MET 33 27.768 35.721 32.944 1.00 0.00 H +ATOM 535 HG3 MET 33 29.450 35.922 33.412 1.00 0.00 H +ATOM 536 SD MET 33 27.974 37.167 34.823 1.00 0.00 S +ATOM 537 CE MET 33 28.261 35.742 35.907 1.00 0.00 C +ATOM 538 HE1 MET 33 29.314 35.459 35.867 1.00 0.00 H +ATOM 539 HE2 MET 33 28.003 36.007 36.933 1.00 0.00 H +ATOM 540 HE3 MET 33 27.645 34.903 35.584 1.00 0.00 H +ATOM 541 C MET 33 31.227 37.692 32.443 1.00 0.00 C +ATOM 542 O MET 33 31.591 37.309 33.553 1.00 0.00 O +ATOM 543 N ALA 34 31.991 37.486 31.363 1.00 0.00 N +ATOM 544 H ALA 34 31.624 37.763 30.463 1.00 0.00 H +ATOM 545 CA ALA 34 33.346 36.933 31.429 1.00 0.00 C +ATOM 546 HA ALA 34 33.346 36.105 32.141 1.00 0.00 H +ATOM 547 CB ALA 34 33.706 36.372 30.049 1.00 0.00 C +ATOM 548 HB1 ALA 34 33.862 37.188 29.344 1.00 0.00 H +ATOM 549 HB2 ALA 34 34.620 35.787 30.134 1.00 0.00 H +ATOM 550 HB3 ALA 34 32.916 35.722 29.680 1.00 0.00 H +ATOM 551 C ALA 34 34.402 37.949 31.923 1.00 0.00 C +ATOM 552 O ALA 34 35.247 37.602 32.748 1.00 0.00 O +ATOM 553 N ASN 35 34.354 39.209 31.473 1.00 0.00 N +ATOM 554 H ASN 35 33.622 39.461 30.819 1.00 0.00 H +ATOM 555 CA ASN 35 35.244 40.278 31.952 1.00 0.00 C +ATOM 556 HA ASN 35 36.252 39.876 32.041 1.00 0.00 H +ATOM 557 CB ASN 35 35.303 41.412 30.916 1.00 0.00 C +ATOM 558 HB2 ASN 35 34.296 41.678 30.598 1.00 0.00 H +ATOM 559 HB3 ASN 35 35.742 42.292 31.385 1.00 0.00 H +ATOM 560 CG ASN 35 36.169 41.059 29.715 1.00 0.00 C +ATOM 561 OD1 ASN 35 37.385 41.143 29.750 1.00 0.00 O +ATOM 562 ND2 ASN 35 35.584 40.646 28.619 1.00 0.00 N +ATOM 563 HD21 ASN 35 36.176 40.421 27.823 1.00 0.00 H +ATOM 564 HD22 ASN 35 34.590 40.470 28.627 1.00 0.00 H +ATOM 565 C ASN 35 34.890 40.777 33.368 1.00 0.00 C +ATOM 566 O ASN 35 35.793 41.160 34.112 1.00 0.00 O +ATOM 567 N ASP 36 33.626 40.672 33.795 1.00 0.00 N +ATOM 568 H ASP 36 32.891 40.468 33.125 1.00 0.00 H +ATOM 569 CA ASP 36 33.221 40.847 35.195 1.00 0.00 C +ATOM 570 HA ASP 36 33.552 41.822 35.548 1.00 0.00 H +ATOM 571 CB ASP 36 31.682 40.816 35.293 1.00 0.00 C +ATOM 572 HB2 ASP 36 31.353 39.864 34.918 1.00 0.00 H +ATOM 573 HB3 ASP 36 31.396 40.835 36.337 1.00 0.00 H +ATOM 574 CG ASP 36 30.911 41.920 34.574 1.00 0.00 C +ATOM 575 OD1 ASP 36 31.494 42.991 34.350 1.00 0.00 O +ATOM 576 OD2 ASP 36 29.688 41.736 34.290 1.00 0.00 O +ATOM 577 C ASP 36 33.853 39.782 36.125 1.00 0.00 C +ATOM 578 O ASP 36 34.127 40.067 37.290 1.00 0.00 O +ATOM 579 N LEU 37 34.120 38.568 35.617 1.00 0.00 N +ATOM 580 H LEU 37 33.811 38.387 34.674 1.00 0.00 H +ATOM 581 CA LEU 37 34.879 37.515 36.309 1.00 0.00 C +ATOM 582 HA LEU 37 34.688 37.622 37.375 1.00 0.00 H +ATOM 583 CB LEU 37 34.318 36.153 35.855 1.00 0.00 C +ATOM 584 HB2 LEU 37 33.247 36.137 36.060 1.00 0.00 H +ATOM 585 HB3 LEU 37 34.449 36.078 34.777 1.00 0.00 H +ATOM 586 CG LEU 37 34.965 34.917 36.511 1.00 0.00 C +ATOM 587 HG LEU 37 36.032 34.903 36.291 1.00 0.00 H +ATOM 588 CD1 LEU 37 34.760 34.871 38.027 1.00 0.00 C +ATOM 589 HD11 LEU 37 33.695 34.919 38.262 1.00 0.00 H +ATOM 590 HD12 LEU 37 35.182 33.951 38.429 1.00 0.00 H +ATOM 591 HD13 LEU 37 35.271 35.715 38.491 1.00 0.00 H +ATOM 592 CD2 LEU 37 34.351 33.646 35.917 1.00 0.00 C +ATOM 593 HD21 LEU 37 34.506 33.633 34.839 1.00 0.00 H +ATOM 594 HD22 LEU 37 34.830 32.771 36.353 1.00 0.00 H +ATOM 595 HD23 LEU 37 33.282 33.616 36.129 1.00 0.00 H +ATOM 596 C LEU 37 36.408 37.638 36.122 1.00 0.00 C +ATOM 597 O LEU 37 37.161 37.217 37.000 1.00 0.00 O +ATOM 598 N GLY 38 36.877 38.224 35.010 1.00 0.00 N +ATOM 599 H GLY 38 36.197 38.523 34.322 1.00 0.00 H +ATOM 600 CA GLY 38 38.270 38.656 34.837 1.00 0.00 C +ATOM 601 HA2 GLY 38 38.370 39.644 35.288 1.00 0.00 H +ATOM 602 HA3 GLY 38 38.922 37.986 35.397 1.00 0.00 H +ATOM 603 C GLY 38 38.840 38.728 33.408 1.00 0.00 C +ATOM 604 O GLY 38 39.887 39.354 33.250 1.00 0.00 O +ATOM 605 N ALA 39 38.236 38.091 32.390 1.00 0.00 N +ATOM 606 H ALA 39 37.380 37.595 32.607 1.00 0.00 H +ATOM 607 CA ALA 39 38.632 38.141 30.960 1.00 0.00 C +ATOM 608 HA ALA 39 38.679 39.186 30.644 1.00 0.00 H +ATOM 609 CB ALA 39 40.016 37.479 30.785 1.00 0.00 C +ATOM 610 HB1 ALA 39 39.988 36.456 31.171 1.00 0.00 H +ATOM 611 HB2 ALA 39 40.271 37.458 29.723 1.00 0.00 H +ATOM 612 HB3 ALA 39 40.781 38.052 31.311 1.00 0.00 H +ATOM 613 C ALA 39 37.631 37.390 30.046 1.00 0.00 C +ATOM 614 O ALA 39 37.072 36.382 30.478 1.00 0.00 O +ATOM 615 N ASP 40 37.437 37.789 28.773 1.00 0.00 N +ATOM 616 H ASP 40 37.910 38.619 28.447 1.00 0.00 H +ATOM 617 CA ASP 40 36.694 36.968 27.791 1.00 0.00 C +ATOM 618 HA ASP 40 35.969 36.395 28.363 1.00 0.00 H +ATOM 619 CB ASP 40 35.850 37.765 26.773 1.00 0.00 C +ATOM 620 HB2 ASP 40 35.276 37.028 26.210 1.00 0.00 H +ATOM 621 HB3 ASP 40 35.120 38.358 27.322 1.00 0.00 H +ATOM 622 CG ASP 40 36.582 38.663 25.770 1.00 0.00 C +ATOM 623 OD1 ASP 40 36.994 39.787 26.183 1.00 0.00 O +ATOM 624 OD2 ASP 40 36.618 38.357 24.551 1.00 0.00 O +ATOM 625 C ASP 40 37.546 35.929 27.041 1.00 0.00 C +ATOM 626 O ASP 40 38.620 36.232 26.526 1.00 0.00 O +ATOM 627 N GLY 41 36.987 34.721 26.910 1.00 0.00 N +ATOM 628 H GLY 41 36.107 34.565 27.376 1.00 0.00 H +ATOM 629 CA GLY 41 37.345 33.747 25.873 1.00 0.00 C +ATOM 630 HA2 GLY 41 38.380 33.888 25.560 1.00 0.00 H +ATOM 631 HA3 GLY 41 37.251 32.741 26.281 1.00 0.00 H +ATOM 632 C GLY 41 36.439 33.863 24.640 1.00 0.00 C +ATOM 633 O GLY 41 35.768 34.878 24.435 1.00 0.00 O +ATOM 634 N GLU 42 36.395 32.809 23.823 1.00 0.00 N +ATOM 635 H GLU 42 36.882 31.965 24.089 1.00 0.00 H +ATOM 636 CA GLU 42 35.562 32.715 22.615 1.00 0.00 C +ATOM 637 HA GLU 42 34.886 33.571 22.565 1.00 0.00 H +ATOM 638 CB GLU 42 36.451 32.720 21.348 1.00 0.00 C +ATOM 639 HB2 GLU 42 36.964 31.758 21.291 1.00 0.00 H +ATOM 640 HB3 GLU 42 35.801 32.788 20.474 1.00 0.00 H +ATOM 641 CG GLU 42 37.530 33.825 21.254 1.00 0.00 C +ATOM 642 HG2 GLU 42 38.271 33.666 22.039 1.00 0.00 H +ATOM 643 HG3 GLU 42 38.051 33.703 20.301 1.00 0.00 H +ATOM 644 CD GLU 42 36.966 35.254 21.340 1.00 0.00 C +ATOM 645 OE1 GLU 42 35.831 35.502 20.921 1.00 0.00 O +ATOM 646 OE2 GLU 42 37.673 36.178 21.855 1.00 0.00 O +ATOM 647 C GLU 42 34.690 31.447 22.657 1.00 0.00 C +ATOM 648 O GLU 42 35.183 30.373 23.018 1.00 0.00 O +ATOM 649 N ASP 43 33.421 31.553 22.245 1.00 0.00 N +ATOM 650 H ASP 43 33.099 32.455 21.932 1.00 0.00 H +ATOM 651 CA ASP 43 32.428 30.474 22.217 1.00 0.00 C +ATOM 652 HA ASP 43 32.899 29.547 22.547 1.00 0.00 H +ATOM 653 CB ASP 43 31.257 30.758 23.187 1.00 0.00 C +ATOM 654 HB2 ASP 43 30.776 31.694 22.884 1.00 0.00 H +ATOM 655 HB3 ASP 43 30.513 29.964 23.067 1.00 0.00 H +ATOM 656 CG ASP 43 31.631 30.859 24.672 1.00 0.00 C +ATOM 657 OD1 ASP 43 32.316 31.827 25.078 1.00 0.00 O +ATOM 658 OD2 ASP 43 31.143 30.012 25.465 1.00 0.00 O +ATOM 659 C ASP 43 31.900 30.239 20.778 1.00 0.00 C +ATOM 660 O ASP 43 31.867 31.158 19.957 1.00 0.00 O +ATOM 661 N THR 44 31.460 29.013 20.489 1.00 0.00 N +ATOM 662 H THR 44 31.457 28.328 21.238 1.00 0.00 H +ATOM 663 CA THR 44 30.746 28.626 19.251 1.00 0.00 C +ATOM 664 HA THR 44 30.994 29.333 18.462 1.00 0.00 H +ATOM 665 CB THR 44 31.221 27.229 18.797 1.00 0.00 C +ATOM 666 HB THR 44 31.210 26.551 19.651 1.00 0.00 H +ATOM 667 CG2 THR 44 30.440 26.587 17.648 1.00 0.00 C +ATOM 668 HG21 THR 44 30.372 27.276 16.808 1.00 0.00 H +ATOM 669 HG22 THR 44 30.945 25.678 17.321 1.00 0.00 H +ATOM 670 HG23 THR 44 29.442 26.311 17.984 1.00 0.00 H +ATOM 671 OG1 THR 44 32.542 27.345 18.315 1.00 0.00 O +ATOM 672 HG1 THR 44 32.918 26.463 18.287 1.00 0.00 H +ATOM 673 C THR 44 29.227 28.706 19.466 1.00 0.00 C +ATOM 674 O THR 44 28.767 28.695 20.606 1.00 0.00 O +ATOM 675 N LYN 45 28.430 28.795 18.393 1.00 0.00 N +ATOM 676 H LYN 45 28.848 28.758 17.476 1.00 0.00 H +ATOM 677 CA LYN 45 26.969 28.948 18.450 1.00 0.00 C +ATOM 678 HA LYN 45 26.612 28.586 19.411 1.00 0.00 H +ATOM 679 CB LYN 45 26.643 30.450 18.347 1.00 0.00 C +ATOM 680 HB2 LYN 45 27.225 30.997 19.088 1.00 0.00 H +ATOM 681 HB3 LYN 45 26.965 30.797 17.370 1.00 0.00 H +ATOM 682 CG LYN 45 25.156 30.791 18.561 1.00 0.00 C +ATOM 683 HG2 LYN 45 24.514 30.017 18.166 1.00 0.00 H +ATOM 684 HG3 LYN 45 24.950 30.847 19.626 1.00 0.00 H +ATOM 685 CD LYN 45 24.738 32.086 17.851 1.00 0.00 C +ATOM 686 HD2 LYN 45 23.701 32.296 18.107 1.00 0.00 H +ATOM 687 HD3 LYN 45 25.348 32.900 18.227 1.00 0.00 H +ATOM 688 CE LYN 45 24.889 31.975 16.327 1.00 0.00 C +ATOM 689 HE2 LYN 45 25.620 32.711 15.986 1.00 0.00 H +ATOM 690 HE3 LYN 45 25.270 30.985 16.080 1.00 0.00 H +ATOM 691 NZ LYN 45 23.622 32.201 15.620 1.00 0.00 N +ATOM 692 HZ2 LYN 45 23.777 32.140 14.622 1.00 0.00 H +ATOM 693 HZ3 LYN 45 23.329 33.153 15.807 1.00 0.00 H +ATOM 694 C LYN 45 26.244 28.161 17.349 1.00 0.00 C +ATOM 695 O LYN 45 26.698 28.126 16.202 1.00 0.00 O +ATOM 696 N ASP 46 25.075 27.612 17.693 1.00 0.00 N +ATOM 697 H ASP 46 24.803 27.678 18.671 1.00 0.00 H +ATOM 698 CA ASP 46 24.054 27.099 16.777 1.00 0.00 C +ATOM 699 HA ASP 46 24.411 27.181 15.749 1.00 0.00 H +ATOM 700 CB ASP 46 23.815 25.615 17.095 1.00 0.00 C +ATOM 701 HB2 ASP 46 24.686 25.026 16.799 1.00 0.00 H +ATOM 702 HB3 ASP 46 23.691 25.510 18.175 1.00 0.00 H +ATOM 703 CG ASP 46 22.565 25.066 16.412 1.00 0.00 C +ATOM 704 OD1 ASP 46 21.773 24.400 17.115 1.00 0.00 O +ATOM 705 OD2 ASP 46 22.344 25.371 15.218 1.00 0.00 O +ATOM 706 C ASP 46 22.734 27.899 16.884 1.00 0.00 C +ATOM 707 O ASP 46 22.220 28.124 17.984 1.00 0.00 O +ATOM 708 N ASP 47 22.144 28.278 15.743 1.00 0.00 N +ATOM 709 H ASP 47 22.578 27.985 14.880 1.00 0.00 H +ATOM 710 CA ASP 47 20.813 28.897 15.671 1.00 0.00 C +ATOM 711 HA ASP 47 20.729 29.648 16.457 1.00 0.00 H +ATOM 712 CB ASP 47 20.627 29.619 14.321 1.00 0.00 C +ATOM 713 HB2 ASP 47 21.348 30.434 14.249 1.00 0.00 H +ATOM 714 HB3 ASP 47 20.816 28.920 13.502 1.00 0.00 H +ATOM 715 CG ASP 47 19.211 30.185 14.195 1.00 0.00 C +ATOM 716 OD1 ASP 47 18.355 29.542 13.541 1.00 0.00 O +ATOM 717 OD2 ASP 47 18.879 31.185 14.874 1.00 0.00 O +ATOM 718 C ASP 47 19.669 27.882 15.878 1.00 0.00 C +ATOM 719 O ASP 47 18.666 28.219 16.510 1.00 0.00 O +ATOM 720 N ALA 48 19.791 26.645 15.388 1.00 0.00 N +ATOM 721 H ALA 48 20.697 26.335 15.035 1.00 0.00 H +ATOM 722 CA ALA 48 18.693 25.671 15.390 1.00 0.00 C +ATOM 723 HA ALA 48 17.829 26.126 14.903 1.00 0.00 H +ATOM 724 CB ALA 48 19.127 24.454 14.567 1.00 0.00 C +ATOM 725 HB1 ALA 48 19.976 23.965 15.047 1.00 0.00 H +ATOM 726 HB2 ALA 48 18.304 23.744 14.490 1.00 0.00 H +ATOM 727 HB3 ALA 48 19.423 24.771 13.567 1.00 0.00 H +ATOM 728 C ALA 48 18.259 25.277 16.816 1.00 0.00 C +ATOM 729 O ALA 48 17.075 25.060 17.072 1.00 0.00 O +ATOM 730 N THR 49 19.205 25.249 17.755 1.00 0.00 N +ATOM 731 H THR 49 20.173 25.255 17.432 1.00 0.00 H +ATOM 732 CA THR 49 18.982 25.117 19.204 1.00 0.00 C +ATOM 733 HA THR 49 17.945 24.815 19.365 1.00 0.00 H +ATOM 734 CB THR 49 19.872 24.014 19.791 1.00 0.00 C +ATOM 735 HB THR 49 19.643 23.926 20.853 1.00 0.00 H +ATOM 736 CG2 THR 49 19.636 22.645 19.159 1.00 0.00 C +ATOM 737 HG21 THR 49 19.902 22.659 18.102 1.00 0.00 H +ATOM 738 HG22 THR 49 20.256 21.908 19.664 1.00 0.00 H +ATOM 739 HG23 THR 49 18.588 22.365 19.260 1.00 0.00 H +ATOM 740 OG1 THR 49 21.241 24.315 19.661 1.00 0.00 O +ATOM 741 HG1 THR 49 21.457 24.269 18.697 1.00 0.00 H +ATOM 742 C THR 49 19.180 26.429 19.975 1.00 0.00 C +ATOM 743 O THR 49 19.114 26.429 21.204 1.00 0.00 O +ATOM 744 N LYS 50 19.413 27.560 19.288 1.00 0.00 N +ATOM 745 H LYS 50 19.437 27.468 18.280 1.00 0.00 H +ATOM 746 CA LYS 50 19.599 28.922 19.844 1.00 0.00 C +ATOM 747 HA LYS 50 20.023 29.534 19.048 1.00 0.00 H +ATOM 748 CB LYS 50 18.228 29.522 20.246 1.00 0.00 C +ATOM 749 HB2 LYS 50 17.808 28.894 21.034 1.00 0.00 H +ATOM 750 HB3 LYS 50 18.383 30.516 20.674 1.00 0.00 H +ATOM 751 CG LYS 50 17.178 29.645 19.129 1.00 0.00 C +ATOM 752 HG2 LYS 50 17.108 28.708 18.572 1.00 0.00 H +ATOM 753 HG3 LYS 50 16.207 29.814 19.605 1.00 0.00 H +ATOM 754 CD LYS 50 17.429 30.818 18.160 1.00 0.00 C +ATOM 755 HD2 LYS 50 17.404 31.746 18.737 1.00 0.00 H +ATOM 756 HD3 LYS 50 18.417 30.724 17.698 1.00 0.00 H +ATOM 757 CE LYS 50 16.340 30.882 17.079 1.00 0.00 C +ATOM 758 HE2 LYS 50 15.374 30.622 17.524 1.00 0.00 H +ATOM 759 HE3 LYS 50 16.281 31.909 16.708 1.00 0.00 H +ATOM 760 NZ LYS 50 16.652 29.991 15.940 1.00 0.00 N +ATOM 761 HZ1 LYS 50 17.058 29.110 16.237 1.00 0.00 H +ATOM 762 HZ2 LYS 50 15.878 29.804 15.314 1.00 0.00 H +ATOM 763 HZ3 LYS 50 17.392 30.410 15.370 1.00 0.00 H +ATOM 764 C LYS 50 20.637 28.968 20.987 1.00 0.00 C +ATOM 765 O LYS 50 20.407 29.633 22.003 1.00 0.00 O +ATOM 766 N THR 51 21.735 28.218 20.849 1.00 0.00 N +ATOM 767 H THR 51 21.909 27.816 19.932 1.00 0.00 H +ATOM 768 CA THR 51 22.646 27.841 21.949 1.00 0.00 C +ATOM 769 HA THR 51 22.394 28.422 22.828 1.00 0.00 H +ATOM 770 CB THR 51 22.467 26.343 22.322 1.00 0.00 C +ATOM 771 HB THR 51 22.611 25.737 21.423 1.00 0.00 H +ATOM 772 CG2 THR 51 23.451 25.851 23.379 1.00 0.00 C +ATOM 773 HG21 THR 51 23.433 26.483 24.265 1.00 0.00 H +ATOM 774 HG22 THR 51 23.222 24.829 23.682 1.00 0.00 H +ATOM 775 HG23 THR 51 24.463 25.841 22.988 1.00 0.00 H +ATOM 776 OG1 THR 51 21.187 26.082 22.858 1.00 0.00 O +ATOM 777 HG1 THR 51 20.519 26.229 22.159 1.00 0.00 H +ATOM 778 C THR 51 24.134 28.130 21.653 1.00 0.00 C +ATOM 779 O THR 51 24.639 27.762 20.598 1.00 0.00 O +ATOM 780 N PHE 52 24.848 28.724 22.617 1.00 0.00 N +ATOM 781 H PHE 52 24.348 29.094 23.416 1.00 0.00 H +ATOM 782 CA PHE 52 26.319 28.802 22.656 1.00 0.00 C +ATOM 783 HA PHE 52 26.688 28.806 21.638 1.00 0.00 H +ATOM 784 CB PHE 52 26.756 30.126 23.325 1.00 0.00 C +ATOM 785 HB2 PHE 52 26.222 30.235 24.266 1.00 0.00 H +ATOM 786 HB3 PHE 52 27.818 30.054 23.558 1.00 0.00 H +ATOM 787 CG PHE 52 26.548 31.378 22.492 1.00 0.00 C +ATOM 788 CD1 PHE 52 25.329 32.082 22.541 1.00 0.00 C +ATOM 789 HD1 PHE 52 24.515 31.712 23.144 1.00 0.00 H +ATOM 790 CE1 PHE 52 25.172 33.278 21.813 1.00 0.00 C +ATOM 791 HE1 PHE 52 24.238 33.821 21.853 1.00 0.00 H +ATOM 792 CZ PHE 52 26.237 33.776 21.042 1.00 0.00 C +ATOM 793 HZ PHE 52 26.124 34.696 20.491 1.00 0.00 H +ATOM 794 CE2 PHE 52 27.454 33.074 20.988 1.00 0.00 C +ATOM 795 HE2 PHE 52 28.276 33.457 20.395 1.00 0.00 H +ATOM 796 CD2 PHE 52 27.606 31.876 21.709 1.00 0.00 C +ATOM 797 HD2 PHE 52 28.545 31.343 21.663 1.00 0.00 H +ATOM 798 C PHE 52 26.972 27.615 23.403 1.00 0.00 C +ATOM 799 O PHE 52 26.436 27.154 24.422 1.00 0.00 O +ATOM 800 N THR 53 28.156 27.174 22.952 1.00 0.00 N +ATOM 801 H THR 53 28.539 27.633 22.127 1.00 0.00 H +ATOM 802 CA THR 53 28.961 26.050 23.493 1.00 0.00 C +ATOM 803 HA THR 53 28.764 25.970 24.561 1.00 0.00 H +ATOM 804 CB THR 53 28.583 24.703 22.833 1.00 0.00 C +ATOM 805 HB THR 53 29.194 23.918 23.284 1.00 0.00 H +ATOM 806 CG2 THR 53 27.122 24.303 23.000 1.00 0.00 C +ATOM 807 HG21 THR 53 26.490 24.954 22.397 1.00 0.00 H +ATOM 808 HG22 THR 53 26.983 23.272 22.670 1.00 0.00 H +ATOM 809 HG23 THR 53 26.834 24.379 24.046 1.00 0.00 H +ATOM 810 OG1 THR 53 28.833 24.716 21.447 1.00 0.00 O +ATOM 811 HG1 THR 53 28.416 23.933 21.073 1.00 0.00 H +ATOM 812 C THR 53 30.481 26.241 23.319 1.00 0.00 C +ATOM 813 O THR 53 30.935 27.030 22.488 1.00 0.00 O +ATOM 814 N LYN 54 31.293 25.485 24.084 1.00 0.00 N +ATOM 815 H LYN 54 30.867 24.864 24.754 1.00 0.00 H +ATOM 816 CA LYN 54 32.750 25.351 23.892 1.00 0.00 C +ATOM 817 HA LYN 54 33.090 26.183 23.273 1.00 0.00 H +ATOM 818 CB LYN 54 33.488 25.489 25.242 1.00 0.00 C +ATOM 819 HB2 LYN 54 34.540 25.654 25.018 1.00 0.00 H +ATOM 820 HB3 LYN 54 33.132 26.378 25.767 1.00 0.00 H +ATOM 821 CG LYN 54 33.370 24.269 26.173 1.00 0.00 C +ATOM 822 HG2 LYN 54 32.445 24.327 26.743 1.00 0.00 H +ATOM 823 HG3 LYN 54 33.334 23.354 25.587 1.00 0.00 H +ATOM 824 CD LYN 54 34.573 24.167 27.121 1.00 0.00 C +ATOM 825 HD2 LYN 54 35.493 24.273 26.549 1.00 0.00 H +ATOM 826 HD3 LYN 54 34.530 24.959 27.865 1.00 0.00 H +ATOM 827 CE LYN 54 34.587 22.806 27.809 1.00 0.00 C +ATOM 828 HE2 LYN 54 33.718 22.744 28.463 1.00 0.00 H +ATOM 829 HE3 LYN 54 34.519 22.024 27.056 1.00 0.00 H +ATOM 830 NZ LYN 54 35.815 22.603 28.604 1.00 0.00 N +ATOM 831 HZ2 LYN 54 35.903 21.609 28.798 1.00 0.00 H +ATOM 832 HZ3 LYN 54 35.803 23.153 29.450 1.00 0.00 H +ATOM 833 C LYN 54 33.155 24.056 23.143 1.00 0.00 C +ATOM 834 O LYN 54 32.318 23.196 22.866 1.00 0.00 O +ATOM 835 N ASH 55 34.456 23.904 22.861 1.00 0.00 N +ATOM 836 H ASH 55 35.093 24.610 23.207 1.00 0.00 H +ATOM 837 CA ASH 55 35.082 22.701 22.282 1.00 0.00 C +ATOM 838 HA ASH 55 34.343 22.216 21.644 1.00 0.00 H +ATOM 839 CB ASH 55 36.254 23.120 21.362 1.00 0.00 C +ATOM 840 HB2 ASH 55 36.802 22.241 21.033 1.00 0.00 H +ATOM 841 HB3 ASH 55 35.828 23.581 20.471 1.00 0.00 H +ATOM 842 CG ASH 55 37.264 24.113 21.950 1.00 0.00 C +ATOM 843 OD1 ASH 55 37.261 24.556 23.089 1.00 0.00 O +ATOM 844 OD2 ASH 55 38.198 24.519 21.062 1.00 0.00 O +ATOM 845 HD2 ASH 55 38.720 25.241 21.453 1.00 0.00 H +ATOM 846 C ASH 55 35.492 21.621 23.327 1.00 0.00 C +ATOM 847 O ASH 55 35.454 21.874 24.527 1.00 0.00 O +ATOM 848 N GLU 56 35.845 20.416 22.846 1.00 0.00 N +ATOM 849 H GLU 56 35.881 20.316 21.846 1.00 0.00 H +ATOM 850 CA GLU 56 36.340 19.234 23.607 1.00 0.00 C +ATOM 851 HA GLU 56 36.000 19.323 24.639 1.00 0.00 H +ATOM 852 CB GLU 56 35.707 17.953 22.997 1.00 0.00 C +ATOM 853 HB2 GLU 56 34.639 17.947 23.211 1.00 0.00 H +ATOM 854 HB3 GLU 56 35.782 18.059 21.914 1.00 0.00 H +ATOM 855 CG GLU 56 36.312 16.561 23.328 1.00 0.00 C +ATOM 856 HG2 GLU 56 36.111 15.927 22.460 1.00 0.00 H +ATOM 857 HG3 GLU 56 37.397 16.627 23.391 1.00 0.00 H +ATOM 858 CD GLU 56 35.748 15.804 24.556 1.00 0.00 C +ATOM 859 OE1 GLU 56 36.418 14.876 25.078 1.00 0.00 O +ATOM 860 OE2 GLU 56 34.575 16.021 24.947 1.00 0.00 O +ATOM 861 C GLU 56 37.881 19.174 23.699 1.00 0.00 C +ATOM 862 O GLU 56 38.391 19.115 24.822 1.00 0.00 O +ATOM 863 OXT GLU 56 38.544 19.174 22.611 1.00 0.00 O +HETATM 864 ZN ZN1 57 26.603 32.487 29.470 1.00 0.00 Zn +HETATM 865 N AN1 58 28.212 33.342 30.330 1.00 0.00 N +HETATM 866 C AN1 58 30.611 34.011 31.085 1.00 0.00 C +HETATM 867 C1 AN1 58 29.262 33.645 30.703 1.00 0.00 C +HETATM 868 H AN1 58 30.632 34.429 32.095 1.00 0.00 H +HETATM 869 H1 AN1 58 30.995 34.752 30.375 1.00 0.00 H +HETATM 870 H2 AN1 58 31.247 33.117 31.056 1.00 0.00 H +HETATM 871 N1 AZI 59 30.729 28.388 31.603 1.00 0.00 N +HETATM 872 N2 AZI 59 30.098 29.423 31.296 1.00 0.00 N +HETATM 873 N3 AZI 59 29.495 30.404 31.023 1.00 0.00 N +CONECT 1 4 3 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 11 12 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 864 +CONECT 88 89 87 95 +CONECT 89 96 86 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 140 142 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 145 139 144 143 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 147 142 +CONECT 146 145 +CONECT 147 148 145 151 +CONECT 148 149 150 147 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 153 152 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 202 189 +CONECT 188 187 +CONECT 189 187 191 195 190 +CONECT 190 189 +CONECT 191 192 194 189 193 +CONECT 192 191 +CONECT 193 191 +CONECT 194 191 +CONECT 195 196 197 189 198 +CONECT 196 195 +CONECT 197 195 +CONECT 198 195 200 199 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 216 204 208 207 +CONECT 207 206 +CONECT 208 209 206 210 211 +CONECT 209 208 +CONECT 210 208 +CONECT 211 208 213 212 +CONECT 212 211 +CONECT 213 215 211 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 217 218 206 +CONECT 217 216 +CONECT 218 220 216 219 +CONECT 219 218 +CONECT 220 221 238 222 218 +CONECT 221 220 +CONECT 222 225 220 223 224 +CONECT 223 222 +CONECT 224 222 +CONECT 225 227 226 228 222 +CONECT 226 225 +CONECT 227 225 +CONECT 228 229 225 230 231 +CONECT 229 228 +CONECT 230 228 +CONECT 231 233 228 234 232 +CONECT 232 231 +CONECT 233 231 +CONECT 234 237 231 236 235 +CONECT 235 234 +CONECT 236 234 +CONECT 237 234 +CONECT 238 239 220 240 +CONECT 239 238 +CONECT 240 238 242 241 +CONECT 241 240 +CONECT 242 245 240 243 244 +CONECT 243 242 +CONECT 244 242 +CONECT 245 246 247 242 +CONECT 246 245 +CONECT 247 249 245 248 +CONECT 248 247 +CONECT 249 251 250 261 247 +CONECT 250 249 +CONECT 251 257 252 253 249 +CONECT 252 251 +CONECT 253 255 251 254 256 +CONECT 254 253 +CONECT 255 253 +CONECT 256 253 +CONECT 257 259 258 260 251 +CONECT 258 257 +CONECT 259 257 +CONECT 260 257 +CONECT 261 263 249 262 +CONECT 262 261 +CONECT 263 273 264 261 +CONECT 264 265 263 274 267 +CONECT 265 266 280 264 +CONECT 266 265 +CONECT 267 264 268 275 276 +CONECT 268 269 270 267 +CONECT 269 272 278 268 +CONECT 270 271 268 277 +CONECT 271 272 279 270 +CONECT 272 864 271 269 +CONECT 273 263 +CONECT 274 264 +CONECT 275 267 +CONECT 276 267 +CONECT 277 270 +CONECT 278 269 +CONECT 279 271 +CONECT 280 282 265 281 +CONECT 281 280 +CONECT 282 283 284 292 280 +CONECT 283 282 +CONECT 284 285 286 282 290 +CONECT 285 284 +CONECT 286 289 288 284 287 +CONECT 287 286 +CONECT 288 286 +CONECT 289 286 +CONECT 290 284 291 +CONECT 291 290 +CONECT 292 294 282 293 +CONECT 293 292 +CONECT 294 304 295 292 +CONECT 295 296 298 294 305 +CONECT 296 297 311 295 +CONECT 297 296 +CONECT 298 306 307 295 299 +CONECT 299 298 300 301 +CONECT 300 309 299 303 +CONECT 301 299 308 302 +CONECT 302 303 301 310 +CONECT 303 300 864 302 +CONECT 304 294 +CONECT 305 295 +CONECT 306 298 +CONECT 307 298 +CONECT 308 301 +CONECT 309 300 +CONECT 310 302 +CONECT 311 313 296 312 +CONECT 312 311 +CONECT 313 324 314 311 315 +CONECT 314 313 +CONECT 315 313 318 317 316 +CONECT 316 315 +CONECT 317 315 +CONECT 318 320 321 315 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 322 323 318 +CONECT 322 321 +CONECT 323 321 +CONECT 324 326 325 313 +CONECT 325 324 +CONECT 326 328 327 324 +CONECT 327 326 +CONECT 328 334 330 329 326 +CONECT 329 328 +CONECT 330 332 331 328 333 +CONECT 331 330 +CONECT 332 330 +CONECT 333 330 +CONECT 334 336 335 328 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 350 340 339 336 +CONECT 339 338 +CONECT 340 341 346 338 342 +CONECT 341 340 +CONECT 342 340 344 345 343 +CONECT 343 342 +CONECT 344 342 +CONECT 345 342 +CONECT 346 347 348 340 349 +CONECT 347 346 +CONECT 348 346 +CONECT 349 346 +CONECT 350 351 352 338 +CONECT 351 350 +CONECT 352 354 350 353 +CONECT 353 352 +CONECT 354 356 355 362 352 +CONECT 355 354 +CONECT 356 359 357 358 354 +CONECT 357 356 +CONECT 358 356 +CONECT 359 360 361 356 +CONECT 360 359 +CONECT 361 359 +CONECT 362 354 364 363 +CONECT 363 362 +CONECT 364 365 366 362 +CONECT 365 364 +CONECT 366 368 364 386 367 +CONECT 367 366 +CONECT 368 371 370 369 366 +CONECT 369 368 +CONECT 370 368 +CONECT 371 372 385 368 +CONECT 372 374 373 371 +CONECT 373 372 +CONECT 374 375 376 372 +CONECT 375 374 +CONECT 376 377 374 385 +CONECT 377 378 379 376 +CONECT 378 377 +CONECT 379 380 377 381 +CONECT 380 379 +CONECT 381 379 382 383 +CONECT 382 381 +CONECT 383 381 385 384 +CONECT 384 383 +CONECT 385 376 383 371 +CONECT 386 388 366 387 +CONECT 387 386 +CONECT 388 389 390 386 +CONECT 389 388 +CONECT 390 392 388 391 396 +CONECT 391 390 +CONECT 392 395 393 394 390 +CONECT 393 392 +CONECT 394 392 +CONECT 395 392 +CONECT 396 390 397 398 +CONECT 397 396 +CONECT 398 396 399 400 +CONECT 399 398 +CONECT 400 398 401 402 411 +CONECT 401 400 +CONECT 402 405 403 400 404 +CONECT 403 402 +CONECT 404 402 +CONECT 405 406 407 408 402 +CONECT 406 405 +CONECT 407 405 +CONECT 408 410 405 409 +CONECT 409 408 +CONECT 410 408 +CONECT 411 400 413 412 +CONECT 412 411 +CONECT 413 414 411 415 +CONECT 414 413 +CONECT 415 413 417 421 416 +CONECT 416 415 +CONECT 417 418 420 415 419 +CONECT 418 417 +CONECT 419 417 +CONECT 420 417 +CONECT 421 423 415 422 +CONECT 422 421 +CONECT 423 424 425 421 +CONECT 424 423 +CONECT 425 427 423 426 436 +CONECT 426 425 +CONECT 427 428 429 430 425 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 432 427 431 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 425 438 437 +CONECT 437 436 +CONECT 438 439 436 440 +CONECT 439 438 +CONECT 440 438 442 441 458 +CONECT 441 440 +CONECT 442 445 443 444 440 +CONECT 443 442 +CONECT 444 442 +CONECT 445 448 447 446 442 +CONECT 446 445 +CONECT 447 445 +CONECT 448 451 449 450 445 +CONECT 449 448 +CONECT 450 448 +CONECT 451 454 452 453 448 +CONECT 452 451 +CONECT 453 451 +CONECT 454 456 455 457 451 +CONECT 455 454 +CONECT 456 454 +CONECT 457 454 +CONECT 458 440 460 459 +CONECT 459 458 +CONECT 460 461 458 462 +CONECT 461 460 +CONECT 462 460 464 463 478 +CONECT 463 462 +CONECT 464 467 465 462 466 +CONECT 465 464 +CONECT 466 464 +CONECT 467 468 476 464 +CONECT 468 470 469 467 +CONECT 469 468 +CONECT 470 471 472 468 +CONECT 471 470 +CONECT 472 473 470 474 +CONECT 473 472 +CONECT 474 472 475 476 +CONECT 475 474 +CONECT 476 474 467 477 +CONECT 477 476 +CONECT 478 462 480 479 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 484 480 492 483 +CONECT 483 482 +CONECT 484 485 490 486 482 +CONECT 485 484 +CONECT 486 488 484 489 487 +CONECT 487 486 +CONECT 488 486 +CONECT 489 486 +CONECT 490 491 484 +CONECT 491 490 +CONECT 492 494 482 493 +CONECT 493 492 +CONECT 494 495 496 492 +CONECT 495 494 +CONECT 496 498 494 497 514 +CONECT 497 496 +CONECT 498 501 499 500 496 +CONECT 499 498 +CONECT 500 498 +CONECT 501 504 503 502 498 +CONECT 502 501 +CONECT 503 501 +CONECT 504 507 505 506 501 +CONECT 505 504 +CONECT 506 504 +CONECT 507 509 508 510 504 +CONECT 508 507 +CONECT 509 507 +CONECT 510 512 507 513 511 +CONECT 511 510 +CONECT 512 510 +CONECT 513 510 +CONECT 514 496 516 515 +CONECT 515 514 +CONECT 516 517 514 518 +CONECT 517 516 +CONECT 518 516 520 519 524 +CONECT 519 518 +CONECT 520 523 521 518 522 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 518 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 530 541 529 +CONECT 529 528 +CONECT 530 532 531 528 533 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 534 535 536 +CONECT 534 533 +CONECT 535 533 +CONECT 536 533 537 +CONECT 537 536 540 538 539 +CONECT 538 537 +CONECT 539 537 +CONECT 540 537 +CONECT 541 543 528 542 +CONECT 542 541 +CONECT 543 544 545 541 +CONECT 544 543 +CONECT 545 547 543 551 546 +CONECT 546 545 +CONECT 547 548 550 549 545 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 545 553 552 +CONECT 552 551 +CONECT 553 554 551 555 +CONECT 554 553 +CONECT 555 557 553 556 565 +CONECT 556 555 +CONECT 557 560 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 562 561 557 +CONECT 561 560 +CONECT 562 563 564 560 +CONECT 563 562 +CONECT 564 562 +CONECT 565 555 567 566 +CONECT 566 565 +CONECT 567 568 565 569 +CONECT 568 567 +CONECT 569 567 571 570 577 +CONECT 570 569 +CONECT 571 574 572 569 573 +CONECT 572 571 +CONECT 573 571 +CONECT 574 576 575 571 +CONECT 575 574 +CONECT 576 574 +CONECT 577 569 579 578 +CONECT 578 577 +CONECT 579 580 577 581 +CONECT 580 579 +CONECT 581 579 583 596 582 +CONECT 582 581 +CONECT 583 585 584 581 586 +CONECT 584 583 +CONECT 585 583 +CONECT 586 583 592 587 588 +CONECT 587 586 +CONECT 588 586 589 590 591 +CONECT 589 588 +CONECT 590 588 +CONECT 591 588 +CONECT 592 593 595 594 586 +CONECT 593 592 +CONECT 594 592 +CONECT 595 592 +CONECT 596 598 581 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 598 601 602 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 613 608 609 605 +CONECT 608 607 +CONECT 609 611 607 610 612 +CONECT 610 609 +CONECT 611 609 +CONECT 612 609 +CONECT 613 615 614 607 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 619 625 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 641 639 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 644 638 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 659 649 652 653 +CONECT 652 651 +CONECT 653 651 654 655 656 +CONECT 654 653 +CONECT 655 653 +CONECT 656 653 657 658 +CONECT 657 656 +CONECT 658 656 +CONECT 659 660 661 651 +CONECT 660 659 +CONECT 661 663 659 662 +CONECT 662 661 +CONECT 663 664 665 673 661 +CONECT 664 663 +CONECT 665 667 671 663 666 +CONECT 666 665 +CONECT 667 668 669 670 665 +CONECT 668 667 +CONECT 669 667 +CONECT 670 667 +CONECT 671 672 665 +CONECT 672 671 +CONECT 673 675 663 674 +CONECT 674 673 +CONECT 675 676 677 673 +CONECT 676 675 +CONECT 677 694 679 675 678 +CONECT 678 677 +CONECT 679 681 677 682 680 +CONECT 680 679 +CONECT 681 679 +CONECT 682 685 683 679 684 +CONECT 683 682 +CONECT 684 682 +CONECT 685 688 686 687 682 +CONECT 686 685 +CONECT 687 685 +CONECT 688 691 689 690 685 +CONECT 689 688 +CONECT 690 688 +CONECT 691 692 693 688 +CONECT 692 691 +CONECT 693 691 +CONECT 694 695 696 677 +CONECT 695 694 +CONECT 696 698 694 697 +CONECT 697 696 +CONECT 698 699 706 700 696 +CONECT 699 698 +CONECT 700 703 698 701 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 705 700 704 +CONECT 704 703 +CONECT 705 703 +CONECT 706 708 698 707 +CONECT 707 706 +CONECT 708 709 710 706 +CONECT 709 708 +CONECT 710 712 708 718 711 +CONECT 711 710 +CONECT 712 714 715 713 710 +CONECT 713 712 +CONECT 714 712 +CONECT 715 716 712 717 +CONECT 716 715 +CONECT 717 715 +CONECT 718 720 710 719 +CONECT 719 718 +CONECT 720 721 722 718 +CONECT 721 720 +CONECT 722 724 723 720 728 +CONECT 723 722 +CONECT 724 727 726 725 722 +CONECT 725 724 +CONECT 726 724 +CONECT 727 724 +CONECT 728 722 729 730 +CONECT 729 728 +CONECT 730 728 731 732 +CONECT 731 730 +CONECT 732 730 733 734 742 +CONECT 733 732 +CONECT 734 736 732 740 735 +CONECT 735 734 +CONECT 736 737 739 738 734 +CONECT 737 736 +CONECT 738 736 +CONECT 739 736 +CONECT 740 741 734 +CONECT 741 740 +CONECT 742 732 744 743 +CONECT 743 742 +CONECT 744 745 746 742 +CONECT 745 744 +CONECT 746 747 744 748 764 +CONECT 747 746 +CONECT 748 751 746 750 749 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 752 753 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 760 759 758 754 +CONECT 758 757 +CONECT 759 757 +CONECT 760 762 763 761 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 760 +CONECT 764 746 766 765 +CONECT 765 764 +CONECT 766 767 764 768 +CONECT 767 766 +CONECT 768 766 778 770 769 +CONECT 769 768 +CONECT 770 771 768 776 772 +CONECT 771 770 +CONECT 772 770 775 774 773 +CONECT 773 772 +CONECT 774 772 +CONECT 775 772 +CONECT 776 777 770 +CONECT 777 776 +CONECT 778 779 768 780 +CONECT 779 778 +CONECT 780 778 782 781 +CONECT 781 780 +CONECT 782 783 780 784 798 +CONECT 783 782 +CONECT 784 787 782 786 785 +CONECT 785 784 +CONECT 786 784 +CONECT 787 796 788 784 +CONECT 788 790 787 789 +CONECT 789 788 +CONECT 790 792 791 788 +CONECT 791 790 +CONECT 792 793 794 790 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 794 797 787 +CONECT 797 796 +CONECT 798 782 800 799 +CONECT 799 798 +CONECT 800 801 798 802 +CONECT 801 800 +CONECT 802 804 800 812 803 +CONECT 803 802 +CONECT 804 810 806 805 802 +CONECT 805 804 +CONECT 806 807 808 804 809 +CONECT 807 806 +CONECT 808 806 +CONECT 809 806 +CONECT 810 811 804 +CONECT 811 810 +CONECT 812 813 802 814 +CONECT 813 812 +CONECT 814 812 816 815 +CONECT 815 814 +CONECT 816 833 817 814 818 +CONECT 817 816 +CONECT 818 816 819 820 821 +CONECT 819 818 +CONECT 820 818 +CONECT 821 818 823 822 824 +CONECT 822 821 +CONECT 823 821 +CONECT 824 821 825 827 826 +CONECT 825 824 +CONECT 826 824 +CONECT 827 829 824 828 830 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 831 832 +CONECT 831 830 +CONECT 832 830 +CONECT 833 835 834 816 +CONECT 834 833 +CONECT 835 837 833 836 +CONECT 836 835 +CONECT 837 839 838 835 846 +CONECT 838 837 +CONECT 839 841 840 842 837 +CONECT 840 839 +CONECT 841 839 +CONECT 842 844 839 843 +CONECT 843 842 +CONECT 844 845 842 +CONECT 845 844 +CONECT 846 837 848 847 +CONECT 847 846 +CONECT 848 849 846 850 +CONECT 849 848 +CONECT 850 848 852 861 851 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 856 852 857 858 +CONECT 856 855 +CONECT 857 855 +CONECT 858 855 860 859 +CONECT 859 858 +CONECT 860 858 +CONECT 861 863 850 862 +CONECT 862 861 +CONECT 863 861 +CONECT 864 87 303 865 272 +CONECT 865 864 867 +CONECT 866 869 867 870 868 +CONECT 867 865 866 +CONECT 868 866 +CONECT 869 866 +CONECT 870 866 +CONECT 871 872 +CONECT 872 873 871 +CONECT 873 872 +MASTER 0 0 0 0 0 0 0 0 873 0 873 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_21.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_21.pdb new file mode 100644 index 0000000..2ec2c07 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_21.pdb @@ -0,0 +1,1751 @@ +COMPND fitness: 0.2006 34.955833333333885 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 P1 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HX1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HX1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HX1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HX1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HX1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HX1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HX1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HX1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N ARG 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H ARG 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA ARG 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 CB ARG 8 32.132 -93.836 -4.510 1.00 0.00 C +ATOM 136 HB2 ARG 8 33.181 -94.067 -4.697 1.00 0.00 H +ATOM 137 HB3 ARG 8 31.847 -92.954 -5.085 1.00 0.00 H +ATOM 138 CG ARG 8 31.930 -93.562 -3.029 1.00 0.00 C +ATOM 139 HG2 ARG 8 30.876 -93.341 -2.857 1.00 0.00 H +ATOM 140 HG3 ARG 8 32.210 -94.454 -2.469 1.00 0.00 H +ATOM 141 CD ARG 8 32.776 -92.387 -2.565 1.00 0.00 C +ATOM 142 HD2 ARG 8 32.675 -92.283 -1.484 1.00 0.00 H +ATOM 143 HD3 ARG 8 33.819 -92.579 -2.815 1.00 0.00 H +ATOM 144 NE ARG 8 32.366 -91.135 -3.195 1.00 0.00 N +ATOM 145 HE ARG 8 31.550 -91.162 -3.789 1.00 0.00 H +ATOM 146 CZ ARG 8 32.999 -89.977 -3.037 1.00 0.00 C +ATOM 147 NH1 ARG 8 32.553 -88.890 -3.652 1.00 0.00 N +ATOM 148 HH11 ARG 8 31.733 -88.946 -4.239 1.00 0.00 H +ATOM 149 HH12 ARG 8 33.036 -88.010 -3.530 1.00 0.00 H +ATOM 150 NH2 ARG 8 34.076 -89.910 -2.268 1.00 0.00 N +ATOM 151 HH21 ARG 8 34.414 -90.741 -1.803 1.00 0.00 H +ATOM 152 HH22 ARG 8 34.555 -89.028 -2.150 1.00 0.00 H +ATOM 153 HA ARG 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 154 C ARG 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 155 O ARG 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 156 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 157 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 158 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 161 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 162 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 163 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 164 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 165 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 166 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 167 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 168 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 169 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 170 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 171 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 172 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 173 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 174 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 175 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 176 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 177 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 178 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 179 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 180 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 181 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 182 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 183 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 184 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 185 N ILE 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 186 H ILE 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 187 CA ILE 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 188 CB ILE 11 32.215-101.571 0.717 1.00 0.00 C +ATOM 189 HB ILE 11 31.857-101.753 1.731 1.00 0.00 H +ATOM 190 CG2 ILE 11 33.468-102.396 0.465 1.00 0.00 C +ATOM 191 HG21 ILE 11 33.825-102.214 -0.549 1.00 0.00 H +ATOM 192 HG22 ILE 11 34.241-102.112 1.179 1.00 0.00 H +ATOM 193 HG23 ILE 11 33.237-103.454 0.583 1.00 0.00 H +ATOM 194 CG1 ILE 11 32.565-100.092 0.545 1.00 0.00 C +ATOM 195 HG12 ILE 11 33.127 -99.998 -0.384 1.00 0.00 H +ATOM 196 HG13 ILE 11 31.625 -99.544 0.459 1.00 0.00 H +ATOM 197 CD1 ILE 11 33.379 -99.520 1.684 1.00 0.00 C +ATOM 198 HD11 ILE 11 34.318-100.066 1.771 1.00 0.00 H +ATOM 199 HD12 ILE 11 33.587 -98.468 1.491 1.00 0.00 H +ATOM 200 HD13 ILE 11 32.818 -99.613 2.615 1.00 0.00 H +ATOM 201 HA ILE 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 202 C ILE 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 203 O ILE 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 204 N ASN 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 205 H ASN 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 206 CA ASN 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 207 CB ASN 12 28.130 -98.237 -0.161 1.00 0.00 C +ATOM 208 HB2 ASN 12 28.768 -97.830 -0.944 1.00 0.00 H +ATOM 209 HB3 ASN 12 27.146 -97.771 -0.217 1.00 0.00 H +ATOM 210 CG ASN 12 28.745 -97.908 1.184 1.00 0.00 C +ATOM 211 OD1 ASN 12 28.878 -98.777 2.046 1.00 0.00 O +ATOM 212 ND2 ASN 12 29.125 -96.650 1.369 1.00 0.00 N +ATOM 213 HD21 ASN 12 29.540 -96.375 2.247 1.00 0.00 H +ATOM 214 HD22 ASN 12 28.996 -95.973 0.630 1.00 0.00 H +ATOM 215 HA ASN 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 216 C ASN 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 217 O ASN 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 218 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 219 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 220 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 221 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 222 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 223 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 224 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 225 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 226 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 227 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 228 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 229 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 230 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 231 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 232 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 233 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 234 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 235 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 236 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 237 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 238 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 239 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 240 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 241 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 242 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 243 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 244 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 245 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 246 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 247 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 248 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 249 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 250 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 251 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 252 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 253 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 254 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 255 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 256 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 257 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 258 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 259 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 260 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 261 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 262 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 263 N HY1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 264 CA HY1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 265 C HY1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 266 O HY1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 267 CB HY1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 268 CG HY1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 269 CD2 HY1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 270 ND1 HY1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 271 CE1 HY1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 272 NE2 HY1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 273 H HY1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 274 HA HY1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 275 HB2 HY1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 276 HB3 HY1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 277 HD1 HY1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 278 HD2 HY1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 279 HE1 HY1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 280 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 281 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 282 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 283 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 284 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 285 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 286 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 287 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 288 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 289 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 290 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 291 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 292 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 293 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 294 N HY2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 295 CA HY2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 296 C HY2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 297 O HY2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 298 CB HY2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 299 CG HY2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 300 CD2 HY2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 301 ND1 HY2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 302 CE1 HY2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 303 NE2 HY2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 304 H HY2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 305 HA HY2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 306 HB2 HY2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 307 HB3 HY2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 308 HD1 HY2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 309 HD2 HY2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 310 HE1 HY2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 311 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 312 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 313 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 314 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 315 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 316 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 317 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 318 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 319 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 320 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 321 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 322 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 323 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 324 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 325 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 326 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 327 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 328 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 329 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 330 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 331 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 332 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 333 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 334 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 335 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 336 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 337 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 338 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 339 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 340 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 341 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 342 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 343 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 344 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 345 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 346 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 347 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 348 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 349 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 350 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 351 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 352 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 353 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 354 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 355 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 356 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 357 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 358 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 359 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 360 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 361 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 362 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 363 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 364 N TRP 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 365 H TRP 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 366 CA TRP 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 367 CB TRP 23 21.411 -85.256 -16.822 1.00 0.00 C +ATOM 368 HB2 TRP 23 22.132 -85.913 -16.338 1.00 0.00 H +ATOM 369 HB3 TRP 23 20.438 -85.734 -16.718 1.00 0.00 H +ATOM 370 CG TRP 23 21.738 -85.227 -18.283 1.00 0.00 C +ATOM 371 CD1 TRP 23 20.859 -85.092 -19.318 1.00 0.00 C +ATOM 372 HD1 TRP 23 19.783 -84.997 -19.203 1.00 0.00 H +ATOM 373 NE1 TRP 23 21.530 -85.108 -20.517 1.00 0.00 N +ATOM 374 HE1 TRP 23 21.113 -85.024 -21.438 1.00 0.00 H +ATOM 375 CE2 TRP 23 22.874 -85.257 -20.268 1.00 0.00 C +ATOM 376 CZ2 TRP 23 23.948 -85.327 -21.155 1.00 0.00 C +ATOM 377 HZ2 TRP 23 23.812 -85.267 -22.225 1.00 0.00 H +ATOM 378 CH2 TRP 23 25.200 -85.477 -20.620 1.00 0.00 C +ATOM 379 HH2 TRP 23 26.050 -85.530 -21.290 1.00 0.00 H +ATOM 380 CZ3 TRP 23 25.394 -85.558 -19.231 1.00 0.00 C +ATOM 381 HZ3 TRP 23 26.400 -85.679 -18.854 1.00 0.00 H +ATOM 382 CE3 TRP 23 24.329 -85.487 -18.351 1.00 0.00 C +ATOM 383 HE3 TRP 23 24.462 -85.551 -17.282 1.00 0.00 H +ATOM 384 CD2 TRP 23 23.042 -85.333 -18.871 1.00 0.00 C +ATOM 385 HA TRP 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 386 C TRP 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 387 O TRP 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 388 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 389 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 390 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 391 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 392 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 393 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 394 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 395 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 396 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 397 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 398 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 399 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 400 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 401 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 402 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 403 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 404 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 405 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 406 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 407 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 408 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 409 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 410 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 411 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 412 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 413 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 414 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 415 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 416 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 417 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 418 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 419 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 420 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 421 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 422 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 423 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 424 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 425 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 426 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 427 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 428 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 429 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 430 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 431 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 432 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 433 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 434 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 435 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 436 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 437 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 438 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 439 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 440 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 441 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 442 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 443 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 444 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 445 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 446 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 447 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 448 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 449 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 450 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 451 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 452 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 453 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 454 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 455 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 456 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 457 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 458 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 459 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 460 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 461 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 462 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 463 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 464 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 465 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 466 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 467 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 468 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 469 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 470 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 471 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 472 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 473 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 474 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 475 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 476 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 477 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 478 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 479 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 480 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 481 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 482 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 483 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 484 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 485 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 486 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 487 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 488 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 489 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 490 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 491 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 492 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 493 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 494 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 495 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 496 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 497 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 498 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 499 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 500 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 501 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 502 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 503 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 504 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 505 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 506 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 507 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 508 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 509 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 510 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 511 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 512 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 513 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 514 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 515 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 516 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 517 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 518 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 519 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 520 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 521 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 522 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 523 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 524 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 525 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 526 N MET 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 527 H MET 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 528 CA MET 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 529 CB MET 33 27.315 -82.525 -3.272 1.00 0.00 C +ATOM 530 HB2 MET 33 26.398 -81.940 -3.214 1.00 0.00 H +ATOM 531 HB3 MET 33 27.389 -82.989 -4.255 1.00 0.00 H +ATOM 532 CG MET 33 27.295 -83.605 -2.204 1.00 0.00 C +ATOM 533 HG2 MET 33 26.492 -84.303 -2.443 1.00 0.00 H +ATOM 534 HG3 MET 33 28.252 -84.128 -2.232 1.00 0.00 H +ATOM 535 SD MET 33 27.030 -82.943 -0.547 1.00 0.00 S +ATOM 536 CE MET 33 27.063 -84.446 0.427 1.00 0.00 C +ATOM 537 HE1 MET 33 28.027 -84.938 0.303 1.00 0.00 H +ATOM 538 HE2 MET 33 26.912 -84.201 1.479 1.00 0.00 H +ATOM 539 HE3 MET 33 26.268 -85.113 0.092 1.00 0.00 H +ATOM 540 HA MET 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 541 C MET 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 542 O MET 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 543 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 544 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 545 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 546 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 547 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 548 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 549 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 550 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 551 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 552 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 553 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 554 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 555 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 556 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 557 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 558 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 559 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 560 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 561 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 562 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 563 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 564 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 565 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 566 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 567 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 568 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 569 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 570 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 571 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 572 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 573 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 574 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 575 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 576 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 577 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 578 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 579 N LEU 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 580 H LEU 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 581 CA LEU 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 582 CB LEU 37 33.048 -83.879 0.496 1.00 0.00 C +ATOM 583 HB2 LEU 37 31.985 -83.889 0.734 1.00 0.00 H +ATOM 584 HB3 LEU 37 33.178 -83.869 -0.586 1.00 0.00 H +ATOM 585 CG LEU 37 33.713 -85.128 1.077 1.00 0.00 C +ATOM 586 HG LEU 37 34.787 -85.068 0.903 1.00 0.00 H +ATOM 587 CD1 LEU 37 33.448 -85.233 2.571 1.00 0.00 C +ATOM 588 HD11 LEU 37 32.374 -85.292 2.747 1.00 0.00 H +ATOM 589 HD12 LEU 37 33.929 -86.128 2.965 1.00 0.00 H +ATOM 590 HD13 LEU 37 33.849 -84.353 3.075 1.00 0.00 H +ATOM 591 CD2 LEU 37 33.176 -86.384 0.410 1.00 0.00 C +ATOM 592 HD21 LEU 37 33.380 -86.342 -0.661 1.00 0.00 H +ATOM 593 HD22 LEU 37 33.662 -87.260 0.838 1.00 0.00 H +ATOM 594 HD23 LEU 37 32.100 -86.450 0.572 1.00 0.00 H +ATOM 595 HA LEU 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 596 C LEU 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 597 O LEU 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 598 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 599 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 600 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 601 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 602 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 603 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 604 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 605 N ALA 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 606 H ALA 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 607 CA ALA 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 608 CB ALA 39 38.874 -82.519 -4.462 1.00 0.00 C +ATOM 609 HB1 ALA 39 39.474 -81.803 -3.899 1.00 0.00 H +ATOM 610 HB2 ALA 39 38.973 -83.508 -4.013 1.00 0.00 H +ATOM 611 HB3 ALA 39 39.223 -82.552 -5.494 1.00 0.00 H +ATOM 612 HA ALA 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 613 C ALA 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 614 O ALA 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 615 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 616 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 617 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 618 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 619 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 620 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 621 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 622 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 623 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 624 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 625 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 626 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 627 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 628 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 629 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 630 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 631 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 632 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 633 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 634 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 635 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 636 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 637 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 638 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 639 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 640 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 641 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 642 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 643 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 644 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 645 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 646 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 647 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 648 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 649 N ASP 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 650 H ASP 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 651 CA ASP 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 652 CB ASP 43 29.884 -89.033 -12.452 1.00 0.00 C +ATOM 653 HB2 ASP 43 29.493 -88.069 -12.779 1.00 0.00 H +ATOM 654 HB3 ASP 43 29.081 -89.770 -12.451 1.00 0.00 H +ATOM 655 CG ASP 43 30.447 -88.899 -11.051 1.00 0.00 C +ATOM 656 OD1 ASP 43 31.651 -88.590 -10.921 1.00 0.00 O +ATOM 657 OD2 ASP 43 29.685 -89.101 -10.082 1.00 0.00 O +ATOM 658 HA ASP 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 659 C ASP 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 660 O ASP 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 661 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 662 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 663 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 664 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 665 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 666 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 667 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 668 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 669 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 670 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 671 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 672 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 673 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 674 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 675 N LYN 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 676 H LYN 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 677 CA LYN 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 678 CB LYN 45 25.266 -89.253 -17.470 1.00 0.00 C +ATOM 679 HB2 LYN 45 25.726 -88.747 -16.621 1.00 0.00 H +ATOM 680 HB3 LYN 45 25.701 -88.876 -18.396 1.00 0.00 H +ATOM 681 CG LYN 45 23.770 -88.987 -17.468 1.00 0.00 C +ATOM 682 HG2 LYN 45 23.323 -89.505 -18.317 1.00 0.00 H +ATOM 683 HG3 LYN 45 23.349 -89.376 -16.541 1.00 0.00 H +ATOM 684 CD LYN 45 23.474 -87.499 -17.571 1.00 0.00 C +ATOM 685 HD2 LYN 45 22.407 -87.345 -17.414 1.00 0.00 H +ATOM 686 HD3 LYN 45 24.035 -86.979 -16.795 1.00 0.00 H +ATOM 687 CE LYN 45 23.868 -86.952 -18.934 1.00 0.00 C +ATOM 688 HE2 LYN 45 24.935 -87.127 -19.077 1.00 0.00 H +ATOM 689 HE3 LYN 45 23.307 -87.493 -19.695 1.00 0.00 H +ATOM 690 NZ LYN 45 23.585 -85.495 -19.050 1.00 0.00 N +ATOM 691 HZ2 LYN 45 23.859 -85.171 -19.966 1.00 0.00 H +ATOM 692 HZ3 LYN 45 22.597 -85.332 -18.918 1.00 0.00 H +ATOM 693 HA LYN 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 694 C LYN 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 695 O LYN 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 696 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 697 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 698 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 699 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 700 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 701 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 702 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 703 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 704 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 705 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 706 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 707 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 708 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 709 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 710 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 711 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 712 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 713 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 714 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 715 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 716 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 717 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 718 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 719 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 720 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 721 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 722 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 723 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 724 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 725 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 726 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 727 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 728 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 729 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 730 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 731 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 732 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 733 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 734 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 735 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 736 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 737 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 738 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 739 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 740 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 741 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 742 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 743 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 744 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 745 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 746 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 747 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 748 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 749 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 750 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 751 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 752 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 753 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 754 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 755 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 756 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 757 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 758 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 759 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 760 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 761 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 762 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 763 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 764 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 765 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 766 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 767 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 768 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 769 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 770 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 771 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 772 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 773 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 774 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 775 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 776 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 777 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 778 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 779 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 780 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 781 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 782 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 783 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 784 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 785 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 786 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 787 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 788 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 789 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 790 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 791 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 792 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 793 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 794 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 795 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 796 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 797 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 798 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 799 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 800 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 801 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 802 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 803 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 804 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 805 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 806 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 807 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 808 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 809 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 810 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 811 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 812 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 813 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 814 N LYN 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 815 H LYN 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 816 CA LYN 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 817 CB LYN 54 32.301 -94.491 -10.199 1.00 0.00 C +ATOM 818 HB2 LYN 54 33.358 -94.431 -10.462 1.00 0.00 H +ATOM 819 HB3 LYN 54 32.026 -93.623 -9.600 1.00 0.00 H +ATOM 820 CG LYN 54 32.050 -95.758 -9.398 1.00 0.00 C +ATOM 821 HG2 LYN 54 30.989 -95.808 -9.152 1.00 0.00 H +ATOM 822 HG3 LYN 54 32.321 -96.617 -10.013 1.00 0.00 H +ATOM 823 CD LYN 54 32.869 -95.774 -8.118 1.00 0.00 C +ATOM 824 HD2 LYN 54 33.925 -95.713 -8.380 1.00 0.00 H +ATOM 825 HD3 LYN 54 32.594 -94.906 -7.518 1.00 0.00 H +ATOM 826 CE LYN 54 32.619 -97.041 -7.318 1.00 0.00 C +ATOM 827 HE2 LYN 54 31.557 -97.090 -7.077 1.00 0.00 H +ATOM 828 HE3 LYN 54 32.889 -97.897 -7.938 1.00 0.00 H +ATOM 829 NZ LYN 54 33.415 -97.070 -6.059 1.00 0.00 N +ATOM 830 HZ2 LYN 54 33.221 -97.925 -5.558 1.00 0.00 H +ATOM 831 HZ3 LYN 54 34.399 -97.026 -6.282 1.00 0.00 H +ATOM 832 HA LYN 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 833 C LYN 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 834 O LYN 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 835 N ASH 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 836 H ASH 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 837 CA ASH 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 838 CB ASH 55 34.660 -96.376 -14.407 1.00 0.00 C +ATOM 839 HB2 ASH 55 34.971 -97.132 -15.128 1.00 0.00 H +ATOM 840 HB3 ASH 55 34.155 -95.564 -14.929 1.00 0.00 H +ATOM 841 CG ASH 55 35.878 -95.832 -13.687 1.00 0.00 C +ATOM 842 OD1 ASH 55 35.823 -95.694 -12.446 1.00 0.00 O +ATOM 843 OD2 ASH 55 36.888 -95.544 -14.362 1.00 0.00 O +ATOM 844 HD2 ASH 55 37.578 -95.214 -13.781 1.00 0.00 H +ATOM 845 HA ASH 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 846 C ASH 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 847 O ASH 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 848 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 849 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 850 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 851 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 852 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 853 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 854 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 855 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 856 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 857 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 858 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 859 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 860 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 861 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 862 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 863 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 864 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 Zn +ATOM 865 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 866 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 867 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 868 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 869 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 870 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +ATOM 871 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 872 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 873 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 17 15 13 16 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 65 60 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 68 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 65 69 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 864 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 104 106 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 111 112 113 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 153 132 154 135 +CONECT 135 136 137 138 134 +CONECT 136 135 +CONECT 137 135 +CONECT 138 135 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 142 143 144 +CONECT 142 141 +CONECT 143 141 +CONECT 144 141 145 146 +CONECT 145 144 +CONECT 146 144 147 150 +CONECT 147 146 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 146 151 152 +CONECT 151 150 +CONECT 152 150 +CONECT 153 134 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 165 169 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 170 175 +CONECT 174 173 +CONECT 175 173 +CONECT 176 178 179 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 182 181 176 180 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 201 202 188 +CONECT 188 189 190 194 187 +CONECT 189 188 +CONECT 190 188 191 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 +CONECT 194 188 195 196 197 +CONECT 195 194 +CONECT 196 194 +CONECT 197 194 198 199 200 +CONECT 198 197 +CONECT 199 197 +CONECT 200 197 +CONECT 201 187 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 216 204 215 207 +CONECT 207 208 209 210 206 +CONECT 208 207 +CONECT 209 207 +CONECT 210 207 211 212 +CONECT 211 210 +CONECT 212 210 213 214 +CONECT 213 212 +CONECT 214 212 +CONECT 215 206 +CONECT 216 217 218 206 +CONECT 217 216 +CONECT 218 220 216 219 +CONECT 219 218 +CONECT 220 221 222 238 218 +CONECT 221 220 +CONECT 222 225 220 223 224 +CONECT 223 222 +CONECT 224 222 +CONECT 225 227 226 228 222 +CONECT 226 225 +CONECT 227 225 +CONECT 228 229 225 231 230 +CONECT 229 228 +CONECT 230 228 +CONECT 231 233 228 234 232 +CONECT 232 231 +CONECT 233 231 +CONECT 234 237 231 235 236 +CONECT 235 234 +CONECT 236 234 +CONECT 237 234 +CONECT 238 239 220 240 +CONECT 239 238 +CONECT 240 238 242 241 +CONECT 241 240 +CONECT 242 245 240 243 244 +CONECT 243 242 +CONECT 244 242 +CONECT 245 246 247 242 +CONECT 246 245 +CONECT 247 249 245 248 +CONECT 248 247 +CONECT 249 251 250 261 247 +CONECT 250 249 +CONECT 251 257 252 253 249 +CONECT 252 251 +CONECT 253 251 256 255 254 +CONECT 254 253 +CONECT 255 253 +CONECT 256 253 +CONECT 257 259 260 258 251 +CONECT 258 257 +CONECT 259 257 +CONECT 260 257 +CONECT 261 263 249 262 +CONECT 262 261 +CONECT 263 273 264 261 +CONECT 264 265 263 274 267 +CONECT 265 266 280 264 +CONECT 266 265 +CONECT 267 264 268 275 276 +CONECT 268 269 270 267 +CONECT 269 272 278 268 +CONECT 270 271 268 277 +CONECT 271 272 279 270 +CONECT 272 864 271 269 +CONECT 273 263 +CONECT 274 264 +CONECT 275 267 +CONECT 276 267 +CONECT 277 270 +CONECT 278 269 +CONECT 279 271 +CONECT 280 282 265 281 +CONECT 281 280 +CONECT 282 283 284 292 280 +CONECT 283 282 +CONECT 284 285 286 282 290 +CONECT 285 284 +CONECT 286 287 288 284 289 +CONECT 287 286 +CONECT 288 286 +CONECT 289 286 +CONECT 290 284 291 +CONECT 291 290 +CONECT 292 294 282 293 +CONECT 293 292 +CONECT 294 304 295 292 +CONECT 295 296 298 294 305 +CONECT 296 297 311 295 +CONECT 297 296 +CONECT 298 306 307 295 299 +CONECT 299 298 300 301 +CONECT 300 309 299 303 +CONECT 301 299 308 302 +CONECT 302 303 301 310 +CONECT 303 300 302 864 +CONECT 304 294 +CONECT 305 295 +CONECT 306 298 +CONECT 307 298 +CONECT 308 301 +CONECT 309 300 +CONECT 310 302 +CONECT 311 313 296 312 +CONECT 312 311 +CONECT 313 324 314 311 315 +CONECT 314 313 +CONECT 315 313 318 317 316 +CONECT 316 315 +CONECT 317 315 +CONECT 318 320 321 315 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 322 318 323 +CONECT 322 321 +CONECT 323 321 +CONECT 324 326 325 313 +CONECT 325 324 +CONECT 326 328 327 324 +CONECT 327 326 +CONECT 328 334 330 329 326 +CONECT 329 328 +CONECT 330 333 332 328 331 +CONECT 331 330 +CONECT 332 330 +CONECT 333 330 +CONECT 334 336 335 328 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 350 340 339 336 +CONECT 339 338 +CONECT 340 341 346 338 342 +CONECT 341 340 +CONECT 342 340 343 345 344 +CONECT 343 342 +CONECT 344 342 +CONECT 345 342 +CONECT 346 349 348 340 347 +CONECT 347 346 +CONECT 348 346 +CONECT 349 346 +CONECT 350 351 352 338 +CONECT 351 350 +CONECT 352 354 350 353 +CONECT 353 352 +CONECT 354 356 355 362 352 +CONECT 355 354 +CONECT 356 359 357 358 354 +CONECT 357 356 +CONECT 358 356 +CONECT 359 360 361 356 +CONECT 360 359 +CONECT 361 359 +CONECT 362 354 364 363 +CONECT 363 362 +CONECT 364 365 362 366 +CONECT 365 364 +CONECT 366 364 386 385 367 +CONECT 367 368 369 370 366 +CONECT 368 367 +CONECT 369 367 +CONECT 370 367 371 384 +CONECT 371 370 372 373 +CONECT 372 371 +CONECT 373 371 374 375 +CONECT 374 373 +CONECT 375 373 376 384 +CONECT 376 375 377 378 +CONECT 377 376 +CONECT 378 376 379 380 +CONECT 379 378 +CONECT 380 378 381 382 +CONECT 381 380 +CONECT 382 380 383 384 +CONECT 383 382 +CONECT 384 370 375 382 +CONECT 385 366 +CONECT 386 388 366 387 +CONECT 387 386 +CONECT 388 389 390 386 +CONECT 389 388 +CONECT 390 392 388 391 396 +CONECT 391 390 +CONECT 392 394 393 395 390 +CONECT 393 392 +CONECT 394 392 +CONECT 395 392 +CONECT 396 390 397 398 +CONECT 397 396 +CONECT 398 396 399 400 +CONECT 399 398 +CONECT 400 398 402 401 411 +CONECT 401 400 +CONECT 402 405 400 403 404 +CONECT 403 402 +CONECT 404 402 +CONECT 405 406 408 407 402 +CONECT 406 405 +CONECT 407 405 +CONECT 408 410 405 409 +CONECT 409 408 +CONECT 410 408 +CONECT 411 400 413 412 +CONECT 412 411 +CONECT 413 414 411 415 +CONECT 414 413 +CONECT 415 413 417 421 416 +CONECT 416 415 +CONECT 417 418 419 415 420 +CONECT 418 417 +CONECT 419 417 +CONECT 420 417 +CONECT 421 423 415 422 +CONECT 422 421 +CONECT 423 424 425 421 +CONECT 424 423 +CONECT 425 427 423 426 436 +CONECT 426 425 +CONECT 427 428 429 430 425 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 427 432 431 +CONECT 431 430 +CONECT 432 430 +CONECT 433 434 435 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 425 438 437 +CONECT 437 436 +CONECT 438 439 436 440 +CONECT 439 438 +CONECT 440 438 442 441 458 +CONECT 441 440 +CONECT 442 445 443 444 440 +CONECT 443 442 +CONECT 444 442 +CONECT 445 448 447 446 442 +CONECT 446 445 +CONECT 447 445 +CONECT 448 451 449 445 450 +CONECT 449 448 +CONECT 450 448 +CONECT 451 454 453 452 448 +CONECT 452 451 +CONECT 453 451 +CONECT 454 457 456 455 451 +CONECT 455 454 +CONECT 456 454 +CONECT 457 454 +CONECT 458 440 460 459 +CONECT 459 458 +CONECT 460 461 458 462 +CONECT 461 460 +CONECT 462 460 464 463 478 +CONECT 463 462 +CONECT 464 467 465 462 466 +CONECT 465 464 +CONECT 466 464 +CONECT 467 468 476 464 +CONECT 468 470 469 467 +CONECT 469 468 +CONECT 470 471 472 468 +CONECT 471 470 +CONECT 472 473 470 474 +CONECT 473 472 +CONECT 474 472 475 476 +CONECT 475 474 +CONECT 476 474 467 477 +CONECT 477 476 +CONECT 478 462 480 479 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 484 480 492 483 +CONECT 483 482 +CONECT 484 485 490 486 482 +CONECT 485 484 +CONECT 486 487 484 488 489 +CONECT 487 486 +CONECT 488 486 +CONECT 489 486 +CONECT 490 491 484 +CONECT 491 490 +CONECT 492 494 482 493 +CONECT 493 492 +CONECT 494 495 496 492 +CONECT 495 494 +CONECT 496 498 494 497 514 +CONECT 497 496 +CONECT 498 501 499 500 496 +CONECT 499 498 +CONECT 500 498 +CONECT 501 504 503 502 498 +CONECT 502 501 +CONECT 503 501 +CONECT 504 507 505 506 501 +CONECT 505 504 +CONECT 506 504 +CONECT 507 509 510 508 504 +CONECT 508 507 +CONECT 509 507 +CONECT 510 512 507 511 513 +CONECT 511 510 +CONECT 512 510 +CONECT 513 510 +CONECT 514 496 516 515 +CONECT 515 514 +CONECT 516 517 514 518 +CONECT 517 516 +CONECT 518 516 520 519 524 +CONECT 519 518 +CONECT 520 522 523 518 521 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 518 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 541 540 529 +CONECT 529 530 531 532 528 +CONECT 530 529 +CONECT 531 529 +CONECT 532 529 533 534 535 +CONECT 533 532 +CONECT 534 532 +CONECT 535 532 536 +CONECT 536 535 537 538 539 +CONECT 537 536 +CONECT 538 536 +CONECT 539 536 +CONECT 540 528 +CONECT 541 543 528 542 +CONECT 542 541 +CONECT 543 544 545 541 +CONECT 544 543 +CONECT 545 547 543 551 546 +CONECT 546 545 +CONECT 547 548 549 550 545 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 553 545 552 +CONECT 552 551 +CONECT 553 554 555 551 +CONECT 554 553 +CONECT 555 557 553 556 565 +CONECT 556 555 +CONECT 557 560 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 562 561 557 +CONECT 561 560 +CONECT 562 564 563 560 +CONECT 563 562 +CONECT 564 562 +CONECT 565 555 567 566 +CONECT 566 565 +CONECT 567 568 565 569 +CONECT 568 567 +CONECT 569 567 570 571 577 +CONECT 570 569 +CONECT 571 572 569 574 573 +CONECT 572 571 +CONECT 573 571 +CONECT 574 575 576 571 +CONECT 575 574 +CONECT 576 574 +CONECT 577 569 579 578 +CONECT 578 577 +CONECT 579 580 577 581 +CONECT 580 579 +CONECT 581 579 596 595 582 +CONECT 582 583 584 585 581 +CONECT 583 582 +CONECT 584 582 +CONECT 585 582 586 587 591 +CONECT 586 585 +CONECT 587 585 588 589 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 585 592 593 594 +CONECT 592 591 +CONECT 593 591 +CONECT 594 591 +CONECT 595 581 +CONECT 596 598 581 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 602 598 601 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 613 612 605 608 +CONECT 608 609 610 611 607 +CONECT 609 608 +CONECT 610 608 +CONECT 611 608 +CONECT 612 607 +CONECT 613 615 614 607 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 619 625 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 641 639 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 644 638 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 659 649 658 652 +CONECT 652 653 654 655 651 +CONECT 653 652 +CONECT 654 652 +CONECT 655 652 656 657 +CONECT 656 655 +CONECT 657 655 +CONECT 658 651 +CONECT 659 660 661 651 +CONECT 660 659 +CONECT 661 663 659 662 +CONECT 662 661 +CONECT 663 664 665 673 661 +CONECT 664 663 +CONECT 665 667 671 663 666 +CONECT 666 665 +CONECT 667 670 669 668 665 +CONECT 668 667 +CONECT 669 667 +CONECT 670 667 +CONECT 671 665 672 +CONECT 672 671 +CONECT 673 675 663 674 +CONECT 674 673 +CONECT 675 676 677 673 +CONECT 676 675 +CONECT 677 694 675 693 678 +CONECT 678 679 680 681 677 +CONECT 679 678 +CONECT 680 678 +CONECT 681 678 682 683 684 +CONECT 682 681 +CONECT 683 681 +CONECT 684 681 685 686 687 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 688 689 690 +CONECT 688 687 +CONECT 689 687 +CONECT 690 687 691 692 +CONECT 691 690 +CONECT 692 690 +CONECT 693 677 +CONECT 694 695 696 677 +CONECT 695 694 +CONECT 696 698 694 697 +CONECT 697 696 +CONECT 698 699 706 700 696 +CONECT 699 698 +CONECT 700 703 698 701 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 705 704 700 +CONECT 704 703 +CONECT 705 703 +CONECT 706 708 698 707 +CONECT 707 706 +CONECT 708 709 710 706 +CONECT 709 708 +CONECT 710 712 708 718 711 +CONECT 711 710 +CONECT 712 714 715 713 710 +CONECT 713 712 +CONECT 714 712 +CONECT 715 716 712 717 +CONECT 716 715 +CONECT 717 715 +CONECT 718 720 710 719 +CONECT 719 718 +CONECT 720 721 722 718 +CONECT 721 720 +CONECT 722 724 723 720 728 +CONECT 723 722 +CONECT 724 727 725 726 722 +CONECT 725 724 +CONECT 726 724 +CONECT 727 724 +CONECT 728 722 729 730 +CONECT 729 728 +CONECT 730 728 731 732 +CONECT 731 730 +CONECT 732 730 733 734 742 +CONECT 733 732 +CONECT 734 736 732 740 735 +CONECT 735 734 +CONECT 736 738 739 737 734 +CONECT 737 736 +CONECT 738 736 +CONECT 739 736 +CONECT 740 741 734 +CONECT 741 740 +CONECT 742 732 744 743 +CONECT 743 742 +CONECT 744 745 746 742 +CONECT 745 744 +CONECT 746 747 744 748 764 +CONECT 747 746 +CONECT 748 751 746 750 749 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 752 753 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 760 759 758 754 +CONECT 758 757 +CONECT 759 757 +CONECT 760 762 761 763 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 760 +CONECT 764 746 766 765 +CONECT 765 764 +CONECT 766 767 764 768 +CONECT 767 766 +CONECT 768 766 778 770 769 +CONECT 769 768 +CONECT 770 771 768 776 772 +CONECT 771 770 +CONECT 772 770 773 774 775 +CONECT 773 772 +CONECT 774 772 +CONECT 775 772 +CONECT 776 777 770 +CONECT 777 776 +CONECT 778 779 768 780 +CONECT 779 778 +CONECT 780 778 782 781 +CONECT 781 780 +CONECT 782 783 780 784 798 +CONECT 783 782 +CONECT 784 787 782 786 785 +CONECT 785 784 +CONECT 786 784 +CONECT 787 796 788 784 +CONECT 788 790 787 789 +CONECT 789 788 +CONECT 790 792 791 788 +CONECT 791 790 +CONECT 792 793 794 790 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 794 797 787 +CONECT 797 796 +CONECT 798 782 800 799 +CONECT 799 798 +CONECT 800 801 798 802 +CONECT 801 800 +CONECT 802 800 804 812 803 +CONECT 803 802 +CONECT 804 810 806 805 802 +CONECT 805 804 +CONECT 806 807 809 804 808 +CONECT 807 806 +CONECT 808 806 +CONECT 809 806 +CONECT 810 811 804 +CONECT 811 810 +CONECT 812 813 802 814 +CONECT 813 812 +CONECT 814 812 816 815 +CONECT 815 814 +CONECT 816 833 832 814 817 +CONECT 817 818 819 820 816 +CONECT 818 817 +CONECT 819 817 +CONECT 820 817 821 822 823 +CONECT 821 820 +CONECT 822 820 +CONECT 823 820 824 825 826 +CONECT 824 823 +CONECT 825 823 +CONECT 826 823 827 828 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 830 831 +CONECT 830 829 +CONECT 831 829 +CONECT 832 816 +CONECT 833 835 834 816 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 845 835 846 838 +CONECT 838 839 840 841 837 +CONECT 839 838 +CONECT 840 838 +CONECT 841 838 842 843 +CONECT 842 841 +CONECT 843 841 844 +CONECT 844 843 +CONECT 845 837 +CONECT 846 837 848 847 +CONECT 847 846 +CONECT 848 849 846 850 +CONECT 849 848 +CONECT 850 852 848 861 851 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 856 852 857 858 +CONECT 856 855 +CONECT 857 855 +CONECT 858 855 859 860 +CONECT 859 858 +CONECT 860 858 +CONECT 861 863 850 862 +CONECT 862 861 +CONECT 863 861 +CONECT 864 87 303 865 272 +CONECT 865 864 867 +CONECT 866 869 867 870 868 +CONECT 867 865 866 +CONECT 868 866 +CONECT 869 866 +CONECT 870 866 +CONECT 871 872 +CONECT 872 871 873 +CONECT 873 872 +MASTER 0 0 0 0 0 0 0 0 873 0 873 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_23.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_23.pdb new file mode 100644 index 0000000..ca39ef4 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_23.pdb @@ -0,0 +1,1799 @@ +COMPND fitness: -2.9699 57.56916666666757 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 58.321 58.077 50.629 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.956 37.949 23.252 1.00 0.00 N +ATOM 2 H1 MET 1 14.980 38.332 24.192 1.00 0.00 H +ATOM 3 H2 MET 1 14.138 38.287 22.772 1.00 0.00 H +ATOM 4 H3 MET 1 15.785 38.295 22.794 1.00 0.00 H +ATOM 5 CA MET 1 15.002 36.474 23.309 1.00 0.00 C +ATOM 6 HA MET 1 14.069 36.131 23.765 1.00 0.00 H +ATOM 7 CB MET 1 15.124 35.857 21.902 1.00 0.00 C +ATOM 8 HB2 MET 1 14.230 36.107 21.333 1.00 0.00 H +ATOM 9 HB3 MET 1 15.988 36.293 21.402 1.00 0.00 H +ATOM 10 CG MET 1 15.297 34.324 21.932 1.00 0.00 C +ATOM 11 HG2 MET 1 16.196 34.087 22.503 1.00 0.00 H +ATOM 12 HG3 MET 1 14.440 33.881 22.449 1.00 0.00 H +ATOM 13 SD MET 1 15.475 33.527 20.312 1.00 0.00 S +ATOM 14 CE MET 1 13.767 33.589 19.696 1.00 0.00 C +ATOM 15 HE1 MET 1 13.425 34.622 19.644 1.00 0.00 H +ATOM 16 HE2 MET 1 13.729 33.152 18.698 1.00 0.00 H +ATOM 17 HE3 MET 1 13.114 33.021 20.359 1.00 0.00 H +ATOM 18 C MET 1 16.150 36.015 24.205 1.00 0.00 C +ATOM 19 O MET 1 17.301 36.332 23.929 1.00 0.00 O +ATOM 20 N GLN 2 15.840 35.222 25.235 1.00 0.00 N +ATOM 21 H GLN 2 14.872 35.057 25.451 1.00 0.00 H +ATOM 22 CA GLN 2 16.825 34.530 26.071 1.00 0.00 C +ATOM 23 HA GLN 2 17.603 35.233 26.370 1.00 0.00 H +ATOM 24 CB GLN 2 16.108 34.038 27.344 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.156 33.590 27.061 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.692 33.259 27.832 1.00 0.00 H +ATOM 27 CG GLN 2 15.842 35.165 28.361 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.520 36.075 27.852 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.027 34.847 29.009 1.00 0.00 H +ATOM 30 CD GLN 2 17.041 35.482 29.255 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.163 35.040 29.053 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.848 36.226 30.319 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.648 36.394 30.901 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.938 36.610 30.509 1.00 0.00 H +ATOM 35 C GLN 2 17.532 33.386 25.299 1.00 0.00 C +ATOM 36 O GLN 2 17.139 32.218 25.389 1.00 0.00 O +ATOM 37 N TYR 3 18.571 33.723 24.526 1.00 0.00 N +ATOM 38 H TYR 3 18.843 34.702 24.521 1.00 0.00 H +ATOM 39 CA TYR 3 19.434 32.771 23.808 1.00 0.00 C +ATOM 40 HA TYR 3 18.817 32.161 23.149 1.00 0.00 H +ATOM 41 CB TYR 3 20.463 33.525 22.955 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.972 34.265 23.577 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.224 32.818 22.619 1.00 0.00 H +ATOM 44 CG TYR 3 19.887 34.209 21.729 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.755 33.488 20.523 1.00 0.00 C +ATOM 46 HD1 TYR 3 20.064 32.450 20.487 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.233 34.122 19.377 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.146 33.593 18.443 1.00 0.00 H +ATOM 49 CZ TYR 3 18.834 35.475 19.443 1.00 0.00 C +ATOM 50 OH TYR 3 18.369 36.111 18.338 1.00 0.00 O +ATOM 51 HH TYR 3 18.180 35.521 17.606 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.957 36.187 20.652 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.649 37.223 20.688 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.488 35.558 21.793 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.593 36.118 22.716 1.00 0.00 H +ATOM 56 C TYR 3 20.165 31.844 24.786 1.00 0.00 C +ATOM 57 O TYR 3 20.561 32.275 25.869 1.00 0.00 O +ATOM 58 N LYS 4 20.355 30.570 24.427 1.00 0.00 N +ATOM 59 H LYS 4 20.162 30.310 23.463 1.00 0.00 H +ATOM 60 CA LYS 4 20.937 29.535 25.303 1.00 0.00 C +ATOM 61 HA LYS 4 20.665 29.747 26.335 1.00 0.00 H +ATOM 62 CB LYS 4 20.368 28.154 24.921 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.355 28.070 23.836 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.042 27.382 25.294 1.00 0.00 H +ATOM 65 CG LYS 4 18.961 27.821 25.453 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.749 26.786 25.184 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.966 27.888 26.541 1.00 0.00 H +ATOM 68 CD LYS 4 17.836 28.702 24.886 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.912 29.707 25.300 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.964 28.771 23.804 1.00 0.00 H +ATOM 71 CE LYS 4 16.431 28.140 25.161 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.708 28.753 24.614 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.375 27.127 24.749 1.00 0.00 H +ATOM 74 NZ LYS 4 16.079 28.129 26.605 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.106 29.068 26.981 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.143 27.759 26.734 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.721 27.546 27.127 1.00 0.00 H +ATOM 78 C LYS 4 22.468 29.532 25.257 1.00 0.00 C +ATOM 79 O LYS 4 23.084 29.863 24.248 1.00 0.00 O +HETATM 80 N HX1 5 23.099 29.093 26.340 1.00 0.00 N +HETATM 81 CA HX1 5 24.550 28.874 26.439 1.00 0.00 C +HETATM 82 C HX1 5 24.807 27.680 27.363 1.00 0.00 C +HETATM 83 O HX1 5 24.366 27.687 28.515 1.00 0.00 O +HETATM 84 CB HX1 5 25.222 30.171 26.926 1.00 0.00 C +HETATM 85 CG HX1 5 26.735 30.197 27.018 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.613 29.209 26.660 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.441 31.266 27.584 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.728 30.877 27.535 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.862 29.636 27.038 1.00 0.00 N +HETATM 90 H HX1 5 22.546 28.943 27.182 1.00 0.00 H +HETATM 91 HA HX1 5 24.953 28.634 25.454 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.821 30.421 27.909 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.927 30.973 26.249 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.397 28.239 26.229 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.549 31.441 27.957 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.695 29.050 27.137 1.00 0.00 H +ATOM 97 N ILE 6 25.449 26.637 26.833 1.00 0.00 N +ATOM 98 H ILE 6 25.789 26.710 25.879 1.00 0.00 H +ATOM 99 CA ILE 6 25.847 25.432 27.572 1.00 0.00 C +ATOM 100 HA ILE 6 25.238 25.360 28.474 1.00 0.00 H +ATOM 101 CB ILE 6 25.566 24.156 26.742 1.00 0.00 C +ATOM 102 HB ILE 6 26.020 24.282 25.761 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.162 22.886 27.383 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.747 22.729 28.378 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.948 22.014 26.768 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.248 22.959 27.445 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.034 24.009 26.574 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.579 23.902 27.558 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.637 24.917 26.119 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.583 22.832 25.701 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.754 21.888 26.221 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.515 22.927 25.503 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.127 22.838 24.755 1.00 0.00 H +ATOM 114 C ILE 6 27.300 25.571 28.052 1.00 0.00 C +ATOM 115 O ILE 6 28.122 26.256 27.446 1.00 0.00 O +ATOM 116 N VAL 7 27.556 24.980 29.213 1.00 0.00 N +ATOM 117 H VAL 7 26.843 24.362 29.580 1.00 0.00 H +ATOM 118 CA VAL 7 28.652 25.309 30.129 1.00 0.00 C +ATOM 119 HA VAL 7 28.692 26.394 30.205 1.00 0.00 H +ATOM 120 CB VAL 7 28.219 24.759 31.504 1.00 0.00 C +ATOM 121 HB VAL 7 27.200 25.102 31.701 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.223 23.228 31.596 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.231 22.835 31.462 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.855 22.918 32.570 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.583 22.799 30.828 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.070 25.293 32.639 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.049 26.379 32.635 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.678 24.946 33.594 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.084 24.939 32.501 1.00 0.00 H +ATOM 130 C VAL 7 30.053 24.831 29.701 1.00 0.00 C +ATOM 131 O VAL 7 30.209 23.725 29.187 1.00 0.00 O +ATOM 132 N LEU 8 31.096 25.626 30.002 1.00 0.00 N +ATOM 133 H LEU 8 30.891 26.594 30.233 1.00 0.00 H +ATOM 134 CA LEU 8 32.513 25.212 29.916 1.00 0.00 C +ATOM 135 HA LEU 8 32.704 24.931 28.876 1.00 0.00 H +ATOM 136 CB LEU 8 33.429 26.416 30.251 1.00 0.00 C +ATOM 137 HB2 LEU 8 33.378 27.070 29.382 1.00 0.00 H +ATOM 138 HB3 LEU 8 33.007 26.969 31.085 1.00 0.00 H +ATOM 139 CG LEU 8 34.922 26.121 30.555 1.00 0.00 C +ATOM 140 HG LEU 8 35.273 25.303 29.918 1.00 0.00 H +ATOM 141 CD1 LEU 8 35.779 27.356 30.267 1.00 0.00 C +ATOM 142 HD11 LEU 8 35.460 28.190 30.895 1.00 0.00 H +ATOM 143 HD12 LEU 8 36.830 27.139 30.464 1.00 0.00 H +ATOM 144 HD13 LEU 8 35.682 27.636 29.218 1.00 0.00 H +ATOM 145 CD2 LEU 8 35.200 25.762 32.025 1.00 0.00 C +ATOM 146 HD21 LEU 8 34.772 24.799 32.281 1.00 0.00 H +ATOM 147 HD22 LEU 8 36.276 25.687 32.182 1.00 0.00 H +ATOM 148 HD23 LEU 8 34.791 26.532 32.680 1.00 0.00 H +ATOM 149 C LEU 8 32.822 23.983 30.782 1.00 0.00 C +ATOM 150 O LEU 8 32.472 23.946 31.966 1.00 0.00 O +ATOM 151 N GLY 9 33.598 23.051 30.225 1.00 0.00 N +ATOM 152 H GLY 9 33.795 23.154 29.243 1.00 0.00 H +ATOM 153 CA GLY 9 34.111 21.855 30.892 1.00 0.00 C +ATOM 154 HA2 GLY 9 35.124 21.662 30.531 1.00 0.00 H +ATOM 155 HA3 GLY 9 34.167 22.045 31.967 1.00 0.00 H +ATOM 156 C GLY 9 33.265 20.599 30.646 1.00 0.00 C +ATOM 157 O GLY 9 32.383 20.585 29.790 1.00 0.00 O +ATOM 158 N LYS 10 33.561 19.536 31.411 1.00 0.00 N +ATOM 159 H LYS 10 34.373 19.607 32.003 1.00 0.00 H +ATOM 160 CA LYS 10 32.876 18.230 31.313 1.00 0.00 C +ATOM 161 HA LYS 10 31.947 18.376 30.753 1.00 0.00 H +ATOM 162 CB LYS 10 33.762 17.267 30.492 1.00 0.00 C +ATOM 163 HB2 LYS 10 34.403 17.848 29.826 1.00 0.00 H +ATOM 164 HB3 LYS 10 34.407 16.691 31.156 1.00 0.00 H +ATOM 165 CG LYS 10 32.947 16.309 29.608 1.00 0.00 C +ATOM 166 HG2 LYS 10 32.357 15.637 30.229 1.00 0.00 H +ATOM 167 HG3 LYS 10 32.266 16.896 28.993 1.00 0.00 H +ATOM 168 CD LYS 10 33.851 15.489 28.678 1.00 0.00 C +ATOM 169 HD2 LYS 10 34.526 16.164 28.154 1.00 0.00 H +ATOM 170 HD3 LYS 10 34.448 14.795 29.267 1.00 0.00 H +ATOM 171 CE LYS 10 33.029 14.713 27.646 1.00 0.00 C +ATOM 172 HE2 LYS 10 32.480 13.919 28.155 1.00 0.00 H +ATOM 173 HE3 LYS 10 32.306 15.400 27.204 1.00 0.00 H +ATOM 174 NZ LYS 10 33.885 14.170 26.567 1.00 0.00 N +ATOM 175 HZ1 LYS 10 34.606 13.562 26.920 1.00 0.00 H +ATOM 176 HZ2 LYS 10 33.350 13.715 25.843 1.00 0.00 H +ATOM 177 HZ3 LYS 10 34.368 14.947 26.091 1.00 0.00 H +ATOM 178 C LYS 10 32.441 17.639 32.667 1.00 0.00 C +ATOM 179 O LYS 10 31.681 16.684 32.711 1.00 0.00 O +ATOM 180 N TYR 11 32.908 18.222 33.777 1.00 0.00 N +ATOM 181 H TYR 11 33.519 19.011 33.670 1.00 0.00 H +ATOM 182 CA TYR 11 32.508 17.866 35.152 1.00 0.00 C +ATOM 183 HA TYR 11 32.353 16.786 35.214 1.00 0.00 H +ATOM 184 CB TYR 11 33.649 18.254 36.107 1.00 0.00 C +ATOM 185 HB2 TYR 11 33.397 17.908 37.112 1.00 0.00 H +ATOM 186 HB3 TYR 11 34.558 17.730 35.807 1.00 0.00 H +ATOM 187 CG TYR 11 33.926 19.748 36.163 1.00 0.00 C +ATOM 188 CD1 TYR 11 34.882 20.328 35.303 1.00 0.00 C +ATOM 189 HD1 TYR 11 35.472 19.701 34.649 1.00 0.00 H +ATOM 190 CE1 TYR 11 35.087 21.722 35.312 1.00 0.00 C +ATOM 191 HE1 TYR 11 35.820 22.167 34.657 1.00 0.00 H +ATOM 192 CZ TYR 11 34.346 22.536 36.198 1.00 0.00 C +ATOM 193 OH TYR 11 34.523 23.881 36.214 1.00 0.00 O +ATOM 194 HH TYR 11 35.260 24.165 35.672 1.00 0.00 H +ATOM 195 CE2 TYR 11 33.413 21.951 37.078 1.00 0.00 C +ATOM 196 HE2 TYR 11 32.870 22.580 37.770 1.00 0.00 H +ATOM 197 CD2 TYR 11 33.200 20.561 37.055 1.00 0.00 C +ATOM 198 HD2 TYR 11 32.472 20.118 37.723 1.00 0.00 H +ATOM 199 C TYR 11 31.196 18.540 35.603 1.00 0.00 C +ATOM 200 O TYR 11 30.610 18.144 36.607 1.00 0.00 O +ATOM 201 N ARG 12 30.754 19.575 34.879 1.00 0.00 N +ATOM 202 H ARG 12 31.275 19.795 34.045 1.00 0.00 H +ATOM 203 CA ARG 12 29.488 20.298 35.053 1.00 0.00 C +ATOM 204 HA ARG 12 28.882 19.755 35.781 1.00 0.00 H +ATOM 205 CB ARG 12 29.739 21.722 35.608 1.00 0.00 C +ATOM 206 HB2 ARG 12 28.776 22.220 35.709 1.00 0.00 H +ATOM 207 HB3 ARG 12 30.158 21.624 36.610 1.00 0.00 H +ATOM 208 CG ARG 12 30.677 22.626 34.778 1.00 0.00 C +ATOM 209 HG2 ARG 12 31.642 22.138 34.645 1.00 0.00 H +ATOM 210 HG3 ARG 12 30.232 22.781 33.794 1.00 0.00 H +ATOM 211 CD ARG 12 30.899 23.992 35.461 1.00 0.00 C +ATOM 212 HD2 ARG 12 29.924 24.405 35.730 1.00 0.00 H +ATOM 213 HD3 ARG 12 31.482 23.851 36.373 1.00 0.00 H +ATOM 214 NE ARG 12 31.597 24.938 34.563 1.00 0.00 N +ATOM 215 HE ARG 12 31.983 24.544 33.708 1.00 0.00 H +ATOM 216 CZ ARG 12 31.481 26.260 34.577 1.00 0.00 C +ATOM 217 NH1 ARG 12 31.763 26.930 33.499 1.00 0.00 N +ATOM 218 HH11 ARG 12 31.994 26.424 32.664 1.00 0.00 H +ATOM 219 HH12 ARG 12 31.409 27.873 33.387 1.00 0.00 H +ATOM 220 NH2 ARG 12 31.046 26.923 35.613 1.00 0.00 N +ATOM 221 HH21 ARG 12 30.906 26.446 36.486 1.00 0.00 H +ATOM 222 HH22 ARG 12 30.960 27.938 35.588 1.00 0.00 H +ATOM 223 C ARG 12 28.733 20.260 33.725 1.00 0.00 C +ATOM 224 O ARG 12 29.364 20.387 32.682 1.00 0.00 O +ATOM 225 N LYS 13 27.412 20.050 33.758 1.00 0.00 N +ATOM 226 H LYS 13 26.999 19.927 34.670 1.00 0.00 H +ATOM 227 CA LYS 13 26.566 19.761 32.574 1.00 0.00 C +ATOM 228 HA LYS 13 27.138 20.023 31.679 1.00 0.00 H +ATOM 229 CB LYS 13 26.287 18.241 32.522 1.00 0.00 C +ATOM 230 HB2 LYS 13 27.174 17.718 32.886 1.00 0.00 H +ATOM 231 HB3 LYS 13 25.464 18.010 33.198 1.00 0.00 H +ATOM 232 CG LYS 13 25.986 17.701 31.109 1.00 0.00 C +ATOM 233 HG2 LYS 13 25.090 18.174 30.703 1.00 0.00 H +ATOM 234 HG3 LYS 13 26.827 17.949 30.458 1.00 0.00 H +ATOM 235 CD LYS 13 25.806 16.170 31.114 1.00 0.00 C +ATOM 236 HD2 LYS 13 25.829 15.812 30.084 1.00 0.00 H +ATOM 237 HD3 LYS 13 26.642 15.716 31.657 1.00 0.00 H +ATOM 238 CE LYS 13 24.465 15.749 31.740 1.00 0.00 C +ATOM 239 HE2 LYS 13 24.274 16.367 32.625 1.00 0.00 H +ATOM 240 HE3 LYS 13 23.669 15.940 31.012 1.00 0.00 H +ATOM 241 NZ LYS 13 24.453 14.315 32.130 1.00 0.00 N +ATOM 242 HZ1 LYS 13 25.152 14.112 32.838 1.00 0.00 H +ATOM 243 HZ2 LYS 13 23.593 14.086 32.611 1.00 0.00 H +ATOM 244 HZ3 LYS 13 24.558 13.673 31.354 1.00 0.00 H +ATOM 245 C LYS 13 25.302 20.641 32.519 1.00 0.00 C +ATOM 246 O LYS 13 24.263 20.237 32.005 1.00 0.00 O +ATOM 247 N GLY 14 25.379 21.829 33.124 1.00 0.00 N +ATOM 248 H GLY 14 26.272 22.097 33.496 1.00 0.00 H +ATOM 249 CA GLY 14 24.294 22.808 33.188 1.00 0.00 C +ATOM 250 HA2 GLY 14 23.351 22.287 33.358 1.00 0.00 H +ATOM 251 HA3 GLY 14 24.461 23.473 34.038 1.00 0.00 H +ATOM 252 C GLY 14 24.142 23.669 31.926 1.00 0.00 C +ATOM 253 O GLY 14 24.958 23.637 31.004 1.00 0.00 O +ATOM 254 N VAL 15 23.083 24.476 31.918 1.00 0.00 N +ATOM 255 H VAL 15 22.486 24.486 32.732 1.00 0.00 H +ATOM 256 CA VAL 15 22.706 25.392 30.836 1.00 0.00 C +ATOM 257 HA VAL 15 23.599 25.631 30.257 1.00 0.00 H +ATOM 258 CB VAL 15 21.694 24.717 29.881 1.00 0.00 C +ATOM 259 HB VAL 15 22.170 23.824 29.475 1.00 0.00 H +ATOM 260 CG1 VAL 15 20.390 24.276 30.568 1.00 0.00 C +ATOM 261 HG11 VAL 15 19.861 25.134 30.985 1.00 0.00 H +ATOM 262 HG12 VAL 15 19.748 23.776 29.841 1.00 0.00 H +ATOM 263 HG13 VAL 15 20.610 23.564 31.362 1.00 0.00 H +ATOM 264 CG2 VAL 15 21.324 25.621 28.698 1.00 0.00 C +ATOM 265 HG21 VAL 15 22.229 25.976 28.206 1.00 0.00 H +ATOM 266 HG22 VAL 15 20.741 25.047 27.977 1.00 0.00 H +ATOM 267 HG23 VAL 15 20.730 26.471 29.034 1.00 0.00 H +ATOM 268 C VAL 15 22.181 26.691 31.445 1.00 0.00 C +ATOM 269 O VAL 15 21.546 26.674 32.497 1.00 0.00 O +HETATM 270 N HY1 16 22.452 27.823 30.799 1.00 0.00 N +HETATM 271 CA HY1 16 21.906 29.134 31.161 1.00 0.00 C +HETATM 272 C HY1 16 21.597 29.940 29.889 1.00 0.00 C +HETATM 273 O HY1 16 21.776 29.444 28.772 1.00 0.00 O +HETATM 274 CB HY1 16 22.868 29.847 32.134 1.00 0.00 C +HETATM 275 CG HY1 16 24.228 30.161 31.557 1.00 0.00 C +HETATM 276 CD2 HY1 16 24.581 31.321 30.923 1.00 0.00 C +HETATM 277 ND1 HY1 16 25.341 29.348 31.572 1.00 0.00 N +HETATM 278 CE1 HY1 16 26.344 30.019 30.971 1.00 0.00 C +HETATM 279 NE2 HY1 16 25.924 31.229 30.545 1.00 0.00 N +HETATM 280 H HY1 16 22.997 27.767 29.940 1.00 0.00 H +HETATM 281 HA HY1 16 20.959 28.990 31.684 1.00 0.00 H +HETATM 282 HB2 HY1 16 22.411 30.778 32.480 1.00 0.00 H +HETATM 283 HB3 HY1 16 22.997 29.223 33.020 1.00 0.00 H +HETATM 284 HD1 HY1 16 25.410 28.439 32.019 1.00 0.00 H +HETATM 285 HD2 HY1 16 23.933 32.170 30.749 1.00 0.00 H +HETATM 286 HE1 HY1 16 27.367 29.650 30.881 1.00 0.00 H +ATOM 287 N THR 17 21.101 31.171 30.036 1.00 0.00 N +ATOM 288 H THR 17 20.948 31.540 30.964 1.00 0.00 H +ATOM 289 CA THR 17 20.669 32.024 28.915 1.00 0.00 C +ATOM 290 HA THR 17 21.107 31.606 28.005 1.00 0.00 H +ATOM 291 CB THR 17 19.145 32.013 28.747 1.00 0.00 C +ATOM 292 HB THR 17 18.881 32.654 27.907 1.00 0.00 H +ATOM 293 CG2 THR 17 18.534 30.634 28.471 1.00 0.00 C +ATOM 294 HG21 THR 17 18.741 29.958 29.298 1.00 0.00 H +ATOM 295 HG22 THR 17 17.463 30.734 28.352 1.00 0.00 H +ATOM 296 HG23 THR 17 18.955 30.232 27.553 1.00 0.00 H +ATOM 297 OG1 THR 17 18.511 32.509 29.899 1.00 0.00 O +ATOM 298 HG1 THR 17 18.514 33.480 29.809 1.00 0.00 H +ATOM 299 C THR 17 21.188 33.458 29.007 1.00 0.00 C +ATOM 300 O THR 17 21.615 33.912 30.066 1.00 0.00 O +HETATM 301 N HY2 18 21.142 34.167 27.880 1.00 0.00 N +HETATM 302 CA HY2 18 21.465 35.591 27.743 1.00 0.00 C +HETATM 303 C HY2 18 20.351 36.301 26.966 1.00 0.00 C +HETATM 304 O HY2 18 20.003 35.863 25.871 1.00 0.00 O +HETATM 305 CB HY2 18 22.815 35.772 27.034 1.00 0.00 C +HETATM 306 CG HY2 18 23.990 35.260 27.840 1.00 0.00 C +HETATM 307 CD2 HY2 18 24.619 34.048 27.704 1.00 0.00 C +HETATM 308 ND1 HY2 18 24.547 35.881 28.937 1.00 0.00 N +HETATM 309 CE1 HY2 18 25.493 35.067 29.429 1.00 0.00 C +HETATM 310 NE2 HY2 18 25.584 33.937 28.713 1.00 0.00 N +HETATM 311 H HY2 18 20.806 33.694 27.048 1.00 0.00 H +HETATM 312 HA HY2 18 21.525 36.048 28.734 1.00 0.00 H +HETATM 313 HB2 HY2 18 22.783 35.265 26.071 1.00 0.00 H +HETATM 314 HB3 HY2 18 22.962 36.834 26.836 1.00 0.00 H +HETATM 315 HD1 HY2 18 24.290 36.786 29.314 1.00 0.00 H +HETATM 316 HD2 HY2 18 24.396 33.300 26.958 1.00 0.00 H +HETATM 317 HE1 HY2 18 26.083 35.283 30.305 1.00 0.00 H +ATOM 318 N GLU 19 19.789 37.374 27.521 1.00 0.00 N +ATOM 319 H GLU 19 20.132 37.707 28.403 1.00 0.00 H +ATOM 320 CA GLU 19 18.766 38.181 26.852 1.00 0.00 C +ATOM 321 HA GLU 19 18.057 37.508 26.378 1.00 0.00 H +ATOM 322 CB GLU 19 18.018 39.025 27.902 1.00 0.00 C +ATOM 323 HB2 GLU 19 17.621 38.357 28.661 1.00 0.00 H +ATOM 324 HB3 GLU 19 18.741 39.684 28.392 1.00 0.00 H +ATOM 325 CG GLU 19 16.859 39.900 27.385 1.00 0.00 C +ATOM 326 HG2 GLU 19 16.440 40.441 28.240 1.00 0.00 H +ATOM 327 HG3 GLU 19 17.257 40.646 26.689 1.00 0.00 H +ATOM 328 CD GLU 19 15.754 39.102 26.690 1.00 0.00 C +ATOM 329 OE1 GLU 19 16.012 38.537 25.604 1.00 0.00 O +ATOM 330 OE2 GLU 19 14.620 39.047 27.208 1.00 0.00 O +ATOM 331 C GLU 19 19.391 39.061 25.754 1.00 0.00 C +ATOM 332 O GLU 19 20.421 39.699 25.983 1.00 0.00 O +ATOM 333 N ALA 20 18.770 39.094 24.569 1.00 0.00 N +ATOM 334 H ALA 20 17.922 38.541 24.472 1.00 0.00 H +ATOM 335 CA ALA 20 19.130 39.993 23.475 1.00 0.00 C +ATOM 336 HA ALA 20 19.288 40.986 23.883 1.00 0.00 H +ATOM 337 CB ALA 20 20.436 39.517 22.823 1.00 0.00 C +ATOM 338 HB1 ALA 20 20.287 38.543 22.357 1.00 0.00 H +ATOM 339 HB2 ALA 20 20.759 40.222 22.058 1.00 0.00 H +ATOM 340 HB3 ALA 20 21.234 39.437 23.559 1.00 0.00 H +ATOM 341 C ALA 20 18.034 40.069 22.405 1.00 0.00 C +ATOM 342 O ALA 20 17.243 39.135 22.236 1.00 0.00 O +ATOM 343 N VAL 21 18.036 41.137 21.589 1.00 0.00 N +ATOM 344 H VAL 21 18.672 41.904 21.803 1.00 0.00 H +ATOM 345 CA VAL 21 17.297 41.158 20.298 1.00 0.00 C +ATOM 346 HA VAL 21 16.312 40.749 20.478 1.00 0.00 H +ATOM 347 CB VAL 21 17.155 42.595 19.756 1.00 0.00 C +ATOM 348 HB VAL 21 16.514 42.525 18.876 1.00 0.00 H +ATOM 349 CG1 VAL 21 16.447 43.502 20.770 1.00 0.00 C +ATOM 350 HG11 VAL 21 17.072 43.672 21.637 1.00 0.00 H +ATOM 351 HG12 VAL 21 16.228 44.453 20.298 1.00 0.00 H +ATOM 352 HG13 VAL 21 15.512 43.052 21.087 1.00 0.00 H +ATOM 353 CG2 VAL 21 18.491 43.234 19.330 1.00 0.00 C +ATOM 354 HG21 VAL 21 18.917 42.669 18.499 1.00 0.00 H +ATOM 355 HG22 VAL 21 18.295 44.248 18.984 1.00 0.00 H +ATOM 356 HG23 VAL 21 19.187 43.253 20.167 1.00 0.00 H +ATOM 357 C VAL 21 17.934 40.273 19.235 1.00 0.00 C +ATOM 358 O VAL 21 17.270 39.791 18.317 1.00 0.00 O +ATOM 359 N ASP 22 19.245 40.037 19.416 1.00 0.00 N +ATOM 360 H ASP 22 19.768 40.442 20.194 1.00 0.00 H +ATOM 361 CA ASP 22 20.021 39.219 18.489 1.00 0.00 C +ATOM 362 HA ASP 22 19.409 38.402 18.068 1.00 0.00 H +ATOM 363 CB ASP 22 20.497 40.066 17.274 1.00 0.00 C +ATOM 364 HB2 ASP 22 19.655 40.653 16.941 1.00 0.00 H +ATOM 365 HB3 ASP 22 21.304 40.722 17.550 1.00 0.00 H +ATOM 366 CG ASP 22 20.932 39.198 16.080 1.00 0.00 C +ATOM 367 OD1 ASP 22 21.842 39.613 15.324 1.00 0.00 O +ATOM 368 OD2 ASP 22 20.298 38.137 15.857 1.00 0.00 O +ATOM 369 C ASP 22 21.263 38.582 19.117 1.00 0.00 C +ATOM 370 O ASP 22 22.097 39.203 19.781 1.00 0.00 O +ATOM 371 N VAL 23 21.523 37.369 18.730 1.00 0.00 N +ATOM 372 H VAL 23 20.714 36.815 18.469 1.00 0.00 H +ATOM 373 CA VAL 23 22.744 37.035 18.010 1.00 0.00 C +ATOM 374 HA VAL 23 22.560 37.361 16.992 1.00 0.00 H +ATOM 375 CB VAL 23 22.923 35.532 17.889 1.00 0.00 C +ATOM 376 HB VAL 23 21.977 35.104 17.597 1.00 0.00 H +ATOM 377 CG1 VAL 23 23.381 34.804 19.173 1.00 0.00 C +ATOM 378 HG11 VAL 23 22.886 35.227 20.047 1.00 0.00 H +ATOM 379 HG12 VAL 23 23.087 33.767 19.123 1.00 0.00 H +ATOM 380 HG13 VAL 23 24.447 34.870 19.318 1.00 0.00 H +ATOM 381 CG2 VAL 23 23.926 35.276 16.721 1.00 0.00 C +ATOM 382 HG21 VAL 23 24.897 35.694 16.888 1.00 0.00 H +ATOM 383 HG22 VAL 23 24.065 34.236 16.568 1.00 0.00 H +ATOM 384 HG23 VAL 23 23.548 35.688 15.793 1.00 0.00 H +ATOM 385 C VAL 23 24.040 37.675 18.496 1.00 0.00 C +ATOM 386 O VAL 23 24.526 37.393 19.606 1.00 0.00 O +ATOM 387 N ALA 24 24.619 38.493 17.619 1.00 0.00 N +ATOM 388 H ALA 24 24.105 38.686 16.760 1.00 0.00 H +ATOM 389 CA ALA 24 25.917 39.150 17.794 1.00 0.00 C +ATOM 390 HA ALA 24 26.644 38.396 18.112 1.00 0.00 H +ATOM 391 CB ALA 24 26.370 39.677 16.435 1.00 0.00 C +ATOM 392 HB1 ALA 24 25.700 40.455 16.051 1.00 0.00 H +ATOM 393 HB2 ALA 24 27.374 40.104 16.494 1.00 0.00 H +ATOM 394 HB3 ALA 24 26.407 38.875 15.695 1.00 0.00 H +ATOM 395 C ALA 24 25.951 40.228 18.903 1.00 0.00 C +ATOM 396 O ALA 24 27.025 40.744 19.206 1.00 0.00 O +ATOM 397 N GLU 25 24.817 40.559 19.550 1.00 0.00 N +ATOM 398 H GLU 25 23.950 40.122 19.260 1.00 0.00 H +ATOM 399 CA GLU 25 24.802 41.295 20.825 1.00 0.00 C +ATOM 400 HA GLU 25 25.698 41.918 20.891 1.00 0.00 H +ATOM 401 CB GLU 25 23.580 42.233 20.902 1.00 0.00 C +ATOM 402 HB2 GLU 25 22.675 41.658 20.717 1.00 0.00 H +ATOM 403 HB3 GLU 25 23.520 42.639 21.905 1.00 0.00 H +ATOM 404 CG GLU 25 23.631 43.417 19.920 1.00 0.00 C +ATOM 405 HG2 GLU 25 23.610 43.020 18.899 1.00 0.00 H +ATOM 406 HG3 GLU 25 22.728 44.019 20.049 1.00 0.00 H +ATOM 407 CD GLU 25 24.870 44.295 20.122 1.00 0.00 C +ATOM 408 OE1 GLU 25 25.007 44.946 21.188 1.00 0.00 O +ATOM 409 OE2 GLU 25 25.742 44.260 19.224 1.00 0.00 O +ATOM 410 C GLU 25 24.861 40.339 22.031 1.00 0.00 C +ATOM 411 O GLU 25 25.626 40.598 22.955 1.00 0.00 O +ATOM 412 N ALA 26 24.161 39.202 21.988 1.00 0.00 N +ATOM 413 H ALA 26 23.559 39.004 21.199 1.00 0.00 H +ATOM 414 CA ALA 26 24.287 38.162 23.029 1.00 0.00 C +ATOM 415 HA ALA 26 24.062 38.616 24.002 1.00 0.00 H +ATOM 416 CB ALA 26 23.300 37.020 22.768 1.00 0.00 C +ATOM 417 HB1 ALA 26 23.547 36.533 21.837 1.00 0.00 H +ATOM 418 HB2 ALA 26 23.360 36.295 23.579 1.00 0.00 H +ATOM 419 HB3 ALA 26 22.299 37.421 22.719 1.00 0.00 H +ATOM 420 C ALA 26 25.735 37.616 23.148 1.00 0.00 C +ATOM 421 O ALA 26 26.174 37.237 24.235 1.00 0.00 O +ATOM 422 N GLU 27 26.474 37.621 22.050 1.00 0.00 N +ATOM 423 H GLU 27 26.023 37.841 21.166 1.00 0.00 H +ATOM 424 CA GLU 27 27.916 37.357 22.046 1.00 0.00 C +ATOM 425 HA GLU 27 28.105 36.375 22.488 1.00 0.00 H +ATOM 426 CB GLU 27 28.385 37.346 20.550 1.00 0.00 C +ATOM 427 HB2 GLU 27 27.788 36.599 20.008 1.00 0.00 H +ATOM 428 HB3 GLU 27 28.240 38.320 20.136 1.00 0.00 H +ATOM 429 CG GLU 27 29.867 36.929 20.328 1.00 0.00 C +ATOM 430 HG2 GLU 27 30.544 37.508 21.077 1.00 0.00 H +ATOM 431 HG3 GLU 27 29.961 35.824 20.635 1.00 0.00 H +ATOM 432 CD GLU 27 30.283 37.101 18.920 1.00 0.00 C +ATOM 433 OE1 GLU 27 31.135 37.943 18.629 1.00 0.00 O +ATOM 434 OE2 GLU 27 29.794 36.371 18.069 1.00 0.00 O +ATOM 435 C GLU 27 28.707 38.401 22.862 1.00 0.00 C +ATOM 436 O GLU 27 29.475 38.046 23.751 1.00 0.00 O +ATOM 437 N LYS 28 28.461 39.695 22.626 1.00 0.00 N +ATOM 438 H LYS 28 27.784 39.939 21.915 1.00 0.00 H +ATOM 439 CA LYS 28 29.065 40.806 23.408 1.00 0.00 C +ATOM 440 HA LYS 28 30.151 40.691 23.381 1.00 0.00 H +ATOM 441 CB LYS 28 28.703 42.170 22.789 1.00 0.00 C +ATOM 442 HB2 LYS 28 27.626 42.298 22.793 1.00 0.00 H +ATOM 443 HB3 LYS 28 29.144 42.951 23.403 1.00 0.00 H +ATOM 444 CG LYS 28 29.227 42.334 21.352 1.00 0.00 C +ATOM 445 HG2 LYS 28 30.307 42.201 21.338 1.00 0.00 H +ATOM 446 HG3 LYS 28 28.788 41.567 20.718 1.00 0.00 H +ATOM 447 CD LYS 28 28.880 43.718 20.789 1.00 0.00 C +ATOM 448 HD2 LYS 28 27.827 43.940 20.964 1.00 0.00 H +ATOM 449 HD3 LYS 28 29.463 44.466 21.330 1.00 0.00 H +ATOM 450 CE LYS 28 29.179 43.834 19.287 1.00 0.00 C +ATOM 451 HE2 LYS 28 29.308 44.891 19.034 1.00 0.00 H +ATOM 452 HE3 LYS 28 30.124 43.331 19.077 1.00 0.00 H +ATOM 453 NZ LYS 28 28.093 43.246 18.469 1.00 0.00 N +ATOM 454 HZ1 LYS 28 27.215 43.737 18.662 1.00 0.00 H +ATOM 455 HZ2 LYS 28 28.263 43.308 17.478 1.00 0.00 H +ATOM 456 HZ3 LYS 28 27.914 42.283 18.741 1.00 0.00 H +ATOM 457 C LYS 28 28.657 40.752 24.883 1.00 0.00 C +ATOM 458 O LYS 28 29.505 40.873 25.758 1.00 0.00 O +ATOM 459 N PHE 29 27.389 40.490 25.177 1.00 0.00 N +ATOM 460 H PHE 29 26.719 40.455 24.417 1.00 0.00 H +ATOM 461 CA PHE 29 26.906 40.294 26.548 1.00 0.00 C +ATOM 462 HA PHE 29 27.225 41.154 27.147 1.00 0.00 H +ATOM 463 CB PHE 29 25.363 40.264 26.566 1.00 0.00 C +ATOM 464 HB2 PHE 29 25.044 39.349 26.073 1.00 0.00 H +ATOM 465 HB3 PHE 29 25.029 40.217 27.602 1.00 0.00 H +ATOM 466 CG PHE 29 24.649 41.442 25.905 1.00 0.00 C +ATOM 467 CD1 PHE 29 23.406 41.230 25.277 1.00 0.00 C +ATOM 468 HD1 PHE 29 22.949 40.252 25.292 1.00 0.00 H +ATOM 469 CE1 PHE 29 22.754 42.285 24.615 1.00 0.00 C +ATOM 470 HE1 PHE 29 21.809 42.103 24.121 1.00 0.00 H +ATOM 471 CZ PHE 29 23.335 43.564 24.583 1.00 0.00 C +ATOM 472 HZ PHE 29 22.857 44.365 24.043 1.00 0.00 H +ATOM 473 CE2 PHE 29 24.553 43.792 25.241 1.00 0.00 C +ATOM 474 HE2 PHE 29 24.999 44.776 25.224 1.00 0.00 H +ATOM 475 CD2 PHE 29 25.207 42.740 25.906 1.00 0.00 C +ATOM 476 HD2 PHE 29 26.144 42.935 26.401 1.00 0.00 H +ATOM 477 C PHE 29 27.510 39.048 27.222 1.00 0.00 C +ATOM 478 O PHE 29 27.704 39.056 28.439 1.00 0.00 O +ATOM 479 N THR 30 27.866 38.009 26.456 1.00 0.00 N +ATOM 480 H THR 30 27.631 38.034 25.476 1.00 0.00 H +ATOM 481 CA THR 30 28.614 36.839 26.949 1.00 0.00 C +ATOM 482 HA THR 30 28.163 36.501 27.879 1.00 0.00 H +ATOM 483 CB THR 30 28.527 35.667 25.949 1.00 0.00 C +ATOM 484 HB THR 30 28.935 35.968 24.984 1.00 0.00 H +ATOM 485 CG2 THR 30 29.310 34.442 26.402 1.00 0.00 C +ATOM 486 HG21 THR 30 29.030 34.145 27.399 1.00 0.00 H +ATOM 487 HG22 THR 30 29.136 33.600 25.753 1.00 0.00 H +ATOM 488 HG23 THR 30 30.379 34.612 26.403 1.00 0.00 H +ATOM 489 OG1 THR 30 27.186 35.256 25.820 1.00 0.00 O +ATOM 490 HG1 THR 30 26.782 35.949 25.271 1.00 0.00 H +ATOM 491 C THR 30 30.080 37.188 27.282 1.00 0.00 C +ATOM 492 O THR 30 30.644 36.659 28.243 1.00 0.00 O +ATOM 493 N LYS 31 30.682 38.139 26.568 1.00 0.00 N +ATOM 494 H LYS 31 30.187 38.500 25.765 1.00 0.00 H +ATOM 495 CA LYS 31 32.009 38.686 26.868 1.00 0.00 C +ATOM 496 HA LYS 31 32.667 37.873 27.164 1.00 0.00 H +ATOM 497 CB LYS 31 32.609 39.327 25.594 1.00 0.00 C +ATOM 498 HB2 LYS 31 31.919 40.053 25.180 1.00 0.00 H +ATOM 499 HB3 LYS 31 33.537 39.834 25.860 1.00 0.00 H +ATOM 500 CG LYS 31 32.937 38.256 24.532 1.00 0.00 C +ATOM 501 HG2 LYS 31 33.666 37.564 24.950 1.00 0.00 H +ATOM 502 HG3 LYS 31 32.044 37.690 24.269 1.00 0.00 H +ATOM 503 CD LYS 31 33.507 38.903 23.266 1.00 0.00 C +ATOM 504 HD2 LYS 31 32.713 39.447 22.755 1.00 0.00 H +ATOM 505 HD3 LYS 31 34.294 39.608 23.529 1.00 0.00 H +ATOM 506 CE LYS 31 34.085 37.861 22.287 1.00 0.00 C +ATOM 507 HE2 LYS 31 33.340 37.093 22.069 1.00 0.00 H +ATOM 508 HE3 LYS 31 34.321 38.367 21.349 1.00 0.00 H +ATOM 509 NZ LYS 31 35.320 37.235 22.811 1.00 0.00 N +ATOM 510 HZ1 LYS 31 35.128 36.422 23.385 1.00 0.00 H +ATOM 511 HZ2 LYS 31 35.886 36.905 22.036 1.00 0.00 H +ATOM 512 HZ3 LYS 31 35.872 37.877 23.386 1.00 0.00 H +ATOM 513 C LYS 31 32.021 39.680 28.036 1.00 0.00 C +ATOM 514 O LYS 31 33.038 39.757 28.731 1.00 0.00 O +ATOM 515 N ALA 32 30.907 40.371 28.303 1.00 0.00 N +ATOM 516 H ALA 32 30.158 40.338 27.621 1.00 0.00 H +ATOM 517 CA ALA 32 30.770 41.272 29.448 1.00 0.00 C +ATOM 518 HA ALA 32 31.556 42.025 29.395 1.00 0.00 H +ATOM 519 CB ALA 32 29.425 42.006 29.365 1.00 0.00 C +ATOM 520 HB1 ALA 32 28.598 41.302 29.421 1.00 0.00 H +ATOM 521 HB2 ALA 32 29.341 42.711 30.195 1.00 0.00 H +ATOM 522 HB3 ALA 32 29.365 42.561 28.428 1.00 0.00 H +ATOM 523 C ALA 32 30.961 40.537 30.791 1.00 0.00 C +ATOM 524 O ALA 32 31.976 40.750 31.456 1.00 0.00 O +ATOM 525 N LEU 33 30.080 39.579 31.132 1.00 0.00 N +ATOM 526 H LEU 33 29.263 39.428 30.555 1.00 0.00 H +ATOM 527 CA LEU 33 30.218 38.812 32.380 1.00 0.00 C +ATOM 528 HA LEU 33 30.350 39.555 33.163 1.00 0.00 H +ATOM 529 CB LEU 33 28.923 38.038 32.729 1.00 0.00 C +ATOM 530 HB2 LEU 33 28.951 37.860 33.807 1.00 0.00 H +ATOM 531 HB3 LEU 33 28.057 38.672 32.546 1.00 0.00 H +ATOM 532 CG LEU 33 28.719 36.670 32.036 1.00 0.00 C +ATOM 533 HG LEU 33 29.625 36.076 32.096 1.00 0.00 H +ATOM 534 CD1 LEU 33 27.602 35.867 32.714 1.00 0.00 C +ATOM 535 HD11 LEU 33 26.670 36.420 32.679 1.00 0.00 H +ATOM 536 HD12 LEU 33 27.462 34.901 32.234 1.00 0.00 H +ATOM 537 HD13 LEU 33 27.851 35.680 33.756 1.00 0.00 H +ATOM 538 CD2 LEU 33 28.330 36.834 30.567 1.00 0.00 C +ATOM 539 HD21 LEU 33 29.097 37.398 30.049 1.00 0.00 H +ATOM 540 HD22 LEU 33 28.244 35.869 30.073 1.00 0.00 H +ATOM 541 HD23 LEU 33 27.392 37.377 30.480 1.00 0.00 H +ATOM 542 C LEU 33 31.470 37.912 32.433 1.00 0.00 C +ATOM 543 O LEU 33 31.799 37.377 33.488 1.00 0.00 O +ATOM 544 N ALA 34 32.167 37.712 31.309 1.00 0.00 N +ATOM 545 H ALA 34 31.835 38.148 30.464 1.00 0.00 H +ATOM 546 CA ALA 34 33.487 37.088 31.286 1.00 0.00 C +ATOM 547 HA ALA 34 33.483 36.255 31.984 1.00 0.00 H +ATOM 548 CB ALA 34 33.738 36.503 29.894 1.00 0.00 C +ATOM 549 HB1 ALA 34 33.888 37.299 29.172 1.00 0.00 H +ATOM 550 HB2 ALA 34 34.625 35.875 29.932 1.00 0.00 H +ATOM 551 HB3 ALA 34 32.899 35.890 29.575 1.00 0.00 H +ATOM 552 C ALA 34 34.603 38.061 31.724 1.00 0.00 C +ATOM 553 O ALA 34 35.476 37.686 32.501 1.00 0.00 O +ATOM 554 N ASN 35 34.562 39.328 31.298 1.00 0.00 N +ATOM 555 H ASN 35 33.796 39.616 30.699 1.00 0.00 H +ATOM 556 CA ASN 35 35.469 40.361 31.813 1.00 0.00 C +ATOM 557 HA ASN 35 36.473 39.937 31.852 1.00 0.00 H +ATOM 558 CB ASN 35 35.535 41.551 30.844 1.00 0.00 C +ATOM 559 HB2 ASN 35 34.534 41.846 30.533 1.00 0.00 H +ATOM 560 HB3 ASN 35 35.997 42.398 31.349 1.00 0.00 H +ATOM 561 CG ASN 35 36.390 41.215 29.635 1.00 0.00 C +ATOM 562 OD1 ASN 35 37.606 41.343 29.640 1.00 0.00 O +ATOM 563 ND2 ASN 35 35.796 40.729 28.576 1.00 0.00 N +ATOM 564 HD21 ASN 35 36.401 40.397 27.826 1.00 0.00 H +ATOM 565 HD22 ASN 35 34.803 40.536 28.596 1.00 0.00 H +ATOM 566 C ASN 35 35.151 40.764 33.264 1.00 0.00 C +ATOM 567 O ASN 35 36.085 41.048 34.010 1.00 0.00 O +ATOM 568 N ASP 36 33.893 40.661 33.714 1.00 0.00 N +ATOM 569 H ASP 36 33.143 40.554 33.037 1.00 0.00 H +ATOM 570 CA ASP 36 33.532 40.798 35.139 1.00 0.00 C +ATOM 571 HA ASP 36 33.869 41.776 35.487 1.00 0.00 H +ATOM 572 CB ASP 36 32.012 40.740 35.330 1.00 0.00 C +ATOM 573 HB2 ASP 36 31.647 39.800 34.925 1.00 0.00 H +ATOM 574 HB3 ASP 36 31.799 40.721 36.398 1.00 0.00 H +ATOM 575 CG ASP 36 31.231 41.914 34.724 1.00 0.00 C +ATOM 576 OD1 ASP 36 31.776 43.044 34.726 1.00 0.00 O +ATOM 577 OD2 ASP 36 30.067 41.678 34.321 1.00 0.00 O +ATOM 578 C ASP 36 34.214 39.742 36.037 1.00 0.00 C +ATOM 579 O ASP 36 34.627 40.061 37.154 1.00 0.00 O +ATOM 580 N ILE 37 34.394 38.499 35.556 1.00 0.00 N +ATOM 581 H ILE 37 33.990 38.272 34.656 1.00 0.00 H +ATOM 582 CA ILE 37 35.223 37.475 36.235 1.00 0.00 C +ATOM 583 HA ILE 37 35.191 37.704 37.300 1.00 0.00 H +ATOM 584 CB ILE 37 34.628 36.044 36.113 1.00 0.00 C +ATOM 585 HB ILE 37 35.229 35.380 36.738 1.00 0.00 H +ATOM 586 CG2 ILE 37 33.207 36.014 36.702 1.00 0.00 C +ATOM 587 HG21 ILE 37 32.526 36.589 36.078 1.00 0.00 H +ATOM 588 HG22 ILE 37 32.840 34.992 36.760 1.00 0.00 H +ATOM 589 HG23 ILE 37 33.201 36.437 37.704 1.00 0.00 H +ATOM 590 CG1 ILE 37 34.579 35.430 34.698 1.00 0.00 C +ATOM 591 HG12 ILE 37 33.916 34.564 34.715 1.00 0.00 H +ATOM 592 HG13 ILE 37 34.139 36.155 34.024 1.00 0.00 H +ATOM 593 CD1 ILE 37 35.922 34.938 34.141 1.00 0.00 C +ATOM 594 HD11 ILE 37 36.377 34.234 34.837 1.00 0.00 H +ATOM 595 HD12 ILE 37 35.757 34.437 33.188 1.00 0.00 H +ATOM 596 HD13 ILE 37 36.604 35.767 33.968 1.00 0.00 H +ATOM 597 C ILE 37 36.722 37.553 35.876 1.00 0.00 C +ATOM 598 O ILE 37 37.523 36.816 36.451 1.00 0.00 O +ATOM 599 N GLY 38 37.118 38.452 34.966 1.00 0.00 N +ATOM 600 H GLY 38 36.394 39.039 34.571 1.00 0.00 H +ATOM 601 CA GLY 38 38.503 38.874 34.726 1.00 0.00 C +ATOM 602 HA2 GLY 38 38.640 39.860 35.174 1.00 0.00 H +ATOM 603 HA3 GLY 38 39.181 38.181 35.224 1.00 0.00 H +ATOM 604 C GLY 38 38.950 38.962 33.259 1.00 0.00 C +ATOM 605 O GLY 38 39.837 39.761 32.962 1.00 0.00 O +ATOM 606 N ARG 39 38.404 38.150 32.340 1.00 0.00 N +ATOM 607 H ARG 39 37.628 37.572 32.642 1.00 0.00 H +ATOM 608 CA ARG 39 38.790 38.081 30.909 1.00 0.00 C +ATOM 609 HA ARG 39 38.783 39.097 30.508 1.00 0.00 H +ATOM 610 CB ARG 39 40.213 37.486 30.800 1.00 0.00 C +ATOM 611 HB2 ARG 39 40.890 38.074 31.419 1.00 0.00 H +ATOM 612 HB3 ARG 39 40.204 36.466 31.189 1.00 0.00 H +ATOM 613 CG ARG 39 40.753 37.472 29.361 1.00 0.00 C +ATOM 614 HG2 ARG 39 40.177 36.752 28.785 1.00 0.00 H +ATOM 615 HG3 ARG 39 40.636 38.460 28.912 1.00 0.00 H +ATOM 616 CD ARG 39 42.224 37.048 29.290 1.00 0.00 C +ATOM 617 HD2 ARG 39 42.334 36.080 29.783 1.00 0.00 H +ATOM 618 HD3 ARG 39 42.487 36.930 28.238 1.00 0.00 H +ATOM 619 NE ARG 39 43.132 38.044 29.897 1.00 0.00 N +ATOM 620 HE ARG 39 42.721 38.925 30.163 1.00 0.00 H +ATOM 621 CZ ARG 39 44.436 37.909 30.064 1.00 0.00 C +ATOM 622 NH1 ARG 39 45.121 38.862 30.637 1.00 0.00 N +ATOM 623 HH11 ARG 39 44.671 39.729 30.875 1.00 0.00 H +ATOM 624 HH12 ARG 39 46.114 38.778 30.781 1.00 0.00 H +ATOM 625 NH2 ARG 39 45.069 36.836 29.670 1.00 0.00 N +ATOM 626 HH21 ARG 39 44.557 36.129 29.152 1.00 0.00 H +ATOM 627 HH22 ARG 39 46.065 36.761 29.750 1.00 0.00 H +ATOM 628 C ARG 39 37.807 37.236 30.083 1.00 0.00 C +ATOM 629 O ARG 39 37.338 36.206 30.560 1.00 0.00 O +ATOM 630 N ASP 40 37.538 37.629 28.835 1.00 0.00 N +ATOM 631 H ASP 40 37.942 38.487 28.479 1.00 0.00 H +ATOM 632 CA ASP 40 36.790 36.809 27.871 1.00 0.00 C +ATOM 633 HA ASP 40 36.103 36.184 28.433 1.00 0.00 H +ATOM 634 CB ASP 40 35.933 37.675 26.938 1.00 0.00 C +ATOM 635 HB2 ASP 40 35.359 37.003 26.296 1.00 0.00 H +ATOM 636 HB3 ASP 40 35.207 38.220 27.538 1.00 0.00 H +ATOM 637 CG ASP 40 36.688 38.676 26.054 1.00 0.00 C +ATOM 638 OD1 ASP 40 37.396 39.561 26.641 1.00 0.00 O +ATOM 639 OD2 ASP 40 36.483 38.647 24.840 1.00 0.00 O +ATOM 640 C ASP 40 37.648 35.831 27.043 1.00 0.00 C +ATOM 641 O ASP 40 38.817 36.075 26.756 1.00 0.00 O +ATOM 642 N GLY 41 37.007 34.739 26.612 1.00 0.00 N +ATOM 643 H GLY 41 36.050 34.627 26.905 1.00 0.00 H +ATOM 644 CA GLY 41 37.461 33.853 25.532 1.00 0.00 C +ATOM 645 HA2 GLY 41 38.456 34.147 25.191 1.00 0.00 H +ATOM 646 HA3 GLY 41 37.514 32.829 25.908 1.00 0.00 H +ATOM 647 C GLY 41 36.504 33.894 24.329 1.00 0.00 C +ATOM 648 O GLY 41 35.685 34.807 24.201 1.00 0.00 O +ATOM 649 N GLU 42 36.573 32.885 23.458 1.00 0.00 N +ATOM 650 H GLU 42 37.209 32.128 23.651 1.00 0.00 H +ATOM 651 CA GLU 42 35.695 32.715 22.287 1.00 0.00 C +ATOM 652 HA GLU 42 34.970 33.527 22.273 1.00 0.00 H +ATOM 653 CB GLU 42 36.508 32.774 20.978 1.00 0.00 C +ATOM 654 HB2 GLU 42 37.232 31.957 20.984 1.00 0.00 H +ATOM 655 HB3 GLU 42 35.834 32.605 20.140 1.00 0.00 H +ATOM 656 CG GLU 42 37.265 34.094 20.728 1.00 0.00 C +ATOM 657 HG2 GLU 42 38.001 34.236 21.527 1.00 0.00 H +ATOM 658 HG3 GLU 42 37.818 34.000 19.792 1.00 0.00 H +ATOM 659 CD GLU 42 36.372 35.334 20.626 1.00 0.00 C +ATOM 660 OE1 GLU 42 35.131 35.214 20.631 1.00 0.00 O +ATOM 661 OE2 GLU 42 36.904 36.469 20.624 1.00 0.00 O +ATOM 662 C GLU 42 34.869 31.423 22.374 1.00 0.00 C +ATOM 663 O GLU 42 35.297 30.445 22.988 1.00 0.00 O +ATOM 664 N ILE 43 33.665 31.431 21.788 1.00 0.00 N +ATOM 665 H ILE 43 33.409 32.241 21.236 1.00 0.00 H +ATOM 666 CA ILE 43 32.614 30.416 21.979 1.00 0.00 C +ATOM 667 HA ILE 43 33.069 29.473 22.292 1.00 0.00 H +ATOM 668 CB ILE 43 31.646 30.897 23.096 1.00 0.00 C +ATOM 669 HB ILE 43 31.245 31.861 22.779 1.00 0.00 H +ATOM 670 CG2 ILE 43 30.447 29.965 23.291 1.00 0.00 C +ATOM 671 HG21 ILE 43 30.778 28.966 23.551 1.00 0.00 H +ATOM 672 HG22 ILE 43 29.817 30.345 24.091 1.00 0.00 H +ATOM 673 HG23 ILE 43 29.860 29.909 22.378 1.00 0.00 H +ATOM 674 CG1 ILE 43 32.299 31.123 24.486 1.00 0.00 C +ATOM 675 HG12 ILE 43 33.132 31.816 24.388 1.00 0.00 H +ATOM 676 HG13 ILE 43 31.570 31.611 25.133 1.00 0.00 H +ATOM 677 CD1 ILE 43 32.793 29.859 25.210 1.00 0.00 C +ATOM 678 HD11 ILE 43 33.457 29.282 24.567 1.00 0.00 H +ATOM 679 HD12 ILE 43 33.339 30.152 26.109 1.00 0.00 H +ATOM 680 HD13 ILE 43 31.948 29.238 25.511 1.00 0.00 H +ATOM 681 C ILE 43 31.881 30.163 20.644 1.00 0.00 C +ATOM 682 O ILE 43 31.529 31.110 19.940 1.00 0.00 O +ATOM 683 N THR 44 31.648 28.895 20.283 1.00 0.00 N +ATOM 684 H THR 44 31.889 28.159 20.937 1.00 0.00 H +ATOM 685 CA THR 44 30.941 28.471 19.053 1.00 0.00 C +ATOM 686 HA THR 44 31.238 29.133 18.240 1.00 0.00 H +ATOM 687 CB THR 44 31.357 27.032 18.684 1.00 0.00 C +ATOM 688 HB THR 44 31.112 26.363 19.513 1.00 0.00 H +ATOM 689 CG2 THR 44 30.726 26.467 17.405 1.00 0.00 C +ATOM 690 HG21 THR 44 30.819 27.184 16.589 1.00 0.00 H +ATOM 691 HG22 THR 44 31.227 25.540 17.127 1.00 0.00 H +ATOM 692 HG23 THR 44 29.676 26.234 17.580 1.00 0.00 H +ATOM 693 OG1 THR 44 32.748 26.977 18.458 1.00 0.00 O +ATOM 694 HG1 THR 44 32.916 27.302 17.569 1.00 0.00 H +ATOM 695 C THR 44 29.413 28.595 19.205 1.00 0.00 C +ATOM 696 O THR 44 28.902 28.657 20.326 1.00 0.00 O +ATOM 697 N ARG 45 28.657 28.632 18.093 1.00 0.00 N +ATOM 698 H ARG 45 29.115 28.544 17.196 1.00 0.00 H +ATOM 699 CA ARG 45 27.194 28.764 18.084 1.00 0.00 C +ATOM 700 HA ARG 45 26.815 28.539 19.076 1.00 0.00 H +ATOM 701 CB ARG 45 26.851 30.237 17.775 1.00 0.00 C +ATOM 702 HB2 ARG 45 27.254 30.880 18.564 1.00 0.00 H +ATOM 703 HB3 ARG 45 27.308 30.530 16.828 1.00 0.00 H +ATOM 704 CG ARG 45 25.332 30.422 17.684 1.00 0.00 C +ATOM 705 HG2 ARG 45 24.965 29.862 16.825 1.00 0.00 H +ATOM 706 HG3 ARG 45 24.874 30.036 18.594 1.00 0.00 H +ATOM 707 CD ARG 45 24.869 31.852 17.472 1.00 0.00 C +ATOM 708 HD2 ARG 45 25.260 32.460 18.288 1.00 0.00 H +ATOM 709 HD3 ARG 45 25.286 32.216 16.535 1.00 0.00 H +ATOM 710 NE ARG 45 23.385 31.892 17.507 1.00 0.00 N +ATOM 711 HE ARG 45 22.983 31.691 18.405 1.00 0.00 H +ATOM 712 CZ ARG 45 22.508 32.108 16.549 1.00 0.00 C +ATOM 713 NH1 ARG 45 22.854 32.201 15.300 1.00 0.00 N +ATOM 714 HH11 ARG 45 23.816 32.071 15.058 1.00 0.00 H +ATOM 715 HH12 ARG 45 22.168 32.413 14.597 1.00 0.00 H +ATOM 716 NH2 ARG 45 21.252 32.199 16.849 1.00 0.00 N +ATOM 717 HH21 ARG 45 20.921 32.136 17.783 1.00 0.00 H +ATOM 718 HH22 ARG 45 20.603 32.040 16.082 1.00 0.00 H +ATOM 719 C ARG 45 26.501 27.807 17.114 1.00 0.00 C +ATOM 720 O ARG 45 27.008 27.553 16.028 1.00 0.00 O +ATOM 721 N ASP 46 25.270 27.408 17.458 1.00 0.00 N +ATOM 722 H ASP 46 24.965 27.637 18.402 1.00 0.00 H +ATOM 723 CA ASP 46 24.207 26.973 16.538 1.00 0.00 C +ATOM 724 HA ASP 46 24.592 27.019 15.511 1.00 0.00 H +ATOM 725 CB ASP 46 23.841 25.516 16.874 1.00 0.00 C +ATOM 726 HB2 ASP 46 24.676 24.840 16.658 1.00 0.00 H +ATOM 727 HB3 ASP 46 23.664 25.480 17.956 1.00 0.00 H +ATOM 728 CG ASP 46 22.594 25.036 16.155 1.00 0.00 C +ATOM 729 OD1 ASP 46 21.743 24.461 16.854 1.00 0.00 O +ATOM 730 OD2 ASP 46 22.407 25.340 14.958 1.00 0.00 O +ATOM 731 C ASP 46 22.968 27.909 16.627 1.00 0.00 C +ATOM 732 O ASP 46 22.654 28.461 17.682 1.00 0.00 O +ATOM 733 N ASP 47 22.251 28.101 15.511 1.00 0.00 N +ATOM 734 H ASP 47 22.548 27.528 14.737 1.00 0.00 H +ATOM 735 CA ASP 47 20.944 28.797 15.398 1.00 0.00 C +ATOM 736 HA ASP 47 20.918 29.566 16.163 1.00 0.00 H +ATOM 737 CB ASP 47 20.780 29.545 14.067 1.00 0.00 C +ATOM 738 HB2 ASP 47 21.676 30.144 13.949 1.00 0.00 H +ATOM 739 HB3 ASP 47 20.740 28.869 13.199 1.00 0.00 H +ATOM 740 CG ASP 47 19.583 30.434 14.154 1.00 0.00 C +ATOM 741 OD1 ASP 47 18.528 30.176 13.547 1.00 0.00 O +ATOM 742 OD2 ASP 47 19.579 31.313 15.046 1.00 0.00 O +ATOM 743 C ASP 47 19.733 27.904 15.643 1.00 0.00 C +ATOM 744 O ASP 47 18.742 28.346 16.243 1.00 0.00 O +ATOM 745 N ALA 48 19.815 26.642 15.209 1.00 0.00 N +ATOM 746 H ALA 48 20.719 26.290 14.869 1.00 0.00 H +ATOM 747 CA ALA 48 18.676 25.730 15.224 1.00 0.00 C +ATOM 748 HA ALA 48 17.841 26.206 14.702 1.00 0.00 H +ATOM 749 CB ALA 48 19.045 24.448 14.464 1.00 0.00 C +ATOM 750 HB1 ALA 48 19.871 23.937 14.948 1.00 0.00 H +ATOM 751 HB2 ALA 48 18.190 23.785 14.444 1.00 0.00 H +ATOM 752 HB3 ALA 48 19.336 24.674 13.443 1.00 0.00 H +ATOM 753 C ALA 48 18.223 25.445 16.663 1.00 0.00 C +ATOM 754 O ALA 48 17.042 25.550 16.983 1.00 0.00 O +ATOM 755 N THR 49 19.174 25.152 17.546 1.00 0.00 N +ATOM 756 H THR 49 20.105 24.964 17.173 1.00 0.00 H +ATOM 757 CA THR 49 19.007 25.063 19.002 1.00 0.00 C +ATOM 758 HA THR 49 17.987 24.719 19.196 1.00 0.00 H +ATOM 759 CB THR 49 20.004 24.052 19.584 1.00 0.00 C +ATOM 760 HB THR 49 19.828 23.977 20.655 1.00 0.00 H +ATOM 761 CG2 THR 49 19.878 22.652 19.003 1.00 0.00 C +ATOM 762 HG21 THR 49 20.114 22.648 17.939 1.00 0.00 H +ATOM 763 HG22 THR 49 20.585 22.008 19.517 1.00 0.00 H +ATOM 764 HG23 THR 49 18.865 22.268 19.143 1.00 0.00 H +ATOM 765 OG1 THR 49 21.330 24.467 19.378 1.00 0.00 O +ATOM 766 HG1 THR 49 21.500 24.365 18.408 1.00 0.00 H +ATOM 767 C THR 49 19.168 26.399 19.745 1.00 0.00 C +ATOM 768 O THR 49 19.084 26.430 20.972 1.00 0.00 O +ATOM 769 N LYS 50 19.418 27.502 19.027 1.00 0.00 N +ATOM 770 H LYS 50 19.403 27.388 18.023 1.00 0.00 H +ATOM 771 CA LYS 50 19.653 28.867 19.552 1.00 0.00 C +ATOM 772 HA LYS 50 20.062 29.454 18.733 1.00 0.00 H +ATOM 773 CB LYS 50 18.295 29.494 19.984 1.00 0.00 C +ATOM 774 HB2 LYS 50 17.859 28.849 20.740 1.00 0.00 H +ATOM 775 HB3 LYS 50 18.480 30.464 20.454 1.00 0.00 H +ATOM 776 CG LYS 50 17.259 29.704 18.856 1.00 0.00 C +ATOM 777 HG2 LYS 50 17.200 28.813 18.230 1.00 0.00 H +ATOM 778 HG3 LYS 50 16.278 29.836 19.329 1.00 0.00 H +ATOM 779 CD LYS 50 17.558 30.946 17.996 1.00 0.00 C +ATOM 780 HD2 LYS 50 17.533 31.823 18.645 1.00 0.00 H +ATOM 781 HD3 LYS 50 18.572 30.862 17.576 1.00 0.00 H +ATOM 782 CE LYS 50 16.532 31.155 16.863 1.00 0.00 C +ATOM 783 HE2 LYS 50 15.554 30.810 17.205 1.00 0.00 H +ATOM 784 HE3 LYS 50 16.435 32.217 16.620 1.00 0.00 H +ATOM 785 NZ LYS 50 16.877 30.378 15.648 1.00 0.00 N +ATOM 786 HZ1 LYS 50 17.155 29.431 15.878 1.00 0.00 H +ATOM 787 HZ2 LYS 50 16.131 30.363 14.971 1.00 0.00 H +ATOM 788 HZ3 LYS 50 17.683 30.740 15.123 1.00 0.00 H +ATOM 789 C LYS 50 20.719 28.910 20.672 1.00 0.00 C +ATOM 790 O LYS 50 20.547 29.646 21.649 1.00 0.00 O +ATOM 791 N THR 51 21.781 28.105 20.554 1.00 0.00 N +ATOM 792 H THR 51 21.911 27.629 19.674 1.00 0.00 H +ATOM 793 CA THR 51 22.708 27.766 21.659 1.00 0.00 C +ATOM 794 HA THR 51 22.444 28.369 22.520 1.00 0.00 H +ATOM 795 CB THR 51 22.534 26.283 22.079 1.00 0.00 C +ATOM 796 HB THR 51 22.706 25.648 21.205 1.00 0.00 H +ATOM 797 CG2 THR 51 23.504 25.840 23.165 1.00 0.00 C +ATOM 798 HG21 THR 51 23.468 26.491 24.033 1.00 0.00 H +ATOM 799 HG22 THR 51 23.274 24.832 23.493 1.00 0.00 H +ATOM 800 HG23 THR 51 24.524 25.817 22.796 1.00 0.00 H +ATOM 801 OG1 THR 51 21.248 26.063 22.613 1.00 0.00 O +ATOM 802 HG1 THR 51 20.611 26.148 21.883 1.00 0.00 H +ATOM 803 C THR 51 24.193 28.073 21.357 1.00 0.00 C +ATOM 804 O THR 51 24.686 27.811 20.265 1.00 0.00 O +ATOM 805 N PHE 52 24.913 28.617 22.342 1.00 0.00 N +ATOM 806 H PHE 52 24.408 28.915 23.164 1.00 0.00 H +ATOM 807 CA PHE 52 26.375 28.740 22.393 1.00 0.00 C +ATOM 808 HA PHE 52 26.766 28.783 21.386 1.00 0.00 H +ATOM 809 CB PHE 52 26.717 30.056 23.121 1.00 0.00 C +ATOM 810 HB2 PHE 52 26.142 30.102 24.039 1.00 0.00 H +ATOM 811 HB3 PHE 52 27.755 30.020 23.417 1.00 0.00 H +ATOM 812 CG PHE 52 26.511 31.343 22.342 1.00 0.00 C +ATOM 813 CD1 PHE 52 25.428 32.190 22.641 1.00 0.00 C +ATOM 814 HD1 PHE 52 24.687 31.889 23.369 1.00 0.00 H +ATOM 815 CE1 PHE 52 25.332 33.451 22.025 1.00 0.00 C +ATOM 816 HE1 PHE 52 24.516 34.116 22.274 1.00 0.00 H +ATOM 817 CZ PHE 52 26.316 33.867 21.113 1.00 0.00 C +ATOM 818 HZ PHE 52 26.261 34.847 20.661 1.00 0.00 H +ATOM 819 CE2 PHE 52 27.380 33.011 20.792 1.00 0.00 C +ATOM 820 HE2 PHE 52 28.145 33.334 20.095 1.00 0.00 H +ATOM 821 CD2 PHE 52 27.478 31.750 21.403 1.00 0.00 C +ATOM 822 HD2 PHE 52 28.318 31.111 21.171 1.00 0.00 H +ATOM 823 C PHE 52 27.067 27.561 23.130 1.00 0.00 C +ATOM 824 O PHE 52 26.538 27.089 24.144 1.00 0.00 O +ATOM 825 N THR 53 28.263 27.132 22.684 1.00 0.00 N +ATOM 826 H THR 53 28.641 27.570 21.843 1.00 0.00 H +ATOM 827 CA THR 53 29.056 25.994 23.229 1.00 0.00 C +ATOM 828 HA THR 53 28.819 25.882 24.287 1.00 0.00 H +ATOM 829 CB THR 53 28.715 24.666 22.524 1.00 0.00 C +ATOM 830 HB THR 53 29.370 23.889 22.922 1.00 0.00 H +ATOM 831 CG2 THR 53 27.274 24.207 22.721 1.00 0.00 C +ATOM 832 HG21 THR 53 26.595 24.877 22.197 1.00 0.00 H +ATOM 833 HG22 THR 53 27.159 23.197 22.328 1.00 0.00 H +ATOM 834 HG23 THR 53 27.042 24.199 23.783 1.00 0.00 H +ATOM 835 OG1 THR 53 28.937 24.769 21.136 1.00 0.00 O +ATOM 836 HG1 THR 53 28.985 23.878 20.776 1.00 0.00 H +ATOM 837 C THR 53 30.586 26.162 23.117 1.00 0.00 C +ATOM 838 O THR 53 31.101 26.876 22.260 1.00 0.00 O +ATOM 839 N THR 54 31.344 25.474 23.985 1.00 0.00 N +ATOM 840 H THR 54 30.878 24.930 24.695 1.00 0.00 H +ATOM 841 CA THR 54 32.822 25.329 23.917 1.00 0.00 C +ATOM 842 HA THR 54 33.226 26.189 23.379 1.00 0.00 H +ATOM 843 CB THR 54 33.431 25.322 25.331 1.00 0.00 C +ATOM 844 HB THR 54 33.179 24.383 25.826 1.00 0.00 H +ATOM 845 CG2 THR 54 34.954 25.512 25.378 1.00 0.00 C +ATOM 846 HG21 THR 54 35.249 26.363 24.762 1.00 0.00 H +ATOM 847 HG22 THR 54 35.275 25.681 26.403 1.00 0.00 H +ATOM 848 HG23 THR 54 35.454 24.613 25.023 1.00 0.00 H +ATOM 849 OG1 THR 54 32.915 26.379 26.110 1.00 0.00 O +ATOM 850 HG1 THR 54 33.250 27.203 25.748 1.00 0.00 H +ATOM 851 C THR 54 33.241 24.063 23.135 1.00 0.00 C +ATOM 852 O THR 54 32.450 23.132 22.990 1.00 0.00 O +ATOM 853 N LEU 55 34.485 24.027 22.638 1.00 0.00 N +ATOM 854 H LEU 55 35.078 24.816 22.827 1.00 0.00 H +ATOM 855 CA LEU 55 35.133 22.882 21.971 1.00 0.00 C +ATOM 856 HA LEU 55 34.378 22.349 21.392 1.00 0.00 H +ATOM 857 CB LEU 55 36.153 23.499 20.985 1.00 0.00 C +ATOM 858 HB2 LEU 55 35.570 24.100 20.285 1.00 0.00 H +ATOM 859 HB3 LEU 55 36.800 24.188 21.529 1.00 0.00 H +ATOM 860 CG LEU 55 37.034 22.526 20.172 1.00 0.00 C +ATOM 861 HG LEU 55 36.527 21.568 20.065 1.00 0.00 H +ATOM 862 CD1 LEU 55 37.287 23.085 18.768 1.00 0.00 C +ATOM 863 HD11 LEU 55 37.761 24.066 18.827 1.00 0.00 H +ATOM 864 HD12 LEU 55 37.937 22.407 18.214 1.00 0.00 H +ATOM 865 HD13 LEU 55 36.343 23.177 18.232 1.00 0.00 H +ATOM 866 CD2 LEU 55 38.399 22.332 20.832 1.00 0.00 C +ATOM 867 HD21 LEU 55 38.275 21.942 21.843 1.00 0.00 H +ATOM 868 HD22 LEU 55 38.980 21.603 20.266 1.00 0.00 H +ATOM 869 HD23 LEU 55 38.941 23.276 20.880 1.00 0.00 H +ATOM 870 C LEU 55 35.726 21.852 22.975 1.00 0.00 C +ATOM 871 O LEU 55 35.967 22.194 24.130 1.00 0.00 O +ATOM 872 N GLU 56 35.932 20.602 22.529 1.00 0.00 N +ATOM 873 H GLU 56 35.775 20.439 21.552 1.00 0.00 H +ATOM 874 CA GLU 56 36.456 19.438 23.296 1.00 0.00 C +ATOM 875 HA GLU 56 36.227 19.593 24.347 1.00 0.00 H +ATOM 876 CB GLU 56 35.693 18.173 22.823 1.00 0.00 C +ATOM 877 HB2 GLU 56 34.626 18.321 22.965 1.00 0.00 H +ATOM 878 HB3 GLU 56 35.844 18.086 21.745 1.00 0.00 H +ATOM 879 CG GLU 56 36.082 16.814 23.453 1.00 0.00 C +ATOM 880 HG2 GLU 56 36.064 16.068 22.651 1.00 0.00 H +ATOM 881 HG3 GLU 56 37.116 16.841 23.779 1.00 0.00 H +ATOM 882 CD GLU 56 35.183 16.309 24.589 1.00 0.00 C +ATOM 883 OE1 GLU 56 35.681 15.972 25.698 1.00 0.00 O +ATOM 884 OE2 GLU 56 33.968 16.066 24.373 1.00 0.00 O +ATOM 885 C GLU 56 37.998 19.269 23.229 1.00 0.00 C +ATOM 886 O GLU 56 38.635 19.282 24.314 1.00 0.00 O +ATOM 887 OXT GLU 56 38.524 19.098 22.101 1.00 0.00 O +HETATM 888 ZN ZN1 57 26.737 32.351 29.113 1.00 0.00 Zn +HETATM 889 N AN1 58 28.448 33.033 30.002 1.00 0.00 N +HETATM 890 C AN1 58 30.847 33.636 30.802 1.00 0.00 C +HETATM 891 C1 AN1 58 29.482 33.295 30.369 1.00 0.00 C +HETATM 892 H AN1 58 30.871 33.892 31.868 1.00 0.00 H +HETATM 893 H1 AN1 58 31.165 34.502 30.220 1.00 0.00 H +HETATM 894 H2 AN1 58 31.533 32.800 30.616 1.00 0.00 H +HETATM 895 N1 AZI 59 30.421 28.759 29.483 1.00 0.00 N +HETATM 896 N2 AZI 59 30.144 28.767 30.670 1.00 0.00 N +HETATM 897 N3 AZI 59 29.859 28.753 31.897 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 888 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 149 +CONECT 135 134 +CONECT 136 137 134 139 138 +CONECT 137 136 +CONECT 138 136 +CONECT 139 140 136 141 145 +CONECT 140 139 +CONECT 141 144 143 139 142 +CONECT 142 141 +CONECT 143 141 +CONECT 144 141 +CONECT 145 139 147 146 148 +CONECT 146 145 +CONECT 147 145 +CONECT 148 145 +CONECT 149 134 151 150 +CONECT 150 149 +CONECT 151 152 149 153 +CONECT 152 151 +CONECT 153 151 154 156 155 +CONECT 154 153 +CONECT 155 153 +CONECT 156 157 153 158 +CONECT 157 156 +CONECT 158 156 160 159 +CONECT 159 158 +CONECT 160 162 161 158 178 +CONECT 161 160 +CONECT 162 165 163 164 160 +CONECT 163 162 +CONECT 164 162 +CONECT 165 168 167 166 162 +CONECT 166 165 +CONECT 167 165 +CONECT 168 171 169 170 165 +CONECT 169 168 +CONECT 170 168 +CONECT 171 174 173 172 168 +CONECT 172 171 +CONECT 173 171 +CONECT 174 176 177 175 171 +CONECT 175 174 +CONECT 176 174 +CONECT 177 174 +CONECT 178 160 179 180 +CONECT 179 178 +CONECT 180 178 181 182 +CONECT 181 180 +CONECT 182 180 183 199 184 +CONECT 183 182 +CONECT 184 182 186 187 185 +CONECT 185 184 +CONECT 186 184 +CONECT 187 188 184 197 +CONECT 188 189 190 187 +CONECT 189 188 +CONECT 190 191 188 192 +CONECT 191 190 +CONECT 192 190 193 195 +CONECT 193 194 192 +CONECT 194 193 +CONECT 195 192 197 196 +CONECT 196 195 +CONECT 197 187 195 198 +CONECT 198 197 +CONECT 199 201 182 200 +CONECT 200 199 +CONECT 201 202 203 199 +CONECT 202 201 +CONECT 203 223 201 205 204 +CONECT 204 203 +CONECT 205 208 203 206 207 +CONECT 206 205 +CONECT 207 205 +CONECT 208 210 209 211 205 +CONECT 209 208 +CONECT 210 208 +CONECT 211 214 208 212 213 +CONECT 212 211 +CONECT 213 211 +CONECT 214 215 216 211 +CONECT 215 214 +CONECT 216 217 214 220 +CONECT 217 218 219 216 +CONECT 218 217 +CONECT 219 217 +CONECT 220 216 222 221 +CONECT 221 220 +CONECT 222 220 +CONECT 223 224 225 203 +CONECT 224 223 +CONECT 225 227 223 226 +CONECT 226 225 +CONECT 227 228 245 229 225 +CONECT 228 227 +CONECT 229 232 227 230 231 +CONECT 230 229 +CONECT 231 229 +CONECT 232 234 233 235 229 +CONECT 233 232 +CONECT 234 232 +CONECT 235 236 232 237 238 +CONECT 236 235 +CONECT 237 235 +CONECT 238 240 235 241 239 +CONECT 239 238 +CONECT 240 238 +CONECT 241 244 238 243 242 +CONECT 242 241 +CONECT 243 241 +CONECT 244 241 +CONECT 245 246 227 247 +CONECT 246 245 +CONECT 247 245 249 248 +CONECT 248 247 +CONECT 249 252 247 250 251 +CONECT 250 249 +CONECT 251 249 +CONECT 252 253 254 249 +CONECT 253 252 +CONECT 254 256 252 255 +CONECT 255 254 +CONECT 256 258 257 268 254 +CONECT 257 256 +CONECT 258 264 259 260 256 +CONECT 259 258 +CONECT 260 262 258 261 263 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 265 267 258 +CONECT 265 264 +CONECT 266 264 +CONECT 267 264 +CONECT 268 270 256 269 +CONECT 269 268 +CONECT 270 280 271 268 +CONECT 271 272 270 281 274 +CONECT 272 273 287 271 +CONECT 273 272 +CONECT 274 271 275 282 283 +CONECT 275 276 277 274 +CONECT 276 279 285 275 +CONECT 277 278 275 284 +CONECT 278 279 286 277 +CONECT 279 888 276 278 +CONECT 280 270 +CONECT 281 271 +CONECT 282 274 +CONECT 283 274 +CONECT 284 277 +CONECT 285 276 +CONECT 286 278 +CONECT 287 289 272 288 +CONECT 288 287 +CONECT 289 290 291 299 287 +CONECT 290 289 +CONECT 291 292 293 289 297 +CONECT 292 291 +CONECT 293 296 295 291 294 +CONECT 294 293 +CONECT 295 293 +CONECT 296 293 +CONECT 297 291 298 +CONECT 298 297 +CONECT 299 301 289 300 +CONECT 300 299 +CONECT 301 311 302 299 +CONECT 302 303 305 301 312 +CONECT 303 304 318 302 +CONECT 304 303 +CONECT 305 313 314 302 306 +CONECT 306 305 307 308 +CONECT 307 316 306 310 +CONECT 308 306 315 309 +CONECT 309 310 308 317 +CONECT 310 307 888 309 +CONECT 311 301 +CONECT 312 302 +CONECT 313 305 +CONECT 314 305 +CONECT 315 308 +CONECT 316 307 +CONECT 317 309 +CONECT 318 320 303 319 +CONECT 319 318 +CONECT 320 331 321 318 322 +CONECT 321 320 +CONECT 322 320 325 324 323 +CONECT 323 322 +CONECT 324 322 +CONECT 325 327 328 322 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 329 330 325 +CONECT 329 328 +CONECT 330 328 +CONECT 331 333 332 320 +CONECT 332 331 +CONECT 333 335 334 331 +CONECT 334 333 +CONECT 335 341 337 336 333 +CONECT 336 335 +CONECT 337 339 338 335 340 +CONECT 338 337 +CONECT 339 337 +CONECT 340 337 +CONECT 341 343 342 335 +CONECT 342 341 +CONECT 343 345 344 341 +CONECT 344 343 +CONECT 345 357 347 346 343 +CONECT 346 345 +CONECT 347 348 353 345 349 +CONECT 348 347 +CONECT 349 347 351 352 350 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 347 356 +CONECT 354 353 +CONECT 355 353 +CONECT 356 353 +CONECT 357 358 359 345 +CONECT 358 357 +CONECT 359 361 357 360 +CONECT 360 359 +CONECT 361 363 362 369 359 +CONECT 362 361 +CONECT 363 366 364 365 361 +CONECT 364 363 +CONECT 365 363 +CONECT 366 367 368 363 +CONECT 367 366 +CONECT 368 366 +CONECT 369 361 371 370 +CONECT 370 369 +CONECT 371 373 372 369 +CONECT 372 371 +CONECT 373 374 375 385 371 +CONECT 374 373 +CONECT 375 381 376 373 377 +CONECT 376 375 +CONECT 377 375 379 380 378 +CONECT 378 377 +CONECT 379 377 +CONECT 380 377 +CONECT 381 384 383 382 375 +CONECT 382 381 +CONECT 383 381 +CONECT 384 381 +CONECT 385 387 373 386 +CONECT 386 385 +CONECT 387 388 389 385 +CONECT 388 387 +CONECT 389 391 387 390 395 +CONECT 390 389 +CONECT 391 394 392 393 389 +CONECT 392 391 +CONECT 393 391 +CONECT 394 391 +CONECT 395 389 396 397 +CONECT 396 395 +CONECT 397 395 398 399 +CONECT 398 397 +CONECT 399 397 400 401 410 +CONECT 400 399 +CONECT 401 404 402 399 403 +CONECT 402 401 +CONECT 403 401 +CONECT 404 405 406 407 401 +CONECT 405 404 +CONECT 406 404 +CONECT 407 409 404 408 +CONECT 408 407 +CONECT 409 407 +CONECT 410 399 412 411 +CONECT 411 410 +CONECT 412 413 410 414 +CONECT 413 412 +CONECT 414 412 416 420 415 +CONECT 415 414 +CONECT 416 417 419 414 418 +CONECT 417 416 +CONECT 418 416 +CONECT 419 416 +CONECT 420 422 414 421 +CONECT 421 420 +CONECT 422 423 424 420 +CONECT 423 422 +CONECT 424 426 422 425 435 +CONECT 425 424 +CONECT 426 427 428 429 424 +CONECT 427 426 +CONECT 428 426 +CONECT 429 432 426 431 430 +CONECT 430 429 +CONECT 431 429 +CONECT 432 434 433 429 +CONECT 433 432 +CONECT 434 432 +CONECT 435 424 437 436 +CONECT 436 435 +CONECT 437 438 435 439 +CONECT 438 437 +CONECT 439 437 441 440 457 +CONECT 440 439 +CONECT 441 444 442 443 439 +CONECT 442 441 +CONECT 443 441 +CONECT 444 446 447 445 441 +CONECT 445 444 +CONECT 446 444 +CONECT 447 450 448 449 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 451 452 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 455 454 456 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 453 +CONECT 457 439 459 458 +CONECT 458 457 +CONECT 459 460 457 461 +CONECT 460 459 +CONECT 461 459 463 462 477 +CONECT 462 461 +CONECT 463 466 464 461 465 +CONECT 464 463 +CONECT 465 463 +CONECT 466 467 475 463 +CONECT 467 469 468 466 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 472 469 473 +CONECT 472 471 +CONECT 473 471 474 475 +CONECT 474 473 +CONECT 475 473 466 476 +CONECT 476 475 +CONECT 477 479 461 478 +CONECT 478 477 +CONECT 479 480 481 477 +CONECT 480 479 +CONECT 481 483 479 491 482 +CONECT 482 481 +CONECT 483 484 489 485 481 +CONECT 484 483 +CONECT 485 487 483 488 486 +CONECT 486 485 +CONECT 487 485 +CONECT 488 485 +CONECT 489 490 483 +CONECT 490 489 +CONECT 491 493 481 492 +CONECT 492 491 +CONECT 493 494 495 491 +CONECT 494 493 +CONECT 495 497 493 496 513 +CONECT 496 495 +CONECT 497 500 498 499 495 +CONECT 498 497 +CONECT 499 497 +CONECT 500 503 502 501 497 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 504 505 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 508 507 509 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 506 510 512 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 495 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 518 523 +CONECT 518 517 +CONECT 519 522 520 517 521 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 +CONECT 523 517 525 524 +CONECT 524 523 +CONECT 525 526 523 527 +CONECT 526 525 +CONECT 527 525 542 529 528 +CONECT 528 527 +CONECT 529 532 527 531 530 +CONECT 530 529 +CONECT 531 529 +CONECT 532 538 533 534 529 +CONECT 533 532 +CONECT 534 532 536 535 537 +CONECT 535 534 +CONECT 536 534 +CONECT 537 534 +CONECT 538 539 540 541 532 +CONECT 539 538 +CONECT 540 538 +CONECT 541 538 +CONECT 542 544 527 543 +CONECT 543 542 +CONECT 544 545 546 542 +CONECT 545 544 +CONECT 546 548 544 552 547 +CONECT 547 546 +CONECT 548 549 551 550 546 +CONECT 549 548 +CONECT 550 548 +CONECT 551 548 +CONECT 552 546 554 553 +CONECT 553 552 +CONECT 554 555 552 556 +CONECT 555 554 +CONECT 556 558 554 557 566 +CONECT 557 556 +CONECT 558 561 559 560 556 +CONECT 559 558 +CONECT 560 558 +CONECT 561 563 562 558 +CONECT 562 561 +CONECT 563 564 565 561 +CONECT 564 563 +CONECT 565 563 +CONECT 566 556 568 567 +CONECT 567 566 +CONECT 568 569 566 570 +CONECT 569 568 +CONECT 570 568 572 571 578 +CONECT 571 570 +CONECT 572 575 573 570 574 +CONECT 573 572 +CONECT 574 572 +CONECT 575 577 576 572 +CONECT 576 575 +CONECT 577 575 +CONECT 578 570 580 579 +CONECT 579 578 +CONECT 580 581 578 582 +CONECT 581 580 +CONECT 582 580 597 584 583 +CONECT 583 582 +CONECT 584 590 582 586 585 +CONECT 585 584 +CONECT 586 587 584 588 589 +CONECT 587 586 +CONECT 588 586 +CONECT 589 586 +CONECT 590 592 593 591 584 +CONECT 591 590 +CONECT 592 590 +CONECT 593 595 596 590 594 +CONECT 594 593 +CONECT 595 593 +CONECT 596 593 +CONECT 597 599 582 598 +CONECT 598 597 +CONECT 599 600 601 597 +CONECT 600 599 +CONECT 601 604 599 602 603 +CONECT 602 601 +CONECT 603 601 +CONECT 604 606 605 601 +CONECT 605 604 +CONECT 606 608 607 604 +CONECT 607 606 +CONECT 608 628 609 610 606 +CONECT 609 608 +CONECT 610 613 608 612 611 +CONECT 611 610 +CONECT 612 610 +CONECT 613 614 615 616 610 +CONECT 614 613 +CONECT 615 613 +CONECT 616 618 613 617 619 +CONECT 617 616 +CONECT 618 616 +CONECT 619 616 621 620 +CONECT 620 619 +CONECT 621 625 619 622 +CONECT 622 621 624 623 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 621 +CONECT 626 625 +CONECT 627 625 +CONECT 628 630 629 608 +CONECT 629 628 +CONECT 630 632 631 628 +CONECT 631 630 +CONECT 632 634 640 633 630 +CONECT 633 632 +CONECT 634 637 635 636 632 +CONECT 635 634 +CONECT 636 634 +CONECT 637 639 638 634 +CONECT 638 637 +CONECT 639 637 +CONECT 640 642 641 632 +CONECT 641 640 +CONECT 642 644 643 640 +CONECT 643 642 +CONECT 644 647 645 646 642 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 648 644 +CONECT 648 647 +CONECT 649 651 650 647 +CONECT 650 649 +CONECT 651 653 652 662 649 +CONECT 652 651 +CONECT 653 655 656 654 651 +CONECT 654 653 +CONECT 655 653 +CONECT 656 658 659 653 657 +CONECT 657 656 +CONECT 658 656 +CONECT 659 661 660 656 +CONECT 660 659 +CONECT 661 659 +CONECT 662 664 651 663 +CONECT 663 662 +CONECT 664 665 666 662 +CONECT 665 664 +CONECT 666 681 664 667 668 +CONECT 667 666 +CONECT 668 666 669 670 674 +CONECT 669 668 +CONECT 670 673 668 671 672 +CONECT 671 670 +CONECT 672 670 +CONECT 673 670 +CONECT 674 668 675 676 677 +CONECT 675 674 +CONECT 676 674 +CONECT 677 674 678 680 679 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 682 683 666 +CONECT 682 681 +CONECT 683 685 681 684 +CONECT 684 683 +CONECT 685 686 687 695 683 +CONECT 686 685 +CONECT 687 689 693 685 688 +CONECT 688 687 +CONECT 689 690 691 692 687 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 +CONECT 693 694 687 +CONECT 694 693 +CONECT 695 697 685 696 +CONECT 696 695 +CONECT 697 698 699 695 +CONECT 698 697 +CONECT 699 719 701 697 700 +CONECT 700 699 +CONECT 701 703 704 699 702 +CONECT 702 701 +CONECT 703 701 +CONECT 704 705 707 701 706 +CONECT 705 704 +CONECT 706 704 +CONECT 707 709 710 704 708 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 707 711 +CONECT 711 710 +CONECT 712 713 716 710 +CONECT 713 715 714 712 +CONECT 714 713 +CONECT 715 713 +CONECT 716 718 712 717 +CONECT 717 716 +CONECT 718 716 +CONECT 719 720 721 699 +CONECT 720 719 +CONECT 721 723 719 722 +CONECT 722 721 +CONECT 723 724 731 725 721 +CONECT 724 723 +CONECT 725 728 723 726 727 +CONECT 726 725 +CONECT 727 725 +CONECT 728 730 729 725 +CONECT 729 728 +CONECT 730 728 +CONECT 731 733 723 732 +CONECT 732 731 +CONECT 733 734 735 731 +CONECT 734 733 +CONECT 735 737 733 743 736 +CONECT 736 735 +CONECT 737 739 738 740 735 +CONECT 738 737 +CONECT 739 737 +CONECT 740 741 737 742 +CONECT 741 740 +CONECT 742 740 +CONECT 743 745 735 744 +CONECT 744 743 +CONECT 745 746 747 743 +CONECT 746 745 +CONECT 747 749 748 745 753 +CONECT 748 747 +CONECT 749 752 751 750 747 +CONECT 750 749 +CONECT 751 749 +CONECT 752 749 +CONECT 753 747 754 755 +CONECT 754 753 +CONECT 755 753 756 757 +CONECT 756 755 +CONECT 757 755 758 759 767 +CONECT 758 757 +CONECT 759 757 761 765 760 +CONECT 760 759 +CONECT 761 762 764 763 759 +CONECT 762 761 +CONECT 763 761 +CONECT 764 761 +CONECT 765 766 759 +CONECT 766 765 +CONECT 767 757 769 768 +CONECT 768 767 +CONECT 769 770 771 767 +CONECT 770 769 +CONECT 771 772 769 773 789 +CONECT 772 771 +CONECT 773 776 771 775 774 +CONECT 774 773 +CONECT 775 773 +CONECT 776 779 777 778 773 +CONECT 777 776 +CONECT 778 776 +CONECT 779 782 781 780 776 +CONECT 780 779 +CONECT 781 779 +CONECT 782 785 784 783 779 +CONECT 783 782 +CONECT 784 782 +CONECT 785 787 788 786 782 +CONECT 786 785 +CONECT 787 785 +CONECT 788 785 +CONECT 789 771 791 790 +CONECT 790 789 +CONECT 791 792 789 793 +CONECT 792 791 +CONECT 793 791 803 795 794 +CONECT 794 793 +CONECT 795 796 793 801 797 +CONECT 796 795 +CONECT 797 795 800 799 798 +CONECT 798 797 +CONECT 799 797 +CONECT 800 797 +CONECT 801 802 795 +CONECT 802 801 +CONECT 803 804 793 805 +CONECT 804 803 +CONECT 805 803 807 806 +CONECT 806 805 +CONECT 807 808 805 809 823 +CONECT 808 807 +CONECT 809 812 807 811 810 +CONECT 810 809 +CONECT 811 809 +CONECT 812 821 813 809 +CONECT 813 815 812 814 +CONECT 814 813 +CONECT 815 817 816 813 +CONECT 816 815 +CONECT 817 818 819 815 +CONECT 818 817 +CONECT 819 820 817 821 +CONECT 820 819 +CONECT 821 819 822 812 +CONECT 822 821 +CONECT 823 807 825 824 +CONECT 824 823 +CONECT 825 826 823 827 +CONECT 826 825 +CONECT 827 829 825 837 828 +CONECT 828 827 +CONECT 829 835 831 830 827 +CONECT 830 829 +CONECT 831 832 833 829 834 +CONECT 832 831 +CONECT 833 831 +CONECT 834 831 +CONECT 835 836 829 +CONECT 836 835 +CONECT 837 838 827 839 +CONECT 838 837 +CONECT 839 837 841 840 +CONECT 840 839 +CONECT 841 851 842 839 843 +CONECT 842 841 +CONECT 843 841 845 844 849 +CONECT 844 843 +CONECT 845 846 848 843 847 +CONECT 846 845 +CONECT 847 845 +CONECT 848 845 +CONECT 849 843 850 +CONECT 850 849 +CONECT 851 853 852 841 +CONECT 852 851 +CONECT 853 855 854 851 +CONECT 854 853 +CONECT 855 857 856 853 870 +CONECT 856 855 +CONECT 857 860 858 859 855 +CONECT 858 857 +CONECT 859 857 +CONECT 860 862 861 866 857 +CONECT 861 860 +CONECT 862 864 865 863 860 +CONECT 863 862 +CONECT 864 862 +CONECT 865 862 +CONECT 866 860 868 869 867 +CONECT 867 866 +CONECT 868 866 +CONECT 869 866 +CONECT 870 855 872 871 +CONECT 871 870 +CONECT 872 873 870 874 +CONECT 873 872 +CONECT 874 872 876 885 875 +CONECT 875 874 +CONECT 876 878 877 874 879 +CONECT 877 876 +CONECT 878 876 +CONECT 879 880 876 881 882 +CONECT 880 879 +CONECT 881 879 +CONECT 882 879 884 883 +CONECT 883 882 +CONECT 884 882 +CONECT 885 887 874 886 +CONECT 886 885 +CONECT 887 885 +CONECT 888 87 310 889 279 +CONECT 889 888 891 +CONECT 890 893 891 894 892 +CONECT 891 889 890 +CONECT 892 890 +CONECT 893 890 +CONECT 894 890 +CONECT 895 896 +CONECT 896 895 897 +CONECT 897 896 +MASTER 0 0 0 0 0 0 0 0 897 0 897 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_28.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_28.pdb new file mode 100644 index 0000000..2ec2c07 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_28.pdb @@ -0,0 +1,1751 @@ +COMPND fitness: 0.2006 34.955833333333885 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 P1 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HX1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HX1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HX1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HX1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HX1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HX1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HX1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HX1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N ARG 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H ARG 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA ARG 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 CB ARG 8 32.132 -93.836 -4.510 1.00 0.00 C +ATOM 136 HB2 ARG 8 33.181 -94.067 -4.697 1.00 0.00 H +ATOM 137 HB3 ARG 8 31.847 -92.954 -5.085 1.00 0.00 H +ATOM 138 CG ARG 8 31.930 -93.562 -3.029 1.00 0.00 C +ATOM 139 HG2 ARG 8 30.876 -93.341 -2.857 1.00 0.00 H +ATOM 140 HG3 ARG 8 32.210 -94.454 -2.469 1.00 0.00 H +ATOM 141 CD ARG 8 32.776 -92.387 -2.565 1.00 0.00 C +ATOM 142 HD2 ARG 8 32.675 -92.283 -1.484 1.00 0.00 H +ATOM 143 HD3 ARG 8 33.819 -92.579 -2.815 1.00 0.00 H +ATOM 144 NE ARG 8 32.366 -91.135 -3.195 1.00 0.00 N +ATOM 145 HE ARG 8 31.550 -91.162 -3.789 1.00 0.00 H +ATOM 146 CZ ARG 8 32.999 -89.977 -3.037 1.00 0.00 C +ATOM 147 NH1 ARG 8 32.553 -88.890 -3.652 1.00 0.00 N +ATOM 148 HH11 ARG 8 31.733 -88.946 -4.239 1.00 0.00 H +ATOM 149 HH12 ARG 8 33.036 -88.010 -3.530 1.00 0.00 H +ATOM 150 NH2 ARG 8 34.076 -89.910 -2.268 1.00 0.00 N +ATOM 151 HH21 ARG 8 34.414 -90.741 -1.803 1.00 0.00 H +ATOM 152 HH22 ARG 8 34.555 -89.028 -2.150 1.00 0.00 H +ATOM 153 HA ARG 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 154 C ARG 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 155 O ARG 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 156 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 157 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 158 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 161 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 162 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 163 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 164 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 165 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 166 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 167 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 168 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 169 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 170 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 171 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 172 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 173 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 174 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 175 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 176 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 177 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 178 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 179 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 180 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 181 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 182 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 183 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 184 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 185 N ILE 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 186 H ILE 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 187 CA ILE 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 188 CB ILE 11 32.215-101.571 0.717 1.00 0.00 C +ATOM 189 HB ILE 11 31.857-101.753 1.731 1.00 0.00 H +ATOM 190 CG2 ILE 11 33.468-102.396 0.465 1.00 0.00 C +ATOM 191 HG21 ILE 11 33.825-102.214 -0.549 1.00 0.00 H +ATOM 192 HG22 ILE 11 34.241-102.112 1.179 1.00 0.00 H +ATOM 193 HG23 ILE 11 33.237-103.454 0.583 1.00 0.00 H +ATOM 194 CG1 ILE 11 32.565-100.092 0.545 1.00 0.00 C +ATOM 195 HG12 ILE 11 33.127 -99.998 -0.384 1.00 0.00 H +ATOM 196 HG13 ILE 11 31.625 -99.544 0.459 1.00 0.00 H +ATOM 197 CD1 ILE 11 33.379 -99.520 1.684 1.00 0.00 C +ATOM 198 HD11 ILE 11 34.318-100.066 1.771 1.00 0.00 H +ATOM 199 HD12 ILE 11 33.587 -98.468 1.491 1.00 0.00 H +ATOM 200 HD13 ILE 11 32.818 -99.613 2.615 1.00 0.00 H +ATOM 201 HA ILE 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 202 C ILE 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 203 O ILE 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 204 N ASN 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 205 H ASN 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 206 CA ASN 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 207 CB ASN 12 28.130 -98.237 -0.161 1.00 0.00 C +ATOM 208 HB2 ASN 12 28.768 -97.830 -0.944 1.00 0.00 H +ATOM 209 HB3 ASN 12 27.146 -97.771 -0.217 1.00 0.00 H +ATOM 210 CG ASN 12 28.745 -97.908 1.184 1.00 0.00 C +ATOM 211 OD1 ASN 12 28.878 -98.777 2.046 1.00 0.00 O +ATOM 212 ND2 ASN 12 29.125 -96.650 1.369 1.00 0.00 N +ATOM 213 HD21 ASN 12 29.540 -96.375 2.247 1.00 0.00 H +ATOM 214 HD22 ASN 12 28.996 -95.973 0.630 1.00 0.00 H +ATOM 215 HA ASN 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 216 C ASN 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 217 O ASN 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 218 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 219 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 220 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 221 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 222 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 223 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 224 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 225 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 226 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 227 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 228 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 229 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 230 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 231 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 232 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 233 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 234 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 235 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 236 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 237 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 238 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 239 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 240 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 241 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 242 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 243 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 244 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 245 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 246 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 247 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 248 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 249 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 250 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 251 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 252 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 253 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 254 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 255 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 256 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 257 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 258 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 259 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 260 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 261 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 262 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 263 N HY1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 264 CA HY1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 265 C HY1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 266 O HY1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 267 CB HY1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 268 CG HY1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 269 CD2 HY1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 270 ND1 HY1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 271 CE1 HY1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 272 NE2 HY1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 273 H HY1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 274 HA HY1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 275 HB2 HY1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 276 HB3 HY1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 277 HD1 HY1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 278 HD2 HY1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 279 HE1 HY1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 280 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 281 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 282 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 283 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 284 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 285 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 286 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 287 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 288 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 289 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 290 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 291 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 292 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 293 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 294 N HY2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 295 CA HY2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 296 C HY2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 297 O HY2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 298 CB HY2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 299 CG HY2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 300 CD2 HY2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 301 ND1 HY2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 302 CE1 HY2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 303 NE2 HY2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 304 H HY2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 305 HA HY2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 306 HB2 HY2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 307 HB3 HY2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 308 HD1 HY2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 309 HD2 HY2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 310 HE1 HY2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 311 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 312 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 313 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 314 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 315 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 316 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 317 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 318 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 319 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 320 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 321 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 322 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 323 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 324 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 325 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 326 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 327 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 328 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 329 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 330 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 331 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 332 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 333 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 334 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 335 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 336 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 337 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 338 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 339 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 340 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 341 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 342 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 343 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 344 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 345 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 346 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 347 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 348 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 349 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 350 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 351 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 352 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 353 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 354 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 355 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 356 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 357 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 358 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 359 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 360 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 361 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 362 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 363 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 364 N TRP 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 365 H TRP 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 366 CA TRP 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 367 CB TRP 23 21.411 -85.256 -16.822 1.00 0.00 C +ATOM 368 HB2 TRP 23 22.132 -85.913 -16.338 1.00 0.00 H +ATOM 369 HB3 TRP 23 20.438 -85.734 -16.718 1.00 0.00 H +ATOM 370 CG TRP 23 21.738 -85.227 -18.283 1.00 0.00 C +ATOM 371 CD1 TRP 23 20.859 -85.092 -19.318 1.00 0.00 C +ATOM 372 HD1 TRP 23 19.783 -84.997 -19.203 1.00 0.00 H +ATOM 373 NE1 TRP 23 21.530 -85.108 -20.517 1.00 0.00 N +ATOM 374 HE1 TRP 23 21.113 -85.024 -21.438 1.00 0.00 H +ATOM 375 CE2 TRP 23 22.874 -85.257 -20.268 1.00 0.00 C +ATOM 376 CZ2 TRP 23 23.948 -85.327 -21.155 1.00 0.00 C +ATOM 377 HZ2 TRP 23 23.812 -85.267 -22.225 1.00 0.00 H +ATOM 378 CH2 TRP 23 25.200 -85.477 -20.620 1.00 0.00 C +ATOM 379 HH2 TRP 23 26.050 -85.530 -21.290 1.00 0.00 H +ATOM 380 CZ3 TRP 23 25.394 -85.558 -19.231 1.00 0.00 C +ATOM 381 HZ3 TRP 23 26.400 -85.679 -18.854 1.00 0.00 H +ATOM 382 CE3 TRP 23 24.329 -85.487 -18.351 1.00 0.00 C +ATOM 383 HE3 TRP 23 24.462 -85.551 -17.282 1.00 0.00 H +ATOM 384 CD2 TRP 23 23.042 -85.333 -18.871 1.00 0.00 C +ATOM 385 HA TRP 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 386 C TRP 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 387 O TRP 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 388 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 389 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 390 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 391 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 392 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 393 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 394 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 395 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 396 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 397 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 398 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 399 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 400 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 401 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 402 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 403 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 404 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 405 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 406 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 407 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 408 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 409 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 410 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 411 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 412 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 413 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 414 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 415 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 416 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 417 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 418 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 419 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 420 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 421 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 422 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 423 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 424 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 425 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 426 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 427 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 428 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 429 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 430 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 431 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 432 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 433 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 434 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 435 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 436 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 437 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 438 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 439 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 440 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 441 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 442 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 443 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 444 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 445 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 446 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 447 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 448 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 449 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 450 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 451 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 452 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 453 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 454 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 455 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 456 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 457 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 458 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 459 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 460 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 461 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 462 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 463 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 464 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 465 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 466 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 467 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 468 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 469 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 470 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 471 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 472 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 473 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 474 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 475 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 476 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 477 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 478 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 479 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 480 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 481 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 482 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 483 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 484 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 485 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 486 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 487 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 488 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 489 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 490 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 491 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 492 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 493 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 494 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 495 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 496 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 497 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 498 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 499 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 500 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 501 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 502 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 503 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 504 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 505 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 506 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 507 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 508 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 509 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 510 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 511 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 512 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 513 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 514 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 515 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 516 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 517 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 518 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 519 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 520 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 521 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 522 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 523 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 524 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 525 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 526 N MET 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 527 H MET 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 528 CA MET 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 529 CB MET 33 27.315 -82.525 -3.272 1.00 0.00 C +ATOM 530 HB2 MET 33 26.398 -81.940 -3.214 1.00 0.00 H +ATOM 531 HB3 MET 33 27.389 -82.989 -4.255 1.00 0.00 H +ATOM 532 CG MET 33 27.295 -83.605 -2.204 1.00 0.00 C +ATOM 533 HG2 MET 33 26.492 -84.303 -2.443 1.00 0.00 H +ATOM 534 HG3 MET 33 28.252 -84.128 -2.232 1.00 0.00 H +ATOM 535 SD MET 33 27.030 -82.943 -0.547 1.00 0.00 S +ATOM 536 CE MET 33 27.063 -84.446 0.427 1.00 0.00 C +ATOM 537 HE1 MET 33 28.027 -84.938 0.303 1.00 0.00 H +ATOM 538 HE2 MET 33 26.912 -84.201 1.479 1.00 0.00 H +ATOM 539 HE3 MET 33 26.268 -85.113 0.092 1.00 0.00 H +ATOM 540 HA MET 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 541 C MET 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 542 O MET 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 543 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 544 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 545 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 546 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 547 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 548 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 549 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 550 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 551 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 552 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 553 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 554 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 555 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 556 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 557 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 558 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 559 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 560 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 561 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 562 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 563 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 564 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 565 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 566 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 567 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 568 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 569 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 570 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 571 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 572 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 573 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 574 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 575 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 576 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 577 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 578 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 579 N LEU 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 580 H LEU 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 581 CA LEU 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 582 CB LEU 37 33.048 -83.879 0.496 1.00 0.00 C +ATOM 583 HB2 LEU 37 31.985 -83.889 0.734 1.00 0.00 H +ATOM 584 HB3 LEU 37 33.178 -83.869 -0.586 1.00 0.00 H +ATOM 585 CG LEU 37 33.713 -85.128 1.077 1.00 0.00 C +ATOM 586 HG LEU 37 34.787 -85.068 0.903 1.00 0.00 H +ATOM 587 CD1 LEU 37 33.448 -85.233 2.571 1.00 0.00 C +ATOM 588 HD11 LEU 37 32.374 -85.292 2.747 1.00 0.00 H +ATOM 589 HD12 LEU 37 33.929 -86.128 2.965 1.00 0.00 H +ATOM 590 HD13 LEU 37 33.849 -84.353 3.075 1.00 0.00 H +ATOM 591 CD2 LEU 37 33.176 -86.384 0.410 1.00 0.00 C +ATOM 592 HD21 LEU 37 33.380 -86.342 -0.661 1.00 0.00 H +ATOM 593 HD22 LEU 37 33.662 -87.260 0.838 1.00 0.00 H +ATOM 594 HD23 LEU 37 32.100 -86.450 0.572 1.00 0.00 H +ATOM 595 HA LEU 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 596 C LEU 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 597 O LEU 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 598 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 599 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 600 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 601 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 602 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 603 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 604 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 605 N ALA 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 606 H ALA 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 607 CA ALA 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 608 CB ALA 39 38.874 -82.519 -4.462 1.00 0.00 C +ATOM 609 HB1 ALA 39 39.474 -81.803 -3.899 1.00 0.00 H +ATOM 610 HB2 ALA 39 38.973 -83.508 -4.013 1.00 0.00 H +ATOM 611 HB3 ALA 39 39.223 -82.552 -5.494 1.00 0.00 H +ATOM 612 HA ALA 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 613 C ALA 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 614 O ALA 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 615 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 616 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 617 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 618 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 619 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 620 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 621 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 622 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 623 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 624 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 625 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 626 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 627 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 628 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 629 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 630 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 631 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 632 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 633 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 634 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 635 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 636 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 637 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 638 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 639 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 640 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 641 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 642 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 643 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 644 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 645 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 646 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 647 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 648 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 649 N ASP 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 650 H ASP 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 651 CA ASP 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 652 CB ASP 43 29.884 -89.033 -12.452 1.00 0.00 C +ATOM 653 HB2 ASP 43 29.493 -88.069 -12.779 1.00 0.00 H +ATOM 654 HB3 ASP 43 29.081 -89.770 -12.451 1.00 0.00 H +ATOM 655 CG ASP 43 30.447 -88.899 -11.051 1.00 0.00 C +ATOM 656 OD1 ASP 43 31.651 -88.590 -10.921 1.00 0.00 O +ATOM 657 OD2 ASP 43 29.685 -89.101 -10.082 1.00 0.00 O +ATOM 658 HA ASP 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 659 C ASP 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 660 O ASP 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 661 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 662 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 663 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 664 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 665 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 666 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 667 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 668 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 669 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 670 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 671 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 672 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 673 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 674 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 675 N LYN 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 676 H LYN 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 677 CA LYN 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 678 CB LYN 45 25.266 -89.253 -17.470 1.00 0.00 C +ATOM 679 HB2 LYN 45 25.726 -88.747 -16.621 1.00 0.00 H +ATOM 680 HB3 LYN 45 25.701 -88.876 -18.396 1.00 0.00 H +ATOM 681 CG LYN 45 23.770 -88.987 -17.468 1.00 0.00 C +ATOM 682 HG2 LYN 45 23.323 -89.505 -18.317 1.00 0.00 H +ATOM 683 HG3 LYN 45 23.349 -89.376 -16.541 1.00 0.00 H +ATOM 684 CD LYN 45 23.474 -87.499 -17.571 1.00 0.00 C +ATOM 685 HD2 LYN 45 22.407 -87.345 -17.414 1.00 0.00 H +ATOM 686 HD3 LYN 45 24.035 -86.979 -16.795 1.00 0.00 H +ATOM 687 CE LYN 45 23.868 -86.952 -18.934 1.00 0.00 C +ATOM 688 HE2 LYN 45 24.935 -87.127 -19.077 1.00 0.00 H +ATOM 689 HE3 LYN 45 23.307 -87.493 -19.695 1.00 0.00 H +ATOM 690 NZ LYN 45 23.585 -85.495 -19.050 1.00 0.00 N +ATOM 691 HZ2 LYN 45 23.859 -85.171 -19.966 1.00 0.00 H +ATOM 692 HZ3 LYN 45 22.597 -85.332 -18.918 1.00 0.00 H +ATOM 693 HA LYN 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 694 C LYN 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 695 O LYN 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 696 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 697 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 698 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 699 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 700 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 701 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 702 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 703 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 704 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 705 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 706 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 707 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 708 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 709 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 710 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 711 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 712 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 713 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 714 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 715 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 716 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 717 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 718 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 719 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 720 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 721 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 722 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 723 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 724 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 725 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 726 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 727 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 728 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 729 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 730 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 731 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 732 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 733 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 734 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 735 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 736 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 737 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 738 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 739 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 740 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 741 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 742 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 743 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 744 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 745 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 746 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 747 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 748 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 749 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 750 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 751 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 752 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 753 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 754 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 755 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 756 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 757 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 758 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 759 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 760 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 761 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 762 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 763 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 764 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 765 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 766 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 767 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 768 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 769 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 770 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 771 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 772 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 773 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 774 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 775 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 776 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 777 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 778 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 779 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 780 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 781 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 782 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 783 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 784 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 785 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 786 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 787 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 788 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 789 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 790 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 791 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 792 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 793 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 794 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 795 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 796 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 797 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 798 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 799 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 800 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 801 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 802 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 803 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 804 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 805 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 806 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 807 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 808 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 809 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 810 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 811 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 812 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 813 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 814 N LYN 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 815 H LYN 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 816 CA LYN 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 817 CB LYN 54 32.301 -94.491 -10.199 1.00 0.00 C +ATOM 818 HB2 LYN 54 33.358 -94.431 -10.462 1.00 0.00 H +ATOM 819 HB3 LYN 54 32.026 -93.623 -9.600 1.00 0.00 H +ATOM 820 CG LYN 54 32.050 -95.758 -9.398 1.00 0.00 C +ATOM 821 HG2 LYN 54 30.989 -95.808 -9.152 1.00 0.00 H +ATOM 822 HG3 LYN 54 32.321 -96.617 -10.013 1.00 0.00 H +ATOM 823 CD LYN 54 32.869 -95.774 -8.118 1.00 0.00 C +ATOM 824 HD2 LYN 54 33.925 -95.713 -8.380 1.00 0.00 H +ATOM 825 HD3 LYN 54 32.594 -94.906 -7.518 1.00 0.00 H +ATOM 826 CE LYN 54 32.619 -97.041 -7.318 1.00 0.00 C +ATOM 827 HE2 LYN 54 31.557 -97.090 -7.077 1.00 0.00 H +ATOM 828 HE3 LYN 54 32.889 -97.897 -7.938 1.00 0.00 H +ATOM 829 NZ LYN 54 33.415 -97.070 -6.059 1.00 0.00 N +ATOM 830 HZ2 LYN 54 33.221 -97.925 -5.558 1.00 0.00 H +ATOM 831 HZ3 LYN 54 34.399 -97.026 -6.282 1.00 0.00 H +ATOM 832 HA LYN 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 833 C LYN 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 834 O LYN 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 835 N ASH 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 836 H ASH 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 837 CA ASH 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 838 CB ASH 55 34.660 -96.376 -14.407 1.00 0.00 C +ATOM 839 HB2 ASH 55 34.971 -97.132 -15.128 1.00 0.00 H +ATOM 840 HB3 ASH 55 34.155 -95.564 -14.929 1.00 0.00 H +ATOM 841 CG ASH 55 35.878 -95.832 -13.687 1.00 0.00 C +ATOM 842 OD1 ASH 55 35.823 -95.694 -12.446 1.00 0.00 O +ATOM 843 OD2 ASH 55 36.888 -95.544 -14.362 1.00 0.00 O +ATOM 844 HD2 ASH 55 37.578 -95.214 -13.781 1.00 0.00 H +ATOM 845 HA ASH 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 846 C ASH 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 847 O ASH 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 848 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 849 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 850 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 851 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 852 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 853 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 854 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 855 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 856 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 857 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 858 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 859 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 860 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 861 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 862 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 863 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 864 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 Zn +ATOM 865 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 866 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 867 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 868 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 869 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 870 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +ATOM 871 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 872 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 873 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 17 15 13 16 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 65 60 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 68 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 65 69 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 864 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 104 106 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 111 112 113 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 153 132 154 135 +CONECT 135 136 137 138 134 +CONECT 136 135 +CONECT 137 135 +CONECT 138 135 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 142 143 144 +CONECT 142 141 +CONECT 143 141 +CONECT 144 141 145 146 +CONECT 145 144 +CONECT 146 144 147 150 +CONECT 147 146 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 146 151 152 +CONECT 151 150 +CONECT 152 150 +CONECT 153 134 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 165 169 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 170 175 +CONECT 174 173 +CONECT 175 173 +CONECT 176 178 179 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 182 181 176 180 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 201 202 188 +CONECT 188 189 190 194 187 +CONECT 189 188 +CONECT 190 188 191 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 +CONECT 194 188 195 196 197 +CONECT 195 194 +CONECT 196 194 +CONECT 197 194 198 199 200 +CONECT 198 197 +CONECT 199 197 +CONECT 200 197 +CONECT 201 187 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 216 204 215 207 +CONECT 207 208 209 210 206 +CONECT 208 207 +CONECT 209 207 +CONECT 210 207 211 212 +CONECT 211 210 +CONECT 212 210 213 214 +CONECT 213 212 +CONECT 214 212 +CONECT 215 206 +CONECT 216 217 218 206 +CONECT 217 216 +CONECT 218 220 216 219 +CONECT 219 218 +CONECT 220 221 222 238 218 +CONECT 221 220 +CONECT 222 225 220 223 224 +CONECT 223 222 +CONECT 224 222 +CONECT 225 227 226 228 222 +CONECT 226 225 +CONECT 227 225 +CONECT 228 229 225 231 230 +CONECT 229 228 +CONECT 230 228 +CONECT 231 233 228 234 232 +CONECT 232 231 +CONECT 233 231 +CONECT 234 237 231 235 236 +CONECT 235 234 +CONECT 236 234 +CONECT 237 234 +CONECT 238 239 220 240 +CONECT 239 238 +CONECT 240 238 242 241 +CONECT 241 240 +CONECT 242 245 240 243 244 +CONECT 243 242 +CONECT 244 242 +CONECT 245 246 247 242 +CONECT 246 245 +CONECT 247 249 245 248 +CONECT 248 247 +CONECT 249 251 250 261 247 +CONECT 250 249 +CONECT 251 257 252 253 249 +CONECT 252 251 +CONECT 253 251 256 255 254 +CONECT 254 253 +CONECT 255 253 +CONECT 256 253 +CONECT 257 259 260 258 251 +CONECT 258 257 +CONECT 259 257 +CONECT 260 257 +CONECT 261 263 249 262 +CONECT 262 261 +CONECT 263 273 264 261 +CONECT 264 265 263 274 267 +CONECT 265 266 280 264 +CONECT 266 265 +CONECT 267 264 268 275 276 +CONECT 268 269 270 267 +CONECT 269 272 278 268 +CONECT 270 271 268 277 +CONECT 271 272 279 270 +CONECT 272 864 271 269 +CONECT 273 263 +CONECT 274 264 +CONECT 275 267 +CONECT 276 267 +CONECT 277 270 +CONECT 278 269 +CONECT 279 271 +CONECT 280 282 265 281 +CONECT 281 280 +CONECT 282 283 284 292 280 +CONECT 283 282 +CONECT 284 285 286 282 290 +CONECT 285 284 +CONECT 286 287 288 284 289 +CONECT 287 286 +CONECT 288 286 +CONECT 289 286 +CONECT 290 284 291 +CONECT 291 290 +CONECT 292 294 282 293 +CONECT 293 292 +CONECT 294 304 295 292 +CONECT 295 296 298 294 305 +CONECT 296 297 311 295 +CONECT 297 296 +CONECT 298 306 307 295 299 +CONECT 299 298 300 301 +CONECT 300 309 299 303 +CONECT 301 299 308 302 +CONECT 302 303 301 310 +CONECT 303 300 302 864 +CONECT 304 294 +CONECT 305 295 +CONECT 306 298 +CONECT 307 298 +CONECT 308 301 +CONECT 309 300 +CONECT 310 302 +CONECT 311 313 296 312 +CONECT 312 311 +CONECT 313 324 314 311 315 +CONECT 314 313 +CONECT 315 313 318 317 316 +CONECT 316 315 +CONECT 317 315 +CONECT 318 320 321 315 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 322 318 323 +CONECT 322 321 +CONECT 323 321 +CONECT 324 326 325 313 +CONECT 325 324 +CONECT 326 328 327 324 +CONECT 327 326 +CONECT 328 334 330 329 326 +CONECT 329 328 +CONECT 330 333 332 328 331 +CONECT 331 330 +CONECT 332 330 +CONECT 333 330 +CONECT 334 336 335 328 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 350 340 339 336 +CONECT 339 338 +CONECT 340 341 346 338 342 +CONECT 341 340 +CONECT 342 340 343 345 344 +CONECT 343 342 +CONECT 344 342 +CONECT 345 342 +CONECT 346 349 348 340 347 +CONECT 347 346 +CONECT 348 346 +CONECT 349 346 +CONECT 350 351 352 338 +CONECT 351 350 +CONECT 352 354 350 353 +CONECT 353 352 +CONECT 354 356 355 362 352 +CONECT 355 354 +CONECT 356 359 357 358 354 +CONECT 357 356 +CONECT 358 356 +CONECT 359 360 361 356 +CONECT 360 359 +CONECT 361 359 +CONECT 362 354 364 363 +CONECT 363 362 +CONECT 364 365 362 366 +CONECT 365 364 +CONECT 366 364 386 385 367 +CONECT 367 368 369 370 366 +CONECT 368 367 +CONECT 369 367 +CONECT 370 367 371 384 +CONECT 371 370 372 373 +CONECT 372 371 +CONECT 373 371 374 375 +CONECT 374 373 +CONECT 375 373 376 384 +CONECT 376 375 377 378 +CONECT 377 376 +CONECT 378 376 379 380 +CONECT 379 378 +CONECT 380 378 381 382 +CONECT 381 380 +CONECT 382 380 383 384 +CONECT 383 382 +CONECT 384 370 375 382 +CONECT 385 366 +CONECT 386 388 366 387 +CONECT 387 386 +CONECT 388 389 390 386 +CONECT 389 388 +CONECT 390 392 388 391 396 +CONECT 391 390 +CONECT 392 394 393 395 390 +CONECT 393 392 +CONECT 394 392 +CONECT 395 392 +CONECT 396 390 397 398 +CONECT 397 396 +CONECT 398 396 399 400 +CONECT 399 398 +CONECT 400 398 402 401 411 +CONECT 401 400 +CONECT 402 405 400 403 404 +CONECT 403 402 +CONECT 404 402 +CONECT 405 406 408 407 402 +CONECT 406 405 +CONECT 407 405 +CONECT 408 410 405 409 +CONECT 409 408 +CONECT 410 408 +CONECT 411 400 413 412 +CONECT 412 411 +CONECT 413 414 411 415 +CONECT 414 413 +CONECT 415 413 417 421 416 +CONECT 416 415 +CONECT 417 418 419 415 420 +CONECT 418 417 +CONECT 419 417 +CONECT 420 417 +CONECT 421 423 415 422 +CONECT 422 421 +CONECT 423 424 425 421 +CONECT 424 423 +CONECT 425 427 423 426 436 +CONECT 426 425 +CONECT 427 428 429 430 425 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 427 432 431 +CONECT 431 430 +CONECT 432 430 +CONECT 433 434 435 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 425 438 437 +CONECT 437 436 +CONECT 438 439 436 440 +CONECT 439 438 +CONECT 440 438 442 441 458 +CONECT 441 440 +CONECT 442 445 443 444 440 +CONECT 443 442 +CONECT 444 442 +CONECT 445 448 447 446 442 +CONECT 446 445 +CONECT 447 445 +CONECT 448 451 449 445 450 +CONECT 449 448 +CONECT 450 448 +CONECT 451 454 453 452 448 +CONECT 452 451 +CONECT 453 451 +CONECT 454 457 456 455 451 +CONECT 455 454 +CONECT 456 454 +CONECT 457 454 +CONECT 458 440 460 459 +CONECT 459 458 +CONECT 460 461 458 462 +CONECT 461 460 +CONECT 462 460 464 463 478 +CONECT 463 462 +CONECT 464 467 465 462 466 +CONECT 465 464 +CONECT 466 464 +CONECT 467 468 476 464 +CONECT 468 470 469 467 +CONECT 469 468 +CONECT 470 471 472 468 +CONECT 471 470 +CONECT 472 473 470 474 +CONECT 473 472 +CONECT 474 472 475 476 +CONECT 475 474 +CONECT 476 474 467 477 +CONECT 477 476 +CONECT 478 462 480 479 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 484 480 492 483 +CONECT 483 482 +CONECT 484 485 490 486 482 +CONECT 485 484 +CONECT 486 487 484 488 489 +CONECT 487 486 +CONECT 488 486 +CONECT 489 486 +CONECT 490 491 484 +CONECT 491 490 +CONECT 492 494 482 493 +CONECT 493 492 +CONECT 494 495 496 492 +CONECT 495 494 +CONECT 496 498 494 497 514 +CONECT 497 496 +CONECT 498 501 499 500 496 +CONECT 499 498 +CONECT 500 498 +CONECT 501 504 503 502 498 +CONECT 502 501 +CONECT 503 501 +CONECT 504 507 505 506 501 +CONECT 505 504 +CONECT 506 504 +CONECT 507 509 510 508 504 +CONECT 508 507 +CONECT 509 507 +CONECT 510 512 507 511 513 +CONECT 511 510 +CONECT 512 510 +CONECT 513 510 +CONECT 514 496 516 515 +CONECT 515 514 +CONECT 516 517 514 518 +CONECT 517 516 +CONECT 518 516 520 519 524 +CONECT 519 518 +CONECT 520 522 523 518 521 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 518 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 541 540 529 +CONECT 529 530 531 532 528 +CONECT 530 529 +CONECT 531 529 +CONECT 532 529 533 534 535 +CONECT 533 532 +CONECT 534 532 +CONECT 535 532 536 +CONECT 536 535 537 538 539 +CONECT 537 536 +CONECT 538 536 +CONECT 539 536 +CONECT 540 528 +CONECT 541 543 528 542 +CONECT 542 541 +CONECT 543 544 545 541 +CONECT 544 543 +CONECT 545 547 543 551 546 +CONECT 546 545 +CONECT 547 548 549 550 545 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 553 545 552 +CONECT 552 551 +CONECT 553 554 555 551 +CONECT 554 553 +CONECT 555 557 553 556 565 +CONECT 556 555 +CONECT 557 560 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 562 561 557 +CONECT 561 560 +CONECT 562 564 563 560 +CONECT 563 562 +CONECT 564 562 +CONECT 565 555 567 566 +CONECT 566 565 +CONECT 567 568 565 569 +CONECT 568 567 +CONECT 569 567 570 571 577 +CONECT 570 569 +CONECT 571 572 569 574 573 +CONECT 572 571 +CONECT 573 571 +CONECT 574 575 576 571 +CONECT 575 574 +CONECT 576 574 +CONECT 577 569 579 578 +CONECT 578 577 +CONECT 579 580 577 581 +CONECT 580 579 +CONECT 581 579 596 595 582 +CONECT 582 583 584 585 581 +CONECT 583 582 +CONECT 584 582 +CONECT 585 582 586 587 591 +CONECT 586 585 +CONECT 587 585 588 589 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 585 592 593 594 +CONECT 592 591 +CONECT 593 591 +CONECT 594 591 +CONECT 595 581 +CONECT 596 598 581 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 602 598 601 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 613 612 605 608 +CONECT 608 609 610 611 607 +CONECT 609 608 +CONECT 610 608 +CONECT 611 608 +CONECT 612 607 +CONECT 613 615 614 607 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 619 625 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 641 639 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 644 638 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 659 649 658 652 +CONECT 652 653 654 655 651 +CONECT 653 652 +CONECT 654 652 +CONECT 655 652 656 657 +CONECT 656 655 +CONECT 657 655 +CONECT 658 651 +CONECT 659 660 661 651 +CONECT 660 659 +CONECT 661 663 659 662 +CONECT 662 661 +CONECT 663 664 665 673 661 +CONECT 664 663 +CONECT 665 667 671 663 666 +CONECT 666 665 +CONECT 667 670 669 668 665 +CONECT 668 667 +CONECT 669 667 +CONECT 670 667 +CONECT 671 665 672 +CONECT 672 671 +CONECT 673 675 663 674 +CONECT 674 673 +CONECT 675 676 677 673 +CONECT 676 675 +CONECT 677 694 675 693 678 +CONECT 678 679 680 681 677 +CONECT 679 678 +CONECT 680 678 +CONECT 681 678 682 683 684 +CONECT 682 681 +CONECT 683 681 +CONECT 684 681 685 686 687 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 688 689 690 +CONECT 688 687 +CONECT 689 687 +CONECT 690 687 691 692 +CONECT 691 690 +CONECT 692 690 +CONECT 693 677 +CONECT 694 695 696 677 +CONECT 695 694 +CONECT 696 698 694 697 +CONECT 697 696 +CONECT 698 699 706 700 696 +CONECT 699 698 +CONECT 700 703 698 701 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 705 704 700 +CONECT 704 703 +CONECT 705 703 +CONECT 706 708 698 707 +CONECT 707 706 +CONECT 708 709 710 706 +CONECT 709 708 +CONECT 710 712 708 718 711 +CONECT 711 710 +CONECT 712 714 715 713 710 +CONECT 713 712 +CONECT 714 712 +CONECT 715 716 712 717 +CONECT 716 715 +CONECT 717 715 +CONECT 718 720 710 719 +CONECT 719 718 +CONECT 720 721 722 718 +CONECT 721 720 +CONECT 722 724 723 720 728 +CONECT 723 722 +CONECT 724 727 725 726 722 +CONECT 725 724 +CONECT 726 724 +CONECT 727 724 +CONECT 728 722 729 730 +CONECT 729 728 +CONECT 730 728 731 732 +CONECT 731 730 +CONECT 732 730 733 734 742 +CONECT 733 732 +CONECT 734 736 732 740 735 +CONECT 735 734 +CONECT 736 738 739 737 734 +CONECT 737 736 +CONECT 738 736 +CONECT 739 736 +CONECT 740 741 734 +CONECT 741 740 +CONECT 742 732 744 743 +CONECT 743 742 +CONECT 744 745 746 742 +CONECT 745 744 +CONECT 746 747 744 748 764 +CONECT 747 746 +CONECT 748 751 746 750 749 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 752 753 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 760 759 758 754 +CONECT 758 757 +CONECT 759 757 +CONECT 760 762 761 763 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 760 +CONECT 764 746 766 765 +CONECT 765 764 +CONECT 766 767 764 768 +CONECT 767 766 +CONECT 768 766 778 770 769 +CONECT 769 768 +CONECT 770 771 768 776 772 +CONECT 771 770 +CONECT 772 770 773 774 775 +CONECT 773 772 +CONECT 774 772 +CONECT 775 772 +CONECT 776 777 770 +CONECT 777 776 +CONECT 778 779 768 780 +CONECT 779 778 +CONECT 780 778 782 781 +CONECT 781 780 +CONECT 782 783 780 784 798 +CONECT 783 782 +CONECT 784 787 782 786 785 +CONECT 785 784 +CONECT 786 784 +CONECT 787 796 788 784 +CONECT 788 790 787 789 +CONECT 789 788 +CONECT 790 792 791 788 +CONECT 791 790 +CONECT 792 793 794 790 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 794 797 787 +CONECT 797 796 +CONECT 798 782 800 799 +CONECT 799 798 +CONECT 800 801 798 802 +CONECT 801 800 +CONECT 802 800 804 812 803 +CONECT 803 802 +CONECT 804 810 806 805 802 +CONECT 805 804 +CONECT 806 807 809 804 808 +CONECT 807 806 +CONECT 808 806 +CONECT 809 806 +CONECT 810 811 804 +CONECT 811 810 +CONECT 812 813 802 814 +CONECT 813 812 +CONECT 814 812 816 815 +CONECT 815 814 +CONECT 816 833 832 814 817 +CONECT 817 818 819 820 816 +CONECT 818 817 +CONECT 819 817 +CONECT 820 817 821 822 823 +CONECT 821 820 +CONECT 822 820 +CONECT 823 820 824 825 826 +CONECT 824 823 +CONECT 825 823 +CONECT 826 823 827 828 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 830 831 +CONECT 830 829 +CONECT 831 829 +CONECT 832 816 +CONECT 833 835 834 816 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 845 835 846 838 +CONECT 838 839 840 841 837 +CONECT 839 838 +CONECT 840 838 +CONECT 841 838 842 843 +CONECT 842 841 +CONECT 843 841 844 +CONECT 844 843 +CONECT 845 837 +CONECT 846 837 848 847 +CONECT 847 846 +CONECT 848 849 846 850 +CONECT 849 848 +CONECT 850 852 848 861 851 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 856 852 857 858 +CONECT 856 855 +CONECT 857 855 +CONECT 858 855 859 860 +CONECT 859 858 +CONECT 860 858 +CONECT 861 863 850 862 +CONECT 862 861 +CONECT 863 861 +CONECT 864 87 303 865 272 +CONECT 865 864 867 +CONECT 866 869 867 870 868 +CONECT 867 865 866 +CONECT 868 866 +CONECT 869 866 +CONECT 870 866 +CONECT 871 872 +CONECT 872 871 873 +CONECT 873 872 +MASTER 0 0 0 0 0 0 0 0 873 0 873 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_29.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_29.pdb new file mode 100644 index 0000000..2ec2c07 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_29.pdb @@ -0,0 +1,1751 @@ +COMPND fitness: 0.2006 34.955833333333885 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 P1 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HX1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HX1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HX1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HX1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HX1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HX1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HX1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HX1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N ARG 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H ARG 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA ARG 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 CB ARG 8 32.132 -93.836 -4.510 1.00 0.00 C +ATOM 136 HB2 ARG 8 33.181 -94.067 -4.697 1.00 0.00 H +ATOM 137 HB3 ARG 8 31.847 -92.954 -5.085 1.00 0.00 H +ATOM 138 CG ARG 8 31.930 -93.562 -3.029 1.00 0.00 C +ATOM 139 HG2 ARG 8 30.876 -93.341 -2.857 1.00 0.00 H +ATOM 140 HG3 ARG 8 32.210 -94.454 -2.469 1.00 0.00 H +ATOM 141 CD ARG 8 32.776 -92.387 -2.565 1.00 0.00 C +ATOM 142 HD2 ARG 8 32.675 -92.283 -1.484 1.00 0.00 H +ATOM 143 HD3 ARG 8 33.819 -92.579 -2.815 1.00 0.00 H +ATOM 144 NE ARG 8 32.366 -91.135 -3.195 1.00 0.00 N +ATOM 145 HE ARG 8 31.550 -91.162 -3.789 1.00 0.00 H +ATOM 146 CZ ARG 8 32.999 -89.977 -3.037 1.00 0.00 C +ATOM 147 NH1 ARG 8 32.553 -88.890 -3.652 1.00 0.00 N +ATOM 148 HH11 ARG 8 31.733 -88.946 -4.239 1.00 0.00 H +ATOM 149 HH12 ARG 8 33.036 -88.010 -3.530 1.00 0.00 H +ATOM 150 NH2 ARG 8 34.076 -89.910 -2.268 1.00 0.00 N +ATOM 151 HH21 ARG 8 34.414 -90.741 -1.803 1.00 0.00 H +ATOM 152 HH22 ARG 8 34.555 -89.028 -2.150 1.00 0.00 H +ATOM 153 HA ARG 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 154 C ARG 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 155 O ARG 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 156 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 157 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 158 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 161 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 162 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 163 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 164 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 165 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 166 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 167 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 168 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 169 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 170 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 171 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 172 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 173 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 174 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 175 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 176 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 177 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 178 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 179 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 180 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 181 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 182 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 183 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 184 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 185 N ILE 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 186 H ILE 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 187 CA ILE 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 188 CB ILE 11 32.215-101.571 0.717 1.00 0.00 C +ATOM 189 HB ILE 11 31.857-101.753 1.731 1.00 0.00 H +ATOM 190 CG2 ILE 11 33.468-102.396 0.465 1.00 0.00 C +ATOM 191 HG21 ILE 11 33.825-102.214 -0.549 1.00 0.00 H +ATOM 192 HG22 ILE 11 34.241-102.112 1.179 1.00 0.00 H +ATOM 193 HG23 ILE 11 33.237-103.454 0.583 1.00 0.00 H +ATOM 194 CG1 ILE 11 32.565-100.092 0.545 1.00 0.00 C +ATOM 195 HG12 ILE 11 33.127 -99.998 -0.384 1.00 0.00 H +ATOM 196 HG13 ILE 11 31.625 -99.544 0.459 1.00 0.00 H +ATOM 197 CD1 ILE 11 33.379 -99.520 1.684 1.00 0.00 C +ATOM 198 HD11 ILE 11 34.318-100.066 1.771 1.00 0.00 H +ATOM 199 HD12 ILE 11 33.587 -98.468 1.491 1.00 0.00 H +ATOM 200 HD13 ILE 11 32.818 -99.613 2.615 1.00 0.00 H +ATOM 201 HA ILE 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 202 C ILE 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 203 O ILE 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 204 N ASN 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 205 H ASN 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 206 CA ASN 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 207 CB ASN 12 28.130 -98.237 -0.161 1.00 0.00 C +ATOM 208 HB2 ASN 12 28.768 -97.830 -0.944 1.00 0.00 H +ATOM 209 HB3 ASN 12 27.146 -97.771 -0.217 1.00 0.00 H +ATOM 210 CG ASN 12 28.745 -97.908 1.184 1.00 0.00 C +ATOM 211 OD1 ASN 12 28.878 -98.777 2.046 1.00 0.00 O +ATOM 212 ND2 ASN 12 29.125 -96.650 1.369 1.00 0.00 N +ATOM 213 HD21 ASN 12 29.540 -96.375 2.247 1.00 0.00 H +ATOM 214 HD22 ASN 12 28.996 -95.973 0.630 1.00 0.00 H +ATOM 215 HA ASN 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 216 C ASN 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 217 O ASN 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 218 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 219 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 220 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 221 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 222 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 223 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 224 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 225 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 226 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 227 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 228 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 229 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 230 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 231 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 232 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 233 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 234 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 235 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 236 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 237 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 238 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 239 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 240 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 241 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 242 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 243 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 244 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 245 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 246 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 247 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 248 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 249 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 250 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 251 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 252 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 253 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 254 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 255 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 256 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 257 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 258 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 259 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 260 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 261 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 262 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 263 N HY1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 264 CA HY1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 265 C HY1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 266 O HY1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 267 CB HY1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 268 CG HY1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 269 CD2 HY1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 270 ND1 HY1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 271 CE1 HY1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 272 NE2 HY1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 273 H HY1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 274 HA HY1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 275 HB2 HY1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 276 HB3 HY1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 277 HD1 HY1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 278 HD2 HY1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 279 HE1 HY1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 280 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 281 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 282 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 283 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 284 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 285 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 286 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 287 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 288 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 289 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 290 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 291 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 292 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 293 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 294 N HY2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 295 CA HY2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 296 C HY2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 297 O HY2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 298 CB HY2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 299 CG HY2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 300 CD2 HY2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 301 ND1 HY2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 302 CE1 HY2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 303 NE2 HY2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 304 H HY2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 305 HA HY2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 306 HB2 HY2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 307 HB3 HY2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 308 HD1 HY2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 309 HD2 HY2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 310 HE1 HY2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 311 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 312 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 313 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 314 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 315 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 316 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 317 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 318 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 319 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 320 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 321 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 322 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 323 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 324 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 325 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 326 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 327 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 328 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 329 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 330 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 331 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 332 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 333 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 334 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 335 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 336 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 337 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 338 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 339 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 340 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 341 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 342 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 343 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 344 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 345 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 346 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 347 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 348 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 349 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 350 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 351 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 352 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 353 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 354 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 355 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 356 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 357 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 358 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 359 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 360 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 361 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 362 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 363 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 364 N TRP 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 365 H TRP 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 366 CA TRP 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 367 CB TRP 23 21.411 -85.256 -16.822 1.00 0.00 C +ATOM 368 HB2 TRP 23 22.132 -85.913 -16.338 1.00 0.00 H +ATOM 369 HB3 TRP 23 20.438 -85.734 -16.718 1.00 0.00 H +ATOM 370 CG TRP 23 21.738 -85.227 -18.283 1.00 0.00 C +ATOM 371 CD1 TRP 23 20.859 -85.092 -19.318 1.00 0.00 C +ATOM 372 HD1 TRP 23 19.783 -84.997 -19.203 1.00 0.00 H +ATOM 373 NE1 TRP 23 21.530 -85.108 -20.517 1.00 0.00 N +ATOM 374 HE1 TRP 23 21.113 -85.024 -21.438 1.00 0.00 H +ATOM 375 CE2 TRP 23 22.874 -85.257 -20.268 1.00 0.00 C +ATOM 376 CZ2 TRP 23 23.948 -85.327 -21.155 1.00 0.00 C +ATOM 377 HZ2 TRP 23 23.812 -85.267 -22.225 1.00 0.00 H +ATOM 378 CH2 TRP 23 25.200 -85.477 -20.620 1.00 0.00 C +ATOM 379 HH2 TRP 23 26.050 -85.530 -21.290 1.00 0.00 H +ATOM 380 CZ3 TRP 23 25.394 -85.558 -19.231 1.00 0.00 C +ATOM 381 HZ3 TRP 23 26.400 -85.679 -18.854 1.00 0.00 H +ATOM 382 CE3 TRP 23 24.329 -85.487 -18.351 1.00 0.00 C +ATOM 383 HE3 TRP 23 24.462 -85.551 -17.282 1.00 0.00 H +ATOM 384 CD2 TRP 23 23.042 -85.333 -18.871 1.00 0.00 C +ATOM 385 HA TRP 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 386 C TRP 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 387 O TRP 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 388 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 389 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 390 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 391 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 392 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 393 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 394 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 395 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 396 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 397 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 398 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 399 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 400 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 401 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 402 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 403 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 404 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 405 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 406 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 407 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 408 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 409 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 410 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 411 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 412 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 413 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 414 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 415 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 416 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 417 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 418 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 419 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 420 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 421 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 422 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 423 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 424 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 425 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 426 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 427 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 428 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 429 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 430 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 431 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 432 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 433 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 434 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 435 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 436 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 437 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 438 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 439 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 440 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 441 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 442 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 443 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 444 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 445 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 446 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 447 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 448 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 449 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 450 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 451 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 452 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 453 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 454 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 455 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 456 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 457 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 458 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 459 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 460 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 461 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 462 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 463 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 464 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 465 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 466 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 467 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 468 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 469 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 470 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 471 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 472 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 473 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 474 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 475 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 476 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 477 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 478 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 479 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 480 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 481 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 482 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 483 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 484 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 485 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 486 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 487 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 488 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 489 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 490 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 491 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 492 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 493 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 494 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 495 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 496 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 497 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 498 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 499 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 500 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 501 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 502 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 503 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 504 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 505 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 506 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 507 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 508 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 509 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 510 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 511 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 512 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 513 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 514 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 515 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 516 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 517 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 518 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 519 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 520 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 521 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 522 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 523 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 524 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 525 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 526 N MET 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 527 H MET 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 528 CA MET 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 529 CB MET 33 27.315 -82.525 -3.272 1.00 0.00 C +ATOM 530 HB2 MET 33 26.398 -81.940 -3.214 1.00 0.00 H +ATOM 531 HB3 MET 33 27.389 -82.989 -4.255 1.00 0.00 H +ATOM 532 CG MET 33 27.295 -83.605 -2.204 1.00 0.00 C +ATOM 533 HG2 MET 33 26.492 -84.303 -2.443 1.00 0.00 H +ATOM 534 HG3 MET 33 28.252 -84.128 -2.232 1.00 0.00 H +ATOM 535 SD MET 33 27.030 -82.943 -0.547 1.00 0.00 S +ATOM 536 CE MET 33 27.063 -84.446 0.427 1.00 0.00 C +ATOM 537 HE1 MET 33 28.027 -84.938 0.303 1.00 0.00 H +ATOM 538 HE2 MET 33 26.912 -84.201 1.479 1.00 0.00 H +ATOM 539 HE3 MET 33 26.268 -85.113 0.092 1.00 0.00 H +ATOM 540 HA MET 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 541 C MET 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 542 O MET 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 543 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 544 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 545 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 546 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 547 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 548 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 549 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 550 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 551 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 552 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 553 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 554 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 555 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 556 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 557 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 558 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 559 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 560 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 561 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 562 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 563 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 564 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 565 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 566 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 567 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 568 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 569 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 570 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 571 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 572 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 573 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 574 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 575 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 576 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 577 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 578 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 579 N LEU 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 580 H LEU 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 581 CA LEU 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 582 CB LEU 37 33.048 -83.879 0.496 1.00 0.00 C +ATOM 583 HB2 LEU 37 31.985 -83.889 0.734 1.00 0.00 H +ATOM 584 HB3 LEU 37 33.178 -83.869 -0.586 1.00 0.00 H +ATOM 585 CG LEU 37 33.713 -85.128 1.077 1.00 0.00 C +ATOM 586 HG LEU 37 34.787 -85.068 0.903 1.00 0.00 H +ATOM 587 CD1 LEU 37 33.448 -85.233 2.571 1.00 0.00 C +ATOM 588 HD11 LEU 37 32.374 -85.292 2.747 1.00 0.00 H +ATOM 589 HD12 LEU 37 33.929 -86.128 2.965 1.00 0.00 H +ATOM 590 HD13 LEU 37 33.849 -84.353 3.075 1.00 0.00 H +ATOM 591 CD2 LEU 37 33.176 -86.384 0.410 1.00 0.00 C +ATOM 592 HD21 LEU 37 33.380 -86.342 -0.661 1.00 0.00 H +ATOM 593 HD22 LEU 37 33.662 -87.260 0.838 1.00 0.00 H +ATOM 594 HD23 LEU 37 32.100 -86.450 0.572 1.00 0.00 H +ATOM 595 HA LEU 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 596 C LEU 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 597 O LEU 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 598 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 599 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 600 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 601 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 602 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 603 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 604 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 605 N ALA 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 606 H ALA 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 607 CA ALA 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 608 CB ALA 39 38.874 -82.519 -4.462 1.00 0.00 C +ATOM 609 HB1 ALA 39 39.474 -81.803 -3.899 1.00 0.00 H +ATOM 610 HB2 ALA 39 38.973 -83.508 -4.013 1.00 0.00 H +ATOM 611 HB3 ALA 39 39.223 -82.552 -5.494 1.00 0.00 H +ATOM 612 HA ALA 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 613 C ALA 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 614 O ALA 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 615 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 616 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 617 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 618 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 619 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 620 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 621 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 622 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 623 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 624 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 625 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 626 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 627 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 628 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 629 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 630 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 631 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 632 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 633 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 634 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 635 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 636 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 637 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 638 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 639 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 640 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 641 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 642 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 643 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 644 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 645 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 646 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 647 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 648 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 649 N ASP 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 650 H ASP 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 651 CA ASP 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 652 CB ASP 43 29.884 -89.033 -12.452 1.00 0.00 C +ATOM 653 HB2 ASP 43 29.493 -88.069 -12.779 1.00 0.00 H +ATOM 654 HB3 ASP 43 29.081 -89.770 -12.451 1.00 0.00 H +ATOM 655 CG ASP 43 30.447 -88.899 -11.051 1.00 0.00 C +ATOM 656 OD1 ASP 43 31.651 -88.590 -10.921 1.00 0.00 O +ATOM 657 OD2 ASP 43 29.685 -89.101 -10.082 1.00 0.00 O +ATOM 658 HA ASP 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 659 C ASP 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 660 O ASP 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 661 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 662 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 663 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 664 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 665 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 666 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 667 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 668 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 669 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 670 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 671 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 672 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 673 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 674 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 675 N LYN 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 676 H LYN 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 677 CA LYN 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 678 CB LYN 45 25.266 -89.253 -17.470 1.00 0.00 C +ATOM 679 HB2 LYN 45 25.726 -88.747 -16.621 1.00 0.00 H +ATOM 680 HB3 LYN 45 25.701 -88.876 -18.396 1.00 0.00 H +ATOM 681 CG LYN 45 23.770 -88.987 -17.468 1.00 0.00 C +ATOM 682 HG2 LYN 45 23.323 -89.505 -18.317 1.00 0.00 H +ATOM 683 HG3 LYN 45 23.349 -89.376 -16.541 1.00 0.00 H +ATOM 684 CD LYN 45 23.474 -87.499 -17.571 1.00 0.00 C +ATOM 685 HD2 LYN 45 22.407 -87.345 -17.414 1.00 0.00 H +ATOM 686 HD3 LYN 45 24.035 -86.979 -16.795 1.00 0.00 H +ATOM 687 CE LYN 45 23.868 -86.952 -18.934 1.00 0.00 C +ATOM 688 HE2 LYN 45 24.935 -87.127 -19.077 1.00 0.00 H +ATOM 689 HE3 LYN 45 23.307 -87.493 -19.695 1.00 0.00 H +ATOM 690 NZ LYN 45 23.585 -85.495 -19.050 1.00 0.00 N +ATOM 691 HZ2 LYN 45 23.859 -85.171 -19.966 1.00 0.00 H +ATOM 692 HZ3 LYN 45 22.597 -85.332 -18.918 1.00 0.00 H +ATOM 693 HA LYN 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 694 C LYN 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 695 O LYN 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 696 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 697 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 698 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 699 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 700 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 701 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 702 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 703 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 704 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 705 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 706 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 707 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 708 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 709 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 710 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 711 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 712 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 713 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 714 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 715 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 716 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 717 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 718 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 719 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 720 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 721 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 722 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 723 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 724 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 725 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 726 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 727 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 728 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 729 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 730 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 731 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 732 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 733 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 734 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 735 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 736 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 737 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 738 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 739 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 740 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 741 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 742 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 743 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 744 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 745 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 746 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 747 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 748 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 749 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 750 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 751 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 752 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 753 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 754 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 755 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 756 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 757 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 758 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 759 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 760 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 761 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 762 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 763 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 764 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 765 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 766 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 767 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 768 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 769 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 770 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 771 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 772 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 773 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 774 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 775 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 776 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 777 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 778 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 779 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 780 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 781 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 782 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 783 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 784 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 785 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 786 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 787 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 788 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 789 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 790 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 791 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 792 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 793 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 794 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 795 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 796 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 797 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 798 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 799 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 800 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 801 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 802 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 803 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 804 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 805 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 806 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 807 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 808 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 809 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 810 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 811 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 812 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 813 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 814 N LYN 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 815 H LYN 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 816 CA LYN 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 817 CB LYN 54 32.301 -94.491 -10.199 1.00 0.00 C +ATOM 818 HB2 LYN 54 33.358 -94.431 -10.462 1.00 0.00 H +ATOM 819 HB3 LYN 54 32.026 -93.623 -9.600 1.00 0.00 H +ATOM 820 CG LYN 54 32.050 -95.758 -9.398 1.00 0.00 C +ATOM 821 HG2 LYN 54 30.989 -95.808 -9.152 1.00 0.00 H +ATOM 822 HG3 LYN 54 32.321 -96.617 -10.013 1.00 0.00 H +ATOM 823 CD LYN 54 32.869 -95.774 -8.118 1.00 0.00 C +ATOM 824 HD2 LYN 54 33.925 -95.713 -8.380 1.00 0.00 H +ATOM 825 HD3 LYN 54 32.594 -94.906 -7.518 1.00 0.00 H +ATOM 826 CE LYN 54 32.619 -97.041 -7.318 1.00 0.00 C +ATOM 827 HE2 LYN 54 31.557 -97.090 -7.077 1.00 0.00 H +ATOM 828 HE3 LYN 54 32.889 -97.897 -7.938 1.00 0.00 H +ATOM 829 NZ LYN 54 33.415 -97.070 -6.059 1.00 0.00 N +ATOM 830 HZ2 LYN 54 33.221 -97.925 -5.558 1.00 0.00 H +ATOM 831 HZ3 LYN 54 34.399 -97.026 -6.282 1.00 0.00 H +ATOM 832 HA LYN 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 833 C LYN 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 834 O LYN 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 835 N ASH 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 836 H ASH 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 837 CA ASH 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 838 CB ASH 55 34.660 -96.376 -14.407 1.00 0.00 C +ATOM 839 HB2 ASH 55 34.971 -97.132 -15.128 1.00 0.00 H +ATOM 840 HB3 ASH 55 34.155 -95.564 -14.929 1.00 0.00 H +ATOM 841 CG ASH 55 35.878 -95.832 -13.687 1.00 0.00 C +ATOM 842 OD1 ASH 55 35.823 -95.694 -12.446 1.00 0.00 O +ATOM 843 OD2 ASH 55 36.888 -95.544 -14.362 1.00 0.00 O +ATOM 844 HD2 ASH 55 37.578 -95.214 -13.781 1.00 0.00 H +ATOM 845 HA ASH 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 846 C ASH 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 847 O ASH 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 848 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 849 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 850 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 851 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 852 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 853 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 854 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 855 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 856 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 857 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 858 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 859 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 860 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 861 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 862 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 863 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 864 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 Zn +ATOM 865 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 866 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 867 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 868 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 869 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 870 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +ATOM 871 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 872 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 873 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 17 15 13 16 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 65 60 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 68 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 65 69 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 864 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 104 106 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 111 112 113 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 153 132 154 135 +CONECT 135 136 137 138 134 +CONECT 136 135 +CONECT 137 135 +CONECT 138 135 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 142 143 144 +CONECT 142 141 +CONECT 143 141 +CONECT 144 141 145 146 +CONECT 145 144 +CONECT 146 144 147 150 +CONECT 147 146 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 146 151 152 +CONECT 151 150 +CONECT 152 150 +CONECT 153 134 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 165 169 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 170 175 +CONECT 174 173 +CONECT 175 173 +CONECT 176 178 179 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 182 181 176 180 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 201 202 188 +CONECT 188 189 190 194 187 +CONECT 189 188 +CONECT 190 188 191 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 +CONECT 194 188 195 196 197 +CONECT 195 194 +CONECT 196 194 +CONECT 197 194 198 199 200 +CONECT 198 197 +CONECT 199 197 +CONECT 200 197 +CONECT 201 187 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 216 204 215 207 +CONECT 207 208 209 210 206 +CONECT 208 207 +CONECT 209 207 +CONECT 210 207 211 212 +CONECT 211 210 +CONECT 212 210 213 214 +CONECT 213 212 +CONECT 214 212 +CONECT 215 206 +CONECT 216 217 218 206 +CONECT 217 216 +CONECT 218 220 216 219 +CONECT 219 218 +CONECT 220 221 222 238 218 +CONECT 221 220 +CONECT 222 225 220 223 224 +CONECT 223 222 +CONECT 224 222 +CONECT 225 227 226 228 222 +CONECT 226 225 +CONECT 227 225 +CONECT 228 229 225 231 230 +CONECT 229 228 +CONECT 230 228 +CONECT 231 233 228 234 232 +CONECT 232 231 +CONECT 233 231 +CONECT 234 237 231 235 236 +CONECT 235 234 +CONECT 236 234 +CONECT 237 234 +CONECT 238 239 220 240 +CONECT 239 238 +CONECT 240 238 242 241 +CONECT 241 240 +CONECT 242 245 240 243 244 +CONECT 243 242 +CONECT 244 242 +CONECT 245 246 247 242 +CONECT 246 245 +CONECT 247 249 245 248 +CONECT 248 247 +CONECT 249 251 250 261 247 +CONECT 250 249 +CONECT 251 257 252 253 249 +CONECT 252 251 +CONECT 253 251 256 255 254 +CONECT 254 253 +CONECT 255 253 +CONECT 256 253 +CONECT 257 259 260 258 251 +CONECT 258 257 +CONECT 259 257 +CONECT 260 257 +CONECT 261 263 249 262 +CONECT 262 261 +CONECT 263 273 264 261 +CONECT 264 265 263 274 267 +CONECT 265 266 280 264 +CONECT 266 265 +CONECT 267 264 268 275 276 +CONECT 268 269 270 267 +CONECT 269 272 278 268 +CONECT 270 271 268 277 +CONECT 271 272 279 270 +CONECT 272 864 271 269 +CONECT 273 263 +CONECT 274 264 +CONECT 275 267 +CONECT 276 267 +CONECT 277 270 +CONECT 278 269 +CONECT 279 271 +CONECT 280 282 265 281 +CONECT 281 280 +CONECT 282 283 284 292 280 +CONECT 283 282 +CONECT 284 285 286 282 290 +CONECT 285 284 +CONECT 286 287 288 284 289 +CONECT 287 286 +CONECT 288 286 +CONECT 289 286 +CONECT 290 284 291 +CONECT 291 290 +CONECT 292 294 282 293 +CONECT 293 292 +CONECT 294 304 295 292 +CONECT 295 296 298 294 305 +CONECT 296 297 311 295 +CONECT 297 296 +CONECT 298 306 307 295 299 +CONECT 299 298 300 301 +CONECT 300 309 299 303 +CONECT 301 299 308 302 +CONECT 302 303 301 310 +CONECT 303 300 302 864 +CONECT 304 294 +CONECT 305 295 +CONECT 306 298 +CONECT 307 298 +CONECT 308 301 +CONECT 309 300 +CONECT 310 302 +CONECT 311 313 296 312 +CONECT 312 311 +CONECT 313 324 314 311 315 +CONECT 314 313 +CONECT 315 313 318 317 316 +CONECT 316 315 +CONECT 317 315 +CONECT 318 320 321 315 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 322 318 323 +CONECT 322 321 +CONECT 323 321 +CONECT 324 326 325 313 +CONECT 325 324 +CONECT 326 328 327 324 +CONECT 327 326 +CONECT 328 334 330 329 326 +CONECT 329 328 +CONECT 330 333 332 328 331 +CONECT 331 330 +CONECT 332 330 +CONECT 333 330 +CONECT 334 336 335 328 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 350 340 339 336 +CONECT 339 338 +CONECT 340 341 346 338 342 +CONECT 341 340 +CONECT 342 340 343 345 344 +CONECT 343 342 +CONECT 344 342 +CONECT 345 342 +CONECT 346 349 348 340 347 +CONECT 347 346 +CONECT 348 346 +CONECT 349 346 +CONECT 350 351 352 338 +CONECT 351 350 +CONECT 352 354 350 353 +CONECT 353 352 +CONECT 354 356 355 362 352 +CONECT 355 354 +CONECT 356 359 357 358 354 +CONECT 357 356 +CONECT 358 356 +CONECT 359 360 361 356 +CONECT 360 359 +CONECT 361 359 +CONECT 362 354 364 363 +CONECT 363 362 +CONECT 364 365 362 366 +CONECT 365 364 +CONECT 366 364 386 385 367 +CONECT 367 368 369 370 366 +CONECT 368 367 +CONECT 369 367 +CONECT 370 367 371 384 +CONECT 371 370 372 373 +CONECT 372 371 +CONECT 373 371 374 375 +CONECT 374 373 +CONECT 375 373 376 384 +CONECT 376 375 377 378 +CONECT 377 376 +CONECT 378 376 379 380 +CONECT 379 378 +CONECT 380 378 381 382 +CONECT 381 380 +CONECT 382 380 383 384 +CONECT 383 382 +CONECT 384 370 375 382 +CONECT 385 366 +CONECT 386 388 366 387 +CONECT 387 386 +CONECT 388 389 390 386 +CONECT 389 388 +CONECT 390 392 388 391 396 +CONECT 391 390 +CONECT 392 394 393 395 390 +CONECT 393 392 +CONECT 394 392 +CONECT 395 392 +CONECT 396 390 397 398 +CONECT 397 396 +CONECT 398 396 399 400 +CONECT 399 398 +CONECT 400 398 402 401 411 +CONECT 401 400 +CONECT 402 405 400 403 404 +CONECT 403 402 +CONECT 404 402 +CONECT 405 406 408 407 402 +CONECT 406 405 +CONECT 407 405 +CONECT 408 410 405 409 +CONECT 409 408 +CONECT 410 408 +CONECT 411 400 413 412 +CONECT 412 411 +CONECT 413 414 411 415 +CONECT 414 413 +CONECT 415 413 417 421 416 +CONECT 416 415 +CONECT 417 418 419 415 420 +CONECT 418 417 +CONECT 419 417 +CONECT 420 417 +CONECT 421 423 415 422 +CONECT 422 421 +CONECT 423 424 425 421 +CONECT 424 423 +CONECT 425 427 423 426 436 +CONECT 426 425 +CONECT 427 428 429 430 425 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 427 432 431 +CONECT 431 430 +CONECT 432 430 +CONECT 433 434 435 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 425 438 437 +CONECT 437 436 +CONECT 438 439 436 440 +CONECT 439 438 +CONECT 440 438 442 441 458 +CONECT 441 440 +CONECT 442 445 443 444 440 +CONECT 443 442 +CONECT 444 442 +CONECT 445 448 447 446 442 +CONECT 446 445 +CONECT 447 445 +CONECT 448 451 449 445 450 +CONECT 449 448 +CONECT 450 448 +CONECT 451 454 453 452 448 +CONECT 452 451 +CONECT 453 451 +CONECT 454 457 456 455 451 +CONECT 455 454 +CONECT 456 454 +CONECT 457 454 +CONECT 458 440 460 459 +CONECT 459 458 +CONECT 460 461 458 462 +CONECT 461 460 +CONECT 462 460 464 463 478 +CONECT 463 462 +CONECT 464 467 465 462 466 +CONECT 465 464 +CONECT 466 464 +CONECT 467 468 476 464 +CONECT 468 470 469 467 +CONECT 469 468 +CONECT 470 471 472 468 +CONECT 471 470 +CONECT 472 473 470 474 +CONECT 473 472 +CONECT 474 472 475 476 +CONECT 475 474 +CONECT 476 474 467 477 +CONECT 477 476 +CONECT 478 462 480 479 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 484 480 492 483 +CONECT 483 482 +CONECT 484 485 490 486 482 +CONECT 485 484 +CONECT 486 487 484 488 489 +CONECT 487 486 +CONECT 488 486 +CONECT 489 486 +CONECT 490 491 484 +CONECT 491 490 +CONECT 492 494 482 493 +CONECT 493 492 +CONECT 494 495 496 492 +CONECT 495 494 +CONECT 496 498 494 497 514 +CONECT 497 496 +CONECT 498 501 499 500 496 +CONECT 499 498 +CONECT 500 498 +CONECT 501 504 503 502 498 +CONECT 502 501 +CONECT 503 501 +CONECT 504 507 505 506 501 +CONECT 505 504 +CONECT 506 504 +CONECT 507 509 510 508 504 +CONECT 508 507 +CONECT 509 507 +CONECT 510 512 507 511 513 +CONECT 511 510 +CONECT 512 510 +CONECT 513 510 +CONECT 514 496 516 515 +CONECT 515 514 +CONECT 516 517 514 518 +CONECT 517 516 +CONECT 518 516 520 519 524 +CONECT 519 518 +CONECT 520 522 523 518 521 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 518 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 541 540 529 +CONECT 529 530 531 532 528 +CONECT 530 529 +CONECT 531 529 +CONECT 532 529 533 534 535 +CONECT 533 532 +CONECT 534 532 +CONECT 535 532 536 +CONECT 536 535 537 538 539 +CONECT 537 536 +CONECT 538 536 +CONECT 539 536 +CONECT 540 528 +CONECT 541 543 528 542 +CONECT 542 541 +CONECT 543 544 545 541 +CONECT 544 543 +CONECT 545 547 543 551 546 +CONECT 546 545 +CONECT 547 548 549 550 545 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 553 545 552 +CONECT 552 551 +CONECT 553 554 555 551 +CONECT 554 553 +CONECT 555 557 553 556 565 +CONECT 556 555 +CONECT 557 560 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 562 561 557 +CONECT 561 560 +CONECT 562 564 563 560 +CONECT 563 562 +CONECT 564 562 +CONECT 565 555 567 566 +CONECT 566 565 +CONECT 567 568 565 569 +CONECT 568 567 +CONECT 569 567 570 571 577 +CONECT 570 569 +CONECT 571 572 569 574 573 +CONECT 572 571 +CONECT 573 571 +CONECT 574 575 576 571 +CONECT 575 574 +CONECT 576 574 +CONECT 577 569 579 578 +CONECT 578 577 +CONECT 579 580 577 581 +CONECT 580 579 +CONECT 581 579 596 595 582 +CONECT 582 583 584 585 581 +CONECT 583 582 +CONECT 584 582 +CONECT 585 582 586 587 591 +CONECT 586 585 +CONECT 587 585 588 589 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 585 592 593 594 +CONECT 592 591 +CONECT 593 591 +CONECT 594 591 +CONECT 595 581 +CONECT 596 598 581 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 602 598 601 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 613 612 605 608 +CONECT 608 609 610 611 607 +CONECT 609 608 +CONECT 610 608 +CONECT 611 608 +CONECT 612 607 +CONECT 613 615 614 607 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 619 625 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 641 639 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 644 638 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 659 649 658 652 +CONECT 652 653 654 655 651 +CONECT 653 652 +CONECT 654 652 +CONECT 655 652 656 657 +CONECT 656 655 +CONECT 657 655 +CONECT 658 651 +CONECT 659 660 661 651 +CONECT 660 659 +CONECT 661 663 659 662 +CONECT 662 661 +CONECT 663 664 665 673 661 +CONECT 664 663 +CONECT 665 667 671 663 666 +CONECT 666 665 +CONECT 667 670 669 668 665 +CONECT 668 667 +CONECT 669 667 +CONECT 670 667 +CONECT 671 665 672 +CONECT 672 671 +CONECT 673 675 663 674 +CONECT 674 673 +CONECT 675 676 677 673 +CONECT 676 675 +CONECT 677 694 675 693 678 +CONECT 678 679 680 681 677 +CONECT 679 678 +CONECT 680 678 +CONECT 681 678 682 683 684 +CONECT 682 681 +CONECT 683 681 +CONECT 684 681 685 686 687 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 688 689 690 +CONECT 688 687 +CONECT 689 687 +CONECT 690 687 691 692 +CONECT 691 690 +CONECT 692 690 +CONECT 693 677 +CONECT 694 695 696 677 +CONECT 695 694 +CONECT 696 698 694 697 +CONECT 697 696 +CONECT 698 699 706 700 696 +CONECT 699 698 +CONECT 700 703 698 701 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 705 704 700 +CONECT 704 703 +CONECT 705 703 +CONECT 706 708 698 707 +CONECT 707 706 +CONECT 708 709 710 706 +CONECT 709 708 +CONECT 710 712 708 718 711 +CONECT 711 710 +CONECT 712 714 715 713 710 +CONECT 713 712 +CONECT 714 712 +CONECT 715 716 712 717 +CONECT 716 715 +CONECT 717 715 +CONECT 718 720 710 719 +CONECT 719 718 +CONECT 720 721 722 718 +CONECT 721 720 +CONECT 722 724 723 720 728 +CONECT 723 722 +CONECT 724 727 725 726 722 +CONECT 725 724 +CONECT 726 724 +CONECT 727 724 +CONECT 728 722 729 730 +CONECT 729 728 +CONECT 730 728 731 732 +CONECT 731 730 +CONECT 732 730 733 734 742 +CONECT 733 732 +CONECT 734 736 732 740 735 +CONECT 735 734 +CONECT 736 738 739 737 734 +CONECT 737 736 +CONECT 738 736 +CONECT 739 736 +CONECT 740 741 734 +CONECT 741 740 +CONECT 742 732 744 743 +CONECT 743 742 +CONECT 744 745 746 742 +CONECT 745 744 +CONECT 746 747 744 748 764 +CONECT 747 746 +CONECT 748 751 746 750 749 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 752 753 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 760 759 758 754 +CONECT 758 757 +CONECT 759 757 +CONECT 760 762 761 763 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 760 +CONECT 764 746 766 765 +CONECT 765 764 +CONECT 766 767 764 768 +CONECT 767 766 +CONECT 768 766 778 770 769 +CONECT 769 768 +CONECT 770 771 768 776 772 +CONECT 771 770 +CONECT 772 770 773 774 775 +CONECT 773 772 +CONECT 774 772 +CONECT 775 772 +CONECT 776 777 770 +CONECT 777 776 +CONECT 778 779 768 780 +CONECT 779 778 +CONECT 780 778 782 781 +CONECT 781 780 +CONECT 782 783 780 784 798 +CONECT 783 782 +CONECT 784 787 782 786 785 +CONECT 785 784 +CONECT 786 784 +CONECT 787 796 788 784 +CONECT 788 790 787 789 +CONECT 789 788 +CONECT 790 792 791 788 +CONECT 791 790 +CONECT 792 793 794 790 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 794 797 787 +CONECT 797 796 +CONECT 798 782 800 799 +CONECT 799 798 +CONECT 800 801 798 802 +CONECT 801 800 +CONECT 802 800 804 812 803 +CONECT 803 802 +CONECT 804 810 806 805 802 +CONECT 805 804 +CONECT 806 807 809 804 808 +CONECT 807 806 +CONECT 808 806 +CONECT 809 806 +CONECT 810 811 804 +CONECT 811 810 +CONECT 812 813 802 814 +CONECT 813 812 +CONECT 814 812 816 815 +CONECT 815 814 +CONECT 816 833 832 814 817 +CONECT 817 818 819 820 816 +CONECT 818 817 +CONECT 819 817 +CONECT 820 817 821 822 823 +CONECT 821 820 +CONECT 822 820 +CONECT 823 820 824 825 826 +CONECT 824 823 +CONECT 825 823 +CONECT 826 823 827 828 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 830 831 +CONECT 830 829 +CONECT 831 829 +CONECT 832 816 +CONECT 833 835 834 816 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 845 835 846 838 +CONECT 838 839 840 841 837 +CONECT 839 838 +CONECT 840 838 +CONECT 841 838 842 843 +CONECT 842 841 +CONECT 843 841 844 +CONECT 844 843 +CONECT 845 837 +CONECT 846 837 848 847 +CONECT 847 846 +CONECT 848 849 846 850 +CONECT 849 848 +CONECT 850 852 848 861 851 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 856 852 857 858 +CONECT 856 855 +CONECT 857 855 +CONECT 858 855 859 860 +CONECT 859 858 +CONECT 860 858 +CONECT 861 863 850 862 +CONECT 862 861 +CONECT 863 861 +CONECT 864 87 303 865 272 +CONECT 865 864 867 +CONECT 866 869 867 870 868 +CONECT 867 865 866 +CONECT 868 866 +CONECT 869 866 +CONECT 870 866 +CONECT 871 872 +CONECT 872 871 873 +CONECT 873 872 +MASTER 0 0 0 0 0 0 0 0 873 0 873 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_36.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_36.pdb new file mode 100644 index 0000000..2ec2c07 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_36.pdb @@ -0,0 +1,1751 @@ +COMPND fitness: 0.2006 34.955833333333885 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 P1 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HX1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HX1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HX1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HX1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HX1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HX1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HX1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HX1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N ARG 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H ARG 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA ARG 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 CB ARG 8 32.132 -93.836 -4.510 1.00 0.00 C +ATOM 136 HB2 ARG 8 33.181 -94.067 -4.697 1.00 0.00 H +ATOM 137 HB3 ARG 8 31.847 -92.954 -5.085 1.00 0.00 H +ATOM 138 CG ARG 8 31.930 -93.562 -3.029 1.00 0.00 C +ATOM 139 HG2 ARG 8 30.876 -93.341 -2.857 1.00 0.00 H +ATOM 140 HG3 ARG 8 32.210 -94.454 -2.469 1.00 0.00 H +ATOM 141 CD ARG 8 32.776 -92.387 -2.565 1.00 0.00 C +ATOM 142 HD2 ARG 8 32.675 -92.283 -1.484 1.00 0.00 H +ATOM 143 HD3 ARG 8 33.819 -92.579 -2.815 1.00 0.00 H +ATOM 144 NE ARG 8 32.366 -91.135 -3.195 1.00 0.00 N +ATOM 145 HE ARG 8 31.550 -91.162 -3.789 1.00 0.00 H +ATOM 146 CZ ARG 8 32.999 -89.977 -3.037 1.00 0.00 C +ATOM 147 NH1 ARG 8 32.553 -88.890 -3.652 1.00 0.00 N +ATOM 148 HH11 ARG 8 31.733 -88.946 -4.239 1.00 0.00 H +ATOM 149 HH12 ARG 8 33.036 -88.010 -3.530 1.00 0.00 H +ATOM 150 NH2 ARG 8 34.076 -89.910 -2.268 1.00 0.00 N +ATOM 151 HH21 ARG 8 34.414 -90.741 -1.803 1.00 0.00 H +ATOM 152 HH22 ARG 8 34.555 -89.028 -2.150 1.00 0.00 H +ATOM 153 HA ARG 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 154 C ARG 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 155 O ARG 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 156 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 157 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 158 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 161 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 162 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 163 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 164 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 165 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 166 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 167 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 168 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 169 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 170 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 171 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 172 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 173 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 174 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 175 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 176 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 177 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 178 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 179 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 180 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 181 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 182 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 183 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 184 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 185 N ILE 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 186 H ILE 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 187 CA ILE 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 188 CB ILE 11 32.215-101.571 0.717 1.00 0.00 C +ATOM 189 HB ILE 11 31.857-101.753 1.731 1.00 0.00 H +ATOM 190 CG2 ILE 11 33.468-102.396 0.465 1.00 0.00 C +ATOM 191 HG21 ILE 11 33.825-102.214 -0.549 1.00 0.00 H +ATOM 192 HG22 ILE 11 34.241-102.112 1.179 1.00 0.00 H +ATOM 193 HG23 ILE 11 33.237-103.454 0.583 1.00 0.00 H +ATOM 194 CG1 ILE 11 32.565-100.092 0.545 1.00 0.00 C +ATOM 195 HG12 ILE 11 33.127 -99.998 -0.384 1.00 0.00 H +ATOM 196 HG13 ILE 11 31.625 -99.544 0.459 1.00 0.00 H +ATOM 197 CD1 ILE 11 33.379 -99.520 1.684 1.00 0.00 C +ATOM 198 HD11 ILE 11 34.318-100.066 1.771 1.00 0.00 H +ATOM 199 HD12 ILE 11 33.587 -98.468 1.491 1.00 0.00 H +ATOM 200 HD13 ILE 11 32.818 -99.613 2.615 1.00 0.00 H +ATOM 201 HA ILE 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 202 C ILE 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 203 O ILE 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 204 N ASN 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 205 H ASN 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 206 CA ASN 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 207 CB ASN 12 28.130 -98.237 -0.161 1.00 0.00 C +ATOM 208 HB2 ASN 12 28.768 -97.830 -0.944 1.00 0.00 H +ATOM 209 HB3 ASN 12 27.146 -97.771 -0.217 1.00 0.00 H +ATOM 210 CG ASN 12 28.745 -97.908 1.184 1.00 0.00 C +ATOM 211 OD1 ASN 12 28.878 -98.777 2.046 1.00 0.00 O +ATOM 212 ND2 ASN 12 29.125 -96.650 1.369 1.00 0.00 N +ATOM 213 HD21 ASN 12 29.540 -96.375 2.247 1.00 0.00 H +ATOM 214 HD22 ASN 12 28.996 -95.973 0.630 1.00 0.00 H +ATOM 215 HA ASN 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 216 C ASN 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 217 O ASN 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 218 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 219 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 220 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 221 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 222 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 223 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 224 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 225 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 226 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 227 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 228 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 229 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 230 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 231 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 232 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 233 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 234 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 235 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 236 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 237 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 238 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 239 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 240 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 241 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 242 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 243 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 244 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 245 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 246 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 247 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 248 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 249 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 250 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 251 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 252 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 253 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 254 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 255 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 256 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 257 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 258 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 259 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 260 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 261 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 262 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 263 N HY1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 264 CA HY1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 265 C HY1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 266 O HY1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 267 CB HY1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 268 CG HY1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 269 CD2 HY1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 270 ND1 HY1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 271 CE1 HY1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 272 NE2 HY1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 273 H HY1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 274 HA HY1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 275 HB2 HY1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 276 HB3 HY1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 277 HD1 HY1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 278 HD2 HY1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 279 HE1 HY1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 280 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 281 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 282 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 283 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 284 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 285 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 286 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 287 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 288 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 289 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 290 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 291 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 292 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 293 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 294 N HY2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 295 CA HY2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 296 C HY2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 297 O HY2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 298 CB HY2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 299 CG HY2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 300 CD2 HY2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 301 ND1 HY2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 302 CE1 HY2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 303 NE2 HY2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 304 H HY2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 305 HA HY2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 306 HB2 HY2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 307 HB3 HY2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 308 HD1 HY2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 309 HD2 HY2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 310 HE1 HY2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 311 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 312 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 313 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 314 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 315 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 316 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 317 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 318 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 319 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 320 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 321 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 322 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 323 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 324 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 325 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 326 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 327 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 328 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 329 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 330 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 331 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 332 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 333 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 334 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 335 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 336 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 337 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 338 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 339 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 340 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 341 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 342 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 343 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 344 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 345 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 346 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 347 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 348 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 349 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 350 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 351 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 352 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 353 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 354 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 355 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 356 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 357 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 358 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 359 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 360 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 361 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 362 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 363 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 364 N TRP 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 365 H TRP 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 366 CA TRP 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 367 CB TRP 23 21.411 -85.256 -16.822 1.00 0.00 C +ATOM 368 HB2 TRP 23 22.132 -85.913 -16.338 1.00 0.00 H +ATOM 369 HB3 TRP 23 20.438 -85.734 -16.718 1.00 0.00 H +ATOM 370 CG TRP 23 21.738 -85.227 -18.283 1.00 0.00 C +ATOM 371 CD1 TRP 23 20.859 -85.092 -19.318 1.00 0.00 C +ATOM 372 HD1 TRP 23 19.783 -84.997 -19.203 1.00 0.00 H +ATOM 373 NE1 TRP 23 21.530 -85.108 -20.517 1.00 0.00 N +ATOM 374 HE1 TRP 23 21.113 -85.024 -21.438 1.00 0.00 H +ATOM 375 CE2 TRP 23 22.874 -85.257 -20.268 1.00 0.00 C +ATOM 376 CZ2 TRP 23 23.948 -85.327 -21.155 1.00 0.00 C +ATOM 377 HZ2 TRP 23 23.812 -85.267 -22.225 1.00 0.00 H +ATOM 378 CH2 TRP 23 25.200 -85.477 -20.620 1.00 0.00 C +ATOM 379 HH2 TRP 23 26.050 -85.530 -21.290 1.00 0.00 H +ATOM 380 CZ3 TRP 23 25.394 -85.558 -19.231 1.00 0.00 C +ATOM 381 HZ3 TRP 23 26.400 -85.679 -18.854 1.00 0.00 H +ATOM 382 CE3 TRP 23 24.329 -85.487 -18.351 1.00 0.00 C +ATOM 383 HE3 TRP 23 24.462 -85.551 -17.282 1.00 0.00 H +ATOM 384 CD2 TRP 23 23.042 -85.333 -18.871 1.00 0.00 C +ATOM 385 HA TRP 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 386 C TRP 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 387 O TRP 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 388 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 389 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 390 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 391 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 392 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 393 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 394 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 395 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 396 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 397 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 398 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 399 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 400 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 401 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 402 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 403 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 404 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 405 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 406 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 407 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 408 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 409 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 410 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 411 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 412 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 413 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 414 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 415 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 416 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 417 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 418 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 419 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 420 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 421 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 422 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 423 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 424 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 425 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 426 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 427 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 428 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 429 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 430 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 431 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 432 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 433 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 434 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 435 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 436 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 437 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 438 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 439 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 440 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 441 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 442 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 443 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 444 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 445 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 446 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 447 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 448 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 449 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 450 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 451 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 452 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 453 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 454 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 455 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 456 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 457 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 458 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 459 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 460 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 461 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 462 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 463 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 464 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 465 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 466 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 467 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 468 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 469 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 470 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 471 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 472 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 473 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 474 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 475 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 476 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 477 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 478 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 479 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 480 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 481 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 482 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 483 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 484 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 485 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 486 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 487 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 488 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 489 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 490 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 491 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 492 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 493 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 494 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 495 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 496 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 497 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 498 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 499 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 500 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 501 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 502 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 503 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 504 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 505 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 506 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 507 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 508 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 509 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 510 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 511 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 512 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 513 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 514 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 515 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 516 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 517 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 518 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 519 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 520 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 521 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 522 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 523 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 524 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 525 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 526 N MET 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 527 H MET 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 528 CA MET 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 529 CB MET 33 27.315 -82.525 -3.272 1.00 0.00 C +ATOM 530 HB2 MET 33 26.398 -81.940 -3.214 1.00 0.00 H +ATOM 531 HB3 MET 33 27.389 -82.989 -4.255 1.00 0.00 H +ATOM 532 CG MET 33 27.295 -83.605 -2.204 1.00 0.00 C +ATOM 533 HG2 MET 33 26.492 -84.303 -2.443 1.00 0.00 H +ATOM 534 HG3 MET 33 28.252 -84.128 -2.232 1.00 0.00 H +ATOM 535 SD MET 33 27.030 -82.943 -0.547 1.00 0.00 S +ATOM 536 CE MET 33 27.063 -84.446 0.427 1.00 0.00 C +ATOM 537 HE1 MET 33 28.027 -84.938 0.303 1.00 0.00 H +ATOM 538 HE2 MET 33 26.912 -84.201 1.479 1.00 0.00 H +ATOM 539 HE3 MET 33 26.268 -85.113 0.092 1.00 0.00 H +ATOM 540 HA MET 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 541 C MET 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 542 O MET 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 543 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 544 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 545 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 546 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 547 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 548 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 549 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 550 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 551 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 552 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 553 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 554 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 555 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 556 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 557 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 558 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 559 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 560 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 561 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 562 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 563 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 564 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 565 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 566 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 567 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 568 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 569 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 570 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 571 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 572 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 573 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 574 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 575 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 576 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 577 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 578 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 579 N LEU 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 580 H LEU 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 581 CA LEU 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 582 CB LEU 37 33.048 -83.879 0.496 1.00 0.00 C +ATOM 583 HB2 LEU 37 31.985 -83.889 0.734 1.00 0.00 H +ATOM 584 HB3 LEU 37 33.178 -83.869 -0.586 1.00 0.00 H +ATOM 585 CG LEU 37 33.713 -85.128 1.077 1.00 0.00 C +ATOM 586 HG LEU 37 34.787 -85.068 0.903 1.00 0.00 H +ATOM 587 CD1 LEU 37 33.448 -85.233 2.571 1.00 0.00 C +ATOM 588 HD11 LEU 37 32.374 -85.292 2.747 1.00 0.00 H +ATOM 589 HD12 LEU 37 33.929 -86.128 2.965 1.00 0.00 H +ATOM 590 HD13 LEU 37 33.849 -84.353 3.075 1.00 0.00 H +ATOM 591 CD2 LEU 37 33.176 -86.384 0.410 1.00 0.00 C +ATOM 592 HD21 LEU 37 33.380 -86.342 -0.661 1.00 0.00 H +ATOM 593 HD22 LEU 37 33.662 -87.260 0.838 1.00 0.00 H +ATOM 594 HD23 LEU 37 32.100 -86.450 0.572 1.00 0.00 H +ATOM 595 HA LEU 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 596 C LEU 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 597 O LEU 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 598 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 599 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 600 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 601 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 602 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 603 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 604 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 605 N ALA 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 606 H ALA 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 607 CA ALA 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 608 CB ALA 39 38.874 -82.519 -4.462 1.00 0.00 C +ATOM 609 HB1 ALA 39 39.474 -81.803 -3.899 1.00 0.00 H +ATOM 610 HB2 ALA 39 38.973 -83.508 -4.013 1.00 0.00 H +ATOM 611 HB3 ALA 39 39.223 -82.552 -5.494 1.00 0.00 H +ATOM 612 HA ALA 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 613 C ALA 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 614 O ALA 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 615 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 616 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 617 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 618 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 619 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 620 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 621 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 622 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 623 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 624 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 625 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 626 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 627 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 628 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 629 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 630 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 631 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 632 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 633 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 634 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 635 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 636 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 637 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 638 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 639 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 640 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 641 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 642 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 643 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 644 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 645 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 646 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 647 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 648 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 649 N ASP 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 650 H ASP 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 651 CA ASP 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 652 CB ASP 43 29.884 -89.033 -12.452 1.00 0.00 C +ATOM 653 HB2 ASP 43 29.493 -88.069 -12.779 1.00 0.00 H +ATOM 654 HB3 ASP 43 29.081 -89.770 -12.451 1.00 0.00 H +ATOM 655 CG ASP 43 30.447 -88.899 -11.051 1.00 0.00 C +ATOM 656 OD1 ASP 43 31.651 -88.590 -10.921 1.00 0.00 O +ATOM 657 OD2 ASP 43 29.685 -89.101 -10.082 1.00 0.00 O +ATOM 658 HA ASP 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 659 C ASP 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 660 O ASP 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 661 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 662 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 663 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 664 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 665 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 666 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 667 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 668 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 669 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 670 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 671 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 672 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 673 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 674 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 675 N LYN 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 676 H LYN 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 677 CA LYN 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 678 CB LYN 45 25.266 -89.253 -17.470 1.00 0.00 C +ATOM 679 HB2 LYN 45 25.726 -88.747 -16.621 1.00 0.00 H +ATOM 680 HB3 LYN 45 25.701 -88.876 -18.396 1.00 0.00 H +ATOM 681 CG LYN 45 23.770 -88.987 -17.468 1.00 0.00 C +ATOM 682 HG2 LYN 45 23.323 -89.505 -18.317 1.00 0.00 H +ATOM 683 HG3 LYN 45 23.349 -89.376 -16.541 1.00 0.00 H +ATOM 684 CD LYN 45 23.474 -87.499 -17.571 1.00 0.00 C +ATOM 685 HD2 LYN 45 22.407 -87.345 -17.414 1.00 0.00 H +ATOM 686 HD3 LYN 45 24.035 -86.979 -16.795 1.00 0.00 H +ATOM 687 CE LYN 45 23.868 -86.952 -18.934 1.00 0.00 C +ATOM 688 HE2 LYN 45 24.935 -87.127 -19.077 1.00 0.00 H +ATOM 689 HE3 LYN 45 23.307 -87.493 -19.695 1.00 0.00 H +ATOM 690 NZ LYN 45 23.585 -85.495 -19.050 1.00 0.00 N +ATOM 691 HZ2 LYN 45 23.859 -85.171 -19.966 1.00 0.00 H +ATOM 692 HZ3 LYN 45 22.597 -85.332 -18.918 1.00 0.00 H +ATOM 693 HA LYN 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 694 C LYN 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 695 O LYN 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 696 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 697 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 698 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 699 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 700 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 701 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 702 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 703 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 704 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 705 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 706 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 707 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 708 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 709 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 710 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 711 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 712 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 713 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 714 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 715 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 716 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 717 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 718 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 719 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 720 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 721 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 722 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 723 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 724 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 725 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 726 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 727 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 728 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 729 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 730 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 731 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 732 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 733 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 734 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 735 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 736 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 737 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 738 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 739 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 740 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 741 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 742 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 743 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 744 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 745 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 746 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 747 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 748 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 749 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 750 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 751 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 752 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 753 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 754 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 755 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 756 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 757 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 758 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 759 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 760 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 761 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 762 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 763 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 764 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 765 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 766 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 767 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 768 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 769 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 770 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 771 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 772 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 773 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 774 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 775 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 776 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 777 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 778 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 779 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 780 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 781 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 782 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 783 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 784 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 785 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 786 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 787 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 788 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 789 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 790 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 791 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 792 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 793 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 794 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 795 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 796 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 797 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 798 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 799 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 800 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 801 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 802 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 803 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 804 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 805 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 806 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 807 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 808 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 809 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 810 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 811 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 812 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 813 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 814 N LYN 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 815 H LYN 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 816 CA LYN 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 817 CB LYN 54 32.301 -94.491 -10.199 1.00 0.00 C +ATOM 818 HB2 LYN 54 33.358 -94.431 -10.462 1.00 0.00 H +ATOM 819 HB3 LYN 54 32.026 -93.623 -9.600 1.00 0.00 H +ATOM 820 CG LYN 54 32.050 -95.758 -9.398 1.00 0.00 C +ATOM 821 HG2 LYN 54 30.989 -95.808 -9.152 1.00 0.00 H +ATOM 822 HG3 LYN 54 32.321 -96.617 -10.013 1.00 0.00 H +ATOM 823 CD LYN 54 32.869 -95.774 -8.118 1.00 0.00 C +ATOM 824 HD2 LYN 54 33.925 -95.713 -8.380 1.00 0.00 H +ATOM 825 HD3 LYN 54 32.594 -94.906 -7.518 1.00 0.00 H +ATOM 826 CE LYN 54 32.619 -97.041 -7.318 1.00 0.00 C +ATOM 827 HE2 LYN 54 31.557 -97.090 -7.077 1.00 0.00 H +ATOM 828 HE3 LYN 54 32.889 -97.897 -7.938 1.00 0.00 H +ATOM 829 NZ LYN 54 33.415 -97.070 -6.059 1.00 0.00 N +ATOM 830 HZ2 LYN 54 33.221 -97.925 -5.558 1.00 0.00 H +ATOM 831 HZ3 LYN 54 34.399 -97.026 -6.282 1.00 0.00 H +ATOM 832 HA LYN 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 833 C LYN 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 834 O LYN 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 835 N ASH 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 836 H ASH 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 837 CA ASH 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 838 CB ASH 55 34.660 -96.376 -14.407 1.00 0.00 C +ATOM 839 HB2 ASH 55 34.971 -97.132 -15.128 1.00 0.00 H +ATOM 840 HB3 ASH 55 34.155 -95.564 -14.929 1.00 0.00 H +ATOM 841 CG ASH 55 35.878 -95.832 -13.687 1.00 0.00 C +ATOM 842 OD1 ASH 55 35.823 -95.694 -12.446 1.00 0.00 O +ATOM 843 OD2 ASH 55 36.888 -95.544 -14.362 1.00 0.00 O +ATOM 844 HD2 ASH 55 37.578 -95.214 -13.781 1.00 0.00 H +ATOM 845 HA ASH 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 846 C ASH 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 847 O ASH 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 848 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 849 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 850 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 851 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 852 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 853 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 854 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 855 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 856 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 857 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 858 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 859 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 860 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 861 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 862 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 863 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 864 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 Zn +ATOM 865 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 866 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 867 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 868 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 869 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 870 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +ATOM 871 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 872 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 873 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 17 15 13 16 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 65 60 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 68 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 65 69 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 864 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 104 106 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 111 112 113 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 153 132 154 135 +CONECT 135 136 137 138 134 +CONECT 136 135 +CONECT 137 135 +CONECT 138 135 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 142 143 144 +CONECT 142 141 +CONECT 143 141 +CONECT 144 141 145 146 +CONECT 145 144 +CONECT 146 144 147 150 +CONECT 147 146 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 146 151 152 +CONECT 151 150 +CONECT 152 150 +CONECT 153 134 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 165 169 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 170 175 +CONECT 174 173 +CONECT 175 173 +CONECT 176 178 179 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 182 181 176 180 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 201 202 188 +CONECT 188 189 190 194 187 +CONECT 189 188 +CONECT 190 188 191 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 +CONECT 194 188 195 196 197 +CONECT 195 194 +CONECT 196 194 +CONECT 197 194 198 199 200 +CONECT 198 197 +CONECT 199 197 +CONECT 200 197 +CONECT 201 187 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 216 204 215 207 +CONECT 207 208 209 210 206 +CONECT 208 207 +CONECT 209 207 +CONECT 210 207 211 212 +CONECT 211 210 +CONECT 212 210 213 214 +CONECT 213 212 +CONECT 214 212 +CONECT 215 206 +CONECT 216 217 218 206 +CONECT 217 216 +CONECT 218 220 216 219 +CONECT 219 218 +CONECT 220 221 222 238 218 +CONECT 221 220 +CONECT 222 225 220 223 224 +CONECT 223 222 +CONECT 224 222 +CONECT 225 227 226 228 222 +CONECT 226 225 +CONECT 227 225 +CONECT 228 229 225 231 230 +CONECT 229 228 +CONECT 230 228 +CONECT 231 233 228 234 232 +CONECT 232 231 +CONECT 233 231 +CONECT 234 237 231 235 236 +CONECT 235 234 +CONECT 236 234 +CONECT 237 234 +CONECT 238 239 220 240 +CONECT 239 238 +CONECT 240 238 242 241 +CONECT 241 240 +CONECT 242 245 240 243 244 +CONECT 243 242 +CONECT 244 242 +CONECT 245 246 247 242 +CONECT 246 245 +CONECT 247 249 245 248 +CONECT 248 247 +CONECT 249 251 250 261 247 +CONECT 250 249 +CONECT 251 257 252 253 249 +CONECT 252 251 +CONECT 253 251 256 255 254 +CONECT 254 253 +CONECT 255 253 +CONECT 256 253 +CONECT 257 259 260 258 251 +CONECT 258 257 +CONECT 259 257 +CONECT 260 257 +CONECT 261 263 249 262 +CONECT 262 261 +CONECT 263 273 264 261 +CONECT 264 265 263 274 267 +CONECT 265 266 280 264 +CONECT 266 265 +CONECT 267 264 268 275 276 +CONECT 268 269 270 267 +CONECT 269 272 278 268 +CONECT 270 271 268 277 +CONECT 271 272 279 270 +CONECT 272 864 271 269 +CONECT 273 263 +CONECT 274 264 +CONECT 275 267 +CONECT 276 267 +CONECT 277 270 +CONECT 278 269 +CONECT 279 271 +CONECT 280 282 265 281 +CONECT 281 280 +CONECT 282 283 284 292 280 +CONECT 283 282 +CONECT 284 285 286 282 290 +CONECT 285 284 +CONECT 286 287 288 284 289 +CONECT 287 286 +CONECT 288 286 +CONECT 289 286 +CONECT 290 284 291 +CONECT 291 290 +CONECT 292 294 282 293 +CONECT 293 292 +CONECT 294 304 295 292 +CONECT 295 296 298 294 305 +CONECT 296 297 311 295 +CONECT 297 296 +CONECT 298 306 307 295 299 +CONECT 299 298 300 301 +CONECT 300 309 299 303 +CONECT 301 299 308 302 +CONECT 302 303 301 310 +CONECT 303 300 302 864 +CONECT 304 294 +CONECT 305 295 +CONECT 306 298 +CONECT 307 298 +CONECT 308 301 +CONECT 309 300 +CONECT 310 302 +CONECT 311 313 296 312 +CONECT 312 311 +CONECT 313 324 314 311 315 +CONECT 314 313 +CONECT 315 313 318 317 316 +CONECT 316 315 +CONECT 317 315 +CONECT 318 320 321 315 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 322 318 323 +CONECT 322 321 +CONECT 323 321 +CONECT 324 326 325 313 +CONECT 325 324 +CONECT 326 328 327 324 +CONECT 327 326 +CONECT 328 334 330 329 326 +CONECT 329 328 +CONECT 330 333 332 328 331 +CONECT 331 330 +CONECT 332 330 +CONECT 333 330 +CONECT 334 336 335 328 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 350 340 339 336 +CONECT 339 338 +CONECT 340 341 346 338 342 +CONECT 341 340 +CONECT 342 340 343 345 344 +CONECT 343 342 +CONECT 344 342 +CONECT 345 342 +CONECT 346 349 348 340 347 +CONECT 347 346 +CONECT 348 346 +CONECT 349 346 +CONECT 350 351 352 338 +CONECT 351 350 +CONECT 352 354 350 353 +CONECT 353 352 +CONECT 354 356 355 362 352 +CONECT 355 354 +CONECT 356 359 357 358 354 +CONECT 357 356 +CONECT 358 356 +CONECT 359 360 361 356 +CONECT 360 359 +CONECT 361 359 +CONECT 362 354 364 363 +CONECT 363 362 +CONECT 364 365 362 366 +CONECT 365 364 +CONECT 366 364 386 385 367 +CONECT 367 368 369 370 366 +CONECT 368 367 +CONECT 369 367 +CONECT 370 367 371 384 +CONECT 371 370 372 373 +CONECT 372 371 +CONECT 373 371 374 375 +CONECT 374 373 +CONECT 375 373 376 384 +CONECT 376 375 377 378 +CONECT 377 376 +CONECT 378 376 379 380 +CONECT 379 378 +CONECT 380 378 381 382 +CONECT 381 380 +CONECT 382 380 383 384 +CONECT 383 382 +CONECT 384 370 375 382 +CONECT 385 366 +CONECT 386 388 366 387 +CONECT 387 386 +CONECT 388 389 390 386 +CONECT 389 388 +CONECT 390 392 388 391 396 +CONECT 391 390 +CONECT 392 394 393 395 390 +CONECT 393 392 +CONECT 394 392 +CONECT 395 392 +CONECT 396 390 397 398 +CONECT 397 396 +CONECT 398 396 399 400 +CONECT 399 398 +CONECT 400 398 402 401 411 +CONECT 401 400 +CONECT 402 405 400 403 404 +CONECT 403 402 +CONECT 404 402 +CONECT 405 406 408 407 402 +CONECT 406 405 +CONECT 407 405 +CONECT 408 410 405 409 +CONECT 409 408 +CONECT 410 408 +CONECT 411 400 413 412 +CONECT 412 411 +CONECT 413 414 411 415 +CONECT 414 413 +CONECT 415 413 417 421 416 +CONECT 416 415 +CONECT 417 418 419 415 420 +CONECT 418 417 +CONECT 419 417 +CONECT 420 417 +CONECT 421 423 415 422 +CONECT 422 421 +CONECT 423 424 425 421 +CONECT 424 423 +CONECT 425 427 423 426 436 +CONECT 426 425 +CONECT 427 428 429 430 425 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 427 432 431 +CONECT 431 430 +CONECT 432 430 +CONECT 433 434 435 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 425 438 437 +CONECT 437 436 +CONECT 438 439 436 440 +CONECT 439 438 +CONECT 440 438 442 441 458 +CONECT 441 440 +CONECT 442 445 443 444 440 +CONECT 443 442 +CONECT 444 442 +CONECT 445 448 447 446 442 +CONECT 446 445 +CONECT 447 445 +CONECT 448 451 449 445 450 +CONECT 449 448 +CONECT 450 448 +CONECT 451 454 453 452 448 +CONECT 452 451 +CONECT 453 451 +CONECT 454 457 456 455 451 +CONECT 455 454 +CONECT 456 454 +CONECT 457 454 +CONECT 458 440 460 459 +CONECT 459 458 +CONECT 460 461 458 462 +CONECT 461 460 +CONECT 462 460 464 463 478 +CONECT 463 462 +CONECT 464 467 465 462 466 +CONECT 465 464 +CONECT 466 464 +CONECT 467 468 476 464 +CONECT 468 470 469 467 +CONECT 469 468 +CONECT 470 471 472 468 +CONECT 471 470 +CONECT 472 473 470 474 +CONECT 473 472 +CONECT 474 472 475 476 +CONECT 475 474 +CONECT 476 474 467 477 +CONECT 477 476 +CONECT 478 462 480 479 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 484 480 492 483 +CONECT 483 482 +CONECT 484 485 490 486 482 +CONECT 485 484 +CONECT 486 487 484 488 489 +CONECT 487 486 +CONECT 488 486 +CONECT 489 486 +CONECT 490 491 484 +CONECT 491 490 +CONECT 492 494 482 493 +CONECT 493 492 +CONECT 494 495 496 492 +CONECT 495 494 +CONECT 496 498 494 497 514 +CONECT 497 496 +CONECT 498 501 499 500 496 +CONECT 499 498 +CONECT 500 498 +CONECT 501 504 503 502 498 +CONECT 502 501 +CONECT 503 501 +CONECT 504 507 505 506 501 +CONECT 505 504 +CONECT 506 504 +CONECT 507 509 510 508 504 +CONECT 508 507 +CONECT 509 507 +CONECT 510 512 507 511 513 +CONECT 511 510 +CONECT 512 510 +CONECT 513 510 +CONECT 514 496 516 515 +CONECT 515 514 +CONECT 516 517 514 518 +CONECT 517 516 +CONECT 518 516 520 519 524 +CONECT 519 518 +CONECT 520 522 523 518 521 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 518 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 541 540 529 +CONECT 529 530 531 532 528 +CONECT 530 529 +CONECT 531 529 +CONECT 532 529 533 534 535 +CONECT 533 532 +CONECT 534 532 +CONECT 535 532 536 +CONECT 536 535 537 538 539 +CONECT 537 536 +CONECT 538 536 +CONECT 539 536 +CONECT 540 528 +CONECT 541 543 528 542 +CONECT 542 541 +CONECT 543 544 545 541 +CONECT 544 543 +CONECT 545 547 543 551 546 +CONECT 546 545 +CONECT 547 548 549 550 545 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 553 545 552 +CONECT 552 551 +CONECT 553 554 555 551 +CONECT 554 553 +CONECT 555 557 553 556 565 +CONECT 556 555 +CONECT 557 560 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 562 561 557 +CONECT 561 560 +CONECT 562 564 563 560 +CONECT 563 562 +CONECT 564 562 +CONECT 565 555 567 566 +CONECT 566 565 +CONECT 567 568 565 569 +CONECT 568 567 +CONECT 569 567 570 571 577 +CONECT 570 569 +CONECT 571 572 569 574 573 +CONECT 572 571 +CONECT 573 571 +CONECT 574 575 576 571 +CONECT 575 574 +CONECT 576 574 +CONECT 577 569 579 578 +CONECT 578 577 +CONECT 579 580 577 581 +CONECT 580 579 +CONECT 581 579 596 595 582 +CONECT 582 583 584 585 581 +CONECT 583 582 +CONECT 584 582 +CONECT 585 582 586 587 591 +CONECT 586 585 +CONECT 587 585 588 589 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 585 592 593 594 +CONECT 592 591 +CONECT 593 591 +CONECT 594 591 +CONECT 595 581 +CONECT 596 598 581 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 602 598 601 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 613 612 605 608 +CONECT 608 609 610 611 607 +CONECT 609 608 +CONECT 610 608 +CONECT 611 608 +CONECT 612 607 +CONECT 613 615 614 607 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 619 625 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 641 639 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 644 638 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 659 649 658 652 +CONECT 652 653 654 655 651 +CONECT 653 652 +CONECT 654 652 +CONECT 655 652 656 657 +CONECT 656 655 +CONECT 657 655 +CONECT 658 651 +CONECT 659 660 661 651 +CONECT 660 659 +CONECT 661 663 659 662 +CONECT 662 661 +CONECT 663 664 665 673 661 +CONECT 664 663 +CONECT 665 667 671 663 666 +CONECT 666 665 +CONECT 667 670 669 668 665 +CONECT 668 667 +CONECT 669 667 +CONECT 670 667 +CONECT 671 665 672 +CONECT 672 671 +CONECT 673 675 663 674 +CONECT 674 673 +CONECT 675 676 677 673 +CONECT 676 675 +CONECT 677 694 675 693 678 +CONECT 678 679 680 681 677 +CONECT 679 678 +CONECT 680 678 +CONECT 681 678 682 683 684 +CONECT 682 681 +CONECT 683 681 +CONECT 684 681 685 686 687 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 688 689 690 +CONECT 688 687 +CONECT 689 687 +CONECT 690 687 691 692 +CONECT 691 690 +CONECT 692 690 +CONECT 693 677 +CONECT 694 695 696 677 +CONECT 695 694 +CONECT 696 698 694 697 +CONECT 697 696 +CONECT 698 699 706 700 696 +CONECT 699 698 +CONECT 700 703 698 701 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 705 704 700 +CONECT 704 703 +CONECT 705 703 +CONECT 706 708 698 707 +CONECT 707 706 +CONECT 708 709 710 706 +CONECT 709 708 +CONECT 710 712 708 718 711 +CONECT 711 710 +CONECT 712 714 715 713 710 +CONECT 713 712 +CONECT 714 712 +CONECT 715 716 712 717 +CONECT 716 715 +CONECT 717 715 +CONECT 718 720 710 719 +CONECT 719 718 +CONECT 720 721 722 718 +CONECT 721 720 +CONECT 722 724 723 720 728 +CONECT 723 722 +CONECT 724 727 725 726 722 +CONECT 725 724 +CONECT 726 724 +CONECT 727 724 +CONECT 728 722 729 730 +CONECT 729 728 +CONECT 730 728 731 732 +CONECT 731 730 +CONECT 732 730 733 734 742 +CONECT 733 732 +CONECT 734 736 732 740 735 +CONECT 735 734 +CONECT 736 738 739 737 734 +CONECT 737 736 +CONECT 738 736 +CONECT 739 736 +CONECT 740 741 734 +CONECT 741 740 +CONECT 742 732 744 743 +CONECT 743 742 +CONECT 744 745 746 742 +CONECT 745 744 +CONECT 746 747 744 748 764 +CONECT 747 746 +CONECT 748 751 746 750 749 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 752 753 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 760 759 758 754 +CONECT 758 757 +CONECT 759 757 +CONECT 760 762 761 763 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 760 +CONECT 764 746 766 765 +CONECT 765 764 +CONECT 766 767 764 768 +CONECT 767 766 +CONECT 768 766 778 770 769 +CONECT 769 768 +CONECT 770 771 768 776 772 +CONECT 771 770 +CONECT 772 770 773 774 775 +CONECT 773 772 +CONECT 774 772 +CONECT 775 772 +CONECT 776 777 770 +CONECT 777 776 +CONECT 778 779 768 780 +CONECT 779 778 +CONECT 780 778 782 781 +CONECT 781 780 +CONECT 782 783 780 784 798 +CONECT 783 782 +CONECT 784 787 782 786 785 +CONECT 785 784 +CONECT 786 784 +CONECT 787 796 788 784 +CONECT 788 790 787 789 +CONECT 789 788 +CONECT 790 792 791 788 +CONECT 791 790 +CONECT 792 793 794 790 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 794 797 787 +CONECT 797 796 +CONECT 798 782 800 799 +CONECT 799 798 +CONECT 800 801 798 802 +CONECT 801 800 +CONECT 802 800 804 812 803 +CONECT 803 802 +CONECT 804 810 806 805 802 +CONECT 805 804 +CONECT 806 807 809 804 808 +CONECT 807 806 +CONECT 808 806 +CONECT 809 806 +CONECT 810 811 804 +CONECT 811 810 +CONECT 812 813 802 814 +CONECT 813 812 +CONECT 814 812 816 815 +CONECT 815 814 +CONECT 816 833 832 814 817 +CONECT 817 818 819 820 816 +CONECT 818 817 +CONECT 819 817 +CONECT 820 817 821 822 823 +CONECT 821 820 +CONECT 822 820 +CONECT 823 820 824 825 826 +CONECT 824 823 +CONECT 825 823 +CONECT 826 823 827 828 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 830 831 +CONECT 830 829 +CONECT 831 829 +CONECT 832 816 +CONECT 833 835 834 816 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 845 835 846 838 +CONECT 838 839 840 841 837 +CONECT 839 838 +CONECT 840 838 +CONECT 841 838 842 843 +CONECT 842 841 +CONECT 843 841 844 +CONECT 844 843 +CONECT 845 837 +CONECT 846 837 848 847 +CONECT 847 846 +CONECT 848 849 846 850 +CONECT 849 848 +CONECT 850 852 848 861 851 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 856 852 857 858 +CONECT 856 855 +CONECT 857 855 +CONECT 858 855 859 860 +CONECT 859 858 +CONECT 860 858 +CONECT 861 863 850 862 +CONECT 862 861 +CONECT 863 861 +CONECT 864 87 303 865 272 +CONECT 865 864 867 +CONECT 866 869 867 870 868 +CONECT 867 865 866 +CONECT 868 866 +CONECT 869 866 +CONECT 870 866 +CONECT 871 872 +CONECT 872 871 873 +CONECT 873 872 +MASTER 0 0 0 0 0 0 0 0 873 0 873 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_37.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_37.pdb new file mode 100644 index 0000000..2ec2c07 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_37.pdb @@ -0,0 +1,1751 @@ +COMPND fitness: 0.2006 34.955833333333885 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 P1 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HX1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HX1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HX1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HX1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HX1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HX1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HX1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HX1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N ARG 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H ARG 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA ARG 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 CB ARG 8 32.132 -93.836 -4.510 1.00 0.00 C +ATOM 136 HB2 ARG 8 33.181 -94.067 -4.697 1.00 0.00 H +ATOM 137 HB3 ARG 8 31.847 -92.954 -5.085 1.00 0.00 H +ATOM 138 CG ARG 8 31.930 -93.562 -3.029 1.00 0.00 C +ATOM 139 HG2 ARG 8 30.876 -93.341 -2.857 1.00 0.00 H +ATOM 140 HG3 ARG 8 32.210 -94.454 -2.469 1.00 0.00 H +ATOM 141 CD ARG 8 32.776 -92.387 -2.565 1.00 0.00 C +ATOM 142 HD2 ARG 8 32.675 -92.283 -1.484 1.00 0.00 H +ATOM 143 HD3 ARG 8 33.819 -92.579 -2.815 1.00 0.00 H +ATOM 144 NE ARG 8 32.366 -91.135 -3.195 1.00 0.00 N +ATOM 145 HE ARG 8 31.550 -91.162 -3.789 1.00 0.00 H +ATOM 146 CZ ARG 8 32.999 -89.977 -3.037 1.00 0.00 C +ATOM 147 NH1 ARG 8 32.553 -88.890 -3.652 1.00 0.00 N +ATOM 148 HH11 ARG 8 31.733 -88.946 -4.239 1.00 0.00 H +ATOM 149 HH12 ARG 8 33.036 -88.010 -3.530 1.00 0.00 H +ATOM 150 NH2 ARG 8 34.076 -89.910 -2.268 1.00 0.00 N +ATOM 151 HH21 ARG 8 34.414 -90.741 -1.803 1.00 0.00 H +ATOM 152 HH22 ARG 8 34.555 -89.028 -2.150 1.00 0.00 H +ATOM 153 HA ARG 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 154 C ARG 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 155 O ARG 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 156 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 157 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 158 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 161 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 162 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 163 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 164 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 165 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 166 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 167 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 168 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 169 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 170 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 171 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 172 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 173 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 174 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 175 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 176 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 177 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 178 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 179 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 180 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 181 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 182 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 183 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 184 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 185 N ILE 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 186 H ILE 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 187 CA ILE 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 188 CB ILE 11 32.215-101.571 0.717 1.00 0.00 C +ATOM 189 HB ILE 11 31.857-101.753 1.731 1.00 0.00 H +ATOM 190 CG2 ILE 11 33.468-102.396 0.465 1.00 0.00 C +ATOM 191 HG21 ILE 11 33.825-102.214 -0.549 1.00 0.00 H +ATOM 192 HG22 ILE 11 34.241-102.112 1.179 1.00 0.00 H +ATOM 193 HG23 ILE 11 33.237-103.454 0.583 1.00 0.00 H +ATOM 194 CG1 ILE 11 32.565-100.092 0.545 1.00 0.00 C +ATOM 195 HG12 ILE 11 33.127 -99.998 -0.384 1.00 0.00 H +ATOM 196 HG13 ILE 11 31.625 -99.544 0.459 1.00 0.00 H +ATOM 197 CD1 ILE 11 33.379 -99.520 1.684 1.00 0.00 C +ATOM 198 HD11 ILE 11 34.318-100.066 1.771 1.00 0.00 H +ATOM 199 HD12 ILE 11 33.587 -98.468 1.491 1.00 0.00 H +ATOM 200 HD13 ILE 11 32.818 -99.613 2.615 1.00 0.00 H +ATOM 201 HA ILE 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 202 C ILE 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 203 O ILE 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 204 N ASN 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 205 H ASN 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 206 CA ASN 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 207 CB ASN 12 28.130 -98.237 -0.161 1.00 0.00 C +ATOM 208 HB2 ASN 12 28.768 -97.830 -0.944 1.00 0.00 H +ATOM 209 HB3 ASN 12 27.146 -97.771 -0.217 1.00 0.00 H +ATOM 210 CG ASN 12 28.745 -97.908 1.184 1.00 0.00 C +ATOM 211 OD1 ASN 12 28.878 -98.777 2.046 1.00 0.00 O +ATOM 212 ND2 ASN 12 29.125 -96.650 1.369 1.00 0.00 N +ATOM 213 HD21 ASN 12 29.540 -96.375 2.247 1.00 0.00 H +ATOM 214 HD22 ASN 12 28.996 -95.973 0.630 1.00 0.00 H +ATOM 215 HA ASN 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 216 C ASN 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 217 O ASN 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 218 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 219 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 220 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 221 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 222 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 223 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 224 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 225 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 226 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 227 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 228 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 229 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 230 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 231 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 232 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 233 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 234 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 235 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 236 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 237 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 238 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 239 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 240 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 241 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 242 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 243 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 244 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 245 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 246 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 247 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 248 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 249 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 250 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 251 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 252 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 253 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 254 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 255 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 256 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 257 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 258 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 259 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 260 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 261 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 262 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 263 N HY1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 264 CA HY1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 265 C HY1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 266 O HY1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 267 CB HY1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 268 CG HY1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 269 CD2 HY1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 270 ND1 HY1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 271 CE1 HY1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 272 NE2 HY1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 273 H HY1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 274 HA HY1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 275 HB2 HY1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 276 HB3 HY1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 277 HD1 HY1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 278 HD2 HY1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 279 HE1 HY1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 280 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 281 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 282 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 283 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 284 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 285 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 286 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 287 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 288 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 289 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 290 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 291 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 292 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 293 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 294 N HY2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 295 CA HY2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 296 C HY2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 297 O HY2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 298 CB HY2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 299 CG HY2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 300 CD2 HY2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 301 ND1 HY2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 302 CE1 HY2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 303 NE2 HY2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 304 H HY2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 305 HA HY2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 306 HB2 HY2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 307 HB3 HY2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 308 HD1 HY2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 309 HD2 HY2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 310 HE1 HY2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 311 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 312 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 313 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 314 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 315 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 316 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 317 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 318 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 319 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 320 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 321 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 322 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 323 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 324 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 325 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 326 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 327 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 328 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 329 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 330 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 331 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 332 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 333 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 334 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 335 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 336 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 337 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 338 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 339 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 340 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 341 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 342 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 343 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 344 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 345 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 346 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 347 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 348 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 349 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 350 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 351 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 352 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 353 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 354 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 355 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 356 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 357 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 358 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 359 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 360 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 361 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 362 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 363 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 364 N TRP 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 365 H TRP 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 366 CA TRP 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 367 CB TRP 23 21.411 -85.256 -16.822 1.00 0.00 C +ATOM 368 HB2 TRP 23 22.132 -85.913 -16.338 1.00 0.00 H +ATOM 369 HB3 TRP 23 20.438 -85.734 -16.718 1.00 0.00 H +ATOM 370 CG TRP 23 21.738 -85.227 -18.283 1.00 0.00 C +ATOM 371 CD1 TRP 23 20.859 -85.092 -19.318 1.00 0.00 C +ATOM 372 HD1 TRP 23 19.783 -84.997 -19.203 1.00 0.00 H +ATOM 373 NE1 TRP 23 21.530 -85.108 -20.517 1.00 0.00 N +ATOM 374 HE1 TRP 23 21.113 -85.024 -21.438 1.00 0.00 H +ATOM 375 CE2 TRP 23 22.874 -85.257 -20.268 1.00 0.00 C +ATOM 376 CZ2 TRP 23 23.948 -85.327 -21.155 1.00 0.00 C +ATOM 377 HZ2 TRP 23 23.812 -85.267 -22.225 1.00 0.00 H +ATOM 378 CH2 TRP 23 25.200 -85.477 -20.620 1.00 0.00 C +ATOM 379 HH2 TRP 23 26.050 -85.530 -21.290 1.00 0.00 H +ATOM 380 CZ3 TRP 23 25.394 -85.558 -19.231 1.00 0.00 C +ATOM 381 HZ3 TRP 23 26.400 -85.679 -18.854 1.00 0.00 H +ATOM 382 CE3 TRP 23 24.329 -85.487 -18.351 1.00 0.00 C +ATOM 383 HE3 TRP 23 24.462 -85.551 -17.282 1.00 0.00 H +ATOM 384 CD2 TRP 23 23.042 -85.333 -18.871 1.00 0.00 C +ATOM 385 HA TRP 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 386 C TRP 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 387 O TRP 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 388 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 389 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 390 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 391 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 392 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 393 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 394 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 395 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 396 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 397 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 398 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 399 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 400 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 401 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 402 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 403 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 404 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 405 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 406 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 407 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 408 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 409 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 410 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 411 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 412 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 413 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 414 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 415 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 416 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 417 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 418 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 419 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 420 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 421 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 422 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 423 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 424 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 425 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 426 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 427 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 428 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 429 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 430 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 431 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 432 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 433 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 434 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 435 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 436 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 437 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 438 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 439 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 440 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 441 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 442 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 443 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 444 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 445 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 446 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 447 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 448 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 449 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 450 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 451 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 452 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 453 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 454 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 455 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 456 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 457 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 458 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 459 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 460 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 461 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 462 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 463 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 464 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 465 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 466 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 467 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 468 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 469 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 470 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 471 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 472 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 473 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 474 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 475 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 476 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 477 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 478 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 479 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 480 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 481 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 482 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 483 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 484 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 485 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 486 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 487 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 488 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 489 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 490 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 491 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 492 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 493 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 494 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 495 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 496 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 497 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 498 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 499 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 500 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 501 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 502 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 503 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 504 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 505 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 506 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 507 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 508 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 509 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 510 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 511 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 512 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 513 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 514 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 515 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 516 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 517 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 518 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 519 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 520 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 521 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 522 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 523 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 524 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 525 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 526 N MET 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 527 H MET 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 528 CA MET 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 529 CB MET 33 27.315 -82.525 -3.272 1.00 0.00 C +ATOM 530 HB2 MET 33 26.398 -81.940 -3.214 1.00 0.00 H +ATOM 531 HB3 MET 33 27.389 -82.989 -4.255 1.00 0.00 H +ATOM 532 CG MET 33 27.295 -83.605 -2.204 1.00 0.00 C +ATOM 533 HG2 MET 33 26.492 -84.303 -2.443 1.00 0.00 H +ATOM 534 HG3 MET 33 28.252 -84.128 -2.232 1.00 0.00 H +ATOM 535 SD MET 33 27.030 -82.943 -0.547 1.00 0.00 S +ATOM 536 CE MET 33 27.063 -84.446 0.427 1.00 0.00 C +ATOM 537 HE1 MET 33 28.027 -84.938 0.303 1.00 0.00 H +ATOM 538 HE2 MET 33 26.912 -84.201 1.479 1.00 0.00 H +ATOM 539 HE3 MET 33 26.268 -85.113 0.092 1.00 0.00 H +ATOM 540 HA MET 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 541 C MET 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 542 O MET 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 543 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 544 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 545 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 546 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 547 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 548 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 549 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 550 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 551 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 552 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 553 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 554 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 555 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 556 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 557 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 558 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 559 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 560 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 561 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 562 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 563 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 564 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 565 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 566 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 567 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 568 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 569 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 570 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 571 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 572 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 573 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 574 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 575 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 576 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 577 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 578 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 579 N LEU 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 580 H LEU 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 581 CA LEU 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 582 CB LEU 37 33.048 -83.879 0.496 1.00 0.00 C +ATOM 583 HB2 LEU 37 31.985 -83.889 0.734 1.00 0.00 H +ATOM 584 HB3 LEU 37 33.178 -83.869 -0.586 1.00 0.00 H +ATOM 585 CG LEU 37 33.713 -85.128 1.077 1.00 0.00 C +ATOM 586 HG LEU 37 34.787 -85.068 0.903 1.00 0.00 H +ATOM 587 CD1 LEU 37 33.448 -85.233 2.571 1.00 0.00 C +ATOM 588 HD11 LEU 37 32.374 -85.292 2.747 1.00 0.00 H +ATOM 589 HD12 LEU 37 33.929 -86.128 2.965 1.00 0.00 H +ATOM 590 HD13 LEU 37 33.849 -84.353 3.075 1.00 0.00 H +ATOM 591 CD2 LEU 37 33.176 -86.384 0.410 1.00 0.00 C +ATOM 592 HD21 LEU 37 33.380 -86.342 -0.661 1.00 0.00 H +ATOM 593 HD22 LEU 37 33.662 -87.260 0.838 1.00 0.00 H +ATOM 594 HD23 LEU 37 32.100 -86.450 0.572 1.00 0.00 H +ATOM 595 HA LEU 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 596 C LEU 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 597 O LEU 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 598 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 599 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 600 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 601 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 602 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 603 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 604 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 605 N ALA 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 606 H ALA 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 607 CA ALA 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 608 CB ALA 39 38.874 -82.519 -4.462 1.00 0.00 C +ATOM 609 HB1 ALA 39 39.474 -81.803 -3.899 1.00 0.00 H +ATOM 610 HB2 ALA 39 38.973 -83.508 -4.013 1.00 0.00 H +ATOM 611 HB3 ALA 39 39.223 -82.552 -5.494 1.00 0.00 H +ATOM 612 HA ALA 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 613 C ALA 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 614 O ALA 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 615 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 616 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 617 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 618 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 619 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 620 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 621 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 622 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 623 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 624 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 625 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 626 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 627 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 628 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 629 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 630 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 631 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 632 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 633 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 634 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 635 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 636 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 637 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 638 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 639 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 640 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 641 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 642 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 643 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 644 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 645 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 646 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 647 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 648 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 649 N ASP 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 650 H ASP 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 651 CA ASP 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 652 CB ASP 43 29.884 -89.033 -12.452 1.00 0.00 C +ATOM 653 HB2 ASP 43 29.493 -88.069 -12.779 1.00 0.00 H +ATOM 654 HB3 ASP 43 29.081 -89.770 -12.451 1.00 0.00 H +ATOM 655 CG ASP 43 30.447 -88.899 -11.051 1.00 0.00 C +ATOM 656 OD1 ASP 43 31.651 -88.590 -10.921 1.00 0.00 O +ATOM 657 OD2 ASP 43 29.685 -89.101 -10.082 1.00 0.00 O +ATOM 658 HA ASP 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 659 C ASP 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 660 O ASP 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 661 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 662 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 663 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 664 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 665 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 666 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 667 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 668 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 669 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 670 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 671 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 672 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 673 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 674 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 675 N LYN 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 676 H LYN 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 677 CA LYN 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 678 CB LYN 45 25.266 -89.253 -17.470 1.00 0.00 C +ATOM 679 HB2 LYN 45 25.726 -88.747 -16.621 1.00 0.00 H +ATOM 680 HB3 LYN 45 25.701 -88.876 -18.396 1.00 0.00 H +ATOM 681 CG LYN 45 23.770 -88.987 -17.468 1.00 0.00 C +ATOM 682 HG2 LYN 45 23.323 -89.505 -18.317 1.00 0.00 H +ATOM 683 HG3 LYN 45 23.349 -89.376 -16.541 1.00 0.00 H +ATOM 684 CD LYN 45 23.474 -87.499 -17.571 1.00 0.00 C +ATOM 685 HD2 LYN 45 22.407 -87.345 -17.414 1.00 0.00 H +ATOM 686 HD3 LYN 45 24.035 -86.979 -16.795 1.00 0.00 H +ATOM 687 CE LYN 45 23.868 -86.952 -18.934 1.00 0.00 C +ATOM 688 HE2 LYN 45 24.935 -87.127 -19.077 1.00 0.00 H +ATOM 689 HE3 LYN 45 23.307 -87.493 -19.695 1.00 0.00 H +ATOM 690 NZ LYN 45 23.585 -85.495 -19.050 1.00 0.00 N +ATOM 691 HZ2 LYN 45 23.859 -85.171 -19.966 1.00 0.00 H +ATOM 692 HZ3 LYN 45 22.597 -85.332 -18.918 1.00 0.00 H +ATOM 693 HA LYN 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 694 C LYN 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 695 O LYN 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 696 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 697 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 698 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 699 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 700 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 701 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 702 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 703 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 704 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 705 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 706 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 707 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 708 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 709 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 710 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 711 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 712 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 713 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 714 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 715 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 716 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 717 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 718 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 719 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 720 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 721 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 722 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 723 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 724 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 725 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 726 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 727 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 728 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 729 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 730 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 731 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 732 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 733 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 734 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 735 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 736 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 737 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 738 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 739 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 740 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 741 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 742 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 743 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 744 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 745 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 746 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 747 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 748 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 749 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 750 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 751 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 752 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 753 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 754 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 755 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 756 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 757 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 758 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 759 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 760 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 761 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 762 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 763 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 764 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 765 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 766 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 767 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 768 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 769 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 770 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 771 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 772 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 773 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 774 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 775 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 776 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 777 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 778 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 779 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 780 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 781 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 782 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 783 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 784 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 785 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 786 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 787 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 788 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 789 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 790 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 791 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 792 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 793 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 794 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 795 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 796 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 797 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 798 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 799 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 800 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 801 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 802 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 803 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 804 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 805 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 806 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 807 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 808 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 809 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 810 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 811 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 812 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 813 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 814 N LYN 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 815 H LYN 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 816 CA LYN 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 817 CB LYN 54 32.301 -94.491 -10.199 1.00 0.00 C +ATOM 818 HB2 LYN 54 33.358 -94.431 -10.462 1.00 0.00 H +ATOM 819 HB3 LYN 54 32.026 -93.623 -9.600 1.00 0.00 H +ATOM 820 CG LYN 54 32.050 -95.758 -9.398 1.00 0.00 C +ATOM 821 HG2 LYN 54 30.989 -95.808 -9.152 1.00 0.00 H +ATOM 822 HG3 LYN 54 32.321 -96.617 -10.013 1.00 0.00 H +ATOM 823 CD LYN 54 32.869 -95.774 -8.118 1.00 0.00 C +ATOM 824 HD2 LYN 54 33.925 -95.713 -8.380 1.00 0.00 H +ATOM 825 HD3 LYN 54 32.594 -94.906 -7.518 1.00 0.00 H +ATOM 826 CE LYN 54 32.619 -97.041 -7.318 1.00 0.00 C +ATOM 827 HE2 LYN 54 31.557 -97.090 -7.077 1.00 0.00 H +ATOM 828 HE3 LYN 54 32.889 -97.897 -7.938 1.00 0.00 H +ATOM 829 NZ LYN 54 33.415 -97.070 -6.059 1.00 0.00 N +ATOM 830 HZ2 LYN 54 33.221 -97.925 -5.558 1.00 0.00 H +ATOM 831 HZ3 LYN 54 34.399 -97.026 -6.282 1.00 0.00 H +ATOM 832 HA LYN 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 833 C LYN 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 834 O LYN 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 835 N ASH 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 836 H ASH 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 837 CA ASH 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 838 CB ASH 55 34.660 -96.376 -14.407 1.00 0.00 C +ATOM 839 HB2 ASH 55 34.971 -97.132 -15.128 1.00 0.00 H +ATOM 840 HB3 ASH 55 34.155 -95.564 -14.929 1.00 0.00 H +ATOM 841 CG ASH 55 35.878 -95.832 -13.687 1.00 0.00 C +ATOM 842 OD1 ASH 55 35.823 -95.694 -12.446 1.00 0.00 O +ATOM 843 OD2 ASH 55 36.888 -95.544 -14.362 1.00 0.00 O +ATOM 844 HD2 ASH 55 37.578 -95.214 -13.781 1.00 0.00 H +ATOM 845 HA ASH 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 846 C ASH 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 847 O ASH 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 848 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 849 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 850 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 851 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 852 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 853 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 854 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 855 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 856 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 857 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 858 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 859 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 860 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 861 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 862 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 863 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 864 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 Zn +ATOM 865 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 866 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 867 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 868 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 869 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 870 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +ATOM 871 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 872 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 873 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 17 15 13 16 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 65 60 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 68 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 65 69 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 864 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 104 106 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 111 112 113 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 153 132 154 135 +CONECT 135 136 137 138 134 +CONECT 136 135 +CONECT 137 135 +CONECT 138 135 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 142 143 144 +CONECT 142 141 +CONECT 143 141 +CONECT 144 141 145 146 +CONECT 145 144 +CONECT 146 144 147 150 +CONECT 147 146 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 146 151 152 +CONECT 151 150 +CONECT 152 150 +CONECT 153 134 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 165 169 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 170 175 +CONECT 174 173 +CONECT 175 173 +CONECT 176 178 179 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 182 181 176 180 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 201 202 188 +CONECT 188 189 190 194 187 +CONECT 189 188 +CONECT 190 188 191 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 +CONECT 194 188 195 196 197 +CONECT 195 194 +CONECT 196 194 +CONECT 197 194 198 199 200 +CONECT 198 197 +CONECT 199 197 +CONECT 200 197 +CONECT 201 187 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 216 204 215 207 +CONECT 207 208 209 210 206 +CONECT 208 207 +CONECT 209 207 +CONECT 210 207 211 212 +CONECT 211 210 +CONECT 212 210 213 214 +CONECT 213 212 +CONECT 214 212 +CONECT 215 206 +CONECT 216 217 218 206 +CONECT 217 216 +CONECT 218 220 216 219 +CONECT 219 218 +CONECT 220 221 222 238 218 +CONECT 221 220 +CONECT 222 225 220 223 224 +CONECT 223 222 +CONECT 224 222 +CONECT 225 227 226 228 222 +CONECT 226 225 +CONECT 227 225 +CONECT 228 229 225 231 230 +CONECT 229 228 +CONECT 230 228 +CONECT 231 233 228 234 232 +CONECT 232 231 +CONECT 233 231 +CONECT 234 237 231 235 236 +CONECT 235 234 +CONECT 236 234 +CONECT 237 234 +CONECT 238 239 220 240 +CONECT 239 238 +CONECT 240 238 242 241 +CONECT 241 240 +CONECT 242 245 240 243 244 +CONECT 243 242 +CONECT 244 242 +CONECT 245 246 247 242 +CONECT 246 245 +CONECT 247 249 245 248 +CONECT 248 247 +CONECT 249 251 250 261 247 +CONECT 250 249 +CONECT 251 257 252 253 249 +CONECT 252 251 +CONECT 253 251 256 255 254 +CONECT 254 253 +CONECT 255 253 +CONECT 256 253 +CONECT 257 259 260 258 251 +CONECT 258 257 +CONECT 259 257 +CONECT 260 257 +CONECT 261 263 249 262 +CONECT 262 261 +CONECT 263 273 264 261 +CONECT 264 265 263 274 267 +CONECT 265 266 280 264 +CONECT 266 265 +CONECT 267 264 268 275 276 +CONECT 268 269 270 267 +CONECT 269 272 278 268 +CONECT 270 271 268 277 +CONECT 271 272 279 270 +CONECT 272 864 271 269 +CONECT 273 263 +CONECT 274 264 +CONECT 275 267 +CONECT 276 267 +CONECT 277 270 +CONECT 278 269 +CONECT 279 271 +CONECT 280 282 265 281 +CONECT 281 280 +CONECT 282 283 284 292 280 +CONECT 283 282 +CONECT 284 285 286 282 290 +CONECT 285 284 +CONECT 286 287 288 284 289 +CONECT 287 286 +CONECT 288 286 +CONECT 289 286 +CONECT 290 284 291 +CONECT 291 290 +CONECT 292 294 282 293 +CONECT 293 292 +CONECT 294 304 295 292 +CONECT 295 296 298 294 305 +CONECT 296 297 311 295 +CONECT 297 296 +CONECT 298 306 307 295 299 +CONECT 299 298 300 301 +CONECT 300 309 299 303 +CONECT 301 299 308 302 +CONECT 302 303 301 310 +CONECT 303 300 302 864 +CONECT 304 294 +CONECT 305 295 +CONECT 306 298 +CONECT 307 298 +CONECT 308 301 +CONECT 309 300 +CONECT 310 302 +CONECT 311 313 296 312 +CONECT 312 311 +CONECT 313 324 314 311 315 +CONECT 314 313 +CONECT 315 313 318 317 316 +CONECT 316 315 +CONECT 317 315 +CONECT 318 320 321 315 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 322 318 323 +CONECT 322 321 +CONECT 323 321 +CONECT 324 326 325 313 +CONECT 325 324 +CONECT 326 328 327 324 +CONECT 327 326 +CONECT 328 334 330 329 326 +CONECT 329 328 +CONECT 330 333 332 328 331 +CONECT 331 330 +CONECT 332 330 +CONECT 333 330 +CONECT 334 336 335 328 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 350 340 339 336 +CONECT 339 338 +CONECT 340 341 346 338 342 +CONECT 341 340 +CONECT 342 340 343 345 344 +CONECT 343 342 +CONECT 344 342 +CONECT 345 342 +CONECT 346 349 348 340 347 +CONECT 347 346 +CONECT 348 346 +CONECT 349 346 +CONECT 350 351 352 338 +CONECT 351 350 +CONECT 352 354 350 353 +CONECT 353 352 +CONECT 354 356 355 362 352 +CONECT 355 354 +CONECT 356 359 357 358 354 +CONECT 357 356 +CONECT 358 356 +CONECT 359 360 361 356 +CONECT 360 359 +CONECT 361 359 +CONECT 362 354 364 363 +CONECT 363 362 +CONECT 364 365 362 366 +CONECT 365 364 +CONECT 366 364 386 385 367 +CONECT 367 368 369 370 366 +CONECT 368 367 +CONECT 369 367 +CONECT 370 367 371 384 +CONECT 371 370 372 373 +CONECT 372 371 +CONECT 373 371 374 375 +CONECT 374 373 +CONECT 375 373 376 384 +CONECT 376 375 377 378 +CONECT 377 376 +CONECT 378 376 379 380 +CONECT 379 378 +CONECT 380 378 381 382 +CONECT 381 380 +CONECT 382 380 383 384 +CONECT 383 382 +CONECT 384 370 375 382 +CONECT 385 366 +CONECT 386 388 366 387 +CONECT 387 386 +CONECT 388 389 390 386 +CONECT 389 388 +CONECT 390 392 388 391 396 +CONECT 391 390 +CONECT 392 394 393 395 390 +CONECT 393 392 +CONECT 394 392 +CONECT 395 392 +CONECT 396 390 397 398 +CONECT 397 396 +CONECT 398 396 399 400 +CONECT 399 398 +CONECT 400 398 402 401 411 +CONECT 401 400 +CONECT 402 405 400 403 404 +CONECT 403 402 +CONECT 404 402 +CONECT 405 406 408 407 402 +CONECT 406 405 +CONECT 407 405 +CONECT 408 410 405 409 +CONECT 409 408 +CONECT 410 408 +CONECT 411 400 413 412 +CONECT 412 411 +CONECT 413 414 411 415 +CONECT 414 413 +CONECT 415 413 417 421 416 +CONECT 416 415 +CONECT 417 418 419 415 420 +CONECT 418 417 +CONECT 419 417 +CONECT 420 417 +CONECT 421 423 415 422 +CONECT 422 421 +CONECT 423 424 425 421 +CONECT 424 423 +CONECT 425 427 423 426 436 +CONECT 426 425 +CONECT 427 428 429 430 425 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 427 432 431 +CONECT 431 430 +CONECT 432 430 +CONECT 433 434 435 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 425 438 437 +CONECT 437 436 +CONECT 438 439 436 440 +CONECT 439 438 +CONECT 440 438 442 441 458 +CONECT 441 440 +CONECT 442 445 443 444 440 +CONECT 443 442 +CONECT 444 442 +CONECT 445 448 447 446 442 +CONECT 446 445 +CONECT 447 445 +CONECT 448 451 449 445 450 +CONECT 449 448 +CONECT 450 448 +CONECT 451 454 453 452 448 +CONECT 452 451 +CONECT 453 451 +CONECT 454 457 456 455 451 +CONECT 455 454 +CONECT 456 454 +CONECT 457 454 +CONECT 458 440 460 459 +CONECT 459 458 +CONECT 460 461 458 462 +CONECT 461 460 +CONECT 462 460 464 463 478 +CONECT 463 462 +CONECT 464 467 465 462 466 +CONECT 465 464 +CONECT 466 464 +CONECT 467 468 476 464 +CONECT 468 470 469 467 +CONECT 469 468 +CONECT 470 471 472 468 +CONECT 471 470 +CONECT 472 473 470 474 +CONECT 473 472 +CONECT 474 472 475 476 +CONECT 475 474 +CONECT 476 474 467 477 +CONECT 477 476 +CONECT 478 462 480 479 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 484 480 492 483 +CONECT 483 482 +CONECT 484 485 490 486 482 +CONECT 485 484 +CONECT 486 487 484 488 489 +CONECT 487 486 +CONECT 488 486 +CONECT 489 486 +CONECT 490 491 484 +CONECT 491 490 +CONECT 492 494 482 493 +CONECT 493 492 +CONECT 494 495 496 492 +CONECT 495 494 +CONECT 496 498 494 497 514 +CONECT 497 496 +CONECT 498 501 499 500 496 +CONECT 499 498 +CONECT 500 498 +CONECT 501 504 503 502 498 +CONECT 502 501 +CONECT 503 501 +CONECT 504 507 505 506 501 +CONECT 505 504 +CONECT 506 504 +CONECT 507 509 510 508 504 +CONECT 508 507 +CONECT 509 507 +CONECT 510 512 507 511 513 +CONECT 511 510 +CONECT 512 510 +CONECT 513 510 +CONECT 514 496 516 515 +CONECT 515 514 +CONECT 516 517 514 518 +CONECT 517 516 +CONECT 518 516 520 519 524 +CONECT 519 518 +CONECT 520 522 523 518 521 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 518 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 541 540 529 +CONECT 529 530 531 532 528 +CONECT 530 529 +CONECT 531 529 +CONECT 532 529 533 534 535 +CONECT 533 532 +CONECT 534 532 +CONECT 535 532 536 +CONECT 536 535 537 538 539 +CONECT 537 536 +CONECT 538 536 +CONECT 539 536 +CONECT 540 528 +CONECT 541 543 528 542 +CONECT 542 541 +CONECT 543 544 545 541 +CONECT 544 543 +CONECT 545 547 543 551 546 +CONECT 546 545 +CONECT 547 548 549 550 545 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 553 545 552 +CONECT 552 551 +CONECT 553 554 555 551 +CONECT 554 553 +CONECT 555 557 553 556 565 +CONECT 556 555 +CONECT 557 560 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 562 561 557 +CONECT 561 560 +CONECT 562 564 563 560 +CONECT 563 562 +CONECT 564 562 +CONECT 565 555 567 566 +CONECT 566 565 +CONECT 567 568 565 569 +CONECT 568 567 +CONECT 569 567 570 571 577 +CONECT 570 569 +CONECT 571 572 569 574 573 +CONECT 572 571 +CONECT 573 571 +CONECT 574 575 576 571 +CONECT 575 574 +CONECT 576 574 +CONECT 577 569 579 578 +CONECT 578 577 +CONECT 579 580 577 581 +CONECT 580 579 +CONECT 581 579 596 595 582 +CONECT 582 583 584 585 581 +CONECT 583 582 +CONECT 584 582 +CONECT 585 582 586 587 591 +CONECT 586 585 +CONECT 587 585 588 589 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 585 592 593 594 +CONECT 592 591 +CONECT 593 591 +CONECT 594 591 +CONECT 595 581 +CONECT 596 598 581 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 602 598 601 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 613 612 605 608 +CONECT 608 609 610 611 607 +CONECT 609 608 +CONECT 610 608 +CONECT 611 608 +CONECT 612 607 +CONECT 613 615 614 607 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 619 625 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 641 639 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 644 638 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 659 649 658 652 +CONECT 652 653 654 655 651 +CONECT 653 652 +CONECT 654 652 +CONECT 655 652 656 657 +CONECT 656 655 +CONECT 657 655 +CONECT 658 651 +CONECT 659 660 661 651 +CONECT 660 659 +CONECT 661 663 659 662 +CONECT 662 661 +CONECT 663 664 665 673 661 +CONECT 664 663 +CONECT 665 667 671 663 666 +CONECT 666 665 +CONECT 667 670 669 668 665 +CONECT 668 667 +CONECT 669 667 +CONECT 670 667 +CONECT 671 665 672 +CONECT 672 671 +CONECT 673 675 663 674 +CONECT 674 673 +CONECT 675 676 677 673 +CONECT 676 675 +CONECT 677 694 675 693 678 +CONECT 678 679 680 681 677 +CONECT 679 678 +CONECT 680 678 +CONECT 681 678 682 683 684 +CONECT 682 681 +CONECT 683 681 +CONECT 684 681 685 686 687 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 688 689 690 +CONECT 688 687 +CONECT 689 687 +CONECT 690 687 691 692 +CONECT 691 690 +CONECT 692 690 +CONECT 693 677 +CONECT 694 695 696 677 +CONECT 695 694 +CONECT 696 698 694 697 +CONECT 697 696 +CONECT 698 699 706 700 696 +CONECT 699 698 +CONECT 700 703 698 701 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 705 704 700 +CONECT 704 703 +CONECT 705 703 +CONECT 706 708 698 707 +CONECT 707 706 +CONECT 708 709 710 706 +CONECT 709 708 +CONECT 710 712 708 718 711 +CONECT 711 710 +CONECT 712 714 715 713 710 +CONECT 713 712 +CONECT 714 712 +CONECT 715 716 712 717 +CONECT 716 715 +CONECT 717 715 +CONECT 718 720 710 719 +CONECT 719 718 +CONECT 720 721 722 718 +CONECT 721 720 +CONECT 722 724 723 720 728 +CONECT 723 722 +CONECT 724 727 725 726 722 +CONECT 725 724 +CONECT 726 724 +CONECT 727 724 +CONECT 728 722 729 730 +CONECT 729 728 +CONECT 730 728 731 732 +CONECT 731 730 +CONECT 732 730 733 734 742 +CONECT 733 732 +CONECT 734 736 732 740 735 +CONECT 735 734 +CONECT 736 738 739 737 734 +CONECT 737 736 +CONECT 738 736 +CONECT 739 736 +CONECT 740 741 734 +CONECT 741 740 +CONECT 742 732 744 743 +CONECT 743 742 +CONECT 744 745 746 742 +CONECT 745 744 +CONECT 746 747 744 748 764 +CONECT 747 746 +CONECT 748 751 746 750 749 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 752 753 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 760 759 758 754 +CONECT 758 757 +CONECT 759 757 +CONECT 760 762 761 763 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 760 +CONECT 764 746 766 765 +CONECT 765 764 +CONECT 766 767 764 768 +CONECT 767 766 +CONECT 768 766 778 770 769 +CONECT 769 768 +CONECT 770 771 768 776 772 +CONECT 771 770 +CONECT 772 770 773 774 775 +CONECT 773 772 +CONECT 774 772 +CONECT 775 772 +CONECT 776 777 770 +CONECT 777 776 +CONECT 778 779 768 780 +CONECT 779 778 +CONECT 780 778 782 781 +CONECT 781 780 +CONECT 782 783 780 784 798 +CONECT 783 782 +CONECT 784 787 782 786 785 +CONECT 785 784 +CONECT 786 784 +CONECT 787 796 788 784 +CONECT 788 790 787 789 +CONECT 789 788 +CONECT 790 792 791 788 +CONECT 791 790 +CONECT 792 793 794 790 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 794 797 787 +CONECT 797 796 +CONECT 798 782 800 799 +CONECT 799 798 +CONECT 800 801 798 802 +CONECT 801 800 +CONECT 802 800 804 812 803 +CONECT 803 802 +CONECT 804 810 806 805 802 +CONECT 805 804 +CONECT 806 807 809 804 808 +CONECT 807 806 +CONECT 808 806 +CONECT 809 806 +CONECT 810 811 804 +CONECT 811 810 +CONECT 812 813 802 814 +CONECT 813 812 +CONECT 814 812 816 815 +CONECT 815 814 +CONECT 816 833 832 814 817 +CONECT 817 818 819 820 816 +CONECT 818 817 +CONECT 819 817 +CONECT 820 817 821 822 823 +CONECT 821 820 +CONECT 822 820 +CONECT 823 820 824 825 826 +CONECT 824 823 +CONECT 825 823 +CONECT 826 823 827 828 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 830 831 +CONECT 830 829 +CONECT 831 829 +CONECT 832 816 +CONECT 833 835 834 816 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 845 835 846 838 +CONECT 838 839 840 841 837 +CONECT 839 838 +CONECT 840 838 +CONECT 841 838 842 843 +CONECT 842 841 +CONECT 843 841 844 +CONECT 844 843 +CONECT 845 837 +CONECT 846 837 848 847 +CONECT 847 846 +CONECT 848 849 846 850 +CONECT 849 848 +CONECT 850 852 848 861 851 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 856 852 857 858 +CONECT 856 855 +CONECT 857 855 +CONECT 858 855 859 860 +CONECT 859 858 +CONECT 860 858 +CONECT 861 863 850 862 +CONECT 862 861 +CONECT 863 861 +CONECT 864 87 303 865 272 +CONECT 865 864 867 +CONECT 866 869 867 870 868 +CONECT 867 865 866 +CONECT 868 866 +CONECT 869 866 +CONECT 870 866 +CONECT 871 872 +CONECT 872 871 873 +CONECT 873 872 +MASTER 0 0 0 0 0 0 0 0 873 0 873 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_4.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_4.pdb new file mode 100644 index 0000000..9984a45 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_4.pdb @@ -0,0 +1,1793 @@ +COMPND fitness: -0.3891 51.34500000000048 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 55.366 58.077 52.650 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.974 37.907 23.853 1.00 0.00 N +ATOM 2 H1 MET 1 14.962 38.311 24.779 1.00 0.00 H +ATOM 3 H2 MET 1 14.210 38.275 23.324 1.00 0.00 H +ATOM 4 H3 MET 1 15.836 38.197 23.429 1.00 0.00 H +ATOM 5 CA MET 1 14.919 36.440 23.934 1.00 0.00 C +ATOM 6 HA MET 1 13.956 36.158 24.362 1.00 0.00 H +ATOM 7 CB MET 1 15.081 35.785 22.548 1.00 0.00 C +ATOM 8 HB2 MET 1 14.229 36.080 21.938 1.00 0.00 H +ATOM 9 HB3 MET 1 15.990 36.158 22.084 1.00 0.00 H +ATOM 10 CG MET 1 15.146 34.242 22.601 1.00 0.00 C +ATOM 11 HG2 MET 1 16.012 33.957 23.214 1.00 0.00 H +ATOM 12 HG3 MET 1 14.239 33.866 23.091 1.00 0.00 H +ATOM 13 SD MET 1 15.334 33.411 20.993 1.00 0.00 S +ATOM 14 CE MET 1 13.668 33.584 20.286 1.00 0.00 C +ATOM 15 HE1 MET 1 13.398 34.637 20.207 1.00 0.00 H +ATOM 16 HE2 MET 1 13.656 33.145 19.287 1.00 0.00 H +ATOM 17 HE3 MET 1 12.938 33.064 20.908 1.00 0.00 H +ATOM 18 C MET 1 16.013 35.966 24.910 1.00 0.00 C +ATOM 19 O MET 1 17.164 36.345 24.741 1.00 0.00 O +ATOM 20 N GLN 2 15.654 35.136 25.886 1.00 0.00 N +ATOM 21 H GLN 2 14.686 34.941 26.060 1.00 0.00 H +ATOM 22 CA GLN 2 16.614 34.446 26.760 1.00 0.00 C +ATOM 23 HA GLN 2 17.406 35.121 27.032 1.00 0.00 H +ATOM 24 CB GLN 2 15.887 34.044 28.061 1.00 0.00 C +ATOM 25 HB2 GLN 2 14.919 33.616 27.825 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.433 33.289 28.592 1.00 0.00 H +ATOM 27 CG GLN 2 15.684 35.224 29.051 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.256 36.058 28.525 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.936 34.887 29.761 1.00 0.00 H +ATOM 30 CD GLN 2 16.918 35.494 29.808 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.020 34.930 29.711 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.816 36.375 30.816 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.550 36.496 31.384 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.884 36.687 31.081 1.00 0.00 H +ATOM 35 C GLN 2 17.313 33.282 26.012 1.00 0.00 C +ATOM 36 O GLN 2 16.997 32.092 26.170 1.00 0.00 O +ATOM 37 N TYR 3 18.269 33.681 25.166 1.00 0.00 N +ATOM 38 H TYR 3 18.447 34.687 25.114 1.00 0.00 H +ATOM 39 CA TYR 3 19.146 32.822 24.374 1.00 0.00 C +ATOM 40 HA TYR 3 18.538 32.197 23.726 1.00 0.00 H +ATOM 41 CB TYR 3 19.997 33.782 23.539 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.350 34.593 24.167 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.892 33.278 23.251 1.00 0.00 H +ATOM 44 CG TYR 3 19.394 34.379 22.281 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.325 33.615 21.098 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.616 32.576 21.104 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.979 34.222 19.870 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.992 33.651 18.948 1.00 0.00 H +ATOM 49 CZ TYR 3 18.663 35.598 19.825 1.00 0.00 C +ATOM 50 OH TYR 3 18.365 36.205 18.642 1.00 0.00 O +ATOM 51 HH TYR 3 18.614 35.683 17.869 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.691 36.355 21.017 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.468 37.412 20.972 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.064 35.748 22.234 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.140 36.351 23.126 1.00 0.00 H +ATOM 56 C TYR 3 20.002 31.916 25.288 1.00 0.00 C +ATOM 57 O TYR 3 20.432 32.353 26.360 1.00 0.00 O +ATOM 58 N LYS 4 20.301 30.659 24.910 1.00 0.00 N +ATOM 59 H LYS 4 20.088 30.369 23.956 1.00 0.00 H +ATOM 60 CA LYS 4 20.905 29.630 25.797 1.00 0.00 C +ATOM 61 HA LYS 4 20.622 29.846 26.826 1.00 0.00 H +ATOM 62 CB LYS 4 20.354 28.224 25.457 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.349 28.090 24.376 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.038 27.470 25.855 1.00 0.00 H +ATOM 65 CG LYS 4 18.957 27.861 25.995 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.787 26.810 25.756 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.956 27.957 27.082 1.00 0.00 H +ATOM 68 CD LYS 4 17.794 28.674 25.409 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.778 29.664 25.859 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.963 28.796 24.338 1.00 0.00 H +ATOM 71 CE LYS 4 16.435 27.983 25.596 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.668 28.587 25.107 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.475 27.021 25.077 1.00 0.00 H +ATOM 74 NZ LYS 4 16.068 27.749 27.014 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.903 28.617 27.502 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.223 27.178 27.050 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.780 27.203 27.481 1.00 0.00 H +ATOM 78 C LYS 4 22.446 29.588 25.785 1.00 0.00 C +ATOM 79 O LYS 4 23.101 29.909 24.800 1.00 0.00 O +HETATM 80 N HX1 5 23.036 29.119 26.886 1.00 0.00 N +HETATM 81 CA HX1 5 24.488 28.900 27.064 1.00 0.00 C +HETATM 82 C HX1 5 24.728 27.705 27.994 1.00 0.00 C +HETATM 83 O HX1 5 24.220 27.697 29.118 1.00 0.00 O +HETATM 84 CB HX1 5 25.116 30.196 27.618 1.00 0.00 C +HETATM 85 CG HX1 5 26.625 30.258 27.775 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.542 29.328 27.358 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.293 31.301 28.436 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.591 30.959 28.378 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.772 29.759 27.799 1.00 0.00 N +HETATM 90 H HX1 5 22.442 28.952 27.696 1.00 0.00 H +HETATM 91 HA HX1 5 24.937 28.680 26.094 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.669 30.411 28.589 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.834 31.017 26.957 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.357 28.370 26.882 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.370 31.473 28.927 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.587 29.158 27.988 1.00 0.00 H +ATOM 97 N ILE 6 25.464 26.687 27.528 1.00 0.00 N +ATOM 98 H ILE 6 25.852 26.749 26.590 1.00 0.00 H +ATOM 99 CA ILE 6 25.857 25.507 28.319 1.00 0.00 C +ATOM 100 HA ILE 6 25.191 25.413 29.177 1.00 0.00 H +ATOM 101 CB ILE 6 25.674 24.217 27.476 1.00 0.00 C +ATOM 102 HB ILE 6 26.190 24.351 26.524 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.260 22.963 28.156 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.777 22.788 29.118 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.120 22.087 27.524 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.336 23.071 28.302 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.161 24.019 27.204 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.641 23.897 28.154 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.763 24.911 26.722 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.800 22.830 26.305 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.976 21.889 26.826 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.741 22.885 26.047 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.391 22.860 25.389 1.00 0.00 H +ATOM 114 C ILE 6 27.273 25.697 28.903 1.00 0.00 C +ATOM 115 O ILE 6 28.086 26.431 28.343 1.00 0.00 O +ATOM 116 N VAL 7 27.523 25.096 30.071 1.00 0.00 N +ATOM 117 H VAL 7 26.805 24.480 30.438 1.00 0.00 H +ATOM 118 CA VAL 7 28.688 25.336 30.942 1.00 0.00 C +ATOM 119 HA VAL 7 28.757 26.414 31.092 1.00 0.00 H +ATOM 120 CB VAL 7 28.398 24.694 32.319 1.00 0.00 C +ATOM 121 HB VAL 7 27.390 24.998 32.614 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.426 23.158 32.292 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.439 22.798 32.103 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.080 22.772 33.246 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.772 22.786 31.504 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.328 25.176 33.437 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.367 26.263 33.448 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.953 24.832 34.400 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.332 24.781 33.301 1.00 0.00 H +ATOM 130 C VAL 7 30.052 24.885 30.383 1.00 0.00 C +ATOM 131 O VAL 7 30.158 23.929 29.619 1.00 0.00 O +ATOM 132 N MET 8 31.111 25.562 30.842 1.00 0.00 N +ATOM 133 H MET 8 30.918 26.406 31.361 1.00 0.00 H +ATOM 134 CA MET 8 32.531 25.194 30.715 1.00 0.00 C +ATOM 135 HA MET 8 32.790 25.179 29.654 1.00 0.00 H +ATOM 136 CB MET 8 33.339 26.319 31.405 1.00 0.00 C +ATOM 137 HB2 MET 8 33.249 27.231 30.811 1.00 0.00 H +ATOM 138 HB3 MET 8 32.884 26.516 32.375 1.00 0.00 H +ATOM 139 CG MET 8 34.826 26.038 31.671 1.00 0.00 C +ATOM 140 HG2 MET 8 35.223 26.859 32.267 1.00 0.00 H +ATOM 141 HG3 MET 8 34.919 25.137 32.274 1.00 0.00 H +ATOM 142 SD MET 8 35.885 25.858 30.209 1.00 0.00 S +ATOM 143 CE MET 8 35.987 27.599 29.701 1.00 0.00 C +ATOM 144 HE1 MET 8 36.341 28.205 30.534 1.00 0.00 H +ATOM 145 HE2 MET 8 36.686 27.696 28.874 1.00 0.00 H +ATOM 146 HE3 MET 8 35.006 27.952 29.387 1.00 0.00 H +ATOM 147 C MET 8 32.875 23.812 31.314 1.00 0.00 C +ATOM 148 O MET 8 32.409 23.450 32.395 1.00 0.00 O +ATOM 149 N GLY 9 33.803 23.092 30.673 1.00 0.00 N +ATOM 150 H GLY 9 34.137 23.439 29.787 1.00 0.00 H +ATOM 151 CA GLY 9 34.384 21.839 31.175 1.00 0.00 C +ATOM 152 HA2 GLY 9 35.356 21.680 30.701 1.00 0.00 H +ATOM 153 HA3 GLY 9 34.556 21.942 32.250 1.00 0.00 H +ATOM 154 C GLY 9 33.522 20.595 30.930 1.00 0.00 C +ATOM 155 O GLY 9 32.752 20.536 29.975 1.00 0.00 O +ATOM 156 N LYS 10 33.687 19.569 31.783 1.00 0.00 N +ATOM 157 H LYS 10 34.423 19.664 32.464 1.00 0.00 H +ATOM 158 CA LYS 10 32.980 18.272 31.683 1.00 0.00 C +ATOM 159 HA LYS 10 32.035 18.452 31.160 1.00 0.00 H +ATOM 160 CB LYS 10 33.827 17.309 30.822 1.00 0.00 C +ATOM 161 HB2 LYS 10 34.432 17.894 30.129 1.00 0.00 H +ATOM 162 HB3 LYS 10 34.507 16.752 31.469 1.00 0.00 H +ATOM 163 CG LYS 10 32.991 16.325 29.983 1.00 0.00 C +ATOM 164 HG2 LYS 10 32.396 15.682 30.631 1.00 0.00 H +ATOM 165 HG3 LYS 10 32.320 16.892 29.337 1.00 0.00 H +ATOM 166 CD LYS 10 33.915 15.459 29.113 1.00 0.00 C +ATOM 167 HD2 LYS 10 34.573 16.115 28.539 1.00 0.00 H +ATOM 168 HD3 LYS 10 34.525 14.824 29.758 1.00 0.00 H +ATOM 169 CE LYS 10 33.124 14.581 28.137 1.00 0.00 C +ATOM 170 HE2 LYS 10 32.585 13.814 28.700 1.00 0.00 H +ATOM 171 HE3 LYS 10 32.389 15.209 27.627 1.00 0.00 H +ATOM 172 NZ LYS 10 34.022 13.969 27.125 1.00 0.00 N +ATOM 173 HZ1 LYS 10 34.787 13.470 27.555 1.00 0.00 H +ATOM 174 HZ2 LYS 10 33.523 13.352 26.499 1.00 0.00 H +ATOM 175 HZ3 LYS 10 34.431 14.710 26.544 1.00 0.00 H +ATOM 176 C LYS 10 32.586 17.644 33.035 1.00 0.00 C +ATOM 177 O LYS 10 32.078 16.525 33.079 1.00 0.00 O +ATOM 178 N ILE 11 32.862 18.333 34.147 1.00 0.00 N +ATOM 179 H ILE 11 33.317 19.222 34.034 1.00 0.00 H +ATOM 180 CA ILE 11 32.415 17.949 35.499 1.00 0.00 C +ATOM 181 HA ILE 11 32.299 16.866 35.545 1.00 0.00 H +ATOM 182 CB ILE 11 33.465 18.348 36.565 1.00 0.00 C +ATOM 183 HB ILE 11 33.028 18.145 37.545 1.00 0.00 H +ATOM 184 CG2 ILE 11 34.700 17.440 36.421 1.00 0.00 C +ATOM 185 HG21 ILE 11 35.224 17.646 35.488 1.00 0.00 H +ATOM 186 HG22 ILE 11 35.387 17.595 37.252 1.00 0.00 H +ATOM 187 HG23 ILE 11 34.395 16.393 36.431 1.00 0.00 H +ATOM 188 CG1 ILE 11 33.854 19.848 36.521 1.00 0.00 C +ATOM 189 HG12 ILE 11 34.373 20.069 35.587 1.00 0.00 H +ATOM 190 HG13 ILE 11 32.951 20.454 36.556 1.00 0.00 H +ATOM 191 CD1 ILE 11 34.743 20.305 37.686 1.00 0.00 C +ATOM 192 HD11 ILE 11 35.718 19.822 37.637 1.00 0.00 H +ATOM 193 HD12 ILE 11 34.889 21.384 37.622 1.00 0.00 H +ATOM 194 HD13 ILE 11 34.261 20.069 38.635 1.00 0.00 H +ATOM 195 C ILE 11 31.023 18.521 35.825 1.00 0.00 C +ATOM 196 O ILE 11 30.214 17.857 36.469 1.00 0.00 O +ATOM 197 N CYS 12 30.718 19.725 35.336 1.00 0.00 N +ATOM 198 H CYS 12 31.414 20.202 34.786 1.00 0.00 H +ATOM 199 CA CYS 12 29.382 20.317 35.361 1.00 0.00 C +ATOM 200 HA CYS 12 28.823 19.901 36.201 1.00 0.00 H +ATOM 201 CB CYS 12 29.514 21.836 35.565 1.00 0.00 C +ATOM 202 HB2 CYS 12 30.065 22.278 34.731 1.00 0.00 H +ATOM 203 HB3 CYS 12 28.520 22.278 35.611 1.00 0.00 H +ATOM 204 SG CYS 12 30.385 22.193 37.127 1.00 0.00 S +ATOM 205 HG CYS 12 29.866 23.408 37.340 1.00 0.00 H +ATOM 206 C CYS 12 28.639 19.979 34.061 1.00 0.00 C +ATOM 207 O CYS 12 29.261 19.839 33.012 1.00 0.00 O +ATOM 208 N LYS 13 27.302 19.901 34.110 1.00 0.00 N +ATOM 209 H LYS 13 26.856 19.938 35.014 1.00 0.00 H +ATOM 210 CA LYS 13 26.432 19.653 32.929 1.00 0.00 C +ATOM 211 HA LYS 13 27.041 19.854 32.031 1.00 0.00 H +ATOM 212 CB LYS 13 26.039 18.153 32.899 1.00 0.00 C +ATOM 213 HB2 LYS 13 26.861 17.579 33.322 1.00 0.00 H +ATOM 214 HB3 LYS 13 25.160 18.007 33.514 1.00 0.00 H +ATOM 215 CG LYS 13 25.793 17.627 31.473 1.00 0.00 C +ATOM 216 HG2 LYS 13 24.918 18.107 31.037 1.00 0.00 H +ATOM 217 HG3 LYS 13 26.660 17.876 30.855 1.00 0.00 H +ATOM 218 CD LYS 13 25.610 16.101 31.427 1.00 0.00 C +ATOM 219 HD2 LYS 13 25.673 15.776 30.387 1.00 0.00 H +ATOM 220 HD3 LYS 13 26.424 15.620 31.975 1.00 0.00 H +ATOM 221 CE LYS 13 24.262 15.641 32.003 1.00 0.00 C +ATOM 222 HE2 LYS 13 24.174 16.005 33.028 1.00 0.00 H +ATOM 223 HE3 LYS 13 23.462 16.093 31.406 1.00 0.00 H +ATOM 224 NZ LYS 13 24.129 14.161 31.975 1.00 0.00 N +ATOM 225 HZ1 LYS 13 24.942 13.708 32.389 1.00 0.00 H +ATOM 226 HZ2 LYS 13 23.293 13.840 32.460 1.00 0.00 H +ATOM 227 HZ3 LYS 13 24.092 13.823 31.015 1.00 0.00 H +ATOM 228 C LYS 13 25.250 20.633 32.829 1.00 0.00 C +ATOM 229 O LYS 13 24.241 20.345 32.193 1.00 0.00 O +ATOM 230 N GLY 14 25.356 21.774 33.519 1.00 0.00 N +ATOM 231 H GLY 14 26.229 21.956 33.973 1.00 0.00 H +ATOM 232 CA GLY 14 24.301 22.774 33.640 1.00 0.00 C +ATOM 233 HA2 GLY 14 23.347 22.272 33.787 1.00 0.00 H +ATOM 234 HA3 GLY 14 24.483 23.393 34.516 1.00 0.00 H +ATOM 235 C GLY 14 24.155 23.716 32.419 1.00 0.00 C +ATOM 236 O GLY 14 25.049 23.818 31.569 1.00 0.00 O +ATOM 237 N VAL 15 23.027 24.443 32.361 1.00 0.00 N +ATOM 238 H VAL 15 22.375 24.340 33.132 1.00 0.00 H +ATOM 239 CA VAL 15 22.652 25.397 31.332 1.00 0.00 C +ATOM 240 HA VAL 15 23.521 25.651 30.732 1.00 0.00 H +ATOM 241 CB VAL 15 21.618 24.752 30.385 1.00 0.00 C +ATOM 242 HB VAL 15 22.067 23.828 29.967 1.00 0.00 H +ATOM 243 CG1 VAL 15 20.297 24.332 31.075 1.00 0.00 C +ATOM 244 HG11 VAL 15 19.800 25.198 31.488 1.00 0.00 H +ATOM 245 HG12 VAL 15 19.642 23.852 30.343 1.00 0.00 H +ATOM 246 HG13 VAL 15 20.503 23.615 31.866 1.00 0.00 H +ATOM 247 CG2 VAL 15 21.256 25.656 29.194 1.00 0.00 C +ATOM 248 HG21 VAL 15 22.167 25.976 28.697 1.00 0.00 H +ATOM 249 HG22 VAL 15 20.650 25.090 28.482 1.00 0.00 H +ATOM 250 HG23 VAL 15 20.691 26.511 29.537 1.00 0.00 H +ATOM 251 C VAL 15 22.131 26.647 31.995 1.00 0.00 C +ATOM 252 O VAL 15 21.588 26.632 33.097 1.00 0.00 O +HETATM 253 N HY1 16 22.314 27.804 31.345 1.00 0.00 N +HETATM 254 CA HY1 16 21.717 29.122 31.665 1.00 0.00 C +HETATM 255 C HY1 16 21.477 29.915 30.382 1.00 0.00 C +HETATM 256 O HY1 16 21.676 29.423 29.284 1.00 0.00 O +HETATM 257 CB HY1 16 22.600 29.816 32.746 1.00 0.00 C +HETATM 258 CG HY1 16 23.963 30.189 32.254 1.00 0.00 C +HETATM 259 CD2 HY1 16 24.304 31.371 31.647 1.00 0.00 C +HETATM 260 ND1 HY1 16 25.088 29.415 32.314 1.00 0.00 N +HETATM 261 CE1 HY1 16 26.096 30.135 31.787 1.00 0.00 C +HETATM 262 NE2 HY1 16 25.670 31.332 31.338 1.00 0.00 N +HETATM 263 H HY1 16 22.818 27.774 30.448 1.00 0.00 H +HETATM 264 HA HY1 16 20.730 28.940 32.121 1.00 0.00 H +HETATM 265 HB2 HY1 16 22.078 30.719 33.098 1.00 0.00 H +HETATM 266 HB3 HY1 16 22.691 29.180 33.619 1.00 0.00 H +HETATM 267 HD1 HY1 16 25.169 28.513 32.757 1.00 0.00 H +HETATM 268 HD2 HY1 16 23.639 32.209 31.457 1.00 0.00 H +HETATM 269 HE1 HY1 16 27.143 29.814 31.758 1.00 0.00 H +ATOM 270 N THR 17 21.024 31.144 30.552 1.00 0.00 N +ATOM 271 H THR 17 20.911 31.487 31.498 1.00 0.00 H +ATOM 272 CA THR 17 20.584 32.073 29.481 1.00 0.00 C +ATOM 273 HA THR 17 20.992 31.671 28.519 1.00 0.00 H +ATOM 274 CB THR 17 19.054 32.046 29.306 1.00 0.00 C +ATOM 275 HB THR 17 18.755 32.641 28.428 1.00 0.00 H +ATOM 276 CG2 THR 17 18.459 30.719 28.967 1.00 0.00 C +ATOM 277 HG21 THR 17 18.673 29.933 29.705 1.00 0.00 H +ATOM 278 HG22 THR 17 17.387 30.720 28.833 1.00 0.00 H +ATOM 279 HG23 THR 17 18.868 30.356 28.002 1.00 0.00 H +ATOM 280 OG1 THR 17 18.357 32.474 30.439 1.00 0.00 O +ATOM 281 HG1 THR 17 18.447 33.452 30.430 1.00 0.00 H +ATOM 282 C THR 17 21.128 33.488 29.521 1.00 0.00 C +ATOM 283 O THR 17 21.644 33.940 30.543 1.00 0.00 O +HETATM 284 N HY2 18 21.011 34.206 28.396 1.00 0.00 N +HETATM 285 CA HY2 18 21.351 35.602 28.295 1.00 0.00 C +HETATM 286 C HY2 18 20.235 36.323 27.509 1.00 0.00 C +HETATM 287 O HY2 18 19.870 35.865 26.433 1.00 0.00 O +HETATM 288 CB HY2 18 22.690 35.795 27.582 1.00 0.00 C +HETATM 289 CG HY2 18 23.913 35.313 28.346 1.00 0.00 C +HETATM 290 CD2 HY2 18 24.319 34.019 28.534 1.00 0.00 C +HETATM 291 ND1 HY2 18 24.839 36.087 28.990 1.00 0.00 N +HETATM 292 CE1 HY2 18 25.758 35.283 29.544 1.00 0.00 C +HETATM 293 NE2 HY2 18 25.480 33.998 29.311 1.00 0.00 N +HETATM 294 H HY2 18 20.648 33.748 27.542 1.00 0.00 H +HETATM 295 HA HY2 18 21.419 36.063 29.280 1.00 0.00 H +HETATM 296 HB2 HY2 18 22.679 35.278 26.611 1.00 0.00 H +HETATM 297 HB3 HY2 18 22.857 36.871 27.355 1.00 0.00 H +HETATM 298 HD1 HY2 18 24.867 37.091 29.020 1.00 0.00 H +HETATM 299 HD2 HY2 18 23.816 33.148 28.170 1.00 0.00 H +HETATM 300 HE1 HY2 18 26.624 35.625 30.086 1.00 0.00 H +ATOM 301 N GLU 19 19.710 37.417 28.053 1.00 0.00 N +ATOM 302 H GLU 19 20.055 37.745 28.951 1.00 0.00 H +ATOM 303 CA GLU 19 18.672 38.239 27.375 1.00 0.00 C +ATOM 304 HA GLU 19 17.952 37.561 26.930 1.00 0.00 H +ATOM 305 CB GLU 19 17.969 39.084 28.438 1.00 0.00 C +ATOM 306 HB2 GLU 19 17.654 38.445 29.254 1.00 0.00 H +ATOM 307 HB3 GLU 19 18.692 39.801 28.846 1.00 0.00 H +ATOM 308 CG GLU 19 16.744 39.844 27.922 1.00 0.00 C +ATOM 309 HG2 GLU 19 16.429 40.532 28.717 1.00 0.00 H +ATOM 310 HG3 GLU 19 17.019 40.455 27.056 1.00 0.00 H +ATOM 311 CD GLU 19 15.597 38.905 27.580 1.00 0.00 C +ATOM 312 OE1 GLU 19 15.524 38.447 26.420 1.00 0.00 O +ATOM 313 OE2 GLU 19 14.792 38.598 28.494 1.00 0.00 O +ATOM 314 C GLU 19 19.301 39.095 26.284 1.00 0.00 C +ATOM 315 O GLU 19 20.281 39.810 26.532 1.00 0.00 O +ATOM 316 N ALA 20 18.731 39.084 25.070 1.00 0.00 N +ATOM 317 H ALA 20 17.963 38.435 24.919 1.00 0.00 H +ATOM 318 CA ALA 20 19.099 39.980 23.973 1.00 0.00 C +ATOM 319 HA ALA 20 19.247 40.984 24.381 1.00 0.00 H +ATOM 320 CB ALA 20 20.422 39.506 23.353 1.00 0.00 C +ATOM 321 HB1 ALA 20 20.281 38.538 22.875 1.00 0.00 H +ATOM 322 HB2 ALA 20 20.768 40.220 22.610 1.00 0.00 H +ATOM 323 HB3 ALA 20 21.189 39.416 24.117 1.00 0.00 H +ATOM 324 C ALA 20 18.010 40.067 22.880 1.00 0.00 C +ATOM 325 O ALA 20 17.168 39.177 22.759 1.00 0.00 O +ATOM 326 N VAL 21 18.065 41.111 22.046 1.00 0.00 N +ATOM 327 H VAL 21 18.750 41.833 22.204 1.00 0.00 H +ATOM 328 CA VAL 21 17.304 41.162 20.778 1.00 0.00 C +ATOM 329 HA VAL 21 16.304 40.751 20.937 1.00 0.00 H +ATOM 330 CB VAL 21 17.132 42.608 20.254 1.00 0.00 C +ATOM 331 HB VAL 21 16.465 42.569 19.386 1.00 0.00 H +ATOM 332 CG1 VAL 21 16.460 43.502 21.301 1.00 0.00 C +ATOM 333 HG11 VAL 21 17.124 43.665 22.146 1.00 0.00 H +ATOM 334 HG12 VAL 21 16.219 44.462 20.848 1.00 0.00 H +ATOM 335 HG13 VAL 21 15.539 43.039 21.647 1.00 0.00 H +ATOM 336 CG2 VAL 21 18.444 43.266 19.801 1.00 0.00 C +ATOM 337 HG21 VAL 21 18.853 42.739 18.940 1.00 0.00 H +ATOM 338 HG22 VAL 21 18.254 44.293 19.492 1.00 0.00 H +ATOM 339 HG23 VAL 21 19.178 43.267 20.603 1.00 0.00 H +ATOM 340 C VAL 21 17.952 40.317 19.666 1.00 0.00 C +ATOM 341 O VAL 21 17.278 39.966 18.704 1.00 0.00 O +ATOM 342 N ASP 22 19.243 40.029 19.813 1.00 0.00 N +ATOM 343 H ASP 22 19.704 40.318 20.655 1.00 0.00 H +ATOM 344 CA ASP 22 20.100 39.419 18.804 1.00 0.00 C +ATOM 345 HA ASP 22 19.497 38.787 18.150 1.00 0.00 H +ATOM 346 CB ASP 22 20.726 40.522 17.944 1.00 0.00 C +ATOM 347 HB2 ASP 22 19.955 41.065 17.402 1.00 0.00 H +ATOM 348 HB3 ASP 22 21.258 41.229 18.582 1.00 0.00 H +ATOM 349 CG ASP 22 21.684 39.915 16.952 1.00 0.00 C +ATOM 350 OD1 ASP 22 22.900 39.923 17.238 1.00 0.00 O +ATOM 351 OD2 ASP 22 21.215 39.285 15.968 1.00 0.00 O +ATOM 352 C ASP 22 21.194 38.552 19.448 1.00 0.00 C +ATOM 353 O ASP 22 21.656 38.814 20.562 1.00 0.00 O +ATOM 354 N TRP 23 21.618 37.513 18.736 1.00 0.00 N +ATOM 355 H TRP 23 21.260 37.424 17.794 1.00 0.00 H +ATOM 356 CA TRP 23 22.592 36.533 19.196 1.00 0.00 C +ATOM 357 HA TRP 23 22.307 36.203 20.193 1.00 0.00 H +ATOM 358 CB TRP 23 22.468 35.355 18.241 1.00 0.00 C +ATOM 359 HB2 TRP 23 21.437 35.006 18.265 1.00 0.00 H +ATOM 360 HB3 TRP 23 22.651 35.708 17.229 1.00 0.00 H +ATOM 361 CG TRP 23 23.345 34.183 18.507 1.00 0.00 C +ATOM 362 CD1 TRP 23 24.327 33.748 17.692 1.00 0.00 C +ATOM 363 HD1 TRP 23 24.622 34.227 16.762 1.00 0.00 H +ATOM 364 NE1 TRP 23 24.843 32.577 18.191 1.00 0.00 N +ATOM 365 HE1 TRP 23 25.589 32.075 17.744 1.00 0.00 H +ATOM 366 CE2 TRP 23 24.205 32.177 19.341 1.00 0.00 C +ATOM 367 CZ2 TRP 23 24.305 31.041 20.154 1.00 0.00 C +ATOM 368 HZ2 TRP 23 24.974 30.231 19.914 1.00 0.00 H +ATOM 369 CH2 TRP 23 23.503 30.982 21.293 1.00 0.00 C +ATOM 370 HH2 TRP 23 23.536 30.162 21.968 1.00 0.00 H +ATOM 371 CZ3 TRP 23 22.656 32.026 21.640 1.00 0.00 C +ATOM 372 HZ3 TRP 23 22.102 31.901 22.548 1.00 0.00 H +ATOM 373 CE3 TRP 23 22.555 33.158 20.816 1.00 0.00 C +ATOM 374 HE3 TRP 23 21.901 33.970 21.077 1.00 0.00 H +ATOM 375 CD2 TRP 23 23.297 33.237 19.620 1.00 0.00 C +ATOM 376 C TRP 23 24.038 37.065 19.291 1.00 0.00 C +ATOM 377 O TRP 23 24.748 36.732 20.243 1.00 0.00 O +ATOM 378 N ALA 24 24.456 37.943 18.378 1.00 0.00 N +ATOM 379 H ALA 24 23.788 38.320 17.705 1.00 0.00 H +ATOM 380 CA ALA 24 25.770 38.591 18.417 1.00 0.00 C +ATOM 381 HA ALA 24 26.523 37.842 18.658 1.00 0.00 H +ATOM 382 CB ALA 24 26.093 39.129 17.019 1.00 0.00 C +ATOM 383 HB1 ALA 24 25.414 39.937 16.750 1.00 0.00 H +ATOM 384 HB2 ALA 24 27.113 39.510 16.990 1.00 0.00 H +ATOM 385 HB3 ALA 24 25.999 38.337 16.277 1.00 0.00 H +ATOM 386 C ALA 24 25.852 39.690 19.499 1.00 0.00 C +ATOM 387 O ALA 24 26.942 40.015 19.974 1.00 0.00 O +ATOM 388 N GLU 25 24.717 40.230 19.956 1.00 0.00 N +ATOM 389 H GLU 25 23.861 40.033 19.446 1.00 0.00 H +ATOM 390 CA GLU 25 24.654 41.013 21.203 1.00 0.00 C +ATOM 391 HA GLU 25 25.521 41.667 21.252 1.00 0.00 H +ATOM 392 CB GLU 25 23.400 41.899 21.224 1.00 0.00 C +ATOM 393 HB2 GLU 25 22.510 41.288 21.082 1.00 0.00 H +ATOM 394 HB3 GLU 25 23.322 42.367 22.203 1.00 0.00 H +ATOM 395 CG GLU 25 23.427 43.014 20.163 1.00 0.00 C +ATOM 396 HG2 GLU 25 23.381 42.559 19.173 1.00 0.00 H +ATOM 397 HG3 GLU 25 22.536 43.634 20.280 1.00 0.00 H +ATOM 398 CD GLU 25 24.682 43.880 20.287 1.00 0.00 C +ATOM 399 OE1 GLU 25 24.871 44.510 21.350 1.00 0.00 O +ATOM 400 OE2 GLU 25 25.522 43.847 19.355 1.00 0.00 O +ATOM 401 C GLU 25 24.739 40.115 22.453 1.00 0.00 C +ATOM 402 O GLU 25 25.485 40.426 23.379 1.00 0.00 O +ATOM 403 N ALA 26 24.079 38.949 22.469 1.00 0.00 N +ATOM 404 H ALA 26 23.460 38.725 21.692 1.00 0.00 H +ATOM 405 CA ALA 26 24.231 37.966 23.555 1.00 0.00 C +ATOM 406 HA ALA 26 23.997 38.473 24.491 1.00 0.00 H +ATOM 407 CB ALA 26 23.229 36.828 23.355 1.00 0.00 C +ATOM 408 HB1 ALA 26 23.465 36.281 22.442 1.00 0.00 H +ATOM 409 HB2 ALA 26 23.277 36.145 24.202 1.00 0.00 H +ATOM 410 HB3 ALA 26 22.221 37.233 23.281 1.00 0.00 H +ATOM 411 C ALA 26 25.681 37.421 23.687 1.00 0.00 C +ATOM 412 O ALA 26 26.072 36.971 24.766 1.00 0.00 O +ATOM 413 N GLU 27 26.475 37.489 22.621 1.00 0.00 N +ATOM 414 H GLU 27 26.057 37.731 21.733 1.00 0.00 H +ATOM 415 CA GLU 27 27.935 37.275 22.668 1.00 0.00 C +ATOM 416 HA GLU 27 28.110 36.335 23.172 1.00 0.00 H +ATOM 417 CB GLU 27 28.501 37.159 21.240 1.00 0.00 C +ATOM 418 HB2 GLU 27 27.858 36.496 20.668 1.00 0.00 H +ATOM 419 HB3 GLU 27 28.521 38.137 20.755 1.00 0.00 H +ATOM 420 CG GLU 27 29.922 36.577 21.246 1.00 0.00 C +ATOM 421 HG2 GLU 27 30.622 37.316 21.655 1.00 0.00 H +ATOM 422 HG3 GLU 27 29.938 35.700 21.917 1.00 0.00 H +ATOM 423 CD GLU 27 30.333 36.159 19.844 1.00 0.00 C +ATOM 424 OE1 GLU 27 30.768 37.041 19.068 1.00 0.00 O +ATOM 425 OE2 GLU 27 30.175 34.953 19.551 1.00 0.00 O +ATOM 426 C GLU 27 28.646 38.358 23.496 1.00 0.00 C +ATOM 427 O GLU 27 29.318 38.035 24.479 1.00 0.00 O +ATOM 428 N LYS 28 28.412 39.636 23.174 1.00 0.00 N +ATOM 429 H LYS 28 27.801 39.819 22.380 1.00 0.00 H +ATOM 430 CA LYS 28 28.954 40.791 23.921 1.00 0.00 C +ATOM 431 HA LYS 28 30.042 40.726 23.917 1.00 0.00 H +ATOM 432 CB LYS 28 28.543 42.111 23.235 1.00 0.00 C +ATOM 433 HB2 LYS 28 27.455 42.207 23.248 1.00 0.00 H +ATOM 434 HB3 LYS 28 28.958 42.934 23.819 1.00 0.00 H +ATOM 435 CG LYS 28 29.040 42.241 21.784 1.00 0.00 C +ATOM 436 HG2 LYS 28 30.122 42.102 21.762 1.00 0.00 H +ATOM 437 HG3 LYS 28 28.581 41.468 21.172 1.00 0.00 H +ATOM 438 CD LYS 28 28.695 43.621 21.197 1.00 0.00 C +ATOM 439 HD2 LYS 28 27.625 43.816 21.309 1.00 0.00 H +ATOM 440 HD3 LYS 28 29.234 44.378 21.768 1.00 0.00 H +ATOM 441 CE LYS 28 29.092 43.749 19.719 1.00 0.00 C +ATOM 442 HE2 LYS 28 29.245 44.811 19.500 1.00 0.00 H +ATOM 443 HE3 LYS 28 30.040 43.231 19.550 1.00 0.00 H +ATOM 444 NZ LYS 28 28.043 43.215 18.818 1.00 0.00 N +ATOM 445 HZ1 LYS 28 27.148 43.676 19.012 1.00 0.00 H +ATOM 446 HZ2 LYS 28 28.250 43.384 17.845 1.00 0.00 H +ATOM 447 HZ3 LYS 28 27.863 42.232 18.978 1.00 0.00 H +ATOM 448 C LYS 28 28.516 40.774 25.382 1.00 0.00 C +ATOM 449 O LYS 28 29.354 40.875 26.282 1.00 0.00 O +ATOM 450 N PHE 29 27.230 40.523 25.671 1.00 0.00 N +ATOM 451 H PHE 29 26.580 40.488 24.887 1.00 0.00 H +ATOM 452 CA PHE 29 26.717 40.381 27.040 1.00 0.00 C +ATOM 453 HA PHE 29 27.028 41.264 27.609 1.00 0.00 H +ATOM 454 CB PHE 29 25.174 40.374 27.017 1.00 0.00 C +ATOM 455 HB2 PHE 29 24.857 39.449 26.532 1.00 0.00 H +ATOM 456 HB3 PHE 29 24.817 40.348 28.045 1.00 0.00 H +ATOM 457 CG PHE 29 24.487 41.545 26.324 1.00 0.00 C +ATOM 458 CD1 PHE 29 23.274 41.325 25.647 1.00 0.00 C +ATOM 459 HD1 PHE 29 22.834 40.341 25.627 1.00 0.00 H +ATOM 460 CE1 PHE 29 22.634 42.384 24.983 1.00 0.00 C +ATOM 461 HE1 PHE 29 21.713 42.203 24.448 1.00 0.00 H +ATOM 462 CZ PHE 29 23.202 43.669 25.000 1.00 0.00 C +ATOM 463 HZ PHE 29 22.721 44.479 24.467 1.00 0.00 H +ATOM 464 CE2 PHE 29 24.393 43.902 25.701 1.00 0.00 C +ATOM 465 HE2 PHE 29 24.824 44.889 25.713 1.00 0.00 H +ATOM 466 CD2 PHE 29 25.032 42.847 26.367 1.00 0.00 C +ATOM 467 HD2 PHE 29 25.949 43.044 26.902 1.00 0.00 H +ATOM 468 C PHE 29 27.235 39.150 27.791 1.00 0.00 C +ATOM 469 O PHE 29 27.109 39.083 29.018 1.00 0.00 O +ATOM 470 N THR 30 27.822 38.171 27.095 1.00 0.00 N +ATOM 471 H THR 30 27.890 38.239 26.095 1.00 0.00 H +ATOM 472 CA THR 30 28.573 37.089 27.760 1.00 0.00 C +ATOM 473 HA THR 30 28.121 36.861 28.736 1.00 0.00 H +ATOM 474 CB THR 30 28.589 35.785 26.951 1.00 0.00 C +ATOM 475 HB THR 30 29.126 35.932 26.020 1.00 0.00 H +ATOM 476 CG2 THR 30 29.291 34.708 27.707 1.00 0.00 C +ATOM 477 HG21 THR 30 29.001 34.665 28.758 1.00 0.00 H +ATOM 478 HG22 THR 30 29.190 33.710 27.309 1.00 0.00 H +ATOM 479 HG23 THR 30 30.396 34.905 27.706 1.00 0.00 H +ATOM 480 OG1 THR 30 27.246 35.347 26.666 1.00 0.00 O +ATOM 481 HG1 THR 30 26.831 36.069 26.125 1.00 0.00 H +ATOM 482 C THR 30 30.015 37.520 28.057 1.00 0.00 C +ATOM 483 O THR 30 30.509 37.256 29.165 1.00 0.00 O +ATOM 484 N LYS 31 30.701 38.226 27.146 1.00 0.00 N +ATOM 485 H LYS 31 30.239 38.432 26.281 1.00 0.00 H +ATOM 486 CA LYS 31 32.033 38.757 27.374 1.00 0.00 C +ATOM 487 HA LYS 31 32.713 37.956 27.669 1.00 0.00 H +ATOM 488 CB LYS 31 32.595 39.350 26.040 1.00 0.00 C +ATOM 489 HB2 LYS 31 31.880 40.043 25.627 1.00 0.00 H +ATOM 490 HB3 LYS 31 33.521 39.882 26.257 1.00 0.00 H +ATOM 491 CG LYS 31 32.908 38.239 25.021 1.00 0.00 C +ATOM 492 HG2 LYS 31 33.616 37.535 25.468 1.00 0.00 H +ATOM 493 HG3 LYS 31 32.001 37.679 24.772 1.00 0.00 H +ATOM 494 CD LYS 31 33.507 38.815 23.745 1.00 0.00 C +ATOM 495 HD2 LYS 31 32.724 39.333 23.190 1.00 0.00 H +ATOM 496 HD3 LYS 31 34.274 39.551 23.997 1.00 0.00 H +ATOM 497 CE LYS 31 34.151 37.756 22.818 1.00 0.00 C +ATOM 498 HE2 LYS 31 33.427 36.967 22.597 1.00 0.00 H +ATOM 499 HE3 LYS 31 34.403 38.229 21.875 1.00 0.00 H +ATOM 500 NZ LYS 31 35.380 37.164 23.401 1.00 0.00 N +ATOM 501 HZ1 LYS 31 35.182 36.369 23.997 1.00 0.00 H +ATOM 502 HZ2 LYS 31 35.964 36.769 22.664 1.00 0.00 H +ATOM 503 HZ3 LYS 31 35.937 37.839 23.926 1.00 0.00 H +ATOM 504 C LYS 31 32.098 39.783 28.503 1.00 0.00 C +ATOM 505 O LYS 31 33.098 39.797 29.236 1.00 0.00 O +ATOM 506 N ALA 32 31.007 40.533 28.748 1.00 0.00 N +ATOM 507 H ALA 32 30.289 40.547 28.024 1.00 0.00 H +ATOM 508 CA ALA 32 30.825 41.326 29.945 1.00 0.00 C +ATOM 509 HA ALA 32 31.623 42.067 30.008 1.00 0.00 H +ATOM 510 CB ALA 32 29.489 42.080 29.856 1.00 0.00 C +ATOM 511 HB1 ALA 32 28.656 41.377 29.781 1.00 0.00 H +ATOM 512 HB2 ALA 32 29.357 42.696 30.751 1.00 0.00 H +ATOM 513 HB3 ALA 32 29.498 42.730 28.980 1.00 0.00 H +ATOM 514 C ALA 32 30.918 40.469 31.230 1.00 0.00 C +ATOM 515 O ALA 32 31.875 40.615 31.989 1.00 0.00 O +ATOM 516 N LYN 33 30.027 39.478 31.414 1.00 0.00 N +ATOM 517 H LYN 33 29.273 39.397 30.746 1.00 0.00 H +ATOM 518 CA LYN 33 30.019 38.600 32.599 1.00 0.00 C +ATOM 519 HA LYN 33 29.905 39.224 33.484 1.00 0.00 H +ATOM 520 CB LYN 33 28.823 37.633 32.537 1.00 0.00 C +ATOM 521 HB2 LYN 33 28.855 37.068 31.598 1.00 0.00 H +ATOM 522 HB3 LYN 33 28.916 36.921 33.362 1.00 0.00 H +ATOM 523 CG LYN 33 27.453 38.320 32.665 1.00 0.00 C +ATOM 524 HG2 LYN 33 27.447 38.962 33.545 1.00 0.00 H +ATOM 525 HG3 LYN 33 27.265 38.928 31.781 1.00 0.00 H +ATOM 526 CD LYN 33 26.345 37.268 32.812 1.00 0.00 C +ATOM 527 HD2 LYN 33 26.425 36.539 32.014 1.00 0.00 H +ATOM 528 HD3 LYN 33 26.468 36.746 33.759 1.00 0.00 H +ATOM 529 CE LYN 33 24.952 37.891 32.766 1.00 0.00 C +ATOM 530 HE2 LYN 33 24.861 38.619 33.571 1.00 0.00 H +ATOM 531 HE3 LYN 33 24.813 38.397 31.810 1.00 0.00 H +ATOM 532 NZ LYN 33 23.905 36.871 32.922 1.00 0.00 N +ATOM 533 HZ2 LYN 33 23.008 37.332 32.970 1.00 0.00 H +ATOM 534 HZ3 LYN 33 23.917 36.241 32.136 1.00 0.00 H +ATOM 535 C LYN 33 31.322 37.801 32.794 1.00 0.00 C +ATOM 536 O LYN 33 31.621 37.372 33.904 1.00 0.00 O +ATOM 537 N ALA 34 32.099 37.570 31.731 1.00 0.00 N +ATOM 538 H ALA 34 31.781 37.901 30.828 1.00 0.00 H +ATOM 539 CA ALA 34 33.426 36.952 31.831 1.00 0.00 C +ATOM 540 HA ALA 34 33.381 36.156 32.576 1.00 0.00 H +ATOM 541 CB ALA 34 33.752 36.314 30.478 1.00 0.00 C +ATOM 542 HB1 ALA 34 33.883 37.091 29.724 1.00 0.00 H +ATOM 543 HB2 ALA 34 34.668 35.737 30.580 1.00 0.00 H +ATOM 544 HB3 ALA 34 32.947 35.645 30.174 1.00 0.00 H +ATOM 545 C ALA 34 34.518 37.937 32.295 1.00 0.00 C +ATOM 546 O ALA 34 35.356 37.574 33.123 1.00 0.00 O +ATOM 547 N ASN 35 34.507 39.192 31.826 1.00 0.00 N +ATOM 548 H ASN 35 33.779 39.466 31.177 1.00 0.00 H +ATOM 549 CA ASN 35 35.407 40.246 32.323 1.00 0.00 C +ATOM 550 HA ASN 35 36.410 39.826 32.419 1.00 0.00 H +ATOM 551 CB ASN 35 35.497 41.390 31.300 1.00 0.00 C +ATOM 552 HB2 ASN 35 34.503 41.660 30.948 1.00 0.00 H +ATOM 553 HB3 ASN 35 35.934 42.262 31.785 1.00 0.00 H +ATOM 554 CG ASN 35 36.402 41.022 30.139 1.00 0.00 C +ATOM 555 OD1 ASN 35 37.618 41.034 30.232 1.00 0.00 O +ATOM 556 ND2 ASN 35 35.850 40.648 29.016 1.00 0.00 N +ATOM 557 HD21 ASN 35 36.490 40.376 28.269 1.00 0.00 H +ATOM 558 HD22 ASN 35 34.848 40.545 28.953 1.00 0.00 H +ATOM 559 C ASN 35 35.039 40.737 33.735 1.00 0.00 C +ATOM 560 O ASN 35 35.938 41.112 34.489 1.00 0.00 O +ATOM 561 N ASP 36 33.767 40.640 34.145 1.00 0.00 N +ATOM 562 H ASP 36 33.044 40.468 33.452 1.00 0.00 H +ATOM 563 CA ASP 36 33.347 40.815 35.542 1.00 0.00 C +ATOM 564 HA ASP 36 33.612 41.817 35.878 1.00 0.00 H +ATOM 565 CB ASP 36 31.820 40.683 35.668 1.00 0.00 C +ATOM 566 HB2 ASP 36 31.534 39.692 35.338 1.00 0.00 H +ATOM 567 HB3 ASP 36 31.551 40.719 36.722 1.00 0.00 H +ATOM 568 CG ASP 36 30.942 41.690 34.922 1.00 0.00 C +ATOM 569 OD1 ASP 36 31.493 42.816 34.631 1.00 0.00 O +ATOM 570 OD2 ASP 36 29.771 41.419 34.688 1.00 0.00 O +ATOM 571 C ASP 36 34.055 39.805 36.478 1.00 0.00 C +ATOM 572 O ASP 36 34.535 40.172 37.554 1.00 0.00 O +ATOM 573 N PHE 37 34.169 38.540 36.047 1.00 0.00 N +ATOM 574 H PHE 37 33.727 38.308 35.169 1.00 0.00 H +ATOM 575 CA PHE 37 34.934 37.497 36.744 1.00 0.00 C +ATOM 576 HA PHE 37 34.690 37.558 37.799 1.00 0.00 H +ATOM 577 CB PHE 37 34.469 36.126 36.228 1.00 0.00 C +ATOM 578 HB2 PHE 37 33.393 36.037 36.395 1.00 0.00 H +ATOM 579 HB3 PHE 37 34.630 36.081 35.150 1.00 0.00 H +ATOM 580 CG PHE 37 35.152 34.933 36.875 1.00 0.00 C +ATOM 581 CD1 PHE 37 34.773 34.523 38.167 1.00 0.00 C +ATOM 582 HD1 PHE 37 34.002 35.061 38.701 1.00 0.00 H +ATOM 583 CE1 PHE 37 35.392 33.410 38.765 1.00 0.00 C +ATOM 584 HE1 PHE 37 35.099 33.099 39.758 1.00 0.00 H +ATOM 585 CZ PHE 37 36.390 32.703 38.072 1.00 0.00 C +ATOM 586 HZ PHE 37 36.864 31.850 38.536 1.00 0.00 H +ATOM 587 CE2 PHE 37 36.770 33.110 36.779 1.00 0.00 C +ATOM 588 HE2 PHE 37 37.535 32.567 36.244 1.00 0.00 H +ATOM 589 CD2 PHE 37 36.152 34.224 36.183 1.00 0.00 C +ATOM 590 HD2 PHE 37 36.442 34.532 35.189 1.00 0.00 H +ATOM 591 C PHE 37 36.459 37.681 36.633 1.00 0.00 C +ATOM 592 O PHE 37 37.181 37.408 37.601 1.00 0.00 O +ATOM 593 N GLY 38 36.946 38.174 35.476 1.00 0.00 N +ATOM 594 H GLY 38 36.274 38.350 34.736 1.00 0.00 H +ATOM 595 CA GLY 38 38.305 38.694 35.283 1.00 0.00 C +ATOM 596 HA2 GLY 38 38.358 39.679 35.738 1.00 0.00 H +ATOM 597 HA3 GLY 38 39.002 38.061 35.822 1.00 0.00 H +ATOM 598 C GLY 38 38.814 38.803 33.840 1.00 0.00 C +ATOM 599 O GLY 38 39.686 39.634 33.577 1.00 0.00 O +ATOM 600 N ARG 39 38.321 37.986 32.886 1.00 0.00 N +ATOM 601 H ARG 39 37.566 37.372 33.173 1.00 0.00 H +ATOM 602 CA ARG 39 38.687 38.004 31.452 1.00 0.00 C +ATOM 603 HA ARG 39 38.623 39.039 31.102 1.00 0.00 H +ATOM 604 CB ARG 39 40.143 37.499 31.293 1.00 0.00 C +ATOM 605 HB2 ARG 39 40.808 38.137 31.879 1.00 0.00 H +ATOM 606 HB3 ARG 39 40.209 36.484 31.698 1.00 0.00 H +ATOM 607 CG ARG 39 40.681 37.476 29.853 1.00 0.00 C +ATOM 608 HG2 ARG 39 41.731 37.183 29.889 1.00 0.00 H +ATOM 609 HG3 ARG 39 40.154 36.707 29.292 1.00 0.00 H +ATOM 610 CD ARG 39 40.572 38.820 29.110 1.00 0.00 C +ATOM 611 HD2 ARG 39 39.529 39.135 29.063 1.00 0.00 H +ATOM 612 HD3 ARG 39 41.138 39.572 29.667 1.00 0.00 H +ATOM 613 NE ARG 39 41.093 38.711 27.733 1.00 0.00 N +ATOM 614 HE ARG 39 41.197 37.781 27.362 1.00 0.00 H +ATOM 615 CZ ARG 39 41.323 39.715 26.902 1.00 0.00 C +ATOM 616 NH1 ARG 39 40.973 40.935 27.194 1.00 0.00 N +ATOM 617 HH11 ARG 39 40.353 41.063 27.975 1.00 0.00 H +ATOM 618 HH12 ARG 39 41.123 41.679 26.541 1.00 0.00 H +ATOM 619 NH2 ARG 39 41.938 39.504 25.770 1.00 0.00 N +ATOM 620 HH21 ARG 39 42.236 38.579 25.530 1.00 0.00 H +ATOM 621 HH22 ARG 39 42.142 40.257 25.126 1.00 0.00 H +ATOM 622 C ARG 39 37.731 37.149 30.600 1.00 0.00 C +ATOM 623 O ARG 39 37.313 36.080 31.034 1.00 0.00 O +ATOM 624 N ASP 40 37.433 37.573 29.370 1.00 0.00 N +ATOM 625 H ASP 40 37.785 38.466 29.050 1.00 0.00 H +ATOM 626 CA ASP 40 36.732 36.767 28.363 1.00 0.00 C +ATOM 627 HA ASP 40 36.012 36.147 28.890 1.00 0.00 H +ATOM 628 CB ASP 40 35.937 37.651 27.386 1.00 0.00 C +ATOM 629 HB2 ASP 40 35.399 36.992 26.707 1.00 0.00 H +ATOM 630 HB3 ASP 40 35.173 38.186 27.950 1.00 0.00 H +ATOM 631 CG ASP 40 36.754 38.652 26.574 1.00 0.00 C +ATOM 632 OD1 ASP 40 37.577 39.373 27.182 1.00 0.00 O +ATOM 633 OD2 ASP 40 36.491 38.780 25.354 1.00 0.00 O +ATOM 634 C ASP 40 37.612 35.797 27.558 1.00 0.00 C +ATOM 635 O ASP 40 38.800 36.022 27.342 1.00 0.00 O +ATOM 636 N GLY 41 36.968 34.739 27.054 1.00 0.00 N +ATOM 637 H GLY 41 35.992 34.654 27.288 1.00 0.00 H +ATOM 638 CA GLY 41 37.454 33.871 25.974 1.00 0.00 C +ATOM 639 HA2 GLY 41 38.383 34.272 25.550 1.00 0.00 H +ATOM 640 HA3 GLY 41 37.646 32.873 26.382 1.00 0.00 H +ATOM 641 C GLY 41 36.419 33.754 24.843 1.00 0.00 C +ATOM 642 O GLY 41 35.478 34.553 24.760 1.00 0.00 O +ATOM 643 N GLU 42 36.564 32.731 23.995 1.00 0.00 N +ATOM 644 H GLU 42 37.314 32.085 24.166 1.00 0.00 H +ATOM 645 CA GLU 42 35.719 32.470 22.820 1.00 0.00 C +ATOM 646 HA GLU 42 34.987 33.274 22.739 1.00 0.00 H +ATOM 647 CB GLU 42 36.560 32.473 21.527 1.00 0.00 C +ATOM 648 HB2 GLU 42 37.201 31.589 21.523 1.00 0.00 H +ATOM 649 HB3 GLU 42 35.878 32.395 20.677 1.00 0.00 H +ATOM 650 CG GLU 42 37.451 33.710 21.310 1.00 0.00 C +ATOM 651 HG2 GLU 42 38.305 33.636 21.989 1.00 0.00 H +ATOM 652 HG3 GLU 42 37.841 33.689 20.290 1.00 0.00 H +ATOM 653 CD GLU 42 36.743 35.051 21.558 1.00 0.00 C +ATOM 654 OE1 GLU 42 35.506 35.156 21.411 1.00 0.00 O +ATOM 655 OE2 GLU 42 37.420 36.011 21.985 1.00 0.00 O +ATOM 656 C GLU 42 34.902 31.171 22.926 1.00 0.00 C +ATOM 657 O GLU 42 35.189 30.297 23.752 1.00 0.00 O +ATOM 658 N ARG 43 33.857 31.073 22.089 1.00 0.00 N +ATOM 659 H ARG 43 33.754 31.781 21.367 1.00 0.00 H +ATOM 660 CA ARG 43 32.715 30.156 22.240 1.00 0.00 C +ATOM 661 HA ARG 43 33.070 29.195 22.605 1.00 0.00 H +ATOM 662 CB ARG 43 31.757 30.741 23.295 1.00 0.00 C +ATOM 663 HB2 ARG 43 30.857 30.131 23.363 1.00 0.00 H +ATOM 664 HB3 ARG 43 32.251 30.680 24.258 1.00 0.00 H +ATOM 665 CG ARG 43 31.347 32.212 23.063 1.00 0.00 C +ATOM 666 HG2 ARG 43 32.157 32.790 22.634 1.00 0.00 H +ATOM 667 HG3 ARG 43 30.532 32.273 22.343 1.00 0.00 H +ATOM 668 CD ARG 43 30.948 32.916 24.353 1.00 0.00 C +ATOM 669 HD2 ARG 43 31.747 32.788 25.065 1.00 0.00 H +ATOM 670 HD3 ARG 43 30.871 33.975 24.176 1.00 0.00 H +ATOM 671 NE ARG 43 29.688 32.389 24.915 1.00 0.00 N +ATOM 672 HE ARG 43 29.764 31.533 25.445 1.00 0.00 H +ATOM 673 CZ ARG 43 28.506 32.979 24.859 1.00 0.00 C +ATOM 674 NH1 ARG 43 28.308 34.021 24.112 1.00 0.00 N +ATOM 675 HH11 ARG 43 29.014 34.251 23.430 1.00 0.00 H +ATOM 676 HH12 ARG 43 27.368 34.336 23.961 1.00 0.00 H +ATOM 677 NH2 ARG 43 27.517 32.541 25.581 1.00 0.00 N +ATOM 678 HH21 ARG 43 27.615 31.710 26.127 1.00 0.00 H +ATOM 679 HH22 ARG 43 26.722 33.143 25.656 1.00 0.00 H +ATOM 680 C ARG 43 32.002 29.904 20.911 1.00 0.00 C +ATOM 681 O ARG 43 31.785 30.843 20.152 1.00 0.00 O +ATOM 682 N THR 44 31.626 28.653 20.654 1.00 0.00 N +ATOM 683 H THR 44 31.760 27.961 21.382 1.00 0.00 H +ATOM 684 CA THR 44 30.964 28.219 19.410 1.00 0.00 C +ATOM 685 HA THR 44 31.281 28.881 18.600 1.00 0.00 H +ATOM 686 CB THR 44 31.419 26.794 19.033 1.00 0.00 C +ATOM 687 HB THR 44 31.189 26.105 19.847 1.00 0.00 H +ATOM 688 CG2 THR 44 30.834 26.244 17.728 1.00 0.00 C +ATOM 689 HG21 THR 44 30.953 26.974 16.926 1.00 0.00 H +ATOM 690 HG22 THR 44 31.345 25.320 17.451 1.00 0.00 H +ATOM 691 HG23 THR 44 29.778 26.010 17.864 1.00 0.00 H +ATOM 692 OG1 THR 44 32.812 26.820 18.838 1.00 0.00 O +ATOM 693 HG1 THR 44 33.066 26.034 18.345 1.00 0.00 H +ATOM 694 C THR 44 29.444 28.346 19.518 1.00 0.00 C +ATOM 695 O THR 44 28.893 28.415 20.625 1.00 0.00 O +ATOM 696 N ILE 45 28.746 28.413 18.370 1.00 0.00 N +ATOM 697 H ILE 45 29.255 28.293 17.506 1.00 0.00 H +ATOM 698 CA ILE 45 27.327 28.740 18.260 1.00 0.00 C +ATOM 699 HA ILE 45 26.903 28.736 19.267 1.00 0.00 H +ATOM 700 CB ILE 45 27.140 30.171 17.691 1.00 0.00 C +ATOM 701 HB ILE 45 26.064 30.352 17.688 1.00 0.00 H +ATOM 702 CG2 ILE 45 27.762 31.185 18.658 1.00 0.00 C +ATOM 703 HG21 ILE 45 28.845 31.067 18.698 1.00 0.00 H +ATOM 704 HG22 ILE 45 27.536 32.208 18.358 1.00 0.00 H +ATOM 705 HG23 ILE 45 27.332 30.996 19.632 1.00 0.00 H +ATOM 706 CG1 ILE 45 27.649 30.451 16.258 1.00 0.00 C +ATOM 707 HG12 ILE 45 27.929 31.498 16.189 1.00 0.00 H +ATOM 708 HG13 ILE 45 28.548 29.877 16.062 1.00 0.00 H +ATOM 709 CD1 ILE 45 26.606 30.205 15.161 1.00 0.00 C +ATOM 710 HD11 ILE 45 25.681 30.736 15.407 1.00 0.00 H +ATOM 711 HD12 ILE 45 26.983 30.585 14.209 1.00 0.00 H +ATOM 712 HD13 ILE 45 26.400 29.138 15.063 1.00 0.00 H +ATOM 713 C ILE 45 26.504 27.715 17.472 1.00 0.00 C +ATOM 714 O ILE 45 27.016 27.025 16.595 1.00 0.00 O +ATOM 715 N ASP 46 25.207 27.689 17.773 1.00 0.00 N +ATOM 716 H ASP 46 24.901 28.170 18.607 1.00 0.00 H +ATOM 717 CA ASP 46 24.135 27.096 16.970 1.00 0.00 C +ATOM 718 HA ASP 46 24.428 27.111 15.916 1.00 0.00 H +ATOM 719 CB ASP 46 23.890 25.642 17.389 1.00 0.00 C +ATOM 720 HB2 ASP 46 24.747 25.024 17.106 1.00 0.00 H +ATOM 721 HB3 ASP 46 23.805 25.612 18.485 1.00 0.00 H +ATOM 722 CG ASP 46 22.620 25.065 16.792 1.00 0.00 C +ATOM 723 OD1 ASP 46 21.857 24.429 17.512 1.00 0.00 O +ATOM 724 OD2 ASP 46 22.343 25.358 15.581 1.00 0.00 O +ATOM 725 C ASP 46 22.846 27.915 17.131 1.00 0.00 C +ATOM 726 O ASP 46 22.423 28.207 18.252 1.00 0.00 O +ATOM 727 N ASP 47 22.202 28.269 16.015 1.00 0.00 N +ATOM 728 H ASP 47 22.559 27.903 15.143 1.00 0.00 H +ATOM 729 CA ASP 47 20.902 28.945 16.002 1.00 0.00 C +ATOM 730 HA ASP 47 20.852 29.629 16.854 1.00 0.00 H +ATOM 731 CB ASP 47 20.771 29.805 14.731 1.00 0.00 C +ATOM 732 HB2 ASP 47 21.603 30.512 14.693 1.00 0.00 H +ATOM 733 HB3 ASP 47 20.827 29.160 13.845 1.00 0.00 H +ATOM 734 CG ASP 47 19.462 30.576 14.734 1.00 0.00 C +ATOM 735 OD1 ASP 47 18.516 30.160 14.029 1.00 0.00 O +ATOM 736 OD2 ASP 47 19.275 31.487 15.577 1.00 0.00 O +ATOM 737 C ASP 47 19.713 27.971 16.131 1.00 0.00 C +ATOM 738 O ASP 47 18.682 28.336 16.701 1.00 0.00 O +ATOM 739 N ALA 48 19.832 26.717 15.678 1.00 0.00 N +ATOM 740 H ALA 48 20.747 26.382 15.376 1.00 0.00 H +ATOM 741 CA ALA 48 18.725 25.756 15.685 1.00 0.00 C +ATOM 742 HA ALA 48 17.869 26.205 15.178 1.00 0.00 H +ATOM 743 CB ALA 48 19.156 24.513 14.893 1.00 0.00 C +ATOM 744 HB1 ALA 48 19.997 24.028 15.391 1.00 0.00 H +ATOM 745 HB2 ALA 48 18.325 23.811 14.828 1.00 0.00 H +ATOM 746 HB3 ALA 48 19.462 24.802 13.888 1.00 0.00 H +ATOM 747 C ALA 48 18.281 25.404 17.113 1.00 0.00 C +ATOM 748 O ALA 48 17.086 25.412 17.426 1.00 0.00 O +ATOM 749 N THR 49 19.236 25.173 18.018 1.00 0.00 N +ATOM 750 H THR 49 20.190 25.052 17.669 1.00 0.00 H +ATOM 751 CA THR 49 19.020 25.058 19.467 1.00 0.00 C +ATOM 752 HA THR 49 17.981 24.772 19.635 1.00 0.00 H +ATOM 753 CB THR 49 19.905 23.959 20.074 1.00 0.00 C +ATOM 754 HB THR 49 19.639 23.852 21.125 1.00 0.00 H +ATOM 755 CG2 THR 49 19.732 22.591 19.421 1.00 0.00 C +ATOM 756 HG21 THR 49 20.040 22.619 18.378 1.00 0.00 H +ATOM 757 HG22 THR 49 20.357 21.871 19.942 1.00 0.00 H +ATOM 758 HG23 THR 49 18.693 22.272 19.476 1.00 0.00 H +ATOM 759 OG1 THR 49 21.268 24.289 20.002 1.00 0.00 O +ATOM 760 HG1 THR 49 21.512 24.256 19.041 1.00 0.00 H +ATOM 761 C THR 49 19.237 26.368 20.233 1.00 0.00 C +ATOM 762 O THR 49 19.126 26.382 21.462 1.00 0.00 O +ATOM 763 N LYS 50 19.543 27.476 19.540 1.00 0.00 N +ATOM 764 H LYS 50 19.597 27.378 18.532 1.00 0.00 H +ATOM 765 CA LYS 50 19.791 28.822 20.106 1.00 0.00 C +ATOM 766 HA LYS 50 20.238 29.428 19.314 1.00 0.00 H +ATOM 767 CB LYS 50 18.438 29.470 20.509 1.00 0.00 C +ATOM 768 HB2 LYS 50 17.996 28.851 21.292 1.00 0.00 H +ATOM 769 HB3 LYS 50 18.632 30.445 20.958 1.00 0.00 H +ATOM 770 CG LYS 50 17.377 29.656 19.402 1.00 0.00 C +ATOM 771 HG2 LYS 50 17.296 28.746 18.807 1.00 0.00 H +ATOM 772 HG3 LYS 50 16.413 29.806 19.894 1.00 0.00 H +ATOM 773 CD LYS 50 17.645 30.872 18.500 1.00 0.00 C +ATOM 774 HD2 LYS 50 17.641 31.759 19.135 1.00 0.00 H +ATOM 775 HD3 LYS 50 18.616 30.785 18.024 1.00 0.00 H +ATOM 776 CE LYS 50 16.543 31.063 17.435 1.00 0.00 C +ATOM 777 HE2 LYS 50 15.565 30.782 17.861 1.00 0.00 H +ATOM 778 HE3 LYS 50 16.500 32.134 17.175 1.00 0.00 H +ATOM 779 NZ LYS 50 16.817 30.302 16.196 1.00 0.00 N +ATOM 780 HZ1 LYS 50 17.174 29.374 16.384 1.00 0.00 H +ATOM 781 HZ2 LYS 50 16.047 30.269 15.554 1.00 0.00 H +ATOM 782 HZ3 LYS 50 17.590 30.734 15.684 1.00 0.00 H +ATOM 783 C LYS 50 20.828 28.802 21.250 1.00 0.00 C +ATOM 784 O LYS 50 20.611 29.450 22.281 1.00 0.00 O +ATOM 785 N THR 51 21.905 28.009 21.119 1.00 0.00 N +ATOM 786 H THR 51 22.084 27.626 20.198 1.00 0.00 H +ATOM 787 CA THR 51 22.804 27.598 22.223 1.00 0.00 C +ATOM 788 HA THR 51 22.558 28.195 23.101 1.00 0.00 H +ATOM 789 CB THR 51 22.558 26.130 22.624 1.00 0.00 C +ATOM 790 HB THR 51 22.679 25.492 21.745 1.00 0.00 H +ATOM 791 CG2 THR 51 23.496 25.627 23.714 1.00 0.00 C +ATOM 792 HG21 THR 51 23.477 26.292 24.579 1.00 0.00 H +ATOM 793 HG22 THR 51 23.200 24.632 24.030 1.00 0.00 H +ATOM 794 HG23 THR 51 24.520 25.560 23.342 1.00 0.00 H +ATOM 795 OG1 THR 51 21.260 25.969 23.160 1.00 0.00 O +ATOM 796 HG1 THR 51 20.617 26.111 22.439 1.00 0.00 H +ATOM 797 C THR 51 24.311 27.830 21.951 1.00 0.00 C +ATOM 798 O THR 51 24.838 27.464 20.904 1.00 0.00 O +ATOM 799 N PHE 52 25.010 28.444 22.922 1.00 0.00 N +ATOM 800 H PHE 52 24.480 28.806 23.702 1.00 0.00 H +ATOM 801 CA PHE 52 26.464 28.630 22.944 1.00 0.00 C +ATOM 802 HA PHE 52 26.848 28.669 21.930 1.00 0.00 H +ATOM 803 CB PHE 52 26.843 29.942 23.659 1.00 0.00 C +ATOM 804 HB2 PHE 52 26.277 30.010 24.588 1.00 0.00 H +ATOM 805 HB3 PHE 52 27.895 29.880 23.947 1.00 0.00 H +ATOM 806 CG PHE 52 26.686 31.243 22.888 1.00 0.00 C +ATOM 807 CD1 PHE 52 25.614 32.113 23.155 1.00 0.00 C +ATOM 808 HD1 PHE 52 24.830 31.811 23.832 1.00 0.00 H +ATOM 809 CE1 PHE 52 25.532 33.364 22.517 1.00 0.00 C +ATOM 810 HE1 PHE 52 24.678 34.008 22.683 1.00 0.00 H +ATOM 811 CZ PHE 52 26.527 33.755 21.609 1.00 0.00 C +ATOM 812 HZ PHE 52 26.446 34.699 21.090 1.00 0.00 H +ATOM 813 CE2 PHE 52 27.628 32.918 21.375 1.00 0.00 C +ATOM 814 HE2 PHE 52 28.408 33.231 20.684 1.00 0.00 H +ATOM 815 CD2 PHE 52 27.706 31.667 22.017 1.00 0.00 C +ATOM 816 HD2 PHE 52 28.549 31.022 21.818 1.00 0.00 H +ATOM 817 C PHE 52 27.162 27.477 23.696 1.00 0.00 C +ATOM 818 O PHE 52 26.681 27.074 24.763 1.00 0.00 O +ATOM 819 N THR 53 28.330 27.045 23.210 1.00 0.00 N +ATOM 820 H THR 53 28.658 27.432 22.326 1.00 0.00 H +ATOM 821 CA THR 53 29.141 25.942 23.785 1.00 0.00 C +ATOM 822 HA THR 53 28.885 25.824 24.835 1.00 0.00 H +ATOM 823 CB THR 53 28.843 24.610 23.072 1.00 0.00 C +ATOM 824 HB THR 53 29.437 23.822 23.538 1.00 0.00 H +ATOM 825 CG2 THR 53 27.377 24.187 23.140 1.00 0.00 C +ATOM 826 HG21 THR 53 26.764 24.851 22.530 1.00 0.00 H +ATOM 827 HG22 THR 53 27.273 23.166 22.771 1.00 0.00 H +ATOM 828 HG23 THR 53 27.034 24.222 24.173 1.00 0.00 H +ATOM 829 OG1 THR 53 29.202 24.691 21.711 1.00 0.00 O +ATOM 830 HG1 THR 53 28.846 23.916 21.267 1.00 0.00 H +ATOM 831 C THR 53 30.659 26.207 23.717 1.00 0.00 C +ATOM 832 O THR 53 31.116 27.162 23.090 1.00 0.00 O +ATOM 833 N ILE 54 31.442 25.345 24.374 1.00 0.00 N +ATOM 834 H ILE 54 31.004 24.594 24.882 1.00 0.00 H +ATOM 835 CA ILE 54 32.909 25.221 24.213 1.00 0.00 C +ATOM 836 HA ILE 54 33.240 26.044 23.577 1.00 0.00 H +ATOM 837 CB ILE 54 33.626 25.401 25.580 1.00 0.00 C +ATOM 838 HB ILE 54 33.304 26.355 25.999 1.00 0.00 H +ATOM 839 CG2 ILE 54 33.247 24.293 26.584 1.00 0.00 C +ATOM 840 HG21 ILE 54 33.569 23.317 26.216 1.00 0.00 H +ATOM 841 HG22 ILE 54 33.722 24.478 27.546 1.00 0.00 H +ATOM 842 HG23 ILE 54 32.168 24.277 26.748 1.00 0.00 H +ATOM 843 CG1 ILE 54 35.160 25.474 25.383 1.00 0.00 C +ATOM 844 HG12 ILE 54 35.543 24.496 25.100 1.00 0.00 H +ATOM 845 HG13 ILE 54 35.377 26.172 24.573 1.00 0.00 H +ATOM 846 CD1 ILE 54 35.950 25.929 26.611 1.00 0.00 C +ATOM 847 HD11 ILE 54 35.874 25.181 27.398 1.00 0.00 H +ATOM 848 HD12 ILE 54 37.002 26.039 26.344 1.00 0.00 H +ATOM 849 HD13 ILE 54 35.566 26.887 26.960 1.00 0.00 H +ATOM 850 C ILE 54 33.281 23.920 23.494 1.00 0.00 C +ATOM 851 O ILE 54 32.554 22.915 23.563 1.00 0.00 O +ATOM 852 N GLN 55 34.431 23.931 22.796 1.00 0.00 N +ATOM 853 H GLN 55 34.936 24.801 22.795 1.00 0.00 H +ATOM 854 CA GLN 55 35.121 22.772 22.222 1.00 0.00 C +ATOM 855 HA GLN 55 34.421 22.277 21.546 1.00 0.00 H +ATOM 856 CB GLN 55 36.307 23.300 21.365 1.00 0.00 C +ATOM 857 HB2 GLN 55 36.791 22.447 20.884 1.00 0.00 H +ATOM 858 HB3 GLN 55 35.899 23.942 20.584 1.00 0.00 H +ATOM 859 CG GLN 55 37.364 24.105 22.163 1.00 0.00 C +ATOM 860 HG2 GLN 55 36.872 24.912 22.709 1.00 0.00 H +ATOM 861 HG3 GLN 55 37.853 23.450 22.885 1.00 0.00 H +ATOM 862 CD GLN 55 38.441 24.723 21.268 1.00 0.00 C +ATOM 863 OE1 GLN 55 38.986 24.095 20.378 1.00 0.00 O +ATOM 864 NE2 GLN 55 38.825 25.969 21.466 1.00 0.00 N +ATOM 865 HE21 GLN 55 39.431 26.369 20.759 1.00 0.00 H +ATOM 866 HE22 GLN 55 38.408 26.538 22.196 1.00 0.00 H +ATOM 867 C GLN 55 35.557 21.728 23.251 1.00 0.00 C +ATOM 868 O GLN 55 35.720 22.036 24.439 1.00 0.00 O +ATOM 869 N GLU 56 35.745 20.453 22.823 1.00 0.00 N +ATOM 870 H GLU 56 35.596 20.314 21.840 1.00 0.00 H +ATOM 871 CA GLU 56 36.107 19.280 23.648 1.00 0.00 C +ATOM 872 HA GLU 56 35.649 19.428 24.630 1.00 0.00 H +ATOM 873 CB GLU 56 35.416 18.033 23.012 1.00 0.00 C +ATOM 874 HB2 GLU 56 34.361 18.110 23.246 1.00 0.00 H +ATOM 875 HB3 GLU 56 35.482 18.109 21.929 1.00 0.00 H +ATOM 876 CG GLU 56 35.888 16.611 23.399 1.00 0.00 C +ATOM 877 HG2 GLU 56 35.227 15.894 22.907 1.00 0.00 H +ATOM 878 HG3 GLU 56 36.860 16.440 22.931 1.00 0.00 H +ATOM 879 CD GLU 56 35.973 16.276 24.876 1.00 0.00 C +ATOM 880 OE1 GLU 56 37.124 16.208 25.412 1.00 0.00 O +ATOM 881 OE2 GLU 56 34.931 15.941 25.517 1.00 0.00 O +ATOM 882 C GLU 56 37.574 19.097 23.925 1.00 0.00 C +ATOM 883 O GLU 56 38.045 19.294 25.096 1.00 0.00 O +ATOM 884 OXT GLU 56 38.337 18.500 23.085 1.00 0.00 O +HETATM 885 ZN ZN1 57 26.532 32.424 29.927 1.00 0.00 Zn +HETATM 886 N AN1 58 28.163 33.271 30.874 1.00 0.00 N +HETATM 887 C AN1 58 30.434 34.061 31.871 1.00 0.00 C +HETATM 888 C1 AN1 58 29.147 33.589 31.334 1.00 0.00 C +HETATM 889 H AN1 58 30.313 34.431 32.897 1.00 0.00 H +HETATM 890 H1 AN1 58 30.837 34.866 31.245 1.00 0.00 H +HETATM 891 H2 AN1 58 31.138 33.224 31.882 1.00 0.00 H +HETATM 892 N1 AZI 59 30.826 28.848 29.728 1.00 0.00 N +HETATM 893 N2 AZI 59 30.154 29.553 30.615 1.00 0.00 N +HETATM 894 N3 AZI 59 29.523 30.210 31.366 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 17 13 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 73 72 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 885 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 147 136 +CONECT 135 134 +CONECT 136 134 137 139 138 +CONECT 137 136 +CONECT 138 136 +CONECT 139 142 136 140 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 139 +CONECT 143 145 146 142 144 +CONECT 144 143 +CONECT 145 143 +CONECT 146 143 +CONECT 147 149 134 148 +CONECT 148 147 +CONECT 149 150 151 147 +CONECT 150 149 +CONECT 151 149 152 154 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 155 151 156 +CONECT 155 154 +CONECT 156 154 158 157 +CONECT 157 156 +CONECT 158 160 159 156 176 +CONECT 159 158 +CONECT 160 163 161 162 158 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 165 164 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 167 168 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 172 171 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 174 175 173 169 +CONECT 173 172 +CONECT 174 172 +CONECT 175 172 +CONECT 176 158 177 178 +CONECT 177 176 +CONECT 178 176 179 180 +CONECT 179 178 +CONECT 180 178 181 195 182 +CONECT 181 180 +CONECT 182 180 184 188 183 +CONECT 183 182 +CONECT 184 185 187 182 186 +CONECT 185 184 +CONECT 186 184 +CONECT 187 184 +CONECT 188 189 190 182 191 +CONECT 189 188 +CONECT 190 188 +CONECT 191 188 193 192 194 +CONECT 192 191 +CONECT 193 191 +CONECT 194 191 +CONECT 195 197 180 196 +CONECT 196 195 +CONECT 197 198 199 195 +CONECT 198 197 +CONECT 199 206 197 201 200 +CONECT 200 199 +CONECT 201 202 199 203 204 +CONECT 202 201 +CONECT 203 201 +CONECT 204 201 205 +CONECT 205 204 +CONECT 206 207 208 199 +CONECT 207 206 +CONECT 208 210 206 209 +CONECT 209 208 +CONECT 210 211 228 212 208 +CONECT 211 210 +CONECT 212 215 210 213 214 +CONECT 213 212 +CONECT 214 212 +CONECT 215 217 216 218 212 +CONECT 216 215 +CONECT 217 215 +CONECT 218 219 215 220 221 +CONECT 219 218 +CONECT 220 218 +CONECT 221 223 218 224 222 +CONECT 222 221 +CONECT 223 221 +CONECT 224 227 221 225 226 +CONECT 225 224 +CONECT 226 224 +CONECT 227 224 +CONECT 228 229 210 230 +CONECT 229 228 +CONECT 230 228 232 231 +CONECT 231 230 +CONECT 232 235 230 233 234 +CONECT 233 232 +CONECT 234 232 +CONECT 235 236 237 232 +CONECT 236 235 +CONECT 237 239 235 238 +CONECT 238 237 +CONECT 239 241 240 251 237 +CONECT 240 239 +CONECT 241 247 242 243 239 +CONECT 242 241 +CONECT 243 245 241 244 246 +CONECT 244 243 +CONECT 245 243 +CONECT 246 243 +CONECT 247 249 248 250 241 +CONECT 248 247 +CONECT 249 247 +CONECT 250 247 +CONECT 251 239 253 252 +CONECT 252 251 +CONECT 253 263 254 251 +CONECT 254 255 253 264 257 +CONECT 255 256 270 254 +CONECT 256 255 +CONECT 257 254 258 265 266 +CONECT 258 259 260 257 +CONECT 259 262 268 258 +CONECT 260 261 258 267 +CONECT 261 262 269 260 +CONECT 262 885 259 261 +CONECT 263 253 +CONECT 264 254 +CONECT 265 257 +CONECT 266 257 +CONECT 267 260 +CONECT 268 259 +CONECT 269 261 +CONECT 270 272 255 271 +CONECT 271 270 +CONECT 272 273 274 282 270 +CONECT 273 272 +CONECT 274 275 276 272 280 +CONECT 275 274 +CONECT 276 279 278 274 277 +CONECT 277 276 +CONECT 278 276 +CONECT 279 276 +CONECT 280 274 281 +CONECT 281 280 +CONECT 282 284 272 283 +CONECT 283 282 +CONECT 284 294 285 282 +CONECT 285 286 288 284 295 +CONECT 286 287 301 285 +CONECT 287 286 +CONECT 288 296 297 285 289 +CONECT 289 288 290 291 +CONECT 290 299 289 293 +CONECT 291 289 298 292 +CONECT 292 291 293 300 +CONECT 293 290 292 885 +CONECT 294 284 +CONECT 295 285 +CONECT 296 288 +CONECT 297 288 +CONECT 298 291 +CONECT 299 290 +CONECT 300 292 +CONECT 301 303 286 302 +CONECT 302 301 +CONECT 303 314 304 301 305 +CONECT 304 303 +CONECT 305 303 308 307 306 +CONECT 306 305 +CONECT 307 305 +CONECT 308 310 311 305 309 +CONECT 309 308 +CONECT 310 308 +CONECT 311 312 308 313 +CONECT 312 311 +CONECT 313 311 +CONECT 314 316 315 303 +CONECT 315 314 +CONECT 316 318 317 314 +CONECT 317 316 +CONECT 318 324 320 319 316 +CONECT 319 318 +CONECT 320 322 321 318 323 +CONECT 321 320 +CONECT 322 320 +CONECT 323 320 +CONECT 324 326 325 318 +CONECT 325 324 +CONECT 326 328 327 324 +CONECT 327 326 +CONECT 328 340 330 329 326 +CONECT 329 328 +CONECT 330 331 336 328 332 +CONECT 331 330 +CONECT 332 330 334 335 333 +CONECT 333 332 +CONECT 334 332 +CONECT 335 332 +CONECT 336 337 338 330 339 +CONECT 337 336 +CONECT 338 336 +CONECT 339 336 +CONECT 340 341 342 328 +CONECT 341 340 +CONECT 342 344 340 343 +CONECT 343 342 +CONECT 344 346 345 352 342 +CONECT 345 344 +CONECT 346 349 347 348 344 +CONECT 347 346 +CONECT 348 346 +CONECT 349 351 350 346 +CONECT 350 349 +CONECT 351 349 +CONECT 352 354 344 353 +CONECT 353 352 +CONECT 354 355 356 352 +CONECT 355 354 +CONECT 356 358 354 376 357 +CONECT 357 356 +CONECT 358 360 359 361 356 +CONECT 359 358 +CONECT 360 358 +CONECT 361 362 358 375 +CONECT 362 363 364 361 +CONECT 363 362 +CONECT 364 362 365 366 +CONECT 365 364 +CONECT 366 364 375 367 +CONECT 367 366 368 369 +CONECT 368 367 +CONECT 369 367 371 370 +CONECT 370 369 +CONECT 371 373 369 372 +CONECT 372 371 +CONECT 373 375 374 371 +CONECT 374 373 +CONECT 375 361 366 373 +CONECT 376 378 356 377 +CONECT 377 376 +CONECT 378 379 380 376 +CONECT 379 378 +CONECT 380 382 378 381 386 +CONECT 381 380 +CONECT 382 385 383 384 380 +CONECT 383 382 +CONECT 384 382 +CONECT 385 382 +CONECT 386 380 388 387 +CONECT 387 386 +CONECT 388 389 386 390 +CONECT 389 388 +CONECT 390 388 392 391 401 +CONECT 391 390 +CONECT 392 395 393 390 394 +CONECT 393 392 +CONECT 394 392 +CONECT 395 396 397 398 392 +CONECT 396 395 +CONECT 397 395 +CONECT 398 400 395 399 +CONECT 399 398 +CONECT 400 398 +CONECT 401 390 403 402 +CONECT 402 401 +CONECT 403 404 401 405 +CONECT 404 403 +CONECT 405 403 407 411 406 +CONECT 406 405 +CONECT 407 408 410 405 409 +CONECT 408 407 +CONECT 409 407 +CONECT 410 407 +CONECT 411 413 405 412 +CONECT 412 411 +CONECT 413 414 415 411 +CONECT 414 413 +CONECT 415 417 413 416 426 +CONECT 416 415 +CONECT 417 418 419 420 415 +CONECT 418 417 +CONECT 419 417 +CONECT 420 423 417 421 422 +CONECT 421 420 +CONECT 422 420 +CONECT 423 424 425 420 +CONECT 424 423 +CONECT 425 423 +CONECT 426 415 428 427 +CONECT 427 426 +CONECT 428 429 426 430 +CONECT 429 428 +CONECT 430 428 432 431 448 +CONECT 431 430 +CONECT 432 435 433 434 430 +CONECT 433 432 +CONECT 434 432 +CONECT 435 437 438 436 432 +CONECT 436 435 +CONECT 437 435 +CONECT 438 441 439 440 435 +CONECT 439 438 +CONECT 440 438 +CONECT 441 444 442 443 438 +CONECT 442 441 +CONECT 443 441 +CONECT 444 446 447 445 441 +CONECT 445 444 +CONECT 446 444 +CONECT 447 444 +CONECT 448 430 450 449 +CONECT 449 448 +CONECT 450 451 448 452 +CONECT 451 450 +CONECT 452 450 454 453 468 +CONECT 453 452 +CONECT 454 457 455 452 456 +CONECT 455 454 +CONECT 456 454 +CONECT 457 458 466 454 +CONECT 458 460 459 457 +CONECT 459 458 +CONECT 460 461 462 458 +CONECT 461 460 +CONECT 462 463 460 464 +CONECT 463 462 +CONECT 464 462 465 466 +CONECT 465 464 +CONECT 466 464 457 467 +CONECT 467 466 +CONECT 468 452 470 469 +CONECT 469 468 +CONECT 470 471 472 468 +CONECT 471 470 +CONECT 472 474 470 482 473 +CONECT 473 472 +CONECT 474 475 480 476 472 +CONECT 475 474 +CONECT 476 474 478 479 477 +CONECT 477 476 +CONECT 478 476 +CONECT 479 476 +CONECT 480 481 474 +CONECT 481 480 +CONECT 482 484 472 483 +CONECT 483 482 +CONECT 484 485 486 482 +CONECT 485 484 +CONECT 486 488 484 487 504 +CONECT 487 486 +CONECT 488 491 489 490 486 +CONECT 489 488 +CONECT 490 488 +CONECT 491 494 493 492 488 +CONECT 492 491 +CONECT 493 491 +CONECT 494 497 495 496 491 +CONECT 495 494 +CONECT 496 494 +CONECT 497 499 498 500 494 +CONECT 498 497 +CONECT 499 497 +CONECT 500 502 497 503 501 +CONECT 501 500 +CONECT 502 500 +CONECT 503 500 +CONECT 504 486 506 505 +CONECT 505 504 +CONECT 506 507 504 508 +CONECT 507 506 +CONECT 508 506 510 509 514 +CONECT 509 508 +CONECT 510 513 511 508 512 +CONECT 511 510 +CONECT 512 510 +CONECT 513 510 +CONECT 514 508 516 515 +CONECT 515 514 +CONECT 516 517 514 518 +CONECT 517 516 +CONECT 518 516 520 535 519 +CONECT 519 518 +CONECT 520 521 518 523 522 +CONECT 521 520 +CONECT 522 520 +CONECT 523 525 520 526 524 +CONECT 524 523 +CONECT 525 523 +CONECT 526 527 523 529 528 +CONECT 527 526 +CONECT 528 526 +CONECT 529 531 526 532 530 +CONECT 530 529 +CONECT 531 529 +CONECT 532 534 529 533 +CONECT 533 532 +CONECT 534 532 +CONECT 535 537 518 536 +CONECT 536 535 +CONECT 537 538 539 535 +CONECT 538 537 +CONECT 539 541 537 545 540 +CONECT 540 539 +CONECT 541 542 544 543 539 +CONECT 542 541 +CONECT 543 541 +CONECT 544 541 +CONECT 545 547 539 546 +CONECT 546 545 +CONECT 547 548 545 549 +CONECT 548 547 +CONECT 549 551 547 550 559 +CONECT 550 549 +CONECT 551 554 552 553 549 +CONECT 552 551 +CONECT 553 551 +CONECT 554 556 555 551 +CONECT 555 554 +CONECT 556 557 558 554 +CONECT 557 556 +CONECT 558 556 +CONECT 559 549 561 560 +CONECT 560 559 +CONECT 561 562 559 563 +CONECT 562 561 +CONECT 563 561 565 564 571 +CONECT 564 563 +CONECT 565 568 566 563 567 +CONECT 566 565 +CONECT 567 565 +CONECT 568 569 570 565 +CONECT 569 568 +CONECT 570 568 +CONECT 571 563 573 572 +CONECT 572 571 +CONECT 573 574 571 575 +CONECT 574 573 +CONECT 575 573 577 591 576 +CONECT 576 575 +CONECT 577 579 578 575 580 +CONECT 578 577 +CONECT 579 577 +CONECT 580 589 577 581 +CONECT 581 580 582 583 +CONECT 582 581 +CONECT 583 585 581 584 +CONECT 584 583 +CONECT 585 587 586 583 +CONECT 586 585 +CONECT 587 589 588 585 +CONECT 588 587 +CONECT 589 590 587 580 +CONECT 590 589 +CONECT 591 593 575 592 +CONECT 592 591 +CONECT 593 594 595 591 +CONECT 594 593 +CONECT 595 598 593 596 597 +CONECT 596 595 +CONECT 597 595 +CONECT 598 600 599 595 +CONECT 599 598 +CONECT 600 602 601 598 +CONECT 601 600 +CONECT 602 622 603 604 600 +CONECT 603 602 +CONECT 604 607 602 606 605 +CONECT 605 604 +CONECT 606 604 +CONECT 607 610 609 608 604 +CONECT 608 607 +CONECT 609 607 +CONECT 610 613 611 612 607 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 610 +CONECT 614 613 +CONECT 615 619 616 613 +CONECT 616 618 615 617 +CONECT 617 616 +CONECT 618 616 +CONECT 619 621 620 615 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 602 +CONECT 623 622 +CONECT 624 626 625 622 +CONECT 625 624 +CONECT 626 628 634 627 624 +CONECT 627 626 +CONECT 628 631 629 630 626 +CONECT 629 628 +CONECT 630 628 +CONECT 631 633 632 628 +CONECT 632 631 +CONECT 633 631 +CONECT 634 636 635 626 +CONECT 635 634 +CONECT 636 638 637 634 +CONECT 637 636 +CONECT 638 641 639 640 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 642 638 +CONECT 642 641 +CONECT 643 645 644 641 +CONECT 644 643 +CONECT 645 647 646 656 643 +CONECT 646 645 +CONECT 647 649 650 648 645 +CONECT 648 647 +CONECT 649 647 +CONECT 650 652 647 653 651 +CONECT 651 650 +CONECT 652 650 +CONECT 653 650 654 655 +CONECT 654 653 +CONECT 655 653 +CONECT 656 658 645 657 +CONECT 657 656 +CONECT 658 659 660 656 +CONECT 659 658 +CONECT 660 680 658 661 662 +CONECT 661 660 +CONECT 662 660 665 663 664 +CONECT 663 662 +CONECT 664 662 +CONECT 665 667 666 662 668 +CONECT 666 665 +CONECT 667 665 +CONECT 668 665 670 671 669 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 673 672 +CONECT 672 671 +CONECT 673 674 671 677 +CONECT 674 675 676 673 +CONECT 675 674 +CONECT 676 674 +CONECT 677 673 679 678 +CONECT 678 677 +CONECT 679 677 +CONECT 680 681 682 660 +CONECT 681 680 +CONECT 682 684 680 683 +CONECT 683 682 +CONECT 684 685 686 694 682 +CONECT 685 684 +CONECT 686 688 692 684 687 +CONECT 687 686 +CONECT 688 689 690 691 686 +CONECT 689 688 +CONECT 690 688 +CONECT 691 688 +CONECT 692 693 686 +CONECT 693 692 +CONECT 694 696 684 695 +CONECT 695 694 +CONECT 696 697 698 694 +CONECT 697 696 +CONECT 698 713 700 696 699 +CONECT 699 698 +CONECT 700 706 701 698 702 +CONECT 701 700 +CONECT 702 700 704 703 705 +CONECT 703 702 +CONECT 704 702 +CONECT 705 702 +CONECT 706 709 708 707 700 +CONECT 707 706 +CONECT 708 706 +CONECT 709 711 712 710 706 +CONECT 710 709 +CONECT 711 709 +CONECT 712 709 +CONECT 713 714 715 698 +CONECT 714 713 +CONECT 715 717 713 716 +CONECT 716 715 +CONECT 717 718 725 719 715 +CONECT 718 717 +CONECT 719 722 717 720 721 +CONECT 720 719 +CONECT 721 719 +CONECT 722 724 719 723 +CONECT 723 722 +CONECT 724 722 +CONECT 725 727 717 726 +CONECT 726 725 +CONECT 727 728 729 725 +CONECT 728 727 +CONECT 729 731 727 737 730 +CONECT 730 729 +CONECT 731 733 732 734 729 +CONECT 732 731 +CONECT 733 731 +CONECT 734 735 731 736 +CONECT 735 734 +CONECT 736 734 +CONECT 737 739 729 738 +CONECT 738 737 +CONECT 739 740 741 737 +CONECT 740 739 +CONECT 741 743 742 739 747 +CONECT 742 741 +CONECT 743 746 745 744 741 +CONECT 744 743 +CONECT 745 743 +CONECT 746 743 +CONECT 747 741 748 749 +CONECT 748 747 +CONECT 749 747 750 751 +CONECT 750 749 +CONECT 751 749 752 753 761 +CONECT 752 751 +CONECT 753 755 751 759 754 +CONECT 754 753 +CONECT 755 756 758 757 753 +CONECT 756 755 +CONECT 757 755 +CONECT 758 755 +CONECT 759 760 753 +CONECT 760 759 +CONECT 761 751 763 762 +CONECT 762 761 +CONECT 763 764 765 761 +CONECT 764 763 +CONECT 765 766 763 767 783 +CONECT 766 765 +CONECT 767 770 765 769 768 +CONECT 768 767 +CONECT 769 767 +CONECT 770 773 771 772 767 +CONECT 771 770 +CONECT 772 770 +CONECT 773 776 775 774 770 +CONECT 774 773 +CONECT 775 773 +CONECT 776 779 778 777 773 +CONECT 777 776 +CONECT 778 776 +CONECT 779 781 782 780 776 +CONECT 780 779 +CONECT 781 779 +CONECT 782 779 +CONECT 783 765 785 784 +CONECT 784 783 +CONECT 785 786 783 787 +CONECT 786 785 +CONECT 787 785 797 789 788 +CONECT 788 787 +CONECT 789 790 787 795 791 +CONECT 790 789 +CONECT 791 789 794 793 792 +CONECT 792 791 +CONECT 793 791 +CONECT 794 791 +CONECT 795 796 789 +CONECT 796 795 +CONECT 797 798 787 799 +CONECT 798 797 +CONECT 799 797 801 800 +CONECT 800 799 +CONECT 801 802 799 803 817 +CONECT 802 801 +CONECT 803 806 801 805 804 +CONECT 804 803 +CONECT 805 803 +CONECT 806 815 807 803 +CONECT 807 809 806 808 +CONECT 808 807 +CONECT 809 811 810 807 +CONECT 810 809 +CONECT 811 812 813 809 +CONECT 812 811 +CONECT 813 814 811 815 +CONECT 814 813 +CONECT 815 813 816 806 +CONECT 816 815 +CONECT 817 801 819 818 +CONECT 818 817 +CONECT 819 820 817 821 +CONECT 820 819 +CONECT 821 823 819 831 822 +CONECT 822 821 +CONECT 823 829 825 824 821 +CONECT 824 823 +CONECT 825 826 827 823 828 +CONECT 826 825 +CONECT 827 825 +CONECT 828 825 +CONECT 829 830 823 +CONECT 830 829 +CONECT 831 832 821 833 +CONECT 832 831 +CONECT 833 831 835 834 +CONECT 834 833 +CONECT 835 850 836 833 837 +CONECT 836 835 +CONECT 837 835 843 838 839 +CONECT 838 837 +CONECT 839 837 840 842 841 +CONECT 840 839 +CONECT 841 839 +CONECT 842 839 +CONECT 843 845 844 837 846 +CONECT 844 843 +CONECT 845 843 +CONECT 846 843 848 849 847 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 +CONECT 850 852 851 835 +CONECT 851 850 +CONECT 852 854 853 850 +CONECT 853 852 +CONECT 854 856 855 852 867 +CONECT 855 854 +CONECT 856 858 857 859 854 +CONECT 857 856 +CONECT 858 856 +CONECT 859 862 856 860 861 +CONECT 860 859 +CONECT 861 859 +CONECT 862 863 864 859 +CONECT 863 862 +CONECT 864 865 862 866 +CONECT 865 864 +CONECT 866 864 +CONECT 867 854 869 868 +CONECT 868 867 +CONECT 869 870 867 871 +CONECT 870 869 +CONECT 871 869 873 882 872 +CONECT 872 871 +CONECT 873 875 874 876 871 +CONECT 874 873 +CONECT 875 873 +CONECT 876 877 878 873 879 +CONECT 877 876 +CONECT 878 876 +CONECT 879 876 880 881 +CONECT 880 879 +CONECT 881 879 +CONECT 882 884 871 883 +CONECT 883 882 +CONECT 884 882 +CONECT 885 87 293 886 262 +CONECT 886 885 888 +CONECT 887 890 888 891 889 +CONECT 888 886 887 +CONECT 889 887 +CONECT 890 887 +CONECT 891 887 +CONECT 892 893 +CONECT 893 892 894 +CONECT 894 893 +MASTER 0 0 0 0 0 0 0 0 894 0 894 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_5.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_5.pdb new file mode 100644 index 0000000..6fcd112 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_5.pdb @@ -0,0 +1,1745 @@ +COMPND fitness: -2.8894 84.35416666666652 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 56.210 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.610 37.835 23.460 1.00 0.00 N +ATOM 2 H1 MET 1 14.587 38.236 24.394 1.00 0.00 H +ATOM 3 H2 MET 1 13.812 38.148 22.935 1.00 0.00 H +ATOM 4 H3 MET 1 15.464 38.178 23.039 1.00 0.00 H +ATOM 5 CA MET 1 14.662 36.367 23.555 1.00 0.00 C +ATOM 6 HA MET 1 13.728 36.021 23.999 1.00 0.00 H +ATOM 7 CB MET 1 14.806 35.736 22.157 1.00 0.00 C +ATOM 8 HB2 MET 1 13.928 35.994 21.567 1.00 0.00 H +ATOM 9 HB3 MET 1 15.682 36.159 21.666 1.00 0.00 H +ATOM 10 CG MET 1 14.957 34.205 22.185 1.00 0.00 C +ATOM 11 HG2 MET 1 15.847 33.953 22.764 1.00 0.00 H +ATOM 12 HG3 MET 1 14.092 33.769 22.688 1.00 0.00 H +ATOM 13 SD MET 1 15.133 33.423 20.557 1.00 0.00 S +ATOM 14 CE MET 1 13.430 33.524 19.932 1.00 0.00 C +ATOM 15 HE1 MET 1 13.103 34.563 19.883 1.00 0.00 H +ATOM 16 HE2 MET 1 13.381 33.092 18.933 1.00 0.00 H +ATOM 17 HE3 MET 1 12.763 32.967 20.591 1.00 0.00 H +ATOM 18 C MET 1 15.802 35.945 24.478 1.00 0.00 C +ATOM 19 O MET 1 16.945 36.312 24.240 1.00 0.00 O +ATOM 20 N GLN 2 15.501 35.116 25.481 1.00 0.00 N +ATOM 21 H GLN 2 14.536 34.897 25.661 1.00 0.00 H +ATOM 22 CA GLN 2 16.493 34.445 26.330 1.00 0.00 C +ATOM 23 HA GLN 2 17.239 35.169 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 15.772 33.892 27.577 1.00 0.00 C +ATOM 25 HB2 GLN 2 14.850 33.401 27.264 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.383 33.136 28.064 1.00 0.00 H +ATOM 27 CG GLN 2 15.424 34.965 28.621 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.944 35.807 28.133 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.697 34.542 29.314 1.00 0.00 H +ATOM 30 CD GLN 2 16.606 35.446 29.461 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.750 35.034 29.311 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.365 36.275 30.448 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.141 36.537 31.027 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.429 36.623 30.586 1.00 0.00 H +ATOM 35 C GLN 2 17.242 33.339 25.554 1.00 0.00 C +ATOM 36 O GLN 2 16.895 32.159 25.641 1.00 0.00 O +ATOM 37 N TYR 3 18.267 33.710 24.779 1.00 0.00 N +ATOM 38 H TYR 3 18.507 34.698 24.761 1.00 0.00 H +ATOM 39 CA TYR 3 19.130 32.772 24.050 1.00 0.00 C +ATOM 40 HA TYR 3 18.508 32.164 23.394 1.00 0.00 H +ATOM 41 CB TYR 3 20.138 33.545 23.190 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.628 34.306 23.802 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.913 32.853 22.855 1.00 0.00 H +ATOM 44 CG TYR 3 19.537 34.200 21.959 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.394 33.447 20.777 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.704 32.411 20.758 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.869 34.045 19.616 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.784 33.476 18.703 1.00 0.00 H +ATOM 49 CZ TYR 3 18.472 35.400 19.642 1.00 0.00 C +ATOM 50 OH TYR 3 17.979 35.981 18.519 1.00 0.00 O +ATOM 51 HH TYR 3 17.916 35.355 17.795 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.600 36.150 20.830 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.290 37.185 20.841 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.136 35.550 21.987 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.235 36.130 22.896 1.00 0.00 H +ATOM 56 C TYR 3 19.865 31.833 25.021 1.00 0.00 C +ATOM 57 O TYR 3 20.356 32.276 26.061 1.00 0.00 O +ATOM 58 N LYS 4 19.933 30.534 24.705 1.00 0.00 N +ATOM 59 H LYS 4 19.658 30.251 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 20.470 29.488 25.599 1.00 0.00 C +ATOM 61 HA LYS 4 20.193 29.725 26.622 1.00 0.00 H +ATOM 62 CB LYS 4 19.857 28.117 25.237 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.784 28.034 24.153 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.538 27.331 25.568 1.00 0.00 H +ATOM 65 CG LYS 4 18.476 27.805 25.856 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.226 26.778 25.589 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.551 27.859 26.942 1.00 0.00 H +ATOM 68 CD LYS 4 17.329 28.710 25.376 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.488 29.726 25.728 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.350 28.733 24.285 1.00 0.00 H +ATOM 71 CE LYS 4 15.930 28.229 25.815 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.191 28.785 25.230 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.824 27.174 25.545 1.00 0.00 H +ATOM 74 NZ LYS 4 15.640 28.425 27.266 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.696 29.397 27.534 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.693 28.146 27.503 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.250 27.898 27.886 1.00 0.00 H +ATOM 78 C LYS 4 22.000 29.450 25.582 1.00 0.00 C +ATOM 79 O LYS 4 22.635 29.697 24.563 1.00 0.00 O +HETATM 80 N HX1 5 22.614 29.087 26.706 1.00 0.00 N +HETATM 81 CA HX1 5 24.068 28.924 26.868 1.00 0.00 C +HETATM 82 C HX1 5 24.352 27.735 27.797 1.00 0.00 C +HETATM 83 O HX1 5 23.963 27.749 28.965 1.00 0.00 O +HETATM 84 CB HX1 5 24.686 30.249 27.361 1.00 0.00 C +HETATM 85 CG HX1 5 26.205 30.328 27.453 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.096 29.341 27.126 1.00 0.00 C +HETATM 87 ND1 HX1 5 26.899 31.425 27.989 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.188 31.059 27.927 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.345 29.815 27.484 1.00 0.00 N +HETATM 90 H HX1 5 22.036 28.964 27.535 1.00 0.00 H +HETATM 91 HA HX1 5 24.511 28.691 25.903 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.270 30.493 28.340 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.367 31.041 26.681 1.00 0.00 H +HETATM 94 HD2 HX1 5 26.901 28.351 26.753 1.00 0.00 H +HETATM 95 HE1 HX1 5 28.999 31.640 28.362 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.166 29.232 27.691 1.00 0.00 H +ATOM 97 N ILE 6 24.976 26.694 27.247 1.00 0.00 N +ATOM 98 H ILE 6 25.273 26.764 26.279 1.00 0.00 H +ATOM 99 CA ILE 6 25.416 25.484 27.957 1.00 0.00 C +ATOM 100 HA ILE 6 24.791 25.350 28.841 1.00 0.00 H +ATOM 101 CB ILE 6 25.219 24.234 27.066 1.00 0.00 C +ATOM 102 HB ILE 6 25.717 24.411 26.111 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.833 22.967 27.697 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.377 22.767 28.667 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.684 22.105 27.049 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.912 23.079 27.816 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.703 24.039 26.816 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.199 23.911 27.773 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.300 24.935 26.343 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.331 22.853 25.919 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.511 21.913 26.441 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.269 22.909 25.674 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.912 22.881 24.996 1.00 0.00 H +ATOM 114 C ILE 6 26.855 25.666 28.457 1.00 0.00 C +ATOM 115 O ILE 6 27.669 26.350 27.833 1.00 0.00 O +ATOM 116 N VAL 7 27.116 25.088 29.628 1.00 0.00 N +ATOM 117 H VAL 7 26.386 24.493 30.005 1.00 0.00 H +ATOM 118 CA VAL 7 28.247 25.361 30.522 1.00 0.00 C +ATOM 119 HA VAL 7 28.279 26.437 30.666 1.00 0.00 H +ATOM 120 CB VAL 7 27.910 24.707 31.877 1.00 0.00 C +ATOM 121 HB VAL 7 26.872 24.951 32.111 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.029 23.177 31.837 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.076 22.879 31.779 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.576 22.749 32.720 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.511 22.784 30.962 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.732 25.253 33.046 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.660 26.340 33.068 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.348 24.861 33.986 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.770 24.958 32.940 1.00 0.00 H +ATOM 130 C VAL 7 29.638 24.925 30.014 1.00 0.00 C +ATOM 131 O VAL 7 29.787 23.876 29.396 1.00 0.00 O +ATOM 132 N ARG 8 30.669 25.690 30.392 1.00 0.00 N +ATOM 133 H ARG 8 30.448 26.631 30.693 1.00 0.00 H +ATOM 134 CA ARG 8 32.095 25.295 30.376 1.00 0.00 C +ATOM 135 HA ARG 8 32.337 25.066 29.335 1.00 0.00 H +ATOM 136 CB ARG 8 33.001 26.478 30.815 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.031 26.191 30.597 1.00 0.00 H +ATOM 138 HB3 ARG 8 32.778 27.341 30.186 1.00 0.00 H +ATOM 139 CG ARG 8 32.964 26.926 32.298 1.00 0.00 C +ATOM 140 HG2 ARG 8 33.166 26.074 32.950 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.772 27.646 32.453 1.00 0.00 H +ATOM 142 CD ARG 8 31.641 27.598 32.706 1.00 0.00 C +ATOM 143 HD2 ARG 8 31.523 28.498 32.102 1.00 0.00 H +ATOM 144 HD3 ARG 8 30.811 26.937 32.492 1.00 0.00 H +ATOM 145 NE ARG 8 31.554 27.975 34.136 1.00 0.00 N +ATOM 146 HE ARG 8 31.477 28.963 34.328 1.00 0.00 H +ATOM 147 CZ ARG 8 31.360 27.181 35.177 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.436 25.880 35.096 1.00 0.00 N +ATOM 149 HH11 ARG 8 31.653 25.451 34.206 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.280 25.329 35.915 1.00 0.00 H +ATOM 151 NH2 ARG 8 31.059 27.706 36.329 1.00 0.00 N +ATOM 152 HH21 ARG 8 30.883 28.704 36.414 1.00 0.00 H +ATOM 153 HH22 ARG 8 30.972 27.170 37.183 1.00 0.00 H +ATOM 154 C ARG 8 32.399 24.032 31.197 1.00 0.00 C +ATOM 155 O ARG 8 31.989 23.928 32.359 1.00 0.00 O +ATOM 156 N GLY 9 33.235 23.149 30.643 1.00 0.00 N +ATOM 157 H GLY 9 33.483 23.302 29.677 1.00 0.00 H +ATOM 158 CA GLY 9 33.803 21.970 31.313 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.769 21.741 30.856 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.977 22.203 32.366 1.00 0.00 H +ATOM 161 C GLY 9 32.930 20.700 31.255 1.00 0.00 C +ATOM 162 O GLY 9 31.748 20.758 30.940 1.00 0.00 O +ATOM 163 N LYS 10 33.531 19.549 31.601 1.00 0.00 N +ATOM 164 H LYS 10 34.504 19.593 31.865 1.00 0.00 H +ATOM 165 CA LYS 10 32.919 18.202 31.470 1.00 0.00 C +ATOM 166 HA LYS 10 31.934 18.338 31.024 1.00 0.00 H +ATOM 167 CB LYS 10 33.740 17.354 30.479 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.240 18.008 29.765 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.509 16.801 31.019 1.00 0.00 H +ATOM 170 CG LYS 10 32.870 16.377 29.670 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.314 15.722 30.339 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.155 16.955 29.085 1.00 0.00 H +ATOM 173 CD LYS 10 33.734 15.532 28.729 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.372 16.192 28.137 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.363 14.862 29.315 1.00 0.00 H +ATOM 176 CE LYS 10 32.861 14.716 27.778 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.249 14.019 28.356 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.207 15.410 27.249 1.00 0.00 H +ATOM 179 NZ LYS 10 33.702 14.007 26.788 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.337 13.350 27.224 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.169 13.532 26.081 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.296 14.687 26.297 1.00 0.00 H +ATOM 183 C LYS 10 32.637 17.486 32.799 1.00 0.00 C +ATOM 184 O LYS 10 32.284 16.311 32.824 1.00 0.00 O +ATOM 185 N TRP 11 32.824 18.177 33.926 1.00 0.00 N +ATOM 186 H TRP 11 33.243 19.090 33.848 1.00 0.00 H +ATOM 187 CA TRP 11 32.126 17.892 35.182 1.00 0.00 C +ATOM 188 HA TRP 11 31.901 16.824 35.268 1.00 0.00 H +ATOM 189 CB TRP 11 33.036 18.283 36.357 1.00 0.00 C +ATOM 190 HB2 TRP 11 32.535 18.015 37.294 1.00 0.00 H +ATOM 191 HB3 TRP 11 33.950 17.689 36.296 1.00 0.00 H +ATOM 192 CG TRP 11 33.419 19.737 36.406 1.00 0.00 C +ATOM 193 CD1 TRP 11 32.861 20.665 37.216 1.00 0.00 C +ATOM 194 HD1 TRP 11 32.089 20.465 37.950 1.00 0.00 H +ATOM 195 NE1 TRP 11 33.403 21.907 36.943 1.00 0.00 N +ATOM 196 HE1 TRP 11 33.141 22.745 37.445 1.00 0.00 H +ATOM 197 CE2 TRP 11 34.318 21.848 35.912 1.00 0.00 C +ATOM 198 CZ2 TRP 11 35.085 22.819 35.250 1.00 0.00 C +ATOM 199 HZ2 TRP 11 35.003 23.862 35.519 1.00 0.00 H +ATOM 200 CH2 TRP 11 35.984 22.415 34.248 1.00 0.00 C +ATOM 201 HH2 TRP 11 36.605 23.145 33.744 1.00 0.00 H +ATOM 202 CZ3 TRP 11 36.107 21.052 33.924 1.00 0.00 C +ATOM 203 HZ3 TRP 11 36.838 20.745 33.183 1.00 0.00 H +ATOM 204 CE3 TRP 11 35.320 20.087 34.584 1.00 0.00 C +ATOM 205 HE3 TRP 11 35.461 19.041 34.352 1.00 0.00 H +ATOM 206 CD2 TRP 11 34.391 20.460 35.583 1.00 0.00 C +ATOM 207 C TRP 11 30.804 18.683 35.243 1.00 0.00 C +ATOM 208 O TRP 11 29.944 18.363 36.056 1.00 0.00 O +ATOM 209 N VAL 12 30.660 19.740 34.430 1.00 0.00 N +ATOM 210 H VAL 12 31.413 19.900 33.802 1.00 0.00 H +ATOM 211 CA VAL 12 29.415 20.530 34.220 1.00 0.00 C +ATOM 212 HA VAL 12 29.656 21.259 33.447 1.00 0.00 H +ATOM 213 CB VAL 12 29.101 21.349 35.518 1.00 0.00 C +ATOM 214 HB VAL 12 29.296 20.712 36.378 1.00 0.00 H +ATOM 215 CG1 VAL 12 27.725 21.975 35.716 1.00 0.00 C +ATOM 216 HG11 VAL 12 26.970 21.208 35.955 1.00 0.00 H +ATOM 217 HG12 VAL 12 27.751 22.645 36.588 1.00 0.00 H +ATOM 218 HG13 VAL 12 27.441 22.553 34.835 1.00 0.00 H +ATOM 219 CG2 VAL 12 30.126 22.530 35.519 1.00 0.00 C +ATOM 220 HG21 VAL 12 29.940 23.175 34.670 1.00 0.00 H +ATOM 221 HG22 VAL 12 30.055 23.143 36.414 1.00 0.00 H +ATOM 222 HG23 VAL 12 31.147 22.192 35.430 1.00 0.00 H +ATOM 223 C VAL 12 28.340 19.651 33.542 1.00 0.00 C +ATOM 224 O VAL 12 28.703 18.718 32.836 1.00 0.00 O +ATOM 225 N LYS 13 27.051 19.990 33.615 1.00 0.00 N +ATOM 226 H LYS 13 26.818 20.626 34.355 1.00 0.00 H +ATOM 227 CA LYS 13 26.031 19.654 32.590 1.00 0.00 C +ATOM 228 HA LYS 13 26.538 19.769 31.626 1.00 0.00 H +ATOM 229 CB LYS 13 25.592 18.175 32.709 1.00 0.00 C +ATOM 230 HB2 LYS 13 26.368 17.610 33.220 1.00 0.00 H +ATOM 231 HB3 LYS 13 24.698 18.118 33.320 1.00 0.00 H +ATOM 232 CG LYS 13 25.353 17.514 31.333 1.00 0.00 C +ATOM 233 HG2 LYS 13 24.456 17.931 30.874 1.00 0.00 H +ATOM 234 HG3 LYS 13 26.197 17.751 30.683 1.00 0.00 H +ATOM 235 CD LYS 13 25.238 15.981 31.410 1.00 0.00 C +ATOM 236 HD2 LYS 13 25.170 15.578 30.397 1.00 0.00 H +ATOM 237 HD3 LYS 13 26.145 15.589 31.878 1.00 0.00 H +ATOM 238 CE LYS 13 24.004 15.541 32.208 1.00 0.00 C +ATOM 239 HE2 LYS 13 23.955 16.153 33.114 1.00 0.00 H +ATOM 240 HE3 LYS 13 23.108 15.743 31.609 1.00 0.00 H +ATOM 241 NZ LYS 13 24.068 14.106 32.592 1.00 0.00 N +ATOM 242 HZ1 LYS 13 24.999 13.834 32.897 1.00 0.00 H +ATOM 243 HZ2 LYS 13 23.472 13.932 33.399 1.00 0.00 H +ATOM 244 HZ3 LYS 13 23.792 13.478 31.849 1.00 0.00 H +ATOM 245 C LYS 13 24.841 20.629 32.531 1.00 0.00 C +ATOM 246 O LYS 13 23.849 20.366 31.856 1.00 0.00 O +ATOM 247 N GLY 14 24.939 21.740 33.268 1.00 0.00 N +ATOM 248 H GLY 14 25.799 21.915 33.754 1.00 0.00 H +ATOM 249 CA GLY 14 23.872 22.731 33.398 1.00 0.00 C +ATOM 250 HA2 GLY 14 22.917 22.216 33.519 1.00 0.00 H +ATOM 251 HA3 GLY 14 24.041 23.329 34.294 1.00 0.00 H +ATOM 252 C GLY 14 23.740 23.693 32.199 1.00 0.00 C +ATOM 253 O GLY 14 24.623 23.800 31.347 1.00 0.00 O +ATOM 254 N VAL 15 22.630 24.433 32.175 1.00 0.00 N +ATOM 255 H VAL 15 21.967 24.310 32.924 1.00 0.00 H +ATOM 256 CA VAL 15 22.258 25.391 31.125 1.00 0.00 C +ATOM 257 HA VAL 15 23.156 25.664 30.577 1.00 0.00 H +ATOM 258 CB VAL 15 21.291 24.727 30.116 1.00 0.00 C +ATOM 259 HB VAL 15 21.791 23.839 29.715 1.00 0.00 H +ATOM 260 CG1 VAL 15 19.966 24.264 30.749 1.00 0.00 C +ATOM 261 HG11 VAL 15 19.406 25.113 31.134 1.00 0.00 H +ATOM 262 HG12 VAL 15 19.365 23.754 29.993 1.00 0.00 H +ATOM 263 HG13 VAL 15 20.160 23.557 31.554 1.00 0.00 H +ATOM 264 CG2 VAL 15 20.963 25.647 28.933 1.00 0.00 C +ATOM 265 HG21 VAL 15 21.883 26.004 28.474 1.00 0.00 H +ATOM 266 HG22 VAL 15 20.402 25.080 28.186 1.00 0.00 H +ATOM 267 HG23 VAL 15 20.358 26.490 29.258 1.00 0.00 H +ATOM 268 C VAL 15 21.686 26.658 31.751 1.00 0.00 C +ATOM 269 O VAL 15 20.993 26.607 32.770 1.00 0.00 O +HETATM 270 N HY1 16 21.983 27.814 31.152 1.00 0.00 N +HETATM 271 CA HY1 16 21.415 29.132 31.476 1.00 0.00 C +HETATM 272 C HY1 16 21.134 29.908 30.177 1.00 0.00 C +HETATM 273 O HY1 16 21.275 29.361 29.086 1.00 0.00 O +HETATM 274 CB HY1 16 22.356 29.875 32.450 1.00 0.00 C +HETATM 275 CG HY1 16 23.709 30.229 31.878 1.00 0.00 C +HETATM 276 CD2 HY1 16 24.068 31.431 31.324 1.00 0.00 C +HETATM 277 ND1 HY1 16 24.813 29.410 31.817 1.00 0.00 N +HETATM 278 CE1 HY1 16 25.816 30.121 31.269 1.00 0.00 C +HETATM 279 NE2 HY1 16 25.412 31.360 30.935 1.00 0.00 N +HETATM 280 H HY1 16 22.553 27.772 30.305 1.00 0.00 H +HETATM 281 HA HY1 16 20.458 28.981 31.988 1.00 0.00 H +HETATM 282 HB2 HY1 16 21.869 30.793 32.788 1.00 0.00 H +HETATM 283 HB3 HY1 16 22.504 29.262 33.342 1.00 0.00 H +HETATM 284 HD1 HY1 16 24.881 28.463 32.165 1.00 0.00 H +HETATM 285 HD2 HY1 16 23.428 32.300 31.222 1.00 0.00 H +HETATM 286 HE1 HY1 16 26.831 29.752 31.127 1.00 0.00 H +ATOM 287 N THR 17 20.733 31.171 30.282 1.00 0.00 N +ATOM 288 H THR 17 20.606 31.590 31.189 1.00 0.00 H +ATOM 289 CA THR 17 20.339 32.027 29.148 1.00 0.00 C +ATOM 290 HA THR 17 20.769 31.599 28.239 1.00 0.00 H +ATOM 291 CB THR 17 18.804 32.054 28.997 1.00 0.00 C +ATOM 292 HB THR 17 18.548 32.701 28.154 1.00 0.00 H +ATOM 293 CG2 THR 17 18.153 30.699 28.714 1.00 0.00 C +ATOM 294 HG21 THR 17 18.358 29.982 29.502 1.00 0.00 H +ATOM 295 HG22 THR 17 17.081 30.790 28.628 1.00 0.00 H +ATOM 296 HG23 THR 17 18.516 30.287 27.783 1.00 0.00 H +ATOM 297 OG1 THR 17 18.212 32.553 30.159 1.00 0.00 O +ATOM 298 HG1 THR 17 18.144 33.518 30.025 1.00 0.00 H +ATOM 299 C THR 17 20.886 33.446 29.236 1.00 0.00 C +ATOM 300 O THR 17 21.350 33.861 30.295 1.00 0.00 O +HETATM 301 N HY2 18 20.813 34.187 28.127 1.00 0.00 N +HETATM 302 CA HY2 18 21.081 35.625 28.066 1.00 0.00 C +HETATM 303 C HY2 18 19.976 36.319 27.265 1.00 0.00 C +HETATM 304 O HY2 18 19.648 35.866 26.170 1.00 0.00 O +HETATM 305 CB HY2 18 22.427 35.918 27.401 1.00 0.00 C +HETATM 306 CG HY2 18 23.623 35.439 28.194 1.00 0.00 C +HETATM 307 CD2 HY2 18 24.155 34.177 28.162 1.00 0.00 C +HETATM 308 ND1 HY2 18 24.312 36.145 29.158 1.00 0.00 N +HETATM 309 CE1 HY2 18 25.247 35.326 29.676 1.00 0.00 C +HETATM 310 NE2 HY2 18 25.185 34.110 29.103 1.00 0.00 N +HETATM 311 H HY2 18 20.458 33.740 27.282 1.00 0.00 H +HETATM 312 HA HY2 18 21.088 36.044 29.084 1.00 0.00 H +HETATM 313 HB2 HY2 18 22.454 35.451 26.408 1.00 0.00 H +HETATM 314 HB3 HY2 18 22.525 37.001 27.258 1.00 0.00 H +HETATM 315 HD1 HY2 18 24.160 37.108 29.430 1.00 0.00 H +HETATM 316 HD2 HY2 18 23.816 33.363 27.535 1.00 0.00 H +HETATM 317 HE1 HY2 18 25.945 35.606 30.456 1.00 0.00 H +ATOM 318 N GLU 19 19.430 37.417 27.787 1.00 0.00 N +ATOM 319 H GLU 19 19.758 37.740 28.682 1.00 0.00 H +ATOM 320 CA GLU 19 18.419 38.226 27.104 1.00 0.00 C +ATOM 321 HA GLU 19 17.699 37.546 26.656 1.00 0.00 H +ATOM 322 CB GLU 19 17.705 39.102 28.147 1.00 0.00 C +ATOM 323 HB2 GLU 19 17.377 38.469 28.971 1.00 0.00 H +ATOM 324 HB3 GLU 19 18.414 39.828 28.557 1.00 0.00 H +ATOM 325 CG GLU 19 16.477 39.854 27.616 1.00 0.00 C +ATOM 326 HG2 GLU 19 15.971 40.349 28.452 1.00 0.00 H +ATOM 327 HG3 GLU 19 16.810 40.632 26.924 1.00 0.00 H +ATOM 328 CD GLU 19 15.524 38.897 26.903 1.00 0.00 C +ATOM 329 OE1 GLU 19 15.614 38.801 25.661 1.00 0.00 O +ATOM 330 OE2 GLU 19 14.785 38.158 27.578 1.00 0.00 O +ATOM 331 C GLU 19 19.040 39.069 25.978 1.00 0.00 C +ATOM 332 O GLU 19 20.090 39.684 26.183 1.00 0.00 O +ATOM 333 N ALA 20 18.406 39.106 24.798 1.00 0.00 N +ATOM 334 H ALA 20 17.526 38.600 24.725 1.00 0.00 H +ATOM 335 CA ALA 20 18.770 39.982 23.679 1.00 0.00 C +ATOM 336 HA ALA 20 18.902 40.994 24.063 1.00 0.00 H +ATOM 337 CB ALA 20 20.096 39.515 23.062 1.00 0.00 C +ATOM 338 HB1 ALA 20 19.972 38.533 22.606 1.00 0.00 H +ATOM 339 HB2 ALA 20 20.416 40.226 22.305 1.00 0.00 H +ATOM 340 HB3 ALA 20 20.879 39.462 23.817 1.00 0.00 H +ATOM 341 C ALA 20 17.694 40.018 22.571 1.00 0.00 C +ATOM 342 O ALA 20 16.874 39.108 22.434 1.00 0.00 O +ATOM 343 N VAL 21 17.756 41.039 21.709 1.00 0.00 N +ATOM 344 H VAL 21 18.418 41.780 21.884 1.00 0.00 H +ATOM 345 CA VAL 21 17.017 41.071 20.423 1.00 0.00 C +ATOM 346 HA VAL 21 16.020 40.661 20.587 1.00 0.00 H +ATOM 347 CB VAL 21 16.842 42.514 19.898 1.00 0.00 C +ATOM 348 HB VAL 21 16.188 42.472 19.027 1.00 0.00 H +ATOM 349 CG1 VAL 21 16.159 43.411 20.937 1.00 0.00 C +ATOM 350 HG11 VAL 21 16.810 43.579 21.795 1.00 0.00 H +ATOM 351 HG12 VAL 21 15.918 44.373 20.486 1.00 0.00 H +ATOM 352 HG13 VAL 21 15.232 42.951 21.279 1.00 0.00 H +ATOM 353 CG2 VAL 21 18.158 43.176 19.464 1.00 0.00 C +ATOM 354 HG21 VAL 21 18.596 42.634 18.626 1.00 0.00 H +ATOM 355 HG22 VAL 21 17.964 44.195 19.129 1.00 0.00 H +ATOM 356 HG23 VAL 21 18.872 43.205 20.287 1.00 0.00 H +ATOM 357 C VAL 21 17.666 40.197 19.339 1.00 0.00 C +ATOM 358 O VAL 21 16.989 39.788 18.400 1.00 0.00 O +ATOM 359 N ASP 22 18.962 39.912 19.481 1.00 0.00 N +ATOM 360 H ASP 22 19.441 40.273 20.289 1.00 0.00 H +ATOM 361 CA ASP 22 19.803 39.155 18.549 1.00 0.00 C +ATOM 362 HA ASP 22 19.204 38.379 18.068 1.00 0.00 H +ATOM 363 CB ASP 22 20.347 40.115 17.467 1.00 0.00 C +ATOM 364 HB2 ASP 22 19.507 40.640 17.014 1.00 0.00 H +ATOM 365 HB3 ASP 22 20.969 40.862 17.961 1.00 0.00 H +ATOM 366 CG ASP 22 21.171 39.445 16.351 1.00 0.00 C +ATOM 367 OD1 ASP 22 21.358 40.133 15.304 1.00 0.00 O +ATOM 368 OD2 ASP 22 21.600 38.297 16.500 1.00 0.00 O +ATOM 369 C ASP 22 20.940 38.484 19.342 1.00 0.00 C +ATOM 370 O ASP 22 21.503 39.076 20.270 1.00 0.00 O +ATOM 371 N LEU 23 21.311 37.261 18.968 1.00 0.00 N +ATOM 372 H LEU 23 20.939 36.925 18.089 1.00 0.00 H +ATOM 373 CA LEU 23 22.452 36.571 19.560 1.00 0.00 C +ATOM 374 HA LEU 23 22.285 36.550 20.632 1.00 0.00 H +ATOM 375 CB LEU 23 22.485 35.111 19.082 1.00 0.00 C +ATOM 376 HB2 LEU 23 21.546 34.665 19.394 1.00 0.00 H +ATOM 377 HB3 LEU 23 22.522 35.056 17.994 1.00 0.00 H +ATOM 378 CG LEU 23 23.640 34.288 19.690 1.00 0.00 C +ATOM 379 HG LEU 23 23.819 34.622 20.711 1.00 0.00 H +ATOM 380 CD1 LEU 23 23.243 32.811 19.763 1.00 0.00 C +ATOM 381 HD11 LEU 23 22.968 32.445 18.779 1.00 0.00 H +ATOM 382 HD12 LEU 23 24.071 32.222 20.159 1.00 0.00 H +ATOM 383 HD13 LEU 23 22.398 32.707 20.441 1.00 0.00 H +ATOM 384 CD2 LEU 23 24.930 34.430 18.880 1.00 0.00 C +ATOM 385 HD21 LEU 23 25.532 35.241 19.277 1.00 0.00 H +ATOM 386 HD22 LEU 23 25.534 33.529 18.950 1.00 0.00 H +ATOM 387 HD23 LEU 23 24.718 34.659 17.839 1.00 0.00 H +ATOM 388 C LEU 23 23.771 37.324 19.343 1.00 0.00 C +ATOM 389 O LEU 23 24.614 37.294 20.233 1.00 0.00 O +ATOM 390 N ALA 24 23.950 38.060 18.242 1.00 0.00 N +ATOM 391 H ALA 24 23.204 38.085 17.546 1.00 0.00 H +ATOM 392 CA ALA 24 25.158 38.865 18.025 1.00 0.00 C +ATOM 393 HA ALA 24 26.018 38.218 18.197 1.00 0.00 H +ATOM 394 CB ALA 24 25.202 39.299 16.558 1.00 0.00 C +ATOM 395 HB1 ALA 24 24.369 39.964 16.325 1.00 0.00 H +ATOM 396 HB2 ALA 24 26.142 39.815 16.363 1.00 0.00 H +ATOM 397 HB3 ALA 24 25.148 38.425 15.906 1.00 0.00 H +ATOM 398 C ALA 24 25.306 40.056 19.005 1.00 0.00 C +ATOM 399 O ALA 24 26.389 40.642 19.118 1.00 0.00 O +ATOM 400 N GLU 25 24.251 40.394 19.761 1.00 0.00 N +ATOM 401 H GLU 25 23.380 39.906 19.598 1.00 0.00 H +ATOM 402 CA GLU 25 24.335 41.202 20.988 1.00 0.00 C +ATOM 403 HA GLU 25 25.200 41.864 20.931 1.00 0.00 H +ATOM 404 CB GLU 25 23.081 42.091 21.112 1.00 0.00 C +ATOM 405 HB2 GLU 25 22.197 41.461 21.036 1.00 0.00 H +ATOM 406 HB3 GLU 25 23.072 42.547 22.099 1.00 0.00 H +ATOM 407 CG GLU 25 22.993 43.209 20.067 1.00 0.00 C +ATOM 408 HG2 GLU 25 23.178 42.799 19.072 1.00 0.00 H +ATOM 409 HG3 GLU 25 21.977 43.613 20.061 1.00 0.00 H +ATOM 410 CD GLU 25 23.989 44.335 20.372 1.00 0.00 C +ATOM 411 OE1 GLU 25 23.587 45.318 21.037 1.00 0.00 O +ATOM 412 OE2 GLU 25 25.166 44.185 19.957 1.00 0.00 O +ATOM 413 C GLU 25 24.520 40.324 22.230 1.00 0.00 C +ATOM 414 O GLU 25 25.355 40.629 23.079 1.00 0.00 O +ATOM 415 N ALA 26 23.838 39.165 22.340 1.00 0.00 N +ATOM 416 H ALA 26 23.144 38.939 21.634 1.00 0.00 H +ATOM 417 CA ALA 26 24.041 38.207 23.435 1.00 0.00 C +ATOM 418 HA ALA 26 23.857 38.735 24.370 1.00 0.00 H +ATOM 419 CB ALA 26 23.053 37.055 23.307 1.00 0.00 C +ATOM 420 HB1 ALA 26 23.352 36.400 22.493 1.00 0.00 H +ATOM 421 HB2 ALA 26 23.041 36.471 24.227 1.00 0.00 H +ATOM 422 HB3 ALA 26 22.059 37.460 23.119 1.00 0.00 H +ATOM 423 C ALA 26 25.475 37.640 23.529 1.00 0.00 C +ATOM 424 O ALA 26 25.878 37.199 24.606 1.00 0.00 O +ATOM 425 N GLU 27 26.225 37.656 22.426 1.00 0.00 N +ATOM 426 H GLU 27 25.728 37.822 21.561 1.00 0.00 H +ATOM 427 CA GLU 27 27.657 37.363 22.351 1.00 0.00 C +ATOM 428 HA GLU 27 27.828 36.387 22.786 1.00 0.00 H +ATOM 429 CB GLU 27 28.049 37.295 20.810 1.00 0.00 C +ATOM 430 HB2 GLU 27 27.320 36.650 20.339 1.00 0.00 H +ATOM 431 HB3 GLU 27 27.974 38.279 20.364 1.00 0.00 H +ATOM 432 CG GLU 27 29.432 36.733 20.511 1.00 0.00 C +ATOM 433 HG2 GLU 27 30.208 37.425 20.927 1.00 0.00 H +ATOM 434 HG3 GLU 27 29.562 35.764 21.055 1.00 0.00 H +ATOM 435 CD GLU 27 29.655 36.541 18.998 1.00 0.00 C +ATOM 436 OE1 GLU 27 30.446 37.312 18.444 1.00 0.00 O +ATOM 437 OE2 GLU 27 29.027 35.659 18.399 1.00 0.00 O +ATOM 438 C GLU 27 28.483 38.382 23.126 1.00 0.00 C +ATOM 439 O GLU 27 29.294 38.026 23.980 1.00 0.00 O +ATOM 440 N LYS 28 28.171 39.676 22.949 1.00 0.00 N +ATOM 441 H LYS 28 27.412 39.874 22.302 1.00 0.00 H +ATOM 442 CA LYS 28 28.730 40.786 23.720 1.00 0.00 C +ATOM 443 HA LYS 28 29.826 40.697 23.712 1.00 0.00 H +ATOM 444 CB LYS 28 28.359 42.145 23.096 1.00 0.00 C +ATOM 445 HB2 LYS 28 27.290 42.317 23.207 1.00 0.00 H +ATOM 446 HB3 LYS 28 28.886 42.916 23.652 1.00 0.00 H +ATOM 447 CG LYS 28 28.732 42.265 21.607 1.00 0.00 C +ATOM 448 HG2 LYS 28 29.789 42.022 21.483 1.00 0.00 H +ATOM 449 HG3 LYS 28 28.138 41.561 21.024 1.00 0.00 H +ATOM 450 CD LYS 28 28.480 43.692 21.087 1.00 0.00 C +ATOM 451 HD2 LYS 28 27.472 44.012 21.359 1.00 0.00 H +ATOM 452 HD3 LYS 28 29.187 44.367 21.577 1.00 0.00 H +ATOM 453 CE LYS 28 28.656 43.806 19.568 1.00 0.00 C +ATOM 454 HE2 LYS 28 28.808 44.863 19.321 1.00 0.00 H +ATOM 455 HE3 LYS 28 29.558 43.270 19.263 1.00 0.00 H +ATOM 456 NZ LYS 28 27.462 43.300 18.844 1.00 0.00 N +ATOM 457 HZ1 LYS 28 26.620 43.776 19.187 1.00 0.00 H +ATOM 458 HZ2 LYS 28 27.524 43.469 17.852 1.00 0.00 H +ATOM 459 HZ3 LYS 28 27.296 42.311 19.010 1.00 0.00 H +ATOM 460 C LYS 28 28.293 40.734 25.190 1.00 0.00 C +ATOM 461 O LYS 28 29.136 40.838 26.076 1.00 0.00 O +ATOM 462 N PHE 29 27.019 40.477 25.467 1.00 0.00 N +ATOM 463 H PHE 29 26.355 40.453 24.698 1.00 0.00 H +ATOM 464 CA PHE 29 26.517 40.332 26.846 1.00 0.00 C +ATOM 465 HA PHE 29 26.806 41.218 27.411 1.00 0.00 H +ATOM 466 CB PHE 29 24.977 40.304 26.842 1.00 0.00 C +ATOM 467 HB2 PHE 29 24.659 39.367 26.390 1.00 0.00 H +ATOM 468 HB3 PHE 29 24.625 40.303 27.880 1.00 0.00 H +ATOM 469 CG PHE 29 24.287 41.460 26.136 1.00 0.00 C +ATOM 470 CD1 PHE 29 23.049 41.246 25.495 1.00 0.00 C +ATOM 471 HD1 PHE 29 22.579 40.275 25.527 1.00 0.00 H +ATOM 472 CE1 PHE 29 22.410 42.297 24.807 1.00 0.00 C +ATOM 473 HE1 PHE 29 21.469 42.116 24.311 1.00 0.00 H +ATOM 474 CZ PHE 29 23.003 43.573 24.765 1.00 0.00 C +ATOM 475 HZ PHE 29 22.524 44.372 24.222 1.00 0.00 H +ATOM 476 CE2 PHE 29 24.219 43.806 25.428 1.00 0.00 C +ATOM 477 HE2 PHE 29 24.669 44.778 25.408 1.00 0.00 H +ATOM 478 CD2 PHE 29 24.853 42.757 26.115 1.00 0.00 C +ATOM 479 HD2 PHE 29 25.782 42.959 26.619 1.00 0.00 H +ATOM 480 C PHE 29 27.097 39.092 27.576 1.00 0.00 C +ATOM 481 O PHE 29 27.242 39.121 28.804 1.00 0.00 O +ATOM 482 N THR 30 27.471 38.019 26.855 1.00 0.00 N +ATOM 483 H THR 30 27.262 38.018 25.867 1.00 0.00 H +ATOM 484 CA THR 30 28.208 36.874 27.383 1.00 0.00 C +ATOM 485 HA THR 30 27.806 36.552 28.340 1.00 0.00 H +ATOM 486 CB THR 30 28.165 35.642 26.355 1.00 0.00 C +ATOM 487 HB THR 30 28.671 35.982 25.465 1.00 0.00 H +ATOM 488 CG2 THR 30 29.010 34.482 26.856 1.00 0.00 C +ATOM 489 HG21 THR 30 28.763 34.155 27.853 1.00 0.00 H +ATOM 490 HG22 THR 30 28.991 33.595 26.210 1.00 0.00 H +ATOM 491 HG23 THR 30 30.047 34.791 26.859 1.00 0.00 H +ATOM 492 OG1 THR 30 26.844 35.210 26.048 1.00 0.00 O +ATOM 493 HG1 THR 30 26.349 35.962 25.650 1.00 0.00 H +ATOM 494 C THR 30 29.681 37.276 27.719 1.00 0.00 C +ATOM 495 O THR 30 30.155 36.942 28.795 1.00 0.00 O +ATOM 496 N LYS 31 30.332 38.079 26.889 1.00 0.00 N +ATOM 497 H LYS 31 29.871 38.384 26.044 1.00 0.00 H +ATOM 498 CA LYS 31 31.674 38.634 27.157 1.00 0.00 C +ATOM 499 HA LYS 31 32.350 37.837 27.474 1.00 0.00 H +ATOM 500 CB LYS 31 32.241 39.245 25.864 1.00 0.00 C +ATOM 501 HB2 LYS 31 31.523 39.940 25.448 1.00 0.00 H +ATOM 502 HB3 LYS 31 33.157 39.786 26.103 1.00 0.00 H +ATOM 503 CG LYS 31 32.581 38.157 24.832 1.00 0.00 C +ATOM 504 HG2 LYS 31 33.317 37.480 25.261 1.00 0.00 H +ATOM 505 HG3 LYS 31 31.704 37.566 24.575 1.00 0.00 H +ATOM 506 CD LYS 31 33.154 38.798 23.560 1.00 0.00 C +ATOM 507 HD2 LYS 31 32.363 39.356 23.055 1.00 0.00 H +ATOM 508 HD3 LYS 31 33.951 39.488 23.827 1.00 0.00 H +ATOM 509 CE LYS 31 33.714 37.746 22.591 1.00 0.00 C +ATOM 510 HE2 LYS 31 32.948 37.001 22.373 1.00 0.00 H +ATOM 511 HE3 LYS 31 33.955 38.245 21.648 1.00 0.00 H +ATOM 512 NZ LYS 31 34.933 37.089 23.115 1.00 0.00 N +ATOM 513 HZ1 LYS 31 34.746 36.340 23.769 1.00 0.00 H +ATOM 514 HZ2 LYS 31 35.437 36.639 22.348 1.00 0.00 H +ATOM 515 HZ3 LYS 31 35.592 37.732 23.552 1.00 0.00 H +ATOM 516 C LYS 31 31.693 39.656 28.305 1.00 0.00 C +ATOM 517 O LYS 31 32.674 39.678 29.044 1.00 0.00 O +ATOM 518 N ALA 32 30.615 40.417 28.505 1.00 0.00 N +ATOM 519 H ALA 32 29.893 40.433 27.798 1.00 0.00 H +ATOM 520 CA ALA 32 30.452 41.245 29.699 1.00 0.00 C +ATOM 521 HA ALA 32 31.287 41.943 29.769 1.00 0.00 H +ATOM 522 CB ALA 32 29.160 42.059 29.583 1.00 0.00 C +ATOM 523 HB1 ALA 32 28.295 41.401 29.522 1.00 0.00 H +ATOM 524 HB2 ALA 32 29.045 42.699 30.464 1.00 0.00 H +ATOM 525 HB3 ALA 32 29.194 42.691 28.695 1.00 0.00 H +ATOM 526 C ALA 32 30.481 40.374 30.974 1.00 0.00 C +ATOM 527 O ALA 32 31.390 40.511 31.786 1.00 0.00 O +ATOM 528 N ALA 33 29.599 39.373 31.058 1.00 0.00 N +ATOM 529 H ALA 33 28.886 39.292 30.345 1.00 0.00 H +ATOM 530 CA ALA 33 29.555 38.428 32.181 1.00 0.00 C +ATOM 531 HA ALA 33 29.465 39.008 33.099 1.00 0.00 H +ATOM 532 CB ALA 33 28.289 37.575 32.028 1.00 0.00 C +ATOM 533 HB1 ALA 33 28.346 36.978 31.119 1.00 0.00 H +ATOM 534 HB2 ALA 33 28.181 36.909 32.886 1.00 0.00 H +ATOM 535 HB3 ALA 33 27.410 38.219 31.981 1.00 0.00 H +ATOM 536 C ALA 33 30.821 37.541 32.333 1.00 0.00 C +ATOM 537 O ALA 33 30.921 36.798 33.305 1.00 0.00 O +ATOM 538 N ALA 34 31.757 37.568 31.379 1.00 0.00 N +ATOM 539 H ALA 34 31.589 38.159 30.584 1.00 0.00 H +ATOM 540 CA ALA 34 33.091 36.966 31.505 1.00 0.00 C +ATOM 541 HA ALA 34 33.037 36.139 32.213 1.00 0.00 H +ATOM 542 CB ALA 34 33.508 36.399 30.143 1.00 0.00 C +ATOM 543 HB1 ALA 34 33.649 37.207 29.426 1.00 0.00 H +ATOM 544 HB2 ALA 34 34.450 35.861 30.259 1.00 0.00 H +ATOM 545 HB3 ALA 34 32.750 35.708 29.774 1.00 0.00 H +ATOM 546 C ALA 34 34.123 37.961 32.063 1.00 0.00 C +ATOM 547 O ALA 34 34.832 37.631 33.008 1.00 0.00 O +ATOM 548 N ASN 35 34.171 39.202 31.560 1.00 0.00 N +ATOM 549 H ASN 35 33.544 39.440 30.800 1.00 0.00 H +ATOM 550 CA ASN 35 35.041 40.256 32.096 1.00 0.00 C +ATOM 551 HA ASN 35 36.050 39.850 32.215 1.00 0.00 H +ATOM 552 CB ASN 35 35.128 41.408 31.082 1.00 0.00 C +ATOM 553 HB2 ASN 35 34.128 41.702 30.765 1.00 0.00 H +ATOM 554 HB3 ASN 35 35.595 42.264 31.566 1.00 0.00 H +ATOM 555 CG ASN 35 35.989 41.053 29.876 1.00 0.00 C +ATOM 556 OD1 ASN 35 37.202 40.998 29.943 1.00 0.00 O +ATOM 557 ND2 ASN 35 35.397 40.799 28.737 1.00 0.00 N +ATOM 558 HD21 ASN 35 36.007 40.585 27.947 1.00 0.00 H +ATOM 559 HD22 ASN 35 34.398 40.684 28.702 1.00 0.00 H +ATOM 560 C ASN 35 34.614 40.741 33.504 1.00 0.00 C +ATOM 561 O ASN 35 35.469 41.137 34.290 1.00 0.00 O +ATOM 562 N ASP 36 33.333 40.617 33.865 1.00 0.00 N +ATOM 563 H ASP 36 32.647 40.420 33.146 1.00 0.00 H +ATOM 564 CA ASP 36 32.837 40.768 35.249 1.00 0.00 C +ATOM 565 HA ASP 36 33.163 41.738 35.630 1.00 0.00 H +ATOM 566 CB ASP 36 31.291 40.753 35.253 1.00 0.00 C +ATOM 567 HB2 ASP 36 30.950 39.847 34.749 1.00 0.00 H +ATOM 568 HB3 ASP 36 30.954 40.684 36.289 1.00 0.00 H +ATOM 569 CG ASP 36 30.604 41.992 34.634 1.00 0.00 C +ATOM 570 OD1 ASP 36 31.204 43.091 34.688 1.00 0.00 O +ATOM 571 OD2 ASP 36 29.439 41.870 34.172 1.00 0.00 O +ATOM 572 C ASP 36 33.415 39.697 36.211 1.00 0.00 C +ATOM 573 O ASP 36 33.441 39.908 37.424 1.00 0.00 O +ATOM 574 N LEU 37 33.904 38.557 35.688 1.00 0.00 N +ATOM 575 H LEU 37 33.842 38.450 34.686 1.00 0.00 H +ATOM 576 CA LEU 37 34.657 37.527 36.423 1.00 0.00 C +ATOM 577 HA LEU 37 34.464 37.650 37.491 1.00 0.00 H +ATOM 578 CB LEU 37 34.109 36.145 35.994 1.00 0.00 C +ATOM 579 HB2 LEU 37 33.040 36.119 36.207 1.00 0.00 H +ATOM 580 HB3 LEU 37 34.231 36.052 34.917 1.00 0.00 H +ATOM 581 CG LEU 37 34.771 34.914 36.645 1.00 0.00 C +ATOM 582 HG LEU 37 35.840 34.913 36.439 1.00 0.00 H +ATOM 583 CD1 LEU 37 34.551 34.857 38.159 1.00 0.00 C +ATOM 584 HD11 LEU 37 33.486 34.879 38.385 1.00 0.00 H +ATOM 585 HD12 LEU 37 34.992 33.944 38.560 1.00 0.00 H +ATOM 586 HD13 LEU 37 35.040 35.710 38.628 1.00 0.00 H +ATOM 587 CD2 LEU 37 34.177 33.637 36.042 1.00 0.00 C +ATOM 588 HD21 LEU 37 34.355 33.629 34.966 1.00 0.00 H +ATOM 589 HD22 LEU 37 34.662 32.764 36.478 1.00 0.00 H +ATOM 590 HD23 LEU 37 33.105 33.596 36.231 1.00 0.00 H +ATOM 591 C LEU 37 36.190 37.649 36.238 1.00 0.00 C +ATOM 592 O LEU 37 36.941 37.271 37.137 1.00 0.00 O +ATOM 593 N GLY 38 36.655 38.181 35.100 1.00 0.00 N +ATOM 594 H GLY 38 35.977 38.417 34.388 1.00 0.00 H +ATOM 595 CA GLY 38 38.057 38.532 34.848 1.00 0.00 C +ATOM 596 HA2 GLY 38 38.314 39.395 35.466 1.00 0.00 H +ATOM 597 HA3 GLY 38 38.690 37.700 35.160 1.00 0.00 H +ATOM 598 C GLY 38 38.413 38.871 33.391 1.00 0.00 C +ATOM 599 O GLY 38 38.929 39.957 33.136 1.00 0.00 O +ATOM 600 N GLU 39 38.171 37.961 32.437 1.00 0.00 N +ATOM 601 H GLU 39 37.657 37.131 32.691 1.00 0.00 H +ATOM 602 CA GLU 39 38.661 38.018 31.042 1.00 0.00 C +ATOM 603 HA GLU 39 38.763 39.061 30.726 1.00 0.00 H +ATOM 604 CB GLU 39 40.065 37.322 30.944 1.00 0.00 C +ATOM 605 HB2 GLU 39 39.944 36.313 31.317 1.00 0.00 H +ATOM 606 HB3 GLU 39 40.335 37.260 29.892 1.00 0.00 H +ATOM 607 CG GLU 39 41.245 37.986 31.688 1.00 0.00 C +ATOM 608 HG2 GLU 39 41.553 38.894 31.136 1.00 0.00 H +ATOM 609 HG3 GLU 39 40.915 38.320 32.684 1.00 0.00 H +ATOM 610 CD GLU 39 42.450 37.039 31.915 1.00 0.00 C +ATOM 611 OE1 GLU 39 42.260 36.003 32.575 1.00 0.00 O +ATOM 612 OE2 GLU 39 43.569 37.372 31.481 1.00 0.00 O +ATOM 613 C GLU 39 37.685 37.298 30.075 1.00 0.00 C +ATOM 614 O GLU 39 37.024 36.351 30.492 1.00 0.00 O +ATOM 615 N ASP 40 37.585 37.685 28.788 1.00 0.00 N +ATOM 616 H ASP 40 38.100 38.498 28.476 1.00 0.00 H +ATOM 617 CA ASP 40 36.738 36.968 27.799 1.00 0.00 C +ATOM 618 HA ASP 40 36.030 36.362 28.365 1.00 0.00 H +ATOM 619 CB ASP 40 35.858 37.913 26.964 1.00 0.00 C +ATOM 620 HB2 ASP 40 35.160 37.288 26.414 1.00 0.00 H +ATOM 621 HB3 ASP 40 35.261 38.533 27.625 1.00 0.00 H +ATOM 622 CG ASP 40 36.587 38.798 25.952 1.00 0.00 C +ATOM 623 OD1 ASP 40 36.893 39.965 26.276 1.00 0.00 O +ATOM 624 OD2 ASP 40 36.761 38.351 24.790 1.00 0.00 O +ATOM 625 C ASP 40 37.475 35.994 26.856 1.00 0.00 C +ATOM 626 O ASP 40 38.374 36.376 26.101 1.00 0.00 O +ATOM 627 N GLY 41 36.973 34.756 26.794 1.00 0.00 N +ATOM 628 H GLY 41 36.288 34.510 27.490 1.00 0.00 H +ATOM 629 CA GLY 41 37.271 33.768 25.747 1.00 0.00 C +ATOM 630 HA2 GLY 41 38.295 33.916 25.381 1.00 0.00 H +ATOM 631 HA3 GLY 41 37.211 32.770 26.191 1.00 0.00 H +ATOM 632 C GLY 41 36.313 33.811 24.533 1.00 0.00 C +ATOM 633 O GLY 41 35.386 34.624 24.460 1.00 0.00 O +ATOM 634 N GLU 42 36.534 32.906 23.574 1.00 0.00 N +ATOM 635 H GLU 42 37.265 32.233 23.726 1.00 0.00 H +ATOM 636 CA GLU 42 35.795 32.783 22.304 1.00 0.00 C +ATOM 637 HA GLU 42 35.112 33.628 22.215 1.00 0.00 H +ATOM 638 CB GLU 42 36.768 32.852 21.111 1.00 0.00 C +ATOM 639 HB2 GLU 42 37.359 31.939 21.083 1.00 0.00 H +ATOM 640 HB3 GLU 42 36.185 32.904 20.190 1.00 0.00 H +ATOM 641 CG GLU 42 37.742 34.046 21.132 1.00 0.00 C +ATOM 642 HG2 GLU 42 38.542 33.823 21.835 1.00 0.00 H +ATOM 643 HG3 GLU 42 38.198 34.176 20.150 1.00 0.00 H +ATOM 644 CD GLU 42 37.078 35.358 21.545 1.00 0.00 C +ATOM 645 OE1 GLU 42 35.962 35.662 21.073 1.00 0.00 O +ATOM 646 OE2 GLU 42 37.603 36.077 22.430 1.00 0.00 O +ATOM 647 C GLU 42 34.925 31.518 22.249 1.00 0.00 C +ATOM 648 O GLU 42 35.177 30.549 22.970 1.00 0.00 O +ATOM 649 N HIP 43 33.822 31.561 21.482 1.00 0.00 N +ATOM 650 H HIP 43 33.691 32.332 20.837 1.00 0.00 H +ATOM 651 CA HIP 43 32.635 30.779 21.863 1.00 0.00 C +ATOM 652 HA HIP 43 32.953 29.805 22.240 1.00 0.00 H +ATOM 653 CB HIP 43 32.036 31.564 23.060 1.00 0.00 C +ATOM 654 HB2 HIP 43 32.780 31.722 23.836 1.00 0.00 H +ATOM 655 HB3 HIP 43 31.707 32.547 22.731 1.00 0.00 H +ATOM 656 CG HIP 43 30.884 30.844 23.669 1.00 0.00 C +ATOM 657 ND1 HIP 43 29.715 30.591 23.008 1.00 0.00 N +ATOM 658 HD1 HIP 43 29.496 30.960 22.088 1.00 0.00 H +ATOM 659 CE1 HIP 43 29.197 29.496 23.532 1.00 0.00 C +ATOM 660 HE1 HIP 43 28.471 28.891 23.007 1.00 0.00 H +ATOM 661 NE2 HIP 43 29.859 29.132 24.623 1.00 0.00 N +ATOM 662 HE2 HIP 43 29.751 28.262 25.124 1.00 0.00 H +ATOM 663 CD2 HIP 43 30.964 29.967 24.715 1.00 0.00 C +ATOM 664 HD2 HIP 43 31.813 29.800 25.339 1.00 0.00 H +ATOM 665 C HIP 43 31.587 30.500 20.744 1.00 0.00 C +ATOM 666 O HIP 43 30.815 31.391 20.404 1.00 0.00 O +ATOM 667 N THR 44 31.412 29.241 20.315 1.00 0.00 N +ATOM 668 H THR 44 32.062 28.545 20.651 1.00 0.00 H +ATOM 669 CA THR 44 30.539 28.792 19.194 1.00 0.00 C +ATOM 670 HA THR 44 30.768 29.416 18.330 1.00 0.00 H +ATOM 671 CB THR 44 30.915 27.341 18.825 1.00 0.00 C +ATOM 672 HB THR 44 30.653 26.672 19.649 1.00 0.00 H +ATOM 673 CG2 THR 44 30.280 26.804 17.538 1.00 0.00 C +ATOM 674 HG21 THR 44 30.421 27.512 16.723 1.00 0.00 H +ATOM 675 HG22 THR 44 30.737 25.852 17.265 1.00 0.00 H +ATOM 676 HG23 THR 44 29.217 26.625 17.692 1.00 0.00 H +ATOM 677 OG1 THR 44 32.307 27.274 18.626 1.00 0.00 O +ATOM 678 HG1 THR 44 32.492 26.533 18.040 1.00 0.00 H +ATOM 679 C THR 44 29.005 28.885 19.426 1.00 0.00 C +ATOM 680 O THR 44 28.541 28.793 20.567 1.00 0.00 O +ATOM 681 N LYS 45 28.231 29.030 18.329 1.00 0.00 N +ATOM 682 H LYS 45 28.718 29.046 17.443 1.00 0.00 H +ATOM 683 CA LYS 45 26.747 29.105 18.236 1.00 0.00 C +ATOM 684 HA LYS 45 26.318 29.062 19.233 1.00 0.00 H +ATOM 685 CB LYS 45 26.374 30.459 17.574 1.00 0.00 C +ATOM 686 HB2 LYS 45 26.571 31.266 18.282 1.00 0.00 H +ATOM 687 HB3 LYS 45 27.024 30.615 16.712 1.00 0.00 H +ATOM 688 CG LYS 45 24.919 30.571 17.071 1.00 0.00 C +ATOM 689 HG2 LYS 45 24.730 29.762 16.369 1.00 0.00 H +ATOM 690 HG3 LYS 45 24.253 30.451 17.926 1.00 0.00 H +ATOM 691 CD LYS 45 24.581 31.864 16.313 1.00 0.00 C +ATOM 692 HD2 LYS 45 24.789 32.715 16.943 1.00 0.00 H +ATOM 693 HD3 LYS 45 25.176 31.930 15.400 1.00 0.00 H +ATOM 694 CE LYS 45 23.091 31.825 15.971 1.00 0.00 C +ATOM 695 HE2 LYS 45 22.923 30.987 15.292 1.00 0.00 H +ATOM 696 HE3 LYS 45 22.532 31.602 16.886 1.00 0.00 H +ATOM 697 NZ LYS 45 22.573 33.072 15.345 1.00 0.00 N +ATOM 698 HZ1 LYS 45 22.962 33.227 14.424 1.00 0.00 H +ATOM 699 HZ2 LYS 45 21.559 32.954 15.239 1.00 0.00 H +ATOM 700 HZ3 LYS 45 22.712 33.892 15.912 1.00 0.00 H +ATOM 701 C LYS 45 26.138 27.945 17.423 1.00 0.00 C +ATOM 702 O LYS 45 26.705 27.569 16.405 1.00 0.00 O +ATOM 703 N ASP 46 24.922 27.524 17.775 1.00 0.00 N +ATOM 704 H ASP 46 24.578 27.808 18.689 1.00 0.00 H +ATOM 705 CA ASP 46 23.873 27.044 16.843 1.00 0.00 C +ATOM 706 HA ASP 46 24.249 27.121 15.818 1.00 0.00 H +ATOM 707 CB ASP 46 23.528 25.569 17.148 1.00 0.00 C +ATOM 708 HB2 ASP 46 24.366 24.916 16.878 1.00 0.00 H +ATOM 709 HB3 ASP 46 23.378 25.489 18.232 1.00 0.00 H +ATOM 710 CG ASP 46 22.266 25.098 16.426 1.00 0.00 C +ATOM 711 OD1 ASP 46 21.392 24.557 17.117 1.00 0.00 O +ATOM 712 OD2 ASP 46 22.087 25.409 15.235 1.00 0.00 O +ATOM 713 C ASP 46 22.613 27.944 16.957 1.00 0.00 C +ATOM 714 O ASP 46 22.294 28.456 18.027 1.00 0.00 O +ATOM 715 N ASP 47 21.897 28.140 15.849 1.00 0.00 N +ATOM 716 H ASP 47 22.146 27.562 15.057 1.00 0.00 H +ATOM 717 CA ASP 47 20.588 28.850 15.794 1.00 0.00 C +ATOM 718 HA ASP 47 20.554 29.519 16.646 1.00 0.00 H +ATOM 719 CB ASP 47 20.475 29.756 14.572 1.00 0.00 C +ATOM 720 HB2 ASP 47 21.461 30.108 14.286 1.00 0.00 H +ATOM 721 HB3 ASP 47 20.085 29.213 13.702 1.00 0.00 H +ATOM 722 CG ASP 47 19.637 30.995 14.888 1.00 0.00 C +ATOM 723 OD1 ASP 47 18.471 31.071 14.473 1.00 0.00 O +ATOM 724 OD2 ASP 47 20.169 31.881 15.573 1.00 0.00 O +ATOM 725 C ASP 47 19.357 27.933 15.861 1.00 0.00 C +ATOM 726 O ASP 47 18.316 28.355 16.366 1.00 0.00 O +ATOM 727 N ALA 48 19.457 26.676 15.411 1.00 0.00 N +ATOM 728 H ALA 48 20.368 26.307 15.139 1.00 0.00 H +ATOM 729 CA ALA 48 18.317 25.752 15.378 1.00 0.00 C +ATOM 730 HA ALA 48 17.480 26.224 14.859 1.00 0.00 H +ATOM 731 CB ALA 48 18.730 24.511 14.577 1.00 0.00 C +ATOM 732 HB1 ALA 48 19.555 24.007 15.072 1.00 0.00 H +ATOM 733 HB2 ALA 48 17.894 23.821 14.498 1.00 0.00 H +ATOM 734 HB3 ALA 48 19.047 24.788 13.575 1.00 0.00 H +ATOM 735 C ALA 48 17.839 25.388 16.792 1.00 0.00 C +ATOM 736 O ALA 48 16.640 25.354 17.075 1.00 0.00 O +ATOM 737 N THR 49 18.778 25.160 17.711 1.00 0.00 N +ATOM 738 H THR 49 19.736 25.037 17.377 1.00 0.00 H +ATOM 739 CA THR 49 18.557 25.051 19.154 1.00 0.00 C +ATOM 740 HA THR 49 17.530 24.709 19.314 1.00 0.00 H +ATOM 741 CB THR 49 19.524 24.022 19.753 1.00 0.00 C +ATOM 742 HB THR 49 19.326 23.946 20.820 1.00 0.00 H +ATOM 743 CG2 THR 49 19.398 22.626 19.153 1.00 0.00 C +ATOM 744 HG21 THR 49 19.665 22.630 18.098 1.00 0.00 H +ATOM 745 HG22 THR 49 20.090 21.979 19.684 1.00 0.00 H +ATOM 746 HG23 THR 49 18.383 22.250 19.269 1.00 0.00 H +ATOM 747 OG1 THR 49 20.861 24.413 19.589 1.00 0.00 O +ATOM 748 HG1 THR 49 21.066 24.338 18.620 1.00 0.00 H +ATOM 749 C THR 49 18.714 26.378 19.910 1.00 0.00 C +ATOM 750 O THR 49 18.618 26.395 21.136 1.00 0.00 O +ATOM 751 N LYS 50 18.968 27.490 19.206 1.00 0.00 N +ATOM 752 H LYS 50 18.980 27.378 18.203 1.00 0.00 H +ATOM 753 CA LYS 50 19.202 28.853 19.749 1.00 0.00 C +ATOM 754 HA LYS 50 19.637 29.449 18.943 1.00 0.00 H +ATOM 755 CB LYS 50 17.845 29.491 20.149 1.00 0.00 C +ATOM 756 HB2 LYS 50 17.408 28.860 20.925 1.00 0.00 H +ATOM 757 HB3 LYS 50 18.038 30.471 20.598 1.00 0.00 H +ATOM 758 CG LYS 50 16.812 29.667 19.017 1.00 0.00 C +ATOM 759 HG2 LYS 50 16.742 28.752 18.424 1.00 0.00 H +ATOM 760 HG3 LYS 50 15.841 29.837 19.491 1.00 0.00 H +ATOM 761 CD LYS 50 17.113 30.878 18.105 1.00 0.00 C +ATOM 762 HD2 LYS 50 17.122 31.775 18.732 1.00 0.00 H +ATOM 763 HD3 LYS 50 18.108 30.766 17.643 1.00 0.00 H +ATOM 764 CE LYS 50 16.028 31.055 17.026 1.00 0.00 C +ATOM 765 HE2 LYS 50 15.056 30.783 17.436 1.00 0.00 H +ATOM 766 HE3 LYS 50 15.985 32.104 16.719 1.00 0.00 H +ATOM 767 NZ LYS 50 16.278 30.207 15.837 1.00 0.00 N +ATOM 768 HZ1 LYS 50 16.593 29.271 16.077 1.00 0.00 H +ATOM 769 HZ2 LYS 50 15.486 30.195 15.189 1.00 0.00 H +ATOM 770 HZ3 LYS 50 17.047 30.589 15.285 1.00 0.00 H +ATOM 771 C LYS 50 20.238 28.865 20.885 1.00 0.00 C +ATOM 772 O LYS 50 20.046 29.552 21.897 1.00 0.00 O +ATOM 773 N THR 51 21.297 28.053 20.758 1.00 0.00 N +ATOM 774 H THR 51 21.447 27.626 19.852 1.00 0.00 H +ATOM 775 CA THR 51 22.186 27.666 21.861 1.00 0.00 C +ATOM 776 HA THR 51 21.925 28.266 22.727 1.00 0.00 H +ATOM 777 CB THR 51 21.978 26.182 22.276 1.00 0.00 C +ATOM 778 HB THR 51 22.103 25.558 21.392 1.00 0.00 H +ATOM 779 CG2 THR 51 22.971 25.680 23.326 1.00 0.00 C +ATOM 780 HG21 THR 51 22.987 26.306 24.214 1.00 0.00 H +ATOM 781 HG22 THR 51 22.722 24.667 23.637 1.00 0.00 H +ATOM 782 HG23 THR 51 23.978 25.634 22.923 1.00 0.00 H +ATOM 783 OG1 THR 51 20.695 26.001 22.835 1.00 0.00 O +ATOM 784 HG1 THR 51 20.033 26.112 22.126 1.00 0.00 H +ATOM 785 C THR 51 23.691 27.954 21.606 1.00 0.00 C +ATOM 786 O THR 51 24.250 27.693 20.552 1.00 0.00 O +ATOM 787 N PHE 52 24.339 28.470 22.636 1.00 0.00 N +ATOM 788 H PHE 52 23.782 28.767 23.426 1.00 0.00 H +ATOM 789 CA PHE 52 25.782 28.625 22.774 1.00 0.00 C +ATOM 790 HA PHE 52 26.236 28.756 21.800 1.00 0.00 H +ATOM 791 CB PHE 52 25.970 29.903 23.630 1.00 0.00 C +ATOM 792 HB2 PHE 52 25.178 29.934 24.366 1.00 0.00 H +ATOM 793 HB3 PHE 52 26.858 29.811 24.241 1.00 0.00 H +ATOM 794 CG PHE 52 25.990 31.261 22.933 1.00 0.00 C +ATOM 795 CD1 PHE 52 25.313 32.345 23.501 1.00 0.00 C +ATOM 796 HD1 PHE 52 24.705 32.206 24.369 1.00 0.00 H +ATOM 797 CE1 PHE 52 25.445 33.639 22.970 1.00 0.00 C +ATOM 798 HE1 PHE 52 24.940 34.476 23.432 1.00 0.00 H +ATOM 799 CZ PHE 52 26.270 33.846 21.867 1.00 0.00 C +ATOM 800 HZ PHE 52 26.395 34.832 21.472 1.00 0.00 H +ATOM 801 CE2 PHE 52 26.935 32.771 21.258 1.00 0.00 C +ATOM 802 HE2 PHE 52 27.570 32.946 20.399 1.00 0.00 H +ATOM 803 CD2 PHE 52 26.777 31.489 21.786 1.00 0.00 C +ATOM 804 HD2 PHE 52 27.285 30.683 21.316 1.00 0.00 H +ATOM 805 C PHE 52 26.423 27.398 23.470 1.00 0.00 C +ATOM 806 O PHE 52 26.087 27.106 24.623 1.00 0.00 O +ATOM 807 N THR 53 27.436 26.751 22.856 1.00 0.00 N +ATOM 808 H THR 53 27.650 26.995 21.888 1.00 0.00 H +ATOM 809 CA THR 53 28.305 25.685 23.436 1.00 0.00 C +ATOM 810 HA THR 53 28.048 25.541 24.487 1.00 0.00 H +ATOM 811 CB THR 53 28.082 24.339 22.718 1.00 0.00 C +ATOM 812 HB THR 53 28.786 23.607 23.118 1.00 0.00 H +ATOM 813 CG2 THR 53 26.676 23.788 22.896 1.00 0.00 C +ATOM 814 HG21 THR 53 25.950 24.428 22.394 1.00 0.00 H +ATOM 815 HG22 THR 53 26.625 22.786 22.468 1.00 0.00 H +ATOM 816 HG23 THR 53 26.442 23.727 23.958 1.00 0.00 H +ATOM 817 OG1 THR 53 28.319 24.486 21.337 1.00 0.00 O +ATOM 818 HG1 THR 53 28.141 23.636 20.917 1.00 0.00 H +ATOM 819 C THR 53 29.812 26.007 23.366 1.00 0.00 C +ATOM 820 O THR 53 30.224 26.906 22.642 1.00 0.00 O +ATOM 821 N THR 54 30.650 25.304 24.140 1.00 0.00 N +ATOM 822 H THR 54 30.284 24.592 24.758 1.00 0.00 H +ATOM 823 CA THR 54 32.131 25.256 23.974 1.00 0.00 C +ATOM 824 HA THR 54 32.450 26.113 23.366 1.00 0.00 H +ATOM 825 CB THR 54 32.874 25.346 25.323 1.00 0.00 C +ATOM 826 HB THR 54 33.948 25.303 25.140 1.00 0.00 H +ATOM 827 CG2 THR 54 32.594 26.656 26.070 1.00 0.00 C +ATOM 828 HG21 THR 54 31.547 26.724 26.352 1.00 0.00 H +ATOM 829 HG22 THR 54 33.190 26.709 26.976 1.00 0.00 H +ATOM 830 HG23 THR 54 32.855 27.511 25.448 1.00 0.00 H +ATOM 831 OG1 THR 54 32.529 24.279 26.170 1.00 0.00 O +ATOM 832 HG1 THR 54 32.961 23.475 25.847 1.00 0.00 H +ATOM 833 C THR 54 32.580 23.997 23.228 1.00 0.00 C +ATOM 834 O THR 54 31.810 23.044 23.101 1.00 0.00 O +ATOM 835 N ALA 55 33.833 23.981 22.756 1.00 0.00 N +ATOM 836 H ALA 55 34.417 24.785 22.911 1.00 0.00 H +ATOM 837 CA ALA 55 34.476 22.803 22.162 1.00 0.00 C +ATOM 838 HA ALA 55 33.773 22.349 21.450 1.00 0.00 H +ATOM 839 CB ALA 55 35.709 23.293 21.391 1.00 0.00 C +ATOM 840 HB1 ALA 55 36.439 23.718 22.088 1.00 0.00 H +ATOM 841 HB2 ALA 55 36.172 22.454 20.859 1.00 0.00 H +ATOM 842 HB3 ALA 55 35.413 24.049 20.657 1.00 0.00 H +ATOM 843 C ALA 55 34.820 21.700 23.201 1.00 0.00 C +ATOM 844 O ALA 55 34.564 21.870 24.395 1.00 0.00 O +ATOM 845 N GLU 56 35.391 20.590 22.719 1.00 0.00 N +ATOM 846 H GLU 56 35.619 20.592 21.742 1.00 0.00 H +ATOM 847 CA GLU 56 35.949 19.442 23.462 1.00 0.00 C +ATOM 848 HA GLU 56 35.837 19.619 24.529 1.00 0.00 H +ATOM 849 CB GLU 56 35.174 18.158 23.066 1.00 0.00 C +ATOM 850 HB2 GLU 56 34.120 18.283 23.304 1.00 0.00 H +ATOM 851 HB3 GLU 56 35.231 18.083 21.976 1.00 0.00 H +ATOM 852 CG GLU 56 35.683 16.816 23.642 1.00 0.00 C +ATOM 853 HG2 GLU 56 35.524 16.058 22.873 1.00 0.00 H +ATOM 854 HG3 GLU 56 36.759 16.858 23.777 1.00 0.00 H +ATOM 855 CD GLU 56 35.019 16.305 24.943 1.00 0.00 C +ATOM 856 OE1 GLU 56 35.650 15.485 25.657 1.00 0.00 O +ATOM 857 OE2 GLU 56 33.830 16.592 25.213 1.00 0.00 O +ATOM 858 C GLU 56 37.466 19.312 23.206 1.00 0.00 C +ATOM 859 O GLU 56 38.207 19.293 24.214 1.00 0.00 O +ATOM 860 OXT GLU 56 37.851 19.278 22.005 1.00 0.00 O +HETATM 861 ZN ZN1 57 26.252 32.500 29.543 1.00 0.00 Zn +HETATM 862 N AN1 58 27.946 33.231 30.455 1.00 0.00 N +HETATM 863 C AN1 58 30.237 34.165 31.270 1.00 0.00 C +HETATM 864 C1 AN1 58 28.941 33.637 30.825 1.00 0.00 C +HETATM 865 H AN1 58 30.152 34.562 32.288 1.00 0.00 H +HETATM 866 H1 AN1 58 30.560 34.975 30.607 1.00 0.00 H +HETATM 867 H2 AN1 58 30.993 33.374 31.265 1.00 0.00 H +HETATM 868 N1 AZI 59 30.423 28.665 29.019 1.00 0.00 N +HETATM 869 N2 AZI 59 29.754 28.732 30.028 1.00 0.00 N +HETATM 870 N3 AZI 59 29.036 28.794 31.085 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 69 71 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 68 73 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 861 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 105 101 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 142 140 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 139 144 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 207 188 189 +CONECT 188 187 +CONECT 189 187 191 192 190 +CONECT 190 189 +CONECT 191 189 +CONECT 192 206 189 193 +CONECT 193 192 195 194 +CONECT 194 193 +CONECT 195 197 193 196 +CONECT 196 195 +CONECT 197 198 206 195 +CONECT 198 200 199 197 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 203 200 204 +CONECT 203 202 +CONECT 204 202 205 206 +CONECT 205 204 +CONECT 206 204 197 192 +CONECT 207 209 187 208 +CONECT 208 207 +CONECT 209 210 211 207 +CONECT 210 209 +CONECT 211 212 223 209 213 +CONECT 212 211 +CONECT 213 211 219 215 214 +CONECT 214 213 +CONECT 215 218 213 216 217 +CONECT 216 215 +CONECT 217 215 +CONECT 218 215 +CONECT 219 220 222 213 221 +CONECT 220 219 +CONECT 221 219 +CONECT 222 219 +CONECT 223 224 225 211 +CONECT 224 223 +CONECT 225 227 223 226 +CONECT 226 225 +CONECT 227 228 245 229 225 +CONECT 228 227 +CONECT 229 232 227 230 231 +CONECT 230 229 +CONECT 231 229 +CONECT 232 234 233 235 229 +CONECT 233 232 +CONECT 234 232 +CONECT 235 236 232 237 238 +CONECT 236 235 +CONECT 237 235 +CONECT 238 235 240 241 239 +CONECT 239 238 +CONECT 240 238 +CONECT 241 244 238 242 243 +CONECT 242 241 +CONECT 243 241 +CONECT 244 241 +CONECT 245 246 227 247 +CONECT 246 245 +CONECT 247 245 249 248 +CONECT 248 247 +CONECT 249 252 247 250 251 +CONECT 250 249 +CONECT 251 249 +CONECT 252 253 254 249 +CONECT 253 252 +CONECT 254 256 252 255 +CONECT 255 254 +CONECT 256 258 257 268 254 +CONECT 257 256 +CONECT 258 264 259 260 256 +CONECT 259 258 +CONECT 260 262 258 261 263 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 265 267 258 +CONECT 265 264 +CONECT 266 264 +CONECT 267 264 +CONECT 268 256 270 269 +CONECT 269 268 +CONECT 270 280 271 268 +CONECT 271 272 270 281 274 +CONECT 272 273 287 271 +CONECT 273 272 +CONECT 274 271 275 282 283 +CONECT 275 276 277 274 +CONECT 276 279 285 275 +CONECT 277 278 275 284 +CONECT 278 279 286 277 +CONECT 279 861 278 276 +CONECT 280 270 +CONECT 281 271 +CONECT 282 274 +CONECT 283 274 +CONECT 284 277 +CONECT 285 276 +CONECT 286 278 +CONECT 287 289 272 288 +CONECT 288 287 +CONECT 289 290 291 299 287 +CONECT 290 289 +CONECT 291 292 293 289 297 +CONECT 292 291 +CONECT 293 296 295 291 294 +CONECT 294 293 +CONECT 295 293 +CONECT 296 293 +CONECT 297 291 298 +CONECT 298 297 +CONECT 299 301 289 300 +CONECT 300 299 +CONECT 301 311 302 299 +CONECT 302 303 305 301 312 +CONECT 303 304 318 302 +CONECT 304 303 +CONECT 305 313 314 302 306 +CONECT 306 305 307 308 +CONECT 307 316 306 310 +CONECT 308 306 315 309 +CONECT 309 310 308 317 +CONECT 310 307 861 309 +CONECT 311 301 +CONECT 312 302 +CONECT 313 305 +CONECT 314 305 +CONECT 315 308 +CONECT 316 307 +CONECT 317 309 +CONECT 318 320 303 319 +CONECT 319 318 +CONECT 320 331 321 318 322 +CONECT 321 320 +CONECT 322 320 325 324 323 +CONECT 323 322 +CONECT 324 322 +CONECT 325 328 327 322 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 329 330 325 +CONECT 329 328 +CONECT 330 328 +CONECT 331 333 332 320 +CONECT 332 331 +CONECT 333 335 334 331 +CONECT 334 333 +CONECT 335 341 337 336 333 +CONECT 336 335 +CONECT 337 339 338 335 340 +CONECT 338 337 +CONECT 339 337 +CONECT 340 337 +CONECT 341 343 342 335 +CONECT 342 341 +CONECT 343 345 344 341 +CONECT 344 343 +CONECT 345 357 347 346 343 +CONECT 346 345 +CONECT 347 348 353 345 349 +CONECT 348 347 +CONECT 349 347 351 352 350 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 347 356 +CONECT 354 353 +CONECT 355 353 +CONECT 356 353 +CONECT 357 358 359 345 +CONECT 358 357 +CONECT 359 361 357 360 +CONECT 360 359 +CONECT 361 363 362 369 359 +CONECT 362 361 +CONECT 363 366 364 365 361 +CONECT 364 363 +CONECT 365 363 +CONECT 366 367 368 363 +CONECT 367 366 +CONECT 368 366 +CONECT 369 361 371 370 +CONECT 370 369 +CONECT 371 372 369 373 +CONECT 372 371 +CONECT 373 371 375 388 374 +CONECT 374 373 +CONECT 375 377 376 373 378 +CONECT 376 375 +CONECT 377 375 +CONECT 378 384 375 380 379 +CONECT 379 378 +CONECT 380 381 378 382 383 +CONECT 381 380 +CONECT 382 380 +CONECT 383 380 +CONECT 384 387 386 385 378 +CONECT 385 384 +CONECT 386 384 +CONECT 387 384 +CONECT 388 390 373 389 +CONECT 389 388 +CONECT 390 391 392 388 +CONECT 391 390 +CONECT 392 394 393 390 398 +CONECT 393 392 +CONECT 394 397 395 396 392 +CONECT 395 394 +CONECT 396 394 +CONECT 397 394 +CONECT 398 392 399 400 +CONECT 399 398 +CONECT 400 398 401 402 +CONECT 401 400 +CONECT 402 400 403 404 413 +CONECT 403 402 +CONECT 404 407 402 405 406 +CONECT 405 404 +CONECT 406 404 +CONECT 407 408 409 410 404 +CONECT 408 407 +CONECT 409 407 +CONECT 410 412 407 411 +CONECT 411 410 +CONECT 412 410 +CONECT 413 402 415 414 +CONECT 414 413 +CONECT 415 416 413 417 +CONECT 416 415 +CONECT 417 415 419 423 418 +CONECT 418 417 +CONECT 419 420 422 417 421 +CONECT 420 419 +CONECT 421 419 +CONECT 422 419 +CONECT 423 425 417 424 +CONECT 424 423 +CONECT 425 426 427 423 +CONECT 426 425 +CONECT 427 429 425 428 438 +CONECT 428 427 +CONECT 429 430 431 432 427 +CONECT 430 429 +CONECT 431 429 +CONECT 432 435 429 433 434 +CONECT 433 432 +CONECT 434 432 +CONECT 435 437 436 432 +CONECT 436 435 +CONECT 437 435 +CONECT 438 427 440 439 +CONECT 439 438 +CONECT 440 441 438 442 +CONECT 441 440 +CONECT 442 440 444 443 460 +CONECT 443 442 +CONECT 444 447 445 446 442 +CONECT 445 444 +CONECT 446 444 +CONECT 447 449 450 448 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 451 452 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 456 455 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 458 459 457 453 +CONECT 457 456 +CONECT 458 456 +CONECT 459 456 +CONECT 460 442 462 461 +CONECT 461 460 +CONECT 462 463 460 464 +CONECT 463 462 +CONECT 464 462 466 465 480 +CONECT 465 464 +CONECT 466 469 467 464 468 +CONECT 467 466 +CONECT 468 466 +CONECT 469 470 478 466 +CONECT 470 472 471 469 +CONECT 471 470 +CONECT 472 473 474 470 +CONECT 473 472 +CONECT 474 475 472 476 +CONECT 475 474 +CONECT 476 474 477 478 +CONECT 477 476 +CONECT 478 476 469 479 +CONECT 479 478 +CONECT 480 464 482 481 +CONECT 481 480 +CONECT 482 483 484 480 +CONECT 483 482 +CONECT 484 486 482 494 485 +CONECT 485 484 +CONECT 486 487 492 488 484 +CONECT 487 486 +CONECT 488 490 486 491 489 +CONECT 489 488 +CONECT 490 488 +CONECT 491 488 +CONECT 492 493 486 +CONECT 493 492 +CONECT 494 496 484 495 +CONECT 495 494 +CONECT 496 497 498 494 +CONECT 497 496 +CONECT 498 500 496 499 516 +CONECT 499 498 +CONECT 500 503 501 502 498 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 505 504 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 509 507 508 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 510 512 506 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 512 +CONECT 516 498 518 517 +CONECT 517 516 +CONECT 518 519 516 520 +CONECT 519 518 +CONECT 520 518 522 521 526 +CONECT 521 520 +CONECT 522 525 523 520 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 522 +CONECT 526 520 528 527 +CONECT 527 526 +CONECT 528 529 526 530 +CONECT 529 528 +CONECT 530 528 532 536 531 +CONECT 531 530 +CONECT 532 533 535 530 534 +CONECT 533 532 +CONECT 534 532 +CONECT 535 532 +CONECT 536 538 530 537 +CONECT 537 536 +CONECT 538 539 540 536 +CONECT 539 538 +CONECT 540 542 538 546 541 +CONECT 541 540 +CONECT 542 543 545 544 540 +CONECT 543 542 +CONECT 544 542 +CONECT 545 542 +CONECT 546 540 548 547 +CONECT 547 546 +CONECT 548 549 546 550 +CONECT 549 548 +CONECT 550 552 548 551 560 +CONECT 551 550 +CONECT 552 555 553 554 550 +CONECT 553 552 +CONECT 554 552 +CONECT 555 557 556 552 +CONECT 556 555 +CONECT 557 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 550 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 566 565 572 +CONECT 565 564 +CONECT 566 569 567 564 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 571 570 566 +CONECT 570 569 +CONECT 571 569 +CONECT 572 564 574 573 +CONECT 573 572 +CONECT 574 575 572 576 +CONECT 575 574 +CONECT 576 574 578 591 577 +CONECT 577 576 +CONECT 578 580 579 576 581 +CONECT 579 578 +CONECT 580 578 +CONECT 581 578 587 582 583 +CONECT 582 581 +CONECT 583 581 584 585 586 +CONECT 584 583 +CONECT 585 583 +CONECT 586 583 +CONECT 587 588 590 589 581 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 593 576 592 +CONECT 592 591 +CONECT 593 594 595 591 +CONECT 594 593 +CONECT 595 598 593 597 596 +CONECT 596 595 +CONECT 597 595 +CONECT 598 600 599 595 +CONECT 599 598 +CONECT 600 602 601 598 +CONECT 601 600 +CONECT 602 613 603 604 600 +CONECT 603 602 +CONECT 604 606 602 605 607 +CONECT 605 604 +CONECT 606 604 +CONECT 607 604 608 610 609 +CONECT 608 607 +CONECT 609 607 +CONECT 610 612 607 611 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 602 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 625 619 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 639 641 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 638 644 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 665 649 652 653 +CONECT 652 651 +CONECT 653 651 655 656 654 +CONECT 654 653 +CONECT 655 653 +CONECT 656 657 653 663 +CONECT 657 658 659 656 +CONECT 658 657 +CONECT 659 660 657 661 +CONECT 660 659 +CONECT 661 659 663 662 +CONECT 662 661 +CONECT 663 656 661 664 +CONECT 664 663 +CONECT 665 667 666 651 +CONECT 666 665 +CONECT 667 669 668 665 +CONECT 668 667 +CONECT 669 670 671 679 667 +CONECT 670 669 +CONECT 671 673 677 669 672 +CONECT 672 671 +CONECT 673 674 675 676 671 +CONECT 674 673 +CONECT 675 673 +CONECT 676 673 +CONECT 677 678 671 +CONECT 678 677 +CONECT 679 681 669 680 +CONECT 680 679 +CONECT 681 682 683 679 +CONECT 682 681 +CONECT 683 701 685 681 684 +CONECT 684 683 +CONECT 685 687 688 683 686 +CONECT 686 685 +CONECT 687 685 +CONECT 688 691 689 685 690 +CONECT 689 688 +CONECT 690 688 +CONECT 691 693 694 692 688 +CONECT 692 691 +CONECT 693 691 +CONECT 694 695 697 691 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 698 699 700 694 +CONECT 698 697 +CONECT 699 697 +CONECT 700 697 +CONECT 701 702 703 683 +CONECT 702 701 +CONECT 703 705 701 704 +CONECT 704 703 +CONECT 705 706 713 707 703 +CONECT 706 705 +CONECT 707 710 705 708 709 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 711 707 +CONECT 711 710 +CONECT 712 710 +CONECT 713 715 705 714 +CONECT 714 713 +CONECT 715 716 717 713 +CONECT 716 715 +CONECT 717 719 715 725 718 +CONECT 718 717 +CONECT 719 721 720 722 717 +CONECT 720 719 +CONECT 721 719 +CONECT 722 723 719 724 +CONECT 723 722 +CONECT 724 722 +CONECT 725 727 717 726 +CONECT 726 725 +CONECT 727 728 729 725 +CONECT 728 727 +CONECT 729 731 730 727 735 +CONECT 730 729 +CONECT 731 734 733 732 729 +CONECT 732 731 +CONECT 733 731 +CONECT 734 731 +CONECT 735 729 736 737 +CONECT 736 735 +CONECT 737 735 738 739 +CONECT 738 737 +CONECT 739 737 740 741 749 +CONECT 740 739 +CONECT 741 743 739 747 742 +CONECT 742 741 +CONECT 743 744 746 745 741 +CONECT 744 743 +CONECT 745 743 +CONECT 746 743 +CONECT 747 748 741 +CONECT 748 747 +CONECT 749 739 751 750 +CONECT 750 749 +CONECT 751 752 753 749 +CONECT 752 751 +CONECT 753 754 751 755 771 +CONECT 754 753 +CONECT 755 758 753 757 756 +CONECT 756 755 +CONECT 757 755 +CONECT 758 761 759 760 755 +CONECT 759 758 +CONECT 760 758 +CONECT 761 764 763 762 758 +CONECT 762 761 +CONECT 763 761 +CONECT 764 767 766 765 761 +CONECT 765 764 +CONECT 766 764 +CONECT 767 769 770 768 764 +CONECT 768 767 +CONECT 769 767 +CONECT 770 767 +CONECT 771 753 773 772 +CONECT 772 771 +CONECT 773 774 771 775 +CONECT 774 773 +CONECT 775 773 785 777 776 +CONECT 776 775 +CONECT 777 778 775 783 779 +CONECT 778 777 +CONECT 779 777 782 781 780 +CONECT 780 779 +CONECT 781 779 +CONECT 782 779 +CONECT 783 784 777 +CONECT 784 783 +CONECT 785 786 775 787 +CONECT 786 785 +CONECT 787 785 789 788 +CONECT 788 787 +CONECT 789 790 787 805 791 +CONECT 790 789 +CONECT 791 789 794 793 792 +CONECT 792 791 +CONECT 793 791 +CONECT 794 803 795 791 +CONECT 795 794 797 796 +CONECT 796 795 +CONECT 797 799 798 795 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 801 804 794 +CONECT 804 803 +CONECT 805 789 807 806 +CONECT 806 805 +CONECT 807 808 809 805 +CONECT 808 807 +CONECT 809 811 807 819 810 +CONECT 810 809 +CONECT 811 817 813 812 809 +CONECT 812 811 +CONECT 813 814 815 811 816 +CONECT 814 813 +CONECT 815 813 +CONECT 816 813 +CONECT 817 818 811 +CONECT 818 817 +CONECT 819 820 809 821 +CONECT 820 819 +CONECT 821 819 823 822 +CONECT 822 821 +CONECT 823 833 824 821 825 +CONECT 824 823 +CONECT 825 823 826 827 831 +CONECT 826 825 +CONECT 827 825 830 828 829 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 825 832 +CONECT 832 831 +CONECT 833 835 834 823 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 839 838 835 843 +CONECT 838 837 +CONECT 839 842 841 840 837 +CONECT 840 839 +CONECT 841 839 +CONECT 842 839 +CONECT 843 837 845 844 +CONECT 844 843 +CONECT 845 846 843 847 +CONECT 846 845 +CONECT 847 845 849 858 848 +CONECT 848 847 +CONECT 849 851 850 847 852 +CONECT 850 849 +CONECT 851 849 +CONECT 852 853 849 854 855 +CONECT 853 852 +CONECT 854 852 +CONECT 855 852 857 856 +CONECT 856 855 +CONECT 857 855 +CONECT 858 860 847 859 +CONECT 859 858 +CONECT 860 858 +CONECT 861 87 310 862 279 +CONECT 862 861 864 +CONECT 863 866 864 867 865 +CONECT 864 862 863 +CONECT 865 863 +CONECT 866 863 +CONECT 867 863 +CONECT 868 869 +CONECT 869 868 870 +CONECT 870 869 +MASTER 0 0 0 0 0 0 0 0 870 0 870 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_6.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_6.pdb new file mode 100644 index 0000000..7a0c97e --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_6.pdb @@ -0,0 +1,1753 @@ +COMPND fitness: -1.2907 59.98833333333391 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 55.366 58.077 52.044 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.215 37.914 23.523 1.00 0.00 N +ATOM 2 H1 MET 1 15.201 38.296 24.464 1.00 0.00 H +ATOM 3 H2 MET 1 14.443 38.284 22.998 1.00 0.00 H +ATOM 4 H3 MET 1 16.084 38.206 23.097 1.00 0.00 H +ATOM 5 CA MET 1 15.167 36.444 23.594 1.00 0.00 C +ATOM 6 HA MET 1 14.223 36.155 24.051 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.794 22.200 1.00 0.00 C +ATOM 8 HB2 MET 1 14.404 36.123 21.604 1.00 0.00 H +ATOM 9 HB3 MET 1 16.168 36.123 21.701 1.00 0.00 H +ATOM 10 CG MET 1 15.256 34.254 22.251 1.00 0.00 C +ATOM 11 HG2 MET 1 16.133 33.929 22.814 1.00 0.00 H +ATOM 12 HG3 MET 1 14.367 33.916 22.786 1.00 0.00 H +ATOM 13 SD MET 1 15.317 33.393 20.646 1.00 0.00 S +ATOM 14 CE MET 1 13.636 33.641 20.008 1.00 0.00 C +ATOM 15 HE1 MET 1 13.415 34.705 19.929 1.00 0.00 H +ATOM 16 HE2 MET 1 13.557 33.192 19.017 1.00 0.00 H +ATOM 17 HE3 MET 1 12.912 33.164 20.670 1.00 0.00 H +ATOM 18 C MET 1 16.285 35.966 24.511 1.00 0.00 C +ATOM 19 O MET 1 17.429 36.370 24.340 1.00 0.00 O +ATOM 20 N GLN 2 15.963 35.099 25.473 1.00 0.00 N +ATOM 21 H GLN 2 14.992 34.874 25.632 1.00 0.00 H +ATOM 22 CA GLN 2 16.928 34.438 26.358 1.00 0.00 C +ATOM 23 HA GLN 2 17.697 35.150 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 16.177 34.003 27.636 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.213 33.562 27.357 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.744 33.245 28.172 1.00 0.00 H +ATOM 27 CG GLN 2 15.930 35.169 28.587 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.504 36.019 28.045 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.177 34.846 29.297 1.00 0.00 H +ATOM 30 CD GLN 2 17.140 35.548 29.441 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.211 34.972 29.368 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.976 36.450 30.363 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.748 36.615 30.982 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.068 36.818 30.542 1.00 0.00 H +ATOM 35 C GLN 2 17.653 33.291 25.623 1.00 0.00 C +ATOM 36 O GLN 2 17.281 32.121 25.734 1.00 0.00 O +ATOM 37 N TYR 3 18.675 33.646 24.841 1.00 0.00 N +ATOM 38 H TYR 3 18.926 34.635 24.813 1.00 0.00 H +ATOM 39 CA TYR 3 19.508 32.709 24.085 1.00 0.00 C +ATOM 40 HA TYR 3 18.854 32.101 23.459 1.00 0.00 H +ATOM 41 CB TYR 3 20.458 33.508 23.197 1.00 0.00 C +ATOM 42 HB2 TYR 3 21.071 34.153 23.827 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.125 32.817 22.690 1.00 0.00 H +ATOM 44 CG TYR 3 19.760 34.349 22.152 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.102 33.711 21.087 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.079 32.633 21.039 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.519 34.465 20.054 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.049 33.973 19.217 1.00 0.00 H +ATOM 49 CZ TYR 3 18.571 35.872 20.103 1.00 0.00 C +ATOM 50 OH TYR 3 18.027 36.608 19.103 1.00 0.00 O +ATOM 51 HH TYR 3 18.041 36.130 18.273 1.00 0.00 H +ATOM 52 CE2 TYR 3 19.176 36.515 21.200 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.196 37.592 21.223 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.774 35.755 22.224 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.247 36.252 23.059 1.00 0.00 H +ATOM 56 C TYR 3 20.295 31.786 25.023 1.00 0.00 C +ATOM 57 O TYR 3 20.806 32.243 26.044 1.00 0.00 O +ATOM 58 N LYS 4 20.410 30.492 24.696 1.00 0.00 N +ATOM 59 H LYS 4 20.118 30.201 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 21.014 29.461 25.566 1.00 0.00 C +ATOM 61 HA LYS 4 20.744 29.654 26.602 1.00 0.00 H +ATOM 62 CB LYS 4 20.480 28.067 25.177 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.496 27.976 24.094 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.160 27.307 25.570 1.00 0.00 H +ATOM 65 CG LYS 4 19.070 27.701 25.676 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.897 26.669 25.374 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.060 27.742 26.766 1.00 0.00 H +ATOM 68 CD LYS 4 17.920 28.560 25.120 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.927 29.535 25.607 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.090 28.713 24.052 1.00 0.00 H +ATOM 71 CE LYS 4 16.533 27.909 25.279 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.777 28.600 24.894 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.509 27.012 24.654 1.00 0.00 H +ATOM 74 NZ LYS 4 16.205 27.518 26.673 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.269 28.291 27.318 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.276 27.107 26.716 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.829 26.763 26.958 1.00 0.00 H +ATOM 78 C LYS 4 22.547 29.475 25.513 1.00 0.00 C +ATOM 79 O LYS 4 23.144 29.819 24.501 1.00 0.00 O +HETATM 80 N HX1 5 23.203 29.039 26.584 1.00 0.00 N +HETATM 81 CA HX1 5 24.662 28.868 26.669 1.00 0.00 C +HETATM 82 C HX1 5 24.985 27.668 27.567 1.00 0.00 C +HETATM 83 O HX1 5 24.522 27.612 28.710 1.00 0.00 O +HETATM 84 CB HX1 5 25.294 30.185 27.169 1.00 0.00 C +HETATM 85 CG HX1 5 26.807 30.275 27.239 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.721 29.336 26.838 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.483 31.361 27.814 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.782 31.031 27.730 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.957 29.808 27.202 1.00 0.00 N +HETATM 90 H HX1 5 22.658 28.869 27.426 1.00 0.00 H +HETATM 91 HA HX1 5 25.052 28.661 25.672 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.899 30.401 28.163 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.958 30.992 26.516 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.539 28.374 26.378 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.578 31.603 28.187 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.812 29.251 27.293 1.00 0.00 H +ATOM 97 N ILE 6 25.726 26.695 27.028 1.00 0.00 N +ATOM 98 H ILE 6 26.046 26.815 26.070 1.00 0.00 H +ATOM 99 CA ILE 6 26.199 25.479 27.709 1.00 0.00 C +ATOM 100 HA ILE 6 25.697 25.404 28.676 1.00 0.00 H +ATOM 101 CB ILE 6 25.811 24.216 26.902 1.00 0.00 C +ATOM 102 HB ILE 6 26.234 24.306 25.901 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.373 22.929 27.541 1.00 0.00 C +ATOM 104 HG21 ILE 6 26.002 22.820 28.562 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.078 22.054 26.963 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.464 22.944 27.545 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.270 24.130 26.784 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.842 24.047 27.783 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.891 25.046 26.331 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.745 22.969 25.931 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.890 22.021 26.449 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.678 23.107 25.758 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.263 22.948 24.971 1.00 0.00 H +ATOM 114 C ILE 6 27.708 25.597 28.003 1.00 0.00 C +ATOM 115 O ILE 6 28.447 26.273 27.288 1.00 0.00 O +ATOM 116 N VAL 7 28.126 24.994 29.115 1.00 0.00 N +ATOM 117 H VAL 7 27.488 24.344 29.551 1.00 0.00 H +ATOM 118 CA VAL 7 29.238 25.447 29.963 1.00 0.00 C +ATOM 119 HA VAL 7 29.296 26.533 29.871 1.00 0.00 H +ATOM 120 CB VAL 7 28.813 25.143 31.416 1.00 0.00 C +ATOM 121 HB VAL 7 27.762 25.424 31.517 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.895 23.654 31.773 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.924 23.309 31.694 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.538 23.499 32.790 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.276 23.071 31.090 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.567 25.988 32.435 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.358 27.041 32.248 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.232 25.736 33.441 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.636 25.813 32.353 1.00 0.00 H +ATOM 130 C VAL 7 30.639 24.901 29.585 1.00 0.00 C +ATOM 131 O VAL 7 30.785 23.764 29.143 1.00 0.00 O +ATOM 132 N GLU 8 31.685 25.707 29.802 1.00 0.00 N +ATOM 133 H GLU 8 31.473 26.676 30.027 1.00 0.00 H +ATOM 134 CA GLU 8 33.119 25.383 29.624 1.00 0.00 C +ATOM 135 HA GLU 8 33.310 25.152 28.575 1.00 0.00 H +ATOM 136 CB GLU 8 33.917 26.667 29.977 1.00 0.00 C +ATOM 137 HB2 GLU 8 33.712 27.426 29.223 1.00 0.00 H +ATOM 138 HB3 GLU 8 33.497 27.048 30.911 1.00 0.00 H +ATOM 139 CG GLU 8 35.447 26.584 30.222 1.00 0.00 C +ATOM 140 HG2 GLU 8 35.729 27.498 30.753 1.00 0.00 H +ATOM 141 HG3 GLU 8 35.683 25.765 30.900 1.00 0.00 H +ATOM 142 CD GLU 8 36.359 26.500 28.992 1.00 0.00 C +ATOM 143 OE1 GLU 8 36.012 27.041 27.916 1.00 0.00 O +ATOM 144 OE2 GLU 8 37.521 26.054 29.135 1.00 0.00 O +ATOM 145 C GLU 8 33.570 24.164 30.464 1.00 0.00 C +ATOM 146 O GLU 8 33.840 24.286 31.658 1.00 0.00 O +ATOM 147 N GLY 9 33.696 22.982 29.849 1.00 0.00 N +ATOM 148 H GLY 9 33.287 22.892 28.929 1.00 0.00 H +ATOM 149 CA GLY 9 34.345 21.797 30.438 1.00 0.00 C +ATOM 150 HA2 GLY 9 35.247 21.575 29.868 1.00 0.00 H +ATOM 151 HA3 GLY 9 34.650 22.011 31.462 1.00 0.00 H +ATOM 152 C GLY 9 33.492 20.522 30.448 1.00 0.00 C +ATOM 153 O GLY 9 32.620 20.332 29.602 1.00 0.00 O +ATOM 154 N LYS 10 33.792 19.600 31.384 1.00 0.00 N +ATOM 155 H LYS 10 34.546 19.810 32.024 1.00 0.00 H +ATOM 156 CA LYS 10 33.231 18.228 31.369 1.00 0.00 C +ATOM 157 HA LYS 10 32.207 18.313 30.994 1.00 0.00 H +ATOM 158 CB LYS 10 34.029 17.371 30.353 1.00 0.00 C +ATOM 159 HB2 LYS 10 34.519 18.019 29.622 1.00 0.00 H +ATOM 160 HB3 LYS 10 34.809 16.806 30.866 1.00 0.00 H +ATOM 161 CG LYS 10 33.125 16.407 29.565 1.00 0.00 C +ATOM 162 HG2 LYS 10 32.575 15.759 30.248 1.00 0.00 H +ATOM 163 HG3 LYS 10 32.406 16.996 28.991 1.00 0.00 H +ATOM 164 CD LYS 10 33.941 15.541 28.595 1.00 0.00 C +ATOM 165 HD2 LYS 10 34.578 16.183 27.985 1.00 0.00 H +ATOM 166 HD3 LYS 10 34.568 14.847 29.158 1.00 0.00 H +ATOM 167 CE LYS 10 32.994 14.759 27.678 1.00 0.00 C +ATOM 168 HE2 LYS 10 32.438 14.025 28.267 1.00 0.00 H +ATOM 169 HE3 LYS 10 32.275 15.460 27.247 1.00 0.00 H +ATOM 170 NZ LYS 10 33.721 14.092 26.575 1.00 0.00 N +ATOM 171 HZ1 LYS 10 34.417 13.448 26.913 1.00 0.00 H +ATOM 172 HZ2 LYS 10 33.061 13.594 25.979 1.00 0.00 H +ATOM 173 HZ3 LYS 10 34.203 14.795 26.004 1.00 0.00 H +ATOM 174 C LYS 10 33.089 17.528 32.737 1.00 0.00 C +ATOM 175 O LYS 10 33.156 16.303 32.800 1.00 0.00 O +ATOM 176 N ARG 11 32.949 18.273 33.841 1.00 0.00 N +ATOM 177 H ARG 11 32.915 19.267 33.709 1.00 0.00 H +ATOM 178 CA ARG 11 32.662 17.722 35.194 1.00 0.00 C +ATOM 179 HA ARG 11 32.758 16.632 35.161 1.00 0.00 H +ATOM 180 CB ARG 11 33.685 18.237 36.231 1.00 0.00 C +ATOM 181 HB2 ARG 11 33.709 19.326 36.208 1.00 0.00 H +ATOM 182 HB3 ARG 11 33.355 17.924 37.222 1.00 0.00 H +ATOM 183 CG ARG 11 35.099 17.680 35.989 1.00 0.00 C +ATOM 184 HG2 ARG 11 35.055 16.589 35.999 1.00 0.00 H +ATOM 185 HG3 ARG 11 35.449 18.007 35.010 1.00 0.00 H +ATOM 186 CD ARG 11 36.103 18.142 37.058 1.00 0.00 C +ATOM 187 HD2 ARG 11 36.071 19.228 37.118 1.00 0.00 H +ATOM 188 HD3 ARG 11 35.803 17.740 38.029 1.00 0.00 H +ATOM 189 NE ARG 11 37.479 17.692 36.740 1.00 0.00 N +ATOM 190 HE ARG 11 37.569 16.946 36.073 1.00 0.00 H +ATOM 191 CZ ARG 11 38.615 18.198 37.201 1.00 0.00 C +ATOM 192 NH1 ARG 11 38.667 19.233 37.987 1.00 0.00 N +ATOM 193 HH11 ARG 11 37.829 19.772 38.112 1.00 0.00 H +ATOM 194 HH12 ARG 11 39.560 19.686 38.132 1.00 0.00 H +ATOM 195 NH2 ARG 11 39.749 17.650 36.875 1.00 0.00 N +ATOM 196 HH21 ARG 11 39.795 16.894 36.219 1.00 0.00 H +ATOM 197 HH22 ARG 11 40.609 18.031 37.266 1.00 0.00 H +ATOM 198 C ARG 11 31.206 17.954 35.609 1.00 0.00 C +ATOM 199 O ARG 11 30.490 17.005 35.900 1.00 0.00 O +ATOM 200 N TYR 12 30.762 19.208 35.566 1.00 0.00 N +ATOM 201 H TYR 12 31.434 19.929 35.379 1.00 0.00 H +ATOM 202 CA TYR 12 29.346 19.607 35.531 1.00 0.00 C +ATOM 203 HA TYR 12 28.789 18.986 36.247 1.00 0.00 H +ATOM 204 CB TYR 12 29.234 21.066 36.001 1.00 0.00 C +ATOM 205 HB2 TYR 12 28.187 21.379 35.945 1.00 0.00 H +ATOM 206 HB3 TYR 12 29.493 21.077 37.062 1.00 0.00 H +ATOM 207 CG TYR 12 30.105 22.126 35.333 1.00 0.00 C +ATOM 208 CD1 TYR 12 30.870 21.891 34.171 1.00 0.00 C +ATOM 209 HD1 TYR 12 30.824 20.950 33.636 1.00 0.00 H +ATOM 210 CE1 TYR 12 31.738 22.879 33.670 1.00 0.00 C +ATOM 211 HE1 TYR 12 32.313 22.692 32.776 1.00 0.00 H +ATOM 212 CZ TYR 12 31.833 24.123 34.322 1.00 0.00 C +ATOM 213 OH TYR 12 32.699 25.074 33.898 1.00 0.00 O +ATOM 214 HH TYR 12 33.108 24.847 33.030 1.00 0.00 H +ATOM 215 CE2 TYR 12 30.999 24.398 35.419 1.00 0.00 C +ATOM 216 HE2 TYR 12 31.006 25.385 35.861 1.00 0.00 H +ATOM 217 CD2 TYR 12 30.158 23.394 35.933 1.00 0.00 C +ATOM 218 HD2 TYR 12 29.558 23.604 36.815 1.00 0.00 H +ATOM 219 C TYR 12 28.690 19.397 34.145 1.00 0.00 C +ATOM 220 O TYR 12 29.368 19.005 33.196 1.00 0.00 O +ATOM 221 N LYS 13 27.382 19.683 34.028 1.00 0.00 N +ATOM 222 H LYS 13 26.894 19.964 34.865 1.00 0.00 H +ATOM 223 CA LYS 13 26.590 19.509 32.789 1.00 0.00 C +ATOM 224 HA LYS 13 27.257 19.685 31.944 1.00 0.00 H +ATOM 225 CB LYS 13 26.113 18.042 32.728 1.00 0.00 C +ATOM 226 HB2 LYS 13 26.870 17.413 33.196 1.00 0.00 H +ATOM 227 HB3 LYS 13 25.191 17.936 33.302 1.00 0.00 H +ATOM 228 CG LYS 13 25.912 17.515 31.295 1.00 0.00 C +ATOM 229 HG2 LYS 13 25.056 18.000 30.825 1.00 0.00 H +ATOM 230 HG3 LYS 13 26.803 17.746 30.711 1.00 0.00 H +ATOM 231 CD LYS 13 25.715 15.990 31.282 1.00 0.00 C +ATOM 232 HD2 LYS 13 25.753 15.643 30.248 1.00 0.00 H +ATOM 233 HD3 LYS 13 26.543 15.525 31.821 1.00 0.00 H +ATOM 234 CE LYS 13 24.376 15.549 31.892 1.00 0.00 C +ATOM 235 HE2 LYS 13 24.136 16.182 32.751 1.00 0.00 H +ATOM 236 HE3 LYS 13 23.603 15.708 31.133 1.00 0.00 H +ATOM 237 NZ LYS 13 24.406 14.121 32.306 1.00 0.00 N +ATOM 238 HZ1 LYS 13 24.934 13.975 33.159 1.00 0.00 H +ATOM 239 HZ2 LYS 13 23.466 13.759 32.451 1.00 0.00 H +ATOM 240 HZ3 LYS 13 24.860 13.553 31.592 1.00 0.00 H +ATOM 241 C LYS 13 25.440 20.533 32.632 1.00 0.00 C +ATOM 242 O LYS 13 24.397 20.233 32.051 1.00 0.00 O +ATOM 243 N GLY 14 25.597 21.720 33.227 1.00 0.00 N +ATOM 244 H GLY 14 26.491 21.921 33.646 1.00 0.00 H +ATOM 245 CA GLY 14 24.547 22.749 33.314 1.00 0.00 C +ATOM 246 HA2 GLY 14 23.595 22.255 33.508 1.00 0.00 H +ATOM 247 HA3 GLY 14 24.753 23.393 34.169 1.00 0.00 H +ATOM 248 C GLY 14 24.384 23.636 32.065 1.00 0.00 C +ATOM 249 O GLY 14 25.241 23.673 31.182 1.00 0.00 O +ATOM 250 N VAL 15 23.283 24.395 32.031 1.00 0.00 N +ATOM 251 H VAL 15 22.640 24.337 32.808 1.00 0.00 H +ATOM 252 CA VAL 15 22.902 25.355 30.981 1.00 0.00 C +ATOM 253 HA VAL 15 23.781 25.595 30.382 1.00 0.00 H +ATOM 254 CB VAL 15 21.857 24.717 30.034 1.00 0.00 C +ATOM 255 HB VAL 15 22.299 23.817 29.609 1.00 0.00 H +ATOM 256 CG1 VAL 15 20.551 24.300 30.731 1.00 0.00 C +ATOM 257 HG11 VAL 15 20.049 25.165 31.169 1.00 0.00 H +ATOM 258 HG12 VAL 15 19.882 23.832 30.007 1.00 0.00 H +ATOM 259 HG13 VAL 15 20.757 23.573 31.519 1.00 0.00 H +ATOM 260 CG2 VAL 15 21.481 25.640 28.867 1.00 0.00 C +ATOM 261 HG21 VAL 15 22.382 25.990 28.366 1.00 0.00 H +ATOM 262 HG22 VAL 15 20.879 25.084 28.146 1.00 0.00 H +ATOM 263 HG23 VAL 15 20.901 26.492 29.221 1.00 0.00 H +ATOM 264 C VAL 15 22.399 26.651 31.633 1.00 0.00 C +ATOM 265 O VAL 15 21.845 26.618 32.728 1.00 0.00 O +HETATM 266 N HY1 16 22.593 27.795 30.980 1.00 0.00 N +HETATM 267 CA HY1 16 22.005 29.092 31.344 1.00 0.00 C +HETATM 268 C HY1 16 21.694 29.890 30.062 1.00 0.00 C +HETATM 269 O HY1 16 21.860 29.375 28.949 1.00 0.00 O +HETATM 270 CB HY1 16 22.928 29.838 32.334 1.00 0.00 C +HETATM 271 CG HY1 16 24.278 30.202 31.763 1.00 0.00 C +HETATM 272 CD2 HY1 16 24.599 31.380 31.142 1.00 0.00 C +HETATM 273 ND1 HY1 16 25.407 29.412 31.750 1.00 0.00 N +HETATM 274 CE1 HY1 16 26.387 30.121 31.164 1.00 0.00 C +HETATM 275 NE2 HY1 16 25.942 31.324 30.761 1.00 0.00 N +HETATM 276 H HY1 16 23.089 27.760 30.095 1.00 0.00 H +HETATM 277 HA HY1 16 21.042 28.937 31.836 1.00 0.00 H +HETATM 278 HB2 HY1 16 22.448 30.747 32.701 1.00 0.00 H +HETATM 279 HB3 HY1 16 23.076 29.209 33.217 1.00 0.00 H +HETATM 280 HD1 HY1 16 25.502 28.501 32.177 1.00 0.00 H +HETATM 281 HD2 HY1 16 23.933 32.219 30.992 1.00 0.00 H +HETATM 282 HE1 HY1 16 27.419 29.794 31.067 1.00 0.00 H +ATOM 283 N THR 17 21.213 31.125 30.221 1.00 0.00 N +ATOM 284 H THR 17 21.084 31.439 31.169 1.00 0.00 H +ATOM 285 CA THR 17 20.771 32.009 29.122 1.00 0.00 C +ATOM 286 HA THR 17 21.190 31.603 28.215 1.00 0.00 H +ATOM 287 CB THR 17 19.244 32.008 28.942 1.00 0.00 C +ATOM 288 HB THR 17 19.023 32.578 28.042 1.00 0.00 H +ATOM 289 CG2 THR 17 18.642 30.640 28.642 1.00 0.00 C +ATOM 290 HG21 THR 17 18.864 29.923 29.430 1.00 0.00 H +ATOM 291 HG22 THR 17 17.562 30.744 28.553 1.00 0.00 H +ATOM 292 HG23 THR 17 19.034 30.311 27.693 1.00 0.00 H +ATOM 293 OG1 THR 17 18.523 32.465 30.065 1.00 0.00 O +ATOM 294 HG1 THR 17 18.606 33.430 30.107 1.00 0.00 H +ATOM 295 C THR 17 21.279 33.458 29.181 1.00 0.00 C +ATOM 296 O THR 17 21.726 33.926 30.226 1.00 0.00 O +HETATM 297 N HY2 18 21.213 34.175 28.055 1.00 0.00 N +HETATM 298 CA HY2 18 21.495 35.612 27.957 1.00 0.00 C +HETATM 299 C HY2 18 20.395 36.305 27.153 1.00 0.00 C +HETATM 300 O HY2 18 20.079 35.863 26.049 1.00 0.00 O +HETATM 301 CB HY2 18 22.848 35.842 27.247 1.00 0.00 C +HETATM 302 CG HY2 18 24.050 35.344 28.020 1.00 0.00 C +HETATM 303 CD2 HY2 18 24.548 34.066 28.017 1.00 0.00 C +HETATM 304 ND1 HY2 18 24.828 36.083 28.888 1.00 0.00 N +HETATM 305 CE1 HY2 18 25.770 35.264 29.383 1.00 0.00 C +HETATM 306 NE2 HY2 18 25.640 34.024 28.889 1.00 0.00 N +HETATM 307 H HY2 18 20.908 33.715 27.202 1.00 0.00 H +HETATM 308 HA HY2 18 21.529 36.051 28.954 1.00 0.00 H +HETATM 309 HB2 HY2 18 22.822 35.342 26.280 1.00 0.00 H +HETATM 310 HB3 HY2 18 22.973 36.910 27.064 1.00 0.00 H +HETATM 311 HD1 HY2 18 24.725 37.067 29.105 1.00 0.00 H +HETATM 312 HD2 HY2 18 24.156 33.232 27.450 1.00 0.00 H +HETATM 313 HE1 HY2 18 26.531 35.559 30.091 1.00 0.00 H +ATOM 314 N GLU 19 19.822 37.382 27.687 1.00 0.00 N +ATOM 315 H GLU 19 20.120 37.688 28.599 1.00 0.00 H +ATOM 316 CA GLU 19 18.828 38.211 26.992 1.00 0.00 C +ATOM 317 HA GLU 19 18.106 37.555 26.510 1.00 0.00 H +ATOM 318 CB GLU 19 18.086 39.074 28.032 1.00 0.00 C +ATOM 319 HB2 GLU 19 17.783 38.444 28.864 1.00 0.00 H +ATOM 320 HB3 GLU 19 18.779 39.814 28.429 1.00 0.00 H +ATOM 321 CG GLU 19 16.839 39.798 27.502 1.00 0.00 C +ATOM 322 HG2 GLU 19 16.549 40.555 28.233 1.00 0.00 H +ATOM 323 HG3 GLU 19 17.073 40.313 26.569 1.00 0.00 H +ATOM 324 CD GLU 19 15.667 38.828 27.300 1.00 0.00 C +ATOM 325 OE1 GLU 19 15.544 38.285 26.172 1.00 0.00 O +ATOM 326 OE2 GLU 19 14.908 38.603 28.271 1.00 0.00 O +ATOM 327 C GLU 19 19.483 39.095 25.913 1.00 0.00 C +ATOM 328 O GLU 19 20.430 39.823 26.208 1.00 0.00 O +ATOM 329 N ALA 20 18.977 39.059 24.676 1.00 0.00 N +ATOM 330 H ALA 20 18.268 38.367 24.467 1.00 0.00 H +ATOM 331 CA ALA 20 19.340 40.004 23.612 1.00 0.00 C +ATOM 332 HA ALA 20 19.410 41.004 24.042 1.00 0.00 H +ATOM 333 CB ALA 20 20.714 39.620 23.042 1.00 0.00 C +ATOM 334 HB1 ALA 20 20.657 38.642 22.573 1.00 0.00 H +ATOM 335 HB2 ALA 20 21.036 40.351 22.302 1.00 0.00 H +ATOM 336 HB3 ALA 20 21.459 39.585 23.834 1.00 0.00 H +ATOM 337 C ALA 20 18.286 40.039 22.486 1.00 0.00 C +ATOM 338 O ALA 20 17.384 39.200 22.439 1.00 0.00 O +ATOM 339 N VAL 21 18.416 40.981 21.545 1.00 0.00 N +ATOM 340 H VAL 21 19.145 41.670 21.653 1.00 0.00 H +ATOM 341 CA VAL 21 17.672 40.975 20.262 1.00 0.00 C +ATOM 342 HA VAL 21 16.689 40.537 20.427 1.00 0.00 H +ATOM 343 CB VAL 21 17.448 42.410 19.731 1.00 0.00 C +ATOM 344 HB VAL 21 16.804 42.345 18.853 1.00 0.00 H +ATOM 345 CG1 VAL 21 16.721 43.284 20.761 1.00 0.00 C +ATOM 346 HG11 VAL 21 17.357 43.476 21.625 1.00 0.00 H +ATOM 347 HG12 VAL 21 16.455 44.237 20.303 1.00 0.00 H +ATOM 348 HG13 VAL 21 15.806 42.790 21.088 1.00 0.00 H +ATOM 349 CG2 VAL 21 18.744 43.117 19.309 1.00 0.00 C +ATOM 350 HG21 VAL 21 19.218 42.578 18.489 1.00 0.00 H +ATOM 351 HG22 VAL 21 18.510 44.121 18.954 1.00 0.00 H +ATOM 352 HG23 VAL 21 19.441 43.191 20.143 1.00 0.00 H +ATOM 353 C VAL 21 18.344 40.117 19.176 1.00 0.00 C +ATOM 354 O VAL 21 17.744 39.875 18.133 1.00 0.00 O +ATOM 355 N ASP 22 19.590 39.693 19.410 1.00 0.00 N +ATOM 356 H ASP 22 20.003 39.905 20.303 1.00 0.00 H +ATOM 357 CA ASP 22 20.496 39.093 18.428 1.00 0.00 C +ATOM 358 HA ASP 22 19.939 38.443 17.752 1.00 0.00 H +ATOM 359 CB ASP 22 21.118 40.245 17.617 1.00 0.00 C +ATOM 360 HB2 ASP 22 20.331 40.741 17.046 1.00 0.00 H +ATOM 361 HB3 ASP 22 21.537 40.973 18.314 1.00 0.00 H +ATOM 362 CG ASP 22 22.212 39.808 16.646 1.00 0.00 C +ATOM 363 OD1 ASP 22 23.135 40.614 16.431 1.00 0.00 O +ATOM 364 OD2 ASP 22 22.150 38.658 16.158 1.00 0.00 O +ATOM 365 C ASP 22 21.589 38.257 19.129 1.00 0.00 C +ATOM 366 O ASP 22 22.026 38.601 20.232 1.00 0.00 O +ATOM 367 N PHE 23 22.075 37.194 18.482 1.00 0.00 N +ATOM 368 H PHE 23 21.801 37.088 17.511 1.00 0.00 H +ATOM 369 CA PHE 23 23.223 36.413 18.957 1.00 0.00 C +ATOM 370 HA PHE 23 23.033 36.100 19.983 1.00 0.00 H +ATOM 371 CB PHE 23 23.435 35.163 18.098 1.00 0.00 C +ATOM 372 HB2 PHE 23 23.449 35.439 17.042 1.00 0.00 H +ATOM 373 HB3 PHE 23 24.415 34.748 18.336 1.00 0.00 H +ATOM 374 CG PHE 23 22.418 34.075 18.332 1.00 0.00 C +ATOM 375 CD1 PHE 23 21.326 33.930 17.460 1.00 0.00 C +ATOM 376 HD1 PHE 23 21.215 34.591 16.613 1.00 0.00 H +ATOM 377 CE1 PHE 23 20.387 32.912 17.686 1.00 0.00 C +ATOM 378 HE1 PHE 23 19.553 32.789 17.010 1.00 0.00 H +ATOM 379 CZ PHE 23 20.545 32.053 18.784 1.00 0.00 C +ATOM 380 HZ PHE 23 19.804 31.307 18.977 1.00 0.00 H +ATOM 381 CE2 PHE 23 21.642 32.183 19.650 1.00 0.00 C +ATOM 382 HE2 PHE 23 21.763 31.512 20.488 1.00 0.00 H +ATOM 383 CD2 PHE 23 22.581 33.199 19.421 1.00 0.00 C +ATOM 384 HD2 PHE 23 23.433 33.303 20.076 1.00 0.00 H +ATOM 385 C PHE 23 24.522 37.216 18.948 1.00 0.00 C +ATOM 386 O PHE 23 25.288 37.123 19.906 1.00 0.00 O +ATOM 387 N ALA 24 24.777 38.032 17.920 1.00 0.00 N +ATOM 388 H ALA 24 24.098 38.127 17.167 1.00 0.00 H +ATOM 389 CA ALA 24 26.004 38.826 17.863 1.00 0.00 C +ATOM 390 HA ALA 24 26.836 38.166 18.118 1.00 0.00 H +ATOM 391 CB ALA 24 26.244 39.297 16.423 1.00 0.00 C +ATOM 392 HB1 ALA 24 25.486 40.016 16.122 1.00 0.00 H +ATOM 393 HB2 ALA 24 27.226 39.763 16.347 1.00 0.00 H +ATOM 394 HB3 ALA 24 26.209 38.442 15.744 1.00 0.00 H +ATOM 395 C ALA 24 26.024 39.969 18.904 1.00 0.00 C +ATOM 396 O ALA 24 27.084 40.536 19.172 1.00 0.00 O +ATOM 397 N GLU 25 24.892 40.281 19.545 1.00 0.00 N +ATOM 398 H GLU 25 24.041 39.856 19.205 1.00 0.00 H +ATOM 399 CA GLU 25 24.819 41.085 20.776 1.00 0.00 C +ATOM 400 HA GLU 25 25.636 41.806 20.796 1.00 0.00 H +ATOM 401 CB GLU 25 23.498 41.871 20.814 1.00 0.00 C +ATOM 402 HB2 GLU 25 22.673 41.163 20.774 1.00 0.00 H +ATOM 403 HB3 GLU 25 23.429 42.408 21.760 1.00 0.00 H +ATOM 404 CG GLU 25 23.310 42.881 19.671 1.00 0.00 C +ATOM 405 HG2 GLU 25 23.577 42.429 18.714 1.00 0.00 H +ATOM 406 HG3 GLU 25 22.247 43.135 19.624 1.00 0.00 H +ATOM 407 CD GLU 25 24.114 44.170 19.880 1.00 0.00 C +ATOM 408 OE1 GLU 25 23.462 45.220 20.101 1.00 0.00 O +ATOM 409 OE2 GLU 25 25.371 44.098 19.811 1.00 0.00 O +ATOM 410 C GLU 25 24.959 40.215 22.041 1.00 0.00 C +ATOM 411 O GLU 25 25.732 40.553 22.938 1.00 0.00 O +ATOM 412 N ALA 26 24.299 39.050 22.103 1.00 0.00 N +ATOM 413 H ALA 26 23.662 38.814 21.352 1.00 0.00 H +ATOM 414 CA ALA 26 24.423 38.100 23.218 1.00 0.00 C +ATOM 415 HA ALA 26 24.130 38.609 24.131 1.00 0.00 H +ATOM 416 CB ALA 26 23.471 36.923 22.993 1.00 0.00 C +ATOM 417 HB1 ALA 26 23.770 36.368 22.108 1.00 0.00 H +ATOM 418 HB2 ALA 26 23.499 36.260 23.854 1.00 0.00 H +ATOM 419 HB3 ALA 26 22.460 37.285 22.860 1.00 0.00 H +ATOM 420 C ALA 26 25.868 37.595 23.424 1.00 0.00 C +ATOM 421 O ALA 26 26.292 37.316 24.550 1.00 0.00 O +ATOM 422 N GLU 27 26.659 37.515 22.348 1.00 0.00 N +ATOM 423 H GLU 27 26.221 37.663 21.441 1.00 0.00 H +ATOM 424 CA GLU 27 28.109 37.261 22.347 1.00 0.00 C +ATOM 425 HA GLU 27 28.316 36.315 22.855 1.00 0.00 H +ATOM 426 CB GLU 27 28.586 37.117 20.887 1.00 0.00 C +ATOM 427 HB2 GLU 27 28.014 36.303 20.438 1.00 0.00 H +ATOM 428 HB3 GLU 27 28.354 38.028 20.337 1.00 0.00 H +ATOM 429 CG GLU 27 30.079 36.836 20.757 1.00 0.00 C +ATOM 430 HG2 GLU 27 30.614 37.779 20.882 1.00 0.00 H +ATOM 431 HG3 GLU 27 30.401 36.162 21.554 1.00 0.00 H +ATOM 432 CD GLU 27 30.366 36.227 19.390 1.00 0.00 C +ATOM 433 OE1 GLU 27 30.986 36.917 18.564 1.00 0.00 O +ATOM 434 OE2 GLU 27 29.944 35.073 19.158 1.00 0.00 O +ATOM 435 C GLU 27 28.855 38.375 23.112 1.00 0.00 C +ATOM 436 O GLU 27 29.633 38.083 24.023 1.00 0.00 O +ATOM 437 N LYS 28 28.553 39.656 22.836 1.00 0.00 N +ATOM 438 H LYS 28 27.822 39.830 22.156 1.00 0.00 H +ATOM 439 CA LYS 28 29.116 40.802 23.576 1.00 0.00 C +ATOM 440 HA LYS 28 30.202 40.719 23.569 1.00 0.00 H +ATOM 441 CB LYS 28 28.725 42.140 22.919 1.00 0.00 C +ATOM 442 HB2 LYS 28 27.648 42.281 22.995 1.00 0.00 H +ATOM 443 HB3 LYS 28 29.205 42.945 23.473 1.00 0.00 H +ATOM 444 CG LYS 28 29.135 42.250 21.442 1.00 0.00 C +ATOM 445 HG2 LYS 28 30.206 42.069 21.341 1.00 0.00 H +ATOM 446 HG3 LYS 28 28.602 41.496 20.871 1.00 0.00 H +ATOM 447 CD LYS 28 28.806 43.646 20.888 1.00 0.00 C +ATOM 448 HD2 LYS 28 27.796 43.939 21.184 1.00 0.00 H +ATOM 449 HD3 LYS 28 29.505 44.362 21.322 1.00 0.00 H +ATOM 450 CE LYS 28 28.917 43.732 19.359 1.00 0.00 C +ATOM 451 HE2 LYS 28 29.049 44.784 19.086 1.00 0.00 H +ATOM 452 HE3 LYS 28 29.802 43.181 19.025 1.00 0.00 H +ATOM 453 NZ LYS 28 27.696 43.214 18.694 1.00 0.00 N +ATOM 454 HZ1 LYS 28 26.858 43.680 19.063 1.00 0.00 H +ATOM 455 HZ2 LYS 28 27.718 43.355 17.696 1.00 0.00 H +ATOM 456 HZ3 LYS 28 27.563 42.223 18.882 1.00 0.00 H +ATOM 457 C LYS 28 28.694 40.774 25.048 1.00 0.00 C +ATOM 458 O LYS 28 29.531 40.971 25.922 1.00 0.00 O +ATOM 459 N PHE 29 27.433 40.461 25.351 1.00 0.00 N +ATOM 460 H PHE 29 26.770 40.367 24.587 1.00 0.00 H +ATOM 461 CA PHE 29 26.956 40.324 26.737 1.00 0.00 C +ATOM 462 HA PHE 29 27.288 41.196 27.301 1.00 0.00 H +ATOM 463 CB PHE 29 25.418 40.308 26.753 1.00 0.00 C +ATOM 464 HB2 PHE 29 25.082 39.379 26.290 1.00 0.00 H +ATOM 465 HB3 PHE 29 25.083 40.298 27.791 1.00 0.00 H +ATOM 466 CG PHE 29 24.734 41.474 26.050 1.00 0.00 C +ATOM 467 CD1 PHE 29 23.512 41.261 25.382 1.00 0.00 C +ATOM 468 HD1 PHE 29 23.048 40.287 25.399 1.00 0.00 H +ATOM 469 CE1 PHE 29 22.881 42.313 24.694 1.00 0.00 C +ATOM 470 HE1 PHE 29 21.946 42.138 24.183 1.00 0.00 H +ATOM 471 CZ PHE 29 23.462 43.592 24.675 1.00 0.00 C +ATOM 472 HZ PHE 29 22.980 44.397 24.138 1.00 0.00 H +ATOM 473 CE2 PHE 29 24.664 43.823 25.367 1.00 0.00 C +ATOM 474 HE2 PHE 29 25.105 44.809 25.369 1.00 0.00 H +ATOM 475 CD2 PHE 29 25.293 42.771 26.056 1.00 0.00 C +ATOM 476 HD2 PHE 29 26.211 42.971 26.586 1.00 0.00 H +ATOM 477 C PHE 29 27.555 39.107 27.465 1.00 0.00 C +ATOM 478 O PHE 29 27.773 39.150 28.677 1.00 0.00 O +ATOM 479 N THR 30 27.896 38.038 26.741 1.00 0.00 N +ATOM 480 H THR 30 27.619 38.016 25.764 1.00 0.00 H +ATOM 481 CA THR 30 28.673 36.905 27.271 1.00 0.00 C +ATOM 482 HA THR 30 28.197 36.550 28.185 1.00 0.00 H +ATOM 483 CB THR 30 28.682 35.736 26.276 1.00 0.00 C +ATOM 484 HB THR 30 29.041 36.062 25.302 1.00 0.00 H +ATOM 485 CG2 THR 30 29.498 34.534 26.746 1.00 0.00 C +ATOM 486 HG21 THR 30 29.142 34.220 27.721 1.00 0.00 H +ATOM 487 HG22 THR 30 29.367 33.720 26.036 1.00 0.00 H +ATOM 488 HG23 THR 30 30.560 34.772 26.807 1.00 0.00 H +ATOM 489 OG1 THR 30 27.360 35.286 26.150 1.00 0.00 O +ATOM 490 HG1 THR 30 26.921 35.901 25.540 1.00 0.00 H +ATOM 491 C THR 30 30.096 37.329 27.627 1.00 0.00 C +ATOM 492 O THR 30 30.588 36.990 28.705 1.00 0.00 O +ATOM 493 N LYS 31 30.738 38.118 26.757 1.00 0.00 N +ATOM 494 H LYS 31 30.278 38.309 25.872 1.00 0.00 H +ATOM 495 CA LYS 31 32.079 38.688 26.976 1.00 0.00 C +ATOM 496 HA LYS 31 32.743 37.884 27.300 1.00 0.00 H +ATOM 497 CB LYS 31 32.621 39.274 25.671 1.00 0.00 C +ATOM 498 HB2 LYS 31 31.903 39.978 25.246 1.00 0.00 H +ATOM 499 HB3 LYS 31 33.541 39.820 25.894 1.00 0.00 H +ATOM 500 CG LYS 31 32.944 38.173 24.651 1.00 0.00 C +ATOM 501 HG2 LYS 31 33.671 37.499 25.091 1.00 0.00 H +ATOM 502 HG3 LYS 31 32.056 37.589 24.426 1.00 0.00 H +ATOM 503 CD LYS 31 33.506 38.765 23.356 1.00 0.00 C +ATOM 504 HD2 LYS 31 32.713 39.327 22.866 1.00 0.00 H +ATOM 505 HD3 LYS 31 34.316 39.458 23.597 1.00 0.00 H +ATOM 506 CE LYS 31 34.009 37.678 22.410 1.00 0.00 C +ATOM 507 HE2 LYS 31 33.210 36.951 22.212 1.00 0.00 H +ATOM 508 HE3 LYS 31 34.294 38.148 21.459 1.00 0.00 H +ATOM 509 NZ LYS 31 35.192 36.994 22.980 1.00 0.00 N +ATOM 510 HZ1 LYS 31 34.970 36.242 23.631 1.00 0.00 H +ATOM 511 HZ2 LYS 31 35.696 36.535 22.223 1.00 0.00 H +ATOM 512 HZ3 LYS 31 35.853 37.636 23.423 1.00 0.00 H +ATOM 513 C LYS 31 32.124 39.737 28.088 1.00 0.00 C +ATOM 514 O LYS 31 33.110 39.767 28.820 1.00 0.00 O +ATOM 515 N ALA 32 31.066 40.529 28.271 1.00 0.00 N +ATOM 516 H ALA 32 30.350 40.537 27.557 1.00 0.00 H +ATOM 517 CA ALA 32 30.916 41.417 29.424 1.00 0.00 C +ATOM 518 HA ALA 32 31.761 42.109 29.453 1.00 0.00 H +ATOM 519 CB ALA 32 29.630 42.243 29.272 1.00 0.00 C +ATOM 520 HB1 ALA 32 28.757 41.591 29.251 1.00 0.00 H +ATOM 521 HB2 ALA 32 29.539 42.927 30.118 1.00 0.00 H +ATOM 522 HB3 ALA 32 29.672 42.826 28.351 1.00 0.00 H +ATOM 523 C ALA 32 30.942 40.605 30.729 1.00 0.00 C +ATOM 524 O ALA 32 31.851 40.784 31.532 1.00 0.00 O +ATOM 525 N GLH 33 30.050 39.611 30.870 1.00 0.00 N +ATOM 526 H GLH 33 29.333 39.496 30.165 1.00 0.00 H +ATOM 527 CA GLH 33 30.047 38.725 32.041 1.00 0.00 C +ATOM 528 HA GLH 33 29.911 39.335 32.935 1.00 0.00 H +ATOM 529 CB GLH 33 28.891 37.715 31.963 1.00 0.00 C +ATOM 530 HB2 GLH 33 28.942 37.165 31.022 1.00 0.00 H +ATOM 531 HB3 GLH 33 29.025 37.002 32.778 1.00 0.00 H +ATOM 532 CG GLH 33 27.500 38.357 32.108 1.00 0.00 C +ATOM 533 HG2 GLH 33 27.504 39.042 32.957 1.00 0.00 H +ATOM 534 HG3 GLH 33 27.261 38.931 31.214 1.00 0.00 H +ATOM 535 CD GLH 33 26.406 37.318 32.358 1.00 0.00 C +ATOM 536 OE1 GLH 33 26.558 36.242 32.918 1.00 0.00 O +ATOM 537 OE2 GLH 33 25.174 37.633 31.910 1.00 0.00 O +ATOM 538 HE2 GLH 33 24.616 36.913 32.215 1.00 0.00 H +ATOM 539 C GLH 33 31.373 37.970 32.231 1.00 0.00 C +ATOM 540 O GLH 33 31.760 37.707 33.362 1.00 0.00 O +ATOM 541 N ALA 34 32.084 37.609 31.158 1.00 0.00 N +ATOM 542 H ALA 34 31.708 37.793 30.237 1.00 0.00 H +ATOM 543 CA ALA 34 33.402 36.984 31.269 1.00 0.00 C +ATOM 544 HA ALA 34 33.329 36.147 31.965 1.00 0.00 H +ATOM 545 CB ALA 34 33.799 36.424 29.900 1.00 0.00 C +ATOM 546 HB1 ALA 34 34.021 37.239 29.214 1.00 0.00 H +ATOM 547 HB2 ALA 34 34.684 35.801 30.018 1.00 0.00 H +ATOM 548 HB3 ALA 34 32.997 35.812 29.491 1.00 0.00 H +ATOM 549 C ALA 34 34.464 37.950 31.840 1.00 0.00 C +ATOM 550 O ALA 34 35.200 37.571 32.750 1.00 0.00 O +ATOM 551 N ASN 35 34.500 39.207 31.376 1.00 0.00 N +ATOM 552 H ASN 35 33.842 39.482 30.658 1.00 0.00 H +ATOM 553 CA ASN 35 35.384 40.242 31.928 1.00 0.00 C +ATOM 554 HA ASN 35 36.374 39.806 32.012 1.00 0.00 H +ATOM 555 CB ASN 35 35.506 41.432 30.957 1.00 0.00 C +ATOM 556 HB2 ASN 35 34.515 41.759 30.649 1.00 0.00 H +ATOM 557 HB3 ASN 35 35.980 42.260 31.484 1.00 0.00 H +ATOM 558 CG ASN 35 36.370 41.137 29.738 1.00 0.00 C +ATOM 559 OD1 ASN 35 37.587 41.194 29.762 1.00 0.00 O +ATOM 560 ND2 ASN 35 35.776 40.836 28.613 1.00 0.00 N +ATOM 561 HD21 ASN 35 36.375 40.628 27.819 1.00 0.00 H +ATOM 562 HD22 ASN 35 34.782 40.669 28.608 1.00 0.00 H +ATOM 563 C ASN 35 34.989 40.686 33.358 1.00 0.00 C +ATOM 564 O ASN 35 35.858 41.125 34.108 1.00 0.00 O +ATOM 565 N ASP 36 33.730 40.502 33.781 1.00 0.00 N +ATOM 566 H ASP 36 33.014 40.300 33.091 1.00 0.00 H +ATOM 567 CA ASP 36 33.323 40.680 35.189 1.00 0.00 C +ATOM 568 HA ASP 36 33.626 41.677 35.506 1.00 0.00 H +ATOM 569 CB ASP 36 31.790 40.605 35.367 1.00 0.00 C +ATOM 570 HB2 ASP 36 31.453 39.608 35.113 1.00 0.00 H +ATOM 571 HB3 ASP 36 31.583 40.721 36.432 1.00 0.00 H +ATOM 572 CG ASP 36 30.936 41.606 34.560 1.00 0.00 C +ATOM 573 OD1 ASP 36 31.454 42.673 34.150 1.00 0.00 O +ATOM 574 OD2 ASP 36 29.729 41.321 34.369 1.00 0.00 O +ATOM 575 C ASP 36 34.022 39.677 36.139 1.00 0.00 C +ATOM 576 O ASP 36 34.366 40.036 37.265 1.00 0.00 O +ATOM 577 N TYR 37 34.279 38.436 35.693 1.00 0.00 N +ATOM 578 H TYR 37 33.929 38.187 34.778 1.00 0.00 H +ATOM 579 CA TYR 37 35.150 37.478 36.405 1.00 0.00 C +ATOM 580 HA TYR 37 35.031 37.637 37.477 1.00 0.00 H +ATOM 581 CB TYR 37 34.728 36.029 36.102 1.00 0.00 C +ATOM 582 HB2 TYR 37 34.894 35.833 35.042 1.00 0.00 H +ATOM 583 HB3 TYR 37 35.387 35.360 36.657 1.00 0.00 H +ATOM 584 CG TYR 37 33.295 35.659 36.456 1.00 0.00 C +ATOM 585 CD1 TYR 37 32.330 35.550 35.437 1.00 0.00 C +ATOM 586 HD1 TYR 37 32.623 35.735 34.416 1.00 0.00 H +ATOM 587 CE1 TYR 37 30.995 35.227 35.746 1.00 0.00 C +ATOM 588 HE1 TYR 37 30.257 35.181 34.963 1.00 0.00 H +ATOM 589 CZ TYR 37 30.630 34.968 37.084 1.00 0.00 C +ATOM 590 OH TYR 37 29.350 34.633 37.395 1.00 0.00 O +ATOM 591 HH TYR 37 28.718 35.000 36.775 1.00 0.00 H +ATOM 592 CE2 TYR 37 31.601 35.043 38.103 1.00 0.00 C +ATOM 593 HE2 TYR 37 31.310 34.844 39.122 1.00 0.00 H +ATOM 594 CD2 TYR 37 32.930 35.393 37.791 1.00 0.00 C +ATOM 595 HD2 TYR 37 33.670 35.453 38.575 1.00 0.00 H +ATOM 596 C TYR 37 36.653 37.661 36.084 1.00 0.00 C +ATOM 597 O TYR 37 37.509 37.230 36.866 1.00 0.00 O +ATOM 598 N GLY 38 36.981 38.278 34.941 1.00 0.00 N +ATOM 599 H GLY 38 36.217 38.563 34.340 1.00 0.00 H +ATOM 600 CA GLY 38 38.332 38.695 34.549 1.00 0.00 C +ATOM 601 HA2 GLY 38 38.510 39.692 34.952 1.00 0.00 H +ATOM 602 HA3 GLY 38 39.067 38.019 34.987 1.00 0.00 H +ATOM 603 C GLY 38 38.572 38.753 33.033 1.00 0.00 C +ATOM 604 O GLY 38 38.680 39.832 32.466 1.00 0.00 O +ATOM 605 N VAL 39 38.769 37.587 32.407 1.00 0.00 N +ATOM 606 H VAL 39 38.528 36.772 32.947 1.00 0.00 H +ATOM 607 CA VAL 39 39.120 37.334 30.982 1.00 0.00 C +ATOM 608 HA VAL 39 39.589 36.353 31.045 1.00 0.00 H +ATOM 609 CB VAL 39 40.278 38.199 30.408 1.00 0.00 C +ATOM 610 HB VAL 39 39.887 39.155 30.060 1.00 0.00 H +ATOM 611 CG1 VAL 39 41.410 38.442 31.429 1.00 0.00 C +ATOM 612 HG11 VAL 39 41.633 37.519 31.969 1.00 0.00 H +ATOM 613 HG12 VAL 39 42.308 38.801 30.921 1.00 0.00 H +ATOM 614 HG13 VAL 39 41.103 39.214 32.136 1.00 0.00 H +ATOM 615 CG2 VAL 39 40.949 37.487 29.219 1.00 0.00 C +ATOM 616 HG21 VAL 39 41.725 38.123 28.799 1.00 0.00 H +ATOM 617 HG22 VAL 39 41.401 36.553 29.543 1.00 0.00 H +ATOM 618 HG23 VAL 39 40.242 37.276 28.424 1.00 0.00 H +ATOM 619 C VAL 39 37.923 37.009 30.055 1.00 0.00 C +ATOM 620 O VAL 39 37.209 36.068 30.396 1.00 0.00 O +ATOM 621 N ASP 40 37.721 37.611 28.865 1.00 0.00 N +ATOM 622 H ASP 40 38.260 38.435 28.629 1.00 0.00 H +ATOM 623 CA ASP 40 36.920 36.948 27.802 1.00 0.00 C +ATOM 624 HA ASP 40 36.182 36.330 28.311 1.00 0.00 H +ATOM 625 CB ASP 40 36.053 37.904 26.947 1.00 0.00 C +ATOM 626 HB2 ASP 40 35.316 37.280 26.435 1.00 0.00 H +ATOM 627 HB3 ASP 40 35.494 38.546 27.614 1.00 0.00 H +ATOM 628 CG ASP 40 36.769 38.774 25.899 1.00 0.00 C +ATOM 629 OD1 ASP 40 37.171 39.908 26.230 1.00 0.00 O +ATOM 630 OD2 ASP 40 36.863 38.346 24.717 1.00 0.00 O +ATOM 631 C ASP 40 37.719 35.999 26.893 1.00 0.00 C +ATOM 632 O ASP 40 38.616 36.413 26.153 1.00 0.00 O +ATOM 633 N GLY 41 37.291 34.734 26.866 1.00 0.00 N +ATOM 634 H GLY 41 36.626 34.447 27.571 1.00 0.00 H +ATOM 635 CA GLY 41 37.610 33.768 25.816 1.00 0.00 C +ATOM 636 HA2 GLY 41 38.623 33.946 25.456 1.00 0.00 H +ATOM 637 HA3 GLY 41 37.580 32.771 26.242 1.00 0.00 H +ATOM 638 C GLY 41 36.655 33.826 24.612 1.00 0.00 C +ATOM 639 O GLY 41 35.774 34.683 24.510 1.00 0.00 O +ATOM 640 N GLU 42 36.792 32.855 23.705 1.00 0.00 N +ATOM 641 H GLU 42 37.487 32.129 23.865 1.00 0.00 H +ATOM 642 CA GLU 42 36.009 32.689 22.461 1.00 0.00 C +ATOM 643 HA GLU 42 35.334 33.540 22.334 1.00 0.00 H +ATOM 644 CB GLU 42 36.923 32.654 21.234 1.00 0.00 C +ATOM 645 HB2 GLU 42 37.390 31.662 21.199 1.00 0.00 H +ATOM 646 HB3 GLU 42 36.257 32.698 20.374 1.00 0.00 H +ATOM 647 CG GLU 42 37.926 33.780 21.144 1.00 0.00 C +ATOM 648 HG2 GLU 42 38.767 33.538 21.797 1.00 0.00 H +ATOM 649 HG3 GLU 42 38.362 33.796 20.165 1.00 0.00 H +ATOM 650 CD GLU 42 37.448 35.144 21.511 1.00 0.00 C +ATOM 651 OE1 GLU 42 36.392 35.531 21.013 1.00 0.00 O +ATOM 652 OE2 GLU 42 38.019 35.817 22.405 1.00 0.00 O +ATOM 653 C GLU 42 35.098 31.428 22.559 1.00 0.00 C +ATOM 654 O GLU 42 35.470 30.440 23.214 1.00 0.00 O +ATOM 655 N ILE 43 33.966 31.444 21.825 1.00 0.00 N +ATOM 656 H ILE 43 33.809 32.250 21.208 1.00 0.00 H +ATOM 657 CA ILE 43 32.887 30.421 21.861 1.00 0.00 C +ATOM 658 HA ILE 43 33.331 29.490 22.218 1.00 0.00 H +ATOM 659 CB ILE 43 31.749 30.833 22.843 1.00 0.00 C +ATOM 660 HB ILE 43 30.876 30.251 22.570 1.00 0.00 H +ATOM 661 CG2 ILE 43 32.120 30.445 24.279 1.00 0.00 C +ATOM 662 HG21 ILE 43 32.995 30.995 24.605 1.00 0.00 H +ATOM 663 HG22 ILE 43 31.282 30.667 24.932 1.00 0.00 H +ATOM 664 HG23 ILE 43 32.325 29.379 24.324 1.00 0.00 H +ATOM 665 CG1 ILE 43 31.340 32.325 22.832 1.00 0.00 C +ATOM 666 HG12 ILE 43 30.451 32.421 23.459 1.00 0.00 H +ATOM 667 HG13 ILE 43 32.122 32.931 23.275 1.00 0.00 H +ATOM 668 CD1 ILE 43 30.995 32.906 21.457 1.00 0.00 C +ATOM 669 HD11 ILE 43 30.366 32.224 20.891 1.00 0.00 H +ATOM 670 HD12 ILE 43 30.466 33.847 21.588 1.00 0.00 H +ATOM 671 HD13 ILE 43 31.907 33.103 20.890 1.00 0.00 H +ATOM 672 C ILE 43 32.351 30.121 20.452 1.00 0.00 C +ATOM 673 O ILE 43 32.559 30.895 19.514 1.00 0.00 O +ATOM 674 N THR 44 31.619 29.018 20.340 1.00 0.00 N +ATOM 675 H THR 44 31.486 28.447 21.169 1.00 0.00 H +ATOM 676 CA THR 44 30.903 28.600 19.128 1.00 0.00 C +ATOM 677 HA THR 44 31.230 29.213 18.290 1.00 0.00 H +ATOM 678 CB THR 44 31.269 27.144 18.781 1.00 0.00 C +ATOM 679 HB THR 44 31.001 26.477 19.600 1.00 0.00 H +ATOM 680 CG2 THR 44 30.624 26.613 17.495 1.00 0.00 C +ATOM 681 HG21 THR 44 30.802 27.305 16.665 1.00 0.00 H +ATOM 682 HG22 THR 44 31.041 25.628 17.235 1.00 0.00 H +ATOM 683 HG23 THR 44 29.544 26.485 17.639 1.00 0.00 H +ATOM 684 OG1 THR 44 32.661 27.056 18.558 1.00 0.00 O +ATOM 685 HG1 THR 44 32.846 26.251 18.066 1.00 0.00 H +ATOM 686 C THR 44 29.392 28.779 19.281 1.00 0.00 C +ATOM 687 O THR 44 28.876 28.725 20.395 1.00 0.00 O +ATOM 688 N GLN 45 28.679 29.026 18.178 1.00 0.00 N +ATOM 689 H GLN 45 29.149 29.020 17.288 1.00 0.00 H +ATOM 690 CA GLN 45 27.222 29.231 18.139 1.00 0.00 C +ATOM 691 HA GLN 45 26.819 29.205 19.153 1.00 0.00 H +ATOM 692 CB GLN 45 26.897 30.607 17.518 1.00 0.00 C +ATOM 693 HB2 GLN 45 27.284 30.625 16.500 1.00 0.00 H +ATOM 694 HB3 GLN 45 25.809 30.696 17.459 1.00 0.00 H +ATOM 695 CG GLN 45 27.454 31.826 18.281 1.00 0.00 C +ATOM 696 HG2 GLN 45 27.104 31.768 19.310 1.00 0.00 H +ATOM 697 HG3 GLN 45 28.542 31.780 18.287 1.00 0.00 H +ATOM 698 CD GLN 45 27.016 33.162 17.659 1.00 0.00 C +ATOM 699 OE1 GLN 45 26.064 33.244 16.898 1.00 0.00 O +ATOM 700 NE2 GLN 45 27.679 34.270 17.903 1.00 0.00 N +ATOM 701 HE21 GLN 45 27.355 35.101 17.453 1.00 0.00 H +ATOM 702 HE22 GLN 45 28.552 34.317 18.441 1.00 0.00 H +ATOM 703 C GLN 45 26.480 28.159 17.312 1.00 0.00 C +ATOM 704 O GLN 45 27.046 27.601 16.370 1.00 0.00 O +ATOM 705 N ASP 46 25.191 27.966 17.604 1.00 0.00 N +ATOM 706 H ASP 46 24.838 28.365 18.468 1.00 0.00 H +ATOM 707 CA ASP 46 24.203 27.294 16.751 1.00 0.00 C +ATOM 708 HA ASP 46 24.528 27.356 15.711 1.00 0.00 H +ATOM 709 CB ASP 46 24.079 25.812 17.147 1.00 0.00 C +ATOM 710 HB2 ASP 46 24.979 25.272 16.851 1.00 0.00 H +ATOM 711 HB3 ASP 46 23.981 25.747 18.230 1.00 0.00 H +ATOM 712 CG ASP 46 22.852 25.158 16.507 1.00 0.00 C +ATOM 713 OD1 ASP 46 22.104 24.474 17.241 1.00 0.00 O +ATOM 714 OD2 ASP 46 22.584 25.407 15.313 1.00 0.00 O +ATOM 715 C ASP 46 22.831 27.991 16.868 1.00 0.00 C +ATOM 716 O ASP 46 22.288 28.138 17.964 1.00 0.00 O +ATOM 717 N ASP 47 22.230 28.373 15.739 1.00 0.00 N +ATOM 718 H ASP 47 22.690 28.167 14.865 1.00 0.00 H +ATOM 719 CA ASP 47 20.867 28.919 15.690 1.00 0.00 C +ATOM 720 HA ASP 47 20.729 29.593 16.537 1.00 0.00 H +ATOM 721 CB ASP 47 20.693 29.766 14.416 1.00 0.00 C +ATOM 722 HB2 ASP 47 21.415 30.585 14.422 1.00 0.00 H +ATOM 723 HB3 ASP 47 20.882 29.148 13.536 1.00 0.00 H +ATOM 724 CG ASP 47 19.278 30.347 14.340 1.00 0.00 C +ATOM 725 OD1 ASP 47 18.430 29.775 13.625 1.00 0.00 O +ATOM 726 OD2 ASP 47 18.941 31.266 15.120 1.00 0.00 O +ATOM 727 C ASP 47 19.773 27.830 15.792 1.00 0.00 C +ATOM 728 O ASP 47 18.707 28.086 16.356 1.00 0.00 O +ATOM 729 N ALA 48 20.006 26.600 15.319 1.00 0.00 N +ATOM 730 H ALA 48 20.951 26.350 15.024 1.00 0.00 H +ATOM 731 CA ALA 48 18.970 25.560 15.236 1.00 0.00 C +ATOM 732 HA ALA 48 18.105 25.984 14.723 1.00 0.00 H +ATOM 733 CB ALA 48 19.510 24.405 14.386 1.00 0.00 C +ATOM 734 HB1 ALA 48 20.362 23.940 14.885 1.00 0.00 H +ATOM 735 HB2 ALA 48 18.729 23.659 14.239 1.00 0.00 H +ATOM 736 HB3 ALA 48 19.832 24.783 13.415 1.00 0.00 H +ATOM 737 C ALA 48 18.489 25.071 16.618 1.00 0.00 C +ATOM 738 O ALA 48 17.304 24.774 16.796 1.00 0.00 O +ATOM 739 N THR 49 19.392 25.037 17.602 1.00 0.00 N +ATOM 740 H THR 49 20.372 25.112 17.325 1.00 0.00 H +ATOM 741 CA THR 49 19.113 24.869 19.043 1.00 0.00 C +ATOM 742 HA THR 49 18.084 24.531 19.159 1.00 0.00 H +ATOM 743 CB THR 49 20.020 23.800 19.672 1.00 0.00 C +ATOM 744 HB THR 49 19.698 23.651 20.702 1.00 0.00 H +ATOM 745 CG2 THR 49 19.958 22.443 18.975 1.00 0.00 C +ATOM 746 HG21 THR 49 20.321 22.522 17.950 1.00 0.00 H +ATOM 747 HG22 THR 49 20.590 21.745 19.521 1.00 0.00 H +ATOM 748 HG23 THR 49 18.931 22.081 18.973 1.00 0.00 H +ATOM 749 OG1 THR 49 21.361 24.217 19.698 1.00 0.00 O +ATOM 750 HG1 THR 49 21.679 24.247 18.761 1.00 0.00 H +ATOM 751 C THR 49 19.231 26.177 19.841 1.00 0.00 C +ATOM 752 O THR 49 19.101 26.167 21.068 1.00 0.00 O +ATOM 753 N LYS 50 19.468 27.312 19.167 1.00 0.00 N +ATOM 754 H LYS 50 19.560 27.226 18.161 1.00 0.00 H +ATOM 755 CA LYS 50 19.589 28.671 19.731 1.00 0.00 C +ATOM 756 HA LYS 50 20.008 29.273 18.928 1.00 0.00 H +ATOM 757 CB LYS 50 18.185 29.226 20.094 1.00 0.00 C +ATOM 758 HB2 LYS 50 17.768 28.587 20.874 1.00 0.00 H +ATOM 759 HB3 LYS 50 18.294 30.221 20.527 1.00 0.00 H +ATOM 760 CG LYS 50 17.144 29.315 18.956 1.00 0.00 C +ATOM 761 HG2 LYS 50 17.135 28.389 18.385 1.00 0.00 H +ATOM 762 HG3 LYS 50 16.161 29.418 19.417 1.00 0.00 H +ATOM 763 CD LYS 50 17.338 30.517 18.014 1.00 0.00 C +ATOM 764 HD2 LYS 50 17.289 31.432 18.604 1.00 0.00 H +ATOM 765 HD3 LYS 50 18.319 30.466 17.544 1.00 0.00 H +ATOM 766 CE LYS 50 16.255 30.586 16.925 1.00 0.00 C +ATOM 767 HE2 LYS 50 15.311 30.225 17.334 1.00 0.00 H +ATOM 768 HE3 LYS 50 16.117 31.628 16.628 1.00 0.00 H +ATOM 769 NZ LYS 50 16.628 29.801 15.728 1.00 0.00 N +ATOM 770 HZ1 LYS 50 17.134 28.955 15.975 1.00 0.00 H +ATOM 771 HZ2 LYS 50 15.839 29.559 15.145 1.00 0.00 H +ATOM 772 HZ3 LYS 50 17.313 30.309 15.154 1.00 0.00 H +ATOM 773 C LYS 50 20.608 28.778 20.892 1.00 0.00 C +ATOM 774 O LYS 50 20.304 29.382 21.927 1.00 0.00 O +ATOM 775 N THR 51 21.791 28.170 20.745 1.00 0.00 N +ATOM 776 H THR 51 22.017 27.827 19.813 1.00 0.00 H +ATOM 777 CA THR 51 22.737 27.843 21.835 1.00 0.00 C +ATOM 778 HA THR 51 22.433 28.389 22.721 1.00 0.00 H +ATOM 779 CB THR 51 22.629 26.341 22.176 1.00 0.00 C +ATOM 780 HB THR 51 22.792 25.755 21.272 1.00 0.00 H +ATOM 781 CG2 THR 51 23.614 25.869 23.247 1.00 0.00 C +ATOM 782 HG21 THR 51 23.549 26.508 24.126 1.00 0.00 H +ATOM 783 HG22 THR 51 23.377 24.843 23.525 1.00 0.00 H +ATOM 784 HG23 THR 51 24.627 25.883 22.852 1.00 0.00 H +ATOM 785 OG1 THR 51 21.358 26.039 22.712 1.00 0.00 O +ATOM 786 HG1 THR 51 20.709 26.084 21.991 1.00 0.00 H +ATOM 787 C THR 51 24.207 28.217 21.545 1.00 0.00 C +ATOM 788 O THR 51 24.716 27.973 20.456 1.00 0.00 O +ATOM 789 N PHE 52 24.918 28.749 22.550 1.00 0.00 N +ATOM 790 H PHE 52 24.402 29.020 23.376 1.00 0.00 H +ATOM 791 CA PHE 52 26.389 28.875 22.610 1.00 0.00 C +ATOM 792 HA PHE 52 26.783 28.971 21.598 1.00 0.00 H +ATOM 793 CB PHE 52 26.774 30.130 23.412 1.00 0.00 C +ATOM 794 HB2 PHE 52 26.267 30.101 24.374 1.00 0.00 H +ATOM 795 HB3 PHE 52 27.845 30.085 23.622 1.00 0.00 H +ATOM 796 CG PHE 52 26.494 31.471 22.766 1.00 0.00 C +ATOM 797 CD1 PHE 52 25.266 32.130 22.966 1.00 0.00 C +ATOM 798 HD1 PHE 52 24.487 31.661 23.545 1.00 0.00 H +ATOM 799 CE1 PHE 52 25.047 33.404 22.412 1.00 0.00 C +ATOM 800 HE1 PHE 52 24.099 33.900 22.556 1.00 0.00 H +ATOM 801 CZ PHE 52 26.060 34.026 21.662 1.00 0.00 C +ATOM 802 HZ PHE 52 25.893 34.995 21.218 1.00 0.00 H +ATOM 803 CE2 PHE 52 27.293 33.379 21.473 1.00 0.00 C +ATOM 804 HE2 PHE 52 28.070 33.856 20.889 1.00 0.00 H +ATOM 805 CD2 PHE 52 27.503 32.100 22.017 1.00 0.00 C +ATOM 806 HD2 PHE 52 28.441 31.592 21.854 1.00 0.00 H +ATOM 807 C PHE 52 27.066 27.661 23.288 1.00 0.00 C +ATOM 808 O PHE 52 26.544 27.156 24.288 1.00 0.00 O +ATOM 809 N THR 53 28.266 27.263 22.839 1.00 0.00 N +ATOM 810 H THR 53 28.641 27.723 22.012 1.00 0.00 H +ATOM 811 CA THR 53 29.074 26.151 23.403 1.00 0.00 C +ATOM 812 HA THR 53 28.798 26.016 24.449 1.00 0.00 H +ATOM 813 CB THR 53 28.800 24.819 22.672 1.00 0.00 C +ATOM 814 HB THR 53 29.387 24.035 23.153 1.00 0.00 H +ATOM 815 CG2 THR 53 27.341 24.373 22.695 1.00 0.00 C +ATOM 816 HG21 THR 53 26.734 25.036 22.079 1.00 0.00 H +ATOM 817 HG22 THR 53 27.264 23.356 22.311 1.00 0.00 H +ATOM 818 HG23 THR 53 26.972 24.389 23.719 1.00 0.00 H +ATOM 819 OG1 THR 53 29.192 24.898 21.323 1.00 0.00 O +ATOM 820 HG1 THR 53 28.756 24.184 20.851 1.00 0.00 H +ATOM 821 C THR 53 30.594 26.406 23.377 1.00 0.00 C +ATOM 822 O THR 53 31.083 27.326 22.718 1.00 0.00 O +ATOM 823 N ALA 54 31.348 25.564 24.100 1.00 0.00 N +ATOM 824 H ALA 54 30.876 24.846 24.626 1.00 0.00 H +ATOM 825 CA ALA 54 32.812 25.456 24.054 1.00 0.00 C +ATOM 826 HA ALA 54 33.210 26.268 23.442 1.00 0.00 H +ATOM 827 CB ALA 54 33.366 25.629 25.475 1.00 0.00 C +ATOM 828 HB1 ALA 54 33.015 24.817 26.113 1.00 0.00 H +ATOM 829 HB2 ALA 54 34.457 25.616 25.456 1.00 0.00 H +ATOM 830 HB3 ALA 54 33.038 26.583 25.891 1.00 0.00 H +ATOM 831 C ALA 54 33.278 24.123 23.415 1.00 0.00 C +ATOM 832 O ALA 54 32.505 23.167 23.298 1.00 0.00 O +ATOM 833 N GLH 55 34.548 24.067 22.999 1.00 0.00 N +ATOM 834 H GLH 55 35.146 24.849 23.215 1.00 0.00 H +ATOM 835 CA GLH 55 35.168 22.922 22.308 1.00 0.00 C +ATOM 836 HA GLH 55 34.398 22.426 21.716 1.00 0.00 H +ATOM 837 CB GLH 55 36.234 23.451 21.327 1.00 0.00 C +ATOM 838 HB2 GLH 55 36.972 24.031 21.884 1.00 0.00 H +ATOM 839 HB3 GLH 55 36.743 22.608 20.858 1.00 0.00 H +ATOM 840 CG GLH 55 35.617 24.327 20.216 1.00 0.00 C +ATOM 841 HG2 GLH 55 34.958 23.714 19.601 1.00 0.00 H +ATOM 842 HG3 GLH 55 35.020 25.129 20.650 1.00 0.00 H +ATOM 843 CD GLH 55 36.655 24.987 19.312 1.00 0.00 C +ATOM 844 OE1 GLH 55 37.842 25.121 19.573 1.00 0.00 O +ATOM 845 OE2 GLH 55 36.155 25.451 18.149 1.00 0.00 O +ATOM 846 HE2 GLH 55 36.883 25.858 17.675 1.00 0.00 H +ATOM 847 C GLH 55 35.736 21.856 23.279 1.00 0.00 C +ATOM 848 O GLH 55 36.043 22.164 24.428 1.00 0.00 O +ATOM 849 N GLU 56 35.854 20.603 22.810 1.00 0.00 N +ATOM 850 H GLU 56 35.627 20.451 21.842 1.00 0.00 H +ATOM 851 CA GLU 56 36.225 19.391 23.580 1.00 0.00 C +ATOM 852 HA GLU 56 35.760 19.455 24.564 1.00 0.00 H +ATOM 853 CB GLU 56 35.617 18.165 22.855 1.00 0.00 C +ATOM 854 HB2 GLU 56 34.541 18.196 23.027 1.00 0.00 H +ATOM 855 HB3 GLU 56 35.768 18.297 21.782 1.00 0.00 H +ATOM 856 CG GLU 56 36.111 16.739 23.193 1.00 0.00 C +ATOM 857 HG2 GLU 56 35.454 16.031 22.680 1.00 0.00 H +ATOM 858 HG3 GLU 56 37.100 16.595 22.754 1.00 0.00 H +ATOM 859 CD GLU 56 36.165 16.375 24.688 1.00 0.00 C +ATOM 860 OE1 GLU 56 37.290 16.354 25.251 1.00 0.00 O +ATOM 861 OE2 GLU 56 35.109 16.022 25.266 1.00 0.00 O +ATOM 862 C GLU 56 37.723 19.244 23.888 1.00 0.00 C +ATOM 863 O GLU 56 38.090 19.361 25.078 1.00 0.00 O +ATOM 864 OXT GLU 56 38.506 18.730 23.060 1.00 0.00 O +HETATM 865 ZN ZN1 57 26.762 32.444 29.336 1.00 0.00 Zn +HETATM 866 N AN1 58 28.364 33.308 30.222 1.00 0.00 N +HETATM 867 C AN1 58 30.678 34.028 31.184 1.00 0.00 C +HETATM 868 C1 AN1 58 29.379 33.629 30.674 1.00 0.00 C +HETATM 869 H AN1 58 30.582 34.423 32.200 1.00 0.00 H +HETATM 870 H1 AN1 58 31.113 34.795 30.535 1.00 0.00 H +HETATM 871 H2 AN1 58 31.336 33.149 31.202 1.00 0.00 H +HETATM 872 N1 AZI 59 30.830 28.620 29.341 1.00 0.00 N +HETATM 873 N2 AZI 59 30.309 29.481 30.054 1.00 0.00 N +HETATM 874 N3 AZI 59 29.759 30.371 30.755 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 73 72 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 865 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 121 122 126 +CONECT 121 120 +CONECT 122 125 120 123 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 127 129 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 145 +CONECT 135 134 +CONECT 136 137 134 139 138 +CONECT 137 136 +CONECT 138 136 +CONECT 139 142 136 140 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 144 139 +CONECT 143 142 +CONECT 144 142 +CONECT 145 134 147 146 +CONECT 146 145 +CONECT 147 148 149 145 +CONECT 148 147 +CONECT 149 147 150 152 151 +CONECT 150 149 +CONECT 151 149 +CONECT 152 153 149 154 +CONECT 153 152 +CONECT 154 152 156 155 +CONECT 155 154 +CONECT 156 158 157 154 174 +CONECT 157 156 +CONECT 158 161 159 160 156 +CONECT 159 158 +CONECT 160 158 +CONECT 161 164 163 162 158 +CONECT 162 161 +CONECT 163 161 +CONECT 164 167 165 166 161 +CONECT 165 164 +CONECT 166 164 +CONECT 167 170 169 168 164 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 170 +CONECT 174 156 175 176 +CONECT 175 174 +CONECT 176 174 177 178 +CONECT 177 176 +CONECT 178 176 179 198 180 +CONECT 179 178 +CONECT 180 178 183 181 182 +CONECT 181 180 +CONECT 182 180 +CONECT 183 185 184 180 186 +CONECT 184 183 +CONECT 185 183 +CONECT 186 183 189 187 188 +CONECT 187 186 +CONECT 188 186 +CONECT 189 190 186 191 +CONECT 190 189 +CONECT 191 189 195 192 +CONECT 192 191 193 194 +CONECT 193 192 +CONECT 194 192 +CONECT 195 196 191 197 +CONECT 196 195 +CONECT 197 195 +CONECT 198 178 200 199 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 219 200 204 203 +CONECT 203 202 +CONECT 204 207 202 205 206 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 217 204 +CONECT 208 209 210 207 +CONECT 209 208 +CONECT 210 211 208 212 +CONECT 211 210 +CONECT 212 210 213 215 +CONECT 213 214 212 +CONECT 214 213 +CONECT 215 212 216 217 +CONECT 216 215 +CONECT 217 207 215 218 +CONECT 218 217 +CONECT 219 220 221 202 +CONECT 220 219 +CONECT 221 223 219 222 +CONECT 222 221 +CONECT 223 224 241 225 221 +CONECT 224 223 +CONECT 225 228 223 226 227 +CONECT 226 225 +CONECT 227 225 +CONECT 228 230 229 231 225 +CONECT 229 228 +CONECT 230 228 +CONECT 231 232 228 233 234 +CONECT 232 231 +CONECT 233 231 +CONECT 234 236 231 237 235 +CONECT 235 234 +CONECT 236 234 +CONECT 237 240 234 239 238 +CONECT 238 237 +CONECT 239 237 +CONECT 240 237 +CONECT 241 242 223 243 +CONECT 242 241 +CONECT 243 241 245 244 +CONECT 244 243 +CONECT 245 248 243 246 247 +CONECT 246 245 +CONECT 247 245 +CONECT 248 249 250 245 +CONECT 249 248 +CONECT 250 252 248 251 +CONECT 251 250 +CONECT 252 254 253 264 250 +CONECT 253 252 +CONECT 254 260 255 256 252 +CONECT 255 254 +CONECT 256 258 254 257 259 +CONECT 257 256 +CONECT 258 256 +CONECT 259 256 +CONECT 260 262 261 263 254 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 252 265 +CONECT 265 264 +CONECT 266 276 267 264 +CONECT 267 268 266 277 270 +CONECT 268 269 283 267 +CONECT 269 268 +CONECT 270 267 271 278 279 +CONECT 271 272 273 270 +CONECT 272 275 281 271 +CONECT 273 274 271 280 +CONECT 274 275 282 273 +CONECT 275 865 272 274 +CONECT 276 266 +CONECT 277 267 +CONECT 278 270 +CONECT 279 270 +CONECT 280 273 +CONECT 281 272 +CONECT 282 274 +CONECT 283 285 268 284 +CONECT 284 283 +CONECT 285 286 287 295 283 +CONECT 286 285 +CONECT 287 288 289 285 293 +CONECT 288 287 +CONECT 289 292 291 287 290 +CONECT 290 289 +CONECT 291 289 +CONECT 292 289 +CONECT 293 287 294 +CONECT 294 293 +CONECT 295 297 285 296 +CONECT 296 295 +CONECT 297 307 298 295 +CONECT 298 299 301 297 308 +CONECT 299 300 314 298 +CONECT 300 299 +CONECT 301 309 310 298 302 +CONECT 302 301 303 304 +CONECT 303 312 302 306 +CONECT 304 302 311 305 +CONECT 305 304 306 313 +CONECT 306 303 865 305 +CONECT 307 297 +CONECT 308 298 +CONECT 309 301 +CONECT 310 301 +CONECT 311 304 +CONECT 312 303 +CONECT 313 305 +CONECT 314 316 299 315 +CONECT 315 314 +CONECT 316 327 317 314 318 +CONECT 317 316 +CONECT 318 316 321 320 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 323 324 318 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 325 321 326 +CONECT 325 324 +CONECT 326 324 +CONECT 327 329 328 316 +CONECT 328 327 +CONECT 329 331 330 327 +CONECT 330 329 +CONECT 331 337 333 332 329 +CONECT 332 331 +CONECT 333 335 334 331 336 +CONECT 334 333 +CONECT 335 333 +CONECT 336 333 +CONECT 337 339 338 331 +CONECT 338 337 +CONECT 339 341 340 337 +CONECT 340 339 +CONECT 341 353 343 342 339 +CONECT 342 341 +CONECT 343 344 349 341 345 +CONECT 344 343 +CONECT 345 343 347 348 346 +CONECT 346 345 +CONECT 347 345 +CONECT 348 345 +CONECT 349 350 351 343 352 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 341 +CONECT 354 353 +CONECT 355 357 353 356 +CONECT 356 355 +CONECT 357 359 358 365 355 +CONECT 358 357 +CONECT 359 362 360 361 357 +CONECT 360 359 +CONECT 361 359 +CONECT 362 364 363 359 +CONECT 363 362 +CONECT 364 362 +CONECT 365 357 367 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 385 370 +CONECT 370 369 +CONECT 371 372 374 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 375 371 383 +CONECT 375 376 377 374 +CONECT 376 375 +CONECT 377 378 375 379 +CONECT 378 377 +CONECT 379 377 380 381 +CONECT 380 379 +CONECT 381 379 383 382 +CONECT 382 381 +CONECT 383 374 381 384 +CONECT 384 383 +CONECT 385 387 369 386 +CONECT 386 385 +CONECT 387 388 389 385 +CONECT 388 387 +CONECT 389 391 387 390 395 +CONECT 390 389 +CONECT 391 394 392 393 389 +CONECT 392 391 +CONECT 393 391 +CONECT 394 391 +CONECT 395 389 396 397 +CONECT 396 395 +CONECT 397 395 398 399 +CONECT 398 397 +CONECT 399 397 400 401 410 +CONECT 400 399 +CONECT 401 404 402 399 403 +CONECT 402 401 +CONECT 403 401 +CONECT 404 405 406 407 401 +CONECT 405 404 +CONECT 406 404 +CONECT 407 404 409 408 +CONECT 408 407 +CONECT 409 407 +CONECT 410 399 412 411 +CONECT 411 410 +CONECT 412 413 410 414 +CONECT 413 412 +CONECT 414 412 416 420 415 +CONECT 415 414 +CONECT 416 417 419 414 418 +CONECT 417 416 +CONECT 418 416 +CONECT 419 416 +CONECT 420 422 414 421 +CONECT 421 420 +CONECT 422 423 424 420 +CONECT 423 422 +CONECT 424 426 422 425 435 +CONECT 425 424 +CONECT 426 428 427 429 424 +CONECT 427 426 +CONECT 428 426 +CONECT 429 432 430 426 431 +CONECT 430 429 +CONECT 431 429 +CONECT 432 433 434 429 +CONECT 433 432 +CONECT 434 432 +CONECT 435 424 437 436 +CONECT 436 435 +CONECT 437 438 435 439 +CONECT 438 437 +CONECT 439 437 441 440 457 +CONECT 440 439 +CONECT 441 444 442 443 439 +CONECT 442 441 +CONECT 443 441 +CONECT 444 446 447 445 441 +CONECT 445 444 +CONECT 446 444 +CONECT 447 450 448 449 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 452 451 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 455 456 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 453 +CONECT 457 439 459 458 +CONECT 458 457 +CONECT 459 460 457 461 +CONECT 460 459 +CONECT 461 459 463 462 477 +CONECT 462 461 +CONECT 463 466 464 461 465 +CONECT 464 463 +CONECT 465 463 +CONECT 466 467 475 463 +CONECT 467 469 468 466 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 472 469 473 +CONECT 472 471 +CONECT 473 471 474 475 +CONECT 474 473 +CONECT 475 473 466 476 +CONECT 476 475 +CONECT 477 461 479 478 +CONECT 478 477 +CONECT 479 480 481 477 +CONECT 480 479 +CONECT 481 483 479 491 482 +CONECT 482 481 +CONECT 483 484 489 485 481 +CONECT 484 483 +CONECT 485 487 483 488 486 +CONECT 486 485 +CONECT 487 485 +CONECT 488 485 +CONECT 489 490 483 +CONECT 490 489 +CONECT 491 493 481 492 +CONECT 492 491 +CONECT 493 494 495 491 +CONECT 494 493 +CONECT 495 497 493 496 513 +CONECT 496 495 +CONECT 497 500 498 499 495 +CONECT 498 497 +CONECT 499 497 +CONECT 500 503 502 501 497 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 504 505 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 508 507 509 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 506 512 510 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 495 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 518 523 +CONECT 518 517 +CONECT 519 522 520 517 521 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 +CONECT 523 517 525 524 +CONECT 524 523 +CONECT 525 526 523 527 +CONECT 526 525 +CONECT 527 525 529 539 528 +CONECT 528 527 +CONECT 529 530 527 532 531 +CONECT 530 529 +CONECT 531 529 +CONECT 532 534 529 535 533 +CONECT 533 532 +CONECT 534 532 +CONECT 535 537 532 536 +CONECT 536 535 +CONECT 537 538 535 +CONECT 538 537 +CONECT 539 541 527 540 +CONECT 540 539 +CONECT 541 542 543 539 +CONECT 542 541 +CONECT 543 545 541 549 544 +CONECT 544 543 +CONECT 545 546 548 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 545 +CONECT 549 543 551 550 +CONECT 550 549 +CONECT 551 552 549 553 +CONECT 552 551 +CONECT 553 555 551 554 563 +CONECT 554 553 +CONECT 555 558 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 560 559 555 +CONECT 559 558 +CONECT 560 561 562 558 +CONECT 561 560 +CONECT 562 560 +CONECT 563 553 565 564 +CONECT 564 563 +CONECT 565 566 563 567 +CONECT 566 565 +CONECT 567 565 569 568 575 +CONECT 568 567 +CONECT 569 572 570 567 571 +CONECT 570 569 +CONECT 571 569 +CONECT 572 573 574 569 +CONECT 573 572 +CONECT 574 572 +CONECT 575 567 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 596 581 580 +CONECT 580 579 +CONECT 581 582 579 584 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 585 581 594 +CONECT 585 586 587 584 +CONECT 586 585 +CONECT 587 588 585 589 +CONECT 588 587 +CONECT 589 587 590 592 +CONECT 590 591 589 +CONECT 591 590 +CONECT 592 589 594 593 +CONECT 593 592 +CONECT 594 584 592 595 +CONECT 595 594 +CONECT 596 598 579 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 598 601 602 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 619 609 608 605 +CONECT 608 607 +CONECT 609 615 610 607 611 +CONECT 610 609 +CONECT 611 609 613 612 614 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 +CONECT 615 618 616 617 609 +CONECT 616 615 +CONECT 617 615 +CONECT 618 615 +CONECT 619 621 620 607 +CONECT 620 619 +CONECT 621 623 622 619 +CONECT 622 621 +CONECT 623 631 625 624 621 +CONECT 624 623 +CONECT 625 628 626 627 623 +CONECT 626 625 +CONECT 627 625 +CONECT 628 630 629 625 +CONECT 629 628 +CONECT 630 628 +CONECT 631 632 633 623 +CONECT 632 631 +CONECT 633 635 631 634 +CONECT 634 633 +CONECT 635 638 636 637 633 +CONECT 636 635 +CONECT 637 635 +CONECT 638 640 639 635 +CONECT 639 638 +CONECT 640 642 641 638 +CONECT 641 640 +CONECT 642 644 643 653 640 +CONECT 643 642 +CONECT 644 646 647 645 642 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 644 650 648 +CONECT 648 647 +CONECT 649 647 +CONECT 650 651 647 652 +CONECT 651 650 +CONECT 652 650 +CONECT 653 655 642 654 +CONECT 654 653 +CONECT 655 656 657 653 +CONECT 656 655 +CONECT 657 672 655 658 659 +CONECT 658 657 +CONECT 659 657 660 665 661 +CONECT 660 659 +CONECT 661 659 664 662 663 +CONECT 662 661 +CONECT 663 661 +CONECT 664 661 +CONECT 665 668 659 667 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 671 669 670 665 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 +CONECT 672 673 674 657 +CONECT 673 672 +CONECT 674 676 672 675 +CONECT 675 674 +CONECT 676 677 678 686 674 +CONECT 677 676 +CONECT 678 680 684 676 679 +CONECT 679 678 +CONECT 680 681 682 683 678 +CONECT 681 680 +CONECT 682 680 +CONECT 683 680 +CONECT 684 685 678 +CONECT 685 684 +CONECT 686 688 676 687 +CONECT 687 686 +CONECT 688 689 690 686 +CONECT 689 688 +CONECT 690 703 692 688 691 +CONECT 691 690 +CONECT 692 693 694 690 695 +CONECT 693 692 +CONECT 694 692 +CONECT 695 692 698 697 696 +CONECT 696 695 +CONECT 697 695 +CONECT 698 699 700 695 +CONECT 699 698 +CONECT 700 701 698 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 704 705 690 +CONECT 704 703 +CONECT 705 707 703 706 +CONECT 706 705 +CONECT 707 708 715 709 705 +CONECT 708 707 +CONECT 709 712 707 710 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 709 713 +CONECT 713 712 +CONECT 714 712 +CONECT 715 717 707 716 +CONECT 716 715 +CONECT 717 718 719 715 +CONECT 718 717 +CONECT 719 721 717 727 720 +CONECT 720 719 +CONECT 721 723 724 722 719 +CONECT 722 721 +CONECT 723 721 +CONECT 724 725 721 726 +CONECT 725 724 +CONECT 726 724 +CONECT 727 729 719 728 +CONECT 728 727 +CONECT 729 730 731 727 +CONECT 730 729 +CONECT 731 733 732 729 737 +CONECT 732 731 +CONECT 733 736 735 734 731 +CONECT 734 733 +CONECT 735 733 +CONECT 736 733 +CONECT 737 731 738 739 +CONECT 738 737 +CONECT 739 737 740 741 +CONECT 740 739 +CONECT 741 739 742 743 751 +CONECT 742 741 +CONECT 743 745 741 749 744 +CONECT 744 743 +CONECT 745 746 748 747 743 +CONECT 746 745 +CONECT 747 745 +CONECT 748 745 +CONECT 749 750 743 +CONECT 750 749 +CONECT 751 741 753 752 +CONECT 752 751 +CONECT 753 754 755 751 +CONECT 754 753 +CONECT 755 756 753 757 773 +CONECT 756 755 +CONECT 757 760 755 759 758 +CONECT 758 757 +CONECT 759 757 +CONECT 760 763 761 762 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 766 765 764 760 +CONECT 764 763 +CONECT 765 763 +CONECT 766 769 768 767 763 +CONECT 767 766 +CONECT 768 766 +CONECT 769 771 772 770 766 +CONECT 770 769 +CONECT 771 769 +CONECT 772 769 +CONECT 773 755 775 774 +CONECT 774 773 +CONECT 775 776 773 777 +CONECT 776 775 +CONECT 777 775 787 779 778 +CONECT 778 777 +CONECT 779 780 777 785 781 +CONECT 780 779 +CONECT 781 779 784 783 782 +CONECT 782 781 +CONECT 783 781 +CONECT 784 781 +CONECT 785 786 779 +CONECT 786 785 +CONECT 787 788 777 789 +CONECT 788 787 +CONECT 789 787 791 790 +CONECT 790 789 +CONECT 791 792 789 807 793 +CONECT 792 791 +CONECT 793 791 796 795 794 +CONECT 794 793 +CONECT 795 793 +CONECT 796 805 797 793 +CONECT 797 799 796 798 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 804 801 805 +CONECT 804 803 +CONECT 805 803 806 796 +CONECT 806 805 +CONECT 807 791 809 808 +CONECT 808 807 +CONECT 809 810 807 811 +CONECT 810 809 +CONECT 811 813 809 821 812 +CONECT 812 811 +CONECT 813 819 815 814 811 +CONECT 814 813 +CONECT 815 816 817 813 818 +CONECT 816 815 +CONECT 817 815 +CONECT 818 815 +CONECT 819 820 813 +CONECT 820 819 +CONECT 821 822 811 823 +CONECT 822 821 +CONECT 823 821 825 824 +CONECT 824 823 +CONECT 825 831 826 823 827 +CONECT 826 825 +CONECT 827 825 829 830 828 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 833 832 825 +CONECT 832 831 +CONECT 833 835 834 831 +CONECT 834 833 +CONECT 835 837 836 833 847 +CONECT 836 835 +CONECT 837 840 839 838 835 +CONECT 838 837 +CONECT 839 837 +CONECT 840 843 841 842 837 +CONECT 841 840 +CONECT 842 840 +CONECT 843 845 844 840 +CONECT 844 843 +CONECT 845 846 843 +CONECT 846 845 +CONECT 847 835 849 848 +CONECT 848 847 +CONECT 849 850 847 851 +CONECT 850 849 +CONECT 851 849 853 862 852 +CONECT 852 851 +CONECT 853 855 854 856 851 +CONECT 854 853 +CONECT 855 853 +CONECT 856 857 858 853 859 +CONECT 857 856 +CONECT 858 856 +CONECT 859 856 860 861 +CONECT 860 859 +CONECT 861 859 +CONECT 862 864 851 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 87 306 866 275 +CONECT 866 865 868 +CONECT 867 870 868 871 869 +CONECT 868 866 867 +CONECT 869 867 +CONECT 870 867 +CONECT 871 867 +CONECT 872 873 +CONECT 873 872 874 +CONECT 874 873 +MASTER 0 0 0 0 0 0 0 0 874 0 874 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_1_front_7.pdb b/tests/nsga2/intermediate_molecules/min_iter_1_front_7.pdb new file mode 100644 index 0000000..7a0c97e --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_1_front_7.pdb @@ -0,0 +1,1753 @@ +COMPND fitness: -1.2907 59.98833333333391 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 55.366 58.077 52.044 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.215 37.914 23.523 1.00 0.00 N +ATOM 2 H1 MET 1 15.201 38.296 24.464 1.00 0.00 H +ATOM 3 H2 MET 1 14.443 38.284 22.998 1.00 0.00 H +ATOM 4 H3 MET 1 16.084 38.206 23.097 1.00 0.00 H +ATOM 5 CA MET 1 15.167 36.444 23.594 1.00 0.00 C +ATOM 6 HA MET 1 14.223 36.155 24.051 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.794 22.200 1.00 0.00 C +ATOM 8 HB2 MET 1 14.404 36.123 21.604 1.00 0.00 H +ATOM 9 HB3 MET 1 16.168 36.123 21.701 1.00 0.00 H +ATOM 10 CG MET 1 15.256 34.254 22.251 1.00 0.00 C +ATOM 11 HG2 MET 1 16.133 33.929 22.814 1.00 0.00 H +ATOM 12 HG3 MET 1 14.367 33.916 22.786 1.00 0.00 H +ATOM 13 SD MET 1 15.317 33.393 20.646 1.00 0.00 S +ATOM 14 CE MET 1 13.636 33.641 20.008 1.00 0.00 C +ATOM 15 HE1 MET 1 13.415 34.705 19.929 1.00 0.00 H +ATOM 16 HE2 MET 1 13.557 33.192 19.017 1.00 0.00 H +ATOM 17 HE3 MET 1 12.912 33.164 20.670 1.00 0.00 H +ATOM 18 C MET 1 16.285 35.966 24.511 1.00 0.00 C +ATOM 19 O MET 1 17.429 36.370 24.340 1.00 0.00 O +ATOM 20 N GLN 2 15.963 35.099 25.473 1.00 0.00 N +ATOM 21 H GLN 2 14.992 34.874 25.632 1.00 0.00 H +ATOM 22 CA GLN 2 16.928 34.438 26.358 1.00 0.00 C +ATOM 23 HA GLN 2 17.697 35.150 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 16.177 34.003 27.636 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.213 33.562 27.357 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.744 33.245 28.172 1.00 0.00 H +ATOM 27 CG GLN 2 15.930 35.169 28.587 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.504 36.019 28.045 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.177 34.846 29.297 1.00 0.00 H +ATOM 30 CD GLN 2 17.140 35.548 29.441 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.211 34.972 29.368 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.976 36.450 30.363 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.748 36.615 30.982 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.068 36.818 30.542 1.00 0.00 H +ATOM 35 C GLN 2 17.653 33.291 25.623 1.00 0.00 C +ATOM 36 O GLN 2 17.281 32.121 25.734 1.00 0.00 O +ATOM 37 N TYR 3 18.675 33.646 24.841 1.00 0.00 N +ATOM 38 H TYR 3 18.926 34.635 24.813 1.00 0.00 H +ATOM 39 CA TYR 3 19.508 32.709 24.085 1.00 0.00 C +ATOM 40 HA TYR 3 18.854 32.101 23.459 1.00 0.00 H +ATOM 41 CB TYR 3 20.458 33.508 23.197 1.00 0.00 C +ATOM 42 HB2 TYR 3 21.071 34.153 23.827 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.125 32.817 22.690 1.00 0.00 H +ATOM 44 CG TYR 3 19.760 34.349 22.152 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.102 33.711 21.087 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.079 32.633 21.039 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.519 34.465 20.054 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.049 33.973 19.217 1.00 0.00 H +ATOM 49 CZ TYR 3 18.571 35.872 20.103 1.00 0.00 C +ATOM 50 OH TYR 3 18.027 36.608 19.103 1.00 0.00 O +ATOM 51 HH TYR 3 18.041 36.130 18.273 1.00 0.00 H +ATOM 52 CE2 TYR 3 19.176 36.515 21.200 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.196 37.592 21.223 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.774 35.755 22.224 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.247 36.252 23.059 1.00 0.00 H +ATOM 56 C TYR 3 20.295 31.786 25.023 1.00 0.00 C +ATOM 57 O TYR 3 20.806 32.243 26.044 1.00 0.00 O +ATOM 58 N LYS 4 20.410 30.492 24.696 1.00 0.00 N +ATOM 59 H LYS 4 20.118 30.201 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 21.014 29.461 25.566 1.00 0.00 C +ATOM 61 HA LYS 4 20.744 29.654 26.602 1.00 0.00 H +ATOM 62 CB LYS 4 20.480 28.067 25.177 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.496 27.976 24.094 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.160 27.307 25.570 1.00 0.00 H +ATOM 65 CG LYS 4 19.070 27.701 25.676 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.897 26.669 25.374 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.060 27.742 26.766 1.00 0.00 H +ATOM 68 CD LYS 4 17.920 28.560 25.120 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.927 29.535 25.607 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.090 28.713 24.052 1.00 0.00 H +ATOM 71 CE LYS 4 16.533 27.909 25.279 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.777 28.600 24.894 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.509 27.012 24.654 1.00 0.00 H +ATOM 74 NZ LYS 4 16.205 27.518 26.673 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.269 28.291 27.318 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.276 27.107 26.716 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.829 26.763 26.958 1.00 0.00 H +ATOM 78 C LYS 4 22.547 29.475 25.513 1.00 0.00 C +ATOM 79 O LYS 4 23.144 29.819 24.501 1.00 0.00 O +HETATM 80 N HX1 5 23.203 29.039 26.584 1.00 0.00 N +HETATM 81 CA HX1 5 24.662 28.868 26.669 1.00 0.00 C +HETATM 82 C HX1 5 24.985 27.668 27.567 1.00 0.00 C +HETATM 83 O HX1 5 24.522 27.612 28.710 1.00 0.00 O +HETATM 84 CB HX1 5 25.294 30.185 27.169 1.00 0.00 C +HETATM 85 CG HX1 5 26.807 30.275 27.239 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.721 29.336 26.838 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.483 31.361 27.814 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.782 31.031 27.730 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.957 29.808 27.202 1.00 0.00 N +HETATM 90 H HX1 5 22.658 28.869 27.426 1.00 0.00 H +HETATM 91 HA HX1 5 25.052 28.661 25.672 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.899 30.401 28.163 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.958 30.992 26.516 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.539 28.374 26.378 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.578 31.603 28.187 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.812 29.251 27.293 1.00 0.00 H +ATOM 97 N ILE 6 25.726 26.695 27.028 1.00 0.00 N +ATOM 98 H ILE 6 26.046 26.815 26.070 1.00 0.00 H +ATOM 99 CA ILE 6 26.199 25.479 27.709 1.00 0.00 C +ATOM 100 HA ILE 6 25.697 25.404 28.676 1.00 0.00 H +ATOM 101 CB ILE 6 25.811 24.216 26.902 1.00 0.00 C +ATOM 102 HB ILE 6 26.234 24.306 25.901 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.373 22.929 27.541 1.00 0.00 C +ATOM 104 HG21 ILE 6 26.002 22.820 28.562 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.078 22.054 26.963 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.464 22.944 27.545 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.270 24.130 26.784 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.842 24.047 27.783 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.891 25.046 26.331 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.745 22.969 25.931 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.890 22.021 26.449 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.678 23.107 25.758 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.263 22.948 24.971 1.00 0.00 H +ATOM 114 C ILE 6 27.708 25.597 28.003 1.00 0.00 C +ATOM 115 O ILE 6 28.447 26.273 27.288 1.00 0.00 O +ATOM 116 N VAL 7 28.126 24.994 29.115 1.00 0.00 N +ATOM 117 H VAL 7 27.488 24.344 29.551 1.00 0.00 H +ATOM 118 CA VAL 7 29.238 25.447 29.963 1.00 0.00 C +ATOM 119 HA VAL 7 29.296 26.533 29.871 1.00 0.00 H +ATOM 120 CB VAL 7 28.813 25.143 31.416 1.00 0.00 C +ATOM 121 HB VAL 7 27.762 25.424 31.517 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.895 23.654 31.773 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.924 23.309 31.694 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.538 23.499 32.790 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.276 23.071 31.090 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.567 25.988 32.435 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.358 27.041 32.248 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.232 25.736 33.441 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.636 25.813 32.353 1.00 0.00 H +ATOM 130 C VAL 7 30.639 24.901 29.585 1.00 0.00 C +ATOM 131 O VAL 7 30.785 23.764 29.143 1.00 0.00 O +ATOM 132 N GLU 8 31.685 25.707 29.802 1.00 0.00 N +ATOM 133 H GLU 8 31.473 26.676 30.027 1.00 0.00 H +ATOM 134 CA GLU 8 33.119 25.383 29.624 1.00 0.00 C +ATOM 135 HA GLU 8 33.310 25.152 28.575 1.00 0.00 H +ATOM 136 CB GLU 8 33.917 26.667 29.977 1.00 0.00 C +ATOM 137 HB2 GLU 8 33.712 27.426 29.223 1.00 0.00 H +ATOM 138 HB3 GLU 8 33.497 27.048 30.911 1.00 0.00 H +ATOM 139 CG GLU 8 35.447 26.584 30.222 1.00 0.00 C +ATOM 140 HG2 GLU 8 35.729 27.498 30.753 1.00 0.00 H +ATOM 141 HG3 GLU 8 35.683 25.765 30.900 1.00 0.00 H +ATOM 142 CD GLU 8 36.359 26.500 28.992 1.00 0.00 C +ATOM 143 OE1 GLU 8 36.012 27.041 27.916 1.00 0.00 O +ATOM 144 OE2 GLU 8 37.521 26.054 29.135 1.00 0.00 O +ATOM 145 C GLU 8 33.570 24.164 30.464 1.00 0.00 C +ATOM 146 O GLU 8 33.840 24.286 31.658 1.00 0.00 O +ATOM 147 N GLY 9 33.696 22.982 29.849 1.00 0.00 N +ATOM 148 H GLY 9 33.287 22.892 28.929 1.00 0.00 H +ATOM 149 CA GLY 9 34.345 21.797 30.438 1.00 0.00 C +ATOM 150 HA2 GLY 9 35.247 21.575 29.868 1.00 0.00 H +ATOM 151 HA3 GLY 9 34.650 22.011 31.462 1.00 0.00 H +ATOM 152 C GLY 9 33.492 20.522 30.448 1.00 0.00 C +ATOM 153 O GLY 9 32.620 20.332 29.602 1.00 0.00 O +ATOM 154 N LYS 10 33.792 19.600 31.384 1.00 0.00 N +ATOM 155 H LYS 10 34.546 19.810 32.024 1.00 0.00 H +ATOM 156 CA LYS 10 33.231 18.228 31.369 1.00 0.00 C +ATOM 157 HA LYS 10 32.207 18.313 30.994 1.00 0.00 H +ATOM 158 CB LYS 10 34.029 17.371 30.353 1.00 0.00 C +ATOM 159 HB2 LYS 10 34.519 18.019 29.622 1.00 0.00 H +ATOM 160 HB3 LYS 10 34.809 16.806 30.866 1.00 0.00 H +ATOM 161 CG LYS 10 33.125 16.407 29.565 1.00 0.00 C +ATOM 162 HG2 LYS 10 32.575 15.759 30.248 1.00 0.00 H +ATOM 163 HG3 LYS 10 32.406 16.996 28.991 1.00 0.00 H +ATOM 164 CD LYS 10 33.941 15.541 28.595 1.00 0.00 C +ATOM 165 HD2 LYS 10 34.578 16.183 27.985 1.00 0.00 H +ATOM 166 HD3 LYS 10 34.568 14.847 29.158 1.00 0.00 H +ATOM 167 CE LYS 10 32.994 14.759 27.678 1.00 0.00 C +ATOM 168 HE2 LYS 10 32.438 14.025 28.267 1.00 0.00 H +ATOM 169 HE3 LYS 10 32.275 15.460 27.247 1.00 0.00 H +ATOM 170 NZ LYS 10 33.721 14.092 26.575 1.00 0.00 N +ATOM 171 HZ1 LYS 10 34.417 13.448 26.913 1.00 0.00 H +ATOM 172 HZ2 LYS 10 33.061 13.594 25.979 1.00 0.00 H +ATOM 173 HZ3 LYS 10 34.203 14.795 26.004 1.00 0.00 H +ATOM 174 C LYS 10 33.089 17.528 32.737 1.00 0.00 C +ATOM 175 O LYS 10 33.156 16.303 32.800 1.00 0.00 O +ATOM 176 N ARG 11 32.949 18.273 33.841 1.00 0.00 N +ATOM 177 H ARG 11 32.915 19.267 33.709 1.00 0.00 H +ATOM 178 CA ARG 11 32.662 17.722 35.194 1.00 0.00 C +ATOM 179 HA ARG 11 32.758 16.632 35.161 1.00 0.00 H +ATOM 180 CB ARG 11 33.685 18.237 36.231 1.00 0.00 C +ATOM 181 HB2 ARG 11 33.709 19.326 36.208 1.00 0.00 H +ATOM 182 HB3 ARG 11 33.355 17.924 37.222 1.00 0.00 H +ATOM 183 CG ARG 11 35.099 17.680 35.989 1.00 0.00 C +ATOM 184 HG2 ARG 11 35.055 16.589 35.999 1.00 0.00 H +ATOM 185 HG3 ARG 11 35.449 18.007 35.010 1.00 0.00 H +ATOM 186 CD ARG 11 36.103 18.142 37.058 1.00 0.00 C +ATOM 187 HD2 ARG 11 36.071 19.228 37.118 1.00 0.00 H +ATOM 188 HD3 ARG 11 35.803 17.740 38.029 1.00 0.00 H +ATOM 189 NE ARG 11 37.479 17.692 36.740 1.00 0.00 N +ATOM 190 HE ARG 11 37.569 16.946 36.073 1.00 0.00 H +ATOM 191 CZ ARG 11 38.615 18.198 37.201 1.00 0.00 C +ATOM 192 NH1 ARG 11 38.667 19.233 37.987 1.00 0.00 N +ATOM 193 HH11 ARG 11 37.829 19.772 38.112 1.00 0.00 H +ATOM 194 HH12 ARG 11 39.560 19.686 38.132 1.00 0.00 H +ATOM 195 NH2 ARG 11 39.749 17.650 36.875 1.00 0.00 N +ATOM 196 HH21 ARG 11 39.795 16.894 36.219 1.00 0.00 H +ATOM 197 HH22 ARG 11 40.609 18.031 37.266 1.00 0.00 H +ATOM 198 C ARG 11 31.206 17.954 35.609 1.00 0.00 C +ATOM 199 O ARG 11 30.490 17.005 35.900 1.00 0.00 O +ATOM 200 N TYR 12 30.762 19.208 35.566 1.00 0.00 N +ATOM 201 H TYR 12 31.434 19.929 35.379 1.00 0.00 H +ATOM 202 CA TYR 12 29.346 19.607 35.531 1.00 0.00 C +ATOM 203 HA TYR 12 28.789 18.986 36.247 1.00 0.00 H +ATOM 204 CB TYR 12 29.234 21.066 36.001 1.00 0.00 C +ATOM 205 HB2 TYR 12 28.187 21.379 35.945 1.00 0.00 H +ATOM 206 HB3 TYR 12 29.493 21.077 37.062 1.00 0.00 H +ATOM 207 CG TYR 12 30.105 22.126 35.333 1.00 0.00 C +ATOM 208 CD1 TYR 12 30.870 21.891 34.171 1.00 0.00 C +ATOM 209 HD1 TYR 12 30.824 20.950 33.636 1.00 0.00 H +ATOM 210 CE1 TYR 12 31.738 22.879 33.670 1.00 0.00 C +ATOM 211 HE1 TYR 12 32.313 22.692 32.776 1.00 0.00 H +ATOM 212 CZ TYR 12 31.833 24.123 34.322 1.00 0.00 C +ATOM 213 OH TYR 12 32.699 25.074 33.898 1.00 0.00 O +ATOM 214 HH TYR 12 33.108 24.847 33.030 1.00 0.00 H +ATOM 215 CE2 TYR 12 30.999 24.398 35.419 1.00 0.00 C +ATOM 216 HE2 TYR 12 31.006 25.385 35.861 1.00 0.00 H +ATOM 217 CD2 TYR 12 30.158 23.394 35.933 1.00 0.00 C +ATOM 218 HD2 TYR 12 29.558 23.604 36.815 1.00 0.00 H +ATOM 219 C TYR 12 28.690 19.397 34.145 1.00 0.00 C +ATOM 220 O TYR 12 29.368 19.005 33.196 1.00 0.00 O +ATOM 221 N LYS 13 27.382 19.683 34.028 1.00 0.00 N +ATOM 222 H LYS 13 26.894 19.964 34.865 1.00 0.00 H +ATOM 223 CA LYS 13 26.590 19.509 32.789 1.00 0.00 C +ATOM 224 HA LYS 13 27.257 19.685 31.944 1.00 0.00 H +ATOM 225 CB LYS 13 26.113 18.042 32.728 1.00 0.00 C +ATOM 226 HB2 LYS 13 26.870 17.413 33.196 1.00 0.00 H +ATOM 227 HB3 LYS 13 25.191 17.936 33.302 1.00 0.00 H +ATOM 228 CG LYS 13 25.912 17.515 31.295 1.00 0.00 C +ATOM 229 HG2 LYS 13 25.056 18.000 30.825 1.00 0.00 H +ATOM 230 HG3 LYS 13 26.803 17.746 30.711 1.00 0.00 H +ATOM 231 CD LYS 13 25.715 15.990 31.282 1.00 0.00 C +ATOM 232 HD2 LYS 13 25.753 15.643 30.248 1.00 0.00 H +ATOM 233 HD3 LYS 13 26.543 15.525 31.821 1.00 0.00 H +ATOM 234 CE LYS 13 24.376 15.549 31.892 1.00 0.00 C +ATOM 235 HE2 LYS 13 24.136 16.182 32.751 1.00 0.00 H +ATOM 236 HE3 LYS 13 23.603 15.708 31.133 1.00 0.00 H +ATOM 237 NZ LYS 13 24.406 14.121 32.306 1.00 0.00 N +ATOM 238 HZ1 LYS 13 24.934 13.975 33.159 1.00 0.00 H +ATOM 239 HZ2 LYS 13 23.466 13.759 32.451 1.00 0.00 H +ATOM 240 HZ3 LYS 13 24.860 13.553 31.592 1.00 0.00 H +ATOM 241 C LYS 13 25.440 20.533 32.632 1.00 0.00 C +ATOM 242 O LYS 13 24.397 20.233 32.051 1.00 0.00 O +ATOM 243 N GLY 14 25.597 21.720 33.227 1.00 0.00 N +ATOM 244 H GLY 14 26.491 21.921 33.646 1.00 0.00 H +ATOM 245 CA GLY 14 24.547 22.749 33.314 1.00 0.00 C +ATOM 246 HA2 GLY 14 23.595 22.255 33.508 1.00 0.00 H +ATOM 247 HA3 GLY 14 24.753 23.393 34.169 1.00 0.00 H +ATOM 248 C GLY 14 24.384 23.636 32.065 1.00 0.00 C +ATOM 249 O GLY 14 25.241 23.673 31.182 1.00 0.00 O +ATOM 250 N VAL 15 23.283 24.395 32.031 1.00 0.00 N +ATOM 251 H VAL 15 22.640 24.337 32.808 1.00 0.00 H +ATOM 252 CA VAL 15 22.902 25.355 30.981 1.00 0.00 C +ATOM 253 HA VAL 15 23.781 25.595 30.382 1.00 0.00 H +ATOM 254 CB VAL 15 21.857 24.717 30.034 1.00 0.00 C +ATOM 255 HB VAL 15 22.299 23.817 29.609 1.00 0.00 H +ATOM 256 CG1 VAL 15 20.551 24.300 30.731 1.00 0.00 C +ATOM 257 HG11 VAL 15 20.049 25.165 31.169 1.00 0.00 H +ATOM 258 HG12 VAL 15 19.882 23.832 30.007 1.00 0.00 H +ATOM 259 HG13 VAL 15 20.757 23.573 31.519 1.00 0.00 H +ATOM 260 CG2 VAL 15 21.481 25.640 28.867 1.00 0.00 C +ATOM 261 HG21 VAL 15 22.382 25.990 28.366 1.00 0.00 H +ATOM 262 HG22 VAL 15 20.879 25.084 28.146 1.00 0.00 H +ATOM 263 HG23 VAL 15 20.901 26.492 29.221 1.00 0.00 H +ATOM 264 C VAL 15 22.399 26.651 31.633 1.00 0.00 C +ATOM 265 O VAL 15 21.845 26.618 32.728 1.00 0.00 O +HETATM 266 N HY1 16 22.593 27.795 30.980 1.00 0.00 N +HETATM 267 CA HY1 16 22.005 29.092 31.344 1.00 0.00 C +HETATM 268 C HY1 16 21.694 29.890 30.062 1.00 0.00 C +HETATM 269 O HY1 16 21.860 29.375 28.949 1.00 0.00 O +HETATM 270 CB HY1 16 22.928 29.838 32.334 1.00 0.00 C +HETATM 271 CG HY1 16 24.278 30.202 31.763 1.00 0.00 C +HETATM 272 CD2 HY1 16 24.599 31.380 31.142 1.00 0.00 C +HETATM 273 ND1 HY1 16 25.407 29.412 31.750 1.00 0.00 N +HETATM 274 CE1 HY1 16 26.387 30.121 31.164 1.00 0.00 C +HETATM 275 NE2 HY1 16 25.942 31.324 30.761 1.00 0.00 N +HETATM 276 H HY1 16 23.089 27.760 30.095 1.00 0.00 H +HETATM 277 HA HY1 16 21.042 28.937 31.836 1.00 0.00 H +HETATM 278 HB2 HY1 16 22.448 30.747 32.701 1.00 0.00 H +HETATM 279 HB3 HY1 16 23.076 29.209 33.217 1.00 0.00 H +HETATM 280 HD1 HY1 16 25.502 28.501 32.177 1.00 0.00 H +HETATM 281 HD2 HY1 16 23.933 32.219 30.992 1.00 0.00 H +HETATM 282 HE1 HY1 16 27.419 29.794 31.067 1.00 0.00 H +ATOM 283 N THR 17 21.213 31.125 30.221 1.00 0.00 N +ATOM 284 H THR 17 21.084 31.439 31.169 1.00 0.00 H +ATOM 285 CA THR 17 20.771 32.009 29.122 1.00 0.00 C +ATOM 286 HA THR 17 21.190 31.603 28.215 1.00 0.00 H +ATOM 287 CB THR 17 19.244 32.008 28.942 1.00 0.00 C +ATOM 288 HB THR 17 19.023 32.578 28.042 1.00 0.00 H +ATOM 289 CG2 THR 17 18.642 30.640 28.642 1.00 0.00 C +ATOM 290 HG21 THR 17 18.864 29.923 29.430 1.00 0.00 H +ATOM 291 HG22 THR 17 17.562 30.744 28.553 1.00 0.00 H +ATOM 292 HG23 THR 17 19.034 30.311 27.693 1.00 0.00 H +ATOM 293 OG1 THR 17 18.523 32.465 30.065 1.00 0.00 O +ATOM 294 HG1 THR 17 18.606 33.430 30.107 1.00 0.00 H +ATOM 295 C THR 17 21.279 33.458 29.181 1.00 0.00 C +ATOM 296 O THR 17 21.726 33.926 30.226 1.00 0.00 O +HETATM 297 N HY2 18 21.213 34.175 28.055 1.00 0.00 N +HETATM 298 CA HY2 18 21.495 35.612 27.957 1.00 0.00 C +HETATM 299 C HY2 18 20.395 36.305 27.153 1.00 0.00 C +HETATM 300 O HY2 18 20.079 35.863 26.049 1.00 0.00 O +HETATM 301 CB HY2 18 22.848 35.842 27.247 1.00 0.00 C +HETATM 302 CG HY2 18 24.050 35.344 28.020 1.00 0.00 C +HETATM 303 CD2 HY2 18 24.548 34.066 28.017 1.00 0.00 C +HETATM 304 ND1 HY2 18 24.828 36.083 28.888 1.00 0.00 N +HETATM 305 CE1 HY2 18 25.770 35.264 29.383 1.00 0.00 C +HETATM 306 NE2 HY2 18 25.640 34.024 28.889 1.00 0.00 N +HETATM 307 H HY2 18 20.908 33.715 27.202 1.00 0.00 H +HETATM 308 HA HY2 18 21.529 36.051 28.954 1.00 0.00 H +HETATM 309 HB2 HY2 18 22.822 35.342 26.280 1.00 0.00 H +HETATM 310 HB3 HY2 18 22.973 36.910 27.064 1.00 0.00 H +HETATM 311 HD1 HY2 18 24.725 37.067 29.105 1.00 0.00 H +HETATM 312 HD2 HY2 18 24.156 33.232 27.450 1.00 0.00 H +HETATM 313 HE1 HY2 18 26.531 35.559 30.091 1.00 0.00 H +ATOM 314 N GLU 19 19.822 37.382 27.687 1.00 0.00 N +ATOM 315 H GLU 19 20.120 37.688 28.599 1.00 0.00 H +ATOM 316 CA GLU 19 18.828 38.211 26.992 1.00 0.00 C +ATOM 317 HA GLU 19 18.106 37.555 26.510 1.00 0.00 H +ATOM 318 CB GLU 19 18.086 39.074 28.032 1.00 0.00 C +ATOM 319 HB2 GLU 19 17.783 38.444 28.864 1.00 0.00 H +ATOM 320 HB3 GLU 19 18.779 39.814 28.429 1.00 0.00 H +ATOM 321 CG GLU 19 16.839 39.798 27.502 1.00 0.00 C +ATOM 322 HG2 GLU 19 16.549 40.555 28.233 1.00 0.00 H +ATOM 323 HG3 GLU 19 17.073 40.313 26.569 1.00 0.00 H +ATOM 324 CD GLU 19 15.667 38.828 27.300 1.00 0.00 C +ATOM 325 OE1 GLU 19 15.544 38.285 26.172 1.00 0.00 O +ATOM 326 OE2 GLU 19 14.908 38.603 28.271 1.00 0.00 O +ATOM 327 C GLU 19 19.483 39.095 25.913 1.00 0.00 C +ATOM 328 O GLU 19 20.430 39.823 26.208 1.00 0.00 O +ATOM 329 N ALA 20 18.977 39.059 24.676 1.00 0.00 N +ATOM 330 H ALA 20 18.268 38.367 24.467 1.00 0.00 H +ATOM 331 CA ALA 20 19.340 40.004 23.612 1.00 0.00 C +ATOM 332 HA ALA 20 19.410 41.004 24.042 1.00 0.00 H +ATOM 333 CB ALA 20 20.714 39.620 23.042 1.00 0.00 C +ATOM 334 HB1 ALA 20 20.657 38.642 22.573 1.00 0.00 H +ATOM 335 HB2 ALA 20 21.036 40.351 22.302 1.00 0.00 H +ATOM 336 HB3 ALA 20 21.459 39.585 23.834 1.00 0.00 H +ATOM 337 C ALA 20 18.286 40.039 22.486 1.00 0.00 C +ATOM 338 O ALA 20 17.384 39.200 22.439 1.00 0.00 O +ATOM 339 N VAL 21 18.416 40.981 21.545 1.00 0.00 N +ATOM 340 H VAL 21 19.145 41.670 21.653 1.00 0.00 H +ATOM 341 CA VAL 21 17.672 40.975 20.262 1.00 0.00 C +ATOM 342 HA VAL 21 16.689 40.537 20.427 1.00 0.00 H +ATOM 343 CB VAL 21 17.448 42.410 19.731 1.00 0.00 C +ATOM 344 HB VAL 21 16.804 42.345 18.853 1.00 0.00 H +ATOM 345 CG1 VAL 21 16.721 43.284 20.761 1.00 0.00 C +ATOM 346 HG11 VAL 21 17.357 43.476 21.625 1.00 0.00 H +ATOM 347 HG12 VAL 21 16.455 44.237 20.303 1.00 0.00 H +ATOM 348 HG13 VAL 21 15.806 42.790 21.088 1.00 0.00 H +ATOM 349 CG2 VAL 21 18.744 43.117 19.309 1.00 0.00 C +ATOM 350 HG21 VAL 21 19.218 42.578 18.489 1.00 0.00 H +ATOM 351 HG22 VAL 21 18.510 44.121 18.954 1.00 0.00 H +ATOM 352 HG23 VAL 21 19.441 43.191 20.143 1.00 0.00 H +ATOM 353 C VAL 21 18.344 40.117 19.176 1.00 0.00 C +ATOM 354 O VAL 21 17.744 39.875 18.133 1.00 0.00 O +ATOM 355 N ASP 22 19.590 39.693 19.410 1.00 0.00 N +ATOM 356 H ASP 22 20.003 39.905 20.303 1.00 0.00 H +ATOM 357 CA ASP 22 20.496 39.093 18.428 1.00 0.00 C +ATOM 358 HA ASP 22 19.939 38.443 17.752 1.00 0.00 H +ATOM 359 CB ASP 22 21.118 40.245 17.617 1.00 0.00 C +ATOM 360 HB2 ASP 22 20.331 40.741 17.046 1.00 0.00 H +ATOM 361 HB3 ASP 22 21.537 40.973 18.314 1.00 0.00 H +ATOM 362 CG ASP 22 22.212 39.808 16.646 1.00 0.00 C +ATOM 363 OD1 ASP 22 23.135 40.614 16.431 1.00 0.00 O +ATOM 364 OD2 ASP 22 22.150 38.658 16.158 1.00 0.00 O +ATOM 365 C ASP 22 21.589 38.257 19.129 1.00 0.00 C +ATOM 366 O ASP 22 22.026 38.601 20.232 1.00 0.00 O +ATOM 367 N PHE 23 22.075 37.194 18.482 1.00 0.00 N +ATOM 368 H PHE 23 21.801 37.088 17.511 1.00 0.00 H +ATOM 369 CA PHE 23 23.223 36.413 18.957 1.00 0.00 C +ATOM 370 HA PHE 23 23.033 36.100 19.983 1.00 0.00 H +ATOM 371 CB PHE 23 23.435 35.163 18.098 1.00 0.00 C +ATOM 372 HB2 PHE 23 23.449 35.439 17.042 1.00 0.00 H +ATOM 373 HB3 PHE 23 24.415 34.748 18.336 1.00 0.00 H +ATOM 374 CG PHE 23 22.418 34.075 18.332 1.00 0.00 C +ATOM 375 CD1 PHE 23 21.326 33.930 17.460 1.00 0.00 C +ATOM 376 HD1 PHE 23 21.215 34.591 16.613 1.00 0.00 H +ATOM 377 CE1 PHE 23 20.387 32.912 17.686 1.00 0.00 C +ATOM 378 HE1 PHE 23 19.553 32.789 17.010 1.00 0.00 H +ATOM 379 CZ PHE 23 20.545 32.053 18.784 1.00 0.00 C +ATOM 380 HZ PHE 23 19.804 31.307 18.977 1.00 0.00 H +ATOM 381 CE2 PHE 23 21.642 32.183 19.650 1.00 0.00 C +ATOM 382 HE2 PHE 23 21.763 31.512 20.488 1.00 0.00 H +ATOM 383 CD2 PHE 23 22.581 33.199 19.421 1.00 0.00 C +ATOM 384 HD2 PHE 23 23.433 33.303 20.076 1.00 0.00 H +ATOM 385 C PHE 23 24.522 37.216 18.948 1.00 0.00 C +ATOM 386 O PHE 23 25.288 37.123 19.906 1.00 0.00 O +ATOM 387 N ALA 24 24.777 38.032 17.920 1.00 0.00 N +ATOM 388 H ALA 24 24.098 38.127 17.167 1.00 0.00 H +ATOM 389 CA ALA 24 26.004 38.826 17.863 1.00 0.00 C +ATOM 390 HA ALA 24 26.836 38.166 18.118 1.00 0.00 H +ATOM 391 CB ALA 24 26.244 39.297 16.423 1.00 0.00 C +ATOM 392 HB1 ALA 24 25.486 40.016 16.122 1.00 0.00 H +ATOM 393 HB2 ALA 24 27.226 39.763 16.347 1.00 0.00 H +ATOM 394 HB3 ALA 24 26.209 38.442 15.744 1.00 0.00 H +ATOM 395 C ALA 24 26.024 39.969 18.904 1.00 0.00 C +ATOM 396 O ALA 24 27.084 40.536 19.172 1.00 0.00 O +ATOM 397 N GLU 25 24.892 40.281 19.545 1.00 0.00 N +ATOM 398 H GLU 25 24.041 39.856 19.205 1.00 0.00 H +ATOM 399 CA GLU 25 24.819 41.085 20.776 1.00 0.00 C +ATOM 400 HA GLU 25 25.636 41.806 20.796 1.00 0.00 H +ATOM 401 CB GLU 25 23.498 41.871 20.814 1.00 0.00 C +ATOM 402 HB2 GLU 25 22.673 41.163 20.774 1.00 0.00 H +ATOM 403 HB3 GLU 25 23.429 42.408 21.760 1.00 0.00 H +ATOM 404 CG GLU 25 23.310 42.881 19.671 1.00 0.00 C +ATOM 405 HG2 GLU 25 23.577 42.429 18.714 1.00 0.00 H +ATOM 406 HG3 GLU 25 22.247 43.135 19.624 1.00 0.00 H +ATOM 407 CD GLU 25 24.114 44.170 19.880 1.00 0.00 C +ATOM 408 OE1 GLU 25 23.462 45.220 20.101 1.00 0.00 O +ATOM 409 OE2 GLU 25 25.371 44.098 19.811 1.00 0.00 O +ATOM 410 C GLU 25 24.959 40.215 22.041 1.00 0.00 C +ATOM 411 O GLU 25 25.732 40.553 22.938 1.00 0.00 O +ATOM 412 N ALA 26 24.299 39.050 22.103 1.00 0.00 N +ATOM 413 H ALA 26 23.662 38.814 21.352 1.00 0.00 H +ATOM 414 CA ALA 26 24.423 38.100 23.218 1.00 0.00 C +ATOM 415 HA ALA 26 24.130 38.609 24.131 1.00 0.00 H +ATOM 416 CB ALA 26 23.471 36.923 22.993 1.00 0.00 C +ATOM 417 HB1 ALA 26 23.770 36.368 22.108 1.00 0.00 H +ATOM 418 HB2 ALA 26 23.499 36.260 23.854 1.00 0.00 H +ATOM 419 HB3 ALA 26 22.460 37.285 22.860 1.00 0.00 H +ATOM 420 C ALA 26 25.868 37.595 23.424 1.00 0.00 C +ATOM 421 O ALA 26 26.292 37.316 24.550 1.00 0.00 O +ATOM 422 N GLU 27 26.659 37.515 22.348 1.00 0.00 N +ATOM 423 H GLU 27 26.221 37.663 21.441 1.00 0.00 H +ATOM 424 CA GLU 27 28.109 37.261 22.347 1.00 0.00 C +ATOM 425 HA GLU 27 28.316 36.315 22.855 1.00 0.00 H +ATOM 426 CB GLU 27 28.586 37.117 20.887 1.00 0.00 C +ATOM 427 HB2 GLU 27 28.014 36.303 20.438 1.00 0.00 H +ATOM 428 HB3 GLU 27 28.354 38.028 20.337 1.00 0.00 H +ATOM 429 CG GLU 27 30.079 36.836 20.757 1.00 0.00 C +ATOM 430 HG2 GLU 27 30.614 37.779 20.882 1.00 0.00 H +ATOM 431 HG3 GLU 27 30.401 36.162 21.554 1.00 0.00 H +ATOM 432 CD GLU 27 30.366 36.227 19.390 1.00 0.00 C +ATOM 433 OE1 GLU 27 30.986 36.917 18.564 1.00 0.00 O +ATOM 434 OE2 GLU 27 29.944 35.073 19.158 1.00 0.00 O +ATOM 435 C GLU 27 28.855 38.375 23.112 1.00 0.00 C +ATOM 436 O GLU 27 29.633 38.083 24.023 1.00 0.00 O +ATOM 437 N LYS 28 28.553 39.656 22.836 1.00 0.00 N +ATOM 438 H LYS 28 27.822 39.830 22.156 1.00 0.00 H +ATOM 439 CA LYS 28 29.116 40.802 23.576 1.00 0.00 C +ATOM 440 HA LYS 28 30.202 40.719 23.569 1.00 0.00 H +ATOM 441 CB LYS 28 28.725 42.140 22.919 1.00 0.00 C +ATOM 442 HB2 LYS 28 27.648 42.281 22.995 1.00 0.00 H +ATOM 443 HB3 LYS 28 29.205 42.945 23.473 1.00 0.00 H +ATOM 444 CG LYS 28 29.135 42.250 21.442 1.00 0.00 C +ATOM 445 HG2 LYS 28 30.206 42.069 21.341 1.00 0.00 H +ATOM 446 HG3 LYS 28 28.602 41.496 20.871 1.00 0.00 H +ATOM 447 CD LYS 28 28.806 43.646 20.888 1.00 0.00 C +ATOM 448 HD2 LYS 28 27.796 43.939 21.184 1.00 0.00 H +ATOM 449 HD3 LYS 28 29.505 44.362 21.322 1.00 0.00 H +ATOM 450 CE LYS 28 28.917 43.732 19.359 1.00 0.00 C +ATOM 451 HE2 LYS 28 29.049 44.784 19.086 1.00 0.00 H +ATOM 452 HE3 LYS 28 29.802 43.181 19.025 1.00 0.00 H +ATOM 453 NZ LYS 28 27.696 43.214 18.694 1.00 0.00 N +ATOM 454 HZ1 LYS 28 26.858 43.680 19.063 1.00 0.00 H +ATOM 455 HZ2 LYS 28 27.718 43.355 17.696 1.00 0.00 H +ATOM 456 HZ3 LYS 28 27.563 42.223 18.882 1.00 0.00 H +ATOM 457 C LYS 28 28.694 40.774 25.048 1.00 0.00 C +ATOM 458 O LYS 28 29.531 40.971 25.922 1.00 0.00 O +ATOM 459 N PHE 29 27.433 40.461 25.351 1.00 0.00 N +ATOM 460 H PHE 29 26.770 40.367 24.587 1.00 0.00 H +ATOM 461 CA PHE 29 26.956 40.324 26.737 1.00 0.00 C +ATOM 462 HA PHE 29 27.288 41.196 27.301 1.00 0.00 H +ATOM 463 CB PHE 29 25.418 40.308 26.753 1.00 0.00 C +ATOM 464 HB2 PHE 29 25.082 39.379 26.290 1.00 0.00 H +ATOM 465 HB3 PHE 29 25.083 40.298 27.791 1.00 0.00 H +ATOM 466 CG PHE 29 24.734 41.474 26.050 1.00 0.00 C +ATOM 467 CD1 PHE 29 23.512 41.261 25.382 1.00 0.00 C +ATOM 468 HD1 PHE 29 23.048 40.287 25.399 1.00 0.00 H +ATOM 469 CE1 PHE 29 22.881 42.313 24.694 1.00 0.00 C +ATOM 470 HE1 PHE 29 21.946 42.138 24.183 1.00 0.00 H +ATOM 471 CZ PHE 29 23.462 43.592 24.675 1.00 0.00 C +ATOM 472 HZ PHE 29 22.980 44.397 24.138 1.00 0.00 H +ATOM 473 CE2 PHE 29 24.664 43.823 25.367 1.00 0.00 C +ATOM 474 HE2 PHE 29 25.105 44.809 25.369 1.00 0.00 H +ATOM 475 CD2 PHE 29 25.293 42.771 26.056 1.00 0.00 C +ATOM 476 HD2 PHE 29 26.211 42.971 26.586 1.00 0.00 H +ATOM 477 C PHE 29 27.555 39.107 27.465 1.00 0.00 C +ATOM 478 O PHE 29 27.773 39.150 28.677 1.00 0.00 O +ATOM 479 N THR 30 27.896 38.038 26.741 1.00 0.00 N +ATOM 480 H THR 30 27.619 38.016 25.764 1.00 0.00 H +ATOM 481 CA THR 30 28.673 36.905 27.271 1.00 0.00 C +ATOM 482 HA THR 30 28.197 36.550 28.185 1.00 0.00 H +ATOM 483 CB THR 30 28.682 35.736 26.276 1.00 0.00 C +ATOM 484 HB THR 30 29.041 36.062 25.302 1.00 0.00 H +ATOM 485 CG2 THR 30 29.498 34.534 26.746 1.00 0.00 C +ATOM 486 HG21 THR 30 29.142 34.220 27.721 1.00 0.00 H +ATOM 487 HG22 THR 30 29.367 33.720 26.036 1.00 0.00 H +ATOM 488 HG23 THR 30 30.560 34.772 26.807 1.00 0.00 H +ATOM 489 OG1 THR 30 27.360 35.286 26.150 1.00 0.00 O +ATOM 490 HG1 THR 30 26.921 35.901 25.540 1.00 0.00 H +ATOM 491 C THR 30 30.096 37.329 27.627 1.00 0.00 C +ATOM 492 O THR 30 30.588 36.990 28.705 1.00 0.00 O +ATOM 493 N LYS 31 30.738 38.118 26.757 1.00 0.00 N +ATOM 494 H LYS 31 30.278 38.309 25.872 1.00 0.00 H +ATOM 495 CA LYS 31 32.079 38.688 26.976 1.00 0.00 C +ATOM 496 HA LYS 31 32.743 37.884 27.300 1.00 0.00 H +ATOM 497 CB LYS 31 32.621 39.274 25.671 1.00 0.00 C +ATOM 498 HB2 LYS 31 31.903 39.978 25.246 1.00 0.00 H +ATOM 499 HB3 LYS 31 33.541 39.820 25.894 1.00 0.00 H +ATOM 500 CG LYS 31 32.944 38.173 24.651 1.00 0.00 C +ATOM 501 HG2 LYS 31 33.671 37.499 25.091 1.00 0.00 H +ATOM 502 HG3 LYS 31 32.056 37.589 24.426 1.00 0.00 H +ATOM 503 CD LYS 31 33.506 38.765 23.356 1.00 0.00 C +ATOM 504 HD2 LYS 31 32.713 39.327 22.866 1.00 0.00 H +ATOM 505 HD3 LYS 31 34.316 39.458 23.597 1.00 0.00 H +ATOM 506 CE LYS 31 34.009 37.678 22.410 1.00 0.00 C +ATOM 507 HE2 LYS 31 33.210 36.951 22.212 1.00 0.00 H +ATOM 508 HE3 LYS 31 34.294 38.148 21.459 1.00 0.00 H +ATOM 509 NZ LYS 31 35.192 36.994 22.980 1.00 0.00 N +ATOM 510 HZ1 LYS 31 34.970 36.242 23.631 1.00 0.00 H +ATOM 511 HZ2 LYS 31 35.696 36.535 22.223 1.00 0.00 H +ATOM 512 HZ3 LYS 31 35.853 37.636 23.423 1.00 0.00 H +ATOM 513 C LYS 31 32.124 39.737 28.088 1.00 0.00 C +ATOM 514 O LYS 31 33.110 39.767 28.820 1.00 0.00 O +ATOM 515 N ALA 32 31.066 40.529 28.271 1.00 0.00 N +ATOM 516 H ALA 32 30.350 40.537 27.557 1.00 0.00 H +ATOM 517 CA ALA 32 30.916 41.417 29.424 1.00 0.00 C +ATOM 518 HA ALA 32 31.761 42.109 29.453 1.00 0.00 H +ATOM 519 CB ALA 32 29.630 42.243 29.272 1.00 0.00 C +ATOM 520 HB1 ALA 32 28.757 41.591 29.251 1.00 0.00 H +ATOM 521 HB2 ALA 32 29.539 42.927 30.118 1.00 0.00 H +ATOM 522 HB3 ALA 32 29.672 42.826 28.351 1.00 0.00 H +ATOM 523 C ALA 32 30.942 40.605 30.729 1.00 0.00 C +ATOM 524 O ALA 32 31.851 40.784 31.532 1.00 0.00 O +ATOM 525 N GLH 33 30.050 39.611 30.870 1.00 0.00 N +ATOM 526 H GLH 33 29.333 39.496 30.165 1.00 0.00 H +ATOM 527 CA GLH 33 30.047 38.725 32.041 1.00 0.00 C +ATOM 528 HA GLH 33 29.911 39.335 32.935 1.00 0.00 H +ATOM 529 CB GLH 33 28.891 37.715 31.963 1.00 0.00 C +ATOM 530 HB2 GLH 33 28.942 37.165 31.022 1.00 0.00 H +ATOM 531 HB3 GLH 33 29.025 37.002 32.778 1.00 0.00 H +ATOM 532 CG GLH 33 27.500 38.357 32.108 1.00 0.00 C +ATOM 533 HG2 GLH 33 27.504 39.042 32.957 1.00 0.00 H +ATOM 534 HG3 GLH 33 27.261 38.931 31.214 1.00 0.00 H +ATOM 535 CD GLH 33 26.406 37.318 32.358 1.00 0.00 C +ATOM 536 OE1 GLH 33 26.558 36.242 32.918 1.00 0.00 O +ATOM 537 OE2 GLH 33 25.174 37.633 31.910 1.00 0.00 O +ATOM 538 HE2 GLH 33 24.616 36.913 32.215 1.00 0.00 H +ATOM 539 C GLH 33 31.373 37.970 32.231 1.00 0.00 C +ATOM 540 O GLH 33 31.760 37.707 33.362 1.00 0.00 O +ATOM 541 N ALA 34 32.084 37.609 31.158 1.00 0.00 N +ATOM 542 H ALA 34 31.708 37.793 30.237 1.00 0.00 H +ATOM 543 CA ALA 34 33.402 36.984 31.269 1.00 0.00 C +ATOM 544 HA ALA 34 33.329 36.147 31.965 1.00 0.00 H +ATOM 545 CB ALA 34 33.799 36.424 29.900 1.00 0.00 C +ATOM 546 HB1 ALA 34 34.021 37.239 29.214 1.00 0.00 H +ATOM 547 HB2 ALA 34 34.684 35.801 30.018 1.00 0.00 H +ATOM 548 HB3 ALA 34 32.997 35.812 29.491 1.00 0.00 H +ATOM 549 C ALA 34 34.464 37.950 31.840 1.00 0.00 C +ATOM 550 O ALA 34 35.200 37.571 32.750 1.00 0.00 O +ATOM 551 N ASN 35 34.500 39.207 31.376 1.00 0.00 N +ATOM 552 H ASN 35 33.842 39.482 30.658 1.00 0.00 H +ATOM 553 CA ASN 35 35.384 40.242 31.928 1.00 0.00 C +ATOM 554 HA ASN 35 36.374 39.806 32.012 1.00 0.00 H +ATOM 555 CB ASN 35 35.506 41.432 30.957 1.00 0.00 C +ATOM 556 HB2 ASN 35 34.515 41.759 30.649 1.00 0.00 H +ATOM 557 HB3 ASN 35 35.980 42.260 31.484 1.00 0.00 H +ATOM 558 CG ASN 35 36.370 41.137 29.738 1.00 0.00 C +ATOM 559 OD1 ASN 35 37.587 41.194 29.762 1.00 0.00 O +ATOM 560 ND2 ASN 35 35.776 40.836 28.613 1.00 0.00 N +ATOM 561 HD21 ASN 35 36.375 40.628 27.819 1.00 0.00 H +ATOM 562 HD22 ASN 35 34.782 40.669 28.608 1.00 0.00 H +ATOM 563 C ASN 35 34.989 40.686 33.358 1.00 0.00 C +ATOM 564 O ASN 35 35.858 41.125 34.108 1.00 0.00 O +ATOM 565 N ASP 36 33.730 40.502 33.781 1.00 0.00 N +ATOM 566 H ASP 36 33.014 40.300 33.091 1.00 0.00 H +ATOM 567 CA ASP 36 33.323 40.680 35.189 1.00 0.00 C +ATOM 568 HA ASP 36 33.626 41.677 35.506 1.00 0.00 H +ATOM 569 CB ASP 36 31.790 40.605 35.367 1.00 0.00 C +ATOM 570 HB2 ASP 36 31.453 39.608 35.113 1.00 0.00 H +ATOM 571 HB3 ASP 36 31.583 40.721 36.432 1.00 0.00 H +ATOM 572 CG ASP 36 30.936 41.606 34.560 1.00 0.00 C +ATOM 573 OD1 ASP 36 31.454 42.673 34.150 1.00 0.00 O +ATOM 574 OD2 ASP 36 29.729 41.321 34.369 1.00 0.00 O +ATOM 575 C ASP 36 34.022 39.677 36.139 1.00 0.00 C +ATOM 576 O ASP 36 34.366 40.036 37.265 1.00 0.00 O +ATOM 577 N TYR 37 34.279 38.436 35.693 1.00 0.00 N +ATOM 578 H TYR 37 33.929 38.187 34.778 1.00 0.00 H +ATOM 579 CA TYR 37 35.150 37.478 36.405 1.00 0.00 C +ATOM 580 HA TYR 37 35.031 37.637 37.477 1.00 0.00 H +ATOM 581 CB TYR 37 34.728 36.029 36.102 1.00 0.00 C +ATOM 582 HB2 TYR 37 34.894 35.833 35.042 1.00 0.00 H +ATOM 583 HB3 TYR 37 35.387 35.360 36.657 1.00 0.00 H +ATOM 584 CG TYR 37 33.295 35.659 36.456 1.00 0.00 C +ATOM 585 CD1 TYR 37 32.330 35.550 35.437 1.00 0.00 C +ATOM 586 HD1 TYR 37 32.623 35.735 34.416 1.00 0.00 H +ATOM 587 CE1 TYR 37 30.995 35.227 35.746 1.00 0.00 C +ATOM 588 HE1 TYR 37 30.257 35.181 34.963 1.00 0.00 H +ATOM 589 CZ TYR 37 30.630 34.968 37.084 1.00 0.00 C +ATOM 590 OH TYR 37 29.350 34.633 37.395 1.00 0.00 O +ATOM 591 HH TYR 37 28.718 35.000 36.775 1.00 0.00 H +ATOM 592 CE2 TYR 37 31.601 35.043 38.103 1.00 0.00 C +ATOM 593 HE2 TYR 37 31.310 34.844 39.122 1.00 0.00 H +ATOM 594 CD2 TYR 37 32.930 35.393 37.791 1.00 0.00 C +ATOM 595 HD2 TYR 37 33.670 35.453 38.575 1.00 0.00 H +ATOM 596 C TYR 37 36.653 37.661 36.084 1.00 0.00 C +ATOM 597 O TYR 37 37.509 37.230 36.866 1.00 0.00 O +ATOM 598 N GLY 38 36.981 38.278 34.941 1.00 0.00 N +ATOM 599 H GLY 38 36.217 38.563 34.340 1.00 0.00 H +ATOM 600 CA GLY 38 38.332 38.695 34.549 1.00 0.00 C +ATOM 601 HA2 GLY 38 38.510 39.692 34.952 1.00 0.00 H +ATOM 602 HA3 GLY 38 39.067 38.019 34.987 1.00 0.00 H +ATOM 603 C GLY 38 38.572 38.753 33.033 1.00 0.00 C +ATOM 604 O GLY 38 38.680 39.832 32.466 1.00 0.00 O +ATOM 605 N VAL 39 38.769 37.587 32.407 1.00 0.00 N +ATOM 606 H VAL 39 38.528 36.772 32.947 1.00 0.00 H +ATOM 607 CA VAL 39 39.120 37.334 30.982 1.00 0.00 C +ATOM 608 HA VAL 39 39.589 36.353 31.045 1.00 0.00 H +ATOM 609 CB VAL 39 40.278 38.199 30.408 1.00 0.00 C +ATOM 610 HB VAL 39 39.887 39.155 30.060 1.00 0.00 H +ATOM 611 CG1 VAL 39 41.410 38.442 31.429 1.00 0.00 C +ATOM 612 HG11 VAL 39 41.633 37.519 31.969 1.00 0.00 H +ATOM 613 HG12 VAL 39 42.308 38.801 30.921 1.00 0.00 H +ATOM 614 HG13 VAL 39 41.103 39.214 32.136 1.00 0.00 H +ATOM 615 CG2 VAL 39 40.949 37.487 29.219 1.00 0.00 C +ATOM 616 HG21 VAL 39 41.725 38.123 28.799 1.00 0.00 H +ATOM 617 HG22 VAL 39 41.401 36.553 29.543 1.00 0.00 H +ATOM 618 HG23 VAL 39 40.242 37.276 28.424 1.00 0.00 H +ATOM 619 C VAL 39 37.923 37.009 30.055 1.00 0.00 C +ATOM 620 O VAL 39 37.209 36.068 30.396 1.00 0.00 O +ATOM 621 N ASP 40 37.721 37.611 28.865 1.00 0.00 N +ATOM 622 H ASP 40 38.260 38.435 28.629 1.00 0.00 H +ATOM 623 CA ASP 40 36.920 36.948 27.802 1.00 0.00 C +ATOM 624 HA ASP 40 36.182 36.330 28.311 1.00 0.00 H +ATOM 625 CB ASP 40 36.053 37.904 26.947 1.00 0.00 C +ATOM 626 HB2 ASP 40 35.316 37.280 26.435 1.00 0.00 H +ATOM 627 HB3 ASP 40 35.494 38.546 27.614 1.00 0.00 H +ATOM 628 CG ASP 40 36.769 38.774 25.899 1.00 0.00 C +ATOM 629 OD1 ASP 40 37.171 39.908 26.230 1.00 0.00 O +ATOM 630 OD2 ASP 40 36.863 38.346 24.717 1.00 0.00 O +ATOM 631 C ASP 40 37.719 35.999 26.893 1.00 0.00 C +ATOM 632 O ASP 40 38.616 36.413 26.153 1.00 0.00 O +ATOM 633 N GLY 41 37.291 34.734 26.866 1.00 0.00 N +ATOM 634 H GLY 41 36.626 34.447 27.571 1.00 0.00 H +ATOM 635 CA GLY 41 37.610 33.768 25.816 1.00 0.00 C +ATOM 636 HA2 GLY 41 38.623 33.946 25.456 1.00 0.00 H +ATOM 637 HA3 GLY 41 37.580 32.771 26.242 1.00 0.00 H +ATOM 638 C GLY 41 36.655 33.826 24.612 1.00 0.00 C +ATOM 639 O GLY 41 35.774 34.683 24.510 1.00 0.00 O +ATOM 640 N GLU 42 36.792 32.855 23.705 1.00 0.00 N +ATOM 641 H GLU 42 37.487 32.129 23.865 1.00 0.00 H +ATOM 642 CA GLU 42 36.009 32.689 22.461 1.00 0.00 C +ATOM 643 HA GLU 42 35.334 33.540 22.334 1.00 0.00 H +ATOM 644 CB GLU 42 36.923 32.654 21.234 1.00 0.00 C +ATOM 645 HB2 GLU 42 37.390 31.662 21.199 1.00 0.00 H +ATOM 646 HB3 GLU 42 36.257 32.698 20.374 1.00 0.00 H +ATOM 647 CG GLU 42 37.926 33.780 21.144 1.00 0.00 C +ATOM 648 HG2 GLU 42 38.767 33.538 21.797 1.00 0.00 H +ATOM 649 HG3 GLU 42 38.362 33.796 20.165 1.00 0.00 H +ATOM 650 CD GLU 42 37.448 35.144 21.511 1.00 0.00 C +ATOM 651 OE1 GLU 42 36.392 35.531 21.013 1.00 0.00 O +ATOM 652 OE2 GLU 42 38.019 35.817 22.405 1.00 0.00 O +ATOM 653 C GLU 42 35.098 31.428 22.559 1.00 0.00 C +ATOM 654 O GLU 42 35.470 30.440 23.214 1.00 0.00 O +ATOM 655 N ILE 43 33.966 31.444 21.825 1.00 0.00 N +ATOM 656 H ILE 43 33.809 32.250 21.208 1.00 0.00 H +ATOM 657 CA ILE 43 32.887 30.421 21.861 1.00 0.00 C +ATOM 658 HA ILE 43 33.331 29.490 22.218 1.00 0.00 H +ATOM 659 CB ILE 43 31.749 30.833 22.843 1.00 0.00 C +ATOM 660 HB ILE 43 30.876 30.251 22.570 1.00 0.00 H +ATOM 661 CG2 ILE 43 32.120 30.445 24.279 1.00 0.00 C +ATOM 662 HG21 ILE 43 32.995 30.995 24.605 1.00 0.00 H +ATOM 663 HG22 ILE 43 31.282 30.667 24.932 1.00 0.00 H +ATOM 664 HG23 ILE 43 32.325 29.379 24.324 1.00 0.00 H +ATOM 665 CG1 ILE 43 31.340 32.325 22.832 1.00 0.00 C +ATOM 666 HG12 ILE 43 30.451 32.421 23.459 1.00 0.00 H +ATOM 667 HG13 ILE 43 32.122 32.931 23.275 1.00 0.00 H +ATOM 668 CD1 ILE 43 30.995 32.906 21.457 1.00 0.00 C +ATOM 669 HD11 ILE 43 30.366 32.224 20.891 1.00 0.00 H +ATOM 670 HD12 ILE 43 30.466 33.847 21.588 1.00 0.00 H +ATOM 671 HD13 ILE 43 31.907 33.103 20.890 1.00 0.00 H +ATOM 672 C ILE 43 32.351 30.121 20.452 1.00 0.00 C +ATOM 673 O ILE 43 32.559 30.895 19.514 1.00 0.00 O +ATOM 674 N THR 44 31.619 29.018 20.340 1.00 0.00 N +ATOM 675 H THR 44 31.486 28.447 21.169 1.00 0.00 H +ATOM 676 CA THR 44 30.903 28.600 19.128 1.00 0.00 C +ATOM 677 HA THR 44 31.230 29.213 18.290 1.00 0.00 H +ATOM 678 CB THR 44 31.269 27.144 18.781 1.00 0.00 C +ATOM 679 HB THR 44 31.001 26.477 19.600 1.00 0.00 H +ATOM 680 CG2 THR 44 30.624 26.613 17.495 1.00 0.00 C +ATOM 681 HG21 THR 44 30.802 27.305 16.665 1.00 0.00 H +ATOM 682 HG22 THR 44 31.041 25.628 17.235 1.00 0.00 H +ATOM 683 HG23 THR 44 29.544 26.485 17.639 1.00 0.00 H +ATOM 684 OG1 THR 44 32.661 27.056 18.558 1.00 0.00 O +ATOM 685 HG1 THR 44 32.846 26.251 18.066 1.00 0.00 H +ATOM 686 C THR 44 29.392 28.779 19.281 1.00 0.00 C +ATOM 687 O THR 44 28.876 28.725 20.395 1.00 0.00 O +ATOM 688 N GLN 45 28.679 29.026 18.178 1.00 0.00 N +ATOM 689 H GLN 45 29.149 29.020 17.288 1.00 0.00 H +ATOM 690 CA GLN 45 27.222 29.231 18.139 1.00 0.00 C +ATOM 691 HA GLN 45 26.819 29.205 19.153 1.00 0.00 H +ATOM 692 CB GLN 45 26.897 30.607 17.518 1.00 0.00 C +ATOM 693 HB2 GLN 45 27.284 30.625 16.500 1.00 0.00 H +ATOM 694 HB3 GLN 45 25.809 30.696 17.459 1.00 0.00 H +ATOM 695 CG GLN 45 27.454 31.826 18.281 1.00 0.00 C +ATOM 696 HG2 GLN 45 27.104 31.768 19.310 1.00 0.00 H +ATOM 697 HG3 GLN 45 28.542 31.780 18.287 1.00 0.00 H +ATOM 698 CD GLN 45 27.016 33.162 17.659 1.00 0.00 C +ATOM 699 OE1 GLN 45 26.064 33.244 16.898 1.00 0.00 O +ATOM 700 NE2 GLN 45 27.679 34.270 17.903 1.00 0.00 N +ATOM 701 HE21 GLN 45 27.355 35.101 17.453 1.00 0.00 H +ATOM 702 HE22 GLN 45 28.552 34.317 18.441 1.00 0.00 H +ATOM 703 C GLN 45 26.480 28.159 17.312 1.00 0.00 C +ATOM 704 O GLN 45 27.046 27.601 16.370 1.00 0.00 O +ATOM 705 N ASP 46 25.191 27.966 17.604 1.00 0.00 N +ATOM 706 H ASP 46 24.838 28.365 18.468 1.00 0.00 H +ATOM 707 CA ASP 46 24.203 27.294 16.751 1.00 0.00 C +ATOM 708 HA ASP 46 24.528 27.356 15.711 1.00 0.00 H +ATOM 709 CB ASP 46 24.079 25.812 17.147 1.00 0.00 C +ATOM 710 HB2 ASP 46 24.979 25.272 16.851 1.00 0.00 H +ATOM 711 HB3 ASP 46 23.981 25.747 18.230 1.00 0.00 H +ATOM 712 CG ASP 46 22.852 25.158 16.507 1.00 0.00 C +ATOM 713 OD1 ASP 46 22.104 24.474 17.241 1.00 0.00 O +ATOM 714 OD2 ASP 46 22.584 25.407 15.313 1.00 0.00 O +ATOM 715 C ASP 46 22.831 27.991 16.868 1.00 0.00 C +ATOM 716 O ASP 46 22.288 28.138 17.964 1.00 0.00 O +ATOM 717 N ASP 47 22.230 28.373 15.739 1.00 0.00 N +ATOM 718 H ASP 47 22.690 28.167 14.865 1.00 0.00 H +ATOM 719 CA ASP 47 20.867 28.919 15.690 1.00 0.00 C +ATOM 720 HA ASP 47 20.729 29.593 16.537 1.00 0.00 H +ATOM 721 CB ASP 47 20.693 29.766 14.416 1.00 0.00 C +ATOM 722 HB2 ASP 47 21.415 30.585 14.422 1.00 0.00 H +ATOM 723 HB3 ASP 47 20.882 29.148 13.536 1.00 0.00 H +ATOM 724 CG ASP 47 19.278 30.347 14.340 1.00 0.00 C +ATOM 725 OD1 ASP 47 18.430 29.775 13.625 1.00 0.00 O +ATOM 726 OD2 ASP 47 18.941 31.266 15.120 1.00 0.00 O +ATOM 727 C ASP 47 19.773 27.830 15.792 1.00 0.00 C +ATOM 728 O ASP 47 18.707 28.086 16.356 1.00 0.00 O +ATOM 729 N ALA 48 20.006 26.600 15.319 1.00 0.00 N +ATOM 730 H ALA 48 20.951 26.350 15.024 1.00 0.00 H +ATOM 731 CA ALA 48 18.970 25.560 15.236 1.00 0.00 C +ATOM 732 HA ALA 48 18.105 25.984 14.723 1.00 0.00 H +ATOM 733 CB ALA 48 19.510 24.405 14.386 1.00 0.00 C +ATOM 734 HB1 ALA 48 20.362 23.940 14.885 1.00 0.00 H +ATOM 735 HB2 ALA 48 18.729 23.659 14.239 1.00 0.00 H +ATOM 736 HB3 ALA 48 19.832 24.783 13.415 1.00 0.00 H +ATOM 737 C ALA 48 18.489 25.071 16.618 1.00 0.00 C +ATOM 738 O ALA 48 17.304 24.774 16.796 1.00 0.00 O +ATOM 739 N THR 49 19.392 25.037 17.602 1.00 0.00 N +ATOM 740 H THR 49 20.372 25.112 17.325 1.00 0.00 H +ATOM 741 CA THR 49 19.113 24.869 19.043 1.00 0.00 C +ATOM 742 HA THR 49 18.084 24.531 19.159 1.00 0.00 H +ATOM 743 CB THR 49 20.020 23.800 19.672 1.00 0.00 C +ATOM 744 HB THR 49 19.698 23.651 20.702 1.00 0.00 H +ATOM 745 CG2 THR 49 19.958 22.443 18.975 1.00 0.00 C +ATOM 746 HG21 THR 49 20.321 22.522 17.950 1.00 0.00 H +ATOM 747 HG22 THR 49 20.590 21.745 19.521 1.00 0.00 H +ATOM 748 HG23 THR 49 18.931 22.081 18.973 1.00 0.00 H +ATOM 749 OG1 THR 49 21.361 24.217 19.698 1.00 0.00 O +ATOM 750 HG1 THR 49 21.679 24.247 18.761 1.00 0.00 H +ATOM 751 C THR 49 19.231 26.177 19.841 1.00 0.00 C +ATOM 752 O THR 49 19.101 26.167 21.068 1.00 0.00 O +ATOM 753 N LYS 50 19.468 27.312 19.167 1.00 0.00 N +ATOM 754 H LYS 50 19.560 27.226 18.161 1.00 0.00 H +ATOM 755 CA LYS 50 19.589 28.671 19.731 1.00 0.00 C +ATOM 756 HA LYS 50 20.008 29.273 18.928 1.00 0.00 H +ATOM 757 CB LYS 50 18.185 29.226 20.094 1.00 0.00 C +ATOM 758 HB2 LYS 50 17.768 28.587 20.874 1.00 0.00 H +ATOM 759 HB3 LYS 50 18.294 30.221 20.527 1.00 0.00 H +ATOM 760 CG LYS 50 17.144 29.315 18.956 1.00 0.00 C +ATOM 761 HG2 LYS 50 17.135 28.389 18.385 1.00 0.00 H +ATOM 762 HG3 LYS 50 16.161 29.418 19.417 1.00 0.00 H +ATOM 763 CD LYS 50 17.338 30.517 18.014 1.00 0.00 C +ATOM 764 HD2 LYS 50 17.289 31.432 18.604 1.00 0.00 H +ATOM 765 HD3 LYS 50 18.319 30.466 17.544 1.00 0.00 H +ATOM 766 CE LYS 50 16.255 30.586 16.925 1.00 0.00 C +ATOM 767 HE2 LYS 50 15.311 30.225 17.334 1.00 0.00 H +ATOM 768 HE3 LYS 50 16.117 31.628 16.628 1.00 0.00 H +ATOM 769 NZ LYS 50 16.628 29.801 15.728 1.00 0.00 N +ATOM 770 HZ1 LYS 50 17.134 28.955 15.975 1.00 0.00 H +ATOM 771 HZ2 LYS 50 15.839 29.559 15.145 1.00 0.00 H +ATOM 772 HZ3 LYS 50 17.313 30.309 15.154 1.00 0.00 H +ATOM 773 C LYS 50 20.608 28.778 20.892 1.00 0.00 C +ATOM 774 O LYS 50 20.304 29.382 21.927 1.00 0.00 O +ATOM 775 N THR 51 21.791 28.170 20.745 1.00 0.00 N +ATOM 776 H THR 51 22.017 27.827 19.813 1.00 0.00 H +ATOM 777 CA THR 51 22.737 27.843 21.835 1.00 0.00 C +ATOM 778 HA THR 51 22.433 28.389 22.721 1.00 0.00 H +ATOM 779 CB THR 51 22.629 26.341 22.176 1.00 0.00 C +ATOM 780 HB THR 51 22.792 25.755 21.272 1.00 0.00 H +ATOM 781 CG2 THR 51 23.614 25.869 23.247 1.00 0.00 C +ATOM 782 HG21 THR 51 23.549 26.508 24.126 1.00 0.00 H +ATOM 783 HG22 THR 51 23.377 24.843 23.525 1.00 0.00 H +ATOM 784 HG23 THR 51 24.627 25.883 22.852 1.00 0.00 H +ATOM 785 OG1 THR 51 21.358 26.039 22.712 1.00 0.00 O +ATOM 786 HG1 THR 51 20.709 26.084 21.991 1.00 0.00 H +ATOM 787 C THR 51 24.207 28.217 21.545 1.00 0.00 C +ATOM 788 O THR 51 24.716 27.973 20.456 1.00 0.00 O +ATOM 789 N PHE 52 24.918 28.749 22.550 1.00 0.00 N +ATOM 790 H PHE 52 24.402 29.020 23.376 1.00 0.00 H +ATOM 791 CA PHE 52 26.389 28.875 22.610 1.00 0.00 C +ATOM 792 HA PHE 52 26.783 28.971 21.598 1.00 0.00 H +ATOM 793 CB PHE 52 26.774 30.130 23.412 1.00 0.00 C +ATOM 794 HB2 PHE 52 26.267 30.101 24.374 1.00 0.00 H +ATOM 795 HB3 PHE 52 27.845 30.085 23.622 1.00 0.00 H +ATOM 796 CG PHE 52 26.494 31.471 22.766 1.00 0.00 C +ATOM 797 CD1 PHE 52 25.266 32.130 22.966 1.00 0.00 C +ATOM 798 HD1 PHE 52 24.487 31.661 23.545 1.00 0.00 H +ATOM 799 CE1 PHE 52 25.047 33.404 22.412 1.00 0.00 C +ATOM 800 HE1 PHE 52 24.099 33.900 22.556 1.00 0.00 H +ATOM 801 CZ PHE 52 26.060 34.026 21.662 1.00 0.00 C +ATOM 802 HZ PHE 52 25.893 34.995 21.218 1.00 0.00 H +ATOM 803 CE2 PHE 52 27.293 33.379 21.473 1.00 0.00 C +ATOM 804 HE2 PHE 52 28.070 33.856 20.889 1.00 0.00 H +ATOM 805 CD2 PHE 52 27.503 32.100 22.017 1.00 0.00 C +ATOM 806 HD2 PHE 52 28.441 31.592 21.854 1.00 0.00 H +ATOM 807 C PHE 52 27.066 27.661 23.288 1.00 0.00 C +ATOM 808 O PHE 52 26.544 27.156 24.288 1.00 0.00 O +ATOM 809 N THR 53 28.266 27.263 22.839 1.00 0.00 N +ATOM 810 H THR 53 28.641 27.723 22.012 1.00 0.00 H +ATOM 811 CA THR 53 29.074 26.151 23.403 1.00 0.00 C +ATOM 812 HA THR 53 28.798 26.016 24.449 1.00 0.00 H +ATOM 813 CB THR 53 28.800 24.819 22.672 1.00 0.00 C +ATOM 814 HB THR 53 29.387 24.035 23.153 1.00 0.00 H +ATOM 815 CG2 THR 53 27.341 24.373 22.695 1.00 0.00 C +ATOM 816 HG21 THR 53 26.734 25.036 22.079 1.00 0.00 H +ATOM 817 HG22 THR 53 27.264 23.356 22.311 1.00 0.00 H +ATOM 818 HG23 THR 53 26.972 24.389 23.719 1.00 0.00 H +ATOM 819 OG1 THR 53 29.192 24.898 21.323 1.00 0.00 O +ATOM 820 HG1 THR 53 28.756 24.184 20.851 1.00 0.00 H +ATOM 821 C THR 53 30.594 26.406 23.377 1.00 0.00 C +ATOM 822 O THR 53 31.083 27.326 22.718 1.00 0.00 O +ATOM 823 N ALA 54 31.348 25.564 24.100 1.00 0.00 N +ATOM 824 H ALA 54 30.876 24.846 24.626 1.00 0.00 H +ATOM 825 CA ALA 54 32.812 25.456 24.054 1.00 0.00 C +ATOM 826 HA ALA 54 33.210 26.268 23.442 1.00 0.00 H +ATOM 827 CB ALA 54 33.366 25.629 25.475 1.00 0.00 C +ATOM 828 HB1 ALA 54 33.015 24.817 26.113 1.00 0.00 H +ATOM 829 HB2 ALA 54 34.457 25.616 25.456 1.00 0.00 H +ATOM 830 HB3 ALA 54 33.038 26.583 25.891 1.00 0.00 H +ATOM 831 C ALA 54 33.278 24.123 23.415 1.00 0.00 C +ATOM 832 O ALA 54 32.505 23.167 23.298 1.00 0.00 O +ATOM 833 N GLH 55 34.548 24.067 22.999 1.00 0.00 N +ATOM 834 H GLH 55 35.146 24.849 23.215 1.00 0.00 H +ATOM 835 CA GLH 55 35.168 22.922 22.308 1.00 0.00 C +ATOM 836 HA GLH 55 34.398 22.426 21.716 1.00 0.00 H +ATOM 837 CB GLH 55 36.234 23.451 21.327 1.00 0.00 C +ATOM 838 HB2 GLH 55 36.972 24.031 21.884 1.00 0.00 H +ATOM 839 HB3 GLH 55 36.743 22.608 20.858 1.00 0.00 H +ATOM 840 CG GLH 55 35.617 24.327 20.216 1.00 0.00 C +ATOM 841 HG2 GLH 55 34.958 23.714 19.601 1.00 0.00 H +ATOM 842 HG3 GLH 55 35.020 25.129 20.650 1.00 0.00 H +ATOM 843 CD GLH 55 36.655 24.987 19.312 1.00 0.00 C +ATOM 844 OE1 GLH 55 37.842 25.121 19.573 1.00 0.00 O +ATOM 845 OE2 GLH 55 36.155 25.451 18.149 1.00 0.00 O +ATOM 846 HE2 GLH 55 36.883 25.858 17.675 1.00 0.00 H +ATOM 847 C GLH 55 35.736 21.856 23.279 1.00 0.00 C +ATOM 848 O GLH 55 36.043 22.164 24.428 1.00 0.00 O +ATOM 849 N GLU 56 35.854 20.603 22.810 1.00 0.00 N +ATOM 850 H GLU 56 35.627 20.451 21.842 1.00 0.00 H +ATOM 851 CA GLU 56 36.225 19.391 23.580 1.00 0.00 C +ATOM 852 HA GLU 56 35.760 19.455 24.564 1.00 0.00 H +ATOM 853 CB GLU 56 35.617 18.165 22.855 1.00 0.00 C +ATOM 854 HB2 GLU 56 34.541 18.196 23.027 1.00 0.00 H +ATOM 855 HB3 GLU 56 35.768 18.297 21.782 1.00 0.00 H +ATOM 856 CG GLU 56 36.111 16.739 23.193 1.00 0.00 C +ATOM 857 HG2 GLU 56 35.454 16.031 22.680 1.00 0.00 H +ATOM 858 HG3 GLU 56 37.100 16.595 22.754 1.00 0.00 H +ATOM 859 CD GLU 56 36.165 16.375 24.688 1.00 0.00 C +ATOM 860 OE1 GLU 56 37.290 16.354 25.251 1.00 0.00 O +ATOM 861 OE2 GLU 56 35.109 16.022 25.266 1.00 0.00 O +ATOM 862 C GLU 56 37.723 19.244 23.888 1.00 0.00 C +ATOM 863 O GLU 56 38.090 19.361 25.078 1.00 0.00 O +ATOM 864 OXT GLU 56 38.506 18.730 23.060 1.00 0.00 O +HETATM 865 ZN ZN1 57 26.762 32.444 29.336 1.00 0.00 Zn +HETATM 866 N AN1 58 28.364 33.308 30.222 1.00 0.00 N +HETATM 867 C AN1 58 30.678 34.028 31.184 1.00 0.00 C +HETATM 868 C1 AN1 58 29.379 33.629 30.674 1.00 0.00 C +HETATM 869 H AN1 58 30.582 34.423 32.200 1.00 0.00 H +HETATM 870 H1 AN1 58 31.113 34.795 30.535 1.00 0.00 H +HETATM 871 H2 AN1 58 31.336 33.149 31.202 1.00 0.00 H +HETATM 872 N1 AZI 59 30.830 28.620 29.341 1.00 0.00 N +HETATM 873 N2 AZI 59 30.309 29.481 30.054 1.00 0.00 N +HETATM 874 N3 AZI 59 29.759 30.371 30.755 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 73 72 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 865 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 121 122 126 +CONECT 121 120 +CONECT 122 125 120 123 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 127 129 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 145 +CONECT 135 134 +CONECT 136 137 134 139 138 +CONECT 137 136 +CONECT 138 136 +CONECT 139 142 136 140 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 144 139 +CONECT 143 142 +CONECT 144 142 +CONECT 145 134 147 146 +CONECT 146 145 +CONECT 147 148 149 145 +CONECT 148 147 +CONECT 149 147 150 152 151 +CONECT 150 149 +CONECT 151 149 +CONECT 152 153 149 154 +CONECT 153 152 +CONECT 154 152 156 155 +CONECT 155 154 +CONECT 156 158 157 154 174 +CONECT 157 156 +CONECT 158 161 159 160 156 +CONECT 159 158 +CONECT 160 158 +CONECT 161 164 163 162 158 +CONECT 162 161 +CONECT 163 161 +CONECT 164 167 165 166 161 +CONECT 165 164 +CONECT 166 164 +CONECT 167 170 169 168 164 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 170 +CONECT 174 156 175 176 +CONECT 175 174 +CONECT 176 174 177 178 +CONECT 177 176 +CONECT 178 176 179 198 180 +CONECT 179 178 +CONECT 180 178 183 181 182 +CONECT 181 180 +CONECT 182 180 +CONECT 183 185 184 180 186 +CONECT 184 183 +CONECT 185 183 +CONECT 186 183 189 187 188 +CONECT 187 186 +CONECT 188 186 +CONECT 189 190 186 191 +CONECT 190 189 +CONECT 191 189 195 192 +CONECT 192 191 193 194 +CONECT 193 192 +CONECT 194 192 +CONECT 195 196 191 197 +CONECT 196 195 +CONECT 197 195 +CONECT 198 178 200 199 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 219 200 204 203 +CONECT 203 202 +CONECT 204 207 202 205 206 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 217 204 +CONECT 208 209 210 207 +CONECT 209 208 +CONECT 210 211 208 212 +CONECT 211 210 +CONECT 212 210 213 215 +CONECT 213 214 212 +CONECT 214 213 +CONECT 215 212 216 217 +CONECT 216 215 +CONECT 217 207 215 218 +CONECT 218 217 +CONECT 219 220 221 202 +CONECT 220 219 +CONECT 221 223 219 222 +CONECT 222 221 +CONECT 223 224 241 225 221 +CONECT 224 223 +CONECT 225 228 223 226 227 +CONECT 226 225 +CONECT 227 225 +CONECT 228 230 229 231 225 +CONECT 229 228 +CONECT 230 228 +CONECT 231 232 228 233 234 +CONECT 232 231 +CONECT 233 231 +CONECT 234 236 231 237 235 +CONECT 235 234 +CONECT 236 234 +CONECT 237 240 234 239 238 +CONECT 238 237 +CONECT 239 237 +CONECT 240 237 +CONECT 241 242 223 243 +CONECT 242 241 +CONECT 243 241 245 244 +CONECT 244 243 +CONECT 245 248 243 246 247 +CONECT 246 245 +CONECT 247 245 +CONECT 248 249 250 245 +CONECT 249 248 +CONECT 250 252 248 251 +CONECT 251 250 +CONECT 252 254 253 264 250 +CONECT 253 252 +CONECT 254 260 255 256 252 +CONECT 255 254 +CONECT 256 258 254 257 259 +CONECT 257 256 +CONECT 258 256 +CONECT 259 256 +CONECT 260 262 261 263 254 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 252 265 +CONECT 265 264 +CONECT 266 276 267 264 +CONECT 267 268 266 277 270 +CONECT 268 269 283 267 +CONECT 269 268 +CONECT 270 267 271 278 279 +CONECT 271 272 273 270 +CONECT 272 275 281 271 +CONECT 273 274 271 280 +CONECT 274 275 282 273 +CONECT 275 865 272 274 +CONECT 276 266 +CONECT 277 267 +CONECT 278 270 +CONECT 279 270 +CONECT 280 273 +CONECT 281 272 +CONECT 282 274 +CONECT 283 285 268 284 +CONECT 284 283 +CONECT 285 286 287 295 283 +CONECT 286 285 +CONECT 287 288 289 285 293 +CONECT 288 287 +CONECT 289 292 291 287 290 +CONECT 290 289 +CONECT 291 289 +CONECT 292 289 +CONECT 293 287 294 +CONECT 294 293 +CONECT 295 297 285 296 +CONECT 296 295 +CONECT 297 307 298 295 +CONECT 298 299 301 297 308 +CONECT 299 300 314 298 +CONECT 300 299 +CONECT 301 309 310 298 302 +CONECT 302 301 303 304 +CONECT 303 312 302 306 +CONECT 304 302 311 305 +CONECT 305 304 306 313 +CONECT 306 303 865 305 +CONECT 307 297 +CONECT 308 298 +CONECT 309 301 +CONECT 310 301 +CONECT 311 304 +CONECT 312 303 +CONECT 313 305 +CONECT 314 316 299 315 +CONECT 315 314 +CONECT 316 327 317 314 318 +CONECT 317 316 +CONECT 318 316 321 320 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 323 324 318 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 325 321 326 +CONECT 325 324 +CONECT 326 324 +CONECT 327 329 328 316 +CONECT 328 327 +CONECT 329 331 330 327 +CONECT 330 329 +CONECT 331 337 333 332 329 +CONECT 332 331 +CONECT 333 335 334 331 336 +CONECT 334 333 +CONECT 335 333 +CONECT 336 333 +CONECT 337 339 338 331 +CONECT 338 337 +CONECT 339 341 340 337 +CONECT 340 339 +CONECT 341 353 343 342 339 +CONECT 342 341 +CONECT 343 344 349 341 345 +CONECT 344 343 +CONECT 345 343 347 348 346 +CONECT 346 345 +CONECT 347 345 +CONECT 348 345 +CONECT 349 350 351 343 352 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 341 +CONECT 354 353 +CONECT 355 357 353 356 +CONECT 356 355 +CONECT 357 359 358 365 355 +CONECT 358 357 +CONECT 359 362 360 361 357 +CONECT 360 359 +CONECT 361 359 +CONECT 362 364 363 359 +CONECT 363 362 +CONECT 364 362 +CONECT 365 357 367 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 385 370 +CONECT 370 369 +CONECT 371 372 374 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 375 371 383 +CONECT 375 376 377 374 +CONECT 376 375 +CONECT 377 378 375 379 +CONECT 378 377 +CONECT 379 377 380 381 +CONECT 380 379 +CONECT 381 379 383 382 +CONECT 382 381 +CONECT 383 374 381 384 +CONECT 384 383 +CONECT 385 387 369 386 +CONECT 386 385 +CONECT 387 388 389 385 +CONECT 388 387 +CONECT 389 391 387 390 395 +CONECT 390 389 +CONECT 391 394 392 393 389 +CONECT 392 391 +CONECT 393 391 +CONECT 394 391 +CONECT 395 389 396 397 +CONECT 396 395 +CONECT 397 395 398 399 +CONECT 398 397 +CONECT 399 397 400 401 410 +CONECT 400 399 +CONECT 401 404 402 399 403 +CONECT 402 401 +CONECT 403 401 +CONECT 404 405 406 407 401 +CONECT 405 404 +CONECT 406 404 +CONECT 407 404 409 408 +CONECT 408 407 +CONECT 409 407 +CONECT 410 399 412 411 +CONECT 411 410 +CONECT 412 413 410 414 +CONECT 413 412 +CONECT 414 412 416 420 415 +CONECT 415 414 +CONECT 416 417 419 414 418 +CONECT 417 416 +CONECT 418 416 +CONECT 419 416 +CONECT 420 422 414 421 +CONECT 421 420 +CONECT 422 423 424 420 +CONECT 423 422 +CONECT 424 426 422 425 435 +CONECT 425 424 +CONECT 426 428 427 429 424 +CONECT 427 426 +CONECT 428 426 +CONECT 429 432 430 426 431 +CONECT 430 429 +CONECT 431 429 +CONECT 432 433 434 429 +CONECT 433 432 +CONECT 434 432 +CONECT 435 424 437 436 +CONECT 436 435 +CONECT 437 438 435 439 +CONECT 438 437 +CONECT 439 437 441 440 457 +CONECT 440 439 +CONECT 441 444 442 443 439 +CONECT 442 441 +CONECT 443 441 +CONECT 444 446 447 445 441 +CONECT 445 444 +CONECT 446 444 +CONECT 447 450 448 449 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 452 451 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 455 456 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 453 +CONECT 457 439 459 458 +CONECT 458 457 +CONECT 459 460 457 461 +CONECT 460 459 +CONECT 461 459 463 462 477 +CONECT 462 461 +CONECT 463 466 464 461 465 +CONECT 464 463 +CONECT 465 463 +CONECT 466 467 475 463 +CONECT 467 469 468 466 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 472 469 473 +CONECT 472 471 +CONECT 473 471 474 475 +CONECT 474 473 +CONECT 475 473 466 476 +CONECT 476 475 +CONECT 477 461 479 478 +CONECT 478 477 +CONECT 479 480 481 477 +CONECT 480 479 +CONECT 481 483 479 491 482 +CONECT 482 481 +CONECT 483 484 489 485 481 +CONECT 484 483 +CONECT 485 487 483 488 486 +CONECT 486 485 +CONECT 487 485 +CONECT 488 485 +CONECT 489 490 483 +CONECT 490 489 +CONECT 491 493 481 492 +CONECT 492 491 +CONECT 493 494 495 491 +CONECT 494 493 +CONECT 495 497 493 496 513 +CONECT 496 495 +CONECT 497 500 498 499 495 +CONECT 498 497 +CONECT 499 497 +CONECT 500 503 502 501 497 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 504 505 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 508 507 509 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 506 512 510 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 495 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 518 523 +CONECT 518 517 +CONECT 519 522 520 517 521 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 +CONECT 523 517 525 524 +CONECT 524 523 +CONECT 525 526 523 527 +CONECT 526 525 +CONECT 527 525 529 539 528 +CONECT 528 527 +CONECT 529 530 527 532 531 +CONECT 530 529 +CONECT 531 529 +CONECT 532 534 529 535 533 +CONECT 533 532 +CONECT 534 532 +CONECT 535 537 532 536 +CONECT 536 535 +CONECT 537 538 535 +CONECT 538 537 +CONECT 539 541 527 540 +CONECT 540 539 +CONECT 541 542 543 539 +CONECT 542 541 +CONECT 543 545 541 549 544 +CONECT 544 543 +CONECT 545 546 548 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 545 +CONECT 549 543 551 550 +CONECT 550 549 +CONECT 551 552 549 553 +CONECT 552 551 +CONECT 553 555 551 554 563 +CONECT 554 553 +CONECT 555 558 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 560 559 555 +CONECT 559 558 +CONECT 560 561 562 558 +CONECT 561 560 +CONECT 562 560 +CONECT 563 553 565 564 +CONECT 564 563 +CONECT 565 566 563 567 +CONECT 566 565 +CONECT 567 565 569 568 575 +CONECT 568 567 +CONECT 569 572 570 567 571 +CONECT 570 569 +CONECT 571 569 +CONECT 572 573 574 569 +CONECT 573 572 +CONECT 574 572 +CONECT 575 567 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 596 581 580 +CONECT 580 579 +CONECT 581 582 579 584 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 585 581 594 +CONECT 585 586 587 584 +CONECT 586 585 +CONECT 587 588 585 589 +CONECT 588 587 +CONECT 589 587 590 592 +CONECT 590 591 589 +CONECT 591 590 +CONECT 592 589 594 593 +CONECT 593 592 +CONECT 594 584 592 595 +CONECT 595 594 +CONECT 596 598 579 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 598 601 602 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 619 609 608 605 +CONECT 608 607 +CONECT 609 615 610 607 611 +CONECT 610 609 +CONECT 611 609 613 612 614 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 +CONECT 615 618 616 617 609 +CONECT 616 615 +CONECT 617 615 +CONECT 618 615 +CONECT 619 621 620 607 +CONECT 620 619 +CONECT 621 623 622 619 +CONECT 622 621 +CONECT 623 631 625 624 621 +CONECT 624 623 +CONECT 625 628 626 627 623 +CONECT 626 625 +CONECT 627 625 +CONECT 628 630 629 625 +CONECT 629 628 +CONECT 630 628 +CONECT 631 632 633 623 +CONECT 632 631 +CONECT 633 635 631 634 +CONECT 634 633 +CONECT 635 638 636 637 633 +CONECT 636 635 +CONECT 637 635 +CONECT 638 640 639 635 +CONECT 639 638 +CONECT 640 642 641 638 +CONECT 641 640 +CONECT 642 644 643 653 640 +CONECT 643 642 +CONECT 644 646 647 645 642 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 644 650 648 +CONECT 648 647 +CONECT 649 647 +CONECT 650 651 647 652 +CONECT 651 650 +CONECT 652 650 +CONECT 653 655 642 654 +CONECT 654 653 +CONECT 655 656 657 653 +CONECT 656 655 +CONECT 657 672 655 658 659 +CONECT 658 657 +CONECT 659 657 660 665 661 +CONECT 660 659 +CONECT 661 659 664 662 663 +CONECT 662 661 +CONECT 663 661 +CONECT 664 661 +CONECT 665 668 659 667 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 671 669 670 665 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 +CONECT 672 673 674 657 +CONECT 673 672 +CONECT 674 676 672 675 +CONECT 675 674 +CONECT 676 677 678 686 674 +CONECT 677 676 +CONECT 678 680 684 676 679 +CONECT 679 678 +CONECT 680 681 682 683 678 +CONECT 681 680 +CONECT 682 680 +CONECT 683 680 +CONECT 684 685 678 +CONECT 685 684 +CONECT 686 688 676 687 +CONECT 687 686 +CONECT 688 689 690 686 +CONECT 689 688 +CONECT 690 703 692 688 691 +CONECT 691 690 +CONECT 692 693 694 690 695 +CONECT 693 692 +CONECT 694 692 +CONECT 695 692 698 697 696 +CONECT 696 695 +CONECT 697 695 +CONECT 698 699 700 695 +CONECT 699 698 +CONECT 700 701 698 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 704 705 690 +CONECT 704 703 +CONECT 705 707 703 706 +CONECT 706 705 +CONECT 707 708 715 709 705 +CONECT 708 707 +CONECT 709 712 707 710 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 709 713 +CONECT 713 712 +CONECT 714 712 +CONECT 715 717 707 716 +CONECT 716 715 +CONECT 717 718 719 715 +CONECT 718 717 +CONECT 719 721 717 727 720 +CONECT 720 719 +CONECT 721 723 724 722 719 +CONECT 722 721 +CONECT 723 721 +CONECT 724 725 721 726 +CONECT 725 724 +CONECT 726 724 +CONECT 727 729 719 728 +CONECT 728 727 +CONECT 729 730 731 727 +CONECT 730 729 +CONECT 731 733 732 729 737 +CONECT 732 731 +CONECT 733 736 735 734 731 +CONECT 734 733 +CONECT 735 733 +CONECT 736 733 +CONECT 737 731 738 739 +CONECT 738 737 +CONECT 739 737 740 741 +CONECT 740 739 +CONECT 741 739 742 743 751 +CONECT 742 741 +CONECT 743 745 741 749 744 +CONECT 744 743 +CONECT 745 746 748 747 743 +CONECT 746 745 +CONECT 747 745 +CONECT 748 745 +CONECT 749 750 743 +CONECT 750 749 +CONECT 751 741 753 752 +CONECT 752 751 +CONECT 753 754 755 751 +CONECT 754 753 +CONECT 755 756 753 757 773 +CONECT 756 755 +CONECT 757 760 755 759 758 +CONECT 758 757 +CONECT 759 757 +CONECT 760 763 761 762 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 766 765 764 760 +CONECT 764 763 +CONECT 765 763 +CONECT 766 769 768 767 763 +CONECT 767 766 +CONECT 768 766 +CONECT 769 771 772 770 766 +CONECT 770 769 +CONECT 771 769 +CONECT 772 769 +CONECT 773 755 775 774 +CONECT 774 773 +CONECT 775 776 773 777 +CONECT 776 775 +CONECT 777 775 787 779 778 +CONECT 778 777 +CONECT 779 780 777 785 781 +CONECT 780 779 +CONECT 781 779 784 783 782 +CONECT 782 781 +CONECT 783 781 +CONECT 784 781 +CONECT 785 786 779 +CONECT 786 785 +CONECT 787 788 777 789 +CONECT 788 787 +CONECT 789 787 791 790 +CONECT 790 789 +CONECT 791 792 789 807 793 +CONECT 792 791 +CONECT 793 791 796 795 794 +CONECT 794 793 +CONECT 795 793 +CONECT 796 805 797 793 +CONECT 797 799 796 798 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 804 801 805 +CONECT 804 803 +CONECT 805 803 806 796 +CONECT 806 805 +CONECT 807 791 809 808 +CONECT 808 807 +CONECT 809 810 807 811 +CONECT 810 809 +CONECT 811 813 809 821 812 +CONECT 812 811 +CONECT 813 819 815 814 811 +CONECT 814 813 +CONECT 815 816 817 813 818 +CONECT 816 815 +CONECT 817 815 +CONECT 818 815 +CONECT 819 820 813 +CONECT 820 819 +CONECT 821 822 811 823 +CONECT 822 821 +CONECT 823 821 825 824 +CONECT 824 823 +CONECT 825 831 826 823 827 +CONECT 826 825 +CONECT 827 825 829 830 828 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 833 832 825 +CONECT 832 831 +CONECT 833 835 834 831 +CONECT 834 833 +CONECT 835 837 836 833 847 +CONECT 836 835 +CONECT 837 840 839 838 835 +CONECT 838 837 +CONECT 839 837 +CONECT 840 843 841 842 837 +CONECT 841 840 +CONECT 842 840 +CONECT 843 845 844 840 +CONECT 844 843 +CONECT 845 846 843 +CONECT 846 845 +CONECT 847 835 849 848 +CONECT 848 847 +CONECT 849 850 847 851 +CONECT 850 849 +CONECT 851 849 853 862 852 +CONECT 852 851 +CONECT 853 855 854 856 851 +CONECT 854 853 +CONECT 855 853 +CONECT 856 857 858 853 859 +CONECT 857 856 +CONECT 858 856 +CONECT 859 856 860 861 +CONECT 860 859 +CONECT 861 859 +CONECT 862 864 851 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 87 306 866 275 +CONECT 866 865 868 +CONECT 867 870 868 871 869 +CONECT 868 866 867 +CONECT 869 867 +CONECT 870 867 +CONECT 871 867 +CONECT 872 873 +CONECT 873 872 874 +CONECT 874 873 +MASTER 0 0 0 0 0 0 0 0 874 0 874 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_2_front_0.pdb b/tests/nsga2/intermediate_molecules/min_iter_2_front_0.pdb new file mode 100644 index 0000000..ab33aa9 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_2_front_0.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.3475 49.977499999999736 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.973 23.612 1.00 0.00 N +ATOM 2 H1 MET 1 15.135 38.357 24.556 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.346 23.089 1.00 0.00 H +ATOM 4 H3 MET 1 16.016 38.284 23.187 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.505 23.670 1.00 0.00 C +ATOM 6 HA MET 1 14.170 36.198 24.097 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.876 22.274 1.00 0.00 C +ATOM 8 HB2 MET 1 14.391 36.152 21.672 1.00 0.00 H +ATOM 9 HB3 MET 1 16.151 36.274 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.373 34.334 22.298 1.00 0.00 C +ATOM 11 HG2 MET 1 16.260 34.066 22.868 1.00 0.00 H +ATOM 12 HG3 MET 1 14.495 33.925 22.807 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.526 20.668 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.572 20.068 1.00 0.00 C +ATOM 15 HE1 MET 1 13.463 34.602 20.016 1.00 0.00 H +ATOM 16 HE2 MET 1 13.776 33.133 19.073 1.00 0.00 H +ATOM 17 HE3 MET 1 13.173 32.997 20.735 1.00 0.00 H +ATOM 18 C MET 1 16.218 36.031 24.600 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.398 24.428 1.00 0.00 O +ATOM 20 N GLN 2 15.878 35.187 25.578 1.00 0.00 N +ATOM 21 H GLN 2 14.912 34.996 25.769 1.00 0.00 H +ATOM 22 CA GLN 2 16.850 34.476 26.430 1.00 0.00 C +ATOM 23 HA GLN 2 17.657 35.151 26.723 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.070 27.723 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.137 33.654 27.496 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.662 33.325 28.279 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.257 28.675 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.459 36.087 28.164 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.214 34.973 29.415 1.00 0.00 H +ATOM 30 CD GLN 2 17.128 35.582 29.524 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.142 34.924 29.513 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.039 36.477 30.468 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.765 36.535 31.087 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.097 36.722 30.761 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.301 25.666 1.00 0.00 C +ATOM 36 O GLN 2 17.102 32.148 25.829 1.00 0.00 O +ATOM 37 N TYR 3 18.478 33.617 24.821 1.00 0.00 N +ATOM 38 H TYR 3 18.752 34.594 24.754 1.00 0.00 H +ATOM 39 CA TYR 3 19.260 32.619 24.100 1.00 0.00 C +ATOM 40 HA TYR 3 18.568 31.967 23.564 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.285 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.866 33.942 23.645 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.481 22.672 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.068 21.937 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.530 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.822 32.423 20.550 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.147 34.204 19.542 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.116 33.738 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.844 35.573 19.676 1.00 0.00 C +ATOM 50 OH TYR 3 18.514 36.309 18.584 1.00 0.00 O +ATOM 51 HH TYR 3 18.772 35.874 17.768 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.189 20.940 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.728 37.250 21.025 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.324 35.441 22.067 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.446 35.934 23.023 1.00 0.00 H +ATOM 56 C TYR 3 20.089 31.764 25.076 1.00 0.00 C +ATOM 57 O TYR 3 20.458 32.245 26.150 1.00 0.00 O +ATOM 58 N LYS 4 20.399 30.504 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.250 30.220 23.771 1.00 0.00 H +ATOM 60 CA LYS 4 21.010 29.502 25.633 1.00 0.00 C +ATOM 61 HA LYS 4 20.726 29.715 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.476 28.101 25.273 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.522 27.982 24.192 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.145 27.345 25.699 1.00 0.00 H +ATOM 65 CG LYS 4 19.052 27.745 25.738 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.888 26.697 25.498 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.995 27.853 26.819 1.00 0.00 H +ATOM 68 CD LYS 4 17.923 28.564 25.084 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.886 29.557 25.526 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.149 28.678 24.022 1.00 0.00 H +ATOM 71 CE LYS 4 16.546 27.888 25.193 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.507 24.665 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.597 26.933 24.667 1.00 0.00 H +ATOM 74 NZ LYS 4 16.095 27.656 26.590 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.985 28.528 27.089 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.207 27.154 26.591 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.756 27.062 27.077 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.619 1.00 0.00 C +ATOM 79 O LYS 4 23.196 29.886 24.647 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.029 26.694 1.00 0.00 N +HETATM 81 CA HX1 5 24.625 28.832 26.820 1.00 0.00 C +HETATM 82 C HX1 5 24.899 27.672 27.782 1.00 0.00 C +HETATM 83 O HX1 5 24.405 27.683 28.910 1.00 0.00 O +HETATM 84 CB HX1 5 25.264 30.145 27.306 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.392 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.072 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.385 27.861 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.095 27.755 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.938 29.837 27.336 1.00 0.00 N +HETATM 90 H HX1 5 22.596 28.839 27.521 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.841 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.383 28.292 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.940 30.947 26.639 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.282 26.701 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.531 31.750 28.083 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.839 29.356 27.352 1.00 0.00 H +ATOM 97 N ILE 6 25.634 26.658 27.326 1.00 0.00 N +ATOM 98 H ILE 6 26.015 26.711 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.003 25.472 28.116 1.00 0.00 C +ATOM 100 HA ILE 6 25.303 25.370 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.851 24.199 27.246 1.00 0.00 C +ATOM 102 HB ILE 6 26.402 24.347 26.317 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.409 22.939 27.935 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.892 22.757 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.288 22.070 27.288 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.481 23.048 28.117 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.345 24.012 26.914 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.791 23.875 27.842 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.968 24.915 26.433 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.011 22.847 25.977 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.180 21.893 26.476 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.956 22.903 25.700 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.617 22.905 25.073 1.00 0.00 H +ATOM 114 C ILE 6 27.391 25.668 28.756 1.00 0.00 C +ATOM 115 O ILE 6 28.227 26.398 28.224 1.00 0.00 O +ATOM 116 N VAL 7 27.598 25.081 29.940 1.00 0.00 N +ATOM 117 H VAL 7 26.867 24.478 30.298 1.00 0.00 H +ATOM 118 CA VAL 7 28.776 25.287 30.804 1.00 0.00 C +ATOM 119 HA VAL 7 28.877 26.362 30.959 1.00 0.00 H +ATOM 120 CB VAL 7 28.499 24.641 32.179 1.00 0.00 C +ATOM 121 HB VAL 7 27.500 24.950 32.487 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.522 23.107 32.134 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.532 22.745 31.926 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.190 22.716 33.090 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.855 22.747 31.351 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.449 25.111 33.285 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.292 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.077 24.778 34.251 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.446 24.702 33.142 1.00 0.00 H +ATOM 130 C VAL 7 30.110 24.804 30.202 1.00 0.00 C +ATOM 131 O VAL 7 30.151 23.918 29.351 1.00 0.00 O +ATOM 132 N THR 8 31.213 25.378 30.689 1.00 0.00 N +ATOM 133 H THR 8 31.110 26.089 31.397 1.00 0.00 H +ATOM 134 CA THR 8 32.596 24.972 30.392 1.00 0.00 C +ATOM 135 HA THR 8 32.687 24.826 29.316 1.00 0.00 H +ATOM 136 CB THR 8 33.570 26.088 30.816 1.00 0.00 C +ATOM 137 HB THR 8 34.595 25.756 30.638 1.00 0.00 H +ATOM 138 CG2 THR 8 33.356 27.393 30.055 1.00 0.00 C +ATOM 139 HG21 THR 8 32.383 27.824 30.296 1.00 0.00 H +ATOM 140 HG22 THR 8 34.132 28.110 30.322 1.00 0.00 H +ATOM 141 HG23 THR 8 33.402 27.211 28.983 1.00 0.00 H +ATOM 142 OG1 THR 8 33.421 26.396 32.182 1.00 0.00 O +ATOM 143 HG1 THR 8 33.806 27.265 32.319 1.00 0.00 H +ATOM 144 C THR 8 33.009 23.656 31.077 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.250 32.105 1.00 0.00 O +ATOM 146 N GLY 9 34.047 23.007 30.532 1.00 0.00 N +ATOM 147 H GLY 9 34.399 23.335 29.647 1.00 0.00 H +ATOM 148 CA GLY 9 34.624 21.774 31.075 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.615 21.618 30.651 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.881 32.155 1.00 0.00 H +ATOM 151 C GLY 9 33.781 20.522 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.016 20.483 29.829 1.00 0.00 O +ATOM 153 N LYS 10 33.954 19.478 31.612 1.00 0.00 N +ATOM 154 H LYS 10 34.677 19.557 32.310 1.00 0.00 H +ATOM 155 CA LYS 10 33.235 18.188 31.477 1.00 0.00 C +ATOM 156 HA LYS 10 32.295 18.399 30.965 1.00 0.00 H +ATOM 157 CB LYS 10 34.063 17.245 30.575 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.683 17.846 29.905 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.730 16.638 31.191 1.00 0.00 H +ATOM 160 CG LYS 10 33.197 16.330 29.689 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.601 15.662 30.311 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.521 16.954 29.102 1.00 0.00 H +ATOM 163 CD LYS 10 34.060 15.496 28.727 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.718 16.162 28.166 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.669 14.795 29.300 1.00 0.00 H +ATOM 166 CE LYS 10 33.176 14.722 27.742 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.970 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.467 15.418 27.287 1.00 0.00 H +ATOM 169 NZ LYS 10 33.968 14.073 26.670 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.727 13.511 27.035 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.369 13.526 26.062 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.418 14.773 26.065 1.00 0.00 H +ATOM 173 C LYS 10 32.827 17.541 32.811 1.00 0.00 C +ATOM 174 O LYS 10 32.345 16.412 32.831 1.00 0.00 O +ATOM 175 N SER 11 33.039 18.242 33.932 1.00 0.00 N +ATOM 176 H SER 11 33.491 19.134 33.839 1.00 0.00 H +ATOM 177 CA SER 11 32.567 17.848 35.278 1.00 0.00 C +ATOM 178 HA SER 11 32.502 16.757 35.338 1.00 0.00 H +ATOM 179 CB SER 11 33.554 18.327 36.351 1.00 0.00 C +ATOM 180 HB2 SER 11 33.584 19.416 36.351 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.982 37.329 1.00 0.00 H +ATOM 182 OG SER 11 34.851 17.824 36.092 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.429 36.454 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.417 35.586 1.00 0.00 C +ATOM 185 O SER 11 30.350 17.745 36.192 1.00 0.00 O +ATOM 186 N CYS 12 30.920 19.653 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.631 20.135 34.631 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.268 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.868 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.352 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.323 22.214 34.524 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.249 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.147 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.147 23.411 37.056 1.00 0.00 H +ATOM 195 C CYS 12 28.852 19.934 33.837 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.664 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.512 19.987 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.061 20.142 34.737 1.00 0.00 H +ATOM 199 CA LYS 13 26.668 19.719 32.664 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.856 31.774 1.00 0.00 H +ATOM 201 CB LYS 13 26.222 18.245 32.710 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.030 17.651 33.147 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.343 18.143 33.363 1.00 0.00 H +ATOM 204 CG LYS 13 25.911 17.632 31.329 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.032 18.104 30.890 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.763 17.815 30.673 1.00 0.00 H +ATOM 207 CD LYS 13 25.679 16.113 31.416 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.682 15.711 30.401 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.513 15.660 31.956 1.00 0.00 H +ATOM 210 CE LYS 13 24.340 15.743 32.074 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.161 16.384 32.939 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.551 15.953 31.349 1.00 0.00 H +ATOM 213 NZ LYS 13 24.295 14.306 32.456 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.868 14.091 33.273 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.348 13.998 32.647 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.676 13.728 31.708 1.00 0.00 H +ATOM 217 C LYS 13 25.489 20.705 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.585 20.485 31.710 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.785 33.297 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.943 33.873 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.751 33.377 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.446 22.191 33.448 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.484 23.328 34.293 1.00 0.00 H +ATOM 224 C GLY 14 24.287 23.715 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.215 23.890 31.406 1.00 0.00 O +ATOM 226 N VAL 15 23.147 24.399 32.109 1.00 0.00 N +ATOM 227 H VAL 15 22.434 24.248 32.807 1.00 0.00 H +ATOM 228 CA VAL 15 22.780 25.390 31.070 1.00 0.00 C +ATOM 229 HA VAL 15 23.676 25.631 30.490 1.00 0.00 H +ATOM 230 CB VAL 15 21.762 24.738 30.086 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.858 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.449 24.323 30.767 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.939 25.182 31.209 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.794 23.862 30.026 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.583 31.546 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.419 25.672 28.928 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.336 26.009 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.822 25.122 28.195 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.846 26.536 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.285 26.687 31.731 1.00 0.00 C +ATOM 241 O VAL 15 21.718 26.631 32.821 1.00 0.00 O +HETATM 242 N HY1 16 22.497 27.830 31.092 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.110 31.451 1.00 0.00 C +HETATM 244 C HY1 16 21.621 29.885 30.134 1.00 0.00 C +HETATM 245 O HY1 16 21.778 29.349 29.016 1.00 0.00 O +HETATM 246 CB HY1 16 22.863 29.871 32.416 1.00 0.00 C +HETATM 247 CG HY1 16 24.211 30.224 31.815 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.548 31.406 31.209 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.320 29.397 31.739 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.302 30.092 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.879 31.315 30.787 1.00 0.00 N +HETATM 252 H HY1 16 22.998 27.783 30.212 1.00 0.00 H +HETATM 253 HA HY1 16 20.967 28.994 31.944 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.401 30.797 32.776 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.027 29.259 33.299 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.398 28.459 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.906 32.259 31.098 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.729 30.997 1.00 0.00 H +ATOM 259 N THR 17 21.169 31.140 30.273 1.00 0.00 N +ATOM 260 H THR 17 21.053 31.461 31.222 1.00 0.00 H +ATOM 261 CA THR 17 20.726 32.026 29.180 1.00 0.00 C +ATOM 262 HA THR 17 21.104 31.634 28.291 1.00 0.00 H +ATOM 263 CB THR 17 19.148 32.016 29.046 1.00 0.00 C +ATOM 264 HB THR 17 18.923 32.603 28.170 1.00 0.00 H +ATOM 265 CG2 THR 17 18.589 30.665 28.720 1.00 0.00 C +ATOM 266 HG21 THR 17 18.790 29.907 29.433 1.00 0.00 H +ATOM 267 HG22 THR 17 17.504 30.697 28.632 1.00 0.00 H +ATOM 268 HG23 THR 17 18.931 30.334 27.781 1.00 0.00 H +ATOM 269 OG1 THR 17 18.484 32.465 30.197 1.00 0.00 O +ATOM 270 HG1 THR 17 18.581 33.451 30.206 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.458 29.234 1.00 0.00 C +ATOM 272 O THR 17 21.706 33.922 30.266 1.00 0.00 O +HETATM 273 N HY2 18 21.133 34.157 28.097 1.00 0.00 N +HETATM 274 CA HY2 18 21.447 35.619 27.968 1.00 0.00 C +HETATM 275 C HY2 18 20.323 36.288 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.983 35.838 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.769 35.819 27.255 1.00 0.00 C +HETATM 278 CG HY2 18 23.998 35.326 28.000 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.419 34.029 28.151 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.941 36.119 28.641 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.317 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.707 27.234 1.00 0.00 H +HETATM 284 HA HY2 18 21.501 36.055 29.015 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.747 35.291 26.296 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.912 36.877 27.054 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.952 37.122 28.679 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.930 33.168 27.777 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.758 35.649 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.806 37.389 27.746 1.00 0.00 N +ATOM 291 H GLU 19 20.137 37.679 28.643 1.00 0.00 H +ATOM 292 CA GLU 19 18.797 38.219 27.105 1.00 0.00 C +ATOM 293 HA GLU 19 18.056 37.553 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.066 39.074 28.153 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.753 38.431 28.965 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.774 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.827 39.851 27.656 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.547 28.418 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.083 40.405 26.761 1.00 0.00 H +ATOM 300 CD GLU 19 15.649 38.897 27.370 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.578 38.371 26.227 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.814 38.685 28.283 1.00 0.00 O +ATOM 303 C GLU 19 19.403 39.112 25.991 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.858 26.275 1.00 0.00 O +ATOM 305 N ALA 20 18.876 39.050 24.758 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.353 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.964 23.687 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.962 24.097 1.00 0.00 H +ATOM 309 CB ALA 20 20.589 39.492 23.095 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.463 38.518 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.950 40.207 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.350 39.402 23.869 1.00 0.00 H +ATOM 313 C ALA 20 18.192 40.038 22.583 1.00 0.00 C +ATOM 314 O ALA 20 17.358 39.136 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.090 21.748 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.829 21.922 1.00 0.00 H +ATOM 317 CA VAL 21 17.459 41.152 20.464 1.00 0.00 C +ATOM 318 HA VAL 21 16.471 40.727 20.628 1.00 0.00 H +ATOM 319 CB VAL 21 17.272 42.602 19.975 1.00 0.00 C +ATOM 320 HB VAL 21 16.617 42.576 19.112 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.594 43.474 21.037 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.250 43.628 21.894 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.346 44.443 20.604 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.670 43.000 21.367 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.581 43.283 19.543 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.005 42.771 18.677 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.378 44.312 19.246 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.314 43.286 20.353 1.00 0.00 H +ATOM 329 C VAL 21 18.120 40.335 19.354 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.995 18.376 1.00 0.00 O +ATOM 331 N ASP 22 19.412 40.053 19.508 1.00 0.00 N +ATOM 332 H ASP 22 19.861 40.330 20.363 1.00 0.00 H +ATOM 333 CA ASP 22 20.292 39.467 18.503 1.00 0.00 C +ATOM 334 HA ASP 22 19.710 38.829 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.939 40.592 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.170 41.084 17.077 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.376 41.328 18.357 1.00 0.00 H +ATOM 338 CG ASP 22 22.019 40.045 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.149 40.566 16.818 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.744 39.033 16.072 1.00 0.00 O +ATOM 341 C ASP 22 21.365 38.599 19.176 1.00 0.00 C +ATOM 342 O ASP 22 21.822 38.878 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.790 37.551 18.485 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.496 17.513 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.613 18.977 1.00 0.00 C +ATOM 346 HA TRP 23 22.544 36.362 20.008 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.353 18.132 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.979 18.209 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.841 35.607 17.088 1.00 0.00 H +ATOM 350 CG TRP 23 23.572 34.246 18.526 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.514 33.704 17.727 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.735 34.018 16.716 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.125 32.677 18.406 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.897 32.152 18.028 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.587 32.476 19.654 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.823 31.539 20.660 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.537 30.742 20.518 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.687 21.884 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.018 22.698 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.769 22.095 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.906 23.078 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.006 33.662 21.051 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.312 34.470 21.209 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.636 33.530 19.792 1.00 0.00 C +ATOM 365 C TRP 23 24.211 37.188 18.977 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.919 1.00 0.00 O +ATOM 367 N ALA 24 24.560 38.026 17.993 1.00 0.00 N +ATOM 368 H ALA 24 23.884 38.270 17.276 1.00 0.00 H +ATOM 369 CA ALA 24 25.849 38.719 17.975 1.00 0.00 C +ATOM 370 HA ALA 24 26.621 38.003 18.265 1.00 0.00 H +ATOM 371 CB ALA 24 26.163 39.147 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.450 39.890 16.191 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.165 39.568 16.485 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.115 38.282 15.875 1.00 0.00 H +ATOM 375 C ALA 24 25.931 39.882 18.996 1.00 0.00 C +ATOM 376 O ALA 24 27.024 40.380 19.278 1.00 0.00 O +ATOM 377 N GLU 25 24.813 40.289 19.607 1.00 0.00 N +ATOM 378 H GLU 25 23.933 39.955 19.233 1.00 0.00 H +ATOM 379 CA GLU 25 24.789 41.076 20.851 1.00 0.00 C +ATOM 380 HA GLU 25 25.640 41.758 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.510 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.645 41.277 20.821 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.448 42.384 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.425 43.037 19.876 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.627 42.632 18.886 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.402 43.419 19.864 1.00 0.00 H +ATOM 387 CD GLU 25 24.366 44.203 20.189 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.896 45.204 20.734 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.592 44.053 19.851 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.098 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.518 23.014 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.004 22.127 1.00 0.00 N +ATOM 393 H ALA 26 23.667 38.776 21.363 1.00 0.00 H +ATOM 394 CA ALA 26 24.459 38.028 23.214 1.00 0.00 C +ATOM 395 HA ALA 26 24.198 38.523 24.143 1.00 0.00 H +ATOM 396 CB ALA 26 23.492 36.861 23.009 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.772 36.287 22.127 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.202 23.878 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.230 22.889 1.00 0.00 H +ATOM 400 C ALA 26 25.919 37.533 23.362 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.229 24.479 1.00 0.00 O +ATOM 402 N GLU 27 26.712 37.509 22.282 1.00 0.00 N +ATOM 403 H GLU 27 26.270 37.639 21.372 1.00 0.00 H +ATOM 404 CA GLU 27 28.168 37.305 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.370 36.352 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.768 37.249 20.914 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.159 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.737 38.253 20.487 1.00 0.00 H +ATOM 409 CG GLU 27 30.213 36.730 20.925 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.144 21.782 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.198 35.646 21.049 1.00 0.00 H +ATOM 412 CD GLU 27 30.995 37.107 19.653 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.755 38.110 19.729 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.384 18.638 1.00 0.00 O +ATOM 415 C GLU 27 28.847 38.398 23.184 1.00 0.00 C +ATOM 416 O GLU 27 29.569 38.095 24.137 1.00 0.00 O +ATOM 417 N LYS 28 28.546 39.674 22.914 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.855 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.819 23.667 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.668 1.00 0.00 H +ATOM 421 CB LYS 28 28.698 42.147 22.994 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.280 23.051 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.171 42.964 23.544 1.00 0.00 H +ATOM 424 CG LYS 28 29.135 42.222 21.520 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.205 42.027 21.442 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.599 41.464 20.951 1.00 0.00 H +ATOM 427 CD LYS 28 28.836 43.606 20.922 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.820 43.913 21.179 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.525 44.332 21.362 1.00 0.00 H +ATOM 430 CE LYS 28 28.996 43.630 19.397 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.091 44.670 19.083 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.914 43.114 19.123 1.00 0.00 H +ATOM 433 NZ LYS 28 27.828 43.021 18.717 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.969 43.488 19.030 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.884 43.102 17.711 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.711 42.039 18.969 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.783 25.133 1.00 0.00 C +ATOM 438 O LYS 28 29.480 40.969 26.020 1.00 0.00 O +ATOM 439 N PHE 29 27.392 40.453 25.418 1.00 0.00 N +ATOM 440 H PHE 29 26.739 40.365 24.641 1.00 0.00 H +ATOM 441 CA PHE 29 26.901 40.285 26.792 1.00 0.00 C +ATOM 442 HA PHE 29 27.227 41.146 27.381 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.262 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.036 39.343 26.309 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.020 40.229 27.831 1.00 0.00 H +ATOM 446 CG PHE 29 24.675 41.444 26.115 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.462 41.234 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.013 40.254 25.408 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.829 42.300 24.768 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.903 42.125 24.236 1.00 0.00 H +ATOM 451 CZ PHE 29 23.396 43.583 24.789 1.00 0.00 C +ATOM 452 HZ PHE 29 22.917 44.395 24.266 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.589 43.803 25.497 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.025 44.796 25.526 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.225 42.742 26.163 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.138 42.936 26.702 1.00 0.00 H +ATOM 457 C PHE 29 27.483 39.049 27.505 1.00 0.00 C +ATOM 458 O PHE 29 27.587 39.036 28.736 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.764 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.043 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.685 36.894 27.317 1.00 0.00 C +ATOM 462 HA THR 30 28.209 36.547 28.224 1.00 0.00 H +ATOM 463 CB THR 30 28.691 35.719 26.332 1.00 0.00 C +ATOM 464 HB THR 30 29.069 36.026 25.354 1.00 0.00 H +ATOM 465 CG2 THR 30 29.495 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.132 34.215 27.800 1.00 0.00 H +ATOM 467 HG22 THR 30 29.364 33.689 26.122 1.00 0.00 H +ATOM 468 HG23 THR 30 30.558 34.743 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.366 35.283 26.192 1.00 0.00 O +ATOM 470 HG1 THR 30 26.961 35.884 25.541 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.981 28.768 1.00 0.00 O +ATOM 473 N LYS 31 30.744 38.121 26.830 1.00 0.00 N +ATOM 474 H LYS 31 30.286 38.318 25.946 1.00 0.00 H +ATOM 475 CA LYS 31 32.077 38.701 27.066 1.00 0.00 C +ATOM 476 HA LYS 31 32.746 37.904 27.373 1.00 0.00 H +ATOM 477 CB LYS 31 32.614 39.317 25.767 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.010 25.345 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.526 39.864 25.984 1.00 0.00 H +ATOM 480 CG LYS 31 32.928 38.207 24.738 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.681 37.552 25.175 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.044 37.631 24.523 1.00 0.00 H +ATOM 483 CD LYS 31 33.460 38.815 23.434 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.383 22.946 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.300 39.496 23.639 1.00 0.00 H +ATOM 486 CE LYS 31 33.922 37.721 22.460 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.110 37.056 22.242 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.219 38.192 21.541 1.00 0.00 H +ATOM 489 NZ LYS 31 35.076 36.972 23.012 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.820 36.242 23.678 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.551 36.467 22.263 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.761 37.564 23.504 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.185 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.781 28.913 1.00 0.00 O +ATOM 495 N ALA 32 31.030 40.509 28.371 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.874 41.413 29.513 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.139 29.502 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.372 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.494 29.373 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.876 30.212 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.556 42.756 28.443 1.00 0.00 H +ATOM 503 C ALA 32 30.964 40.640 30.836 1.00 0.00 C +ATOM 504 O ALA 32 31.880 40.889 31.614 1.00 0.00 O +ATOM 505 N LYN 33 30.119 39.614 31.029 1.00 0.00 N +ATOM 506 H LYN 33 29.393 39.457 30.345 1.00 0.00 H +ATOM 507 CA LYN 33 30.159 38.756 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.026 39.385 33.109 1.00 0.00 H +ATOM 509 CB LYN 33 29.011 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.063 37.156 31.263 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.143 37.040 33.026 1.00 0.00 H +ATOM 512 CG LYN 33 27.613 38.360 32.313 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.566 38.985 33.205 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.415 38.982 31.441 1.00 0.00 H +ATOM 515 CD LYN 33 26.538 37.269 32.411 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.694 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.634 36.750 33.364 1.00 0.00 H +ATOM 518 CE LYN 33 25.125 37.836 32.286 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.936 38.516 33.109 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.037 38.375 31.345 1.00 0.00 H +ATOM 521 NZ LYN 33 24.119 36.762 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.186 37.155 32.262 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.255 36.114 31.546 1.00 0.00 H +ATOM 524 C LYN 33 31.513 38.043 32.390 1.00 0.00 C +ATOM 525 O LYN 33 32.011 37.922 33.504 1.00 0.00 O +ATOM 526 N ALA 34 32.145 37.587 31.303 1.00 0.00 N +ATOM 527 H ALA 34 31.697 37.679 30.398 1.00 0.00 H +ATOM 528 CA ALA 34 33.472 36.969 31.385 1.00 0.00 C +ATOM 529 HA ALA 34 33.431 36.162 32.122 1.00 0.00 H +ATOM 530 CB ALA 34 33.818 36.357 30.025 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.964 37.148 29.291 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.777 30.128 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.697 29.695 1.00 0.00 H +ATOM 534 C ALA 34 34.575 37.949 31.862 1.00 0.00 C +ATOM 535 O ALA 34 35.472 37.543 32.601 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.228 31.485 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.508 30.883 1.00 0.00 H +ATOM 538 CA ASN 35 35.366 40.292 31.998 1.00 0.00 C +ATOM 539 HA ASN 35 36.365 39.875 32.114 1.00 0.00 H +ATOM 540 CB ASN 35 35.477 41.419 30.965 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.487 41.705 30.621 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.289 31.446 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.032 29.797 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.582 41.001 29.896 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.708 28.665 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.450 27.893 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.606 28.624 1.00 0.00 H +ATOM 548 C ASN 35 34.979 40.792 33.401 1.00 0.00 C +ATOM 549 O ASN 35 35.862 41.217 34.149 1.00 0.00 O +ATOM 550 N ASP 36 33.716 40.637 33.828 1.00 0.00 N +ATOM 551 H ASP 36 32.980 40.415 33.164 1.00 0.00 H +ATOM 552 CA ASP 36 33.336 40.771 35.246 1.00 0.00 C +ATOM 553 HA ASP 36 33.662 41.747 35.601 1.00 0.00 H +ATOM 554 CB ASP 36 31.821 40.770 35.436 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.447 39.787 35.228 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.605 40.869 36.494 1.00 0.00 H +ATOM 557 CG ASP 36 30.980 41.783 34.656 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.511 42.875 34.375 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.773 41.517 34.399 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.709 36.121 1.00 0.00 C +ATOM 561 O ASP 36 34.483 40.005 37.231 1.00 0.00 O +ATOM 562 N PHE 37 34.225 38.482 35.605 1.00 0.00 N +ATOM 563 H PHE 37 33.748 38.284 34.733 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.460 36.169 1.00 0.00 C +ATOM 565 HA PHE 37 35.119 37.613 37.247 1.00 0.00 H +ATOM 566 CB PHE 37 34.572 36.046 35.924 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.659 35.830 34.863 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.338 36.433 1.00 0.00 H +ATOM 569 CG PHE 37 33.149 35.766 36.381 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.137 35.554 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.369 35.612 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.307 35.837 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.038 35.189 35.100 1.00 0.00 H +ATOM 574 CZ PHE 37 30.512 35.237 37.203 1.00 0.00 C +ATOM 575 HZ PHE 37 29.500 35.052 37.516 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.521 35.411 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.278 35.363 39.212 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.836 35.675 37.747 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.604 35.826 38.483 1.00 0.00 H +ATOM 580 C PHE 37 36.605 37.583 35.730 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.678 35.998 1.00 0.00 O +ATOM 582 N GLY 38 36.994 38.685 35.076 1.00 0.00 N +ATOM 583 H GLY 38 36.290 39.389 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.388 39.099 34.834 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.496 40.119 35.199 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.053 38.480 35.433 1.00 0.00 H +ATOM 587 C GLY 38 38.924 39.067 33.387 1.00 0.00 C +ATOM 588 O GLY 38 39.870 39.802 33.105 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.230 32.483 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.729 32.758 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.054 31.088 1.00 0.00 C +ATOM 592 HA ARG 39 38.947 39.047 30.642 1.00 0.00 H +ATOM 593 CB ARG 39 40.303 37.441 31.074 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.636 37.432 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.986 38.107 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.521 36.014 31.626 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.035 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.754 31.462 1.00 0.00 H +ATOM 599 CD ARG 39 40.216 35.825 33.129 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.853 36.510 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.175 36.078 33.336 1.00 0.00 H +ATOM 602 NE ARG 39 40.443 34.444 33.597 1.00 0.00 N +ATOM 603 HE ARG 39 41.200 34.298 34.242 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.298 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.466 32.486 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.428 34.356 32.087 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.300 32.617 32.077 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.956 32.225 33.814 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.695 32.096 34.486 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.340 31.449 33.597 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.227 30.190 1.00 0.00 C +ATOM 612 O ARG 39 37.524 36.139 30.601 1.00 0.00 O +ATOM 613 N ASP 40 37.649 37.680 28.957 1.00 0.00 N +ATOM 614 H ASP 40 38.027 38.575 28.671 1.00 0.00 H +ATOM 615 CA ASP 40 36.888 36.895 27.965 1.00 0.00 C +ATOM 616 HA ASP 40 36.165 36.313 28.528 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.736 26.967 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.446 37.041 26.398 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.370 38.354 27.534 1.00 0.00 H +ATOM 620 CG ASP 40 36.827 38.629 25.966 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.259 39.727 26.388 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.844 38.320 24.740 1.00 0.00 O +ATOM 623 C ASP 40 37.718 35.863 27.180 1.00 0.00 C +ATOM 624 O ASP 40 38.884 36.079 26.863 1.00 0.00 O +ATOM 625 N GLY 41 37.053 34.763 26.809 1.00 0.00 N +ATOM 626 H GLY 41 36.096 34.687 27.112 1.00 0.00 H +ATOM 627 CA GLY 41 37.470 33.830 25.756 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.458 34.102 25.380 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.530 32.827 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.480 33.816 24.578 1.00 0.00 C +ATOM 631 O GLY 41 35.572 34.649 24.502 1.00 0.00 O +ATOM 632 N GLU 42 36.641 32.855 23.669 1.00 0.00 N +ATOM 633 H GLU 42 37.356 32.161 23.819 1.00 0.00 H +ATOM 634 CA GLU 42 35.802 32.668 22.472 1.00 0.00 C +ATOM 635 HA GLU 42 35.115 33.509 22.372 1.00 0.00 H +ATOM 636 CB GLU 42 36.689 32.632 21.211 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.165 31.653 21.165 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.044 32.715 20.336 1.00 0.00 H +ATOM 639 CG GLU 42 37.807 33.696 21.110 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.580 33.458 21.845 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.278 33.628 20.127 1.00 0.00 H +ATOM 642 CD GLU 42 37.351 35.145 21.325 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.164 35.460 21.116 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.176 36.004 21.723 1.00 0.00 O +ATOM 645 C GLU 42 34.953 31.386 22.575 1.00 0.00 C +ATOM 646 O GLU 42 35.399 30.400 23.169 1.00 0.00 O +ATOM 647 N ALA 43 33.750 31.390 21.987 1.00 0.00 N +ATOM 648 H ALA 43 33.482 32.195 21.439 1.00 0.00 H +ATOM 649 CA ALA 43 32.763 30.304 22.059 1.00 0.00 C +ATOM 650 HA ALA 43 33.255 29.386 22.386 1.00 0.00 H +ATOM 651 CB ALA 43 31.699 30.668 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.186 31.588 22.813 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.966 29.860 23.179 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.172 30.808 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.115 30.014 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.888 30.928 19.897 1.00 0.00 O +ATOM 657 N THR 44 31.800 28.743 20.425 1.00 0.00 N +ATOM 658 H THR 44 31.921 28.066 21.171 1.00 0.00 H +ATOM 659 CA THR 44 31.132 28.280 19.197 1.00 0.00 C +ATOM 660 HA THR 44 31.427 28.942 18.384 1.00 0.00 H +ATOM 661 CB THR 44 31.609 26.864 18.828 1.00 0.00 C +ATOM 662 HB THR 44 31.426 26.183 19.661 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.277 17.557 1.00 0.00 C +ATOM 664 HG21 THR 44 31.074 26.985 16.731 1.00 0.00 H +ATOM 665 HG22 THR 44 31.501 25.353 17.284 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.035 17.728 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.918 18.568 1.00 0.00 O +ATOM 668 HG1 THR 44 33.233 26.114 18.102 1.00 0.00 H +ATOM 669 C THR 44 29.607 28.380 19.330 1.00 0.00 C +ATOM 670 O THR 44 29.074 28.429 20.439 1.00 0.00 O +ATOM 671 N ILE 45 28.902 28.457 18.195 1.00 0.00 N +ATOM 672 H ILE 45 29.375 28.320 17.316 1.00 0.00 H +ATOM 673 CA ILE 45 27.480 28.839 18.125 1.00 0.00 C +ATOM 674 HA ILE 45 27.062 28.755 19.129 1.00 0.00 H +ATOM 675 CB ILE 45 27.333 30.312 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.272 30.526 17.776 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.068 31.232 18.675 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.152 31.107 18.585 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.832 32.280 18.494 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.767 30.970 19.686 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.759 30.685 16.250 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.026 31.742 16.230 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.656 30.128 15.967 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.502 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.734 30.942 15.528 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.979 31.006 14.266 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.520 29.448 14.962 1.00 0.00 H +ATOM 688 C ILE 45 26.631 27.921 17.246 1.00 0.00 C +ATOM 689 O ILE 45 27.124 27.339 16.280 1.00 0.00 O +ATOM 690 N ASP 46 25.331 27.876 17.547 1.00 0.00 N +ATOM 691 H ASP 46 25.033 28.294 18.423 1.00 0.00 H +ATOM 692 CA ASP 46 24.283 27.257 16.737 1.00 0.00 C +ATOM 693 HA ASP 46 24.587 27.262 15.685 1.00 0.00 H +ATOM 694 CB ASP 46 24.078 25.805 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.217 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.957 25.786 18.268 1.00 0.00 H +ATOM 697 CG ASP 46 22.842 25.167 16.545 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.473 17.282 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.562 25.433 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.960 28.047 16.852 1.00 0.00 C +ATOM 701 O ASP 46 22.512 28.361 17.957 1.00 0.00 O +ATOM 702 N ASP 47 22.310 28.329 15.718 1.00 0.00 N +ATOM 703 H ASP 47 22.680 27.938 14.863 1.00 0.00 H +ATOM 704 CA ASP 47 20.971 28.922 15.676 1.00 0.00 C +ATOM 705 HA ASP 47 20.879 29.650 16.488 1.00 0.00 H +ATOM 706 CB ASP 47 20.780 29.672 14.348 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.524 30.465 14.258 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.918 28.977 13.517 1.00 0.00 H +ATOM 709 CG ASP 47 19.369 30.276 14.272 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.488 29.678 13.612 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.067 31.233 15.020 1.00 0.00 O +ATOM 712 C ASP 47 19.855 27.874 15.879 1.00 0.00 C +ATOM 713 O ASP 47 18.845 28.182 16.515 1.00 0.00 O +ATOM 714 N ALA 48 20.003 26.633 15.397 1.00 0.00 N +ATOM 715 H ALA 48 20.918 26.339 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.935 25.624 15.414 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.052 14.933 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.422 14.585 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.277 23.964 15.055 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.682 14.517 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.673 24.751 13.581 1.00 0.00 H +ATOM 722 C ALA 48 18.526 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.930 17.102 1.00 0.00 O +ATOM 724 N THR 49 19.478 25.244 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.438 25.291 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.267 25.119 19.230 1.00 0.00 C +ATOM 727 HA THR 49 18.217 24.871 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.101 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.822 23.860 20.869 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.626 19.138 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.663 18.100 1.00 0.00 H +ATOM 732 HG22 THR 49 20.431 21.855 19.655 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.166 1.00 0.00 H +ATOM 734 OG1 THR 49 21.479 24.241 19.772 1.00 0.00 O +ATOM 735 HG1 THR 49 21.731 24.265 18.814 1.00 0.00 H +ATOM 736 C THR 49 19.506 26.430 20.000 1.00 0.00 C +ATOM 737 O THR 49 19.425 26.431 21.224 1.00 0.00 O +ATOM 738 N LYS 50 19.768 27.552 19.311 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.294 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.905 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.356 29.539 19.085 1.00 0.00 H +ATOM 742 CB LYS 50 18.568 29.470 20.294 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.163 28.830 21.071 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.701 30.460 20.734 1.00 0.00 H +ATOM 745 CG LYS 50 17.490 29.595 19.184 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.427 28.653 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.736 19.684 1.00 0.00 H +ATOM 748 CD LYS 50 17.702 30.770 18.225 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.701 31.693 18.812 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.686 17.722 1.00 0.00 H +ATOM 751 CE LYS 50 16.567 30.866 17.186 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.595 17.663 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.503 31.892 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.995 16.015 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.233 29.097 16.281 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.015 29.834 15.433 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.545 30.416 15.422 1.00 0.00 H +ATOM 758 C LYS 50 20.985 28.947 21.017 1.00 0.00 C +ATOM 759 O LYS 50 20.690 29.519 22.087 1.00 0.00 O +ATOM 760 N THR 51 22.149 28.291 20.853 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.965 19.930 1.00 0.00 H +ATOM 762 CA THR 51 23.056 27.909 21.961 1.00 0.00 C +ATOM 763 HA THR 51 22.764 28.428 22.859 1.00 0.00 H +ATOM 764 CB THR 51 22.887 26.405 22.276 1.00 0.00 C +ATOM 765 HB THR 51 22.977 25.816 21.351 1.00 0.00 H +ATOM 766 CG2 THR 51 23.852 25.861 23.315 1.00 0.00 C +ATOM 767 HG21 THR 51 23.811 26.476 24.217 1.00 0.00 H +ATOM 768 HG22 THR 51 23.574 24.839 23.587 1.00 0.00 H +ATOM 769 HG23 THR 51 24.879 25.834 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.642 26.171 22.880 1.00 0.00 O +ATOM 771 HG1 THR 51 20.952 26.250 22.187 1.00 0.00 H +ATOM 772 C THR 51 24.558 28.226 21.727 1.00 0.00 C +ATOM 773 O THR 51 25.088 27.999 20.643 1.00 0.00 O +ATOM 774 N PHE 52 25.247 28.694 22.774 1.00 0.00 N +ATOM 775 H PHE 52 24.711 28.955 23.594 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.776 22.877 1.00 0.00 C +ATOM 777 HA PHE 52 27.143 28.936 21.901 1.00 0.00 H +ATOM 778 CB PHE 52 27.150 29.949 23.826 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.478 29.957 24.658 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.734 24.192 1.00 0.00 H +ATOM 781 CG PHE 52 27.216 31.350 23.227 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.432 32.382 23.751 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.753 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.448 33.649 23.160 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.778 34.433 23.517 1.00 0.00 H +ATOM 786 CZ PHE 52 27.282 33.889 22.068 1.00 0.00 C +ATOM 787 HZ PHE 52 27.247 34.834 21.561 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.159 32.900 21.619 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.839 33.106 20.790 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.629 22.200 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.776 30.856 21.829 1.00 0.00 H +ATOM 792 C PHE 52 27.330 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.807 27.009 24.507 1.00 0.00 O +ATOM 794 N THR 53 28.485 27.065 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.850 27.522 22.148 1.00 0.00 H +ATOM 796 CA THR 53 29.279 25.926 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.045 25.794 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.933 24.610 22.780 1.00 0.00 C +ATOM 799 HB THR 53 29.508 23.801 23.237 1.00 0.00 H +ATOM 800 CG2 THR 53 27.457 24.224 22.859 1.00 0.00 C +ATOM 801 HG21 THR 53 26.863 24.906 22.251 1.00 0.00 H +ATOM 802 HG22 THR 53 27.322 23.209 22.490 1.00 0.00 H +ATOM 803 HG23 THR 53 27.120 24.269 23.894 1.00 0.00 H +ATOM 804 OG1 THR 53 29.270 24.680 21.419 1.00 0.00 O +ATOM 805 HG1 THR 53 28.753 24.016 20.952 1.00 0.00 H +ATOM 806 C THR 53 30.801 26.146 23.414 1.00 0.00 C +ATOM 807 O THR 53 31.285 27.021 22.692 1.00 0.00 O +ATOM 808 N THR 54 31.568 25.322 24.142 1.00 0.00 N +ATOM 809 H THR 54 31.108 24.646 24.732 1.00 0.00 H +ATOM 810 CA THR 54 33.040 25.237 24.079 1.00 0.00 C +ATOM 811 HA THR 54 33.413 26.032 23.433 1.00 0.00 H +ATOM 812 CB THR 54 33.664 25.450 25.472 1.00 0.00 C +ATOM 813 HB THR 54 33.370 24.631 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.192 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.513 26.333 24.768 1.00 0.00 H +ATOM 816 HG22 THR 54 35.549 25.815 26.469 1.00 0.00 H +ATOM 817 HG23 THR 54 35.638 24.608 25.194 1.00 0.00 H +ATOM 818 OG1 THR 54 33.199 26.661 26.022 1.00 0.00 O +ATOM 819 HG1 THR 54 33.873 26.996 26.616 1.00 0.00 H +ATOM 820 C THR 54 33.478 23.891 23.475 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.889 23.606 1.00 0.00 O +ATOM 822 N GLN 55 34.634 23.874 22.804 1.00 0.00 N +ATOM 823 H GLN 55 35.155 24.736 22.760 1.00 0.00 H +ATOM 824 CA GLN 55 35.263 22.689 22.197 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.160 21.641 1.00 0.00 H +ATOM 826 CB GLN 55 36.318 23.157 21.174 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.731 22.289 20.660 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.803 23.768 20.429 1.00 0.00 H +ATOM 829 CG GLN 55 37.480 23.990 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.094 24.710 22.481 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.176 23.332 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.246 24.768 20.685 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.322 24.390 19.522 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.828 25.897 21.030 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.406 26.349 20.327 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.721 26.270 21.959 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.678 23.227 1.00 0.00 C +ATOM 838 O GLN 55 36.115 22.046 24.365 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.411 22.806 1.00 0.00 N +ATOM 840 H GLU 56 35.791 20.230 21.834 1.00 0.00 H +ATOM 841 CA GLU 56 36.494 19.248 23.574 1.00 0.00 C +ATOM 842 HA GLU 56 36.158 19.336 24.606 1.00 0.00 H +ATOM 843 CB GLU 56 35.887 17.954 22.970 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.807 17.983 23.079 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.991 21.899 1.00 0.00 H +ATOM 846 CG GLU 56 36.406 16.581 23.466 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.470 15.932 22.595 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.421 16.670 23.824 1.00 0.00 H +ATOM 849 CD GLU 56 35.546 15.853 24.519 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.084 15.362 25.545 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.329 15.640 24.294 1.00 0.00 O +ATOM 852 C GLU 56 38.033 19.203 23.640 1.00 0.00 C +ATOM 853 O GLU 56 38.543 19.194 24.791 1.00 0.00 O +ATOM 854 OXT GLU 56 38.679 19.135 22.573 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.719 32.459 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.327 33.243 30.276 1.00 0.00 N +HETATM 857 C AN1 58 30.687 33.879 31.201 1.00 0.00 C +HETATM 858 C1 AN1 58 29.383 33.533 30.715 1.00 0.00 C +HETATM 859 H AN1 58 30.624 34.272 32.222 1.00 0.00 H +HETATM 860 H1 AN1 58 31.138 34.632 30.547 1.00 0.00 H +HETATM 861 H2 AN1 58 31.318 32.977 31.202 1.00 0.00 H +HETATM 862 N1 AZI 59 31.274 30.374 29.435 1.00 0.00 N +HETATM 863 N2 AZI 59 30.476 30.257 30.351 1.00 0.00 N +HETATM 864 N3 AZI 59 29.630 30.157 31.296 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 148 144 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 639 643 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_2_front_1.pdb b/tests/nsga2/intermediate_molecules/min_iter_2_front_1.pdb new file mode 100644 index 0000000..6fcd112 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_2_front_1.pdb @@ -0,0 +1,1745 @@ +COMPND fitness: -2.8894 84.35416666666652 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 56.210 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.610 37.835 23.460 1.00 0.00 N +ATOM 2 H1 MET 1 14.587 38.236 24.394 1.00 0.00 H +ATOM 3 H2 MET 1 13.812 38.148 22.935 1.00 0.00 H +ATOM 4 H3 MET 1 15.464 38.178 23.039 1.00 0.00 H +ATOM 5 CA MET 1 14.662 36.367 23.555 1.00 0.00 C +ATOM 6 HA MET 1 13.728 36.021 23.999 1.00 0.00 H +ATOM 7 CB MET 1 14.806 35.736 22.157 1.00 0.00 C +ATOM 8 HB2 MET 1 13.928 35.994 21.567 1.00 0.00 H +ATOM 9 HB3 MET 1 15.682 36.159 21.666 1.00 0.00 H +ATOM 10 CG MET 1 14.957 34.205 22.185 1.00 0.00 C +ATOM 11 HG2 MET 1 15.847 33.953 22.764 1.00 0.00 H +ATOM 12 HG3 MET 1 14.092 33.769 22.688 1.00 0.00 H +ATOM 13 SD MET 1 15.133 33.423 20.557 1.00 0.00 S +ATOM 14 CE MET 1 13.430 33.524 19.932 1.00 0.00 C +ATOM 15 HE1 MET 1 13.103 34.563 19.883 1.00 0.00 H +ATOM 16 HE2 MET 1 13.381 33.092 18.933 1.00 0.00 H +ATOM 17 HE3 MET 1 12.763 32.967 20.591 1.00 0.00 H +ATOM 18 C MET 1 15.802 35.945 24.478 1.00 0.00 C +ATOM 19 O MET 1 16.945 36.312 24.240 1.00 0.00 O +ATOM 20 N GLN 2 15.501 35.116 25.481 1.00 0.00 N +ATOM 21 H GLN 2 14.536 34.897 25.661 1.00 0.00 H +ATOM 22 CA GLN 2 16.493 34.445 26.330 1.00 0.00 C +ATOM 23 HA GLN 2 17.239 35.169 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 15.772 33.892 27.577 1.00 0.00 C +ATOM 25 HB2 GLN 2 14.850 33.401 27.264 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.383 33.136 28.064 1.00 0.00 H +ATOM 27 CG GLN 2 15.424 34.965 28.621 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.944 35.807 28.133 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.697 34.542 29.314 1.00 0.00 H +ATOM 30 CD GLN 2 16.606 35.446 29.461 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.750 35.034 29.311 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.365 36.275 30.448 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.141 36.537 31.027 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.429 36.623 30.586 1.00 0.00 H +ATOM 35 C GLN 2 17.242 33.339 25.554 1.00 0.00 C +ATOM 36 O GLN 2 16.895 32.159 25.641 1.00 0.00 O +ATOM 37 N TYR 3 18.267 33.710 24.779 1.00 0.00 N +ATOM 38 H TYR 3 18.507 34.698 24.761 1.00 0.00 H +ATOM 39 CA TYR 3 19.130 32.772 24.050 1.00 0.00 C +ATOM 40 HA TYR 3 18.508 32.164 23.394 1.00 0.00 H +ATOM 41 CB TYR 3 20.138 33.545 23.190 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.628 34.306 23.802 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.913 32.853 22.855 1.00 0.00 H +ATOM 44 CG TYR 3 19.537 34.200 21.959 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.394 33.447 20.777 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.704 32.411 20.758 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.869 34.045 19.616 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.784 33.476 18.703 1.00 0.00 H +ATOM 49 CZ TYR 3 18.472 35.400 19.642 1.00 0.00 C +ATOM 50 OH TYR 3 17.979 35.981 18.519 1.00 0.00 O +ATOM 51 HH TYR 3 17.916 35.355 17.795 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.600 36.150 20.830 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.290 37.185 20.841 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.136 35.550 21.987 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.235 36.130 22.896 1.00 0.00 H +ATOM 56 C TYR 3 19.865 31.833 25.021 1.00 0.00 C +ATOM 57 O TYR 3 20.356 32.276 26.061 1.00 0.00 O +ATOM 58 N LYS 4 19.933 30.534 24.705 1.00 0.00 N +ATOM 59 H LYS 4 19.658 30.251 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 20.470 29.488 25.599 1.00 0.00 C +ATOM 61 HA LYS 4 20.193 29.725 26.622 1.00 0.00 H +ATOM 62 CB LYS 4 19.857 28.117 25.237 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.784 28.034 24.153 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.538 27.331 25.568 1.00 0.00 H +ATOM 65 CG LYS 4 18.476 27.805 25.856 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.226 26.778 25.589 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.551 27.859 26.942 1.00 0.00 H +ATOM 68 CD LYS 4 17.329 28.710 25.376 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.488 29.726 25.728 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.350 28.733 24.285 1.00 0.00 H +ATOM 71 CE LYS 4 15.930 28.229 25.815 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.191 28.785 25.230 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.824 27.174 25.545 1.00 0.00 H +ATOM 74 NZ LYS 4 15.640 28.425 27.266 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.696 29.397 27.534 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.693 28.146 27.503 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.250 27.898 27.886 1.00 0.00 H +ATOM 78 C LYS 4 22.000 29.450 25.582 1.00 0.00 C +ATOM 79 O LYS 4 22.635 29.697 24.563 1.00 0.00 O +HETATM 80 N HX1 5 22.614 29.087 26.706 1.00 0.00 N +HETATM 81 CA HX1 5 24.068 28.924 26.868 1.00 0.00 C +HETATM 82 C HX1 5 24.352 27.735 27.797 1.00 0.00 C +HETATM 83 O HX1 5 23.963 27.749 28.965 1.00 0.00 O +HETATM 84 CB HX1 5 24.686 30.249 27.361 1.00 0.00 C +HETATM 85 CG HX1 5 26.205 30.328 27.453 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.096 29.341 27.126 1.00 0.00 C +HETATM 87 ND1 HX1 5 26.899 31.425 27.989 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.188 31.059 27.927 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.345 29.815 27.484 1.00 0.00 N +HETATM 90 H HX1 5 22.036 28.964 27.535 1.00 0.00 H +HETATM 91 HA HX1 5 24.511 28.691 25.903 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.270 30.493 28.340 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.367 31.041 26.681 1.00 0.00 H +HETATM 94 HD2 HX1 5 26.901 28.351 26.753 1.00 0.00 H +HETATM 95 HE1 HX1 5 28.999 31.640 28.362 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.166 29.232 27.691 1.00 0.00 H +ATOM 97 N ILE 6 24.976 26.694 27.247 1.00 0.00 N +ATOM 98 H ILE 6 25.273 26.764 26.279 1.00 0.00 H +ATOM 99 CA ILE 6 25.416 25.484 27.957 1.00 0.00 C +ATOM 100 HA ILE 6 24.791 25.350 28.841 1.00 0.00 H +ATOM 101 CB ILE 6 25.219 24.234 27.066 1.00 0.00 C +ATOM 102 HB ILE 6 25.717 24.411 26.111 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.833 22.967 27.697 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.377 22.767 28.667 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.684 22.105 27.049 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.912 23.079 27.816 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.703 24.039 26.816 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.199 23.911 27.773 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.300 24.935 26.343 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.331 22.853 25.919 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.511 21.913 26.441 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.269 22.909 25.674 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.912 22.881 24.996 1.00 0.00 H +ATOM 114 C ILE 6 26.855 25.666 28.457 1.00 0.00 C +ATOM 115 O ILE 6 27.669 26.350 27.833 1.00 0.00 O +ATOM 116 N VAL 7 27.116 25.088 29.628 1.00 0.00 N +ATOM 117 H VAL 7 26.386 24.493 30.005 1.00 0.00 H +ATOM 118 CA VAL 7 28.247 25.361 30.522 1.00 0.00 C +ATOM 119 HA VAL 7 28.279 26.437 30.666 1.00 0.00 H +ATOM 120 CB VAL 7 27.910 24.707 31.877 1.00 0.00 C +ATOM 121 HB VAL 7 26.872 24.951 32.111 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.029 23.177 31.837 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.076 22.879 31.779 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.576 22.749 32.720 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.511 22.784 30.962 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.732 25.253 33.046 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.660 26.340 33.068 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.348 24.861 33.986 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.770 24.958 32.940 1.00 0.00 H +ATOM 130 C VAL 7 29.638 24.925 30.014 1.00 0.00 C +ATOM 131 O VAL 7 29.787 23.876 29.396 1.00 0.00 O +ATOM 132 N ARG 8 30.669 25.690 30.392 1.00 0.00 N +ATOM 133 H ARG 8 30.448 26.631 30.693 1.00 0.00 H +ATOM 134 CA ARG 8 32.095 25.295 30.376 1.00 0.00 C +ATOM 135 HA ARG 8 32.337 25.066 29.335 1.00 0.00 H +ATOM 136 CB ARG 8 33.001 26.478 30.815 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.031 26.191 30.597 1.00 0.00 H +ATOM 138 HB3 ARG 8 32.778 27.341 30.186 1.00 0.00 H +ATOM 139 CG ARG 8 32.964 26.926 32.298 1.00 0.00 C +ATOM 140 HG2 ARG 8 33.166 26.074 32.950 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.772 27.646 32.453 1.00 0.00 H +ATOM 142 CD ARG 8 31.641 27.598 32.706 1.00 0.00 C +ATOM 143 HD2 ARG 8 31.523 28.498 32.102 1.00 0.00 H +ATOM 144 HD3 ARG 8 30.811 26.937 32.492 1.00 0.00 H +ATOM 145 NE ARG 8 31.554 27.975 34.136 1.00 0.00 N +ATOM 146 HE ARG 8 31.477 28.963 34.328 1.00 0.00 H +ATOM 147 CZ ARG 8 31.360 27.181 35.177 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.436 25.880 35.096 1.00 0.00 N +ATOM 149 HH11 ARG 8 31.653 25.451 34.206 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.280 25.329 35.915 1.00 0.00 H +ATOM 151 NH2 ARG 8 31.059 27.706 36.329 1.00 0.00 N +ATOM 152 HH21 ARG 8 30.883 28.704 36.414 1.00 0.00 H +ATOM 153 HH22 ARG 8 30.972 27.170 37.183 1.00 0.00 H +ATOM 154 C ARG 8 32.399 24.032 31.197 1.00 0.00 C +ATOM 155 O ARG 8 31.989 23.928 32.359 1.00 0.00 O +ATOM 156 N GLY 9 33.235 23.149 30.643 1.00 0.00 N +ATOM 157 H GLY 9 33.483 23.302 29.677 1.00 0.00 H +ATOM 158 CA GLY 9 33.803 21.970 31.313 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.769 21.741 30.856 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.977 22.203 32.366 1.00 0.00 H +ATOM 161 C GLY 9 32.930 20.700 31.255 1.00 0.00 C +ATOM 162 O GLY 9 31.748 20.758 30.940 1.00 0.00 O +ATOM 163 N LYS 10 33.531 19.549 31.601 1.00 0.00 N +ATOM 164 H LYS 10 34.504 19.593 31.865 1.00 0.00 H +ATOM 165 CA LYS 10 32.919 18.202 31.470 1.00 0.00 C +ATOM 166 HA LYS 10 31.934 18.338 31.024 1.00 0.00 H +ATOM 167 CB LYS 10 33.740 17.354 30.479 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.240 18.008 29.765 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.509 16.801 31.019 1.00 0.00 H +ATOM 170 CG LYS 10 32.870 16.377 29.670 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.314 15.722 30.339 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.155 16.955 29.085 1.00 0.00 H +ATOM 173 CD LYS 10 33.734 15.532 28.729 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.372 16.192 28.137 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.363 14.862 29.315 1.00 0.00 H +ATOM 176 CE LYS 10 32.861 14.716 27.778 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.249 14.019 28.356 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.207 15.410 27.249 1.00 0.00 H +ATOM 179 NZ LYS 10 33.702 14.007 26.788 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.337 13.350 27.224 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.169 13.532 26.081 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.296 14.687 26.297 1.00 0.00 H +ATOM 183 C LYS 10 32.637 17.486 32.799 1.00 0.00 C +ATOM 184 O LYS 10 32.284 16.311 32.824 1.00 0.00 O +ATOM 185 N TRP 11 32.824 18.177 33.926 1.00 0.00 N +ATOM 186 H TRP 11 33.243 19.090 33.848 1.00 0.00 H +ATOM 187 CA TRP 11 32.126 17.892 35.182 1.00 0.00 C +ATOM 188 HA TRP 11 31.901 16.824 35.268 1.00 0.00 H +ATOM 189 CB TRP 11 33.036 18.283 36.357 1.00 0.00 C +ATOM 190 HB2 TRP 11 32.535 18.015 37.294 1.00 0.00 H +ATOM 191 HB3 TRP 11 33.950 17.689 36.296 1.00 0.00 H +ATOM 192 CG TRP 11 33.419 19.737 36.406 1.00 0.00 C +ATOM 193 CD1 TRP 11 32.861 20.665 37.216 1.00 0.00 C +ATOM 194 HD1 TRP 11 32.089 20.465 37.950 1.00 0.00 H +ATOM 195 NE1 TRP 11 33.403 21.907 36.943 1.00 0.00 N +ATOM 196 HE1 TRP 11 33.141 22.745 37.445 1.00 0.00 H +ATOM 197 CE2 TRP 11 34.318 21.848 35.912 1.00 0.00 C +ATOM 198 CZ2 TRP 11 35.085 22.819 35.250 1.00 0.00 C +ATOM 199 HZ2 TRP 11 35.003 23.862 35.519 1.00 0.00 H +ATOM 200 CH2 TRP 11 35.984 22.415 34.248 1.00 0.00 C +ATOM 201 HH2 TRP 11 36.605 23.145 33.744 1.00 0.00 H +ATOM 202 CZ3 TRP 11 36.107 21.052 33.924 1.00 0.00 C +ATOM 203 HZ3 TRP 11 36.838 20.745 33.183 1.00 0.00 H +ATOM 204 CE3 TRP 11 35.320 20.087 34.584 1.00 0.00 C +ATOM 205 HE3 TRP 11 35.461 19.041 34.352 1.00 0.00 H +ATOM 206 CD2 TRP 11 34.391 20.460 35.583 1.00 0.00 C +ATOM 207 C TRP 11 30.804 18.683 35.243 1.00 0.00 C +ATOM 208 O TRP 11 29.944 18.363 36.056 1.00 0.00 O +ATOM 209 N VAL 12 30.660 19.740 34.430 1.00 0.00 N +ATOM 210 H VAL 12 31.413 19.900 33.802 1.00 0.00 H +ATOM 211 CA VAL 12 29.415 20.530 34.220 1.00 0.00 C +ATOM 212 HA VAL 12 29.656 21.259 33.447 1.00 0.00 H +ATOM 213 CB VAL 12 29.101 21.349 35.518 1.00 0.00 C +ATOM 214 HB VAL 12 29.296 20.712 36.378 1.00 0.00 H +ATOM 215 CG1 VAL 12 27.725 21.975 35.716 1.00 0.00 C +ATOM 216 HG11 VAL 12 26.970 21.208 35.955 1.00 0.00 H +ATOM 217 HG12 VAL 12 27.751 22.645 36.588 1.00 0.00 H +ATOM 218 HG13 VAL 12 27.441 22.553 34.835 1.00 0.00 H +ATOM 219 CG2 VAL 12 30.126 22.530 35.519 1.00 0.00 C +ATOM 220 HG21 VAL 12 29.940 23.175 34.670 1.00 0.00 H +ATOM 221 HG22 VAL 12 30.055 23.143 36.414 1.00 0.00 H +ATOM 222 HG23 VAL 12 31.147 22.192 35.430 1.00 0.00 H +ATOM 223 C VAL 12 28.340 19.651 33.542 1.00 0.00 C +ATOM 224 O VAL 12 28.703 18.718 32.836 1.00 0.00 O +ATOM 225 N LYS 13 27.051 19.990 33.615 1.00 0.00 N +ATOM 226 H LYS 13 26.818 20.626 34.355 1.00 0.00 H +ATOM 227 CA LYS 13 26.031 19.654 32.590 1.00 0.00 C +ATOM 228 HA LYS 13 26.538 19.769 31.626 1.00 0.00 H +ATOM 229 CB LYS 13 25.592 18.175 32.709 1.00 0.00 C +ATOM 230 HB2 LYS 13 26.368 17.610 33.220 1.00 0.00 H +ATOM 231 HB3 LYS 13 24.698 18.118 33.320 1.00 0.00 H +ATOM 232 CG LYS 13 25.353 17.514 31.333 1.00 0.00 C +ATOM 233 HG2 LYS 13 24.456 17.931 30.874 1.00 0.00 H +ATOM 234 HG3 LYS 13 26.197 17.751 30.683 1.00 0.00 H +ATOM 235 CD LYS 13 25.238 15.981 31.410 1.00 0.00 C +ATOM 236 HD2 LYS 13 25.170 15.578 30.397 1.00 0.00 H +ATOM 237 HD3 LYS 13 26.145 15.589 31.878 1.00 0.00 H +ATOM 238 CE LYS 13 24.004 15.541 32.208 1.00 0.00 C +ATOM 239 HE2 LYS 13 23.955 16.153 33.114 1.00 0.00 H +ATOM 240 HE3 LYS 13 23.108 15.743 31.609 1.00 0.00 H +ATOM 241 NZ LYS 13 24.068 14.106 32.592 1.00 0.00 N +ATOM 242 HZ1 LYS 13 24.999 13.834 32.897 1.00 0.00 H +ATOM 243 HZ2 LYS 13 23.472 13.932 33.399 1.00 0.00 H +ATOM 244 HZ3 LYS 13 23.792 13.478 31.849 1.00 0.00 H +ATOM 245 C LYS 13 24.841 20.629 32.531 1.00 0.00 C +ATOM 246 O LYS 13 23.849 20.366 31.856 1.00 0.00 O +ATOM 247 N GLY 14 24.939 21.740 33.268 1.00 0.00 N +ATOM 248 H GLY 14 25.799 21.915 33.754 1.00 0.00 H +ATOM 249 CA GLY 14 23.872 22.731 33.398 1.00 0.00 C +ATOM 250 HA2 GLY 14 22.917 22.216 33.519 1.00 0.00 H +ATOM 251 HA3 GLY 14 24.041 23.329 34.294 1.00 0.00 H +ATOM 252 C GLY 14 23.740 23.693 32.199 1.00 0.00 C +ATOM 253 O GLY 14 24.623 23.800 31.347 1.00 0.00 O +ATOM 254 N VAL 15 22.630 24.433 32.175 1.00 0.00 N +ATOM 255 H VAL 15 21.967 24.310 32.924 1.00 0.00 H +ATOM 256 CA VAL 15 22.258 25.391 31.125 1.00 0.00 C +ATOM 257 HA VAL 15 23.156 25.664 30.577 1.00 0.00 H +ATOM 258 CB VAL 15 21.291 24.727 30.116 1.00 0.00 C +ATOM 259 HB VAL 15 21.791 23.839 29.715 1.00 0.00 H +ATOM 260 CG1 VAL 15 19.966 24.264 30.749 1.00 0.00 C +ATOM 261 HG11 VAL 15 19.406 25.113 31.134 1.00 0.00 H +ATOM 262 HG12 VAL 15 19.365 23.754 29.993 1.00 0.00 H +ATOM 263 HG13 VAL 15 20.160 23.557 31.554 1.00 0.00 H +ATOM 264 CG2 VAL 15 20.963 25.647 28.933 1.00 0.00 C +ATOM 265 HG21 VAL 15 21.883 26.004 28.474 1.00 0.00 H +ATOM 266 HG22 VAL 15 20.402 25.080 28.186 1.00 0.00 H +ATOM 267 HG23 VAL 15 20.358 26.490 29.258 1.00 0.00 H +ATOM 268 C VAL 15 21.686 26.658 31.751 1.00 0.00 C +ATOM 269 O VAL 15 20.993 26.607 32.770 1.00 0.00 O +HETATM 270 N HY1 16 21.983 27.814 31.152 1.00 0.00 N +HETATM 271 CA HY1 16 21.415 29.132 31.476 1.00 0.00 C +HETATM 272 C HY1 16 21.134 29.908 30.177 1.00 0.00 C +HETATM 273 O HY1 16 21.275 29.361 29.086 1.00 0.00 O +HETATM 274 CB HY1 16 22.356 29.875 32.450 1.00 0.00 C +HETATM 275 CG HY1 16 23.709 30.229 31.878 1.00 0.00 C +HETATM 276 CD2 HY1 16 24.068 31.431 31.324 1.00 0.00 C +HETATM 277 ND1 HY1 16 24.813 29.410 31.817 1.00 0.00 N +HETATM 278 CE1 HY1 16 25.816 30.121 31.269 1.00 0.00 C +HETATM 279 NE2 HY1 16 25.412 31.360 30.935 1.00 0.00 N +HETATM 280 H HY1 16 22.553 27.772 30.305 1.00 0.00 H +HETATM 281 HA HY1 16 20.458 28.981 31.988 1.00 0.00 H +HETATM 282 HB2 HY1 16 21.869 30.793 32.788 1.00 0.00 H +HETATM 283 HB3 HY1 16 22.504 29.262 33.342 1.00 0.00 H +HETATM 284 HD1 HY1 16 24.881 28.463 32.165 1.00 0.00 H +HETATM 285 HD2 HY1 16 23.428 32.300 31.222 1.00 0.00 H +HETATM 286 HE1 HY1 16 26.831 29.752 31.127 1.00 0.00 H +ATOM 287 N THR 17 20.733 31.171 30.282 1.00 0.00 N +ATOM 288 H THR 17 20.606 31.590 31.189 1.00 0.00 H +ATOM 289 CA THR 17 20.339 32.027 29.148 1.00 0.00 C +ATOM 290 HA THR 17 20.769 31.599 28.239 1.00 0.00 H +ATOM 291 CB THR 17 18.804 32.054 28.997 1.00 0.00 C +ATOM 292 HB THR 17 18.548 32.701 28.154 1.00 0.00 H +ATOM 293 CG2 THR 17 18.153 30.699 28.714 1.00 0.00 C +ATOM 294 HG21 THR 17 18.358 29.982 29.502 1.00 0.00 H +ATOM 295 HG22 THR 17 17.081 30.790 28.628 1.00 0.00 H +ATOM 296 HG23 THR 17 18.516 30.287 27.783 1.00 0.00 H +ATOM 297 OG1 THR 17 18.212 32.553 30.159 1.00 0.00 O +ATOM 298 HG1 THR 17 18.144 33.518 30.025 1.00 0.00 H +ATOM 299 C THR 17 20.886 33.446 29.236 1.00 0.00 C +ATOM 300 O THR 17 21.350 33.861 30.295 1.00 0.00 O +HETATM 301 N HY2 18 20.813 34.187 28.127 1.00 0.00 N +HETATM 302 CA HY2 18 21.081 35.625 28.066 1.00 0.00 C +HETATM 303 C HY2 18 19.976 36.319 27.265 1.00 0.00 C +HETATM 304 O HY2 18 19.648 35.866 26.170 1.00 0.00 O +HETATM 305 CB HY2 18 22.427 35.918 27.401 1.00 0.00 C +HETATM 306 CG HY2 18 23.623 35.439 28.194 1.00 0.00 C +HETATM 307 CD2 HY2 18 24.155 34.177 28.162 1.00 0.00 C +HETATM 308 ND1 HY2 18 24.312 36.145 29.158 1.00 0.00 N +HETATM 309 CE1 HY2 18 25.247 35.326 29.676 1.00 0.00 C +HETATM 310 NE2 HY2 18 25.185 34.110 29.103 1.00 0.00 N +HETATM 311 H HY2 18 20.458 33.740 27.282 1.00 0.00 H +HETATM 312 HA HY2 18 21.088 36.044 29.084 1.00 0.00 H +HETATM 313 HB2 HY2 18 22.454 35.451 26.408 1.00 0.00 H +HETATM 314 HB3 HY2 18 22.525 37.001 27.258 1.00 0.00 H +HETATM 315 HD1 HY2 18 24.160 37.108 29.430 1.00 0.00 H +HETATM 316 HD2 HY2 18 23.816 33.363 27.535 1.00 0.00 H +HETATM 317 HE1 HY2 18 25.945 35.606 30.456 1.00 0.00 H +ATOM 318 N GLU 19 19.430 37.417 27.787 1.00 0.00 N +ATOM 319 H GLU 19 19.758 37.740 28.682 1.00 0.00 H +ATOM 320 CA GLU 19 18.419 38.226 27.104 1.00 0.00 C +ATOM 321 HA GLU 19 17.699 37.546 26.656 1.00 0.00 H +ATOM 322 CB GLU 19 17.705 39.102 28.147 1.00 0.00 C +ATOM 323 HB2 GLU 19 17.377 38.469 28.971 1.00 0.00 H +ATOM 324 HB3 GLU 19 18.414 39.828 28.557 1.00 0.00 H +ATOM 325 CG GLU 19 16.477 39.854 27.616 1.00 0.00 C +ATOM 326 HG2 GLU 19 15.971 40.349 28.452 1.00 0.00 H +ATOM 327 HG3 GLU 19 16.810 40.632 26.924 1.00 0.00 H +ATOM 328 CD GLU 19 15.524 38.897 26.903 1.00 0.00 C +ATOM 329 OE1 GLU 19 15.614 38.801 25.661 1.00 0.00 O +ATOM 330 OE2 GLU 19 14.785 38.158 27.578 1.00 0.00 O +ATOM 331 C GLU 19 19.040 39.069 25.978 1.00 0.00 C +ATOM 332 O GLU 19 20.090 39.684 26.183 1.00 0.00 O +ATOM 333 N ALA 20 18.406 39.106 24.798 1.00 0.00 N +ATOM 334 H ALA 20 17.526 38.600 24.725 1.00 0.00 H +ATOM 335 CA ALA 20 18.770 39.982 23.679 1.00 0.00 C +ATOM 336 HA ALA 20 18.902 40.994 24.063 1.00 0.00 H +ATOM 337 CB ALA 20 20.096 39.515 23.062 1.00 0.00 C +ATOM 338 HB1 ALA 20 19.972 38.533 22.606 1.00 0.00 H +ATOM 339 HB2 ALA 20 20.416 40.226 22.305 1.00 0.00 H +ATOM 340 HB3 ALA 20 20.879 39.462 23.817 1.00 0.00 H +ATOM 341 C ALA 20 17.694 40.018 22.571 1.00 0.00 C +ATOM 342 O ALA 20 16.874 39.108 22.434 1.00 0.00 O +ATOM 343 N VAL 21 17.756 41.039 21.709 1.00 0.00 N +ATOM 344 H VAL 21 18.418 41.780 21.884 1.00 0.00 H +ATOM 345 CA VAL 21 17.017 41.071 20.423 1.00 0.00 C +ATOM 346 HA VAL 21 16.020 40.661 20.587 1.00 0.00 H +ATOM 347 CB VAL 21 16.842 42.514 19.898 1.00 0.00 C +ATOM 348 HB VAL 21 16.188 42.472 19.027 1.00 0.00 H +ATOM 349 CG1 VAL 21 16.159 43.411 20.937 1.00 0.00 C +ATOM 350 HG11 VAL 21 16.810 43.579 21.795 1.00 0.00 H +ATOM 351 HG12 VAL 21 15.918 44.373 20.486 1.00 0.00 H +ATOM 352 HG13 VAL 21 15.232 42.951 21.279 1.00 0.00 H +ATOM 353 CG2 VAL 21 18.158 43.176 19.464 1.00 0.00 C +ATOM 354 HG21 VAL 21 18.596 42.634 18.626 1.00 0.00 H +ATOM 355 HG22 VAL 21 17.964 44.195 19.129 1.00 0.00 H +ATOM 356 HG23 VAL 21 18.872 43.205 20.287 1.00 0.00 H +ATOM 357 C VAL 21 17.666 40.197 19.339 1.00 0.00 C +ATOM 358 O VAL 21 16.989 39.788 18.400 1.00 0.00 O +ATOM 359 N ASP 22 18.962 39.912 19.481 1.00 0.00 N +ATOM 360 H ASP 22 19.441 40.273 20.289 1.00 0.00 H +ATOM 361 CA ASP 22 19.803 39.155 18.549 1.00 0.00 C +ATOM 362 HA ASP 22 19.204 38.379 18.068 1.00 0.00 H +ATOM 363 CB ASP 22 20.347 40.115 17.467 1.00 0.00 C +ATOM 364 HB2 ASP 22 19.507 40.640 17.014 1.00 0.00 H +ATOM 365 HB3 ASP 22 20.969 40.862 17.961 1.00 0.00 H +ATOM 366 CG ASP 22 21.171 39.445 16.351 1.00 0.00 C +ATOM 367 OD1 ASP 22 21.358 40.133 15.304 1.00 0.00 O +ATOM 368 OD2 ASP 22 21.600 38.297 16.500 1.00 0.00 O +ATOM 369 C ASP 22 20.940 38.484 19.342 1.00 0.00 C +ATOM 370 O ASP 22 21.503 39.076 20.270 1.00 0.00 O +ATOM 371 N LEU 23 21.311 37.261 18.968 1.00 0.00 N +ATOM 372 H LEU 23 20.939 36.925 18.089 1.00 0.00 H +ATOM 373 CA LEU 23 22.452 36.571 19.560 1.00 0.00 C +ATOM 374 HA LEU 23 22.285 36.550 20.632 1.00 0.00 H +ATOM 375 CB LEU 23 22.485 35.111 19.082 1.00 0.00 C +ATOM 376 HB2 LEU 23 21.546 34.665 19.394 1.00 0.00 H +ATOM 377 HB3 LEU 23 22.522 35.056 17.994 1.00 0.00 H +ATOM 378 CG LEU 23 23.640 34.288 19.690 1.00 0.00 C +ATOM 379 HG LEU 23 23.819 34.622 20.711 1.00 0.00 H +ATOM 380 CD1 LEU 23 23.243 32.811 19.763 1.00 0.00 C +ATOM 381 HD11 LEU 23 22.968 32.445 18.779 1.00 0.00 H +ATOM 382 HD12 LEU 23 24.071 32.222 20.159 1.00 0.00 H +ATOM 383 HD13 LEU 23 22.398 32.707 20.441 1.00 0.00 H +ATOM 384 CD2 LEU 23 24.930 34.430 18.880 1.00 0.00 C +ATOM 385 HD21 LEU 23 25.532 35.241 19.277 1.00 0.00 H +ATOM 386 HD22 LEU 23 25.534 33.529 18.950 1.00 0.00 H +ATOM 387 HD23 LEU 23 24.718 34.659 17.839 1.00 0.00 H +ATOM 388 C LEU 23 23.771 37.324 19.343 1.00 0.00 C +ATOM 389 O LEU 23 24.614 37.294 20.233 1.00 0.00 O +ATOM 390 N ALA 24 23.950 38.060 18.242 1.00 0.00 N +ATOM 391 H ALA 24 23.204 38.085 17.546 1.00 0.00 H +ATOM 392 CA ALA 24 25.158 38.865 18.025 1.00 0.00 C +ATOM 393 HA ALA 24 26.018 38.218 18.197 1.00 0.00 H +ATOM 394 CB ALA 24 25.202 39.299 16.558 1.00 0.00 C +ATOM 395 HB1 ALA 24 24.369 39.964 16.325 1.00 0.00 H +ATOM 396 HB2 ALA 24 26.142 39.815 16.363 1.00 0.00 H +ATOM 397 HB3 ALA 24 25.148 38.425 15.906 1.00 0.00 H +ATOM 398 C ALA 24 25.306 40.056 19.005 1.00 0.00 C +ATOM 399 O ALA 24 26.389 40.642 19.118 1.00 0.00 O +ATOM 400 N GLU 25 24.251 40.394 19.761 1.00 0.00 N +ATOM 401 H GLU 25 23.380 39.906 19.598 1.00 0.00 H +ATOM 402 CA GLU 25 24.335 41.202 20.988 1.00 0.00 C +ATOM 403 HA GLU 25 25.200 41.864 20.931 1.00 0.00 H +ATOM 404 CB GLU 25 23.081 42.091 21.112 1.00 0.00 C +ATOM 405 HB2 GLU 25 22.197 41.461 21.036 1.00 0.00 H +ATOM 406 HB3 GLU 25 23.072 42.547 22.099 1.00 0.00 H +ATOM 407 CG GLU 25 22.993 43.209 20.067 1.00 0.00 C +ATOM 408 HG2 GLU 25 23.178 42.799 19.072 1.00 0.00 H +ATOM 409 HG3 GLU 25 21.977 43.613 20.061 1.00 0.00 H +ATOM 410 CD GLU 25 23.989 44.335 20.372 1.00 0.00 C +ATOM 411 OE1 GLU 25 23.587 45.318 21.037 1.00 0.00 O +ATOM 412 OE2 GLU 25 25.166 44.185 19.957 1.00 0.00 O +ATOM 413 C GLU 25 24.520 40.324 22.230 1.00 0.00 C +ATOM 414 O GLU 25 25.355 40.629 23.079 1.00 0.00 O +ATOM 415 N ALA 26 23.838 39.165 22.340 1.00 0.00 N +ATOM 416 H ALA 26 23.144 38.939 21.634 1.00 0.00 H +ATOM 417 CA ALA 26 24.041 38.207 23.435 1.00 0.00 C +ATOM 418 HA ALA 26 23.857 38.735 24.370 1.00 0.00 H +ATOM 419 CB ALA 26 23.053 37.055 23.307 1.00 0.00 C +ATOM 420 HB1 ALA 26 23.352 36.400 22.493 1.00 0.00 H +ATOM 421 HB2 ALA 26 23.041 36.471 24.227 1.00 0.00 H +ATOM 422 HB3 ALA 26 22.059 37.460 23.119 1.00 0.00 H +ATOM 423 C ALA 26 25.475 37.640 23.529 1.00 0.00 C +ATOM 424 O ALA 26 25.878 37.199 24.606 1.00 0.00 O +ATOM 425 N GLU 27 26.225 37.656 22.426 1.00 0.00 N +ATOM 426 H GLU 27 25.728 37.822 21.561 1.00 0.00 H +ATOM 427 CA GLU 27 27.657 37.363 22.351 1.00 0.00 C +ATOM 428 HA GLU 27 27.828 36.387 22.786 1.00 0.00 H +ATOM 429 CB GLU 27 28.049 37.295 20.810 1.00 0.00 C +ATOM 430 HB2 GLU 27 27.320 36.650 20.339 1.00 0.00 H +ATOM 431 HB3 GLU 27 27.974 38.279 20.364 1.00 0.00 H +ATOM 432 CG GLU 27 29.432 36.733 20.511 1.00 0.00 C +ATOM 433 HG2 GLU 27 30.208 37.425 20.927 1.00 0.00 H +ATOM 434 HG3 GLU 27 29.562 35.764 21.055 1.00 0.00 H +ATOM 435 CD GLU 27 29.655 36.541 18.998 1.00 0.00 C +ATOM 436 OE1 GLU 27 30.446 37.312 18.444 1.00 0.00 O +ATOM 437 OE2 GLU 27 29.027 35.659 18.399 1.00 0.00 O +ATOM 438 C GLU 27 28.483 38.382 23.126 1.00 0.00 C +ATOM 439 O GLU 27 29.294 38.026 23.980 1.00 0.00 O +ATOM 440 N LYS 28 28.171 39.676 22.949 1.00 0.00 N +ATOM 441 H LYS 28 27.412 39.874 22.302 1.00 0.00 H +ATOM 442 CA LYS 28 28.730 40.786 23.720 1.00 0.00 C +ATOM 443 HA LYS 28 29.826 40.697 23.712 1.00 0.00 H +ATOM 444 CB LYS 28 28.359 42.145 23.096 1.00 0.00 C +ATOM 445 HB2 LYS 28 27.290 42.317 23.207 1.00 0.00 H +ATOM 446 HB3 LYS 28 28.886 42.916 23.652 1.00 0.00 H +ATOM 447 CG LYS 28 28.732 42.265 21.607 1.00 0.00 C +ATOM 448 HG2 LYS 28 29.789 42.022 21.483 1.00 0.00 H +ATOM 449 HG3 LYS 28 28.138 41.561 21.024 1.00 0.00 H +ATOM 450 CD LYS 28 28.480 43.692 21.087 1.00 0.00 C +ATOM 451 HD2 LYS 28 27.472 44.012 21.359 1.00 0.00 H +ATOM 452 HD3 LYS 28 29.187 44.367 21.577 1.00 0.00 H +ATOM 453 CE LYS 28 28.656 43.806 19.568 1.00 0.00 C +ATOM 454 HE2 LYS 28 28.808 44.863 19.321 1.00 0.00 H +ATOM 455 HE3 LYS 28 29.558 43.270 19.263 1.00 0.00 H +ATOM 456 NZ LYS 28 27.462 43.300 18.844 1.00 0.00 N +ATOM 457 HZ1 LYS 28 26.620 43.776 19.187 1.00 0.00 H +ATOM 458 HZ2 LYS 28 27.524 43.469 17.852 1.00 0.00 H +ATOM 459 HZ3 LYS 28 27.296 42.311 19.010 1.00 0.00 H +ATOM 460 C LYS 28 28.293 40.734 25.190 1.00 0.00 C +ATOM 461 O LYS 28 29.136 40.838 26.076 1.00 0.00 O +ATOM 462 N PHE 29 27.019 40.477 25.467 1.00 0.00 N +ATOM 463 H PHE 29 26.355 40.453 24.698 1.00 0.00 H +ATOM 464 CA PHE 29 26.517 40.332 26.846 1.00 0.00 C +ATOM 465 HA PHE 29 26.806 41.218 27.411 1.00 0.00 H +ATOM 466 CB PHE 29 24.977 40.304 26.842 1.00 0.00 C +ATOM 467 HB2 PHE 29 24.659 39.367 26.390 1.00 0.00 H +ATOM 468 HB3 PHE 29 24.625 40.303 27.880 1.00 0.00 H +ATOM 469 CG PHE 29 24.287 41.460 26.136 1.00 0.00 C +ATOM 470 CD1 PHE 29 23.049 41.246 25.495 1.00 0.00 C +ATOM 471 HD1 PHE 29 22.579 40.275 25.527 1.00 0.00 H +ATOM 472 CE1 PHE 29 22.410 42.297 24.807 1.00 0.00 C +ATOM 473 HE1 PHE 29 21.469 42.116 24.311 1.00 0.00 H +ATOM 474 CZ PHE 29 23.003 43.573 24.765 1.00 0.00 C +ATOM 475 HZ PHE 29 22.524 44.372 24.222 1.00 0.00 H +ATOM 476 CE2 PHE 29 24.219 43.806 25.428 1.00 0.00 C +ATOM 477 HE2 PHE 29 24.669 44.778 25.408 1.00 0.00 H +ATOM 478 CD2 PHE 29 24.853 42.757 26.115 1.00 0.00 C +ATOM 479 HD2 PHE 29 25.782 42.959 26.619 1.00 0.00 H +ATOM 480 C PHE 29 27.097 39.092 27.576 1.00 0.00 C +ATOM 481 O PHE 29 27.242 39.121 28.804 1.00 0.00 O +ATOM 482 N THR 30 27.471 38.019 26.855 1.00 0.00 N +ATOM 483 H THR 30 27.262 38.018 25.867 1.00 0.00 H +ATOM 484 CA THR 30 28.208 36.874 27.383 1.00 0.00 C +ATOM 485 HA THR 30 27.806 36.552 28.340 1.00 0.00 H +ATOM 486 CB THR 30 28.165 35.642 26.355 1.00 0.00 C +ATOM 487 HB THR 30 28.671 35.982 25.465 1.00 0.00 H +ATOM 488 CG2 THR 30 29.010 34.482 26.856 1.00 0.00 C +ATOM 489 HG21 THR 30 28.763 34.155 27.853 1.00 0.00 H +ATOM 490 HG22 THR 30 28.991 33.595 26.210 1.00 0.00 H +ATOM 491 HG23 THR 30 30.047 34.791 26.859 1.00 0.00 H +ATOM 492 OG1 THR 30 26.844 35.210 26.048 1.00 0.00 O +ATOM 493 HG1 THR 30 26.349 35.962 25.650 1.00 0.00 H +ATOM 494 C THR 30 29.681 37.276 27.719 1.00 0.00 C +ATOM 495 O THR 30 30.155 36.942 28.795 1.00 0.00 O +ATOM 496 N LYS 31 30.332 38.079 26.889 1.00 0.00 N +ATOM 497 H LYS 31 29.871 38.384 26.044 1.00 0.00 H +ATOM 498 CA LYS 31 31.674 38.634 27.157 1.00 0.00 C +ATOM 499 HA LYS 31 32.350 37.837 27.474 1.00 0.00 H +ATOM 500 CB LYS 31 32.241 39.245 25.864 1.00 0.00 C +ATOM 501 HB2 LYS 31 31.523 39.940 25.448 1.00 0.00 H +ATOM 502 HB3 LYS 31 33.157 39.786 26.103 1.00 0.00 H +ATOM 503 CG LYS 31 32.581 38.157 24.832 1.00 0.00 C +ATOM 504 HG2 LYS 31 33.317 37.480 25.261 1.00 0.00 H +ATOM 505 HG3 LYS 31 31.704 37.566 24.575 1.00 0.00 H +ATOM 506 CD LYS 31 33.154 38.798 23.560 1.00 0.00 C +ATOM 507 HD2 LYS 31 32.363 39.356 23.055 1.00 0.00 H +ATOM 508 HD3 LYS 31 33.951 39.488 23.827 1.00 0.00 H +ATOM 509 CE LYS 31 33.714 37.746 22.591 1.00 0.00 C +ATOM 510 HE2 LYS 31 32.948 37.001 22.373 1.00 0.00 H +ATOM 511 HE3 LYS 31 33.955 38.245 21.648 1.00 0.00 H +ATOM 512 NZ LYS 31 34.933 37.089 23.115 1.00 0.00 N +ATOM 513 HZ1 LYS 31 34.746 36.340 23.769 1.00 0.00 H +ATOM 514 HZ2 LYS 31 35.437 36.639 22.348 1.00 0.00 H +ATOM 515 HZ3 LYS 31 35.592 37.732 23.552 1.00 0.00 H +ATOM 516 C LYS 31 31.693 39.656 28.305 1.00 0.00 C +ATOM 517 O LYS 31 32.674 39.678 29.044 1.00 0.00 O +ATOM 518 N ALA 32 30.615 40.417 28.505 1.00 0.00 N +ATOM 519 H ALA 32 29.893 40.433 27.798 1.00 0.00 H +ATOM 520 CA ALA 32 30.452 41.245 29.699 1.00 0.00 C +ATOM 521 HA ALA 32 31.287 41.943 29.769 1.00 0.00 H +ATOM 522 CB ALA 32 29.160 42.059 29.583 1.00 0.00 C +ATOM 523 HB1 ALA 32 28.295 41.401 29.522 1.00 0.00 H +ATOM 524 HB2 ALA 32 29.045 42.699 30.464 1.00 0.00 H +ATOM 525 HB3 ALA 32 29.194 42.691 28.695 1.00 0.00 H +ATOM 526 C ALA 32 30.481 40.374 30.974 1.00 0.00 C +ATOM 527 O ALA 32 31.390 40.511 31.786 1.00 0.00 O +ATOM 528 N ALA 33 29.599 39.373 31.058 1.00 0.00 N +ATOM 529 H ALA 33 28.886 39.292 30.345 1.00 0.00 H +ATOM 530 CA ALA 33 29.555 38.428 32.181 1.00 0.00 C +ATOM 531 HA ALA 33 29.465 39.008 33.099 1.00 0.00 H +ATOM 532 CB ALA 33 28.289 37.575 32.028 1.00 0.00 C +ATOM 533 HB1 ALA 33 28.346 36.978 31.119 1.00 0.00 H +ATOM 534 HB2 ALA 33 28.181 36.909 32.886 1.00 0.00 H +ATOM 535 HB3 ALA 33 27.410 38.219 31.981 1.00 0.00 H +ATOM 536 C ALA 33 30.821 37.541 32.333 1.00 0.00 C +ATOM 537 O ALA 33 30.921 36.798 33.305 1.00 0.00 O +ATOM 538 N ALA 34 31.757 37.568 31.379 1.00 0.00 N +ATOM 539 H ALA 34 31.589 38.159 30.584 1.00 0.00 H +ATOM 540 CA ALA 34 33.091 36.966 31.505 1.00 0.00 C +ATOM 541 HA ALA 34 33.037 36.139 32.213 1.00 0.00 H +ATOM 542 CB ALA 34 33.508 36.399 30.143 1.00 0.00 C +ATOM 543 HB1 ALA 34 33.649 37.207 29.426 1.00 0.00 H +ATOM 544 HB2 ALA 34 34.450 35.861 30.259 1.00 0.00 H +ATOM 545 HB3 ALA 34 32.750 35.708 29.774 1.00 0.00 H +ATOM 546 C ALA 34 34.123 37.961 32.063 1.00 0.00 C +ATOM 547 O ALA 34 34.832 37.631 33.008 1.00 0.00 O +ATOM 548 N ASN 35 34.171 39.202 31.560 1.00 0.00 N +ATOM 549 H ASN 35 33.544 39.440 30.800 1.00 0.00 H +ATOM 550 CA ASN 35 35.041 40.256 32.096 1.00 0.00 C +ATOM 551 HA ASN 35 36.050 39.850 32.215 1.00 0.00 H +ATOM 552 CB ASN 35 35.128 41.408 31.082 1.00 0.00 C +ATOM 553 HB2 ASN 35 34.128 41.702 30.765 1.00 0.00 H +ATOM 554 HB3 ASN 35 35.595 42.264 31.566 1.00 0.00 H +ATOM 555 CG ASN 35 35.989 41.053 29.876 1.00 0.00 C +ATOM 556 OD1 ASN 35 37.202 40.998 29.943 1.00 0.00 O +ATOM 557 ND2 ASN 35 35.397 40.799 28.737 1.00 0.00 N +ATOM 558 HD21 ASN 35 36.007 40.585 27.947 1.00 0.00 H +ATOM 559 HD22 ASN 35 34.398 40.684 28.702 1.00 0.00 H +ATOM 560 C ASN 35 34.614 40.741 33.504 1.00 0.00 C +ATOM 561 O ASN 35 35.469 41.137 34.290 1.00 0.00 O +ATOM 562 N ASP 36 33.333 40.617 33.865 1.00 0.00 N +ATOM 563 H ASP 36 32.647 40.420 33.146 1.00 0.00 H +ATOM 564 CA ASP 36 32.837 40.768 35.249 1.00 0.00 C +ATOM 565 HA ASP 36 33.163 41.738 35.630 1.00 0.00 H +ATOM 566 CB ASP 36 31.291 40.753 35.253 1.00 0.00 C +ATOM 567 HB2 ASP 36 30.950 39.847 34.749 1.00 0.00 H +ATOM 568 HB3 ASP 36 30.954 40.684 36.289 1.00 0.00 H +ATOM 569 CG ASP 36 30.604 41.992 34.634 1.00 0.00 C +ATOM 570 OD1 ASP 36 31.204 43.091 34.688 1.00 0.00 O +ATOM 571 OD2 ASP 36 29.439 41.870 34.172 1.00 0.00 O +ATOM 572 C ASP 36 33.415 39.697 36.211 1.00 0.00 C +ATOM 573 O ASP 36 33.441 39.908 37.424 1.00 0.00 O +ATOM 574 N LEU 37 33.904 38.557 35.688 1.00 0.00 N +ATOM 575 H LEU 37 33.842 38.450 34.686 1.00 0.00 H +ATOM 576 CA LEU 37 34.657 37.527 36.423 1.00 0.00 C +ATOM 577 HA LEU 37 34.464 37.650 37.491 1.00 0.00 H +ATOM 578 CB LEU 37 34.109 36.145 35.994 1.00 0.00 C +ATOM 579 HB2 LEU 37 33.040 36.119 36.207 1.00 0.00 H +ATOM 580 HB3 LEU 37 34.231 36.052 34.917 1.00 0.00 H +ATOM 581 CG LEU 37 34.771 34.914 36.645 1.00 0.00 C +ATOM 582 HG LEU 37 35.840 34.913 36.439 1.00 0.00 H +ATOM 583 CD1 LEU 37 34.551 34.857 38.159 1.00 0.00 C +ATOM 584 HD11 LEU 37 33.486 34.879 38.385 1.00 0.00 H +ATOM 585 HD12 LEU 37 34.992 33.944 38.560 1.00 0.00 H +ATOM 586 HD13 LEU 37 35.040 35.710 38.628 1.00 0.00 H +ATOM 587 CD2 LEU 37 34.177 33.637 36.042 1.00 0.00 C +ATOM 588 HD21 LEU 37 34.355 33.629 34.966 1.00 0.00 H +ATOM 589 HD22 LEU 37 34.662 32.764 36.478 1.00 0.00 H +ATOM 590 HD23 LEU 37 33.105 33.596 36.231 1.00 0.00 H +ATOM 591 C LEU 37 36.190 37.649 36.238 1.00 0.00 C +ATOM 592 O LEU 37 36.941 37.271 37.137 1.00 0.00 O +ATOM 593 N GLY 38 36.655 38.181 35.100 1.00 0.00 N +ATOM 594 H GLY 38 35.977 38.417 34.388 1.00 0.00 H +ATOM 595 CA GLY 38 38.057 38.532 34.848 1.00 0.00 C +ATOM 596 HA2 GLY 38 38.314 39.395 35.466 1.00 0.00 H +ATOM 597 HA3 GLY 38 38.690 37.700 35.160 1.00 0.00 H +ATOM 598 C GLY 38 38.413 38.871 33.391 1.00 0.00 C +ATOM 599 O GLY 38 38.929 39.957 33.136 1.00 0.00 O +ATOM 600 N GLU 39 38.171 37.961 32.437 1.00 0.00 N +ATOM 601 H GLU 39 37.657 37.131 32.691 1.00 0.00 H +ATOM 602 CA GLU 39 38.661 38.018 31.042 1.00 0.00 C +ATOM 603 HA GLU 39 38.763 39.061 30.726 1.00 0.00 H +ATOM 604 CB GLU 39 40.065 37.322 30.944 1.00 0.00 C +ATOM 605 HB2 GLU 39 39.944 36.313 31.317 1.00 0.00 H +ATOM 606 HB3 GLU 39 40.335 37.260 29.892 1.00 0.00 H +ATOM 607 CG GLU 39 41.245 37.986 31.688 1.00 0.00 C +ATOM 608 HG2 GLU 39 41.553 38.894 31.136 1.00 0.00 H +ATOM 609 HG3 GLU 39 40.915 38.320 32.684 1.00 0.00 H +ATOM 610 CD GLU 39 42.450 37.039 31.915 1.00 0.00 C +ATOM 611 OE1 GLU 39 42.260 36.003 32.575 1.00 0.00 O +ATOM 612 OE2 GLU 39 43.569 37.372 31.481 1.00 0.00 O +ATOM 613 C GLU 39 37.685 37.298 30.075 1.00 0.00 C +ATOM 614 O GLU 39 37.024 36.351 30.492 1.00 0.00 O +ATOM 615 N ASP 40 37.585 37.685 28.788 1.00 0.00 N +ATOM 616 H ASP 40 38.100 38.498 28.476 1.00 0.00 H +ATOM 617 CA ASP 40 36.738 36.968 27.799 1.00 0.00 C +ATOM 618 HA ASP 40 36.030 36.362 28.365 1.00 0.00 H +ATOM 619 CB ASP 40 35.858 37.913 26.964 1.00 0.00 C +ATOM 620 HB2 ASP 40 35.160 37.288 26.414 1.00 0.00 H +ATOM 621 HB3 ASP 40 35.261 38.533 27.625 1.00 0.00 H +ATOM 622 CG ASP 40 36.587 38.798 25.952 1.00 0.00 C +ATOM 623 OD1 ASP 40 36.893 39.965 26.276 1.00 0.00 O +ATOM 624 OD2 ASP 40 36.761 38.351 24.790 1.00 0.00 O +ATOM 625 C ASP 40 37.475 35.994 26.856 1.00 0.00 C +ATOM 626 O ASP 40 38.374 36.376 26.101 1.00 0.00 O +ATOM 627 N GLY 41 36.973 34.756 26.794 1.00 0.00 N +ATOM 628 H GLY 41 36.288 34.510 27.490 1.00 0.00 H +ATOM 629 CA GLY 41 37.271 33.768 25.747 1.00 0.00 C +ATOM 630 HA2 GLY 41 38.295 33.916 25.381 1.00 0.00 H +ATOM 631 HA3 GLY 41 37.211 32.770 26.191 1.00 0.00 H +ATOM 632 C GLY 41 36.313 33.811 24.533 1.00 0.00 C +ATOM 633 O GLY 41 35.386 34.624 24.460 1.00 0.00 O +ATOM 634 N GLU 42 36.534 32.906 23.574 1.00 0.00 N +ATOM 635 H GLU 42 37.265 32.233 23.726 1.00 0.00 H +ATOM 636 CA GLU 42 35.795 32.783 22.304 1.00 0.00 C +ATOM 637 HA GLU 42 35.112 33.628 22.215 1.00 0.00 H +ATOM 638 CB GLU 42 36.768 32.852 21.111 1.00 0.00 C +ATOM 639 HB2 GLU 42 37.359 31.939 21.083 1.00 0.00 H +ATOM 640 HB3 GLU 42 36.185 32.904 20.190 1.00 0.00 H +ATOM 641 CG GLU 42 37.742 34.046 21.132 1.00 0.00 C +ATOM 642 HG2 GLU 42 38.542 33.823 21.835 1.00 0.00 H +ATOM 643 HG3 GLU 42 38.198 34.176 20.150 1.00 0.00 H +ATOM 644 CD GLU 42 37.078 35.358 21.545 1.00 0.00 C +ATOM 645 OE1 GLU 42 35.962 35.662 21.073 1.00 0.00 O +ATOM 646 OE2 GLU 42 37.603 36.077 22.430 1.00 0.00 O +ATOM 647 C GLU 42 34.925 31.518 22.249 1.00 0.00 C +ATOM 648 O GLU 42 35.177 30.549 22.970 1.00 0.00 O +ATOM 649 N HIP 43 33.822 31.561 21.482 1.00 0.00 N +ATOM 650 H HIP 43 33.691 32.332 20.837 1.00 0.00 H +ATOM 651 CA HIP 43 32.635 30.779 21.863 1.00 0.00 C +ATOM 652 HA HIP 43 32.953 29.805 22.240 1.00 0.00 H +ATOM 653 CB HIP 43 32.036 31.564 23.060 1.00 0.00 C +ATOM 654 HB2 HIP 43 32.780 31.722 23.836 1.00 0.00 H +ATOM 655 HB3 HIP 43 31.707 32.547 22.731 1.00 0.00 H +ATOM 656 CG HIP 43 30.884 30.844 23.669 1.00 0.00 C +ATOM 657 ND1 HIP 43 29.715 30.591 23.008 1.00 0.00 N +ATOM 658 HD1 HIP 43 29.496 30.960 22.088 1.00 0.00 H +ATOM 659 CE1 HIP 43 29.197 29.496 23.532 1.00 0.00 C +ATOM 660 HE1 HIP 43 28.471 28.891 23.007 1.00 0.00 H +ATOM 661 NE2 HIP 43 29.859 29.132 24.623 1.00 0.00 N +ATOM 662 HE2 HIP 43 29.751 28.262 25.124 1.00 0.00 H +ATOM 663 CD2 HIP 43 30.964 29.967 24.715 1.00 0.00 C +ATOM 664 HD2 HIP 43 31.813 29.800 25.339 1.00 0.00 H +ATOM 665 C HIP 43 31.587 30.500 20.744 1.00 0.00 C +ATOM 666 O HIP 43 30.815 31.391 20.404 1.00 0.00 O +ATOM 667 N THR 44 31.412 29.241 20.315 1.00 0.00 N +ATOM 668 H THR 44 32.062 28.545 20.651 1.00 0.00 H +ATOM 669 CA THR 44 30.539 28.792 19.194 1.00 0.00 C +ATOM 670 HA THR 44 30.768 29.416 18.330 1.00 0.00 H +ATOM 671 CB THR 44 30.915 27.341 18.825 1.00 0.00 C +ATOM 672 HB THR 44 30.653 26.672 19.649 1.00 0.00 H +ATOM 673 CG2 THR 44 30.280 26.804 17.538 1.00 0.00 C +ATOM 674 HG21 THR 44 30.421 27.512 16.723 1.00 0.00 H +ATOM 675 HG22 THR 44 30.737 25.852 17.265 1.00 0.00 H +ATOM 676 HG23 THR 44 29.217 26.625 17.692 1.00 0.00 H +ATOM 677 OG1 THR 44 32.307 27.274 18.626 1.00 0.00 O +ATOM 678 HG1 THR 44 32.492 26.533 18.040 1.00 0.00 H +ATOM 679 C THR 44 29.005 28.885 19.426 1.00 0.00 C +ATOM 680 O THR 44 28.541 28.793 20.567 1.00 0.00 O +ATOM 681 N LYS 45 28.231 29.030 18.329 1.00 0.00 N +ATOM 682 H LYS 45 28.718 29.046 17.443 1.00 0.00 H +ATOM 683 CA LYS 45 26.747 29.105 18.236 1.00 0.00 C +ATOM 684 HA LYS 45 26.318 29.062 19.233 1.00 0.00 H +ATOM 685 CB LYS 45 26.374 30.459 17.574 1.00 0.00 C +ATOM 686 HB2 LYS 45 26.571 31.266 18.282 1.00 0.00 H +ATOM 687 HB3 LYS 45 27.024 30.615 16.712 1.00 0.00 H +ATOM 688 CG LYS 45 24.919 30.571 17.071 1.00 0.00 C +ATOM 689 HG2 LYS 45 24.730 29.762 16.369 1.00 0.00 H +ATOM 690 HG3 LYS 45 24.253 30.451 17.926 1.00 0.00 H +ATOM 691 CD LYS 45 24.581 31.864 16.313 1.00 0.00 C +ATOM 692 HD2 LYS 45 24.789 32.715 16.943 1.00 0.00 H +ATOM 693 HD3 LYS 45 25.176 31.930 15.400 1.00 0.00 H +ATOM 694 CE LYS 45 23.091 31.825 15.971 1.00 0.00 C +ATOM 695 HE2 LYS 45 22.923 30.987 15.292 1.00 0.00 H +ATOM 696 HE3 LYS 45 22.532 31.602 16.886 1.00 0.00 H +ATOM 697 NZ LYS 45 22.573 33.072 15.345 1.00 0.00 N +ATOM 698 HZ1 LYS 45 22.962 33.227 14.424 1.00 0.00 H +ATOM 699 HZ2 LYS 45 21.559 32.954 15.239 1.00 0.00 H +ATOM 700 HZ3 LYS 45 22.712 33.892 15.912 1.00 0.00 H +ATOM 701 C LYS 45 26.138 27.945 17.423 1.00 0.00 C +ATOM 702 O LYS 45 26.705 27.569 16.405 1.00 0.00 O +ATOM 703 N ASP 46 24.922 27.524 17.775 1.00 0.00 N +ATOM 704 H ASP 46 24.578 27.808 18.689 1.00 0.00 H +ATOM 705 CA ASP 46 23.873 27.044 16.843 1.00 0.00 C +ATOM 706 HA ASP 46 24.249 27.121 15.818 1.00 0.00 H +ATOM 707 CB ASP 46 23.528 25.569 17.148 1.00 0.00 C +ATOM 708 HB2 ASP 46 24.366 24.916 16.878 1.00 0.00 H +ATOM 709 HB3 ASP 46 23.378 25.489 18.232 1.00 0.00 H +ATOM 710 CG ASP 46 22.266 25.098 16.426 1.00 0.00 C +ATOM 711 OD1 ASP 46 21.392 24.557 17.117 1.00 0.00 O +ATOM 712 OD2 ASP 46 22.087 25.409 15.235 1.00 0.00 O +ATOM 713 C ASP 46 22.613 27.944 16.957 1.00 0.00 C +ATOM 714 O ASP 46 22.294 28.456 18.027 1.00 0.00 O +ATOM 715 N ASP 47 21.897 28.140 15.849 1.00 0.00 N +ATOM 716 H ASP 47 22.146 27.562 15.057 1.00 0.00 H +ATOM 717 CA ASP 47 20.588 28.850 15.794 1.00 0.00 C +ATOM 718 HA ASP 47 20.554 29.519 16.646 1.00 0.00 H +ATOM 719 CB ASP 47 20.475 29.756 14.572 1.00 0.00 C +ATOM 720 HB2 ASP 47 21.461 30.108 14.286 1.00 0.00 H +ATOM 721 HB3 ASP 47 20.085 29.213 13.702 1.00 0.00 H +ATOM 722 CG ASP 47 19.637 30.995 14.888 1.00 0.00 C +ATOM 723 OD1 ASP 47 18.471 31.071 14.473 1.00 0.00 O +ATOM 724 OD2 ASP 47 20.169 31.881 15.573 1.00 0.00 O +ATOM 725 C ASP 47 19.357 27.933 15.861 1.00 0.00 C +ATOM 726 O ASP 47 18.316 28.355 16.366 1.00 0.00 O +ATOM 727 N ALA 48 19.457 26.676 15.411 1.00 0.00 N +ATOM 728 H ALA 48 20.368 26.307 15.139 1.00 0.00 H +ATOM 729 CA ALA 48 18.317 25.752 15.378 1.00 0.00 C +ATOM 730 HA ALA 48 17.480 26.224 14.859 1.00 0.00 H +ATOM 731 CB ALA 48 18.730 24.511 14.577 1.00 0.00 C +ATOM 732 HB1 ALA 48 19.555 24.007 15.072 1.00 0.00 H +ATOM 733 HB2 ALA 48 17.894 23.821 14.498 1.00 0.00 H +ATOM 734 HB3 ALA 48 19.047 24.788 13.575 1.00 0.00 H +ATOM 735 C ALA 48 17.839 25.388 16.792 1.00 0.00 C +ATOM 736 O ALA 48 16.640 25.354 17.075 1.00 0.00 O +ATOM 737 N THR 49 18.778 25.160 17.711 1.00 0.00 N +ATOM 738 H THR 49 19.736 25.037 17.377 1.00 0.00 H +ATOM 739 CA THR 49 18.557 25.051 19.154 1.00 0.00 C +ATOM 740 HA THR 49 17.530 24.709 19.314 1.00 0.00 H +ATOM 741 CB THR 49 19.524 24.022 19.753 1.00 0.00 C +ATOM 742 HB THR 49 19.326 23.946 20.820 1.00 0.00 H +ATOM 743 CG2 THR 49 19.398 22.626 19.153 1.00 0.00 C +ATOM 744 HG21 THR 49 19.665 22.630 18.098 1.00 0.00 H +ATOM 745 HG22 THR 49 20.090 21.979 19.684 1.00 0.00 H +ATOM 746 HG23 THR 49 18.383 22.250 19.269 1.00 0.00 H +ATOM 747 OG1 THR 49 20.861 24.413 19.589 1.00 0.00 O +ATOM 748 HG1 THR 49 21.066 24.338 18.620 1.00 0.00 H +ATOM 749 C THR 49 18.714 26.378 19.910 1.00 0.00 C +ATOM 750 O THR 49 18.618 26.395 21.136 1.00 0.00 O +ATOM 751 N LYS 50 18.968 27.490 19.206 1.00 0.00 N +ATOM 752 H LYS 50 18.980 27.378 18.203 1.00 0.00 H +ATOM 753 CA LYS 50 19.202 28.853 19.749 1.00 0.00 C +ATOM 754 HA LYS 50 19.637 29.449 18.943 1.00 0.00 H +ATOM 755 CB LYS 50 17.845 29.491 20.149 1.00 0.00 C +ATOM 756 HB2 LYS 50 17.408 28.860 20.925 1.00 0.00 H +ATOM 757 HB3 LYS 50 18.038 30.471 20.598 1.00 0.00 H +ATOM 758 CG LYS 50 16.812 29.667 19.017 1.00 0.00 C +ATOM 759 HG2 LYS 50 16.742 28.752 18.424 1.00 0.00 H +ATOM 760 HG3 LYS 50 15.841 29.837 19.491 1.00 0.00 H +ATOM 761 CD LYS 50 17.113 30.878 18.105 1.00 0.00 C +ATOM 762 HD2 LYS 50 17.122 31.775 18.732 1.00 0.00 H +ATOM 763 HD3 LYS 50 18.108 30.766 17.643 1.00 0.00 H +ATOM 764 CE LYS 50 16.028 31.055 17.026 1.00 0.00 C +ATOM 765 HE2 LYS 50 15.056 30.783 17.436 1.00 0.00 H +ATOM 766 HE3 LYS 50 15.985 32.104 16.719 1.00 0.00 H +ATOM 767 NZ LYS 50 16.278 30.207 15.837 1.00 0.00 N +ATOM 768 HZ1 LYS 50 16.593 29.271 16.077 1.00 0.00 H +ATOM 769 HZ2 LYS 50 15.486 30.195 15.189 1.00 0.00 H +ATOM 770 HZ3 LYS 50 17.047 30.589 15.285 1.00 0.00 H +ATOM 771 C LYS 50 20.238 28.865 20.885 1.00 0.00 C +ATOM 772 O LYS 50 20.046 29.552 21.897 1.00 0.00 O +ATOM 773 N THR 51 21.297 28.053 20.758 1.00 0.00 N +ATOM 774 H THR 51 21.447 27.626 19.852 1.00 0.00 H +ATOM 775 CA THR 51 22.186 27.666 21.861 1.00 0.00 C +ATOM 776 HA THR 51 21.925 28.266 22.727 1.00 0.00 H +ATOM 777 CB THR 51 21.978 26.182 22.276 1.00 0.00 C +ATOM 778 HB THR 51 22.103 25.558 21.392 1.00 0.00 H +ATOM 779 CG2 THR 51 22.971 25.680 23.326 1.00 0.00 C +ATOM 780 HG21 THR 51 22.987 26.306 24.214 1.00 0.00 H +ATOM 781 HG22 THR 51 22.722 24.667 23.637 1.00 0.00 H +ATOM 782 HG23 THR 51 23.978 25.634 22.923 1.00 0.00 H +ATOM 783 OG1 THR 51 20.695 26.001 22.835 1.00 0.00 O +ATOM 784 HG1 THR 51 20.033 26.112 22.126 1.00 0.00 H +ATOM 785 C THR 51 23.691 27.954 21.606 1.00 0.00 C +ATOM 786 O THR 51 24.250 27.693 20.552 1.00 0.00 O +ATOM 787 N PHE 52 24.339 28.470 22.636 1.00 0.00 N +ATOM 788 H PHE 52 23.782 28.767 23.426 1.00 0.00 H +ATOM 789 CA PHE 52 25.782 28.625 22.774 1.00 0.00 C +ATOM 790 HA PHE 52 26.236 28.756 21.800 1.00 0.00 H +ATOM 791 CB PHE 52 25.970 29.903 23.630 1.00 0.00 C +ATOM 792 HB2 PHE 52 25.178 29.934 24.366 1.00 0.00 H +ATOM 793 HB3 PHE 52 26.858 29.811 24.241 1.00 0.00 H +ATOM 794 CG PHE 52 25.990 31.261 22.933 1.00 0.00 C +ATOM 795 CD1 PHE 52 25.313 32.345 23.501 1.00 0.00 C +ATOM 796 HD1 PHE 52 24.705 32.206 24.369 1.00 0.00 H +ATOM 797 CE1 PHE 52 25.445 33.639 22.970 1.00 0.00 C +ATOM 798 HE1 PHE 52 24.940 34.476 23.432 1.00 0.00 H +ATOM 799 CZ PHE 52 26.270 33.846 21.867 1.00 0.00 C +ATOM 800 HZ PHE 52 26.395 34.832 21.472 1.00 0.00 H +ATOM 801 CE2 PHE 52 26.935 32.771 21.258 1.00 0.00 C +ATOM 802 HE2 PHE 52 27.570 32.946 20.399 1.00 0.00 H +ATOM 803 CD2 PHE 52 26.777 31.489 21.786 1.00 0.00 C +ATOM 804 HD2 PHE 52 27.285 30.683 21.316 1.00 0.00 H +ATOM 805 C PHE 52 26.423 27.398 23.470 1.00 0.00 C +ATOM 806 O PHE 52 26.087 27.106 24.623 1.00 0.00 O +ATOM 807 N THR 53 27.436 26.751 22.856 1.00 0.00 N +ATOM 808 H THR 53 27.650 26.995 21.888 1.00 0.00 H +ATOM 809 CA THR 53 28.305 25.685 23.436 1.00 0.00 C +ATOM 810 HA THR 53 28.048 25.541 24.487 1.00 0.00 H +ATOM 811 CB THR 53 28.082 24.339 22.718 1.00 0.00 C +ATOM 812 HB THR 53 28.786 23.607 23.118 1.00 0.00 H +ATOM 813 CG2 THR 53 26.676 23.788 22.896 1.00 0.00 C +ATOM 814 HG21 THR 53 25.950 24.428 22.394 1.00 0.00 H +ATOM 815 HG22 THR 53 26.625 22.786 22.468 1.00 0.00 H +ATOM 816 HG23 THR 53 26.442 23.727 23.958 1.00 0.00 H +ATOM 817 OG1 THR 53 28.319 24.486 21.337 1.00 0.00 O +ATOM 818 HG1 THR 53 28.141 23.636 20.917 1.00 0.00 H +ATOM 819 C THR 53 29.812 26.007 23.366 1.00 0.00 C +ATOM 820 O THR 53 30.224 26.906 22.642 1.00 0.00 O +ATOM 821 N THR 54 30.650 25.304 24.140 1.00 0.00 N +ATOM 822 H THR 54 30.284 24.592 24.758 1.00 0.00 H +ATOM 823 CA THR 54 32.131 25.256 23.974 1.00 0.00 C +ATOM 824 HA THR 54 32.450 26.113 23.366 1.00 0.00 H +ATOM 825 CB THR 54 32.874 25.346 25.323 1.00 0.00 C +ATOM 826 HB THR 54 33.948 25.303 25.140 1.00 0.00 H +ATOM 827 CG2 THR 54 32.594 26.656 26.070 1.00 0.00 C +ATOM 828 HG21 THR 54 31.547 26.724 26.352 1.00 0.00 H +ATOM 829 HG22 THR 54 33.190 26.709 26.976 1.00 0.00 H +ATOM 830 HG23 THR 54 32.855 27.511 25.448 1.00 0.00 H +ATOM 831 OG1 THR 54 32.529 24.279 26.170 1.00 0.00 O +ATOM 832 HG1 THR 54 32.961 23.475 25.847 1.00 0.00 H +ATOM 833 C THR 54 32.580 23.997 23.228 1.00 0.00 C +ATOM 834 O THR 54 31.810 23.044 23.101 1.00 0.00 O +ATOM 835 N ALA 55 33.833 23.981 22.756 1.00 0.00 N +ATOM 836 H ALA 55 34.417 24.785 22.911 1.00 0.00 H +ATOM 837 CA ALA 55 34.476 22.803 22.162 1.00 0.00 C +ATOM 838 HA ALA 55 33.773 22.349 21.450 1.00 0.00 H +ATOM 839 CB ALA 55 35.709 23.293 21.391 1.00 0.00 C +ATOM 840 HB1 ALA 55 36.439 23.718 22.088 1.00 0.00 H +ATOM 841 HB2 ALA 55 36.172 22.454 20.859 1.00 0.00 H +ATOM 842 HB3 ALA 55 35.413 24.049 20.657 1.00 0.00 H +ATOM 843 C ALA 55 34.820 21.700 23.201 1.00 0.00 C +ATOM 844 O ALA 55 34.564 21.870 24.395 1.00 0.00 O +ATOM 845 N GLU 56 35.391 20.590 22.719 1.00 0.00 N +ATOM 846 H GLU 56 35.619 20.592 21.742 1.00 0.00 H +ATOM 847 CA GLU 56 35.949 19.442 23.462 1.00 0.00 C +ATOM 848 HA GLU 56 35.837 19.619 24.529 1.00 0.00 H +ATOM 849 CB GLU 56 35.174 18.158 23.066 1.00 0.00 C +ATOM 850 HB2 GLU 56 34.120 18.283 23.304 1.00 0.00 H +ATOM 851 HB3 GLU 56 35.231 18.083 21.976 1.00 0.00 H +ATOM 852 CG GLU 56 35.683 16.816 23.642 1.00 0.00 C +ATOM 853 HG2 GLU 56 35.524 16.058 22.873 1.00 0.00 H +ATOM 854 HG3 GLU 56 36.759 16.858 23.777 1.00 0.00 H +ATOM 855 CD GLU 56 35.019 16.305 24.943 1.00 0.00 C +ATOM 856 OE1 GLU 56 35.650 15.485 25.657 1.00 0.00 O +ATOM 857 OE2 GLU 56 33.830 16.592 25.213 1.00 0.00 O +ATOM 858 C GLU 56 37.466 19.312 23.206 1.00 0.00 C +ATOM 859 O GLU 56 38.207 19.293 24.214 1.00 0.00 O +ATOM 860 OXT GLU 56 37.851 19.278 22.005 1.00 0.00 O +HETATM 861 ZN ZN1 57 26.252 32.500 29.543 1.00 0.00 Zn +HETATM 862 N AN1 58 27.946 33.231 30.455 1.00 0.00 N +HETATM 863 C AN1 58 30.237 34.165 31.270 1.00 0.00 C +HETATM 864 C1 AN1 58 28.941 33.637 30.825 1.00 0.00 C +HETATM 865 H AN1 58 30.152 34.562 32.288 1.00 0.00 H +HETATM 866 H1 AN1 58 30.560 34.975 30.607 1.00 0.00 H +HETATM 867 H2 AN1 58 30.993 33.374 31.265 1.00 0.00 H +HETATM 868 N1 AZI 59 30.423 28.665 29.019 1.00 0.00 N +HETATM 869 N2 AZI 59 29.754 28.732 30.028 1.00 0.00 N +HETATM 870 N3 AZI 59 29.036 28.794 31.085 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 69 71 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 68 73 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 861 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 105 101 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 142 140 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 139 144 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 207 188 189 +CONECT 188 187 +CONECT 189 187 191 192 190 +CONECT 190 189 +CONECT 191 189 +CONECT 192 206 189 193 +CONECT 193 192 195 194 +CONECT 194 193 +CONECT 195 197 193 196 +CONECT 196 195 +CONECT 197 198 206 195 +CONECT 198 200 199 197 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 203 200 204 +CONECT 203 202 +CONECT 204 202 205 206 +CONECT 205 204 +CONECT 206 204 197 192 +CONECT 207 209 187 208 +CONECT 208 207 +CONECT 209 210 211 207 +CONECT 210 209 +CONECT 211 212 223 209 213 +CONECT 212 211 +CONECT 213 211 219 215 214 +CONECT 214 213 +CONECT 215 218 213 216 217 +CONECT 216 215 +CONECT 217 215 +CONECT 218 215 +CONECT 219 220 222 213 221 +CONECT 220 219 +CONECT 221 219 +CONECT 222 219 +CONECT 223 224 225 211 +CONECT 224 223 +CONECT 225 227 223 226 +CONECT 226 225 +CONECT 227 228 245 229 225 +CONECT 228 227 +CONECT 229 232 227 230 231 +CONECT 230 229 +CONECT 231 229 +CONECT 232 234 233 235 229 +CONECT 233 232 +CONECT 234 232 +CONECT 235 236 232 237 238 +CONECT 236 235 +CONECT 237 235 +CONECT 238 235 240 241 239 +CONECT 239 238 +CONECT 240 238 +CONECT 241 244 238 242 243 +CONECT 242 241 +CONECT 243 241 +CONECT 244 241 +CONECT 245 246 227 247 +CONECT 246 245 +CONECT 247 245 249 248 +CONECT 248 247 +CONECT 249 252 247 250 251 +CONECT 250 249 +CONECT 251 249 +CONECT 252 253 254 249 +CONECT 253 252 +CONECT 254 256 252 255 +CONECT 255 254 +CONECT 256 258 257 268 254 +CONECT 257 256 +CONECT 258 264 259 260 256 +CONECT 259 258 +CONECT 260 262 258 261 263 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 265 267 258 +CONECT 265 264 +CONECT 266 264 +CONECT 267 264 +CONECT 268 256 270 269 +CONECT 269 268 +CONECT 270 280 271 268 +CONECT 271 272 270 281 274 +CONECT 272 273 287 271 +CONECT 273 272 +CONECT 274 271 275 282 283 +CONECT 275 276 277 274 +CONECT 276 279 285 275 +CONECT 277 278 275 284 +CONECT 278 279 286 277 +CONECT 279 861 278 276 +CONECT 280 270 +CONECT 281 271 +CONECT 282 274 +CONECT 283 274 +CONECT 284 277 +CONECT 285 276 +CONECT 286 278 +CONECT 287 289 272 288 +CONECT 288 287 +CONECT 289 290 291 299 287 +CONECT 290 289 +CONECT 291 292 293 289 297 +CONECT 292 291 +CONECT 293 296 295 291 294 +CONECT 294 293 +CONECT 295 293 +CONECT 296 293 +CONECT 297 291 298 +CONECT 298 297 +CONECT 299 301 289 300 +CONECT 300 299 +CONECT 301 311 302 299 +CONECT 302 303 305 301 312 +CONECT 303 304 318 302 +CONECT 304 303 +CONECT 305 313 314 302 306 +CONECT 306 305 307 308 +CONECT 307 316 306 310 +CONECT 308 306 315 309 +CONECT 309 310 308 317 +CONECT 310 307 861 309 +CONECT 311 301 +CONECT 312 302 +CONECT 313 305 +CONECT 314 305 +CONECT 315 308 +CONECT 316 307 +CONECT 317 309 +CONECT 318 320 303 319 +CONECT 319 318 +CONECT 320 331 321 318 322 +CONECT 321 320 +CONECT 322 320 325 324 323 +CONECT 323 322 +CONECT 324 322 +CONECT 325 328 327 322 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 329 330 325 +CONECT 329 328 +CONECT 330 328 +CONECT 331 333 332 320 +CONECT 332 331 +CONECT 333 335 334 331 +CONECT 334 333 +CONECT 335 341 337 336 333 +CONECT 336 335 +CONECT 337 339 338 335 340 +CONECT 338 337 +CONECT 339 337 +CONECT 340 337 +CONECT 341 343 342 335 +CONECT 342 341 +CONECT 343 345 344 341 +CONECT 344 343 +CONECT 345 357 347 346 343 +CONECT 346 345 +CONECT 347 348 353 345 349 +CONECT 348 347 +CONECT 349 347 351 352 350 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 347 356 +CONECT 354 353 +CONECT 355 353 +CONECT 356 353 +CONECT 357 358 359 345 +CONECT 358 357 +CONECT 359 361 357 360 +CONECT 360 359 +CONECT 361 363 362 369 359 +CONECT 362 361 +CONECT 363 366 364 365 361 +CONECT 364 363 +CONECT 365 363 +CONECT 366 367 368 363 +CONECT 367 366 +CONECT 368 366 +CONECT 369 361 371 370 +CONECT 370 369 +CONECT 371 372 369 373 +CONECT 372 371 +CONECT 373 371 375 388 374 +CONECT 374 373 +CONECT 375 377 376 373 378 +CONECT 376 375 +CONECT 377 375 +CONECT 378 384 375 380 379 +CONECT 379 378 +CONECT 380 381 378 382 383 +CONECT 381 380 +CONECT 382 380 +CONECT 383 380 +CONECT 384 387 386 385 378 +CONECT 385 384 +CONECT 386 384 +CONECT 387 384 +CONECT 388 390 373 389 +CONECT 389 388 +CONECT 390 391 392 388 +CONECT 391 390 +CONECT 392 394 393 390 398 +CONECT 393 392 +CONECT 394 397 395 396 392 +CONECT 395 394 +CONECT 396 394 +CONECT 397 394 +CONECT 398 392 399 400 +CONECT 399 398 +CONECT 400 398 401 402 +CONECT 401 400 +CONECT 402 400 403 404 413 +CONECT 403 402 +CONECT 404 407 402 405 406 +CONECT 405 404 +CONECT 406 404 +CONECT 407 408 409 410 404 +CONECT 408 407 +CONECT 409 407 +CONECT 410 412 407 411 +CONECT 411 410 +CONECT 412 410 +CONECT 413 402 415 414 +CONECT 414 413 +CONECT 415 416 413 417 +CONECT 416 415 +CONECT 417 415 419 423 418 +CONECT 418 417 +CONECT 419 420 422 417 421 +CONECT 420 419 +CONECT 421 419 +CONECT 422 419 +CONECT 423 425 417 424 +CONECT 424 423 +CONECT 425 426 427 423 +CONECT 426 425 +CONECT 427 429 425 428 438 +CONECT 428 427 +CONECT 429 430 431 432 427 +CONECT 430 429 +CONECT 431 429 +CONECT 432 435 429 433 434 +CONECT 433 432 +CONECT 434 432 +CONECT 435 437 436 432 +CONECT 436 435 +CONECT 437 435 +CONECT 438 427 440 439 +CONECT 439 438 +CONECT 440 441 438 442 +CONECT 441 440 +CONECT 442 440 444 443 460 +CONECT 443 442 +CONECT 444 447 445 446 442 +CONECT 445 444 +CONECT 446 444 +CONECT 447 449 450 448 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 451 452 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 456 455 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 458 459 457 453 +CONECT 457 456 +CONECT 458 456 +CONECT 459 456 +CONECT 460 442 462 461 +CONECT 461 460 +CONECT 462 463 460 464 +CONECT 463 462 +CONECT 464 462 466 465 480 +CONECT 465 464 +CONECT 466 469 467 464 468 +CONECT 467 466 +CONECT 468 466 +CONECT 469 470 478 466 +CONECT 470 472 471 469 +CONECT 471 470 +CONECT 472 473 474 470 +CONECT 473 472 +CONECT 474 475 472 476 +CONECT 475 474 +CONECT 476 474 477 478 +CONECT 477 476 +CONECT 478 476 469 479 +CONECT 479 478 +CONECT 480 464 482 481 +CONECT 481 480 +CONECT 482 483 484 480 +CONECT 483 482 +CONECT 484 486 482 494 485 +CONECT 485 484 +CONECT 486 487 492 488 484 +CONECT 487 486 +CONECT 488 490 486 491 489 +CONECT 489 488 +CONECT 490 488 +CONECT 491 488 +CONECT 492 493 486 +CONECT 493 492 +CONECT 494 496 484 495 +CONECT 495 494 +CONECT 496 497 498 494 +CONECT 497 496 +CONECT 498 500 496 499 516 +CONECT 499 498 +CONECT 500 503 501 502 498 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 505 504 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 509 507 508 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 510 512 506 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 512 +CONECT 516 498 518 517 +CONECT 517 516 +CONECT 518 519 516 520 +CONECT 519 518 +CONECT 520 518 522 521 526 +CONECT 521 520 +CONECT 522 525 523 520 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 522 +CONECT 526 520 528 527 +CONECT 527 526 +CONECT 528 529 526 530 +CONECT 529 528 +CONECT 530 528 532 536 531 +CONECT 531 530 +CONECT 532 533 535 530 534 +CONECT 533 532 +CONECT 534 532 +CONECT 535 532 +CONECT 536 538 530 537 +CONECT 537 536 +CONECT 538 539 540 536 +CONECT 539 538 +CONECT 540 542 538 546 541 +CONECT 541 540 +CONECT 542 543 545 544 540 +CONECT 543 542 +CONECT 544 542 +CONECT 545 542 +CONECT 546 540 548 547 +CONECT 547 546 +CONECT 548 549 546 550 +CONECT 549 548 +CONECT 550 552 548 551 560 +CONECT 551 550 +CONECT 552 555 553 554 550 +CONECT 553 552 +CONECT 554 552 +CONECT 555 557 556 552 +CONECT 556 555 +CONECT 557 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 550 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 566 565 572 +CONECT 565 564 +CONECT 566 569 567 564 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 571 570 566 +CONECT 570 569 +CONECT 571 569 +CONECT 572 564 574 573 +CONECT 573 572 +CONECT 574 575 572 576 +CONECT 575 574 +CONECT 576 574 578 591 577 +CONECT 577 576 +CONECT 578 580 579 576 581 +CONECT 579 578 +CONECT 580 578 +CONECT 581 578 587 582 583 +CONECT 582 581 +CONECT 583 581 584 585 586 +CONECT 584 583 +CONECT 585 583 +CONECT 586 583 +CONECT 587 588 590 589 581 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 593 576 592 +CONECT 592 591 +CONECT 593 594 595 591 +CONECT 594 593 +CONECT 595 598 593 597 596 +CONECT 596 595 +CONECT 597 595 +CONECT 598 600 599 595 +CONECT 599 598 +CONECT 600 602 601 598 +CONECT 601 600 +CONECT 602 613 603 604 600 +CONECT 603 602 +CONECT 604 606 602 605 607 +CONECT 605 604 +CONECT 606 604 +CONECT 607 604 608 610 609 +CONECT 608 607 +CONECT 609 607 +CONECT 610 612 607 611 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 602 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 625 619 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 639 641 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 638 644 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 665 649 652 653 +CONECT 652 651 +CONECT 653 651 655 656 654 +CONECT 654 653 +CONECT 655 653 +CONECT 656 657 653 663 +CONECT 657 658 659 656 +CONECT 658 657 +CONECT 659 660 657 661 +CONECT 660 659 +CONECT 661 659 663 662 +CONECT 662 661 +CONECT 663 656 661 664 +CONECT 664 663 +CONECT 665 667 666 651 +CONECT 666 665 +CONECT 667 669 668 665 +CONECT 668 667 +CONECT 669 670 671 679 667 +CONECT 670 669 +CONECT 671 673 677 669 672 +CONECT 672 671 +CONECT 673 674 675 676 671 +CONECT 674 673 +CONECT 675 673 +CONECT 676 673 +CONECT 677 678 671 +CONECT 678 677 +CONECT 679 681 669 680 +CONECT 680 679 +CONECT 681 682 683 679 +CONECT 682 681 +CONECT 683 701 685 681 684 +CONECT 684 683 +CONECT 685 687 688 683 686 +CONECT 686 685 +CONECT 687 685 +CONECT 688 691 689 685 690 +CONECT 689 688 +CONECT 690 688 +CONECT 691 693 694 692 688 +CONECT 692 691 +CONECT 693 691 +CONECT 694 695 697 691 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 698 699 700 694 +CONECT 698 697 +CONECT 699 697 +CONECT 700 697 +CONECT 701 702 703 683 +CONECT 702 701 +CONECT 703 705 701 704 +CONECT 704 703 +CONECT 705 706 713 707 703 +CONECT 706 705 +CONECT 707 710 705 708 709 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 711 707 +CONECT 711 710 +CONECT 712 710 +CONECT 713 715 705 714 +CONECT 714 713 +CONECT 715 716 717 713 +CONECT 716 715 +CONECT 717 719 715 725 718 +CONECT 718 717 +CONECT 719 721 720 722 717 +CONECT 720 719 +CONECT 721 719 +CONECT 722 723 719 724 +CONECT 723 722 +CONECT 724 722 +CONECT 725 727 717 726 +CONECT 726 725 +CONECT 727 728 729 725 +CONECT 728 727 +CONECT 729 731 730 727 735 +CONECT 730 729 +CONECT 731 734 733 732 729 +CONECT 732 731 +CONECT 733 731 +CONECT 734 731 +CONECT 735 729 736 737 +CONECT 736 735 +CONECT 737 735 738 739 +CONECT 738 737 +CONECT 739 737 740 741 749 +CONECT 740 739 +CONECT 741 743 739 747 742 +CONECT 742 741 +CONECT 743 744 746 745 741 +CONECT 744 743 +CONECT 745 743 +CONECT 746 743 +CONECT 747 748 741 +CONECT 748 747 +CONECT 749 739 751 750 +CONECT 750 749 +CONECT 751 752 753 749 +CONECT 752 751 +CONECT 753 754 751 755 771 +CONECT 754 753 +CONECT 755 758 753 757 756 +CONECT 756 755 +CONECT 757 755 +CONECT 758 761 759 760 755 +CONECT 759 758 +CONECT 760 758 +CONECT 761 764 763 762 758 +CONECT 762 761 +CONECT 763 761 +CONECT 764 767 766 765 761 +CONECT 765 764 +CONECT 766 764 +CONECT 767 769 770 768 764 +CONECT 768 767 +CONECT 769 767 +CONECT 770 767 +CONECT 771 753 773 772 +CONECT 772 771 +CONECT 773 774 771 775 +CONECT 774 773 +CONECT 775 773 785 777 776 +CONECT 776 775 +CONECT 777 778 775 783 779 +CONECT 778 777 +CONECT 779 777 782 781 780 +CONECT 780 779 +CONECT 781 779 +CONECT 782 779 +CONECT 783 784 777 +CONECT 784 783 +CONECT 785 786 775 787 +CONECT 786 785 +CONECT 787 785 789 788 +CONECT 788 787 +CONECT 789 790 787 805 791 +CONECT 790 789 +CONECT 791 789 794 793 792 +CONECT 792 791 +CONECT 793 791 +CONECT 794 803 795 791 +CONECT 795 794 797 796 +CONECT 796 795 +CONECT 797 799 798 795 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 801 804 794 +CONECT 804 803 +CONECT 805 789 807 806 +CONECT 806 805 +CONECT 807 808 809 805 +CONECT 808 807 +CONECT 809 811 807 819 810 +CONECT 810 809 +CONECT 811 817 813 812 809 +CONECT 812 811 +CONECT 813 814 815 811 816 +CONECT 814 813 +CONECT 815 813 +CONECT 816 813 +CONECT 817 818 811 +CONECT 818 817 +CONECT 819 820 809 821 +CONECT 820 819 +CONECT 821 819 823 822 +CONECT 822 821 +CONECT 823 833 824 821 825 +CONECT 824 823 +CONECT 825 823 826 827 831 +CONECT 826 825 +CONECT 827 825 830 828 829 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 825 832 +CONECT 832 831 +CONECT 833 835 834 823 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 839 838 835 843 +CONECT 838 837 +CONECT 839 842 841 840 837 +CONECT 840 839 +CONECT 841 839 +CONECT 842 839 +CONECT 843 837 845 844 +CONECT 844 843 +CONECT 845 846 843 847 +CONECT 846 845 +CONECT 847 845 849 858 848 +CONECT 848 847 +CONECT 849 851 850 847 852 +CONECT 850 849 +CONECT 851 849 +CONECT 852 853 849 854 855 +CONECT 853 852 +CONECT 854 852 +CONECT 855 852 857 856 +CONECT 856 855 +CONECT 857 855 +CONECT 858 860 847 859 +CONECT 859 858 +CONECT 860 858 +CONECT 861 87 310 862 279 +CONECT 862 861 864 +CONECT 863 866 864 867 865 +CONECT 864 862 863 +CONECT 865 863 +CONECT 866 863 +CONECT 867 863 +CONECT 868 869 +CONECT 869 868 870 +CONECT 870 869 +MASTER 0 0 0 0 0 0 0 0 870 0 870 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_2_front_2.pdb b/tests/nsga2/intermediate_molecules/min_iter_2_front_2.pdb new file mode 100644 index 0000000..7a0c97e --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_2_front_2.pdb @@ -0,0 +1,1753 @@ +COMPND fitness: -1.2907 59.98833333333391 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 55.366 58.077 52.044 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.215 37.914 23.523 1.00 0.00 N +ATOM 2 H1 MET 1 15.201 38.296 24.464 1.00 0.00 H +ATOM 3 H2 MET 1 14.443 38.284 22.998 1.00 0.00 H +ATOM 4 H3 MET 1 16.084 38.206 23.097 1.00 0.00 H +ATOM 5 CA MET 1 15.167 36.444 23.594 1.00 0.00 C +ATOM 6 HA MET 1 14.223 36.155 24.051 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.794 22.200 1.00 0.00 C +ATOM 8 HB2 MET 1 14.404 36.123 21.604 1.00 0.00 H +ATOM 9 HB3 MET 1 16.168 36.123 21.701 1.00 0.00 H +ATOM 10 CG MET 1 15.256 34.254 22.251 1.00 0.00 C +ATOM 11 HG2 MET 1 16.133 33.929 22.814 1.00 0.00 H +ATOM 12 HG3 MET 1 14.367 33.916 22.786 1.00 0.00 H +ATOM 13 SD MET 1 15.317 33.393 20.646 1.00 0.00 S +ATOM 14 CE MET 1 13.636 33.641 20.008 1.00 0.00 C +ATOM 15 HE1 MET 1 13.415 34.705 19.929 1.00 0.00 H +ATOM 16 HE2 MET 1 13.557 33.192 19.017 1.00 0.00 H +ATOM 17 HE3 MET 1 12.912 33.164 20.670 1.00 0.00 H +ATOM 18 C MET 1 16.285 35.966 24.511 1.00 0.00 C +ATOM 19 O MET 1 17.429 36.370 24.340 1.00 0.00 O +ATOM 20 N GLN 2 15.963 35.099 25.473 1.00 0.00 N +ATOM 21 H GLN 2 14.992 34.874 25.632 1.00 0.00 H +ATOM 22 CA GLN 2 16.928 34.438 26.358 1.00 0.00 C +ATOM 23 HA GLN 2 17.697 35.150 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 16.177 34.003 27.636 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.213 33.562 27.357 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.744 33.245 28.172 1.00 0.00 H +ATOM 27 CG GLN 2 15.930 35.169 28.587 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.504 36.019 28.045 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.177 34.846 29.297 1.00 0.00 H +ATOM 30 CD GLN 2 17.140 35.548 29.441 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.211 34.972 29.368 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.976 36.450 30.363 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.748 36.615 30.982 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.068 36.818 30.542 1.00 0.00 H +ATOM 35 C GLN 2 17.653 33.291 25.623 1.00 0.00 C +ATOM 36 O GLN 2 17.281 32.121 25.734 1.00 0.00 O +ATOM 37 N TYR 3 18.675 33.646 24.841 1.00 0.00 N +ATOM 38 H TYR 3 18.926 34.635 24.813 1.00 0.00 H +ATOM 39 CA TYR 3 19.508 32.709 24.085 1.00 0.00 C +ATOM 40 HA TYR 3 18.854 32.101 23.459 1.00 0.00 H +ATOM 41 CB TYR 3 20.458 33.508 23.197 1.00 0.00 C +ATOM 42 HB2 TYR 3 21.071 34.153 23.827 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.125 32.817 22.690 1.00 0.00 H +ATOM 44 CG TYR 3 19.760 34.349 22.152 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.102 33.711 21.087 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.079 32.633 21.039 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.519 34.465 20.054 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.049 33.973 19.217 1.00 0.00 H +ATOM 49 CZ TYR 3 18.571 35.872 20.103 1.00 0.00 C +ATOM 50 OH TYR 3 18.027 36.608 19.103 1.00 0.00 O +ATOM 51 HH TYR 3 18.041 36.130 18.273 1.00 0.00 H +ATOM 52 CE2 TYR 3 19.176 36.515 21.200 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.196 37.592 21.223 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.774 35.755 22.224 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.247 36.252 23.059 1.00 0.00 H +ATOM 56 C TYR 3 20.295 31.786 25.023 1.00 0.00 C +ATOM 57 O TYR 3 20.806 32.243 26.044 1.00 0.00 O +ATOM 58 N LYS 4 20.410 30.492 24.696 1.00 0.00 N +ATOM 59 H LYS 4 20.118 30.201 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 21.014 29.461 25.566 1.00 0.00 C +ATOM 61 HA LYS 4 20.744 29.654 26.602 1.00 0.00 H +ATOM 62 CB LYS 4 20.480 28.067 25.177 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.496 27.976 24.094 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.160 27.307 25.570 1.00 0.00 H +ATOM 65 CG LYS 4 19.070 27.701 25.676 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.897 26.669 25.374 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.060 27.742 26.766 1.00 0.00 H +ATOM 68 CD LYS 4 17.920 28.560 25.120 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.927 29.535 25.607 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.090 28.713 24.052 1.00 0.00 H +ATOM 71 CE LYS 4 16.533 27.909 25.279 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.777 28.600 24.894 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.509 27.012 24.654 1.00 0.00 H +ATOM 74 NZ LYS 4 16.205 27.518 26.673 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.269 28.291 27.318 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.276 27.107 26.716 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.829 26.763 26.958 1.00 0.00 H +ATOM 78 C LYS 4 22.547 29.475 25.513 1.00 0.00 C +ATOM 79 O LYS 4 23.144 29.819 24.501 1.00 0.00 O +HETATM 80 N HX1 5 23.203 29.039 26.584 1.00 0.00 N +HETATM 81 CA HX1 5 24.662 28.868 26.669 1.00 0.00 C +HETATM 82 C HX1 5 24.985 27.668 27.567 1.00 0.00 C +HETATM 83 O HX1 5 24.522 27.612 28.710 1.00 0.00 O +HETATM 84 CB HX1 5 25.294 30.185 27.169 1.00 0.00 C +HETATM 85 CG HX1 5 26.807 30.275 27.239 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.721 29.336 26.838 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.483 31.361 27.814 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.782 31.031 27.730 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.957 29.808 27.202 1.00 0.00 N +HETATM 90 H HX1 5 22.658 28.869 27.426 1.00 0.00 H +HETATM 91 HA HX1 5 25.052 28.661 25.672 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.899 30.401 28.163 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.958 30.992 26.516 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.539 28.374 26.378 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.578 31.603 28.187 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.812 29.251 27.293 1.00 0.00 H +ATOM 97 N ILE 6 25.726 26.695 27.028 1.00 0.00 N +ATOM 98 H ILE 6 26.046 26.815 26.070 1.00 0.00 H +ATOM 99 CA ILE 6 26.199 25.479 27.709 1.00 0.00 C +ATOM 100 HA ILE 6 25.697 25.404 28.676 1.00 0.00 H +ATOM 101 CB ILE 6 25.811 24.216 26.902 1.00 0.00 C +ATOM 102 HB ILE 6 26.234 24.306 25.901 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.373 22.929 27.541 1.00 0.00 C +ATOM 104 HG21 ILE 6 26.002 22.820 28.562 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.078 22.054 26.963 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.464 22.944 27.545 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.270 24.130 26.784 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.842 24.047 27.783 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.891 25.046 26.331 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.745 22.969 25.931 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.890 22.021 26.449 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.678 23.107 25.758 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.263 22.948 24.971 1.00 0.00 H +ATOM 114 C ILE 6 27.708 25.597 28.003 1.00 0.00 C +ATOM 115 O ILE 6 28.447 26.273 27.288 1.00 0.00 O +ATOM 116 N VAL 7 28.126 24.994 29.115 1.00 0.00 N +ATOM 117 H VAL 7 27.488 24.344 29.551 1.00 0.00 H +ATOM 118 CA VAL 7 29.238 25.447 29.963 1.00 0.00 C +ATOM 119 HA VAL 7 29.296 26.533 29.871 1.00 0.00 H +ATOM 120 CB VAL 7 28.813 25.143 31.416 1.00 0.00 C +ATOM 121 HB VAL 7 27.762 25.424 31.517 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.895 23.654 31.773 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.924 23.309 31.694 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.538 23.499 32.790 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.276 23.071 31.090 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.567 25.988 32.435 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.358 27.041 32.248 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.232 25.736 33.441 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.636 25.813 32.353 1.00 0.00 H +ATOM 130 C VAL 7 30.639 24.901 29.585 1.00 0.00 C +ATOM 131 O VAL 7 30.785 23.764 29.143 1.00 0.00 O +ATOM 132 N GLU 8 31.685 25.707 29.802 1.00 0.00 N +ATOM 133 H GLU 8 31.473 26.676 30.027 1.00 0.00 H +ATOM 134 CA GLU 8 33.119 25.383 29.624 1.00 0.00 C +ATOM 135 HA GLU 8 33.310 25.152 28.575 1.00 0.00 H +ATOM 136 CB GLU 8 33.917 26.667 29.977 1.00 0.00 C +ATOM 137 HB2 GLU 8 33.712 27.426 29.223 1.00 0.00 H +ATOM 138 HB3 GLU 8 33.497 27.048 30.911 1.00 0.00 H +ATOM 139 CG GLU 8 35.447 26.584 30.222 1.00 0.00 C +ATOM 140 HG2 GLU 8 35.729 27.498 30.753 1.00 0.00 H +ATOM 141 HG3 GLU 8 35.683 25.765 30.900 1.00 0.00 H +ATOM 142 CD GLU 8 36.359 26.500 28.992 1.00 0.00 C +ATOM 143 OE1 GLU 8 36.012 27.041 27.916 1.00 0.00 O +ATOM 144 OE2 GLU 8 37.521 26.054 29.135 1.00 0.00 O +ATOM 145 C GLU 8 33.570 24.164 30.464 1.00 0.00 C +ATOM 146 O GLU 8 33.840 24.286 31.658 1.00 0.00 O +ATOM 147 N GLY 9 33.696 22.982 29.849 1.00 0.00 N +ATOM 148 H GLY 9 33.287 22.892 28.929 1.00 0.00 H +ATOM 149 CA GLY 9 34.345 21.797 30.438 1.00 0.00 C +ATOM 150 HA2 GLY 9 35.247 21.575 29.868 1.00 0.00 H +ATOM 151 HA3 GLY 9 34.650 22.011 31.462 1.00 0.00 H +ATOM 152 C GLY 9 33.492 20.522 30.448 1.00 0.00 C +ATOM 153 O GLY 9 32.620 20.332 29.602 1.00 0.00 O +ATOM 154 N LYS 10 33.792 19.600 31.384 1.00 0.00 N +ATOM 155 H LYS 10 34.546 19.810 32.024 1.00 0.00 H +ATOM 156 CA LYS 10 33.231 18.228 31.369 1.00 0.00 C +ATOM 157 HA LYS 10 32.207 18.313 30.994 1.00 0.00 H +ATOM 158 CB LYS 10 34.029 17.371 30.353 1.00 0.00 C +ATOM 159 HB2 LYS 10 34.519 18.019 29.622 1.00 0.00 H +ATOM 160 HB3 LYS 10 34.809 16.806 30.866 1.00 0.00 H +ATOM 161 CG LYS 10 33.125 16.407 29.565 1.00 0.00 C +ATOM 162 HG2 LYS 10 32.575 15.759 30.248 1.00 0.00 H +ATOM 163 HG3 LYS 10 32.406 16.996 28.991 1.00 0.00 H +ATOM 164 CD LYS 10 33.941 15.541 28.595 1.00 0.00 C +ATOM 165 HD2 LYS 10 34.578 16.183 27.985 1.00 0.00 H +ATOM 166 HD3 LYS 10 34.568 14.847 29.158 1.00 0.00 H +ATOM 167 CE LYS 10 32.994 14.759 27.678 1.00 0.00 C +ATOM 168 HE2 LYS 10 32.438 14.025 28.267 1.00 0.00 H +ATOM 169 HE3 LYS 10 32.275 15.460 27.247 1.00 0.00 H +ATOM 170 NZ LYS 10 33.721 14.092 26.575 1.00 0.00 N +ATOM 171 HZ1 LYS 10 34.417 13.448 26.913 1.00 0.00 H +ATOM 172 HZ2 LYS 10 33.061 13.594 25.979 1.00 0.00 H +ATOM 173 HZ3 LYS 10 34.203 14.795 26.004 1.00 0.00 H +ATOM 174 C LYS 10 33.089 17.528 32.737 1.00 0.00 C +ATOM 175 O LYS 10 33.156 16.303 32.800 1.00 0.00 O +ATOM 176 N ARG 11 32.949 18.273 33.841 1.00 0.00 N +ATOM 177 H ARG 11 32.915 19.267 33.709 1.00 0.00 H +ATOM 178 CA ARG 11 32.662 17.722 35.194 1.00 0.00 C +ATOM 179 HA ARG 11 32.758 16.632 35.161 1.00 0.00 H +ATOM 180 CB ARG 11 33.685 18.237 36.231 1.00 0.00 C +ATOM 181 HB2 ARG 11 33.709 19.326 36.208 1.00 0.00 H +ATOM 182 HB3 ARG 11 33.355 17.924 37.222 1.00 0.00 H +ATOM 183 CG ARG 11 35.099 17.680 35.989 1.00 0.00 C +ATOM 184 HG2 ARG 11 35.055 16.589 35.999 1.00 0.00 H +ATOM 185 HG3 ARG 11 35.449 18.007 35.010 1.00 0.00 H +ATOM 186 CD ARG 11 36.103 18.142 37.058 1.00 0.00 C +ATOM 187 HD2 ARG 11 36.071 19.228 37.118 1.00 0.00 H +ATOM 188 HD3 ARG 11 35.803 17.740 38.029 1.00 0.00 H +ATOM 189 NE ARG 11 37.479 17.692 36.740 1.00 0.00 N +ATOM 190 HE ARG 11 37.569 16.946 36.073 1.00 0.00 H +ATOM 191 CZ ARG 11 38.615 18.198 37.201 1.00 0.00 C +ATOM 192 NH1 ARG 11 38.667 19.233 37.987 1.00 0.00 N +ATOM 193 HH11 ARG 11 37.829 19.772 38.112 1.00 0.00 H +ATOM 194 HH12 ARG 11 39.560 19.686 38.132 1.00 0.00 H +ATOM 195 NH2 ARG 11 39.749 17.650 36.875 1.00 0.00 N +ATOM 196 HH21 ARG 11 39.795 16.894 36.219 1.00 0.00 H +ATOM 197 HH22 ARG 11 40.609 18.031 37.266 1.00 0.00 H +ATOM 198 C ARG 11 31.206 17.954 35.609 1.00 0.00 C +ATOM 199 O ARG 11 30.490 17.005 35.900 1.00 0.00 O +ATOM 200 N TYR 12 30.762 19.208 35.566 1.00 0.00 N +ATOM 201 H TYR 12 31.434 19.929 35.379 1.00 0.00 H +ATOM 202 CA TYR 12 29.346 19.607 35.531 1.00 0.00 C +ATOM 203 HA TYR 12 28.789 18.986 36.247 1.00 0.00 H +ATOM 204 CB TYR 12 29.234 21.066 36.001 1.00 0.00 C +ATOM 205 HB2 TYR 12 28.187 21.379 35.945 1.00 0.00 H +ATOM 206 HB3 TYR 12 29.493 21.077 37.062 1.00 0.00 H +ATOM 207 CG TYR 12 30.105 22.126 35.333 1.00 0.00 C +ATOM 208 CD1 TYR 12 30.870 21.891 34.171 1.00 0.00 C +ATOM 209 HD1 TYR 12 30.824 20.950 33.636 1.00 0.00 H +ATOM 210 CE1 TYR 12 31.738 22.879 33.670 1.00 0.00 C +ATOM 211 HE1 TYR 12 32.313 22.692 32.776 1.00 0.00 H +ATOM 212 CZ TYR 12 31.833 24.123 34.322 1.00 0.00 C +ATOM 213 OH TYR 12 32.699 25.074 33.898 1.00 0.00 O +ATOM 214 HH TYR 12 33.108 24.847 33.030 1.00 0.00 H +ATOM 215 CE2 TYR 12 30.999 24.398 35.419 1.00 0.00 C +ATOM 216 HE2 TYR 12 31.006 25.385 35.861 1.00 0.00 H +ATOM 217 CD2 TYR 12 30.158 23.394 35.933 1.00 0.00 C +ATOM 218 HD2 TYR 12 29.558 23.604 36.815 1.00 0.00 H +ATOM 219 C TYR 12 28.690 19.397 34.145 1.00 0.00 C +ATOM 220 O TYR 12 29.368 19.005 33.196 1.00 0.00 O +ATOM 221 N LYS 13 27.382 19.683 34.028 1.00 0.00 N +ATOM 222 H LYS 13 26.894 19.964 34.865 1.00 0.00 H +ATOM 223 CA LYS 13 26.590 19.509 32.789 1.00 0.00 C +ATOM 224 HA LYS 13 27.257 19.685 31.944 1.00 0.00 H +ATOM 225 CB LYS 13 26.113 18.042 32.728 1.00 0.00 C +ATOM 226 HB2 LYS 13 26.870 17.413 33.196 1.00 0.00 H +ATOM 227 HB3 LYS 13 25.191 17.936 33.302 1.00 0.00 H +ATOM 228 CG LYS 13 25.912 17.515 31.295 1.00 0.00 C +ATOM 229 HG2 LYS 13 25.056 18.000 30.825 1.00 0.00 H +ATOM 230 HG3 LYS 13 26.803 17.746 30.711 1.00 0.00 H +ATOM 231 CD LYS 13 25.715 15.990 31.282 1.00 0.00 C +ATOM 232 HD2 LYS 13 25.753 15.643 30.248 1.00 0.00 H +ATOM 233 HD3 LYS 13 26.543 15.525 31.821 1.00 0.00 H +ATOM 234 CE LYS 13 24.376 15.549 31.892 1.00 0.00 C +ATOM 235 HE2 LYS 13 24.136 16.182 32.751 1.00 0.00 H +ATOM 236 HE3 LYS 13 23.603 15.708 31.133 1.00 0.00 H +ATOM 237 NZ LYS 13 24.406 14.121 32.306 1.00 0.00 N +ATOM 238 HZ1 LYS 13 24.934 13.975 33.159 1.00 0.00 H +ATOM 239 HZ2 LYS 13 23.466 13.759 32.451 1.00 0.00 H +ATOM 240 HZ3 LYS 13 24.860 13.553 31.592 1.00 0.00 H +ATOM 241 C LYS 13 25.440 20.533 32.632 1.00 0.00 C +ATOM 242 O LYS 13 24.397 20.233 32.051 1.00 0.00 O +ATOM 243 N GLY 14 25.597 21.720 33.227 1.00 0.00 N +ATOM 244 H GLY 14 26.491 21.921 33.646 1.00 0.00 H +ATOM 245 CA GLY 14 24.547 22.749 33.314 1.00 0.00 C +ATOM 246 HA2 GLY 14 23.595 22.255 33.508 1.00 0.00 H +ATOM 247 HA3 GLY 14 24.753 23.393 34.169 1.00 0.00 H +ATOM 248 C GLY 14 24.384 23.636 32.065 1.00 0.00 C +ATOM 249 O GLY 14 25.241 23.673 31.182 1.00 0.00 O +ATOM 250 N VAL 15 23.283 24.395 32.031 1.00 0.00 N +ATOM 251 H VAL 15 22.640 24.337 32.808 1.00 0.00 H +ATOM 252 CA VAL 15 22.902 25.355 30.981 1.00 0.00 C +ATOM 253 HA VAL 15 23.781 25.595 30.382 1.00 0.00 H +ATOM 254 CB VAL 15 21.857 24.717 30.034 1.00 0.00 C +ATOM 255 HB VAL 15 22.299 23.817 29.609 1.00 0.00 H +ATOM 256 CG1 VAL 15 20.551 24.300 30.731 1.00 0.00 C +ATOM 257 HG11 VAL 15 20.049 25.165 31.169 1.00 0.00 H +ATOM 258 HG12 VAL 15 19.882 23.832 30.007 1.00 0.00 H +ATOM 259 HG13 VAL 15 20.757 23.573 31.519 1.00 0.00 H +ATOM 260 CG2 VAL 15 21.481 25.640 28.867 1.00 0.00 C +ATOM 261 HG21 VAL 15 22.382 25.990 28.366 1.00 0.00 H +ATOM 262 HG22 VAL 15 20.879 25.084 28.146 1.00 0.00 H +ATOM 263 HG23 VAL 15 20.901 26.492 29.221 1.00 0.00 H +ATOM 264 C VAL 15 22.399 26.651 31.633 1.00 0.00 C +ATOM 265 O VAL 15 21.845 26.618 32.728 1.00 0.00 O +HETATM 266 N HY1 16 22.593 27.795 30.980 1.00 0.00 N +HETATM 267 CA HY1 16 22.005 29.092 31.344 1.00 0.00 C +HETATM 268 C HY1 16 21.694 29.890 30.062 1.00 0.00 C +HETATM 269 O HY1 16 21.860 29.375 28.949 1.00 0.00 O +HETATM 270 CB HY1 16 22.928 29.838 32.334 1.00 0.00 C +HETATM 271 CG HY1 16 24.278 30.202 31.763 1.00 0.00 C +HETATM 272 CD2 HY1 16 24.599 31.380 31.142 1.00 0.00 C +HETATM 273 ND1 HY1 16 25.407 29.412 31.750 1.00 0.00 N +HETATM 274 CE1 HY1 16 26.387 30.121 31.164 1.00 0.00 C +HETATM 275 NE2 HY1 16 25.942 31.324 30.761 1.00 0.00 N +HETATM 276 H HY1 16 23.089 27.760 30.095 1.00 0.00 H +HETATM 277 HA HY1 16 21.042 28.937 31.836 1.00 0.00 H +HETATM 278 HB2 HY1 16 22.448 30.747 32.701 1.00 0.00 H +HETATM 279 HB3 HY1 16 23.076 29.209 33.217 1.00 0.00 H +HETATM 280 HD1 HY1 16 25.502 28.501 32.177 1.00 0.00 H +HETATM 281 HD2 HY1 16 23.933 32.219 30.992 1.00 0.00 H +HETATM 282 HE1 HY1 16 27.419 29.794 31.067 1.00 0.00 H +ATOM 283 N THR 17 21.213 31.125 30.221 1.00 0.00 N +ATOM 284 H THR 17 21.084 31.439 31.169 1.00 0.00 H +ATOM 285 CA THR 17 20.771 32.009 29.122 1.00 0.00 C +ATOM 286 HA THR 17 21.190 31.603 28.215 1.00 0.00 H +ATOM 287 CB THR 17 19.244 32.008 28.942 1.00 0.00 C +ATOM 288 HB THR 17 19.023 32.578 28.042 1.00 0.00 H +ATOM 289 CG2 THR 17 18.642 30.640 28.642 1.00 0.00 C +ATOM 290 HG21 THR 17 18.864 29.923 29.430 1.00 0.00 H +ATOM 291 HG22 THR 17 17.562 30.744 28.553 1.00 0.00 H +ATOM 292 HG23 THR 17 19.034 30.311 27.693 1.00 0.00 H +ATOM 293 OG1 THR 17 18.523 32.465 30.065 1.00 0.00 O +ATOM 294 HG1 THR 17 18.606 33.430 30.107 1.00 0.00 H +ATOM 295 C THR 17 21.279 33.458 29.181 1.00 0.00 C +ATOM 296 O THR 17 21.726 33.926 30.226 1.00 0.00 O +HETATM 297 N HY2 18 21.213 34.175 28.055 1.00 0.00 N +HETATM 298 CA HY2 18 21.495 35.612 27.957 1.00 0.00 C +HETATM 299 C HY2 18 20.395 36.305 27.153 1.00 0.00 C +HETATM 300 O HY2 18 20.079 35.863 26.049 1.00 0.00 O +HETATM 301 CB HY2 18 22.848 35.842 27.247 1.00 0.00 C +HETATM 302 CG HY2 18 24.050 35.344 28.020 1.00 0.00 C +HETATM 303 CD2 HY2 18 24.548 34.066 28.017 1.00 0.00 C +HETATM 304 ND1 HY2 18 24.828 36.083 28.888 1.00 0.00 N +HETATM 305 CE1 HY2 18 25.770 35.264 29.383 1.00 0.00 C +HETATM 306 NE2 HY2 18 25.640 34.024 28.889 1.00 0.00 N +HETATM 307 H HY2 18 20.908 33.715 27.202 1.00 0.00 H +HETATM 308 HA HY2 18 21.529 36.051 28.954 1.00 0.00 H +HETATM 309 HB2 HY2 18 22.822 35.342 26.280 1.00 0.00 H +HETATM 310 HB3 HY2 18 22.973 36.910 27.064 1.00 0.00 H +HETATM 311 HD1 HY2 18 24.725 37.067 29.105 1.00 0.00 H +HETATM 312 HD2 HY2 18 24.156 33.232 27.450 1.00 0.00 H +HETATM 313 HE1 HY2 18 26.531 35.559 30.091 1.00 0.00 H +ATOM 314 N GLU 19 19.822 37.382 27.687 1.00 0.00 N +ATOM 315 H GLU 19 20.120 37.688 28.599 1.00 0.00 H +ATOM 316 CA GLU 19 18.828 38.211 26.992 1.00 0.00 C +ATOM 317 HA GLU 19 18.106 37.555 26.510 1.00 0.00 H +ATOM 318 CB GLU 19 18.086 39.074 28.032 1.00 0.00 C +ATOM 319 HB2 GLU 19 17.783 38.444 28.864 1.00 0.00 H +ATOM 320 HB3 GLU 19 18.779 39.814 28.429 1.00 0.00 H +ATOM 321 CG GLU 19 16.839 39.798 27.502 1.00 0.00 C +ATOM 322 HG2 GLU 19 16.549 40.555 28.233 1.00 0.00 H +ATOM 323 HG3 GLU 19 17.073 40.313 26.569 1.00 0.00 H +ATOM 324 CD GLU 19 15.667 38.828 27.300 1.00 0.00 C +ATOM 325 OE1 GLU 19 15.544 38.285 26.172 1.00 0.00 O +ATOM 326 OE2 GLU 19 14.908 38.603 28.271 1.00 0.00 O +ATOM 327 C GLU 19 19.483 39.095 25.913 1.00 0.00 C +ATOM 328 O GLU 19 20.430 39.823 26.208 1.00 0.00 O +ATOM 329 N ALA 20 18.977 39.059 24.676 1.00 0.00 N +ATOM 330 H ALA 20 18.268 38.367 24.467 1.00 0.00 H +ATOM 331 CA ALA 20 19.340 40.004 23.612 1.00 0.00 C +ATOM 332 HA ALA 20 19.410 41.004 24.042 1.00 0.00 H +ATOM 333 CB ALA 20 20.714 39.620 23.042 1.00 0.00 C +ATOM 334 HB1 ALA 20 20.657 38.642 22.573 1.00 0.00 H +ATOM 335 HB2 ALA 20 21.036 40.351 22.302 1.00 0.00 H +ATOM 336 HB3 ALA 20 21.459 39.585 23.834 1.00 0.00 H +ATOM 337 C ALA 20 18.286 40.039 22.486 1.00 0.00 C +ATOM 338 O ALA 20 17.384 39.200 22.439 1.00 0.00 O +ATOM 339 N VAL 21 18.416 40.981 21.545 1.00 0.00 N +ATOM 340 H VAL 21 19.145 41.670 21.653 1.00 0.00 H +ATOM 341 CA VAL 21 17.672 40.975 20.262 1.00 0.00 C +ATOM 342 HA VAL 21 16.689 40.537 20.427 1.00 0.00 H +ATOM 343 CB VAL 21 17.448 42.410 19.731 1.00 0.00 C +ATOM 344 HB VAL 21 16.804 42.345 18.853 1.00 0.00 H +ATOM 345 CG1 VAL 21 16.721 43.284 20.761 1.00 0.00 C +ATOM 346 HG11 VAL 21 17.357 43.476 21.625 1.00 0.00 H +ATOM 347 HG12 VAL 21 16.455 44.237 20.303 1.00 0.00 H +ATOM 348 HG13 VAL 21 15.806 42.790 21.088 1.00 0.00 H +ATOM 349 CG2 VAL 21 18.744 43.117 19.309 1.00 0.00 C +ATOM 350 HG21 VAL 21 19.218 42.578 18.489 1.00 0.00 H +ATOM 351 HG22 VAL 21 18.510 44.121 18.954 1.00 0.00 H +ATOM 352 HG23 VAL 21 19.441 43.191 20.143 1.00 0.00 H +ATOM 353 C VAL 21 18.344 40.117 19.176 1.00 0.00 C +ATOM 354 O VAL 21 17.744 39.875 18.133 1.00 0.00 O +ATOM 355 N ASP 22 19.590 39.693 19.410 1.00 0.00 N +ATOM 356 H ASP 22 20.003 39.905 20.303 1.00 0.00 H +ATOM 357 CA ASP 22 20.496 39.093 18.428 1.00 0.00 C +ATOM 358 HA ASP 22 19.939 38.443 17.752 1.00 0.00 H +ATOM 359 CB ASP 22 21.118 40.245 17.617 1.00 0.00 C +ATOM 360 HB2 ASP 22 20.331 40.741 17.046 1.00 0.00 H +ATOM 361 HB3 ASP 22 21.537 40.973 18.314 1.00 0.00 H +ATOM 362 CG ASP 22 22.212 39.808 16.646 1.00 0.00 C +ATOM 363 OD1 ASP 22 23.135 40.614 16.431 1.00 0.00 O +ATOM 364 OD2 ASP 22 22.150 38.658 16.158 1.00 0.00 O +ATOM 365 C ASP 22 21.589 38.257 19.129 1.00 0.00 C +ATOM 366 O ASP 22 22.026 38.601 20.232 1.00 0.00 O +ATOM 367 N PHE 23 22.075 37.194 18.482 1.00 0.00 N +ATOM 368 H PHE 23 21.801 37.088 17.511 1.00 0.00 H +ATOM 369 CA PHE 23 23.223 36.413 18.957 1.00 0.00 C +ATOM 370 HA PHE 23 23.033 36.100 19.983 1.00 0.00 H +ATOM 371 CB PHE 23 23.435 35.163 18.098 1.00 0.00 C +ATOM 372 HB2 PHE 23 23.449 35.439 17.042 1.00 0.00 H +ATOM 373 HB3 PHE 23 24.415 34.748 18.336 1.00 0.00 H +ATOM 374 CG PHE 23 22.418 34.075 18.332 1.00 0.00 C +ATOM 375 CD1 PHE 23 21.326 33.930 17.460 1.00 0.00 C +ATOM 376 HD1 PHE 23 21.215 34.591 16.613 1.00 0.00 H +ATOM 377 CE1 PHE 23 20.387 32.912 17.686 1.00 0.00 C +ATOM 378 HE1 PHE 23 19.553 32.789 17.010 1.00 0.00 H +ATOM 379 CZ PHE 23 20.545 32.053 18.784 1.00 0.00 C +ATOM 380 HZ PHE 23 19.804 31.307 18.977 1.00 0.00 H +ATOM 381 CE2 PHE 23 21.642 32.183 19.650 1.00 0.00 C +ATOM 382 HE2 PHE 23 21.763 31.512 20.488 1.00 0.00 H +ATOM 383 CD2 PHE 23 22.581 33.199 19.421 1.00 0.00 C +ATOM 384 HD2 PHE 23 23.433 33.303 20.076 1.00 0.00 H +ATOM 385 C PHE 23 24.522 37.216 18.948 1.00 0.00 C +ATOM 386 O PHE 23 25.288 37.123 19.906 1.00 0.00 O +ATOM 387 N ALA 24 24.777 38.032 17.920 1.00 0.00 N +ATOM 388 H ALA 24 24.098 38.127 17.167 1.00 0.00 H +ATOM 389 CA ALA 24 26.004 38.826 17.863 1.00 0.00 C +ATOM 390 HA ALA 24 26.836 38.166 18.118 1.00 0.00 H +ATOM 391 CB ALA 24 26.244 39.297 16.423 1.00 0.00 C +ATOM 392 HB1 ALA 24 25.486 40.016 16.122 1.00 0.00 H +ATOM 393 HB2 ALA 24 27.226 39.763 16.347 1.00 0.00 H +ATOM 394 HB3 ALA 24 26.209 38.442 15.744 1.00 0.00 H +ATOM 395 C ALA 24 26.024 39.969 18.904 1.00 0.00 C +ATOM 396 O ALA 24 27.084 40.536 19.172 1.00 0.00 O +ATOM 397 N GLU 25 24.892 40.281 19.545 1.00 0.00 N +ATOM 398 H GLU 25 24.041 39.856 19.205 1.00 0.00 H +ATOM 399 CA GLU 25 24.819 41.085 20.776 1.00 0.00 C +ATOM 400 HA GLU 25 25.636 41.806 20.796 1.00 0.00 H +ATOM 401 CB GLU 25 23.498 41.871 20.814 1.00 0.00 C +ATOM 402 HB2 GLU 25 22.673 41.163 20.774 1.00 0.00 H +ATOM 403 HB3 GLU 25 23.429 42.408 21.760 1.00 0.00 H +ATOM 404 CG GLU 25 23.310 42.881 19.671 1.00 0.00 C +ATOM 405 HG2 GLU 25 23.577 42.429 18.714 1.00 0.00 H +ATOM 406 HG3 GLU 25 22.247 43.135 19.624 1.00 0.00 H +ATOM 407 CD GLU 25 24.114 44.170 19.880 1.00 0.00 C +ATOM 408 OE1 GLU 25 23.462 45.220 20.101 1.00 0.00 O +ATOM 409 OE2 GLU 25 25.371 44.098 19.811 1.00 0.00 O +ATOM 410 C GLU 25 24.959 40.215 22.041 1.00 0.00 C +ATOM 411 O GLU 25 25.732 40.553 22.938 1.00 0.00 O +ATOM 412 N ALA 26 24.299 39.050 22.103 1.00 0.00 N +ATOM 413 H ALA 26 23.662 38.814 21.352 1.00 0.00 H +ATOM 414 CA ALA 26 24.423 38.100 23.218 1.00 0.00 C +ATOM 415 HA ALA 26 24.130 38.609 24.131 1.00 0.00 H +ATOM 416 CB ALA 26 23.471 36.923 22.993 1.00 0.00 C +ATOM 417 HB1 ALA 26 23.770 36.368 22.108 1.00 0.00 H +ATOM 418 HB2 ALA 26 23.499 36.260 23.854 1.00 0.00 H +ATOM 419 HB3 ALA 26 22.460 37.285 22.860 1.00 0.00 H +ATOM 420 C ALA 26 25.868 37.595 23.424 1.00 0.00 C +ATOM 421 O ALA 26 26.292 37.316 24.550 1.00 0.00 O +ATOM 422 N GLU 27 26.659 37.515 22.348 1.00 0.00 N +ATOM 423 H GLU 27 26.221 37.663 21.441 1.00 0.00 H +ATOM 424 CA GLU 27 28.109 37.261 22.347 1.00 0.00 C +ATOM 425 HA GLU 27 28.316 36.315 22.855 1.00 0.00 H +ATOM 426 CB GLU 27 28.586 37.117 20.887 1.00 0.00 C +ATOM 427 HB2 GLU 27 28.014 36.303 20.438 1.00 0.00 H +ATOM 428 HB3 GLU 27 28.354 38.028 20.337 1.00 0.00 H +ATOM 429 CG GLU 27 30.079 36.836 20.757 1.00 0.00 C +ATOM 430 HG2 GLU 27 30.614 37.779 20.882 1.00 0.00 H +ATOM 431 HG3 GLU 27 30.401 36.162 21.554 1.00 0.00 H +ATOM 432 CD GLU 27 30.366 36.227 19.390 1.00 0.00 C +ATOM 433 OE1 GLU 27 30.986 36.917 18.564 1.00 0.00 O +ATOM 434 OE2 GLU 27 29.944 35.073 19.158 1.00 0.00 O +ATOM 435 C GLU 27 28.855 38.375 23.112 1.00 0.00 C +ATOM 436 O GLU 27 29.633 38.083 24.023 1.00 0.00 O +ATOM 437 N LYS 28 28.553 39.656 22.836 1.00 0.00 N +ATOM 438 H LYS 28 27.822 39.830 22.156 1.00 0.00 H +ATOM 439 CA LYS 28 29.116 40.802 23.576 1.00 0.00 C +ATOM 440 HA LYS 28 30.202 40.719 23.569 1.00 0.00 H +ATOM 441 CB LYS 28 28.725 42.140 22.919 1.00 0.00 C +ATOM 442 HB2 LYS 28 27.648 42.281 22.995 1.00 0.00 H +ATOM 443 HB3 LYS 28 29.205 42.945 23.473 1.00 0.00 H +ATOM 444 CG LYS 28 29.135 42.250 21.442 1.00 0.00 C +ATOM 445 HG2 LYS 28 30.206 42.069 21.341 1.00 0.00 H +ATOM 446 HG3 LYS 28 28.602 41.496 20.871 1.00 0.00 H +ATOM 447 CD LYS 28 28.806 43.646 20.888 1.00 0.00 C +ATOM 448 HD2 LYS 28 27.796 43.939 21.184 1.00 0.00 H +ATOM 449 HD3 LYS 28 29.505 44.362 21.322 1.00 0.00 H +ATOM 450 CE LYS 28 28.917 43.732 19.359 1.00 0.00 C +ATOM 451 HE2 LYS 28 29.049 44.784 19.086 1.00 0.00 H +ATOM 452 HE3 LYS 28 29.802 43.181 19.025 1.00 0.00 H +ATOM 453 NZ LYS 28 27.696 43.214 18.694 1.00 0.00 N +ATOM 454 HZ1 LYS 28 26.858 43.680 19.063 1.00 0.00 H +ATOM 455 HZ2 LYS 28 27.718 43.355 17.696 1.00 0.00 H +ATOM 456 HZ3 LYS 28 27.563 42.223 18.882 1.00 0.00 H +ATOM 457 C LYS 28 28.694 40.774 25.048 1.00 0.00 C +ATOM 458 O LYS 28 29.531 40.971 25.922 1.00 0.00 O +ATOM 459 N PHE 29 27.433 40.461 25.351 1.00 0.00 N +ATOM 460 H PHE 29 26.770 40.367 24.587 1.00 0.00 H +ATOM 461 CA PHE 29 26.956 40.324 26.737 1.00 0.00 C +ATOM 462 HA PHE 29 27.288 41.196 27.301 1.00 0.00 H +ATOM 463 CB PHE 29 25.418 40.308 26.753 1.00 0.00 C +ATOM 464 HB2 PHE 29 25.082 39.379 26.290 1.00 0.00 H +ATOM 465 HB3 PHE 29 25.083 40.298 27.791 1.00 0.00 H +ATOM 466 CG PHE 29 24.734 41.474 26.050 1.00 0.00 C +ATOM 467 CD1 PHE 29 23.512 41.261 25.382 1.00 0.00 C +ATOM 468 HD1 PHE 29 23.048 40.287 25.399 1.00 0.00 H +ATOM 469 CE1 PHE 29 22.881 42.313 24.694 1.00 0.00 C +ATOM 470 HE1 PHE 29 21.946 42.138 24.183 1.00 0.00 H +ATOM 471 CZ PHE 29 23.462 43.592 24.675 1.00 0.00 C +ATOM 472 HZ PHE 29 22.980 44.397 24.138 1.00 0.00 H +ATOM 473 CE2 PHE 29 24.664 43.823 25.367 1.00 0.00 C +ATOM 474 HE2 PHE 29 25.105 44.809 25.369 1.00 0.00 H +ATOM 475 CD2 PHE 29 25.293 42.771 26.056 1.00 0.00 C +ATOM 476 HD2 PHE 29 26.211 42.971 26.586 1.00 0.00 H +ATOM 477 C PHE 29 27.555 39.107 27.465 1.00 0.00 C +ATOM 478 O PHE 29 27.773 39.150 28.677 1.00 0.00 O +ATOM 479 N THR 30 27.896 38.038 26.741 1.00 0.00 N +ATOM 480 H THR 30 27.619 38.016 25.764 1.00 0.00 H +ATOM 481 CA THR 30 28.673 36.905 27.271 1.00 0.00 C +ATOM 482 HA THR 30 28.197 36.550 28.185 1.00 0.00 H +ATOM 483 CB THR 30 28.682 35.736 26.276 1.00 0.00 C +ATOM 484 HB THR 30 29.041 36.062 25.302 1.00 0.00 H +ATOM 485 CG2 THR 30 29.498 34.534 26.746 1.00 0.00 C +ATOM 486 HG21 THR 30 29.142 34.220 27.721 1.00 0.00 H +ATOM 487 HG22 THR 30 29.367 33.720 26.036 1.00 0.00 H +ATOM 488 HG23 THR 30 30.560 34.772 26.807 1.00 0.00 H +ATOM 489 OG1 THR 30 27.360 35.286 26.150 1.00 0.00 O +ATOM 490 HG1 THR 30 26.921 35.901 25.540 1.00 0.00 H +ATOM 491 C THR 30 30.096 37.329 27.627 1.00 0.00 C +ATOM 492 O THR 30 30.588 36.990 28.705 1.00 0.00 O +ATOM 493 N LYS 31 30.738 38.118 26.757 1.00 0.00 N +ATOM 494 H LYS 31 30.278 38.309 25.872 1.00 0.00 H +ATOM 495 CA LYS 31 32.079 38.688 26.976 1.00 0.00 C +ATOM 496 HA LYS 31 32.743 37.884 27.300 1.00 0.00 H +ATOM 497 CB LYS 31 32.621 39.274 25.671 1.00 0.00 C +ATOM 498 HB2 LYS 31 31.903 39.978 25.246 1.00 0.00 H +ATOM 499 HB3 LYS 31 33.541 39.820 25.894 1.00 0.00 H +ATOM 500 CG LYS 31 32.944 38.173 24.651 1.00 0.00 C +ATOM 501 HG2 LYS 31 33.671 37.499 25.091 1.00 0.00 H +ATOM 502 HG3 LYS 31 32.056 37.589 24.426 1.00 0.00 H +ATOM 503 CD LYS 31 33.506 38.765 23.356 1.00 0.00 C +ATOM 504 HD2 LYS 31 32.713 39.327 22.866 1.00 0.00 H +ATOM 505 HD3 LYS 31 34.316 39.458 23.597 1.00 0.00 H +ATOM 506 CE LYS 31 34.009 37.678 22.410 1.00 0.00 C +ATOM 507 HE2 LYS 31 33.210 36.951 22.212 1.00 0.00 H +ATOM 508 HE3 LYS 31 34.294 38.148 21.459 1.00 0.00 H +ATOM 509 NZ LYS 31 35.192 36.994 22.980 1.00 0.00 N +ATOM 510 HZ1 LYS 31 34.970 36.242 23.631 1.00 0.00 H +ATOM 511 HZ2 LYS 31 35.696 36.535 22.223 1.00 0.00 H +ATOM 512 HZ3 LYS 31 35.853 37.636 23.423 1.00 0.00 H +ATOM 513 C LYS 31 32.124 39.737 28.088 1.00 0.00 C +ATOM 514 O LYS 31 33.110 39.767 28.820 1.00 0.00 O +ATOM 515 N ALA 32 31.066 40.529 28.271 1.00 0.00 N +ATOM 516 H ALA 32 30.350 40.537 27.557 1.00 0.00 H +ATOM 517 CA ALA 32 30.916 41.417 29.424 1.00 0.00 C +ATOM 518 HA ALA 32 31.761 42.109 29.453 1.00 0.00 H +ATOM 519 CB ALA 32 29.630 42.243 29.272 1.00 0.00 C +ATOM 520 HB1 ALA 32 28.757 41.591 29.251 1.00 0.00 H +ATOM 521 HB2 ALA 32 29.539 42.927 30.118 1.00 0.00 H +ATOM 522 HB3 ALA 32 29.672 42.826 28.351 1.00 0.00 H +ATOM 523 C ALA 32 30.942 40.605 30.729 1.00 0.00 C +ATOM 524 O ALA 32 31.851 40.784 31.532 1.00 0.00 O +ATOM 525 N GLH 33 30.050 39.611 30.870 1.00 0.00 N +ATOM 526 H GLH 33 29.333 39.496 30.165 1.00 0.00 H +ATOM 527 CA GLH 33 30.047 38.725 32.041 1.00 0.00 C +ATOM 528 HA GLH 33 29.911 39.335 32.935 1.00 0.00 H +ATOM 529 CB GLH 33 28.891 37.715 31.963 1.00 0.00 C +ATOM 530 HB2 GLH 33 28.942 37.165 31.022 1.00 0.00 H +ATOM 531 HB3 GLH 33 29.025 37.002 32.778 1.00 0.00 H +ATOM 532 CG GLH 33 27.500 38.357 32.108 1.00 0.00 C +ATOM 533 HG2 GLH 33 27.504 39.042 32.957 1.00 0.00 H +ATOM 534 HG3 GLH 33 27.261 38.931 31.214 1.00 0.00 H +ATOM 535 CD GLH 33 26.406 37.318 32.358 1.00 0.00 C +ATOM 536 OE1 GLH 33 26.558 36.242 32.918 1.00 0.00 O +ATOM 537 OE2 GLH 33 25.174 37.633 31.910 1.00 0.00 O +ATOM 538 HE2 GLH 33 24.616 36.913 32.215 1.00 0.00 H +ATOM 539 C GLH 33 31.373 37.970 32.231 1.00 0.00 C +ATOM 540 O GLH 33 31.760 37.707 33.362 1.00 0.00 O +ATOM 541 N ALA 34 32.084 37.609 31.158 1.00 0.00 N +ATOM 542 H ALA 34 31.708 37.793 30.237 1.00 0.00 H +ATOM 543 CA ALA 34 33.402 36.984 31.269 1.00 0.00 C +ATOM 544 HA ALA 34 33.329 36.147 31.965 1.00 0.00 H +ATOM 545 CB ALA 34 33.799 36.424 29.900 1.00 0.00 C +ATOM 546 HB1 ALA 34 34.021 37.239 29.214 1.00 0.00 H +ATOM 547 HB2 ALA 34 34.684 35.801 30.018 1.00 0.00 H +ATOM 548 HB3 ALA 34 32.997 35.812 29.491 1.00 0.00 H +ATOM 549 C ALA 34 34.464 37.950 31.840 1.00 0.00 C +ATOM 550 O ALA 34 35.200 37.571 32.750 1.00 0.00 O +ATOM 551 N ASN 35 34.500 39.207 31.376 1.00 0.00 N +ATOM 552 H ASN 35 33.842 39.482 30.658 1.00 0.00 H +ATOM 553 CA ASN 35 35.384 40.242 31.928 1.00 0.00 C +ATOM 554 HA ASN 35 36.374 39.806 32.012 1.00 0.00 H +ATOM 555 CB ASN 35 35.506 41.432 30.957 1.00 0.00 C +ATOM 556 HB2 ASN 35 34.515 41.759 30.649 1.00 0.00 H +ATOM 557 HB3 ASN 35 35.980 42.260 31.484 1.00 0.00 H +ATOM 558 CG ASN 35 36.370 41.137 29.738 1.00 0.00 C +ATOM 559 OD1 ASN 35 37.587 41.194 29.762 1.00 0.00 O +ATOM 560 ND2 ASN 35 35.776 40.836 28.613 1.00 0.00 N +ATOM 561 HD21 ASN 35 36.375 40.628 27.819 1.00 0.00 H +ATOM 562 HD22 ASN 35 34.782 40.669 28.608 1.00 0.00 H +ATOM 563 C ASN 35 34.989 40.686 33.358 1.00 0.00 C +ATOM 564 O ASN 35 35.858 41.125 34.108 1.00 0.00 O +ATOM 565 N ASP 36 33.730 40.502 33.781 1.00 0.00 N +ATOM 566 H ASP 36 33.014 40.300 33.091 1.00 0.00 H +ATOM 567 CA ASP 36 33.323 40.680 35.189 1.00 0.00 C +ATOM 568 HA ASP 36 33.626 41.677 35.506 1.00 0.00 H +ATOM 569 CB ASP 36 31.790 40.605 35.367 1.00 0.00 C +ATOM 570 HB2 ASP 36 31.453 39.608 35.113 1.00 0.00 H +ATOM 571 HB3 ASP 36 31.583 40.721 36.432 1.00 0.00 H +ATOM 572 CG ASP 36 30.936 41.606 34.560 1.00 0.00 C +ATOM 573 OD1 ASP 36 31.454 42.673 34.150 1.00 0.00 O +ATOM 574 OD2 ASP 36 29.729 41.321 34.369 1.00 0.00 O +ATOM 575 C ASP 36 34.022 39.677 36.139 1.00 0.00 C +ATOM 576 O ASP 36 34.366 40.036 37.265 1.00 0.00 O +ATOM 577 N TYR 37 34.279 38.436 35.693 1.00 0.00 N +ATOM 578 H TYR 37 33.929 38.187 34.778 1.00 0.00 H +ATOM 579 CA TYR 37 35.150 37.478 36.405 1.00 0.00 C +ATOM 580 HA TYR 37 35.031 37.637 37.477 1.00 0.00 H +ATOM 581 CB TYR 37 34.728 36.029 36.102 1.00 0.00 C +ATOM 582 HB2 TYR 37 34.894 35.833 35.042 1.00 0.00 H +ATOM 583 HB3 TYR 37 35.387 35.360 36.657 1.00 0.00 H +ATOM 584 CG TYR 37 33.295 35.659 36.456 1.00 0.00 C +ATOM 585 CD1 TYR 37 32.330 35.550 35.437 1.00 0.00 C +ATOM 586 HD1 TYR 37 32.623 35.735 34.416 1.00 0.00 H +ATOM 587 CE1 TYR 37 30.995 35.227 35.746 1.00 0.00 C +ATOM 588 HE1 TYR 37 30.257 35.181 34.963 1.00 0.00 H +ATOM 589 CZ TYR 37 30.630 34.968 37.084 1.00 0.00 C +ATOM 590 OH TYR 37 29.350 34.633 37.395 1.00 0.00 O +ATOM 591 HH TYR 37 28.718 35.000 36.775 1.00 0.00 H +ATOM 592 CE2 TYR 37 31.601 35.043 38.103 1.00 0.00 C +ATOM 593 HE2 TYR 37 31.310 34.844 39.122 1.00 0.00 H +ATOM 594 CD2 TYR 37 32.930 35.393 37.791 1.00 0.00 C +ATOM 595 HD2 TYR 37 33.670 35.453 38.575 1.00 0.00 H +ATOM 596 C TYR 37 36.653 37.661 36.084 1.00 0.00 C +ATOM 597 O TYR 37 37.509 37.230 36.866 1.00 0.00 O +ATOM 598 N GLY 38 36.981 38.278 34.941 1.00 0.00 N +ATOM 599 H GLY 38 36.217 38.563 34.340 1.00 0.00 H +ATOM 600 CA GLY 38 38.332 38.695 34.549 1.00 0.00 C +ATOM 601 HA2 GLY 38 38.510 39.692 34.952 1.00 0.00 H +ATOM 602 HA3 GLY 38 39.067 38.019 34.987 1.00 0.00 H +ATOM 603 C GLY 38 38.572 38.753 33.033 1.00 0.00 C +ATOM 604 O GLY 38 38.680 39.832 32.466 1.00 0.00 O +ATOM 605 N VAL 39 38.769 37.587 32.407 1.00 0.00 N +ATOM 606 H VAL 39 38.528 36.772 32.947 1.00 0.00 H +ATOM 607 CA VAL 39 39.120 37.334 30.982 1.00 0.00 C +ATOM 608 HA VAL 39 39.589 36.353 31.045 1.00 0.00 H +ATOM 609 CB VAL 39 40.278 38.199 30.408 1.00 0.00 C +ATOM 610 HB VAL 39 39.887 39.155 30.060 1.00 0.00 H +ATOM 611 CG1 VAL 39 41.410 38.442 31.429 1.00 0.00 C +ATOM 612 HG11 VAL 39 41.633 37.519 31.969 1.00 0.00 H +ATOM 613 HG12 VAL 39 42.308 38.801 30.921 1.00 0.00 H +ATOM 614 HG13 VAL 39 41.103 39.214 32.136 1.00 0.00 H +ATOM 615 CG2 VAL 39 40.949 37.487 29.219 1.00 0.00 C +ATOM 616 HG21 VAL 39 41.725 38.123 28.799 1.00 0.00 H +ATOM 617 HG22 VAL 39 41.401 36.553 29.543 1.00 0.00 H +ATOM 618 HG23 VAL 39 40.242 37.276 28.424 1.00 0.00 H +ATOM 619 C VAL 39 37.923 37.009 30.055 1.00 0.00 C +ATOM 620 O VAL 39 37.209 36.068 30.396 1.00 0.00 O +ATOM 621 N ASP 40 37.721 37.611 28.865 1.00 0.00 N +ATOM 622 H ASP 40 38.260 38.435 28.629 1.00 0.00 H +ATOM 623 CA ASP 40 36.920 36.948 27.802 1.00 0.00 C +ATOM 624 HA ASP 40 36.182 36.330 28.311 1.00 0.00 H +ATOM 625 CB ASP 40 36.053 37.904 26.947 1.00 0.00 C +ATOM 626 HB2 ASP 40 35.316 37.280 26.435 1.00 0.00 H +ATOM 627 HB3 ASP 40 35.494 38.546 27.614 1.00 0.00 H +ATOM 628 CG ASP 40 36.769 38.774 25.899 1.00 0.00 C +ATOM 629 OD1 ASP 40 37.171 39.908 26.230 1.00 0.00 O +ATOM 630 OD2 ASP 40 36.863 38.346 24.717 1.00 0.00 O +ATOM 631 C ASP 40 37.719 35.999 26.893 1.00 0.00 C +ATOM 632 O ASP 40 38.616 36.413 26.153 1.00 0.00 O +ATOM 633 N GLY 41 37.291 34.734 26.866 1.00 0.00 N +ATOM 634 H GLY 41 36.626 34.447 27.571 1.00 0.00 H +ATOM 635 CA GLY 41 37.610 33.768 25.816 1.00 0.00 C +ATOM 636 HA2 GLY 41 38.623 33.946 25.456 1.00 0.00 H +ATOM 637 HA3 GLY 41 37.580 32.771 26.242 1.00 0.00 H +ATOM 638 C GLY 41 36.655 33.826 24.612 1.00 0.00 C +ATOM 639 O GLY 41 35.774 34.683 24.510 1.00 0.00 O +ATOM 640 N GLU 42 36.792 32.855 23.705 1.00 0.00 N +ATOM 641 H GLU 42 37.487 32.129 23.865 1.00 0.00 H +ATOM 642 CA GLU 42 36.009 32.689 22.461 1.00 0.00 C +ATOM 643 HA GLU 42 35.334 33.540 22.334 1.00 0.00 H +ATOM 644 CB GLU 42 36.923 32.654 21.234 1.00 0.00 C +ATOM 645 HB2 GLU 42 37.390 31.662 21.199 1.00 0.00 H +ATOM 646 HB3 GLU 42 36.257 32.698 20.374 1.00 0.00 H +ATOM 647 CG GLU 42 37.926 33.780 21.144 1.00 0.00 C +ATOM 648 HG2 GLU 42 38.767 33.538 21.797 1.00 0.00 H +ATOM 649 HG3 GLU 42 38.362 33.796 20.165 1.00 0.00 H +ATOM 650 CD GLU 42 37.448 35.144 21.511 1.00 0.00 C +ATOM 651 OE1 GLU 42 36.392 35.531 21.013 1.00 0.00 O +ATOM 652 OE2 GLU 42 38.019 35.817 22.405 1.00 0.00 O +ATOM 653 C GLU 42 35.098 31.428 22.559 1.00 0.00 C +ATOM 654 O GLU 42 35.470 30.440 23.214 1.00 0.00 O +ATOM 655 N ILE 43 33.966 31.444 21.825 1.00 0.00 N +ATOM 656 H ILE 43 33.809 32.250 21.208 1.00 0.00 H +ATOM 657 CA ILE 43 32.887 30.421 21.861 1.00 0.00 C +ATOM 658 HA ILE 43 33.331 29.490 22.218 1.00 0.00 H +ATOM 659 CB ILE 43 31.749 30.833 22.843 1.00 0.00 C +ATOM 660 HB ILE 43 30.876 30.251 22.570 1.00 0.00 H +ATOM 661 CG2 ILE 43 32.120 30.445 24.279 1.00 0.00 C +ATOM 662 HG21 ILE 43 32.995 30.995 24.605 1.00 0.00 H +ATOM 663 HG22 ILE 43 31.282 30.667 24.932 1.00 0.00 H +ATOM 664 HG23 ILE 43 32.325 29.379 24.324 1.00 0.00 H +ATOM 665 CG1 ILE 43 31.340 32.325 22.832 1.00 0.00 C +ATOM 666 HG12 ILE 43 30.451 32.421 23.459 1.00 0.00 H +ATOM 667 HG13 ILE 43 32.122 32.931 23.275 1.00 0.00 H +ATOM 668 CD1 ILE 43 30.995 32.906 21.457 1.00 0.00 C +ATOM 669 HD11 ILE 43 30.366 32.224 20.891 1.00 0.00 H +ATOM 670 HD12 ILE 43 30.466 33.847 21.588 1.00 0.00 H +ATOM 671 HD13 ILE 43 31.907 33.103 20.890 1.00 0.00 H +ATOM 672 C ILE 43 32.351 30.121 20.452 1.00 0.00 C +ATOM 673 O ILE 43 32.559 30.895 19.514 1.00 0.00 O +ATOM 674 N THR 44 31.619 29.018 20.340 1.00 0.00 N +ATOM 675 H THR 44 31.486 28.447 21.169 1.00 0.00 H +ATOM 676 CA THR 44 30.903 28.600 19.128 1.00 0.00 C +ATOM 677 HA THR 44 31.230 29.213 18.290 1.00 0.00 H +ATOM 678 CB THR 44 31.269 27.144 18.781 1.00 0.00 C +ATOM 679 HB THR 44 31.001 26.477 19.600 1.00 0.00 H +ATOM 680 CG2 THR 44 30.624 26.613 17.495 1.00 0.00 C +ATOM 681 HG21 THR 44 30.802 27.305 16.665 1.00 0.00 H +ATOM 682 HG22 THR 44 31.041 25.628 17.235 1.00 0.00 H +ATOM 683 HG23 THR 44 29.544 26.485 17.639 1.00 0.00 H +ATOM 684 OG1 THR 44 32.661 27.056 18.558 1.00 0.00 O +ATOM 685 HG1 THR 44 32.846 26.251 18.066 1.00 0.00 H +ATOM 686 C THR 44 29.392 28.779 19.281 1.00 0.00 C +ATOM 687 O THR 44 28.876 28.725 20.395 1.00 0.00 O +ATOM 688 N GLN 45 28.679 29.026 18.178 1.00 0.00 N +ATOM 689 H GLN 45 29.149 29.020 17.288 1.00 0.00 H +ATOM 690 CA GLN 45 27.222 29.231 18.139 1.00 0.00 C +ATOM 691 HA GLN 45 26.819 29.205 19.153 1.00 0.00 H +ATOM 692 CB GLN 45 26.897 30.607 17.518 1.00 0.00 C +ATOM 693 HB2 GLN 45 27.284 30.625 16.500 1.00 0.00 H +ATOM 694 HB3 GLN 45 25.809 30.696 17.459 1.00 0.00 H +ATOM 695 CG GLN 45 27.454 31.826 18.281 1.00 0.00 C +ATOM 696 HG2 GLN 45 27.104 31.768 19.310 1.00 0.00 H +ATOM 697 HG3 GLN 45 28.542 31.780 18.287 1.00 0.00 H +ATOM 698 CD GLN 45 27.016 33.162 17.659 1.00 0.00 C +ATOM 699 OE1 GLN 45 26.064 33.244 16.898 1.00 0.00 O +ATOM 700 NE2 GLN 45 27.679 34.270 17.903 1.00 0.00 N +ATOM 701 HE21 GLN 45 27.355 35.101 17.453 1.00 0.00 H +ATOM 702 HE22 GLN 45 28.552 34.317 18.441 1.00 0.00 H +ATOM 703 C GLN 45 26.480 28.159 17.312 1.00 0.00 C +ATOM 704 O GLN 45 27.046 27.601 16.370 1.00 0.00 O +ATOM 705 N ASP 46 25.191 27.966 17.604 1.00 0.00 N +ATOM 706 H ASP 46 24.838 28.365 18.468 1.00 0.00 H +ATOM 707 CA ASP 46 24.203 27.294 16.751 1.00 0.00 C +ATOM 708 HA ASP 46 24.528 27.356 15.711 1.00 0.00 H +ATOM 709 CB ASP 46 24.079 25.812 17.147 1.00 0.00 C +ATOM 710 HB2 ASP 46 24.979 25.272 16.851 1.00 0.00 H +ATOM 711 HB3 ASP 46 23.981 25.747 18.230 1.00 0.00 H +ATOM 712 CG ASP 46 22.852 25.158 16.507 1.00 0.00 C +ATOM 713 OD1 ASP 46 22.104 24.474 17.241 1.00 0.00 O +ATOM 714 OD2 ASP 46 22.584 25.407 15.313 1.00 0.00 O +ATOM 715 C ASP 46 22.831 27.991 16.868 1.00 0.00 C +ATOM 716 O ASP 46 22.288 28.138 17.964 1.00 0.00 O +ATOM 717 N ASP 47 22.230 28.373 15.739 1.00 0.00 N +ATOM 718 H ASP 47 22.690 28.167 14.865 1.00 0.00 H +ATOM 719 CA ASP 47 20.867 28.919 15.690 1.00 0.00 C +ATOM 720 HA ASP 47 20.729 29.593 16.537 1.00 0.00 H +ATOM 721 CB ASP 47 20.693 29.766 14.416 1.00 0.00 C +ATOM 722 HB2 ASP 47 21.415 30.585 14.422 1.00 0.00 H +ATOM 723 HB3 ASP 47 20.882 29.148 13.536 1.00 0.00 H +ATOM 724 CG ASP 47 19.278 30.347 14.340 1.00 0.00 C +ATOM 725 OD1 ASP 47 18.430 29.775 13.625 1.00 0.00 O +ATOM 726 OD2 ASP 47 18.941 31.266 15.120 1.00 0.00 O +ATOM 727 C ASP 47 19.773 27.830 15.792 1.00 0.00 C +ATOM 728 O ASP 47 18.707 28.086 16.356 1.00 0.00 O +ATOM 729 N ALA 48 20.006 26.600 15.319 1.00 0.00 N +ATOM 730 H ALA 48 20.951 26.350 15.024 1.00 0.00 H +ATOM 731 CA ALA 48 18.970 25.560 15.236 1.00 0.00 C +ATOM 732 HA ALA 48 18.105 25.984 14.723 1.00 0.00 H +ATOM 733 CB ALA 48 19.510 24.405 14.386 1.00 0.00 C +ATOM 734 HB1 ALA 48 20.362 23.940 14.885 1.00 0.00 H +ATOM 735 HB2 ALA 48 18.729 23.659 14.239 1.00 0.00 H +ATOM 736 HB3 ALA 48 19.832 24.783 13.415 1.00 0.00 H +ATOM 737 C ALA 48 18.489 25.071 16.618 1.00 0.00 C +ATOM 738 O ALA 48 17.304 24.774 16.796 1.00 0.00 O +ATOM 739 N THR 49 19.392 25.037 17.602 1.00 0.00 N +ATOM 740 H THR 49 20.372 25.112 17.325 1.00 0.00 H +ATOM 741 CA THR 49 19.113 24.869 19.043 1.00 0.00 C +ATOM 742 HA THR 49 18.084 24.531 19.159 1.00 0.00 H +ATOM 743 CB THR 49 20.020 23.800 19.672 1.00 0.00 C +ATOM 744 HB THR 49 19.698 23.651 20.702 1.00 0.00 H +ATOM 745 CG2 THR 49 19.958 22.443 18.975 1.00 0.00 C +ATOM 746 HG21 THR 49 20.321 22.522 17.950 1.00 0.00 H +ATOM 747 HG22 THR 49 20.590 21.745 19.521 1.00 0.00 H +ATOM 748 HG23 THR 49 18.931 22.081 18.973 1.00 0.00 H +ATOM 749 OG1 THR 49 21.361 24.217 19.698 1.00 0.00 O +ATOM 750 HG1 THR 49 21.679 24.247 18.761 1.00 0.00 H +ATOM 751 C THR 49 19.231 26.177 19.841 1.00 0.00 C +ATOM 752 O THR 49 19.101 26.167 21.068 1.00 0.00 O +ATOM 753 N LYS 50 19.468 27.312 19.167 1.00 0.00 N +ATOM 754 H LYS 50 19.560 27.226 18.161 1.00 0.00 H +ATOM 755 CA LYS 50 19.589 28.671 19.731 1.00 0.00 C +ATOM 756 HA LYS 50 20.008 29.273 18.928 1.00 0.00 H +ATOM 757 CB LYS 50 18.185 29.226 20.094 1.00 0.00 C +ATOM 758 HB2 LYS 50 17.768 28.587 20.874 1.00 0.00 H +ATOM 759 HB3 LYS 50 18.294 30.221 20.527 1.00 0.00 H +ATOM 760 CG LYS 50 17.144 29.315 18.956 1.00 0.00 C +ATOM 761 HG2 LYS 50 17.135 28.389 18.385 1.00 0.00 H +ATOM 762 HG3 LYS 50 16.161 29.418 19.417 1.00 0.00 H +ATOM 763 CD LYS 50 17.338 30.517 18.014 1.00 0.00 C +ATOM 764 HD2 LYS 50 17.289 31.432 18.604 1.00 0.00 H +ATOM 765 HD3 LYS 50 18.319 30.466 17.544 1.00 0.00 H +ATOM 766 CE LYS 50 16.255 30.586 16.925 1.00 0.00 C +ATOM 767 HE2 LYS 50 15.311 30.225 17.334 1.00 0.00 H +ATOM 768 HE3 LYS 50 16.117 31.628 16.628 1.00 0.00 H +ATOM 769 NZ LYS 50 16.628 29.801 15.728 1.00 0.00 N +ATOM 770 HZ1 LYS 50 17.134 28.955 15.975 1.00 0.00 H +ATOM 771 HZ2 LYS 50 15.839 29.559 15.145 1.00 0.00 H +ATOM 772 HZ3 LYS 50 17.313 30.309 15.154 1.00 0.00 H +ATOM 773 C LYS 50 20.608 28.778 20.892 1.00 0.00 C +ATOM 774 O LYS 50 20.304 29.382 21.927 1.00 0.00 O +ATOM 775 N THR 51 21.791 28.170 20.745 1.00 0.00 N +ATOM 776 H THR 51 22.017 27.827 19.813 1.00 0.00 H +ATOM 777 CA THR 51 22.737 27.843 21.835 1.00 0.00 C +ATOM 778 HA THR 51 22.433 28.389 22.721 1.00 0.00 H +ATOM 779 CB THR 51 22.629 26.341 22.176 1.00 0.00 C +ATOM 780 HB THR 51 22.792 25.755 21.272 1.00 0.00 H +ATOM 781 CG2 THR 51 23.614 25.869 23.247 1.00 0.00 C +ATOM 782 HG21 THR 51 23.549 26.508 24.126 1.00 0.00 H +ATOM 783 HG22 THR 51 23.377 24.843 23.525 1.00 0.00 H +ATOM 784 HG23 THR 51 24.627 25.883 22.852 1.00 0.00 H +ATOM 785 OG1 THR 51 21.358 26.039 22.712 1.00 0.00 O +ATOM 786 HG1 THR 51 20.709 26.084 21.991 1.00 0.00 H +ATOM 787 C THR 51 24.207 28.217 21.545 1.00 0.00 C +ATOM 788 O THR 51 24.716 27.973 20.456 1.00 0.00 O +ATOM 789 N PHE 52 24.918 28.749 22.550 1.00 0.00 N +ATOM 790 H PHE 52 24.402 29.020 23.376 1.00 0.00 H +ATOM 791 CA PHE 52 26.389 28.875 22.610 1.00 0.00 C +ATOM 792 HA PHE 52 26.783 28.971 21.598 1.00 0.00 H +ATOM 793 CB PHE 52 26.774 30.130 23.412 1.00 0.00 C +ATOM 794 HB2 PHE 52 26.267 30.101 24.374 1.00 0.00 H +ATOM 795 HB3 PHE 52 27.845 30.085 23.622 1.00 0.00 H +ATOM 796 CG PHE 52 26.494 31.471 22.766 1.00 0.00 C +ATOM 797 CD1 PHE 52 25.266 32.130 22.966 1.00 0.00 C +ATOM 798 HD1 PHE 52 24.487 31.661 23.545 1.00 0.00 H +ATOM 799 CE1 PHE 52 25.047 33.404 22.412 1.00 0.00 C +ATOM 800 HE1 PHE 52 24.099 33.900 22.556 1.00 0.00 H +ATOM 801 CZ PHE 52 26.060 34.026 21.662 1.00 0.00 C +ATOM 802 HZ PHE 52 25.893 34.995 21.218 1.00 0.00 H +ATOM 803 CE2 PHE 52 27.293 33.379 21.473 1.00 0.00 C +ATOM 804 HE2 PHE 52 28.070 33.856 20.889 1.00 0.00 H +ATOM 805 CD2 PHE 52 27.503 32.100 22.017 1.00 0.00 C +ATOM 806 HD2 PHE 52 28.441 31.592 21.854 1.00 0.00 H +ATOM 807 C PHE 52 27.066 27.661 23.288 1.00 0.00 C +ATOM 808 O PHE 52 26.544 27.156 24.288 1.00 0.00 O +ATOM 809 N THR 53 28.266 27.263 22.839 1.00 0.00 N +ATOM 810 H THR 53 28.641 27.723 22.012 1.00 0.00 H +ATOM 811 CA THR 53 29.074 26.151 23.403 1.00 0.00 C +ATOM 812 HA THR 53 28.798 26.016 24.449 1.00 0.00 H +ATOM 813 CB THR 53 28.800 24.819 22.672 1.00 0.00 C +ATOM 814 HB THR 53 29.387 24.035 23.153 1.00 0.00 H +ATOM 815 CG2 THR 53 27.341 24.373 22.695 1.00 0.00 C +ATOM 816 HG21 THR 53 26.734 25.036 22.079 1.00 0.00 H +ATOM 817 HG22 THR 53 27.264 23.356 22.311 1.00 0.00 H +ATOM 818 HG23 THR 53 26.972 24.389 23.719 1.00 0.00 H +ATOM 819 OG1 THR 53 29.192 24.898 21.323 1.00 0.00 O +ATOM 820 HG1 THR 53 28.756 24.184 20.851 1.00 0.00 H +ATOM 821 C THR 53 30.594 26.406 23.377 1.00 0.00 C +ATOM 822 O THR 53 31.083 27.326 22.718 1.00 0.00 O +ATOM 823 N ALA 54 31.348 25.564 24.100 1.00 0.00 N +ATOM 824 H ALA 54 30.876 24.846 24.626 1.00 0.00 H +ATOM 825 CA ALA 54 32.812 25.456 24.054 1.00 0.00 C +ATOM 826 HA ALA 54 33.210 26.268 23.442 1.00 0.00 H +ATOM 827 CB ALA 54 33.366 25.629 25.475 1.00 0.00 C +ATOM 828 HB1 ALA 54 33.015 24.817 26.113 1.00 0.00 H +ATOM 829 HB2 ALA 54 34.457 25.616 25.456 1.00 0.00 H +ATOM 830 HB3 ALA 54 33.038 26.583 25.891 1.00 0.00 H +ATOM 831 C ALA 54 33.278 24.123 23.415 1.00 0.00 C +ATOM 832 O ALA 54 32.505 23.167 23.298 1.00 0.00 O +ATOM 833 N GLH 55 34.548 24.067 22.999 1.00 0.00 N +ATOM 834 H GLH 55 35.146 24.849 23.215 1.00 0.00 H +ATOM 835 CA GLH 55 35.168 22.922 22.308 1.00 0.00 C +ATOM 836 HA GLH 55 34.398 22.426 21.716 1.00 0.00 H +ATOM 837 CB GLH 55 36.234 23.451 21.327 1.00 0.00 C +ATOM 838 HB2 GLH 55 36.972 24.031 21.884 1.00 0.00 H +ATOM 839 HB3 GLH 55 36.743 22.608 20.858 1.00 0.00 H +ATOM 840 CG GLH 55 35.617 24.327 20.216 1.00 0.00 C +ATOM 841 HG2 GLH 55 34.958 23.714 19.601 1.00 0.00 H +ATOM 842 HG3 GLH 55 35.020 25.129 20.650 1.00 0.00 H +ATOM 843 CD GLH 55 36.655 24.987 19.312 1.00 0.00 C +ATOM 844 OE1 GLH 55 37.842 25.121 19.573 1.00 0.00 O +ATOM 845 OE2 GLH 55 36.155 25.451 18.149 1.00 0.00 O +ATOM 846 HE2 GLH 55 36.883 25.858 17.675 1.00 0.00 H +ATOM 847 C GLH 55 35.736 21.856 23.279 1.00 0.00 C +ATOM 848 O GLH 55 36.043 22.164 24.428 1.00 0.00 O +ATOM 849 N GLU 56 35.854 20.603 22.810 1.00 0.00 N +ATOM 850 H GLU 56 35.627 20.451 21.842 1.00 0.00 H +ATOM 851 CA GLU 56 36.225 19.391 23.580 1.00 0.00 C +ATOM 852 HA GLU 56 35.760 19.455 24.564 1.00 0.00 H +ATOM 853 CB GLU 56 35.617 18.165 22.855 1.00 0.00 C +ATOM 854 HB2 GLU 56 34.541 18.196 23.027 1.00 0.00 H +ATOM 855 HB3 GLU 56 35.768 18.297 21.782 1.00 0.00 H +ATOM 856 CG GLU 56 36.111 16.739 23.193 1.00 0.00 C +ATOM 857 HG2 GLU 56 35.454 16.031 22.680 1.00 0.00 H +ATOM 858 HG3 GLU 56 37.100 16.595 22.754 1.00 0.00 H +ATOM 859 CD GLU 56 36.165 16.375 24.688 1.00 0.00 C +ATOM 860 OE1 GLU 56 37.290 16.354 25.251 1.00 0.00 O +ATOM 861 OE2 GLU 56 35.109 16.022 25.266 1.00 0.00 O +ATOM 862 C GLU 56 37.723 19.244 23.888 1.00 0.00 C +ATOM 863 O GLU 56 38.090 19.361 25.078 1.00 0.00 O +ATOM 864 OXT GLU 56 38.506 18.730 23.060 1.00 0.00 O +HETATM 865 ZN ZN1 57 26.762 32.444 29.336 1.00 0.00 Zn +HETATM 866 N AN1 58 28.364 33.308 30.222 1.00 0.00 N +HETATM 867 C AN1 58 30.678 34.028 31.184 1.00 0.00 C +HETATM 868 C1 AN1 58 29.379 33.629 30.674 1.00 0.00 C +HETATM 869 H AN1 58 30.582 34.423 32.200 1.00 0.00 H +HETATM 870 H1 AN1 58 31.113 34.795 30.535 1.00 0.00 H +HETATM 871 H2 AN1 58 31.336 33.149 31.202 1.00 0.00 H +HETATM 872 N1 AZI 59 30.830 28.620 29.341 1.00 0.00 N +HETATM 873 N2 AZI 59 30.309 29.481 30.054 1.00 0.00 N +HETATM 874 N3 AZI 59 29.759 30.371 30.755 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 73 72 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 865 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 121 122 126 +CONECT 121 120 +CONECT 122 125 120 123 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 127 129 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 145 +CONECT 135 134 +CONECT 136 137 134 139 138 +CONECT 137 136 +CONECT 138 136 +CONECT 139 142 136 140 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 144 139 +CONECT 143 142 +CONECT 144 142 +CONECT 145 134 147 146 +CONECT 146 145 +CONECT 147 148 149 145 +CONECT 148 147 +CONECT 149 147 150 152 151 +CONECT 150 149 +CONECT 151 149 +CONECT 152 153 149 154 +CONECT 153 152 +CONECT 154 152 156 155 +CONECT 155 154 +CONECT 156 158 157 154 174 +CONECT 157 156 +CONECT 158 161 159 160 156 +CONECT 159 158 +CONECT 160 158 +CONECT 161 164 163 162 158 +CONECT 162 161 +CONECT 163 161 +CONECT 164 167 165 166 161 +CONECT 165 164 +CONECT 166 164 +CONECT 167 170 169 168 164 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 170 +CONECT 174 156 175 176 +CONECT 175 174 +CONECT 176 174 177 178 +CONECT 177 176 +CONECT 178 176 179 198 180 +CONECT 179 178 +CONECT 180 178 183 181 182 +CONECT 181 180 +CONECT 182 180 +CONECT 183 185 184 180 186 +CONECT 184 183 +CONECT 185 183 +CONECT 186 183 189 187 188 +CONECT 187 186 +CONECT 188 186 +CONECT 189 190 186 191 +CONECT 190 189 +CONECT 191 189 195 192 +CONECT 192 191 193 194 +CONECT 193 192 +CONECT 194 192 +CONECT 195 196 191 197 +CONECT 196 195 +CONECT 197 195 +CONECT 198 178 200 199 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 219 200 204 203 +CONECT 203 202 +CONECT 204 207 202 205 206 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 217 204 +CONECT 208 209 210 207 +CONECT 209 208 +CONECT 210 211 208 212 +CONECT 211 210 +CONECT 212 210 213 215 +CONECT 213 214 212 +CONECT 214 213 +CONECT 215 212 216 217 +CONECT 216 215 +CONECT 217 207 215 218 +CONECT 218 217 +CONECT 219 220 221 202 +CONECT 220 219 +CONECT 221 223 219 222 +CONECT 222 221 +CONECT 223 224 241 225 221 +CONECT 224 223 +CONECT 225 228 223 226 227 +CONECT 226 225 +CONECT 227 225 +CONECT 228 230 229 231 225 +CONECT 229 228 +CONECT 230 228 +CONECT 231 232 228 233 234 +CONECT 232 231 +CONECT 233 231 +CONECT 234 236 231 237 235 +CONECT 235 234 +CONECT 236 234 +CONECT 237 240 234 239 238 +CONECT 238 237 +CONECT 239 237 +CONECT 240 237 +CONECT 241 242 223 243 +CONECT 242 241 +CONECT 243 241 245 244 +CONECT 244 243 +CONECT 245 248 243 246 247 +CONECT 246 245 +CONECT 247 245 +CONECT 248 249 250 245 +CONECT 249 248 +CONECT 250 252 248 251 +CONECT 251 250 +CONECT 252 254 253 264 250 +CONECT 253 252 +CONECT 254 260 255 256 252 +CONECT 255 254 +CONECT 256 258 254 257 259 +CONECT 257 256 +CONECT 258 256 +CONECT 259 256 +CONECT 260 262 261 263 254 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 252 265 +CONECT 265 264 +CONECT 266 276 267 264 +CONECT 267 268 266 277 270 +CONECT 268 269 283 267 +CONECT 269 268 +CONECT 270 267 271 278 279 +CONECT 271 272 273 270 +CONECT 272 275 281 271 +CONECT 273 274 271 280 +CONECT 274 275 282 273 +CONECT 275 865 272 274 +CONECT 276 266 +CONECT 277 267 +CONECT 278 270 +CONECT 279 270 +CONECT 280 273 +CONECT 281 272 +CONECT 282 274 +CONECT 283 285 268 284 +CONECT 284 283 +CONECT 285 286 287 295 283 +CONECT 286 285 +CONECT 287 288 289 285 293 +CONECT 288 287 +CONECT 289 292 291 287 290 +CONECT 290 289 +CONECT 291 289 +CONECT 292 289 +CONECT 293 287 294 +CONECT 294 293 +CONECT 295 297 285 296 +CONECT 296 295 +CONECT 297 307 298 295 +CONECT 298 299 301 297 308 +CONECT 299 300 314 298 +CONECT 300 299 +CONECT 301 309 310 298 302 +CONECT 302 301 303 304 +CONECT 303 312 302 306 +CONECT 304 302 311 305 +CONECT 305 304 306 313 +CONECT 306 303 865 305 +CONECT 307 297 +CONECT 308 298 +CONECT 309 301 +CONECT 310 301 +CONECT 311 304 +CONECT 312 303 +CONECT 313 305 +CONECT 314 316 299 315 +CONECT 315 314 +CONECT 316 327 317 314 318 +CONECT 317 316 +CONECT 318 316 321 320 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 323 324 318 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 325 321 326 +CONECT 325 324 +CONECT 326 324 +CONECT 327 329 328 316 +CONECT 328 327 +CONECT 329 331 330 327 +CONECT 330 329 +CONECT 331 337 333 332 329 +CONECT 332 331 +CONECT 333 335 334 331 336 +CONECT 334 333 +CONECT 335 333 +CONECT 336 333 +CONECT 337 339 338 331 +CONECT 338 337 +CONECT 339 341 340 337 +CONECT 340 339 +CONECT 341 353 343 342 339 +CONECT 342 341 +CONECT 343 344 349 341 345 +CONECT 344 343 +CONECT 345 343 347 348 346 +CONECT 346 345 +CONECT 347 345 +CONECT 348 345 +CONECT 349 350 351 343 352 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 341 +CONECT 354 353 +CONECT 355 357 353 356 +CONECT 356 355 +CONECT 357 359 358 365 355 +CONECT 358 357 +CONECT 359 362 360 361 357 +CONECT 360 359 +CONECT 361 359 +CONECT 362 364 363 359 +CONECT 363 362 +CONECT 364 362 +CONECT 365 357 367 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 385 370 +CONECT 370 369 +CONECT 371 372 374 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 375 371 383 +CONECT 375 376 377 374 +CONECT 376 375 +CONECT 377 378 375 379 +CONECT 378 377 +CONECT 379 377 380 381 +CONECT 380 379 +CONECT 381 379 383 382 +CONECT 382 381 +CONECT 383 374 381 384 +CONECT 384 383 +CONECT 385 387 369 386 +CONECT 386 385 +CONECT 387 388 389 385 +CONECT 388 387 +CONECT 389 391 387 390 395 +CONECT 390 389 +CONECT 391 394 392 393 389 +CONECT 392 391 +CONECT 393 391 +CONECT 394 391 +CONECT 395 389 396 397 +CONECT 396 395 +CONECT 397 395 398 399 +CONECT 398 397 +CONECT 399 397 400 401 410 +CONECT 400 399 +CONECT 401 404 402 399 403 +CONECT 402 401 +CONECT 403 401 +CONECT 404 405 406 407 401 +CONECT 405 404 +CONECT 406 404 +CONECT 407 404 409 408 +CONECT 408 407 +CONECT 409 407 +CONECT 410 399 412 411 +CONECT 411 410 +CONECT 412 413 410 414 +CONECT 413 412 +CONECT 414 412 416 420 415 +CONECT 415 414 +CONECT 416 417 419 414 418 +CONECT 417 416 +CONECT 418 416 +CONECT 419 416 +CONECT 420 422 414 421 +CONECT 421 420 +CONECT 422 423 424 420 +CONECT 423 422 +CONECT 424 426 422 425 435 +CONECT 425 424 +CONECT 426 428 427 429 424 +CONECT 427 426 +CONECT 428 426 +CONECT 429 432 430 426 431 +CONECT 430 429 +CONECT 431 429 +CONECT 432 433 434 429 +CONECT 433 432 +CONECT 434 432 +CONECT 435 424 437 436 +CONECT 436 435 +CONECT 437 438 435 439 +CONECT 438 437 +CONECT 439 437 441 440 457 +CONECT 440 439 +CONECT 441 444 442 443 439 +CONECT 442 441 +CONECT 443 441 +CONECT 444 446 447 445 441 +CONECT 445 444 +CONECT 446 444 +CONECT 447 450 448 449 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 452 451 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 455 456 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 453 +CONECT 457 439 459 458 +CONECT 458 457 +CONECT 459 460 457 461 +CONECT 460 459 +CONECT 461 459 463 462 477 +CONECT 462 461 +CONECT 463 466 464 461 465 +CONECT 464 463 +CONECT 465 463 +CONECT 466 467 475 463 +CONECT 467 469 468 466 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 472 469 473 +CONECT 472 471 +CONECT 473 471 474 475 +CONECT 474 473 +CONECT 475 473 466 476 +CONECT 476 475 +CONECT 477 461 479 478 +CONECT 478 477 +CONECT 479 480 481 477 +CONECT 480 479 +CONECT 481 483 479 491 482 +CONECT 482 481 +CONECT 483 484 489 485 481 +CONECT 484 483 +CONECT 485 487 483 488 486 +CONECT 486 485 +CONECT 487 485 +CONECT 488 485 +CONECT 489 490 483 +CONECT 490 489 +CONECT 491 493 481 492 +CONECT 492 491 +CONECT 493 494 495 491 +CONECT 494 493 +CONECT 495 497 493 496 513 +CONECT 496 495 +CONECT 497 500 498 499 495 +CONECT 498 497 +CONECT 499 497 +CONECT 500 503 502 501 497 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 504 505 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 508 507 509 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 506 512 510 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 495 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 518 523 +CONECT 518 517 +CONECT 519 522 520 517 521 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 +CONECT 523 517 525 524 +CONECT 524 523 +CONECT 525 526 523 527 +CONECT 526 525 +CONECT 527 525 529 539 528 +CONECT 528 527 +CONECT 529 530 527 532 531 +CONECT 530 529 +CONECT 531 529 +CONECT 532 534 529 535 533 +CONECT 533 532 +CONECT 534 532 +CONECT 535 537 532 536 +CONECT 536 535 +CONECT 537 538 535 +CONECT 538 537 +CONECT 539 541 527 540 +CONECT 540 539 +CONECT 541 542 543 539 +CONECT 542 541 +CONECT 543 545 541 549 544 +CONECT 544 543 +CONECT 545 546 548 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 545 +CONECT 549 543 551 550 +CONECT 550 549 +CONECT 551 552 549 553 +CONECT 552 551 +CONECT 553 555 551 554 563 +CONECT 554 553 +CONECT 555 558 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 560 559 555 +CONECT 559 558 +CONECT 560 561 562 558 +CONECT 561 560 +CONECT 562 560 +CONECT 563 553 565 564 +CONECT 564 563 +CONECT 565 566 563 567 +CONECT 566 565 +CONECT 567 565 569 568 575 +CONECT 568 567 +CONECT 569 572 570 567 571 +CONECT 570 569 +CONECT 571 569 +CONECT 572 573 574 569 +CONECT 573 572 +CONECT 574 572 +CONECT 575 567 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 596 581 580 +CONECT 580 579 +CONECT 581 582 579 584 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 585 581 594 +CONECT 585 586 587 584 +CONECT 586 585 +CONECT 587 588 585 589 +CONECT 588 587 +CONECT 589 587 590 592 +CONECT 590 591 589 +CONECT 591 590 +CONECT 592 589 594 593 +CONECT 593 592 +CONECT 594 584 592 595 +CONECT 595 594 +CONECT 596 598 579 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 598 601 602 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 619 609 608 605 +CONECT 608 607 +CONECT 609 615 610 607 611 +CONECT 610 609 +CONECT 611 609 613 612 614 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 +CONECT 615 618 616 617 609 +CONECT 616 615 +CONECT 617 615 +CONECT 618 615 +CONECT 619 621 620 607 +CONECT 620 619 +CONECT 621 623 622 619 +CONECT 622 621 +CONECT 623 631 625 624 621 +CONECT 624 623 +CONECT 625 628 626 627 623 +CONECT 626 625 +CONECT 627 625 +CONECT 628 630 629 625 +CONECT 629 628 +CONECT 630 628 +CONECT 631 632 633 623 +CONECT 632 631 +CONECT 633 635 631 634 +CONECT 634 633 +CONECT 635 638 636 637 633 +CONECT 636 635 +CONECT 637 635 +CONECT 638 640 639 635 +CONECT 639 638 +CONECT 640 642 641 638 +CONECT 641 640 +CONECT 642 644 643 653 640 +CONECT 643 642 +CONECT 644 646 647 645 642 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 644 650 648 +CONECT 648 647 +CONECT 649 647 +CONECT 650 651 647 652 +CONECT 651 650 +CONECT 652 650 +CONECT 653 655 642 654 +CONECT 654 653 +CONECT 655 656 657 653 +CONECT 656 655 +CONECT 657 672 655 658 659 +CONECT 658 657 +CONECT 659 657 660 665 661 +CONECT 660 659 +CONECT 661 659 664 662 663 +CONECT 662 661 +CONECT 663 661 +CONECT 664 661 +CONECT 665 668 659 667 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 671 669 670 665 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 +CONECT 672 673 674 657 +CONECT 673 672 +CONECT 674 676 672 675 +CONECT 675 674 +CONECT 676 677 678 686 674 +CONECT 677 676 +CONECT 678 680 684 676 679 +CONECT 679 678 +CONECT 680 681 682 683 678 +CONECT 681 680 +CONECT 682 680 +CONECT 683 680 +CONECT 684 685 678 +CONECT 685 684 +CONECT 686 688 676 687 +CONECT 687 686 +CONECT 688 689 690 686 +CONECT 689 688 +CONECT 690 703 692 688 691 +CONECT 691 690 +CONECT 692 693 694 690 695 +CONECT 693 692 +CONECT 694 692 +CONECT 695 692 698 697 696 +CONECT 696 695 +CONECT 697 695 +CONECT 698 699 700 695 +CONECT 699 698 +CONECT 700 701 698 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 704 705 690 +CONECT 704 703 +CONECT 705 707 703 706 +CONECT 706 705 +CONECT 707 708 715 709 705 +CONECT 708 707 +CONECT 709 712 707 710 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 709 713 +CONECT 713 712 +CONECT 714 712 +CONECT 715 717 707 716 +CONECT 716 715 +CONECT 717 718 719 715 +CONECT 718 717 +CONECT 719 721 717 727 720 +CONECT 720 719 +CONECT 721 723 724 722 719 +CONECT 722 721 +CONECT 723 721 +CONECT 724 725 721 726 +CONECT 725 724 +CONECT 726 724 +CONECT 727 729 719 728 +CONECT 728 727 +CONECT 729 730 731 727 +CONECT 730 729 +CONECT 731 733 732 729 737 +CONECT 732 731 +CONECT 733 736 735 734 731 +CONECT 734 733 +CONECT 735 733 +CONECT 736 733 +CONECT 737 731 738 739 +CONECT 738 737 +CONECT 739 737 740 741 +CONECT 740 739 +CONECT 741 739 742 743 751 +CONECT 742 741 +CONECT 743 745 741 749 744 +CONECT 744 743 +CONECT 745 746 748 747 743 +CONECT 746 745 +CONECT 747 745 +CONECT 748 745 +CONECT 749 750 743 +CONECT 750 749 +CONECT 751 741 753 752 +CONECT 752 751 +CONECT 753 754 755 751 +CONECT 754 753 +CONECT 755 756 753 757 773 +CONECT 756 755 +CONECT 757 760 755 759 758 +CONECT 758 757 +CONECT 759 757 +CONECT 760 763 761 762 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 766 765 764 760 +CONECT 764 763 +CONECT 765 763 +CONECT 766 769 768 767 763 +CONECT 767 766 +CONECT 768 766 +CONECT 769 771 772 770 766 +CONECT 770 769 +CONECT 771 769 +CONECT 772 769 +CONECT 773 755 775 774 +CONECT 774 773 +CONECT 775 776 773 777 +CONECT 776 775 +CONECT 777 775 787 779 778 +CONECT 778 777 +CONECT 779 780 777 785 781 +CONECT 780 779 +CONECT 781 779 784 783 782 +CONECT 782 781 +CONECT 783 781 +CONECT 784 781 +CONECT 785 786 779 +CONECT 786 785 +CONECT 787 788 777 789 +CONECT 788 787 +CONECT 789 787 791 790 +CONECT 790 789 +CONECT 791 792 789 807 793 +CONECT 792 791 +CONECT 793 791 796 795 794 +CONECT 794 793 +CONECT 795 793 +CONECT 796 805 797 793 +CONECT 797 799 796 798 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 804 801 805 +CONECT 804 803 +CONECT 805 803 806 796 +CONECT 806 805 +CONECT 807 791 809 808 +CONECT 808 807 +CONECT 809 810 807 811 +CONECT 810 809 +CONECT 811 813 809 821 812 +CONECT 812 811 +CONECT 813 819 815 814 811 +CONECT 814 813 +CONECT 815 816 817 813 818 +CONECT 816 815 +CONECT 817 815 +CONECT 818 815 +CONECT 819 820 813 +CONECT 820 819 +CONECT 821 822 811 823 +CONECT 822 821 +CONECT 823 821 825 824 +CONECT 824 823 +CONECT 825 831 826 823 827 +CONECT 826 825 +CONECT 827 825 829 830 828 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 833 832 825 +CONECT 832 831 +CONECT 833 835 834 831 +CONECT 834 833 +CONECT 835 837 836 833 847 +CONECT 836 835 +CONECT 837 840 839 838 835 +CONECT 838 837 +CONECT 839 837 +CONECT 840 843 841 842 837 +CONECT 841 840 +CONECT 842 840 +CONECT 843 845 844 840 +CONECT 844 843 +CONECT 845 846 843 +CONECT 846 845 +CONECT 847 835 849 848 +CONECT 848 847 +CONECT 849 850 847 851 +CONECT 850 849 +CONECT 851 849 853 862 852 +CONECT 852 851 +CONECT 853 855 854 856 851 +CONECT 854 853 +CONECT 855 853 +CONECT 856 857 858 853 859 +CONECT 857 856 +CONECT 858 856 +CONECT 859 856 860 861 +CONECT 860 859 +CONECT 861 859 +CONECT 862 864 851 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 87 306 866 275 +CONECT 866 865 868 +CONECT 867 870 868 871 869 +CONECT 868 866 867 +CONECT 869 867 +CONECT 870 867 +CONECT 871 867 +CONECT 872 873 +CONECT 873 872 874 +CONECT 874 873 +MASTER 0 0 0 0 0 0 0 0 874 0 874 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_2_front_3.pdb b/tests/nsga2/intermediate_molecules/min_iter_2_front_3.pdb new file mode 100644 index 0000000..7a0c97e --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_2_front_3.pdb @@ -0,0 +1,1753 @@ +COMPND fitness: -1.2907 59.98833333333391 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 55.366 58.077 52.044 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.215 37.914 23.523 1.00 0.00 N +ATOM 2 H1 MET 1 15.201 38.296 24.464 1.00 0.00 H +ATOM 3 H2 MET 1 14.443 38.284 22.998 1.00 0.00 H +ATOM 4 H3 MET 1 16.084 38.206 23.097 1.00 0.00 H +ATOM 5 CA MET 1 15.167 36.444 23.594 1.00 0.00 C +ATOM 6 HA MET 1 14.223 36.155 24.051 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.794 22.200 1.00 0.00 C +ATOM 8 HB2 MET 1 14.404 36.123 21.604 1.00 0.00 H +ATOM 9 HB3 MET 1 16.168 36.123 21.701 1.00 0.00 H +ATOM 10 CG MET 1 15.256 34.254 22.251 1.00 0.00 C +ATOM 11 HG2 MET 1 16.133 33.929 22.814 1.00 0.00 H +ATOM 12 HG3 MET 1 14.367 33.916 22.786 1.00 0.00 H +ATOM 13 SD MET 1 15.317 33.393 20.646 1.00 0.00 S +ATOM 14 CE MET 1 13.636 33.641 20.008 1.00 0.00 C +ATOM 15 HE1 MET 1 13.415 34.705 19.929 1.00 0.00 H +ATOM 16 HE2 MET 1 13.557 33.192 19.017 1.00 0.00 H +ATOM 17 HE3 MET 1 12.912 33.164 20.670 1.00 0.00 H +ATOM 18 C MET 1 16.285 35.966 24.511 1.00 0.00 C +ATOM 19 O MET 1 17.429 36.370 24.340 1.00 0.00 O +ATOM 20 N GLN 2 15.963 35.099 25.473 1.00 0.00 N +ATOM 21 H GLN 2 14.992 34.874 25.632 1.00 0.00 H +ATOM 22 CA GLN 2 16.928 34.438 26.358 1.00 0.00 C +ATOM 23 HA GLN 2 17.697 35.150 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 16.177 34.003 27.636 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.213 33.562 27.357 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.744 33.245 28.172 1.00 0.00 H +ATOM 27 CG GLN 2 15.930 35.169 28.587 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.504 36.019 28.045 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.177 34.846 29.297 1.00 0.00 H +ATOM 30 CD GLN 2 17.140 35.548 29.441 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.211 34.972 29.368 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.976 36.450 30.363 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.748 36.615 30.982 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.068 36.818 30.542 1.00 0.00 H +ATOM 35 C GLN 2 17.653 33.291 25.623 1.00 0.00 C +ATOM 36 O GLN 2 17.281 32.121 25.734 1.00 0.00 O +ATOM 37 N TYR 3 18.675 33.646 24.841 1.00 0.00 N +ATOM 38 H TYR 3 18.926 34.635 24.813 1.00 0.00 H +ATOM 39 CA TYR 3 19.508 32.709 24.085 1.00 0.00 C +ATOM 40 HA TYR 3 18.854 32.101 23.459 1.00 0.00 H +ATOM 41 CB TYR 3 20.458 33.508 23.197 1.00 0.00 C +ATOM 42 HB2 TYR 3 21.071 34.153 23.827 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.125 32.817 22.690 1.00 0.00 H +ATOM 44 CG TYR 3 19.760 34.349 22.152 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.102 33.711 21.087 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.079 32.633 21.039 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.519 34.465 20.054 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.049 33.973 19.217 1.00 0.00 H +ATOM 49 CZ TYR 3 18.571 35.872 20.103 1.00 0.00 C +ATOM 50 OH TYR 3 18.027 36.608 19.103 1.00 0.00 O +ATOM 51 HH TYR 3 18.041 36.130 18.273 1.00 0.00 H +ATOM 52 CE2 TYR 3 19.176 36.515 21.200 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.196 37.592 21.223 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.774 35.755 22.224 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.247 36.252 23.059 1.00 0.00 H +ATOM 56 C TYR 3 20.295 31.786 25.023 1.00 0.00 C +ATOM 57 O TYR 3 20.806 32.243 26.044 1.00 0.00 O +ATOM 58 N LYS 4 20.410 30.492 24.696 1.00 0.00 N +ATOM 59 H LYS 4 20.118 30.201 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 21.014 29.461 25.566 1.00 0.00 C +ATOM 61 HA LYS 4 20.744 29.654 26.602 1.00 0.00 H +ATOM 62 CB LYS 4 20.480 28.067 25.177 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.496 27.976 24.094 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.160 27.307 25.570 1.00 0.00 H +ATOM 65 CG LYS 4 19.070 27.701 25.676 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.897 26.669 25.374 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.060 27.742 26.766 1.00 0.00 H +ATOM 68 CD LYS 4 17.920 28.560 25.120 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.927 29.535 25.607 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.090 28.713 24.052 1.00 0.00 H +ATOM 71 CE LYS 4 16.533 27.909 25.279 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.777 28.600 24.894 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.509 27.012 24.654 1.00 0.00 H +ATOM 74 NZ LYS 4 16.205 27.518 26.673 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.269 28.291 27.318 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.276 27.107 26.716 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.829 26.763 26.958 1.00 0.00 H +ATOM 78 C LYS 4 22.547 29.475 25.513 1.00 0.00 C +ATOM 79 O LYS 4 23.144 29.819 24.501 1.00 0.00 O +HETATM 80 N HX1 5 23.203 29.039 26.584 1.00 0.00 N +HETATM 81 CA HX1 5 24.662 28.868 26.669 1.00 0.00 C +HETATM 82 C HX1 5 24.985 27.668 27.567 1.00 0.00 C +HETATM 83 O HX1 5 24.522 27.612 28.710 1.00 0.00 O +HETATM 84 CB HX1 5 25.294 30.185 27.169 1.00 0.00 C +HETATM 85 CG HX1 5 26.807 30.275 27.239 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.721 29.336 26.838 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.483 31.361 27.814 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.782 31.031 27.730 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.957 29.808 27.202 1.00 0.00 N +HETATM 90 H HX1 5 22.658 28.869 27.426 1.00 0.00 H +HETATM 91 HA HX1 5 25.052 28.661 25.672 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.899 30.401 28.163 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.958 30.992 26.516 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.539 28.374 26.378 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.578 31.603 28.187 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.812 29.251 27.293 1.00 0.00 H +ATOM 97 N ILE 6 25.726 26.695 27.028 1.00 0.00 N +ATOM 98 H ILE 6 26.046 26.815 26.070 1.00 0.00 H +ATOM 99 CA ILE 6 26.199 25.479 27.709 1.00 0.00 C +ATOM 100 HA ILE 6 25.697 25.404 28.676 1.00 0.00 H +ATOM 101 CB ILE 6 25.811 24.216 26.902 1.00 0.00 C +ATOM 102 HB ILE 6 26.234 24.306 25.901 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.373 22.929 27.541 1.00 0.00 C +ATOM 104 HG21 ILE 6 26.002 22.820 28.562 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.078 22.054 26.963 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.464 22.944 27.545 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.270 24.130 26.784 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.842 24.047 27.783 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.891 25.046 26.331 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.745 22.969 25.931 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.890 22.021 26.449 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.678 23.107 25.758 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.263 22.948 24.971 1.00 0.00 H +ATOM 114 C ILE 6 27.708 25.597 28.003 1.00 0.00 C +ATOM 115 O ILE 6 28.447 26.273 27.288 1.00 0.00 O +ATOM 116 N VAL 7 28.126 24.994 29.115 1.00 0.00 N +ATOM 117 H VAL 7 27.488 24.344 29.551 1.00 0.00 H +ATOM 118 CA VAL 7 29.238 25.447 29.963 1.00 0.00 C +ATOM 119 HA VAL 7 29.296 26.533 29.871 1.00 0.00 H +ATOM 120 CB VAL 7 28.813 25.143 31.416 1.00 0.00 C +ATOM 121 HB VAL 7 27.762 25.424 31.517 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.895 23.654 31.773 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.924 23.309 31.694 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.538 23.499 32.790 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.276 23.071 31.090 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.567 25.988 32.435 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.358 27.041 32.248 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.232 25.736 33.441 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.636 25.813 32.353 1.00 0.00 H +ATOM 130 C VAL 7 30.639 24.901 29.585 1.00 0.00 C +ATOM 131 O VAL 7 30.785 23.764 29.143 1.00 0.00 O +ATOM 132 N GLU 8 31.685 25.707 29.802 1.00 0.00 N +ATOM 133 H GLU 8 31.473 26.676 30.027 1.00 0.00 H +ATOM 134 CA GLU 8 33.119 25.383 29.624 1.00 0.00 C +ATOM 135 HA GLU 8 33.310 25.152 28.575 1.00 0.00 H +ATOM 136 CB GLU 8 33.917 26.667 29.977 1.00 0.00 C +ATOM 137 HB2 GLU 8 33.712 27.426 29.223 1.00 0.00 H +ATOM 138 HB3 GLU 8 33.497 27.048 30.911 1.00 0.00 H +ATOM 139 CG GLU 8 35.447 26.584 30.222 1.00 0.00 C +ATOM 140 HG2 GLU 8 35.729 27.498 30.753 1.00 0.00 H +ATOM 141 HG3 GLU 8 35.683 25.765 30.900 1.00 0.00 H +ATOM 142 CD GLU 8 36.359 26.500 28.992 1.00 0.00 C +ATOM 143 OE1 GLU 8 36.012 27.041 27.916 1.00 0.00 O +ATOM 144 OE2 GLU 8 37.521 26.054 29.135 1.00 0.00 O +ATOM 145 C GLU 8 33.570 24.164 30.464 1.00 0.00 C +ATOM 146 O GLU 8 33.840 24.286 31.658 1.00 0.00 O +ATOM 147 N GLY 9 33.696 22.982 29.849 1.00 0.00 N +ATOM 148 H GLY 9 33.287 22.892 28.929 1.00 0.00 H +ATOM 149 CA GLY 9 34.345 21.797 30.438 1.00 0.00 C +ATOM 150 HA2 GLY 9 35.247 21.575 29.868 1.00 0.00 H +ATOM 151 HA3 GLY 9 34.650 22.011 31.462 1.00 0.00 H +ATOM 152 C GLY 9 33.492 20.522 30.448 1.00 0.00 C +ATOM 153 O GLY 9 32.620 20.332 29.602 1.00 0.00 O +ATOM 154 N LYS 10 33.792 19.600 31.384 1.00 0.00 N +ATOM 155 H LYS 10 34.546 19.810 32.024 1.00 0.00 H +ATOM 156 CA LYS 10 33.231 18.228 31.369 1.00 0.00 C +ATOM 157 HA LYS 10 32.207 18.313 30.994 1.00 0.00 H +ATOM 158 CB LYS 10 34.029 17.371 30.353 1.00 0.00 C +ATOM 159 HB2 LYS 10 34.519 18.019 29.622 1.00 0.00 H +ATOM 160 HB3 LYS 10 34.809 16.806 30.866 1.00 0.00 H +ATOM 161 CG LYS 10 33.125 16.407 29.565 1.00 0.00 C +ATOM 162 HG2 LYS 10 32.575 15.759 30.248 1.00 0.00 H +ATOM 163 HG3 LYS 10 32.406 16.996 28.991 1.00 0.00 H +ATOM 164 CD LYS 10 33.941 15.541 28.595 1.00 0.00 C +ATOM 165 HD2 LYS 10 34.578 16.183 27.985 1.00 0.00 H +ATOM 166 HD3 LYS 10 34.568 14.847 29.158 1.00 0.00 H +ATOM 167 CE LYS 10 32.994 14.759 27.678 1.00 0.00 C +ATOM 168 HE2 LYS 10 32.438 14.025 28.267 1.00 0.00 H +ATOM 169 HE3 LYS 10 32.275 15.460 27.247 1.00 0.00 H +ATOM 170 NZ LYS 10 33.721 14.092 26.575 1.00 0.00 N +ATOM 171 HZ1 LYS 10 34.417 13.448 26.913 1.00 0.00 H +ATOM 172 HZ2 LYS 10 33.061 13.594 25.979 1.00 0.00 H +ATOM 173 HZ3 LYS 10 34.203 14.795 26.004 1.00 0.00 H +ATOM 174 C LYS 10 33.089 17.528 32.737 1.00 0.00 C +ATOM 175 O LYS 10 33.156 16.303 32.800 1.00 0.00 O +ATOM 176 N ARG 11 32.949 18.273 33.841 1.00 0.00 N +ATOM 177 H ARG 11 32.915 19.267 33.709 1.00 0.00 H +ATOM 178 CA ARG 11 32.662 17.722 35.194 1.00 0.00 C +ATOM 179 HA ARG 11 32.758 16.632 35.161 1.00 0.00 H +ATOM 180 CB ARG 11 33.685 18.237 36.231 1.00 0.00 C +ATOM 181 HB2 ARG 11 33.709 19.326 36.208 1.00 0.00 H +ATOM 182 HB3 ARG 11 33.355 17.924 37.222 1.00 0.00 H +ATOM 183 CG ARG 11 35.099 17.680 35.989 1.00 0.00 C +ATOM 184 HG2 ARG 11 35.055 16.589 35.999 1.00 0.00 H +ATOM 185 HG3 ARG 11 35.449 18.007 35.010 1.00 0.00 H +ATOM 186 CD ARG 11 36.103 18.142 37.058 1.00 0.00 C +ATOM 187 HD2 ARG 11 36.071 19.228 37.118 1.00 0.00 H +ATOM 188 HD3 ARG 11 35.803 17.740 38.029 1.00 0.00 H +ATOM 189 NE ARG 11 37.479 17.692 36.740 1.00 0.00 N +ATOM 190 HE ARG 11 37.569 16.946 36.073 1.00 0.00 H +ATOM 191 CZ ARG 11 38.615 18.198 37.201 1.00 0.00 C +ATOM 192 NH1 ARG 11 38.667 19.233 37.987 1.00 0.00 N +ATOM 193 HH11 ARG 11 37.829 19.772 38.112 1.00 0.00 H +ATOM 194 HH12 ARG 11 39.560 19.686 38.132 1.00 0.00 H +ATOM 195 NH2 ARG 11 39.749 17.650 36.875 1.00 0.00 N +ATOM 196 HH21 ARG 11 39.795 16.894 36.219 1.00 0.00 H +ATOM 197 HH22 ARG 11 40.609 18.031 37.266 1.00 0.00 H +ATOM 198 C ARG 11 31.206 17.954 35.609 1.00 0.00 C +ATOM 199 O ARG 11 30.490 17.005 35.900 1.00 0.00 O +ATOM 200 N TYR 12 30.762 19.208 35.566 1.00 0.00 N +ATOM 201 H TYR 12 31.434 19.929 35.379 1.00 0.00 H +ATOM 202 CA TYR 12 29.346 19.607 35.531 1.00 0.00 C +ATOM 203 HA TYR 12 28.789 18.986 36.247 1.00 0.00 H +ATOM 204 CB TYR 12 29.234 21.066 36.001 1.00 0.00 C +ATOM 205 HB2 TYR 12 28.187 21.379 35.945 1.00 0.00 H +ATOM 206 HB3 TYR 12 29.493 21.077 37.062 1.00 0.00 H +ATOM 207 CG TYR 12 30.105 22.126 35.333 1.00 0.00 C +ATOM 208 CD1 TYR 12 30.870 21.891 34.171 1.00 0.00 C +ATOM 209 HD1 TYR 12 30.824 20.950 33.636 1.00 0.00 H +ATOM 210 CE1 TYR 12 31.738 22.879 33.670 1.00 0.00 C +ATOM 211 HE1 TYR 12 32.313 22.692 32.776 1.00 0.00 H +ATOM 212 CZ TYR 12 31.833 24.123 34.322 1.00 0.00 C +ATOM 213 OH TYR 12 32.699 25.074 33.898 1.00 0.00 O +ATOM 214 HH TYR 12 33.108 24.847 33.030 1.00 0.00 H +ATOM 215 CE2 TYR 12 30.999 24.398 35.419 1.00 0.00 C +ATOM 216 HE2 TYR 12 31.006 25.385 35.861 1.00 0.00 H +ATOM 217 CD2 TYR 12 30.158 23.394 35.933 1.00 0.00 C +ATOM 218 HD2 TYR 12 29.558 23.604 36.815 1.00 0.00 H +ATOM 219 C TYR 12 28.690 19.397 34.145 1.00 0.00 C +ATOM 220 O TYR 12 29.368 19.005 33.196 1.00 0.00 O +ATOM 221 N LYS 13 27.382 19.683 34.028 1.00 0.00 N +ATOM 222 H LYS 13 26.894 19.964 34.865 1.00 0.00 H +ATOM 223 CA LYS 13 26.590 19.509 32.789 1.00 0.00 C +ATOM 224 HA LYS 13 27.257 19.685 31.944 1.00 0.00 H +ATOM 225 CB LYS 13 26.113 18.042 32.728 1.00 0.00 C +ATOM 226 HB2 LYS 13 26.870 17.413 33.196 1.00 0.00 H +ATOM 227 HB3 LYS 13 25.191 17.936 33.302 1.00 0.00 H +ATOM 228 CG LYS 13 25.912 17.515 31.295 1.00 0.00 C +ATOM 229 HG2 LYS 13 25.056 18.000 30.825 1.00 0.00 H +ATOM 230 HG3 LYS 13 26.803 17.746 30.711 1.00 0.00 H +ATOM 231 CD LYS 13 25.715 15.990 31.282 1.00 0.00 C +ATOM 232 HD2 LYS 13 25.753 15.643 30.248 1.00 0.00 H +ATOM 233 HD3 LYS 13 26.543 15.525 31.821 1.00 0.00 H +ATOM 234 CE LYS 13 24.376 15.549 31.892 1.00 0.00 C +ATOM 235 HE2 LYS 13 24.136 16.182 32.751 1.00 0.00 H +ATOM 236 HE3 LYS 13 23.603 15.708 31.133 1.00 0.00 H +ATOM 237 NZ LYS 13 24.406 14.121 32.306 1.00 0.00 N +ATOM 238 HZ1 LYS 13 24.934 13.975 33.159 1.00 0.00 H +ATOM 239 HZ2 LYS 13 23.466 13.759 32.451 1.00 0.00 H +ATOM 240 HZ3 LYS 13 24.860 13.553 31.592 1.00 0.00 H +ATOM 241 C LYS 13 25.440 20.533 32.632 1.00 0.00 C +ATOM 242 O LYS 13 24.397 20.233 32.051 1.00 0.00 O +ATOM 243 N GLY 14 25.597 21.720 33.227 1.00 0.00 N +ATOM 244 H GLY 14 26.491 21.921 33.646 1.00 0.00 H +ATOM 245 CA GLY 14 24.547 22.749 33.314 1.00 0.00 C +ATOM 246 HA2 GLY 14 23.595 22.255 33.508 1.00 0.00 H +ATOM 247 HA3 GLY 14 24.753 23.393 34.169 1.00 0.00 H +ATOM 248 C GLY 14 24.384 23.636 32.065 1.00 0.00 C +ATOM 249 O GLY 14 25.241 23.673 31.182 1.00 0.00 O +ATOM 250 N VAL 15 23.283 24.395 32.031 1.00 0.00 N +ATOM 251 H VAL 15 22.640 24.337 32.808 1.00 0.00 H +ATOM 252 CA VAL 15 22.902 25.355 30.981 1.00 0.00 C +ATOM 253 HA VAL 15 23.781 25.595 30.382 1.00 0.00 H +ATOM 254 CB VAL 15 21.857 24.717 30.034 1.00 0.00 C +ATOM 255 HB VAL 15 22.299 23.817 29.609 1.00 0.00 H +ATOM 256 CG1 VAL 15 20.551 24.300 30.731 1.00 0.00 C +ATOM 257 HG11 VAL 15 20.049 25.165 31.169 1.00 0.00 H +ATOM 258 HG12 VAL 15 19.882 23.832 30.007 1.00 0.00 H +ATOM 259 HG13 VAL 15 20.757 23.573 31.519 1.00 0.00 H +ATOM 260 CG2 VAL 15 21.481 25.640 28.867 1.00 0.00 C +ATOM 261 HG21 VAL 15 22.382 25.990 28.366 1.00 0.00 H +ATOM 262 HG22 VAL 15 20.879 25.084 28.146 1.00 0.00 H +ATOM 263 HG23 VAL 15 20.901 26.492 29.221 1.00 0.00 H +ATOM 264 C VAL 15 22.399 26.651 31.633 1.00 0.00 C +ATOM 265 O VAL 15 21.845 26.618 32.728 1.00 0.00 O +HETATM 266 N HY1 16 22.593 27.795 30.980 1.00 0.00 N +HETATM 267 CA HY1 16 22.005 29.092 31.344 1.00 0.00 C +HETATM 268 C HY1 16 21.694 29.890 30.062 1.00 0.00 C +HETATM 269 O HY1 16 21.860 29.375 28.949 1.00 0.00 O +HETATM 270 CB HY1 16 22.928 29.838 32.334 1.00 0.00 C +HETATM 271 CG HY1 16 24.278 30.202 31.763 1.00 0.00 C +HETATM 272 CD2 HY1 16 24.599 31.380 31.142 1.00 0.00 C +HETATM 273 ND1 HY1 16 25.407 29.412 31.750 1.00 0.00 N +HETATM 274 CE1 HY1 16 26.387 30.121 31.164 1.00 0.00 C +HETATM 275 NE2 HY1 16 25.942 31.324 30.761 1.00 0.00 N +HETATM 276 H HY1 16 23.089 27.760 30.095 1.00 0.00 H +HETATM 277 HA HY1 16 21.042 28.937 31.836 1.00 0.00 H +HETATM 278 HB2 HY1 16 22.448 30.747 32.701 1.00 0.00 H +HETATM 279 HB3 HY1 16 23.076 29.209 33.217 1.00 0.00 H +HETATM 280 HD1 HY1 16 25.502 28.501 32.177 1.00 0.00 H +HETATM 281 HD2 HY1 16 23.933 32.219 30.992 1.00 0.00 H +HETATM 282 HE1 HY1 16 27.419 29.794 31.067 1.00 0.00 H +ATOM 283 N THR 17 21.213 31.125 30.221 1.00 0.00 N +ATOM 284 H THR 17 21.084 31.439 31.169 1.00 0.00 H +ATOM 285 CA THR 17 20.771 32.009 29.122 1.00 0.00 C +ATOM 286 HA THR 17 21.190 31.603 28.215 1.00 0.00 H +ATOM 287 CB THR 17 19.244 32.008 28.942 1.00 0.00 C +ATOM 288 HB THR 17 19.023 32.578 28.042 1.00 0.00 H +ATOM 289 CG2 THR 17 18.642 30.640 28.642 1.00 0.00 C +ATOM 290 HG21 THR 17 18.864 29.923 29.430 1.00 0.00 H +ATOM 291 HG22 THR 17 17.562 30.744 28.553 1.00 0.00 H +ATOM 292 HG23 THR 17 19.034 30.311 27.693 1.00 0.00 H +ATOM 293 OG1 THR 17 18.523 32.465 30.065 1.00 0.00 O +ATOM 294 HG1 THR 17 18.606 33.430 30.107 1.00 0.00 H +ATOM 295 C THR 17 21.279 33.458 29.181 1.00 0.00 C +ATOM 296 O THR 17 21.726 33.926 30.226 1.00 0.00 O +HETATM 297 N HY2 18 21.213 34.175 28.055 1.00 0.00 N +HETATM 298 CA HY2 18 21.495 35.612 27.957 1.00 0.00 C +HETATM 299 C HY2 18 20.395 36.305 27.153 1.00 0.00 C +HETATM 300 O HY2 18 20.079 35.863 26.049 1.00 0.00 O +HETATM 301 CB HY2 18 22.848 35.842 27.247 1.00 0.00 C +HETATM 302 CG HY2 18 24.050 35.344 28.020 1.00 0.00 C +HETATM 303 CD2 HY2 18 24.548 34.066 28.017 1.00 0.00 C +HETATM 304 ND1 HY2 18 24.828 36.083 28.888 1.00 0.00 N +HETATM 305 CE1 HY2 18 25.770 35.264 29.383 1.00 0.00 C +HETATM 306 NE2 HY2 18 25.640 34.024 28.889 1.00 0.00 N +HETATM 307 H HY2 18 20.908 33.715 27.202 1.00 0.00 H +HETATM 308 HA HY2 18 21.529 36.051 28.954 1.00 0.00 H +HETATM 309 HB2 HY2 18 22.822 35.342 26.280 1.00 0.00 H +HETATM 310 HB3 HY2 18 22.973 36.910 27.064 1.00 0.00 H +HETATM 311 HD1 HY2 18 24.725 37.067 29.105 1.00 0.00 H +HETATM 312 HD2 HY2 18 24.156 33.232 27.450 1.00 0.00 H +HETATM 313 HE1 HY2 18 26.531 35.559 30.091 1.00 0.00 H +ATOM 314 N GLU 19 19.822 37.382 27.687 1.00 0.00 N +ATOM 315 H GLU 19 20.120 37.688 28.599 1.00 0.00 H +ATOM 316 CA GLU 19 18.828 38.211 26.992 1.00 0.00 C +ATOM 317 HA GLU 19 18.106 37.555 26.510 1.00 0.00 H +ATOM 318 CB GLU 19 18.086 39.074 28.032 1.00 0.00 C +ATOM 319 HB2 GLU 19 17.783 38.444 28.864 1.00 0.00 H +ATOM 320 HB3 GLU 19 18.779 39.814 28.429 1.00 0.00 H +ATOM 321 CG GLU 19 16.839 39.798 27.502 1.00 0.00 C +ATOM 322 HG2 GLU 19 16.549 40.555 28.233 1.00 0.00 H +ATOM 323 HG3 GLU 19 17.073 40.313 26.569 1.00 0.00 H +ATOM 324 CD GLU 19 15.667 38.828 27.300 1.00 0.00 C +ATOM 325 OE1 GLU 19 15.544 38.285 26.172 1.00 0.00 O +ATOM 326 OE2 GLU 19 14.908 38.603 28.271 1.00 0.00 O +ATOM 327 C GLU 19 19.483 39.095 25.913 1.00 0.00 C +ATOM 328 O GLU 19 20.430 39.823 26.208 1.00 0.00 O +ATOM 329 N ALA 20 18.977 39.059 24.676 1.00 0.00 N +ATOM 330 H ALA 20 18.268 38.367 24.467 1.00 0.00 H +ATOM 331 CA ALA 20 19.340 40.004 23.612 1.00 0.00 C +ATOM 332 HA ALA 20 19.410 41.004 24.042 1.00 0.00 H +ATOM 333 CB ALA 20 20.714 39.620 23.042 1.00 0.00 C +ATOM 334 HB1 ALA 20 20.657 38.642 22.573 1.00 0.00 H +ATOM 335 HB2 ALA 20 21.036 40.351 22.302 1.00 0.00 H +ATOM 336 HB3 ALA 20 21.459 39.585 23.834 1.00 0.00 H +ATOM 337 C ALA 20 18.286 40.039 22.486 1.00 0.00 C +ATOM 338 O ALA 20 17.384 39.200 22.439 1.00 0.00 O +ATOM 339 N VAL 21 18.416 40.981 21.545 1.00 0.00 N +ATOM 340 H VAL 21 19.145 41.670 21.653 1.00 0.00 H +ATOM 341 CA VAL 21 17.672 40.975 20.262 1.00 0.00 C +ATOM 342 HA VAL 21 16.689 40.537 20.427 1.00 0.00 H +ATOM 343 CB VAL 21 17.448 42.410 19.731 1.00 0.00 C +ATOM 344 HB VAL 21 16.804 42.345 18.853 1.00 0.00 H +ATOM 345 CG1 VAL 21 16.721 43.284 20.761 1.00 0.00 C +ATOM 346 HG11 VAL 21 17.357 43.476 21.625 1.00 0.00 H +ATOM 347 HG12 VAL 21 16.455 44.237 20.303 1.00 0.00 H +ATOM 348 HG13 VAL 21 15.806 42.790 21.088 1.00 0.00 H +ATOM 349 CG2 VAL 21 18.744 43.117 19.309 1.00 0.00 C +ATOM 350 HG21 VAL 21 19.218 42.578 18.489 1.00 0.00 H +ATOM 351 HG22 VAL 21 18.510 44.121 18.954 1.00 0.00 H +ATOM 352 HG23 VAL 21 19.441 43.191 20.143 1.00 0.00 H +ATOM 353 C VAL 21 18.344 40.117 19.176 1.00 0.00 C +ATOM 354 O VAL 21 17.744 39.875 18.133 1.00 0.00 O +ATOM 355 N ASP 22 19.590 39.693 19.410 1.00 0.00 N +ATOM 356 H ASP 22 20.003 39.905 20.303 1.00 0.00 H +ATOM 357 CA ASP 22 20.496 39.093 18.428 1.00 0.00 C +ATOM 358 HA ASP 22 19.939 38.443 17.752 1.00 0.00 H +ATOM 359 CB ASP 22 21.118 40.245 17.617 1.00 0.00 C +ATOM 360 HB2 ASP 22 20.331 40.741 17.046 1.00 0.00 H +ATOM 361 HB3 ASP 22 21.537 40.973 18.314 1.00 0.00 H +ATOM 362 CG ASP 22 22.212 39.808 16.646 1.00 0.00 C +ATOM 363 OD1 ASP 22 23.135 40.614 16.431 1.00 0.00 O +ATOM 364 OD2 ASP 22 22.150 38.658 16.158 1.00 0.00 O +ATOM 365 C ASP 22 21.589 38.257 19.129 1.00 0.00 C +ATOM 366 O ASP 22 22.026 38.601 20.232 1.00 0.00 O +ATOM 367 N PHE 23 22.075 37.194 18.482 1.00 0.00 N +ATOM 368 H PHE 23 21.801 37.088 17.511 1.00 0.00 H +ATOM 369 CA PHE 23 23.223 36.413 18.957 1.00 0.00 C +ATOM 370 HA PHE 23 23.033 36.100 19.983 1.00 0.00 H +ATOM 371 CB PHE 23 23.435 35.163 18.098 1.00 0.00 C +ATOM 372 HB2 PHE 23 23.449 35.439 17.042 1.00 0.00 H +ATOM 373 HB3 PHE 23 24.415 34.748 18.336 1.00 0.00 H +ATOM 374 CG PHE 23 22.418 34.075 18.332 1.00 0.00 C +ATOM 375 CD1 PHE 23 21.326 33.930 17.460 1.00 0.00 C +ATOM 376 HD1 PHE 23 21.215 34.591 16.613 1.00 0.00 H +ATOM 377 CE1 PHE 23 20.387 32.912 17.686 1.00 0.00 C +ATOM 378 HE1 PHE 23 19.553 32.789 17.010 1.00 0.00 H +ATOM 379 CZ PHE 23 20.545 32.053 18.784 1.00 0.00 C +ATOM 380 HZ PHE 23 19.804 31.307 18.977 1.00 0.00 H +ATOM 381 CE2 PHE 23 21.642 32.183 19.650 1.00 0.00 C +ATOM 382 HE2 PHE 23 21.763 31.512 20.488 1.00 0.00 H +ATOM 383 CD2 PHE 23 22.581 33.199 19.421 1.00 0.00 C +ATOM 384 HD2 PHE 23 23.433 33.303 20.076 1.00 0.00 H +ATOM 385 C PHE 23 24.522 37.216 18.948 1.00 0.00 C +ATOM 386 O PHE 23 25.288 37.123 19.906 1.00 0.00 O +ATOM 387 N ALA 24 24.777 38.032 17.920 1.00 0.00 N +ATOM 388 H ALA 24 24.098 38.127 17.167 1.00 0.00 H +ATOM 389 CA ALA 24 26.004 38.826 17.863 1.00 0.00 C +ATOM 390 HA ALA 24 26.836 38.166 18.118 1.00 0.00 H +ATOM 391 CB ALA 24 26.244 39.297 16.423 1.00 0.00 C +ATOM 392 HB1 ALA 24 25.486 40.016 16.122 1.00 0.00 H +ATOM 393 HB2 ALA 24 27.226 39.763 16.347 1.00 0.00 H +ATOM 394 HB3 ALA 24 26.209 38.442 15.744 1.00 0.00 H +ATOM 395 C ALA 24 26.024 39.969 18.904 1.00 0.00 C +ATOM 396 O ALA 24 27.084 40.536 19.172 1.00 0.00 O +ATOM 397 N GLU 25 24.892 40.281 19.545 1.00 0.00 N +ATOM 398 H GLU 25 24.041 39.856 19.205 1.00 0.00 H +ATOM 399 CA GLU 25 24.819 41.085 20.776 1.00 0.00 C +ATOM 400 HA GLU 25 25.636 41.806 20.796 1.00 0.00 H +ATOM 401 CB GLU 25 23.498 41.871 20.814 1.00 0.00 C +ATOM 402 HB2 GLU 25 22.673 41.163 20.774 1.00 0.00 H +ATOM 403 HB3 GLU 25 23.429 42.408 21.760 1.00 0.00 H +ATOM 404 CG GLU 25 23.310 42.881 19.671 1.00 0.00 C +ATOM 405 HG2 GLU 25 23.577 42.429 18.714 1.00 0.00 H +ATOM 406 HG3 GLU 25 22.247 43.135 19.624 1.00 0.00 H +ATOM 407 CD GLU 25 24.114 44.170 19.880 1.00 0.00 C +ATOM 408 OE1 GLU 25 23.462 45.220 20.101 1.00 0.00 O +ATOM 409 OE2 GLU 25 25.371 44.098 19.811 1.00 0.00 O +ATOM 410 C GLU 25 24.959 40.215 22.041 1.00 0.00 C +ATOM 411 O GLU 25 25.732 40.553 22.938 1.00 0.00 O +ATOM 412 N ALA 26 24.299 39.050 22.103 1.00 0.00 N +ATOM 413 H ALA 26 23.662 38.814 21.352 1.00 0.00 H +ATOM 414 CA ALA 26 24.423 38.100 23.218 1.00 0.00 C +ATOM 415 HA ALA 26 24.130 38.609 24.131 1.00 0.00 H +ATOM 416 CB ALA 26 23.471 36.923 22.993 1.00 0.00 C +ATOM 417 HB1 ALA 26 23.770 36.368 22.108 1.00 0.00 H +ATOM 418 HB2 ALA 26 23.499 36.260 23.854 1.00 0.00 H +ATOM 419 HB3 ALA 26 22.460 37.285 22.860 1.00 0.00 H +ATOM 420 C ALA 26 25.868 37.595 23.424 1.00 0.00 C +ATOM 421 O ALA 26 26.292 37.316 24.550 1.00 0.00 O +ATOM 422 N GLU 27 26.659 37.515 22.348 1.00 0.00 N +ATOM 423 H GLU 27 26.221 37.663 21.441 1.00 0.00 H +ATOM 424 CA GLU 27 28.109 37.261 22.347 1.00 0.00 C +ATOM 425 HA GLU 27 28.316 36.315 22.855 1.00 0.00 H +ATOM 426 CB GLU 27 28.586 37.117 20.887 1.00 0.00 C +ATOM 427 HB2 GLU 27 28.014 36.303 20.438 1.00 0.00 H +ATOM 428 HB3 GLU 27 28.354 38.028 20.337 1.00 0.00 H +ATOM 429 CG GLU 27 30.079 36.836 20.757 1.00 0.00 C +ATOM 430 HG2 GLU 27 30.614 37.779 20.882 1.00 0.00 H +ATOM 431 HG3 GLU 27 30.401 36.162 21.554 1.00 0.00 H +ATOM 432 CD GLU 27 30.366 36.227 19.390 1.00 0.00 C +ATOM 433 OE1 GLU 27 30.986 36.917 18.564 1.00 0.00 O +ATOM 434 OE2 GLU 27 29.944 35.073 19.158 1.00 0.00 O +ATOM 435 C GLU 27 28.855 38.375 23.112 1.00 0.00 C +ATOM 436 O GLU 27 29.633 38.083 24.023 1.00 0.00 O +ATOM 437 N LYS 28 28.553 39.656 22.836 1.00 0.00 N +ATOM 438 H LYS 28 27.822 39.830 22.156 1.00 0.00 H +ATOM 439 CA LYS 28 29.116 40.802 23.576 1.00 0.00 C +ATOM 440 HA LYS 28 30.202 40.719 23.569 1.00 0.00 H +ATOM 441 CB LYS 28 28.725 42.140 22.919 1.00 0.00 C +ATOM 442 HB2 LYS 28 27.648 42.281 22.995 1.00 0.00 H +ATOM 443 HB3 LYS 28 29.205 42.945 23.473 1.00 0.00 H +ATOM 444 CG LYS 28 29.135 42.250 21.442 1.00 0.00 C +ATOM 445 HG2 LYS 28 30.206 42.069 21.341 1.00 0.00 H +ATOM 446 HG3 LYS 28 28.602 41.496 20.871 1.00 0.00 H +ATOM 447 CD LYS 28 28.806 43.646 20.888 1.00 0.00 C +ATOM 448 HD2 LYS 28 27.796 43.939 21.184 1.00 0.00 H +ATOM 449 HD3 LYS 28 29.505 44.362 21.322 1.00 0.00 H +ATOM 450 CE LYS 28 28.917 43.732 19.359 1.00 0.00 C +ATOM 451 HE2 LYS 28 29.049 44.784 19.086 1.00 0.00 H +ATOM 452 HE3 LYS 28 29.802 43.181 19.025 1.00 0.00 H +ATOM 453 NZ LYS 28 27.696 43.214 18.694 1.00 0.00 N +ATOM 454 HZ1 LYS 28 26.858 43.680 19.063 1.00 0.00 H +ATOM 455 HZ2 LYS 28 27.718 43.355 17.696 1.00 0.00 H +ATOM 456 HZ3 LYS 28 27.563 42.223 18.882 1.00 0.00 H +ATOM 457 C LYS 28 28.694 40.774 25.048 1.00 0.00 C +ATOM 458 O LYS 28 29.531 40.971 25.922 1.00 0.00 O +ATOM 459 N PHE 29 27.433 40.461 25.351 1.00 0.00 N +ATOM 460 H PHE 29 26.770 40.367 24.587 1.00 0.00 H +ATOM 461 CA PHE 29 26.956 40.324 26.737 1.00 0.00 C +ATOM 462 HA PHE 29 27.288 41.196 27.301 1.00 0.00 H +ATOM 463 CB PHE 29 25.418 40.308 26.753 1.00 0.00 C +ATOM 464 HB2 PHE 29 25.082 39.379 26.290 1.00 0.00 H +ATOM 465 HB3 PHE 29 25.083 40.298 27.791 1.00 0.00 H +ATOM 466 CG PHE 29 24.734 41.474 26.050 1.00 0.00 C +ATOM 467 CD1 PHE 29 23.512 41.261 25.382 1.00 0.00 C +ATOM 468 HD1 PHE 29 23.048 40.287 25.399 1.00 0.00 H +ATOM 469 CE1 PHE 29 22.881 42.313 24.694 1.00 0.00 C +ATOM 470 HE1 PHE 29 21.946 42.138 24.183 1.00 0.00 H +ATOM 471 CZ PHE 29 23.462 43.592 24.675 1.00 0.00 C +ATOM 472 HZ PHE 29 22.980 44.397 24.138 1.00 0.00 H +ATOM 473 CE2 PHE 29 24.664 43.823 25.367 1.00 0.00 C +ATOM 474 HE2 PHE 29 25.105 44.809 25.369 1.00 0.00 H +ATOM 475 CD2 PHE 29 25.293 42.771 26.056 1.00 0.00 C +ATOM 476 HD2 PHE 29 26.211 42.971 26.586 1.00 0.00 H +ATOM 477 C PHE 29 27.555 39.107 27.465 1.00 0.00 C +ATOM 478 O PHE 29 27.773 39.150 28.677 1.00 0.00 O +ATOM 479 N THR 30 27.896 38.038 26.741 1.00 0.00 N +ATOM 480 H THR 30 27.619 38.016 25.764 1.00 0.00 H +ATOM 481 CA THR 30 28.673 36.905 27.271 1.00 0.00 C +ATOM 482 HA THR 30 28.197 36.550 28.185 1.00 0.00 H +ATOM 483 CB THR 30 28.682 35.736 26.276 1.00 0.00 C +ATOM 484 HB THR 30 29.041 36.062 25.302 1.00 0.00 H +ATOM 485 CG2 THR 30 29.498 34.534 26.746 1.00 0.00 C +ATOM 486 HG21 THR 30 29.142 34.220 27.721 1.00 0.00 H +ATOM 487 HG22 THR 30 29.367 33.720 26.036 1.00 0.00 H +ATOM 488 HG23 THR 30 30.560 34.772 26.807 1.00 0.00 H +ATOM 489 OG1 THR 30 27.360 35.286 26.150 1.00 0.00 O +ATOM 490 HG1 THR 30 26.921 35.901 25.540 1.00 0.00 H +ATOM 491 C THR 30 30.096 37.329 27.627 1.00 0.00 C +ATOM 492 O THR 30 30.588 36.990 28.705 1.00 0.00 O +ATOM 493 N LYS 31 30.738 38.118 26.757 1.00 0.00 N +ATOM 494 H LYS 31 30.278 38.309 25.872 1.00 0.00 H +ATOM 495 CA LYS 31 32.079 38.688 26.976 1.00 0.00 C +ATOM 496 HA LYS 31 32.743 37.884 27.300 1.00 0.00 H +ATOM 497 CB LYS 31 32.621 39.274 25.671 1.00 0.00 C +ATOM 498 HB2 LYS 31 31.903 39.978 25.246 1.00 0.00 H +ATOM 499 HB3 LYS 31 33.541 39.820 25.894 1.00 0.00 H +ATOM 500 CG LYS 31 32.944 38.173 24.651 1.00 0.00 C +ATOM 501 HG2 LYS 31 33.671 37.499 25.091 1.00 0.00 H +ATOM 502 HG3 LYS 31 32.056 37.589 24.426 1.00 0.00 H +ATOM 503 CD LYS 31 33.506 38.765 23.356 1.00 0.00 C +ATOM 504 HD2 LYS 31 32.713 39.327 22.866 1.00 0.00 H +ATOM 505 HD3 LYS 31 34.316 39.458 23.597 1.00 0.00 H +ATOM 506 CE LYS 31 34.009 37.678 22.410 1.00 0.00 C +ATOM 507 HE2 LYS 31 33.210 36.951 22.212 1.00 0.00 H +ATOM 508 HE3 LYS 31 34.294 38.148 21.459 1.00 0.00 H +ATOM 509 NZ LYS 31 35.192 36.994 22.980 1.00 0.00 N +ATOM 510 HZ1 LYS 31 34.970 36.242 23.631 1.00 0.00 H +ATOM 511 HZ2 LYS 31 35.696 36.535 22.223 1.00 0.00 H +ATOM 512 HZ3 LYS 31 35.853 37.636 23.423 1.00 0.00 H +ATOM 513 C LYS 31 32.124 39.737 28.088 1.00 0.00 C +ATOM 514 O LYS 31 33.110 39.767 28.820 1.00 0.00 O +ATOM 515 N ALA 32 31.066 40.529 28.271 1.00 0.00 N +ATOM 516 H ALA 32 30.350 40.537 27.557 1.00 0.00 H +ATOM 517 CA ALA 32 30.916 41.417 29.424 1.00 0.00 C +ATOM 518 HA ALA 32 31.761 42.109 29.453 1.00 0.00 H +ATOM 519 CB ALA 32 29.630 42.243 29.272 1.00 0.00 C +ATOM 520 HB1 ALA 32 28.757 41.591 29.251 1.00 0.00 H +ATOM 521 HB2 ALA 32 29.539 42.927 30.118 1.00 0.00 H +ATOM 522 HB3 ALA 32 29.672 42.826 28.351 1.00 0.00 H +ATOM 523 C ALA 32 30.942 40.605 30.729 1.00 0.00 C +ATOM 524 O ALA 32 31.851 40.784 31.532 1.00 0.00 O +ATOM 525 N GLH 33 30.050 39.611 30.870 1.00 0.00 N +ATOM 526 H GLH 33 29.333 39.496 30.165 1.00 0.00 H +ATOM 527 CA GLH 33 30.047 38.725 32.041 1.00 0.00 C +ATOM 528 HA GLH 33 29.911 39.335 32.935 1.00 0.00 H +ATOM 529 CB GLH 33 28.891 37.715 31.963 1.00 0.00 C +ATOM 530 HB2 GLH 33 28.942 37.165 31.022 1.00 0.00 H +ATOM 531 HB3 GLH 33 29.025 37.002 32.778 1.00 0.00 H +ATOM 532 CG GLH 33 27.500 38.357 32.108 1.00 0.00 C +ATOM 533 HG2 GLH 33 27.504 39.042 32.957 1.00 0.00 H +ATOM 534 HG3 GLH 33 27.261 38.931 31.214 1.00 0.00 H +ATOM 535 CD GLH 33 26.406 37.318 32.358 1.00 0.00 C +ATOM 536 OE1 GLH 33 26.558 36.242 32.918 1.00 0.00 O +ATOM 537 OE2 GLH 33 25.174 37.633 31.910 1.00 0.00 O +ATOM 538 HE2 GLH 33 24.616 36.913 32.215 1.00 0.00 H +ATOM 539 C GLH 33 31.373 37.970 32.231 1.00 0.00 C +ATOM 540 O GLH 33 31.760 37.707 33.362 1.00 0.00 O +ATOM 541 N ALA 34 32.084 37.609 31.158 1.00 0.00 N +ATOM 542 H ALA 34 31.708 37.793 30.237 1.00 0.00 H +ATOM 543 CA ALA 34 33.402 36.984 31.269 1.00 0.00 C +ATOM 544 HA ALA 34 33.329 36.147 31.965 1.00 0.00 H +ATOM 545 CB ALA 34 33.799 36.424 29.900 1.00 0.00 C +ATOM 546 HB1 ALA 34 34.021 37.239 29.214 1.00 0.00 H +ATOM 547 HB2 ALA 34 34.684 35.801 30.018 1.00 0.00 H +ATOM 548 HB3 ALA 34 32.997 35.812 29.491 1.00 0.00 H +ATOM 549 C ALA 34 34.464 37.950 31.840 1.00 0.00 C +ATOM 550 O ALA 34 35.200 37.571 32.750 1.00 0.00 O +ATOM 551 N ASN 35 34.500 39.207 31.376 1.00 0.00 N +ATOM 552 H ASN 35 33.842 39.482 30.658 1.00 0.00 H +ATOM 553 CA ASN 35 35.384 40.242 31.928 1.00 0.00 C +ATOM 554 HA ASN 35 36.374 39.806 32.012 1.00 0.00 H +ATOM 555 CB ASN 35 35.506 41.432 30.957 1.00 0.00 C +ATOM 556 HB2 ASN 35 34.515 41.759 30.649 1.00 0.00 H +ATOM 557 HB3 ASN 35 35.980 42.260 31.484 1.00 0.00 H +ATOM 558 CG ASN 35 36.370 41.137 29.738 1.00 0.00 C +ATOM 559 OD1 ASN 35 37.587 41.194 29.762 1.00 0.00 O +ATOM 560 ND2 ASN 35 35.776 40.836 28.613 1.00 0.00 N +ATOM 561 HD21 ASN 35 36.375 40.628 27.819 1.00 0.00 H +ATOM 562 HD22 ASN 35 34.782 40.669 28.608 1.00 0.00 H +ATOM 563 C ASN 35 34.989 40.686 33.358 1.00 0.00 C +ATOM 564 O ASN 35 35.858 41.125 34.108 1.00 0.00 O +ATOM 565 N ASP 36 33.730 40.502 33.781 1.00 0.00 N +ATOM 566 H ASP 36 33.014 40.300 33.091 1.00 0.00 H +ATOM 567 CA ASP 36 33.323 40.680 35.189 1.00 0.00 C +ATOM 568 HA ASP 36 33.626 41.677 35.506 1.00 0.00 H +ATOM 569 CB ASP 36 31.790 40.605 35.367 1.00 0.00 C +ATOM 570 HB2 ASP 36 31.453 39.608 35.113 1.00 0.00 H +ATOM 571 HB3 ASP 36 31.583 40.721 36.432 1.00 0.00 H +ATOM 572 CG ASP 36 30.936 41.606 34.560 1.00 0.00 C +ATOM 573 OD1 ASP 36 31.454 42.673 34.150 1.00 0.00 O +ATOM 574 OD2 ASP 36 29.729 41.321 34.369 1.00 0.00 O +ATOM 575 C ASP 36 34.022 39.677 36.139 1.00 0.00 C +ATOM 576 O ASP 36 34.366 40.036 37.265 1.00 0.00 O +ATOM 577 N TYR 37 34.279 38.436 35.693 1.00 0.00 N +ATOM 578 H TYR 37 33.929 38.187 34.778 1.00 0.00 H +ATOM 579 CA TYR 37 35.150 37.478 36.405 1.00 0.00 C +ATOM 580 HA TYR 37 35.031 37.637 37.477 1.00 0.00 H +ATOM 581 CB TYR 37 34.728 36.029 36.102 1.00 0.00 C +ATOM 582 HB2 TYR 37 34.894 35.833 35.042 1.00 0.00 H +ATOM 583 HB3 TYR 37 35.387 35.360 36.657 1.00 0.00 H +ATOM 584 CG TYR 37 33.295 35.659 36.456 1.00 0.00 C +ATOM 585 CD1 TYR 37 32.330 35.550 35.437 1.00 0.00 C +ATOM 586 HD1 TYR 37 32.623 35.735 34.416 1.00 0.00 H +ATOM 587 CE1 TYR 37 30.995 35.227 35.746 1.00 0.00 C +ATOM 588 HE1 TYR 37 30.257 35.181 34.963 1.00 0.00 H +ATOM 589 CZ TYR 37 30.630 34.968 37.084 1.00 0.00 C +ATOM 590 OH TYR 37 29.350 34.633 37.395 1.00 0.00 O +ATOM 591 HH TYR 37 28.718 35.000 36.775 1.00 0.00 H +ATOM 592 CE2 TYR 37 31.601 35.043 38.103 1.00 0.00 C +ATOM 593 HE2 TYR 37 31.310 34.844 39.122 1.00 0.00 H +ATOM 594 CD2 TYR 37 32.930 35.393 37.791 1.00 0.00 C +ATOM 595 HD2 TYR 37 33.670 35.453 38.575 1.00 0.00 H +ATOM 596 C TYR 37 36.653 37.661 36.084 1.00 0.00 C +ATOM 597 O TYR 37 37.509 37.230 36.866 1.00 0.00 O +ATOM 598 N GLY 38 36.981 38.278 34.941 1.00 0.00 N +ATOM 599 H GLY 38 36.217 38.563 34.340 1.00 0.00 H +ATOM 600 CA GLY 38 38.332 38.695 34.549 1.00 0.00 C +ATOM 601 HA2 GLY 38 38.510 39.692 34.952 1.00 0.00 H +ATOM 602 HA3 GLY 38 39.067 38.019 34.987 1.00 0.00 H +ATOM 603 C GLY 38 38.572 38.753 33.033 1.00 0.00 C +ATOM 604 O GLY 38 38.680 39.832 32.466 1.00 0.00 O +ATOM 605 N VAL 39 38.769 37.587 32.407 1.00 0.00 N +ATOM 606 H VAL 39 38.528 36.772 32.947 1.00 0.00 H +ATOM 607 CA VAL 39 39.120 37.334 30.982 1.00 0.00 C +ATOM 608 HA VAL 39 39.589 36.353 31.045 1.00 0.00 H +ATOM 609 CB VAL 39 40.278 38.199 30.408 1.00 0.00 C +ATOM 610 HB VAL 39 39.887 39.155 30.060 1.00 0.00 H +ATOM 611 CG1 VAL 39 41.410 38.442 31.429 1.00 0.00 C +ATOM 612 HG11 VAL 39 41.633 37.519 31.969 1.00 0.00 H +ATOM 613 HG12 VAL 39 42.308 38.801 30.921 1.00 0.00 H +ATOM 614 HG13 VAL 39 41.103 39.214 32.136 1.00 0.00 H +ATOM 615 CG2 VAL 39 40.949 37.487 29.219 1.00 0.00 C +ATOM 616 HG21 VAL 39 41.725 38.123 28.799 1.00 0.00 H +ATOM 617 HG22 VAL 39 41.401 36.553 29.543 1.00 0.00 H +ATOM 618 HG23 VAL 39 40.242 37.276 28.424 1.00 0.00 H +ATOM 619 C VAL 39 37.923 37.009 30.055 1.00 0.00 C +ATOM 620 O VAL 39 37.209 36.068 30.396 1.00 0.00 O +ATOM 621 N ASP 40 37.721 37.611 28.865 1.00 0.00 N +ATOM 622 H ASP 40 38.260 38.435 28.629 1.00 0.00 H +ATOM 623 CA ASP 40 36.920 36.948 27.802 1.00 0.00 C +ATOM 624 HA ASP 40 36.182 36.330 28.311 1.00 0.00 H +ATOM 625 CB ASP 40 36.053 37.904 26.947 1.00 0.00 C +ATOM 626 HB2 ASP 40 35.316 37.280 26.435 1.00 0.00 H +ATOM 627 HB3 ASP 40 35.494 38.546 27.614 1.00 0.00 H +ATOM 628 CG ASP 40 36.769 38.774 25.899 1.00 0.00 C +ATOM 629 OD1 ASP 40 37.171 39.908 26.230 1.00 0.00 O +ATOM 630 OD2 ASP 40 36.863 38.346 24.717 1.00 0.00 O +ATOM 631 C ASP 40 37.719 35.999 26.893 1.00 0.00 C +ATOM 632 O ASP 40 38.616 36.413 26.153 1.00 0.00 O +ATOM 633 N GLY 41 37.291 34.734 26.866 1.00 0.00 N +ATOM 634 H GLY 41 36.626 34.447 27.571 1.00 0.00 H +ATOM 635 CA GLY 41 37.610 33.768 25.816 1.00 0.00 C +ATOM 636 HA2 GLY 41 38.623 33.946 25.456 1.00 0.00 H +ATOM 637 HA3 GLY 41 37.580 32.771 26.242 1.00 0.00 H +ATOM 638 C GLY 41 36.655 33.826 24.612 1.00 0.00 C +ATOM 639 O GLY 41 35.774 34.683 24.510 1.00 0.00 O +ATOM 640 N GLU 42 36.792 32.855 23.705 1.00 0.00 N +ATOM 641 H GLU 42 37.487 32.129 23.865 1.00 0.00 H +ATOM 642 CA GLU 42 36.009 32.689 22.461 1.00 0.00 C +ATOM 643 HA GLU 42 35.334 33.540 22.334 1.00 0.00 H +ATOM 644 CB GLU 42 36.923 32.654 21.234 1.00 0.00 C +ATOM 645 HB2 GLU 42 37.390 31.662 21.199 1.00 0.00 H +ATOM 646 HB3 GLU 42 36.257 32.698 20.374 1.00 0.00 H +ATOM 647 CG GLU 42 37.926 33.780 21.144 1.00 0.00 C +ATOM 648 HG2 GLU 42 38.767 33.538 21.797 1.00 0.00 H +ATOM 649 HG3 GLU 42 38.362 33.796 20.165 1.00 0.00 H +ATOM 650 CD GLU 42 37.448 35.144 21.511 1.00 0.00 C +ATOM 651 OE1 GLU 42 36.392 35.531 21.013 1.00 0.00 O +ATOM 652 OE2 GLU 42 38.019 35.817 22.405 1.00 0.00 O +ATOM 653 C GLU 42 35.098 31.428 22.559 1.00 0.00 C +ATOM 654 O GLU 42 35.470 30.440 23.214 1.00 0.00 O +ATOM 655 N ILE 43 33.966 31.444 21.825 1.00 0.00 N +ATOM 656 H ILE 43 33.809 32.250 21.208 1.00 0.00 H +ATOM 657 CA ILE 43 32.887 30.421 21.861 1.00 0.00 C +ATOM 658 HA ILE 43 33.331 29.490 22.218 1.00 0.00 H +ATOM 659 CB ILE 43 31.749 30.833 22.843 1.00 0.00 C +ATOM 660 HB ILE 43 30.876 30.251 22.570 1.00 0.00 H +ATOM 661 CG2 ILE 43 32.120 30.445 24.279 1.00 0.00 C +ATOM 662 HG21 ILE 43 32.995 30.995 24.605 1.00 0.00 H +ATOM 663 HG22 ILE 43 31.282 30.667 24.932 1.00 0.00 H +ATOM 664 HG23 ILE 43 32.325 29.379 24.324 1.00 0.00 H +ATOM 665 CG1 ILE 43 31.340 32.325 22.832 1.00 0.00 C +ATOM 666 HG12 ILE 43 30.451 32.421 23.459 1.00 0.00 H +ATOM 667 HG13 ILE 43 32.122 32.931 23.275 1.00 0.00 H +ATOM 668 CD1 ILE 43 30.995 32.906 21.457 1.00 0.00 C +ATOM 669 HD11 ILE 43 30.366 32.224 20.891 1.00 0.00 H +ATOM 670 HD12 ILE 43 30.466 33.847 21.588 1.00 0.00 H +ATOM 671 HD13 ILE 43 31.907 33.103 20.890 1.00 0.00 H +ATOM 672 C ILE 43 32.351 30.121 20.452 1.00 0.00 C +ATOM 673 O ILE 43 32.559 30.895 19.514 1.00 0.00 O +ATOM 674 N THR 44 31.619 29.018 20.340 1.00 0.00 N +ATOM 675 H THR 44 31.486 28.447 21.169 1.00 0.00 H +ATOM 676 CA THR 44 30.903 28.600 19.128 1.00 0.00 C +ATOM 677 HA THR 44 31.230 29.213 18.290 1.00 0.00 H +ATOM 678 CB THR 44 31.269 27.144 18.781 1.00 0.00 C +ATOM 679 HB THR 44 31.001 26.477 19.600 1.00 0.00 H +ATOM 680 CG2 THR 44 30.624 26.613 17.495 1.00 0.00 C +ATOM 681 HG21 THR 44 30.802 27.305 16.665 1.00 0.00 H +ATOM 682 HG22 THR 44 31.041 25.628 17.235 1.00 0.00 H +ATOM 683 HG23 THR 44 29.544 26.485 17.639 1.00 0.00 H +ATOM 684 OG1 THR 44 32.661 27.056 18.558 1.00 0.00 O +ATOM 685 HG1 THR 44 32.846 26.251 18.066 1.00 0.00 H +ATOM 686 C THR 44 29.392 28.779 19.281 1.00 0.00 C +ATOM 687 O THR 44 28.876 28.725 20.395 1.00 0.00 O +ATOM 688 N GLN 45 28.679 29.026 18.178 1.00 0.00 N +ATOM 689 H GLN 45 29.149 29.020 17.288 1.00 0.00 H +ATOM 690 CA GLN 45 27.222 29.231 18.139 1.00 0.00 C +ATOM 691 HA GLN 45 26.819 29.205 19.153 1.00 0.00 H +ATOM 692 CB GLN 45 26.897 30.607 17.518 1.00 0.00 C +ATOM 693 HB2 GLN 45 27.284 30.625 16.500 1.00 0.00 H +ATOM 694 HB3 GLN 45 25.809 30.696 17.459 1.00 0.00 H +ATOM 695 CG GLN 45 27.454 31.826 18.281 1.00 0.00 C +ATOM 696 HG2 GLN 45 27.104 31.768 19.310 1.00 0.00 H +ATOM 697 HG3 GLN 45 28.542 31.780 18.287 1.00 0.00 H +ATOM 698 CD GLN 45 27.016 33.162 17.659 1.00 0.00 C +ATOM 699 OE1 GLN 45 26.064 33.244 16.898 1.00 0.00 O +ATOM 700 NE2 GLN 45 27.679 34.270 17.903 1.00 0.00 N +ATOM 701 HE21 GLN 45 27.355 35.101 17.453 1.00 0.00 H +ATOM 702 HE22 GLN 45 28.552 34.317 18.441 1.00 0.00 H +ATOM 703 C GLN 45 26.480 28.159 17.312 1.00 0.00 C +ATOM 704 O GLN 45 27.046 27.601 16.370 1.00 0.00 O +ATOM 705 N ASP 46 25.191 27.966 17.604 1.00 0.00 N +ATOM 706 H ASP 46 24.838 28.365 18.468 1.00 0.00 H +ATOM 707 CA ASP 46 24.203 27.294 16.751 1.00 0.00 C +ATOM 708 HA ASP 46 24.528 27.356 15.711 1.00 0.00 H +ATOM 709 CB ASP 46 24.079 25.812 17.147 1.00 0.00 C +ATOM 710 HB2 ASP 46 24.979 25.272 16.851 1.00 0.00 H +ATOM 711 HB3 ASP 46 23.981 25.747 18.230 1.00 0.00 H +ATOM 712 CG ASP 46 22.852 25.158 16.507 1.00 0.00 C +ATOM 713 OD1 ASP 46 22.104 24.474 17.241 1.00 0.00 O +ATOM 714 OD2 ASP 46 22.584 25.407 15.313 1.00 0.00 O +ATOM 715 C ASP 46 22.831 27.991 16.868 1.00 0.00 C +ATOM 716 O ASP 46 22.288 28.138 17.964 1.00 0.00 O +ATOM 717 N ASP 47 22.230 28.373 15.739 1.00 0.00 N +ATOM 718 H ASP 47 22.690 28.167 14.865 1.00 0.00 H +ATOM 719 CA ASP 47 20.867 28.919 15.690 1.00 0.00 C +ATOM 720 HA ASP 47 20.729 29.593 16.537 1.00 0.00 H +ATOM 721 CB ASP 47 20.693 29.766 14.416 1.00 0.00 C +ATOM 722 HB2 ASP 47 21.415 30.585 14.422 1.00 0.00 H +ATOM 723 HB3 ASP 47 20.882 29.148 13.536 1.00 0.00 H +ATOM 724 CG ASP 47 19.278 30.347 14.340 1.00 0.00 C +ATOM 725 OD1 ASP 47 18.430 29.775 13.625 1.00 0.00 O +ATOM 726 OD2 ASP 47 18.941 31.266 15.120 1.00 0.00 O +ATOM 727 C ASP 47 19.773 27.830 15.792 1.00 0.00 C +ATOM 728 O ASP 47 18.707 28.086 16.356 1.00 0.00 O +ATOM 729 N ALA 48 20.006 26.600 15.319 1.00 0.00 N +ATOM 730 H ALA 48 20.951 26.350 15.024 1.00 0.00 H +ATOM 731 CA ALA 48 18.970 25.560 15.236 1.00 0.00 C +ATOM 732 HA ALA 48 18.105 25.984 14.723 1.00 0.00 H +ATOM 733 CB ALA 48 19.510 24.405 14.386 1.00 0.00 C +ATOM 734 HB1 ALA 48 20.362 23.940 14.885 1.00 0.00 H +ATOM 735 HB2 ALA 48 18.729 23.659 14.239 1.00 0.00 H +ATOM 736 HB3 ALA 48 19.832 24.783 13.415 1.00 0.00 H +ATOM 737 C ALA 48 18.489 25.071 16.618 1.00 0.00 C +ATOM 738 O ALA 48 17.304 24.774 16.796 1.00 0.00 O +ATOM 739 N THR 49 19.392 25.037 17.602 1.00 0.00 N +ATOM 740 H THR 49 20.372 25.112 17.325 1.00 0.00 H +ATOM 741 CA THR 49 19.113 24.869 19.043 1.00 0.00 C +ATOM 742 HA THR 49 18.084 24.531 19.159 1.00 0.00 H +ATOM 743 CB THR 49 20.020 23.800 19.672 1.00 0.00 C +ATOM 744 HB THR 49 19.698 23.651 20.702 1.00 0.00 H +ATOM 745 CG2 THR 49 19.958 22.443 18.975 1.00 0.00 C +ATOM 746 HG21 THR 49 20.321 22.522 17.950 1.00 0.00 H +ATOM 747 HG22 THR 49 20.590 21.745 19.521 1.00 0.00 H +ATOM 748 HG23 THR 49 18.931 22.081 18.973 1.00 0.00 H +ATOM 749 OG1 THR 49 21.361 24.217 19.698 1.00 0.00 O +ATOM 750 HG1 THR 49 21.679 24.247 18.761 1.00 0.00 H +ATOM 751 C THR 49 19.231 26.177 19.841 1.00 0.00 C +ATOM 752 O THR 49 19.101 26.167 21.068 1.00 0.00 O +ATOM 753 N LYS 50 19.468 27.312 19.167 1.00 0.00 N +ATOM 754 H LYS 50 19.560 27.226 18.161 1.00 0.00 H +ATOM 755 CA LYS 50 19.589 28.671 19.731 1.00 0.00 C +ATOM 756 HA LYS 50 20.008 29.273 18.928 1.00 0.00 H +ATOM 757 CB LYS 50 18.185 29.226 20.094 1.00 0.00 C +ATOM 758 HB2 LYS 50 17.768 28.587 20.874 1.00 0.00 H +ATOM 759 HB3 LYS 50 18.294 30.221 20.527 1.00 0.00 H +ATOM 760 CG LYS 50 17.144 29.315 18.956 1.00 0.00 C +ATOM 761 HG2 LYS 50 17.135 28.389 18.385 1.00 0.00 H +ATOM 762 HG3 LYS 50 16.161 29.418 19.417 1.00 0.00 H +ATOM 763 CD LYS 50 17.338 30.517 18.014 1.00 0.00 C +ATOM 764 HD2 LYS 50 17.289 31.432 18.604 1.00 0.00 H +ATOM 765 HD3 LYS 50 18.319 30.466 17.544 1.00 0.00 H +ATOM 766 CE LYS 50 16.255 30.586 16.925 1.00 0.00 C +ATOM 767 HE2 LYS 50 15.311 30.225 17.334 1.00 0.00 H +ATOM 768 HE3 LYS 50 16.117 31.628 16.628 1.00 0.00 H +ATOM 769 NZ LYS 50 16.628 29.801 15.728 1.00 0.00 N +ATOM 770 HZ1 LYS 50 17.134 28.955 15.975 1.00 0.00 H +ATOM 771 HZ2 LYS 50 15.839 29.559 15.145 1.00 0.00 H +ATOM 772 HZ3 LYS 50 17.313 30.309 15.154 1.00 0.00 H +ATOM 773 C LYS 50 20.608 28.778 20.892 1.00 0.00 C +ATOM 774 O LYS 50 20.304 29.382 21.927 1.00 0.00 O +ATOM 775 N THR 51 21.791 28.170 20.745 1.00 0.00 N +ATOM 776 H THR 51 22.017 27.827 19.813 1.00 0.00 H +ATOM 777 CA THR 51 22.737 27.843 21.835 1.00 0.00 C +ATOM 778 HA THR 51 22.433 28.389 22.721 1.00 0.00 H +ATOM 779 CB THR 51 22.629 26.341 22.176 1.00 0.00 C +ATOM 780 HB THR 51 22.792 25.755 21.272 1.00 0.00 H +ATOM 781 CG2 THR 51 23.614 25.869 23.247 1.00 0.00 C +ATOM 782 HG21 THR 51 23.549 26.508 24.126 1.00 0.00 H +ATOM 783 HG22 THR 51 23.377 24.843 23.525 1.00 0.00 H +ATOM 784 HG23 THR 51 24.627 25.883 22.852 1.00 0.00 H +ATOM 785 OG1 THR 51 21.358 26.039 22.712 1.00 0.00 O +ATOM 786 HG1 THR 51 20.709 26.084 21.991 1.00 0.00 H +ATOM 787 C THR 51 24.207 28.217 21.545 1.00 0.00 C +ATOM 788 O THR 51 24.716 27.973 20.456 1.00 0.00 O +ATOM 789 N PHE 52 24.918 28.749 22.550 1.00 0.00 N +ATOM 790 H PHE 52 24.402 29.020 23.376 1.00 0.00 H +ATOM 791 CA PHE 52 26.389 28.875 22.610 1.00 0.00 C +ATOM 792 HA PHE 52 26.783 28.971 21.598 1.00 0.00 H +ATOM 793 CB PHE 52 26.774 30.130 23.412 1.00 0.00 C +ATOM 794 HB2 PHE 52 26.267 30.101 24.374 1.00 0.00 H +ATOM 795 HB3 PHE 52 27.845 30.085 23.622 1.00 0.00 H +ATOM 796 CG PHE 52 26.494 31.471 22.766 1.00 0.00 C +ATOM 797 CD1 PHE 52 25.266 32.130 22.966 1.00 0.00 C +ATOM 798 HD1 PHE 52 24.487 31.661 23.545 1.00 0.00 H +ATOM 799 CE1 PHE 52 25.047 33.404 22.412 1.00 0.00 C +ATOM 800 HE1 PHE 52 24.099 33.900 22.556 1.00 0.00 H +ATOM 801 CZ PHE 52 26.060 34.026 21.662 1.00 0.00 C +ATOM 802 HZ PHE 52 25.893 34.995 21.218 1.00 0.00 H +ATOM 803 CE2 PHE 52 27.293 33.379 21.473 1.00 0.00 C +ATOM 804 HE2 PHE 52 28.070 33.856 20.889 1.00 0.00 H +ATOM 805 CD2 PHE 52 27.503 32.100 22.017 1.00 0.00 C +ATOM 806 HD2 PHE 52 28.441 31.592 21.854 1.00 0.00 H +ATOM 807 C PHE 52 27.066 27.661 23.288 1.00 0.00 C +ATOM 808 O PHE 52 26.544 27.156 24.288 1.00 0.00 O +ATOM 809 N THR 53 28.266 27.263 22.839 1.00 0.00 N +ATOM 810 H THR 53 28.641 27.723 22.012 1.00 0.00 H +ATOM 811 CA THR 53 29.074 26.151 23.403 1.00 0.00 C +ATOM 812 HA THR 53 28.798 26.016 24.449 1.00 0.00 H +ATOM 813 CB THR 53 28.800 24.819 22.672 1.00 0.00 C +ATOM 814 HB THR 53 29.387 24.035 23.153 1.00 0.00 H +ATOM 815 CG2 THR 53 27.341 24.373 22.695 1.00 0.00 C +ATOM 816 HG21 THR 53 26.734 25.036 22.079 1.00 0.00 H +ATOM 817 HG22 THR 53 27.264 23.356 22.311 1.00 0.00 H +ATOM 818 HG23 THR 53 26.972 24.389 23.719 1.00 0.00 H +ATOM 819 OG1 THR 53 29.192 24.898 21.323 1.00 0.00 O +ATOM 820 HG1 THR 53 28.756 24.184 20.851 1.00 0.00 H +ATOM 821 C THR 53 30.594 26.406 23.377 1.00 0.00 C +ATOM 822 O THR 53 31.083 27.326 22.718 1.00 0.00 O +ATOM 823 N ALA 54 31.348 25.564 24.100 1.00 0.00 N +ATOM 824 H ALA 54 30.876 24.846 24.626 1.00 0.00 H +ATOM 825 CA ALA 54 32.812 25.456 24.054 1.00 0.00 C +ATOM 826 HA ALA 54 33.210 26.268 23.442 1.00 0.00 H +ATOM 827 CB ALA 54 33.366 25.629 25.475 1.00 0.00 C +ATOM 828 HB1 ALA 54 33.015 24.817 26.113 1.00 0.00 H +ATOM 829 HB2 ALA 54 34.457 25.616 25.456 1.00 0.00 H +ATOM 830 HB3 ALA 54 33.038 26.583 25.891 1.00 0.00 H +ATOM 831 C ALA 54 33.278 24.123 23.415 1.00 0.00 C +ATOM 832 O ALA 54 32.505 23.167 23.298 1.00 0.00 O +ATOM 833 N GLH 55 34.548 24.067 22.999 1.00 0.00 N +ATOM 834 H GLH 55 35.146 24.849 23.215 1.00 0.00 H +ATOM 835 CA GLH 55 35.168 22.922 22.308 1.00 0.00 C +ATOM 836 HA GLH 55 34.398 22.426 21.716 1.00 0.00 H +ATOM 837 CB GLH 55 36.234 23.451 21.327 1.00 0.00 C +ATOM 838 HB2 GLH 55 36.972 24.031 21.884 1.00 0.00 H +ATOM 839 HB3 GLH 55 36.743 22.608 20.858 1.00 0.00 H +ATOM 840 CG GLH 55 35.617 24.327 20.216 1.00 0.00 C +ATOM 841 HG2 GLH 55 34.958 23.714 19.601 1.00 0.00 H +ATOM 842 HG3 GLH 55 35.020 25.129 20.650 1.00 0.00 H +ATOM 843 CD GLH 55 36.655 24.987 19.312 1.00 0.00 C +ATOM 844 OE1 GLH 55 37.842 25.121 19.573 1.00 0.00 O +ATOM 845 OE2 GLH 55 36.155 25.451 18.149 1.00 0.00 O +ATOM 846 HE2 GLH 55 36.883 25.858 17.675 1.00 0.00 H +ATOM 847 C GLH 55 35.736 21.856 23.279 1.00 0.00 C +ATOM 848 O GLH 55 36.043 22.164 24.428 1.00 0.00 O +ATOM 849 N GLU 56 35.854 20.603 22.810 1.00 0.00 N +ATOM 850 H GLU 56 35.627 20.451 21.842 1.00 0.00 H +ATOM 851 CA GLU 56 36.225 19.391 23.580 1.00 0.00 C +ATOM 852 HA GLU 56 35.760 19.455 24.564 1.00 0.00 H +ATOM 853 CB GLU 56 35.617 18.165 22.855 1.00 0.00 C +ATOM 854 HB2 GLU 56 34.541 18.196 23.027 1.00 0.00 H +ATOM 855 HB3 GLU 56 35.768 18.297 21.782 1.00 0.00 H +ATOM 856 CG GLU 56 36.111 16.739 23.193 1.00 0.00 C +ATOM 857 HG2 GLU 56 35.454 16.031 22.680 1.00 0.00 H +ATOM 858 HG3 GLU 56 37.100 16.595 22.754 1.00 0.00 H +ATOM 859 CD GLU 56 36.165 16.375 24.688 1.00 0.00 C +ATOM 860 OE1 GLU 56 37.290 16.354 25.251 1.00 0.00 O +ATOM 861 OE2 GLU 56 35.109 16.022 25.266 1.00 0.00 O +ATOM 862 C GLU 56 37.723 19.244 23.888 1.00 0.00 C +ATOM 863 O GLU 56 38.090 19.361 25.078 1.00 0.00 O +ATOM 864 OXT GLU 56 38.506 18.730 23.060 1.00 0.00 O +HETATM 865 ZN ZN1 57 26.762 32.444 29.336 1.00 0.00 Zn +HETATM 866 N AN1 58 28.364 33.308 30.222 1.00 0.00 N +HETATM 867 C AN1 58 30.678 34.028 31.184 1.00 0.00 C +HETATM 868 C1 AN1 58 29.379 33.629 30.674 1.00 0.00 C +HETATM 869 H AN1 58 30.582 34.423 32.200 1.00 0.00 H +HETATM 870 H1 AN1 58 31.113 34.795 30.535 1.00 0.00 H +HETATM 871 H2 AN1 58 31.336 33.149 31.202 1.00 0.00 H +HETATM 872 N1 AZI 59 30.830 28.620 29.341 1.00 0.00 N +HETATM 873 N2 AZI 59 30.309 29.481 30.054 1.00 0.00 N +HETATM 874 N3 AZI 59 29.759 30.371 30.755 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 73 72 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 865 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 121 122 126 +CONECT 121 120 +CONECT 122 125 120 123 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 127 129 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 145 +CONECT 135 134 +CONECT 136 137 134 139 138 +CONECT 137 136 +CONECT 138 136 +CONECT 139 142 136 140 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 144 139 +CONECT 143 142 +CONECT 144 142 +CONECT 145 134 147 146 +CONECT 146 145 +CONECT 147 148 149 145 +CONECT 148 147 +CONECT 149 147 150 152 151 +CONECT 150 149 +CONECT 151 149 +CONECT 152 153 149 154 +CONECT 153 152 +CONECT 154 152 156 155 +CONECT 155 154 +CONECT 156 158 157 154 174 +CONECT 157 156 +CONECT 158 161 159 160 156 +CONECT 159 158 +CONECT 160 158 +CONECT 161 164 163 162 158 +CONECT 162 161 +CONECT 163 161 +CONECT 164 167 165 166 161 +CONECT 165 164 +CONECT 166 164 +CONECT 167 170 169 168 164 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 170 +CONECT 174 156 175 176 +CONECT 175 174 +CONECT 176 174 177 178 +CONECT 177 176 +CONECT 178 176 179 198 180 +CONECT 179 178 +CONECT 180 178 183 181 182 +CONECT 181 180 +CONECT 182 180 +CONECT 183 185 184 180 186 +CONECT 184 183 +CONECT 185 183 +CONECT 186 183 189 187 188 +CONECT 187 186 +CONECT 188 186 +CONECT 189 190 186 191 +CONECT 190 189 +CONECT 191 189 195 192 +CONECT 192 191 193 194 +CONECT 193 192 +CONECT 194 192 +CONECT 195 196 191 197 +CONECT 196 195 +CONECT 197 195 +CONECT 198 178 200 199 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 219 200 204 203 +CONECT 203 202 +CONECT 204 207 202 205 206 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 217 204 +CONECT 208 209 210 207 +CONECT 209 208 +CONECT 210 211 208 212 +CONECT 211 210 +CONECT 212 210 213 215 +CONECT 213 214 212 +CONECT 214 213 +CONECT 215 212 216 217 +CONECT 216 215 +CONECT 217 207 215 218 +CONECT 218 217 +CONECT 219 220 221 202 +CONECT 220 219 +CONECT 221 223 219 222 +CONECT 222 221 +CONECT 223 224 241 225 221 +CONECT 224 223 +CONECT 225 228 223 226 227 +CONECT 226 225 +CONECT 227 225 +CONECT 228 230 229 231 225 +CONECT 229 228 +CONECT 230 228 +CONECT 231 232 228 233 234 +CONECT 232 231 +CONECT 233 231 +CONECT 234 236 231 237 235 +CONECT 235 234 +CONECT 236 234 +CONECT 237 240 234 239 238 +CONECT 238 237 +CONECT 239 237 +CONECT 240 237 +CONECT 241 242 223 243 +CONECT 242 241 +CONECT 243 241 245 244 +CONECT 244 243 +CONECT 245 248 243 246 247 +CONECT 246 245 +CONECT 247 245 +CONECT 248 249 250 245 +CONECT 249 248 +CONECT 250 252 248 251 +CONECT 251 250 +CONECT 252 254 253 264 250 +CONECT 253 252 +CONECT 254 260 255 256 252 +CONECT 255 254 +CONECT 256 258 254 257 259 +CONECT 257 256 +CONECT 258 256 +CONECT 259 256 +CONECT 260 262 261 263 254 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 252 265 +CONECT 265 264 +CONECT 266 276 267 264 +CONECT 267 268 266 277 270 +CONECT 268 269 283 267 +CONECT 269 268 +CONECT 270 267 271 278 279 +CONECT 271 272 273 270 +CONECT 272 275 281 271 +CONECT 273 274 271 280 +CONECT 274 275 282 273 +CONECT 275 865 272 274 +CONECT 276 266 +CONECT 277 267 +CONECT 278 270 +CONECT 279 270 +CONECT 280 273 +CONECT 281 272 +CONECT 282 274 +CONECT 283 285 268 284 +CONECT 284 283 +CONECT 285 286 287 295 283 +CONECT 286 285 +CONECT 287 288 289 285 293 +CONECT 288 287 +CONECT 289 292 291 287 290 +CONECT 290 289 +CONECT 291 289 +CONECT 292 289 +CONECT 293 287 294 +CONECT 294 293 +CONECT 295 297 285 296 +CONECT 296 295 +CONECT 297 307 298 295 +CONECT 298 299 301 297 308 +CONECT 299 300 314 298 +CONECT 300 299 +CONECT 301 309 310 298 302 +CONECT 302 301 303 304 +CONECT 303 312 302 306 +CONECT 304 302 311 305 +CONECT 305 304 306 313 +CONECT 306 303 865 305 +CONECT 307 297 +CONECT 308 298 +CONECT 309 301 +CONECT 310 301 +CONECT 311 304 +CONECT 312 303 +CONECT 313 305 +CONECT 314 316 299 315 +CONECT 315 314 +CONECT 316 327 317 314 318 +CONECT 317 316 +CONECT 318 316 321 320 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 323 324 318 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 325 321 326 +CONECT 325 324 +CONECT 326 324 +CONECT 327 329 328 316 +CONECT 328 327 +CONECT 329 331 330 327 +CONECT 330 329 +CONECT 331 337 333 332 329 +CONECT 332 331 +CONECT 333 335 334 331 336 +CONECT 334 333 +CONECT 335 333 +CONECT 336 333 +CONECT 337 339 338 331 +CONECT 338 337 +CONECT 339 341 340 337 +CONECT 340 339 +CONECT 341 353 343 342 339 +CONECT 342 341 +CONECT 343 344 349 341 345 +CONECT 344 343 +CONECT 345 343 347 348 346 +CONECT 346 345 +CONECT 347 345 +CONECT 348 345 +CONECT 349 350 351 343 352 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 341 +CONECT 354 353 +CONECT 355 357 353 356 +CONECT 356 355 +CONECT 357 359 358 365 355 +CONECT 358 357 +CONECT 359 362 360 361 357 +CONECT 360 359 +CONECT 361 359 +CONECT 362 364 363 359 +CONECT 363 362 +CONECT 364 362 +CONECT 365 357 367 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 385 370 +CONECT 370 369 +CONECT 371 372 374 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 375 371 383 +CONECT 375 376 377 374 +CONECT 376 375 +CONECT 377 378 375 379 +CONECT 378 377 +CONECT 379 377 380 381 +CONECT 380 379 +CONECT 381 379 383 382 +CONECT 382 381 +CONECT 383 374 381 384 +CONECT 384 383 +CONECT 385 387 369 386 +CONECT 386 385 +CONECT 387 388 389 385 +CONECT 388 387 +CONECT 389 391 387 390 395 +CONECT 390 389 +CONECT 391 394 392 393 389 +CONECT 392 391 +CONECT 393 391 +CONECT 394 391 +CONECT 395 389 396 397 +CONECT 396 395 +CONECT 397 395 398 399 +CONECT 398 397 +CONECT 399 397 400 401 410 +CONECT 400 399 +CONECT 401 404 402 399 403 +CONECT 402 401 +CONECT 403 401 +CONECT 404 405 406 407 401 +CONECT 405 404 +CONECT 406 404 +CONECT 407 404 409 408 +CONECT 408 407 +CONECT 409 407 +CONECT 410 399 412 411 +CONECT 411 410 +CONECT 412 413 410 414 +CONECT 413 412 +CONECT 414 412 416 420 415 +CONECT 415 414 +CONECT 416 417 419 414 418 +CONECT 417 416 +CONECT 418 416 +CONECT 419 416 +CONECT 420 422 414 421 +CONECT 421 420 +CONECT 422 423 424 420 +CONECT 423 422 +CONECT 424 426 422 425 435 +CONECT 425 424 +CONECT 426 428 427 429 424 +CONECT 427 426 +CONECT 428 426 +CONECT 429 432 430 426 431 +CONECT 430 429 +CONECT 431 429 +CONECT 432 433 434 429 +CONECT 433 432 +CONECT 434 432 +CONECT 435 424 437 436 +CONECT 436 435 +CONECT 437 438 435 439 +CONECT 438 437 +CONECT 439 437 441 440 457 +CONECT 440 439 +CONECT 441 444 442 443 439 +CONECT 442 441 +CONECT 443 441 +CONECT 444 446 447 445 441 +CONECT 445 444 +CONECT 446 444 +CONECT 447 450 448 449 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 452 451 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 455 456 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 453 +CONECT 457 439 459 458 +CONECT 458 457 +CONECT 459 460 457 461 +CONECT 460 459 +CONECT 461 459 463 462 477 +CONECT 462 461 +CONECT 463 466 464 461 465 +CONECT 464 463 +CONECT 465 463 +CONECT 466 467 475 463 +CONECT 467 469 468 466 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 472 469 473 +CONECT 472 471 +CONECT 473 471 474 475 +CONECT 474 473 +CONECT 475 473 466 476 +CONECT 476 475 +CONECT 477 461 479 478 +CONECT 478 477 +CONECT 479 480 481 477 +CONECT 480 479 +CONECT 481 483 479 491 482 +CONECT 482 481 +CONECT 483 484 489 485 481 +CONECT 484 483 +CONECT 485 487 483 488 486 +CONECT 486 485 +CONECT 487 485 +CONECT 488 485 +CONECT 489 490 483 +CONECT 490 489 +CONECT 491 493 481 492 +CONECT 492 491 +CONECT 493 494 495 491 +CONECT 494 493 +CONECT 495 497 493 496 513 +CONECT 496 495 +CONECT 497 500 498 499 495 +CONECT 498 497 +CONECT 499 497 +CONECT 500 503 502 501 497 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 504 505 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 508 507 509 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 506 512 510 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 495 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 518 523 +CONECT 518 517 +CONECT 519 522 520 517 521 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 +CONECT 523 517 525 524 +CONECT 524 523 +CONECT 525 526 523 527 +CONECT 526 525 +CONECT 527 525 529 539 528 +CONECT 528 527 +CONECT 529 530 527 532 531 +CONECT 530 529 +CONECT 531 529 +CONECT 532 534 529 535 533 +CONECT 533 532 +CONECT 534 532 +CONECT 535 537 532 536 +CONECT 536 535 +CONECT 537 538 535 +CONECT 538 537 +CONECT 539 541 527 540 +CONECT 540 539 +CONECT 541 542 543 539 +CONECT 542 541 +CONECT 543 545 541 549 544 +CONECT 544 543 +CONECT 545 546 548 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 545 +CONECT 549 543 551 550 +CONECT 550 549 +CONECT 551 552 549 553 +CONECT 552 551 +CONECT 553 555 551 554 563 +CONECT 554 553 +CONECT 555 558 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 560 559 555 +CONECT 559 558 +CONECT 560 561 562 558 +CONECT 561 560 +CONECT 562 560 +CONECT 563 553 565 564 +CONECT 564 563 +CONECT 565 566 563 567 +CONECT 566 565 +CONECT 567 565 569 568 575 +CONECT 568 567 +CONECT 569 572 570 567 571 +CONECT 570 569 +CONECT 571 569 +CONECT 572 573 574 569 +CONECT 573 572 +CONECT 574 572 +CONECT 575 567 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 596 581 580 +CONECT 580 579 +CONECT 581 582 579 584 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 585 581 594 +CONECT 585 586 587 584 +CONECT 586 585 +CONECT 587 588 585 589 +CONECT 588 587 +CONECT 589 587 590 592 +CONECT 590 591 589 +CONECT 591 590 +CONECT 592 589 594 593 +CONECT 593 592 +CONECT 594 584 592 595 +CONECT 595 594 +CONECT 596 598 579 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 598 601 602 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 619 609 608 605 +CONECT 608 607 +CONECT 609 615 610 607 611 +CONECT 610 609 +CONECT 611 609 613 612 614 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 +CONECT 615 618 616 617 609 +CONECT 616 615 +CONECT 617 615 +CONECT 618 615 +CONECT 619 621 620 607 +CONECT 620 619 +CONECT 621 623 622 619 +CONECT 622 621 +CONECT 623 631 625 624 621 +CONECT 624 623 +CONECT 625 628 626 627 623 +CONECT 626 625 +CONECT 627 625 +CONECT 628 630 629 625 +CONECT 629 628 +CONECT 630 628 +CONECT 631 632 633 623 +CONECT 632 631 +CONECT 633 635 631 634 +CONECT 634 633 +CONECT 635 638 636 637 633 +CONECT 636 635 +CONECT 637 635 +CONECT 638 640 639 635 +CONECT 639 638 +CONECT 640 642 641 638 +CONECT 641 640 +CONECT 642 644 643 653 640 +CONECT 643 642 +CONECT 644 646 647 645 642 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 644 650 648 +CONECT 648 647 +CONECT 649 647 +CONECT 650 651 647 652 +CONECT 651 650 +CONECT 652 650 +CONECT 653 655 642 654 +CONECT 654 653 +CONECT 655 656 657 653 +CONECT 656 655 +CONECT 657 672 655 658 659 +CONECT 658 657 +CONECT 659 657 660 665 661 +CONECT 660 659 +CONECT 661 659 664 662 663 +CONECT 662 661 +CONECT 663 661 +CONECT 664 661 +CONECT 665 668 659 667 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 671 669 670 665 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 +CONECT 672 673 674 657 +CONECT 673 672 +CONECT 674 676 672 675 +CONECT 675 674 +CONECT 676 677 678 686 674 +CONECT 677 676 +CONECT 678 680 684 676 679 +CONECT 679 678 +CONECT 680 681 682 683 678 +CONECT 681 680 +CONECT 682 680 +CONECT 683 680 +CONECT 684 685 678 +CONECT 685 684 +CONECT 686 688 676 687 +CONECT 687 686 +CONECT 688 689 690 686 +CONECT 689 688 +CONECT 690 703 692 688 691 +CONECT 691 690 +CONECT 692 693 694 690 695 +CONECT 693 692 +CONECT 694 692 +CONECT 695 692 698 697 696 +CONECT 696 695 +CONECT 697 695 +CONECT 698 699 700 695 +CONECT 699 698 +CONECT 700 701 698 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 704 705 690 +CONECT 704 703 +CONECT 705 707 703 706 +CONECT 706 705 +CONECT 707 708 715 709 705 +CONECT 708 707 +CONECT 709 712 707 710 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 709 713 +CONECT 713 712 +CONECT 714 712 +CONECT 715 717 707 716 +CONECT 716 715 +CONECT 717 718 719 715 +CONECT 718 717 +CONECT 719 721 717 727 720 +CONECT 720 719 +CONECT 721 723 724 722 719 +CONECT 722 721 +CONECT 723 721 +CONECT 724 725 721 726 +CONECT 725 724 +CONECT 726 724 +CONECT 727 729 719 728 +CONECT 728 727 +CONECT 729 730 731 727 +CONECT 730 729 +CONECT 731 733 732 729 737 +CONECT 732 731 +CONECT 733 736 735 734 731 +CONECT 734 733 +CONECT 735 733 +CONECT 736 733 +CONECT 737 731 738 739 +CONECT 738 737 +CONECT 739 737 740 741 +CONECT 740 739 +CONECT 741 739 742 743 751 +CONECT 742 741 +CONECT 743 745 741 749 744 +CONECT 744 743 +CONECT 745 746 748 747 743 +CONECT 746 745 +CONECT 747 745 +CONECT 748 745 +CONECT 749 750 743 +CONECT 750 749 +CONECT 751 741 753 752 +CONECT 752 751 +CONECT 753 754 755 751 +CONECT 754 753 +CONECT 755 756 753 757 773 +CONECT 756 755 +CONECT 757 760 755 759 758 +CONECT 758 757 +CONECT 759 757 +CONECT 760 763 761 762 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 766 765 764 760 +CONECT 764 763 +CONECT 765 763 +CONECT 766 769 768 767 763 +CONECT 767 766 +CONECT 768 766 +CONECT 769 771 772 770 766 +CONECT 770 769 +CONECT 771 769 +CONECT 772 769 +CONECT 773 755 775 774 +CONECT 774 773 +CONECT 775 776 773 777 +CONECT 776 775 +CONECT 777 775 787 779 778 +CONECT 778 777 +CONECT 779 780 777 785 781 +CONECT 780 779 +CONECT 781 779 784 783 782 +CONECT 782 781 +CONECT 783 781 +CONECT 784 781 +CONECT 785 786 779 +CONECT 786 785 +CONECT 787 788 777 789 +CONECT 788 787 +CONECT 789 787 791 790 +CONECT 790 789 +CONECT 791 792 789 807 793 +CONECT 792 791 +CONECT 793 791 796 795 794 +CONECT 794 793 +CONECT 795 793 +CONECT 796 805 797 793 +CONECT 797 799 796 798 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 804 801 805 +CONECT 804 803 +CONECT 805 803 806 796 +CONECT 806 805 +CONECT 807 791 809 808 +CONECT 808 807 +CONECT 809 810 807 811 +CONECT 810 809 +CONECT 811 813 809 821 812 +CONECT 812 811 +CONECT 813 819 815 814 811 +CONECT 814 813 +CONECT 815 816 817 813 818 +CONECT 816 815 +CONECT 817 815 +CONECT 818 815 +CONECT 819 820 813 +CONECT 820 819 +CONECT 821 822 811 823 +CONECT 822 821 +CONECT 823 821 825 824 +CONECT 824 823 +CONECT 825 831 826 823 827 +CONECT 826 825 +CONECT 827 825 829 830 828 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 833 832 825 +CONECT 832 831 +CONECT 833 835 834 831 +CONECT 834 833 +CONECT 835 837 836 833 847 +CONECT 836 835 +CONECT 837 840 839 838 835 +CONECT 838 837 +CONECT 839 837 +CONECT 840 843 841 842 837 +CONECT 841 840 +CONECT 842 840 +CONECT 843 845 844 840 +CONECT 844 843 +CONECT 845 846 843 +CONECT 846 845 +CONECT 847 835 849 848 +CONECT 848 847 +CONECT 849 850 847 851 +CONECT 850 849 +CONECT 851 849 853 862 852 +CONECT 852 851 +CONECT 853 855 854 856 851 +CONECT 854 853 +CONECT 855 853 +CONECT 856 857 858 853 859 +CONECT 857 856 +CONECT 858 856 +CONECT 859 856 860 861 +CONECT 860 859 +CONECT 861 859 +CONECT 862 864 851 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 87 306 866 275 +CONECT 866 865 868 +CONECT 867 870 868 871 869 +CONECT 868 866 867 +CONECT 869 867 +CONECT 870 867 +CONECT 871 867 +CONECT 872 873 +CONECT 873 872 874 +CONECT 874 873 +MASTER 0 0 0 0 0 0 0 0 874 0 874 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_2_front_35.pdb b/tests/nsga2/intermediate_molecules/min_iter_2_front_35.pdb new file mode 100644 index 0000000..f4e1d44 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_2_front_35.pdb @@ -0,0 +1,1809 @@ +COMPND fitness: -6.1199 19.879166666667516 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 57.635 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.745 37.880 23.487 1.00 0.00 N +ATOM 2 H1 MET 1 14.743 38.279 24.420 1.00 0.00 H +ATOM 3 H2 MET 1 13.924 38.185 22.990 1.00 0.00 H +ATOM 4 H3 MET 1 15.584 38.222 23.038 1.00 0.00 H +ATOM 5 CA MET 1 14.801 36.414 23.587 1.00 0.00 C +ATOM 6 HA MET 1 13.868 36.071 24.040 1.00 0.00 H +ATOM 7 CB MET 1 14.943 35.769 22.196 1.00 0.00 C +ATOM 8 HB2 MET 1 14.067 36.025 21.603 1.00 0.00 H +ATOM 9 HB3 MET 1 15.824 36.180 21.702 1.00 0.00 H +ATOM 10 CG MET 1 15.085 34.236 22.246 1.00 0.00 C +ATOM 11 HG2 MET 1 15.982 33.988 22.816 1.00 0.00 H +ATOM 12 HG3 MET 1 14.226 33.815 22.774 1.00 0.00 H +ATOM 13 SD MET 1 15.227 33.414 20.634 1.00 0.00 S +ATOM 14 CE MET 1 13.530 33.558 20.004 1.00 0.00 C +ATOM 15 HE1 MET 1 13.241 34.606 19.936 1.00 0.00 H +ATOM 16 HE2 MET 1 13.475 33.113 19.010 1.00 0.00 H +ATOM 17 HE3 MET 1 12.843 33.031 20.667 1.00 0.00 H +ATOM 18 C MET 1 15.946 35.999 24.505 1.00 0.00 C +ATOM 19 O MET 1 17.087 36.378 24.269 1.00 0.00 O +ATOM 20 N GLN 2 15.652 35.162 25.502 1.00 0.00 N +ATOM 21 H GLN 2 14.688 34.926 25.672 1.00 0.00 H +ATOM 22 CA GLN 2 16.650 34.489 26.338 1.00 0.00 C +ATOM 23 HA GLN 2 17.401 35.211 26.661 1.00 0.00 H +ATOM 24 CB GLN 2 15.939 33.935 27.589 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.024 33.433 27.274 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.557 33.182 28.073 1.00 0.00 H +ATOM 27 CG GLN 2 15.578 35.021 28.622 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.170 35.889 28.114 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.796 34.626 29.271 1.00 0.00 H +ATOM 30 CD GLN 2 16.740 35.472 29.510 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.899 35.123 29.320 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.470 36.226 30.553 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.236 36.483 31.149 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.538 36.595 30.674 1.00 0.00 H +ATOM 35 C GLN 2 17.384 33.383 25.545 1.00 0.00 C +ATOM 36 O GLN 2 17.017 32.207 25.612 1.00 0.00 O +ATOM 37 N TYR 3 18.415 33.754 24.776 1.00 0.00 N +ATOM 38 H TYR 3 18.672 34.737 24.784 1.00 0.00 H +ATOM 39 CA TYR 3 19.293 32.819 24.056 1.00 0.00 C +ATOM 40 HA TYR 3 18.690 32.202 23.391 1.00 0.00 H +ATOM 41 CB TYR 3 20.316 33.592 23.211 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.783 34.366 23.824 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.108 32.904 22.908 1.00 0.00 H +ATOM 44 CG TYR 3 19.745 34.221 21.954 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.718 33.475 20.759 1.00 0.00 C +ATOM 46 HD1 TYR 3 20.099 32.463 20.744 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.216 34.050 19.576 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.217 33.484 18.656 1.00 0.00 H +ATOM 49 CZ TYR 3 18.731 35.375 19.591 1.00 0.00 C +ATOM 50 OH TYR 3 18.254 35.929 18.445 1.00 0.00 O +ATOM 51 HH TYR 3 18.362 35.332 17.703 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.750 36.120 20.789 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.381 37.136 20.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.261 35.544 21.968 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.284 36.121 22.884 1.00 0.00 H +ATOM 56 C TYR 3 20.022 31.895 25.041 1.00 0.00 C +ATOM 57 O TYR 3 20.486 32.348 26.088 1.00 0.00 O +ATOM 58 N LYS 4 20.123 30.598 24.730 1.00 0.00 N +ATOM 59 H LYS 4 19.879 30.314 23.783 1.00 0.00 H +ATOM 60 CA LYS 4 20.696 29.568 25.612 1.00 0.00 C +ATOM 61 HA LYS 4 20.439 29.804 26.640 1.00 0.00 H +ATOM 62 CB LYS 4 20.090 28.188 25.268 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.075 28.074 24.185 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.749 27.410 25.655 1.00 0.00 H +ATOM 65 CG LYS 4 18.669 27.887 25.806 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.439 26.854 25.543 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.674 27.958 26.893 1.00 0.00 H +ATOM 68 CD LYS 4 17.550 28.780 25.238 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.638 29.780 25.654 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.696 28.853 24.158 1.00 0.00 H +ATOM 71 CE LYS 4 16.122 28.248 25.478 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.440 28.810 24.832 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.077 27.204 25.151 1.00 0.00 H +ATOM 74 NZ LYS 4 15.647 28.365 26.885 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.629 29.324 27.205 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.687 28.020 26.967 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.204 27.822 27.526 1.00 0.00 H +ATOM 78 C LYS 4 22.232 29.564 25.559 1.00 0.00 C +ATOM 79 O LYS 4 22.855 29.929 24.566 1.00 0.00 O +HETATM 80 N HX1 5 22.868 29.121 26.637 1.00 0.00 N +HETATM 81 CA HX1 5 24.328 28.966 26.746 1.00 0.00 C +HETATM 82 C HX1 5 24.644 27.767 27.648 1.00 0.00 C +HETATM 83 O HX1 5 24.241 27.736 28.815 1.00 0.00 O +HETATM 84 CB HX1 5 24.946 30.288 27.253 1.00 0.00 C +HETATM 85 CG HX1 5 26.463 30.365 27.331 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.358 29.400 26.951 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.165 31.437 27.907 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.456 31.069 27.837 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.601 29.836 27.330 1.00 0.00 N +HETATM 90 H HX1 5 22.307 28.946 27.469 1.00 0.00 H +HETATM 91 HA HX1 5 24.744 28.768 25.756 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.545 30.506 28.244 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.612 31.089 26.591 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.156 28.436 26.505 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.272 31.637 28.263 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.424 29.244 27.468 1.00 0.00 H +ATOM 97 N ILE 6 25.313 26.762 27.080 1.00 0.00 N +ATOM 98 H ILE 6 25.599 26.868 26.110 1.00 0.00 H +ATOM 99 CA ILE 6 25.772 25.537 27.743 1.00 0.00 C +ATOM 100 HA ILE 6 25.214 25.427 28.675 1.00 0.00 H +ATOM 101 CB ILE 6 25.437 24.293 26.876 1.00 0.00 C +ATOM 102 HB ILE 6 25.854 24.450 25.882 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.025 22.981 27.435 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.628 22.777 28.430 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.778 22.146 26.781 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.114 23.024 27.466 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.895 24.173 26.763 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.472 24.081 27.763 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.496 25.083 26.315 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.387 22.996 25.921 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.533 22.057 26.456 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.318 23.123 25.738 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.913 22.962 24.966 1.00 0.00 H +ATOM 114 C ILE 6 27.256 25.666 28.148 1.00 0.00 C +ATOM 115 O ILE 6 28.024 26.454 27.599 1.00 0.00 O +ATOM 116 N VAL 7 27.595 24.921 29.192 1.00 0.00 N +ATOM 117 H VAL 7 26.900 24.243 29.472 1.00 0.00 H +ATOM 118 CA VAL 7 28.705 25.068 30.140 1.00 0.00 C +ATOM 119 HA VAL 7 28.740 26.119 30.429 1.00 0.00 H +ATOM 120 CB VAL 7 28.280 24.241 31.372 1.00 0.00 C +ATOM 121 HB VAL 7 27.391 24.718 31.794 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.919 22.777 31.067 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.760 22.265 30.603 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.660 22.271 31.989 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.054 22.703 30.413 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.329 24.209 32.477 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.759 25.195 32.628 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.844 23.866 33.384 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.111 23.501 32.211 1.00 0.00 H +ATOM 130 C VAL 7 30.127 24.713 29.652 1.00 0.00 C +ATOM 131 O VAL 7 30.332 23.769 28.890 1.00 0.00 O +ATOM 132 N ARG 8 31.125 25.450 30.180 1.00 0.00 N +ATOM 133 H ARG 8 30.852 26.293 30.666 1.00 0.00 H +ATOM 134 CA ARG 8 32.575 25.156 30.106 1.00 0.00 C +ATOM 135 HA ARG 8 32.815 25.008 29.054 1.00 0.00 H +ATOM 136 CB ARG 8 33.392 26.376 30.609 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.441 26.212 30.365 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.064 27.266 30.070 1.00 0.00 H +ATOM 139 CG ARG 8 33.288 26.649 32.130 1.00 0.00 C +ATOM 140 HG2 ARG 8 32.239 26.784 32.407 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.668 25.782 32.674 1.00 0.00 H +ATOM 142 CD ARG 8 34.101 27.865 32.617 1.00 0.00 C +ATOM 143 HD2 ARG 8 34.159 27.834 33.705 1.00 0.00 H +ATOM 144 HD3 ARG 8 35.114 27.783 32.229 1.00 0.00 H +ATOM 145 NE ARG 8 33.501 29.153 32.193 1.00 0.00 N +ATOM 146 HE ARG 8 33.869 29.569 31.335 1.00 0.00 H +ATOM 147 CZ ARG 8 32.399 29.712 32.664 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.825 29.373 33.779 1.00 0.00 N +ATOM 149 HH11 ARG 8 32.364 28.901 34.498 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.036 29.918 34.060 1.00 0.00 H +ATOM 151 NH2 ARG 8 31.795 30.641 32.009 1.00 0.00 N +ATOM 152 HH21 ARG 8 32.258 30.954 31.157 1.00 0.00 H +ATOM 153 HH22 ARG 8 30.792 30.544 31.969 1.00 0.00 H +ATOM 154 C ARG 8 32.985 23.867 30.846 1.00 0.00 C +ATOM 155 O ARG 8 32.551 23.619 31.970 1.00 0.00 O +ATOM 156 N GLY 9 33.918 23.104 30.275 1.00 0.00 N +ATOM 157 H GLY 9 34.237 23.351 29.353 1.00 0.00 H +ATOM 158 CA GLY 9 34.416 21.849 30.859 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.343 21.560 30.361 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.641 22.013 31.914 1.00 0.00 H +ATOM 161 C GLY 9 33.425 20.677 30.745 1.00 0.00 C +ATOM 162 O GLY 9 32.500 20.714 29.939 1.00 0.00 O +ATOM 163 N LYS 10 33.641 19.621 31.549 1.00 0.00 N +ATOM 164 H LYS 10 34.478 19.643 32.112 1.00 0.00 H +ATOM 165 CA LYS 10 32.889 18.344 31.470 1.00 0.00 C +ATOM 166 HA LYS 10 31.953 18.539 30.939 1.00 0.00 H +ATOM 167 CB LYS 10 33.714 17.348 30.623 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.348 17.919 29.942 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.370 16.773 31.279 1.00 0.00 H +ATOM 170 CG LYS 10 32.884 16.383 29.753 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.281 15.727 30.381 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.221 16.964 29.110 1.00 0.00 H +ATOM 173 CD LYS 10 33.829 15.541 28.876 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.522 16.211 28.365 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.400 14.864 29.512 1.00 0.00 H +ATOM 176 CE LYS 10 33.093 14.728 27.806 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.499 13.950 28.294 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.409 15.397 27.278 1.00 0.00 H +ATOM 179 NZ LYS 10 34.051 14.137 26.834 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.729 13.531 27.281 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.583 13.630 26.098 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.594 14.875 26.363 1.00 0.00 H +ATOM 183 C LYS 10 32.471 17.756 32.836 1.00 0.00 C +ATOM 184 O LYS 10 31.962 16.645 32.897 1.00 0.00 O +ATOM 185 N ILE 11 32.723 18.474 33.940 1.00 0.00 N +ATOM 186 H ILE 11 33.161 19.370 33.808 1.00 0.00 H +ATOM 187 CA ILE 11 32.381 18.064 35.327 1.00 0.00 C +ATOM 188 HA ILE 11 32.234 16.984 35.348 1.00 0.00 H +ATOM 189 CB ILE 11 33.537 18.395 36.300 1.00 0.00 C +ATOM 190 HB ILE 11 33.191 18.153 37.308 1.00 0.00 H +ATOM 191 CG2 ILE 11 34.744 17.487 36.018 1.00 0.00 C +ATOM 192 HG21 ILE 11 35.173 17.710 35.044 1.00 0.00 H +ATOM 193 HG22 ILE 11 35.506 17.627 36.782 1.00 0.00 H +ATOM 194 HG23 ILE 11 34.431 16.445 36.042 1.00 0.00 H +ATOM 195 CG1 ILE 11 33.906 19.897 36.275 1.00 0.00 C +ATOM 196 HG12 ILE 11 34.429 20.131 35.346 1.00 0.00 H +ATOM 197 HG13 ILE 11 32.996 20.492 36.308 1.00 0.00 H +ATOM 198 CD1 ILE 11 34.776 20.336 37.457 1.00 0.00 C +ATOM 199 HD11 ILE 11 35.742 19.835 37.427 1.00 0.00 H +ATOM 200 HD12 ILE 11 34.939 21.413 37.399 1.00 0.00 H +ATOM 201 HD13 ILE 11 34.269 20.105 38.395 1.00 0.00 H +ATOM 202 C ILE 11 31.064 18.665 35.861 1.00 0.00 C +ATOM 203 O ILE 11 30.565 18.230 36.894 1.00 0.00 O +ATOM 204 N ARG 12 30.508 19.655 35.159 1.00 0.00 N +ATOM 205 H ARG 12 30.941 19.901 34.276 1.00 0.00 H +ATOM 206 CA ARG 12 29.178 20.231 35.367 1.00 0.00 C +ATOM 207 HA ARG 12 28.599 19.577 36.007 1.00 0.00 H +ATOM 208 CB ARG 12 29.277 21.614 36.069 1.00 0.00 C +ATOM 209 HB2 ARG 12 28.298 22.070 36.051 1.00 0.00 H +ATOM 210 HB3 ARG 12 29.512 21.466 37.120 1.00 0.00 H +ATOM 211 CG ARG 12 30.294 22.589 35.497 1.00 0.00 C +ATOM 212 HG2 ARG 12 31.298 22.220 35.713 1.00 0.00 H +ATOM 213 HG3 ARG 12 30.250 22.582 34.418 1.00 0.00 H +ATOM 214 CD ARG 12 30.193 24.039 36.012 1.00 0.00 C +ATOM 215 HD2 ARG 12 30.524 24.038 37.044 1.00 0.00 H +ATOM 216 HD3 ARG 12 30.903 24.655 35.474 1.00 0.00 H +ATOM 217 NE ARG 12 28.856 24.677 35.872 1.00 0.00 N +ATOM 218 HE ARG 12 28.065 24.120 36.214 1.00 0.00 H +ATOM 219 CZ ARG 12 28.532 25.842 35.358 1.00 0.00 C +ATOM 220 NH1 ARG 12 29.393 26.656 34.823 1.00 0.00 N +ATOM 221 HH11 ARG 12 30.377 26.413 34.786 1.00 0.00 H +ATOM 222 HH12 ARG 12 29.088 27.511 34.386 1.00 0.00 H +ATOM 223 NH2 ARG 12 27.293 26.200 35.364 1.00 0.00 N +ATOM 224 HH21 ARG 12 26.608 25.544 35.780 1.00 0.00 H +ATOM 225 HH22 ARG 12 27.017 27.128 35.097 1.00 0.00 H +ATOM 226 C ARG 12 28.466 20.290 34.018 1.00 0.00 C +ATOM 227 O ARG 12 29.150 20.405 33.006 1.00 0.00 O +ATOM 228 N LYS 13 27.136 20.152 33.998 1.00 0.00 N +ATOM 229 H LYS 13 26.668 20.087 34.894 1.00 0.00 H +ATOM 230 CA LYS 13 26.351 19.835 32.776 1.00 0.00 C +ATOM 231 HA LYS 13 26.980 20.030 31.898 1.00 0.00 H +ATOM 232 CB LYS 13 26.024 18.319 32.784 1.00 0.00 C +ATOM 233 HB2 LYS 13 26.879 17.787 33.210 1.00 0.00 H +ATOM 234 HB3 LYS 13 25.161 18.152 33.432 1.00 0.00 H +ATOM 235 CG LYS 13 25.764 17.711 31.386 1.00 0.00 C +ATOM 236 HG2 LYS 13 24.880 18.159 30.928 1.00 0.00 H +ATOM 237 HG3 LYS 13 26.625 17.923 30.748 1.00 0.00 H +ATOM 238 CD LYS 13 25.570 16.182 31.449 1.00 0.00 C +ATOM 239 HD2 LYS 13 25.570 15.786 30.433 1.00 0.00 H +ATOM 240 HD3 LYS 13 26.416 15.745 31.986 1.00 0.00 H +ATOM 241 CE LYS 13 24.252 15.786 32.134 1.00 0.00 C +ATOM 242 HE2 LYS 13 24.095 16.445 32.993 1.00 0.00 H +ATOM 243 HE3 LYS 13 23.424 15.954 31.438 1.00 0.00 H +ATOM 244 NZ LYS 13 24.262 14.377 32.606 1.00 0.00 N +ATOM 245 HZ1 LYS 13 25.102 14.163 33.127 1.00 0.00 H +ATOM 246 HZ2 LYS 13 23.528 14.229 33.297 1.00 0.00 H +ATOM 247 HZ3 LYS 13 24.146 13.696 31.866 1.00 0.00 H +ATOM 248 C LYS 13 25.104 20.721 32.577 1.00 0.00 C +ATOM 249 O LYS 13 24.270 20.440 31.718 1.00 0.00 O +ATOM 250 N GLY 14 24.945 21.766 33.390 1.00 0.00 N +ATOM 251 H GLY 14 25.642 21.970 34.094 1.00 0.00 H +ATOM 252 CA GLY 14 23.783 22.651 33.338 1.00 0.00 C +ATOM 253 HA2 GLY 14 22.880 22.052 33.218 1.00 0.00 H +ATOM 254 HA3 GLY 14 23.681 23.189 34.276 1.00 0.00 H +ATOM 255 C GLY 14 23.811 23.690 32.212 1.00 0.00 C +ATOM 256 O GLY 14 24.766 23.831 31.445 1.00 0.00 O +ATOM 257 N VAL 15 22.721 24.450 32.144 1.00 0.00 N +ATOM 258 H VAL 15 22.014 24.309 32.852 1.00 0.00 H +ATOM 259 CA VAL 15 22.409 25.408 31.081 1.00 0.00 C +ATOM 260 HA VAL 15 23.327 25.645 30.547 1.00 0.00 H +ATOM 261 CB VAL 15 21.440 24.759 30.063 1.00 0.00 C +ATOM 262 HB VAL 15 21.940 23.879 29.651 1.00 0.00 H +ATOM 263 CG1 VAL 15 20.118 24.286 30.694 1.00 0.00 C +ATOM 264 HG11 VAL 15 19.568 25.126 31.115 1.00 0.00 H +ATOM 265 HG12 VAL 15 19.508 23.798 29.931 1.00 0.00 H +ATOM 266 HG13 VAL 15 20.316 23.552 31.473 1.00 0.00 H +ATOM 267 CG2 VAL 15 21.108 25.689 28.890 1.00 0.00 C +ATOM 268 HG21 VAL 15 22.028 26.061 28.439 1.00 0.00 H +ATOM 269 HG22 VAL 15 20.558 25.127 28.133 1.00 0.00 H +ATOM 270 HG23 VAL 15 20.494 26.524 29.221 1.00 0.00 H +ATOM 271 C VAL 15 21.874 26.701 31.690 1.00 0.00 C +ATOM 272 O VAL 15 21.209 26.686 32.723 1.00 0.00 O +HETATM 273 N HY1 16 22.179 27.840 31.067 1.00 0.00 N +HETATM 274 CA HY1 16 21.637 29.164 31.415 1.00 0.00 C +HETATM 275 C HY1 16 21.358 29.956 30.137 1.00 0.00 C +HETATM 276 O HY1 16 21.535 29.437 29.033 1.00 0.00 O +HETATM 277 CB HY1 16 22.600 29.885 32.384 1.00 0.00 C +HETATM 278 CG HY1 16 23.951 30.212 31.794 1.00 0.00 C +HETATM 279 CD2 HY1 16 24.360 31.433 31.319 1.00 0.00 C +HETATM 280 ND1 HY1 16 24.986 29.330 31.591 1.00 0.00 N +HETATM 281 CE1 HY1 16 26.002 30.017 31.040 1.00 0.00 C +HETATM 282 NE2 HY1 16 25.671 31.306 30.841 1.00 0.00 N +HETATM 283 H HY1 16 22.717 27.786 30.202 1.00 0.00 H +HETATM 284 HA HY1 16 20.684 29.025 31.937 1.00 0.00 H +HETATM 285 HB2 HY1 16 22.132 30.813 32.726 1.00 0.00 H +HETATM 286 HB3 HY1 16 22.742 29.270 33.272 1.00 0.00 H +HETATM 287 HD1 HY1 16 24.980 28.341 31.806 1.00 0.00 H +HETATM 288 HD2 HY1 16 23.768 32.339 31.311 1.00 0.00 H +HETATM 289 HE1 HY1 16 26.965 29.587 30.773 1.00 0.00 H +ATOM 290 N THR 17 20.915 31.207 30.262 1.00 0.00 N +ATOM 291 H THR 17 20.754 31.606 31.175 1.00 0.00 H +ATOM 292 CA THR 17 20.507 32.058 29.135 1.00 0.00 C +ATOM 293 HA THR 17 20.947 31.627 28.224 1.00 0.00 H +ATOM 294 CB THR 17 18.994 32.085 28.987 1.00 0.00 C +ATOM 295 HB THR 17 18.726 32.742 28.158 1.00 0.00 H +ATOM 296 CG2 THR 17 18.331 30.715 28.713 1.00 0.00 C +ATOM 297 HG21 THR 17 18.539 30.018 29.521 1.00 0.00 H +ATOM 298 HG22 THR 17 17.266 30.825 28.622 1.00 0.00 H +ATOM 299 HG23 THR 17 18.711 30.299 27.787 1.00 0.00 H +ATOM 300 OG1 THR 17 18.393 32.588 30.157 1.00 0.00 O +ATOM 301 HG1 THR 17 18.304 33.550 30.019 1.00 0.00 H +ATOM 302 C THR 17 21.063 33.477 29.238 1.00 0.00 C +ATOM 303 O THR 17 21.520 33.894 30.300 1.00 0.00 O +HETATM 304 N HY2 18 20.996 34.217 28.131 1.00 0.00 N +HETATM 305 CA HY2 18 21.281 35.654 28.049 1.00 0.00 C +HETATM 306 C HY2 18 20.167 36.344 27.255 1.00 0.00 C +HETATM 307 O HY2 18 19.828 35.891 26.162 1.00 0.00 O +HETATM 308 CB HY2 18 22.628 35.911 27.367 1.00 0.00 C +HETATM 309 CG HY2 18 23.821 35.424 28.161 1.00 0.00 C +HETATM 310 CD2 HY2 18 24.353 34.161 28.129 1.00 0.00 C +HETATM 311 ND1 HY2 18 24.518 36.134 29.116 1.00 0.00 N +HETATM 312 CE1 HY2 18 25.458 35.316 29.624 1.00 0.00 C +HETATM 313 NE2 HY2 18 25.394 34.097 29.060 1.00 0.00 N +HETATM 314 H HY2 18 20.641 33.770 27.293 1.00 0.00 H +HETATM 315 HA HY2 18 21.304 36.085 29.058 1.00 0.00 H +HETATM 316 HB2 HY2 18 22.635 35.430 26.383 1.00 0.00 H +HETATM 317 HB3 HY2 18 22.739 36.989 27.205 1.00 0.00 H +HETATM 318 HD1 HY2 18 24.367 37.099 29.382 1.00 0.00 H +HETATM 319 HD2 HY2 18 24.012 33.350 27.501 1.00 0.00 H +HETATM 320 HE1 HY2 18 26.167 35.602 30.392 1.00 0.00 H +ATOM 321 N GLU 19 19.615 37.434 27.786 1.00 0.00 N +ATOM 322 H GLU 19 19.943 37.760 28.677 1.00 0.00 H +ATOM 323 CA GLU 19 18.587 38.233 27.115 1.00 0.00 C +ATOM 324 HA GLU 19 17.861 37.556 26.675 1.00 0.00 H +ATOM 325 CB GLU 19 17.882 39.109 28.164 1.00 0.00 C +ATOM 326 HB2 GLU 19 17.550 38.477 28.984 1.00 0.00 H +ATOM 327 HB3 GLU 19 18.599 39.827 28.572 1.00 0.00 H +ATOM 328 CG GLU 19 16.663 39.880 27.633 1.00 0.00 C +ATOM 329 HG2 GLU 19 16.210 40.435 28.462 1.00 0.00 H +ATOM 330 HG3 GLU 19 16.998 40.613 26.891 1.00 0.00 H +ATOM 331 CD GLU 19 15.641 38.932 27.015 1.00 0.00 C +ATOM 332 OE1 GLU 19 15.701 38.733 25.782 1.00 0.00 O +ATOM 333 OE2 GLU 19 14.849 38.325 27.761 1.00 0.00 O +ATOM 334 C GLU 19 19.198 39.080 25.980 1.00 0.00 C +ATOM 335 O GLU 19 20.203 39.758 26.202 1.00 0.00 O +ATOM 336 N ALA 20 18.606 39.044 24.780 1.00 0.00 N +ATOM 337 H ALA 20 17.784 38.457 24.675 1.00 0.00 H +ATOM 338 CA ALA 20 18.996 39.888 23.650 1.00 0.00 C +ATOM 339 HA ALA 20 19.136 40.905 24.010 1.00 0.00 H +ATOM 340 CB ALA 20 20.326 39.388 23.068 1.00 0.00 C +ATOM 341 HB1 ALA 20 20.194 38.398 22.628 1.00 0.00 H +ATOM 342 HB2 ALA 20 20.680 40.074 22.299 1.00 0.00 H +ATOM 343 HB3 ALA 20 21.089 39.333 23.842 1.00 0.00 H +ATOM 344 C ALA 20 17.932 39.914 22.538 1.00 0.00 C +ATOM 345 O ALA 20 17.063 39.040 22.433 1.00 0.00 O +ATOM 346 N VAL 21 18.034 40.899 21.634 1.00 0.00 N +ATOM 347 H VAL 21 18.741 41.611 21.783 1.00 0.00 H +ATOM 348 CA VAL 21 17.311 40.921 20.337 1.00 0.00 C +ATOM 349 HA VAL 21 16.315 40.503 20.494 1.00 0.00 H +ATOM 350 CB VAL 21 17.117 42.377 19.835 1.00 0.00 C +ATOM 351 HB VAL 21 16.476 42.332 18.947 1.00 0.00 H +ATOM 352 CG1 VAL 21 16.400 43.250 20.877 1.00 0.00 C +ATOM 353 HG11 VAL 21 17.035 43.407 21.741 1.00 0.00 H +ATOM 354 HG12 VAL 21 16.158 44.208 20.432 1.00 0.00 H +ATOM 355 HG13 VAL 21 15.480 42.767 21.188 1.00 0.00 H +ATOM 356 CG2 VAL 21 18.435 43.063 19.429 1.00 0.00 C +ATOM 357 HG21 VAL 21 18.896 42.530 18.601 1.00 0.00 H +ATOM 358 HG22 VAL 21 18.226 44.076 19.094 1.00 0.00 H +ATOM 359 HG23 VAL 21 19.124 43.099 20.266 1.00 0.00 H +ATOM 360 C VAL 21 17.985 40.079 19.258 1.00 0.00 C +ATOM 361 O VAL 21 17.384 39.819 18.224 1.00 0.00 O +ATOM 362 N ASP 22 19.237 39.669 19.479 1.00 0.00 N +ATOM 363 H ASP 22 19.664 39.908 20.358 1.00 0.00 H +ATOM 364 CA ASP 22 20.121 39.001 18.509 1.00 0.00 C +ATOM 365 HA ASP 22 19.522 38.298 17.910 1.00 0.00 H +ATOM 366 CB ASP 22 20.738 40.062 17.585 1.00 0.00 C +ATOM 367 HB2 ASP 22 19.920 40.726 17.225 1.00 0.00 H +ATOM 368 HB3 ASP 22 21.434 40.689 18.195 1.00 0.00 H +ATOM 369 CG ASP 22 21.487 39.505 16.380 1.00 0.00 C +ATOM 370 OD1 ASP 22 21.692 40.286 15.421 1.00 0.00 O +ATOM 371 OD2 ASP 22 21.818 38.319 16.355 1.00 0.00 O +ATOM 372 C ASP 22 21.198 38.190 19.263 1.00 0.00 C +ATOM 373 O ASP 22 21.715 38.640 20.295 1.00 0.00 O +ATOM 374 N TRP 23 21.599 37.030 18.739 1.00 0.00 N +ATOM 375 H TRP 23 21.333 36.859 17.782 1.00 0.00 H +ATOM 376 CA TRP 23 22.727 36.273 19.261 1.00 0.00 C +ATOM 377 HA TRP 23 22.535 36.070 20.312 1.00 0.00 H +ATOM 378 CB TRP 23 22.844 34.916 18.533 1.00 0.00 C +ATOM 379 HB2 TRP 23 23.609 34.330 19.040 1.00 0.00 H +ATOM 380 HB3 TRP 23 21.903 34.386 18.649 1.00 0.00 H +ATOM 381 CG TRP 23 23.201 34.978 17.077 1.00 0.00 C +ATOM 382 CD1 TRP 23 22.341 34.797 16.050 1.00 0.00 C +ATOM 383 HD1 TRP 23 21.289 34.555 16.149 1.00 0.00 H +ATOM 384 NE1 TRP 23 23.000 34.999 14.853 1.00 0.00 N +ATOM 385 HE1 TRP 23 22.550 34.927 13.950 1.00 0.00 H +ATOM 386 CE2 TRP 23 24.321 35.337 15.049 1.00 0.00 C +ATOM 387 CZ2 TRP 23 25.364 35.685 14.176 1.00 0.00 C +ATOM 388 HZ2 TRP 23 25.185 35.741 13.114 1.00 0.00 H +ATOM 389 CH2 TRP 23 26.642 35.948 14.705 1.00 0.00 C +ATOM 390 HH2 TRP 23 27.458 36.213 14.048 1.00 0.00 H +ATOM 391 CZ3 TRP 23 26.864 35.838 16.091 1.00 0.00 C +ATOM 392 HZ3 TRP 23 27.848 36.029 16.497 1.00 0.00 H +ATOM 393 CE3 TRP 23 25.807 35.490 16.954 1.00 0.00 C +ATOM 394 HE3 TRP 23 25.994 35.420 18.014 1.00 0.00 H +ATOM 395 CD2 TRP 23 24.500 35.261 16.463 1.00 0.00 C +ATOM 396 C TRP 23 24.040 37.075 19.169 1.00 0.00 C +ATOM 397 O TRP 23 24.894 36.943 20.048 1.00 0.00 O +ATOM 398 N ALA 24 24.184 37.965 18.176 1.00 0.00 N +ATOM 399 H ALA 24 23.462 38.002 17.455 1.00 0.00 H +ATOM 400 CA ALA 24 25.376 38.794 17.993 1.00 0.00 C +ATOM 401 HA ALA 24 26.255 38.161 18.097 1.00 0.00 H +ATOM 402 CB ALA 24 25.364 39.327 16.558 1.00 0.00 C +ATOM 403 HB1 ALA 24 24.523 40.002 16.408 1.00 0.00 H +ATOM 404 HB2 ALA 24 26.286 39.864 16.345 1.00 0.00 H +ATOM 405 HB3 ALA 24 25.274 38.503 15.853 1.00 0.00 H +ATOM 406 C ALA 24 25.526 39.930 19.031 1.00 0.00 C +ATOM 407 O ALA 24 26.612 40.504 19.178 1.00 0.00 O +ATOM 408 N GLU 25 24.461 40.240 19.781 1.00 0.00 N +ATOM 409 H GLU 25 23.598 39.752 19.579 1.00 0.00 H +ATOM 410 CA GLU 25 24.521 41.028 21.020 1.00 0.00 C +ATOM 411 HA GLU 25 25.414 41.652 21.013 1.00 0.00 H +ATOM 412 CB GLU 25 23.299 41.958 21.109 1.00 0.00 C +ATOM 413 HB2 GLU 25 22.392 41.374 20.932 1.00 0.00 H +ATOM 414 HB3 GLU 25 23.240 42.359 22.117 1.00 0.00 H +ATOM 415 CG GLU 25 23.352 43.133 20.127 1.00 0.00 C +ATOM 416 HG2 GLU 25 23.344 42.734 19.107 1.00 0.00 H +ATOM 417 HG3 GLU 25 22.443 43.734 20.238 1.00 0.00 H +ATOM 418 CD GLU 25 24.586 44.016 20.336 1.00 0.00 C +ATOM 419 OE1 GLU 25 24.776 44.550 21.451 1.00 0.00 O +ATOM 420 OE2 GLU 25 25.400 44.101 19.390 1.00 0.00 O +ATOM 421 C GLU 25 24.643 40.121 22.256 1.00 0.00 C +ATOM 422 O GLU 25 25.414 40.427 23.158 1.00 0.00 O +ATOM 423 N ALA 26 23.983 38.952 22.288 1.00 0.00 N +ATOM 424 H ALA 26 23.329 38.727 21.539 1.00 0.00 H +ATOM 425 CA ALA 26 24.158 37.964 23.369 1.00 0.00 C +ATOM 426 HA ALA 26 23.916 38.460 24.308 1.00 0.00 H +ATOM 427 CB ALA 26 23.209 36.801 23.149 1.00 0.00 C +ATOM 428 HB1 ALA 26 23.516 36.235 22.269 1.00 0.00 H +ATOM 429 HB2 ALA 26 23.227 36.133 24.012 1.00 0.00 H +ATOM 430 HB3 ALA 26 22.193 37.177 23.007 1.00 0.00 H +ATOM 431 C ALA 26 25.616 37.461 23.493 1.00 0.00 C +ATOM 432 O ALA 26 26.033 37.105 24.597 1.00 0.00 O +ATOM 433 N GLU 27 26.385 37.472 22.405 1.00 0.00 N +ATOM 434 H GLU 27 25.919 37.575 21.510 1.00 0.00 H +ATOM 435 CA GLU 27 27.839 37.249 22.409 1.00 0.00 C +ATOM 436 HA GLU 27 28.023 36.289 22.873 1.00 0.00 H +ATOM 437 CB GLU 27 28.353 37.215 20.928 1.00 0.00 C +ATOM 438 HB2 GLU 27 27.749 36.501 20.373 1.00 0.00 H +ATOM 439 HB3 GLU 27 28.212 38.197 20.486 1.00 0.00 H +ATOM 440 CG GLU 27 29.821 36.798 20.795 1.00 0.00 C +ATOM 441 HG2 GLU 27 30.422 37.267 21.594 1.00 0.00 H +ATOM 442 HG3 GLU 27 29.880 35.709 20.957 1.00 0.00 H +ATOM 443 CD GLU 27 30.417 37.140 19.425 1.00 0.00 C +ATOM 444 OE1 GLU 27 30.946 38.262 19.264 1.00 0.00 O +ATOM 445 OE2 GLU 27 30.381 36.288 18.514 1.00 0.00 O +ATOM 446 C GLU 27 28.584 38.323 23.219 1.00 0.00 C +ATOM 447 O GLU 27 29.362 38.004 24.113 1.00 0.00 O +ATOM 448 N LYS 28 28.272 39.598 22.969 1.00 0.00 N +ATOM 449 H LYS 28 27.573 39.781 22.256 1.00 0.00 H +ATOM 450 CA LYS 28 28.831 40.744 23.711 1.00 0.00 C +ATOM 451 HA LYS 28 29.920 40.668 23.681 1.00 0.00 H +ATOM 452 CB LYS 28 28.422 42.074 23.050 1.00 0.00 C +ATOM 453 HB2 LYS 28 27.340 42.201 23.106 1.00 0.00 H +ATOM 454 HB3 LYS 28 28.887 42.881 23.615 1.00 0.00 H +ATOM 455 CG LYS 28 28.863 42.187 21.579 1.00 0.00 C +ATOM 456 HG2 LYS 28 29.932 41.982 21.510 1.00 0.00 H +ATOM 457 HG3 LYS 28 28.328 41.446 20.984 1.00 0.00 H +ATOM 458 CD LYS 28 28.582 43.591 21.013 1.00 0.00 C +ATOM 459 HD2 LYS 28 27.543 43.865 21.197 1.00 0.00 H +ATOM 460 HD3 LYS 28 29.214 44.309 21.539 1.00 0.00 H +ATOM 461 CE LYS 28 28.875 43.679 19.507 1.00 0.00 C +ATOM 462 HE2 LYS 28 29.000 44.736 19.247 1.00 0.00 H +ATOM 463 HE3 LYS 28 29.822 43.178 19.298 1.00 0.00 H +ATOM 464 NZ LYS 28 27.780 43.091 18.697 1.00 0.00 N +ATOM 465 HZ1 LYS 28 26.904 43.581 18.901 1.00 0.00 H +ATOM 466 HZ2 LYS 28 27.934 43.179 17.705 1.00 0.00 H +ATOM 467 HZ3 LYS 28 27.597 42.121 18.938 1.00 0.00 H +ATOM 468 C LYS 28 28.421 40.717 25.185 1.00 0.00 C +ATOM 469 O LYS 28 29.269 40.868 26.061 1.00 0.00 O +ATOM 470 N PHE 29 27.153 40.430 25.485 1.00 0.00 N +ATOM 471 H PHE 29 26.486 40.365 24.716 1.00 0.00 H +ATOM 472 CA PHE 29 26.665 40.284 26.863 1.00 0.00 C +ATOM 473 HA PHE 29 26.967 41.156 27.431 1.00 0.00 H +ATOM 474 CB PHE 29 25.125 40.255 26.861 1.00 0.00 C +ATOM 475 HB2 PHE 29 24.805 39.326 26.395 1.00 0.00 H +ATOM 476 HB3 PHE 29 24.774 40.241 27.899 1.00 0.00 H +ATOM 477 CG PHE 29 24.438 41.418 26.164 1.00 0.00 C +ATOM 478 CD1 PHE 29 23.215 41.204 25.493 1.00 0.00 C +ATOM 479 HD1 PHE 29 22.758 40.227 25.499 1.00 0.00 H +ATOM 480 CE1 PHE 29 22.585 42.256 24.799 1.00 0.00 C +ATOM 481 HE1 PHE 29 21.665 42.072 24.277 1.00 0.00 H +ATOM 482 CZ PHE 29 23.179 43.532 24.772 1.00 0.00 C +ATOM 483 HZ PHE 29 22.721 44.327 24.207 1.00 0.00 H +ATOM 484 CE2 PHE 29 24.377 43.770 25.466 1.00 0.00 C +ATOM 485 HE2 PHE 29 24.825 44.740 25.450 1.00 0.00 H +ATOM 486 CD2 PHE 29 24.999 42.719 26.166 1.00 0.00 C +ATOM 487 HD2 PHE 29 25.919 42.918 26.685 1.00 0.00 H +ATOM 488 C PHE 29 27.252 39.031 27.583 1.00 0.00 C +ATOM 489 O PHE 29 27.391 39.054 28.809 1.00 0.00 O +ATOM 490 N THR 30 27.631 37.984 26.848 1.00 0.00 N +ATOM 491 H THR 30 27.430 37.988 25.856 1.00 0.00 H +ATOM 492 CA THR 30 28.387 36.854 27.387 1.00 0.00 C +ATOM 493 HA THR 30 27.976 36.517 28.319 1.00 0.00 H +ATOM 494 CB THR 30 28.369 35.616 26.356 1.00 0.00 C +ATOM 495 HB THR 30 28.820 35.954 25.447 1.00 0.00 H +ATOM 496 CG2 THR 30 29.240 34.485 26.845 1.00 0.00 C +ATOM 497 HG21 THR 30 28.995 34.128 27.826 1.00 0.00 H +ATOM 498 HG22 THR 30 29.216 33.608 26.175 1.00 0.00 H +ATOM 499 HG23 THR 30 30.280 34.792 26.852 1.00 0.00 H +ATOM 500 OG1 THR 30 27.058 35.144 26.133 1.00 0.00 O +ATOM 501 HG1 THR 30 26.557 35.852 25.666 1.00 0.00 H +ATOM 502 C THR 30 29.848 37.270 27.711 1.00 0.00 C +ATOM 503 O THR 30 30.323 36.962 28.799 1.00 0.00 O +ATOM 504 N LYS 31 30.505 38.057 26.862 1.00 0.00 N +ATOM 505 H LYS 31 30.045 38.319 25.997 1.00 0.00 H +ATOM 506 CA LYS 31 31.840 38.605 27.115 1.00 0.00 C +ATOM 507 HA LYS 31 32.524 37.806 27.399 1.00 0.00 H +ATOM 508 CB LYS 31 32.394 39.247 25.814 1.00 0.00 C +ATOM 509 HB2 LYS 31 31.669 39.946 25.426 1.00 0.00 H +ATOM 510 HB3 LYS 31 33.307 39.783 26.056 1.00 0.00 H +ATOM 511 CG LYS 31 32.729 38.185 24.750 1.00 0.00 C +ATOM 512 HG2 LYS 31 33.484 37.513 25.148 1.00 0.00 H +ATOM 513 HG3 LYS 31 31.855 37.590 24.497 1.00 0.00 H +ATOM 514 CD LYS 31 33.265 38.860 23.478 1.00 0.00 C +ATOM 515 HD2 LYS 31 32.453 39.402 22.997 1.00 0.00 H +ATOM 516 HD3 LYS 31 34.038 39.574 23.747 1.00 0.00 H +ATOM 517 CE LYS 31 33.852 37.860 22.457 1.00 0.00 C +ATOM 518 HE2 LYS 31 33.109 37.103 22.211 1.00 0.00 H +ATOM 519 HE3 LYS 31 34.078 38.405 21.540 1.00 0.00 H +ATOM 520 NZ LYS 31 35.090 37.214 22.956 1.00 0.00 N +ATOM 521 HZ1 LYS 31 34.884 36.467 23.594 1.00 0.00 H +ATOM 522 HZ2 LYS 31 35.630 36.803 22.189 1.00 0.00 H +ATOM 523 HZ3 LYS 31 35.688 37.863 23.478 1.00 0.00 H +ATOM 524 C LYS 31 31.875 39.604 28.282 1.00 0.00 C +ATOM 525 O LYS 31 32.866 39.609 29.014 1.00 0.00 O +ATOM 526 N ALA 32 30.799 40.361 28.521 1.00 0.00 N +ATOM 527 H ALA 32 30.066 40.386 27.821 1.00 0.00 H +ATOM 528 CA ALA 32 30.664 41.193 29.719 1.00 0.00 C +ATOM 529 HA ALA 32 31.491 41.903 29.749 1.00 0.00 H +ATOM 530 CB ALA 32 29.359 41.990 29.637 1.00 0.00 C +ATOM 531 HB1 ALA 32 28.498 41.320 29.604 1.00 0.00 H +ATOM 532 HB2 ALA 32 29.265 42.632 30.518 1.00 0.00 H +ATOM 533 HB3 ALA 32 29.360 42.618 28.745 1.00 0.00 H +ATOM 534 C ALA 32 30.757 40.346 31.006 1.00 0.00 C +ATOM 535 O ALA 32 31.714 40.486 31.766 1.00 0.00 O +ATOM 536 N MET 33 29.862 39.359 31.165 1.00 0.00 N +ATOM 537 H MET 33 29.116 39.293 30.484 1.00 0.00 H +ATOM 538 CA MET 33 29.829 38.444 32.321 1.00 0.00 C +ATOM 539 HA MET 33 29.671 39.040 33.221 1.00 0.00 H +ATOM 540 CB MET 33 28.619 37.507 32.134 1.00 0.00 C +ATOM 541 HB2 MET 33 27.713 38.110 32.048 1.00 0.00 H +ATOM 542 HB3 MET 33 28.745 36.961 31.196 1.00 0.00 H +ATOM 543 CG MET 33 28.400 36.473 33.250 1.00 0.00 C +ATOM 544 HG2 MET 33 27.622 35.779 32.928 1.00 0.00 H +ATOM 545 HG3 MET 33 29.310 35.893 33.391 1.00 0.00 H +ATOM 546 SD MET 33 27.891 37.160 34.845 1.00 0.00 S +ATOM 547 CE MET 33 28.165 35.719 35.909 1.00 0.00 C +ATOM 548 HE1 MET 33 29.213 35.421 35.855 1.00 0.00 H +ATOM 549 HE2 MET 33 27.919 35.978 36.940 1.00 0.00 H +ATOM 550 HE3 MET 33 27.530 34.894 35.583 1.00 0.00 H +ATOM 551 C MET 33 31.141 37.654 32.526 1.00 0.00 C +ATOM 552 O MET 33 31.423 37.185 33.627 1.00 0.00 O +ATOM 553 N ALA 34 31.955 37.472 31.479 1.00 0.00 N +ATOM 554 H ALA 34 31.675 37.852 30.587 1.00 0.00 H +ATOM 555 CA ALA 34 33.295 36.891 31.598 1.00 0.00 C +ATOM 556 HA ALA 34 33.269 36.098 32.346 1.00 0.00 H +ATOM 557 CB ALA 34 33.661 36.252 30.258 1.00 0.00 C +ATOM 558 HB1 ALA 34 33.789 37.025 29.503 1.00 0.00 H +ATOM 559 HB2 ALA 34 34.586 35.693 30.383 1.00 0.00 H +ATOM 560 HB3 ALA 34 32.890 35.559 29.932 1.00 0.00 H +ATOM 561 C ALA 34 34.361 37.908 32.061 1.00 0.00 C +ATOM 562 O ALA 34 35.201 37.573 32.893 1.00 0.00 O +ATOM 563 N ASN 35 34.323 39.158 31.587 1.00 0.00 N +ATOM 564 H ASN 35 33.586 39.411 30.938 1.00 0.00 H +ATOM 565 CA ASN 35 35.217 40.225 32.061 1.00 0.00 C +ATOM 566 HA ASN 35 36.233 39.828 32.101 1.00 0.00 H +ATOM 567 CB ASN 35 35.225 41.390 31.060 1.00 0.00 C +ATOM 568 HB2 ASN 35 34.212 41.623 30.737 1.00 0.00 H +ATOM 569 HB3 ASN 35 35.642 42.274 31.543 1.00 0.00 H +ATOM 570 CG ASN 35 36.110 41.066 29.875 1.00 0.00 C +ATOM 571 OD1 ASN 35 37.325 41.124 29.946 1.00 0.00 O +ATOM 572 ND2 ASN 35 35.543 40.671 28.767 1.00 0.00 N +ATOM 573 HD21 ASN 35 36.169 40.327 28.036 1.00 0.00 H +ATOM 574 HD22 ASN 35 34.552 40.478 28.754 1.00 0.00 H +ATOM 575 C ASN 35 34.906 40.685 33.496 1.00 0.00 C +ATOM 576 O ASN 35 35.840 40.994 34.232 1.00 0.00 O +ATOM 577 N ASP 36 33.645 40.618 33.935 1.00 0.00 N +ATOM 578 H ASP 36 32.903 40.472 33.257 1.00 0.00 H +ATOM 579 CA ASP 36 33.264 40.776 35.350 1.00 0.00 C +ATOM 580 HA ASP 36 33.615 41.749 35.702 1.00 0.00 H +ATOM 581 CB ASP 36 31.733 40.747 35.473 1.00 0.00 C +ATOM 582 HB2 ASP 36 31.358 39.823 35.024 1.00 0.00 H +ATOM 583 HB3 ASP 36 31.470 40.725 36.533 1.00 0.00 H +ATOM 584 CG ASP 36 31.031 41.957 34.843 1.00 0.00 C +ATOM 585 OD1 ASP 36 31.533 43.090 35.035 1.00 0.00 O +ATOM 586 OD2 ASP 36 29.966 41.744 34.217 1.00 0.00 O +ATOM 587 C ASP 36 33.907 39.703 36.258 1.00 0.00 C +ATOM 588 O ASP 36 34.247 39.982 37.409 1.00 0.00 O +ATOM 589 N LEU 37 34.124 38.485 35.736 1.00 0.00 N +ATOM 590 H LEU 37 33.787 38.316 34.799 1.00 0.00 H +ATOM 591 CA LEU 37 34.901 37.423 36.394 1.00 0.00 C +ATOM 592 HA LEU 37 34.727 37.504 37.465 1.00 0.00 H +ATOM 593 CB LEU 37 34.343 36.066 35.914 1.00 0.00 C +ATOM 594 HB2 LEU 37 33.266 36.054 36.096 1.00 0.00 H +ATOM 595 HB3 LEU 37 34.494 35.994 34.837 1.00 0.00 H +ATOM 596 CG LEU 37 34.962 34.815 36.568 1.00 0.00 C +ATOM 597 HG LEU 37 36.029 34.779 36.363 1.00 0.00 H +ATOM 598 CD1 LEU 37 34.737 34.768 38.082 1.00 0.00 C +ATOM 599 HD11 LEU 37 33.672 34.841 38.306 1.00 0.00 H +ATOM 600 HD12 LEU 37 35.131 33.837 38.487 1.00 0.00 H +ATOM 601 HD13 LEU 37 35.263 35.597 38.555 1.00 0.00 H +ATOM 602 CD2 LEU 37 34.327 33.558 35.966 1.00 0.00 C +ATOM 603 HD21 LEU 37 34.496 33.547 34.888 1.00 0.00 H +ATOM 604 HD22 LEU 37 34.785 32.670 36.401 1.00 0.00 H +ATOM 605 HD23 LEU 37 33.255 33.549 36.163 1.00 0.00 H +ATOM 606 C LEU 37 36.429 37.565 36.184 1.00 0.00 C +ATOM 607 O LEU 37 37.214 37.039 36.976 1.00 0.00 O +ATOM 608 N GLY 38 36.861 38.293 35.146 1.00 0.00 N +ATOM 609 H GLY 38 36.147 38.677 34.540 1.00 0.00 H +ATOM 610 CA GLY 38 38.229 38.796 34.965 1.00 0.00 C +ATOM 611 HA2 GLY 38 38.289 39.788 35.412 1.00 0.00 H +ATOM 612 HA3 GLY 38 38.920 38.149 35.501 1.00 0.00 H +ATOM 613 C GLY 38 38.739 38.896 33.517 1.00 0.00 C +ATOM 614 O GLY 38 39.656 39.677 33.270 1.00 0.00 O +ATOM 615 N ARG 39 38.211 38.106 32.567 1.00 0.00 N +ATOM 616 H ARG 39 37.431 37.520 32.844 1.00 0.00 H +ATOM 617 CA ARG 39 38.616 38.058 31.138 1.00 0.00 C +ATOM 618 HA ARG 39 38.611 39.074 30.737 1.00 0.00 H +ATOM 619 CB ARG 39 40.038 37.457 31.037 1.00 0.00 C +ATOM 620 HB2 ARG 39 40.704 38.039 31.673 1.00 0.00 H +ATOM 621 HB3 ARG 39 40.019 36.431 31.412 1.00 0.00 H +ATOM 622 CG ARG 39 40.617 37.460 29.611 1.00 0.00 C +ATOM 623 HG2 ARG 39 40.037 36.773 28.994 1.00 0.00 H +ATOM 624 HG3 ARG 39 40.539 38.461 29.183 1.00 0.00 H +ATOM 625 CD ARG 39 42.085 37.001 29.575 1.00 0.00 C +ATOM 626 HD2 ARG 39 42.171 36.028 30.058 1.00 0.00 H +ATOM 627 HD3 ARG 39 42.366 36.866 28.528 1.00 0.00 H +ATOM 628 NE ARG 39 43.008 37.988 30.181 1.00 0.00 N +ATOM 629 HE ARG 39 43.213 38.797 29.616 1.00 0.00 H +ATOM 630 CZ ARG 39 43.620 37.922 31.353 1.00 0.00 C +ATOM 631 NH1 ARG 39 43.462 36.920 32.175 1.00 0.00 N +ATOM 632 HH11 ARG 39 42.901 36.142 31.881 1.00 0.00 H +ATOM 633 HH12 ARG 39 43.924 36.912 33.064 1.00 0.00 H +ATOM 634 NH2 ARG 39 44.416 38.883 31.731 1.00 0.00 N +ATOM 635 HH21 ARG 39 44.562 39.678 31.135 1.00 0.00 H +ATOM 636 HH22 ARG 39 44.928 38.822 32.594 1.00 0.00 H +ATOM 637 C ARG 39 37.628 37.212 30.321 1.00 0.00 C +ATOM 638 O ARG 39 37.146 36.204 30.831 1.00 0.00 O +ATOM 639 N ASP 40 37.354 37.571 29.065 1.00 0.00 N +ATOM 640 H ASP 40 37.758 38.416 28.677 1.00 0.00 H +ATOM 641 CA ASP 40 36.561 36.737 28.150 1.00 0.00 C +ATOM 642 HA ASP 40 35.897 36.130 28.754 1.00 0.00 H +ATOM 643 CB ASP 40 35.662 37.581 27.236 1.00 0.00 C +ATOM 644 HB2 ASP 40 35.054 36.898 26.645 1.00 0.00 H +ATOM 645 HB3 ASP 40 34.972 38.147 27.858 1.00 0.00 H +ATOM 646 CG ASP 40 36.388 38.553 26.305 1.00 0.00 C +ATOM 647 OD1 ASP 40 37.088 39.453 26.822 1.00 0.00 O +ATOM 648 OD2 ASP 40 36.142 38.463 25.082 1.00 0.00 O +ATOM 649 C ASP 40 37.366 35.731 27.310 1.00 0.00 C +ATOM 650 O ASP 40 38.517 35.966 26.951 1.00 0.00 O +ATOM 651 N GLY 41 36.695 34.633 26.945 1.00 0.00 N +ATOM 652 H GLY 41 35.773 34.509 27.334 1.00 0.00 H +ATOM 653 CA GLY 41 37.097 33.692 25.889 1.00 0.00 C +ATOM 654 HA2 GLY 41 37.998 34.064 25.388 1.00 0.00 H +ATOM 655 HA3 GLY 41 37.321 32.718 26.335 1.00 0.00 H +ATOM 656 C GLY 41 35.998 33.504 24.829 1.00 0.00 C +ATOM 657 O GLY 41 34.857 33.955 24.984 1.00 0.00 O +ATOM 658 N GLU 42 36.330 32.838 23.724 1.00 0.00 N +ATOM 659 H GLU 42 37.259 32.459 23.666 1.00 0.00 H +ATOM 660 CA GLU 42 35.426 32.613 22.589 1.00 0.00 C +ATOM 661 HA GLU 42 34.763 33.471 22.533 1.00 0.00 H +ATOM 662 CB GLU 42 36.220 32.532 21.271 1.00 0.00 C +ATOM 663 HB2 GLU 42 36.851 31.643 21.295 1.00 0.00 H +ATOM 664 HB3 GLU 42 35.513 32.414 20.449 1.00 0.00 H +ATOM 665 CG GLU 42 37.113 33.752 20.965 1.00 0.00 C +ATOM 666 HG2 GLU 42 37.953 33.741 21.664 1.00 0.00 H +ATOM 667 HG3 GLU 42 37.524 33.639 19.960 1.00 0.00 H +ATOM 668 CD GLU 42 36.395 35.108 21.069 1.00 0.00 C +ATOM 669 OE1 GLU 42 35.146 35.162 21.033 1.00 0.00 O +ATOM 670 OE2 GLU 42 37.068 36.138 21.285 1.00 0.00 O +ATOM 671 C GLU 42 34.494 31.403 22.759 1.00 0.00 C +ATOM 672 O GLU 42 34.758 30.510 23.563 1.00 0.00 O +ATOM 673 N HIP 43 33.370 31.399 22.026 1.00 0.00 N +ATOM 674 H HIP 43 33.245 32.127 21.331 1.00 0.00 H +ATOM 675 CA HIP 43 32.308 30.384 22.122 1.00 0.00 C +ATOM 676 HA HIP 43 32.731 29.459 22.517 1.00 0.00 H +ATOM 677 CB HIP 43 31.202 30.851 23.088 1.00 0.00 C +ATOM 678 HB2 HIP 43 30.740 31.756 22.689 1.00 0.00 H +ATOM 679 HB3 HIP 43 30.423 30.087 23.129 1.00 0.00 H +ATOM 680 CG HIP 43 31.675 31.132 24.490 1.00 0.00 C +ATOM 681 ND1 HIP 43 32.339 32.269 24.917 1.00 0.00 N +ATOM 682 HD1 HIP 43 32.666 33.031 24.335 1.00 0.00 H +ATOM 683 CE1 HIP 43 32.725 32.065 26.185 1.00 0.00 C +ATOM 684 HE1 HIP 43 33.373 32.718 26.769 1.00 0.00 H +ATOM 685 NE2 HIP 43 32.306 30.849 26.582 1.00 0.00 N +ATOM 686 HE2 HIP 43 32.558 30.447 27.494 1.00 0.00 H +ATOM 687 CD2 HIP 43 31.660 30.237 25.525 1.00 0.00 C +ATOM 688 HD2 HIP 43 31.302 29.216 25.476 1.00 0.00 H +ATOM 689 C HIP 43 31.704 30.075 20.749 1.00 0.00 C +ATOM 690 O HIP 43 31.426 31.004 19.996 1.00 0.00 O +ATOM 691 N THR 44 31.467 28.799 20.455 1.00 0.00 N +ATOM 692 H THR 44 31.691 28.104 21.150 1.00 0.00 H +ATOM 693 CA THR 44 30.721 28.358 19.259 1.00 0.00 C +ATOM 694 HA THR 44 31.003 28.994 18.420 1.00 0.00 H +ATOM 695 CB THR 44 31.096 26.905 18.900 1.00 0.00 C +ATOM 696 HB THR 44 30.801 26.240 19.713 1.00 0.00 H +ATOM 697 CG2 THR 44 30.480 26.400 17.592 1.00 0.00 C +ATOM 698 HG21 THR 44 30.622 27.136 16.799 1.00 0.00 H +ATOM 699 HG22 THR 44 30.950 25.463 17.294 1.00 0.00 H +ATOM 700 HG23 THR 44 29.416 26.208 17.728 1.00 0.00 H +ATOM 701 OG1 THR 44 32.492 26.824 18.732 1.00 0.00 O +ATOM 702 HG1 THR 44 32.707 25.932 18.442 1.00 0.00 H +ATOM 703 C THR 44 29.210 28.535 19.479 1.00 0.00 C +ATOM 704 O THR 44 28.772 28.651 20.626 1.00 0.00 O +ATOM 705 N LYN 45 28.408 28.579 18.411 1.00 0.00 N +ATOM 706 H LYN 45 28.811 28.432 17.499 1.00 0.00 H +ATOM 707 CA LYN 45 26.955 28.754 18.461 1.00 0.00 C +ATOM 708 HA LYN 45 26.617 28.502 19.463 1.00 0.00 H +ATOM 709 CB LYN 45 26.603 30.233 18.198 1.00 0.00 C +ATOM 710 HB2 LYN 45 25.542 30.379 18.411 1.00 0.00 H +ATOM 711 HB3 LYN 45 27.169 30.868 18.882 1.00 0.00 H +ATOM 712 CG LYN 45 26.888 30.667 16.744 1.00 0.00 C +ATOM 713 HG2 LYN 45 27.965 30.622 16.563 1.00 0.00 H +ATOM 714 HG3 LYN 45 26.389 29.982 16.058 1.00 0.00 H +ATOM 715 CD LYN 45 26.379 32.090 16.469 1.00 0.00 C +ATOM 716 HD2 LYN 45 25.313 32.140 16.685 1.00 0.00 H +ATOM 717 HD3 LYN 45 26.905 32.782 17.129 1.00 0.00 H +ATOM 718 CE LYN 45 26.624 32.508 15.011 1.00 0.00 C +ATOM 719 HE2 LYN 45 26.349 33.551 14.878 1.00 0.00 H +ATOM 720 HE3 LYN 45 27.683 32.403 14.776 1.00 0.00 H +ATOM 721 NZ LYN 45 25.869 31.687 14.057 1.00 0.00 N +ATOM 722 HZ2 LYN 45 25.501 32.274 13.322 1.00 0.00 H +ATOM 723 HZ3 LYN 45 26.480 30.997 13.666 1.00 0.00 H +ATOM 724 C LYN 45 26.206 27.832 17.493 1.00 0.00 C +ATOM 725 O LYN 45 26.775 27.348 16.516 1.00 0.00 O +ATOM 726 N ASP 46 24.906 27.668 17.732 1.00 0.00 N +ATOM 727 H ASP 46 24.546 28.022 18.614 1.00 0.00 H +ATOM 728 CA ASP 46 23.913 27.112 16.809 1.00 0.00 C +ATOM 729 HA ASP 46 24.283 27.216 15.786 1.00 0.00 H +ATOM 730 CB ASP 46 23.691 25.622 17.116 1.00 0.00 C +ATOM 731 HB2 ASP 46 24.567 25.035 16.818 1.00 0.00 H +ATOM 732 HB3 ASP 46 23.581 25.521 18.203 1.00 0.00 H +ATOM 733 CG ASP 46 22.445 25.080 16.433 1.00 0.00 C +ATOM 734 OD1 ASP 46 21.629 24.455 17.138 1.00 0.00 O +ATOM 735 OD2 ASP 46 22.249 25.346 15.231 1.00 0.00 O +ATOM 736 C ASP 46 22.595 27.881 16.952 1.00 0.00 C +ATOM 737 O ASP 46 22.077 28.053 18.056 1.00 0.00 O +ATOM 738 N ASP 47 22.016 28.321 15.829 1.00 0.00 N +ATOM 739 H ASP 47 22.470 28.102 14.955 1.00 0.00 H +ATOM 740 CA ASP 47 20.701 29.003 15.792 1.00 0.00 C +ATOM 741 HA ASP 47 20.677 29.711 16.618 1.00 0.00 H +ATOM 742 CB ASP 47 20.545 29.865 14.542 1.00 0.00 C +ATOM 743 HB2 ASP 47 21.376 30.565 14.533 1.00 0.00 H +ATOM 744 HB3 ASP 47 20.609 29.233 13.631 1.00 0.00 H +ATOM 745 CG ASP 47 19.284 30.686 14.619 1.00 0.00 C +ATOM 746 OD1 ASP 47 18.283 30.395 13.928 1.00 0.00 O +ATOM 747 OD2 ASP 47 19.195 31.526 15.535 1.00 0.00 O +ATOM 748 C ASP 47 19.511 28.047 15.935 1.00 0.00 C +ATOM 749 O ASP 47 18.482 28.421 16.500 1.00 0.00 O +ATOM 750 N ALA 48 19.623 26.797 15.469 1.00 0.00 N +ATOM 751 H ALA 48 20.532 26.476 15.127 1.00 0.00 H +ATOM 752 CA ALA 48 18.509 25.839 15.497 1.00 0.00 C +ATOM 753 HA ALA 48 17.651 26.291 14.991 1.00 0.00 H +ATOM 754 CB ALA 48 18.910 24.576 14.726 1.00 0.00 C +ATOM 755 HB1 ALA 48 19.754 24.092 15.215 1.00 0.00 H +ATOM 756 HB2 ALA 48 18.072 23.886 14.699 1.00 0.00 H +ATOM 757 HB3 ALA 48 19.194 24.825 13.704 1.00 0.00 H +ATOM 758 C ALA 48 18.085 25.533 16.943 1.00 0.00 C +ATOM 759 O ALA 48 16.905 25.617 17.296 1.00 0.00 O +ATOM 760 N THR 49 19.052 25.242 17.814 1.00 0.00 N +ATOM 761 H THR 49 19.989 25.070 17.445 1.00 0.00 H +ATOM 762 CA THR 49 18.878 25.118 19.268 1.00 0.00 C +ATOM 763 HA THR 49 17.852 24.783 19.449 1.00 0.00 H +ATOM 764 CB THR 49 19.833 24.058 19.831 1.00 0.00 C +ATOM 765 HB THR 49 19.634 23.969 20.896 1.00 0.00 H +ATOM 766 CG2 THR 49 19.654 22.674 19.212 1.00 0.00 C +ATOM 767 HG21 THR 49 19.909 22.682 18.152 1.00 0.00 H +ATOM 768 HG22 THR 49 20.317 21.983 19.725 1.00 0.00 H +ATOM 769 HG23 THR 49 18.622 22.340 19.325 1.00 0.00 H +ATOM 770 OG1 THR 49 21.179 24.426 19.670 1.00 0.00 O +ATOM 771 HG1 THR 49 21.386 24.355 18.705 1.00 0.00 H +ATOM 772 C THR 49 19.059 26.435 20.038 1.00 0.00 C +ATOM 773 O THR 49 18.985 26.432 21.267 1.00 0.00 O +ATOM 774 N LYS 50 19.285 27.561 19.346 1.00 0.00 N +ATOM 775 H LYS 50 19.342 27.461 18.343 1.00 0.00 H +ATOM 776 CA LYS 50 19.472 28.925 19.901 1.00 0.00 C +ATOM 777 HA LYS 50 19.880 29.543 19.099 1.00 0.00 H +ATOM 778 CB LYS 50 18.098 29.509 20.332 1.00 0.00 C +ATOM 779 HB2 LYS 50 17.673 28.838 21.076 1.00 0.00 H +ATOM 780 HB3 LYS 50 18.261 30.477 20.819 1.00 0.00 H +ATOM 781 CG LYS 50 17.067 29.712 19.206 1.00 0.00 C +ATOM 782 HG2 LYS 50 17.014 28.822 18.574 1.00 0.00 H +ATOM 783 HG3 LYS 50 16.086 29.850 19.676 1.00 0.00 H +ATOM 784 CD LYS 50 17.372 30.959 18.352 1.00 0.00 C +ATOM 785 HD2 LYS 50 17.360 31.833 19.010 1.00 0.00 H +ATOM 786 HD3 LYS 50 18.383 30.868 17.915 1.00 0.00 H +ATOM 787 CE LYS 50 16.321 31.169 17.250 1.00 0.00 C +ATOM 788 HE2 LYS 50 15.339 30.864 17.626 1.00 0.00 H +ATOM 789 HE3 LYS 50 16.298 32.229 16.981 1.00 0.00 H +ATOM 790 NZ LYS 50 16.645 30.380 16.040 1.00 0.00 N +ATOM 791 HZ1 LYS 50 16.985 29.446 16.254 1.00 0.00 H +ATOM 792 HZ2 LYS 50 15.920 30.335 15.344 1.00 0.00 H +ATOM 793 HZ3 LYS 50 17.445 30.779 15.533 1.00 0.00 H +ATOM 794 C LYS 50 20.528 28.972 21.028 1.00 0.00 C +ATOM 795 O LYS 50 20.302 29.623 22.053 1.00 0.00 O +ATOM 796 N THR 51 21.628 28.236 20.869 1.00 0.00 N +ATOM 797 H THR 51 21.791 27.829 19.955 1.00 0.00 H +ATOM 798 CA THR 51 22.554 27.872 21.959 1.00 0.00 C +ATOM 799 HA THR 51 22.299 28.448 22.834 1.00 0.00 H +ATOM 800 CB THR 51 22.378 26.369 22.345 1.00 0.00 C +ATOM 801 HB THR 51 22.510 25.765 21.446 1.00 0.00 H +ATOM 802 CG2 THR 51 23.395 25.880 23.366 1.00 0.00 C +ATOM 803 HG21 THR 51 23.419 26.502 24.256 1.00 0.00 H +ATOM 804 HG22 THR 51 23.175 24.858 23.676 1.00 0.00 H +ATOM 805 HG23 THR 51 24.392 25.856 22.938 1.00 0.00 H +ATOM 806 OG1 THR 51 21.107 26.133 22.906 1.00 0.00 O +ATOM 807 HG1 THR 51 20.438 26.248 22.201 1.00 0.00 H +ATOM 808 C THR 51 24.039 28.178 21.666 1.00 0.00 C +ATOM 809 O THR 51 24.559 27.818 20.615 1.00 0.00 O +ATOM 810 N PHE 52 24.754 28.785 22.624 1.00 0.00 N +ATOM 811 H PHE 52 24.245 29.156 23.420 1.00 0.00 H +ATOM 812 CA PHE 52 26.225 28.839 22.664 1.00 0.00 C +ATOM 813 HA PHE 52 26.606 28.820 21.650 1.00 0.00 H +ATOM 814 CB PHE 52 26.691 30.157 23.319 1.00 0.00 C +ATOM 815 HB2 PHE 52 26.175 30.279 24.269 1.00 0.00 H +ATOM 816 HB3 PHE 52 27.757 30.073 23.534 1.00 0.00 H +ATOM 817 CG PHE 52 26.488 31.402 22.476 1.00 0.00 C +ATOM 818 CD1 PHE 52 25.306 32.159 22.590 1.00 0.00 C +ATOM 819 HD1 PHE 52 24.515 31.835 23.247 1.00 0.00 H +ATOM 820 CE1 PHE 52 25.154 33.342 21.843 1.00 0.00 C +ATOM 821 HE1 PHE 52 24.247 33.923 21.925 1.00 0.00 H +ATOM 822 CZ PHE 52 26.182 33.771 20.985 1.00 0.00 C +ATOM 823 HZ PHE 52 26.064 34.677 20.408 1.00 0.00 H +ATOM 824 CE2 PHE 52 27.359 33.013 20.861 1.00 0.00 C +ATOM 825 HE2 PHE 52 28.144 33.340 20.192 1.00 0.00 H +ATOM 826 CD2 PHE 52 27.508 31.826 21.600 1.00 0.00 C +ATOM 827 HD2 PHE 52 28.408 31.240 21.488 1.00 0.00 H +ATOM 828 C PHE 52 26.849 27.661 23.434 1.00 0.00 C +ATOM 829 O PHE 52 26.291 27.206 24.437 1.00 0.00 O +ATOM 830 N THR 53 28.052 27.225 23.033 1.00 0.00 N +ATOM 831 H THR 53 28.445 27.656 22.197 1.00 0.00 H +ATOM 832 CA THR 53 28.833 26.103 23.617 1.00 0.00 C +ATOM 833 HA THR 53 28.496 25.936 24.641 1.00 0.00 H +ATOM 834 CB THR 53 28.598 24.796 22.824 1.00 0.00 C +ATOM 835 HB THR 53 29.153 23.993 23.309 1.00 0.00 H +ATOM 836 CG2 THR 53 27.139 24.356 22.749 1.00 0.00 C +ATOM 837 HG21 THR 53 26.566 25.047 22.132 1.00 0.00 H +ATOM 838 HG22 THR 53 27.084 23.357 22.319 1.00 0.00 H +ATOM 839 HG23 THR 53 26.718 24.323 23.751 1.00 0.00 H +ATOM 840 OG1 THR 53 29.077 24.934 21.508 1.00 0.00 O +ATOM 841 HG1 THR 53 28.772 24.169 21.009 1.00 0.00 H +ATOM 842 C THR 53 30.351 26.388 23.677 1.00 0.00 C +ATOM 843 O THR 53 30.807 27.474 23.312 1.00 0.00 O +ATOM 844 N SER 54 31.141 25.416 24.151 1.00 0.00 N +ATOM 845 H SER 54 30.703 24.551 24.431 1.00 0.00 H +ATOM 846 CA SER 54 32.612 25.391 24.076 1.00 0.00 C +ATOM 847 HA SER 54 32.945 26.191 23.418 1.00 0.00 H +ATOM 848 CB SER 54 33.238 25.631 25.454 1.00 0.00 C +ATOM 849 HB2 SER 54 32.859 26.571 25.851 1.00 0.00 H +ATOM 850 HB3 SER 54 32.962 24.823 26.133 1.00 0.00 H +ATOM 851 OG SER 54 34.649 25.706 25.359 1.00 0.00 O +ATOM 852 HG SER 54 35.032 24.827 25.477 1.00 0.00 H +ATOM 853 C SER 54 33.114 24.057 23.467 1.00 0.00 C +ATOM 854 O SER 54 32.442 23.034 23.590 1.00 0.00 O +ATOM 855 N LYS 55 34.283 24.082 22.819 1.00 0.00 N +ATOM 856 H LYS 55 34.809 24.944 22.852 1.00 0.00 H +ATOM 857 CA LYS 55 34.904 22.919 22.151 1.00 0.00 C +ATOM 858 HA LYS 55 34.124 22.409 21.592 1.00 0.00 H +ATOM 859 CB LYS 55 35.957 23.408 21.137 1.00 0.00 C +ATOM 860 HB2 LYS 55 36.270 22.561 20.521 1.00 0.00 H +ATOM 861 HB3 LYS 55 35.496 24.142 20.463 1.00 0.00 H +ATOM 862 CG LYS 55 37.213 24.036 21.787 1.00 0.00 C +ATOM 863 HG2 LYS 55 36.902 24.877 22.418 1.00 0.00 H +ATOM 864 HG3 LYS 55 37.703 23.296 22.427 1.00 0.00 H +ATOM 865 CD LYS 55 38.245 24.537 20.766 1.00 0.00 C +ATOM 866 HD2 LYS 55 37.767 25.286 20.129 1.00 0.00 H +ATOM 867 HD3 LYS 55 39.054 25.020 21.305 1.00 0.00 H +ATOM 868 CE LYS 55 38.852 23.433 19.879 1.00 0.00 C +ATOM 869 HE2 LYS 55 38.069 23.015 19.214 1.00 0.00 H +ATOM 870 HE3 LYS 55 39.592 23.940 19.254 1.00 0.00 H +ATOM 871 NZ LYS 55 39.577 22.376 20.638 1.00 0.00 N +ATOM 872 HZ1 LYS 55 38.967 21.625 20.958 1.00 0.00 H +ATOM 873 HZ2 LYS 55 40.265 21.931 20.041 1.00 0.00 H +ATOM 874 HZ3 LYS 55 40.055 22.736 21.441 1.00 0.00 H +ATOM 875 C LYS 55 35.499 21.888 23.119 1.00 0.00 C +ATOM 876 O LYS 55 35.824 22.210 24.256 1.00 0.00 O +ATOM 877 N GLU 56 35.657 20.680 22.583 1.00 0.00 N +ATOM 878 H GLU 56 35.333 20.577 21.640 1.00 0.00 H +ATOM 879 CA GLU 56 36.595 19.613 23.024 1.00 0.00 C +ATOM 880 HA GLU 56 36.752 19.726 24.093 1.00 0.00 H +ATOM 881 CB GLU 56 35.909 18.246 22.778 1.00 0.00 C +ATOM 882 HB2 GLU 56 34.836 18.349 22.920 1.00 0.00 H +ATOM 883 HB3 GLU 56 36.020 18.002 21.730 1.00 0.00 H +ATOM 884 CG GLU 56 36.394 17.029 23.608 1.00 0.00 C +ATOM 885 HG2 GLU 56 36.489 16.183 22.937 1.00 0.00 H +ATOM 886 HG3 GLU 56 37.387 17.233 23.979 1.00 0.00 H +ATOM 887 CD GLU 56 35.508 16.555 24.805 1.00 0.00 C +ATOM 888 OE1 GLU 56 35.904 15.565 25.479 1.00 0.00 O +ATOM 889 OE2 GLU 56 34.413 17.114 25.072 1.00 0.00 O +ATOM 890 C GLU 56 37.964 19.768 22.371 1.00 0.00 C +ATOM 891 O GLU 56 39.015 19.514 22.996 1.00 0.00 O +ATOM 892 OXT GLU 56 37.993 20.269 21.212 1.00 0.00 O +HETATM 893 ZN ZN1 57 26.498 32.489 29.471 1.00 0.00 Zn +HETATM 894 N AN1 58 28.214 33.192 30.364 1.00 0.00 N +HETATM 895 C AN1 58 30.576 34.103 31.003 1.00 0.00 C +HETATM 896 C1 AN1 58 29.261 33.584 30.680 1.00 0.00 C +HETATM 897 H AN1 58 30.650 34.367 32.063 1.00 0.00 H +HETATM 898 H1 AN1 58 30.768 35.002 30.407 1.00 0.00 H +HETATM 899 H2 AN1 58 31.353 33.365 30.766 1.00 0.00 H +HETATM 900 N1 AZI 59 30.233 28.753 29.524 1.00 0.00 N +HETATM 901 N2 AZI 59 29.712 28.995 30.612 1.00 0.00 N +HETATM 902 N3 AZI 59 29.208 29.261 31.731 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 893 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 105 101 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 118 132 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 140 142 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 139 145 144 143 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 142 147 +CONECT 146 145 +CONECT 147 151 145 148 +CONECT 148 147 150 149 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 153 147 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 202 189 +CONECT 188 187 +CONECT 189 187 191 195 190 +CONECT 190 189 +CONECT 191 192 194 189 193 +CONECT 192 191 +CONECT 193 191 +CONECT 194 191 +CONECT 195 196 189 197 198 +CONECT 196 195 +CONECT 197 195 +CONECT 198 195 200 199 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 226 204 207 208 +CONECT 207 206 +CONECT 208 206 211 209 210 +CONECT 209 208 +CONECT 210 208 +CONECT 211 213 212 214 208 +CONECT 212 211 +CONECT 213 211 +CONECT 214 216 211 217 215 +CONECT 215 214 +CONECT 216 214 +CONECT 217 219 214 218 +CONECT 218 217 +CONECT 219 220 223 217 +CONECT 220 222 221 219 +CONECT 221 220 +CONECT 222 220 +CONECT 223 225 219 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 227 228 206 +CONECT 227 226 +CONECT 228 230 226 229 +CONECT 229 228 +CONECT 230 231 248 232 228 +CONECT 231 230 +CONECT 232 235 230 233 234 +CONECT 233 232 +CONECT 234 232 +CONECT 235 237 236 238 232 +CONECT 236 235 +CONECT 237 235 +CONECT 238 239 235 240 241 +CONECT 239 238 +CONECT 240 238 +CONECT 241 243 238 244 242 +CONECT 242 241 +CONECT 243 241 +CONECT 244 247 241 245 246 +CONECT 245 244 +CONECT 246 244 +CONECT 247 244 +CONECT 248 249 230 250 +CONECT 249 248 +CONECT 250 248 252 251 +CONECT 251 250 +CONECT 252 255 253 250 254 +CONECT 253 252 +CONECT 254 252 +CONECT 255 256 257 252 +CONECT 256 255 +CONECT 257 259 255 258 +CONECT 258 257 +CONECT 259 261 260 271 257 +CONECT 260 259 +CONECT 261 267 262 263 259 +CONECT 262 261 +CONECT 263 265 261 264 266 +CONECT 264 263 +CONECT 265 263 +CONECT 266 263 +CONECT 267 269 268 270 261 +CONECT 268 267 +CONECT 269 267 +CONECT 270 267 +CONECT 271 273 259 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 273 284 277 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 274 278 285 286 +CONECT 278 279 280 277 +CONECT 279 282 288 278 +CONECT 280 281 278 287 +CONECT 281 289 282 280 +CONECT 282 893 281 279 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 293 294 302 290 +CONECT 293 292 +CONECT 294 295 296 292 300 +CONECT 295 294 +CONECT 296 299 298 294 297 +CONECT 297 296 +CONECT 298 296 +CONECT 299 296 +CONECT 300 294 301 +CONECT 301 300 +CONECT 302 304 292 303 +CONECT 303 302 +CONECT 304 314 305 302 +CONECT 305 306 308 304 315 +CONECT 306 307 321 305 +CONECT 307 306 +CONECT 308 316 317 305 309 +CONECT 309 308 310 311 +CONECT 310 319 309 313 +CONECT 311 309 318 312 +CONECT 312 313 311 320 +CONECT 313 310 893 312 +CONECT 314 304 +CONECT 315 305 +CONECT 316 308 +CONECT 317 308 +CONECT 318 311 +CONECT 319 310 +CONECT 320 312 +CONECT 321 323 306 322 +CONECT 322 321 +CONECT 323 334 324 321 325 +CONECT 324 323 +CONECT 325 323 328 327 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 330 331 325 329 +CONECT 329 328 +CONECT 330 328 +CONECT 331 332 328 333 +CONECT 332 331 +CONECT 333 331 +CONECT 334 336 335 323 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 344 340 339 336 +CONECT 339 338 +CONECT 340 342 341 338 343 +CONECT 341 340 +CONECT 342 340 +CONECT 343 340 +CONECT 344 346 345 338 +CONECT 345 344 +CONECT 346 348 347 344 +CONECT 347 346 +CONECT 348 360 350 349 346 +CONECT 349 348 +CONECT 350 351 356 348 352 +CONECT 351 350 +CONECT 352 350 354 355 353 +CONECT 353 352 +CONECT 354 352 +CONECT 355 352 +CONECT 356 357 358 350 359 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 +CONECT 360 361 362 348 +CONECT 361 360 +CONECT 362 364 360 363 +CONECT 363 362 +CONECT 364 366 365 372 362 +CONECT 365 364 +CONECT 366 369 367 368 364 +CONECT 367 366 +CONECT 368 366 +CONECT 369 370 371 366 +CONECT 370 369 +CONECT 371 369 +CONECT 372 364 374 373 +CONECT 373 372 +CONECT 374 375 376 372 +CONECT 375 374 +CONECT 376 378 374 396 377 +CONECT 377 376 +CONECT 378 381 380 379 376 +CONECT 379 378 +CONECT 380 378 +CONECT 381 382 395 378 +CONECT 382 384 383 381 +CONECT 383 382 +CONECT 384 385 386 382 +CONECT 385 384 +CONECT 386 387 384 395 +CONECT 387 388 389 386 +CONECT 388 387 +CONECT 389 390 387 391 +CONECT 390 389 +CONECT 391 389 392 393 +CONECT 392 391 +CONECT 393 391 395 394 +CONECT 394 393 +CONECT 395 386 393 381 +CONECT 396 398 376 397 +CONECT 397 396 +CONECT 398 399 400 396 +CONECT 399 398 +CONECT 400 402 401 398 406 +CONECT 401 400 +CONECT 402 405 404 403 400 +CONECT 403 402 +CONECT 404 402 +CONECT 405 402 +CONECT 406 400 407 408 +CONECT 407 406 +CONECT 408 406 409 410 +CONECT 409 408 +CONECT 410 408 411 412 421 +CONECT 411 410 +CONECT 412 415 413 410 414 +CONECT 413 412 +CONECT 414 412 +CONECT 415 416 417 418 412 +CONECT 416 415 +CONECT 417 415 +CONECT 418 420 415 419 +CONECT 419 418 +CONECT 420 418 +CONECT 421 410 423 422 +CONECT 422 421 +CONECT 423 424 421 425 +CONECT 424 423 +CONECT 425 423 427 431 426 +CONECT 426 425 +CONECT 427 428 430 425 429 +CONECT 428 427 +CONECT 429 427 +CONECT 430 427 +CONECT 431 433 425 432 +CONECT 432 431 +CONECT 433 434 435 431 +CONECT 434 433 +CONECT 435 437 433 436 446 +CONECT 436 435 +CONECT 437 438 439 440 435 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 437 442 441 +CONECT 441 440 +CONECT 442 440 +CONECT 443 445 444 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 435 448 447 +CONECT 447 446 +CONECT 448 449 446 450 +CONECT 449 448 +CONECT 450 448 452 451 468 +CONECT 451 450 +CONECT 452 455 453 454 450 +CONECT 453 452 +CONECT 454 452 +CONECT 455 457 458 456 452 +CONECT 456 455 +CONECT 457 455 +CONECT 458 461 459 460 455 +CONECT 459 458 +CONECT 460 458 +CONECT 461 464 462 463 458 +CONECT 462 461 +CONECT 463 461 +CONECT 464 466 465 467 461 +CONECT 465 464 +CONECT 466 464 +CONECT 467 464 +CONECT 468 450 470 469 +CONECT 469 468 +CONECT 470 471 468 472 +CONECT 471 470 +CONECT 472 470 474 473 488 +CONECT 473 472 +CONECT 474 477 475 472 476 +CONECT 475 474 +CONECT 476 474 +CONECT 477 478 486 474 +CONECT 478 480 479 477 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 483 480 484 +CONECT 483 482 +CONECT 484 482 485 486 +CONECT 485 484 +CONECT 486 484 477 487 +CONECT 487 486 +CONECT 488 490 472 489 +CONECT 489 488 +CONECT 490 491 492 488 +CONECT 491 490 +CONECT 492 494 490 502 493 +CONECT 493 492 +CONECT 494 495 500 496 492 +CONECT 495 494 +CONECT 496 498 494 499 497 +CONECT 497 496 +CONECT 498 496 +CONECT 499 496 +CONECT 500 501 494 +CONECT 501 500 +CONECT 502 504 492 503 +CONECT 503 502 +CONECT 504 505 506 502 +CONECT 505 504 +CONECT 506 508 504 507 524 +CONECT 507 506 +CONECT 508 511 509 510 506 +CONECT 509 508 +CONECT 510 508 +CONECT 511 514 513 512 508 +CONECT 512 511 +CONECT 513 511 +CONECT 514 517 515 516 511 +CONECT 515 514 +CONECT 516 514 +CONECT 517 519 518 520 514 +CONECT 518 517 +CONECT 519 517 +CONECT 520 522 517 523 521 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 506 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 530 529 534 +CONECT 529 528 +CONECT 530 533 531 528 532 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 536 540 551 539 +CONECT 539 538 +CONECT 540 542 541 538 543 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 544 545 546 +CONECT 544 543 +CONECT 545 543 +CONECT 546 543 547 +CONECT 547 546 550 548 549 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 553 538 552 +CONECT 552 551 +CONECT 553 554 555 551 +CONECT 554 553 +CONECT 555 557 553 561 556 +CONECT 556 555 +CONECT 557 558 560 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 557 +CONECT 561 563 555 562 +CONECT 562 561 +CONECT 563 564 565 561 +CONECT 564 563 +CONECT 565 567 563 566 575 +CONECT 566 565 +CONECT 567 570 568 569 565 +CONECT 568 567 +CONECT 569 567 +CONECT 570 572 571 567 +CONECT 571 570 +CONECT 572 573 574 570 +CONECT 573 572 +CONECT 574 572 +CONECT 575 565 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 581 580 587 +CONECT 580 579 +CONECT 581 584 582 579 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 586 585 581 +CONECT 585 584 +CONECT 586 584 +CONECT 587 579 589 588 +CONECT 588 587 +CONECT 589 590 587 591 +CONECT 590 589 +CONECT 591 589 593 606 592 +CONECT 592 591 +CONECT 593 595 594 591 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 593 602 597 598 +CONECT 597 596 +CONECT 598 596 599 600 601 +CONECT 599 598 +CONECT 600 598 +CONECT 601 598 +CONECT 602 603 605 604 596 +CONECT 603 602 +CONECT 604 602 +CONECT 605 602 +CONECT 606 608 591 607 +CONECT 607 606 +CONECT 608 609 610 606 +CONECT 609 608 +CONECT 610 613 608 611 612 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 610 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 637 618 619 615 +CONECT 618 617 +CONECT 619 622 617 621 620 +CONECT 620 619 +CONECT 621 619 +CONECT 622 623 624 625 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 627 622 626 628 +CONECT 626 625 +CONECT 627 625 +CONECT 628 625 629 630 +CONECT 629 628 +CONECT 630 628 634 631 +CONECT 631 630 632 633 +CONECT 632 631 +CONECT 633 631 +CONECT 634 635 630 636 +CONECT 635 634 +CONECT 636 634 +CONECT 637 639 638 617 +CONECT 638 637 +CONECT 639 641 640 637 +CONECT 640 639 +CONECT 641 643 649 642 639 +CONECT 642 641 +CONECT 643 646 644 645 641 +CONECT 644 643 +CONECT 645 643 +CONECT 646 648 647 643 +CONECT 647 646 +CONECT 648 646 +CONECT 649 651 650 641 +CONECT 650 649 +CONECT 651 653 649 652 +CONECT 652 651 +CONECT 653 656 654 655 651 +CONECT 654 653 +CONECT 655 653 +CONECT 656 658 657 653 +CONECT 657 656 +CONECT 658 660 659 656 +CONECT 659 658 +CONECT 660 662 661 671 658 +CONECT 661 660 +CONECT 662 664 665 663 660 +CONECT 663 662 +CONECT 664 662 +CONECT 665 667 668 662 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 665 669 670 +CONECT 669 668 +CONECT 670 668 +CONECT 671 673 660 672 +CONECT 672 671 +CONECT 673 674 675 671 +CONECT 674 673 +CONECT 675 689 673 676 677 +CONECT 676 675 +CONECT 677 675 678 679 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 681 687 +CONECT 681 682 680 683 +CONECT 682 681 +CONECT 683 681 685 684 +CONECT 684 683 +CONECT 685 687 683 686 +CONECT 686 685 +CONECT 687 680 688 685 +CONECT 688 687 +CONECT 689 690 691 675 +CONECT 690 689 +CONECT 691 693 689 692 +CONECT 692 691 +CONECT 693 694 695 703 691 +CONECT 694 693 +CONECT 695 697 701 693 696 +CONECT 696 695 +CONECT 697 698 699 700 695 +CONECT 698 697 +CONECT 699 697 +CONECT 700 697 +CONECT 701 702 695 +CONECT 702 701 +CONECT 703 705 693 704 +CONECT 704 703 +CONECT 705 706 707 703 +CONECT 706 705 +CONECT 707 724 709 705 708 +CONECT 708 707 +CONECT 709 712 710 707 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 715 713 709 +CONECT 713 712 +CONECT 714 712 +CONECT 715 718 716 712 717 +CONECT 716 715 +CONECT 717 715 +CONECT 718 721 720 719 715 +CONECT 719 718 +CONECT 720 718 +CONECT 721 722 723 718 +CONECT 722 721 +CONECT 723 721 +CONECT 724 725 726 707 +CONECT 725 724 +CONECT 726 728 724 727 +CONECT 727 726 +CONECT 728 729 736 730 726 +CONECT 729 728 +CONECT 730 733 728 731 732 +CONECT 731 730 +CONECT 732 730 +CONECT 733 735 730 734 +CONECT 734 733 +CONECT 735 733 +CONECT 736 738 728 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 742 738 748 741 +CONECT 741 740 +CONECT 742 744 743 745 740 +CONECT 743 742 +CONECT 744 742 +CONECT 745 746 742 747 +CONECT 746 745 +CONECT 747 745 +CONECT 748 750 740 749 +CONECT 749 748 +CONECT 750 751 752 748 +CONECT 751 750 +CONECT 752 754 753 750 758 +CONECT 753 752 +CONECT 754 757 756 755 752 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 752 759 760 +CONECT 759 758 +CONECT 760 758 761 762 +CONECT 761 760 +CONECT 762 760 763 764 772 +CONECT 763 762 +CONECT 764 766 762 770 765 +CONECT 765 764 +CONECT 766 767 769 768 764 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 762 774 773 +CONECT 773 772 +CONECT 774 775 776 772 +CONECT 775 774 +CONECT 776 777 774 778 794 +CONECT 777 776 +CONECT 778 781 776 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 784 782 783 778 +CONECT 782 781 +CONECT 783 781 +CONECT 784 787 786 785 781 +CONECT 785 784 +CONECT 786 784 +CONECT 787 790 789 788 784 +CONECT 788 787 +CONECT 789 787 +CONECT 790 792 793 791 787 +CONECT 791 790 +CONECT 792 790 +CONECT 793 790 +CONECT 794 776 796 795 +CONECT 795 794 +CONECT 796 797 794 798 +CONECT 797 796 +CONECT 798 796 808 800 799 +CONECT 799 798 +CONECT 800 801 798 806 802 +CONECT 801 800 +CONECT 802 800 805 804 803 +CONECT 803 802 +CONECT 804 802 +CONECT 805 802 +CONECT 806 807 800 +CONECT 807 806 +CONECT 808 809 798 810 +CONECT 809 808 +CONECT 810 808 812 811 +CONECT 811 810 +CONECT 812 813 810 814 828 +CONECT 813 812 +CONECT 814 817 812 816 815 +CONECT 815 814 +CONECT 816 814 +CONECT 817 826 818 814 +CONECT 818 820 817 819 +CONECT 819 818 +CONECT 820 822 821 818 +CONECT 821 820 +CONECT 822 823 824 820 +CONECT 823 822 +CONECT 824 825 822 826 +CONECT 825 824 +CONECT 826 824 827 817 +CONECT 827 826 +CONECT 828 812 830 829 +CONECT 829 828 +CONECT 830 831 828 832 +CONECT 831 830 +CONECT 832 834 830 842 833 +CONECT 833 832 +CONECT 834 840 836 835 832 +CONECT 835 834 +CONECT 836 837 838 834 839 +CONECT 837 836 +CONECT 838 836 +CONECT 839 836 +CONECT 840 841 834 +CONECT 841 840 +CONECT 842 843 832 844 +CONECT 843 842 +CONECT 844 842 846 845 +CONECT 845 844 +CONECT 846 847 853 844 848 +CONECT 847 846 +CONECT 848 846 851 849 850 +CONECT 849 848 +CONECT 850 848 +CONECT 851 848 852 +CONECT 852 851 +CONECT 853 855 854 846 +CONECT 854 853 +CONECT 855 857 856 853 +CONECT 856 855 +CONECT 857 859 858 855 875 +CONECT 858 857 +CONECT 859 861 860 862 857 +CONECT 860 859 +CONECT 861 859 +CONECT 862 865 859 863 864 +CONECT 863 862 +CONECT 864 862 +CONECT 865 868 866 867 862 +CONECT 866 865 +CONECT 867 865 +CONECT 868 869 870 871 865 +CONECT 869 868 +CONECT 870 868 +CONECT 871 868 873 872 874 +CONECT 872 871 +CONECT 873 871 +CONECT 874 871 +CONECT 875 857 877 876 +CONECT 876 875 +CONECT 877 878 879 875 +CONECT 878 877 +CONECT 879 890 877 881 880 +CONECT 880 879 +CONECT 881 883 882 879 884 +CONECT 882 881 +CONECT 883 881 +CONECT 884 881 885 886 887 +CONECT 885 884 +CONECT 886 884 +CONECT 887 884 889 888 +CONECT 888 887 +CONECT 889 887 +CONECT 890 892 891 879 +CONECT 891 890 +CONECT 892 890 +CONECT 893 87 313 894 282 +CONECT 894 893 896 +CONECT 895 898 896 899 897 +CONECT 896 894 895 +CONECT 897 895 +CONECT 898 895 +CONECT 899 895 +CONECT 900 901 +CONECT 901 900 902 +CONECT 902 901 +MASTER 0 0 0 0 0 0 0 0 902 0 902 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_2_front_4.pdb b/tests/nsga2/intermediate_molecules/min_iter_2_front_4.pdb new file mode 100644 index 0000000..ab33aa9 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_2_front_4.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.3475 49.977499999999736 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.973 23.612 1.00 0.00 N +ATOM 2 H1 MET 1 15.135 38.357 24.556 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.346 23.089 1.00 0.00 H +ATOM 4 H3 MET 1 16.016 38.284 23.187 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.505 23.670 1.00 0.00 C +ATOM 6 HA MET 1 14.170 36.198 24.097 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.876 22.274 1.00 0.00 C +ATOM 8 HB2 MET 1 14.391 36.152 21.672 1.00 0.00 H +ATOM 9 HB3 MET 1 16.151 36.274 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.373 34.334 22.298 1.00 0.00 C +ATOM 11 HG2 MET 1 16.260 34.066 22.868 1.00 0.00 H +ATOM 12 HG3 MET 1 14.495 33.925 22.807 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.526 20.668 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.572 20.068 1.00 0.00 C +ATOM 15 HE1 MET 1 13.463 34.602 20.016 1.00 0.00 H +ATOM 16 HE2 MET 1 13.776 33.133 19.073 1.00 0.00 H +ATOM 17 HE3 MET 1 13.173 32.997 20.735 1.00 0.00 H +ATOM 18 C MET 1 16.218 36.031 24.600 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.398 24.428 1.00 0.00 O +ATOM 20 N GLN 2 15.878 35.187 25.578 1.00 0.00 N +ATOM 21 H GLN 2 14.912 34.996 25.769 1.00 0.00 H +ATOM 22 CA GLN 2 16.850 34.476 26.430 1.00 0.00 C +ATOM 23 HA GLN 2 17.657 35.151 26.723 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.070 27.723 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.137 33.654 27.496 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.662 33.325 28.279 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.257 28.675 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.459 36.087 28.164 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.214 34.973 29.415 1.00 0.00 H +ATOM 30 CD GLN 2 17.128 35.582 29.524 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.142 34.924 29.513 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.039 36.477 30.468 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.765 36.535 31.087 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.097 36.722 30.761 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.301 25.666 1.00 0.00 C +ATOM 36 O GLN 2 17.102 32.148 25.829 1.00 0.00 O +ATOM 37 N TYR 3 18.478 33.617 24.821 1.00 0.00 N +ATOM 38 H TYR 3 18.752 34.594 24.754 1.00 0.00 H +ATOM 39 CA TYR 3 19.260 32.619 24.100 1.00 0.00 C +ATOM 40 HA TYR 3 18.568 31.967 23.564 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.285 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.866 33.942 23.645 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.481 22.672 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.068 21.937 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.530 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.822 32.423 20.550 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.147 34.204 19.542 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.116 33.738 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.844 35.573 19.676 1.00 0.00 C +ATOM 50 OH TYR 3 18.514 36.309 18.584 1.00 0.00 O +ATOM 51 HH TYR 3 18.772 35.874 17.768 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.189 20.940 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.728 37.250 21.025 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.324 35.441 22.067 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.446 35.934 23.023 1.00 0.00 H +ATOM 56 C TYR 3 20.089 31.764 25.076 1.00 0.00 C +ATOM 57 O TYR 3 20.458 32.245 26.150 1.00 0.00 O +ATOM 58 N LYS 4 20.399 30.504 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.250 30.220 23.771 1.00 0.00 H +ATOM 60 CA LYS 4 21.010 29.502 25.633 1.00 0.00 C +ATOM 61 HA LYS 4 20.726 29.715 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.476 28.101 25.273 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.522 27.982 24.192 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.145 27.345 25.699 1.00 0.00 H +ATOM 65 CG LYS 4 19.052 27.745 25.738 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.888 26.697 25.498 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.995 27.853 26.819 1.00 0.00 H +ATOM 68 CD LYS 4 17.923 28.564 25.084 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.886 29.557 25.526 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.149 28.678 24.022 1.00 0.00 H +ATOM 71 CE LYS 4 16.546 27.888 25.193 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.507 24.665 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.597 26.933 24.667 1.00 0.00 H +ATOM 74 NZ LYS 4 16.095 27.656 26.590 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.985 28.528 27.089 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.207 27.154 26.591 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.756 27.062 27.077 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.619 1.00 0.00 C +ATOM 79 O LYS 4 23.196 29.886 24.647 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.029 26.694 1.00 0.00 N +HETATM 81 CA HX1 5 24.625 28.832 26.820 1.00 0.00 C +HETATM 82 C HX1 5 24.899 27.672 27.782 1.00 0.00 C +HETATM 83 O HX1 5 24.405 27.683 28.910 1.00 0.00 O +HETATM 84 CB HX1 5 25.264 30.145 27.306 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.392 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.072 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.385 27.861 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.095 27.755 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.938 29.837 27.336 1.00 0.00 N +HETATM 90 H HX1 5 22.596 28.839 27.521 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.841 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.383 28.292 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.940 30.947 26.639 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.282 26.701 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.531 31.750 28.083 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.839 29.356 27.352 1.00 0.00 H +ATOM 97 N ILE 6 25.634 26.658 27.326 1.00 0.00 N +ATOM 98 H ILE 6 26.015 26.711 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.003 25.472 28.116 1.00 0.00 C +ATOM 100 HA ILE 6 25.303 25.370 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.851 24.199 27.246 1.00 0.00 C +ATOM 102 HB ILE 6 26.402 24.347 26.317 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.409 22.939 27.935 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.892 22.757 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.288 22.070 27.288 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.481 23.048 28.117 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.345 24.012 26.914 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.791 23.875 27.842 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.968 24.915 26.433 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.011 22.847 25.977 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.180 21.893 26.476 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.956 22.903 25.700 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.617 22.905 25.073 1.00 0.00 H +ATOM 114 C ILE 6 27.391 25.668 28.756 1.00 0.00 C +ATOM 115 O ILE 6 28.227 26.398 28.224 1.00 0.00 O +ATOM 116 N VAL 7 27.598 25.081 29.940 1.00 0.00 N +ATOM 117 H VAL 7 26.867 24.478 30.298 1.00 0.00 H +ATOM 118 CA VAL 7 28.776 25.287 30.804 1.00 0.00 C +ATOM 119 HA VAL 7 28.877 26.362 30.959 1.00 0.00 H +ATOM 120 CB VAL 7 28.499 24.641 32.179 1.00 0.00 C +ATOM 121 HB VAL 7 27.500 24.950 32.487 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.522 23.107 32.134 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.532 22.745 31.926 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.190 22.716 33.090 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.855 22.747 31.351 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.449 25.111 33.285 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.292 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.077 24.778 34.251 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.446 24.702 33.142 1.00 0.00 H +ATOM 130 C VAL 7 30.110 24.804 30.202 1.00 0.00 C +ATOM 131 O VAL 7 30.151 23.918 29.351 1.00 0.00 O +ATOM 132 N THR 8 31.213 25.378 30.689 1.00 0.00 N +ATOM 133 H THR 8 31.110 26.089 31.397 1.00 0.00 H +ATOM 134 CA THR 8 32.596 24.972 30.392 1.00 0.00 C +ATOM 135 HA THR 8 32.687 24.826 29.316 1.00 0.00 H +ATOM 136 CB THR 8 33.570 26.088 30.816 1.00 0.00 C +ATOM 137 HB THR 8 34.595 25.756 30.638 1.00 0.00 H +ATOM 138 CG2 THR 8 33.356 27.393 30.055 1.00 0.00 C +ATOM 139 HG21 THR 8 32.383 27.824 30.296 1.00 0.00 H +ATOM 140 HG22 THR 8 34.132 28.110 30.322 1.00 0.00 H +ATOM 141 HG23 THR 8 33.402 27.211 28.983 1.00 0.00 H +ATOM 142 OG1 THR 8 33.421 26.396 32.182 1.00 0.00 O +ATOM 143 HG1 THR 8 33.806 27.265 32.319 1.00 0.00 H +ATOM 144 C THR 8 33.009 23.656 31.077 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.250 32.105 1.00 0.00 O +ATOM 146 N GLY 9 34.047 23.007 30.532 1.00 0.00 N +ATOM 147 H GLY 9 34.399 23.335 29.647 1.00 0.00 H +ATOM 148 CA GLY 9 34.624 21.774 31.075 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.615 21.618 30.651 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.881 32.155 1.00 0.00 H +ATOM 151 C GLY 9 33.781 20.522 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.016 20.483 29.829 1.00 0.00 O +ATOM 153 N LYS 10 33.954 19.478 31.612 1.00 0.00 N +ATOM 154 H LYS 10 34.677 19.557 32.310 1.00 0.00 H +ATOM 155 CA LYS 10 33.235 18.188 31.477 1.00 0.00 C +ATOM 156 HA LYS 10 32.295 18.399 30.965 1.00 0.00 H +ATOM 157 CB LYS 10 34.063 17.245 30.575 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.683 17.846 29.905 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.730 16.638 31.191 1.00 0.00 H +ATOM 160 CG LYS 10 33.197 16.330 29.689 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.601 15.662 30.311 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.521 16.954 29.102 1.00 0.00 H +ATOM 163 CD LYS 10 34.060 15.496 28.727 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.718 16.162 28.166 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.669 14.795 29.300 1.00 0.00 H +ATOM 166 CE LYS 10 33.176 14.722 27.742 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.970 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.467 15.418 27.287 1.00 0.00 H +ATOM 169 NZ LYS 10 33.968 14.073 26.670 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.727 13.511 27.035 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.369 13.526 26.062 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.418 14.773 26.065 1.00 0.00 H +ATOM 173 C LYS 10 32.827 17.541 32.811 1.00 0.00 C +ATOM 174 O LYS 10 32.345 16.412 32.831 1.00 0.00 O +ATOM 175 N SER 11 33.039 18.242 33.932 1.00 0.00 N +ATOM 176 H SER 11 33.491 19.134 33.839 1.00 0.00 H +ATOM 177 CA SER 11 32.567 17.848 35.278 1.00 0.00 C +ATOM 178 HA SER 11 32.502 16.757 35.338 1.00 0.00 H +ATOM 179 CB SER 11 33.554 18.327 36.351 1.00 0.00 C +ATOM 180 HB2 SER 11 33.584 19.416 36.351 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.982 37.329 1.00 0.00 H +ATOM 182 OG SER 11 34.851 17.824 36.092 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.429 36.454 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.417 35.586 1.00 0.00 C +ATOM 185 O SER 11 30.350 17.745 36.192 1.00 0.00 O +ATOM 186 N CYS 12 30.920 19.653 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.631 20.135 34.631 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.268 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.868 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.352 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.323 22.214 34.524 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.249 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.147 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.147 23.411 37.056 1.00 0.00 H +ATOM 195 C CYS 12 28.852 19.934 33.837 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.664 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.512 19.987 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.061 20.142 34.737 1.00 0.00 H +ATOM 199 CA LYS 13 26.668 19.719 32.664 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.856 31.774 1.00 0.00 H +ATOM 201 CB LYS 13 26.222 18.245 32.710 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.030 17.651 33.147 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.343 18.143 33.363 1.00 0.00 H +ATOM 204 CG LYS 13 25.911 17.632 31.329 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.032 18.104 30.890 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.763 17.815 30.673 1.00 0.00 H +ATOM 207 CD LYS 13 25.679 16.113 31.416 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.682 15.711 30.401 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.513 15.660 31.956 1.00 0.00 H +ATOM 210 CE LYS 13 24.340 15.743 32.074 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.161 16.384 32.939 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.551 15.953 31.349 1.00 0.00 H +ATOM 213 NZ LYS 13 24.295 14.306 32.456 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.868 14.091 33.273 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.348 13.998 32.647 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.676 13.728 31.708 1.00 0.00 H +ATOM 217 C LYS 13 25.489 20.705 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.585 20.485 31.710 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.785 33.297 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.943 33.873 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.751 33.377 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.446 22.191 33.448 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.484 23.328 34.293 1.00 0.00 H +ATOM 224 C GLY 14 24.287 23.715 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.215 23.890 31.406 1.00 0.00 O +ATOM 226 N VAL 15 23.147 24.399 32.109 1.00 0.00 N +ATOM 227 H VAL 15 22.434 24.248 32.807 1.00 0.00 H +ATOM 228 CA VAL 15 22.780 25.390 31.070 1.00 0.00 C +ATOM 229 HA VAL 15 23.676 25.631 30.490 1.00 0.00 H +ATOM 230 CB VAL 15 21.762 24.738 30.086 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.858 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.449 24.323 30.767 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.939 25.182 31.209 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.794 23.862 30.026 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.583 31.546 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.419 25.672 28.928 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.336 26.009 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.822 25.122 28.195 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.846 26.536 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.285 26.687 31.731 1.00 0.00 C +ATOM 241 O VAL 15 21.718 26.631 32.821 1.00 0.00 O +HETATM 242 N HY1 16 22.497 27.830 31.092 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.110 31.451 1.00 0.00 C +HETATM 244 C HY1 16 21.621 29.885 30.134 1.00 0.00 C +HETATM 245 O HY1 16 21.778 29.349 29.016 1.00 0.00 O +HETATM 246 CB HY1 16 22.863 29.871 32.416 1.00 0.00 C +HETATM 247 CG HY1 16 24.211 30.224 31.815 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.548 31.406 31.209 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.320 29.397 31.739 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.302 30.092 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.879 31.315 30.787 1.00 0.00 N +HETATM 252 H HY1 16 22.998 27.783 30.212 1.00 0.00 H +HETATM 253 HA HY1 16 20.967 28.994 31.944 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.401 30.797 32.776 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.027 29.259 33.299 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.398 28.459 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.906 32.259 31.098 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.729 30.997 1.00 0.00 H +ATOM 259 N THR 17 21.169 31.140 30.273 1.00 0.00 N +ATOM 260 H THR 17 21.053 31.461 31.222 1.00 0.00 H +ATOM 261 CA THR 17 20.726 32.026 29.180 1.00 0.00 C +ATOM 262 HA THR 17 21.104 31.634 28.291 1.00 0.00 H +ATOM 263 CB THR 17 19.148 32.016 29.046 1.00 0.00 C +ATOM 264 HB THR 17 18.923 32.603 28.170 1.00 0.00 H +ATOM 265 CG2 THR 17 18.589 30.665 28.720 1.00 0.00 C +ATOM 266 HG21 THR 17 18.790 29.907 29.433 1.00 0.00 H +ATOM 267 HG22 THR 17 17.504 30.697 28.632 1.00 0.00 H +ATOM 268 HG23 THR 17 18.931 30.334 27.781 1.00 0.00 H +ATOM 269 OG1 THR 17 18.484 32.465 30.197 1.00 0.00 O +ATOM 270 HG1 THR 17 18.581 33.451 30.206 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.458 29.234 1.00 0.00 C +ATOM 272 O THR 17 21.706 33.922 30.266 1.00 0.00 O +HETATM 273 N HY2 18 21.133 34.157 28.097 1.00 0.00 N +HETATM 274 CA HY2 18 21.447 35.619 27.968 1.00 0.00 C +HETATM 275 C HY2 18 20.323 36.288 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.983 35.838 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.769 35.819 27.255 1.00 0.00 C +HETATM 278 CG HY2 18 23.998 35.326 28.000 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.419 34.029 28.151 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.941 36.119 28.641 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.317 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.707 27.234 1.00 0.00 H +HETATM 284 HA HY2 18 21.501 36.055 29.015 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.747 35.291 26.296 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.912 36.877 27.054 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.952 37.122 28.679 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.930 33.168 27.777 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.758 35.649 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.806 37.389 27.746 1.00 0.00 N +ATOM 291 H GLU 19 20.137 37.679 28.643 1.00 0.00 H +ATOM 292 CA GLU 19 18.797 38.219 27.105 1.00 0.00 C +ATOM 293 HA GLU 19 18.056 37.553 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.066 39.074 28.153 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.753 38.431 28.965 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.774 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.827 39.851 27.656 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.547 28.418 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.083 40.405 26.761 1.00 0.00 H +ATOM 300 CD GLU 19 15.649 38.897 27.370 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.578 38.371 26.227 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.814 38.685 28.283 1.00 0.00 O +ATOM 303 C GLU 19 19.403 39.112 25.991 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.858 26.275 1.00 0.00 O +ATOM 305 N ALA 20 18.876 39.050 24.758 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.353 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.964 23.687 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.962 24.097 1.00 0.00 H +ATOM 309 CB ALA 20 20.589 39.492 23.095 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.463 38.518 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.950 40.207 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.350 39.402 23.869 1.00 0.00 H +ATOM 313 C ALA 20 18.192 40.038 22.583 1.00 0.00 C +ATOM 314 O ALA 20 17.358 39.136 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.090 21.748 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.829 21.922 1.00 0.00 H +ATOM 317 CA VAL 21 17.459 41.152 20.464 1.00 0.00 C +ATOM 318 HA VAL 21 16.471 40.727 20.628 1.00 0.00 H +ATOM 319 CB VAL 21 17.272 42.602 19.975 1.00 0.00 C +ATOM 320 HB VAL 21 16.617 42.576 19.112 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.594 43.474 21.037 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.250 43.628 21.894 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.346 44.443 20.604 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.670 43.000 21.367 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.581 43.283 19.543 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.005 42.771 18.677 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.378 44.312 19.246 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.314 43.286 20.353 1.00 0.00 H +ATOM 329 C VAL 21 18.120 40.335 19.354 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.995 18.376 1.00 0.00 O +ATOM 331 N ASP 22 19.412 40.053 19.508 1.00 0.00 N +ATOM 332 H ASP 22 19.861 40.330 20.363 1.00 0.00 H +ATOM 333 CA ASP 22 20.292 39.467 18.503 1.00 0.00 C +ATOM 334 HA ASP 22 19.710 38.829 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.939 40.592 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.170 41.084 17.077 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.376 41.328 18.357 1.00 0.00 H +ATOM 338 CG ASP 22 22.019 40.045 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.149 40.566 16.818 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.744 39.033 16.072 1.00 0.00 O +ATOM 341 C ASP 22 21.365 38.599 19.176 1.00 0.00 C +ATOM 342 O ASP 22 21.822 38.878 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.790 37.551 18.485 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.496 17.513 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.613 18.977 1.00 0.00 C +ATOM 346 HA TRP 23 22.544 36.362 20.008 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.353 18.132 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.979 18.209 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.841 35.607 17.088 1.00 0.00 H +ATOM 350 CG TRP 23 23.572 34.246 18.526 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.514 33.704 17.727 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.735 34.018 16.716 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.125 32.677 18.406 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.897 32.152 18.028 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.587 32.476 19.654 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.823 31.539 20.660 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.537 30.742 20.518 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.687 21.884 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.018 22.698 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.769 22.095 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.906 23.078 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.006 33.662 21.051 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.312 34.470 21.209 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.636 33.530 19.792 1.00 0.00 C +ATOM 365 C TRP 23 24.211 37.188 18.977 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.919 1.00 0.00 O +ATOM 367 N ALA 24 24.560 38.026 17.993 1.00 0.00 N +ATOM 368 H ALA 24 23.884 38.270 17.276 1.00 0.00 H +ATOM 369 CA ALA 24 25.849 38.719 17.975 1.00 0.00 C +ATOM 370 HA ALA 24 26.621 38.003 18.265 1.00 0.00 H +ATOM 371 CB ALA 24 26.163 39.147 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.450 39.890 16.191 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.165 39.568 16.485 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.115 38.282 15.875 1.00 0.00 H +ATOM 375 C ALA 24 25.931 39.882 18.996 1.00 0.00 C +ATOM 376 O ALA 24 27.024 40.380 19.278 1.00 0.00 O +ATOM 377 N GLU 25 24.813 40.289 19.607 1.00 0.00 N +ATOM 378 H GLU 25 23.933 39.955 19.233 1.00 0.00 H +ATOM 379 CA GLU 25 24.789 41.076 20.851 1.00 0.00 C +ATOM 380 HA GLU 25 25.640 41.758 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.510 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.645 41.277 20.821 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.448 42.384 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.425 43.037 19.876 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.627 42.632 18.886 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.402 43.419 19.864 1.00 0.00 H +ATOM 387 CD GLU 25 24.366 44.203 20.189 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.896 45.204 20.734 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.592 44.053 19.851 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.098 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.518 23.014 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.004 22.127 1.00 0.00 N +ATOM 393 H ALA 26 23.667 38.776 21.363 1.00 0.00 H +ATOM 394 CA ALA 26 24.459 38.028 23.214 1.00 0.00 C +ATOM 395 HA ALA 26 24.198 38.523 24.143 1.00 0.00 H +ATOM 396 CB ALA 26 23.492 36.861 23.009 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.772 36.287 22.127 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.202 23.878 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.230 22.889 1.00 0.00 H +ATOM 400 C ALA 26 25.919 37.533 23.362 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.229 24.479 1.00 0.00 O +ATOM 402 N GLU 27 26.712 37.509 22.282 1.00 0.00 N +ATOM 403 H GLU 27 26.270 37.639 21.372 1.00 0.00 H +ATOM 404 CA GLU 27 28.168 37.305 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.370 36.352 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.768 37.249 20.914 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.159 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.737 38.253 20.487 1.00 0.00 H +ATOM 409 CG GLU 27 30.213 36.730 20.925 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.144 21.782 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.198 35.646 21.049 1.00 0.00 H +ATOM 412 CD GLU 27 30.995 37.107 19.653 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.755 38.110 19.729 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.384 18.638 1.00 0.00 O +ATOM 415 C GLU 27 28.847 38.398 23.184 1.00 0.00 C +ATOM 416 O GLU 27 29.569 38.095 24.137 1.00 0.00 O +ATOM 417 N LYS 28 28.546 39.674 22.914 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.855 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.819 23.667 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.668 1.00 0.00 H +ATOM 421 CB LYS 28 28.698 42.147 22.994 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.280 23.051 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.171 42.964 23.544 1.00 0.00 H +ATOM 424 CG LYS 28 29.135 42.222 21.520 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.205 42.027 21.442 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.599 41.464 20.951 1.00 0.00 H +ATOM 427 CD LYS 28 28.836 43.606 20.922 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.820 43.913 21.179 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.525 44.332 21.362 1.00 0.00 H +ATOM 430 CE LYS 28 28.996 43.630 19.397 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.091 44.670 19.083 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.914 43.114 19.123 1.00 0.00 H +ATOM 433 NZ LYS 28 27.828 43.021 18.717 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.969 43.488 19.030 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.884 43.102 17.711 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.711 42.039 18.969 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.783 25.133 1.00 0.00 C +ATOM 438 O LYS 28 29.480 40.969 26.020 1.00 0.00 O +ATOM 439 N PHE 29 27.392 40.453 25.418 1.00 0.00 N +ATOM 440 H PHE 29 26.739 40.365 24.641 1.00 0.00 H +ATOM 441 CA PHE 29 26.901 40.285 26.792 1.00 0.00 C +ATOM 442 HA PHE 29 27.227 41.146 27.381 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.262 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.036 39.343 26.309 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.020 40.229 27.831 1.00 0.00 H +ATOM 446 CG PHE 29 24.675 41.444 26.115 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.462 41.234 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.013 40.254 25.408 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.829 42.300 24.768 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.903 42.125 24.236 1.00 0.00 H +ATOM 451 CZ PHE 29 23.396 43.583 24.789 1.00 0.00 C +ATOM 452 HZ PHE 29 22.917 44.395 24.266 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.589 43.803 25.497 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.025 44.796 25.526 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.225 42.742 26.163 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.138 42.936 26.702 1.00 0.00 H +ATOM 457 C PHE 29 27.483 39.049 27.505 1.00 0.00 C +ATOM 458 O PHE 29 27.587 39.036 28.736 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.764 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.043 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.685 36.894 27.317 1.00 0.00 C +ATOM 462 HA THR 30 28.209 36.547 28.224 1.00 0.00 H +ATOM 463 CB THR 30 28.691 35.719 26.332 1.00 0.00 C +ATOM 464 HB THR 30 29.069 36.026 25.354 1.00 0.00 H +ATOM 465 CG2 THR 30 29.495 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.132 34.215 27.800 1.00 0.00 H +ATOM 467 HG22 THR 30 29.364 33.689 26.122 1.00 0.00 H +ATOM 468 HG23 THR 30 30.558 34.743 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.366 35.283 26.192 1.00 0.00 O +ATOM 470 HG1 THR 30 26.961 35.884 25.541 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.981 28.768 1.00 0.00 O +ATOM 473 N LYS 31 30.744 38.121 26.830 1.00 0.00 N +ATOM 474 H LYS 31 30.286 38.318 25.946 1.00 0.00 H +ATOM 475 CA LYS 31 32.077 38.701 27.066 1.00 0.00 C +ATOM 476 HA LYS 31 32.746 37.904 27.373 1.00 0.00 H +ATOM 477 CB LYS 31 32.614 39.317 25.767 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.010 25.345 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.526 39.864 25.984 1.00 0.00 H +ATOM 480 CG LYS 31 32.928 38.207 24.738 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.681 37.552 25.175 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.044 37.631 24.523 1.00 0.00 H +ATOM 483 CD LYS 31 33.460 38.815 23.434 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.383 22.946 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.300 39.496 23.639 1.00 0.00 H +ATOM 486 CE LYS 31 33.922 37.721 22.460 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.110 37.056 22.242 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.219 38.192 21.541 1.00 0.00 H +ATOM 489 NZ LYS 31 35.076 36.972 23.012 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.820 36.242 23.678 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.551 36.467 22.263 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.761 37.564 23.504 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.185 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.781 28.913 1.00 0.00 O +ATOM 495 N ALA 32 31.030 40.509 28.371 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.874 41.413 29.513 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.139 29.502 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.372 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.494 29.373 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.876 30.212 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.556 42.756 28.443 1.00 0.00 H +ATOM 503 C ALA 32 30.964 40.640 30.836 1.00 0.00 C +ATOM 504 O ALA 32 31.880 40.889 31.614 1.00 0.00 O +ATOM 505 N LYN 33 30.119 39.614 31.029 1.00 0.00 N +ATOM 506 H LYN 33 29.393 39.457 30.345 1.00 0.00 H +ATOM 507 CA LYN 33 30.159 38.756 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.026 39.385 33.109 1.00 0.00 H +ATOM 509 CB LYN 33 29.011 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.063 37.156 31.263 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.143 37.040 33.026 1.00 0.00 H +ATOM 512 CG LYN 33 27.613 38.360 32.313 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.566 38.985 33.205 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.415 38.982 31.441 1.00 0.00 H +ATOM 515 CD LYN 33 26.538 37.269 32.411 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.694 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.634 36.750 33.364 1.00 0.00 H +ATOM 518 CE LYN 33 25.125 37.836 32.286 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.936 38.516 33.109 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.037 38.375 31.345 1.00 0.00 H +ATOM 521 NZ LYN 33 24.119 36.762 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.186 37.155 32.262 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.255 36.114 31.546 1.00 0.00 H +ATOM 524 C LYN 33 31.513 38.043 32.390 1.00 0.00 C +ATOM 525 O LYN 33 32.011 37.922 33.504 1.00 0.00 O +ATOM 526 N ALA 34 32.145 37.587 31.303 1.00 0.00 N +ATOM 527 H ALA 34 31.697 37.679 30.398 1.00 0.00 H +ATOM 528 CA ALA 34 33.472 36.969 31.385 1.00 0.00 C +ATOM 529 HA ALA 34 33.431 36.162 32.122 1.00 0.00 H +ATOM 530 CB ALA 34 33.818 36.357 30.025 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.964 37.148 29.291 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.777 30.128 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.697 29.695 1.00 0.00 H +ATOM 534 C ALA 34 34.575 37.949 31.862 1.00 0.00 C +ATOM 535 O ALA 34 35.472 37.543 32.601 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.228 31.485 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.508 30.883 1.00 0.00 H +ATOM 538 CA ASN 35 35.366 40.292 31.998 1.00 0.00 C +ATOM 539 HA ASN 35 36.365 39.875 32.114 1.00 0.00 H +ATOM 540 CB ASN 35 35.477 41.419 30.965 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.487 41.705 30.621 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.289 31.446 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.032 29.797 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.582 41.001 29.896 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.708 28.665 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.450 27.893 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.606 28.624 1.00 0.00 H +ATOM 548 C ASN 35 34.979 40.792 33.401 1.00 0.00 C +ATOM 549 O ASN 35 35.862 41.217 34.149 1.00 0.00 O +ATOM 550 N ASP 36 33.716 40.637 33.828 1.00 0.00 N +ATOM 551 H ASP 36 32.980 40.415 33.164 1.00 0.00 H +ATOM 552 CA ASP 36 33.336 40.771 35.246 1.00 0.00 C +ATOM 553 HA ASP 36 33.662 41.747 35.601 1.00 0.00 H +ATOM 554 CB ASP 36 31.821 40.770 35.436 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.447 39.787 35.228 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.605 40.869 36.494 1.00 0.00 H +ATOM 557 CG ASP 36 30.980 41.783 34.656 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.511 42.875 34.375 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.773 41.517 34.399 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.709 36.121 1.00 0.00 C +ATOM 561 O ASP 36 34.483 40.005 37.231 1.00 0.00 O +ATOM 562 N PHE 37 34.225 38.482 35.605 1.00 0.00 N +ATOM 563 H PHE 37 33.748 38.284 34.733 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.460 36.169 1.00 0.00 C +ATOM 565 HA PHE 37 35.119 37.613 37.247 1.00 0.00 H +ATOM 566 CB PHE 37 34.572 36.046 35.924 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.659 35.830 34.863 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.338 36.433 1.00 0.00 H +ATOM 569 CG PHE 37 33.149 35.766 36.381 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.137 35.554 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.369 35.612 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.307 35.837 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.038 35.189 35.100 1.00 0.00 H +ATOM 574 CZ PHE 37 30.512 35.237 37.203 1.00 0.00 C +ATOM 575 HZ PHE 37 29.500 35.052 37.516 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.521 35.411 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.278 35.363 39.212 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.836 35.675 37.747 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.604 35.826 38.483 1.00 0.00 H +ATOM 580 C PHE 37 36.605 37.583 35.730 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.678 35.998 1.00 0.00 O +ATOM 582 N GLY 38 36.994 38.685 35.076 1.00 0.00 N +ATOM 583 H GLY 38 36.290 39.389 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.388 39.099 34.834 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.496 40.119 35.199 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.053 38.480 35.433 1.00 0.00 H +ATOM 587 C GLY 38 38.924 39.067 33.387 1.00 0.00 C +ATOM 588 O GLY 38 39.870 39.802 33.105 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.230 32.483 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.729 32.758 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.054 31.088 1.00 0.00 C +ATOM 592 HA ARG 39 38.947 39.047 30.642 1.00 0.00 H +ATOM 593 CB ARG 39 40.303 37.441 31.074 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.636 37.432 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.986 38.107 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.521 36.014 31.626 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.035 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.754 31.462 1.00 0.00 H +ATOM 599 CD ARG 39 40.216 35.825 33.129 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.853 36.510 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.175 36.078 33.336 1.00 0.00 H +ATOM 602 NE ARG 39 40.443 34.444 33.597 1.00 0.00 N +ATOM 603 HE ARG 39 41.200 34.298 34.242 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.298 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.466 32.486 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.428 34.356 32.087 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.300 32.617 32.077 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.956 32.225 33.814 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.695 32.096 34.486 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.340 31.449 33.597 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.227 30.190 1.00 0.00 C +ATOM 612 O ARG 39 37.524 36.139 30.601 1.00 0.00 O +ATOM 613 N ASP 40 37.649 37.680 28.957 1.00 0.00 N +ATOM 614 H ASP 40 38.027 38.575 28.671 1.00 0.00 H +ATOM 615 CA ASP 40 36.888 36.895 27.965 1.00 0.00 C +ATOM 616 HA ASP 40 36.165 36.313 28.528 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.736 26.967 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.446 37.041 26.398 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.370 38.354 27.534 1.00 0.00 H +ATOM 620 CG ASP 40 36.827 38.629 25.966 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.259 39.727 26.388 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.844 38.320 24.740 1.00 0.00 O +ATOM 623 C ASP 40 37.718 35.863 27.180 1.00 0.00 C +ATOM 624 O ASP 40 38.884 36.079 26.863 1.00 0.00 O +ATOM 625 N GLY 41 37.053 34.763 26.809 1.00 0.00 N +ATOM 626 H GLY 41 36.096 34.687 27.112 1.00 0.00 H +ATOM 627 CA GLY 41 37.470 33.830 25.756 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.458 34.102 25.380 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.530 32.827 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.480 33.816 24.578 1.00 0.00 C +ATOM 631 O GLY 41 35.572 34.649 24.502 1.00 0.00 O +ATOM 632 N GLU 42 36.641 32.855 23.669 1.00 0.00 N +ATOM 633 H GLU 42 37.356 32.161 23.819 1.00 0.00 H +ATOM 634 CA GLU 42 35.802 32.668 22.472 1.00 0.00 C +ATOM 635 HA GLU 42 35.115 33.509 22.372 1.00 0.00 H +ATOM 636 CB GLU 42 36.689 32.632 21.211 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.165 31.653 21.165 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.044 32.715 20.336 1.00 0.00 H +ATOM 639 CG GLU 42 37.807 33.696 21.110 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.580 33.458 21.845 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.278 33.628 20.127 1.00 0.00 H +ATOM 642 CD GLU 42 37.351 35.145 21.325 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.164 35.460 21.116 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.176 36.004 21.723 1.00 0.00 O +ATOM 645 C GLU 42 34.953 31.386 22.575 1.00 0.00 C +ATOM 646 O GLU 42 35.399 30.400 23.169 1.00 0.00 O +ATOM 647 N ALA 43 33.750 31.390 21.987 1.00 0.00 N +ATOM 648 H ALA 43 33.482 32.195 21.439 1.00 0.00 H +ATOM 649 CA ALA 43 32.763 30.304 22.059 1.00 0.00 C +ATOM 650 HA ALA 43 33.255 29.386 22.386 1.00 0.00 H +ATOM 651 CB ALA 43 31.699 30.668 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.186 31.588 22.813 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.966 29.860 23.179 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.172 30.808 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.115 30.014 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.888 30.928 19.897 1.00 0.00 O +ATOM 657 N THR 44 31.800 28.743 20.425 1.00 0.00 N +ATOM 658 H THR 44 31.921 28.066 21.171 1.00 0.00 H +ATOM 659 CA THR 44 31.132 28.280 19.197 1.00 0.00 C +ATOM 660 HA THR 44 31.427 28.942 18.384 1.00 0.00 H +ATOM 661 CB THR 44 31.609 26.864 18.828 1.00 0.00 C +ATOM 662 HB THR 44 31.426 26.183 19.661 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.277 17.557 1.00 0.00 C +ATOM 664 HG21 THR 44 31.074 26.985 16.731 1.00 0.00 H +ATOM 665 HG22 THR 44 31.501 25.353 17.284 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.035 17.728 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.918 18.568 1.00 0.00 O +ATOM 668 HG1 THR 44 33.233 26.114 18.102 1.00 0.00 H +ATOM 669 C THR 44 29.607 28.380 19.330 1.00 0.00 C +ATOM 670 O THR 44 29.074 28.429 20.439 1.00 0.00 O +ATOM 671 N ILE 45 28.902 28.457 18.195 1.00 0.00 N +ATOM 672 H ILE 45 29.375 28.320 17.316 1.00 0.00 H +ATOM 673 CA ILE 45 27.480 28.839 18.125 1.00 0.00 C +ATOM 674 HA ILE 45 27.062 28.755 19.129 1.00 0.00 H +ATOM 675 CB ILE 45 27.333 30.312 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.272 30.526 17.776 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.068 31.232 18.675 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.152 31.107 18.585 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.832 32.280 18.494 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.767 30.970 19.686 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.759 30.685 16.250 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.026 31.742 16.230 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.656 30.128 15.967 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.502 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.734 30.942 15.528 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.979 31.006 14.266 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.520 29.448 14.962 1.00 0.00 H +ATOM 688 C ILE 45 26.631 27.921 17.246 1.00 0.00 C +ATOM 689 O ILE 45 27.124 27.339 16.280 1.00 0.00 O +ATOM 690 N ASP 46 25.331 27.876 17.547 1.00 0.00 N +ATOM 691 H ASP 46 25.033 28.294 18.423 1.00 0.00 H +ATOM 692 CA ASP 46 24.283 27.257 16.737 1.00 0.00 C +ATOM 693 HA ASP 46 24.587 27.262 15.685 1.00 0.00 H +ATOM 694 CB ASP 46 24.078 25.805 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.217 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.957 25.786 18.268 1.00 0.00 H +ATOM 697 CG ASP 46 22.842 25.167 16.545 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.473 17.282 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.562 25.433 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.960 28.047 16.852 1.00 0.00 C +ATOM 701 O ASP 46 22.512 28.361 17.957 1.00 0.00 O +ATOM 702 N ASP 47 22.310 28.329 15.718 1.00 0.00 N +ATOM 703 H ASP 47 22.680 27.938 14.863 1.00 0.00 H +ATOM 704 CA ASP 47 20.971 28.922 15.676 1.00 0.00 C +ATOM 705 HA ASP 47 20.879 29.650 16.488 1.00 0.00 H +ATOM 706 CB ASP 47 20.780 29.672 14.348 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.524 30.465 14.258 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.918 28.977 13.517 1.00 0.00 H +ATOM 709 CG ASP 47 19.369 30.276 14.272 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.488 29.678 13.612 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.067 31.233 15.020 1.00 0.00 O +ATOM 712 C ASP 47 19.855 27.874 15.879 1.00 0.00 C +ATOM 713 O ASP 47 18.845 28.182 16.515 1.00 0.00 O +ATOM 714 N ALA 48 20.003 26.633 15.397 1.00 0.00 N +ATOM 715 H ALA 48 20.918 26.339 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.935 25.624 15.414 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.052 14.933 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.422 14.585 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.277 23.964 15.055 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.682 14.517 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.673 24.751 13.581 1.00 0.00 H +ATOM 722 C ALA 48 18.526 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.930 17.102 1.00 0.00 O +ATOM 724 N THR 49 19.478 25.244 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.438 25.291 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.267 25.119 19.230 1.00 0.00 C +ATOM 727 HA THR 49 18.217 24.871 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.101 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.822 23.860 20.869 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.626 19.138 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.663 18.100 1.00 0.00 H +ATOM 732 HG22 THR 49 20.431 21.855 19.655 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.166 1.00 0.00 H +ATOM 734 OG1 THR 49 21.479 24.241 19.772 1.00 0.00 O +ATOM 735 HG1 THR 49 21.731 24.265 18.814 1.00 0.00 H +ATOM 736 C THR 49 19.506 26.430 20.000 1.00 0.00 C +ATOM 737 O THR 49 19.425 26.431 21.224 1.00 0.00 O +ATOM 738 N LYS 50 19.768 27.552 19.311 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.294 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.905 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.356 29.539 19.085 1.00 0.00 H +ATOM 742 CB LYS 50 18.568 29.470 20.294 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.163 28.830 21.071 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.701 30.460 20.734 1.00 0.00 H +ATOM 745 CG LYS 50 17.490 29.595 19.184 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.427 28.653 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.736 19.684 1.00 0.00 H +ATOM 748 CD LYS 50 17.702 30.770 18.225 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.701 31.693 18.812 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.686 17.722 1.00 0.00 H +ATOM 751 CE LYS 50 16.567 30.866 17.186 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.595 17.663 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.503 31.892 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.995 16.015 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.233 29.097 16.281 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.015 29.834 15.433 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.545 30.416 15.422 1.00 0.00 H +ATOM 758 C LYS 50 20.985 28.947 21.017 1.00 0.00 C +ATOM 759 O LYS 50 20.690 29.519 22.087 1.00 0.00 O +ATOM 760 N THR 51 22.149 28.291 20.853 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.965 19.930 1.00 0.00 H +ATOM 762 CA THR 51 23.056 27.909 21.961 1.00 0.00 C +ATOM 763 HA THR 51 22.764 28.428 22.859 1.00 0.00 H +ATOM 764 CB THR 51 22.887 26.405 22.276 1.00 0.00 C +ATOM 765 HB THR 51 22.977 25.816 21.351 1.00 0.00 H +ATOM 766 CG2 THR 51 23.852 25.861 23.315 1.00 0.00 C +ATOM 767 HG21 THR 51 23.811 26.476 24.217 1.00 0.00 H +ATOM 768 HG22 THR 51 23.574 24.839 23.587 1.00 0.00 H +ATOM 769 HG23 THR 51 24.879 25.834 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.642 26.171 22.880 1.00 0.00 O +ATOM 771 HG1 THR 51 20.952 26.250 22.187 1.00 0.00 H +ATOM 772 C THR 51 24.558 28.226 21.727 1.00 0.00 C +ATOM 773 O THR 51 25.088 27.999 20.643 1.00 0.00 O +ATOM 774 N PHE 52 25.247 28.694 22.774 1.00 0.00 N +ATOM 775 H PHE 52 24.711 28.955 23.594 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.776 22.877 1.00 0.00 C +ATOM 777 HA PHE 52 27.143 28.936 21.901 1.00 0.00 H +ATOM 778 CB PHE 52 27.150 29.949 23.826 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.478 29.957 24.658 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.734 24.192 1.00 0.00 H +ATOM 781 CG PHE 52 27.216 31.350 23.227 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.432 32.382 23.751 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.753 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.448 33.649 23.160 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.778 34.433 23.517 1.00 0.00 H +ATOM 786 CZ PHE 52 27.282 33.889 22.068 1.00 0.00 C +ATOM 787 HZ PHE 52 27.247 34.834 21.561 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.159 32.900 21.619 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.839 33.106 20.790 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.629 22.200 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.776 30.856 21.829 1.00 0.00 H +ATOM 792 C PHE 52 27.330 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.807 27.009 24.507 1.00 0.00 O +ATOM 794 N THR 53 28.485 27.065 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.850 27.522 22.148 1.00 0.00 H +ATOM 796 CA THR 53 29.279 25.926 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.045 25.794 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.933 24.610 22.780 1.00 0.00 C +ATOM 799 HB THR 53 29.508 23.801 23.237 1.00 0.00 H +ATOM 800 CG2 THR 53 27.457 24.224 22.859 1.00 0.00 C +ATOM 801 HG21 THR 53 26.863 24.906 22.251 1.00 0.00 H +ATOM 802 HG22 THR 53 27.322 23.209 22.490 1.00 0.00 H +ATOM 803 HG23 THR 53 27.120 24.269 23.894 1.00 0.00 H +ATOM 804 OG1 THR 53 29.270 24.680 21.419 1.00 0.00 O +ATOM 805 HG1 THR 53 28.753 24.016 20.952 1.00 0.00 H +ATOM 806 C THR 53 30.801 26.146 23.414 1.00 0.00 C +ATOM 807 O THR 53 31.285 27.021 22.692 1.00 0.00 O +ATOM 808 N THR 54 31.568 25.322 24.142 1.00 0.00 N +ATOM 809 H THR 54 31.108 24.646 24.732 1.00 0.00 H +ATOM 810 CA THR 54 33.040 25.237 24.079 1.00 0.00 C +ATOM 811 HA THR 54 33.413 26.032 23.433 1.00 0.00 H +ATOM 812 CB THR 54 33.664 25.450 25.472 1.00 0.00 C +ATOM 813 HB THR 54 33.370 24.631 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.192 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.513 26.333 24.768 1.00 0.00 H +ATOM 816 HG22 THR 54 35.549 25.815 26.469 1.00 0.00 H +ATOM 817 HG23 THR 54 35.638 24.608 25.194 1.00 0.00 H +ATOM 818 OG1 THR 54 33.199 26.661 26.022 1.00 0.00 O +ATOM 819 HG1 THR 54 33.873 26.996 26.616 1.00 0.00 H +ATOM 820 C THR 54 33.478 23.891 23.475 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.889 23.606 1.00 0.00 O +ATOM 822 N GLN 55 34.634 23.874 22.804 1.00 0.00 N +ATOM 823 H GLN 55 35.155 24.736 22.760 1.00 0.00 H +ATOM 824 CA GLN 55 35.263 22.689 22.197 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.160 21.641 1.00 0.00 H +ATOM 826 CB GLN 55 36.318 23.157 21.174 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.731 22.289 20.660 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.803 23.768 20.429 1.00 0.00 H +ATOM 829 CG GLN 55 37.480 23.990 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.094 24.710 22.481 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.176 23.332 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.246 24.768 20.685 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.322 24.390 19.522 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.828 25.897 21.030 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.406 26.349 20.327 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.721 26.270 21.959 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.678 23.227 1.00 0.00 C +ATOM 838 O GLN 55 36.115 22.046 24.365 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.411 22.806 1.00 0.00 N +ATOM 840 H GLU 56 35.791 20.230 21.834 1.00 0.00 H +ATOM 841 CA GLU 56 36.494 19.248 23.574 1.00 0.00 C +ATOM 842 HA GLU 56 36.158 19.336 24.606 1.00 0.00 H +ATOM 843 CB GLU 56 35.887 17.954 22.970 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.807 17.983 23.079 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.991 21.899 1.00 0.00 H +ATOM 846 CG GLU 56 36.406 16.581 23.466 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.470 15.932 22.595 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.421 16.670 23.824 1.00 0.00 H +ATOM 849 CD GLU 56 35.546 15.853 24.519 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.084 15.362 25.545 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.329 15.640 24.294 1.00 0.00 O +ATOM 852 C GLU 56 38.033 19.203 23.640 1.00 0.00 C +ATOM 853 O GLU 56 38.543 19.194 24.791 1.00 0.00 O +ATOM 854 OXT GLU 56 38.679 19.135 22.573 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.719 32.459 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.327 33.243 30.276 1.00 0.00 N +HETATM 857 C AN1 58 30.687 33.879 31.201 1.00 0.00 C +HETATM 858 C1 AN1 58 29.383 33.533 30.715 1.00 0.00 C +HETATM 859 H AN1 58 30.624 34.272 32.222 1.00 0.00 H +HETATM 860 H1 AN1 58 31.138 34.632 30.547 1.00 0.00 H +HETATM 861 H2 AN1 58 31.318 32.977 31.202 1.00 0.00 H +HETATM 862 N1 AZI 59 31.274 30.374 29.435 1.00 0.00 N +HETATM 863 N2 AZI 59 30.476 30.257 30.351 1.00 0.00 N +HETATM 864 N3 AZI 59 29.630 30.157 31.296 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 148 144 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 639 643 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_2_front_7.pdb b/tests/nsga2/intermediate_molecules/min_iter_2_front_7.pdb new file mode 100644 index 0000000..48f1266 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_2_front_7.pdb @@ -0,0 +1,1759 @@ +COMPND fitness: -3.7512 86.6599999999994 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 56.210 58.077 52.044 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.606 37.843 23.332 1.00 0.00 N +ATOM 2 H1 MET 1 14.561 38.256 24.258 1.00 0.00 H +ATOM 3 H2 MET 1 13.827 38.164 22.783 1.00 0.00 H +ATOM 4 H3 MET 1 15.475 38.170 22.930 1.00 0.00 H +ATOM 5 CA MET 1 14.630 36.376 23.447 1.00 0.00 C +ATOM 6 HA MET 1 13.686 36.053 23.885 1.00 0.00 H +ATOM 7 CB MET 1 14.779 35.725 22.058 1.00 0.00 C +ATOM 8 HB2 MET 1 13.905 35.984 21.460 1.00 0.00 H +ATOM 9 HB3 MET 1 15.663 36.132 21.565 1.00 0.00 H +ATOM 10 CG MET 1 14.914 34.195 22.110 1.00 0.00 C +ATOM 11 HG2 MET 1 15.809 33.940 22.680 1.00 0.00 H +ATOM 12 HG3 MET 1 14.049 33.777 22.629 1.00 0.00 H +ATOM 13 SD MET 1 15.062 33.382 20.493 1.00 0.00 S +ATOM 14 CE MET 1 13.359 33.515 19.876 1.00 0.00 C +ATOM 15 HE1 MET 1 13.058 34.560 19.812 1.00 0.00 H +ATOM 16 HE2 MET 1 13.297 33.070 18.883 1.00 0.00 H +ATOM 17 HE3 MET 1 12.684 32.982 20.546 1.00 0.00 H +ATOM 18 C MET 1 15.751 35.940 24.383 1.00 0.00 C +ATOM 19 O MET 1 16.896 36.328 24.187 1.00 0.00 O +ATOM 20 N GLN 2 15.440 35.074 25.351 1.00 0.00 N +ATOM 21 H GLN 2 14.472 34.834 25.495 1.00 0.00 H +ATOM 22 CA GLN 2 16.413 34.386 26.209 1.00 0.00 C +ATOM 23 HA GLN 2 17.163 35.101 26.548 1.00 0.00 H +ATOM 24 CB GLN 2 15.660 33.839 27.442 1.00 0.00 C +ATOM 25 HB2 GLN 2 14.728 33.382 27.108 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.234 33.053 27.924 1.00 0.00 H +ATOM 27 CG GLN 2 15.332 34.909 28.498 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.887 35.771 28.013 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.582 34.501 29.177 1.00 0.00 H +ATOM 30 CD GLN 2 16.524 35.361 29.339 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.655 34.909 29.191 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.312 36.233 30.300 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.089 36.502 30.869 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.408 36.678 30.366 1.00 0.00 H +ATOM 35 C GLN 2 17.162 33.270 25.440 1.00 0.00 C +ATOM 36 O GLN 2 16.821 32.092 25.554 1.00 0.00 O +ATOM 37 N TYR 3 18.180 33.629 24.652 1.00 0.00 N +ATOM 38 H TYR 3 18.418 34.618 24.614 1.00 0.00 H +ATOM 39 CA TYR 3 19.046 32.686 23.920 1.00 0.00 C +ATOM 40 HA TYR 3 18.430 32.099 23.237 1.00 0.00 H +ATOM 41 CB TYR 3 20.075 33.468 23.090 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.560 34.213 23.724 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.851 32.777 22.757 1.00 0.00 H +ATOM 44 CG TYR 3 19.504 34.151 21.860 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.421 33.432 20.651 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.751 32.402 20.611 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.934 34.054 19.487 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.898 33.509 18.555 1.00 0.00 H +ATOM 49 CZ TYR 3 18.516 35.401 19.533 1.00 0.00 C +ATOM 50 OH TYR 3 18.068 36.006 18.402 1.00 0.00 O +ATOM 51 HH TYR 3 18.265 35.478 17.625 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.582 36.118 20.747 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.264 37.151 20.769 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.081 35.495 21.908 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.142 36.054 22.834 1.00 0.00 H +ATOM 56 C TYR 3 19.758 31.718 24.880 1.00 0.00 C +ATOM 57 O TYR 3 20.253 32.137 25.927 1.00 0.00 O +ATOM 58 N LYS 4 19.814 30.420 24.558 1.00 0.00 N +ATOM 59 H LYS 4 19.564 30.159 23.606 1.00 0.00 H +ATOM 60 CA LYS 4 20.327 29.351 25.441 1.00 0.00 C +ATOM 61 HA LYS 4 20.068 29.589 26.469 1.00 0.00 H +ATOM 62 CB LYS 4 19.670 28.002 25.066 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.603 27.928 23.981 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.325 27.194 25.394 1.00 0.00 H +ATOM 65 CG LYS 4 18.278 27.723 25.675 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.001 26.705 25.397 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.346 27.765 26.762 1.00 0.00 H +ATOM 68 CD LYS 4 17.162 28.667 25.194 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.336 29.665 25.587 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.218 28.723 24.104 1.00 0.00 H +ATOM 71 CE LYS 4 15.739 28.200 25.570 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.031 28.787 24.974 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.626 27.156 25.262 1.00 0.00 H +ATOM 74 NZ LYS 4 15.398 28.355 27.015 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.453 29.321 27.308 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.441 28.062 27.197 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.999 27.808 27.619 1.00 0.00 H +ATOM 78 C LYS 4 21.859 29.250 25.406 1.00 0.00 C +ATOM 79 O LYS 4 22.510 29.627 24.436 1.00 0.00 O +HETATM 80 N HX1 5 22.468 28.722 26.466 1.00 0.00 N +HETATM 81 CA HX1 5 23.925 28.531 26.561 1.00 0.00 C +HETATM 82 C HX1 5 24.291 27.414 27.546 1.00 0.00 C +HETATM 83 O HX1 5 23.816 27.403 28.683 1.00 0.00 O +HETATM 84 CB HX1 5 24.559 29.858 26.974 1.00 0.00 C +HETATM 85 CG HX1 5 26.066 29.960 27.018 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.022 29.042 26.675 1.00 0.00 C +HETATM 87 ND1 HX1 5 26.676 31.061 27.599 1.00 0.00 N +HETATM 88 CE1 HX1 5 27.991 30.818 27.497 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.228 29.585 27.032 1.00 0.00 N +HETATM 90 H HX1 5 21.913 28.579 27.306 1.00 0.00 H +HETATM 91 HA HX1 5 24.318 28.260 25.581 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.179 30.134 27.959 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.214 30.629 26.287 1.00 0.00 H +HETATM 94 HD2 HX1 5 26.886 28.045 26.285 1.00 0.00 H +HETATM 95 HE1 HX1 5 28.763 31.447 27.914 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.102 29.078 27.222 1.00 0.00 H +ATOM 97 N ILE 6 25.132 26.489 27.085 1.00 0.00 N +ATOM 98 H ILE 6 25.458 26.571 26.126 1.00 0.00 H +ATOM 99 CA ILE 6 25.644 25.322 27.819 1.00 0.00 C +ATOM 100 HA ILE 6 25.110 25.241 28.770 1.00 0.00 H +ATOM 101 CB ILE 6 25.327 24.038 27.013 1.00 0.00 C +ATOM 102 HB ILE 6 25.787 24.132 26.028 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.904 22.774 27.676 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.503 22.652 28.681 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.658 21.888 27.095 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.991 22.817 27.722 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.792 23.903 26.833 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.330 23.794 27.813 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.398 24.811 26.380 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.329 22.747 25.939 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.496 21.792 26.437 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.260 22.854 25.747 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.867 22.770 24.990 1.00 0.00 H +ATOM 114 C ILE 6 27.131 25.511 28.167 1.00 0.00 C +ATOM 115 O ILE 6 27.874 26.246 27.505 1.00 0.00 O +ATOM 116 N VAL 7 27.523 24.924 29.300 1.00 0.00 N +ATOM 117 H VAL 7 26.889 24.232 29.696 1.00 0.00 H +ATOM 118 CA VAL 7 28.566 25.434 30.206 1.00 0.00 C +ATOM 119 HA VAL 7 28.518 26.524 30.150 1.00 0.00 H +ATOM 120 CB VAL 7 28.126 25.043 31.634 1.00 0.00 C +ATOM 121 HB VAL 7 27.059 25.240 31.715 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.312 23.552 31.929 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.350 23.255 31.825 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.977 23.323 32.941 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.718 22.960 31.234 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.754 25.899 32.738 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.446 26.934 32.614 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.393 25.561 33.711 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.836 25.844 32.729 1.00 0.00 H +ATOM 130 C VAL 7 30.027 25.023 29.878 1.00 0.00 C +ATOM 131 O VAL 7 30.259 23.980 29.272 1.00 0.00 O +ATOM 132 N ARG 8 31.025 25.803 30.343 1.00 0.00 N +ATOM 133 H ARG 8 30.730 26.642 30.829 1.00 0.00 H +ATOM 134 CA ARG 8 32.494 25.697 30.079 1.00 0.00 C +ATOM 135 HA ARG 8 32.641 25.654 29.002 1.00 0.00 H +ATOM 136 CB ARG 8 33.190 27.021 30.529 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.243 26.980 30.258 1.00 0.00 H +ATOM 138 HB3 ARG 8 32.752 27.856 29.977 1.00 0.00 H +ATOM 139 CG ARG 8 33.078 27.338 32.034 1.00 0.00 C +ATOM 140 HG2 ARG 8 32.080 27.673 32.284 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.275 26.434 32.583 1.00 0.00 H +ATOM 142 CD ARG 8 34.135 28.324 32.567 1.00 0.00 C +ATOM 143 HD2 ARG 8 35.114 28.005 32.227 1.00 0.00 H +ATOM 144 HD3 ARG 8 33.944 29.313 32.150 1.00 0.00 H +ATOM 145 NE ARG 8 34.140 28.392 34.050 1.00 0.00 N +ATOM 146 HE ARG 8 33.745 29.220 34.456 1.00 0.00 H +ATOM 147 CZ ARG 8 34.700 27.536 34.893 1.00 0.00 C +ATOM 148 NH1 ARG 8 35.207 26.395 34.516 1.00 0.00 N +ATOM 149 HH11 ARG 8 35.120 26.109 33.554 1.00 0.00 H +ATOM 150 HH12 ARG 8 35.645 25.786 35.187 1.00 0.00 H +ATOM 151 NH2 ARG 8 34.752 27.809 36.166 1.00 0.00 N +ATOM 152 HH21 ARG 8 34.458 28.703 36.519 1.00 0.00 H +ATOM 153 HH22 ARG 8 35.271 27.201 36.780 1.00 0.00 H +ATOM 154 C ARG 8 33.221 24.420 30.618 1.00 0.00 C +ATOM 155 O ARG 8 34.140 24.545 31.425 1.00 0.00 O +ATOM 156 N GLY 9 32.794 23.192 30.314 1.00 0.00 N +ATOM 157 H GLY 9 31.936 23.085 29.778 1.00 0.00 H +ATOM 158 CA GLY 9 33.551 21.973 30.680 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.358 21.821 29.958 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.023 22.124 31.650 1.00 0.00 H +ATOM 161 C GLY 9 32.693 20.696 30.769 1.00 0.00 C +ATOM 162 O GLY 9 31.554 20.681 30.307 1.00 0.00 O +ATOM 163 N LYS 10 33.209 19.638 31.434 1.00 0.00 N +ATOM 164 H LYS 10 34.139 19.753 31.822 1.00 0.00 H +ATOM 165 CA LYS 10 32.675 18.250 31.389 1.00 0.00 C +ATOM 166 HA LYS 10 31.669 18.289 30.975 1.00 0.00 H +ATOM 167 CB LYS 10 33.543 17.448 30.389 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.001 18.124 29.659 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.358 16.937 30.916 1.00 0.00 H +ATOM 170 CG LYS 10 32.733 16.420 29.582 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.183 15.759 30.254 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.013 16.957 28.963 1.00 0.00 H +ATOM 173 CD LYS 10 33.643 15.574 28.686 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.296 16.229 28.107 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.260 14.923 29.303 1.00 0.00 H +ATOM 176 CE LYS 10 32.827 14.724 27.709 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.193 14.038 28.269 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.190 15.392 27.127 1.00 0.00 H +ATOM 179 NZ LYS 10 33.711 13.988 26.778 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.326 13.343 27.264 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.201 13.485 26.071 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.315 14.654 26.284 1.00 0.00 H +ATOM 183 C LYS 10 32.518 17.528 32.747 1.00 0.00 C +ATOM 184 O LYS 10 32.596 16.307 32.801 1.00 0.00 O +ATOM 185 N ASN 11 32.378 18.251 33.862 1.00 0.00 N +ATOM 186 H ASN 11 32.311 19.238 33.729 1.00 0.00 H +ATOM 187 CA ASN 11 32.101 17.706 35.213 1.00 0.00 C +ATOM 188 HA ASN 11 32.387 16.648 35.230 1.00 0.00 H +ATOM 189 CB ASN 11 33.024 18.458 36.211 1.00 0.00 C +ATOM 190 HB2 ASN 11 34.053 18.194 36.010 1.00 0.00 H +ATOM 191 HB3 ASN 11 32.920 19.530 36.035 1.00 0.00 H +ATOM 192 CG ASN 11 32.702 18.222 37.671 1.00 0.00 C +ATOM 193 OD1 ASN 11 31.653 18.588 38.170 1.00 0.00 O +ATOM 194 ND2 ASN 11 33.609 17.657 38.430 1.00 0.00 N +ATOM 195 HD21 ASN 11 33.341 17.524 39.395 1.00 0.00 H +ATOM 196 HD22 ASN 11 34.511 17.380 38.074 1.00 0.00 H +ATOM 197 C ASN 11 30.600 17.753 35.520 1.00 0.00 C +ATOM 198 O ASN 11 29.907 16.749 35.462 1.00 0.00 O +ATOM 199 N TYR 12 30.095 18.967 35.742 1.00 0.00 N +ATOM 200 H TYR 12 30.736 19.709 35.899 1.00 0.00 H +ATOM 201 CA TYR 12 28.678 19.398 35.675 1.00 0.00 C +ATOM 202 HA TYR 12 28.082 18.749 36.359 1.00 0.00 H +ATOM 203 CB TYR 12 28.666 20.825 36.150 1.00 0.00 C +ATOM 204 HB2 TYR 12 27.626 21.198 36.151 1.00 0.00 H +ATOM 205 HB3 TYR 12 28.941 20.842 37.215 1.00 0.00 H +ATOM 206 CG TYR 12 29.561 21.851 35.412 1.00 0.00 C +ATOM 207 CD1 TYR 12 30.331 21.560 34.255 1.00 0.00 C +ATOM 208 HD1 TYR 12 30.263 20.582 33.755 1.00 0.00 H +ATOM 209 CE1 TYR 12 31.155 22.501 33.648 1.00 0.00 C +ATOM 210 HE1 TYR 12 31.680 22.275 32.733 1.00 0.00 H +ATOM 211 CZ TYR 12 31.213 23.780 34.184 1.00 0.00 C +ATOM 212 OH TYR 12 31.987 24.732 33.569 1.00 0.00 O +ATOM 213 HH TYR 12 32.324 24.387 32.701 1.00 0.00 H +ATOM 214 CE2 TYR 12 30.474 24.127 35.305 1.00 0.00 C +ATOM 215 HE2 TYR 12 30.501 25.147 35.689 1.00 0.00 H +ATOM 216 CD2 TYR 12 29.651 23.171 35.908 1.00 0.00 C +ATOM 217 HD2 TYR 12 29.043 23.443 36.787 1.00 0.00 H +ATOM 218 C TYR 12 28.090 19.253 34.250 1.00 0.00 C +ATOM 219 O TYR 12 28.788 18.862 33.309 1.00 0.00 O +ATOM 220 N LYS 13 26.821 19.647 34.065 1.00 0.00 N +ATOM 221 H LYS 13 26.305 19.925 34.884 1.00 0.00 H +ATOM 222 CA LYS 13 26.094 19.541 32.776 1.00 0.00 C +ATOM 223 HA LYS 13 26.805 19.717 31.969 1.00 0.00 H +ATOM 224 CB LYS 13 25.593 18.087 32.650 1.00 0.00 C +ATOM 225 HB2 LYS 13 26.320 17.429 33.127 1.00 0.00 H +ATOM 226 HB3 LYS 13 24.654 17.988 33.195 1.00 0.00 H +ATOM 227 CG LYS 13 25.425 17.587 31.203 1.00 0.00 C +ATOM 228 HG2 LYS 13 24.549 18.045 30.741 1.00 0.00 H +ATOM 229 HG3 LYS 13 26.302 17.868 30.624 1.00 0.00 H +ATOM 230 CD LYS 13 25.291 16.049 31.158 1.00 0.00 C +ATOM 231 HD2 LYS 13 25.230 15.725 30.117 1.00 0.00 H +ATOM 232 HD3 LYS 13 26.195 15.616 31.594 1.00 0.00 H +ATOM 233 CE LYS 13 24.053 15.554 31.925 1.00 0.00 C +ATOM 234 HE2 LYS 13 23.979 16.117 32.855 1.00 0.00 H +ATOM 235 HE3 LYS 13 23.165 15.772 31.325 1.00 0.00 H +ATOM 236 NZ LYS 13 24.127 14.113 32.260 1.00 0.00 N +ATOM 237 HZ1 LYS 13 25.032 13.871 32.657 1.00 0.00 H +ATOM 238 HZ2 LYS 13 23.461 13.886 32.994 1.00 0.00 H +ATOM 239 HZ3 LYS 13 23.964 13.519 31.457 1.00 0.00 H +ATOM 240 C LYS 13 24.980 20.595 32.595 1.00 0.00 C +ATOM 241 O LYS 13 23.956 20.338 31.967 1.00 0.00 O +ATOM 242 N GLY 14 25.140 21.770 33.215 1.00 0.00 N +ATOM 243 H GLY 14 26.023 21.941 33.667 1.00 0.00 H +ATOM 244 CA GLY 14 24.092 22.793 33.319 1.00 0.00 C +ATOM 245 HA2 GLY 14 23.148 22.298 33.541 1.00 0.00 H +ATOM 246 HA3 GLY 14 24.315 23.453 34.156 1.00 0.00 H +ATOM 247 C GLY 14 23.874 23.669 32.071 1.00 0.00 C +ATOM 248 O GLY 14 24.749 23.819 31.213 1.00 0.00 O +ATOM 249 N VAL 15 22.695 24.302 32.017 1.00 0.00 N +ATOM 250 H VAL 15 22.053 24.151 32.781 1.00 0.00 H +ATOM 251 CA VAL 15 22.244 25.234 30.969 1.00 0.00 C +ATOM 252 HA VAL 15 23.112 25.536 30.386 1.00 0.00 H +ATOM 253 CB VAL 15 21.252 24.543 30.003 1.00 0.00 C +ATOM 254 HB VAL 15 21.734 23.644 29.616 1.00 0.00 H +ATOM 255 CG1 VAL 15 19.942 24.128 30.686 1.00 0.00 C +ATOM 256 HG11 VAL 15 19.401 25.000 31.051 1.00 0.00 H +ATOM 257 HG12 VAL 15 19.310 23.599 29.968 1.00 0.00 H +ATOM 258 HG13 VAL 15 20.149 23.452 31.516 1.00 0.00 H +ATOM 259 CG2 VAL 15 20.890 25.430 28.802 1.00 0.00 C +ATOM 260 HG21 VAL 15 21.796 25.776 28.306 1.00 0.00 H +ATOM 261 HG22 VAL 15 20.312 24.845 28.084 1.00 0.00 H +ATOM 262 HG23 VAL 15 20.288 26.282 29.113 1.00 0.00 H +ATOM 263 C VAL 15 21.642 26.495 31.603 1.00 0.00 C +ATOM 264 O VAL 15 21.073 26.439 32.694 1.00 0.00 O +HETATM 265 N HY1 16 21.783 27.631 30.929 1.00 0.00 N +HETATM 266 CA HY1 16 21.218 28.928 31.326 1.00 0.00 C +HETATM 267 C HY1 16 21.036 29.822 30.068 1.00 0.00 C +HETATM 268 O HY1 16 21.371 29.383 28.958 1.00 0.00 O +HETATM 269 CB HY1 16 22.137 29.545 32.394 1.00 0.00 C +HETATM 270 CG HY1 16 23.542 29.763 31.898 1.00 0.00 C +HETATM 271 CD2 HY1 16 23.897 30.825 31.132 1.00 0.00 C +HETATM 272 ND1 HY1 16 24.612 28.888 31.897 1.00 0.00 N +HETATM 273 CE1 HY1 16 25.588 29.437 31.139 1.00 0.00 C +HETATM 274 NE2 HY1 16 25.183 30.623 30.647 1.00 0.00 N +HETATM 275 H HY1 16 22.297 27.605 30.055 1.00 0.00 H +HETATM 276 HA HY1 16 20.231 28.774 31.762 1.00 0.00 H +HETATM 277 HB2 HY1 16 21.721 30.492 32.738 1.00 0.00 H +HETATM 278 HB3 HY1 16 22.169 28.880 33.267 1.00 0.00 H +HETATM 279 HD1 HY1 16 24.657 28.001 32.388 1.00 0.00 H +HETATM 280 HD2 HY1 16 23.233 31.636 30.872 1.00 0.00 H +HETATM 281 HE1 HY1 16 26.569 28.993 30.965 1.00 0.00 H +ATOM 282 N THR 17 20.509 31.046 30.201 1.00 0.00 N +ATOM 283 H THR 17 20.226 31.383 31.101 1.00 0.00 H +ATOM 284 CA THR 17 20.080 31.865 29.044 1.00 0.00 C +ATOM 285 HA THR 17 20.517 31.448 28.143 1.00 0.00 H +ATOM 286 CB THR 17 18.549 31.829 28.895 1.00 0.00 C +ATOM 287 HB THR 17 18.274 32.454 28.059 1.00 0.00 H +ATOM 288 CG2 THR 17 17.977 30.425 28.652 1.00 0.00 C +ATOM 289 HG21 THR 17 18.205 29.759 29.472 1.00 0.00 H +ATOM 290 HG22 THR 17 16.890 30.494 28.552 1.00 0.00 H +ATOM 291 HG23 THR 17 18.376 30.025 27.734 1.00 0.00 H +ATOM 292 OG1 THR 17 17.946 32.336 30.061 1.00 0.00 O +ATOM 293 HG1 THR 17 17.908 33.302 29.951 1.00 0.00 H +ATOM 294 C THR 17 20.520 33.329 29.097 1.00 0.00 C +ATOM 295 O THR 17 20.892 33.824 30.166 1.00 0.00 O +HETATM 296 N HY2 18 20.484 34.015 27.941 1.00 0.00 N +HETATM 297 CA HY2 18 20.882 35.411 27.722 1.00 0.00 C +HETATM 298 C HY2 18 19.851 36.210 26.928 1.00 0.00 C +HETATM 299 O HY2 18 19.572 35.885 25.778 1.00 0.00 O +HETATM 300 CB HY2 18 22.273 35.475 27.050 1.00 0.00 C +HETATM 301 CG HY2 18 23.272 34.804 27.979 1.00 0.00 C +HETATM 302 CD2 HY2 18 23.969 33.646 27.739 1.00 0.00 C +HETATM 303 ND1 HY2 18 23.279 34.994 29.343 1.00 0.00 N +HETATM 304 CE1 HY2 18 23.808 33.906 29.896 1.00 0.00 C +HETATM 305 NE2 HY2 18 24.364 33.102 28.972 1.00 0.00 N +HETATM 306 H HY2 18 20.201 33.487 27.121 1.00 0.00 H +HETATM 307 HA HY2 18 20.970 35.912 28.681 1.00 0.00 H +HETATM 308 HB2 HY2 18 22.237 34.978 26.082 1.00 0.00 H +HETATM 309 HB3 HY2 18 22.557 36.514 26.883 1.00 0.00 H +HETATM 310 HD1 HY2 18 22.704 35.669 29.851 1.00 0.00 H +HETATM 311 HD2 HY2 18 24.054 33.162 26.778 1.00 0.00 H +HETATM 312 HE1 HY2 18 23.733 33.703 30.955 1.00 0.00 H +ATOM 313 N GLU 19 19.305 37.253 27.550 1.00 0.00 N +ATOM 314 H GLU 19 19.560 37.468 28.502 1.00 0.00 H +ATOM 315 CA GLU 19 18.335 38.139 26.909 1.00 0.00 C +ATOM 316 HA GLU 19 17.580 37.512 26.437 1.00 0.00 H +ATOM 317 CB GLU 19 17.681 39.005 27.999 1.00 0.00 C +ATOM 318 HB2 GLU 19 17.352 38.353 28.807 1.00 0.00 H +ATOM 319 HB3 GLU 19 18.428 39.691 28.402 1.00 0.00 H +ATOM 320 CG GLU 19 16.471 39.813 27.518 1.00 0.00 C +ATOM 321 HG2 GLU 19 16.008 40.295 28.382 1.00 0.00 H +ATOM 322 HG3 GLU 19 16.809 40.595 26.832 1.00 0.00 H +ATOM 323 CD GLU 19 15.468 38.898 26.817 1.00 0.00 C +ATOM 324 OE1 GLU 19 15.493 38.853 25.568 1.00 0.00 O +ATOM 325 OE2 GLU 19 14.771 38.123 27.500 1.00 0.00 O +ATOM 326 C GLU 19 18.993 39.011 25.829 1.00 0.00 C +ATOM 327 O GLU 19 20.034 39.622 26.077 1.00 0.00 O +ATOM 328 N ALA 20 18.393 39.062 24.639 1.00 0.00 N +ATOM 329 H ALA 20 17.534 38.535 24.527 1.00 0.00 H +ATOM 330 CA ALA 20 18.794 39.928 23.528 1.00 0.00 C +ATOM 331 HA ALA 20 18.938 40.939 23.911 1.00 0.00 H +ATOM 332 CB ALA 20 20.120 39.430 22.936 1.00 0.00 C +ATOM 333 HB1 ALA 20 19.981 38.442 22.498 1.00 0.00 H +ATOM 334 HB2 ALA 20 20.463 40.118 22.165 1.00 0.00 H +ATOM 335 HB3 ALA 20 20.891 39.377 23.704 1.00 0.00 H +ATOM 336 C ALA 20 17.730 39.970 22.414 1.00 0.00 C +ATOM 337 O ALA 20 16.877 39.085 22.300 1.00 0.00 O +ATOM 338 N VAL 21 17.828 40.967 21.527 1.00 0.00 N +ATOM 339 H VAL 21 18.517 41.687 21.688 1.00 0.00 H +ATOM 340 CA VAL 21 17.108 40.983 20.235 1.00 0.00 C +ATOM 341 HA VAL 21 16.112 40.569 20.390 1.00 0.00 H +ATOM 342 CB VAL 21 16.922 42.424 19.708 1.00 0.00 C +ATOM 343 HB VAL 21 16.284 42.377 18.825 1.00 0.00 H +ATOM 344 CG1 VAL 21 16.207 43.312 20.736 1.00 0.00 C +ATOM 345 HG11 VAL 21 16.841 43.487 21.604 1.00 0.00 H +ATOM 346 HG12 VAL 21 15.962 44.273 20.283 1.00 0.00 H +ATOM 347 HG13 VAL 21 15.281 42.837 21.061 1.00 0.00 H +ATOM 348 CG2 VAL 21 18.238 43.102 19.302 1.00 0.00 C +ATOM 349 HG21 VAL 21 18.700 42.562 18.476 1.00 0.00 H +ATOM 350 HG22 VAL 21 18.040 44.118 18.959 1.00 0.00 H +ATOM 351 HG23 VAL 21 18.934 43.140 20.139 1.00 0.00 H +ATOM 352 C VAL 21 17.781 40.114 19.160 1.00 0.00 C +ATOM 353 O VAL 21 17.147 39.785 18.160 1.00 0.00 O +ATOM 354 N ASP 22 19.050 39.749 19.368 1.00 0.00 N +ATOM 355 H ASP 22 19.476 40.007 20.243 1.00 0.00 H +ATOM 356 CA ASP 22 19.944 39.093 18.406 1.00 0.00 C +ATOM 357 HA ASP 22 19.370 38.425 17.764 1.00 0.00 H +ATOM 358 CB ASP 22 20.556 40.186 17.509 1.00 0.00 C +ATOM 359 HB2 ASP 22 19.748 40.807 17.120 1.00 0.00 H +ATOM 360 HB3 ASP 22 21.211 40.830 18.090 1.00 0.00 H +ATOM 361 CG ASP 22 21.364 39.655 16.331 1.00 0.00 C +ATOM 362 OD1 ASP 22 21.470 40.449 15.361 1.00 0.00 O +ATOM 363 OD2 ASP 22 21.882 38.534 16.368 1.00 0.00 O +ATOM 364 C ASP 22 21.010 38.262 19.152 1.00 0.00 C +ATOM 365 O ASP 22 21.519 38.679 20.197 1.00 0.00 O +ATOM 366 N LEU 23 21.373 37.097 18.612 1.00 0.00 N +ATOM 367 H LEU 23 21.060 36.924 17.665 1.00 0.00 H +ATOM 368 CA LEU 23 22.451 36.256 19.128 1.00 0.00 C +ATOM 369 HA LEU 23 22.232 36.042 20.172 1.00 0.00 H +ATOM 370 CB LEU 23 22.427 34.919 18.362 1.00 0.00 C +ATOM 371 HB2 LEU 23 21.429 34.495 18.470 1.00 0.00 H +ATOM 372 HB3 LEU 23 22.588 35.105 17.300 1.00 0.00 H +ATOM 373 CG LEU 23 23.460 33.898 18.881 1.00 0.00 C +ATOM 374 HG LEU 23 23.719 34.148 19.908 1.00 0.00 H +ATOM 375 CD1 LEU 23 22.889 32.478 18.888 1.00 0.00 C +ATOM 376 HD11 LEU 23 22.614 32.176 17.877 1.00 0.00 H +ATOM 377 HD12 LEU 23 23.634 31.788 19.283 1.00 0.00 H +ATOM 378 HD13 LEU 23 22.009 32.440 19.528 1.00 0.00 H +ATOM 379 CD2 LEU 23 24.722 33.893 18.016 1.00 0.00 C +ATOM 380 HD21 LEU 23 25.158 34.890 17.970 1.00 0.00 H +ATOM 381 HD22 LEU 23 25.459 33.219 18.446 1.00 0.00 H +ATOM 382 HD23 LEU 23 24.480 33.567 17.004 1.00 0.00 H +ATOM 383 C LEU 23 23.818 36.971 19.075 1.00 0.00 C +ATOM 384 O LEU 23 24.632 36.796 19.983 1.00 0.00 O +ATOM 385 N ALA 24 24.054 37.834 18.081 1.00 0.00 N +ATOM 386 H ALA 24 23.334 37.955 17.366 1.00 0.00 H +ATOM 387 CA ALA 24 25.275 38.639 17.954 1.00 0.00 C +ATOM 388 HA ALA 24 26.125 37.990 18.164 1.00 0.00 H +ATOM 389 CB ALA 24 25.385 39.106 16.501 1.00 0.00 C +ATOM 390 HB1 ALA 24 24.557 39.771 16.254 1.00 0.00 H +ATOM 391 HB2 ALA 24 26.329 39.629 16.356 1.00 0.00 H +ATOM 392 HB3 ALA 24 25.359 38.244 15.834 1.00 0.00 H +ATOM 393 C ALA 24 25.361 39.827 18.944 1.00 0.00 C +ATOM 394 O ALA 24 26.433 40.412 19.133 1.00 0.00 O +ATOM 395 N GLU 25 24.256 40.178 19.611 1.00 0.00 N +ATOM 396 H GLU 25 23.395 39.702 19.373 1.00 0.00 H +ATOM 397 CA GLU 25 24.264 41.004 20.827 1.00 0.00 C +ATOM 398 HA GLU 25 25.120 41.680 20.813 1.00 0.00 H +ATOM 399 CB GLU 25 22.987 41.862 20.899 1.00 0.00 C +ATOM 400 HB2 GLU 25 22.123 41.221 20.735 1.00 0.00 H +ATOM 401 HB3 GLU 25 22.902 42.280 21.899 1.00 0.00 H +ATOM 402 CG GLU 25 22.951 43.019 19.891 1.00 0.00 C +ATOM 403 HG2 GLU 25 23.195 42.648 18.896 1.00 0.00 H +ATOM 404 HG3 GLU 25 21.933 43.412 19.851 1.00 0.00 H +ATOM 405 CD GLU 25 23.913 44.144 20.293 1.00 0.00 C +ATOM 406 OE1 GLU 25 23.478 45.087 20.985 1.00 0.00 O +ATOM 407 OE2 GLU 25 25.113 44.027 19.919 1.00 0.00 O +ATOM 408 C GLU 25 24.432 40.126 22.081 1.00 0.00 C +ATOM 409 O GLU 25 25.224 40.456 22.965 1.00 0.00 O +ATOM 410 N ALA 26 23.788 38.950 22.138 1.00 0.00 N +ATOM 411 H ALA 26 23.138 38.715 21.394 1.00 0.00 H +ATOM 412 CA ALA 26 23.981 37.984 23.225 1.00 0.00 C +ATOM 413 HA ALA 26 23.762 38.494 24.162 1.00 0.00 H +ATOM 414 CB ALA 26 22.974 36.842 23.061 1.00 0.00 C +ATOM 415 HB1 ALA 26 23.199 36.283 22.157 1.00 0.00 H +ATOM 416 HB2 ALA 26 23.034 36.172 23.915 1.00 0.00 H +ATOM 417 HB3 ALA 26 21.964 37.238 22.992 1.00 0.00 H +ATOM 418 C ALA 26 25.427 37.446 23.335 1.00 0.00 C +ATOM 419 O ALA 26 25.824 37.003 24.418 1.00 0.00 O +ATOM 420 N GLU 27 26.226 37.506 22.263 1.00 0.00 N +ATOM 421 H GLU 27 25.786 37.697 21.366 1.00 0.00 H +ATOM 422 CA GLU 27 27.682 37.297 22.299 1.00 0.00 C +ATOM 423 HA GLU 27 27.873 36.349 22.802 1.00 0.00 H +ATOM 424 CB GLU 27 28.250 37.195 20.869 1.00 0.00 C +ATOM 425 HB2 GLU 27 27.652 36.495 20.285 1.00 0.00 H +ATOM 426 HB3 GLU 27 28.190 38.174 20.391 1.00 0.00 H +ATOM 427 CG GLU 27 29.709 36.707 20.879 1.00 0.00 C +ATOM 428 HG2 GLU 27 30.246 37.147 21.723 1.00 0.00 H +ATOM 429 HG3 GLU 27 29.712 35.623 21.031 1.00 0.00 H +ATOM 430 CD GLU 27 30.466 37.088 19.601 1.00 0.00 C +ATOM 431 OE1 GLU 27 30.854 38.276 19.503 1.00 0.00 O +ATOM 432 OE2 GLU 27 30.694 36.185 18.769 1.00 0.00 O +ATOM 433 C GLU 27 28.399 38.403 23.095 1.00 0.00 C +ATOM 434 O GLU 27 29.144 38.111 24.035 1.00 0.00 O +ATOM 435 N LYS 28 28.111 39.679 22.804 1.00 0.00 N +ATOM 436 H LYS 28 27.456 39.856 22.053 1.00 0.00 H +ATOM 437 CA LYS 28 28.669 40.829 23.542 1.00 0.00 C +ATOM 438 HA LYS 28 29.757 40.759 23.523 1.00 0.00 H +ATOM 439 CB LYS 28 28.255 42.157 22.883 1.00 0.00 C +ATOM 440 HB2 LYS 28 27.172 42.278 22.942 1.00 0.00 H +ATOM 441 HB3 LYS 28 28.719 42.971 23.444 1.00 0.00 H +ATOM 442 CG LYS 28 28.686 42.263 21.411 1.00 0.00 C +ATOM 443 HG2 LYS 28 29.750 42.034 21.326 1.00 0.00 H +ATOM 444 HG3 LYS 28 28.124 41.540 20.822 1.00 0.00 H +ATOM 445 CD LYS 28 28.432 43.680 20.873 1.00 0.00 C +ATOM 446 HD2 LYS 28 27.437 44.018 21.168 1.00 0.00 H +ATOM 447 HD3 LYS 28 29.160 44.358 21.322 1.00 0.00 H +ATOM 448 CE LYS 28 28.554 43.752 19.344 1.00 0.00 C +ATOM 449 HE2 LYS 28 28.652 44.804 19.060 1.00 0.00 H +ATOM 450 HE3 LYS 28 29.462 43.233 19.027 1.00 0.00 H +ATOM 451 NZ LYS 28 27.361 43.170 18.683 1.00 0.00 N +ATOM 452 HZ1 LYS 28 26.512 43.612 19.055 1.00 0.00 H +ATOM 453 HZ2 LYS 28 27.376 43.317 17.686 1.00 0.00 H +ATOM 454 HZ3 LYS 28 27.262 42.177 18.881 1.00 0.00 H +ATOM 455 C LYS 28 28.248 40.810 25.012 1.00 0.00 C +ATOM 456 O LYS 28 29.093 40.897 25.903 1.00 0.00 O +ATOM 457 N PHE 29 26.965 40.568 25.284 1.00 0.00 N +ATOM 458 H PHE 29 26.308 40.561 24.505 1.00 0.00 H +ATOM 459 CA PHE 29 26.454 40.372 26.647 1.00 0.00 C +ATOM 460 HA PHE 29 26.755 41.229 27.250 1.00 0.00 H +ATOM 461 CB PHE 29 24.918 40.333 26.629 1.00 0.00 C +ATOM 462 HB2 PHE 29 24.608 39.412 26.136 1.00 0.00 H +ATOM 463 HB3 PHE 29 24.565 40.293 27.662 1.00 0.00 H +ATOM 464 CG PHE 29 24.218 41.505 25.955 1.00 0.00 C +ATOM 465 CD1 PHE 29 22.999 41.289 25.282 1.00 0.00 C +ATOM 466 HD1 PHE 29 22.551 40.307 25.269 1.00 0.00 H +ATOM 467 CE1 PHE 29 22.362 42.347 24.611 1.00 0.00 C +ATOM 468 HE1 PHE 29 21.440 42.167 24.079 1.00 0.00 H +ATOM 469 CZ PHE 29 22.937 43.630 24.611 1.00 0.00 C +ATOM 470 HZ PHE 29 22.467 44.436 24.065 1.00 0.00 H +ATOM 471 CE2 PHE 29 24.132 43.861 25.313 1.00 0.00 C +ATOM 472 HE2 PHE 29 24.573 44.845 25.321 1.00 0.00 H +ATOM 473 CD2 PHE 29 24.766 42.805 25.989 1.00 0.00 C +ATOM 474 HD2 PHE 29 25.684 43.004 26.519 1.00 0.00 H +ATOM 475 C PHE 29 27.025 39.110 27.331 1.00 0.00 C +ATOM 476 O PHE 29 27.057 39.034 28.559 1.00 0.00 O +ATOM 477 N THR 30 27.519 38.123 26.569 1.00 0.00 N +ATOM 478 H THR 30 27.472 38.226 25.559 1.00 0.00 H +ATOM 479 CA THR 30 28.282 36.990 27.101 1.00 0.00 C +ATOM 480 HA THR 30 27.799 36.696 28.022 1.00 0.00 H +ATOM 481 CB THR 30 28.255 35.769 26.144 1.00 0.00 C +ATOM 482 HB THR 30 28.535 36.074 25.144 1.00 0.00 H +ATOM 483 CG2 THR 30 29.213 34.641 26.549 1.00 0.00 C +ATOM 484 HG21 THR 30 29.091 34.356 27.586 1.00 0.00 H +ATOM 485 HG22 THR 30 29.060 33.765 25.915 1.00 0.00 H +ATOM 486 HG23 THR 30 30.235 34.981 26.383 1.00 0.00 H +ATOM 487 OG1 THR 30 26.949 35.222 26.159 1.00 0.00 O +ATOM 488 HG1 THR 30 26.411 35.804 25.580 1.00 0.00 H +ATOM 489 C THR 30 29.697 37.395 27.517 1.00 0.00 C +ATOM 490 O THR 30 30.116 36.977 28.596 1.00 0.00 O +ATOM 491 N LYS 31 30.396 38.237 26.743 1.00 0.00 N +ATOM 492 H LYS 31 29.969 38.548 25.875 1.00 0.00 H +ATOM 493 CA LYS 31 31.759 38.733 27.030 1.00 0.00 C +ATOM 494 HA LYS 31 32.393 37.903 27.349 1.00 0.00 H +ATOM 495 CB LYS 31 32.356 39.316 25.742 1.00 0.00 C +ATOM 496 HB2 LYS 31 31.677 40.067 25.331 1.00 0.00 H +ATOM 497 HB3 LYS 31 33.304 39.811 25.970 1.00 0.00 H +ATOM 498 CG LYS 31 32.616 38.226 24.689 1.00 0.00 C +ATOM 499 HG2 LYS 31 33.308 37.492 25.095 1.00 0.00 H +ATOM 500 HG3 LYS 31 31.691 37.710 24.439 1.00 0.00 H +ATOM 501 CD LYS 31 33.202 38.836 23.409 1.00 0.00 C +ATOM 502 HD2 LYS 31 32.420 39.421 22.919 1.00 0.00 H +ATOM 503 HD3 LYS 31 34.019 39.511 23.668 1.00 0.00 H +ATOM 504 CE LYS 31 33.717 37.773 22.435 1.00 0.00 C +ATOM 505 HE2 LYS 31 32.924 37.052 22.218 1.00 0.00 H +ATOM 506 HE3 LYS 31 33.962 38.263 21.487 1.00 0.00 H +ATOM 507 NZ LYS 31 34.922 37.074 22.949 1.00 0.00 N +ATOM 508 HZ1 LYS 31 34.715 36.322 23.594 1.00 0.00 H +ATOM 509 HZ2 LYS 31 35.427 36.621 22.180 1.00 0.00 H +ATOM 510 HZ3 LYS 31 35.585 37.695 23.408 1.00 0.00 H +ATOM 511 C LYS 31 31.821 39.756 28.169 1.00 0.00 C +ATOM 512 O LYS 31 32.781 39.726 28.936 1.00 0.00 O +ATOM 513 N ALA 32 30.796 40.598 28.331 1.00 0.00 N +ATOM 514 H ALA 32 30.099 40.631 27.594 1.00 0.00 H +ATOM 515 CA ALA 32 30.739 41.633 29.373 1.00 0.00 C +ATOM 516 HA ALA 32 31.499 42.384 29.163 1.00 0.00 H +ATOM 517 CB ALA 32 29.356 42.306 29.300 1.00 0.00 C +ATOM 518 HB1 ALA 32 28.554 41.574 29.415 1.00 0.00 H +ATOM 519 HB2 ALA 32 29.262 43.050 30.092 1.00 0.00 H +ATOM 520 HB3 ALA 32 29.243 42.801 28.337 1.00 0.00 H +ATOM 521 C ALA 32 31.031 41.072 30.780 1.00 0.00 C +ATOM 522 O ALA 32 32.064 41.340 31.385 1.00 0.00 O +ATOM 523 N ARG 33 30.166 40.171 31.235 1.00 0.00 N +ATOM 524 H ARG 33 29.351 39.998 30.664 1.00 0.00 H +ATOM 525 CA ARG 33 30.294 39.444 32.510 1.00 0.00 C +ATOM 526 HA ARG 33 30.422 40.178 33.297 1.00 0.00 H +ATOM 527 CB ARG 33 28.995 38.699 32.794 1.00 0.00 C +ATOM 528 HB2 ARG 33 29.130 38.075 33.679 1.00 0.00 H +ATOM 529 HB3 ARG 33 28.177 39.395 32.979 1.00 0.00 H +ATOM 530 CG ARG 33 28.687 37.855 31.561 1.00 0.00 C +ATOM 531 HG2 ARG 33 28.076 38.434 30.871 1.00 0.00 H +ATOM 532 HG3 ARG 33 29.601 37.582 31.040 1.00 0.00 H +ATOM 533 CD ARG 33 27.984 36.569 31.880 1.00 0.00 C +ATOM 534 HD2 ARG 33 28.538 36.004 32.635 1.00 0.00 H +ATOM 535 HD3 ARG 33 26.985 36.812 32.252 1.00 0.00 H +ATOM 536 NE ARG 33 27.901 35.843 30.611 1.00 0.00 N +ATOM 537 HE ARG 33 28.490 36.185 29.860 1.00 0.00 H +ATOM 538 CZ ARG 33 26.904 35.066 30.309 1.00 0.00 C +ATOM 539 NH1 ARG 33 26.635 34.799 29.061 1.00 0.00 N +ATOM 540 HH11 ARG 33 27.186 35.168 28.300 1.00 0.00 H +ATOM 541 HH12 ARG 33 25.727 34.451 28.800 1.00 0.00 H +ATOM 542 NH2 ARG 33 26.203 34.541 31.276 1.00 0.00 N +ATOM 543 HH21 ARG 33 26.473 34.757 32.221 1.00 0.00 H +ATOM 544 HH22 ARG 33 25.586 33.777 31.106 1.00 0.00 H +ATOM 545 C ARG 33 31.465 38.449 32.604 1.00 0.00 C +ATOM 546 O ARG 33 31.778 37.990 33.697 1.00 0.00 O +ATOM 547 N ALA 34 32.072 38.042 31.482 1.00 0.00 N +ATOM 548 H ALA 34 31.783 38.439 30.604 1.00 0.00 H +ATOM 549 CA ALA 34 33.302 37.246 31.503 1.00 0.00 C +ATOM 550 HA ALA 34 33.202 36.446 32.236 1.00 0.00 H +ATOM 551 CB ALA 34 33.538 36.601 30.123 1.00 0.00 C +ATOM 552 HB1 ALA 34 33.762 37.355 29.372 1.00 0.00 H +ATOM 553 HB2 ALA 34 34.384 35.912 30.170 1.00 0.00 H +ATOM 554 HB3 ALA 34 32.660 36.035 29.815 1.00 0.00 H +ATOM 555 C ALA 34 34.457 38.136 31.984 1.00 0.00 C +ATOM 556 O ALA 34 35.219 37.724 32.850 1.00 0.00 O +ATOM 557 N ASN 35 34.474 39.401 31.551 1.00 0.00 N +ATOM 558 H ASN 35 33.784 39.677 30.864 1.00 0.00 H +ATOM 559 CA ASN 35 35.325 40.453 32.107 1.00 0.00 C +ATOM 560 HA ASN 35 36.327 40.046 32.242 1.00 0.00 H +ATOM 561 CB ASN 35 35.440 41.586 31.075 1.00 0.00 C +ATOM 562 HB2 ASN 35 34.453 41.945 30.796 1.00 0.00 H +ATOM 563 HB3 ASN 35 35.979 42.414 31.532 1.00 0.00 H +ATOM 564 CG ASN 35 36.209 41.162 29.832 1.00 0.00 C +ATOM 565 OD1 ASN 35 37.424 41.107 29.816 1.00 0.00 O +ATOM 566 ND2 ASN 35 35.544 40.847 28.746 1.00 0.00 N +ATOM 567 HD21 ASN 35 36.101 40.597 27.934 1.00 0.00 H +ATOM 568 HD22 ASN 35 34.541 40.769 28.766 1.00 0.00 H +ATOM 569 C ASN 35 34.886 40.937 33.515 1.00 0.00 C +ATOM 570 O ASN 35 35.755 41.332 34.288 1.00 0.00 O +ATOM 571 N ASP 36 33.604 40.835 33.915 1.00 0.00 N +ATOM 572 H ASP 36 32.883 40.704 33.220 1.00 0.00 H +ATOM 573 CA ASP 36 33.222 40.978 35.343 1.00 0.00 C +ATOM 574 HA ASP 36 33.609 41.930 35.704 1.00 0.00 H +ATOM 575 CB ASP 36 31.690 41.001 35.561 1.00 0.00 C +ATOM 576 HB2 ASP 36 31.275 40.064 35.211 1.00 0.00 H +ATOM 577 HB3 ASP 36 31.510 41.010 36.635 1.00 0.00 H +ATOM 578 CG ASP 36 30.917 42.200 34.975 1.00 0.00 C +ATOM 579 OD1 ASP 36 31.468 43.323 35.011 1.00 0.00 O +ATOM 580 OD2 ASP 36 29.741 42.011 34.563 1.00 0.00 O +ATOM 581 C ASP 36 33.862 39.877 36.225 1.00 0.00 C +ATOM 582 O ASP 36 34.232 40.144 37.368 1.00 0.00 O +ATOM 583 N LEU 37 34.028 38.649 35.706 1.00 0.00 N +ATOM 584 H LEU 37 33.645 38.474 34.786 1.00 0.00 H +ATOM 585 CA LEU 37 34.769 37.561 36.371 1.00 0.00 C +ATOM 586 HA LEU 37 34.582 37.645 37.443 1.00 0.00 H +ATOM 587 CB LEU 37 34.192 36.213 35.882 1.00 0.00 C +ATOM 588 HB2 LEU 37 33.118 36.210 36.069 1.00 0.00 H +ATOM 589 HB3 LEU 37 34.342 36.154 34.805 1.00 0.00 H +ATOM 590 CG LEU 37 34.805 34.945 36.516 1.00 0.00 C +ATOM 591 HG LEU 37 35.876 34.913 36.321 1.00 0.00 H +ATOM 592 CD1 LEU 37 34.566 34.864 38.026 1.00 0.00 C +ATOM 593 HD11 LEU 37 33.499 34.915 38.242 1.00 0.00 H +ATOM 594 HD12 LEU 37 34.975 33.932 38.415 1.00 0.00 H +ATOM 595 HD13 LEU 37 35.076 35.691 38.518 1.00 0.00 H +ATOM 596 CD2 LEU 37 34.181 33.694 35.888 1.00 0.00 C +ATOM 597 HD21 LEU 37 34.363 33.701 34.813 1.00 0.00 H +ATOM 598 HD22 LEU 37 34.644 32.804 36.314 1.00 0.00 H +ATOM 599 HD23 LEU 37 33.108 33.675 36.077 1.00 0.00 H +ATOM 600 C LEU 37 36.304 37.655 36.183 1.00 0.00 C +ATOM 601 O LEU 37 37.049 37.195 37.049 1.00 0.00 O +ATOM 602 N GLY 38 36.774 38.237 35.074 1.00 0.00 N +ATOM 603 H GLY 38 36.097 38.511 34.376 1.00 0.00 H +ATOM 604 CA GLY 38 38.182 38.550 34.809 1.00 0.00 C +ATOM 605 HA2 GLY 38 38.459 39.417 35.411 1.00 0.00 H +ATOM 606 HA3 GLY 38 38.795 37.709 35.131 1.00 0.00 H +ATOM 607 C GLY 38 38.540 38.860 33.342 1.00 0.00 C +ATOM 608 O GLY 38 39.143 39.896 33.084 1.00 0.00 O +ATOM 609 N GLU 39 38.201 37.985 32.384 1.00 0.00 N +ATOM 610 H GLU 39 37.589 37.219 32.631 1.00 0.00 H +ATOM 611 CA GLU 39 38.667 38.020 30.972 1.00 0.00 C +ATOM 612 HA GLU 39 38.785 39.059 30.656 1.00 0.00 H +ATOM 613 CB GLU 39 40.040 37.296 30.846 1.00 0.00 C +ATOM 614 HB2 GLU 39 39.905 36.277 31.208 1.00 0.00 H +ATOM 615 HB3 GLU 39 40.298 37.242 29.788 1.00 0.00 H +ATOM 616 CG GLU 39 41.235 37.941 31.588 1.00 0.00 C +ATOM 617 HG2 GLU 39 41.429 38.925 31.147 1.00 0.00 H +ATOM 618 HG3 GLU 39 40.970 38.086 32.638 1.00 0.00 H +ATOM 619 CD GLU 39 42.521 37.093 31.582 1.00 0.00 C +ATOM 620 OE1 GLU 39 42.422 35.846 31.671 1.00 0.00 O +ATOM 621 OE2 GLU 39 43.632 37.676 31.560 1.00 0.00 O +ATOM 622 C GLU 39 37.648 37.338 30.014 1.00 0.00 C +ATOM 623 O GLU 39 36.929 36.433 30.444 1.00 0.00 O +ATOM 624 N ASP 40 37.580 37.703 28.713 1.00 0.00 N +ATOM 625 H ASP 40 38.152 38.477 28.401 1.00 0.00 H +ATOM 626 CA ASP 40 36.731 37.006 27.712 1.00 0.00 C +ATOM 627 HA ASP 40 36.019 36.400 28.273 1.00 0.00 H +ATOM 628 CB ASP 40 35.856 37.950 26.869 1.00 0.00 C +ATOM 629 HB2 ASP 40 35.149 37.321 26.332 1.00 0.00 H +ATOM 630 HB3 ASP 40 35.268 38.580 27.529 1.00 0.00 H +ATOM 631 CG ASP 40 36.582 38.819 25.835 1.00 0.00 C +ATOM 632 OD1 ASP 40 36.945 39.969 26.162 1.00 0.00 O +ATOM 633 OD2 ASP 40 36.695 38.391 24.657 1.00 0.00 O +ATOM 634 C ASP 40 37.463 36.031 26.766 1.00 0.00 C +ATOM 635 O ASP 40 38.376 36.411 26.026 1.00 0.00 O +ATOM 636 N GLY 41 36.937 34.801 26.687 1.00 0.00 N +ATOM 637 H GLY 41 36.209 34.568 27.343 1.00 0.00 H +ATOM 638 CA GLY 41 37.260 33.807 25.655 1.00 0.00 C +ATOM 639 HA2 GLY 41 38.284 33.968 25.307 1.00 0.00 H +ATOM 640 HA3 GLY 41 37.212 32.809 26.099 1.00 0.00 H +ATOM 641 C GLY 41 36.319 33.835 24.428 1.00 0.00 C +ATOM 642 O GLY 41 35.379 34.632 24.345 1.00 0.00 O +ATOM 643 N GLU 42 36.572 32.930 23.480 1.00 0.00 N +ATOM 644 H GLU 42 37.303 32.262 23.657 1.00 0.00 H +ATOM 645 CA GLU 42 35.849 32.773 22.198 1.00 0.00 C +ATOM 646 HA GLU 42 35.155 33.605 22.083 1.00 0.00 H +ATOM 647 CB GLU 42 36.832 32.823 21.014 1.00 0.00 C +ATOM 648 HB2 GLU 42 37.410 31.899 20.996 1.00 0.00 H +ATOM 649 HB3 GLU 42 36.250 32.852 20.091 1.00 0.00 H +ATOM 650 CG GLU 42 37.808 34.026 21.041 1.00 0.00 C +ATOM 651 HG2 GLU 42 38.582 33.822 21.785 1.00 0.00 H +ATOM 652 HG3 GLU 42 38.302 34.092 20.068 1.00 0.00 H +ATOM 653 CD GLU 42 37.130 35.373 21.376 1.00 0.00 C +ATOM 654 OE1 GLU 42 35.967 35.572 20.965 1.00 0.00 O +ATOM 655 OE2 GLU 42 37.694 36.214 22.124 1.00 0.00 O +ATOM 656 C GLU 42 34.999 31.500 22.160 1.00 0.00 C +ATOM 657 O GLU 42 35.269 30.539 22.888 1.00 0.00 O +ATOM 658 N HIP 43 33.891 31.517 21.396 1.00 0.00 N +ATOM 659 H HIP 43 33.753 32.283 20.746 1.00 0.00 H +ATOM 660 CA HIP 43 32.711 30.745 21.803 1.00 0.00 C +ATOM 661 HA HIP 43 33.033 29.779 22.194 1.00 0.00 H +ATOM 662 CB HIP 43 32.123 31.562 22.981 1.00 0.00 C +ATOM 663 HB2 HIP 43 32.868 31.705 23.765 1.00 0.00 H +ATOM 664 HB3 HIP 43 31.824 32.549 22.633 1.00 0.00 H +ATOM 665 CG HIP 43 30.942 30.884 23.586 1.00 0.00 C +ATOM 666 ND1 HIP 43 29.754 30.730 22.930 1.00 0.00 N +ATOM 667 HD1 HIP 43 29.562 31.132 22.014 1.00 0.00 H +ATOM 668 CE1 HIP 43 29.202 29.607 23.386 1.00 0.00 C +ATOM 669 HE1 HIP 43 28.474 29.044 22.833 1.00 0.00 H +ATOM 670 NE2 HIP 43 29.897 29.146 24.436 1.00 0.00 N +ATOM 671 HE2 HIP 43 29.817 28.199 24.785 1.00 0.00 H +ATOM 672 CD2 HIP 43 31.021 29.930 24.558 1.00 0.00 C +ATOM 673 HD2 HIP 43 31.900 29.678 25.124 1.00 0.00 H +ATOM 674 C HIP 43 31.650 30.454 20.697 1.00 0.00 C +ATOM 675 O HIP 43 30.841 31.328 20.397 1.00 0.00 O +ATOM 676 N THR 44 31.523 29.200 20.247 1.00 0.00 N +ATOM 677 H THR 44 32.201 28.523 20.559 1.00 0.00 H +ATOM 678 CA THR 44 30.635 28.728 19.143 1.00 0.00 C +ATOM 679 HA THR 44 30.827 29.355 18.270 1.00 0.00 H +ATOM 680 CB THR 44 31.019 27.279 18.766 1.00 0.00 C +ATOM 681 HB THR 44 30.729 26.605 19.575 1.00 0.00 H +ATOM 682 CG2 THR 44 30.403 26.764 17.461 1.00 0.00 C +ATOM 683 HG21 THR 44 30.532 27.498 16.665 1.00 0.00 H +ATOM 684 HG22 THR 44 30.870 25.825 17.164 1.00 0.00 H +ATOM 685 HG23 THR 44 29.340 26.566 17.601 1.00 0.00 H +ATOM 686 OG1 THR 44 32.417 27.197 18.606 1.00 0.00 O +ATOM 687 HG1 THR 44 32.604 26.452 18.027 1.00 0.00 H +ATOM 688 C THR 44 29.114 28.795 19.411 1.00 0.00 C +ATOM 689 O THR 44 28.661 28.721 20.558 1.00 0.00 O +ATOM 690 N GLN 45 28.319 28.898 18.337 1.00 0.00 N +ATOM 691 H GLN 45 28.789 29.017 17.446 1.00 0.00 H +ATOM 692 CA GLN 45 26.865 29.110 18.294 1.00 0.00 C +ATOM 693 HA GLN 45 26.462 28.962 19.295 1.00 0.00 H +ATOM 694 CB GLN 45 26.599 30.578 17.884 1.00 0.00 C +ATOM 695 HB2 GLN 45 25.572 30.804 18.169 1.00 0.00 H +ATOM 696 HB3 GLN 45 27.242 31.234 18.473 1.00 0.00 H +ATOM 697 CG GLN 45 26.741 30.947 16.382 1.00 0.00 C +ATOM 698 HG2 GLN 45 26.052 30.342 15.794 1.00 0.00 H +ATOM 699 HG3 GLN 45 26.425 31.983 16.257 1.00 0.00 H +ATOM 700 CD GLN 45 28.143 30.823 15.768 1.00 0.00 C +ATOM 701 OE1 GLN 45 29.158 30.708 16.436 1.00 0.00 O +ATOM 702 NE2 GLN 45 28.276 30.835 14.462 1.00 0.00 N +ATOM 703 HE21 GLN 45 29.214 30.785 14.109 1.00 0.00 H +ATOM 704 HE22 GLN 45 27.485 30.864 13.826 1.00 0.00 H +ATOM 705 C GLN 45 26.106 28.148 17.353 1.00 0.00 C +ATOM 706 O GLN 45 26.651 27.691 16.350 1.00 0.00 O +ATOM 707 N ASP 46 24.816 27.938 17.631 1.00 0.00 N +ATOM 708 H ASP 46 24.469 28.232 18.538 1.00 0.00 H +ATOM 709 CA ASP 46 23.806 27.349 16.739 1.00 0.00 C +ATOM 710 HA ASP 46 24.147 27.428 15.708 1.00 0.00 H +ATOM 711 CB ASP 46 23.590 25.860 17.075 1.00 0.00 C +ATOM 712 HB2 ASP 46 24.463 25.284 16.756 1.00 0.00 H +ATOM 713 HB3 ASP 46 23.496 25.765 18.157 1.00 0.00 H +ATOM 714 CG ASP 46 22.341 25.292 16.395 1.00 0.00 C +ATOM 715 OD1 ASP 46 21.515 24.680 17.113 1.00 0.00 O +ATOM 716 OD2 ASP 46 22.135 25.545 15.195 1.00 0.00 O +ATOM 717 C ASP 46 22.471 28.108 16.864 1.00 0.00 C +ATOM 718 O ASP 46 22.025 28.431 17.966 1.00 0.00 O +ATOM 719 N ASP 47 21.809 28.361 15.735 1.00 0.00 N +ATOM 720 H ASP 47 22.178 27.953 14.884 1.00 0.00 H +ATOM 721 CA ASP 47 20.481 28.990 15.695 1.00 0.00 C +ATOM 722 HA ASP 47 20.396 29.652 16.550 1.00 0.00 H +ATOM 723 CB ASP 47 20.358 29.872 14.438 1.00 0.00 C +ATOM 724 HB2 ASP 47 21.220 30.541 14.390 1.00 0.00 H +ATOM 725 HB3 ASP 47 20.363 29.240 13.547 1.00 0.00 H +ATOM 726 CG ASP 47 19.084 30.708 14.499 1.00 0.00 C +ATOM 727 OD1 ASP 47 18.127 30.409 13.761 1.00 0.00 O +ATOM 728 OD2 ASP 47 18.939 31.541 15.419 1.00 0.00 O +ATOM 729 C ASP 47 19.313 27.985 15.776 1.00 0.00 C +ATOM 730 O ASP 47 18.260 28.318 16.326 1.00 0.00 O +ATOM 731 N ALA 48 19.476 26.741 15.304 1.00 0.00 N +ATOM 732 H ALA 48 20.408 26.439 15.014 1.00 0.00 H +ATOM 733 CA ALA 48 18.394 25.746 15.250 1.00 0.00 C +ATOM 734 HA ALA 48 17.536 26.176 14.732 1.00 0.00 H +ATOM 735 CB ALA 48 18.895 24.541 14.445 1.00 0.00 C +ATOM 736 HB1 ALA 48 19.748 24.085 14.950 1.00 0.00 H +ATOM 737 HB2 ALA 48 18.099 23.805 14.350 1.00 0.00 H +ATOM 738 HB3 ALA 48 19.206 24.861 13.450 1.00 0.00 H +ATOM 739 C ALA 48 17.916 25.322 16.650 1.00 0.00 C +ATOM 740 O ALA 48 16.721 25.152 16.897 1.00 0.00 O +ATOM 741 N THR 49 18.847 25.199 17.595 1.00 0.00 N +ATOM 742 H THR 49 19.823 25.180 17.290 1.00 0.00 H +ATOM 743 CA THR 49 18.582 25.048 19.034 1.00 0.00 C +ATOM 744 HA THR 49 17.557 24.704 19.161 1.00 0.00 H +ATOM 745 CB THR 49 19.520 23.996 19.644 1.00 0.00 C +ATOM 746 HB THR 49 19.269 23.888 20.697 1.00 0.00 H +ATOM 747 CG2 THR 49 19.421 22.621 18.993 1.00 0.00 C +ATOM 748 HG21 THR 49 19.747 22.665 17.954 1.00 0.00 H +ATOM 749 HG22 THR 49 20.077 21.947 19.538 1.00 0.00 H +ATOM 750 HG23 THR 49 18.398 22.254 19.040 1.00 0.00 H +ATOM 751 OG1 THR 49 20.859 24.396 19.551 1.00 0.00 O +ATOM 752 HG1 THR 49 21.108 24.393 18.591 1.00 0.00 H +ATOM 753 C THR 49 18.705 26.359 19.819 1.00 0.00 C +ATOM 754 O THR 49 18.601 26.347 21.047 1.00 0.00 O +ATOM 755 N LYS 50 18.935 27.492 19.139 1.00 0.00 N +ATOM 756 H LYS 50 18.973 27.403 18.132 1.00 0.00 H +ATOM 757 CA LYS 50 19.167 28.835 19.712 1.00 0.00 C +ATOM 758 HA LYS 50 19.597 29.451 18.919 1.00 0.00 H +ATOM 759 CB LYS 50 17.826 29.468 20.157 1.00 0.00 C +ATOM 760 HB2 LYS 50 17.370 28.808 20.900 1.00 0.00 H +ATOM 761 HB3 LYS 50 18.015 30.425 20.646 1.00 0.00 H +ATOM 762 CG LYS 50 16.794 29.705 19.037 1.00 0.00 C +ATOM 763 HG2 LYS 50 16.716 28.820 18.405 1.00 0.00 H +ATOM 764 HG3 LYS 50 15.824 29.873 19.507 1.00 0.00 H +ATOM 765 CD LYS 50 17.127 30.944 18.184 1.00 0.00 C +ATOM 766 HD2 LYS 50 17.102 31.820 18.837 1.00 0.00 H +ATOM 767 HD3 LYS 50 18.129 30.854 17.760 1.00 0.00 H +ATOM 768 CE LYS 50 16.090 31.145 17.073 1.00 0.00 C +ATOM 769 HE2 LYS 50 15.096 30.898 17.457 1.00 0.00 H +ATOM 770 HE3 LYS 50 16.103 32.201 16.787 1.00 0.00 H +ATOM 771 NZ LYS 50 16.421 30.345 15.873 1.00 0.00 N +ATOM 772 HZ1 LYS 50 16.767 29.414 16.087 1.00 0.00 H +ATOM 773 HZ2 LYS 50 15.699 30.310 15.174 1.00 0.00 H +ATOM 774 HZ3 LYS 50 17.223 30.766 15.390 1.00 0.00 H +ATOM 775 C LYS 50 20.222 28.825 20.831 1.00 0.00 C +ATOM 776 O LYS 50 20.055 29.510 21.843 1.00 0.00 O +ATOM 777 N THR 51 21.259 27.993 20.691 1.00 0.00 N +ATOM 778 H THR 51 21.409 27.592 19.762 1.00 0.00 H +ATOM 779 CA THR 51 22.172 27.599 21.771 1.00 0.00 C +ATOM 780 HA THR 51 21.917 28.210 22.629 1.00 0.00 H +ATOM 781 CB THR 51 21.970 26.124 22.200 1.00 0.00 C +ATOM 782 HB THR 51 22.136 25.481 21.351 1.00 0.00 H +ATOM 783 CG2 THR 51 22.951 25.655 23.296 1.00 0.00 C +ATOM 784 HG21 THR 51 22.956 26.297 24.162 1.00 0.00 H +ATOM 785 HG22 THR 51 22.722 24.643 23.608 1.00 0.00 H +ATOM 786 HG23 THR 51 23.956 25.620 22.870 1.00 0.00 H +ATOM 787 OG1 THR 51 20.670 25.917 22.733 1.00 0.00 O +ATOM 788 HG1 THR 51 20.030 26.045 22.006 1.00 0.00 H +ATOM 789 C THR 51 23.652 27.888 21.483 1.00 0.00 C +ATOM 790 O THR 51 24.206 27.618 20.424 1.00 0.00 O +ATOM 791 N PHE 52 24.319 28.422 22.500 1.00 0.00 N +ATOM 792 H PHE 52 23.768 28.734 23.281 1.00 0.00 H +ATOM 793 CA PHE 52 25.768 28.588 22.617 1.00 0.00 C +ATOM 794 HA PHE 52 26.209 28.718 21.624 1.00 0.00 H +ATOM 795 CB PHE 52 25.934 29.876 23.433 1.00 0.00 C +ATOM 796 HB2 PHE 52 25.158 29.901 24.199 1.00 0.00 H +ATOM 797 HB3 PHE 52 26.852 29.852 24.017 1.00 0.00 H +ATOM 798 CG PHE 52 25.885 31.198 22.680 1.00 0.00 C +ATOM 799 CD1 PHE 52 25.012 32.221 23.103 1.00 0.00 C +ATOM 800 HD1 PHE 52 24.320 32.041 23.903 1.00 0.00 H +ATOM 801 CE1 PHE 52 25.045 33.487 22.491 1.00 0.00 C +ATOM 802 HE1 PHE 52 24.379 34.268 22.818 1.00 0.00 H +ATOM 803 CZ PHE 52 25.956 33.741 21.454 1.00 0.00 C +ATOM 804 HZ PHE 52 25.988 34.712 20.988 1.00 0.00 H +ATOM 805 CE2 PHE 52 26.810 32.725 21.004 1.00 0.00 C +ATOM 806 HE2 PHE 52 27.499 32.922 20.194 1.00 0.00 H +ATOM 807 CD2 PHE 52 26.762 31.458 21.608 1.00 0.00 C +ATOM 808 HD2 PHE 52 27.415 30.692 21.242 1.00 0.00 H +ATOM 809 C PHE 52 26.431 27.347 23.282 1.00 0.00 C +ATOM 810 O PHE 52 26.004 26.944 24.366 1.00 0.00 O +ATOM 811 N THR 53 27.533 26.805 22.728 1.00 0.00 N +ATOM 812 H THR 53 27.815 27.125 21.802 1.00 0.00 H +ATOM 813 CA THR 53 28.350 25.688 23.289 1.00 0.00 C +ATOM 814 HA THR 53 28.083 25.538 24.333 1.00 0.00 H +ATOM 815 CB THR 53 28.074 24.368 22.548 1.00 0.00 C +ATOM 816 HB THR 53 28.722 23.593 22.958 1.00 0.00 H +ATOM 817 CG2 THR 53 26.632 23.889 22.679 1.00 0.00 C +ATOM 818 HG21 THR 53 25.960 24.557 22.139 1.00 0.00 H +ATOM 819 HG22 THR 53 26.550 22.885 22.263 1.00 0.00 H +ATOM 820 HG23 THR 53 26.352 23.855 23.730 1.00 0.00 H +ATOM 821 OG1 THR 53 28.366 24.524 21.181 1.00 0.00 O +ATOM 822 HG1 THR 53 28.124 23.708 20.725 1.00 0.00 H +ATOM 823 C THR 53 29.872 25.956 23.241 1.00 0.00 C +ATOM 824 O THR 53 30.300 26.968 22.690 1.00 0.00 O +ATOM 825 N MET 54 30.713 25.105 23.856 1.00 0.00 N +ATOM 826 H MET 54 30.334 24.273 24.286 1.00 0.00 H +ATOM 827 CA MET 54 32.182 25.105 23.663 1.00 0.00 C +ATOM 828 HA MET 54 32.446 25.938 23.009 1.00 0.00 H +ATOM 829 CB MET 54 32.941 25.336 24.987 1.00 0.00 C +ATOM 830 HB2 MET 54 33.969 25.599 24.737 1.00 0.00 H +ATOM 831 HB3 MET 54 32.509 26.192 25.507 1.00 0.00 H +ATOM 832 CG MET 54 32.985 24.135 25.949 1.00 0.00 C +ATOM 833 HG2 MET 54 31.992 23.991 26.371 1.00 0.00 H +ATOM 834 HG3 MET 54 33.253 23.231 25.406 1.00 0.00 H +ATOM 835 SD MET 54 34.168 24.322 27.314 1.00 0.00 S +ATOM 836 CE MET 54 35.724 23.824 26.523 1.00 0.00 C +ATOM 837 HE1 MET 54 35.888 24.409 25.619 1.00 0.00 H +ATOM 838 HE2 MET 54 36.551 23.987 27.212 1.00 0.00 H +ATOM 839 HE3 MET 54 35.680 22.766 26.267 1.00 0.00 H +ATOM 840 C MET 54 32.662 23.829 22.946 1.00 0.00 C +ATOM 841 O MET 54 31.929 22.843 22.877 1.00 0.00 O +ATOM 842 N ALA 55 33.892 23.859 22.423 1.00 0.00 N +ATOM 843 H ALA 55 34.450 24.686 22.561 1.00 0.00 H +ATOM 844 CA ALA 55 34.554 22.718 21.782 1.00 0.00 C +ATOM 845 HA ALA 55 33.844 22.246 21.100 1.00 0.00 H +ATOM 846 CB ALA 55 35.732 23.266 20.959 1.00 0.00 C +ATOM 847 HB1 ALA 55 36.461 23.734 21.623 1.00 0.00 H +ATOM 848 HB2 ALA 55 36.219 22.451 20.421 1.00 0.00 H +ATOM 849 HB3 ALA 55 35.371 24.000 20.235 1.00 0.00 H +ATOM 850 C ALA 55 35.017 21.628 22.779 1.00 0.00 C +ATOM 851 O ALA 55 35.021 21.847 23.989 1.00 0.00 O +ATOM 852 N GLU 56 35.431 20.479 22.234 1.00 0.00 N +ATOM 853 H GLU 56 35.452 20.421 21.231 1.00 0.00 H +ATOM 854 CA GLU 56 36.104 19.352 22.911 1.00 0.00 C +ATOM 855 HA GLU 56 36.199 19.575 23.974 1.00 0.00 H +ATOM 856 CB GLU 56 35.238 18.076 22.755 1.00 0.00 C +ATOM 857 HB2 GLU 56 34.213 18.295 23.051 1.00 0.00 H +ATOM 858 HB3 GLU 56 35.204 17.849 21.688 1.00 0.00 H +ATOM 859 CG GLU 56 35.736 16.811 23.492 1.00 0.00 C +ATOM 860 HG2 GLU 56 35.664 15.981 22.790 1.00 0.00 H +ATOM 861 HG3 GLU 56 36.794 16.912 23.710 1.00 0.00 H +ATOM 862 CD GLU 56 34.988 16.399 24.782 1.00 0.00 C +ATOM 863 OE1 GLU 56 35.523 15.530 25.516 1.00 0.00 O +ATOM 864 OE2 GLU 56 33.843 16.839 25.048 1.00 0.00 O +ATOM 865 C GLU 56 37.541 19.172 22.368 1.00 0.00 C +ATOM 866 O GLU 56 38.465 19.135 23.205 1.00 0.00 O +ATOM 867 OXT GLU 56 37.715 19.114 21.119 1.00 0.00 O +HETATM 868 ZN ZN1 57 25.930 31.773 29.258 1.00 0.00 Zn +HETATM 869 N AN1 58 27.732 32.212 30.227 1.00 0.00 N +HETATM 870 C AN1 58 30.202 32.363 31.070 1.00 0.00 C +HETATM 871 C1 AN1 58 28.815 32.265 30.631 1.00 0.00 C +HETATM 872 H AN1 58 30.258 32.653 32.123 1.00 0.00 H +HETATM 873 H1 AN1 58 30.745 33.103 30.462 1.00 0.00 H +HETATM 874 H2 AN1 58 30.695 31.392 30.947 1.00 0.00 H +HETATM 875 N1 AZI 59 30.363 29.082 28.864 1.00 0.00 N +HETATM 876 N2 AZI 59 29.718 29.024 29.896 1.00 0.00 N +HETATM 877 N3 AZI 59 29.034 28.987 30.964 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 68 73 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 868 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 121 122 126 +CONECT 121 120 +CONECT 122 125 120 123 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 127 129 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 118 132 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 140 142 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 139 144 143 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 159 156 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 197 189 +CONECT 188 187 +CONECT 189 187 190 191 192 +CONECT 190 189 +CONECT 191 189 +CONECT 192 189 193 194 +CONECT 193 192 +CONECT 194 192 196 195 +CONECT 195 194 +CONECT 196 194 +CONECT 197 187 198 199 +CONECT 198 197 +CONECT 199 197 201 200 +CONECT 200 199 +CONECT 201 218 199 203 202 +CONECT 202 201 +CONECT 203 206 201 204 205 +CONECT 204 203 +CONECT 205 203 +CONECT 206 207 216 203 +CONECT 207 209 208 206 +CONECT 208 207 +CONECT 209 210 211 207 +CONECT 210 209 +CONECT 211 212 209 214 +CONECT 212 213 211 +CONECT 213 212 +CONECT 214 211 215 216 +CONECT 215 214 +CONECT 216 214 206 217 +CONECT 217 216 +CONECT 218 219 220 201 +CONECT 219 218 +CONECT 220 222 218 221 +CONECT 221 220 +CONECT 222 223 240 224 220 +CONECT 223 222 +CONECT 224 227 222 225 226 +CONECT 225 224 +CONECT 226 224 +CONECT 227 229 228 230 224 +CONECT 228 227 +CONECT 229 227 +CONECT 230 231 227 232 233 +CONECT 231 230 +CONECT 232 230 +CONECT 233 230 235 236 234 +CONECT 234 233 +CONECT 235 233 +CONECT 236 239 233 237 238 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 241 222 242 +CONECT 241 240 +CONECT 242 240 244 243 +CONECT 243 242 +CONECT 244 247 242 245 246 +CONECT 245 244 +CONECT 246 244 +CONECT 247 248 249 244 +CONECT 248 247 +CONECT 249 251 247 250 +CONECT 250 249 +CONECT 251 253 252 263 249 +CONECT 252 251 +CONECT 253 259 254 255 251 +CONECT 254 253 +CONECT 255 257 253 256 258 +CONECT 256 255 +CONECT 257 255 +CONECT 258 255 +CONECT 259 261 260 262 253 +CONECT 260 259 +CONECT 261 259 +CONECT 262 259 +CONECT 263 265 251 264 +CONECT 264 263 +CONECT 265 275 266 263 +CONECT 266 267 265 276 269 +CONECT 267 268 282 266 +CONECT 268 267 +CONECT 269 266 270 277 278 +CONECT 270 271 272 269 +CONECT 271 274 280 270 +CONECT 272 273 270 279 +CONECT 273 274 281 272 +CONECT 274 868 271 273 +CONECT 275 265 +CONECT 276 266 +CONECT 277 269 +CONECT 278 269 +CONECT 279 272 +CONECT 280 271 +CONECT 281 273 +CONECT 282 284 267 283 +CONECT 283 282 +CONECT 284 285 286 294 282 +CONECT 285 284 +CONECT 286 287 288 284 292 +CONECT 287 286 +CONECT 288 291 290 286 289 +CONECT 289 288 +CONECT 290 288 +CONECT 291 288 +CONECT 292 286 293 +CONECT 293 292 +CONECT 294 296 284 295 +CONECT 295 294 +CONECT 296 306 297 294 +CONECT 297 298 300 296 307 +CONECT 298 299 313 297 +CONECT 299 298 +CONECT 300 308 309 297 301 +CONECT 301 300 302 303 +CONECT 302 311 301 305 +CONECT 303 301 310 304 +CONECT 304 305 303 312 +CONECT 305 302 868 304 +CONECT 306 296 +CONECT 307 297 +CONECT 308 300 +CONECT 309 300 +CONECT 310 303 +CONECT 311 302 +CONECT 312 304 +CONECT 313 315 298 314 +CONECT 314 313 +CONECT 315 326 316 313 317 +CONECT 316 315 +CONECT 317 315 320 319 318 +CONECT 318 317 +CONECT 319 317 +CONECT 320 323 322 317 321 +CONECT 321 320 +CONECT 322 320 +CONECT 323 324 325 320 +CONECT 324 323 +CONECT 325 323 +CONECT 326 328 327 315 +CONECT 327 326 +CONECT 328 330 329 326 +CONECT 329 328 +CONECT 330 336 332 331 328 +CONECT 331 330 +CONECT 332 334 333 330 335 +CONECT 333 332 +CONECT 334 332 +CONECT 335 332 +CONECT 336 338 337 330 +CONECT 337 336 +CONECT 338 340 339 336 +CONECT 339 338 +CONECT 340 352 342 341 338 +CONECT 341 340 +CONECT 342 343 348 340 344 +CONECT 343 342 +CONECT 344 342 346 347 345 +CONECT 345 344 +CONECT 346 344 +CONECT 347 344 +CONECT 348 349 350 342 351 +CONECT 349 348 +CONECT 350 348 +CONECT 351 348 +CONECT 352 353 354 340 +CONECT 353 352 +CONECT 354 356 352 355 +CONECT 355 354 +CONECT 356 358 357 364 354 +CONECT 357 356 +CONECT 358 361 359 360 356 +CONECT 359 358 +CONECT 360 358 +CONECT 361 362 363 358 +CONECT 362 361 +CONECT 363 361 +CONECT 364 356 366 365 +CONECT 365 364 +CONECT 366 367 368 364 +CONECT 367 366 +CONECT 368 370 366 383 369 +CONECT 369 368 +CONECT 370 372 371 373 368 +CONECT 371 370 +CONECT 372 370 +CONECT 373 379 370 375 374 +CONECT 374 373 +CONECT 375 376 373 377 378 +CONECT 376 375 +CONECT 377 375 +CONECT 378 375 +CONECT 379 382 380 381 373 +CONECT 380 379 +CONECT 381 379 +CONECT 382 379 +CONECT 383 385 368 384 +CONECT 384 383 +CONECT 385 386 387 383 +CONECT 386 385 +CONECT 387 389 385 388 393 +CONECT 388 387 +CONECT 389 392 390 391 387 +CONECT 390 389 +CONECT 391 389 +CONECT 392 389 +CONECT 393 387 394 395 +CONECT 394 393 +CONECT 395 393 396 397 +CONECT 396 395 +CONECT 397 395 398 399 408 +CONECT 398 397 +CONECT 399 402 400 397 401 +CONECT 400 399 +CONECT 401 399 +CONECT 402 403 404 405 399 +CONECT 403 402 +CONECT 404 402 +CONECT 405 402 407 406 +CONECT 406 405 +CONECT 407 405 +CONECT 408 397 410 409 +CONECT 409 408 +CONECT 410 411 408 412 +CONECT 411 410 +CONECT 412 410 414 418 413 +CONECT 413 412 +CONECT 414 415 417 412 416 +CONECT 415 414 +CONECT 416 414 +CONECT 417 414 +CONECT 418 420 412 419 +CONECT 419 418 +CONECT 420 421 422 418 +CONECT 421 420 +CONECT 422 424 420 423 433 +CONECT 423 422 +CONECT 424 425 426 427 422 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 424 429 428 +CONECT 428 427 +CONECT 429 427 +CONECT 430 432 431 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 422 435 434 +CONECT 434 433 +CONECT 435 436 433 437 +CONECT 436 435 +CONECT 437 435 439 438 455 +CONECT 438 437 +CONECT 439 442 440 441 437 +CONECT 440 439 +CONECT 441 439 +CONECT 442 444 445 443 439 +CONECT 443 442 +CONECT 444 442 +CONECT 445 448 446 447 442 +CONECT 446 445 +CONECT 447 445 +CONECT 448 451 450 449 445 +CONECT 449 448 +CONECT 450 448 +CONECT 451 453 454 452 448 +CONECT 452 451 +CONECT 453 451 +CONECT 454 451 +CONECT 455 437 457 456 +CONECT 456 455 +CONECT 457 458 455 459 +CONECT 458 457 +CONECT 459 457 461 460 475 +CONECT 460 459 +CONECT 461 464 462 459 463 +CONECT 462 461 +CONECT 463 461 +CONECT 464 465 473 461 +CONECT 465 467 466 464 +CONECT 466 465 +CONECT 467 468 469 465 +CONECT 468 467 +CONECT 469 470 467 471 +CONECT 470 469 +CONECT 471 469 472 473 +CONECT 472 471 +CONECT 473 471 464 474 +CONECT 474 473 +CONECT 475 477 459 476 +CONECT 476 475 +CONECT 477 478 479 475 +CONECT 478 477 +CONECT 479 481 477 489 480 +CONECT 480 479 +CONECT 481 482 487 483 479 +CONECT 482 481 +CONECT 483 485 481 486 484 +CONECT 484 483 +CONECT 485 483 +CONECT 486 483 +CONECT 487 488 481 +CONECT 488 487 +CONECT 489 491 479 490 +CONECT 490 489 +CONECT 491 492 493 489 +CONECT 492 491 +CONECT 493 495 491 494 511 +CONECT 494 493 +CONECT 495 498 496 497 493 +CONECT 496 495 +CONECT 497 495 +CONECT 498 501 500 499 495 +CONECT 499 498 +CONECT 500 498 +CONECT 501 504 502 503 498 +CONECT 502 501 +CONECT 503 501 +CONECT 504 506 505 507 501 +CONECT 505 504 +CONECT 506 504 +CONECT 507 509 504 510 508 +CONECT 508 507 +CONECT 509 507 +CONECT 510 507 +CONECT 511 493 513 512 +CONECT 512 511 +CONECT 513 514 511 515 +CONECT 514 513 +CONECT 515 513 516 517 521 +CONECT 516 515 +CONECT 517 520 515 518 519 +CONECT 518 517 +CONECT 519 517 +CONECT 520 517 +CONECT 521 515 523 522 +CONECT 522 521 +CONECT 523 524 521 525 +CONECT 524 523 +CONECT 525 523 545 527 526 +CONECT 526 525 +CONECT 527 530 525 529 528 +CONECT 528 527 +CONECT 529 527 +CONECT 530 531 532 533 527 +CONECT 531 530 +CONECT 532 530 +CONECT 533 536 530 535 534 +CONECT 534 533 +CONECT 535 533 +CONECT 536 537 538 533 +CONECT 537 536 +CONECT 538 539 536 542 +CONECT 539 540 541 538 +CONECT 540 539 +CONECT 541 539 +CONECT 542 538 544 543 +CONECT 543 542 +CONECT 544 542 +CONECT 545 547 525 546 +CONECT 546 545 +CONECT 547 548 549 545 +CONECT 548 547 +CONECT 549 551 547 555 550 +CONECT 550 549 +CONECT 551 552 554 553 549 +CONECT 552 551 +CONECT 553 551 +CONECT 554 551 +CONECT 555 549 557 556 +CONECT 556 555 +CONECT 557 558 555 559 +CONECT 558 557 +CONECT 559 561 557 560 569 +CONECT 560 559 +CONECT 561 564 562 563 559 +CONECT 562 561 +CONECT 563 561 +CONECT 564 566 565 561 +CONECT 565 564 +CONECT 566 567 568 564 +CONECT 567 566 +CONECT 568 566 +CONECT 569 559 571 570 +CONECT 570 569 +CONECT 571 572 569 573 +CONECT 572 571 +CONECT 573 571 575 574 581 +CONECT 574 573 +CONECT 575 578 576 573 577 +CONECT 576 575 +CONECT 577 575 +CONECT 578 580 579 575 +CONECT 579 578 +CONECT 580 578 +CONECT 581 573 583 582 +CONECT 582 581 +CONECT 583 584 581 585 +CONECT 584 583 +CONECT 585 583 587 600 586 +CONECT 586 585 +CONECT 587 589 588 585 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 596 591 592 +CONECT 591 590 +CONECT 592 590 593 594 595 +CONECT 593 592 +CONECT 594 592 +CONECT 595 592 +CONECT 596 597 599 598 590 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 +CONECT 600 602 585 601 +CONECT 601 600 +CONECT 602 603 604 600 +CONECT 603 602 +CONECT 604 607 602 606 605 +CONECT 605 604 +CONECT 606 604 +CONECT 607 609 608 604 +CONECT 608 607 +CONECT 609 611 610 607 +CONECT 610 609 +CONECT 611 622 612 613 609 +CONECT 612 611 +CONECT 613 615 611 614 616 +CONECT 614 613 +CONECT 615 613 +CONECT 616 613 617 619 618 +CONECT 617 616 +CONECT 618 616 +CONECT 619 621 616 620 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 611 +CONECT 623 622 +CONECT 624 626 625 622 +CONECT 625 624 +CONECT 626 634 628 627 624 +CONECT 627 626 +CONECT 628 631 629 630 626 +CONECT 629 628 +CONECT 630 628 +CONECT 631 633 632 628 +CONECT 632 631 +CONECT 633 631 +CONECT 634 635 636 626 +CONECT 635 634 +CONECT 636 638 634 637 +CONECT 637 636 +CONECT 638 641 639 640 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 642 638 +CONECT 642 641 +CONECT 643 645 644 641 +CONECT 644 643 +CONECT 645 647 646 656 643 +CONECT 646 645 +CONECT 647 649 648 650 645 +CONECT 648 647 +CONECT 649 647 +CONECT 650 652 647 653 651 +CONECT 651 650 +CONECT 652 650 +CONECT 653 654 650 655 +CONECT 654 653 +CONECT 655 653 +CONECT 656 658 645 657 +CONECT 657 656 +CONECT 658 659 660 656 +CONECT 659 658 +CONECT 660 674 658 661 662 +CONECT 661 660 +CONECT 662 660 664 665 663 +CONECT 663 662 +CONECT 664 662 +CONECT 665 666 662 672 +CONECT 666 667 668 665 +CONECT 667 666 +CONECT 668 669 666 670 +CONECT 669 668 +CONECT 670 668 672 671 +CONECT 671 670 +CONECT 672 665 670 673 +CONECT 673 672 +CONECT 674 676 675 660 +CONECT 675 674 +CONECT 676 678 677 674 +CONECT 677 676 +CONECT 678 679 680 688 676 +CONECT 679 678 +CONECT 680 682 686 678 681 +CONECT 681 680 +CONECT 682 683 684 685 680 +CONECT 683 682 +CONECT 684 682 +CONECT 685 682 +CONECT 686 687 680 +CONECT 687 686 +CONECT 688 690 678 689 +CONECT 689 688 +CONECT 690 691 692 688 +CONECT 691 690 +CONECT 692 705 694 690 693 +CONECT 693 692 +CONECT 694 697 695 692 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 700 698 699 694 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 697 701 +CONECT 701 700 +CONECT 702 704 703 700 +CONECT 703 702 +CONECT 704 702 +CONECT 705 706 707 692 +CONECT 706 705 +CONECT 707 709 705 708 +CONECT 708 707 +CONECT 709 710 717 711 707 +CONECT 710 709 +CONECT 711 714 709 712 713 +CONECT 712 711 +CONECT 713 711 +CONECT 714 716 711 715 +CONECT 715 714 +CONECT 716 714 +CONECT 717 719 709 718 +CONECT 718 717 +CONECT 719 720 721 717 +CONECT 720 719 +CONECT 721 723 719 729 722 +CONECT 722 721 +CONECT 723 725 724 726 721 +CONECT 724 723 +CONECT 725 723 +CONECT 726 727 723 728 +CONECT 727 726 +CONECT 728 726 +CONECT 729 731 721 730 +CONECT 730 729 +CONECT 731 732 733 729 +CONECT 732 731 +CONECT 733 735 734 731 739 +CONECT 734 733 +CONECT 735 738 737 736 733 +CONECT 736 735 +CONECT 737 735 +CONECT 738 735 +CONECT 739 733 740 741 +CONECT 740 739 +CONECT 741 739 742 743 +CONECT 742 741 +CONECT 743 741 744 745 753 +CONECT 744 743 +CONECT 745 747 743 751 746 +CONECT 746 745 +CONECT 747 748 750 749 745 +CONECT 748 747 +CONECT 749 747 +CONECT 750 747 +CONECT 751 752 745 +CONECT 752 751 +CONECT 753 743 755 754 +CONECT 754 753 +CONECT 755 756 757 753 +CONECT 756 755 +CONECT 757 758 755 759 775 +CONECT 758 757 +CONECT 759 762 757 761 760 +CONECT 760 759 +CONECT 761 759 +CONECT 762 765 763 764 759 +CONECT 763 762 +CONECT 764 762 +CONECT 765 768 767 766 762 +CONECT 766 765 +CONECT 767 765 +CONECT 768 771 770 769 765 +CONECT 769 768 +CONECT 770 768 +CONECT 771 773 774 772 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 771 +CONECT 775 757 777 776 +CONECT 776 775 +CONECT 777 778 775 779 +CONECT 778 777 +CONECT 779 777 789 781 780 +CONECT 780 779 +CONECT 781 782 779 787 783 +CONECT 782 781 +CONECT 783 781 786 785 784 +CONECT 784 783 +CONECT 785 783 +CONECT 786 783 +CONECT 787 788 781 +CONECT 788 787 +CONECT 789 790 779 791 +CONECT 790 789 +CONECT 791 789 793 792 +CONECT 792 791 +CONECT 793 794 791 809 795 +CONECT 794 793 +CONECT 795 793 798 797 796 +CONECT 796 795 +CONECT 797 795 +CONECT 798 807 799 795 +CONECT 799 801 798 800 +CONECT 800 799 +CONECT 801 803 802 799 +CONECT 802 801 +CONECT 803 804 805 801 +CONECT 804 803 +CONECT 805 806 803 807 +CONECT 806 805 +CONECT 807 805 808 798 +CONECT 808 807 +CONECT 809 793 811 810 +CONECT 810 809 +CONECT 811 812 809 813 +CONECT 812 811 +CONECT 813 815 811 823 814 +CONECT 814 813 +CONECT 815 821 817 816 813 +CONECT 816 815 +CONECT 817 818 819 815 820 +CONECT 818 817 +CONECT 819 817 +CONECT 820 817 +CONECT 821 822 815 +CONECT 822 821 +CONECT 823 824 813 825 +CONECT 824 823 +CONECT 825 823 827 826 +CONECT 826 825 +CONECT 827 840 828 825 829 +CONECT 828 827 +CONECT 829 827 830 831 832 +CONECT 830 829 +CONECT 831 829 +CONECT 832 829 834 833 835 +CONECT 833 832 +CONECT 834 832 +CONECT 835 832 836 +CONECT 836 837 839 838 835 +CONECT 837 836 +CONECT 838 836 +CONECT 839 836 +CONECT 840 842 841 827 +CONECT 841 840 +CONECT 842 844 843 840 +CONECT 843 842 +CONECT 844 846 845 842 850 +CONECT 845 844 +CONECT 846 849 848 847 844 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 +CONECT 850 844 852 851 +CONECT 851 850 +CONECT 852 853 850 854 +CONECT 853 852 +CONECT 854 852 865 856 855 +CONECT 855 854 +CONECT 856 858 854 857 859 +CONECT 857 856 +CONECT 858 856 +CONECT 859 856 860 861 862 +CONECT 860 859 +CONECT 861 859 +CONECT 862 859 864 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 867 854 866 +CONECT 866 865 +CONECT 867 865 +CONECT 868 87 305 869 274 +CONECT 869 868 871 +CONECT 870 873 871 874 872 +CONECT 871 869 870 +CONECT 872 870 +CONECT 873 870 +CONECT 874 870 +CONECT 875 876 +CONECT 876 875 877 +CONECT 877 876 +MASTER 0 0 0 0 0 0 0 0 877 0 877 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_3_front_0.pdb b/tests/nsga2/intermediate_molecules/min_iter_3_front_0.pdb new file mode 100644 index 0000000..c2d6518 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_3_front_0.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.331 51.38249999999948 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.971 23.610 1.00 0.00 N +ATOM 2 H1 MET 1 15.141 38.355 24.553 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.345 23.090 1.00 0.00 H +ATOM 4 H3 MET 1 16.014 38.281 23.181 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.500 23.668 1.00 0.00 C +ATOM 6 HA MET 1 14.171 36.197 24.096 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.872 22.269 1.00 0.00 C +ATOM 8 HB2 MET 1 14.392 36.151 21.668 1.00 0.00 H +ATOM 9 HB3 MET 1 16.153 36.270 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.371 34.332 22.296 1.00 0.00 C +ATOM 11 HG2 MET 1 16.259 34.062 22.867 1.00 0.00 H +ATOM 12 HG3 MET 1 14.494 33.923 22.804 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.525 20.666 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.569 20.066 1.00 0.00 C +ATOM 15 HE1 MET 1 13.461 34.598 20.015 1.00 0.00 H +ATOM 16 HE2 MET 1 13.777 33.132 19.069 1.00 0.00 H +ATOM 17 HE3 MET 1 13.174 32.990 20.731 1.00 0.00 H +ATOM 18 C MET 1 16.221 36.029 24.598 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.397 24.423 1.00 0.00 O +ATOM 20 N GLN 2 15.881 35.189 25.579 1.00 0.00 N +ATOM 21 H GLN 2 14.910 34.997 25.765 1.00 0.00 H +ATOM 22 CA GLN 2 16.846 34.478 26.432 1.00 0.00 C +ATOM 23 HA GLN 2 17.652 35.157 26.726 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.072 27.724 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.138 33.651 27.491 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.661 33.315 28.273 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.253 28.684 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.469 36.090 28.161 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.204 34.973 29.418 1.00 0.00 H +ATOM 30 CD GLN 2 17.129 35.580 29.525 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.164 34.935 29.495 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.031 36.470 30.481 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.772 36.536 31.097 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.109 36.732 30.769 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.304 25.672 1.00 0.00 C +ATOM 36 O GLN 2 17.101 32.148 25.833 1.00 0.00 O +ATOM 37 N TYR 3 18.476 33.620 24.822 1.00 0.00 N +ATOM 38 H TYR 3 18.753 34.594 24.753 1.00 0.00 H +ATOM 39 CA TYR 3 19.257 32.618 24.101 1.00 0.00 C +ATOM 40 HA TYR 3 18.571 31.964 23.563 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.286 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.865 33.945 23.646 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.482 22.671 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.069 21.936 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.528 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.821 32.423 20.552 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.146 34.202 19.540 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.115 33.734 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.845 35.572 19.674 1.00 0.00 C +ATOM 50 OH TYR 3 18.515 36.305 18.581 1.00 0.00 O +ATOM 51 HH TYR 3 18.774 35.870 17.765 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.190 20.937 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.729 37.250 21.020 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.323 35.442 22.065 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.447 35.936 23.020 1.00 0.00 H +ATOM 56 C TYR 3 20.090 31.765 25.077 1.00 0.00 C +ATOM 57 O TYR 3 20.461 32.246 26.149 1.00 0.00 O +ATOM 58 N LYS 4 20.401 30.506 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.251 30.222 23.770 1.00 0.00 H +ATOM 60 CA LYS 4 21.012 29.502 25.631 1.00 0.00 C +ATOM 61 HA LYS 4 20.728 29.716 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.477 28.101 25.270 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.521 27.983 24.189 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.144 27.345 25.695 1.00 0.00 H +ATOM 65 CG LYS 4 19.051 27.747 25.735 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.886 26.697 25.494 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.996 27.852 26.817 1.00 0.00 H +ATOM 68 CD LYS 4 17.924 28.566 25.082 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.889 29.561 25.522 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.146 28.677 24.019 1.00 0.00 H +ATOM 71 CE LYS 4 16.545 27.894 25.197 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.511 24.666 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.594 26.934 24.678 1.00 0.00 H +ATOM 74 NZ LYS 4 16.096 27.673 26.597 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.986 28.550 27.087 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.208 27.171 26.603 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.759 27.086 27.088 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.617 1.00 0.00 C +ATOM 79 O LYS 4 23.197 29.888 24.646 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.028 26.695 1.00 0.00 N +HETATM 81 CA HX1 5 24.626 28.831 26.818 1.00 0.00 C +HETATM 82 C HX1 5 24.900 27.673 27.781 1.00 0.00 C +HETATM 83 O HX1 5 24.403 27.682 28.908 1.00 0.00 O +HETATM 84 CB HX1 5 25.263 30.146 27.306 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.390 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.070 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.386 27.859 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.096 27.752 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.937 29.837 27.334 1.00 0.00 N +HETATM 90 H HX1 5 22.597 28.839 27.518 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.840 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.382 28.291 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.939 30.946 26.638 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.281 26.698 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.530 31.749 28.082 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.838 29.357 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.635 26.658 27.325 1.00 0.00 N +ATOM 98 H ILE 6 26.017 26.713 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.005 25.472 28.115 1.00 0.00 C +ATOM 100 HA ILE 6 25.305 25.371 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.849 24.199 27.245 1.00 0.00 C +ATOM 102 HB ILE 6 26.399 24.347 26.315 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.408 22.939 27.933 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.891 22.758 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.284 22.071 27.286 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.479 23.047 28.114 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.343 24.015 26.915 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.790 23.879 27.844 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.966 24.918 26.434 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.005 22.849 25.979 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.174 21.896 26.480 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.950 22.908 25.704 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.610 22.906 25.075 1.00 0.00 H +ATOM 114 C ILE 6 27.394 25.667 28.753 1.00 0.00 C +ATOM 115 O ILE 6 28.229 26.397 28.221 1.00 0.00 O +ATOM 116 N VAL 7 27.601 25.080 29.936 1.00 0.00 N +ATOM 117 H VAL 7 26.870 24.477 30.295 1.00 0.00 H +ATOM 118 CA VAL 7 28.779 25.286 30.801 1.00 0.00 C +ATOM 119 HA VAL 7 28.879 26.361 30.956 1.00 0.00 H +ATOM 120 CB VAL 7 28.501 24.640 32.176 1.00 0.00 C +ATOM 121 HB VAL 7 27.502 24.948 32.483 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.525 23.106 32.131 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.535 22.744 31.923 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.192 22.714 33.086 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.858 22.745 31.347 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.450 25.110 33.283 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.290 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.078 24.777 34.249 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.448 24.701 33.140 1.00 0.00 H +ATOM 130 C VAL 7 30.113 24.804 30.200 1.00 0.00 C +ATOM 131 O VAL 7 30.155 23.918 29.349 1.00 0.00 O +ATOM 132 N THR 8 31.216 25.379 30.688 1.00 0.00 N +ATOM 133 H THR 8 31.111 26.090 31.396 1.00 0.00 H +ATOM 134 CA THR 8 32.599 24.973 30.394 1.00 0.00 C +ATOM 135 HA THR 8 32.693 24.829 29.317 1.00 0.00 H +ATOM 136 CB THR 8 33.573 26.088 30.820 1.00 0.00 C +ATOM 137 HB THR 8 34.598 25.756 30.643 1.00 0.00 H +ATOM 138 CG2 THR 8 33.360 27.395 30.062 1.00 0.00 C +ATOM 139 HG21 THR 8 32.387 27.825 30.304 1.00 0.00 H +ATOM 140 HG22 THR 8 34.136 28.111 30.331 1.00 0.00 H +ATOM 141 HG23 THR 8 33.406 27.215 28.989 1.00 0.00 H +ATOM 142 OG1 THR 8 33.423 26.394 32.187 1.00 0.00 O +ATOM 143 HG1 THR 8 33.805 27.264 32.325 1.00 0.00 H +ATOM 144 C THR 8 33.011 23.656 31.078 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.249 32.104 1.00 0.00 O +ATOM 146 N GLY 9 34.050 23.008 30.534 1.00 0.00 N +ATOM 147 H GLY 9 34.405 23.337 29.651 1.00 0.00 H +ATOM 148 CA GLY 9 34.626 21.773 31.078 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.617 21.618 30.655 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.880 32.158 1.00 0.00 H +ATOM 151 C GLY 9 33.783 20.523 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.022 20.484 29.825 1.00 0.00 O +ATOM 153 N LYS 10 33.951 19.480 31.615 1.00 0.00 N +ATOM 154 H LYS 10 34.670 19.560 32.316 1.00 0.00 H +ATOM 155 CA LYS 10 33.230 18.191 31.479 1.00 0.00 C +ATOM 156 HA LYS 10 32.289 18.403 30.967 1.00 0.00 H +ATOM 157 CB LYS 10 34.057 17.246 30.577 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.677 17.847 29.907 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.724 16.640 31.194 1.00 0.00 H +ATOM 160 CG LYS 10 33.192 16.330 29.692 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.593 15.666 30.313 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.519 16.953 29.100 1.00 0.00 H +ATOM 163 CD LYS 10 34.058 15.492 28.736 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.721 16.156 28.178 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.661 14.791 29.314 1.00 0.00 H +ATOM 166 CE LYS 10 33.179 14.718 27.746 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.965 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.471 15.413 27.288 1.00 0.00 H +ATOM 169 NZ LYS 10 33.977 14.072 26.676 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.736 13.512 27.043 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.382 13.524 26.065 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.427 14.774 26.073 1.00 0.00 H +ATOM 173 C LYS 10 32.821 17.544 32.814 1.00 0.00 C +ATOM 174 O LYS 10 32.336 16.416 32.832 1.00 0.00 O +ATOM 175 N SER 11 33.037 18.243 33.935 1.00 0.00 N +ATOM 176 H SER 11 33.494 19.132 33.842 1.00 0.00 H +ATOM 177 CA SER 11 32.566 17.848 35.279 1.00 0.00 C +ATOM 178 HA SER 11 32.499 16.758 35.340 1.00 0.00 H +ATOM 179 CB SER 11 33.553 18.325 36.353 1.00 0.00 C +ATOM 180 HB2 SER 11 33.585 19.415 36.355 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.980 37.332 1.00 0.00 H +ATOM 182 OG SER 11 34.850 17.821 36.094 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.425 36.456 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.420 35.589 1.00 0.00 C +ATOM 185 O SER 11 30.351 17.750 36.199 1.00 0.00 O +ATOM 186 N CYS 12 30.919 19.655 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.630 20.134 34.627 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.270 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.870 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.351 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.324 22.215 34.523 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.251 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.149 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.145 23.412 37.057 1.00 0.00 H +ATOM 195 C CYS 12 28.853 19.936 33.838 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.667 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.513 19.990 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.060 20.142 34.736 1.00 0.00 H +ATOM 199 CA LYS 13 26.667 19.722 32.662 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.862 31.773 1.00 0.00 H +ATOM 201 CB LYS 13 26.223 18.247 32.706 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.032 17.655 33.143 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.346 18.144 33.358 1.00 0.00 H +ATOM 204 CG LYS 13 25.915 17.636 31.324 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.036 18.108 30.884 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.767 17.822 30.669 1.00 0.00 H +ATOM 207 CD LYS 13 25.684 16.116 31.406 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.690 15.716 30.391 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.518 15.663 31.947 1.00 0.00 H +ATOM 210 CE LYS 13 24.346 15.744 32.064 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.165 16.386 32.929 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.553 15.951 31.340 1.00 0.00 H +ATOM 213 NZ LYS 13 24.304 14.308 32.452 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.875 14.098 33.271 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.357 13.998 32.643 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.687 13.729 31.706 1.00 0.00 H +ATOM 217 C LYS 13 25.488 20.707 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.584 20.487 31.712 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.786 33.298 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.945 33.874 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.754 33.376 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.445 22.193 33.447 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.483 23.331 34.294 1.00 0.00 H +ATOM 224 C GLY 14 24.286 23.716 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.214 23.892 31.407 1.00 0.00 O +ATOM 226 N VAL 15 23.145 24.399 32.111 1.00 0.00 N +ATOM 227 H VAL 15 22.435 24.245 32.812 1.00 0.00 H +ATOM 228 CA VAL 15 22.778 25.387 31.071 1.00 0.00 C +ATOM 229 HA VAL 15 23.675 25.626 30.492 1.00 0.00 H +ATOM 230 CB VAL 15 21.760 24.738 30.089 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.856 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.449 24.318 30.766 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.938 25.178 31.211 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.793 23.856 30.028 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.579 31.548 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.416 25.668 28.927 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.331 26.008 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.820 25.120 28.196 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.841 26.533 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.282 26.685 31.729 1.00 0.00 C +ATOM 241 O VAL 15 21.714 26.632 32.818 1.00 0.00 O +HETATM 242 N HY1 16 22.496 27.830 31.091 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.109 31.450 1.00 0.00 C +HETATM 244 C HY1 16 21.616 29.886 30.135 1.00 0.00 C +HETATM 245 O HY1 16 21.780 29.350 29.023 1.00 0.00 O +HETATM 246 CB HY1 16 22.864 29.868 32.413 1.00 0.00 C +HETATM 247 CG HY1 16 24.212 30.223 31.813 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.549 31.404 31.207 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.321 29.396 31.740 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.303 30.091 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.880 31.315 30.788 1.00 0.00 N +HETATM 252 H HY1 16 22.997 27.783 30.210 1.00 0.00 H +HETATM 253 HA HY1 16 20.968 28.987 31.945 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.396 30.793 32.773 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.026 29.256 33.296 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.399 28.458 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.907 32.258 31.095 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.728 30.996 1.00 0.00 H +ATOM 259 N THR 17 21.166 31.142 30.265 1.00 0.00 N +ATOM 260 H THR 17 21.050 31.473 31.216 1.00 0.00 H +ATOM 261 CA THR 17 20.736 32.026 29.172 1.00 0.00 C +ATOM 262 HA THR 17 21.120 31.634 28.284 1.00 0.00 H +ATOM 263 CB THR 17 19.152 32.017 29.049 1.00 0.00 C +ATOM 264 HB THR 17 18.937 32.609 28.167 1.00 0.00 H +ATOM 265 CG2 THR 17 18.596 30.675 28.723 1.00 0.00 C +ATOM 266 HG21 THR 17 18.786 29.900 29.421 1.00 0.00 H +ATOM 267 HG22 THR 17 17.506 30.690 28.630 1.00 0.00 H +ATOM 268 HG23 THR 17 18.925 30.322 27.780 1.00 0.00 H +ATOM 269 OG1 THR 17 18.479 32.473 30.205 1.00 0.00 O +ATOM 270 HG1 THR 17 18.568 33.453 30.221 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.458 29.233 1.00 0.00 C +ATOM 272 O THR 17 21.702 33.916 30.265 1.00 0.00 O +HETATM 273 N HY2 18 21.139 34.162 28.101 1.00 0.00 N +HETATM 274 CA HY2 18 21.450 35.620 27.971 1.00 0.00 C +HETATM 275 C HY2 18 20.329 36.290 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.985 35.837 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.774 35.820 27.259 1.00 0.00 C +HETATM 278 CG HY2 18 24.005 35.327 28.003 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.420 34.030 28.155 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.943 36.119 28.644 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.315 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.707 27.237 1.00 0.00 H +HETATM 284 HA HY2 18 21.503 36.046 29.014 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.748 35.296 26.297 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.910 36.879 27.057 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.955 37.127 28.681 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.926 33.165 27.774 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.761 35.647 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.807 37.387 27.748 1.00 0.00 N +ATOM 291 H GLU 19 20.142 37.684 28.644 1.00 0.00 H +ATOM 292 CA GLU 19 18.798 38.219 27.101 1.00 0.00 C +ATOM 293 HA GLU 19 18.058 37.555 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.065 39.079 28.156 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.754 38.431 28.967 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.775 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.833 39.851 27.657 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.550 28.422 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.089 40.412 26.764 1.00 0.00 H +ATOM 300 CD GLU 19 15.654 38.901 27.366 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.588 38.373 26.224 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.813 38.691 28.275 1.00 0.00 O +ATOM 303 C GLU 19 19.405 39.113 25.992 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.857 26.273 1.00 0.00 O +ATOM 305 N ALA 20 18.878 39.052 24.762 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.354 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.961 23.686 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.963 24.094 1.00 0.00 H +ATOM 309 CB ALA 20 20.592 39.489 23.094 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.465 38.517 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.951 40.206 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.351 39.401 23.870 1.00 0.00 H +ATOM 313 C ALA 20 18.191 40.036 22.579 1.00 0.00 C +ATOM 314 O ALA 20 17.360 39.133 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.087 21.745 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.824 21.920 1.00 0.00 H +ATOM 317 CA VAL 21 17.460 41.147 20.465 1.00 0.00 C +ATOM 318 HA VAL 21 16.471 40.723 20.625 1.00 0.00 H +ATOM 319 CB VAL 21 17.274 42.597 19.972 1.00 0.00 C +ATOM 320 HB VAL 21 16.616 42.570 19.108 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.597 43.470 21.033 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.255 43.626 21.888 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.349 44.439 20.598 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.674 42.997 21.365 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.583 43.276 19.536 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.004 42.764 18.670 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.380 44.306 19.239 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.315 43.278 20.344 1.00 0.00 H +ATOM 329 C VAL 21 18.121 40.330 19.353 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.986 18.375 1.00 0.00 O +ATOM 331 N ASP 22 19.414 40.050 19.506 1.00 0.00 N +ATOM 332 H ASP 22 19.863 40.329 20.361 1.00 0.00 H +ATOM 333 CA ASP 22 20.295 39.463 18.502 1.00 0.00 C +ATOM 334 HA ASP 22 19.714 38.825 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.941 40.588 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.174 41.079 17.075 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.377 41.324 18.356 1.00 0.00 H +ATOM 338 CG ASP 22 22.025 40.044 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.147 40.586 16.800 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.762 39.018 16.087 1.00 0.00 O +ATOM 341 C ASP 22 21.366 38.597 19.178 1.00 0.00 C +ATOM 342 O ASP 22 21.825 38.880 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.789 37.545 18.492 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.489 17.520 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.608 18.984 1.00 0.00 C +ATOM 346 HA TRP 23 22.545 36.357 20.016 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.348 18.138 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.975 18.216 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.840 35.604 17.094 1.00 0.00 H +ATOM 350 CG TRP 23 23.573 34.244 18.531 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.517 33.704 17.733 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.739 34.020 16.723 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.129 32.678 18.412 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.903 32.155 18.035 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.589 32.475 19.659 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.825 31.536 20.665 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.540 30.741 20.523 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.682 21.888 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.012 22.701 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.765 22.099 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.900 23.082 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.005 33.658 21.055 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.310 34.465 21.213 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.637 33.527 19.797 1.00 0.00 C +ATOM 365 C TRP 23 24.210 37.185 18.982 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.925 1.00 0.00 O +ATOM 367 N ALA 24 24.557 38.022 17.997 1.00 0.00 N +ATOM 368 H ALA 24 23.880 38.262 17.279 1.00 0.00 H +ATOM 369 CA ALA 24 25.846 38.717 17.976 1.00 0.00 C +ATOM 370 HA ALA 24 26.618 38.001 18.267 1.00 0.00 H +ATOM 371 CB ALA 24 26.158 39.140 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.444 39.882 16.189 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.160 39.562 16.482 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.110 38.274 15.877 1.00 0.00 H +ATOM 375 C ALA 24 25.929 39.882 18.994 1.00 0.00 C +ATOM 376 O ALA 24 27.022 40.384 19.270 1.00 0.00 O +ATOM 377 N GLU 25 24.812 40.285 19.610 1.00 0.00 N +ATOM 378 H GLU 25 23.932 39.945 19.243 1.00 0.00 H +ATOM 379 CA GLU 25 24.791 41.075 20.852 1.00 0.00 C +ATOM 380 HA GLU 25 25.642 41.755 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.512 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.646 41.279 20.820 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.451 42.386 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.432 43.037 19.875 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.632 42.630 18.884 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.410 43.424 19.863 1.00 0.00 H +ATOM 387 CD GLU 25 24.381 44.197 20.185 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.918 45.196 20.744 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.601 44.048 19.836 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.102 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.517 23.016 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.005 22.132 1.00 0.00 N +ATOM 393 H ALA 26 23.666 38.775 21.366 1.00 0.00 H +ATOM 394 CA ALA 26 24.460 38.029 23.217 1.00 0.00 C +ATOM 395 HA ALA 26 24.199 38.524 24.148 1.00 0.00 H +ATOM 396 CB ALA 26 23.491 36.862 23.015 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.771 36.287 22.133 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.204 23.883 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.230 22.894 1.00 0.00 H +ATOM 400 C ALA 26 25.918 37.533 23.365 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.227 24.482 1.00 0.00 O +ATOM 402 N GLU 27 26.710 37.510 22.283 1.00 0.00 N +ATOM 403 H GLU 27 26.268 37.638 21.376 1.00 0.00 H +ATOM 404 CA GLU 27 28.167 37.303 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.369 36.351 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.763 37.247 20.913 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.152 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.735 38.251 20.486 1.00 0.00 H +ATOM 409 CG GLU 27 30.208 36.724 20.921 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.145 21.771 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.190 35.641 21.055 1.00 0.00 H +ATOM 412 CD GLU 27 30.982 37.089 19.641 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.725 38.106 19.697 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.344 18.641 1.00 0.00 O +ATOM 415 C GLU 27 28.849 38.396 23.183 1.00 0.00 C +ATOM 416 O GLU 27 29.572 38.094 24.134 1.00 0.00 O +ATOM 417 N LYS 28 28.547 39.673 22.914 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.853 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.817 23.666 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.667 1.00 0.00 H +ATOM 421 CB LYS 28 28.699 42.145 22.993 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.278 23.048 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.170 42.963 23.542 1.00 0.00 H +ATOM 424 CG LYS 28 29.137 42.221 21.519 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.207 42.027 21.443 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.604 41.462 20.949 1.00 0.00 H +ATOM 427 CD LYS 28 28.837 43.604 20.920 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.819 43.907 21.172 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.521 44.332 21.364 1.00 0.00 H +ATOM 430 CE LYS 28 29.006 43.629 19.396 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.103 44.670 19.084 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.926 43.113 19.127 1.00 0.00 H +ATOM 433 NZ LYS 28 27.841 43.021 18.708 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.981 43.489 19.017 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.904 43.103 17.704 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.722 42.040 18.958 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.782 25.132 1.00 0.00 C +ATOM 438 O LYS 28 29.482 40.969 26.019 1.00 0.00 O +ATOM 439 N PHE 29 27.393 40.452 25.417 1.00 0.00 N +ATOM 440 H PHE 29 26.740 40.365 24.642 1.00 0.00 H +ATOM 441 CA PHE 29 26.903 40.286 26.793 1.00 0.00 C +ATOM 442 HA PHE 29 27.228 41.146 27.379 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.264 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.038 39.343 26.310 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.022 40.230 27.832 1.00 0.00 H +ATOM 446 CG PHE 29 24.678 41.443 26.116 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.465 41.235 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.015 40.254 25.407 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.830 42.300 24.767 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.907 42.126 24.234 1.00 0.00 H +ATOM 451 CZ PHE 29 23.399 43.584 24.790 1.00 0.00 C +ATOM 452 HZ PHE 29 22.919 44.396 24.265 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.591 43.806 25.498 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.027 44.796 25.527 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.226 42.742 26.165 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.139 42.936 26.704 1.00 0.00 H +ATOM 457 C PHE 29 27.484 39.050 27.507 1.00 0.00 C +ATOM 458 O PHE 29 27.589 39.038 28.735 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.768 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.042 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.683 36.892 27.316 1.00 0.00 C +ATOM 462 HA THR 30 28.208 36.545 28.226 1.00 0.00 H +ATOM 463 CB THR 30 28.692 35.717 26.333 1.00 0.00 C +ATOM 464 HB THR 30 29.073 36.025 25.356 1.00 0.00 H +ATOM 465 CG2 THR 30 29.496 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.137 34.212 27.801 1.00 0.00 H +ATOM 467 HG22 THR 30 29.369 33.689 26.123 1.00 0.00 H +ATOM 468 HG23 THR 30 30.559 34.746 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.365 35.280 26.189 1.00 0.00 O +ATOM 470 HG1 THR 30 26.960 35.883 25.542 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.982 28.769 1.00 0.00 O +ATOM 473 N LYS 31 30.746 38.122 26.832 1.00 0.00 N +ATOM 474 H LYS 31 30.287 38.320 25.947 1.00 0.00 H +ATOM 475 CA LYS 31 32.078 38.702 27.069 1.00 0.00 C +ATOM 476 HA LYS 31 32.749 37.905 27.376 1.00 0.00 H +ATOM 477 CB LYS 31 32.616 39.317 25.766 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.011 25.348 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.529 39.865 25.987 1.00 0.00 H +ATOM 480 CG LYS 31 32.930 38.210 24.744 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.684 37.553 25.176 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.044 37.629 24.525 1.00 0.00 H +ATOM 483 CD LYS 31 33.459 38.818 23.435 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.384 22.952 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.299 39.497 23.642 1.00 0.00 H +ATOM 486 CE LYS 31 33.923 37.725 22.467 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.107 37.055 22.246 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.217 38.195 21.540 1.00 0.00 H +ATOM 489 NZ LYS 31 35.077 36.976 23.015 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.822 36.247 23.679 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.553 36.469 22.265 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.760 37.567 23.503 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.188 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.780 28.917 1.00 0.00 O +ATOM 495 N ALA 32 31.031 40.509 28.373 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.873 41.412 29.515 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.138 29.505 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.375 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.495 29.375 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.875 30.215 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.557 42.757 28.446 1.00 0.00 H +ATOM 503 C ALA 32 30.963 40.638 30.838 1.00 0.00 C +ATOM 504 O ALA 32 31.881 40.886 31.616 1.00 0.00 O +ATOM 505 N LYN 33 30.117 39.613 31.030 1.00 0.00 N +ATOM 506 H LYN 33 29.390 39.457 30.346 1.00 0.00 H +ATOM 507 CA LYN 33 30.156 38.755 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.022 39.383 33.110 1.00 0.00 H +ATOM 509 CB LYN 33 29.008 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.061 37.156 31.262 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.141 37.038 33.024 1.00 0.00 H +ATOM 512 CG LYN 33 27.610 38.358 32.315 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.564 38.982 33.207 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.412 38.981 31.444 1.00 0.00 H +ATOM 515 CD LYN 33 26.535 37.267 32.412 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.691 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.632 36.748 33.365 1.00 0.00 H +ATOM 518 CE LYN 33 25.122 37.835 32.288 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.934 38.514 33.114 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.035 38.378 31.349 1.00 0.00 H +ATOM 521 NZ LYN 33 24.115 36.761 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.184 37.154 32.261 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.253 36.113 31.547 1.00 0.00 H +ATOM 524 C LYN 33 31.510 38.042 32.391 1.00 0.00 C +ATOM 525 O LYN 33 32.008 37.922 33.505 1.00 0.00 O +ATOM 526 N ALA 34 32.143 37.585 31.305 1.00 0.00 N +ATOM 527 H ALA 34 31.696 37.677 30.400 1.00 0.00 H +ATOM 528 CA ALA 34 33.470 36.966 31.389 1.00 0.00 C +ATOM 529 HA ALA 34 33.428 36.160 32.125 1.00 0.00 H +ATOM 530 CB ALA 34 33.816 36.355 30.029 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.962 37.145 29.294 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.776 30.132 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.693 29.698 1.00 0.00 H +ATOM 534 C ALA 34 34.573 37.946 31.865 1.00 0.00 C +ATOM 535 O ALA 34 35.469 37.540 32.604 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.224 31.488 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.504 30.885 1.00 0.00 H +ATOM 538 CA ASN 35 35.368 40.286 32.000 1.00 0.00 C +ATOM 539 HA ASN 35 36.366 39.870 32.113 1.00 0.00 H +ATOM 540 CB ASN 35 35.476 41.416 30.969 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.486 41.702 30.624 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.287 31.449 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.031 29.800 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.581 41.002 29.898 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.705 28.668 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.448 27.895 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.600 28.628 1.00 0.00 H +ATOM 548 C ASN 35 34.981 40.786 33.404 1.00 0.00 C +ATOM 549 O ASN 35 35.867 41.207 34.150 1.00 0.00 O +ATOM 550 N ASP 36 33.718 40.635 33.831 1.00 0.00 N +ATOM 551 H ASP 36 32.984 40.413 33.166 1.00 0.00 H +ATOM 552 CA ASP 36 33.339 40.772 35.249 1.00 0.00 C +ATOM 553 HA ASP 36 33.668 41.747 35.602 1.00 0.00 H +ATOM 554 CB ASP 36 31.819 40.767 35.440 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.448 39.783 35.230 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.607 40.875 36.498 1.00 0.00 H +ATOM 557 CG ASP 36 30.981 41.783 34.657 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.512 42.876 34.366 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.778 41.516 34.402 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.708 36.125 1.00 0.00 C +ATOM 561 O ASP 36 34.482 40.004 37.236 1.00 0.00 O +ATOM 562 N PHE 37 34.227 38.480 35.608 1.00 0.00 N +ATOM 563 H PHE 37 33.751 38.279 34.737 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.459 36.179 1.00 0.00 C +ATOM 565 HA PHE 37 35.118 37.611 37.257 1.00 0.00 H +ATOM 566 CB PHE 37 34.574 36.041 35.932 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.663 35.826 34.870 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.334 36.446 1.00 0.00 H +ATOM 569 CG PHE 37 33.150 35.763 36.385 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.139 35.558 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.374 35.619 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.312 35.834 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.039 35.198 35.094 1.00 0.00 H +ATOM 574 CZ PHE 37 30.507 35.235 37.199 1.00 0.00 C +ATOM 575 HZ PHE 37 29.492 35.053 37.510 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.515 35.404 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.270 35.352 39.212 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.834 35.668 37.752 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.601 35.814 38.491 1.00 0.00 H +ATOM 580 C PHE 37 36.607 37.580 35.742 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.679 36.016 1.00 0.00 O +ATOM 582 N GLY 38 36.998 38.676 35.079 1.00 0.00 N +ATOM 583 H GLY 38 36.291 39.378 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.389 39.091 34.839 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.499 40.111 35.207 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.054 38.469 35.438 1.00 0.00 H +ATOM 587 C GLY 38 38.925 39.060 33.393 1.00 0.00 C +ATOM 588 O GLY 38 39.874 39.792 33.112 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.227 32.486 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.727 32.761 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.052 31.090 1.00 0.00 C +ATOM 592 HA ARG 39 38.944 39.045 30.646 1.00 0.00 H +ATOM 593 CB ARG 39 40.304 37.440 31.075 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.635 37.431 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.987 38.106 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.522 36.013 31.628 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.039 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.753 31.461 1.00 0.00 H +ATOM 599 CD ARG 39 40.222 35.826 33.132 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.861 36.507 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.182 36.080 33.342 1.00 0.00 H +ATOM 602 NE ARG 39 40.446 34.443 33.599 1.00 0.00 N +ATOM 603 HE ARG 39 41.205 34.297 34.244 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.303 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.469 32.493 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.428 34.360 32.093 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.296 32.621 32.084 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.954 32.226 33.819 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.694 32.095 34.491 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.336 31.450 33.602 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.225 30.193 1.00 0.00 C +ATOM 612 O ARG 39 37.522 36.137 30.605 1.00 0.00 O +ATOM 613 N ASP 40 37.650 37.678 28.959 1.00 0.00 N +ATOM 614 H ASP 40 38.029 38.573 28.674 1.00 0.00 H +ATOM 615 CA ASP 40 36.889 36.892 27.966 1.00 0.00 C +ATOM 616 HA ASP 40 36.166 36.309 28.530 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.733 26.970 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.444 37.038 26.402 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.369 38.350 27.538 1.00 0.00 H +ATOM 620 CG ASP 40 36.824 38.628 25.969 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.257 39.725 26.392 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.837 38.322 24.743 1.00 0.00 O +ATOM 623 C ASP 40 37.720 35.861 27.181 1.00 0.00 C +ATOM 624 O ASP 40 38.885 36.078 26.862 1.00 0.00 O +ATOM 625 N GLY 41 37.056 34.760 26.814 1.00 0.00 N +ATOM 626 H GLY 41 36.099 34.682 27.117 1.00 0.00 H +ATOM 627 CA GLY 41 37.471 33.828 25.758 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.459 34.099 25.383 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.531 32.823 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.482 33.818 24.581 1.00 0.00 C +ATOM 631 O GLY 41 35.578 34.655 24.504 1.00 0.00 O +ATOM 632 N GLU 42 36.638 32.853 23.674 1.00 0.00 N +ATOM 633 H GLU 42 37.348 32.156 23.828 1.00 0.00 H +ATOM 634 CA GLU 42 35.799 32.668 22.476 1.00 0.00 C +ATOM 635 HA GLU 42 35.112 33.509 22.376 1.00 0.00 H +ATOM 636 CB GLU 42 36.683 32.630 21.214 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.158 31.650 21.168 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.035 32.711 20.341 1.00 0.00 H +ATOM 639 CG GLU 42 37.803 33.694 21.111 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.575 33.457 21.850 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.277 33.620 20.129 1.00 0.00 H +ATOM 642 CD GLU 42 37.343 35.144 21.318 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.154 35.459 21.111 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.167 36.006 21.711 1.00 0.00 O +ATOM 645 C GLU 42 34.948 31.386 22.578 1.00 0.00 C +ATOM 646 O GLU 42 35.393 30.398 23.170 1.00 0.00 O +ATOM 647 N ALA 43 33.745 31.391 21.989 1.00 0.00 N +ATOM 648 H ALA 43 33.480 32.196 21.440 1.00 0.00 H +ATOM 649 CA ALA 43 32.756 30.306 22.060 1.00 0.00 C +ATOM 650 HA ALA 43 33.248 29.388 22.388 1.00 0.00 H +ATOM 651 CB ALA 43 31.692 30.672 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.181 31.592 22.812 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.959 29.866 23.177 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.164 30.811 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.110 30.017 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.882 30.932 19.898 1.00 0.00 O +ATOM 657 N THR 44 31.798 28.746 20.423 1.00 0.00 N +ATOM 658 H THR 44 31.919 28.067 21.168 1.00 0.00 H +ATOM 659 CA THR 44 31.131 28.283 19.194 1.00 0.00 C +ATOM 660 HA THR 44 31.425 28.947 18.381 1.00 0.00 H +ATOM 661 CB THR 44 31.610 26.868 18.823 1.00 0.00 C +ATOM 662 HB THR 44 31.430 26.188 19.657 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.281 17.554 1.00 0.00 C +ATOM 664 HG21 THR 44 31.071 26.989 16.727 1.00 0.00 H +ATOM 665 HG22 THR 44 31.502 25.358 17.280 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.037 17.727 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.927 18.561 1.00 0.00 O +ATOM 668 HG1 THR 44 33.234 26.124 18.092 1.00 0.00 H +ATOM 669 C THR 44 29.605 28.381 19.326 1.00 0.00 C +ATOM 670 O THR 44 29.072 28.429 20.436 1.00 0.00 O +ATOM 671 N ILE 45 28.899 28.459 18.193 1.00 0.00 N +ATOM 672 H ILE 45 29.373 28.324 17.314 1.00 0.00 H +ATOM 673 CA ILE 45 27.479 28.840 18.123 1.00 0.00 C +ATOM 674 HA ILE 45 27.060 28.756 19.126 1.00 0.00 H +ATOM 675 CB ILE 45 27.332 30.316 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.271 30.529 17.778 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.069 31.232 18.677 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.151 31.108 18.586 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.833 32.282 18.498 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.768 30.969 19.687 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.759 30.692 16.252 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.018 31.752 16.233 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.657 30.140 15.968 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.506 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.730 30.935 15.529 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.975 31.017 14.269 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.530 29.452 14.955 1.00 0.00 H +ATOM 688 C ILE 45 26.629 27.925 17.243 1.00 0.00 C +ATOM 689 O ILE 45 27.122 27.343 16.276 1.00 0.00 O +ATOM 690 N ASP 46 25.329 27.880 17.545 1.00 0.00 N +ATOM 691 H ASP 46 25.032 28.297 18.421 1.00 0.00 H +ATOM 692 CA ASP 46 24.280 27.260 16.735 1.00 0.00 C +ATOM 693 HA ASP 46 24.584 27.263 15.684 1.00 0.00 H +ATOM 694 CB ASP 46 24.077 25.807 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.221 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.955 25.788 18.267 1.00 0.00 H +ATOM 697 CG ASP 46 22.841 25.170 16.544 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.475 17.281 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.561 25.439 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.957 28.050 16.850 1.00 0.00 C +ATOM 701 O ASP 46 22.507 28.363 17.955 1.00 0.00 O +ATOM 702 N ASP 47 22.309 28.333 15.716 1.00 0.00 N +ATOM 703 H ASP 47 22.678 27.944 14.861 1.00 0.00 H +ATOM 704 CA ASP 47 20.969 28.925 15.674 1.00 0.00 C +ATOM 705 HA ASP 47 20.875 29.653 16.485 1.00 0.00 H +ATOM 706 CB ASP 47 20.776 29.674 14.345 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.520 30.467 14.253 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.912 28.978 13.514 1.00 0.00 H +ATOM 709 CG ASP 47 19.366 30.275 14.271 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.485 29.674 13.613 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.064 31.235 15.016 1.00 0.00 O +ATOM 712 C ASP 47 19.852 27.876 15.878 1.00 0.00 C +ATOM 713 O ASP 47 18.842 28.184 16.513 1.00 0.00 O +ATOM 714 N ALA 48 20.002 26.636 15.396 1.00 0.00 N +ATOM 715 H ALA 48 20.917 26.342 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.934 25.626 15.412 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.054 14.931 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.425 14.583 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.276 23.967 15.053 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.686 14.514 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.674 24.756 13.580 1.00 0.00 H +ATOM 722 C ALA 48 18.524 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.929 17.099 1.00 0.00 O +ATOM 724 N THR 49 19.475 25.245 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.436 25.295 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.265 25.120 19.229 1.00 0.00 C +ATOM 727 HA THR 49 18.215 24.872 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.099 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.818 23.859 20.868 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.628 19.137 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.666 18.098 1.00 0.00 H +ATOM 732 HG22 THR 49 20.434 21.857 19.654 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.165 1.00 0.00 H +ATOM 734 OG1 THR 49 21.478 24.244 19.774 1.00 0.00 O +ATOM 735 HG1 THR 49 21.730 24.270 18.816 1.00 0.00 H +ATOM 736 C THR 49 19.505 26.429 19.997 1.00 0.00 C +ATOM 737 O THR 49 19.426 26.431 21.226 1.00 0.00 O +ATOM 738 N LYS 50 19.766 27.551 19.307 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.297 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.906 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.354 29.538 19.086 1.00 0.00 H +ATOM 742 CB LYS 50 18.564 29.472 20.292 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.160 28.830 21.074 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.701 30.459 20.736 1.00 0.00 H +ATOM 745 CG LYS 50 17.492 29.593 19.188 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.426 28.657 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.740 19.683 1.00 0.00 H +ATOM 748 CD LYS 50 17.704 30.775 18.223 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.703 31.695 18.813 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.688 17.723 1.00 0.00 H +ATOM 751 CE LYS 50 16.571 30.869 17.187 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.603 17.664 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.507 31.899 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.997 16.018 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.231 29.102 16.282 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.013 29.838 15.434 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.544 30.418 15.421 1.00 0.00 H +ATOM 758 C LYS 50 20.986 28.948 21.020 1.00 0.00 C +ATOM 759 O LYS 50 20.693 29.519 22.082 1.00 0.00 O +ATOM 760 N THR 51 22.146 28.292 20.857 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.962 19.926 1.00 0.00 H +ATOM 762 CA THR 51 23.055 27.904 21.959 1.00 0.00 C +ATOM 763 HA THR 51 22.763 28.429 22.858 1.00 0.00 H +ATOM 764 CB THR 51 22.885 26.404 22.277 1.00 0.00 C +ATOM 765 HB THR 51 22.979 25.814 21.354 1.00 0.00 H +ATOM 766 CG2 THR 51 23.850 25.861 23.317 1.00 0.00 C +ATOM 767 HG21 THR 51 23.812 26.474 24.218 1.00 0.00 H +ATOM 768 HG22 THR 51 23.577 24.841 23.588 1.00 0.00 H +ATOM 769 HG23 THR 51 24.876 25.835 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.633 26.168 22.876 1.00 0.00 O +ATOM 771 HG1 THR 51 20.954 26.250 22.182 1.00 0.00 H +ATOM 772 C THR 51 24.556 28.224 21.725 1.00 0.00 C +ATOM 773 O THR 51 25.085 28.000 20.641 1.00 0.00 O +ATOM 774 N PHE 52 25.248 28.694 22.772 1.00 0.00 N +ATOM 775 H PHE 52 24.712 28.952 23.592 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.779 22.880 1.00 0.00 C +ATOM 777 HA PHE 52 27.145 28.937 21.899 1.00 0.00 H +ATOM 778 CB PHE 52 27.149 29.952 23.820 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.476 29.958 24.659 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.735 24.193 1.00 0.00 H +ATOM 781 CG PHE 52 27.217 31.347 23.228 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.428 32.382 23.752 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.751 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.443 33.652 23.161 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.777 34.431 23.515 1.00 0.00 H +ATOM 786 CZ PHE 52 27.281 33.893 22.066 1.00 0.00 C +ATOM 787 HZ PHE 52 27.244 34.837 21.559 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.160 32.902 21.616 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.836 33.108 20.791 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.628 22.199 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.778 30.857 21.828 1.00 0.00 H +ATOM 792 C PHE 52 27.331 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.809 27.010 24.505 1.00 0.00 O +ATOM 794 N THR 53 28.487 27.066 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.851 27.522 22.147 1.00 0.00 H +ATOM 796 CA THR 53 29.281 25.929 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.048 25.798 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.936 24.611 22.782 1.00 0.00 C +ATOM 799 HB THR 53 29.512 23.804 23.241 1.00 0.00 H +ATOM 800 CG2 THR 53 27.461 24.225 22.862 1.00 0.00 C +ATOM 801 HG21 THR 53 26.865 24.906 22.254 1.00 0.00 H +ATOM 802 HG22 THR 53 27.326 23.209 22.494 1.00 0.00 H +ATOM 803 HG23 THR 53 27.124 24.270 23.898 1.00 0.00 H +ATOM 804 OG1 THR 53 29.273 24.680 21.420 1.00 0.00 O +ATOM 805 HG1 THR 53 28.756 24.016 20.955 1.00 0.00 H +ATOM 806 C THR 53 30.804 26.149 23.413 1.00 0.00 C +ATOM 807 O THR 53 31.287 27.022 22.688 1.00 0.00 O +ATOM 808 N THR 54 31.571 25.328 24.145 1.00 0.00 N +ATOM 809 H THR 54 31.111 24.655 24.737 1.00 0.00 H +ATOM 810 CA THR 54 33.043 25.241 24.080 1.00 0.00 C +ATOM 811 HA THR 54 33.416 26.036 23.436 1.00 0.00 H +ATOM 812 CB THR 54 33.668 25.452 25.473 1.00 0.00 C +ATOM 813 HB THR 54 33.373 24.632 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.195 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.517 26.335 24.770 1.00 0.00 H +ATOM 816 HG22 THR 54 35.553 25.813 26.470 1.00 0.00 H +ATOM 817 HG23 THR 54 35.642 24.609 25.193 1.00 0.00 H +ATOM 818 OG1 THR 54 33.203 26.662 26.026 1.00 0.00 O +ATOM 819 HG1 THR 54 33.876 26.992 26.625 1.00 0.00 H +ATOM 820 C THR 54 33.479 23.896 23.474 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.895 23.605 1.00 0.00 O +ATOM 822 N GLN 55 34.635 23.879 22.803 1.00 0.00 N +ATOM 823 H GLN 55 35.156 24.739 22.761 1.00 0.00 H +ATOM 824 CA GLN 55 35.264 22.693 22.195 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.165 21.639 1.00 0.00 H +ATOM 826 CB GLN 55 36.319 23.163 21.173 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.730 22.295 20.657 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.804 23.775 20.430 1.00 0.00 H +ATOM 829 CG GLN 55 37.482 23.993 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.096 24.713 22.482 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.177 23.334 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.249 24.773 20.686 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.326 24.397 19.523 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.831 25.902 21.034 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.408 26.355 20.331 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.724 26.275 21.962 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.679 23.225 1.00 0.00 C +ATOM 838 O GLN 55 36.112 22.047 24.363 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.413 22.804 1.00 0.00 N +ATOM 840 H GLU 56 35.794 20.234 21.832 1.00 0.00 H +ATOM 841 CA GLU 56 36.491 19.249 23.573 1.00 0.00 C +ATOM 842 HA GLU 56 36.152 19.337 24.602 1.00 0.00 H +ATOM 843 CB GLU 56 35.885 17.954 22.967 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.804 17.985 23.074 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.993 21.896 1.00 0.00 H +ATOM 846 CG GLU 56 36.403 16.582 23.463 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.459 15.931 22.591 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.423 16.669 23.812 1.00 0.00 H +ATOM 849 CD GLU 56 35.548 15.855 24.520 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.094 15.347 25.534 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.325 15.660 24.312 1.00 0.00 O +ATOM 852 C GLU 56 38.030 19.202 23.644 1.00 0.00 C +ATOM 853 O GLU 56 38.535 19.186 24.795 1.00 0.00 O +ATOM 854 OXT GLU 56 38.680 19.141 22.578 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.717 32.457 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.342 33.248 30.282 1.00 0.00 N +HETATM 857 C AN1 58 30.690 33.885 31.200 1.00 0.00 C +HETATM 858 C1 AN1 58 29.362 33.529 30.704 1.00 0.00 C +HETATM 859 H AN1 58 30.622 34.282 32.217 1.00 0.00 H +HETATM 860 H1 AN1 58 31.134 34.634 30.540 1.00 0.00 H +HETATM 861 H2 AN1 58 31.317 32.983 31.203 1.00 0.00 H +HETATM 862 N1 AZI 59 31.272 30.355 29.425 1.00 0.00 N +HETATM 863 N2 AZI 59 30.474 30.251 30.345 1.00 0.00 N +HETATM 864 N3 AZI 59 29.631 30.164 31.291 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 148 144 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 643 639 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_3_front_1.pdb b/tests/nsga2/intermediate_molecules/min_iter_3_front_1.pdb new file mode 100644 index 0000000..c2d6518 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_3_front_1.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.331 51.38249999999948 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.971 23.610 1.00 0.00 N +ATOM 2 H1 MET 1 15.141 38.355 24.553 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.345 23.090 1.00 0.00 H +ATOM 4 H3 MET 1 16.014 38.281 23.181 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.500 23.668 1.00 0.00 C +ATOM 6 HA MET 1 14.171 36.197 24.096 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.872 22.269 1.00 0.00 C +ATOM 8 HB2 MET 1 14.392 36.151 21.668 1.00 0.00 H +ATOM 9 HB3 MET 1 16.153 36.270 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.371 34.332 22.296 1.00 0.00 C +ATOM 11 HG2 MET 1 16.259 34.062 22.867 1.00 0.00 H +ATOM 12 HG3 MET 1 14.494 33.923 22.804 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.525 20.666 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.569 20.066 1.00 0.00 C +ATOM 15 HE1 MET 1 13.461 34.598 20.015 1.00 0.00 H +ATOM 16 HE2 MET 1 13.777 33.132 19.069 1.00 0.00 H +ATOM 17 HE3 MET 1 13.174 32.990 20.731 1.00 0.00 H +ATOM 18 C MET 1 16.221 36.029 24.598 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.397 24.423 1.00 0.00 O +ATOM 20 N GLN 2 15.881 35.189 25.579 1.00 0.00 N +ATOM 21 H GLN 2 14.910 34.997 25.765 1.00 0.00 H +ATOM 22 CA GLN 2 16.846 34.478 26.432 1.00 0.00 C +ATOM 23 HA GLN 2 17.652 35.157 26.726 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.072 27.724 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.138 33.651 27.491 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.661 33.315 28.273 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.253 28.684 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.469 36.090 28.161 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.204 34.973 29.418 1.00 0.00 H +ATOM 30 CD GLN 2 17.129 35.580 29.525 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.164 34.935 29.495 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.031 36.470 30.481 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.772 36.536 31.097 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.109 36.732 30.769 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.304 25.672 1.00 0.00 C +ATOM 36 O GLN 2 17.101 32.148 25.833 1.00 0.00 O +ATOM 37 N TYR 3 18.476 33.620 24.822 1.00 0.00 N +ATOM 38 H TYR 3 18.753 34.594 24.753 1.00 0.00 H +ATOM 39 CA TYR 3 19.257 32.618 24.101 1.00 0.00 C +ATOM 40 HA TYR 3 18.571 31.964 23.563 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.286 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.865 33.945 23.646 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.482 22.671 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.069 21.936 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.528 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.821 32.423 20.552 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.146 34.202 19.540 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.115 33.734 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.845 35.572 19.674 1.00 0.00 C +ATOM 50 OH TYR 3 18.515 36.305 18.581 1.00 0.00 O +ATOM 51 HH TYR 3 18.774 35.870 17.765 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.190 20.937 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.729 37.250 21.020 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.323 35.442 22.065 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.447 35.936 23.020 1.00 0.00 H +ATOM 56 C TYR 3 20.090 31.765 25.077 1.00 0.00 C +ATOM 57 O TYR 3 20.461 32.246 26.149 1.00 0.00 O +ATOM 58 N LYS 4 20.401 30.506 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.251 30.222 23.770 1.00 0.00 H +ATOM 60 CA LYS 4 21.012 29.502 25.631 1.00 0.00 C +ATOM 61 HA LYS 4 20.728 29.716 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.477 28.101 25.270 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.521 27.983 24.189 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.144 27.345 25.695 1.00 0.00 H +ATOM 65 CG LYS 4 19.051 27.747 25.735 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.886 26.697 25.494 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.996 27.852 26.817 1.00 0.00 H +ATOM 68 CD LYS 4 17.924 28.566 25.082 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.889 29.561 25.522 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.146 28.677 24.019 1.00 0.00 H +ATOM 71 CE LYS 4 16.545 27.894 25.197 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.511 24.666 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.594 26.934 24.678 1.00 0.00 H +ATOM 74 NZ LYS 4 16.096 27.673 26.597 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.986 28.550 27.087 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.208 27.171 26.603 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.759 27.086 27.088 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.617 1.00 0.00 C +ATOM 79 O LYS 4 23.197 29.888 24.646 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.028 26.695 1.00 0.00 N +HETATM 81 CA HX1 5 24.626 28.831 26.818 1.00 0.00 C +HETATM 82 C HX1 5 24.900 27.673 27.781 1.00 0.00 C +HETATM 83 O HX1 5 24.403 27.682 28.908 1.00 0.00 O +HETATM 84 CB HX1 5 25.263 30.146 27.306 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.390 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.070 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.386 27.859 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.096 27.752 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.937 29.837 27.334 1.00 0.00 N +HETATM 90 H HX1 5 22.597 28.839 27.518 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.840 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.382 28.291 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.939 30.946 26.638 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.281 26.698 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.530 31.749 28.082 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.838 29.357 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.635 26.658 27.325 1.00 0.00 N +ATOM 98 H ILE 6 26.017 26.713 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.005 25.472 28.115 1.00 0.00 C +ATOM 100 HA ILE 6 25.305 25.371 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.849 24.199 27.245 1.00 0.00 C +ATOM 102 HB ILE 6 26.399 24.347 26.315 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.408 22.939 27.933 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.891 22.758 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.284 22.071 27.286 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.479 23.047 28.114 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.343 24.015 26.915 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.790 23.879 27.844 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.966 24.918 26.434 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.005 22.849 25.979 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.174 21.896 26.480 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.950 22.908 25.704 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.610 22.906 25.075 1.00 0.00 H +ATOM 114 C ILE 6 27.394 25.667 28.753 1.00 0.00 C +ATOM 115 O ILE 6 28.229 26.397 28.221 1.00 0.00 O +ATOM 116 N VAL 7 27.601 25.080 29.936 1.00 0.00 N +ATOM 117 H VAL 7 26.870 24.477 30.295 1.00 0.00 H +ATOM 118 CA VAL 7 28.779 25.286 30.801 1.00 0.00 C +ATOM 119 HA VAL 7 28.879 26.361 30.956 1.00 0.00 H +ATOM 120 CB VAL 7 28.501 24.640 32.176 1.00 0.00 C +ATOM 121 HB VAL 7 27.502 24.948 32.483 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.525 23.106 32.131 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.535 22.744 31.923 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.192 22.714 33.086 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.858 22.745 31.347 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.450 25.110 33.283 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.290 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.078 24.777 34.249 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.448 24.701 33.140 1.00 0.00 H +ATOM 130 C VAL 7 30.113 24.804 30.200 1.00 0.00 C +ATOM 131 O VAL 7 30.155 23.918 29.349 1.00 0.00 O +ATOM 132 N THR 8 31.216 25.379 30.688 1.00 0.00 N +ATOM 133 H THR 8 31.111 26.090 31.396 1.00 0.00 H +ATOM 134 CA THR 8 32.599 24.973 30.394 1.00 0.00 C +ATOM 135 HA THR 8 32.693 24.829 29.317 1.00 0.00 H +ATOM 136 CB THR 8 33.573 26.088 30.820 1.00 0.00 C +ATOM 137 HB THR 8 34.598 25.756 30.643 1.00 0.00 H +ATOM 138 CG2 THR 8 33.360 27.395 30.062 1.00 0.00 C +ATOM 139 HG21 THR 8 32.387 27.825 30.304 1.00 0.00 H +ATOM 140 HG22 THR 8 34.136 28.111 30.331 1.00 0.00 H +ATOM 141 HG23 THR 8 33.406 27.215 28.989 1.00 0.00 H +ATOM 142 OG1 THR 8 33.423 26.394 32.187 1.00 0.00 O +ATOM 143 HG1 THR 8 33.805 27.264 32.325 1.00 0.00 H +ATOM 144 C THR 8 33.011 23.656 31.078 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.249 32.104 1.00 0.00 O +ATOM 146 N GLY 9 34.050 23.008 30.534 1.00 0.00 N +ATOM 147 H GLY 9 34.405 23.337 29.651 1.00 0.00 H +ATOM 148 CA GLY 9 34.626 21.773 31.078 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.617 21.618 30.655 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.880 32.158 1.00 0.00 H +ATOM 151 C GLY 9 33.783 20.523 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.022 20.484 29.825 1.00 0.00 O +ATOM 153 N LYS 10 33.951 19.480 31.615 1.00 0.00 N +ATOM 154 H LYS 10 34.670 19.560 32.316 1.00 0.00 H +ATOM 155 CA LYS 10 33.230 18.191 31.479 1.00 0.00 C +ATOM 156 HA LYS 10 32.289 18.403 30.967 1.00 0.00 H +ATOM 157 CB LYS 10 34.057 17.246 30.577 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.677 17.847 29.907 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.724 16.640 31.194 1.00 0.00 H +ATOM 160 CG LYS 10 33.192 16.330 29.692 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.593 15.666 30.313 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.519 16.953 29.100 1.00 0.00 H +ATOM 163 CD LYS 10 34.058 15.492 28.736 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.721 16.156 28.178 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.661 14.791 29.314 1.00 0.00 H +ATOM 166 CE LYS 10 33.179 14.718 27.746 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.965 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.471 15.413 27.288 1.00 0.00 H +ATOM 169 NZ LYS 10 33.977 14.072 26.676 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.736 13.512 27.043 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.382 13.524 26.065 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.427 14.774 26.073 1.00 0.00 H +ATOM 173 C LYS 10 32.821 17.544 32.814 1.00 0.00 C +ATOM 174 O LYS 10 32.336 16.416 32.832 1.00 0.00 O +ATOM 175 N SER 11 33.037 18.243 33.935 1.00 0.00 N +ATOM 176 H SER 11 33.494 19.132 33.842 1.00 0.00 H +ATOM 177 CA SER 11 32.566 17.848 35.279 1.00 0.00 C +ATOM 178 HA SER 11 32.499 16.758 35.340 1.00 0.00 H +ATOM 179 CB SER 11 33.553 18.325 36.353 1.00 0.00 C +ATOM 180 HB2 SER 11 33.585 19.415 36.355 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.980 37.332 1.00 0.00 H +ATOM 182 OG SER 11 34.850 17.821 36.094 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.425 36.456 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.420 35.589 1.00 0.00 C +ATOM 185 O SER 11 30.351 17.750 36.199 1.00 0.00 O +ATOM 186 N CYS 12 30.919 19.655 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.630 20.134 34.627 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.270 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.870 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.351 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.324 22.215 34.523 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.251 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.149 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.145 23.412 37.057 1.00 0.00 H +ATOM 195 C CYS 12 28.853 19.936 33.838 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.667 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.513 19.990 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.060 20.142 34.736 1.00 0.00 H +ATOM 199 CA LYS 13 26.667 19.722 32.662 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.862 31.773 1.00 0.00 H +ATOM 201 CB LYS 13 26.223 18.247 32.706 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.032 17.655 33.143 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.346 18.144 33.358 1.00 0.00 H +ATOM 204 CG LYS 13 25.915 17.636 31.324 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.036 18.108 30.884 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.767 17.822 30.669 1.00 0.00 H +ATOM 207 CD LYS 13 25.684 16.116 31.406 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.690 15.716 30.391 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.518 15.663 31.947 1.00 0.00 H +ATOM 210 CE LYS 13 24.346 15.744 32.064 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.165 16.386 32.929 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.553 15.951 31.340 1.00 0.00 H +ATOM 213 NZ LYS 13 24.304 14.308 32.452 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.875 14.098 33.271 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.357 13.998 32.643 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.687 13.729 31.706 1.00 0.00 H +ATOM 217 C LYS 13 25.488 20.707 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.584 20.487 31.712 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.786 33.298 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.945 33.874 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.754 33.376 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.445 22.193 33.447 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.483 23.331 34.294 1.00 0.00 H +ATOM 224 C GLY 14 24.286 23.716 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.214 23.892 31.407 1.00 0.00 O +ATOM 226 N VAL 15 23.145 24.399 32.111 1.00 0.00 N +ATOM 227 H VAL 15 22.435 24.245 32.812 1.00 0.00 H +ATOM 228 CA VAL 15 22.778 25.387 31.071 1.00 0.00 C +ATOM 229 HA VAL 15 23.675 25.626 30.492 1.00 0.00 H +ATOM 230 CB VAL 15 21.760 24.738 30.089 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.856 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.449 24.318 30.766 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.938 25.178 31.211 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.793 23.856 30.028 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.579 31.548 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.416 25.668 28.927 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.331 26.008 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.820 25.120 28.196 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.841 26.533 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.282 26.685 31.729 1.00 0.00 C +ATOM 241 O VAL 15 21.714 26.632 32.818 1.00 0.00 O +HETATM 242 N HY1 16 22.496 27.830 31.091 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.109 31.450 1.00 0.00 C +HETATM 244 C HY1 16 21.616 29.886 30.135 1.00 0.00 C +HETATM 245 O HY1 16 21.780 29.350 29.023 1.00 0.00 O +HETATM 246 CB HY1 16 22.864 29.868 32.413 1.00 0.00 C +HETATM 247 CG HY1 16 24.212 30.223 31.813 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.549 31.404 31.207 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.321 29.396 31.740 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.303 30.091 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.880 31.315 30.788 1.00 0.00 N +HETATM 252 H HY1 16 22.997 27.783 30.210 1.00 0.00 H +HETATM 253 HA HY1 16 20.968 28.987 31.945 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.396 30.793 32.773 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.026 29.256 33.296 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.399 28.458 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.907 32.258 31.095 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.728 30.996 1.00 0.00 H +ATOM 259 N THR 17 21.166 31.142 30.265 1.00 0.00 N +ATOM 260 H THR 17 21.050 31.473 31.216 1.00 0.00 H +ATOM 261 CA THR 17 20.736 32.026 29.172 1.00 0.00 C +ATOM 262 HA THR 17 21.120 31.634 28.284 1.00 0.00 H +ATOM 263 CB THR 17 19.152 32.017 29.049 1.00 0.00 C +ATOM 264 HB THR 17 18.937 32.609 28.167 1.00 0.00 H +ATOM 265 CG2 THR 17 18.596 30.675 28.723 1.00 0.00 C +ATOM 266 HG21 THR 17 18.786 29.900 29.421 1.00 0.00 H +ATOM 267 HG22 THR 17 17.506 30.690 28.630 1.00 0.00 H +ATOM 268 HG23 THR 17 18.925 30.322 27.780 1.00 0.00 H +ATOM 269 OG1 THR 17 18.479 32.473 30.205 1.00 0.00 O +ATOM 270 HG1 THR 17 18.568 33.453 30.221 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.458 29.233 1.00 0.00 C +ATOM 272 O THR 17 21.702 33.916 30.265 1.00 0.00 O +HETATM 273 N HY2 18 21.139 34.162 28.101 1.00 0.00 N +HETATM 274 CA HY2 18 21.450 35.620 27.971 1.00 0.00 C +HETATM 275 C HY2 18 20.329 36.290 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.985 35.837 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.774 35.820 27.259 1.00 0.00 C +HETATM 278 CG HY2 18 24.005 35.327 28.003 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.420 34.030 28.155 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.943 36.119 28.644 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.315 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.707 27.237 1.00 0.00 H +HETATM 284 HA HY2 18 21.503 36.046 29.014 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.748 35.296 26.297 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.910 36.879 27.057 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.955 37.127 28.681 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.926 33.165 27.774 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.761 35.647 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.807 37.387 27.748 1.00 0.00 N +ATOM 291 H GLU 19 20.142 37.684 28.644 1.00 0.00 H +ATOM 292 CA GLU 19 18.798 38.219 27.101 1.00 0.00 C +ATOM 293 HA GLU 19 18.058 37.555 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.065 39.079 28.156 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.754 38.431 28.967 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.775 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.833 39.851 27.657 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.550 28.422 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.089 40.412 26.764 1.00 0.00 H +ATOM 300 CD GLU 19 15.654 38.901 27.366 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.588 38.373 26.224 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.813 38.691 28.275 1.00 0.00 O +ATOM 303 C GLU 19 19.405 39.113 25.992 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.857 26.273 1.00 0.00 O +ATOM 305 N ALA 20 18.878 39.052 24.762 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.354 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.961 23.686 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.963 24.094 1.00 0.00 H +ATOM 309 CB ALA 20 20.592 39.489 23.094 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.465 38.517 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.951 40.206 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.351 39.401 23.870 1.00 0.00 H +ATOM 313 C ALA 20 18.191 40.036 22.579 1.00 0.00 C +ATOM 314 O ALA 20 17.360 39.133 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.087 21.745 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.824 21.920 1.00 0.00 H +ATOM 317 CA VAL 21 17.460 41.147 20.465 1.00 0.00 C +ATOM 318 HA VAL 21 16.471 40.723 20.625 1.00 0.00 H +ATOM 319 CB VAL 21 17.274 42.597 19.972 1.00 0.00 C +ATOM 320 HB VAL 21 16.616 42.570 19.108 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.597 43.470 21.033 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.255 43.626 21.888 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.349 44.439 20.598 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.674 42.997 21.365 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.583 43.276 19.536 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.004 42.764 18.670 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.380 44.306 19.239 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.315 43.278 20.344 1.00 0.00 H +ATOM 329 C VAL 21 18.121 40.330 19.353 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.986 18.375 1.00 0.00 O +ATOM 331 N ASP 22 19.414 40.050 19.506 1.00 0.00 N +ATOM 332 H ASP 22 19.863 40.329 20.361 1.00 0.00 H +ATOM 333 CA ASP 22 20.295 39.463 18.502 1.00 0.00 C +ATOM 334 HA ASP 22 19.714 38.825 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.941 40.588 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.174 41.079 17.075 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.377 41.324 18.356 1.00 0.00 H +ATOM 338 CG ASP 22 22.025 40.044 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.147 40.586 16.800 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.762 39.018 16.087 1.00 0.00 O +ATOM 341 C ASP 22 21.366 38.597 19.178 1.00 0.00 C +ATOM 342 O ASP 22 21.825 38.880 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.789 37.545 18.492 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.489 17.520 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.608 18.984 1.00 0.00 C +ATOM 346 HA TRP 23 22.545 36.357 20.016 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.348 18.138 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.975 18.216 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.840 35.604 17.094 1.00 0.00 H +ATOM 350 CG TRP 23 23.573 34.244 18.531 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.517 33.704 17.733 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.739 34.020 16.723 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.129 32.678 18.412 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.903 32.155 18.035 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.589 32.475 19.659 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.825 31.536 20.665 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.540 30.741 20.523 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.682 21.888 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.012 22.701 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.765 22.099 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.900 23.082 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.005 33.658 21.055 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.310 34.465 21.213 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.637 33.527 19.797 1.00 0.00 C +ATOM 365 C TRP 23 24.210 37.185 18.982 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.925 1.00 0.00 O +ATOM 367 N ALA 24 24.557 38.022 17.997 1.00 0.00 N +ATOM 368 H ALA 24 23.880 38.262 17.279 1.00 0.00 H +ATOM 369 CA ALA 24 25.846 38.717 17.976 1.00 0.00 C +ATOM 370 HA ALA 24 26.618 38.001 18.267 1.00 0.00 H +ATOM 371 CB ALA 24 26.158 39.140 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.444 39.882 16.189 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.160 39.562 16.482 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.110 38.274 15.877 1.00 0.00 H +ATOM 375 C ALA 24 25.929 39.882 18.994 1.00 0.00 C +ATOM 376 O ALA 24 27.022 40.384 19.270 1.00 0.00 O +ATOM 377 N GLU 25 24.812 40.285 19.610 1.00 0.00 N +ATOM 378 H GLU 25 23.932 39.945 19.243 1.00 0.00 H +ATOM 379 CA GLU 25 24.791 41.075 20.852 1.00 0.00 C +ATOM 380 HA GLU 25 25.642 41.755 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.512 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.646 41.279 20.820 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.451 42.386 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.432 43.037 19.875 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.632 42.630 18.884 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.410 43.424 19.863 1.00 0.00 H +ATOM 387 CD GLU 25 24.381 44.197 20.185 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.918 45.196 20.744 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.601 44.048 19.836 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.102 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.517 23.016 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.005 22.132 1.00 0.00 N +ATOM 393 H ALA 26 23.666 38.775 21.366 1.00 0.00 H +ATOM 394 CA ALA 26 24.460 38.029 23.217 1.00 0.00 C +ATOM 395 HA ALA 26 24.199 38.524 24.148 1.00 0.00 H +ATOM 396 CB ALA 26 23.491 36.862 23.015 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.771 36.287 22.133 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.204 23.883 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.230 22.894 1.00 0.00 H +ATOM 400 C ALA 26 25.918 37.533 23.365 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.227 24.482 1.00 0.00 O +ATOM 402 N GLU 27 26.710 37.510 22.283 1.00 0.00 N +ATOM 403 H GLU 27 26.268 37.638 21.376 1.00 0.00 H +ATOM 404 CA GLU 27 28.167 37.303 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.369 36.351 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.763 37.247 20.913 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.152 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.735 38.251 20.486 1.00 0.00 H +ATOM 409 CG GLU 27 30.208 36.724 20.921 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.145 21.771 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.190 35.641 21.055 1.00 0.00 H +ATOM 412 CD GLU 27 30.982 37.089 19.641 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.725 38.106 19.697 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.344 18.641 1.00 0.00 O +ATOM 415 C GLU 27 28.849 38.396 23.183 1.00 0.00 C +ATOM 416 O GLU 27 29.572 38.094 24.134 1.00 0.00 O +ATOM 417 N LYS 28 28.547 39.673 22.914 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.853 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.817 23.666 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.667 1.00 0.00 H +ATOM 421 CB LYS 28 28.699 42.145 22.993 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.278 23.048 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.170 42.963 23.542 1.00 0.00 H +ATOM 424 CG LYS 28 29.137 42.221 21.519 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.207 42.027 21.443 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.604 41.462 20.949 1.00 0.00 H +ATOM 427 CD LYS 28 28.837 43.604 20.920 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.819 43.907 21.172 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.521 44.332 21.364 1.00 0.00 H +ATOM 430 CE LYS 28 29.006 43.629 19.396 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.103 44.670 19.084 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.926 43.113 19.127 1.00 0.00 H +ATOM 433 NZ LYS 28 27.841 43.021 18.708 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.981 43.489 19.017 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.904 43.103 17.704 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.722 42.040 18.958 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.782 25.132 1.00 0.00 C +ATOM 438 O LYS 28 29.482 40.969 26.019 1.00 0.00 O +ATOM 439 N PHE 29 27.393 40.452 25.417 1.00 0.00 N +ATOM 440 H PHE 29 26.740 40.365 24.642 1.00 0.00 H +ATOM 441 CA PHE 29 26.903 40.286 26.793 1.00 0.00 C +ATOM 442 HA PHE 29 27.228 41.146 27.379 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.264 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.038 39.343 26.310 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.022 40.230 27.832 1.00 0.00 H +ATOM 446 CG PHE 29 24.678 41.443 26.116 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.465 41.235 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.015 40.254 25.407 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.830 42.300 24.767 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.907 42.126 24.234 1.00 0.00 H +ATOM 451 CZ PHE 29 23.399 43.584 24.790 1.00 0.00 C +ATOM 452 HZ PHE 29 22.919 44.396 24.265 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.591 43.806 25.498 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.027 44.796 25.527 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.226 42.742 26.165 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.139 42.936 26.704 1.00 0.00 H +ATOM 457 C PHE 29 27.484 39.050 27.507 1.00 0.00 C +ATOM 458 O PHE 29 27.589 39.038 28.735 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.768 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.042 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.683 36.892 27.316 1.00 0.00 C +ATOM 462 HA THR 30 28.208 36.545 28.226 1.00 0.00 H +ATOM 463 CB THR 30 28.692 35.717 26.333 1.00 0.00 C +ATOM 464 HB THR 30 29.073 36.025 25.356 1.00 0.00 H +ATOM 465 CG2 THR 30 29.496 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.137 34.212 27.801 1.00 0.00 H +ATOM 467 HG22 THR 30 29.369 33.689 26.123 1.00 0.00 H +ATOM 468 HG23 THR 30 30.559 34.746 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.365 35.280 26.189 1.00 0.00 O +ATOM 470 HG1 THR 30 26.960 35.883 25.542 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.982 28.769 1.00 0.00 O +ATOM 473 N LYS 31 30.746 38.122 26.832 1.00 0.00 N +ATOM 474 H LYS 31 30.287 38.320 25.947 1.00 0.00 H +ATOM 475 CA LYS 31 32.078 38.702 27.069 1.00 0.00 C +ATOM 476 HA LYS 31 32.749 37.905 27.376 1.00 0.00 H +ATOM 477 CB LYS 31 32.616 39.317 25.766 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.011 25.348 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.529 39.865 25.987 1.00 0.00 H +ATOM 480 CG LYS 31 32.930 38.210 24.744 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.684 37.553 25.176 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.044 37.629 24.525 1.00 0.00 H +ATOM 483 CD LYS 31 33.459 38.818 23.435 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.384 22.952 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.299 39.497 23.642 1.00 0.00 H +ATOM 486 CE LYS 31 33.923 37.725 22.467 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.107 37.055 22.246 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.217 38.195 21.540 1.00 0.00 H +ATOM 489 NZ LYS 31 35.077 36.976 23.015 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.822 36.247 23.679 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.553 36.469 22.265 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.760 37.567 23.503 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.188 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.780 28.917 1.00 0.00 O +ATOM 495 N ALA 32 31.031 40.509 28.373 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.873 41.412 29.515 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.138 29.505 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.375 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.495 29.375 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.875 30.215 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.557 42.757 28.446 1.00 0.00 H +ATOM 503 C ALA 32 30.963 40.638 30.838 1.00 0.00 C +ATOM 504 O ALA 32 31.881 40.886 31.616 1.00 0.00 O +ATOM 505 N LYN 33 30.117 39.613 31.030 1.00 0.00 N +ATOM 506 H LYN 33 29.390 39.457 30.346 1.00 0.00 H +ATOM 507 CA LYN 33 30.156 38.755 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.022 39.383 33.110 1.00 0.00 H +ATOM 509 CB LYN 33 29.008 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.061 37.156 31.262 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.141 37.038 33.024 1.00 0.00 H +ATOM 512 CG LYN 33 27.610 38.358 32.315 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.564 38.982 33.207 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.412 38.981 31.444 1.00 0.00 H +ATOM 515 CD LYN 33 26.535 37.267 32.412 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.691 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.632 36.748 33.365 1.00 0.00 H +ATOM 518 CE LYN 33 25.122 37.835 32.288 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.934 38.514 33.114 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.035 38.378 31.349 1.00 0.00 H +ATOM 521 NZ LYN 33 24.115 36.761 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.184 37.154 32.261 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.253 36.113 31.547 1.00 0.00 H +ATOM 524 C LYN 33 31.510 38.042 32.391 1.00 0.00 C +ATOM 525 O LYN 33 32.008 37.922 33.505 1.00 0.00 O +ATOM 526 N ALA 34 32.143 37.585 31.305 1.00 0.00 N +ATOM 527 H ALA 34 31.696 37.677 30.400 1.00 0.00 H +ATOM 528 CA ALA 34 33.470 36.966 31.389 1.00 0.00 C +ATOM 529 HA ALA 34 33.428 36.160 32.125 1.00 0.00 H +ATOM 530 CB ALA 34 33.816 36.355 30.029 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.962 37.145 29.294 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.776 30.132 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.693 29.698 1.00 0.00 H +ATOM 534 C ALA 34 34.573 37.946 31.865 1.00 0.00 C +ATOM 535 O ALA 34 35.469 37.540 32.604 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.224 31.488 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.504 30.885 1.00 0.00 H +ATOM 538 CA ASN 35 35.368 40.286 32.000 1.00 0.00 C +ATOM 539 HA ASN 35 36.366 39.870 32.113 1.00 0.00 H +ATOM 540 CB ASN 35 35.476 41.416 30.969 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.486 41.702 30.624 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.287 31.449 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.031 29.800 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.581 41.002 29.898 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.705 28.668 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.448 27.895 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.600 28.628 1.00 0.00 H +ATOM 548 C ASN 35 34.981 40.786 33.404 1.00 0.00 C +ATOM 549 O ASN 35 35.867 41.207 34.150 1.00 0.00 O +ATOM 550 N ASP 36 33.718 40.635 33.831 1.00 0.00 N +ATOM 551 H ASP 36 32.984 40.413 33.166 1.00 0.00 H +ATOM 552 CA ASP 36 33.339 40.772 35.249 1.00 0.00 C +ATOM 553 HA ASP 36 33.668 41.747 35.602 1.00 0.00 H +ATOM 554 CB ASP 36 31.819 40.767 35.440 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.448 39.783 35.230 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.607 40.875 36.498 1.00 0.00 H +ATOM 557 CG ASP 36 30.981 41.783 34.657 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.512 42.876 34.366 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.778 41.516 34.402 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.708 36.125 1.00 0.00 C +ATOM 561 O ASP 36 34.482 40.004 37.236 1.00 0.00 O +ATOM 562 N PHE 37 34.227 38.480 35.608 1.00 0.00 N +ATOM 563 H PHE 37 33.751 38.279 34.737 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.459 36.179 1.00 0.00 C +ATOM 565 HA PHE 37 35.118 37.611 37.257 1.00 0.00 H +ATOM 566 CB PHE 37 34.574 36.041 35.932 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.663 35.826 34.870 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.334 36.446 1.00 0.00 H +ATOM 569 CG PHE 37 33.150 35.763 36.385 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.139 35.558 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.374 35.619 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.312 35.834 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.039 35.198 35.094 1.00 0.00 H +ATOM 574 CZ PHE 37 30.507 35.235 37.199 1.00 0.00 C +ATOM 575 HZ PHE 37 29.492 35.053 37.510 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.515 35.404 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.270 35.352 39.212 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.834 35.668 37.752 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.601 35.814 38.491 1.00 0.00 H +ATOM 580 C PHE 37 36.607 37.580 35.742 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.679 36.016 1.00 0.00 O +ATOM 582 N GLY 38 36.998 38.676 35.079 1.00 0.00 N +ATOM 583 H GLY 38 36.291 39.378 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.389 39.091 34.839 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.499 40.111 35.207 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.054 38.469 35.438 1.00 0.00 H +ATOM 587 C GLY 38 38.925 39.060 33.393 1.00 0.00 C +ATOM 588 O GLY 38 39.874 39.792 33.112 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.227 32.486 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.727 32.761 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.052 31.090 1.00 0.00 C +ATOM 592 HA ARG 39 38.944 39.045 30.646 1.00 0.00 H +ATOM 593 CB ARG 39 40.304 37.440 31.075 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.635 37.431 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.987 38.106 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.522 36.013 31.628 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.039 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.753 31.461 1.00 0.00 H +ATOM 599 CD ARG 39 40.222 35.826 33.132 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.861 36.507 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.182 36.080 33.342 1.00 0.00 H +ATOM 602 NE ARG 39 40.446 34.443 33.599 1.00 0.00 N +ATOM 603 HE ARG 39 41.205 34.297 34.244 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.303 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.469 32.493 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.428 34.360 32.093 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.296 32.621 32.084 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.954 32.226 33.819 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.694 32.095 34.491 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.336 31.450 33.602 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.225 30.193 1.00 0.00 C +ATOM 612 O ARG 39 37.522 36.137 30.605 1.00 0.00 O +ATOM 613 N ASP 40 37.650 37.678 28.959 1.00 0.00 N +ATOM 614 H ASP 40 38.029 38.573 28.674 1.00 0.00 H +ATOM 615 CA ASP 40 36.889 36.892 27.966 1.00 0.00 C +ATOM 616 HA ASP 40 36.166 36.309 28.530 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.733 26.970 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.444 37.038 26.402 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.369 38.350 27.538 1.00 0.00 H +ATOM 620 CG ASP 40 36.824 38.628 25.969 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.257 39.725 26.392 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.837 38.322 24.743 1.00 0.00 O +ATOM 623 C ASP 40 37.720 35.861 27.181 1.00 0.00 C +ATOM 624 O ASP 40 38.885 36.078 26.862 1.00 0.00 O +ATOM 625 N GLY 41 37.056 34.760 26.814 1.00 0.00 N +ATOM 626 H GLY 41 36.099 34.682 27.117 1.00 0.00 H +ATOM 627 CA GLY 41 37.471 33.828 25.758 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.459 34.099 25.383 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.531 32.823 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.482 33.818 24.581 1.00 0.00 C +ATOM 631 O GLY 41 35.578 34.655 24.504 1.00 0.00 O +ATOM 632 N GLU 42 36.638 32.853 23.674 1.00 0.00 N +ATOM 633 H GLU 42 37.348 32.156 23.828 1.00 0.00 H +ATOM 634 CA GLU 42 35.799 32.668 22.476 1.00 0.00 C +ATOM 635 HA GLU 42 35.112 33.509 22.376 1.00 0.00 H +ATOM 636 CB GLU 42 36.683 32.630 21.214 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.158 31.650 21.168 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.035 32.711 20.341 1.00 0.00 H +ATOM 639 CG GLU 42 37.803 33.694 21.111 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.575 33.457 21.850 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.277 33.620 20.129 1.00 0.00 H +ATOM 642 CD GLU 42 37.343 35.144 21.318 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.154 35.459 21.111 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.167 36.006 21.711 1.00 0.00 O +ATOM 645 C GLU 42 34.948 31.386 22.578 1.00 0.00 C +ATOM 646 O GLU 42 35.393 30.398 23.170 1.00 0.00 O +ATOM 647 N ALA 43 33.745 31.391 21.989 1.00 0.00 N +ATOM 648 H ALA 43 33.480 32.196 21.440 1.00 0.00 H +ATOM 649 CA ALA 43 32.756 30.306 22.060 1.00 0.00 C +ATOM 650 HA ALA 43 33.248 29.388 22.388 1.00 0.00 H +ATOM 651 CB ALA 43 31.692 30.672 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.181 31.592 22.812 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.959 29.866 23.177 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.164 30.811 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.110 30.017 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.882 30.932 19.898 1.00 0.00 O +ATOM 657 N THR 44 31.798 28.746 20.423 1.00 0.00 N +ATOM 658 H THR 44 31.919 28.067 21.168 1.00 0.00 H +ATOM 659 CA THR 44 31.131 28.283 19.194 1.00 0.00 C +ATOM 660 HA THR 44 31.425 28.947 18.381 1.00 0.00 H +ATOM 661 CB THR 44 31.610 26.868 18.823 1.00 0.00 C +ATOM 662 HB THR 44 31.430 26.188 19.657 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.281 17.554 1.00 0.00 C +ATOM 664 HG21 THR 44 31.071 26.989 16.727 1.00 0.00 H +ATOM 665 HG22 THR 44 31.502 25.358 17.280 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.037 17.727 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.927 18.561 1.00 0.00 O +ATOM 668 HG1 THR 44 33.234 26.124 18.092 1.00 0.00 H +ATOM 669 C THR 44 29.605 28.381 19.326 1.00 0.00 C +ATOM 670 O THR 44 29.072 28.429 20.436 1.00 0.00 O +ATOM 671 N ILE 45 28.899 28.459 18.193 1.00 0.00 N +ATOM 672 H ILE 45 29.373 28.324 17.314 1.00 0.00 H +ATOM 673 CA ILE 45 27.479 28.840 18.123 1.00 0.00 C +ATOM 674 HA ILE 45 27.060 28.756 19.126 1.00 0.00 H +ATOM 675 CB ILE 45 27.332 30.316 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.271 30.529 17.778 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.069 31.232 18.677 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.151 31.108 18.586 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.833 32.282 18.498 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.768 30.969 19.687 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.759 30.692 16.252 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.018 31.752 16.233 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.657 30.140 15.968 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.506 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.730 30.935 15.529 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.975 31.017 14.269 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.530 29.452 14.955 1.00 0.00 H +ATOM 688 C ILE 45 26.629 27.925 17.243 1.00 0.00 C +ATOM 689 O ILE 45 27.122 27.343 16.276 1.00 0.00 O +ATOM 690 N ASP 46 25.329 27.880 17.545 1.00 0.00 N +ATOM 691 H ASP 46 25.032 28.297 18.421 1.00 0.00 H +ATOM 692 CA ASP 46 24.280 27.260 16.735 1.00 0.00 C +ATOM 693 HA ASP 46 24.584 27.263 15.684 1.00 0.00 H +ATOM 694 CB ASP 46 24.077 25.807 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.221 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.955 25.788 18.267 1.00 0.00 H +ATOM 697 CG ASP 46 22.841 25.170 16.544 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.475 17.281 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.561 25.439 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.957 28.050 16.850 1.00 0.00 C +ATOM 701 O ASP 46 22.507 28.363 17.955 1.00 0.00 O +ATOM 702 N ASP 47 22.309 28.333 15.716 1.00 0.00 N +ATOM 703 H ASP 47 22.678 27.944 14.861 1.00 0.00 H +ATOM 704 CA ASP 47 20.969 28.925 15.674 1.00 0.00 C +ATOM 705 HA ASP 47 20.875 29.653 16.485 1.00 0.00 H +ATOM 706 CB ASP 47 20.776 29.674 14.345 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.520 30.467 14.253 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.912 28.978 13.514 1.00 0.00 H +ATOM 709 CG ASP 47 19.366 30.275 14.271 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.485 29.674 13.613 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.064 31.235 15.016 1.00 0.00 O +ATOM 712 C ASP 47 19.852 27.876 15.878 1.00 0.00 C +ATOM 713 O ASP 47 18.842 28.184 16.513 1.00 0.00 O +ATOM 714 N ALA 48 20.002 26.636 15.396 1.00 0.00 N +ATOM 715 H ALA 48 20.917 26.342 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.934 25.626 15.412 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.054 14.931 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.425 14.583 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.276 23.967 15.053 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.686 14.514 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.674 24.756 13.580 1.00 0.00 H +ATOM 722 C ALA 48 18.524 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.929 17.099 1.00 0.00 O +ATOM 724 N THR 49 19.475 25.245 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.436 25.295 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.265 25.120 19.229 1.00 0.00 C +ATOM 727 HA THR 49 18.215 24.872 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.099 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.818 23.859 20.868 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.628 19.137 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.666 18.098 1.00 0.00 H +ATOM 732 HG22 THR 49 20.434 21.857 19.654 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.165 1.00 0.00 H +ATOM 734 OG1 THR 49 21.478 24.244 19.774 1.00 0.00 O +ATOM 735 HG1 THR 49 21.730 24.270 18.816 1.00 0.00 H +ATOM 736 C THR 49 19.505 26.429 19.997 1.00 0.00 C +ATOM 737 O THR 49 19.426 26.431 21.226 1.00 0.00 O +ATOM 738 N LYS 50 19.766 27.551 19.307 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.297 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.906 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.354 29.538 19.086 1.00 0.00 H +ATOM 742 CB LYS 50 18.564 29.472 20.292 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.160 28.830 21.074 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.701 30.459 20.736 1.00 0.00 H +ATOM 745 CG LYS 50 17.492 29.593 19.188 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.426 28.657 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.740 19.683 1.00 0.00 H +ATOM 748 CD LYS 50 17.704 30.775 18.223 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.703 31.695 18.813 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.688 17.723 1.00 0.00 H +ATOM 751 CE LYS 50 16.571 30.869 17.187 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.603 17.664 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.507 31.899 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.997 16.018 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.231 29.102 16.282 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.013 29.838 15.434 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.544 30.418 15.421 1.00 0.00 H +ATOM 758 C LYS 50 20.986 28.948 21.020 1.00 0.00 C +ATOM 759 O LYS 50 20.693 29.519 22.082 1.00 0.00 O +ATOM 760 N THR 51 22.146 28.292 20.857 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.962 19.926 1.00 0.00 H +ATOM 762 CA THR 51 23.055 27.904 21.959 1.00 0.00 C +ATOM 763 HA THR 51 22.763 28.429 22.858 1.00 0.00 H +ATOM 764 CB THR 51 22.885 26.404 22.277 1.00 0.00 C +ATOM 765 HB THR 51 22.979 25.814 21.354 1.00 0.00 H +ATOM 766 CG2 THR 51 23.850 25.861 23.317 1.00 0.00 C +ATOM 767 HG21 THR 51 23.812 26.474 24.218 1.00 0.00 H +ATOM 768 HG22 THR 51 23.577 24.841 23.588 1.00 0.00 H +ATOM 769 HG23 THR 51 24.876 25.835 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.633 26.168 22.876 1.00 0.00 O +ATOM 771 HG1 THR 51 20.954 26.250 22.182 1.00 0.00 H +ATOM 772 C THR 51 24.556 28.224 21.725 1.00 0.00 C +ATOM 773 O THR 51 25.085 28.000 20.641 1.00 0.00 O +ATOM 774 N PHE 52 25.248 28.694 22.772 1.00 0.00 N +ATOM 775 H PHE 52 24.712 28.952 23.592 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.779 22.880 1.00 0.00 C +ATOM 777 HA PHE 52 27.145 28.937 21.899 1.00 0.00 H +ATOM 778 CB PHE 52 27.149 29.952 23.820 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.476 29.958 24.659 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.735 24.193 1.00 0.00 H +ATOM 781 CG PHE 52 27.217 31.347 23.228 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.428 32.382 23.752 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.751 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.443 33.652 23.161 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.777 34.431 23.515 1.00 0.00 H +ATOM 786 CZ PHE 52 27.281 33.893 22.066 1.00 0.00 C +ATOM 787 HZ PHE 52 27.244 34.837 21.559 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.160 32.902 21.616 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.836 33.108 20.791 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.628 22.199 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.778 30.857 21.828 1.00 0.00 H +ATOM 792 C PHE 52 27.331 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.809 27.010 24.505 1.00 0.00 O +ATOM 794 N THR 53 28.487 27.066 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.851 27.522 22.147 1.00 0.00 H +ATOM 796 CA THR 53 29.281 25.929 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.048 25.798 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.936 24.611 22.782 1.00 0.00 C +ATOM 799 HB THR 53 29.512 23.804 23.241 1.00 0.00 H +ATOM 800 CG2 THR 53 27.461 24.225 22.862 1.00 0.00 C +ATOM 801 HG21 THR 53 26.865 24.906 22.254 1.00 0.00 H +ATOM 802 HG22 THR 53 27.326 23.209 22.494 1.00 0.00 H +ATOM 803 HG23 THR 53 27.124 24.270 23.898 1.00 0.00 H +ATOM 804 OG1 THR 53 29.273 24.680 21.420 1.00 0.00 O +ATOM 805 HG1 THR 53 28.756 24.016 20.955 1.00 0.00 H +ATOM 806 C THR 53 30.804 26.149 23.413 1.00 0.00 C +ATOM 807 O THR 53 31.287 27.022 22.688 1.00 0.00 O +ATOM 808 N THR 54 31.571 25.328 24.145 1.00 0.00 N +ATOM 809 H THR 54 31.111 24.655 24.737 1.00 0.00 H +ATOM 810 CA THR 54 33.043 25.241 24.080 1.00 0.00 C +ATOM 811 HA THR 54 33.416 26.036 23.436 1.00 0.00 H +ATOM 812 CB THR 54 33.668 25.452 25.473 1.00 0.00 C +ATOM 813 HB THR 54 33.373 24.632 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.195 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.517 26.335 24.770 1.00 0.00 H +ATOM 816 HG22 THR 54 35.553 25.813 26.470 1.00 0.00 H +ATOM 817 HG23 THR 54 35.642 24.609 25.193 1.00 0.00 H +ATOM 818 OG1 THR 54 33.203 26.662 26.026 1.00 0.00 O +ATOM 819 HG1 THR 54 33.876 26.992 26.625 1.00 0.00 H +ATOM 820 C THR 54 33.479 23.896 23.474 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.895 23.605 1.00 0.00 O +ATOM 822 N GLN 55 34.635 23.879 22.803 1.00 0.00 N +ATOM 823 H GLN 55 35.156 24.739 22.761 1.00 0.00 H +ATOM 824 CA GLN 55 35.264 22.693 22.195 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.165 21.639 1.00 0.00 H +ATOM 826 CB GLN 55 36.319 23.163 21.173 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.730 22.295 20.657 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.804 23.775 20.430 1.00 0.00 H +ATOM 829 CG GLN 55 37.482 23.993 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.096 24.713 22.482 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.177 23.334 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.249 24.773 20.686 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.326 24.397 19.523 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.831 25.902 21.034 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.408 26.355 20.331 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.724 26.275 21.962 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.679 23.225 1.00 0.00 C +ATOM 838 O GLN 55 36.112 22.047 24.363 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.413 22.804 1.00 0.00 N +ATOM 840 H GLU 56 35.794 20.234 21.832 1.00 0.00 H +ATOM 841 CA GLU 56 36.491 19.249 23.573 1.00 0.00 C +ATOM 842 HA GLU 56 36.152 19.337 24.602 1.00 0.00 H +ATOM 843 CB GLU 56 35.885 17.954 22.967 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.804 17.985 23.074 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.993 21.896 1.00 0.00 H +ATOM 846 CG GLU 56 36.403 16.582 23.463 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.459 15.931 22.591 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.423 16.669 23.812 1.00 0.00 H +ATOM 849 CD GLU 56 35.548 15.855 24.520 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.094 15.347 25.534 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.325 15.660 24.312 1.00 0.00 O +ATOM 852 C GLU 56 38.030 19.202 23.644 1.00 0.00 C +ATOM 853 O GLU 56 38.535 19.186 24.795 1.00 0.00 O +ATOM 854 OXT GLU 56 38.680 19.141 22.578 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.717 32.457 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.342 33.248 30.282 1.00 0.00 N +HETATM 857 C AN1 58 30.690 33.885 31.200 1.00 0.00 C +HETATM 858 C1 AN1 58 29.362 33.529 30.704 1.00 0.00 C +HETATM 859 H AN1 58 30.622 34.282 32.217 1.00 0.00 H +HETATM 860 H1 AN1 58 31.134 34.634 30.540 1.00 0.00 H +HETATM 861 H2 AN1 58 31.317 32.983 31.203 1.00 0.00 H +HETATM 862 N1 AZI 59 31.272 30.355 29.425 1.00 0.00 N +HETATM 863 N2 AZI 59 30.474 30.251 30.345 1.00 0.00 N +HETATM 864 N3 AZI 59 29.631 30.164 31.291 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 148 144 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 643 639 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_3_front_2.pdb b/tests/nsga2/intermediate_molecules/min_iter_3_front_2.pdb new file mode 100644 index 0000000..48f1266 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_3_front_2.pdb @@ -0,0 +1,1759 @@ +COMPND fitness: -3.7512 86.6599999999994 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 56.210 58.077 52.044 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.606 37.843 23.332 1.00 0.00 N +ATOM 2 H1 MET 1 14.561 38.256 24.258 1.00 0.00 H +ATOM 3 H2 MET 1 13.827 38.164 22.783 1.00 0.00 H +ATOM 4 H3 MET 1 15.475 38.170 22.930 1.00 0.00 H +ATOM 5 CA MET 1 14.630 36.376 23.447 1.00 0.00 C +ATOM 6 HA MET 1 13.686 36.053 23.885 1.00 0.00 H +ATOM 7 CB MET 1 14.779 35.725 22.058 1.00 0.00 C +ATOM 8 HB2 MET 1 13.905 35.984 21.460 1.00 0.00 H +ATOM 9 HB3 MET 1 15.663 36.132 21.565 1.00 0.00 H +ATOM 10 CG MET 1 14.914 34.195 22.110 1.00 0.00 C +ATOM 11 HG2 MET 1 15.809 33.940 22.680 1.00 0.00 H +ATOM 12 HG3 MET 1 14.049 33.777 22.629 1.00 0.00 H +ATOM 13 SD MET 1 15.062 33.382 20.493 1.00 0.00 S +ATOM 14 CE MET 1 13.359 33.515 19.876 1.00 0.00 C +ATOM 15 HE1 MET 1 13.058 34.560 19.812 1.00 0.00 H +ATOM 16 HE2 MET 1 13.297 33.070 18.883 1.00 0.00 H +ATOM 17 HE3 MET 1 12.684 32.982 20.546 1.00 0.00 H +ATOM 18 C MET 1 15.751 35.940 24.383 1.00 0.00 C +ATOM 19 O MET 1 16.896 36.328 24.187 1.00 0.00 O +ATOM 20 N GLN 2 15.440 35.074 25.351 1.00 0.00 N +ATOM 21 H GLN 2 14.472 34.834 25.495 1.00 0.00 H +ATOM 22 CA GLN 2 16.413 34.386 26.209 1.00 0.00 C +ATOM 23 HA GLN 2 17.163 35.101 26.548 1.00 0.00 H +ATOM 24 CB GLN 2 15.660 33.839 27.442 1.00 0.00 C +ATOM 25 HB2 GLN 2 14.728 33.382 27.108 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.234 33.053 27.924 1.00 0.00 H +ATOM 27 CG GLN 2 15.332 34.909 28.498 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.887 35.771 28.013 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.582 34.501 29.177 1.00 0.00 H +ATOM 30 CD GLN 2 16.524 35.361 29.339 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.655 34.909 29.191 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.312 36.233 30.300 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.089 36.502 30.869 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.408 36.678 30.366 1.00 0.00 H +ATOM 35 C GLN 2 17.162 33.270 25.440 1.00 0.00 C +ATOM 36 O GLN 2 16.821 32.092 25.554 1.00 0.00 O +ATOM 37 N TYR 3 18.180 33.629 24.652 1.00 0.00 N +ATOM 38 H TYR 3 18.418 34.618 24.614 1.00 0.00 H +ATOM 39 CA TYR 3 19.046 32.686 23.920 1.00 0.00 C +ATOM 40 HA TYR 3 18.430 32.099 23.237 1.00 0.00 H +ATOM 41 CB TYR 3 20.075 33.468 23.090 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.560 34.213 23.724 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.851 32.777 22.757 1.00 0.00 H +ATOM 44 CG TYR 3 19.504 34.151 21.860 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.421 33.432 20.651 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.751 32.402 20.611 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.934 34.054 19.487 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.898 33.509 18.555 1.00 0.00 H +ATOM 49 CZ TYR 3 18.516 35.401 19.533 1.00 0.00 C +ATOM 50 OH TYR 3 18.068 36.006 18.402 1.00 0.00 O +ATOM 51 HH TYR 3 18.265 35.478 17.625 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.582 36.118 20.747 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.264 37.151 20.769 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.081 35.495 21.908 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.142 36.054 22.834 1.00 0.00 H +ATOM 56 C TYR 3 19.758 31.718 24.880 1.00 0.00 C +ATOM 57 O TYR 3 20.253 32.137 25.927 1.00 0.00 O +ATOM 58 N LYS 4 19.814 30.420 24.558 1.00 0.00 N +ATOM 59 H LYS 4 19.564 30.159 23.606 1.00 0.00 H +ATOM 60 CA LYS 4 20.327 29.351 25.441 1.00 0.00 C +ATOM 61 HA LYS 4 20.068 29.589 26.469 1.00 0.00 H +ATOM 62 CB LYS 4 19.670 28.002 25.066 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.603 27.928 23.981 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.325 27.194 25.394 1.00 0.00 H +ATOM 65 CG LYS 4 18.278 27.723 25.675 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.001 26.705 25.397 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.346 27.765 26.762 1.00 0.00 H +ATOM 68 CD LYS 4 17.162 28.667 25.194 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.336 29.665 25.587 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.218 28.723 24.104 1.00 0.00 H +ATOM 71 CE LYS 4 15.739 28.200 25.570 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.031 28.787 24.974 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.626 27.156 25.262 1.00 0.00 H +ATOM 74 NZ LYS 4 15.398 28.355 27.015 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.453 29.321 27.308 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.441 28.062 27.197 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.999 27.808 27.619 1.00 0.00 H +ATOM 78 C LYS 4 21.859 29.250 25.406 1.00 0.00 C +ATOM 79 O LYS 4 22.510 29.627 24.436 1.00 0.00 O +HETATM 80 N HX1 5 22.468 28.722 26.466 1.00 0.00 N +HETATM 81 CA HX1 5 23.925 28.531 26.561 1.00 0.00 C +HETATM 82 C HX1 5 24.291 27.414 27.546 1.00 0.00 C +HETATM 83 O HX1 5 23.816 27.403 28.683 1.00 0.00 O +HETATM 84 CB HX1 5 24.559 29.858 26.974 1.00 0.00 C +HETATM 85 CG HX1 5 26.066 29.960 27.018 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.022 29.042 26.675 1.00 0.00 C +HETATM 87 ND1 HX1 5 26.676 31.061 27.599 1.00 0.00 N +HETATM 88 CE1 HX1 5 27.991 30.818 27.497 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.228 29.585 27.032 1.00 0.00 N +HETATM 90 H HX1 5 21.913 28.579 27.306 1.00 0.00 H +HETATM 91 HA HX1 5 24.318 28.260 25.581 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.179 30.134 27.959 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.214 30.629 26.287 1.00 0.00 H +HETATM 94 HD2 HX1 5 26.886 28.045 26.285 1.00 0.00 H +HETATM 95 HE1 HX1 5 28.763 31.447 27.914 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.102 29.078 27.222 1.00 0.00 H +ATOM 97 N ILE 6 25.132 26.489 27.085 1.00 0.00 N +ATOM 98 H ILE 6 25.458 26.571 26.126 1.00 0.00 H +ATOM 99 CA ILE 6 25.644 25.322 27.819 1.00 0.00 C +ATOM 100 HA ILE 6 25.110 25.241 28.770 1.00 0.00 H +ATOM 101 CB ILE 6 25.327 24.038 27.013 1.00 0.00 C +ATOM 102 HB ILE 6 25.787 24.132 26.028 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.904 22.774 27.676 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.503 22.652 28.681 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.658 21.888 27.095 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.991 22.817 27.722 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.792 23.903 26.833 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.330 23.794 27.813 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.398 24.811 26.380 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.329 22.747 25.939 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.496 21.792 26.437 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.260 22.854 25.747 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.867 22.770 24.990 1.00 0.00 H +ATOM 114 C ILE 6 27.131 25.511 28.167 1.00 0.00 C +ATOM 115 O ILE 6 27.874 26.246 27.505 1.00 0.00 O +ATOM 116 N VAL 7 27.523 24.924 29.300 1.00 0.00 N +ATOM 117 H VAL 7 26.889 24.232 29.696 1.00 0.00 H +ATOM 118 CA VAL 7 28.566 25.434 30.206 1.00 0.00 C +ATOM 119 HA VAL 7 28.518 26.524 30.150 1.00 0.00 H +ATOM 120 CB VAL 7 28.126 25.043 31.634 1.00 0.00 C +ATOM 121 HB VAL 7 27.059 25.240 31.715 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.312 23.552 31.929 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.350 23.255 31.825 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.977 23.323 32.941 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.718 22.960 31.234 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.754 25.899 32.738 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.446 26.934 32.614 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.393 25.561 33.711 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.836 25.844 32.729 1.00 0.00 H +ATOM 130 C VAL 7 30.027 25.023 29.878 1.00 0.00 C +ATOM 131 O VAL 7 30.259 23.980 29.272 1.00 0.00 O +ATOM 132 N ARG 8 31.025 25.803 30.343 1.00 0.00 N +ATOM 133 H ARG 8 30.730 26.642 30.829 1.00 0.00 H +ATOM 134 CA ARG 8 32.494 25.697 30.079 1.00 0.00 C +ATOM 135 HA ARG 8 32.641 25.654 29.002 1.00 0.00 H +ATOM 136 CB ARG 8 33.190 27.021 30.529 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.243 26.980 30.258 1.00 0.00 H +ATOM 138 HB3 ARG 8 32.752 27.856 29.977 1.00 0.00 H +ATOM 139 CG ARG 8 33.078 27.338 32.034 1.00 0.00 C +ATOM 140 HG2 ARG 8 32.080 27.673 32.284 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.275 26.434 32.583 1.00 0.00 H +ATOM 142 CD ARG 8 34.135 28.324 32.567 1.00 0.00 C +ATOM 143 HD2 ARG 8 35.114 28.005 32.227 1.00 0.00 H +ATOM 144 HD3 ARG 8 33.944 29.313 32.150 1.00 0.00 H +ATOM 145 NE ARG 8 34.140 28.392 34.050 1.00 0.00 N +ATOM 146 HE ARG 8 33.745 29.220 34.456 1.00 0.00 H +ATOM 147 CZ ARG 8 34.700 27.536 34.893 1.00 0.00 C +ATOM 148 NH1 ARG 8 35.207 26.395 34.516 1.00 0.00 N +ATOM 149 HH11 ARG 8 35.120 26.109 33.554 1.00 0.00 H +ATOM 150 HH12 ARG 8 35.645 25.786 35.187 1.00 0.00 H +ATOM 151 NH2 ARG 8 34.752 27.809 36.166 1.00 0.00 N +ATOM 152 HH21 ARG 8 34.458 28.703 36.519 1.00 0.00 H +ATOM 153 HH22 ARG 8 35.271 27.201 36.780 1.00 0.00 H +ATOM 154 C ARG 8 33.221 24.420 30.618 1.00 0.00 C +ATOM 155 O ARG 8 34.140 24.545 31.425 1.00 0.00 O +ATOM 156 N GLY 9 32.794 23.192 30.314 1.00 0.00 N +ATOM 157 H GLY 9 31.936 23.085 29.778 1.00 0.00 H +ATOM 158 CA GLY 9 33.551 21.973 30.680 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.358 21.821 29.958 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.023 22.124 31.650 1.00 0.00 H +ATOM 161 C GLY 9 32.693 20.696 30.769 1.00 0.00 C +ATOM 162 O GLY 9 31.554 20.681 30.307 1.00 0.00 O +ATOM 163 N LYS 10 33.209 19.638 31.434 1.00 0.00 N +ATOM 164 H LYS 10 34.139 19.753 31.822 1.00 0.00 H +ATOM 165 CA LYS 10 32.675 18.250 31.389 1.00 0.00 C +ATOM 166 HA LYS 10 31.669 18.289 30.975 1.00 0.00 H +ATOM 167 CB LYS 10 33.543 17.448 30.389 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.001 18.124 29.659 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.358 16.937 30.916 1.00 0.00 H +ATOM 170 CG LYS 10 32.733 16.420 29.582 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.183 15.759 30.254 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.013 16.957 28.963 1.00 0.00 H +ATOM 173 CD LYS 10 33.643 15.574 28.686 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.296 16.229 28.107 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.260 14.923 29.303 1.00 0.00 H +ATOM 176 CE LYS 10 32.827 14.724 27.709 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.193 14.038 28.269 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.190 15.392 27.127 1.00 0.00 H +ATOM 179 NZ LYS 10 33.711 13.988 26.778 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.326 13.343 27.264 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.201 13.485 26.071 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.315 14.654 26.284 1.00 0.00 H +ATOM 183 C LYS 10 32.518 17.528 32.747 1.00 0.00 C +ATOM 184 O LYS 10 32.596 16.307 32.801 1.00 0.00 O +ATOM 185 N ASN 11 32.378 18.251 33.862 1.00 0.00 N +ATOM 186 H ASN 11 32.311 19.238 33.729 1.00 0.00 H +ATOM 187 CA ASN 11 32.101 17.706 35.213 1.00 0.00 C +ATOM 188 HA ASN 11 32.387 16.648 35.230 1.00 0.00 H +ATOM 189 CB ASN 11 33.024 18.458 36.211 1.00 0.00 C +ATOM 190 HB2 ASN 11 34.053 18.194 36.010 1.00 0.00 H +ATOM 191 HB3 ASN 11 32.920 19.530 36.035 1.00 0.00 H +ATOM 192 CG ASN 11 32.702 18.222 37.671 1.00 0.00 C +ATOM 193 OD1 ASN 11 31.653 18.588 38.170 1.00 0.00 O +ATOM 194 ND2 ASN 11 33.609 17.657 38.430 1.00 0.00 N +ATOM 195 HD21 ASN 11 33.341 17.524 39.395 1.00 0.00 H +ATOM 196 HD22 ASN 11 34.511 17.380 38.074 1.00 0.00 H +ATOM 197 C ASN 11 30.600 17.753 35.520 1.00 0.00 C +ATOM 198 O ASN 11 29.907 16.749 35.462 1.00 0.00 O +ATOM 199 N TYR 12 30.095 18.967 35.742 1.00 0.00 N +ATOM 200 H TYR 12 30.736 19.709 35.899 1.00 0.00 H +ATOM 201 CA TYR 12 28.678 19.398 35.675 1.00 0.00 C +ATOM 202 HA TYR 12 28.082 18.749 36.359 1.00 0.00 H +ATOM 203 CB TYR 12 28.666 20.825 36.150 1.00 0.00 C +ATOM 204 HB2 TYR 12 27.626 21.198 36.151 1.00 0.00 H +ATOM 205 HB3 TYR 12 28.941 20.842 37.215 1.00 0.00 H +ATOM 206 CG TYR 12 29.561 21.851 35.412 1.00 0.00 C +ATOM 207 CD1 TYR 12 30.331 21.560 34.255 1.00 0.00 C +ATOM 208 HD1 TYR 12 30.263 20.582 33.755 1.00 0.00 H +ATOM 209 CE1 TYR 12 31.155 22.501 33.648 1.00 0.00 C +ATOM 210 HE1 TYR 12 31.680 22.275 32.733 1.00 0.00 H +ATOM 211 CZ TYR 12 31.213 23.780 34.184 1.00 0.00 C +ATOM 212 OH TYR 12 31.987 24.732 33.569 1.00 0.00 O +ATOM 213 HH TYR 12 32.324 24.387 32.701 1.00 0.00 H +ATOM 214 CE2 TYR 12 30.474 24.127 35.305 1.00 0.00 C +ATOM 215 HE2 TYR 12 30.501 25.147 35.689 1.00 0.00 H +ATOM 216 CD2 TYR 12 29.651 23.171 35.908 1.00 0.00 C +ATOM 217 HD2 TYR 12 29.043 23.443 36.787 1.00 0.00 H +ATOM 218 C TYR 12 28.090 19.253 34.250 1.00 0.00 C +ATOM 219 O TYR 12 28.788 18.862 33.309 1.00 0.00 O +ATOM 220 N LYS 13 26.821 19.647 34.065 1.00 0.00 N +ATOM 221 H LYS 13 26.305 19.925 34.884 1.00 0.00 H +ATOM 222 CA LYS 13 26.094 19.541 32.776 1.00 0.00 C +ATOM 223 HA LYS 13 26.805 19.717 31.969 1.00 0.00 H +ATOM 224 CB LYS 13 25.593 18.087 32.650 1.00 0.00 C +ATOM 225 HB2 LYS 13 26.320 17.429 33.127 1.00 0.00 H +ATOM 226 HB3 LYS 13 24.654 17.988 33.195 1.00 0.00 H +ATOM 227 CG LYS 13 25.425 17.587 31.203 1.00 0.00 C +ATOM 228 HG2 LYS 13 24.549 18.045 30.741 1.00 0.00 H +ATOM 229 HG3 LYS 13 26.302 17.868 30.624 1.00 0.00 H +ATOM 230 CD LYS 13 25.291 16.049 31.158 1.00 0.00 C +ATOM 231 HD2 LYS 13 25.230 15.725 30.117 1.00 0.00 H +ATOM 232 HD3 LYS 13 26.195 15.616 31.594 1.00 0.00 H +ATOM 233 CE LYS 13 24.053 15.554 31.925 1.00 0.00 C +ATOM 234 HE2 LYS 13 23.979 16.117 32.855 1.00 0.00 H +ATOM 235 HE3 LYS 13 23.165 15.772 31.325 1.00 0.00 H +ATOM 236 NZ LYS 13 24.127 14.113 32.260 1.00 0.00 N +ATOM 237 HZ1 LYS 13 25.032 13.871 32.657 1.00 0.00 H +ATOM 238 HZ2 LYS 13 23.461 13.886 32.994 1.00 0.00 H +ATOM 239 HZ3 LYS 13 23.964 13.519 31.457 1.00 0.00 H +ATOM 240 C LYS 13 24.980 20.595 32.595 1.00 0.00 C +ATOM 241 O LYS 13 23.956 20.338 31.967 1.00 0.00 O +ATOM 242 N GLY 14 25.140 21.770 33.215 1.00 0.00 N +ATOM 243 H GLY 14 26.023 21.941 33.667 1.00 0.00 H +ATOM 244 CA GLY 14 24.092 22.793 33.319 1.00 0.00 C +ATOM 245 HA2 GLY 14 23.148 22.298 33.541 1.00 0.00 H +ATOM 246 HA3 GLY 14 24.315 23.453 34.156 1.00 0.00 H +ATOM 247 C GLY 14 23.874 23.669 32.071 1.00 0.00 C +ATOM 248 O GLY 14 24.749 23.819 31.213 1.00 0.00 O +ATOM 249 N VAL 15 22.695 24.302 32.017 1.00 0.00 N +ATOM 250 H VAL 15 22.053 24.151 32.781 1.00 0.00 H +ATOM 251 CA VAL 15 22.244 25.234 30.969 1.00 0.00 C +ATOM 252 HA VAL 15 23.112 25.536 30.386 1.00 0.00 H +ATOM 253 CB VAL 15 21.252 24.543 30.003 1.00 0.00 C +ATOM 254 HB VAL 15 21.734 23.644 29.616 1.00 0.00 H +ATOM 255 CG1 VAL 15 19.942 24.128 30.686 1.00 0.00 C +ATOM 256 HG11 VAL 15 19.401 25.000 31.051 1.00 0.00 H +ATOM 257 HG12 VAL 15 19.310 23.599 29.968 1.00 0.00 H +ATOM 258 HG13 VAL 15 20.149 23.452 31.516 1.00 0.00 H +ATOM 259 CG2 VAL 15 20.890 25.430 28.802 1.00 0.00 C +ATOM 260 HG21 VAL 15 21.796 25.776 28.306 1.00 0.00 H +ATOM 261 HG22 VAL 15 20.312 24.845 28.084 1.00 0.00 H +ATOM 262 HG23 VAL 15 20.288 26.282 29.113 1.00 0.00 H +ATOM 263 C VAL 15 21.642 26.495 31.603 1.00 0.00 C +ATOM 264 O VAL 15 21.073 26.439 32.694 1.00 0.00 O +HETATM 265 N HY1 16 21.783 27.631 30.929 1.00 0.00 N +HETATM 266 CA HY1 16 21.218 28.928 31.326 1.00 0.00 C +HETATM 267 C HY1 16 21.036 29.822 30.068 1.00 0.00 C +HETATM 268 O HY1 16 21.371 29.383 28.958 1.00 0.00 O +HETATM 269 CB HY1 16 22.137 29.545 32.394 1.00 0.00 C +HETATM 270 CG HY1 16 23.542 29.763 31.898 1.00 0.00 C +HETATM 271 CD2 HY1 16 23.897 30.825 31.132 1.00 0.00 C +HETATM 272 ND1 HY1 16 24.612 28.888 31.897 1.00 0.00 N +HETATM 273 CE1 HY1 16 25.588 29.437 31.139 1.00 0.00 C +HETATM 274 NE2 HY1 16 25.183 30.623 30.647 1.00 0.00 N +HETATM 275 H HY1 16 22.297 27.605 30.055 1.00 0.00 H +HETATM 276 HA HY1 16 20.231 28.774 31.762 1.00 0.00 H +HETATM 277 HB2 HY1 16 21.721 30.492 32.738 1.00 0.00 H +HETATM 278 HB3 HY1 16 22.169 28.880 33.267 1.00 0.00 H +HETATM 279 HD1 HY1 16 24.657 28.001 32.388 1.00 0.00 H +HETATM 280 HD2 HY1 16 23.233 31.636 30.872 1.00 0.00 H +HETATM 281 HE1 HY1 16 26.569 28.993 30.965 1.00 0.00 H +ATOM 282 N THR 17 20.509 31.046 30.201 1.00 0.00 N +ATOM 283 H THR 17 20.226 31.383 31.101 1.00 0.00 H +ATOM 284 CA THR 17 20.080 31.865 29.044 1.00 0.00 C +ATOM 285 HA THR 17 20.517 31.448 28.143 1.00 0.00 H +ATOM 286 CB THR 17 18.549 31.829 28.895 1.00 0.00 C +ATOM 287 HB THR 17 18.274 32.454 28.059 1.00 0.00 H +ATOM 288 CG2 THR 17 17.977 30.425 28.652 1.00 0.00 C +ATOM 289 HG21 THR 17 18.205 29.759 29.472 1.00 0.00 H +ATOM 290 HG22 THR 17 16.890 30.494 28.552 1.00 0.00 H +ATOM 291 HG23 THR 17 18.376 30.025 27.734 1.00 0.00 H +ATOM 292 OG1 THR 17 17.946 32.336 30.061 1.00 0.00 O +ATOM 293 HG1 THR 17 17.908 33.302 29.951 1.00 0.00 H +ATOM 294 C THR 17 20.520 33.329 29.097 1.00 0.00 C +ATOM 295 O THR 17 20.892 33.824 30.166 1.00 0.00 O +HETATM 296 N HY2 18 20.484 34.015 27.941 1.00 0.00 N +HETATM 297 CA HY2 18 20.882 35.411 27.722 1.00 0.00 C +HETATM 298 C HY2 18 19.851 36.210 26.928 1.00 0.00 C +HETATM 299 O HY2 18 19.572 35.885 25.778 1.00 0.00 O +HETATM 300 CB HY2 18 22.273 35.475 27.050 1.00 0.00 C +HETATM 301 CG HY2 18 23.272 34.804 27.979 1.00 0.00 C +HETATM 302 CD2 HY2 18 23.969 33.646 27.739 1.00 0.00 C +HETATM 303 ND1 HY2 18 23.279 34.994 29.343 1.00 0.00 N +HETATM 304 CE1 HY2 18 23.808 33.906 29.896 1.00 0.00 C +HETATM 305 NE2 HY2 18 24.364 33.102 28.972 1.00 0.00 N +HETATM 306 H HY2 18 20.201 33.487 27.121 1.00 0.00 H +HETATM 307 HA HY2 18 20.970 35.912 28.681 1.00 0.00 H +HETATM 308 HB2 HY2 18 22.237 34.978 26.082 1.00 0.00 H +HETATM 309 HB3 HY2 18 22.557 36.514 26.883 1.00 0.00 H +HETATM 310 HD1 HY2 18 22.704 35.669 29.851 1.00 0.00 H +HETATM 311 HD2 HY2 18 24.054 33.162 26.778 1.00 0.00 H +HETATM 312 HE1 HY2 18 23.733 33.703 30.955 1.00 0.00 H +ATOM 313 N GLU 19 19.305 37.253 27.550 1.00 0.00 N +ATOM 314 H GLU 19 19.560 37.468 28.502 1.00 0.00 H +ATOM 315 CA GLU 19 18.335 38.139 26.909 1.00 0.00 C +ATOM 316 HA GLU 19 17.580 37.512 26.437 1.00 0.00 H +ATOM 317 CB GLU 19 17.681 39.005 27.999 1.00 0.00 C +ATOM 318 HB2 GLU 19 17.352 38.353 28.807 1.00 0.00 H +ATOM 319 HB3 GLU 19 18.428 39.691 28.402 1.00 0.00 H +ATOM 320 CG GLU 19 16.471 39.813 27.518 1.00 0.00 C +ATOM 321 HG2 GLU 19 16.008 40.295 28.382 1.00 0.00 H +ATOM 322 HG3 GLU 19 16.809 40.595 26.832 1.00 0.00 H +ATOM 323 CD GLU 19 15.468 38.898 26.817 1.00 0.00 C +ATOM 324 OE1 GLU 19 15.493 38.853 25.568 1.00 0.00 O +ATOM 325 OE2 GLU 19 14.771 38.123 27.500 1.00 0.00 O +ATOM 326 C GLU 19 18.993 39.011 25.829 1.00 0.00 C +ATOM 327 O GLU 19 20.034 39.622 26.077 1.00 0.00 O +ATOM 328 N ALA 20 18.393 39.062 24.639 1.00 0.00 N +ATOM 329 H ALA 20 17.534 38.535 24.527 1.00 0.00 H +ATOM 330 CA ALA 20 18.794 39.928 23.528 1.00 0.00 C +ATOM 331 HA ALA 20 18.938 40.939 23.911 1.00 0.00 H +ATOM 332 CB ALA 20 20.120 39.430 22.936 1.00 0.00 C +ATOM 333 HB1 ALA 20 19.981 38.442 22.498 1.00 0.00 H +ATOM 334 HB2 ALA 20 20.463 40.118 22.165 1.00 0.00 H +ATOM 335 HB3 ALA 20 20.891 39.377 23.704 1.00 0.00 H +ATOM 336 C ALA 20 17.730 39.970 22.414 1.00 0.00 C +ATOM 337 O ALA 20 16.877 39.085 22.300 1.00 0.00 O +ATOM 338 N VAL 21 17.828 40.967 21.527 1.00 0.00 N +ATOM 339 H VAL 21 18.517 41.687 21.688 1.00 0.00 H +ATOM 340 CA VAL 21 17.108 40.983 20.235 1.00 0.00 C +ATOM 341 HA VAL 21 16.112 40.569 20.390 1.00 0.00 H +ATOM 342 CB VAL 21 16.922 42.424 19.708 1.00 0.00 C +ATOM 343 HB VAL 21 16.284 42.377 18.825 1.00 0.00 H +ATOM 344 CG1 VAL 21 16.207 43.312 20.736 1.00 0.00 C +ATOM 345 HG11 VAL 21 16.841 43.487 21.604 1.00 0.00 H +ATOM 346 HG12 VAL 21 15.962 44.273 20.283 1.00 0.00 H +ATOM 347 HG13 VAL 21 15.281 42.837 21.061 1.00 0.00 H +ATOM 348 CG2 VAL 21 18.238 43.102 19.302 1.00 0.00 C +ATOM 349 HG21 VAL 21 18.700 42.562 18.476 1.00 0.00 H +ATOM 350 HG22 VAL 21 18.040 44.118 18.959 1.00 0.00 H +ATOM 351 HG23 VAL 21 18.934 43.140 20.139 1.00 0.00 H +ATOM 352 C VAL 21 17.781 40.114 19.160 1.00 0.00 C +ATOM 353 O VAL 21 17.147 39.785 18.160 1.00 0.00 O +ATOM 354 N ASP 22 19.050 39.749 19.368 1.00 0.00 N +ATOM 355 H ASP 22 19.476 40.007 20.243 1.00 0.00 H +ATOM 356 CA ASP 22 19.944 39.093 18.406 1.00 0.00 C +ATOM 357 HA ASP 22 19.370 38.425 17.764 1.00 0.00 H +ATOM 358 CB ASP 22 20.556 40.186 17.509 1.00 0.00 C +ATOM 359 HB2 ASP 22 19.748 40.807 17.120 1.00 0.00 H +ATOM 360 HB3 ASP 22 21.211 40.830 18.090 1.00 0.00 H +ATOM 361 CG ASP 22 21.364 39.655 16.331 1.00 0.00 C +ATOM 362 OD1 ASP 22 21.470 40.449 15.361 1.00 0.00 O +ATOM 363 OD2 ASP 22 21.882 38.534 16.368 1.00 0.00 O +ATOM 364 C ASP 22 21.010 38.262 19.152 1.00 0.00 C +ATOM 365 O ASP 22 21.519 38.679 20.197 1.00 0.00 O +ATOM 366 N LEU 23 21.373 37.097 18.612 1.00 0.00 N +ATOM 367 H LEU 23 21.060 36.924 17.665 1.00 0.00 H +ATOM 368 CA LEU 23 22.451 36.256 19.128 1.00 0.00 C +ATOM 369 HA LEU 23 22.232 36.042 20.172 1.00 0.00 H +ATOM 370 CB LEU 23 22.427 34.919 18.362 1.00 0.00 C +ATOM 371 HB2 LEU 23 21.429 34.495 18.470 1.00 0.00 H +ATOM 372 HB3 LEU 23 22.588 35.105 17.300 1.00 0.00 H +ATOM 373 CG LEU 23 23.460 33.898 18.881 1.00 0.00 C +ATOM 374 HG LEU 23 23.719 34.148 19.908 1.00 0.00 H +ATOM 375 CD1 LEU 23 22.889 32.478 18.888 1.00 0.00 C +ATOM 376 HD11 LEU 23 22.614 32.176 17.877 1.00 0.00 H +ATOM 377 HD12 LEU 23 23.634 31.788 19.283 1.00 0.00 H +ATOM 378 HD13 LEU 23 22.009 32.440 19.528 1.00 0.00 H +ATOM 379 CD2 LEU 23 24.722 33.893 18.016 1.00 0.00 C +ATOM 380 HD21 LEU 23 25.158 34.890 17.970 1.00 0.00 H +ATOM 381 HD22 LEU 23 25.459 33.219 18.446 1.00 0.00 H +ATOM 382 HD23 LEU 23 24.480 33.567 17.004 1.00 0.00 H +ATOM 383 C LEU 23 23.818 36.971 19.075 1.00 0.00 C +ATOM 384 O LEU 23 24.632 36.796 19.983 1.00 0.00 O +ATOM 385 N ALA 24 24.054 37.834 18.081 1.00 0.00 N +ATOM 386 H ALA 24 23.334 37.955 17.366 1.00 0.00 H +ATOM 387 CA ALA 24 25.275 38.639 17.954 1.00 0.00 C +ATOM 388 HA ALA 24 26.125 37.990 18.164 1.00 0.00 H +ATOM 389 CB ALA 24 25.385 39.106 16.501 1.00 0.00 C +ATOM 390 HB1 ALA 24 24.557 39.771 16.254 1.00 0.00 H +ATOM 391 HB2 ALA 24 26.329 39.629 16.356 1.00 0.00 H +ATOM 392 HB3 ALA 24 25.359 38.244 15.834 1.00 0.00 H +ATOM 393 C ALA 24 25.361 39.827 18.944 1.00 0.00 C +ATOM 394 O ALA 24 26.433 40.412 19.133 1.00 0.00 O +ATOM 395 N GLU 25 24.256 40.178 19.611 1.00 0.00 N +ATOM 396 H GLU 25 23.395 39.702 19.373 1.00 0.00 H +ATOM 397 CA GLU 25 24.264 41.004 20.827 1.00 0.00 C +ATOM 398 HA GLU 25 25.120 41.680 20.813 1.00 0.00 H +ATOM 399 CB GLU 25 22.987 41.862 20.899 1.00 0.00 C +ATOM 400 HB2 GLU 25 22.123 41.221 20.735 1.00 0.00 H +ATOM 401 HB3 GLU 25 22.902 42.280 21.899 1.00 0.00 H +ATOM 402 CG GLU 25 22.951 43.019 19.891 1.00 0.00 C +ATOM 403 HG2 GLU 25 23.195 42.648 18.896 1.00 0.00 H +ATOM 404 HG3 GLU 25 21.933 43.412 19.851 1.00 0.00 H +ATOM 405 CD GLU 25 23.913 44.144 20.293 1.00 0.00 C +ATOM 406 OE1 GLU 25 23.478 45.087 20.985 1.00 0.00 O +ATOM 407 OE2 GLU 25 25.113 44.027 19.919 1.00 0.00 O +ATOM 408 C GLU 25 24.432 40.126 22.081 1.00 0.00 C +ATOM 409 O GLU 25 25.224 40.456 22.965 1.00 0.00 O +ATOM 410 N ALA 26 23.788 38.950 22.138 1.00 0.00 N +ATOM 411 H ALA 26 23.138 38.715 21.394 1.00 0.00 H +ATOM 412 CA ALA 26 23.981 37.984 23.225 1.00 0.00 C +ATOM 413 HA ALA 26 23.762 38.494 24.162 1.00 0.00 H +ATOM 414 CB ALA 26 22.974 36.842 23.061 1.00 0.00 C +ATOM 415 HB1 ALA 26 23.199 36.283 22.157 1.00 0.00 H +ATOM 416 HB2 ALA 26 23.034 36.172 23.915 1.00 0.00 H +ATOM 417 HB3 ALA 26 21.964 37.238 22.992 1.00 0.00 H +ATOM 418 C ALA 26 25.427 37.446 23.335 1.00 0.00 C +ATOM 419 O ALA 26 25.824 37.003 24.418 1.00 0.00 O +ATOM 420 N GLU 27 26.226 37.506 22.263 1.00 0.00 N +ATOM 421 H GLU 27 25.786 37.697 21.366 1.00 0.00 H +ATOM 422 CA GLU 27 27.682 37.297 22.299 1.00 0.00 C +ATOM 423 HA GLU 27 27.873 36.349 22.802 1.00 0.00 H +ATOM 424 CB GLU 27 28.250 37.195 20.869 1.00 0.00 C +ATOM 425 HB2 GLU 27 27.652 36.495 20.285 1.00 0.00 H +ATOM 426 HB3 GLU 27 28.190 38.174 20.391 1.00 0.00 H +ATOM 427 CG GLU 27 29.709 36.707 20.879 1.00 0.00 C +ATOM 428 HG2 GLU 27 30.246 37.147 21.723 1.00 0.00 H +ATOM 429 HG3 GLU 27 29.712 35.623 21.031 1.00 0.00 H +ATOM 430 CD GLU 27 30.466 37.088 19.601 1.00 0.00 C +ATOM 431 OE1 GLU 27 30.854 38.276 19.503 1.00 0.00 O +ATOM 432 OE2 GLU 27 30.694 36.185 18.769 1.00 0.00 O +ATOM 433 C GLU 27 28.399 38.403 23.095 1.00 0.00 C +ATOM 434 O GLU 27 29.144 38.111 24.035 1.00 0.00 O +ATOM 435 N LYS 28 28.111 39.679 22.804 1.00 0.00 N +ATOM 436 H LYS 28 27.456 39.856 22.053 1.00 0.00 H +ATOM 437 CA LYS 28 28.669 40.829 23.542 1.00 0.00 C +ATOM 438 HA LYS 28 29.757 40.759 23.523 1.00 0.00 H +ATOM 439 CB LYS 28 28.255 42.157 22.883 1.00 0.00 C +ATOM 440 HB2 LYS 28 27.172 42.278 22.942 1.00 0.00 H +ATOM 441 HB3 LYS 28 28.719 42.971 23.444 1.00 0.00 H +ATOM 442 CG LYS 28 28.686 42.263 21.411 1.00 0.00 C +ATOM 443 HG2 LYS 28 29.750 42.034 21.326 1.00 0.00 H +ATOM 444 HG3 LYS 28 28.124 41.540 20.822 1.00 0.00 H +ATOM 445 CD LYS 28 28.432 43.680 20.873 1.00 0.00 C +ATOM 446 HD2 LYS 28 27.437 44.018 21.168 1.00 0.00 H +ATOM 447 HD3 LYS 28 29.160 44.358 21.322 1.00 0.00 H +ATOM 448 CE LYS 28 28.554 43.752 19.344 1.00 0.00 C +ATOM 449 HE2 LYS 28 28.652 44.804 19.060 1.00 0.00 H +ATOM 450 HE3 LYS 28 29.462 43.233 19.027 1.00 0.00 H +ATOM 451 NZ LYS 28 27.361 43.170 18.683 1.00 0.00 N +ATOM 452 HZ1 LYS 28 26.512 43.612 19.055 1.00 0.00 H +ATOM 453 HZ2 LYS 28 27.376 43.317 17.686 1.00 0.00 H +ATOM 454 HZ3 LYS 28 27.262 42.177 18.881 1.00 0.00 H +ATOM 455 C LYS 28 28.248 40.810 25.012 1.00 0.00 C +ATOM 456 O LYS 28 29.093 40.897 25.903 1.00 0.00 O +ATOM 457 N PHE 29 26.965 40.568 25.284 1.00 0.00 N +ATOM 458 H PHE 29 26.308 40.561 24.505 1.00 0.00 H +ATOM 459 CA PHE 29 26.454 40.372 26.647 1.00 0.00 C +ATOM 460 HA PHE 29 26.755 41.229 27.250 1.00 0.00 H +ATOM 461 CB PHE 29 24.918 40.333 26.629 1.00 0.00 C +ATOM 462 HB2 PHE 29 24.608 39.412 26.136 1.00 0.00 H +ATOM 463 HB3 PHE 29 24.565 40.293 27.662 1.00 0.00 H +ATOM 464 CG PHE 29 24.218 41.505 25.955 1.00 0.00 C +ATOM 465 CD1 PHE 29 22.999 41.289 25.282 1.00 0.00 C +ATOM 466 HD1 PHE 29 22.551 40.307 25.269 1.00 0.00 H +ATOM 467 CE1 PHE 29 22.362 42.347 24.611 1.00 0.00 C +ATOM 468 HE1 PHE 29 21.440 42.167 24.079 1.00 0.00 H +ATOM 469 CZ PHE 29 22.937 43.630 24.611 1.00 0.00 C +ATOM 470 HZ PHE 29 22.467 44.436 24.065 1.00 0.00 H +ATOM 471 CE2 PHE 29 24.132 43.861 25.313 1.00 0.00 C +ATOM 472 HE2 PHE 29 24.573 44.845 25.321 1.00 0.00 H +ATOM 473 CD2 PHE 29 24.766 42.805 25.989 1.00 0.00 C +ATOM 474 HD2 PHE 29 25.684 43.004 26.519 1.00 0.00 H +ATOM 475 C PHE 29 27.025 39.110 27.331 1.00 0.00 C +ATOM 476 O PHE 29 27.057 39.034 28.559 1.00 0.00 O +ATOM 477 N THR 30 27.519 38.123 26.569 1.00 0.00 N +ATOM 478 H THR 30 27.472 38.226 25.559 1.00 0.00 H +ATOM 479 CA THR 30 28.282 36.990 27.101 1.00 0.00 C +ATOM 480 HA THR 30 27.799 36.696 28.022 1.00 0.00 H +ATOM 481 CB THR 30 28.255 35.769 26.144 1.00 0.00 C +ATOM 482 HB THR 30 28.535 36.074 25.144 1.00 0.00 H +ATOM 483 CG2 THR 30 29.213 34.641 26.549 1.00 0.00 C +ATOM 484 HG21 THR 30 29.091 34.356 27.586 1.00 0.00 H +ATOM 485 HG22 THR 30 29.060 33.765 25.915 1.00 0.00 H +ATOM 486 HG23 THR 30 30.235 34.981 26.383 1.00 0.00 H +ATOM 487 OG1 THR 30 26.949 35.222 26.159 1.00 0.00 O +ATOM 488 HG1 THR 30 26.411 35.804 25.580 1.00 0.00 H +ATOM 489 C THR 30 29.697 37.395 27.517 1.00 0.00 C +ATOM 490 O THR 30 30.116 36.977 28.596 1.00 0.00 O +ATOM 491 N LYS 31 30.396 38.237 26.743 1.00 0.00 N +ATOM 492 H LYS 31 29.969 38.548 25.875 1.00 0.00 H +ATOM 493 CA LYS 31 31.759 38.733 27.030 1.00 0.00 C +ATOM 494 HA LYS 31 32.393 37.903 27.349 1.00 0.00 H +ATOM 495 CB LYS 31 32.356 39.316 25.742 1.00 0.00 C +ATOM 496 HB2 LYS 31 31.677 40.067 25.331 1.00 0.00 H +ATOM 497 HB3 LYS 31 33.304 39.811 25.970 1.00 0.00 H +ATOM 498 CG LYS 31 32.616 38.226 24.689 1.00 0.00 C +ATOM 499 HG2 LYS 31 33.308 37.492 25.095 1.00 0.00 H +ATOM 500 HG3 LYS 31 31.691 37.710 24.439 1.00 0.00 H +ATOM 501 CD LYS 31 33.202 38.836 23.409 1.00 0.00 C +ATOM 502 HD2 LYS 31 32.420 39.421 22.919 1.00 0.00 H +ATOM 503 HD3 LYS 31 34.019 39.511 23.668 1.00 0.00 H +ATOM 504 CE LYS 31 33.717 37.773 22.435 1.00 0.00 C +ATOM 505 HE2 LYS 31 32.924 37.052 22.218 1.00 0.00 H +ATOM 506 HE3 LYS 31 33.962 38.263 21.487 1.00 0.00 H +ATOM 507 NZ LYS 31 34.922 37.074 22.949 1.00 0.00 N +ATOM 508 HZ1 LYS 31 34.715 36.322 23.594 1.00 0.00 H +ATOM 509 HZ2 LYS 31 35.427 36.621 22.180 1.00 0.00 H +ATOM 510 HZ3 LYS 31 35.585 37.695 23.408 1.00 0.00 H +ATOM 511 C LYS 31 31.821 39.756 28.169 1.00 0.00 C +ATOM 512 O LYS 31 32.781 39.726 28.936 1.00 0.00 O +ATOM 513 N ALA 32 30.796 40.598 28.331 1.00 0.00 N +ATOM 514 H ALA 32 30.099 40.631 27.594 1.00 0.00 H +ATOM 515 CA ALA 32 30.739 41.633 29.373 1.00 0.00 C +ATOM 516 HA ALA 32 31.499 42.384 29.163 1.00 0.00 H +ATOM 517 CB ALA 32 29.356 42.306 29.300 1.00 0.00 C +ATOM 518 HB1 ALA 32 28.554 41.574 29.415 1.00 0.00 H +ATOM 519 HB2 ALA 32 29.262 43.050 30.092 1.00 0.00 H +ATOM 520 HB3 ALA 32 29.243 42.801 28.337 1.00 0.00 H +ATOM 521 C ALA 32 31.031 41.072 30.780 1.00 0.00 C +ATOM 522 O ALA 32 32.064 41.340 31.385 1.00 0.00 O +ATOM 523 N ARG 33 30.166 40.171 31.235 1.00 0.00 N +ATOM 524 H ARG 33 29.351 39.998 30.664 1.00 0.00 H +ATOM 525 CA ARG 33 30.294 39.444 32.510 1.00 0.00 C +ATOM 526 HA ARG 33 30.422 40.178 33.297 1.00 0.00 H +ATOM 527 CB ARG 33 28.995 38.699 32.794 1.00 0.00 C +ATOM 528 HB2 ARG 33 29.130 38.075 33.679 1.00 0.00 H +ATOM 529 HB3 ARG 33 28.177 39.395 32.979 1.00 0.00 H +ATOM 530 CG ARG 33 28.687 37.855 31.561 1.00 0.00 C +ATOM 531 HG2 ARG 33 28.076 38.434 30.871 1.00 0.00 H +ATOM 532 HG3 ARG 33 29.601 37.582 31.040 1.00 0.00 H +ATOM 533 CD ARG 33 27.984 36.569 31.880 1.00 0.00 C +ATOM 534 HD2 ARG 33 28.538 36.004 32.635 1.00 0.00 H +ATOM 535 HD3 ARG 33 26.985 36.812 32.252 1.00 0.00 H +ATOM 536 NE ARG 33 27.901 35.843 30.611 1.00 0.00 N +ATOM 537 HE ARG 33 28.490 36.185 29.860 1.00 0.00 H +ATOM 538 CZ ARG 33 26.904 35.066 30.309 1.00 0.00 C +ATOM 539 NH1 ARG 33 26.635 34.799 29.061 1.00 0.00 N +ATOM 540 HH11 ARG 33 27.186 35.168 28.300 1.00 0.00 H +ATOM 541 HH12 ARG 33 25.727 34.451 28.800 1.00 0.00 H +ATOM 542 NH2 ARG 33 26.203 34.541 31.276 1.00 0.00 N +ATOM 543 HH21 ARG 33 26.473 34.757 32.221 1.00 0.00 H +ATOM 544 HH22 ARG 33 25.586 33.777 31.106 1.00 0.00 H +ATOM 545 C ARG 33 31.465 38.449 32.604 1.00 0.00 C +ATOM 546 O ARG 33 31.778 37.990 33.697 1.00 0.00 O +ATOM 547 N ALA 34 32.072 38.042 31.482 1.00 0.00 N +ATOM 548 H ALA 34 31.783 38.439 30.604 1.00 0.00 H +ATOM 549 CA ALA 34 33.302 37.246 31.503 1.00 0.00 C +ATOM 550 HA ALA 34 33.202 36.446 32.236 1.00 0.00 H +ATOM 551 CB ALA 34 33.538 36.601 30.123 1.00 0.00 C +ATOM 552 HB1 ALA 34 33.762 37.355 29.372 1.00 0.00 H +ATOM 553 HB2 ALA 34 34.384 35.912 30.170 1.00 0.00 H +ATOM 554 HB3 ALA 34 32.660 36.035 29.815 1.00 0.00 H +ATOM 555 C ALA 34 34.457 38.136 31.984 1.00 0.00 C +ATOM 556 O ALA 34 35.219 37.724 32.850 1.00 0.00 O +ATOM 557 N ASN 35 34.474 39.401 31.551 1.00 0.00 N +ATOM 558 H ASN 35 33.784 39.677 30.864 1.00 0.00 H +ATOM 559 CA ASN 35 35.325 40.453 32.107 1.00 0.00 C +ATOM 560 HA ASN 35 36.327 40.046 32.242 1.00 0.00 H +ATOM 561 CB ASN 35 35.440 41.586 31.075 1.00 0.00 C +ATOM 562 HB2 ASN 35 34.453 41.945 30.796 1.00 0.00 H +ATOM 563 HB3 ASN 35 35.979 42.414 31.532 1.00 0.00 H +ATOM 564 CG ASN 35 36.209 41.162 29.832 1.00 0.00 C +ATOM 565 OD1 ASN 35 37.424 41.107 29.816 1.00 0.00 O +ATOM 566 ND2 ASN 35 35.544 40.847 28.746 1.00 0.00 N +ATOM 567 HD21 ASN 35 36.101 40.597 27.934 1.00 0.00 H +ATOM 568 HD22 ASN 35 34.541 40.769 28.766 1.00 0.00 H +ATOM 569 C ASN 35 34.886 40.937 33.515 1.00 0.00 C +ATOM 570 O ASN 35 35.755 41.332 34.288 1.00 0.00 O +ATOM 571 N ASP 36 33.604 40.835 33.915 1.00 0.00 N +ATOM 572 H ASP 36 32.883 40.704 33.220 1.00 0.00 H +ATOM 573 CA ASP 36 33.222 40.978 35.343 1.00 0.00 C +ATOM 574 HA ASP 36 33.609 41.930 35.704 1.00 0.00 H +ATOM 575 CB ASP 36 31.690 41.001 35.561 1.00 0.00 C +ATOM 576 HB2 ASP 36 31.275 40.064 35.211 1.00 0.00 H +ATOM 577 HB3 ASP 36 31.510 41.010 36.635 1.00 0.00 H +ATOM 578 CG ASP 36 30.917 42.200 34.975 1.00 0.00 C +ATOM 579 OD1 ASP 36 31.468 43.323 35.011 1.00 0.00 O +ATOM 580 OD2 ASP 36 29.741 42.011 34.563 1.00 0.00 O +ATOM 581 C ASP 36 33.862 39.877 36.225 1.00 0.00 C +ATOM 582 O ASP 36 34.232 40.144 37.368 1.00 0.00 O +ATOM 583 N LEU 37 34.028 38.649 35.706 1.00 0.00 N +ATOM 584 H LEU 37 33.645 38.474 34.786 1.00 0.00 H +ATOM 585 CA LEU 37 34.769 37.561 36.371 1.00 0.00 C +ATOM 586 HA LEU 37 34.582 37.645 37.443 1.00 0.00 H +ATOM 587 CB LEU 37 34.192 36.213 35.882 1.00 0.00 C +ATOM 588 HB2 LEU 37 33.118 36.210 36.069 1.00 0.00 H +ATOM 589 HB3 LEU 37 34.342 36.154 34.805 1.00 0.00 H +ATOM 590 CG LEU 37 34.805 34.945 36.516 1.00 0.00 C +ATOM 591 HG LEU 37 35.876 34.913 36.321 1.00 0.00 H +ATOM 592 CD1 LEU 37 34.566 34.864 38.026 1.00 0.00 C +ATOM 593 HD11 LEU 37 33.499 34.915 38.242 1.00 0.00 H +ATOM 594 HD12 LEU 37 34.975 33.932 38.415 1.00 0.00 H +ATOM 595 HD13 LEU 37 35.076 35.691 38.518 1.00 0.00 H +ATOM 596 CD2 LEU 37 34.181 33.694 35.888 1.00 0.00 C +ATOM 597 HD21 LEU 37 34.363 33.701 34.813 1.00 0.00 H +ATOM 598 HD22 LEU 37 34.644 32.804 36.314 1.00 0.00 H +ATOM 599 HD23 LEU 37 33.108 33.675 36.077 1.00 0.00 H +ATOM 600 C LEU 37 36.304 37.655 36.183 1.00 0.00 C +ATOM 601 O LEU 37 37.049 37.195 37.049 1.00 0.00 O +ATOM 602 N GLY 38 36.774 38.237 35.074 1.00 0.00 N +ATOM 603 H GLY 38 36.097 38.511 34.376 1.00 0.00 H +ATOM 604 CA GLY 38 38.182 38.550 34.809 1.00 0.00 C +ATOM 605 HA2 GLY 38 38.459 39.417 35.411 1.00 0.00 H +ATOM 606 HA3 GLY 38 38.795 37.709 35.131 1.00 0.00 H +ATOM 607 C GLY 38 38.540 38.860 33.342 1.00 0.00 C +ATOM 608 O GLY 38 39.143 39.896 33.084 1.00 0.00 O +ATOM 609 N GLU 39 38.201 37.985 32.384 1.00 0.00 N +ATOM 610 H GLU 39 37.589 37.219 32.631 1.00 0.00 H +ATOM 611 CA GLU 39 38.667 38.020 30.972 1.00 0.00 C +ATOM 612 HA GLU 39 38.785 39.059 30.656 1.00 0.00 H +ATOM 613 CB GLU 39 40.040 37.296 30.846 1.00 0.00 C +ATOM 614 HB2 GLU 39 39.905 36.277 31.208 1.00 0.00 H +ATOM 615 HB3 GLU 39 40.298 37.242 29.788 1.00 0.00 H +ATOM 616 CG GLU 39 41.235 37.941 31.588 1.00 0.00 C +ATOM 617 HG2 GLU 39 41.429 38.925 31.147 1.00 0.00 H +ATOM 618 HG3 GLU 39 40.970 38.086 32.638 1.00 0.00 H +ATOM 619 CD GLU 39 42.521 37.093 31.582 1.00 0.00 C +ATOM 620 OE1 GLU 39 42.422 35.846 31.671 1.00 0.00 O +ATOM 621 OE2 GLU 39 43.632 37.676 31.560 1.00 0.00 O +ATOM 622 C GLU 39 37.648 37.338 30.014 1.00 0.00 C +ATOM 623 O GLU 39 36.929 36.433 30.444 1.00 0.00 O +ATOM 624 N ASP 40 37.580 37.703 28.713 1.00 0.00 N +ATOM 625 H ASP 40 38.152 38.477 28.401 1.00 0.00 H +ATOM 626 CA ASP 40 36.731 37.006 27.712 1.00 0.00 C +ATOM 627 HA ASP 40 36.019 36.400 28.273 1.00 0.00 H +ATOM 628 CB ASP 40 35.856 37.950 26.869 1.00 0.00 C +ATOM 629 HB2 ASP 40 35.149 37.321 26.332 1.00 0.00 H +ATOM 630 HB3 ASP 40 35.268 38.580 27.529 1.00 0.00 H +ATOM 631 CG ASP 40 36.582 38.819 25.835 1.00 0.00 C +ATOM 632 OD1 ASP 40 36.945 39.969 26.162 1.00 0.00 O +ATOM 633 OD2 ASP 40 36.695 38.391 24.657 1.00 0.00 O +ATOM 634 C ASP 40 37.463 36.031 26.766 1.00 0.00 C +ATOM 635 O ASP 40 38.376 36.411 26.026 1.00 0.00 O +ATOM 636 N GLY 41 36.937 34.801 26.687 1.00 0.00 N +ATOM 637 H GLY 41 36.209 34.568 27.343 1.00 0.00 H +ATOM 638 CA GLY 41 37.260 33.807 25.655 1.00 0.00 C +ATOM 639 HA2 GLY 41 38.284 33.968 25.307 1.00 0.00 H +ATOM 640 HA3 GLY 41 37.212 32.809 26.099 1.00 0.00 H +ATOM 641 C GLY 41 36.319 33.835 24.428 1.00 0.00 C +ATOM 642 O GLY 41 35.379 34.632 24.345 1.00 0.00 O +ATOM 643 N GLU 42 36.572 32.930 23.480 1.00 0.00 N +ATOM 644 H GLU 42 37.303 32.262 23.657 1.00 0.00 H +ATOM 645 CA GLU 42 35.849 32.773 22.198 1.00 0.00 C +ATOM 646 HA GLU 42 35.155 33.605 22.083 1.00 0.00 H +ATOM 647 CB GLU 42 36.832 32.823 21.014 1.00 0.00 C +ATOM 648 HB2 GLU 42 37.410 31.899 20.996 1.00 0.00 H +ATOM 649 HB3 GLU 42 36.250 32.852 20.091 1.00 0.00 H +ATOM 650 CG GLU 42 37.808 34.026 21.041 1.00 0.00 C +ATOM 651 HG2 GLU 42 38.582 33.822 21.785 1.00 0.00 H +ATOM 652 HG3 GLU 42 38.302 34.092 20.068 1.00 0.00 H +ATOM 653 CD GLU 42 37.130 35.373 21.376 1.00 0.00 C +ATOM 654 OE1 GLU 42 35.967 35.572 20.965 1.00 0.00 O +ATOM 655 OE2 GLU 42 37.694 36.214 22.124 1.00 0.00 O +ATOM 656 C GLU 42 34.999 31.500 22.160 1.00 0.00 C +ATOM 657 O GLU 42 35.269 30.539 22.888 1.00 0.00 O +ATOM 658 N HIP 43 33.891 31.517 21.396 1.00 0.00 N +ATOM 659 H HIP 43 33.753 32.283 20.746 1.00 0.00 H +ATOM 660 CA HIP 43 32.711 30.745 21.803 1.00 0.00 C +ATOM 661 HA HIP 43 33.033 29.779 22.194 1.00 0.00 H +ATOM 662 CB HIP 43 32.123 31.562 22.981 1.00 0.00 C +ATOM 663 HB2 HIP 43 32.868 31.705 23.765 1.00 0.00 H +ATOM 664 HB3 HIP 43 31.824 32.549 22.633 1.00 0.00 H +ATOM 665 CG HIP 43 30.942 30.884 23.586 1.00 0.00 C +ATOM 666 ND1 HIP 43 29.754 30.730 22.930 1.00 0.00 N +ATOM 667 HD1 HIP 43 29.562 31.132 22.014 1.00 0.00 H +ATOM 668 CE1 HIP 43 29.202 29.607 23.386 1.00 0.00 C +ATOM 669 HE1 HIP 43 28.474 29.044 22.833 1.00 0.00 H +ATOM 670 NE2 HIP 43 29.897 29.146 24.436 1.00 0.00 N +ATOM 671 HE2 HIP 43 29.817 28.199 24.785 1.00 0.00 H +ATOM 672 CD2 HIP 43 31.021 29.930 24.558 1.00 0.00 C +ATOM 673 HD2 HIP 43 31.900 29.678 25.124 1.00 0.00 H +ATOM 674 C HIP 43 31.650 30.454 20.697 1.00 0.00 C +ATOM 675 O HIP 43 30.841 31.328 20.397 1.00 0.00 O +ATOM 676 N THR 44 31.523 29.200 20.247 1.00 0.00 N +ATOM 677 H THR 44 32.201 28.523 20.559 1.00 0.00 H +ATOM 678 CA THR 44 30.635 28.728 19.143 1.00 0.00 C +ATOM 679 HA THR 44 30.827 29.355 18.270 1.00 0.00 H +ATOM 680 CB THR 44 31.019 27.279 18.766 1.00 0.00 C +ATOM 681 HB THR 44 30.729 26.605 19.575 1.00 0.00 H +ATOM 682 CG2 THR 44 30.403 26.764 17.461 1.00 0.00 C +ATOM 683 HG21 THR 44 30.532 27.498 16.665 1.00 0.00 H +ATOM 684 HG22 THR 44 30.870 25.825 17.164 1.00 0.00 H +ATOM 685 HG23 THR 44 29.340 26.566 17.601 1.00 0.00 H +ATOM 686 OG1 THR 44 32.417 27.197 18.606 1.00 0.00 O +ATOM 687 HG1 THR 44 32.604 26.452 18.027 1.00 0.00 H +ATOM 688 C THR 44 29.114 28.795 19.411 1.00 0.00 C +ATOM 689 O THR 44 28.661 28.721 20.558 1.00 0.00 O +ATOM 690 N GLN 45 28.319 28.898 18.337 1.00 0.00 N +ATOM 691 H GLN 45 28.789 29.017 17.446 1.00 0.00 H +ATOM 692 CA GLN 45 26.865 29.110 18.294 1.00 0.00 C +ATOM 693 HA GLN 45 26.462 28.962 19.295 1.00 0.00 H +ATOM 694 CB GLN 45 26.599 30.578 17.884 1.00 0.00 C +ATOM 695 HB2 GLN 45 25.572 30.804 18.169 1.00 0.00 H +ATOM 696 HB3 GLN 45 27.242 31.234 18.473 1.00 0.00 H +ATOM 697 CG GLN 45 26.741 30.947 16.382 1.00 0.00 C +ATOM 698 HG2 GLN 45 26.052 30.342 15.794 1.00 0.00 H +ATOM 699 HG3 GLN 45 26.425 31.983 16.257 1.00 0.00 H +ATOM 700 CD GLN 45 28.143 30.823 15.768 1.00 0.00 C +ATOM 701 OE1 GLN 45 29.158 30.708 16.436 1.00 0.00 O +ATOM 702 NE2 GLN 45 28.276 30.835 14.462 1.00 0.00 N +ATOM 703 HE21 GLN 45 29.214 30.785 14.109 1.00 0.00 H +ATOM 704 HE22 GLN 45 27.485 30.864 13.826 1.00 0.00 H +ATOM 705 C GLN 45 26.106 28.148 17.353 1.00 0.00 C +ATOM 706 O GLN 45 26.651 27.691 16.350 1.00 0.00 O +ATOM 707 N ASP 46 24.816 27.938 17.631 1.00 0.00 N +ATOM 708 H ASP 46 24.469 28.232 18.538 1.00 0.00 H +ATOM 709 CA ASP 46 23.806 27.349 16.739 1.00 0.00 C +ATOM 710 HA ASP 46 24.147 27.428 15.708 1.00 0.00 H +ATOM 711 CB ASP 46 23.590 25.860 17.075 1.00 0.00 C +ATOM 712 HB2 ASP 46 24.463 25.284 16.756 1.00 0.00 H +ATOM 713 HB3 ASP 46 23.496 25.765 18.157 1.00 0.00 H +ATOM 714 CG ASP 46 22.341 25.292 16.395 1.00 0.00 C +ATOM 715 OD1 ASP 46 21.515 24.680 17.113 1.00 0.00 O +ATOM 716 OD2 ASP 46 22.135 25.545 15.195 1.00 0.00 O +ATOM 717 C ASP 46 22.471 28.108 16.864 1.00 0.00 C +ATOM 718 O ASP 46 22.025 28.431 17.966 1.00 0.00 O +ATOM 719 N ASP 47 21.809 28.361 15.735 1.00 0.00 N +ATOM 720 H ASP 47 22.178 27.953 14.884 1.00 0.00 H +ATOM 721 CA ASP 47 20.481 28.990 15.695 1.00 0.00 C +ATOM 722 HA ASP 47 20.396 29.652 16.550 1.00 0.00 H +ATOM 723 CB ASP 47 20.358 29.872 14.438 1.00 0.00 C +ATOM 724 HB2 ASP 47 21.220 30.541 14.390 1.00 0.00 H +ATOM 725 HB3 ASP 47 20.363 29.240 13.547 1.00 0.00 H +ATOM 726 CG ASP 47 19.084 30.708 14.499 1.00 0.00 C +ATOM 727 OD1 ASP 47 18.127 30.409 13.761 1.00 0.00 O +ATOM 728 OD2 ASP 47 18.939 31.541 15.419 1.00 0.00 O +ATOM 729 C ASP 47 19.313 27.985 15.776 1.00 0.00 C +ATOM 730 O ASP 47 18.260 28.318 16.326 1.00 0.00 O +ATOM 731 N ALA 48 19.476 26.741 15.304 1.00 0.00 N +ATOM 732 H ALA 48 20.408 26.439 15.014 1.00 0.00 H +ATOM 733 CA ALA 48 18.394 25.746 15.250 1.00 0.00 C +ATOM 734 HA ALA 48 17.536 26.176 14.732 1.00 0.00 H +ATOM 735 CB ALA 48 18.895 24.541 14.445 1.00 0.00 C +ATOM 736 HB1 ALA 48 19.748 24.085 14.950 1.00 0.00 H +ATOM 737 HB2 ALA 48 18.099 23.805 14.350 1.00 0.00 H +ATOM 738 HB3 ALA 48 19.206 24.861 13.450 1.00 0.00 H +ATOM 739 C ALA 48 17.916 25.322 16.650 1.00 0.00 C +ATOM 740 O ALA 48 16.721 25.152 16.897 1.00 0.00 O +ATOM 741 N THR 49 18.847 25.199 17.595 1.00 0.00 N +ATOM 742 H THR 49 19.823 25.180 17.290 1.00 0.00 H +ATOM 743 CA THR 49 18.582 25.048 19.034 1.00 0.00 C +ATOM 744 HA THR 49 17.557 24.704 19.161 1.00 0.00 H +ATOM 745 CB THR 49 19.520 23.996 19.644 1.00 0.00 C +ATOM 746 HB THR 49 19.269 23.888 20.697 1.00 0.00 H +ATOM 747 CG2 THR 49 19.421 22.621 18.993 1.00 0.00 C +ATOM 748 HG21 THR 49 19.747 22.665 17.954 1.00 0.00 H +ATOM 749 HG22 THR 49 20.077 21.947 19.538 1.00 0.00 H +ATOM 750 HG23 THR 49 18.398 22.254 19.040 1.00 0.00 H +ATOM 751 OG1 THR 49 20.859 24.396 19.551 1.00 0.00 O +ATOM 752 HG1 THR 49 21.108 24.393 18.591 1.00 0.00 H +ATOM 753 C THR 49 18.705 26.359 19.819 1.00 0.00 C +ATOM 754 O THR 49 18.601 26.347 21.047 1.00 0.00 O +ATOM 755 N LYS 50 18.935 27.492 19.139 1.00 0.00 N +ATOM 756 H LYS 50 18.973 27.403 18.132 1.00 0.00 H +ATOM 757 CA LYS 50 19.167 28.835 19.712 1.00 0.00 C +ATOM 758 HA LYS 50 19.597 29.451 18.919 1.00 0.00 H +ATOM 759 CB LYS 50 17.826 29.468 20.157 1.00 0.00 C +ATOM 760 HB2 LYS 50 17.370 28.808 20.900 1.00 0.00 H +ATOM 761 HB3 LYS 50 18.015 30.425 20.646 1.00 0.00 H +ATOM 762 CG LYS 50 16.794 29.705 19.037 1.00 0.00 C +ATOM 763 HG2 LYS 50 16.716 28.820 18.405 1.00 0.00 H +ATOM 764 HG3 LYS 50 15.824 29.873 19.507 1.00 0.00 H +ATOM 765 CD LYS 50 17.127 30.944 18.184 1.00 0.00 C +ATOM 766 HD2 LYS 50 17.102 31.820 18.837 1.00 0.00 H +ATOM 767 HD3 LYS 50 18.129 30.854 17.760 1.00 0.00 H +ATOM 768 CE LYS 50 16.090 31.145 17.073 1.00 0.00 C +ATOM 769 HE2 LYS 50 15.096 30.898 17.457 1.00 0.00 H +ATOM 770 HE3 LYS 50 16.103 32.201 16.787 1.00 0.00 H +ATOM 771 NZ LYS 50 16.421 30.345 15.873 1.00 0.00 N +ATOM 772 HZ1 LYS 50 16.767 29.414 16.087 1.00 0.00 H +ATOM 773 HZ2 LYS 50 15.699 30.310 15.174 1.00 0.00 H +ATOM 774 HZ3 LYS 50 17.223 30.766 15.390 1.00 0.00 H +ATOM 775 C LYS 50 20.222 28.825 20.831 1.00 0.00 C +ATOM 776 O LYS 50 20.055 29.510 21.843 1.00 0.00 O +ATOM 777 N THR 51 21.259 27.993 20.691 1.00 0.00 N +ATOM 778 H THR 51 21.409 27.592 19.762 1.00 0.00 H +ATOM 779 CA THR 51 22.172 27.599 21.771 1.00 0.00 C +ATOM 780 HA THR 51 21.917 28.210 22.629 1.00 0.00 H +ATOM 781 CB THR 51 21.970 26.124 22.200 1.00 0.00 C +ATOM 782 HB THR 51 22.136 25.481 21.351 1.00 0.00 H +ATOM 783 CG2 THR 51 22.951 25.655 23.296 1.00 0.00 C +ATOM 784 HG21 THR 51 22.956 26.297 24.162 1.00 0.00 H +ATOM 785 HG22 THR 51 22.722 24.643 23.608 1.00 0.00 H +ATOM 786 HG23 THR 51 23.956 25.620 22.870 1.00 0.00 H +ATOM 787 OG1 THR 51 20.670 25.917 22.733 1.00 0.00 O +ATOM 788 HG1 THR 51 20.030 26.045 22.006 1.00 0.00 H +ATOM 789 C THR 51 23.652 27.888 21.483 1.00 0.00 C +ATOM 790 O THR 51 24.206 27.618 20.424 1.00 0.00 O +ATOM 791 N PHE 52 24.319 28.422 22.500 1.00 0.00 N +ATOM 792 H PHE 52 23.768 28.734 23.281 1.00 0.00 H +ATOM 793 CA PHE 52 25.768 28.588 22.617 1.00 0.00 C +ATOM 794 HA PHE 52 26.209 28.718 21.624 1.00 0.00 H +ATOM 795 CB PHE 52 25.934 29.876 23.433 1.00 0.00 C +ATOM 796 HB2 PHE 52 25.158 29.901 24.199 1.00 0.00 H +ATOM 797 HB3 PHE 52 26.852 29.852 24.017 1.00 0.00 H +ATOM 798 CG PHE 52 25.885 31.198 22.680 1.00 0.00 C +ATOM 799 CD1 PHE 52 25.012 32.221 23.103 1.00 0.00 C +ATOM 800 HD1 PHE 52 24.320 32.041 23.903 1.00 0.00 H +ATOM 801 CE1 PHE 52 25.045 33.487 22.491 1.00 0.00 C +ATOM 802 HE1 PHE 52 24.379 34.268 22.818 1.00 0.00 H +ATOM 803 CZ PHE 52 25.956 33.741 21.454 1.00 0.00 C +ATOM 804 HZ PHE 52 25.988 34.712 20.988 1.00 0.00 H +ATOM 805 CE2 PHE 52 26.810 32.725 21.004 1.00 0.00 C +ATOM 806 HE2 PHE 52 27.499 32.922 20.194 1.00 0.00 H +ATOM 807 CD2 PHE 52 26.762 31.458 21.608 1.00 0.00 C +ATOM 808 HD2 PHE 52 27.415 30.692 21.242 1.00 0.00 H +ATOM 809 C PHE 52 26.431 27.347 23.282 1.00 0.00 C +ATOM 810 O PHE 52 26.004 26.944 24.366 1.00 0.00 O +ATOM 811 N THR 53 27.533 26.805 22.728 1.00 0.00 N +ATOM 812 H THR 53 27.815 27.125 21.802 1.00 0.00 H +ATOM 813 CA THR 53 28.350 25.688 23.289 1.00 0.00 C +ATOM 814 HA THR 53 28.083 25.538 24.333 1.00 0.00 H +ATOM 815 CB THR 53 28.074 24.368 22.548 1.00 0.00 C +ATOM 816 HB THR 53 28.722 23.593 22.958 1.00 0.00 H +ATOM 817 CG2 THR 53 26.632 23.889 22.679 1.00 0.00 C +ATOM 818 HG21 THR 53 25.960 24.557 22.139 1.00 0.00 H +ATOM 819 HG22 THR 53 26.550 22.885 22.263 1.00 0.00 H +ATOM 820 HG23 THR 53 26.352 23.855 23.730 1.00 0.00 H +ATOM 821 OG1 THR 53 28.366 24.524 21.181 1.00 0.00 O +ATOM 822 HG1 THR 53 28.124 23.708 20.725 1.00 0.00 H +ATOM 823 C THR 53 29.872 25.956 23.241 1.00 0.00 C +ATOM 824 O THR 53 30.300 26.968 22.690 1.00 0.00 O +ATOM 825 N MET 54 30.713 25.105 23.856 1.00 0.00 N +ATOM 826 H MET 54 30.334 24.273 24.286 1.00 0.00 H +ATOM 827 CA MET 54 32.182 25.105 23.663 1.00 0.00 C +ATOM 828 HA MET 54 32.446 25.938 23.009 1.00 0.00 H +ATOM 829 CB MET 54 32.941 25.336 24.987 1.00 0.00 C +ATOM 830 HB2 MET 54 33.969 25.599 24.737 1.00 0.00 H +ATOM 831 HB3 MET 54 32.509 26.192 25.507 1.00 0.00 H +ATOM 832 CG MET 54 32.985 24.135 25.949 1.00 0.00 C +ATOM 833 HG2 MET 54 31.992 23.991 26.371 1.00 0.00 H +ATOM 834 HG3 MET 54 33.253 23.231 25.406 1.00 0.00 H +ATOM 835 SD MET 54 34.168 24.322 27.314 1.00 0.00 S +ATOM 836 CE MET 54 35.724 23.824 26.523 1.00 0.00 C +ATOM 837 HE1 MET 54 35.888 24.409 25.619 1.00 0.00 H +ATOM 838 HE2 MET 54 36.551 23.987 27.212 1.00 0.00 H +ATOM 839 HE3 MET 54 35.680 22.766 26.267 1.00 0.00 H +ATOM 840 C MET 54 32.662 23.829 22.946 1.00 0.00 C +ATOM 841 O MET 54 31.929 22.843 22.877 1.00 0.00 O +ATOM 842 N ALA 55 33.892 23.859 22.423 1.00 0.00 N +ATOM 843 H ALA 55 34.450 24.686 22.561 1.00 0.00 H +ATOM 844 CA ALA 55 34.554 22.718 21.782 1.00 0.00 C +ATOM 845 HA ALA 55 33.844 22.246 21.100 1.00 0.00 H +ATOM 846 CB ALA 55 35.732 23.266 20.959 1.00 0.00 C +ATOM 847 HB1 ALA 55 36.461 23.734 21.623 1.00 0.00 H +ATOM 848 HB2 ALA 55 36.219 22.451 20.421 1.00 0.00 H +ATOM 849 HB3 ALA 55 35.371 24.000 20.235 1.00 0.00 H +ATOM 850 C ALA 55 35.017 21.628 22.779 1.00 0.00 C +ATOM 851 O ALA 55 35.021 21.847 23.989 1.00 0.00 O +ATOM 852 N GLU 56 35.431 20.479 22.234 1.00 0.00 N +ATOM 853 H GLU 56 35.452 20.421 21.231 1.00 0.00 H +ATOM 854 CA GLU 56 36.104 19.352 22.911 1.00 0.00 C +ATOM 855 HA GLU 56 36.199 19.575 23.974 1.00 0.00 H +ATOM 856 CB GLU 56 35.238 18.076 22.755 1.00 0.00 C +ATOM 857 HB2 GLU 56 34.213 18.295 23.051 1.00 0.00 H +ATOM 858 HB3 GLU 56 35.204 17.849 21.688 1.00 0.00 H +ATOM 859 CG GLU 56 35.736 16.811 23.492 1.00 0.00 C +ATOM 860 HG2 GLU 56 35.664 15.981 22.790 1.00 0.00 H +ATOM 861 HG3 GLU 56 36.794 16.912 23.710 1.00 0.00 H +ATOM 862 CD GLU 56 34.988 16.399 24.782 1.00 0.00 C +ATOM 863 OE1 GLU 56 35.523 15.530 25.516 1.00 0.00 O +ATOM 864 OE2 GLU 56 33.843 16.839 25.048 1.00 0.00 O +ATOM 865 C GLU 56 37.541 19.172 22.368 1.00 0.00 C +ATOM 866 O GLU 56 38.465 19.135 23.205 1.00 0.00 O +ATOM 867 OXT GLU 56 37.715 19.114 21.119 1.00 0.00 O +HETATM 868 ZN ZN1 57 25.930 31.773 29.258 1.00 0.00 Zn +HETATM 869 N AN1 58 27.732 32.212 30.227 1.00 0.00 N +HETATM 870 C AN1 58 30.202 32.363 31.070 1.00 0.00 C +HETATM 871 C1 AN1 58 28.815 32.265 30.631 1.00 0.00 C +HETATM 872 H AN1 58 30.258 32.653 32.123 1.00 0.00 H +HETATM 873 H1 AN1 58 30.745 33.103 30.462 1.00 0.00 H +HETATM 874 H2 AN1 58 30.695 31.392 30.947 1.00 0.00 H +HETATM 875 N1 AZI 59 30.363 29.082 28.864 1.00 0.00 N +HETATM 876 N2 AZI 59 29.718 29.024 29.896 1.00 0.00 N +HETATM 877 N3 AZI 59 29.034 28.987 30.964 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 68 73 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 868 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 121 122 126 +CONECT 121 120 +CONECT 122 125 120 123 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 127 129 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 118 132 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 140 142 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 139 144 143 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 159 156 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 197 189 +CONECT 188 187 +CONECT 189 187 190 191 192 +CONECT 190 189 +CONECT 191 189 +CONECT 192 189 193 194 +CONECT 193 192 +CONECT 194 192 196 195 +CONECT 195 194 +CONECT 196 194 +CONECT 197 187 198 199 +CONECT 198 197 +CONECT 199 197 201 200 +CONECT 200 199 +CONECT 201 218 199 203 202 +CONECT 202 201 +CONECT 203 206 201 204 205 +CONECT 204 203 +CONECT 205 203 +CONECT 206 207 216 203 +CONECT 207 209 208 206 +CONECT 208 207 +CONECT 209 210 211 207 +CONECT 210 209 +CONECT 211 212 209 214 +CONECT 212 213 211 +CONECT 213 212 +CONECT 214 211 215 216 +CONECT 215 214 +CONECT 216 214 206 217 +CONECT 217 216 +CONECT 218 219 220 201 +CONECT 219 218 +CONECT 220 222 218 221 +CONECT 221 220 +CONECT 222 223 240 224 220 +CONECT 223 222 +CONECT 224 227 222 225 226 +CONECT 225 224 +CONECT 226 224 +CONECT 227 229 228 230 224 +CONECT 228 227 +CONECT 229 227 +CONECT 230 231 227 232 233 +CONECT 231 230 +CONECT 232 230 +CONECT 233 230 235 236 234 +CONECT 234 233 +CONECT 235 233 +CONECT 236 239 233 237 238 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 241 222 242 +CONECT 241 240 +CONECT 242 240 244 243 +CONECT 243 242 +CONECT 244 247 242 245 246 +CONECT 245 244 +CONECT 246 244 +CONECT 247 248 249 244 +CONECT 248 247 +CONECT 249 251 247 250 +CONECT 250 249 +CONECT 251 253 252 263 249 +CONECT 252 251 +CONECT 253 259 254 255 251 +CONECT 254 253 +CONECT 255 257 253 256 258 +CONECT 256 255 +CONECT 257 255 +CONECT 258 255 +CONECT 259 261 260 262 253 +CONECT 260 259 +CONECT 261 259 +CONECT 262 259 +CONECT 263 265 251 264 +CONECT 264 263 +CONECT 265 275 266 263 +CONECT 266 267 265 276 269 +CONECT 267 268 282 266 +CONECT 268 267 +CONECT 269 266 270 277 278 +CONECT 270 271 272 269 +CONECT 271 274 280 270 +CONECT 272 273 270 279 +CONECT 273 274 281 272 +CONECT 274 868 271 273 +CONECT 275 265 +CONECT 276 266 +CONECT 277 269 +CONECT 278 269 +CONECT 279 272 +CONECT 280 271 +CONECT 281 273 +CONECT 282 284 267 283 +CONECT 283 282 +CONECT 284 285 286 294 282 +CONECT 285 284 +CONECT 286 287 288 284 292 +CONECT 287 286 +CONECT 288 291 290 286 289 +CONECT 289 288 +CONECT 290 288 +CONECT 291 288 +CONECT 292 286 293 +CONECT 293 292 +CONECT 294 296 284 295 +CONECT 295 294 +CONECT 296 306 297 294 +CONECT 297 298 300 296 307 +CONECT 298 299 313 297 +CONECT 299 298 +CONECT 300 308 309 297 301 +CONECT 301 300 302 303 +CONECT 302 311 301 305 +CONECT 303 301 310 304 +CONECT 304 305 303 312 +CONECT 305 302 868 304 +CONECT 306 296 +CONECT 307 297 +CONECT 308 300 +CONECT 309 300 +CONECT 310 303 +CONECT 311 302 +CONECT 312 304 +CONECT 313 315 298 314 +CONECT 314 313 +CONECT 315 326 316 313 317 +CONECT 316 315 +CONECT 317 315 320 319 318 +CONECT 318 317 +CONECT 319 317 +CONECT 320 323 322 317 321 +CONECT 321 320 +CONECT 322 320 +CONECT 323 324 325 320 +CONECT 324 323 +CONECT 325 323 +CONECT 326 328 327 315 +CONECT 327 326 +CONECT 328 330 329 326 +CONECT 329 328 +CONECT 330 336 332 331 328 +CONECT 331 330 +CONECT 332 334 333 330 335 +CONECT 333 332 +CONECT 334 332 +CONECT 335 332 +CONECT 336 338 337 330 +CONECT 337 336 +CONECT 338 340 339 336 +CONECT 339 338 +CONECT 340 352 342 341 338 +CONECT 341 340 +CONECT 342 343 348 340 344 +CONECT 343 342 +CONECT 344 342 346 347 345 +CONECT 345 344 +CONECT 346 344 +CONECT 347 344 +CONECT 348 349 350 342 351 +CONECT 349 348 +CONECT 350 348 +CONECT 351 348 +CONECT 352 353 354 340 +CONECT 353 352 +CONECT 354 356 352 355 +CONECT 355 354 +CONECT 356 358 357 364 354 +CONECT 357 356 +CONECT 358 361 359 360 356 +CONECT 359 358 +CONECT 360 358 +CONECT 361 362 363 358 +CONECT 362 361 +CONECT 363 361 +CONECT 364 356 366 365 +CONECT 365 364 +CONECT 366 367 368 364 +CONECT 367 366 +CONECT 368 370 366 383 369 +CONECT 369 368 +CONECT 370 372 371 373 368 +CONECT 371 370 +CONECT 372 370 +CONECT 373 379 370 375 374 +CONECT 374 373 +CONECT 375 376 373 377 378 +CONECT 376 375 +CONECT 377 375 +CONECT 378 375 +CONECT 379 382 380 381 373 +CONECT 380 379 +CONECT 381 379 +CONECT 382 379 +CONECT 383 385 368 384 +CONECT 384 383 +CONECT 385 386 387 383 +CONECT 386 385 +CONECT 387 389 385 388 393 +CONECT 388 387 +CONECT 389 392 390 391 387 +CONECT 390 389 +CONECT 391 389 +CONECT 392 389 +CONECT 393 387 394 395 +CONECT 394 393 +CONECT 395 393 396 397 +CONECT 396 395 +CONECT 397 395 398 399 408 +CONECT 398 397 +CONECT 399 402 400 397 401 +CONECT 400 399 +CONECT 401 399 +CONECT 402 403 404 405 399 +CONECT 403 402 +CONECT 404 402 +CONECT 405 402 407 406 +CONECT 406 405 +CONECT 407 405 +CONECT 408 397 410 409 +CONECT 409 408 +CONECT 410 411 408 412 +CONECT 411 410 +CONECT 412 410 414 418 413 +CONECT 413 412 +CONECT 414 415 417 412 416 +CONECT 415 414 +CONECT 416 414 +CONECT 417 414 +CONECT 418 420 412 419 +CONECT 419 418 +CONECT 420 421 422 418 +CONECT 421 420 +CONECT 422 424 420 423 433 +CONECT 423 422 +CONECT 424 425 426 427 422 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 424 429 428 +CONECT 428 427 +CONECT 429 427 +CONECT 430 432 431 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 422 435 434 +CONECT 434 433 +CONECT 435 436 433 437 +CONECT 436 435 +CONECT 437 435 439 438 455 +CONECT 438 437 +CONECT 439 442 440 441 437 +CONECT 440 439 +CONECT 441 439 +CONECT 442 444 445 443 439 +CONECT 443 442 +CONECT 444 442 +CONECT 445 448 446 447 442 +CONECT 446 445 +CONECT 447 445 +CONECT 448 451 450 449 445 +CONECT 449 448 +CONECT 450 448 +CONECT 451 453 454 452 448 +CONECT 452 451 +CONECT 453 451 +CONECT 454 451 +CONECT 455 437 457 456 +CONECT 456 455 +CONECT 457 458 455 459 +CONECT 458 457 +CONECT 459 457 461 460 475 +CONECT 460 459 +CONECT 461 464 462 459 463 +CONECT 462 461 +CONECT 463 461 +CONECT 464 465 473 461 +CONECT 465 467 466 464 +CONECT 466 465 +CONECT 467 468 469 465 +CONECT 468 467 +CONECT 469 470 467 471 +CONECT 470 469 +CONECT 471 469 472 473 +CONECT 472 471 +CONECT 473 471 464 474 +CONECT 474 473 +CONECT 475 477 459 476 +CONECT 476 475 +CONECT 477 478 479 475 +CONECT 478 477 +CONECT 479 481 477 489 480 +CONECT 480 479 +CONECT 481 482 487 483 479 +CONECT 482 481 +CONECT 483 485 481 486 484 +CONECT 484 483 +CONECT 485 483 +CONECT 486 483 +CONECT 487 488 481 +CONECT 488 487 +CONECT 489 491 479 490 +CONECT 490 489 +CONECT 491 492 493 489 +CONECT 492 491 +CONECT 493 495 491 494 511 +CONECT 494 493 +CONECT 495 498 496 497 493 +CONECT 496 495 +CONECT 497 495 +CONECT 498 501 500 499 495 +CONECT 499 498 +CONECT 500 498 +CONECT 501 504 502 503 498 +CONECT 502 501 +CONECT 503 501 +CONECT 504 506 505 507 501 +CONECT 505 504 +CONECT 506 504 +CONECT 507 509 504 510 508 +CONECT 508 507 +CONECT 509 507 +CONECT 510 507 +CONECT 511 493 513 512 +CONECT 512 511 +CONECT 513 514 511 515 +CONECT 514 513 +CONECT 515 513 516 517 521 +CONECT 516 515 +CONECT 517 520 515 518 519 +CONECT 518 517 +CONECT 519 517 +CONECT 520 517 +CONECT 521 515 523 522 +CONECT 522 521 +CONECT 523 524 521 525 +CONECT 524 523 +CONECT 525 523 545 527 526 +CONECT 526 525 +CONECT 527 530 525 529 528 +CONECT 528 527 +CONECT 529 527 +CONECT 530 531 532 533 527 +CONECT 531 530 +CONECT 532 530 +CONECT 533 536 530 535 534 +CONECT 534 533 +CONECT 535 533 +CONECT 536 537 538 533 +CONECT 537 536 +CONECT 538 539 536 542 +CONECT 539 540 541 538 +CONECT 540 539 +CONECT 541 539 +CONECT 542 538 544 543 +CONECT 543 542 +CONECT 544 542 +CONECT 545 547 525 546 +CONECT 546 545 +CONECT 547 548 549 545 +CONECT 548 547 +CONECT 549 551 547 555 550 +CONECT 550 549 +CONECT 551 552 554 553 549 +CONECT 552 551 +CONECT 553 551 +CONECT 554 551 +CONECT 555 549 557 556 +CONECT 556 555 +CONECT 557 558 555 559 +CONECT 558 557 +CONECT 559 561 557 560 569 +CONECT 560 559 +CONECT 561 564 562 563 559 +CONECT 562 561 +CONECT 563 561 +CONECT 564 566 565 561 +CONECT 565 564 +CONECT 566 567 568 564 +CONECT 567 566 +CONECT 568 566 +CONECT 569 559 571 570 +CONECT 570 569 +CONECT 571 572 569 573 +CONECT 572 571 +CONECT 573 571 575 574 581 +CONECT 574 573 +CONECT 575 578 576 573 577 +CONECT 576 575 +CONECT 577 575 +CONECT 578 580 579 575 +CONECT 579 578 +CONECT 580 578 +CONECT 581 573 583 582 +CONECT 582 581 +CONECT 583 584 581 585 +CONECT 584 583 +CONECT 585 583 587 600 586 +CONECT 586 585 +CONECT 587 589 588 585 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 596 591 592 +CONECT 591 590 +CONECT 592 590 593 594 595 +CONECT 593 592 +CONECT 594 592 +CONECT 595 592 +CONECT 596 597 599 598 590 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 +CONECT 600 602 585 601 +CONECT 601 600 +CONECT 602 603 604 600 +CONECT 603 602 +CONECT 604 607 602 606 605 +CONECT 605 604 +CONECT 606 604 +CONECT 607 609 608 604 +CONECT 608 607 +CONECT 609 611 610 607 +CONECT 610 609 +CONECT 611 622 612 613 609 +CONECT 612 611 +CONECT 613 615 611 614 616 +CONECT 614 613 +CONECT 615 613 +CONECT 616 613 617 619 618 +CONECT 617 616 +CONECT 618 616 +CONECT 619 621 616 620 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 611 +CONECT 623 622 +CONECT 624 626 625 622 +CONECT 625 624 +CONECT 626 634 628 627 624 +CONECT 627 626 +CONECT 628 631 629 630 626 +CONECT 629 628 +CONECT 630 628 +CONECT 631 633 632 628 +CONECT 632 631 +CONECT 633 631 +CONECT 634 635 636 626 +CONECT 635 634 +CONECT 636 638 634 637 +CONECT 637 636 +CONECT 638 641 639 640 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 642 638 +CONECT 642 641 +CONECT 643 645 644 641 +CONECT 644 643 +CONECT 645 647 646 656 643 +CONECT 646 645 +CONECT 647 649 648 650 645 +CONECT 648 647 +CONECT 649 647 +CONECT 650 652 647 653 651 +CONECT 651 650 +CONECT 652 650 +CONECT 653 654 650 655 +CONECT 654 653 +CONECT 655 653 +CONECT 656 658 645 657 +CONECT 657 656 +CONECT 658 659 660 656 +CONECT 659 658 +CONECT 660 674 658 661 662 +CONECT 661 660 +CONECT 662 660 664 665 663 +CONECT 663 662 +CONECT 664 662 +CONECT 665 666 662 672 +CONECT 666 667 668 665 +CONECT 667 666 +CONECT 668 669 666 670 +CONECT 669 668 +CONECT 670 668 672 671 +CONECT 671 670 +CONECT 672 665 670 673 +CONECT 673 672 +CONECT 674 676 675 660 +CONECT 675 674 +CONECT 676 678 677 674 +CONECT 677 676 +CONECT 678 679 680 688 676 +CONECT 679 678 +CONECT 680 682 686 678 681 +CONECT 681 680 +CONECT 682 683 684 685 680 +CONECT 683 682 +CONECT 684 682 +CONECT 685 682 +CONECT 686 687 680 +CONECT 687 686 +CONECT 688 690 678 689 +CONECT 689 688 +CONECT 690 691 692 688 +CONECT 691 690 +CONECT 692 705 694 690 693 +CONECT 693 692 +CONECT 694 697 695 692 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 700 698 699 694 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 697 701 +CONECT 701 700 +CONECT 702 704 703 700 +CONECT 703 702 +CONECT 704 702 +CONECT 705 706 707 692 +CONECT 706 705 +CONECT 707 709 705 708 +CONECT 708 707 +CONECT 709 710 717 711 707 +CONECT 710 709 +CONECT 711 714 709 712 713 +CONECT 712 711 +CONECT 713 711 +CONECT 714 716 711 715 +CONECT 715 714 +CONECT 716 714 +CONECT 717 719 709 718 +CONECT 718 717 +CONECT 719 720 721 717 +CONECT 720 719 +CONECT 721 723 719 729 722 +CONECT 722 721 +CONECT 723 725 724 726 721 +CONECT 724 723 +CONECT 725 723 +CONECT 726 727 723 728 +CONECT 727 726 +CONECT 728 726 +CONECT 729 731 721 730 +CONECT 730 729 +CONECT 731 732 733 729 +CONECT 732 731 +CONECT 733 735 734 731 739 +CONECT 734 733 +CONECT 735 738 737 736 733 +CONECT 736 735 +CONECT 737 735 +CONECT 738 735 +CONECT 739 733 740 741 +CONECT 740 739 +CONECT 741 739 742 743 +CONECT 742 741 +CONECT 743 741 744 745 753 +CONECT 744 743 +CONECT 745 747 743 751 746 +CONECT 746 745 +CONECT 747 748 750 749 745 +CONECT 748 747 +CONECT 749 747 +CONECT 750 747 +CONECT 751 752 745 +CONECT 752 751 +CONECT 753 743 755 754 +CONECT 754 753 +CONECT 755 756 757 753 +CONECT 756 755 +CONECT 757 758 755 759 775 +CONECT 758 757 +CONECT 759 762 757 761 760 +CONECT 760 759 +CONECT 761 759 +CONECT 762 765 763 764 759 +CONECT 763 762 +CONECT 764 762 +CONECT 765 768 767 766 762 +CONECT 766 765 +CONECT 767 765 +CONECT 768 771 770 769 765 +CONECT 769 768 +CONECT 770 768 +CONECT 771 773 774 772 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 771 +CONECT 775 757 777 776 +CONECT 776 775 +CONECT 777 778 775 779 +CONECT 778 777 +CONECT 779 777 789 781 780 +CONECT 780 779 +CONECT 781 782 779 787 783 +CONECT 782 781 +CONECT 783 781 786 785 784 +CONECT 784 783 +CONECT 785 783 +CONECT 786 783 +CONECT 787 788 781 +CONECT 788 787 +CONECT 789 790 779 791 +CONECT 790 789 +CONECT 791 789 793 792 +CONECT 792 791 +CONECT 793 794 791 809 795 +CONECT 794 793 +CONECT 795 793 798 797 796 +CONECT 796 795 +CONECT 797 795 +CONECT 798 807 799 795 +CONECT 799 801 798 800 +CONECT 800 799 +CONECT 801 803 802 799 +CONECT 802 801 +CONECT 803 804 805 801 +CONECT 804 803 +CONECT 805 806 803 807 +CONECT 806 805 +CONECT 807 805 808 798 +CONECT 808 807 +CONECT 809 793 811 810 +CONECT 810 809 +CONECT 811 812 809 813 +CONECT 812 811 +CONECT 813 815 811 823 814 +CONECT 814 813 +CONECT 815 821 817 816 813 +CONECT 816 815 +CONECT 817 818 819 815 820 +CONECT 818 817 +CONECT 819 817 +CONECT 820 817 +CONECT 821 822 815 +CONECT 822 821 +CONECT 823 824 813 825 +CONECT 824 823 +CONECT 825 823 827 826 +CONECT 826 825 +CONECT 827 840 828 825 829 +CONECT 828 827 +CONECT 829 827 830 831 832 +CONECT 830 829 +CONECT 831 829 +CONECT 832 829 834 833 835 +CONECT 833 832 +CONECT 834 832 +CONECT 835 832 836 +CONECT 836 837 839 838 835 +CONECT 837 836 +CONECT 838 836 +CONECT 839 836 +CONECT 840 842 841 827 +CONECT 841 840 +CONECT 842 844 843 840 +CONECT 843 842 +CONECT 844 846 845 842 850 +CONECT 845 844 +CONECT 846 849 848 847 844 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 +CONECT 850 844 852 851 +CONECT 851 850 +CONECT 852 853 850 854 +CONECT 853 852 +CONECT 854 852 865 856 855 +CONECT 855 854 +CONECT 856 858 854 857 859 +CONECT 857 856 +CONECT 858 856 +CONECT 859 856 860 861 862 +CONECT 860 859 +CONECT 861 859 +CONECT 862 859 864 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 867 854 866 +CONECT 866 865 +CONECT 867 865 +CONECT 868 87 305 869 274 +CONECT 869 868 871 +CONECT 870 873 871 874 872 +CONECT 871 869 870 +CONECT 872 870 +CONECT 873 870 +CONECT 874 870 +CONECT 875 876 +CONECT 876 875 877 +CONECT 877 876 +MASTER 0 0 0 0 0 0 0 0 877 0 877 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_3_front_3.pdb b/tests/nsga2/intermediate_molecules/min_iter_3_front_3.pdb new file mode 100644 index 0000000..0f703bf --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_3_front_3.pdb @@ -0,0 +1,1745 @@ +COMPND fitness: -2.8843 83.41749999999979 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 56.210 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.610 37.835 23.460 1.00 0.00 N +ATOM 2 H1 MET 1 14.587 38.236 24.394 1.00 0.00 H +ATOM 3 H2 MET 1 13.812 38.148 22.935 1.00 0.00 H +ATOM 4 H3 MET 1 15.464 38.178 23.039 1.00 0.00 H +ATOM 5 CA MET 1 14.662 36.367 23.555 1.00 0.00 C +ATOM 6 HA MET 1 13.728 36.021 23.999 1.00 0.00 H +ATOM 7 CB MET 1 14.806 35.736 22.157 1.00 0.00 C +ATOM 8 HB2 MET 1 13.928 35.994 21.567 1.00 0.00 H +ATOM 9 HB3 MET 1 15.682 36.159 21.666 1.00 0.00 H +ATOM 10 CG MET 1 14.957 34.205 22.185 1.00 0.00 C +ATOM 11 HG2 MET 1 15.847 33.953 22.764 1.00 0.00 H +ATOM 12 HG3 MET 1 14.092 33.769 22.688 1.00 0.00 H +ATOM 13 SD MET 1 15.133 33.423 20.557 1.00 0.00 S +ATOM 14 CE MET 1 13.430 33.524 19.932 1.00 0.00 C +ATOM 15 HE1 MET 1 13.103 34.563 19.883 1.00 0.00 H +ATOM 16 HE2 MET 1 13.381 33.092 18.933 1.00 0.00 H +ATOM 17 HE3 MET 1 12.763 32.967 20.591 1.00 0.00 H +ATOM 18 C MET 1 15.802 35.945 24.478 1.00 0.00 C +ATOM 19 O MET 1 16.945 36.312 24.240 1.00 0.00 O +ATOM 20 N GLN 2 15.501 35.116 25.481 1.00 0.00 N +ATOM 21 H GLN 2 14.536 34.897 25.661 1.00 0.00 H +ATOM 22 CA GLN 2 16.493 34.445 26.330 1.00 0.00 C +ATOM 23 HA GLN 2 17.239 35.169 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 15.772 33.892 27.577 1.00 0.00 C +ATOM 25 HB2 GLN 2 14.850 33.401 27.264 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.383 33.136 28.064 1.00 0.00 H +ATOM 27 CG GLN 2 15.424 34.965 28.621 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.944 35.807 28.133 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.697 34.542 29.314 1.00 0.00 H +ATOM 30 CD GLN 2 16.606 35.446 29.461 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.750 35.034 29.311 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.365 36.275 30.448 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.141 36.537 31.027 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.429 36.623 30.586 1.00 0.00 H +ATOM 35 C GLN 2 17.242 33.339 25.554 1.00 0.00 C +ATOM 36 O GLN 2 16.895 32.159 25.641 1.00 0.00 O +ATOM 37 N TYR 3 18.267 33.710 24.779 1.00 0.00 N +ATOM 38 H TYR 3 18.507 34.698 24.761 1.00 0.00 H +ATOM 39 CA TYR 3 19.130 32.772 24.050 1.00 0.00 C +ATOM 40 HA TYR 3 18.508 32.164 23.394 1.00 0.00 H +ATOM 41 CB TYR 3 20.138 33.545 23.190 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.628 34.306 23.802 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.913 32.853 22.855 1.00 0.00 H +ATOM 44 CG TYR 3 19.537 34.200 21.959 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.394 33.447 20.777 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.704 32.411 20.758 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.869 34.045 19.616 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.784 33.476 18.703 1.00 0.00 H +ATOM 49 CZ TYR 3 18.472 35.400 19.642 1.00 0.00 C +ATOM 50 OH TYR 3 17.979 35.981 18.519 1.00 0.00 O +ATOM 51 HH TYR 3 17.916 35.355 17.795 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.600 36.150 20.830 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.290 37.185 20.841 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.136 35.550 21.987 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.235 36.130 22.896 1.00 0.00 H +ATOM 56 C TYR 3 19.865 31.833 25.021 1.00 0.00 C +ATOM 57 O TYR 3 20.356 32.276 26.061 1.00 0.00 O +ATOM 58 N LYS 4 19.933 30.534 24.705 1.00 0.00 N +ATOM 59 H LYS 4 19.658 30.251 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 20.470 29.488 25.599 1.00 0.00 C +ATOM 61 HA LYS 4 20.193 29.725 26.622 1.00 0.00 H +ATOM 62 CB LYS 4 19.857 28.117 25.237 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.784 28.034 24.153 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.538 27.331 25.568 1.00 0.00 H +ATOM 65 CG LYS 4 18.476 27.805 25.856 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.226 26.778 25.589 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.551 27.859 26.942 1.00 0.00 H +ATOM 68 CD LYS 4 17.329 28.710 25.376 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.488 29.726 25.728 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.350 28.733 24.285 1.00 0.00 H +ATOM 71 CE LYS 4 15.930 28.229 25.815 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.191 28.785 25.230 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.824 27.174 25.545 1.00 0.00 H +ATOM 74 NZ LYS 4 15.640 28.425 27.266 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.696 29.397 27.534 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.693 28.146 27.503 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.250 27.898 27.886 1.00 0.00 H +ATOM 78 C LYS 4 22.000 29.450 25.582 1.00 0.00 C +ATOM 79 O LYS 4 22.635 29.697 24.563 1.00 0.00 O +HETATM 80 N HX1 5 22.614 29.087 26.706 1.00 0.00 N +HETATM 81 CA HX1 5 24.068 28.924 26.868 1.00 0.00 C +HETATM 82 C HX1 5 24.352 27.735 27.797 1.00 0.00 C +HETATM 83 O HX1 5 23.963 27.749 28.965 1.00 0.00 O +HETATM 84 CB HX1 5 24.686 30.249 27.361 1.00 0.00 C +HETATM 85 CG HX1 5 26.205 30.328 27.453 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.096 29.341 27.126 1.00 0.00 C +HETATM 87 ND1 HX1 5 26.899 31.425 27.989 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.188 31.059 27.927 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.345 29.815 27.484 1.00 0.00 N +HETATM 90 H HX1 5 22.036 28.964 27.535 1.00 0.00 H +HETATM 91 HA HX1 5 24.511 28.691 25.903 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.270 30.493 28.340 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.367 31.041 26.681 1.00 0.00 H +HETATM 94 HD2 HX1 5 26.901 28.351 26.753 1.00 0.00 H +HETATM 95 HE1 HX1 5 28.999 31.640 28.362 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.166 29.232 27.691 1.00 0.00 H +ATOM 97 N ILE 6 24.976 26.694 27.247 1.00 0.00 N +ATOM 98 H ILE 6 25.273 26.764 26.279 1.00 0.00 H +ATOM 99 CA ILE 6 25.416 25.484 27.957 1.00 0.00 C +ATOM 100 HA ILE 6 24.791 25.350 28.841 1.00 0.00 H +ATOM 101 CB ILE 6 25.219 24.234 27.066 1.00 0.00 C +ATOM 102 HB ILE 6 25.717 24.411 26.111 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.833 22.967 27.697 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.377 22.767 28.667 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.684 22.105 27.049 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.912 23.079 27.816 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.703 24.039 26.816 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.199 23.911 27.773 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.300 24.935 26.343 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.331 22.853 25.919 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.511 21.913 26.441 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.269 22.909 25.674 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.912 22.881 24.996 1.00 0.00 H +ATOM 114 C ILE 6 26.855 25.666 28.457 1.00 0.00 C +ATOM 115 O ILE 6 27.669 26.350 27.833 1.00 0.00 O +ATOM 116 N VAL 7 27.116 25.088 29.628 1.00 0.00 N +ATOM 117 H VAL 7 26.386 24.493 30.005 1.00 0.00 H +ATOM 118 CA VAL 7 28.247 25.361 30.522 1.00 0.00 C +ATOM 119 HA VAL 7 28.279 26.437 30.666 1.00 0.00 H +ATOM 120 CB VAL 7 27.910 24.707 31.877 1.00 0.00 C +ATOM 121 HB VAL 7 26.872 24.951 32.111 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.029 23.177 31.837 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.076 22.879 31.779 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.576 22.749 32.720 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.511 22.784 30.962 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.732 25.253 33.046 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.660 26.340 33.068 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.348 24.861 33.986 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.770 24.958 32.940 1.00 0.00 H +ATOM 130 C VAL 7 29.638 24.925 30.014 1.00 0.00 C +ATOM 131 O VAL 7 29.787 23.876 29.396 1.00 0.00 O +ATOM 132 N ARG 8 30.669 25.690 30.392 1.00 0.00 N +ATOM 133 H ARG 8 30.448 26.631 30.693 1.00 0.00 H +ATOM 134 CA ARG 8 32.095 25.295 30.376 1.00 0.00 C +ATOM 135 HA ARG 8 32.337 25.066 29.335 1.00 0.00 H +ATOM 136 CB ARG 8 33.001 26.478 30.815 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.031 26.191 30.597 1.00 0.00 H +ATOM 138 HB3 ARG 8 32.778 27.341 30.186 1.00 0.00 H +ATOM 139 CG ARG 8 32.964 26.926 32.298 1.00 0.00 C +ATOM 140 HG2 ARG 8 33.166 26.074 32.950 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.772 27.646 32.453 1.00 0.00 H +ATOM 142 CD ARG 8 31.641 27.598 32.706 1.00 0.00 C +ATOM 143 HD2 ARG 8 31.523 28.498 32.102 1.00 0.00 H +ATOM 144 HD3 ARG 8 30.811 26.937 32.492 1.00 0.00 H +ATOM 145 NE ARG 8 31.554 27.975 34.136 1.00 0.00 N +ATOM 146 HE ARG 8 31.477 28.963 34.328 1.00 0.00 H +ATOM 147 CZ ARG 8 31.360 27.181 35.177 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.436 25.880 35.096 1.00 0.00 N +ATOM 149 HH11 ARG 8 31.653 25.451 34.206 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.280 25.329 35.915 1.00 0.00 H +ATOM 151 NH2 ARG 8 31.059 27.706 36.329 1.00 0.00 N +ATOM 152 HH21 ARG 8 30.883 28.704 36.414 1.00 0.00 H +ATOM 153 HH22 ARG 8 30.972 27.170 37.183 1.00 0.00 H +ATOM 154 C ARG 8 32.399 24.032 31.197 1.00 0.00 C +ATOM 155 O ARG 8 31.989 23.928 32.359 1.00 0.00 O +ATOM 156 N GLY 9 33.235 23.149 30.643 1.00 0.00 N +ATOM 157 H GLY 9 33.483 23.302 29.677 1.00 0.00 H +ATOM 158 CA GLY 9 33.803 21.970 31.313 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.769 21.741 30.856 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.977 22.203 32.366 1.00 0.00 H +ATOM 161 C GLY 9 32.930 20.700 31.255 1.00 0.00 C +ATOM 162 O GLY 9 31.748 20.758 30.940 1.00 0.00 O +ATOM 163 N LYS 10 33.531 19.549 31.601 1.00 0.00 N +ATOM 164 H LYS 10 34.504 19.593 31.865 1.00 0.00 H +ATOM 165 CA LYS 10 32.919 18.202 31.470 1.00 0.00 C +ATOM 166 HA LYS 10 31.934 18.338 31.024 1.00 0.00 H +ATOM 167 CB LYS 10 33.740 17.354 30.479 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.240 18.008 29.765 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.509 16.801 31.019 1.00 0.00 H +ATOM 170 CG LYS 10 32.870 16.377 29.670 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.314 15.722 30.339 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.155 16.955 29.085 1.00 0.00 H +ATOM 173 CD LYS 10 33.734 15.532 28.729 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.372 16.192 28.137 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.363 14.862 29.315 1.00 0.00 H +ATOM 176 CE LYS 10 32.861 14.716 27.778 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.249 14.019 28.356 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.207 15.410 27.249 1.00 0.00 H +ATOM 179 NZ LYS 10 33.702 14.007 26.788 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.337 13.350 27.224 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.169 13.532 26.081 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.296 14.687 26.297 1.00 0.00 H +ATOM 183 C LYS 10 32.637 17.486 32.799 1.00 0.00 C +ATOM 184 O LYS 10 32.284 16.311 32.824 1.00 0.00 O +ATOM 185 N TRP 11 32.824 18.177 33.926 1.00 0.00 N +ATOM 186 H TRP 11 33.243 19.090 33.848 1.00 0.00 H +ATOM 187 CA TRP 11 32.126 17.892 35.182 1.00 0.00 C +ATOM 188 HA TRP 11 31.901 16.824 35.268 1.00 0.00 H +ATOM 189 CB TRP 11 33.036 18.283 36.357 1.00 0.00 C +ATOM 190 HB2 TRP 11 32.535 18.015 37.294 1.00 0.00 H +ATOM 191 HB3 TRP 11 33.950 17.689 36.296 1.00 0.00 H +ATOM 192 CG TRP 11 33.419 19.737 36.406 1.00 0.00 C +ATOM 193 CD1 TRP 11 32.861 20.665 37.216 1.00 0.00 C +ATOM 194 HD1 TRP 11 32.089 20.465 37.950 1.00 0.00 H +ATOM 195 NE1 TRP 11 33.403 21.907 36.943 1.00 0.00 N +ATOM 196 HE1 TRP 11 33.141 22.745 37.445 1.00 0.00 H +ATOM 197 CE2 TRP 11 34.318 21.848 35.912 1.00 0.00 C +ATOM 198 CZ2 TRP 11 35.085 22.819 35.250 1.00 0.00 C +ATOM 199 HZ2 TRP 11 35.003 23.862 35.519 1.00 0.00 H +ATOM 200 CH2 TRP 11 35.984 22.415 34.248 1.00 0.00 C +ATOM 201 HH2 TRP 11 36.605 23.145 33.744 1.00 0.00 H +ATOM 202 CZ3 TRP 11 36.107 21.052 33.924 1.00 0.00 C +ATOM 203 HZ3 TRP 11 36.838 20.745 33.183 1.00 0.00 H +ATOM 204 CE3 TRP 11 35.320 20.087 34.584 1.00 0.00 C +ATOM 205 HE3 TRP 11 35.461 19.041 34.352 1.00 0.00 H +ATOM 206 CD2 TRP 11 34.391 20.460 35.583 1.00 0.00 C +ATOM 207 C TRP 11 30.804 18.683 35.243 1.00 0.00 C +ATOM 208 O TRP 11 29.944 18.363 36.056 1.00 0.00 O +ATOM 209 N VAL 12 30.660 19.740 34.430 1.00 0.00 N +ATOM 210 H VAL 12 31.413 19.900 33.802 1.00 0.00 H +ATOM 211 CA VAL 12 29.415 20.530 34.220 1.00 0.00 C +ATOM 212 HA VAL 12 29.656 21.259 33.447 1.00 0.00 H +ATOM 213 CB VAL 12 29.101 21.349 35.518 1.00 0.00 C +ATOM 214 HB VAL 12 29.296 20.712 36.378 1.00 0.00 H +ATOM 215 CG1 VAL 12 27.725 21.975 35.716 1.00 0.00 C +ATOM 216 HG11 VAL 12 26.970 21.208 35.955 1.00 0.00 H +ATOM 217 HG12 VAL 12 27.751 22.645 36.588 1.00 0.00 H +ATOM 218 HG13 VAL 12 27.441 22.553 34.835 1.00 0.00 H +ATOM 219 CG2 VAL 12 30.126 22.530 35.519 1.00 0.00 C +ATOM 220 HG21 VAL 12 29.940 23.175 34.670 1.00 0.00 H +ATOM 221 HG22 VAL 12 30.055 23.143 36.414 1.00 0.00 H +ATOM 222 HG23 VAL 12 31.147 22.192 35.430 1.00 0.00 H +ATOM 223 C VAL 12 28.340 19.651 33.542 1.00 0.00 C +ATOM 224 O VAL 12 28.703 18.718 32.836 1.00 0.00 O +ATOM 225 N LYS 13 27.051 19.990 33.615 1.00 0.00 N +ATOM 226 H LYS 13 26.818 20.626 34.355 1.00 0.00 H +ATOM 227 CA LYS 13 26.031 19.654 32.590 1.00 0.00 C +ATOM 228 HA LYS 13 26.538 19.769 31.626 1.00 0.00 H +ATOM 229 CB LYS 13 25.592 18.175 32.709 1.00 0.00 C +ATOM 230 HB2 LYS 13 26.368 17.610 33.220 1.00 0.00 H +ATOM 231 HB3 LYS 13 24.698 18.118 33.320 1.00 0.00 H +ATOM 232 CG LYS 13 25.353 17.514 31.333 1.00 0.00 C +ATOM 233 HG2 LYS 13 24.456 17.931 30.874 1.00 0.00 H +ATOM 234 HG3 LYS 13 26.197 17.751 30.683 1.00 0.00 H +ATOM 235 CD LYS 13 25.238 15.981 31.410 1.00 0.00 C +ATOM 236 HD2 LYS 13 25.170 15.578 30.397 1.00 0.00 H +ATOM 237 HD3 LYS 13 26.145 15.589 31.878 1.00 0.00 H +ATOM 238 CE LYS 13 24.004 15.541 32.208 1.00 0.00 C +ATOM 239 HE2 LYS 13 23.955 16.153 33.114 1.00 0.00 H +ATOM 240 HE3 LYS 13 23.108 15.743 31.609 1.00 0.00 H +ATOM 241 NZ LYS 13 24.068 14.106 32.592 1.00 0.00 N +ATOM 242 HZ1 LYS 13 24.999 13.834 32.897 1.00 0.00 H +ATOM 243 HZ2 LYS 13 23.472 13.932 33.399 1.00 0.00 H +ATOM 244 HZ3 LYS 13 23.792 13.478 31.849 1.00 0.00 H +ATOM 245 C LYS 13 24.841 20.629 32.531 1.00 0.00 C +ATOM 246 O LYS 13 23.849 20.366 31.856 1.00 0.00 O +ATOM 247 N GLY 14 24.939 21.740 33.268 1.00 0.00 N +ATOM 248 H GLY 14 25.799 21.915 33.754 1.00 0.00 H +ATOM 249 CA GLY 14 23.872 22.731 33.398 1.00 0.00 C +ATOM 250 HA2 GLY 14 22.917 22.216 33.519 1.00 0.00 H +ATOM 251 HA3 GLY 14 24.041 23.329 34.294 1.00 0.00 H +ATOM 252 C GLY 14 23.740 23.693 32.199 1.00 0.00 C +ATOM 253 O GLY 14 24.623 23.800 31.347 1.00 0.00 O +ATOM 254 N VAL 15 22.630 24.433 32.175 1.00 0.00 N +ATOM 255 H VAL 15 21.967 24.310 32.924 1.00 0.00 H +ATOM 256 CA VAL 15 22.258 25.391 31.125 1.00 0.00 C +ATOM 257 HA VAL 15 23.156 25.664 30.577 1.00 0.00 H +ATOM 258 CB VAL 15 21.291 24.727 30.116 1.00 0.00 C +ATOM 259 HB VAL 15 21.791 23.839 29.715 1.00 0.00 H +ATOM 260 CG1 VAL 15 19.966 24.264 30.749 1.00 0.00 C +ATOM 261 HG11 VAL 15 19.406 25.113 31.134 1.00 0.00 H +ATOM 262 HG12 VAL 15 19.365 23.754 29.993 1.00 0.00 H +ATOM 263 HG13 VAL 15 20.160 23.557 31.554 1.00 0.00 H +ATOM 264 CG2 VAL 15 20.963 25.647 28.933 1.00 0.00 C +ATOM 265 HG21 VAL 15 21.883 26.004 28.474 1.00 0.00 H +ATOM 266 HG22 VAL 15 20.402 25.080 28.186 1.00 0.00 H +ATOM 267 HG23 VAL 15 20.358 26.490 29.258 1.00 0.00 H +ATOM 268 C VAL 15 21.686 26.658 31.751 1.00 0.00 C +ATOM 269 O VAL 15 20.993 26.607 32.770 1.00 0.00 O +HETATM 270 N HY1 16 21.983 27.814 31.152 1.00 0.00 N +HETATM 271 CA HY1 16 21.415 29.132 31.476 1.00 0.00 C +HETATM 272 C HY1 16 21.134 29.908 30.177 1.00 0.00 C +HETATM 273 O HY1 16 21.275 29.361 29.086 1.00 0.00 O +HETATM 274 CB HY1 16 22.356 29.875 32.450 1.00 0.00 C +HETATM 275 CG HY1 16 23.709 30.229 31.878 1.00 0.00 C +HETATM 276 CD2 HY1 16 24.068 31.431 31.324 1.00 0.00 C +HETATM 277 ND1 HY1 16 24.813 29.410 31.817 1.00 0.00 N +HETATM 278 CE1 HY1 16 25.816 30.121 31.269 1.00 0.00 C +HETATM 279 NE2 HY1 16 25.412 31.360 30.935 1.00 0.00 N +HETATM 280 H HY1 16 22.553 27.772 30.305 1.00 0.00 H +HETATM 281 HA HY1 16 20.458 28.981 31.988 1.00 0.00 H +HETATM 282 HB2 HY1 16 21.869 30.793 32.788 1.00 0.00 H +HETATM 283 HB3 HY1 16 22.504 29.262 33.342 1.00 0.00 H +HETATM 284 HD1 HY1 16 24.881 28.463 32.165 1.00 0.00 H +HETATM 285 HD2 HY1 16 23.428 32.300 31.222 1.00 0.00 H +HETATM 286 HE1 HY1 16 26.831 29.752 31.127 1.00 0.00 H +ATOM 287 N THR 17 20.733 31.171 30.282 1.00 0.00 N +ATOM 288 H THR 17 20.606 31.590 31.189 1.00 0.00 H +ATOM 289 CA THR 17 20.339 32.027 29.148 1.00 0.00 C +ATOM 290 HA THR 17 20.769 31.599 28.239 1.00 0.00 H +ATOM 291 CB THR 17 18.804 32.054 28.997 1.00 0.00 C +ATOM 292 HB THR 17 18.548 32.701 28.154 1.00 0.00 H +ATOM 293 CG2 THR 17 18.153 30.699 28.714 1.00 0.00 C +ATOM 294 HG21 THR 17 18.358 29.982 29.502 1.00 0.00 H +ATOM 295 HG22 THR 17 17.081 30.790 28.628 1.00 0.00 H +ATOM 296 HG23 THR 17 18.516 30.287 27.783 1.00 0.00 H +ATOM 297 OG1 THR 17 18.212 32.553 30.159 1.00 0.00 O +ATOM 298 HG1 THR 17 18.144 33.518 30.025 1.00 0.00 H +ATOM 299 C THR 17 20.886 33.446 29.236 1.00 0.00 C +ATOM 300 O THR 17 21.350 33.861 30.295 1.00 0.00 O +HETATM 301 N HY2 18 20.813 34.187 28.127 1.00 0.00 N +HETATM 302 CA HY2 18 21.081 35.625 28.066 1.00 0.00 C +HETATM 303 C HY2 18 19.976 36.319 27.265 1.00 0.00 C +HETATM 304 O HY2 18 19.648 35.866 26.170 1.00 0.00 O +HETATM 305 CB HY2 18 22.427 35.918 27.401 1.00 0.00 C +HETATM 306 CG HY2 18 23.623 35.439 28.194 1.00 0.00 C +HETATM 307 CD2 HY2 18 24.155 34.177 28.162 1.00 0.00 C +HETATM 308 ND1 HY2 18 24.312 36.145 29.158 1.00 0.00 N +HETATM 309 CE1 HY2 18 25.247 35.326 29.676 1.00 0.00 C +HETATM 310 NE2 HY2 18 25.185 34.110 29.103 1.00 0.00 N +HETATM 311 H HY2 18 20.458 33.740 27.282 1.00 0.00 H +HETATM 312 HA HY2 18 21.088 36.044 29.084 1.00 0.00 H +HETATM 313 HB2 HY2 18 22.454 35.451 26.408 1.00 0.00 H +HETATM 314 HB3 HY2 18 22.525 37.001 27.258 1.00 0.00 H +HETATM 315 HD1 HY2 18 24.160 37.108 29.430 1.00 0.00 H +HETATM 316 HD2 HY2 18 23.816 33.363 27.535 1.00 0.00 H +HETATM 317 HE1 HY2 18 25.945 35.606 30.456 1.00 0.00 H +ATOM 318 N GLU 19 19.430 37.417 27.787 1.00 0.00 N +ATOM 319 H GLU 19 19.758 37.740 28.682 1.00 0.00 H +ATOM 320 CA GLU 19 18.419 38.226 27.104 1.00 0.00 C +ATOM 321 HA GLU 19 17.699 37.546 26.656 1.00 0.00 H +ATOM 322 CB GLU 19 17.705 39.102 28.147 1.00 0.00 C +ATOM 323 HB2 GLU 19 17.377 38.469 28.971 1.00 0.00 H +ATOM 324 HB3 GLU 19 18.414 39.828 28.557 1.00 0.00 H +ATOM 325 CG GLU 19 16.477 39.854 27.616 1.00 0.00 C +ATOM 326 HG2 GLU 19 15.971 40.349 28.452 1.00 0.00 H +ATOM 327 HG3 GLU 19 16.810 40.632 26.924 1.00 0.00 H +ATOM 328 CD GLU 19 15.524 38.897 26.903 1.00 0.00 C +ATOM 329 OE1 GLU 19 15.614 38.801 25.661 1.00 0.00 O +ATOM 330 OE2 GLU 19 14.785 38.158 27.578 1.00 0.00 O +ATOM 331 C GLU 19 19.040 39.069 25.978 1.00 0.00 C +ATOM 332 O GLU 19 20.090 39.684 26.183 1.00 0.00 O +ATOM 333 N ALA 20 18.406 39.106 24.798 1.00 0.00 N +ATOM 334 H ALA 20 17.526 38.600 24.725 1.00 0.00 H +ATOM 335 CA ALA 20 18.770 39.982 23.679 1.00 0.00 C +ATOM 336 HA ALA 20 18.902 40.994 24.063 1.00 0.00 H +ATOM 337 CB ALA 20 20.096 39.515 23.062 1.00 0.00 C +ATOM 338 HB1 ALA 20 19.972 38.533 22.606 1.00 0.00 H +ATOM 339 HB2 ALA 20 20.416 40.226 22.305 1.00 0.00 H +ATOM 340 HB3 ALA 20 20.879 39.462 23.817 1.00 0.00 H +ATOM 341 C ALA 20 17.694 40.018 22.571 1.00 0.00 C +ATOM 342 O ALA 20 16.874 39.108 22.434 1.00 0.00 O +ATOM 343 N VAL 21 17.756 41.039 21.709 1.00 0.00 N +ATOM 344 H VAL 21 18.418 41.780 21.884 1.00 0.00 H +ATOM 345 CA VAL 21 17.017 41.071 20.423 1.00 0.00 C +ATOM 346 HA VAL 21 16.020 40.661 20.587 1.00 0.00 H +ATOM 347 CB VAL 21 16.842 42.514 19.898 1.00 0.00 C +ATOM 348 HB VAL 21 16.188 42.472 19.027 1.00 0.00 H +ATOM 349 CG1 VAL 21 16.159 43.411 20.937 1.00 0.00 C +ATOM 350 HG11 VAL 21 16.810 43.579 21.795 1.00 0.00 H +ATOM 351 HG12 VAL 21 15.918 44.373 20.486 1.00 0.00 H +ATOM 352 HG13 VAL 21 15.232 42.951 21.279 1.00 0.00 H +ATOM 353 CG2 VAL 21 18.158 43.176 19.464 1.00 0.00 C +ATOM 354 HG21 VAL 21 18.596 42.634 18.626 1.00 0.00 H +ATOM 355 HG22 VAL 21 17.964 44.195 19.129 1.00 0.00 H +ATOM 356 HG23 VAL 21 18.872 43.205 20.287 1.00 0.00 H +ATOM 357 C VAL 21 17.666 40.197 19.339 1.00 0.00 C +ATOM 358 O VAL 21 16.989 39.788 18.400 1.00 0.00 O +ATOM 359 N ASP 22 18.962 39.912 19.481 1.00 0.00 N +ATOM 360 H ASP 22 19.441 40.273 20.289 1.00 0.00 H +ATOM 361 CA ASP 22 19.803 39.155 18.549 1.00 0.00 C +ATOM 362 HA ASP 22 19.204 38.379 18.068 1.00 0.00 H +ATOM 363 CB ASP 22 20.347 40.115 17.467 1.00 0.00 C +ATOM 364 HB2 ASP 22 19.507 40.640 17.014 1.00 0.00 H +ATOM 365 HB3 ASP 22 20.969 40.862 17.961 1.00 0.00 H +ATOM 366 CG ASP 22 21.171 39.445 16.351 1.00 0.00 C +ATOM 367 OD1 ASP 22 21.358 40.133 15.304 1.00 0.00 O +ATOM 368 OD2 ASP 22 21.600 38.297 16.500 1.00 0.00 O +ATOM 369 C ASP 22 20.940 38.484 19.342 1.00 0.00 C +ATOM 370 O ASP 22 21.503 39.076 20.270 1.00 0.00 O +ATOM 371 N LEU 23 21.311 37.261 18.968 1.00 0.00 N +ATOM 372 H LEU 23 20.939 36.925 18.089 1.00 0.00 H +ATOM 373 CA LEU 23 22.452 36.571 19.560 1.00 0.00 C +ATOM 374 HA LEU 23 22.285 36.550 20.632 1.00 0.00 H +ATOM 375 CB LEU 23 22.485 35.111 19.082 1.00 0.00 C +ATOM 376 HB2 LEU 23 21.546 34.665 19.394 1.00 0.00 H +ATOM 377 HB3 LEU 23 22.522 35.056 17.994 1.00 0.00 H +ATOM 378 CG LEU 23 23.640 34.288 19.690 1.00 0.00 C +ATOM 379 HG LEU 23 23.819 34.622 20.711 1.00 0.00 H +ATOM 380 CD1 LEU 23 23.243 32.811 19.763 1.00 0.00 C +ATOM 381 HD11 LEU 23 22.968 32.445 18.779 1.00 0.00 H +ATOM 382 HD12 LEU 23 24.071 32.222 20.159 1.00 0.00 H +ATOM 383 HD13 LEU 23 22.398 32.707 20.441 1.00 0.00 H +ATOM 384 CD2 LEU 23 24.930 34.430 18.880 1.00 0.00 C +ATOM 385 HD21 LEU 23 25.532 35.241 19.277 1.00 0.00 H +ATOM 386 HD22 LEU 23 25.534 33.529 18.950 1.00 0.00 H +ATOM 387 HD23 LEU 23 24.718 34.659 17.839 1.00 0.00 H +ATOM 388 C LEU 23 23.771 37.324 19.343 1.00 0.00 C +ATOM 389 O LEU 23 24.614 37.294 20.233 1.00 0.00 O +ATOM 390 N ALA 24 23.950 38.060 18.242 1.00 0.00 N +ATOM 391 H ALA 24 23.204 38.085 17.546 1.00 0.00 H +ATOM 392 CA ALA 24 25.158 38.865 18.025 1.00 0.00 C +ATOM 393 HA ALA 24 26.018 38.218 18.197 1.00 0.00 H +ATOM 394 CB ALA 24 25.202 39.299 16.558 1.00 0.00 C +ATOM 395 HB1 ALA 24 24.369 39.964 16.325 1.00 0.00 H +ATOM 396 HB2 ALA 24 26.142 39.815 16.363 1.00 0.00 H +ATOM 397 HB3 ALA 24 25.148 38.425 15.906 1.00 0.00 H +ATOM 398 C ALA 24 25.306 40.056 19.005 1.00 0.00 C +ATOM 399 O ALA 24 26.389 40.642 19.118 1.00 0.00 O +ATOM 400 N GLU 25 24.251 40.394 19.761 1.00 0.00 N +ATOM 401 H GLU 25 23.380 39.906 19.598 1.00 0.00 H +ATOM 402 CA GLU 25 24.335 41.202 20.988 1.00 0.00 C +ATOM 403 HA GLU 25 25.200 41.864 20.931 1.00 0.00 H +ATOM 404 CB GLU 25 23.081 42.091 21.112 1.00 0.00 C +ATOM 405 HB2 GLU 25 22.197 41.461 21.036 1.00 0.00 H +ATOM 406 HB3 GLU 25 23.072 42.547 22.099 1.00 0.00 H +ATOM 407 CG GLU 25 22.993 43.209 20.067 1.00 0.00 C +ATOM 408 HG2 GLU 25 23.178 42.799 19.072 1.00 0.00 H +ATOM 409 HG3 GLU 25 21.977 43.613 20.061 1.00 0.00 H +ATOM 410 CD GLU 25 23.989 44.335 20.372 1.00 0.00 C +ATOM 411 OE1 GLU 25 23.587 45.318 21.037 1.00 0.00 O +ATOM 412 OE2 GLU 25 25.166 44.185 19.957 1.00 0.00 O +ATOM 413 C GLU 25 24.520 40.324 22.230 1.00 0.00 C +ATOM 414 O GLU 25 25.355 40.629 23.079 1.00 0.00 O +ATOM 415 N ALA 26 23.838 39.165 22.340 1.00 0.00 N +ATOM 416 H ALA 26 23.144 38.939 21.634 1.00 0.00 H +ATOM 417 CA ALA 26 24.041 38.207 23.435 1.00 0.00 C +ATOM 418 HA ALA 26 23.857 38.735 24.370 1.00 0.00 H +ATOM 419 CB ALA 26 23.053 37.055 23.307 1.00 0.00 C +ATOM 420 HB1 ALA 26 23.352 36.400 22.493 1.00 0.00 H +ATOM 421 HB2 ALA 26 23.041 36.471 24.227 1.00 0.00 H +ATOM 422 HB3 ALA 26 22.059 37.460 23.119 1.00 0.00 H +ATOM 423 C ALA 26 25.475 37.640 23.529 1.00 0.00 C +ATOM 424 O ALA 26 25.878 37.199 24.606 1.00 0.00 O +ATOM 425 N GLU 27 26.225 37.656 22.426 1.00 0.00 N +ATOM 426 H GLU 27 25.728 37.822 21.561 1.00 0.00 H +ATOM 427 CA GLU 27 27.657 37.363 22.351 1.00 0.00 C +ATOM 428 HA GLU 27 27.828 36.387 22.786 1.00 0.00 H +ATOM 429 CB GLU 27 28.049 37.295 20.810 1.00 0.00 C +ATOM 430 HB2 GLU 27 27.320 36.650 20.339 1.00 0.00 H +ATOM 431 HB3 GLU 27 27.974 38.279 20.364 1.00 0.00 H +ATOM 432 CG GLU 27 29.432 36.733 20.511 1.00 0.00 C +ATOM 433 HG2 GLU 27 30.208 37.425 20.927 1.00 0.00 H +ATOM 434 HG3 GLU 27 29.562 35.764 21.055 1.00 0.00 H +ATOM 435 CD GLU 27 29.655 36.541 18.998 1.00 0.00 C +ATOM 436 OE1 GLU 27 30.446 37.312 18.444 1.00 0.00 O +ATOM 437 OE2 GLU 27 29.027 35.659 18.399 1.00 0.00 O +ATOM 438 C GLU 27 28.483 38.382 23.126 1.00 0.00 C +ATOM 439 O GLU 27 29.294 38.026 23.980 1.00 0.00 O +ATOM 440 N LYS 28 28.171 39.676 22.949 1.00 0.00 N +ATOM 441 H LYS 28 27.412 39.874 22.302 1.00 0.00 H +ATOM 442 CA LYS 28 28.730 40.786 23.720 1.00 0.00 C +ATOM 443 HA LYS 28 29.826 40.697 23.712 1.00 0.00 H +ATOM 444 CB LYS 28 28.359 42.145 23.096 1.00 0.00 C +ATOM 445 HB2 LYS 28 27.290 42.317 23.207 1.00 0.00 H +ATOM 446 HB3 LYS 28 28.886 42.916 23.652 1.00 0.00 H +ATOM 447 CG LYS 28 28.732 42.265 21.607 1.00 0.00 C +ATOM 448 HG2 LYS 28 29.789 42.022 21.483 1.00 0.00 H +ATOM 449 HG3 LYS 28 28.138 41.561 21.024 1.00 0.00 H +ATOM 450 CD LYS 28 28.480 43.692 21.087 1.00 0.00 C +ATOM 451 HD2 LYS 28 27.472 44.012 21.359 1.00 0.00 H +ATOM 452 HD3 LYS 28 29.187 44.367 21.577 1.00 0.00 H +ATOM 453 CE LYS 28 28.656 43.806 19.568 1.00 0.00 C +ATOM 454 HE2 LYS 28 28.808 44.863 19.321 1.00 0.00 H +ATOM 455 HE3 LYS 28 29.558 43.270 19.263 1.00 0.00 H +ATOM 456 NZ LYS 28 27.462 43.300 18.844 1.00 0.00 N +ATOM 457 HZ1 LYS 28 26.620 43.776 19.187 1.00 0.00 H +ATOM 458 HZ2 LYS 28 27.524 43.469 17.852 1.00 0.00 H +ATOM 459 HZ3 LYS 28 27.296 42.311 19.010 1.00 0.00 H +ATOM 460 C LYS 28 28.293 40.734 25.190 1.00 0.00 C +ATOM 461 O LYS 28 29.136 40.838 26.076 1.00 0.00 O +ATOM 462 N PHE 29 27.019 40.477 25.467 1.00 0.00 N +ATOM 463 H PHE 29 26.355 40.453 24.698 1.00 0.00 H +ATOM 464 CA PHE 29 26.517 40.332 26.846 1.00 0.00 C +ATOM 465 HA PHE 29 26.806 41.218 27.411 1.00 0.00 H +ATOM 466 CB PHE 29 24.977 40.304 26.842 1.00 0.00 C +ATOM 467 HB2 PHE 29 24.659 39.367 26.390 1.00 0.00 H +ATOM 468 HB3 PHE 29 24.625 40.303 27.880 1.00 0.00 H +ATOM 469 CG PHE 29 24.287 41.460 26.136 1.00 0.00 C +ATOM 470 CD1 PHE 29 23.049 41.246 25.495 1.00 0.00 C +ATOM 471 HD1 PHE 29 22.579 40.275 25.527 1.00 0.00 H +ATOM 472 CE1 PHE 29 22.410 42.297 24.807 1.00 0.00 C +ATOM 473 HE1 PHE 29 21.469 42.116 24.311 1.00 0.00 H +ATOM 474 CZ PHE 29 23.003 43.573 24.765 1.00 0.00 C +ATOM 475 HZ PHE 29 22.524 44.372 24.222 1.00 0.00 H +ATOM 476 CE2 PHE 29 24.219 43.806 25.428 1.00 0.00 C +ATOM 477 HE2 PHE 29 24.669 44.778 25.408 1.00 0.00 H +ATOM 478 CD2 PHE 29 24.853 42.757 26.115 1.00 0.00 C +ATOM 479 HD2 PHE 29 25.782 42.959 26.619 1.00 0.00 H +ATOM 480 C PHE 29 27.097 39.092 27.576 1.00 0.00 C +ATOM 481 O PHE 29 27.242 39.121 28.804 1.00 0.00 O +ATOM 482 N THR 30 27.471 38.019 26.855 1.00 0.00 N +ATOM 483 H THR 30 27.262 38.018 25.867 1.00 0.00 H +ATOM 484 CA THR 30 28.208 36.874 27.383 1.00 0.00 C +ATOM 485 HA THR 30 27.806 36.552 28.340 1.00 0.00 H +ATOM 486 CB THR 30 28.165 35.642 26.355 1.00 0.00 C +ATOM 487 HB THR 30 28.671 35.982 25.465 1.00 0.00 H +ATOM 488 CG2 THR 30 29.010 34.482 26.856 1.00 0.00 C +ATOM 489 HG21 THR 30 28.763 34.155 27.853 1.00 0.00 H +ATOM 490 HG22 THR 30 28.991 33.595 26.210 1.00 0.00 H +ATOM 491 HG23 THR 30 30.047 34.791 26.859 1.00 0.00 H +ATOM 492 OG1 THR 30 26.844 35.210 26.048 1.00 0.00 O +ATOM 493 HG1 THR 30 26.349 35.962 25.650 1.00 0.00 H +ATOM 494 C THR 30 29.681 37.276 27.719 1.00 0.00 C +ATOM 495 O THR 30 30.155 36.942 28.795 1.00 0.00 O +ATOM 496 N LYS 31 30.332 38.079 26.889 1.00 0.00 N +ATOM 497 H LYS 31 29.871 38.384 26.044 1.00 0.00 H +ATOM 498 CA LYS 31 31.674 38.634 27.157 1.00 0.00 C +ATOM 499 HA LYS 31 32.350 37.837 27.474 1.00 0.00 H +ATOM 500 CB LYS 31 32.241 39.245 25.864 1.00 0.00 C +ATOM 501 HB2 LYS 31 31.523 39.940 25.448 1.00 0.00 H +ATOM 502 HB3 LYS 31 33.157 39.786 26.103 1.00 0.00 H +ATOM 503 CG LYS 31 32.581 38.157 24.832 1.00 0.00 C +ATOM 504 HG2 LYS 31 33.317 37.480 25.261 1.00 0.00 H +ATOM 505 HG3 LYS 31 31.704 37.566 24.575 1.00 0.00 H +ATOM 506 CD LYS 31 33.154 38.798 23.560 1.00 0.00 C +ATOM 507 HD2 LYS 31 32.363 39.356 23.055 1.00 0.00 H +ATOM 508 HD3 LYS 31 33.951 39.488 23.827 1.00 0.00 H +ATOM 509 CE LYS 31 33.714 37.746 22.591 1.00 0.00 C +ATOM 510 HE2 LYS 31 32.948 37.001 22.373 1.00 0.00 H +ATOM 511 HE3 LYS 31 33.955 38.245 21.648 1.00 0.00 H +ATOM 512 NZ LYS 31 34.933 37.089 23.115 1.00 0.00 N +ATOM 513 HZ1 LYS 31 34.746 36.340 23.769 1.00 0.00 H +ATOM 514 HZ2 LYS 31 35.437 36.639 22.348 1.00 0.00 H +ATOM 515 HZ3 LYS 31 35.592 37.732 23.552 1.00 0.00 H +ATOM 516 C LYS 31 31.693 39.656 28.305 1.00 0.00 C +ATOM 517 O LYS 31 32.674 39.678 29.044 1.00 0.00 O +ATOM 518 N ALA 32 30.615 40.417 28.505 1.00 0.00 N +ATOM 519 H ALA 32 29.893 40.433 27.798 1.00 0.00 H +ATOM 520 CA ALA 32 30.452 41.245 29.699 1.00 0.00 C +ATOM 521 HA ALA 32 31.287 41.943 29.769 1.00 0.00 H +ATOM 522 CB ALA 32 29.160 42.059 29.583 1.00 0.00 C +ATOM 523 HB1 ALA 32 28.295 41.401 29.522 1.00 0.00 H +ATOM 524 HB2 ALA 32 29.045 42.699 30.464 1.00 0.00 H +ATOM 525 HB3 ALA 32 29.194 42.691 28.695 1.00 0.00 H +ATOM 526 C ALA 32 30.481 40.374 30.974 1.00 0.00 C +ATOM 527 O ALA 32 31.390 40.511 31.786 1.00 0.00 O +ATOM 528 N ALA 33 29.599 39.373 31.058 1.00 0.00 N +ATOM 529 H ALA 33 28.886 39.292 30.345 1.00 0.00 H +ATOM 530 CA ALA 33 29.555 38.428 32.181 1.00 0.00 C +ATOM 531 HA ALA 33 29.465 39.008 33.099 1.00 0.00 H +ATOM 532 CB ALA 33 28.289 37.575 32.028 1.00 0.00 C +ATOM 533 HB1 ALA 33 28.346 36.978 31.119 1.00 0.00 H +ATOM 534 HB2 ALA 33 28.181 36.909 32.886 1.00 0.00 H +ATOM 535 HB3 ALA 33 27.410 38.219 31.981 1.00 0.00 H +ATOM 536 C ALA 33 30.821 37.541 32.333 1.00 0.00 C +ATOM 537 O ALA 33 30.921 36.798 33.305 1.00 0.00 O +ATOM 538 N ALA 34 31.757 37.568 31.379 1.00 0.00 N +ATOM 539 H ALA 34 31.589 38.159 30.584 1.00 0.00 H +ATOM 540 CA ALA 34 33.091 36.966 31.505 1.00 0.00 C +ATOM 541 HA ALA 34 33.037 36.139 32.213 1.00 0.00 H +ATOM 542 CB ALA 34 33.508 36.399 30.143 1.00 0.00 C +ATOM 543 HB1 ALA 34 33.649 37.207 29.426 1.00 0.00 H +ATOM 544 HB2 ALA 34 34.450 35.861 30.259 1.00 0.00 H +ATOM 545 HB3 ALA 34 32.750 35.708 29.774 1.00 0.00 H +ATOM 546 C ALA 34 34.123 37.961 32.063 1.00 0.00 C +ATOM 547 O ALA 34 34.832 37.631 33.008 1.00 0.00 O +ATOM 548 N ASN 35 34.171 39.202 31.560 1.00 0.00 N +ATOM 549 H ASN 35 33.544 39.440 30.800 1.00 0.00 H +ATOM 550 CA ASN 35 35.041 40.256 32.096 1.00 0.00 C +ATOM 551 HA ASN 35 36.050 39.850 32.215 1.00 0.00 H +ATOM 552 CB ASN 35 35.128 41.408 31.082 1.00 0.00 C +ATOM 553 HB2 ASN 35 34.128 41.702 30.765 1.00 0.00 H +ATOM 554 HB3 ASN 35 35.595 42.264 31.566 1.00 0.00 H +ATOM 555 CG ASN 35 35.989 41.053 29.876 1.00 0.00 C +ATOM 556 OD1 ASN 35 37.202 40.998 29.943 1.00 0.00 O +ATOM 557 ND2 ASN 35 35.397 40.799 28.737 1.00 0.00 N +ATOM 558 HD21 ASN 35 36.007 40.585 27.947 1.00 0.00 H +ATOM 559 HD22 ASN 35 34.398 40.684 28.702 1.00 0.00 H +ATOM 560 C ASN 35 34.614 40.741 33.504 1.00 0.00 C +ATOM 561 O ASN 35 35.469 41.137 34.290 1.00 0.00 O +ATOM 562 N ASP 36 33.333 40.617 33.865 1.00 0.00 N +ATOM 563 H ASP 36 32.647 40.420 33.146 1.00 0.00 H +ATOM 564 CA ASP 36 32.837 40.768 35.249 1.00 0.00 C +ATOM 565 HA ASP 36 33.163 41.738 35.630 1.00 0.00 H +ATOM 566 CB ASP 36 31.291 40.753 35.253 1.00 0.00 C +ATOM 567 HB2 ASP 36 30.950 39.847 34.749 1.00 0.00 H +ATOM 568 HB3 ASP 36 30.954 40.684 36.289 1.00 0.00 H +ATOM 569 CG ASP 36 30.604 41.992 34.634 1.00 0.00 C +ATOM 570 OD1 ASP 36 31.204 43.091 34.688 1.00 0.00 O +ATOM 571 OD2 ASP 36 29.439 41.870 34.172 1.00 0.00 O +ATOM 572 C ASP 36 33.415 39.697 36.211 1.00 0.00 C +ATOM 573 O ASP 36 33.441 39.908 37.424 1.00 0.00 O +ATOM 574 N LEU 37 33.904 38.557 35.688 1.00 0.00 N +ATOM 575 H LEU 37 33.842 38.450 34.686 1.00 0.00 H +ATOM 576 CA LEU 37 34.657 37.527 36.423 1.00 0.00 C +ATOM 577 HA LEU 37 34.464 37.650 37.491 1.00 0.00 H +ATOM 578 CB LEU 37 34.109 36.145 35.994 1.00 0.00 C +ATOM 579 HB2 LEU 37 33.040 36.119 36.207 1.00 0.00 H +ATOM 580 HB3 LEU 37 34.231 36.052 34.917 1.00 0.00 H +ATOM 581 CG LEU 37 34.771 34.914 36.645 1.00 0.00 C +ATOM 582 HG LEU 37 35.840 34.913 36.439 1.00 0.00 H +ATOM 583 CD1 LEU 37 34.551 34.857 38.159 1.00 0.00 C +ATOM 584 HD11 LEU 37 33.486 34.879 38.385 1.00 0.00 H +ATOM 585 HD12 LEU 37 34.992 33.944 38.560 1.00 0.00 H +ATOM 586 HD13 LEU 37 35.040 35.710 38.628 1.00 0.00 H +ATOM 587 CD2 LEU 37 34.177 33.637 36.042 1.00 0.00 C +ATOM 588 HD21 LEU 37 34.355 33.629 34.966 1.00 0.00 H +ATOM 589 HD22 LEU 37 34.662 32.764 36.478 1.00 0.00 H +ATOM 590 HD23 LEU 37 33.105 33.596 36.231 1.00 0.00 H +ATOM 591 C LEU 37 36.190 37.649 36.238 1.00 0.00 C +ATOM 592 O LEU 37 36.941 37.271 37.137 1.00 0.00 O +ATOM 593 N GLY 38 36.655 38.181 35.100 1.00 0.00 N +ATOM 594 H GLY 38 35.977 38.417 34.388 1.00 0.00 H +ATOM 595 CA GLY 38 38.057 38.532 34.848 1.00 0.00 C +ATOM 596 HA2 GLY 38 38.314 39.395 35.466 1.00 0.00 H +ATOM 597 HA3 GLY 38 38.690 37.700 35.160 1.00 0.00 H +ATOM 598 C GLY 38 38.413 38.871 33.391 1.00 0.00 C +ATOM 599 O GLY 38 38.929 39.957 33.136 1.00 0.00 O +ATOM 600 N GLU 39 38.171 37.961 32.437 1.00 0.00 N +ATOM 601 H GLU 39 37.657 37.131 32.691 1.00 0.00 H +ATOM 602 CA GLU 39 38.661 38.018 31.042 1.00 0.00 C +ATOM 603 HA GLU 39 38.763 39.061 30.726 1.00 0.00 H +ATOM 604 CB GLU 39 40.065 37.322 30.944 1.00 0.00 C +ATOM 605 HB2 GLU 39 39.944 36.313 31.317 1.00 0.00 H +ATOM 606 HB3 GLU 39 40.335 37.260 29.892 1.00 0.00 H +ATOM 607 CG GLU 39 41.245 37.986 31.688 1.00 0.00 C +ATOM 608 HG2 GLU 39 41.553 38.894 31.136 1.00 0.00 H +ATOM 609 HG3 GLU 39 40.915 38.320 32.684 1.00 0.00 H +ATOM 610 CD GLU 39 42.450 37.039 31.915 1.00 0.00 C +ATOM 611 OE1 GLU 39 42.260 36.003 32.575 1.00 0.00 O +ATOM 612 OE2 GLU 39 43.569 37.372 31.481 1.00 0.00 O +ATOM 613 C GLU 39 37.685 37.298 30.075 1.00 0.00 C +ATOM 614 O GLU 39 37.024 36.351 30.492 1.00 0.00 O +ATOM 615 N ASP 40 37.585 37.685 28.788 1.00 0.00 N +ATOM 616 H ASP 40 38.100 38.498 28.476 1.00 0.00 H +ATOM 617 CA ASP 40 36.738 36.968 27.799 1.00 0.00 C +ATOM 618 HA ASP 40 36.030 36.362 28.365 1.00 0.00 H +ATOM 619 CB ASP 40 35.858 37.913 26.964 1.00 0.00 C +ATOM 620 HB2 ASP 40 35.160 37.288 26.414 1.00 0.00 H +ATOM 621 HB3 ASP 40 35.261 38.533 27.625 1.00 0.00 H +ATOM 622 CG ASP 40 36.587 38.798 25.952 1.00 0.00 C +ATOM 623 OD1 ASP 40 36.893 39.965 26.276 1.00 0.00 O +ATOM 624 OD2 ASP 40 36.761 38.351 24.790 1.00 0.00 O +ATOM 625 C ASP 40 37.475 35.994 26.856 1.00 0.00 C +ATOM 626 O ASP 40 38.374 36.376 26.101 1.00 0.00 O +ATOM 627 N GLY 41 36.973 34.756 26.794 1.00 0.00 N +ATOM 628 H GLY 41 36.288 34.510 27.490 1.00 0.00 H +ATOM 629 CA GLY 41 37.271 33.768 25.747 1.00 0.00 C +ATOM 630 HA2 GLY 41 38.295 33.916 25.381 1.00 0.00 H +ATOM 631 HA3 GLY 41 37.211 32.770 26.191 1.00 0.00 H +ATOM 632 C GLY 41 36.313 33.811 24.533 1.00 0.00 C +ATOM 633 O GLY 41 35.386 34.624 24.460 1.00 0.00 O +ATOM 634 N GLU 42 36.534 32.906 23.574 1.00 0.00 N +ATOM 635 H GLU 42 37.265 32.233 23.726 1.00 0.00 H +ATOM 636 CA GLU 42 35.795 32.783 22.304 1.00 0.00 C +ATOM 637 HA GLU 42 35.112 33.628 22.215 1.00 0.00 H +ATOM 638 CB GLU 42 36.768 32.852 21.111 1.00 0.00 C +ATOM 639 HB2 GLU 42 37.359 31.939 21.083 1.00 0.00 H +ATOM 640 HB3 GLU 42 36.185 32.904 20.190 1.00 0.00 H +ATOM 641 CG GLU 42 37.742 34.046 21.132 1.00 0.00 C +ATOM 642 HG2 GLU 42 38.542 33.823 21.835 1.00 0.00 H +ATOM 643 HG3 GLU 42 38.198 34.176 20.150 1.00 0.00 H +ATOM 644 CD GLU 42 37.078 35.358 21.545 1.00 0.00 C +ATOM 645 OE1 GLU 42 35.962 35.662 21.073 1.00 0.00 O +ATOM 646 OE2 GLU 42 37.603 36.077 22.430 1.00 0.00 O +ATOM 647 C GLU 42 34.925 31.518 22.249 1.00 0.00 C +ATOM 648 O GLU 42 35.177 30.549 22.970 1.00 0.00 O +ATOM 649 N HIP 43 33.822 31.561 21.482 1.00 0.00 N +ATOM 650 H HIP 43 33.691 32.332 20.837 1.00 0.00 H +ATOM 651 CA HIP 43 32.635 30.779 21.863 1.00 0.00 C +ATOM 652 HA HIP 43 32.953 29.805 22.240 1.00 0.00 H +ATOM 653 CB HIP 43 32.036 31.564 23.060 1.00 0.00 C +ATOM 654 HB2 HIP 43 32.780 31.722 23.836 1.00 0.00 H +ATOM 655 HB3 HIP 43 31.707 32.547 22.731 1.00 0.00 H +ATOM 656 CG HIP 43 30.884 30.844 23.669 1.00 0.00 C +ATOM 657 ND1 HIP 43 29.715 30.591 23.008 1.00 0.00 N +ATOM 658 HD1 HIP 43 29.496 30.960 22.088 1.00 0.00 H +ATOM 659 CE1 HIP 43 29.197 29.496 23.532 1.00 0.00 C +ATOM 660 HE1 HIP 43 28.471 28.891 23.007 1.00 0.00 H +ATOM 661 NE2 HIP 43 29.859 29.132 24.623 1.00 0.00 N +ATOM 662 HE2 HIP 43 29.751 28.262 25.124 1.00 0.00 H +ATOM 663 CD2 HIP 43 30.964 29.967 24.715 1.00 0.00 C +ATOM 664 HD2 HIP 43 31.813 29.800 25.339 1.00 0.00 H +ATOM 665 C HIP 43 31.587 30.500 20.744 1.00 0.00 C +ATOM 666 O HIP 43 30.815 31.391 20.404 1.00 0.00 O +ATOM 667 N THR 44 31.412 29.241 20.315 1.00 0.00 N +ATOM 668 H THR 44 32.062 28.545 20.651 1.00 0.00 H +ATOM 669 CA THR 44 30.539 28.792 19.194 1.00 0.00 C +ATOM 670 HA THR 44 30.768 29.416 18.330 1.00 0.00 H +ATOM 671 CB THR 44 30.915 27.341 18.825 1.00 0.00 C +ATOM 672 HB THR 44 30.653 26.672 19.649 1.00 0.00 H +ATOM 673 CG2 THR 44 30.280 26.804 17.538 1.00 0.00 C +ATOM 674 HG21 THR 44 30.421 27.512 16.723 1.00 0.00 H +ATOM 675 HG22 THR 44 30.737 25.852 17.265 1.00 0.00 H +ATOM 676 HG23 THR 44 29.217 26.625 17.692 1.00 0.00 H +ATOM 677 OG1 THR 44 32.307 27.274 18.626 1.00 0.00 O +ATOM 678 HG1 THR 44 32.492 26.533 18.040 1.00 0.00 H +ATOM 679 C THR 44 29.005 28.885 19.426 1.00 0.00 C +ATOM 680 O THR 44 28.541 28.793 20.567 1.00 0.00 O +ATOM 681 N LYS 45 28.231 29.030 18.329 1.00 0.00 N +ATOM 682 H LYS 45 28.718 29.046 17.443 1.00 0.00 H +ATOM 683 CA LYS 45 26.747 29.105 18.236 1.00 0.00 C +ATOM 684 HA LYS 45 26.318 29.062 19.233 1.00 0.00 H +ATOM 685 CB LYS 45 26.374 30.459 17.574 1.00 0.00 C +ATOM 686 HB2 LYS 45 26.571 31.266 18.282 1.00 0.00 H +ATOM 687 HB3 LYS 45 27.024 30.615 16.712 1.00 0.00 H +ATOM 688 CG LYS 45 24.919 30.571 17.071 1.00 0.00 C +ATOM 689 HG2 LYS 45 24.730 29.762 16.369 1.00 0.00 H +ATOM 690 HG3 LYS 45 24.253 30.451 17.926 1.00 0.00 H +ATOM 691 CD LYS 45 24.581 31.864 16.313 1.00 0.00 C +ATOM 692 HD2 LYS 45 24.789 32.715 16.943 1.00 0.00 H +ATOM 693 HD3 LYS 45 25.176 31.930 15.400 1.00 0.00 H +ATOM 694 CE LYS 45 23.091 31.825 15.971 1.00 0.00 C +ATOM 695 HE2 LYS 45 22.923 30.987 15.292 1.00 0.00 H +ATOM 696 HE3 LYS 45 22.532 31.602 16.886 1.00 0.00 H +ATOM 697 NZ LYS 45 22.573 33.072 15.345 1.00 0.00 N +ATOM 698 HZ1 LYS 45 22.962 33.227 14.424 1.00 0.00 H +ATOM 699 HZ2 LYS 45 21.559 32.954 15.239 1.00 0.00 H +ATOM 700 HZ3 LYS 45 22.712 33.892 15.912 1.00 0.00 H +ATOM 701 C LYS 45 26.138 27.945 17.423 1.00 0.00 C +ATOM 702 O LYS 45 26.705 27.569 16.405 1.00 0.00 O +ATOM 703 N ASP 46 24.922 27.524 17.775 1.00 0.00 N +ATOM 704 H ASP 46 24.578 27.808 18.689 1.00 0.00 H +ATOM 705 CA ASP 46 23.873 27.044 16.843 1.00 0.00 C +ATOM 706 HA ASP 46 24.249 27.121 15.818 1.00 0.00 H +ATOM 707 CB ASP 46 23.528 25.569 17.148 1.00 0.00 C +ATOM 708 HB2 ASP 46 24.366 24.916 16.878 1.00 0.00 H +ATOM 709 HB3 ASP 46 23.378 25.489 18.232 1.00 0.00 H +ATOM 710 CG ASP 46 22.266 25.098 16.426 1.00 0.00 C +ATOM 711 OD1 ASP 46 21.392 24.557 17.117 1.00 0.00 O +ATOM 712 OD2 ASP 46 22.087 25.409 15.235 1.00 0.00 O +ATOM 713 C ASP 46 22.613 27.944 16.957 1.00 0.00 C +ATOM 714 O ASP 46 22.294 28.456 18.027 1.00 0.00 O +ATOM 715 N ASP 47 21.897 28.140 15.849 1.00 0.00 N +ATOM 716 H ASP 47 22.146 27.562 15.057 1.00 0.00 H +ATOM 717 CA ASP 47 20.588 28.850 15.794 1.00 0.00 C +ATOM 718 HA ASP 47 20.554 29.519 16.646 1.00 0.00 H +ATOM 719 CB ASP 47 20.475 29.756 14.572 1.00 0.00 C +ATOM 720 HB2 ASP 47 21.461 30.108 14.286 1.00 0.00 H +ATOM 721 HB3 ASP 47 20.085 29.213 13.702 1.00 0.00 H +ATOM 722 CG ASP 47 19.637 30.995 14.888 1.00 0.00 C +ATOM 723 OD1 ASP 47 18.471 31.071 14.473 1.00 0.00 O +ATOM 724 OD2 ASP 47 20.169 31.881 15.573 1.00 0.00 O +ATOM 725 C ASP 47 19.357 27.933 15.861 1.00 0.00 C +ATOM 726 O ASP 47 18.316 28.355 16.366 1.00 0.00 O +ATOM 727 N ALA 48 19.457 26.676 15.411 1.00 0.00 N +ATOM 728 H ALA 48 20.368 26.307 15.139 1.00 0.00 H +ATOM 729 CA ALA 48 18.317 25.752 15.378 1.00 0.00 C +ATOM 730 HA ALA 48 17.480 26.224 14.859 1.00 0.00 H +ATOM 731 CB ALA 48 18.730 24.511 14.577 1.00 0.00 C +ATOM 732 HB1 ALA 48 19.555 24.007 15.072 1.00 0.00 H +ATOM 733 HB2 ALA 48 17.894 23.821 14.498 1.00 0.00 H +ATOM 734 HB3 ALA 48 19.047 24.788 13.575 1.00 0.00 H +ATOM 735 C ALA 48 17.839 25.388 16.792 1.00 0.00 C +ATOM 736 O ALA 48 16.640 25.354 17.075 1.00 0.00 O +ATOM 737 N THR 49 18.778 25.160 17.711 1.00 0.00 N +ATOM 738 H THR 49 19.736 25.037 17.377 1.00 0.00 H +ATOM 739 CA THR 49 18.557 25.051 19.154 1.00 0.00 C +ATOM 740 HA THR 49 17.530 24.709 19.314 1.00 0.00 H +ATOM 741 CB THR 49 19.524 24.022 19.753 1.00 0.00 C +ATOM 742 HB THR 49 19.326 23.946 20.820 1.00 0.00 H +ATOM 743 CG2 THR 49 19.398 22.626 19.153 1.00 0.00 C +ATOM 744 HG21 THR 49 19.665 22.630 18.098 1.00 0.00 H +ATOM 745 HG22 THR 49 20.090 21.979 19.684 1.00 0.00 H +ATOM 746 HG23 THR 49 18.383 22.250 19.269 1.00 0.00 H +ATOM 747 OG1 THR 49 20.861 24.413 19.589 1.00 0.00 O +ATOM 748 HG1 THR 49 21.066 24.338 18.620 1.00 0.00 H +ATOM 749 C THR 49 18.714 26.378 19.910 1.00 0.00 C +ATOM 750 O THR 49 18.618 26.395 21.136 1.00 0.00 O +ATOM 751 N LYS 50 18.968 27.490 19.206 1.00 0.00 N +ATOM 752 H LYS 50 18.980 27.378 18.203 1.00 0.00 H +ATOM 753 CA LYS 50 19.202 28.853 19.749 1.00 0.00 C +ATOM 754 HA LYS 50 19.637 29.449 18.943 1.00 0.00 H +ATOM 755 CB LYS 50 17.845 29.491 20.149 1.00 0.00 C +ATOM 756 HB2 LYS 50 17.408 28.860 20.925 1.00 0.00 H +ATOM 757 HB3 LYS 50 18.038 30.471 20.598 1.00 0.00 H +ATOM 758 CG LYS 50 16.812 29.667 19.017 1.00 0.00 C +ATOM 759 HG2 LYS 50 16.742 28.752 18.424 1.00 0.00 H +ATOM 760 HG3 LYS 50 15.841 29.837 19.491 1.00 0.00 H +ATOM 761 CD LYS 50 17.113 30.878 18.105 1.00 0.00 C +ATOM 762 HD2 LYS 50 17.122 31.775 18.732 1.00 0.00 H +ATOM 763 HD3 LYS 50 18.108 30.766 17.643 1.00 0.00 H +ATOM 764 CE LYS 50 16.028 31.055 17.026 1.00 0.00 C +ATOM 765 HE2 LYS 50 15.056 30.783 17.436 1.00 0.00 H +ATOM 766 HE3 LYS 50 15.985 32.104 16.719 1.00 0.00 H +ATOM 767 NZ LYS 50 16.278 30.207 15.837 1.00 0.00 N +ATOM 768 HZ1 LYS 50 16.593 29.271 16.077 1.00 0.00 H +ATOM 769 HZ2 LYS 50 15.486 30.195 15.189 1.00 0.00 H +ATOM 770 HZ3 LYS 50 17.047 30.589 15.285 1.00 0.00 H +ATOM 771 C LYS 50 20.238 28.865 20.885 1.00 0.00 C +ATOM 772 O LYS 50 20.046 29.552 21.897 1.00 0.00 O +ATOM 773 N THR 51 21.297 28.053 20.758 1.00 0.00 N +ATOM 774 H THR 51 21.447 27.626 19.852 1.00 0.00 H +ATOM 775 CA THR 51 22.186 27.666 21.861 1.00 0.00 C +ATOM 776 HA THR 51 21.925 28.266 22.727 1.00 0.00 H +ATOM 777 CB THR 51 21.978 26.182 22.276 1.00 0.00 C +ATOM 778 HB THR 51 22.103 25.558 21.392 1.00 0.00 H +ATOM 779 CG2 THR 51 22.971 25.680 23.326 1.00 0.00 C +ATOM 780 HG21 THR 51 22.987 26.306 24.214 1.00 0.00 H +ATOM 781 HG22 THR 51 22.722 24.667 23.637 1.00 0.00 H +ATOM 782 HG23 THR 51 23.978 25.634 22.923 1.00 0.00 H +ATOM 783 OG1 THR 51 20.695 26.001 22.835 1.00 0.00 O +ATOM 784 HG1 THR 51 20.033 26.112 22.126 1.00 0.00 H +ATOM 785 C THR 51 23.691 27.954 21.606 1.00 0.00 C +ATOM 786 O THR 51 24.250 27.693 20.552 1.00 0.00 O +ATOM 787 N PHE 52 24.339 28.470 22.636 1.00 0.00 N +ATOM 788 H PHE 52 23.782 28.767 23.426 1.00 0.00 H +ATOM 789 CA PHE 52 25.782 28.625 22.774 1.00 0.00 C +ATOM 790 HA PHE 52 26.236 28.756 21.800 1.00 0.00 H +ATOM 791 CB PHE 52 25.970 29.903 23.630 1.00 0.00 C +ATOM 792 HB2 PHE 52 25.178 29.934 24.366 1.00 0.00 H +ATOM 793 HB3 PHE 52 26.858 29.811 24.241 1.00 0.00 H +ATOM 794 CG PHE 52 25.990 31.261 22.933 1.00 0.00 C +ATOM 795 CD1 PHE 52 25.313 32.345 23.501 1.00 0.00 C +ATOM 796 HD1 PHE 52 24.705 32.206 24.369 1.00 0.00 H +ATOM 797 CE1 PHE 52 25.445 33.639 22.970 1.00 0.00 C +ATOM 798 HE1 PHE 52 24.940 34.476 23.432 1.00 0.00 H +ATOM 799 CZ PHE 52 26.270 33.846 21.867 1.00 0.00 C +ATOM 800 HZ PHE 52 26.395 34.832 21.472 1.00 0.00 H +ATOM 801 CE2 PHE 52 26.935 32.771 21.258 1.00 0.00 C +ATOM 802 HE2 PHE 52 27.570 32.946 20.399 1.00 0.00 H +ATOM 803 CD2 PHE 52 26.777 31.489 21.786 1.00 0.00 C +ATOM 804 HD2 PHE 52 27.285 30.683 21.316 1.00 0.00 H +ATOM 805 C PHE 52 26.423 27.398 23.470 1.00 0.00 C +ATOM 806 O PHE 52 26.087 27.106 24.623 1.00 0.00 O +ATOM 807 N THR 53 27.436 26.751 22.856 1.00 0.00 N +ATOM 808 H THR 53 27.650 26.995 21.888 1.00 0.00 H +ATOM 809 CA THR 53 28.305 25.685 23.436 1.00 0.00 C +ATOM 810 HA THR 53 28.048 25.541 24.487 1.00 0.00 H +ATOM 811 CB THR 53 28.082 24.339 22.718 1.00 0.00 C +ATOM 812 HB THR 53 28.786 23.607 23.118 1.00 0.00 H +ATOM 813 CG2 THR 53 26.676 23.788 22.896 1.00 0.00 C +ATOM 814 HG21 THR 53 25.950 24.428 22.394 1.00 0.00 H +ATOM 815 HG22 THR 53 26.625 22.786 22.468 1.00 0.00 H +ATOM 816 HG23 THR 53 26.442 23.727 23.958 1.00 0.00 H +ATOM 817 OG1 THR 53 28.319 24.486 21.337 1.00 0.00 O +ATOM 818 HG1 THR 53 28.141 23.636 20.917 1.00 0.00 H +ATOM 819 C THR 53 29.812 26.007 23.366 1.00 0.00 C +ATOM 820 O THR 53 30.224 26.906 22.642 1.00 0.00 O +ATOM 821 N THR 54 30.650 25.304 24.140 1.00 0.00 N +ATOM 822 H THR 54 30.284 24.592 24.758 1.00 0.00 H +ATOM 823 CA THR 54 32.131 25.256 23.974 1.00 0.00 C +ATOM 824 HA THR 54 32.450 26.113 23.366 1.00 0.00 H +ATOM 825 CB THR 54 32.874 25.346 25.323 1.00 0.00 C +ATOM 826 HB THR 54 33.948 25.303 25.140 1.00 0.00 H +ATOM 827 CG2 THR 54 32.594 26.656 26.070 1.00 0.00 C +ATOM 828 HG21 THR 54 31.547 26.724 26.352 1.00 0.00 H +ATOM 829 HG22 THR 54 33.190 26.709 26.976 1.00 0.00 H +ATOM 830 HG23 THR 54 32.855 27.511 25.448 1.00 0.00 H +ATOM 831 OG1 THR 54 32.529 24.279 26.170 1.00 0.00 O +ATOM 832 HG1 THR 54 32.961 23.475 25.847 1.00 0.00 H +ATOM 833 C THR 54 32.580 23.997 23.228 1.00 0.00 C +ATOM 834 O THR 54 31.810 23.044 23.101 1.00 0.00 O +ATOM 835 N ALA 55 33.833 23.981 22.756 1.00 0.00 N +ATOM 836 H ALA 55 34.417 24.785 22.911 1.00 0.00 H +ATOM 837 CA ALA 55 34.476 22.803 22.162 1.00 0.00 C +ATOM 838 HA ALA 55 33.773 22.349 21.450 1.00 0.00 H +ATOM 839 CB ALA 55 35.709 23.293 21.391 1.00 0.00 C +ATOM 840 HB1 ALA 55 36.439 23.718 22.088 1.00 0.00 H +ATOM 841 HB2 ALA 55 36.172 22.454 20.859 1.00 0.00 H +ATOM 842 HB3 ALA 55 35.413 24.049 20.657 1.00 0.00 H +ATOM 843 C ALA 55 34.820 21.700 23.201 1.00 0.00 C +ATOM 844 O ALA 55 34.564 21.870 24.395 1.00 0.00 O +ATOM 845 N GLU 56 35.391 20.590 22.719 1.00 0.00 N +ATOM 846 H GLU 56 35.619 20.592 21.742 1.00 0.00 H +ATOM 847 CA GLU 56 35.949 19.442 23.462 1.00 0.00 C +ATOM 848 HA GLU 56 35.837 19.619 24.529 1.00 0.00 H +ATOM 849 CB GLU 56 35.174 18.158 23.066 1.00 0.00 C +ATOM 850 HB2 GLU 56 34.120 18.283 23.304 1.00 0.00 H +ATOM 851 HB3 GLU 56 35.231 18.083 21.976 1.00 0.00 H +ATOM 852 CG GLU 56 35.683 16.816 23.642 1.00 0.00 C +ATOM 853 HG2 GLU 56 35.524 16.058 22.873 1.00 0.00 H +ATOM 854 HG3 GLU 56 36.759 16.858 23.777 1.00 0.00 H +ATOM 855 CD GLU 56 35.019 16.305 24.943 1.00 0.00 C +ATOM 856 OE1 GLU 56 35.650 15.485 25.657 1.00 0.00 O +ATOM 857 OE2 GLU 56 33.830 16.592 25.213 1.00 0.00 O +ATOM 858 C GLU 56 37.466 19.312 23.206 1.00 0.00 C +ATOM 859 O GLU 56 38.207 19.293 24.214 1.00 0.00 O +ATOM 860 OXT GLU 56 37.851 19.278 22.005 1.00 0.00 O +HETATM 861 ZN ZN1 57 26.252 32.500 29.543 1.00 0.00 Zn +HETATM 862 N AN1 58 27.946 33.231 30.455 1.00 0.00 N +HETATM 863 C AN1 58 30.237 34.165 31.270 1.00 0.00 C +HETATM 864 C1 AN1 58 28.941 33.637 30.825 1.00 0.00 C +HETATM 865 H AN1 58 30.152 34.562 32.288 1.00 0.00 H +HETATM 866 H1 AN1 58 30.560 34.975 30.607 1.00 0.00 H +HETATM 867 H2 AN1 58 30.993 33.374 31.265 1.00 0.00 H +HETATM 868 N1 AZI 59 30.423 28.665 29.019 1.00 0.00 N +HETATM 869 N2 AZI 59 29.754 28.732 30.028 1.00 0.00 N +HETATM 870 N3 AZI 59 29.036 28.794 31.085 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 69 71 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 68 73 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 861 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 105 101 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 142 140 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 139 144 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 207 188 189 +CONECT 188 187 +CONECT 189 187 191 192 190 +CONECT 190 189 +CONECT 191 189 +CONECT 192 206 189 193 +CONECT 193 192 195 194 +CONECT 194 193 +CONECT 195 197 193 196 +CONECT 196 195 +CONECT 197 198 206 195 +CONECT 198 200 199 197 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 203 200 204 +CONECT 203 202 +CONECT 204 202 205 206 +CONECT 205 204 +CONECT 206 204 197 192 +CONECT 207 209 187 208 +CONECT 208 207 +CONECT 209 210 211 207 +CONECT 210 209 +CONECT 211 212 223 209 213 +CONECT 212 211 +CONECT 213 211 219 215 214 +CONECT 214 213 +CONECT 215 218 213 216 217 +CONECT 216 215 +CONECT 217 215 +CONECT 218 215 +CONECT 219 220 222 213 221 +CONECT 220 219 +CONECT 221 219 +CONECT 222 219 +CONECT 223 224 225 211 +CONECT 224 223 +CONECT 225 227 223 226 +CONECT 226 225 +CONECT 227 228 245 229 225 +CONECT 228 227 +CONECT 229 232 227 230 231 +CONECT 230 229 +CONECT 231 229 +CONECT 232 234 233 235 229 +CONECT 233 232 +CONECT 234 232 +CONECT 235 236 232 237 238 +CONECT 236 235 +CONECT 237 235 +CONECT 238 235 240 241 239 +CONECT 239 238 +CONECT 240 238 +CONECT 241 244 238 242 243 +CONECT 242 241 +CONECT 243 241 +CONECT 244 241 +CONECT 245 246 227 247 +CONECT 246 245 +CONECT 247 245 249 248 +CONECT 248 247 +CONECT 249 252 247 250 251 +CONECT 250 249 +CONECT 251 249 +CONECT 252 253 254 249 +CONECT 253 252 +CONECT 254 256 252 255 +CONECT 255 254 +CONECT 256 258 257 268 254 +CONECT 257 256 +CONECT 258 264 259 260 256 +CONECT 259 258 +CONECT 260 262 258 261 263 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 265 267 258 +CONECT 265 264 +CONECT 266 264 +CONECT 267 264 +CONECT 268 256 270 269 +CONECT 269 268 +CONECT 270 280 271 268 +CONECT 271 272 270 281 274 +CONECT 272 273 287 271 +CONECT 273 272 +CONECT 274 271 275 282 283 +CONECT 275 276 277 274 +CONECT 276 279 285 275 +CONECT 277 278 275 284 +CONECT 278 279 286 277 +CONECT 279 861 278 276 +CONECT 280 270 +CONECT 281 271 +CONECT 282 274 +CONECT 283 274 +CONECT 284 277 +CONECT 285 276 +CONECT 286 278 +CONECT 287 289 272 288 +CONECT 288 287 +CONECT 289 290 291 299 287 +CONECT 290 289 +CONECT 291 292 293 289 297 +CONECT 292 291 +CONECT 293 296 295 291 294 +CONECT 294 293 +CONECT 295 293 +CONECT 296 293 +CONECT 297 291 298 +CONECT 298 297 +CONECT 299 301 289 300 +CONECT 300 299 +CONECT 301 311 302 299 +CONECT 302 303 305 301 312 +CONECT 303 304 318 302 +CONECT 304 303 +CONECT 305 313 314 302 306 +CONECT 306 305 307 308 +CONECT 307 316 306 310 +CONECT 308 306 315 309 +CONECT 309 310 308 317 +CONECT 310 307 861 309 +CONECT 311 301 +CONECT 312 302 +CONECT 313 305 +CONECT 314 305 +CONECT 315 308 +CONECT 316 307 +CONECT 317 309 +CONECT 318 320 303 319 +CONECT 319 318 +CONECT 320 331 321 318 322 +CONECT 321 320 +CONECT 322 320 325 324 323 +CONECT 323 322 +CONECT 324 322 +CONECT 325 328 327 322 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 329 330 325 +CONECT 329 328 +CONECT 330 328 +CONECT 331 333 332 320 +CONECT 332 331 +CONECT 333 335 334 331 +CONECT 334 333 +CONECT 335 341 337 336 333 +CONECT 336 335 +CONECT 337 339 338 335 340 +CONECT 338 337 +CONECT 339 337 +CONECT 340 337 +CONECT 341 343 342 335 +CONECT 342 341 +CONECT 343 345 344 341 +CONECT 344 343 +CONECT 345 357 347 346 343 +CONECT 346 345 +CONECT 347 348 353 345 349 +CONECT 348 347 +CONECT 349 347 351 352 350 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 347 356 +CONECT 354 353 +CONECT 355 353 +CONECT 356 353 +CONECT 357 358 359 345 +CONECT 358 357 +CONECT 359 361 357 360 +CONECT 360 359 +CONECT 361 363 362 369 359 +CONECT 362 361 +CONECT 363 366 364 365 361 +CONECT 364 363 +CONECT 365 363 +CONECT 366 367 368 363 +CONECT 367 366 +CONECT 368 366 +CONECT 369 361 371 370 +CONECT 370 369 +CONECT 371 372 369 373 +CONECT 372 371 +CONECT 373 371 375 388 374 +CONECT 374 373 +CONECT 375 377 376 373 378 +CONECT 376 375 +CONECT 377 375 +CONECT 378 384 375 380 379 +CONECT 379 378 +CONECT 380 381 378 382 383 +CONECT 381 380 +CONECT 382 380 +CONECT 383 380 +CONECT 384 387 386 385 378 +CONECT 385 384 +CONECT 386 384 +CONECT 387 384 +CONECT 388 390 373 389 +CONECT 389 388 +CONECT 390 391 392 388 +CONECT 391 390 +CONECT 392 394 393 390 398 +CONECT 393 392 +CONECT 394 397 395 396 392 +CONECT 395 394 +CONECT 396 394 +CONECT 397 394 +CONECT 398 392 399 400 +CONECT 399 398 +CONECT 400 398 401 402 +CONECT 401 400 +CONECT 402 400 403 404 413 +CONECT 403 402 +CONECT 404 407 402 405 406 +CONECT 405 404 +CONECT 406 404 +CONECT 407 408 409 410 404 +CONECT 408 407 +CONECT 409 407 +CONECT 410 412 407 411 +CONECT 411 410 +CONECT 412 410 +CONECT 413 402 415 414 +CONECT 414 413 +CONECT 415 416 413 417 +CONECT 416 415 +CONECT 417 415 419 423 418 +CONECT 418 417 +CONECT 419 420 422 417 421 +CONECT 420 419 +CONECT 421 419 +CONECT 422 419 +CONECT 423 425 417 424 +CONECT 424 423 +CONECT 425 426 427 423 +CONECT 426 425 +CONECT 427 429 425 428 438 +CONECT 428 427 +CONECT 429 430 431 432 427 +CONECT 430 429 +CONECT 431 429 +CONECT 432 435 429 433 434 +CONECT 433 432 +CONECT 434 432 +CONECT 435 437 436 432 +CONECT 436 435 +CONECT 437 435 +CONECT 438 427 440 439 +CONECT 439 438 +CONECT 440 441 438 442 +CONECT 441 440 +CONECT 442 440 444 443 460 +CONECT 443 442 +CONECT 444 447 445 446 442 +CONECT 445 444 +CONECT 446 444 +CONECT 447 449 450 448 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 451 452 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 456 455 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 458 459 457 453 +CONECT 457 456 +CONECT 458 456 +CONECT 459 456 +CONECT 460 442 462 461 +CONECT 461 460 +CONECT 462 463 460 464 +CONECT 463 462 +CONECT 464 462 466 465 480 +CONECT 465 464 +CONECT 466 469 467 464 468 +CONECT 467 466 +CONECT 468 466 +CONECT 469 470 478 466 +CONECT 470 472 471 469 +CONECT 471 470 +CONECT 472 473 474 470 +CONECT 473 472 +CONECT 474 475 472 476 +CONECT 475 474 +CONECT 476 474 477 478 +CONECT 477 476 +CONECT 478 476 469 479 +CONECT 479 478 +CONECT 480 464 482 481 +CONECT 481 480 +CONECT 482 483 484 480 +CONECT 483 482 +CONECT 484 486 482 494 485 +CONECT 485 484 +CONECT 486 487 492 488 484 +CONECT 487 486 +CONECT 488 490 486 491 489 +CONECT 489 488 +CONECT 490 488 +CONECT 491 488 +CONECT 492 493 486 +CONECT 493 492 +CONECT 494 496 484 495 +CONECT 495 494 +CONECT 496 497 498 494 +CONECT 497 496 +CONECT 498 500 496 499 516 +CONECT 499 498 +CONECT 500 503 501 502 498 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 505 504 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 509 507 508 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 510 512 506 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 512 +CONECT 516 498 518 517 +CONECT 517 516 +CONECT 518 519 516 520 +CONECT 519 518 +CONECT 520 518 522 521 526 +CONECT 521 520 +CONECT 522 525 523 520 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 522 +CONECT 526 520 528 527 +CONECT 527 526 +CONECT 528 529 526 530 +CONECT 529 528 +CONECT 530 528 532 536 531 +CONECT 531 530 +CONECT 532 533 535 530 534 +CONECT 533 532 +CONECT 534 532 +CONECT 535 532 +CONECT 536 538 530 537 +CONECT 537 536 +CONECT 538 539 540 536 +CONECT 539 538 +CONECT 540 542 538 546 541 +CONECT 541 540 +CONECT 542 543 545 544 540 +CONECT 543 542 +CONECT 544 542 +CONECT 545 542 +CONECT 546 540 548 547 +CONECT 547 546 +CONECT 548 549 546 550 +CONECT 549 548 +CONECT 550 552 548 551 560 +CONECT 551 550 +CONECT 552 555 553 554 550 +CONECT 553 552 +CONECT 554 552 +CONECT 555 557 556 552 +CONECT 556 555 +CONECT 557 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 550 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 566 565 572 +CONECT 565 564 +CONECT 566 569 567 564 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 571 570 566 +CONECT 570 569 +CONECT 571 569 +CONECT 572 564 574 573 +CONECT 573 572 +CONECT 574 575 572 576 +CONECT 575 574 +CONECT 576 574 578 591 577 +CONECT 577 576 +CONECT 578 580 579 576 581 +CONECT 579 578 +CONECT 580 578 +CONECT 581 578 587 582 583 +CONECT 582 581 +CONECT 583 581 584 585 586 +CONECT 584 583 +CONECT 585 583 +CONECT 586 583 +CONECT 587 588 590 589 581 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 593 576 592 +CONECT 592 591 +CONECT 593 594 595 591 +CONECT 594 593 +CONECT 595 598 593 597 596 +CONECT 596 595 +CONECT 597 595 +CONECT 598 600 599 595 +CONECT 599 598 +CONECT 600 602 601 598 +CONECT 601 600 +CONECT 602 613 603 604 600 +CONECT 603 602 +CONECT 604 606 602 605 607 +CONECT 605 604 +CONECT 606 604 +CONECT 607 604 608 610 609 +CONECT 608 607 +CONECT 609 607 +CONECT 610 612 607 611 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 602 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 625 619 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 639 641 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 638 644 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 665 649 652 653 +CONECT 652 651 +CONECT 653 651 655 656 654 +CONECT 654 653 +CONECT 655 653 +CONECT 656 657 653 663 +CONECT 657 658 659 656 +CONECT 658 657 +CONECT 659 660 657 661 +CONECT 660 659 +CONECT 661 659 663 662 +CONECT 662 661 +CONECT 663 656 661 664 +CONECT 664 663 +CONECT 665 667 666 651 +CONECT 666 665 +CONECT 667 669 668 665 +CONECT 668 667 +CONECT 669 670 671 679 667 +CONECT 670 669 +CONECT 671 673 677 669 672 +CONECT 672 671 +CONECT 673 674 675 676 671 +CONECT 674 673 +CONECT 675 673 +CONECT 676 673 +CONECT 677 678 671 +CONECT 678 677 +CONECT 679 681 669 680 +CONECT 680 679 +CONECT 681 682 683 679 +CONECT 682 681 +CONECT 683 701 685 681 684 +CONECT 684 683 +CONECT 685 687 688 683 686 +CONECT 686 685 +CONECT 687 685 +CONECT 688 691 689 685 690 +CONECT 689 688 +CONECT 690 688 +CONECT 691 693 694 692 688 +CONECT 692 691 +CONECT 693 691 +CONECT 694 695 697 691 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 698 699 700 694 +CONECT 698 697 +CONECT 699 697 +CONECT 700 697 +CONECT 701 702 703 683 +CONECT 702 701 +CONECT 703 705 701 704 +CONECT 704 703 +CONECT 705 706 713 707 703 +CONECT 706 705 +CONECT 707 710 705 708 709 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 711 707 +CONECT 711 710 +CONECT 712 710 +CONECT 713 715 705 714 +CONECT 714 713 +CONECT 715 716 717 713 +CONECT 716 715 +CONECT 717 719 715 725 718 +CONECT 718 717 +CONECT 719 721 720 722 717 +CONECT 720 719 +CONECT 721 719 +CONECT 722 723 719 724 +CONECT 723 722 +CONECT 724 722 +CONECT 725 727 717 726 +CONECT 726 725 +CONECT 727 728 729 725 +CONECT 728 727 +CONECT 729 731 730 727 735 +CONECT 730 729 +CONECT 731 734 733 732 729 +CONECT 732 731 +CONECT 733 731 +CONECT 734 731 +CONECT 735 729 736 737 +CONECT 736 735 +CONECT 737 735 738 739 +CONECT 738 737 +CONECT 739 737 740 741 749 +CONECT 740 739 +CONECT 741 743 739 747 742 +CONECT 742 741 +CONECT 743 744 746 745 741 +CONECT 744 743 +CONECT 745 743 +CONECT 746 743 +CONECT 747 748 741 +CONECT 748 747 +CONECT 749 739 751 750 +CONECT 750 749 +CONECT 751 752 753 749 +CONECT 752 751 +CONECT 753 754 751 755 771 +CONECT 754 753 +CONECT 755 758 753 757 756 +CONECT 756 755 +CONECT 757 755 +CONECT 758 761 759 760 755 +CONECT 759 758 +CONECT 760 758 +CONECT 761 764 763 762 758 +CONECT 762 761 +CONECT 763 761 +CONECT 764 767 766 765 761 +CONECT 765 764 +CONECT 766 764 +CONECT 767 769 770 768 764 +CONECT 768 767 +CONECT 769 767 +CONECT 770 767 +CONECT 771 753 773 772 +CONECT 772 771 +CONECT 773 774 771 775 +CONECT 774 773 +CONECT 775 773 785 777 776 +CONECT 776 775 +CONECT 777 778 775 783 779 +CONECT 778 777 +CONECT 779 777 782 781 780 +CONECT 780 779 +CONECT 781 779 +CONECT 782 779 +CONECT 783 784 777 +CONECT 784 783 +CONECT 785 786 775 787 +CONECT 786 785 +CONECT 787 785 789 788 +CONECT 788 787 +CONECT 789 790 787 805 791 +CONECT 790 789 +CONECT 791 789 794 793 792 +CONECT 792 791 +CONECT 793 791 +CONECT 794 803 795 791 +CONECT 795 794 797 796 +CONECT 796 795 +CONECT 797 799 798 795 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 801 804 794 +CONECT 804 803 +CONECT 805 789 807 806 +CONECT 806 805 +CONECT 807 808 809 805 +CONECT 808 807 +CONECT 809 811 807 819 810 +CONECT 810 809 +CONECT 811 817 813 812 809 +CONECT 812 811 +CONECT 813 814 815 811 816 +CONECT 814 813 +CONECT 815 813 +CONECT 816 813 +CONECT 817 818 811 +CONECT 818 817 +CONECT 819 820 809 821 +CONECT 820 819 +CONECT 821 819 823 822 +CONECT 822 821 +CONECT 823 833 824 821 825 +CONECT 824 823 +CONECT 825 823 826 827 831 +CONECT 826 825 +CONECT 827 825 830 828 829 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 825 832 +CONECT 832 831 +CONECT 833 835 834 823 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 839 838 835 843 +CONECT 838 837 +CONECT 839 842 841 840 837 +CONECT 840 839 +CONECT 841 839 +CONECT 842 839 +CONECT 843 837 845 844 +CONECT 844 843 +CONECT 845 846 843 847 +CONECT 846 845 +CONECT 847 845 849 858 848 +CONECT 848 847 +CONECT 849 851 850 847 852 +CONECT 850 849 +CONECT 851 849 +CONECT 852 853 849 854 855 +CONECT 853 852 +CONECT 854 852 +CONECT 855 852 857 856 +CONECT 856 855 +CONECT 857 855 +CONECT 858 860 847 859 +CONECT 859 858 +CONECT 860 858 +CONECT 861 87 310 862 279 +CONECT 862 861 864 +CONECT 863 866 864 867 865 +CONECT 864 862 863 +CONECT 865 863 +CONECT 866 863 +CONECT 867 863 +CONECT 868 869 +CONECT 869 868 870 +CONECT 870 869 +MASTER 0 0 0 0 0 0 0 0 870 0 870 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_3_front_4.pdb b/tests/nsga2/intermediate_molecules/min_iter_3_front_4.pdb new file mode 100644 index 0000000..0f703bf --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_3_front_4.pdb @@ -0,0 +1,1745 @@ +COMPND fitness: -2.8843 83.41749999999979 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 56.210 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.610 37.835 23.460 1.00 0.00 N +ATOM 2 H1 MET 1 14.587 38.236 24.394 1.00 0.00 H +ATOM 3 H2 MET 1 13.812 38.148 22.935 1.00 0.00 H +ATOM 4 H3 MET 1 15.464 38.178 23.039 1.00 0.00 H +ATOM 5 CA MET 1 14.662 36.367 23.555 1.00 0.00 C +ATOM 6 HA MET 1 13.728 36.021 23.999 1.00 0.00 H +ATOM 7 CB MET 1 14.806 35.736 22.157 1.00 0.00 C +ATOM 8 HB2 MET 1 13.928 35.994 21.567 1.00 0.00 H +ATOM 9 HB3 MET 1 15.682 36.159 21.666 1.00 0.00 H +ATOM 10 CG MET 1 14.957 34.205 22.185 1.00 0.00 C +ATOM 11 HG2 MET 1 15.847 33.953 22.764 1.00 0.00 H +ATOM 12 HG3 MET 1 14.092 33.769 22.688 1.00 0.00 H +ATOM 13 SD MET 1 15.133 33.423 20.557 1.00 0.00 S +ATOM 14 CE MET 1 13.430 33.524 19.932 1.00 0.00 C +ATOM 15 HE1 MET 1 13.103 34.563 19.883 1.00 0.00 H +ATOM 16 HE2 MET 1 13.381 33.092 18.933 1.00 0.00 H +ATOM 17 HE3 MET 1 12.763 32.967 20.591 1.00 0.00 H +ATOM 18 C MET 1 15.802 35.945 24.478 1.00 0.00 C +ATOM 19 O MET 1 16.945 36.312 24.240 1.00 0.00 O +ATOM 20 N GLN 2 15.501 35.116 25.481 1.00 0.00 N +ATOM 21 H GLN 2 14.536 34.897 25.661 1.00 0.00 H +ATOM 22 CA GLN 2 16.493 34.445 26.330 1.00 0.00 C +ATOM 23 HA GLN 2 17.239 35.169 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 15.772 33.892 27.577 1.00 0.00 C +ATOM 25 HB2 GLN 2 14.850 33.401 27.264 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.383 33.136 28.064 1.00 0.00 H +ATOM 27 CG GLN 2 15.424 34.965 28.621 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.944 35.807 28.133 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.697 34.542 29.314 1.00 0.00 H +ATOM 30 CD GLN 2 16.606 35.446 29.461 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.750 35.034 29.311 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.365 36.275 30.448 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.141 36.537 31.027 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.429 36.623 30.586 1.00 0.00 H +ATOM 35 C GLN 2 17.242 33.339 25.554 1.00 0.00 C +ATOM 36 O GLN 2 16.895 32.159 25.641 1.00 0.00 O +ATOM 37 N TYR 3 18.267 33.710 24.779 1.00 0.00 N +ATOM 38 H TYR 3 18.507 34.698 24.761 1.00 0.00 H +ATOM 39 CA TYR 3 19.130 32.772 24.050 1.00 0.00 C +ATOM 40 HA TYR 3 18.508 32.164 23.394 1.00 0.00 H +ATOM 41 CB TYR 3 20.138 33.545 23.190 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.628 34.306 23.802 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.913 32.853 22.855 1.00 0.00 H +ATOM 44 CG TYR 3 19.537 34.200 21.959 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.394 33.447 20.777 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.704 32.411 20.758 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.869 34.045 19.616 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.784 33.476 18.703 1.00 0.00 H +ATOM 49 CZ TYR 3 18.472 35.400 19.642 1.00 0.00 C +ATOM 50 OH TYR 3 17.979 35.981 18.519 1.00 0.00 O +ATOM 51 HH TYR 3 17.916 35.355 17.795 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.600 36.150 20.830 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.290 37.185 20.841 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.136 35.550 21.987 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.235 36.130 22.896 1.00 0.00 H +ATOM 56 C TYR 3 19.865 31.833 25.021 1.00 0.00 C +ATOM 57 O TYR 3 20.356 32.276 26.061 1.00 0.00 O +ATOM 58 N LYS 4 19.933 30.534 24.705 1.00 0.00 N +ATOM 59 H LYS 4 19.658 30.251 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 20.470 29.488 25.599 1.00 0.00 C +ATOM 61 HA LYS 4 20.193 29.725 26.622 1.00 0.00 H +ATOM 62 CB LYS 4 19.857 28.117 25.237 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.784 28.034 24.153 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.538 27.331 25.568 1.00 0.00 H +ATOM 65 CG LYS 4 18.476 27.805 25.856 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.226 26.778 25.589 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.551 27.859 26.942 1.00 0.00 H +ATOM 68 CD LYS 4 17.329 28.710 25.376 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.488 29.726 25.728 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.350 28.733 24.285 1.00 0.00 H +ATOM 71 CE LYS 4 15.930 28.229 25.815 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.191 28.785 25.230 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.824 27.174 25.545 1.00 0.00 H +ATOM 74 NZ LYS 4 15.640 28.425 27.266 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.696 29.397 27.534 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.693 28.146 27.503 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.250 27.898 27.886 1.00 0.00 H +ATOM 78 C LYS 4 22.000 29.450 25.582 1.00 0.00 C +ATOM 79 O LYS 4 22.635 29.697 24.563 1.00 0.00 O +HETATM 80 N HX1 5 22.614 29.087 26.706 1.00 0.00 N +HETATM 81 CA HX1 5 24.068 28.924 26.868 1.00 0.00 C +HETATM 82 C HX1 5 24.352 27.735 27.797 1.00 0.00 C +HETATM 83 O HX1 5 23.963 27.749 28.965 1.00 0.00 O +HETATM 84 CB HX1 5 24.686 30.249 27.361 1.00 0.00 C +HETATM 85 CG HX1 5 26.205 30.328 27.453 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.096 29.341 27.126 1.00 0.00 C +HETATM 87 ND1 HX1 5 26.899 31.425 27.989 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.188 31.059 27.927 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.345 29.815 27.484 1.00 0.00 N +HETATM 90 H HX1 5 22.036 28.964 27.535 1.00 0.00 H +HETATM 91 HA HX1 5 24.511 28.691 25.903 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.270 30.493 28.340 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.367 31.041 26.681 1.00 0.00 H +HETATM 94 HD2 HX1 5 26.901 28.351 26.753 1.00 0.00 H +HETATM 95 HE1 HX1 5 28.999 31.640 28.362 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.166 29.232 27.691 1.00 0.00 H +ATOM 97 N ILE 6 24.976 26.694 27.247 1.00 0.00 N +ATOM 98 H ILE 6 25.273 26.764 26.279 1.00 0.00 H +ATOM 99 CA ILE 6 25.416 25.484 27.957 1.00 0.00 C +ATOM 100 HA ILE 6 24.791 25.350 28.841 1.00 0.00 H +ATOM 101 CB ILE 6 25.219 24.234 27.066 1.00 0.00 C +ATOM 102 HB ILE 6 25.717 24.411 26.111 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.833 22.967 27.697 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.377 22.767 28.667 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.684 22.105 27.049 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.912 23.079 27.816 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.703 24.039 26.816 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.199 23.911 27.773 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.300 24.935 26.343 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.331 22.853 25.919 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.511 21.913 26.441 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.269 22.909 25.674 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.912 22.881 24.996 1.00 0.00 H +ATOM 114 C ILE 6 26.855 25.666 28.457 1.00 0.00 C +ATOM 115 O ILE 6 27.669 26.350 27.833 1.00 0.00 O +ATOM 116 N VAL 7 27.116 25.088 29.628 1.00 0.00 N +ATOM 117 H VAL 7 26.386 24.493 30.005 1.00 0.00 H +ATOM 118 CA VAL 7 28.247 25.361 30.522 1.00 0.00 C +ATOM 119 HA VAL 7 28.279 26.437 30.666 1.00 0.00 H +ATOM 120 CB VAL 7 27.910 24.707 31.877 1.00 0.00 C +ATOM 121 HB VAL 7 26.872 24.951 32.111 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.029 23.177 31.837 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.076 22.879 31.779 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.576 22.749 32.720 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.511 22.784 30.962 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.732 25.253 33.046 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.660 26.340 33.068 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.348 24.861 33.986 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.770 24.958 32.940 1.00 0.00 H +ATOM 130 C VAL 7 29.638 24.925 30.014 1.00 0.00 C +ATOM 131 O VAL 7 29.787 23.876 29.396 1.00 0.00 O +ATOM 132 N ARG 8 30.669 25.690 30.392 1.00 0.00 N +ATOM 133 H ARG 8 30.448 26.631 30.693 1.00 0.00 H +ATOM 134 CA ARG 8 32.095 25.295 30.376 1.00 0.00 C +ATOM 135 HA ARG 8 32.337 25.066 29.335 1.00 0.00 H +ATOM 136 CB ARG 8 33.001 26.478 30.815 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.031 26.191 30.597 1.00 0.00 H +ATOM 138 HB3 ARG 8 32.778 27.341 30.186 1.00 0.00 H +ATOM 139 CG ARG 8 32.964 26.926 32.298 1.00 0.00 C +ATOM 140 HG2 ARG 8 33.166 26.074 32.950 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.772 27.646 32.453 1.00 0.00 H +ATOM 142 CD ARG 8 31.641 27.598 32.706 1.00 0.00 C +ATOM 143 HD2 ARG 8 31.523 28.498 32.102 1.00 0.00 H +ATOM 144 HD3 ARG 8 30.811 26.937 32.492 1.00 0.00 H +ATOM 145 NE ARG 8 31.554 27.975 34.136 1.00 0.00 N +ATOM 146 HE ARG 8 31.477 28.963 34.328 1.00 0.00 H +ATOM 147 CZ ARG 8 31.360 27.181 35.177 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.436 25.880 35.096 1.00 0.00 N +ATOM 149 HH11 ARG 8 31.653 25.451 34.206 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.280 25.329 35.915 1.00 0.00 H +ATOM 151 NH2 ARG 8 31.059 27.706 36.329 1.00 0.00 N +ATOM 152 HH21 ARG 8 30.883 28.704 36.414 1.00 0.00 H +ATOM 153 HH22 ARG 8 30.972 27.170 37.183 1.00 0.00 H +ATOM 154 C ARG 8 32.399 24.032 31.197 1.00 0.00 C +ATOM 155 O ARG 8 31.989 23.928 32.359 1.00 0.00 O +ATOM 156 N GLY 9 33.235 23.149 30.643 1.00 0.00 N +ATOM 157 H GLY 9 33.483 23.302 29.677 1.00 0.00 H +ATOM 158 CA GLY 9 33.803 21.970 31.313 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.769 21.741 30.856 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.977 22.203 32.366 1.00 0.00 H +ATOM 161 C GLY 9 32.930 20.700 31.255 1.00 0.00 C +ATOM 162 O GLY 9 31.748 20.758 30.940 1.00 0.00 O +ATOM 163 N LYS 10 33.531 19.549 31.601 1.00 0.00 N +ATOM 164 H LYS 10 34.504 19.593 31.865 1.00 0.00 H +ATOM 165 CA LYS 10 32.919 18.202 31.470 1.00 0.00 C +ATOM 166 HA LYS 10 31.934 18.338 31.024 1.00 0.00 H +ATOM 167 CB LYS 10 33.740 17.354 30.479 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.240 18.008 29.765 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.509 16.801 31.019 1.00 0.00 H +ATOM 170 CG LYS 10 32.870 16.377 29.670 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.314 15.722 30.339 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.155 16.955 29.085 1.00 0.00 H +ATOM 173 CD LYS 10 33.734 15.532 28.729 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.372 16.192 28.137 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.363 14.862 29.315 1.00 0.00 H +ATOM 176 CE LYS 10 32.861 14.716 27.778 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.249 14.019 28.356 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.207 15.410 27.249 1.00 0.00 H +ATOM 179 NZ LYS 10 33.702 14.007 26.788 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.337 13.350 27.224 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.169 13.532 26.081 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.296 14.687 26.297 1.00 0.00 H +ATOM 183 C LYS 10 32.637 17.486 32.799 1.00 0.00 C +ATOM 184 O LYS 10 32.284 16.311 32.824 1.00 0.00 O +ATOM 185 N TRP 11 32.824 18.177 33.926 1.00 0.00 N +ATOM 186 H TRP 11 33.243 19.090 33.848 1.00 0.00 H +ATOM 187 CA TRP 11 32.126 17.892 35.182 1.00 0.00 C +ATOM 188 HA TRP 11 31.901 16.824 35.268 1.00 0.00 H +ATOM 189 CB TRP 11 33.036 18.283 36.357 1.00 0.00 C +ATOM 190 HB2 TRP 11 32.535 18.015 37.294 1.00 0.00 H +ATOM 191 HB3 TRP 11 33.950 17.689 36.296 1.00 0.00 H +ATOM 192 CG TRP 11 33.419 19.737 36.406 1.00 0.00 C +ATOM 193 CD1 TRP 11 32.861 20.665 37.216 1.00 0.00 C +ATOM 194 HD1 TRP 11 32.089 20.465 37.950 1.00 0.00 H +ATOM 195 NE1 TRP 11 33.403 21.907 36.943 1.00 0.00 N +ATOM 196 HE1 TRP 11 33.141 22.745 37.445 1.00 0.00 H +ATOM 197 CE2 TRP 11 34.318 21.848 35.912 1.00 0.00 C +ATOM 198 CZ2 TRP 11 35.085 22.819 35.250 1.00 0.00 C +ATOM 199 HZ2 TRP 11 35.003 23.862 35.519 1.00 0.00 H +ATOM 200 CH2 TRP 11 35.984 22.415 34.248 1.00 0.00 C +ATOM 201 HH2 TRP 11 36.605 23.145 33.744 1.00 0.00 H +ATOM 202 CZ3 TRP 11 36.107 21.052 33.924 1.00 0.00 C +ATOM 203 HZ3 TRP 11 36.838 20.745 33.183 1.00 0.00 H +ATOM 204 CE3 TRP 11 35.320 20.087 34.584 1.00 0.00 C +ATOM 205 HE3 TRP 11 35.461 19.041 34.352 1.00 0.00 H +ATOM 206 CD2 TRP 11 34.391 20.460 35.583 1.00 0.00 C +ATOM 207 C TRP 11 30.804 18.683 35.243 1.00 0.00 C +ATOM 208 O TRP 11 29.944 18.363 36.056 1.00 0.00 O +ATOM 209 N VAL 12 30.660 19.740 34.430 1.00 0.00 N +ATOM 210 H VAL 12 31.413 19.900 33.802 1.00 0.00 H +ATOM 211 CA VAL 12 29.415 20.530 34.220 1.00 0.00 C +ATOM 212 HA VAL 12 29.656 21.259 33.447 1.00 0.00 H +ATOM 213 CB VAL 12 29.101 21.349 35.518 1.00 0.00 C +ATOM 214 HB VAL 12 29.296 20.712 36.378 1.00 0.00 H +ATOM 215 CG1 VAL 12 27.725 21.975 35.716 1.00 0.00 C +ATOM 216 HG11 VAL 12 26.970 21.208 35.955 1.00 0.00 H +ATOM 217 HG12 VAL 12 27.751 22.645 36.588 1.00 0.00 H +ATOM 218 HG13 VAL 12 27.441 22.553 34.835 1.00 0.00 H +ATOM 219 CG2 VAL 12 30.126 22.530 35.519 1.00 0.00 C +ATOM 220 HG21 VAL 12 29.940 23.175 34.670 1.00 0.00 H +ATOM 221 HG22 VAL 12 30.055 23.143 36.414 1.00 0.00 H +ATOM 222 HG23 VAL 12 31.147 22.192 35.430 1.00 0.00 H +ATOM 223 C VAL 12 28.340 19.651 33.542 1.00 0.00 C +ATOM 224 O VAL 12 28.703 18.718 32.836 1.00 0.00 O +ATOM 225 N LYS 13 27.051 19.990 33.615 1.00 0.00 N +ATOM 226 H LYS 13 26.818 20.626 34.355 1.00 0.00 H +ATOM 227 CA LYS 13 26.031 19.654 32.590 1.00 0.00 C +ATOM 228 HA LYS 13 26.538 19.769 31.626 1.00 0.00 H +ATOM 229 CB LYS 13 25.592 18.175 32.709 1.00 0.00 C +ATOM 230 HB2 LYS 13 26.368 17.610 33.220 1.00 0.00 H +ATOM 231 HB3 LYS 13 24.698 18.118 33.320 1.00 0.00 H +ATOM 232 CG LYS 13 25.353 17.514 31.333 1.00 0.00 C +ATOM 233 HG2 LYS 13 24.456 17.931 30.874 1.00 0.00 H +ATOM 234 HG3 LYS 13 26.197 17.751 30.683 1.00 0.00 H +ATOM 235 CD LYS 13 25.238 15.981 31.410 1.00 0.00 C +ATOM 236 HD2 LYS 13 25.170 15.578 30.397 1.00 0.00 H +ATOM 237 HD3 LYS 13 26.145 15.589 31.878 1.00 0.00 H +ATOM 238 CE LYS 13 24.004 15.541 32.208 1.00 0.00 C +ATOM 239 HE2 LYS 13 23.955 16.153 33.114 1.00 0.00 H +ATOM 240 HE3 LYS 13 23.108 15.743 31.609 1.00 0.00 H +ATOM 241 NZ LYS 13 24.068 14.106 32.592 1.00 0.00 N +ATOM 242 HZ1 LYS 13 24.999 13.834 32.897 1.00 0.00 H +ATOM 243 HZ2 LYS 13 23.472 13.932 33.399 1.00 0.00 H +ATOM 244 HZ3 LYS 13 23.792 13.478 31.849 1.00 0.00 H +ATOM 245 C LYS 13 24.841 20.629 32.531 1.00 0.00 C +ATOM 246 O LYS 13 23.849 20.366 31.856 1.00 0.00 O +ATOM 247 N GLY 14 24.939 21.740 33.268 1.00 0.00 N +ATOM 248 H GLY 14 25.799 21.915 33.754 1.00 0.00 H +ATOM 249 CA GLY 14 23.872 22.731 33.398 1.00 0.00 C +ATOM 250 HA2 GLY 14 22.917 22.216 33.519 1.00 0.00 H +ATOM 251 HA3 GLY 14 24.041 23.329 34.294 1.00 0.00 H +ATOM 252 C GLY 14 23.740 23.693 32.199 1.00 0.00 C +ATOM 253 O GLY 14 24.623 23.800 31.347 1.00 0.00 O +ATOM 254 N VAL 15 22.630 24.433 32.175 1.00 0.00 N +ATOM 255 H VAL 15 21.967 24.310 32.924 1.00 0.00 H +ATOM 256 CA VAL 15 22.258 25.391 31.125 1.00 0.00 C +ATOM 257 HA VAL 15 23.156 25.664 30.577 1.00 0.00 H +ATOM 258 CB VAL 15 21.291 24.727 30.116 1.00 0.00 C +ATOM 259 HB VAL 15 21.791 23.839 29.715 1.00 0.00 H +ATOM 260 CG1 VAL 15 19.966 24.264 30.749 1.00 0.00 C +ATOM 261 HG11 VAL 15 19.406 25.113 31.134 1.00 0.00 H +ATOM 262 HG12 VAL 15 19.365 23.754 29.993 1.00 0.00 H +ATOM 263 HG13 VAL 15 20.160 23.557 31.554 1.00 0.00 H +ATOM 264 CG2 VAL 15 20.963 25.647 28.933 1.00 0.00 C +ATOM 265 HG21 VAL 15 21.883 26.004 28.474 1.00 0.00 H +ATOM 266 HG22 VAL 15 20.402 25.080 28.186 1.00 0.00 H +ATOM 267 HG23 VAL 15 20.358 26.490 29.258 1.00 0.00 H +ATOM 268 C VAL 15 21.686 26.658 31.751 1.00 0.00 C +ATOM 269 O VAL 15 20.993 26.607 32.770 1.00 0.00 O +HETATM 270 N HY1 16 21.983 27.814 31.152 1.00 0.00 N +HETATM 271 CA HY1 16 21.415 29.132 31.476 1.00 0.00 C +HETATM 272 C HY1 16 21.134 29.908 30.177 1.00 0.00 C +HETATM 273 O HY1 16 21.275 29.361 29.086 1.00 0.00 O +HETATM 274 CB HY1 16 22.356 29.875 32.450 1.00 0.00 C +HETATM 275 CG HY1 16 23.709 30.229 31.878 1.00 0.00 C +HETATM 276 CD2 HY1 16 24.068 31.431 31.324 1.00 0.00 C +HETATM 277 ND1 HY1 16 24.813 29.410 31.817 1.00 0.00 N +HETATM 278 CE1 HY1 16 25.816 30.121 31.269 1.00 0.00 C +HETATM 279 NE2 HY1 16 25.412 31.360 30.935 1.00 0.00 N +HETATM 280 H HY1 16 22.553 27.772 30.305 1.00 0.00 H +HETATM 281 HA HY1 16 20.458 28.981 31.988 1.00 0.00 H +HETATM 282 HB2 HY1 16 21.869 30.793 32.788 1.00 0.00 H +HETATM 283 HB3 HY1 16 22.504 29.262 33.342 1.00 0.00 H +HETATM 284 HD1 HY1 16 24.881 28.463 32.165 1.00 0.00 H +HETATM 285 HD2 HY1 16 23.428 32.300 31.222 1.00 0.00 H +HETATM 286 HE1 HY1 16 26.831 29.752 31.127 1.00 0.00 H +ATOM 287 N THR 17 20.733 31.171 30.282 1.00 0.00 N +ATOM 288 H THR 17 20.606 31.590 31.189 1.00 0.00 H +ATOM 289 CA THR 17 20.339 32.027 29.148 1.00 0.00 C +ATOM 290 HA THR 17 20.769 31.599 28.239 1.00 0.00 H +ATOM 291 CB THR 17 18.804 32.054 28.997 1.00 0.00 C +ATOM 292 HB THR 17 18.548 32.701 28.154 1.00 0.00 H +ATOM 293 CG2 THR 17 18.153 30.699 28.714 1.00 0.00 C +ATOM 294 HG21 THR 17 18.358 29.982 29.502 1.00 0.00 H +ATOM 295 HG22 THR 17 17.081 30.790 28.628 1.00 0.00 H +ATOM 296 HG23 THR 17 18.516 30.287 27.783 1.00 0.00 H +ATOM 297 OG1 THR 17 18.212 32.553 30.159 1.00 0.00 O +ATOM 298 HG1 THR 17 18.144 33.518 30.025 1.00 0.00 H +ATOM 299 C THR 17 20.886 33.446 29.236 1.00 0.00 C +ATOM 300 O THR 17 21.350 33.861 30.295 1.00 0.00 O +HETATM 301 N HY2 18 20.813 34.187 28.127 1.00 0.00 N +HETATM 302 CA HY2 18 21.081 35.625 28.066 1.00 0.00 C +HETATM 303 C HY2 18 19.976 36.319 27.265 1.00 0.00 C +HETATM 304 O HY2 18 19.648 35.866 26.170 1.00 0.00 O +HETATM 305 CB HY2 18 22.427 35.918 27.401 1.00 0.00 C +HETATM 306 CG HY2 18 23.623 35.439 28.194 1.00 0.00 C +HETATM 307 CD2 HY2 18 24.155 34.177 28.162 1.00 0.00 C +HETATM 308 ND1 HY2 18 24.312 36.145 29.158 1.00 0.00 N +HETATM 309 CE1 HY2 18 25.247 35.326 29.676 1.00 0.00 C +HETATM 310 NE2 HY2 18 25.185 34.110 29.103 1.00 0.00 N +HETATM 311 H HY2 18 20.458 33.740 27.282 1.00 0.00 H +HETATM 312 HA HY2 18 21.088 36.044 29.084 1.00 0.00 H +HETATM 313 HB2 HY2 18 22.454 35.451 26.408 1.00 0.00 H +HETATM 314 HB3 HY2 18 22.525 37.001 27.258 1.00 0.00 H +HETATM 315 HD1 HY2 18 24.160 37.108 29.430 1.00 0.00 H +HETATM 316 HD2 HY2 18 23.816 33.363 27.535 1.00 0.00 H +HETATM 317 HE1 HY2 18 25.945 35.606 30.456 1.00 0.00 H +ATOM 318 N GLU 19 19.430 37.417 27.787 1.00 0.00 N +ATOM 319 H GLU 19 19.758 37.740 28.682 1.00 0.00 H +ATOM 320 CA GLU 19 18.419 38.226 27.104 1.00 0.00 C +ATOM 321 HA GLU 19 17.699 37.546 26.656 1.00 0.00 H +ATOM 322 CB GLU 19 17.705 39.102 28.147 1.00 0.00 C +ATOM 323 HB2 GLU 19 17.377 38.469 28.971 1.00 0.00 H +ATOM 324 HB3 GLU 19 18.414 39.828 28.557 1.00 0.00 H +ATOM 325 CG GLU 19 16.477 39.854 27.616 1.00 0.00 C +ATOM 326 HG2 GLU 19 15.971 40.349 28.452 1.00 0.00 H +ATOM 327 HG3 GLU 19 16.810 40.632 26.924 1.00 0.00 H +ATOM 328 CD GLU 19 15.524 38.897 26.903 1.00 0.00 C +ATOM 329 OE1 GLU 19 15.614 38.801 25.661 1.00 0.00 O +ATOM 330 OE2 GLU 19 14.785 38.158 27.578 1.00 0.00 O +ATOM 331 C GLU 19 19.040 39.069 25.978 1.00 0.00 C +ATOM 332 O GLU 19 20.090 39.684 26.183 1.00 0.00 O +ATOM 333 N ALA 20 18.406 39.106 24.798 1.00 0.00 N +ATOM 334 H ALA 20 17.526 38.600 24.725 1.00 0.00 H +ATOM 335 CA ALA 20 18.770 39.982 23.679 1.00 0.00 C +ATOM 336 HA ALA 20 18.902 40.994 24.063 1.00 0.00 H +ATOM 337 CB ALA 20 20.096 39.515 23.062 1.00 0.00 C +ATOM 338 HB1 ALA 20 19.972 38.533 22.606 1.00 0.00 H +ATOM 339 HB2 ALA 20 20.416 40.226 22.305 1.00 0.00 H +ATOM 340 HB3 ALA 20 20.879 39.462 23.817 1.00 0.00 H +ATOM 341 C ALA 20 17.694 40.018 22.571 1.00 0.00 C +ATOM 342 O ALA 20 16.874 39.108 22.434 1.00 0.00 O +ATOM 343 N VAL 21 17.756 41.039 21.709 1.00 0.00 N +ATOM 344 H VAL 21 18.418 41.780 21.884 1.00 0.00 H +ATOM 345 CA VAL 21 17.017 41.071 20.423 1.00 0.00 C +ATOM 346 HA VAL 21 16.020 40.661 20.587 1.00 0.00 H +ATOM 347 CB VAL 21 16.842 42.514 19.898 1.00 0.00 C +ATOM 348 HB VAL 21 16.188 42.472 19.027 1.00 0.00 H +ATOM 349 CG1 VAL 21 16.159 43.411 20.937 1.00 0.00 C +ATOM 350 HG11 VAL 21 16.810 43.579 21.795 1.00 0.00 H +ATOM 351 HG12 VAL 21 15.918 44.373 20.486 1.00 0.00 H +ATOM 352 HG13 VAL 21 15.232 42.951 21.279 1.00 0.00 H +ATOM 353 CG2 VAL 21 18.158 43.176 19.464 1.00 0.00 C +ATOM 354 HG21 VAL 21 18.596 42.634 18.626 1.00 0.00 H +ATOM 355 HG22 VAL 21 17.964 44.195 19.129 1.00 0.00 H +ATOM 356 HG23 VAL 21 18.872 43.205 20.287 1.00 0.00 H +ATOM 357 C VAL 21 17.666 40.197 19.339 1.00 0.00 C +ATOM 358 O VAL 21 16.989 39.788 18.400 1.00 0.00 O +ATOM 359 N ASP 22 18.962 39.912 19.481 1.00 0.00 N +ATOM 360 H ASP 22 19.441 40.273 20.289 1.00 0.00 H +ATOM 361 CA ASP 22 19.803 39.155 18.549 1.00 0.00 C +ATOM 362 HA ASP 22 19.204 38.379 18.068 1.00 0.00 H +ATOM 363 CB ASP 22 20.347 40.115 17.467 1.00 0.00 C +ATOM 364 HB2 ASP 22 19.507 40.640 17.014 1.00 0.00 H +ATOM 365 HB3 ASP 22 20.969 40.862 17.961 1.00 0.00 H +ATOM 366 CG ASP 22 21.171 39.445 16.351 1.00 0.00 C +ATOM 367 OD1 ASP 22 21.358 40.133 15.304 1.00 0.00 O +ATOM 368 OD2 ASP 22 21.600 38.297 16.500 1.00 0.00 O +ATOM 369 C ASP 22 20.940 38.484 19.342 1.00 0.00 C +ATOM 370 O ASP 22 21.503 39.076 20.270 1.00 0.00 O +ATOM 371 N LEU 23 21.311 37.261 18.968 1.00 0.00 N +ATOM 372 H LEU 23 20.939 36.925 18.089 1.00 0.00 H +ATOM 373 CA LEU 23 22.452 36.571 19.560 1.00 0.00 C +ATOM 374 HA LEU 23 22.285 36.550 20.632 1.00 0.00 H +ATOM 375 CB LEU 23 22.485 35.111 19.082 1.00 0.00 C +ATOM 376 HB2 LEU 23 21.546 34.665 19.394 1.00 0.00 H +ATOM 377 HB3 LEU 23 22.522 35.056 17.994 1.00 0.00 H +ATOM 378 CG LEU 23 23.640 34.288 19.690 1.00 0.00 C +ATOM 379 HG LEU 23 23.819 34.622 20.711 1.00 0.00 H +ATOM 380 CD1 LEU 23 23.243 32.811 19.763 1.00 0.00 C +ATOM 381 HD11 LEU 23 22.968 32.445 18.779 1.00 0.00 H +ATOM 382 HD12 LEU 23 24.071 32.222 20.159 1.00 0.00 H +ATOM 383 HD13 LEU 23 22.398 32.707 20.441 1.00 0.00 H +ATOM 384 CD2 LEU 23 24.930 34.430 18.880 1.00 0.00 C +ATOM 385 HD21 LEU 23 25.532 35.241 19.277 1.00 0.00 H +ATOM 386 HD22 LEU 23 25.534 33.529 18.950 1.00 0.00 H +ATOM 387 HD23 LEU 23 24.718 34.659 17.839 1.00 0.00 H +ATOM 388 C LEU 23 23.771 37.324 19.343 1.00 0.00 C +ATOM 389 O LEU 23 24.614 37.294 20.233 1.00 0.00 O +ATOM 390 N ALA 24 23.950 38.060 18.242 1.00 0.00 N +ATOM 391 H ALA 24 23.204 38.085 17.546 1.00 0.00 H +ATOM 392 CA ALA 24 25.158 38.865 18.025 1.00 0.00 C +ATOM 393 HA ALA 24 26.018 38.218 18.197 1.00 0.00 H +ATOM 394 CB ALA 24 25.202 39.299 16.558 1.00 0.00 C +ATOM 395 HB1 ALA 24 24.369 39.964 16.325 1.00 0.00 H +ATOM 396 HB2 ALA 24 26.142 39.815 16.363 1.00 0.00 H +ATOM 397 HB3 ALA 24 25.148 38.425 15.906 1.00 0.00 H +ATOM 398 C ALA 24 25.306 40.056 19.005 1.00 0.00 C +ATOM 399 O ALA 24 26.389 40.642 19.118 1.00 0.00 O +ATOM 400 N GLU 25 24.251 40.394 19.761 1.00 0.00 N +ATOM 401 H GLU 25 23.380 39.906 19.598 1.00 0.00 H +ATOM 402 CA GLU 25 24.335 41.202 20.988 1.00 0.00 C +ATOM 403 HA GLU 25 25.200 41.864 20.931 1.00 0.00 H +ATOM 404 CB GLU 25 23.081 42.091 21.112 1.00 0.00 C +ATOM 405 HB2 GLU 25 22.197 41.461 21.036 1.00 0.00 H +ATOM 406 HB3 GLU 25 23.072 42.547 22.099 1.00 0.00 H +ATOM 407 CG GLU 25 22.993 43.209 20.067 1.00 0.00 C +ATOM 408 HG2 GLU 25 23.178 42.799 19.072 1.00 0.00 H +ATOM 409 HG3 GLU 25 21.977 43.613 20.061 1.00 0.00 H +ATOM 410 CD GLU 25 23.989 44.335 20.372 1.00 0.00 C +ATOM 411 OE1 GLU 25 23.587 45.318 21.037 1.00 0.00 O +ATOM 412 OE2 GLU 25 25.166 44.185 19.957 1.00 0.00 O +ATOM 413 C GLU 25 24.520 40.324 22.230 1.00 0.00 C +ATOM 414 O GLU 25 25.355 40.629 23.079 1.00 0.00 O +ATOM 415 N ALA 26 23.838 39.165 22.340 1.00 0.00 N +ATOM 416 H ALA 26 23.144 38.939 21.634 1.00 0.00 H +ATOM 417 CA ALA 26 24.041 38.207 23.435 1.00 0.00 C +ATOM 418 HA ALA 26 23.857 38.735 24.370 1.00 0.00 H +ATOM 419 CB ALA 26 23.053 37.055 23.307 1.00 0.00 C +ATOM 420 HB1 ALA 26 23.352 36.400 22.493 1.00 0.00 H +ATOM 421 HB2 ALA 26 23.041 36.471 24.227 1.00 0.00 H +ATOM 422 HB3 ALA 26 22.059 37.460 23.119 1.00 0.00 H +ATOM 423 C ALA 26 25.475 37.640 23.529 1.00 0.00 C +ATOM 424 O ALA 26 25.878 37.199 24.606 1.00 0.00 O +ATOM 425 N GLU 27 26.225 37.656 22.426 1.00 0.00 N +ATOM 426 H GLU 27 25.728 37.822 21.561 1.00 0.00 H +ATOM 427 CA GLU 27 27.657 37.363 22.351 1.00 0.00 C +ATOM 428 HA GLU 27 27.828 36.387 22.786 1.00 0.00 H +ATOM 429 CB GLU 27 28.049 37.295 20.810 1.00 0.00 C +ATOM 430 HB2 GLU 27 27.320 36.650 20.339 1.00 0.00 H +ATOM 431 HB3 GLU 27 27.974 38.279 20.364 1.00 0.00 H +ATOM 432 CG GLU 27 29.432 36.733 20.511 1.00 0.00 C +ATOM 433 HG2 GLU 27 30.208 37.425 20.927 1.00 0.00 H +ATOM 434 HG3 GLU 27 29.562 35.764 21.055 1.00 0.00 H +ATOM 435 CD GLU 27 29.655 36.541 18.998 1.00 0.00 C +ATOM 436 OE1 GLU 27 30.446 37.312 18.444 1.00 0.00 O +ATOM 437 OE2 GLU 27 29.027 35.659 18.399 1.00 0.00 O +ATOM 438 C GLU 27 28.483 38.382 23.126 1.00 0.00 C +ATOM 439 O GLU 27 29.294 38.026 23.980 1.00 0.00 O +ATOM 440 N LYS 28 28.171 39.676 22.949 1.00 0.00 N +ATOM 441 H LYS 28 27.412 39.874 22.302 1.00 0.00 H +ATOM 442 CA LYS 28 28.730 40.786 23.720 1.00 0.00 C +ATOM 443 HA LYS 28 29.826 40.697 23.712 1.00 0.00 H +ATOM 444 CB LYS 28 28.359 42.145 23.096 1.00 0.00 C +ATOM 445 HB2 LYS 28 27.290 42.317 23.207 1.00 0.00 H +ATOM 446 HB3 LYS 28 28.886 42.916 23.652 1.00 0.00 H +ATOM 447 CG LYS 28 28.732 42.265 21.607 1.00 0.00 C +ATOM 448 HG2 LYS 28 29.789 42.022 21.483 1.00 0.00 H +ATOM 449 HG3 LYS 28 28.138 41.561 21.024 1.00 0.00 H +ATOM 450 CD LYS 28 28.480 43.692 21.087 1.00 0.00 C +ATOM 451 HD2 LYS 28 27.472 44.012 21.359 1.00 0.00 H +ATOM 452 HD3 LYS 28 29.187 44.367 21.577 1.00 0.00 H +ATOM 453 CE LYS 28 28.656 43.806 19.568 1.00 0.00 C +ATOM 454 HE2 LYS 28 28.808 44.863 19.321 1.00 0.00 H +ATOM 455 HE3 LYS 28 29.558 43.270 19.263 1.00 0.00 H +ATOM 456 NZ LYS 28 27.462 43.300 18.844 1.00 0.00 N +ATOM 457 HZ1 LYS 28 26.620 43.776 19.187 1.00 0.00 H +ATOM 458 HZ2 LYS 28 27.524 43.469 17.852 1.00 0.00 H +ATOM 459 HZ3 LYS 28 27.296 42.311 19.010 1.00 0.00 H +ATOM 460 C LYS 28 28.293 40.734 25.190 1.00 0.00 C +ATOM 461 O LYS 28 29.136 40.838 26.076 1.00 0.00 O +ATOM 462 N PHE 29 27.019 40.477 25.467 1.00 0.00 N +ATOM 463 H PHE 29 26.355 40.453 24.698 1.00 0.00 H +ATOM 464 CA PHE 29 26.517 40.332 26.846 1.00 0.00 C +ATOM 465 HA PHE 29 26.806 41.218 27.411 1.00 0.00 H +ATOM 466 CB PHE 29 24.977 40.304 26.842 1.00 0.00 C +ATOM 467 HB2 PHE 29 24.659 39.367 26.390 1.00 0.00 H +ATOM 468 HB3 PHE 29 24.625 40.303 27.880 1.00 0.00 H +ATOM 469 CG PHE 29 24.287 41.460 26.136 1.00 0.00 C +ATOM 470 CD1 PHE 29 23.049 41.246 25.495 1.00 0.00 C +ATOM 471 HD1 PHE 29 22.579 40.275 25.527 1.00 0.00 H +ATOM 472 CE1 PHE 29 22.410 42.297 24.807 1.00 0.00 C +ATOM 473 HE1 PHE 29 21.469 42.116 24.311 1.00 0.00 H +ATOM 474 CZ PHE 29 23.003 43.573 24.765 1.00 0.00 C +ATOM 475 HZ PHE 29 22.524 44.372 24.222 1.00 0.00 H +ATOM 476 CE2 PHE 29 24.219 43.806 25.428 1.00 0.00 C +ATOM 477 HE2 PHE 29 24.669 44.778 25.408 1.00 0.00 H +ATOM 478 CD2 PHE 29 24.853 42.757 26.115 1.00 0.00 C +ATOM 479 HD2 PHE 29 25.782 42.959 26.619 1.00 0.00 H +ATOM 480 C PHE 29 27.097 39.092 27.576 1.00 0.00 C +ATOM 481 O PHE 29 27.242 39.121 28.804 1.00 0.00 O +ATOM 482 N THR 30 27.471 38.019 26.855 1.00 0.00 N +ATOM 483 H THR 30 27.262 38.018 25.867 1.00 0.00 H +ATOM 484 CA THR 30 28.208 36.874 27.383 1.00 0.00 C +ATOM 485 HA THR 30 27.806 36.552 28.340 1.00 0.00 H +ATOM 486 CB THR 30 28.165 35.642 26.355 1.00 0.00 C +ATOM 487 HB THR 30 28.671 35.982 25.465 1.00 0.00 H +ATOM 488 CG2 THR 30 29.010 34.482 26.856 1.00 0.00 C +ATOM 489 HG21 THR 30 28.763 34.155 27.853 1.00 0.00 H +ATOM 490 HG22 THR 30 28.991 33.595 26.210 1.00 0.00 H +ATOM 491 HG23 THR 30 30.047 34.791 26.859 1.00 0.00 H +ATOM 492 OG1 THR 30 26.844 35.210 26.048 1.00 0.00 O +ATOM 493 HG1 THR 30 26.349 35.962 25.650 1.00 0.00 H +ATOM 494 C THR 30 29.681 37.276 27.719 1.00 0.00 C +ATOM 495 O THR 30 30.155 36.942 28.795 1.00 0.00 O +ATOM 496 N LYS 31 30.332 38.079 26.889 1.00 0.00 N +ATOM 497 H LYS 31 29.871 38.384 26.044 1.00 0.00 H +ATOM 498 CA LYS 31 31.674 38.634 27.157 1.00 0.00 C +ATOM 499 HA LYS 31 32.350 37.837 27.474 1.00 0.00 H +ATOM 500 CB LYS 31 32.241 39.245 25.864 1.00 0.00 C +ATOM 501 HB2 LYS 31 31.523 39.940 25.448 1.00 0.00 H +ATOM 502 HB3 LYS 31 33.157 39.786 26.103 1.00 0.00 H +ATOM 503 CG LYS 31 32.581 38.157 24.832 1.00 0.00 C +ATOM 504 HG2 LYS 31 33.317 37.480 25.261 1.00 0.00 H +ATOM 505 HG3 LYS 31 31.704 37.566 24.575 1.00 0.00 H +ATOM 506 CD LYS 31 33.154 38.798 23.560 1.00 0.00 C +ATOM 507 HD2 LYS 31 32.363 39.356 23.055 1.00 0.00 H +ATOM 508 HD3 LYS 31 33.951 39.488 23.827 1.00 0.00 H +ATOM 509 CE LYS 31 33.714 37.746 22.591 1.00 0.00 C +ATOM 510 HE2 LYS 31 32.948 37.001 22.373 1.00 0.00 H +ATOM 511 HE3 LYS 31 33.955 38.245 21.648 1.00 0.00 H +ATOM 512 NZ LYS 31 34.933 37.089 23.115 1.00 0.00 N +ATOM 513 HZ1 LYS 31 34.746 36.340 23.769 1.00 0.00 H +ATOM 514 HZ2 LYS 31 35.437 36.639 22.348 1.00 0.00 H +ATOM 515 HZ3 LYS 31 35.592 37.732 23.552 1.00 0.00 H +ATOM 516 C LYS 31 31.693 39.656 28.305 1.00 0.00 C +ATOM 517 O LYS 31 32.674 39.678 29.044 1.00 0.00 O +ATOM 518 N ALA 32 30.615 40.417 28.505 1.00 0.00 N +ATOM 519 H ALA 32 29.893 40.433 27.798 1.00 0.00 H +ATOM 520 CA ALA 32 30.452 41.245 29.699 1.00 0.00 C +ATOM 521 HA ALA 32 31.287 41.943 29.769 1.00 0.00 H +ATOM 522 CB ALA 32 29.160 42.059 29.583 1.00 0.00 C +ATOM 523 HB1 ALA 32 28.295 41.401 29.522 1.00 0.00 H +ATOM 524 HB2 ALA 32 29.045 42.699 30.464 1.00 0.00 H +ATOM 525 HB3 ALA 32 29.194 42.691 28.695 1.00 0.00 H +ATOM 526 C ALA 32 30.481 40.374 30.974 1.00 0.00 C +ATOM 527 O ALA 32 31.390 40.511 31.786 1.00 0.00 O +ATOM 528 N ALA 33 29.599 39.373 31.058 1.00 0.00 N +ATOM 529 H ALA 33 28.886 39.292 30.345 1.00 0.00 H +ATOM 530 CA ALA 33 29.555 38.428 32.181 1.00 0.00 C +ATOM 531 HA ALA 33 29.465 39.008 33.099 1.00 0.00 H +ATOM 532 CB ALA 33 28.289 37.575 32.028 1.00 0.00 C +ATOM 533 HB1 ALA 33 28.346 36.978 31.119 1.00 0.00 H +ATOM 534 HB2 ALA 33 28.181 36.909 32.886 1.00 0.00 H +ATOM 535 HB3 ALA 33 27.410 38.219 31.981 1.00 0.00 H +ATOM 536 C ALA 33 30.821 37.541 32.333 1.00 0.00 C +ATOM 537 O ALA 33 30.921 36.798 33.305 1.00 0.00 O +ATOM 538 N ALA 34 31.757 37.568 31.379 1.00 0.00 N +ATOM 539 H ALA 34 31.589 38.159 30.584 1.00 0.00 H +ATOM 540 CA ALA 34 33.091 36.966 31.505 1.00 0.00 C +ATOM 541 HA ALA 34 33.037 36.139 32.213 1.00 0.00 H +ATOM 542 CB ALA 34 33.508 36.399 30.143 1.00 0.00 C +ATOM 543 HB1 ALA 34 33.649 37.207 29.426 1.00 0.00 H +ATOM 544 HB2 ALA 34 34.450 35.861 30.259 1.00 0.00 H +ATOM 545 HB3 ALA 34 32.750 35.708 29.774 1.00 0.00 H +ATOM 546 C ALA 34 34.123 37.961 32.063 1.00 0.00 C +ATOM 547 O ALA 34 34.832 37.631 33.008 1.00 0.00 O +ATOM 548 N ASN 35 34.171 39.202 31.560 1.00 0.00 N +ATOM 549 H ASN 35 33.544 39.440 30.800 1.00 0.00 H +ATOM 550 CA ASN 35 35.041 40.256 32.096 1.00 0.00 C +ATOM 551 HA ASN 35 36.050 39.850 32.215 1.00 0.00 H +ATOM 552 CB ASN 35 35.128 41.408 31.082 1.00 0.00 C +ATOM 553 HB2 ASN 35 34.128 41.702 30.765 1.00 0.00 H +ATOM 554 HB3 ASN 35 35.595 42.264 31.566 1.00 0.00 H +ATOM 555 CG ASN 35 35.989 41.053 29.876 1.00 0.00 C +ATOM 556 OD1 ASN 35 37.202 40.998 29.943 1.00 0.00 O +ATOM 557 ND2 ASN 35 35.397 40.799 28.737 1.00 0.00 N +ATOM 558 HD21 ASN 35 36.007 40.585 27.947 1.00 0.00 H +ATOM 559 HD22 ASN 35 34.398 40.684 28.702 1.00 0.00 H +ATOM 560 C ASN 35 34.614 40.741 33.504 1.00 0.00 C +ATOM 561 O ASN 35 35.469 41.137 34.290 1.00 0.00 O +ATOM 562 N ASP 36 33.333 40.617 33.865 1.00 0.00 N +ATOM 563 H ASP 36 32.647 40.420 33.146 1.00 0.00 H +ATOM 564 CA ASP 36 32.837 40.768 35.249 1.00 0.00 C +ATOM 565 HA ASP 36 33.163 41.738 35.630 1.00 0.00 H +ATOM 566 CB ASP 36 31.291 40.753 35.253 1.00 0.00 C +ATOM 567 HB2 ASP 36 30.950 39.847 34.749 1.00 0.00 H +ATOM 568 HB3 ASP 36 30.954 40.684 36.289 1.00 0.00 H +ATOM 569 CG ASP 36 30.604 41.992 34.634 1.00 0.00 C +ATOM 570 OD1 ASP 36 31.204 43.091 34.688 1.00 0.00 O +ATOM 571 OD2 ASP 36 29.439 41.870 34.172 1.00 0.00 O +ATOM 572 C ASP 36 33.415 39.697 36.211 1.00 0.00 C +ATOM 573 O ASP 36 33.441 39.908 37.424 1.00 0.00 O +ATOM 574 N LEU 37 33.904 38.557 35.688 1.00 0.00 N +ATOM 575 H LEU 37 33.842 38.450 34.686 1.00 0.00 H +ATOM 576 CA LEU 37 34.657 37.527 36.423 1.00 0.00 C +ATOM 577 HA LEU 37 34.464 37.650 37.491 1.00 0.00 H +ATOM 578 CB LEU 37 34.109 36.145 35.994 1.00 0.00 C +ATOM 579 HB2 LEU 37 33.040 36.119 36.207 1.00 0.00 H +ATOM 580 HB3 LEU 37 34.231 36.052 34.917 1.00 0.00 H +ATOM 581 CG LEU 37 34.771 34.914 36.645 1.00 0.00 C +ATOM 582 HG LEU 37 35.840 34.913 36.439 1.00 0.00 H +ATOM 583 CD1 LEU 37 34.551 34.857 38.159 1.00 0.00 C +ATOM 584 HD11 LEU 37 33.486 34.879 38.385 1.00 0.00 H +ATOM 585 HD12 LEU 37 34.992 33.944 38.560 1.00 0.00 H +ATOM 586 HD13 LEU 37 35.040 35.710 38.628 1.00 0.00 H +ATOM 587 CD2 LEU 37 34.177 33.637 36.042 1.00 0.00 C +ATOM 588 HD21 LEU 37 34.355 33.629 34.966 1.00 0.00 H +ATOM 589 HD22 LEU 37 34.662 32.764 36.478 1.00 0.00 H +ATOM 590 HD23 LEU 37 33.105 33.596 36.231 1.00 0.00 H +ATOM 591 C LEU 37 36.190 37.649 36.238 1.00 0.00 C +ATOM 592 O LEU 37 36.941 37.271 37.137 1.00 0.00 O +ATOM 593 N GLY 38 36.655 38.181 35.100 1.00 0.00 N +ATOM 594 H GLY 38 35.977 38.417 34.388 1.00 0.00 H +ATOM 595 CA GLY 38 38.057 38.532 34.848 1.00 0.00 C +ATOM 596 HA2 GLY 38 38.314 39.395 35.466 1.00 0.00 H +ATOM 597 HA3 GLY 38 38.690 37.700 35.160 1.00 0.00 H +ATOM 598 C GLY 38 38.413 38.871 33.391 1.00 0.00 C +ATOM 599 O GLY 38 38.929 39.957 33.136 1.00 0.00 O +ATOM 600 N GLU 39 38.171 37.961 32.437 1.00 0.00 N +ATOM 601 H GLU 39 37.657 37.131 32.691 1.00 0.00 H +ATOM 602 CA GLU 39 38.661 38.018 31.042 1.00 0.00 C +ATOM 603 HA GLU 39 38.763 39.061 30.726 1.00 0.00 H +ATOM 604 CB GLU 39 40.065 37.322 30.944 1.00 0.00 C +ATOM 605 HB2 GLU 39 39.944 36.313 31.317 1.00 0.00 H +ATOM 606 HB3 GLU 39 40.335 37.260 29.892 1.00 0.00 H +ATOM 607 CG GLU 39 41.245 37.986 31.688 1.00 0.00 C +ATOM 608 HG2 GLU 39 41.553 38.894 31.136 1.00 0.00 H +ATOM 609 HG3 GLU 39 40.915 38.320 32.684 1.00 0.00 H +ATOM 610 CD GLU 39 42.450 37.039 31.915 1.00 0.00 C +ATOM 611 OE1 GLU 39 42.260 36.003 32.575 1.00 0.00 O +ATOM 612 OE2 GLU 39 43.569 37.372 31.481 1.00 0.00 O +ATOM 613 C GLU 39 37.685 37.298 30.075 1.00 0.00 C +ATOM 614 O GLU 39 37.024 36.351 30.492 1.00 0.00 O +ATOM 615 N ASP 40 37.585 37.685 28.788 1.00 0.00 N +ATOM 616 H ASP 40 38.100 38.498 28.476 1.00 0.00 H +ATOM 617 CA ASP 40 36.738 36.968 27.799 1.00 0.00 C +ATOM 618 HA ASP 40 36.030 36.362 28.365 1.00 0.00 H +ATOM 619 CB ASP 40 35.858 37.913 26.964 1.00 0.00 C +ATOM 620 HB2 ASP 40 35.160 37.288 26.414 1.00 0.00 H +ATOM 621 HB3 ASP 40 35.261 38.533 27.625 1.00 0.00 H +ATOM 622 CG ASP 40 36.587 38.798 25.952 1.00 0.00 C +ATOM 623 OD1 ASP 40 36.893 39.965 26.276 1.00 0.00 O +ATOM 624 OD2 ASP 40 36.761 38.351 24.790 1.00 0.00 O +ATOM 625 C ASP 40 37.475 35.994 26.856 1.00 0.00 C +ATOM 626 O ASP 40 38.374 36.376 26.101 1.00 0.00 O +ATOM 627 N GLY 41 36.973 34.756 26.794 1.00 0.00 N +ATOM 628 H GLY 41 36.288 34.510 27.490 1.00 0.00 H +ATOM 629 CA GLY 41 37.271 33.768 25.747 1.00 0.00 C +ATOM 630 HA2 GLY 41 38.295 33.916 25.381 1.00 0.00 H +ATOM 631 HA3 GLY 41 37.211 32.770 26.191 1.00 0.00 H +ATOM 632 C GLY 41 36.313 33.811 24.533 1.00 0.00 C +ATOM 633 O GLY 41 35.386 34.624 24.460 1.00 0.00 O +ATOM 634 N GLU 42 36.534 32.906 23.574 1.00 0.00 N +ATOM 635 H GLU 42 37.265 32.233 23.726 1.00 0.00 H +ATOM 636 CA GLU 42 35.795 32.783 22.304 1.00 0.00 C +ATOM 637 HA GLU 42 35.112 33.628 22.215 1.00 0.00 H +ATOM 638 CB GLU 42 36.768 32.852 21.111 1.00 0.00 C +ATOM 639 HB2 GLU 42 37.359 31.939 21.083 1.00 0.00 H +ATOM 640 HB3 GLU 42 36.185 32.904 20.190 1.00 0.00 H +ATOM 641 CG GLU 42 37.742 34.046 21.132 1.00 0.00 C +ATOM 642 HG2 GLU 42 38.542 33.823 21.835 1.00 0.00 H +ATOM 643 HG3 GLU 42 38.198 34.176 20.150 1.00 0.00 H +ATOM 644 CD GLU 42 37.078 35.358 21.545 1.00 0.00 C +ATOM 645 OE1 GLU 42 35.962 35.662 21.073 1.00 0.00 O +ATOM 646 OE2 GLU 42 37.603 36.077 22.430 1.00 0.00 O +ATOM 647 C GLU 42 34.925 31.518 22.249 1.00 0.00 C +ATOM 648 O GLU 42 35.177 30.549 22.970 1.00 0.00 O +ATOM 649 N HIP 43 33.822 31.561 21.482 1.00 0.00 N +ATOM 650 H HIP 43 33.691 32.332 20.837 1.00 0.00 H +ATOM 651 CA HIP 43 32.635 30.779 21.863 1.00 0.00 C +ATOM 652 HA HIP 43 32.953 29.805 22.240 1.00 0.00 H +ATOM 653 CB HIP 43 32.036 31.564 23.060 1.00 0.00 C +ATOM 654 HB2 HIP 43 32.780 31.722 23.836 1.00 0.00 H +ATOM 655 HB3 HIP 43 31.707 32.547 22.731 1.00 0.00 H +ATOM 656 CG HIP 43 30.884 30.844 23.669 1.00 0.00 C +ATOM 657 ND1 HIP 43 29.715 30.591 23.008 1.00 0.00 N +ATOM 658 HD1 HIP 43 29.496 30.960 22.088 1.00 0.00 H +ATOM 659 CE1 HIP 43 29.197 29.496 23.532 1.00 0.00 C +ATOM 660 HE1 HIP 43 28.471 28.891 23.007 1.00 0.00 H +ATOM 661 NE2 HIP 43 29.859 29.132 24.623 1.00 0.00 N +ATOM 662 HE2 HIP 43 29.751 28.262 25.124 1.00 0.00 H +ATOM 663 CD2 HIP 43 30.964 29.967 24.715 1.00 0.00 C +ATOM 664 HD2 HIP 43 31.813 29.800 25.339 1.00 0.00 H +ATOM 665 C HIP 43 31.587 30.500 20.744 1.00 0.00 C +ATOM 666 O HIP 43 30.815 31.391 20.404 1.00 0.00 O +ATOM 667 N THR 44 31.412 29.241 20.315 1.00 0.00 N +ATOM 668 H THR 44 32.062 28.545 20.651 1.00 0.00 H +ATOM 669 CA THR 44 30.539 28.792 19.194 1.00 0.00 C +ATOM 670 HA THR 44 30.768 29.416 18.330 1.00 0.00 H +ATOM 671 CB THR 44 30.915 27.341 18.825 1.00 0.00 C +ATOM 672 HB THR 44 30.653 26.672 19.649 1.00 0.00 H +ATOM 673 CG2 THR 44 30.280 26.804 17.538 1.00 0.00 C +ATOM 674 HG21 THR 44 30.421 27.512 16.723 1.00 0.00 H +ATOM 675 HG22 THR 44 30.737 25.852 17.265 1.00 0.00 H +ATOM 676 HG23 THR 44 29.217 26.625 17.692 1.00 0.00 H +ATOM 677 OG1 THR 44 32.307 27.274 18.626 1.00 0.00 O +ATOM 678 HG1 THR 44 32.492 26.533 18.040 1.00 0.00 H +ATOM 679 C THR 44 29.005 28.885 19.426 1.00 0.00 C +ATOM 680 O THR 44 28.541 28.793 20.567 1.00 0.00 O +ATOM 681 N LYS 45 28.231 29.030 18.329 1.00 0.00 N +ATOM 682 H LYS 45 28.718 29.046 17.443 1.00 0.00 H +ATOM 683 CA LYS 45 26.747 29.105 18.236 1.00 0.00 C +ATOM 684 HA LYS 45 26.318 29.062 19.233 1.00 0.00 H +ATOM 685 CB LYS 45 26.374 30.459 17.574 1.00 0.00 C +ATOM 686 HB2 LYS 45 26.571 31.266 18.282 1.00 0.00 H +ATOM 687 HB3 LYS 45 27.024 30.615 16.712 1.00 0.00 H +ATOM 688 CG LYS 45 24.919 30.571 17.071 1.00 0.00 C +ATOM 689 HG2 LYS 45 24.730 29.762 16.369 1.00 0.00 H +ATOM 690 HG3 LYS 45 24.253 30.451 17.926 1.00 0.00 H +ATOM 691 CD LYS 45 24.581 31.864 16.313 1.00 0.00 C +ATOM 692 HD2 LYS 45 24.789 32.715 16.943 1.00 0.00 H +ATOM 693 HD3 LYS 45 25.176 31.930 15.400 1.00 0.00 H +ATOM 694 CE LYS 45 23.091 31.825 15.971 1.00 0.00 C +ATOM 695 HE2 LYS 45 22.923 30.987 15.292 1.00 0.00 H +ATOM 696 HE3 LYS 45 22.532 31.602 16.886 1.00 0.00 H +ATOM 697 NZ LYS 45 22.573 33.072 15.345 1.00 0.00 N +ATOM 698 HZ1 LYS 45 22.962 33.227 14.424 1.00 0.00 H +ATOM 699 HZ2 LYS 45 21.559 32.954 15.239 1.00 0.00 H +ATOM 700 HZ3 LYS 45 22.712 33.892 15.912 1.00 0.00 H +ATOM 701 C LYS 45 26.138 27.945 17.423 1.00 0.00 C +ATOM 702 O LYS 45 26.705 27.569 16.405 1.00 0.00 O +ATOM 703 N ASP 46 24.922 27.524 17.775 1.00 0.00 N +ATOM 704 H ASP 46 24.578 27.808 18.689 1.00 0.00 H +ATOM 705 CA ASP 46 23.873 27.044 16.843 1.00 0.00 C +ATOM 706 HA ASP 46 24.249 27.121 15.818 1.00 0.00 H +ATOM 707 CB ASP 46 23.528 25.569 17.148 1.00 0.00 C +ATOM 708 HB2 ASP 46 24.366 24.916 16.878 1.00 0.00 H +ATOM 709 HB3 ASP 46 23.378 25.489 18.232 1.00 0.00 H +ATOM 710 CG ASP 46 22.266 25.098 16.426 1.00 0.00 C +ATOM 711 OD1 ASP 46 21.392 24.557 17.117 1.00 0.00 O +ATOM 712 OD2 ASP 46 22.087 25.409 15.235 1.00 0.00 O +ATOM 713 C ASP 46 22.613 27.944 16.957 1.00 0.00 C +ATOM 714 O ASP 46 22.294 28.456 18.027 1.00 0.00 O +ATOM 715 N ASP 47 21.897 28.140 15.849 1.00 0.00 N +ATOM 716 H ASP 47 22.146 27.562 15.057 1.00 0.00 H +ATOM 717 CA ASP 47 20.588 28.850 15.794 1.00 0.00 C +ATOM 718 HA ASP 47 20.554 29.519 16.646 1.00 0.00 H +ATOM 719 CB ASP 47 20.475 29.756 14.572 1.00 0.00 C +ATOM 720 HB2 ASP 47 21.461 30.108 14.286 1.00 0.00 H +ATOM 721 HB3 ASP 47 20.085 29.213 13.702 1.00 0.00 H +ATOM 722 CG ASP 47 19.637 30.995 14.888 1.00 0.00 C +ATOM 723 OD1 ASP 47 18.471 31.071 14.473 1.00 0.00 O +ATOM 724 OD2 ASP 47 20.169 31.881 15.573 1.00 0.00 O +ATOM 725 C ASP 47 19.357 27.933 15.861 1.00 0.00 C +ATOM 726 O ASP 47 18.316 28.355 16.366 1.00 0.00 O +ATOM 727 N ALA 48 19.457 26.676 15.411 1.00 0.00 N +ATOM 728 H ALA 48 20.368 26.307 15.139 1.00 0.00 H +ATOM 729 CA ALA 48 18.317 25.752 15.378 1.00 0.00 C +ATOM 730 HA ALA 48 17.480 26.224 14.859 1.00 0.00 H +ATOM 731 CB ALA 48 18.730 24.511 14.577 1.00 0.00 C +ATOM 732 HB1 ALA 48 19.555 24.007 15.072 1.00 0.00 H +ATOM 733 HB2 ALA 48 17.894 23.821 14.498 1.00 0.00 H +ATOM 734 HB3 ALA 48 19.047 24.788 13.575 1.00 0.00 H +ATOM 735 C ALA 48 17.839 25.388 16.792 1.00 0.00 C +ATOM 736 O ALA 48 16.640 25.354 17.075 1.00 0.00 O +ATOM 737 N THR 49 18.778 25.160 17.711 1.00 0.00 N +ATOM 738 H THR 49 19.736 25.037 17.377 1.00 0.00 H +ATOM 739 CA THR 49 18.557 25.051 19.154 1.00 0.00 C +ATOM 740 HA THR 49 17.530 24.709 19.314 1.00 0.00 H +ATOM 741 CB THR 49 19.524 24.022 19.753 1.00 0.00 C +ATOM 742 HB THR 49 19.326 23.946 20.820 1.00 0.00 H +ATOM 743 CG2 THR 49 19.398 22.626 19.153 1.00 0.00 C +ATOM 744 HG21 THR 49 19.665 22.630 18.098 1.00 0.00 H +ATOM 745 HG22 THR 49 20.090 21.979 19.684 1.00 0.00 H +ATOM 746 HG23 THR 49 18.383 22.250 19.269 1.00 0.00 H +ATOM 747 OG1 THR 49 20.861 24.413 19.589 1.00 0.00 O +ATOM 748 HG1 THR 49 21.066 24.338 18.620 1.00 0.00 H +ATOM 749 C THR 49 18.714 26.378 19.910 1.00 0.00 C +ATOM 750 O THR 49 18.618 26.395 21.136 1.00 0.00 O +ATOM 751 N LYS 50 18.968 27.490 19.206 1.00 0.00 N +ATOM 752 H LYS 50 18.980 27.378 18.203 1.00 0.00 H +ATOM 753 CA LYS 50 19.202 28.853 19.749 1.00 0.00 C +ATOM 754 HA LYS 50 19.637 29.449 18.943 1.00 0.00 H +ATOM 755 CB LYS 50 17.845 29.491 20.149 1.00 0.00 C +ATOM 756 HB2 LYS 50 17.408 28.860 20.925 1.00 0.00 H +ATOM 757 HB3 LYS 50 18.038 30.471 20.598 1.00 0.00 H +ATOM 758 CG LYS 50 16.812 29.667 19.017 1.00 0.00 C +ATOM 759 HG2 LYS 50 16.742 28.752 18.424 1.00 0.00 H +ATOM 760 HG3 LYS 50 15.841 29.837 19.491 1.00 0.00 H +ATOM 761 CD LYS 50 17.113 30.878 18.105 1.00 0.00 C +ATOM 762 HD2 LYS 50 17.122 31.775 18.732 1.00 0.00 H +ATOM 763 HD3 LYS 50 18.108 30.766 17.643 1.00 0.00 H +ATOM 764 CE LYS 50 16.028 31.055 17.026 1.00 0.00 C +ATOM 765 HE2 LYS 50 15.056 30.783 17.436 1.00 0.00 H +ATOM 766 HE3 LYS 50 15.985 32.104 16.719 1.00 0.00 H +ATOM 767 NZ LYS 50 16.278 30.207 15.837 1.00 0.00 N +ATOM 768 HZ1 LYS 50 16.593 29.271 16.077 1.00 0.00 H +ATOM 769 HZ2 LYS 50 15.486 30.195 15.189 1.00 0.00 H +ATOM 770 HZ3 LYS 50 17.047 30.589 15.285 1.00 0.00 H +ATOM 771 C LYS 50 20.238 28.865 20.885 1.00 0.00 C +ATOM 772 O LYS 50 20.046 29.552 21.897 1.00 0.00 O +ATOM 773 N THR 51 21.297 28.053 20.758 1.00 0.00 N +ATOM 774 H THR 51 21.447 27.626 19.852 1.00 0.00 H +ATOM 775 CA THR 51 22.186 27.666 21.861 1.00 0.00 C +ATOM 776 HA THR 51 21.925 28.266 22.727 1.00 0.00 H +ATOM 777 CB THR 51 21.978 26.182 22.276 1.00 0.00 C +ATOM 778 HB THR 51 22.103 25.558 21.392 1.00 0.00 H +ATOM 779 CG2 THR 51 22.971 25.680 23.326 1.00 0.00 C +ATOM 780 HG21 THR 51 22.987 26.306 24.214 1.00 0.00 H +ATOM 781 HG22 THR 51 22.722 24.667 23.637 1.00 0.00 H +ATOM 782 HG23 THR 51 23.978 25.634 22.923 1.00 0.00 H +ATOM 783 OG1 THR 51 20.695 26.001 22.835 1.00 0.00 O +ATOM 784 HG1 THR 51 20.033 26.112 22.126 1.00 0.00 H +ATOM 785 C THR 51 23.691 27.954 21.606 1.00 0.00 C +ATOM 786 O THR 51 24.250 27.693 20.552 1.00 0.00 O +ATOM 787 N PHE 52 24.339 28.470 22.636 1.00 0.00 N +ATOM 788 H PHE 52 23.782 28.767 23.426 1.00 0.00 H +ATOM 789 CA PHE 52 25.782 28.625 22.774 1.00 0.00 C +ATOM 790 HA PHE 52 26.236 28.756 21.800 1.00 0.00 H +ATOM 791 CB PHE 52 25.970 29.903 23.630 1.00 0.00 C +ATOM 792 HB2 PHE 52 25.178 29.934 24.366 1.00 0.00 H +ATOM 793 HB3 PHE 52 26.858 29.811 24.241 1.00 0.00 H +ATOM 794 CG PHE 52 25.990 31.261 22.933 1.00 0.00 C +ATOM 795 CD1 PHE 52 25.313 32.345 23.501 1.00 0.00 C +ATOM 796 HD1 PHE 52 24.705 32.206 24.369 1.00 0.00 H +ATOM 797 CE1 PHE 52 25.445 33.639 22.970 1.00 0.00 C +ATOM 798 HE1 PHE 52 24.940 34.476 23.432 1.00 0.00 H +ATOM 799 CZ PHE 52 26.270 33.846 21.867 1.00 0.00 C +ATOM 800 HZ PHE 52 26.395 34.832 21.472 1.00 0.00 H +ATOM 801 CE2 PHE 52 26.935 32.771 21.258 1.00 0.00 C +ATOM 802 HE2 PHE 52 27.570 32.946 20.399 1.00 0.00 H +ATOM 803 CD2 PHE 52 26.777 31.489 21.786 1.00 0.00 C +ATOM 804 HD2 PHE 52 27.285 30.683 21.316 1.00 0.00 H +ATOM 805 C PHE 52 26.423 27.398 23.470 1.00 0.00 C +ATOM 806 O PHE 52 26.087 27.106 24.623 1.00 0.00 O +ATOM 807 N THR 53 27.436 26.751 22.856 1.00 0.00 N +ATOM 808 H THR 53 27.650 26.995 21.888 1.00 0.00 H +ATOM 809 CA THR 53 28.305 25.685 23.436 1.00 0.00 C +ATOM 810 HA THR 53 28.048 25.541 24.487 1.00 0.00 H +ATOM 811 CB THR 53 28.082 24.339 22.718 1.00 0.00 C +ATOM 812 HB THR 53 28.786 23.607 23.118 1.00 0.00 H +ATOM 813 CG2 THR 53 26.676 23.788 22.896 1.00 0.00 C +ATOM 814 HG21 THR 53 25.950 24.428 22.394 1.00 0.00 H +ATOM 815 HG22 THR 53 26.625 22.786 22.468 1.00 0.00 H +ATOM 816 HG23 THR 53 26.442 23.727 23.958 1.00 0.00 H +ATOM 817 OG1 THR 53 28.319 24.486 21.337 1.00 0.00 O +ATOM 818 HG1 THR 53 28.141 23.636 20.917 1.00 0.00 H +ATOM 819 C THR 53 29.812 26.007 23.366 1.00 0.00 C +ATOM 820 O THR 53 30.224 26.906 22.642 1.00 0.00 O +ATOM 821 N THR 54 30.650 25.304 24.140 1.00 0.00 N +ATOM 822 H THR 54 30.284 24.592 24.758 1.00 0.00 H +ATOM 823 CA THR 54 32.131 25.256 23.974 1.00 0.00 C +ATOM 824 HA THR 54 32.450 26.113 23.366 1.00 0.00 H +ATOM 825 CB THR 54 32.874 25.346 25.323 1.00 0.00 C +ATOM 826 HB THR 54 33.948 25.303 25.140 1.00 0.00 H +ATOM 827 CG2 THR 54 32.594 26.656 26.070 1.00 0.00 C +ATOM 828 HG21 THR 54 31.547 26.724 26.352 1.00 0.00 H +ATOM 829 HG22 THR 54 33.190 26.709 26.976 1.00 0.00 H +ATOM 830 HG23 THR 54 32.855 27.511 25.448 1.00 0.00 H +ATOM 831 OG1 THR 54 32.529 24.279 26.170 1.00 0.00 O +ATOM 832 HG1 THR 54 32.961 23.475 25.847 1.00 0.00 H +ATOM 833 C THR 54 32.580 23.997 23.228 1.00 0.00 C +ATOM 834 O THR 54 31.810 23.044 23.101 1.00 0.00 O +ATOM 835 N ALA 55 33.833 23.981 22.756 1.00 0.00 N +ATOM 836 H ALA 55 34.417 24.785 22.911 1.00 0.00 H +ATOM 837 CA ALA 55 34.476 22.803 22.162 1.00 0.00 C +ATOM 838 HA ALA 55 33.773 22.349 21.450 1.00 0.00 H +ATOM 839 CB ALA 55 35.709 23.293 21.391 1.00 0.00 C +ATOM 840 HB1 ALA 55 36.439 23.718 22.088 1.00 0.00 H +ATOM 841 HB2 ALA 55 36.172 22.454 20.859 1.00 0.00 H +ATOM 842 HB3 ALA 55 35.413 24.049 20.657 1.00 0.00 H +ATOM 843 C ALA 55 34.820 21.700 23.201 1.00 0.00 C +ATOM 844 O ALA 55 34.564 21.870 24.395 1.00 0.00 O +ATOM 845 N GLU 56 35.391 20.590 22.719 1.00 0.00 N +ATOM 846 H GLU 56 35.619 20.592 21.742 1.00 0.00 H +ATOM 847 CA GLU 56 35.949 19.442 23.462 1.00 0.00 C +ATOM 848 HA GLU 56 35.837 19.619 24.529 1.00 0.00 H +ATOM 849 CB GLU 56 35.174 18.158 23.066 1.00 0.00 C +ATOM 850 HB2 GLU 56 34.120 18.283 23.304 1.00 0.00 H +ATOM 851 HB3 GLU 56 35.231 18.083 21.976 1.00 0.00 H +ATOM 852 CG GLU 56 35.683 16.816 23.642 1.00 0.00 C +ATOM 853 HG2 GLU 56 35.524 16.058 22.873 1.00 0.00 H +ATOM 854 HG3 GLU 56 36.759 16.858 23.777 1.00 0.00 H +ATOM 855 CD GLU 56 35.019 16.305 24.943 1.00 0.00 C +ATOM 856 OE1 GLU 56 35.650 15.485 25.657 1.00 0.00 O +ATOM 857 OE2 GLU 56 33.830 16.592 25.213 1.00 0.00 O +ATOM 858 C GLU 56 37.466 19.312 23.206 1.00 0.00 C +ATOM 859 O GLU 56 38.207 19.293 24.214 1.00 0.00 O +ATOM 860 OXT GLU 56 37.851 19.278 22.005 1.00 0.00 O +HETATM 861 ZN ZN1 57 26.252 32.500 29.543 1.00 0.00 Zn +HETATM 862 N AN1 58 27.946 33.231 30.455 1.00 0.00 N +HETATM 863 C AN1 58 30.237 34.165 31.270 1.00 0.00 C +HETATM 864 C1 AN1 58 28.941 33.637 30.825 1.00 0.00 C +HETATM 865 H AN1 58 30.152 34.562 32.288 1.00 0.00 H +HETATM 866 H1 AN1 58 30.560 34.975 30.607 1.00 0.00 H +HETATM 867 H2 AN1 58 30.993 33.374 31.265 1.00 0.00 H +HETATM 868 N1 AZI 59 30.423 28.665 29.019 1.00 0.00 N +HETATM 869 N2 AZI 59 29.754 28.732 30.028 1.00 0.00 N +HETATM 870 N3 AZI 59 29.036 28.794 31.085 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 69 71 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 68 73 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 861 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 105 101 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 142 140 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 139 144 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 207 188 189 +CONECT 188 187 +CONECT 189 187 191 192 190 +CONECT 190 189 +CONECT 191 189 +CONECT 192 206 189 193 +CONECT 193 192 195 194 +CONECT 194 193 +CONECT 195 197 193 196 +CONECT 196 195 +CONECT 197 198 206 195 +CONECT 198 200 199 197 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 203 200 204 +CONECT 203 202 +CONECT 204 202 205 206 +CONECT 205 204 +CONECT 206 204 197 192 +CONECT 207 209 187 208 +CONECT 208 207 +CONECT 209 210 211 207 +CONECT 210 209 +CONECT 211 212 223 209 213 +CONECT 212 211 +CONECT 213 211 219 215 214 +CONECT 214 213 +CONECT 215 218 213 216 217 +CONECT 216 215 +CONECT 217 215 +CONECT 218 215 +CONECT 219 220 222 213 221 +CONECT 220 219 +CONECT 221 219 +CONECT 222 219 +CONECT 223 224 225 211 +CONECT 224 223 +CONECT 225 227 223 226 +CONECT 226 225 +CONECT 227 228 245 229 225 +CONECT 228 227 +CONECT 229 232 227 230 231 +CONECT 230 229 +CONECT 231 229 +CONECT 232 234 233 235 229 +CONECT 233 232 +CONECT 234 232 +CONECT 235 236 232 237 238 +CONECT 236 235 +CONECT 237 235 +CONECT 238 235 240 241 239 +CONECT 239 238 +CONECT 240 238 +CONECT 241 244 238 242 243 +CONECT 242 241 +CONECT 243 241 +CONECT 244 241 +CONECT 245 246 227 247 +CONECT 246 245 +CONECT 247 245 249 248 +CONECT 248 247 +CONECT 249 252 247 250 251 +CONECT 250 249 +CONECT 251 249 +CONECT 252 253 254 249 +CONECT 253 252 +CONECT 254 256 252 255 +CONECT 255 254 +CONECT 256 258 257 268 254 +CONECT 257 256 +CONECT 258 264 259 260 256 +CONECT 259 258 +CONECT 260 262 258 261 263 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 265 267 258 +CONECT 265 264 +CONECT 266 264 +CONECT 267 264 +CONECT 268 256 270 269 +CONECT 269 268 +CONECT 270 280 271 268 +CONECT 271 272 270 281 274 +CONECT 272 273 287 271 +CONECT 273 272 +CONECT 274 271 275 282 283 +CONECT 275 276 277 274 +CONECT 276 279 285 275 +CONECT 277 278 275 284 +CONECT 278 279 286 277 +CONECT 279 861 278 276 +CONECT 280 270 +CONECT 281 271 +CONECT 282 274 +CONECT 283 274 +CONECT 284 277 +CONECT 285 276 +CONECT 286 278 +CONECT 287 289 272 288 +CONECT 288 287 +CONECT 289 290 291 299 287 +CONECT 290 289 +CONECT 291 292 293 289 297 +CONECT 292 291 +CONECT 293 296 295 291 294 +CONECT 294 293 +CONECT 295 293 +CONECT 296 293 +CONECT 297 291 298 +CONECT 298 297 +CONECT 299 301 289 300 +CONECT 300 299 +CONECT 301 311 302 299 +CONECT 302 303 305 301 312 +CONECT 303 304 318 302 +CONECT 304 303 +CONECT 305 313 314 302 306 +CONECT 306 305 307 308 +CONECT 307 316 306 310 +CONECT 308 306 315 309 +CONECT 309 310 308 317 +CONECT 310 307 861 309 +CONECT 311 301 +CONECT 312 302 +CONECT 313 305 +CONECT 314 305 +CONECT 315 308 +CONECT 316 307 +CONECT 317 309 +CONECT 318 320 303 319 +CONECT 319 318 +CONECT 320 331 321 318 322 +CONECT 321 320 +CONECT 322 320 325 324 323 +CONECT 323 322 +CONECT 324 322 +CONECT 325 328 327 322 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 329 330 325 +CONECT 329 328 +CONECT 330 328 +CONECT 331 333 332 320 +CONECT 332 331 +CONECT 333 335 334 331 +CONECT 334 333 +CONECT 335 341 337 336 333 +CONECT 336 335 +CONECT 337 339 338 335 340 +CONECT 338 337 +CONECT 339 337 +CONECT 340 337 +CONECT 341 343 342 335 +CONECT 342 341 +CONECT 343 345 344 341 +CONECT 344 343 +CONECT 345 357 347 346 343 +CONECT 346 345 +CONECT 347 348 353 345 349 +CONECT 348 347 +CONECT 349 347 351 352 350 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 347 356 +CONECT 354 353 +CONECT 355 353 +CONECT 356 353 +CONECT 357 358 359 345 +CONECT 358 357 +CONECT 359 361 357 360 +CONECT 360 359 +CONECT 361 363 362 369 359 +CONECT 362 361 +CONECT 363 366 364 365 361 +CONECT 364 363 +CONECT 365 363 +CONECT 366 367 368 363 +CONECT 367 366 +CONECT 368 366 +CONECT 369 361 371 370 +CONECT 370 369 +CONECT 371 372 369 373 +CONECT 372 371 +CONECT 373 371 375 388 374 +CONECT 374 373 +CONECT 375 377 376 373 378 +CONECT 376 375 +CONECT 377 375 +CONECT 378 384 375 380 379 +CONECT 379 378 +CONECT 380 381 378 382 383 +CONECT 381 380 +CONECT 382 380 +CONECT 383 380 +CONECT 384 387 386 385 378 +CONECT 385 384 +CONECT 386 384 +CONECT 387 384 +CONECT 388 390 373 389 +CONECT 389 388 +CONECT 390 391 392 388 +CONECT 391 390 +CONECT 392 394 393 390 398 +CONECT 393 392 +CONECT 394 397 395 396 392 +CONECT 395 394 +CONECT 396 394 +CONECT 397 394 +CONECT 398 392 399 400 +CONECT 399 398 +CONECT 400 398 401 402 +CONECT 401 400 +CONECT 402 400 403 404 413 +CONECT 403 402 +CONECT 404 407 402 405 406 +CONECT 405 404 +CONECT 406 404 +CONECT 407 408 409 410 404 +CONECT 408 407 +CONECT 409 407 +CONECT 410 412 407 411 +CONECT 411 410 +CONECT 412 410 +CONECT 413 402 415 414 +CONECT 414 413 +CONECT 415 416 413 417 +CONECT 416 415 +CONECT 417 415 419 423 418 +CONECT 418 417 +CONECT 419 420 422 417 421 +CONECT 420 419 +CONECT 421 419 +CONECT 422 419 +CONECT 423 425 417 424 +CONECT 424 423 +CONECT 425 426 427 423 +CONECT 426 425 +CONECT 427 429 425 428 438 +CONECT 428 427 +CONECT 429 430 431 432 427 +CONECT 430 429 +CONECT 431 429 +CONECT 432 435 429 433 434 +CONECT 433 432 +CONECT 434 432 +CONECT 435 437 436 432 +CONECT 436 435 +CONECT 437 435 +CONECT 438 427 440 439 +CONECT 439 438 +CONECT 440 441 438 442 +CONECT 441 440 +CONECT 442 440 444 443 460 +CONECT 443 442 +CONECT 444 447 445 446 442 +CONECT 445 444 +CONECT 446 444 +CONECT 447 449 450 448 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 451 452 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 456 455 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 458 459 457 453 +CONECT 457 456 +CONECT 458 456 +CONECT 459 456 +CONECT 460 442 462 461 +CONECT 461 460 +CONECT 462 463 460 464 +CONECT 463 462 +CONECT 464 462 466 465 480 +CONECT 465 464 +CONECT 466 469 467 464 468 +CONECT 467 466 +CONECT 468 466 +CONECT 469 470 478 466 +CONECT 470 472 471 469 +CONECT 471 470 +CONECT 472 473 474 470 +CONECT 473 472 +CONECT 474 475 472 476 +CONECT 475 474 +CONECT 476 474 477 478 +CONECT 477 476 +CONECT 478 476 469 479 +CONECT 479 478 +CONECT 480 464 482 481 +CONECT 481 480 +CONECT 482 483 484 480 +CONECT 483 482 +CONECT 484 486 482 494 485 +CONECT 485 484 +CONECT 486 487 492 488 484 +CONECT 487 486 +CONECT 488 490 486 491 489 +CONECT 489 488 +CONECT 490 488 +CONECT 491 488 +CONECT 492 493 486 +CONECT 493 492 +CONECT 494 496 484 495 +CONECT 495 494 +CONECT 496 497 498 494 +CONECT 497 496 +CONECT 498 500 496 499 516 +CONECT 499 498 +CONECT 500 503 501 502 498 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 505 504 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 509 507 508 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 510 512 506 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 512 +CONECT 516 498 518 517 +CONECT 517 516 +CONECT 518 519 516 520 +CONECT 519 518 +CONECT 520 518 522 521 526 +CONECT 521 520 +CONECT 522 525 523 520 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 522 +CONECT 526 520 528 527 +CONECT 527 526 +CONECT 528 529 526 530 +CONECT 529 528 +CONECT 530 528 532 536 531 +CONECT 531 530 +CONECT 532 533 535 530 534 +CONECT 533 532 +CONECT 534 532 +CONECT 535 532 +CONECT 536 538 530 537 +CONECT 537 536 +CONECT 538 539 540 536 +CONECT 539 538 +CONECT 540 542 538 546 541 +CONECT 541 540 +CONECT 542 543 545 544 540 +CONECT 543 542 +CONECT 544 542 +CONECT 545 542 +CONECT 546 540 548 547 +CONECT 547 546 +CONECT 548 549 546 550 +CONECT 549 548 +CONECT 550 552 548 551 560 +CONECT 551 550 +CONECT 552 555 553 554 550 +CONECT 553 552 +CONECT 554 552 +CONECT 555 557 556 552 +CONECT 556 555 +CONECT 557 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 550 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 566 565 572 +CONECT 565 564 +CONECT 566 569 567 564 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 571 570 566 +CONECT 570 569 +CONECT 571 569 +CONECT 572 564 574 573 +CONECT 573 572 +CONECT 574 575 572 576 +CONECT 575 574 +CONECT 576 574 578 591 577 +CONECT 577 576 +CONECT 578 580 579 576 581 +CONECT 579 578 +CONECT 580 578 +CONECT 581 578 587 582 583 +CONECT 582 581 +CONECT 583 581 584 585 586 +CONECT 584 583 +CONECT 585 583 +CONECT 586 583 +CONECT 587 588 590 589 581 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 593 576 592 +CONECT 592 591 +CONECT 593 594 595 591 +CONECT 594 593 +CONECT 595 598 593 597 596 +CONECT 596 595 +CONECT 597 595 +CONECT 598 600 599 595 +CONECT 599 598 +CONECT 600 602 601 598 +CONECT 601 600 +CONECT 602 613 603 604 600 +CONECT 603 602 +CONECT 604 606 602 605 607 +CONECT 605 604 +CONECT 606 604 +CONECT 607 604 608 610 609 +CONECT 608 607 +CONECT 609 607 +CONECT 610 612 607 611 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 602 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 625 619 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 639 641 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 638 644 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 665 649 652 653 +CONECT 652 651 +CONECT 653 651 655 656 654 +CONECT 654 653 +CONECT 655 653 +CONECT 656 657 653 663 +CONECT 657 658 659 656 +CONECT 658 657 +CONECT 659 660 657 661 +CONECT 660 659 +CONECT 661 659 663 662 +CONECT 662 661 +CONECT 663 656 661 664 +CONECT 664 663 +CONECT 665 667 666 651 +CONECT 666 665 +CONECT 667 669 668 665 +CONECT 668 667 +CONECT 669 670 671 679 667 +CONECT 670 669 +CONECT 671 673 677 669 672 +CONECT 672 671 +CONECT 673 674 675 676 671 +CONECT 674 673 +CONECT 675 673 +CONECT 676 673 +CONECT 677 678 671 +CONECT 678 677 +CONECT 679 681 669 680 +CONECT 680 679 +CONECT 681 682 683 679 +CONECT 682 681 +CONECT 683 701 685 681 684 +CONECT 684 683 +CONECT 685 687 688 683 686 +CONECT 686 685 +CONECT 687 685 +CONECT 688 691 689 685 690 +CONECT 689 688 +CONECT 690 688 +CONECT 691 693 694 692 688 +CONECT 692 691 +CONECT 693 691 +CONECT 694 695 697 691 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 698 699 700 694 +CONECT 698 697 +CONECT 699 697 +CONECT 700 697 +CONECT 701 702 703 683 +CONECT 702 701 +CONECT 703 705 701 704 +CONECT 704 703 +CONECT 705 706 713 707 703 +CONECT 706 705 +CONECT 707 710 705 708 709 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 711 707 +CONECT 711 710 +CONECT 712 710 +CONECT 713 715 705 714 +CONECT 714 713 +CONECT 715 716 717 713 +CONECT 716 715 +CONECT 717 719 715 725 718 +CONECT 718 717 +CONECT 719 721 720 722 717 +CONECT 720 719 +CONECT 721 719 +CONECT 722 723 719 724 +CONECT 723 722 +CONECT 724 722 +CONECT 725 727 717 726 +CONECT 726 725 +CONECT 727 728 729 725 +CONECT 728 727 +CONECT 729 731 730 727 735 +CONECT 730 729 +CONECT 731 734 733 732 729 +CONECT 732 731 +CONECT 733 731 +CONECT 734 731 +CONECT 735 729 736 737 +CONECT 736 735 +CONECT 737 735 738 739 +CONECT 738 737 +CONECT 739 737 740 741 749 +CONECT 740 739 +CONECT 741 743 739 747 742 +CONECT 742 741 +CONECT 743 744 746 745 741 +CONECT 744 743 +CONECT 745 743 +CONECT 746 743 +CONECT 747 748 741 +CONECT 748 747 +CONECT 749 739 751 750 +CONECT 750 749 +CONECT 751 752 753 749 +CONECT 752 751 +CONECT 753 754 751 755 771 +CONECT 754 753 +CONECT 755 758 753 757 756 +CONECT 756 755 +CONECT 757 755 +CONECT 758 761 759 760 755 +CONECT 759 758 +CONECT 760 758 +CONECT 761 764 763 762 758 +CONECT 762 761 +CONECT 763 761 +CONECT 764 767 766 765 761 +CONECT 765 764 +CONECT 766 764 +CONECT 767 769 770 768 764 +CONECT 768 767 +CONECT 769 767 +CONECT 770 767 +CONECT 771 753 773 772 +CONECT 772 771 +CONECT 773 774 771 775 +CONECT 774 773 +CONECT 775 773 785 777 776 +CONECT 776 775 +CONECT 777 778 775 783 779 +CONECT 778 777 +CONECT 779 777 782 781 780 +CONECT 780 779 +CONECT 781 779 +CONECT 782 779 +CONECT 783 784 777 +CONECT 784 783 +CONECT 785 786 775 787 +CONECT 786 785 +CONECT 787 785 789 788 +CONECT 788 787 +CONECT 789 790 787 805 791 +CONECT 790 789 +CONECT 791 789 794 793 792 +CONECT 792 791 +CONECT 793 791 +CONECT 794 803 795 791 +CONECT 795 794 797 796 +CONECT 796 795 +CONECT 797 799 798 795 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 801 804 794 +CONECT 804 803 +CONECT 805 789 807 806 +CONECT 806 805 +CONECT 807 808 809 805 +CONECT 808 807 +CONECT 809 811 807 819 810 +CONECT 810 809 +CONECT 811 817 813 812 809 +CONECT 812 811 +CONECT 813 814 815 811 816 +CONECT 814 813 +CONECT 815 813 +CONECT 816 813 +CONECT 817 818 811 +CONECT 818 817 +CONECT 819 820 809 821 +CONECT 820 819 +CONECT 821 819 823 822 +CONECT 822 821 +CONECT 823 833 824 821 825 +CONECT 824 823 +CONECT 825 823 826 827 831 +CONECT 826 825 +CONECT 827 825 830 828 829 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 825 832 +CONECT 832 831 +CONECT 833 835 834 823 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 839 838 835 843 +CONECT 838 837 +CONECT 839 842 841 840 837 +CONECT 840 839 +CONECT 841 839 +CONECT 842 839 +CONECT 843 837 845 844 +CONECT 844 843 +CONECT 845 846 843 847 +CONECT 846 845 +CONECT 847 845 849 858 848 +CONECT 848 847 +CONECT 849 851 850 847 852 +CONECT 850 849 +CONECT 851 849 +CONECT 852 853 849 854 855 +CONECT 853 852 +CONECT 854 852 +CONECT 855 852 857 856 +CONECT 856 855 +CONECT 857 855 +CONECT 858 860 847 859 +CONECT 859 858 +CONECT 860 858 +CONECT 861 87 310 862 279 +CONECT 862 861 864 +CONECT 863 866 864 867 865 +CONECT 864 862 863 +CONECT 865 863 +CONECT 866 863 +CONECT 867 863 +CONECT 868 869 +CONECT 869 868 870 +CONECT 870 869 +MASTER 0 0 0 0 0 0 0 0 870 0 870 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_3_front_5.pdb b/tests/nsga2/intermediate_molecules/min_iter_3_front_5.pdb new file mode 100644 index 0000000..c2d6518 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_3_front_5.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.331 51.38249999999948 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.971 23.610 1.00 0.00 N +ATOM 2 H1 MET 1 15.141 38.355 24.553 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.345 23.090 1.00 0.00 H +ATOM 4 H3 MET 1 16.014 38.281 23.181 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.500 23.668 1.00 0.00 C +ATOM 6 HA MET 1 14.171 36.197 24.096 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.872 22.269 1.00 0.00 C +ATOM 8 HB2 MET 1 14.392 36.151 21.668 1.00 0.00 H +ATOM 9 HB3 MET 1 16.153 36.270 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.371 34.332 22.296 1.00 0.00 C +ATOM 11 HG2 MET 1 16.259 34.062 22.867 1.00 0.00 H +ATOM 12 HG3 MET 1 14.494 33.923 22.804 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.525 20.666 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.569 20.066 1.00 0.00 C +ATOM 15 HE1 MET 1 13.461 34.598 20.015 1.00 0.00 H +ATOM 16 HE2 MET 1 13.777 33.132 19.069 1.00 0.00 H +ATOM 17 HE3 MET 1 13.174 32.990 20.731 1.00 0.00 H +ATOM 18 C MET 1 16.221 36.029 24.598 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.397 24.423 1.00 0.00 O +ATOM 20 N GLN 2 15.881 35.189 25.579 1.00 0.00 N +ATOM 21 H GLN 2 14.910 34.997 25.765 1.00 0.00 H +ATOM 22 CA GLN 2 16.846 34.478 26.432 1.00 0.00 C +ATOM 23 HA GLN 2 17.652 35.157 26.726 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.072 27.724 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.138 33.651 27.491 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.661 33.315 28.273 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.253 28.684 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.469 36.090 28.161 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.204 34.973 29.418 1.00 0.00 H +ATOM 30 CD GLN 2 17.129 35.580 29.525 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.164 34.935 29.495 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.031 36.470 30.481 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.772 36.536 31.097 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.109 36.732 30.769 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.304 25.672 1.00 0.00 C +ATOM 36 O GLN 2 17.101 32.148 25.833 1.00 0.00 O +ATOM 37 N TYR 3 18.476 33.620 24.822 1.00 0.00 N +ATOM 38 H TYR 3 18.753 34.594 24.753 1.00 0.00 H +ATOM 39 CA TYR 3 19.257 32.618 24.101 1.00 0.00 C +ATOM 40 HA TYR 3 18.571 31.964 23.563 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.286 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.865 33.945 23.646 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.482 22.671 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.069 21.936 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.528 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.821 32.423 20.552 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.146 34.202 19.540 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.115 33.734 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.845 35.572 19.674 1.00 0.00 C +ATOM 50 OH TYR 3 18.515 36.305 18.581 1.00 0.00 O +ATOM 51 HH TYR 3 18.774 35.870 17.765 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.190 20.937 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.729 37.250 21.020 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.323 35.442 22.065 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.447 35.936 23.020 1.00 0.00 H +ATOM 56 C TYR 3 20.090 31.765 25.077 1.00 0.00 C +ATOM 57 O TYR 3 20.461 32.246 26.149 1.00 0.00 O +ATOM 58 N LYS 4 20.401 30.506 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.251 30.222 23.770 1.00 0.00 H +ATOM 60 CA LYS 4 21.012 29.502 25.631 1.00 0.00 C +ATOM 61 HA LYS 4 20.728 29.716 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.477 28.101 25.270 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.521 27.983 24.189 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.144 27.345 25.695 1.00 0.00 H +ATOM 65 CG LYS 4 19.051 27.747 25.735 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.886 26.697 25.494 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.996 27.852 26.817 1.00 0.00 H +ATOM 68 CD LYS 4 17.924 28.566 25.082 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.889 29.561 25.522 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.146 28.677 24.019 1.00 0.00 H +ATOM 71 CE LYS 4 16.545 27.894 25.197 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.511 24.666 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.594 26.934 24.678 1.00 0.00 H +ATOM 74 NZ LYS 4 16.096 27.673 26.597 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.986 28.550 27.087 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.208 27.171 26.603 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.759 27.086 27.088 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.617 1.00 0.00 C +ATOM 79 O LYS 4 23.197 29.888 24.646 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.028 26.695 1.00 0.00 N +HETATM 81 CA HX1 5 24.626 28.831 26.818 1.00 0.00 C +HETATM 82 C HX1 5 24.900 27.673 27.781 1.00 0.00 C +HETATM 83 O HX1 5 24.403 27.682 28.908 1.00 0.00 O +HETATM 84 CB HX1 5 25.263 30.146 27.306 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.390 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.070 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.386 27.859 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.096 27.752 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.937 29.837 27.334 1.00 0.00 N +HETATM 90 H HX1 5 22.597 28.839 27.518 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.840 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.382 28.291 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.939 30.946 26.638 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.281 26.698 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.530 31.749 28.082 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.838 29.357 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.635 26.658 27.325 1.00 0.00 N +ATOM 98 H ILE 6 26.017 26.713 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.005 25.472 28.115 1.00 0.00 C +ATOM 100 HA ILE 6 25.305 25.371 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.849 24.199 27.245 1.00 0.00 C +ATOM 102 HB ILE 6 26.399 24.347 26.315 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.408 22.939 27.933 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.891 22.758 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.284 22.071 27.286 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.479 23.047 28.114 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.343 24.015 26.915 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.790 23.879 27.844 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.966 24.918 26.434 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.005 22.849 25.979 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.174 21.896 26.480 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.950 22.908 25.704 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.610 22.906 25.075 1.00 0.00 H +ATOM 114 C ILE 6 27.394 25.667 28.753 1.00 0.00 C +ATOM 115 O ILE 6 28.229 26.397 28.221 1.00 0.00 O +ATOM 116 N VAL 7 27.601 25.080 29.936 1.00 0.00 N +ATOM 117 H VAL 7 26.870 24.477 30.295 1.00 0.00 H +ATOM 118 CA VAL 7 28.779 25.286 30.801 1.00 0.00 C +ATOM 119 HA VAL 7 28.879 26.361 30.956 1.00 0.00 H +ATOM 120 CB VAL 7 28.501 24.640 32.176 1.00 0.00 C +ATOM 121 HB VAL 7 27.502 24.948 32.483 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.525 23.106 32.131 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.535 22.744 31.923 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.192 22.714 33.086 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.858 22.745 31.347 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.450 25.110 33.283 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.290 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.078 24.777 34.249 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.448 24.701 33.140 1.00 0.00 H +ATOM 130 C VAL 7 30.113 24.804 30.200 1.00 0.00 C +ATOM 131 O VAL 7 30.155 23.918 29.349 1.00 0.00 O +ATOM 132 N THR 8 31.216 25.379 30.688 1.00 0.00 N +ATOM 133 H THR 8 31.111 26.090 31.396 1.00 0.00 H +ATOM 134 CA THR 8 32.599 24.973 30.394 1.00 0.00 C +ATOM 135 HA THR 8 32.693 24.829 29.317 1.00 0.00 H +ATOM 136 CB THR 8 33.573 26.088 30.820 1.00 0.00 C +ATOM 137 HB THR 8 34.598 25.756 30.643 1.00 0.00 H +ATOM 138 CG2 THR 8 33.360 27.395 30.062 1.00 0.00 C +ATOM 139 HG21 THR 8 32.387 27.825 30.304 1.00 0.00 H +ATOM 140 HG22 THR 8 34.136 28.111 30.331 1.00 0.00 H +ATOM 141 HG23 THR 8 33.406 27.215 28.989 1.00 0.00 H +ATOM 142 OG1 THR 8 33.423 26.394 32.187 1.00 0.00 O +ATOM 143 HG1 THR 8 33.805 27.264 32.325 1.00 0.00 H +ATOM 144 C THR 8 33.011 23.656 31.078 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.249 32.104 1.00 0.00 O +ATOM 146 N GLY 9 34.050 23.008 30.534 1.00 0.00 N +ATOM 147 H GLY 9 34.405 23.337 29.651 1.00 0.00 H +ATOM 148 CA GLY 9 34.626 21.773 31.078 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.617 21.618 30.655 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.880 32.158 1.00 0.00 H +ATOM 151 C GLY 9 33.783 20.523 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.022 20.484 29.825 1.00 0.00 O +ATOM 153 N LYS 10 33.951 19.480 31.615 1.00 0.00 N +ATOM 154 H LYS 10 34.670 19.560 32.316 1.00 0.00 H +ATOM 155 CA LYS 10 33.230 18.191 31.479 1.00 0.00 C +ATOM 156 HA LYS 10 32.289 18.403 30.967 1.00 0.00 H +ATOM 157 CB LYS 10 34.057 17.246 30.577 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.677 17.847 29.907 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.724 16.640 31.194 1.00 0.00 H +ATOM 160 CG LYS 10 33.192 16.330 29.692 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.593 15.666 30.313 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.519 16.953 29.100 1.00 0.00 H +ATOM 163 CD LYS 10 34.058 15.492 28.736 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.721 16.156 28.178 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.661 14.791 29.314 1.00 0.00 H +ATOM 166 CE LYS 10 33.179 14.718 27.746 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.965 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.471 15.413 27.288 1.00 0.00 H +ATOM 169 NZ LYS 10 33.977 14.072 26.676 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.736 13.512 27.043 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.382 13.524 26.065 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.427 14.774 26.073 1.00 0.00 H +ATOM 173 C LYS 10 32.821 17.544 32.814 1.00 0.00 C +ATOM 174 O LYS 10 32.336 16.416 32.832 1.00 0.00 O +ATOM 175 N SER 11 33.037 18.243 33.935 1.00 0.00 N +ATOM 176 H SER 11 33.494 19.132 33.842 1.00 0.00 H +ATOM 177 CA SER 11 32.566 17.848 35.279 1.00 0.00 C +ATOM 178 HA SER 11 32.499 16.758 35.340 1.00 0.00 H +ATOM 179 CB SER 11 33.553 18.325 36.353 1.00 0.00 C +ATOM 180 HB2 SER 11 33.585 19.415 36.355 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.980 37.332 1.00 0.00 H +ATOM 182 OG SER 11 34.850 17.821 36.094 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.425 36.456 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.420 35.589 1.00 0.00 C +ATOM 185 O SER 11 30.351 17.750 36.199 1.00 0.00 O +ATOM 186 N CYS 12 30.919 19.655 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.630 20.134 34.627 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.270 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.870 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.351 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.324 22.215 34.523 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.251 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.149 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.145 23.412 37.057 1.00 0.00 H +ATOM 195 C CYS 12 28.853 19.936 33.838 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.667 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.513 19.990 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.060 20.142 34.736 1.00 0.00 H +ATOM 199 CA LYS 13 26.667 19.722 32.662 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.862 31.773 1.00 0.00 H +ATOM 201 CB LYS 13 26.223 18.247 32.706 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.032 17.655 33.143 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.346 18.144 33.358 1.00 0.00 H +ATOM 204 CG LYS 13 25.915 17.636 31.324 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.036 18.108 30.884 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.767 17.822 30.669 1.00 0.00 H +ATOM 207 CD LYS 13 25.684 16.116 31.406 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.690 15.716 30.391 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.518 15.663 31.947 1.00 0.00 H +ATOM 210 CE LYS 13 24.346 15.744 32.064 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.165 16.386 32.929 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.553 15.951 31.340 1.00 0.00 H +ATOM 213 NZ LYS 13 24.304 14.308 32.452 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.875 14.098 33.271 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.357 13.998 32.643 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.687 13.729 31.706 1.00 0.00 H +ATOM 217 C LYS 13 25.488 20.707 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.584 20.487 31.712 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.786 33.298 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.945 33.874 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.754 33.376 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.445 22.193 33.447 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.483 23.331 34.294 1.00 0.00 H +ATOM 224 C GLY 14 24.286 23.716 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.214 23.892 31.407 1.00 0.00 O +ATOM 226 N VAL 15 23.145 24.399 32.111 1.00 0.00 N +ATOM 227 H VAL 15 22.435 24.245 32.812 1.00 0.00 H +ATOM 228 CA VAL 15 22.778 25.387 31.071 1.00 0.00 C +ATOM 229 HA VAL 15 23.675 25.626 30.492 1.00 0.00 H +ATOM 230 CB VAL 15 21.760 24.738 30.089 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.856 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.449 24.318 30.766 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.938 25.178 31.211 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.793 23.856 30.028 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.579 31.548 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.416 25.668 28.927 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.331 26.008 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.820 25.120 28.196 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.841 26.533 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.282 26.685 31.729 1.00 0.00 C +ATOM 241 O VAL 15 21.714 26.632 32.818 1.00 0.00 O +HETATM 242 N HY1 16 22.496 27.830 31.091 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.109 31.450 1.00 0.00 C +HETATM 244 C HY1 16 21.616 29.886 30.135 1.00 0.00 C +HETATM 245 O HY1 16 21.780 29.350 29.023 1.00 0.00 O +HETATM 246 CB HY1 16 22.864 29.868 32.413 1.00 0.00 C +HETATM 247 CG HY1 16 24.212 30.223 31.813 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.549 31.404 31.207 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.321 29.396 31.740 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.303 30.091 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.880 31.315 30.788 1.00 0.00 N +HETATM 252 H HY1 16 22.997 27.783 30.210 1.00 0.00 H +HETATM 253 HA HY1 16 20.968 28.987 31.945 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.396 30.793 32.773 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.026 29.256 33.296 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.399 28.458 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.907 32.258 31.095 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.728 30.996 1.00 0.00 H +ATOM 259 N THR 17 21.166 31.142 30.265 1.00 0.00 N +ATOM 260 H THR 17 21.050 31.473 31.216 1.00 0.00 H +ATOM 261 CA THR 17 20.736 32.026 29.172 1.00 0.00 C +ATOM 262 HA THR 17 21.120 31.634 28.284 1.00 0.00 H +ATOM 263 CB THR 17 19.152 32.017 29.049 1.00 0.00 C +ATOM 264 HB THR 17 18.937 32.609 28.167 1.00 0.00 H +ATOM 265 CG2 THR 17 18.596 30.675 28.723 1.00 0.00 C +ATOM 266 HG21 THR 17 18.786 29.900 29.421 1.00 0.00 H +ATOM 267 HG22 THR 17 17.506 30.690 28.630 1.00 0.00 H +ATOM 268 HG23 THR 17 18.925 30.322 27.780 1.00 0.00 H +ATOM 269 OG1 THR 17 18.479 32.473 30.205 1.00 0.00 O +ATOM 270 HG1 THR 17 18.568 33.453 30.221 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.458 29.233 1.00 0.00 C +ATOM 272 O THR 17 21.702 33.916 30.265 1.00 0.00 O +HETATM 273 N HY2 18 21.139 34.162 28.101 1.00 0.00 N +HETATM 274 CA HY2 18 21.450 35.620 27.971 1.00 0.00 C +HETATM 275 C HY2 18 20.329 36.290 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.985 35.837 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.774 35.820 27.259 1.00 0.00 C +HETATM 278 CG HY2 18 24.005 35.327 28.003 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.420 34.030 28.155 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.943 36.119 28.644 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.315 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.707 27.237 1.00 0.00 H +HETATM 284 HA HY2 18 21.503 36.046 29.014 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.748 35.296 26.297 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.910 36.879 27.057 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.955 37.127 28.681 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.926 33.165 27.774 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.761 35.647 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.807 37.387 27.748 1.00 0.00 N +ATOM 291 H GLU 19 20.142 37.684 28.644 1.00 0.00 H +ATOM 292 CA GLU 19 18.798 38.219 27.101 1.00 0.00 C +ATOM 293 HA GLU 19 18.058 37.555 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.065 39.079 28.156 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.754 38.431 28.967 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.775 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.833 39.851 27.657 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.550 28.422 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.089 40.412 26.764 1.00 0.00 H +ATOM 300 CD GLU 19 15.654 38.901 27.366 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.588 38.373 26.224 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.813 38.691 28.275 1.00 0.00 O +ATOM 303 C GLU 19 19.405 39.113 25.992 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.857 26.273 1.00 0.00 O +ATOM 305 N ALA 20 18.878 39.052 24.762 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.354 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.961 23.686 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.963 24.094 1.00 0.00 H +ATOM 309 CB ALA 20 20.592 39.489 23.094 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.465 38.517 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.951 40.206 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.351 39.401 23.870 1.00 0.00 H +ATOM 313 C ALA 20 18.191 40.036 22.579 1.00 0.00 C +ATOM 314 O ALA 20 17.360 39.133 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.087 21.745 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.824 21.920 1.00 0.00 H +ATOM 317 CA VAL 21 17.460 41.147 20.465 1.00 0.00 C +ATOM 318 HA VAL 21 16.471 40.723 20.625 1.00 0.00 H +ATOM 319 CB VAL 21 17.274 42.597 19.972 1.00 0.00 C +ATOM 320 HB VAL 21 16.616 42.570 19.108 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.597 43.470 21.033 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.255 43.626 21.888 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.349 44.439 20.598 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.674 42.997 21.365 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.583 43.276 19.536 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.004 42.764 18.670 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.380 44.306 19.239 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.315 43.278 20.344 1.00 0.00 H +ATOM 329 C VAL 21 18.121 40.330 19.353 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.986 18.375 1.00 0.00 O +ATOM 331 N ASP 22 19.414 40.050 19.506 1.00 0.00 N +ATOM 332 H ASP 22 19.863 40.329 20.361 1.00 0.00 H +ATOM 333 CA ASP 22 20.295 39.463 18.502 1.00 0.00 C +ATOM 334 HA ASP 22 19.714 38.825 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.941 40.588 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.174 41.079 17.075 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.377 41.324 18.356 1.00 0.00 H +ATOM 338 CG ASP 22 22.025 40.044 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.147 40.586 16.800 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.762 39.018 16.087 1.00 0.00 O +ATOM 341 C ASP 22 21.366 38.597 19.178 1.00 0.00 C +ATOM 342 O ASP 22 21.825 38.880 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.789 37.545 18.492 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.489 17.520 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.608 18.984 1.00 0.00 C +ATOM 346 HA TRP 23 22.545 36.357 20.016 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.348 18.138 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.975 18.216 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.840 35.604 17.094 1.00 0.00 H +ATOM 350 CG TRP 23 23.573 34.244 18.531 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.517 33.704 17.733 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.739 34.020 16.723 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.129 32.678 18.412 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.903 32.155 18.035 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.589 32.475 19.659 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.825 31.536 20.665 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.540 30.741 20.523 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.682 21.888 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.012 22.701 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.765 22.099 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.900 23.082 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.005 33.658 21.055 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.310 34.465 21.213 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.637 33.527 19.797 1.00 0.00 C +ATOM 365 C TRP 23 24.210 37.185 18.982 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.925 1.00 0.00 O +ATOM 367 N ALA 24 24.557 38.022 17.997 1.00 0.00 N +ATOM 368 H ALA 24 23.880 38.262 17.279 1.00 0.00 H +ATOM 369 CA ALA 24 25.846 38.717 17.976 1.00 0.00 C +ATOM 370 HA ALA 24 26.618 38.001 18.267 1.00 0.00 H +ATOM 371 CB ALA 24 26.158 39.140 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.444 39.882 16.189 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.160 39.562 16.482 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.110 38.274 15.877 1.00 0.00 H +ATOM 375 C ALA 24 25.929 39.882 18.994 1.00 0.00 C +ATOM 376 O ALA 24 27.022 40.384 19.270 1.00 0.00 O +ATOM 377 N GLU 25 24.812 40.285 19.610 1.00 0.00 N +ATOM 378 H GLU 25 23.932 39.945 19.243 1.00 0.00 H +ATOM 379 CA GLU 25 24.791 41.075 20.852 1.00 0.00 C +ATOM 380 HA GLU 25 25.642 41.755 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.512 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.646 41.279 20.820 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.451 42.386 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.432 43.037 19.875 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.632 42.630 18.884 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.410 43.424 19.863 1.00 0.00 H +ATOM 387 CD GLU 25 24.381 44.197 20.185 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.918 45.196 20.744 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.601 44.048 19.836 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.102 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.517 23.016 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.005 22.132 1.00 0.00 N +ATOM 393 H ALA 26 23.666 38.775 21.366 1.00 0.00 H +ATOM 394 CA ALA 26 24.460 38.029 23.217 1.00 0.00 C +ATOM 395 HA ALA 26 24.199 38.524 24.148 1.00 0.00 H +ATOM 396 CB ALA 26 23.491 36.862 23.015 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.771 36.287 22.133 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.204 23.883 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.230 22.894 1.00 0.00 H +ATOM 400 C ALA 26 25.918 37.533 23.365 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.227 24.482 1.00 0.00 O +ATOM 402 N GLU 27 26.710 37.510 22.283 1.00 0.00 N +ATOM 403 H GLU 27 26.268 37.638 21.376 1.00 0.00 H +ATOM 404 CA GLU 27 28.167 37.303 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.369 36.351 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.763 37.247 20.913 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.152 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.735 38.251 20.486 1.00 0.00 H +ATOM 409 CG GLU 27 30.208 36.724 20.921 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.145 21.771 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.190 35.641 21.055 1.00 0.00 H +ATOM 412 CD GLU 27 30.982 37.089 19.641 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.725 38.106 19.697 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.344 18.641 1.00 0.00 O +ATOM 415 C GLU 27 28.849 38.396 23.183 1.00 0.00 C +ATOM 416 O GLU 27 29.572 38.094 24.134 1.00 0.00 O +ATOM 417 N LYS 28 28.547 39.673 22.914 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.853 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.817 23.666 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.667 1.00 0.00 H +ATOM 421 CB LYS 28 28.699 42.145 22.993 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.278 23.048 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.170 42.963 23.542 1.00 0.00 H +ATOM 424 CG LYS 28 29.137 42.221 21.519 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.207 42.027 21.443 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.604 41.462 20.949 1.00 0.00 H +ATOM 427 CD LYS 28 28.837 43.604 20.920 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.819 43.907 21.172 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.521 44.332 21.364 1.00 0.00 H +ATOM 430 CE LYS 28 29.006 43.629 19.396 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.103 44.670 19.084 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.926 43.113 19.127 1.00 0.00 H +ATOM 433 NZ LYS 28 27.841 43.021 18.708 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.981 43.489 19.017 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.904 43.103 17.704 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.722 42.040 18.958 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.782 25.132 1.00 0.00 C +ATOM 438 O LYS 28 29.482 40.969 26.019 1.00 0.00 O +ATOM 439 N PHE 29 27.393 40.452 25.417 1.00 0.00 N +ATOM 440 H PHE 29 26.740 40.365 24.642 1.00 0.00 H +ATOM 441 CA PHE 29 26.903 40.286 26.793 1.00 0.00 C +ATOM 442 HA PHE 29 27.228 41.146 27.379 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.264 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.038 39.343 26.310 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.022 40.230 27.832 1.00 0.00 H +ATOM 446 CG PHE 29 24.678 41.443 26.116 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.465 41.235 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.015 40.254 25.407 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.830 42.300 24.767 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.907 42.126 24.234 1.00 0.00 H +ATOM 451 CZ PHE 29 23.399 43.584 24.790 1.00 0.00 C +ATOM 452 HZ PHE 29 22.919 44.396 24.265 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.591 43.806 25.498 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.027 44.796 25.527 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.226 42.742 26.165 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.139 42.936 26.704 1.00 0.00 H +ATOM 457 C PHE 29 27.484 39.050 27.507 1.00 0.00 C +ATOM 458 O PHE 29 27.589 39.038 28.735 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.768 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.042 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.683 36.892 27.316 1.00 0.00 C +ATOM 462 HA THR 30 28.208 36.545 28.226 1.00 0.00 H +ATOM 463 CB THR 30 28.692 35.717 26.333 1.00 0.00 C +ATOM 464 HB THR 30 29.073 36.025 25.356 1.00 0.00 H +ATOM 465 CG2 THR 30 29.496 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.137 34.212 27.801 1.00 0.00 H +ATOM 467 HG22 THR 30 29.369 33.689 26.123 1.00 0.00 H +ATOM 468 HG23 THR 30 30.559 34.746 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.365 35.280 26.189 1.00 0.00 O +ATOM 470 HG1 THR 30 26.960 35.883 25.542 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.982 28.769 1.00 0.00 O +ATOM 473 N LYS 31 30.746 38.122 26.832 1.00 0.00 N +ATOM 474 H LYS 31 30.287 38.320 25.947 1.00 0.00 H +ATOM 475 CA LYS 31 32.078 38.702 27.069 1.00 0.00 C +ATOM 476 HA LYS 31 32.749 37.905 27.376 1.00 0.00 H +ATOM 477 CB LYS 31 32.616 39.317 25.766 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.011 25.348 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.529 39.865 25.987 1.00 0.00 H +ATOM 480 CG LYS 31 32.930 38.210 24.744 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.684 37.553 25.176 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.044 37.629 24.525 1.00 0.00 H +ATOM 483 CD LYS 31 33.459 38.818 23.435 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.384 22.952 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.299 39.497 23.642 1.00 0.00 H +ATOM 486 CE LYS 31 33.923 37.725 22.467 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.107 37.055 22.246 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.217 38.195 21.540 1.00 0.00 H +ATOM 489 NZ LYS 31 35.077 36.976 23.015 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.822 36.247 23.679 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.553 36.469 22.265 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.760 37.567 23.503 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.188 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.780 28.917 1.00 0.00 O +ATOM 495 N ALA 32 31.031 40.509 28.373 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.873 41.412 29.515 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.138 29.505 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.375 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.495 29.375 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.875 30.215 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.557 42.757 28.446 1.00 0.00 H +ATOM 503 C ALA 32 30.963 40.638 30.838 1.00 0.00 C +ATOM 504 O ALA 32 31.881 40.886 31.616 1.00 0.00 O +ATOM 505 N LYN 33 30.117 39.613 31.030 1.00 0.00 N +ATOM 506 H LYN 33 29.390 39.457 30.346 1.00 0.00 H +ATOM 507 CA LYN 33 30.156 38.755 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.022 39.383 33.110 1.00 0.00 H +ATOM 509 CB LYN 33 29.008 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.061 37.156 31.262 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.141 37.038 33.024 1.00 0.00 H +ATOM 512 CG LYN 33 27.610 38.358 32.315 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.564 38.982 33.207 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.412 38.981 31.444 1.00 0.00 H +ATOM 515 CD LYN 33 26.535 37.267 32.412 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.691 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.632 36.748 33.365 1.00 0.00 H +ATOM 518 CE LYN 33 25.122 37.835 32.288 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.934 38.514 33.114 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.035 38.378 31.349 1.00 0.00 H +ATOM 521 NZ LYN 33 24.115 36.761 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.184 37.154 32.261 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.253 36.113 31.547 1.00 0.00 H +ATOM 524 C LYN 33 31.510 38.042 32.391 1.00 0.00 C +ATOM 525 O LYN 33 32.008 37.922 33.505 1.00 0.00 O +ATOM 526 N ALA 34 32.143 37.585 31.305 1.00 0.00 N +ATOM 527 H ALA 34 31.696 37.677 30.400 1.00 0.00 H +ATOM 528 CA ALA 34 33.470 36.966 31.389 1.00 0.00 C +ATOM 529 HA ALA 34 33.428 36.160 32.125 1.00 0.00 H +ATOM 530 CB ALA 34 33.816 36.355 30.029 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.962 37.145 29.294 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.776 30.132 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.693 29.698 1.00 0.00 H +ATOM 534 C ALA 34 34.573 37.946 31.865 1.00 0.00 C +ATOM 535 O ALA 34 35.469 37.540 32.604 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.224 31.488 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.504 30.885 1.00 0.00 H +ATOM 538 CA ASN 35 35.368 40.286 32.000 1.00 0.00 C +ATOM 539 HA ASN 35 36.366 39.870 32.113 1.00 0.00 H +ATOM 540 CB ASN 35 35.476 41.416 30.969 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.486 41.702 30.624 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.287 31.449 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.031 29.800 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.581 41.002 29.898 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.705 28.668 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.448 27.895 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.600 28.628 1.00 0.00 H +ATOM 548 C ASN 35 34.981 40.786 33.404 1.00 0.00 C +ATOM 549 O ASN 35 35.867 41.207 34.150 1.00 0.00 O +ATOM 550 N ASP 36 33.718 40.635 33.831 1.00 0.00 N +ATOM 551 H ASP 36 32.984 40.413 33.166 1.00 0.00 H +ATOM 552 CA ASP 36 33.339 40.772 35.249 1.00 0.00 C +ATOM 553 HA ASP 36 33.668 41.747 35.602 1.00 0.00 H +ATOM 554 CB ASP 36 31.819 40.767 35.440 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.448 39.783 35.230 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.607 40.875 36.498 1.00 0.00 H +ATOM 557 CG ASP 36 30.981 41.783 34.657 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.512 42.876 34.366 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.778 41.516 34.402 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.708 36.125 1.00 0.00 C +ATOM 561 O ASP 36 34.482 40.004 37.236 1.00 0.00 O +ATOM 562 N PHE 37 34.227 38.480 35.608 1.00 0.00 N +ATOM 563 H PHE 37 33.751 38.279 34.737 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.459 36.179 1.00 0.00 C +ATOM 565 HA PHE 37 35.118 37.611 37.257 1.00 0.00 H +ATOM 566 CB PHE 37 34.574 36.041 35.932 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.663 35.826 34.870 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.334 36.446 1.00 0.00 H +ATOM 569 CG PHE 37 33.150 35.763 36.385 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.139 35.558 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.374 35.619 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.312 35.834 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.039 35.198 35.094 1.00 0.00 H +ATOM 574 CZ PHE 37 30.507 35.235 37.199 1.00 0.00 C +ATOM 575 HZ PHE 37 29.492 35.053 37.510 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.515 35.404 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.270 35.352 39.212 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.834 35.668 37.752 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.601 35.814 38.491 1.00 0.00 H +ATOM 580 C PHE 37 36.607 37.580 35.742 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.679 36.016 1.00 0.00 O +ATOM 582 N GLY 38 36.998 38.676 35.079 1.00 0.00 N +ATOM 583 H GLY 38 36.291 39.378 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.389 39.091 34.839 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.499 40.111 35.207 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.054 38.469 35.438 1.00 0.00 H +ATOM 587 C GLY 38 38.925 39.060 33.393 1.00 0.00 C +ATOM 588 O GLY 38 39.874 39.792 33.112 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.227 32.486 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.727 32.761 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.052 31.090 1.00 0.00 C +ATOM 592 HA ARG 39 38.944 39.045 30.646 1.00 0.00 H +ATOM 593 CB ARG 39 40.304 37.440 31.075 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.635 37.431 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.987 38.106 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.522 36.013 31.628 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.039 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.753 31.461 1.00 0.00 H +ATOM 599 CD ARG 39 40.222 35.826 33.132 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.861 36.507 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.182 36.080 33.342 1.00 0.00 H +ATOM 602 NE ARG 39 40.446 34.443 33.599 1.00 0.00 N +ATOM 603 HE ARG 39 41.205 34.297 34.244 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.303 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.469 32.493 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.428 34.360 32.093 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.296 32.621 32.084 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.954 32.226 33.819 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.694 32.095 34.491 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.336 31.450 33.602 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.225 30.193 1.00 0.00 C +ATOM 612 O ARG 39 37.522 36.137 30.605 1.00 0.00 O +ATOM 613 N ASP 40 37.650 37.678 28.959 1.00 0.00 N +ATOM 614 H ASP 40 38.029 38.573 28.674 1.00 0.00 H +ATOM 615 CA ASP 40 36.889 36.892 27.966 1.00 0.00 C +ATOM 616 HA ASP 40 36.166 36.309 28.530 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.733 26.970 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.444 37.038 26.402 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.369 38.350 27.538 1.00 0.00 H +ATOM 620 CG ASP 40 36.824 38.628 25.969 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.257 39.725 26.392 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.837 38.322 24.743 1.00 0.00 O +ATOM 623 C ASP 40 37.720 35.861 27.181 1.00 0.00 C +ATOM 624 O ASP 40 38.885 36.078 26.862 1.00 0.00 O +ATOM 625 N GLY 41 37.056 34.760 26.814 1.00 0.00 N +ATOM 626 H GLY 41 36.099 34.682 27.117 1.00 0.00 H +ATOM 627 CA GLY 41 37.471 33.828 25.758 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.459 34.099 25.383 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.531 32.823 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.482 33.818 24.581 1.00 0.00 C +ATOM 631 O GLY 41 35.578 34.655 24.504 1.00 0.00 O +ATOM 632 N GLU 42 36.638 32.853 23.674 1.00 0.00 N +ATOM 633 H GLU 42 37.348 32.156 23.828 1.00 0.00 H +ATOM 634 CA GLU 42 35.799 32.668 22.476 1.00 0.00 C +ATOM 635 HA GLU 42 35.112 33.509 22.376 1.00 0.00 H +ATOM 636 CB GLU 42 36.683 32.630 21.214 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.158 31.650 21.168 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.035 32.711 20.341 1.00 0.00 H +ATOM 639 CG GLU 42 37.803 33.694 21.111 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.575 33.457 21.850 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.277 33.620 20.129 1.00 0.00 H +ATOM 642 CD GLU 42 37.343 35.144 21.318 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.154 35.459 21.111 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.167 36.006 21.711 1.00 0.00 O +ATOM 645 C GLU 42 34.948 31.386 22.578 1.00 0.00 C +ATOM 646 O GLU 42 35.393 30.398 23.170 1.00 0.00 O +ATOM 647 N ALA 43 33.745 31.391 21.989 1.00 0.00 N +ATOM 648 H ALA 43 33.480 32.196 21.440 1.00 0.00 H +ATOM 649 CA ALA 43 32.756 30.306 22.060 1.00 0.00 C +ATOM 650 HA ALA 43 33.248 29.388 22.388 1.00 0.00 H +ATOM 651 CB ALA 43 31.692 30.672 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.181 31.592 22.812 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.959 29.866 23.177 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.164 30.811 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.110 30.017 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.882 30.932 19.898 1.00 0.00 O +ATOM 657 N THR 44 31.798 28.746 20.423 1.00 0.00 N +ATOM 658 H THR 44 31.919 28.067 21.168 1.00 0.00 H +ATOM 659 CA THR 44 31.131 28.283 19.194 1.00 0.00 C +ATOM 660 HA THR 44 31.425 28.947 18.381 1.00 0.00 H +ATOM 661 CB THR 44 31.610 26.868 18.823 1.00 0.00 C +ATOM 662 HB THR 44 31.430 26.188 19.657 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.281 17.554 1.00 0.00 C +ATOM 664 HG21 THR 44 31.071 26.989 16.727 1.00 0.00 H +ATOM 665 HG22 THR 44 31.502 25.358 17.280 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.037 17.727 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.927 18.561 1.00 0.00 O +ATOM 668 HG1 THR 44 33.234 26.124 18.092 1.00 0.00 H +ATOM 669 C THR 44 29.605 28.381 19.326 1.00 0.00 C +ATOM 670 O THR 44 29.072 28.429 20.436 1.00 0.00 O +ATOM 671 N ILE 45 28.899 28.459 18.193 1.00 0.00 N +ATOM 672 H ILE 45 29.373 28.324 17.314 1.00 0.00 H +ATOM 673 CA ILE 45 27.479 28.840 18.123 1.00 0.00 C +ATOM 674 HA ILE 45 27.060 28.756 19.126 1.00 0.00 H +ATOM 675 CB ILE 45 27.332 30.316 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.271 30.529 17.778 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.069 31.232 18.677 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.151 31.108 18.586 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.833 32.282 18.498 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.768 30.969 19.687 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.759 30.692 16.252 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.018 31.752 16.233 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.657 30.140 15.968 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.506 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.730 30.935 15.529 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.975 31.017 14.269 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.530 29.452 14.955 1.00 0.00 H +ATOM 688 C ILE 45 26.629 27.925 17.243 1.00 0.00 C +ATOM 689 O ILE 45 27.122 27.343 16.276 1.00 0.00 O +ATOM 690 N ASP 46 25.329 27.880 17.545 1.00 0.00 N +ATOM 691 H ASP 46 25.032 28.297 18.421 1.00 0.00 H +ATOM 692 CA ASP 46 24.280 27.260 16.735 1.00 0.00 C +ATOM 693 HA ASP 46 24.584 27.263 15.684 1.00 0.00 H +ATOM 694 CB ASP 46 24.077 25.807 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.221 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.955 25.788 18.267 1.00 0.00 H +ATOM 697 CG ASP 46 22.841 25.170 16.544 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.475 17.281 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.561 25.439 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.957 28.050 16.850 1.00 0.00 C +ATOM 701 O ASP 46 22.507 28.363 17.955 1.00 0.00 O +ATOM 702 N ASP 47 22.309 28.333 15.716 1.00 0.00 N +ATOM 703 H ASP 47 22.678 27.944 14.861 1.00 0.00 H +ATOM 704 CA ASP 47 20.969 28.925 15.674 1.00 0.00 C +ATOM 705 HA ASP 47 20.875 29.653 16.485 1.00 0.00 H +ATOM 706 CB ASP 47 20.776 29.674 14.345 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.520 30.467 14.253 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.912 28.978 13.514 1.00 0.00 H +ATOM 709 CG ASP 47 19.366 30.275 14.271 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.485 29.674 13.613 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.064 31.235 15.016 1.00 0.00 O +ATOM 712 C ASP 47 19.852 27.876 15.878 1.00 0.00 C +ATOM 713 O ASP 47 18.842 28.184 16.513 1.00 0.00 O +ATOM 714 N ALA 48 20.002 26.636 15.396 1.00 0.00 N +ATOM 715 H ALA 48 20.917 26.342 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.934 25.626 15.412 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.054 14.931 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.425 14.583 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.276 23.967 15.053 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.686 14.514 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.674 24.756 13.580 1.00 0.00 H +ATOM 722 C ALA 48 18.524 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.929 17.099 1.00 0.00 O +ATOM 724 N THR 49 19.475 25.245 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.436 25.295 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.265 25.120 19.229 1.00 0.00 C +ATOM 727 HA THR 49 18.215 24.872 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.099 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.818 23.859 20.868 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.628 19.137 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.666 18.098 1.00 0.00 H +ATOM 732 HG22 THR 49 20.434 21.857 19.654 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.165 1.00 0.00 H +ATOM 734 OG1 THR 49 21.478 24.244 19.774 1.00 0.00 O +ATOM 735 HG1 THR 49 21.730 24.270 18.816 1.00 0.00 H +ATOM 736 C THR 49 19.505 26.429 19.997 1.00 0.00 C +ATOM 737 O THR 49 19.426 26.431 21.226 1.00 0.00 O +ATOM 738 N LYS 50 19.766 27.551 19.307 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.297 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.906 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.354 29.538 19.086 1.00 0.00 H +ATOM 742 CB LYS 50 18.564 29.472 20.292 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.160 28.830 21.074 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.701 30.459 20.736 1.00 0.00 H +ATOM 745 CG LYS 50 17.492 29.593 19.188 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.426 28.657 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.740 19.683 1.00 0.00 H +ATOM 748 CD LYS 50 17.704 30.775 18.223 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.703 31.695 18.813 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.688 17.723 1.00 0.00 H +ATOM 751 CE LYS 50 16.571 30.869 17.187 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.603 17.664 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.507 31.899 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.997 16.018 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.231 29.102 16.282 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.013 29.838 15.434 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.544 30.418 15.421 1.00 0.00 H +ATOM 758 C LYS 50 20.986 28.948 21.020 1.00 0.00 C +ATOM 759 O LYS 50 20.693 29.519 22.082 1.00 0.00 O +ATOM 760 N THR 51 22.146 28.292 20.857 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.962 19.926 1.00 0.00 H +ATOM 762 CA THR 51 23.055 27.904 21.959 1.00 0.00 C +ATOM 763 HA THR 51 22.763 28.429 22.858 1.00 0.00 H +ATOM 764 CB THR 51 22.885 26.404 22.277 1.00 0.00 C +ATOM 765 HB THR 51 22.979 25.814 21.354 1.00 0.00 H +ATOM 766 CG2 THR 51 23.850 25.861 23.317 1.00 0.00 C +ATOM 767 HG21 THR 51 23.812 26.474 24.218 1.00 0.00 H +ATOM 768 HG22 THR 51 23.577 24.841 23.588 1.00 0.00 H +ATOM 769 HG23 THR 51 24.876 25.835 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.633 26.168 22.876 1.00 0.00 O +ATOM 771 HG1 THR 51 20.954 26.250 22.182 1.00 0.00 H +ATOM 772 C THR 51 24.556 28.224 21.725 1.00 0.00 C +ATOM 773 O THR 51 25.085 28.000 20.641 1.00 0.00 O +ATOM 774 N PHE 52 25.248 28.694 22.772 1.00 0.00 N +ATOM 775 H PHE 52 24.712 28.952 23.592 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.779 22.880 1.00 0.00 C +ATOM 777 HA PHE 52 27.145 28.937 21.899 1.00 0.00 H +ATOM 778 CB PHE 52 27.149 29.952 23.820 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.476 29.958 24.659 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.735 24.193 1.00 0.00 H +ATOM 781 CG PHE 52 27.217 31.347 23.228 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.428 32.382 23.752 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.751 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.443 33.652 23.161 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.777 34.431 23.515 1.00 0.00 H +ATOM 786 CZ PHE 52 27.281 33.893 22.066 1.00 0.00 C +ATOM 787 HZ PHE 52 27.244 34.837 21.559 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.160 32.902 21.616 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.836 33.108 20.791 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.628 22.199 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.778 30.857 21.828 1.00 0.00 H +ATOM 792 C PHE 52 27.331 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.809 27.010 24.505 1.00 0.00 O +ATOM 794 N THR 53 28.487 27.066 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.851 27.522 22.147 1.00 0.00 H +ATOM 796 CA THR 53 29.281 25.929 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.048 25.798 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.936 24.611 22.782 1.00 0.00 C +ATOM 799 HB THR 53 29.512 23.804 23.241 1.00 0.00 H +ATOM 800 CG2 THR 53 27.461 24.225 22.862 1.00 0.00 C +ATOM 801 HG21 THR 53 26.865 24.906 22.254 1.00 0.00 H +ATOM 802 HG22 THR 53 27.326 23.209 22.494 1.00 0.00 H +ATOM 803 HG23 THR 53 27.124 24.270 23.898 1.00 0.00 H +ATOM 804 OG1 THR 53 29.273 24.680 21.420 1.00 0.00 O +ATOM 805 HG1 THR 53 28.756 24.016 20.955 1.00 0.00 H +ATOM 806 C THR 53 30.804 26.149 23.413 1.00 0.00 C +ATOM 807 O THR 53 31.287 27.022 22.688 1.00 0.00 O +ATOM 808 N THR 54 31.571 25.328 24.145 1.00 0.00 N +ATOM 809 H THR 54 31.111 24.655 24.737 1.00 0.00 H +ATOM 810 CA THR 54 33.043 25.241 24.080 1.00 0.00 C +ATOM 811 HA THR 54 33.416 26.036 23.436 1.00 0.00 H +ATOM 812 CB THR 54 33.668 25.452 25.473 1.00 0.00 C +ATOM 813 HB THR 54 33.373 24.632 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.195 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.517 26.335 24.770 1.00 0.00 H +ATOM 816 HG22 THR 54 35.553 25.813 26.470 1.00 0.00 H +ATOM 817 HG23 THR 54 35.642 24.609 25.193 1.00 0.00 H +ATOM 818 OG1 THR 54 33.203 26.662 26.026 1.00 0.00 O +ATOM 819 HG1 THR 54 33.876 26.992 26.625 1.00 0.00 H +ATOM 820 C THR 54 33.479 23.896 23.474 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.895 23.605 1.00 0.00 O +ATOM 822 N GLN 55 34.635 23.879 22.803 1.00 0.00 N +ATOM 823 H GLN 55 35.156 24.739 22.761 1.00 0.00 H +ATOM 824 CA GLN 55 35.264 22.693 22.195 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.165 21.639 1.00 0.00 H +ATOM 826 CB GLN 55 36.319 23.163 21.173 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.730 22.295 20.657 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.804 23.775 20.430 1.00 0.00 H +ATOM 829 CG GLN 55 37.482 23.993 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.096 24.713 22.482 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.177 23.334 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.249 24.773 20.686 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.326 24.397 19.523 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.831 25.902 21.034 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.408 26.355 20.331 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.724 26.275 21.962 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.679 23.225 1.00 0.00 C +ATOM 838 O GLN 55 36.112 22.047 24.363 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.413 22.804 1.00 0.00 N +ATOM 840 H GLU 56 35.794 20.234 21.832 1.00 0.00 H +ATOM 841 CA GLU 56 36.491 19.249 23.573 1.00 0.00 C +ATOM 842 HA GLU 56 36.152 19.337 24.602 1.00 0.00 H +ATOM 843 CB GLU 56 35.885 17.954 22.967 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.804 17.985 23.074 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.993 21.896 1.00 0.00 H +ATOM 846 CG GLU 56 36.403 16.582 23.463 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.459 15.931 22.591 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.423 16.669 23.812 1.00 0.00 H +ATOM 849 CD GLU 56 35.548 15.855 24.520 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.094 15.347 25.534 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.325 15.660 24.312 1.00 0.00 O +ATOM 852 C GLU 56 38.030 19.202 23.644 1.00 0.00 C +ATOM 853 O GLU 56 38.535 19.186 24.795 1.00 0.00 O +ATOM 854 OXT GLU 56 38.680 19.141 22.578 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.717 32.457 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.342 33.248 30.282 1.00 0.00 N +HETATM 857 C AN1 58 30.690 33.885 31.200 1.00 0.00 C +HETATM 858 C1 AN1 58 29.362 33.529 30.704 1.00 0.00 C +HETATM 859 H AN1 58 30.622 34.282 32.217 1.00 0.00 H +HETATM 860 H1 AN1 58 31.134 34.634 30.540 1.00 0.00 H +HETATM 861 H2 AN1 58 31.317 32.983 31.203 1.00 0.00 H +HETATM 862 N1 AZI 59 31.272 30.355 29.425 1.00 0.00 N +HETATM 863 N2 AZI 59 30.474 30.251 30.345 1.00 0.00 N +HETATM 864 N3 AZI 59 29.631 30.164 31.291 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 148 144 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 643 639 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_3_front_7.pdb b/tests/nsga2/intermediate_molecules/min_iter_3_front_7.pdb new file mode 100644 index 0000000..93ef165 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_3_front_7.pdb @@ -0,0 +1,1785 @@ +COMPND fitness: -6.2239 90.03083333333325 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 50.124 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.128 37.937 23.379 1.00 0.00 N +ATOM 2 H1 MET 1 15.115 38.352 24.304 1.00 0.00 H +ATOM 3 H2 MET 1 14.353 38.281 22.845 1.00 0.00 H +ATOM 4 H3 MET 1 15.989 38.231 22.950 1.00 0.00 H +ATOM 5 CA MET 1 15.114 36.469 23.492 1.00 0.00 C +ATOM 6 HA MET 1 14.154 36.172 23.930 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.810 22.104 1.00 0.00 C +ATOM 8 HB2 MET 1 14.395 36.081 21.502 1.00 0.00 H +ATOM 9 HB3 MET 1 16.151 36.200 21.624 1.00 0.00 H +ATOM 10 CG MET 1 15.368 34.269 22.154 1.00 0.00 C +ATOM 11 HG2 MET 1 16.256 34.008 22.740 1.00 0.00 H +ATOM 12 HG3 MET 1 14.490 33.864 22.670 1.00 0.00 H +ATOM 13 SD MET 1 15.523 33.454 20.540 1.00 0.00 S +ATOM 14 CE MET 1 13.825 33.570 19.902 1.00 0.00 C +ATOM 15 HE1 MET 1 13.514 34.612 19.846 1.00 0.00 H +ATOM 16 HE2 MET 1 13.786 33.136 18.902 1.00 0.00 H +ATOM 17 HE3 MET 1 13.144 33.019 20.553 1.00 0.00 H +ATOM 18 C MET 1 16.215 36.013 24.449 1.00 0.00 C +ATOM 19 O MET 1 17.372 36.346 24.223 1.00 0.00 O +ATOM 20 N GLN 2 15.871 35.224 25.474 1.00 0.00 N +ATOM 21 H GLN 2 14.897 35.087 25.675 1.00 0.00 H +ATOM 22 CA GLN 2 16.831 34.496 26.306 1.00 0.00 C +ATOM 23 HA GLN 2 17.643 35.162 26.593 1.00 0.00 H +ATOM 24 CB GLN 2 16.127 34.008 27.587 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.159 33.579 27.318 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.708 33.210 28.060 1.00 0.00 H +ATOM 27 CG GLN 2 15.903 35.114 28.632 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.477 35.983 28.143 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.171 34.756 29.353 1.00 0.00 H +ATOM 30 CD GLN 2 17.153 35.508 29.416 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.264 35.044 29.192 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.019 36.331 30.429 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.839 36.559 30.955 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.114 36.721 30.646 1.00 0.00 H +ATOM 35 C GLN 2 17.469 33.325 25.522 1.00 0.00 C +ATOM 36 O GLN 2 17.052 32.167 25.651 1.00 0.00 O +ATOM 37 N TYR 3 18.463 33.623 24.678 1.00 0.00 N +ATOM 38 H TYR 3 18.765 34.592 24.628 1.00 0.00 H +ATOM 39 CA TYR 3 19.234 32.609 23.954 1.00 0.00 C +ATOM 40 HA TYR 3 18.545 31.959 23.422 1.00 0.00 H +ATOM 41 CB TYR 3 20.170 33.262 22.941 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.877 33.900 23.476 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.723 32.438 22.497 1.00 0.00 H +ATOM 44 CG TYR 3 19.600 34.062 21.781 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.519 33.459 20.512 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.802 32.423 20.390 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.149 34.213 19.385 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.118 33.754 18.409 1.00 0.00 H +ATOM 49 CZ TYR 3 18.855 35.585 19.528 1.00 0.00 C +ATOM 50 OH TYR 3 18.517 36.324 18.441 1.00 0.00 O +ATOM 51 HH TYR 3 18.718 35.875 17.614 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.941 36.195 20.795 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.739 37.253 20.885 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.327 35.436 21.918 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.448 35.924 22.876 1.00 0.00 H +ATOM 56 C TYR 3 20.072 31.754 24.926 1.00 0.00 C +ATOM 57 O TYR 3 20.489 32.242 25.980 1.00 0.00 O +ATOM 58 N LYS 4 20.339 30.479 24.600 1.00 0.00 N +ATOM 59 H LYS 4 20.151 30.180 23.644 1.00 0.00 H +ATOM 60 CA LYS 4 20.960 29.479 25.496 1.00 0.00 C +ATOM 61 HA LYS 4 20.692 29.716 26.523 1.00 0.00 H +ATOM 62 CB LYS 4 20.389 28.078 25.169 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.359 27.961 24.086 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.082 27.325 25.544 1.00 0.00 H +ATOM 65 CG LYS 4 18.993 27.726 25.738 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.817 26.675 25.502 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.009 27.823 26.824 1.00 0.00 H +ATOM 68 CD LYS 4 17.809 28.534 25.173 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.798 29.537 25.609 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.962 28.643 24.097 1.00 0.00 H +ATOM 71 CE LYS 4 16.441 27.842 25.378 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.715 28.351 24.738 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.517 26.807 25.026 1.00 0.00 H +ATOM 74 NZ LYS 4 15.935 27.871 26.782 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.755 28.812 27.098 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.064 27.350 26.889 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.572 27.463 27.463 1.00 0.00 H +ATOM 78 C LYS 4 22.499 29.490 25.466 1.00 0.00 C +ATOM 79 O LYS 4 23.140 29.867 24.490 1.00 0.00 O +HETATM 80 N HX1 5 23.130 29.035 26.548 1.00 0.00 N +HETATM 81 CA HX1 5 24.591 28.856 26.679 1.00 0.00 C +HETATM 82 C HX1 5 24.878 27.688 27.631 1.00 0.00 C +HETATM 83 O HX1 5 24.428 27.708 28.777 1.00 0.00 O +HETATM 84 CB HX1 5 25.222 30.175 27.180 1.00 0.00 C +HETATM 85 CG HX1 5 26.737 30.247 27.288 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.646 29.286 26.930 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.420 31.336 27.850 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.719 30.994 27.776 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.886 29.754 27.285 1.00 0.00 N +HETATM 90 H HX1 5 22.559 28.844 27.370 1.00 0.00 H +HETATM 91 HA HX1 5 25.018 28.612 25.702 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.806 30.413 28.160 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.913 30.973 26.501 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.458 28.305 26.513 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.519 31.581 28.203 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.738 29.194 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.579 26.661 27.147 1.00 0.00 N +ATOM 98 H ILE 6 25.921 26.711 26.193 1.00 0.00 H +ATOM 99 CA ILE 6 25.970 25.469 27.917 1.00 0.00 C +ATOM 100 HA ILE 6 25.283 25.357 28.755 1.00 0.00 H +ATOM 101 CB ILE 6 25.813 24.203 27.035 1.00 0.00 C +ATOM 102 HB ILE 6 26.347 24.367 26.099 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.392 22.937 27.698 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.889 22.736 28.645 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.267 22.079 27.038 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.465 23.049 27.864 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.304 24.011 26.726 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.764 23.868 27.661 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.914 24.914 26.252 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.964 22.843 25.793 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.140 21.891 26.293 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.908 22.895 25.523 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.564 22.899 24.885 1.00 0.00 H +ATOM 114 C ILE 6 27.370 25.661 28.537 1.00 0.00 C +ATOM 115 O ILE 6 28.186 26.422 28.017 1.00 0.00 O +ATOM 116 N VAL 7 27.605 25.035 29.694 1.00 0.00 N +ATOM 117 H VAL 7 26.884 24.405 30.032 1.00 0.00 H +ATOM 118 CA VAL 7 28.769 25.251 30.572 1.00 0.00 C +ATOM 119 HA VAL 7 28.849 26.325 30.732 1.00 0.00 H +ATOM 120 CB VAL 7 28.470 24.592 31.936 1.00 0.00 C +ATOM 121 HB VAL 7 27.460 24.891 32.229 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.498 23.060 31.893 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.507 22.695 31.701 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.158 22.662 32.842 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.845 22.689 31.104 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.397 25.060 33.063 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.408 26.149 33.096 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.024 24.680 34.015 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.403 24.676 32.902 1.00 0.00 H +ATOM 130 C VAL 7 30.119 24.780 29.995 1.00 0.00 C +ATOM 131 O VAL 7 30.207 23.763 29.310 1.00 0.00 O +ATOM 132 N ARG 8 31.201 25.497 30.343 1.00 0.00 N +ATOM 133 H ARG 8 31.031 26.423 30.713 1.00 0.00 H +ATOM 134 CA ARG 8 32.608 25.082 30.154 1.00 0.00 C +ATOM 135 HA ARG 8 32.717 24.857 29.094 1.00 0.00 H +ATOM 136 CB ARG 8 33.575 26.241 30.501 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.546 25.995 30.072 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.247 27.151 30.004 1.00 0.00 H +ATOM 139 CG ARG 8 33.814 26.544 32.001 1.00 0.00 C +ATOM 140 HG2 ARG 8 34.126 25.632 32.506 1.00 0.00 H +ATOM 141 HG3 ARG 8 34.652 27.235 32.093 1.00 0.00 H +ATOM 142 CD ARG 8 32.636 27.142 32.778 1.00 0.00 C +ATOM 143 HD2 ARG 8 31.766 26.524 32.631 1.00 0.00 H +ATOM 144 HD3 ARG 8 32.851 27.100 33.836 1.00 0.00 H +ATOM 145 NE ARG 8 32.321 28.531 32.389 1.00 0.00 N +ATOM 146 HE ARG 8 31.868 28.645 31.483 1.00 0.00 H +ATOM 147 CZ ARG 8 32.417 29.619 33.139 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.818 30.717 32.782 1.00 0.00 N +ATOM 149 HH11 ARG 8 31.188 30.675 31.981 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.731 31.448 33.453 1.00 0.00 H +ATOM 151 NH2 ARG 8 33.086 29.637 34.256 1.00 0.00 N +ATOM 152 HH21 ARG 8 33.619 28.829 34.514 1.00 0.00 H +ATOM 153 HH22 ARG 8 33.065 30.431 34.886 1.00 0.00 H +ATOM 154 C ARG 8 32.993 23.796 30.906 1.00 0.00 C +ATOM 155 O ARG 8 32.490 23.532 31.997 1.00 0.00 O +ATOM 156 N GLY 9 33.997 23.086 30.385 1.00 0.00 N +ATOM 157 H GLY 9 34.336 23.350 29.474 1.00 0.00 H +ATOM 158 CA GLY 9 34.544 21.859 30.982 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.546 21.680 30.585 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.627 21.989 32.066 1.00 0.00 H +ATOM 161 C GLY 9 33.690 20.615 30.703 1.00 0.00 C +ATOM 162 O GLY 9 32.893 20.602 29.772 1.00 0.00 O +ATOM 163 N LYS 10 33.877 19.558 31.507 1.00 0.00 N +ATOM 164 H LYS 10 34.624 19.619 32.176 1.00 0.00 H +ATOM 165 CA LYS 10 33.145 18.277 31.372 1.00 0.00 C +ATOM 166 HA LYS 10 32.234 18.481 30.799 1.00 0.00 H +ATOM 167 CB LYS 10 34.004 17.293 30.544 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.660 17.868 29.891 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.633 16.707 31.215 1.00 0.00 H +ATOM 170 CG LYS 10 33.182 16.351 29.644 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.576 15.685 30.259 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.517 16.953 29.025 1.00 0.00 H +ATOM 173 CD LYS 10 34.095 15.518 28.728 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.765 16.189 28.186 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.693 14.843 29.337 1.00 0.00 H +ATOM 176 CE LYS 10 33.287 14.702 27.711 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.727 13.931 28.247 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.567 15.368 27.228 1.00 0.00 H +ATOM 179 NZ LYS 10 34.153 14.097 26.667 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.950 13.593 27.047 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.637 13.513 26.029 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.558 14.828 26.065 1.00 0.00 H +ATOM 183 C LYS 10 32.647 17.678 32.701 1.00 0.00 C +ATOM 184 O LYS 10 31.863 16.738 32.687 1.00 0.00 O +ATOM 185 N SER 11 33.082 18.223 33.848 1.00 0.00 N +ATOM 186 H SER 11 33.752 18.967 33.790 1.00 0.00 H +ATOM 187 CA SER 11 32.570 17.839 35.182 1.00 0.00 C +ATOM 188 HA SER 11 32.446 16.755 35.225 1.00 0.00 H +ATOM 189 CB SER 11 33.539 18.260 36.295 1.00 0.00 C +ATOM 190 HB2 SER 11 33.665 19.345 36.284 1.00 0.00 H +ATOM 191 HB3 SER 11 33.107 17.977 37.259 1.00 0.00 H +ATOM 192 OG SER 11 34.809 17.642 36.180 1.00 0.00 O +ATOM 193 HG SER 11 35.427 18.251 35.756 1.00 0.00 H +ATOM 194 C SER 11 31.199 18.462 35.496 1.00 0.00 C +ATOM 195 O SER 11 30.406 17.878 36.230 1.00 0.00 O +ATOM 196 N CYS 12 30.923 19.656 34.964 1.00 0.00 N +ATOM 197 H CYS 12 31.599 20.053 34.332 1.00 0.00 H +ATOM 198 CA CYS 12 29.611 20.301 35.006 1.00 0.00 C +ATOM 199 HA CYS 12 29.036 19.906 35.847 1.00 0.00 H +ATOM 200 CB CYS 12 29.796 21.821 35.196 1.00 0.00 C +ATOM 201 HB2 CYS 12 30.330 22.228 34.334 1.00 0.00 H +ATOM 202 HB3 CYS 12 28.812 22.284 35.254 1.00 0.00 H +ATOM 203 SG CYS 12 30.722 22.206 36.721 1.00 0.00 S +ATOM 204 HG CYS 12 29.845 23.085 37.226 1.00 0.00 H +ATOM 205 C CYS 12 28.846 19.994 33.710 1.00 0.00 C +ATOM 206 O CYS 12 29.461 19.846 32.657 1.00 0.00 O +ATOM 207 N LYS 13 27.505 19.956 33.760 1.00 0.00 N +ATOM 208 H LYS 13 27.067 20.025 34.666 1.00 0.00 H +ATOM 209 CA LYS 13 26.638 19.689 32.587 1.00 0.00 C +ATOM 210 HA LYS 13 27.243 19.869 31.686 1.00 0.00 H +ATOM 211 CB LYS 13 26.243 18.193 32.591 1.00 0.00 C +ATOM 212 HB2 LYS 13 27.073 17.620 33.007 1.00 0.00 H +ATOM 213 HB3 LYS 13 25.379 18.062 33.237 1.00 0.00 H +ATOM 214 CG LYS 13 25.952 17.630 31.186 1.00 0.00 C +ATOM 215 HG2 LYS 13 25.065 18.101 30.761 1.00 0.00 H +ATOM 216 HG3 LYS 13 26.801 17.853 30.536 1.00 0.00 H +ATOM 217 CD LYS 13 25.755 16.105 31.210 1.00 0.00 C +ATOM 218 HD2 LYS 13 25.746 15.739 30.181 1.00 0.00 H +ATOM 219 HD3 LYS 13 26.602 15.645 31.726 1.00 0.00 H +ATOM 220 CE LYS 13 24.441 15.690 31.887 1.00 0.00 C +ATOM 221 HE2 LYS 13 24.310 16.264 32.808 1.00 0.00 H +ATOM 222 HE3 LYS 13 23.614 15.945 31.214 1.00 0.00 H +ATOM 223 NZ LYS 13 24.411 14.238 32.200 1.00 0.00 N +ATOM 224 HZ1 LYS 13 25.113 13.979 32.890 1.00 0.00 H +ATOM 225 HZ2 LYS 13 23.525 13.972 32.618 1.00 0.00 H +ATOM 226 HZ3 LYS 13 24.608 13.675 31.375 1.00 0.00 H +ATOM 227 C LYS 13 25.442 20.651 32.462 1.00 0.00 C +ATOM 228 O LYS 13 24.474 20.361 31.772 1.00 0.00 O +ATOM 229 N GLY 14 25.489 21.778 33.176 1.00 0.00 N +ATOM 230 H GLY 14 26.334 21.976 33.674 1.00 0.00 H +ATOM 231 CA GLY 14 24.400 22.746 33.252 1.00 0.00 C +ATOM 232 HA2 GLY 14 23.453 22.214 33.347 1.00 0.00 H +ATOM 233 HA3 GLY 14 24.522 23.365 34.139 1.00 0.00 H +ATOM 234 C GLY 14 24.283 23.694 32.040 1.00 0.00 C +ATOM 235 O GLY 14 25.205 23.839 31.229 1.00 0.00 O +ATOM 236 N VAL 15 23.147 24.397 31.969 1.00 0.00 N +ATOM 237 H VAL 15 22.465 24.249 32.702 1.00 0.00 H +ATOM 238 CA VAL 15 22.785 25.364 30.936 1.00 0.00 C +ATOM 239 HA VAL 15 23.676 25.622 30.371 1.00 0.00 H +ATOM 240 CB VAL 15 21.782 24.726 29.948 1.00 0.00 C +ATOM 241 HB VAL 15 22.261 23.828 29.523 1.00 0.00 H +ATOM 242 CG1 VAL 15 20.463 24.268 30.608 1.00 0.00 C +ATOM 243 HG11 VAL 15 19.940 25.116 31.035 1.00 0.00 H +ATOM 244 HG12 VAL 15 19.832 23.789 29.857 1.00 0.00 H +ATOM 245 HG13 VAL 15 20.672 23.536 31.384 1.00 0.00 H +ATOM 246 CG2 VAL 15 21.431 25.652 28.775 1.00 0.00 C +ATOM 247 HG21 VAL 15 22.344 26.000 28.296 1.00 0.00 H +ATOM 248 HG22 VAL 15 20.849 25.095 28.039 1.00 0.00 H +ATOM 249 HG23 VAL 15 20.845 26.497 29.121 1.00 0.00 H +ATOM 250 C VAL 15 22.255 26.634 31.587 1.00 0.00 C +ATOM 251 O VAL 15 21.634 26.597 32.639 1.00 0.00 O +HETATM 252 N HY1 16 22.503 27.793 30.973 1.00 0.00 N +HETATM 253 CA HY1 16 21.907 29.109 31.309 1.00 0.00 C +HETATM 254 C HY1 16 21.626 29.889 30.030 1.00 0.00 C +HETATM 255 O HY1 16 21.803 29.384 28.934 1.00 0.00 O +HETATM 256 CB HY1 16 22.834 29.825 32.330 1.00 0.00 C +HETATM 257 CG HY1 16 24.188 30.197 31.783 1.00 0.00 C +HETATM 258 CD2 HY1 16 24.521 31.376 31.162 1.00 0.00 C +HETATM 259 ND1 HY1 16 25.320 29.420 31.809 1.00 0.00 N +HETATM 260 CE1 HY1 16 26.313 30.124 31.227 1.00 0.00 C +HETATM 261 NE2 HY1 16 25.875 31.326 30.803 1.00 0.00 N +HETATM 262 H HY1 16 23.045 27.766 30.100 1.00 0.00 H +HETATM 263 HA HY1 16 20.949 28.916 31.823 1.00 0.00 H +HETATM 264 HB2 HY1 16 22.325 30.741 32.671 1.00 0.00 H +HETATM 265 HB3 HY1 16 22.960 29.204 33.207 1.00 0.00 H +HETATM 266 HD1 HY1 16 25.420 28.523 32.269 1.00 0.00 H +HETATM 267 HD2 HY1 16 23.853 32.210 30.983 1.00 0.00 H +HETATM 268 HE1 HY1 16 27.347 29.785 31.131 1.00 0.00 H +ATOM 269 N THR 17 21.180 31.133 30.157 1.00 0.00 N +ATOM 270 H THR 17 21.010 31.533 31.074 1.00 0.00 H +ATOM 271 CA THR 17 20.738 32.013 29.045 1.00 0.00 C +ATOM 272 HA THR 17 21.170 31.561 28.112 1.00 0.00 H +ATOM 273 CB THR 17 19.231 32.020 28.904 1.00 0.00 C +ATOM 274 HB THR 17 18.946 32.674 28.050 1.00 0.00 H +ATOM 275 CG2 THR 17 18.569 30.688 28.614 1.00 0.00 C +ATOM 276 HG21 THR 17 18.780 29.952 29.396 1.00 0.00 H +ATOM 277 HG22 THR 17 17.520 30.750 28.519 1.00 0.00 H +ATOM 278 HG23 THR 17 18.943 30.252 27.683 1.00 0.00 H +ATOM 279 OG1 THR 17 18.633 32.525 30.065 1.00 0.00 O +ATOM 280 HG1 THR 17 18.590 33.499 29.935 1.00 0.00 H +ATOM 281 C THR 17 21.325 33.419 29.080 1.00 0.00 C +ATOM 282 O THR 17 21.830 33.841 30.105 1.00 0.00 O +HETATM 283 N HY2 18 21.199 34.131 27.962 1.00 0.00 N +HETATM 284 CA HY2 18 21.498 35.567 27.862 1.00 0.00 C +HETATM 285 C HY2 18 20.379 36.266 27.075 1.00 0.00 C +HETATM 286 O HY2 18 20.033 35.823 25.984 1.00 0.00 O +HETATM 287 CB HY2 18 22.831 35.804 27.169 1.00 0.00 C +HETATM 288 CG HY2 18 24.029 35.337 27.962 1.00 0.00 C +HETATM 289 CD2 HY2 18 24.563 34.072 27.954 1.00 0.00 C +HETATM 290 ND1 HY2 18 24.707 36.053 28.927 1.00 0.00 N +HETATM 291 CE1 HY2 18 25.640 35.241 29.456 1.00 0.00 C +HETATM 292 NE2 HY2 18 25.591 34.016 28.902 1.00 0.00 N +HETATM 293 H HY2 18 20.786 33.675 27.148 1.00 0.00 H +HETATM 294 HA HY2 18 21.526 36.010 28.879 1.00 0.00 H +HETATM 295 HB2 HY2 18 22.841 35.309 26.183 1.00 0.00 H +HETATM 296 HB3 HY2 18 22.951 36.890 26.989 1.00 0.00 H +HETATM 297 HD1 HY2 18 24.548 37.015 29.189 1.00 0.00 H +HETATM 298 HD2 HY2 18 24.231 33.250 27.332 1.00 0.00 H +HETATM 299 HE1 HY2 18 26.337 35.534 30.234 1.00 0.00 H +ATOM 300 N GLU 19 19.854 37.365 27.613 1.00 0.00 N +ATOM 301 H GLU 19 20.181 37.657 28.514 1.00 0.00 H +ATOM 302 CA GLU 19 18.861 38.214 26.953 1.00 0.00 C +ATOM 303 HA GLU 19 18.118 37.567 26.510 1.00 0.00 H +ATOM 304 CB GLU 19 18.201 39.105 28.007 1.00 0.00 C +ATOM 305 HB2 GLU 19 17.888 38.497 28.852 1.00 0.00 H +ATOM 306 HB3 GLU 19 18.937 39.829 28.382 1.00 0.00 H +ATOM 307 CG GLU 19 16.971 39.870 27.494 1.00 0.00 C +ATOM 308 HG2 GLU 19 16.593 40.510 28.305 1.00 0.00 H +ATOM 309 HG3 GLU 19 17.267 40.530 26.668 1.00 0.00 H +ATOM 310 CD GLU 19 15.891 38.899 27.051 1.00 0.00 C +ATOM 311 OE1 GLU 19 15.841 38.587 25.838 1.00 0.00 O +ATOM 312 OE2 GLU 19 15.168 38.381 27.921 1.00 0.00 O +ATOM 313 C GLU 19 19.511 39.051 25.841 1.00 0.00 C +ATOM 314 O GLU 19 20.557 39.666 26.070 1.00 0.00 O +ATOM 315 N ALA 20 18.896 39.088 24.651 1.00 0.00 N +ATOM 316 H ALA 20 18.064 38.515 24.532 1.00 0.00 H +ATOM 317 CA ALA 20 19.271 39.983 23.548 1.00 0.00 C +ATOM 318 HA ALA 20 19.436 40.983 23.947 1.00 0.00 H +ATOM 319 CB ALA 20 20.578 39.484 22.920 1.00 0.00 C +ATOM 320 HB1 ALA 20 20.424 38.505 22.460 1.00 0.00 H +ATOM 321 HB2 ALA 20 20.915 40.186 22.161 1.00 0.00 H +ATOM 322 HB3 ALA 20 21.364 39.400 23.667 1.00 0.00 H +ATOM 323 C ALA 20 18.183 40.055 22.465 1.00 0.00 C +ATOM 324 O ALA 20 17.362 39.144 22.322 1.00 0.00 O +ATOM 325 N VAL 21 18.199 41.109 21.636 1.00 0.00 N +ATOM 326 H VAL 21 18.866 41.851 21.810 1.00 0.00 H +ATOM 327 CA VAL 21 17.428 41.159 20.367 1.00 0.00 C +ATOM 328 HA VAL 21 16.429 40.760 20.548 1.00 0.00 H +ATOM 329 CB VAL 21 17.259 42.610 19.852 1.00 0.00 C +ATOM 330 HB VAL 21 16.584 42.573 18.993 1.00 0.00 H +ATOM 331 CG1 VAL 21 16.606 43.510 20.912 1.00 0.00 C +ATOM 332 HG11 VAL 21 17.283 43.665 21.747 1.00 0.00 H +ATOM 333 HG12 VAL 21 16.368 44.469 20.461 1.00 0.00 H +ATOM 334 HG13 VAL 21 15.686 43.051 21.264 1.00 0.00 H +ATOM 335 CG2 VAL 21 18.574 43.260 19.386 1.00 0.00 C +ATOM 336 HG21 VAL 21 18.969 42.728 18.522 1.00 0.00 H +ATOM 337 HG22 VAL 21 18.382 44.286 19.080 1.00 0.00 H +ATOM 338 HG23 VAL 21 19.313 43.256 20.184 1.00 0.00 H +ATOM 339 C VAL 21 18.056 40.311 19.265 1.00 0.00 C +ATOM 340 O VAL 21 17.372 39.908 18.335 1.00 0.00 O +ATOM 341 N ASP 22 19.356 40.045 19.380 1.00 0.00 N +ATOM 342 H ASP 22 19.840 40.370 20.200 1.00 0.00 H +ATOM 343 CA ASP 22 20.203 39.414 18.367 1.00 0.00 C +ATOM 344 HA ASP 22 19.591 38.740 17.749 1.00 0.00 H +ATOM 345 CB ASP 22 20.808 40.497 17.447 1.00 0.00 C +ATOM 346 HB2 ASP 22 20.011 40.913 16.813 1.00 0.00 H +ATOM 347 HB3 ASP 22 21.216 41.310 18.079 1.00 0.00 H +ATOM 348 CG ASP 22 21.904 39.924 16.576 1.00 0.00 C +ATOM 349 OD1 ASP 22 23.061 40.332 16.776 1.00 0.00 O +ATOM 350 OD2 ASP 22 21.645 38.936 15.850 1.00 0.00 O +ATOM 351 C ASP 22 21.312 38.577 19.024 1.00 0.00 C +ATOM 352 O ASP 22 21.786 38.862 20.125 1.00 0.00 O +ATOM 353 N TRP 23 21.758 37.546 18.320 1.00 0.00 N +ATOM 354 H TRP 23 21.457 37.488 17.356 1.00 0.00 H +ATOM 355 CA TRP 23 22.777 36.618 18.774 1.00 0.00 C +ATOM 356 HA TRP 23 22.545 36.338 19.799 1.00 0.00 H +ATOM 357 CB TRP 23 22.654 35.377 17.900 1.00 0.00 C +ATOM 358 HB2 TRP 23 21.626 35.019 17.952 1.00 0.00 H +ATOM 359 HB3 TRP 23 22.841 35.665 16.862 1.00 0.00 H +ATOM 360 CG TRP 23 23.539 34.241 18.269 1.00 0.00 C +ATOM 361 CD1 TRP 23 24.465 33.691 17.461 1.00 0.00 C +ATOM 362 HD1 TRP 23 24.709 34.023 16.459 1.00 0.00 H +ATOM 363 NE1 TRP 23 25.028 32.616 18.105 1.00 0.00 N +ATOM 364 HE1 TRP 23 25.775 32.071 17.710 1.00 0.00 H +ATOM 365 CE2 TRP 23 24.471 32.396 19.344 1.00 0.00 C +ATOM 366 CZ2 TRP 23 24.645 31.401 20.312 1.00 0.00 C +ATOM 367 HZ2 TRP 23 25.308 30.566 20.135 1.00 0.00 H +ATOM 368 CH2 TRP 23 23.967 31.535 21.529 1.00 0.00 C +ATOM 369 HH2 TRP 23 24.088 30.820 22.312 1.00 0.00 H +ATOM 370 CZ3 TRP 23 23.194 32.666 21.795 1.00 0.00 C +ATOM 371 HZ3 TRP 23 22.789 32.798 22.788 1.00 0.00 H +ATOM 372 CE3 TRP 23 22.960 33.611 20.781 1.00 0.00 C +ATOM 373 HE3 TRP 23 22.305 34.442 20.972 1.00 0.00 H +ATOM 374 CD2 TRP 23 23.577 33.487 19.517 1.00 0.00 C +ATOM 375 C TRP 23 24.201 37.200 18.775 1.00 0.00 C +ATOM 376 O TRP 23 24.979 36.883 19.677 1.00 0.00 O +ATOM 377 N ALA 24 24.536 38.109 17.850 1.00 0.00 N +ATOM 378 H ALA 24 23.837 38.430 17.182 1.00 0.00 H +ATOM 379 CA ALA 24 25.826 38.805 17.840 1.00 0.00 C +ATOM 380 HA ALA 24 26.592 38.098 18.148 1.00 0.00 H +ATOM 381 CB ALA 24 26.163 39.206 16.400 1.00 0.00 C +ATOM 382 HB1 ALA 24 25.465 39.956 16.034 1.00 0.00 H +ATOM 383 HB2 ALA 24 27.173 39.612 16.353 1.00 0.00 H +ATOM 384 HB3 ALA 24 26.113 38.333 15.751 1.00 0.00 H +ATOM 385 C ALA 24 25.896 39.988 18.834 1.00 0.00 C +ATOM 386 O ALA 24 26.984 40.488 19.139 1.00 0.00 O +ATOM 387 N GLU 25 24.765 40.408 19.414 1.00 0.00 N +ATOM 388 H GLU 25 23.891 40.105 18.996 1.00 0.00 H +ATOM 389 CA GLU 25 24.725 41.188 20.666 1.00 0.00 C +ATOM 390 HA GLU 25 25.581 41.863 20.687 1.00 0.00 H +ATOM 391 CB GLU 25 23.451 42.045 20.730 1.00 0.00 C +ATOM 392 HB2 GLU 25 22.582 41.422 20.516 1.00 0.00 H +ATOM 393 HB3 GLU 25 23.342 42.425 21.740 1.00 0.00 H +ATOM 394 CG GLU 25 23.468 43.249 19.777 1.00 0.00 C +ATOM 395 HG2 GLU 25 23.540 42.881 18.748 1.00 0.00 H +ATOM 396 HG3 GLU 25 22.512 43.776 19.855 1.00 0.00 H +ATOM 397 CD GLU 25 24.619 44.199 20.081 1.00 0.00 C +ATOM 398 OE1 GLU 25 24.524 44.975 21.065 1.00 0.00 O +ATOM 399 OE2 GLU 25 25.648 44.107 19.362 1.00 0.00 O +ATOM 400 C GLU 25 24.874 40.287 21.906 1.00 0.00 C +ATOM 401 O GLU 25 25.688 40.579 22.784 1.00 0.00 O +ATOM 402 N ALA 26 24.201 39.125 21.956 1.00 0.00 N +ATOM 403 H ALA 26 23.518 38.919 21.232 1.00 0.00 H +ATOM 404 CA ALA 26 24.463 38.107 22.990 1.00 0.00 C +ATOM 405 HA ALA 26 24.293 38.571 23.963 1.00 0.00 H +ATOM 406 CB ALA 26 23.482 36.944 22.834 1.00 0.00 C +ATOM 407 HB1 ALA 26 23.667 36.421 21.901 1.00 0.00 H +ATOM 408 HB2 ALA 26 23.605 36.247 23.660 1.00 0.00 H +ATOM 409 HB3 ALA 26 22.458 37.314 22.841 1.00 0.00 H +ATOM 410 C ALA 26 25.930 37.609 22.973 1.00 0.00 C +ATOM 411 O ALA 26 26.453 37.180 24.015 1.00 0.00 O +ATOM 412 N GLU 27 26.614 37.710 21.825 1.00 0.00 N +ATOM 413 H GLU 27 26.089 37.904 20.980 1.00 0.00 H +ATOM 414 CA GLU 27 28.052 37.490 21.713 1.00 0.00 C +ATOM 415 HA GLU 27 28.210 36.457 21.940 1.00 0.00 H +ATOM 416 CB GLU 27 28.583 37.614 20.270 1.00 0.00 C +ATOM 417 HB2 GLU 27 27.924 37.058 19.610 1.00 0.00 H +ATOM 418 HB3 GLU 27 28.620 38.658 19.970 1.00 0.00 H +ATOM 419 CG GLU 27 29.988 36.996 20.197 1.00 0.00 C +ATOM 420 HG2 GLU 27 30.676 37.588 20.819 1.00 0.00 H +ATOM 421 HG3 GLU 27 29.956 35.983 20.634 1.00 0.00 H +ATOM 422 CD GLU 27 30.513 36.934 18.769 1.00 0.00 C +ATOM 423 OE1 GLU 27 30.943 38.000 18.278 1.00 0.00 O +ATOM 424 OE2 GLU 27 30.501 35.827 18.191 1.00 0.00 O +ATOM 425 C GLU 27 28.828 38.374 22.706 1.00 0.00 C +ATOM 426 O GLU 27 29.568 37.849 23.548 1.00 0.00 O +ATOM 427 N LYS 28 28.541 39.682 22.661 1.00 0.00 N +ATOM 428 H LYS 28 27.831 39.957 21.987 1.00 0.00 H +ATOM 429 CA LYS 28 29.121 40.758 23.481 1.00 0.00 C +ATOM 430 HA LYS 28 30.206 40.658 23.479 1.00 0.00 H +ATOM 431 CB LYS 28 28.761 42.131 22.873 1.00 0.00 C +ATOM 432 HB2 LYS 28 27.685 42.299 22.951 1.00 0.00 H +ATOM 433 HB3 LYS 28 29.264 42.909 23.451 1.00 0.00 H +ATOM 434 CG LYS 28 29.172 42.274 21.396 1.00 0.00 C +ATOM 435 HG2 LYS 28 30.244 42.100 21.301 1.00 0.00 H +ATOM 436 HG3 LYS 28 28.646 41.528 20.802 1.00 0.00 H +ATOM 437 CD LYS 28 28.833 43.668 20.845 1.00 0.00 C +ATOM 438 HD2 LYS 28 27.793 43.910 21.048 1.00 0.00 H +ATOM 439 HD3 LYS 28 29.453 44.406 21.356 1.00 0.00 H +ATOM 440 CE LYS 28 29.082 43.754 19.331 1.00 0.00 C +ATOM 441 HE2 LYS 28 29.159 44.812 19.054 1.00 0.00 H +ATOM 442 HE3 LYS 28 30.045 43.295 19.106 1.00 0.00 H +ATOM 443 NZ LYS 28 27.999 43.108 18.548 1.00 0.00 N +ATOM 444 HZ1 LYS 28 27.111 43.575 18.756 1.00 0.00 H +ATOM 445 HZ2 LYS 28 28.147 43.172 17.552 1.00 0.00 H +ATOM 446 HZ3 LYS 28 27.858 42.139 18.817 1.00 0.00 H +ATOM 447 C LYS 28 28.671 40.699 24.942 1.00 0.00 C +ATOM 448 O LYS 28 29.516 40.726 25.833 1.00 0.00 O +ATOM 449 N PHE 29 27.376 40.527 25.225 1.00 0.00 N +ATOM 450 H PHE 29 26.709 40.552 24.455 1.00 0.00 H +ATOM 451 CA PHE 29 26.873 40.474 26.615 1.00 0.00 C +ATOM 452 HA PHE 29 27.188 41.382 27.129 1.00 0.00 H +ATOM 453 CB PHE 29 25.335 40.437 26.615 1.00 0.00 C +ATOM 454 HB2 PHE 29 25.018 39.493 26.171 1.00 0.00 H +ATOM 455 HB3 PHE 29 24.990 40.451 27.649 1.00 0.00 H +ATOM 456 CG PHE 29 24.643 41.578 25.884 1.00 0.00 C +ATOM 457 CD1 PHE 29 23.461 41.323 25.164 1.00 0.00 C +ATOM 458 HD1 PHE 29 23.037 40.333 25.146 1.00 0.00 H +ATOM 459 CE1 PHE 29 22.822 42.359 24.462 1.00 0.00 C +ATOM 460 HE1 PHE 29 21.922 42.155 23.902 1.00 0.00 H +ATOM 461 CZ PHE 29 23.361 43.658 24.478 1.00 0.00 C +ATOM 462 HZ PHE 29 22.885 44.450 23.917 1.00 0.00 H +ATOM 463 CE2 PHE 29 24.520 43.928 25.225 1.00 0.00 C +ATOM 464 HE2 PHE 29 24.924 44.927 25.252 1.00 0.00 H +ATOM 465 CD2 PHE 29 25.155 42.893 25.932 1.00 0.00 C +ATOM 466 HD2 PHE 29 26.038 43.124 26.504 1.00 0.00 H +ATOM 467 C PHE 29 27.437 39.300 27.430 1.00 0.00 C +ATOM 468 O PHE 29 27.531 39.370 28.654 1.00 0.00 O +ATOM 469 N THR 30 27.865 38.222 26.770 1.00 0.00 N +ATOM 470 H THR 30 27.724 38.182 25.766 1.00 0.00 H +ATOM 471 CA THR 30 28.618 37.144 27.427 1.00 0.00 C +ATOM 472 HA THR 30 28.163 36.900 28.387 1.00 0.00 H +ATOM 473 CB THR 30 28.621 35.900 26.536 1.00 0.00 C +ATOM 474 HB THR 30 29.132 36.191 25.639 1.00 0.00 H +ATOM 475 CG2 THR 30 29.346 34.706 27.138 1.00 0.00 C +ATOM 476 HG21 THR 30 28.984 34.522 28.133 1.00 0.00 H +ATOM 477 HG22 THR 30 29.193 33.814 26.546 1.00 0.00 H +ATOM 478 HG23 THR 30 30.428 34.887 27.191 1.00 0.00 H +ATOM 479 OG1 THR 30 27.298 35.471 26.245 1.00 0.00 O +ATOM 480 HG1 THR 30 26.888 36.131 25.657 1.00 0.00 H +ATOM 481 C THR 30 30.081 37.537 27.695 1.00 0.00 C +ATOM 482 O THR 30 30.624 37.146 28.731 1.00 0.00 O +ATOM 483 N LYS 31 30.720 38.306 26.804 1.00 0.00 N +ATOM 484 H LYS 31 30.198 38.651 26.014 1.00 0.00 H +ATOM 485 CA LYS 31 32.070 38.835 27.005 1.00 0.00 C +ATOM 486 HA LYS 31 32.733 38.032 27.315 1.00 0.00 H +ATOM 487 CB LYS 31 32.647 39.415 25.683 1.00 0.00 C +ATOM 488 HB2 LYS 31 31.948 40.110 25.246 1.00 0.00 H +ATOM 489 HB3 LYS 31 33.566 39.953 25.914 1.00 0.00 H +ATOM 490 CG LYS 31 32.996 38.312 24.666 1.00 0.00 C +ATOM 491 HG2 LYS 31 33.730 37.640 25.106 1.00 0.00 H +ATOM 492 HG3 LYS 31 32.107 37.731 24.423 1.00 0.00 H +ATOM 493 CD LYS 31 33.567 38.923 23.384 1.00 0.00 C +ATOM 494 HD2 LYS 31 32.778 39.479 22.879 1.00 0.00 H +ATOM 495 HD3 LYS 31 34.355 39.629 23.638 1.00 0.00 H +ATOM 496 CE LYS 31 34.151 37.892 22.391 1.00 0.00 C +ATOM 497 HE2 LYS 31 33.409 37.129 22.159 1.00 0.00 H +ATOM 498 HE3 LYS 31 34.379 38.403 21.457 1.00 0.00 H +ATOM 499 NZ LYS 31 35.390 37.255 22.898 1.00 0.00 N +ATOM 500 HZ1 LYS 31 35.201 36.470 23.500 1.00 0.00 H +ATOM 501 HZ2 LYS 31 35.932 36.859 22.126 1.00 0.00 H +ATOM 502 HZ3 LYS 31 35.985 37.896 23.428 1.00 0.00 H +ATOM 503 C LYS 31 32.129 39.879 28.130 1.00 0.00 C +ATOM 504 O LYS 31 33.139 39.914 28.834 1.00 0.00 O +ATOM 505 N ALA 32 31.036 40.609 28.382 1.00 0.00 N +ATOM 506 H ALA 32 30.297 40.611 27.689 1.00 0.00 H +ATOM 507 CA ALA 32 30.856 41.387 29.608 1.00 0.00 C +ATOM 508 HA ALA 32 31.679 42.095 29.692 1.00 0.00 H +ATOM 509 CB ALA 32 29.558 42.200 29.527 1.00 0.00 C +ATOM 510 HB1 ALA 32 28.691 41.544 29.473 1.00 0.00 H +ATOM 511 HB2 ALA 32 29.463 42.823 30.421 1.00 0.00 H +ATOM 512 HB3 ALA 32 29.578 42.846 28.650 1.00 0.00 H +ATOM 513 C ALA 32 30.927 40.489 30.858 1.00 0.00 C +ATOM 514 O ALA 32 31.924 40.546 31.574 1.00 0.00 O +ATOM 515 N LYN 33 29.996 39.531 31.025 1.00 0.00 N +ATOM 516 H LYN 33 29.190 39.542 30.415 1.00 0.00 H +ATOM 517 CA LYN 33 30.009 38.573 32.151 1.00 0.00 C +ATOM 518 HA LYN 33 29.910 39.148 33.071 1.00 0.00 H +ATOM 519 CB LYN 33 28.774 37.649 32.038 1.00 0.00 C +ATOM 520 HB2 LYN 33 27.879 38.255 31.901 1.00 0.00 H +ATOM 521 HB3 LYN 33 28.890 37.020 31.159 1.00 0.00 H +ATOM 522 CG LYN 33 28.554 36.757 33.275 1.00 0.00 C +ATOM 523 HG2 LYN 33 29.439 36.152 33.441 1.00 0.00 H +ATOM 524 HG3 LYN 33 28.421 37.387 34.152 1.00 0.00 H +ATOM 525 CD LYN 33 27.373 35.776 33.182 1.00 0.00 C +ATOM 526 HD2 LYN 33 27.409 35.248 32.236 1.00 0.00 H +ATOM 527 HD3 LYN 33 27.480 35.041 33.977 1.00 0.00 H +ATOM 528 CE LYN 33 26.005 36.448 33.325 1.00 0.00 C +ATOM 529 HE2 LYN 33 26.005 37.059 34.229 1.00 0.00 H +ATOM 530 HE3 LYN 33 25.827 37.088 32.462 1.00 0.00 H +ATOM 531 NZ LYN 33 24.926 35.449 33.420 1.00 0.00 N +ATOM 532 HZ2 LYN 33 24.037 35.924 33.515 1.00 0.00 H +ATOM 533 HZ3 LYN 33 24.894 34.884 32.590 1.00 0.00 H +ATOM 534 C LYN 33 31.326 37.768 32.264 1.00 0.00 C +ATOM 535 O LYN 33 31.650 37.212 33.313 1.00 0.00 O +ATOM 536 N ALA 34 32.102 37.650 31.186 1.00 0.00 N +ATOM 537 H ALA 34 31.786 38.093 30.336 1.00 0.00 H +ATOM 538 CA ALA 34 33.415 37.025 31.197 1.00 0.00 C +ATOM 539 HA ALA 34 33.379 36.199 31.902 1.00 0.00 H +ATOM 540 CB ALA 34 33.660 36.419 29.822 1.00 0.00 C +ATOM 541 HB1 ALA 34 33.759 37.224 29.100 1.00 0.00 H +ATOM 542 HB2 ALA 34 34.569 35.830 29.857 1.00 0.00 H +ATOM 543 HB3 ALA 34 32.833 35.773 29.533 1.00 0.00 H +ATOM 544 C ALA 34 34.561 37.964 31.644 1.00 0.00 C +ATOM 545 O ALA 34 35.485 37.474 32.295 1.00 0.00 O +ATOM 546 N ASN 35 34.515 39.269 31.348 1.00 0.00 N +ATOM 547 H ASN 35 33.732 39.616 30.804 1.00 0.00 H +ATOM 548 CA ASN 35 35.446 40.284 31.873 1.00 0.00 C +ATOM 549 HA ASN 35 36.435 39.832 31.976 1.00 0.00 H +ATOM 550 CB ASN 35 35.582 41.433 30.859 1.00 0.00 C +ATOM 551 HB2 ASN 35 34.603 41.733 30.493 1.00 0.00 H +ATOM 552 HB3 ASN 35 36.033 42.295 31.352 1.00 0.00 H +ATOM 553 CG ASN 35 36.493 41.030 29.719 1.00 0.00 C +ATOM 554 OD1 ASN 35 37.698 40.971 29.868 1.00 0.00 O +ATOM 555 ND2 ASN 35 35.956 40.693 28.578 1.00 0.00 N +ATOM 556 HD21 ASN 35 36.601 40.354 27.860 1.00 0.00 H +ATOM 557 HD22 ASN 35 34.954 40.631 28.488 1.00 0.00 H +ATOM 558 C ASN 35 35.078 40.777 33.276 1.00 0.00 C +ATOM 559 O ASN 35 35.967 41.126 34.052 1.00 0.00 O +ATOM 560 N ASP 36 33.802 40.685 33.673 1.00 0.00 N +ATOM 561 H ASP 36 33.078 40.563 32.970 1.00 0.00 H +ATOM 562 CA ASP 36 33.357 40.843 35.067 1.00 0.00 C +ATOM 563 HA ASP 36 33.630 41.847 35.410 1.00 0.00 H +ATOM 564 CB ASP 36 31.839 40.739 35.150 1.00 0.00 C +ATOM 565 HB2 ASP 36 31.563 39.728 34.867 1.00 0.00 H +ATOM 566 HB3 ASP 36 31.542 40.818 36.195 1.00 0.00 H +ATOM 567 CG ASP 36 30.985 41.711 34.324 1.00 0.00 C +ATOM 568 OD1 ASP 36 31.462 42.836 34.035 1.00 0.00 O +ATOM 569 OD2 ASP 36 29.825 41.345 33.996 1.00 0.00 O +ATOM 570 C ASP 36 34.066 39.828 35.995 1.00 0.00 C +ATOM 571 O ASP 36 34.498 40.176 37.098 1.00 0.00 O +ATOM 572 N LYS 37 34.277 38.580 35.528 1.00 0.00 N +ATOM 573 H LYS 37 33.863 38.350 34.636 1.00 0.00 H +ATOM 574 CA LYS 37 35.150 37.580 36.183 1.00 0.00 C +ATOM 575 HA LYS 37 35.130 37.789 37.253 1.00 0.00 H +ATOM 576 CB LYS 37 34.565 36.152 36.027 1.00 0.00 C +ATOM 577 HB2 LYS 37 35.078 35.490 36.724 1.00 0.00 H +ATOM 578 HB3 LYS 37 33.508 36.149 36.288 1.00 0.00 H +ATOM 579 CG LYS 37 34.759 35.601 34.608 1.00 0.00 C +ATOM 580 HG2 LYS 37 34.139 36.177 33.928 1.00 0.00 H +ATOM 581 HG3 LYS 37 35.798 35.735 34.318 1.00 0.00 H +ATOM 582 CD LYS 37 34.436 34.122 34.422 1.00 0.00 C +ATOM 583 HD2 LYS 37 34.578 33.610 35.373 1.00 0.00 H +ATOM 584 HD3 LYS 37 33.395 34.014 34.154 1.00 0.00 H +ATOM 585 CE LYS 37 35.328 33.472 33.330 1.00 0.00 C +ATOM 586 HE2 LYS 37 36.315 33.292 33.762 1.00 0.00 H +ATOM 587 HE3 LYS 37 34.983 32.454 33.128 1.00 0.00 H +ATOM 588 NZ LYS 37 35.470 34.267 32.074 1.00 0.00 N +ATOM 589 HZ1 LYS 37 35.901 35.166 32.277 1.00 0.00 H +ATOM 590 HZ2 LYS 37 36.069 33.816 31.389 1.00 0.00 H +ATOM 591 HZ3 LYS 37 34.567 34.433 31.674 1.00 0.00 H +ATOM 592 C LYS 37 36.641 37.666 35.797 1.00 0.00 C +ATOM 593 O LYS 37 37.388 36.717 36.024 1.00 0.00 O +ATOM 594 N GLY 38 37.093 38.753 35.163 1.00 0.00 N +ATOM 595 H GLY 38 36.427 39.500 35.014 1.00 0.00 H +ATOM 596 CA GLY 38 38.497 39.081 34.900 1.00 0.00 C +ATOM 597 HA2 GLY 38 38.673 40.099 35.250 1.00 0.00 H +ATOM 598 HA3 GLY 38 39.136 38.422 35.493 1.00 0.00 H +ATOM 599 C GLY 38 38.992 39.003 33.451 1.00 0.00 C +ATOM 600 O GLY 38 39.908 39.749 33.113 1.00 0.00 O +ATOM 601 N ARG 39 38.439 38.123 32.592 1.00 0.00 N +ATOM 602 H ARG 39 37.620 37.630 32.924 1.00 0.00 H +ATOM 603 CA ARG 39 38.850 37.918 31.183 1.00 0.00 C +ATOM 604 HA ARG 39 38.819 38.900 30.702 1.00 0.00 H +ATOM 605 CB ARG 39 40.315 37.408 31.055 1.00 0.00 C +ATOM 606 HB2 ARG 39 40.570 37.429 29.993 1.00 0.00 H +ATOM 607 HB3 ARG 39 40.992 38.115 31.533 1.00 0.00 H +ATOM 608 CG ARG 39 40.642 35.990 31.575 1.00 0.00 C +ATOM 609 HG2 ARG 39 40.011 35.274 31.049 1.00 0.00 H +ATOM 610 HG3 ARG 39 41.676 35.759 31.313 1.00 0.00 H +ATOM 611 CD ARG 39 40.486 35.825 33.102 1.00 0.00 C +ATOM 612 HD2 ARG 39 41.184 36.504 33.600 1.00 0.00 H +ATOM 613 HD3 ARG 39 39.476 36.100 33.403 1.00 0.00 H +ATOM 614 NE ARG 39 40.739 34.451 33.582 1.00 0.00 N +ATOM 615 HE ARG 39 41.505 34.326 34.228 1.00 0.00 H +ATOM 616 CZ ARG 39 39.961 33.401 33.419 1.00 0.00 C +ATOM 617 NH1 ARG 39 38.912 33.425 32.650 1.00 0.00 N +ATOM 618 HH11 ARG 39 38.753 34.219 32.059 1.00 0.00 H +ATOM 619 HH12 ARG 39 38.395 32.553 32.564 1.00 0.00 H +ATOM 620 NH2 ARG 39 40.208 32.279 34.029 1.00 0.00 N +ATOM 621 HH21 ARG 39 41.021 32.194 34.618 1.00 0.00 H +ATOM 622 HH22 ARG 39 39.586 31.492 33.869 1.00 0.00 H +ATOM 623 C ARG 39 37.906 37.010 30.382 1.00 0.00 C +ATOM 624 O ARG 39 37.450 35.970 30.889 1.00 0.00 O +ATOM 625 N ASP 40 37.643 37.373 29.123 1.00 0.00 N +ATOM 626 H ASP 40 38.049 38.236 28.768 1.00 0.00 H +ATOM 627 CA ASP 40 36.914 36.559 28.147 1.00 0.00 C +ATOM 628 HA ASP 40 36.250 35.909 28.701 1.00 0.00 H +ATOM 629 CB ASP 40 36.024 37.438 27.250 1.00 0.00 C +ATOM 630 HB2 ASP 40 35.359 36.797 26.672 1.00 0.00 H +ATOM 631 HB3 ASP 40 35.373 38.034 27.885 1.00 0.00 H +ATOM 632 CG ASP 40 36.757 38.385 26.309 1.00 0.00 C +ATOM 633 OD1 ASP 40 37.565 39.185 26.826 1.00 0.00 O +ATOM 634 OD2 ASP 40 36.426 38.367 25.105 1.00 0.00 O +ATOM 635 C ASP 40 37.774 35.579 27.330 1.00 0.00 C +ATOM 636 O ASP 40 38.983 35.480 27.496 1.00 0.00 O +ATOM 637 N GLY 41 37.089 34.803 26.488 1.00 0.00 N +ATOM 638 H GLY 41 36.101 34.991 26.421 1.00 0.00 H +ATOM 639 CA GLY 41 37.618 33.880 25.478 1.00 0.00 C +ATOM 640 HA2 GLY 41 38.494 34.335 24.987 1.00 0.00 H +ATOM 641 HA3 GLY 41 37.896 32.927 25.956 1.00 0.00 H +ATOM 642 C GLY 41 36.528 33.613 24.424 1.00 0.00 C +ATOM 643 O GLY 41 35.445 34.207 24.475 1.00 0.00 O +ATOM 644 N GLU 42 36.788 32.709 23.482 1.00 0.00 N +ATOM 645 H GLU 42 37.670 32.237 23.523 1.00 0.00 H +ATOM 646 CA GLU 42 35.905 32.412 22.347 1.00 0.00 C +ATOM 647 HA GLU 42 35.125 33.167 22.344 1.00 0.00 H +ATOM 648 CB GLU 42 36.664 32.525 21.011 1.00 0.00 C +ATOM 649 HB2 GLU 42 37.366 31.695 20.944 1.00 0.00 H +ATOM 650 HB3 GLU 42 35.944 32.414 20.201 1.00 0.00 H +ATOM 651 CG GLU 42 37.443 33.834 20.782 1.00 0.00 C +ATOM 652 HG2 GLU 42 38.311 33.827 21.446 1.00 0.00 H +ATOM 653 HG3 GLU 42 37.826 33.837 19.759 1.00 0.00 H +ATOM 654 CD GLU 42 36.645 35.123 21.033 1.00 0.00 C +ATOM 655 OE1 GLU 42 35.399 35.099 21.148 1.00 0.00 O +ATOM 656 OE2 GLU 42 37.273 36.191 21.218 1.00 0.00 O +ATOM 657 C GLU 42 35.155 31.079 22.449 1.00 0.00 C +ATOM 658 O GLU 42 35.545 30.177 23.201 1.00 0.00 O +ATOM 659 N ARG 43 34.045 30.983 21.696 1.00 0.00 N +ATOM 660 H ARG 43 33.859 31.729 21.028 1.00 0.00 H +ATOM 661 CA ARG 43 33.015 29.940 21.796 1.00 0.00 C +ATOM 662 HA ARG 43 33.495 28.981 22.001 1.00 0.00 H +ATOM 663 CB ARG 43 32.087 30.275 22.974 1.00 0.00 C +ATOM 664 HB2 ARG 43 31.317 29.508 23.057 1.00 0.00 H +ATOM 665 HB3 ARG 43 32.669 30.262 23.897 1.00 0.00 H +ATOM 666 CG ARG 43 31.391 31.637 22.844 1.00 0.00 C +ATOM 667 HG2 ARG 43 32.110 32.434 22.660 1.00 0.00 H +ATOM 668 HG3 ARG 43 30.694 31.612 22.010 1.00 0.00 H +ATOM 669 CD ARG 43 30.634 31.967 24.121 1.00 0.00 C +ATOM 670 HD2 ARG 43 30.147 31.059 24.480 1.00 0.00 H +ATOM 671 HD3 ARG 43 31.339 32.284 24.887 1.00 0.00 H +ATOM 672 NE ARG 43 29.619 32.996 23.893 1.00 0.00 N +ATOM 673 HE ARG 43 28.685 32.661 23.712 1.00 0.00 H +ATOM 674 CZ ARG 43 29.781 34.291 23.756 1.00 0.00 C +ATOM 675 NH1 ARG 43 30.924 34.915 23.764 1.00 0.00 N +ATOM 676 HH11 ARG 43 31.776 34.380 23.737 1.00 0.00 H +ATOM 677 HH12 ARG 43 30.928 35.903 23.564 1.00 0.00 H +ATOM 678 NH2 ARG 43 28.724 35.010 23.622 1.00 0.00 N +ATOM 679 HH21 ARG 43 27.818 34.575 23.525 1.00 0.00 H +ATOM 680 HH22 ARG 43 28.806 36.015 23.611 1.00 0.00 H +ATOM 681 C ARG 43 32.226 29.788 20.491 1.00 0.00 C +ATOM 682 O ARG 43 32.016 30.775 19.792 1.00 0.00 O +ATOM 683 N THR 44 31.769 28.574 20.199 1.00 0.00 N +ATOM 684 H THR 44 31.893 27.856 20.903 1.00 0.00 H +ATOM 685 CA THR 44 31.059 28.197 18.965 1.00 0.00 C +ATOM 686 HA THR 44 31.367 28.878 18.171 1.00 0.00 H +ATOM 687 CB THR 44 31.491 26.779 18.541 1.00 0.00 C +ATOM 688 HB THR 44 31.284 26.073 19.347 1.00 0.00 H +ATOM 689 CG2 THR 44 30.877 26.255 17.242 1.00 0.00 C +ATOM 690 HG21 THR 44 30.980 26.998 16.449 1.00 0.00 H +ATOM 691 HG22 THR 44 31.383 25.337 16.935 1.00 0.00 H +ATOM 692 HG23 THR 44 29.824 26.016 17.397 1.00 0.00 H +ATOM 693 OG1 THR 44 32.880 26.818 18.313 1.00 0.00 O +ATOM 694 HG1 THR 44 33.143 26.013 17.857 1.00 0.00 H +ATOM 695 C THR 44 29.537 28.364 19.112 1.00 0.00 C +ATOM 696 O THR 44 29.024 28.513 20.225 1.00 0.00 O +ATOM 697 N ILE 45 28.813 28.404 17.984 1.00 0.00 N +ATOM 698 H ILE 45 29.281 28.200 17.114 1.00 0.00 H +ATOM 699 CA ILE 45 27.405 28.808 17.888 1.00 0.00 C +ATOM 700 HA ILE 45 26.992 28.796 18.898 1.00 0.00 H +ATOM 701 CB ILE 45 27.300 30.258 17.349 1.00 0.00 C +ATOM 702 HB ILE 45 26.234 30.493 17.386 1.00 0.00 H +ATOM 703 CG2 ILE 45 28.017 31.233 18.293 1.00 0.00 C +ATOM 704 HG21 ILE 45 29.094 31.074 18.238 1.00 0.00 H +ATOM 705 HG22 ILE 45 27.806 32.268 18.025 1.00 0.00 H +ATOM 706 HG23 ILE 45 27.671 31.042 19.300 1.00 0.00 H +ATOM 707 CG1 ILE 45 27.759 30.525 15.895 1.00 0.00 C +ATOM 708 HG12 ILE 45 28.047 31.568 15.812 1.00 0.00 H +ATOM 709 HG13 ILE 45 28.654 29.949 15.680 1.00 0.00 H +ATOM 710 CD1 ILE 45 26.691 30.279 14.822 1.00 0.00 C +ATOM 711 HD11 ILE 45 25.759 30.773 15.114 1.00 0.00 H +ATOM 712 HD12 ILE 45 27.018 30.695 13.866 1.00 0.00 H +ATOM 713 HD13 ILE 45 26.512 29.212 14.695 1.00 0.00 H +ATOM 714 C ILE 45 26.527 27.858 17.072 1.00 0.00 C +ATOM 715 O ILE 45 27.017 27.114 16.226 1.00 0.00 O +ATOM 716 N ASP 46 25.216 27.950 17.304 1.00 0.00 N +ATOM 717 H ASP 46 24.910 28.475 18.111 1.00 0.00 H +ATOM 718 CA ASP 46 24.153 27.357 16.483 1.00 0.00 C +ATOM 719 HA ASP 46 24.474 27.365 15.437 1.00 0.00 H +ATOM 720 CB ASP 46 23.935 25.904 16.910 1.00 0.00 C +ATOM 721 HB2 ASP 46 24.821 25.306 16.686 1.00 0.00 H +ATOM 722 HB3 ASP 46 23.790 25.882 17.995 1.00 0.00 H +ATOM 723 CG ASP 46 22.728 25.281 16.224 1.00 0.00 C +ATOM 724 OD1 ASP 46 21.961 24.603 16.947 1.00 0.00 O +ATOM 725 OD2 ASP 46 22.511 25.554 15.040 1.00 0.00 O +ATOM 726 C ASP 46 22.834 28.159 16.594 1.00 0.00 C +ATOM 727 O ASP 46 22.399 28.488 17.698 1.00 0.00 O +ATOM 728 N ASP 47 22.184 28.437 15.458 1.00 0.00 N +ATOM 729 H ASP 47 22.559 28.038 14.608 1.00 0.00 H +ATOM 730 CA ASP 47 20.840 29.039 15.391 1.00 0.00 C +ATOM 731 HA ASP 47 20.745 29.781 16.186 1.00 0.00 H +ATOM 732 CB ASP 47 20.651 29.780 14.049 1.00 0.00 C +ATOM 733 HB2 ASP 47 21.371 30.599 13.994 1.00 0.00 H +ATOM 734 HB3 ASP 47 20.869 29.092 13.229 1.00 0.00 H +ATOM 735 CG ASP 47 19.236 30.338 13.866 1.00 0.00 C +ATOM 736 OD1 ASP 47 18.366 29.642 13.294 1.00 0.00 O +ATOM 737 OD2 ASP 47 18.910 31.439 14.376 1.00 0.00 O +ATOM 738 C ASP 47 19.712 28.006 15.601 1.00 0.00 C +ATOM 739 O ASP 47 18.680 28.354 16.177 1.00 0.00 O +ATOM 740 N ALA 48 19.891 26.748 15.189 1.00 0.00 N +ATOM 741 H ALA 48 20.815 26.444 14.883 1.00 0.00 H +ATOM 742 CA ALA 48 18.830 25.738 15.223 1.00 0.00 C +ATOM 743 HA ALA 48 17.947 26.136 14.721 1.00 0.00 H +ATOM 744 CB ALA 48 19.314 24.506 14.451 1.00 0.00 C +ATOM 745 HB1 ALA 48 20.173 24.065 14.961 1.00 0.00 H +ATOM 746 HB2 ALA 48 18.518 23.764 14.391 1.00 0.00 H +ATOM 747 HB3 ALA 48 19.617 24.791 13.444 1.00 0.00 H +ATOM 748 C ALA 48 18.413 25.386 16.665 1.00 0.00 C +ATOM 749 O ALA 48 17.226 25.293 16.965 1.00 0.00 O +ATOM 750 N THR 49 19.383 25.251 17.569 1.00 0.00 N +ATOM 751 H THR 49 20.338 25.173 17.219 1.00 0.00 H +ATOM 752 CA THR 49 19.192 25.102 19.021 1.00 0.00 C +ATOM 753 HA THR 49 18.164 24.774 19.188 1.00 0.00 H +ATOM 754 CB THR 49 20.126 24.025 19.584 1.00 0.00 C +ATOM 755 HB THR 49 19.898 23.910 20.645 1.00 0.00 H +ATOM 756 CG2 THR 49 19.960 22.658 18.926 1.00 0.00 C +ATOM 757 HG21 THR 49 20.258 22.695 17.880 1.00 0.00 H +ATOM 758 HG22 THR 49 20.593 21.942 19.444 1.00 0.00 H +ATOM 759 HG23 THR 49 18.922 22.334 18.992 1.00 0.00 H +ATOM 760 OG1 THR 49 21.483 24.396 19.468 1.00 0.00 O +ATOM 761 HG1 THR 49 21.694 24.365 18.500 1.00 0.00 H +ATOM 762 C THR 49 19.397 26.401 19.808 1.00 0.00 C +ATOM 763 O THR 49 19.269 26.396 21.031 1.00 0.00 O +ATOM 764 N LYS 50 19.705 27.522 19.134 1.00 0.00 N +ATOM 765 H LYS 50 19.806 27.421 18.131 1.00 0.00 H +ATOM 766 CA LYS 50 19.900 28.882 19.702 1.00 0.00 C +ATOM 767 HA LYS 50 20.324 29.504 18.914 1.00 0.00 H +ATOM 768 CB LYS 50 18.514 29.466 20.090 1.00 0.00 C +ATOM 769 HB2 LYS 50 18.082 28.812 20.847 1.00 0.00 H +ATOM 770 HB3 LYS 50 18.662 30.440 20.569 1.00 0.00 H +ATOM 771 CG LYS 50 17.483 29.640 18.962 1.00 0.00 C +ATOM 772 HG2 LYS 50 17.406 28.724 18.377 1.00 0.00 H +ATOM 773 HG3 LYS 50 16.511 29.807 19.436 1.00 0.00 H +ATOM 774 CD LYS 50 17.771 30.842 18.048 1.00 0.00 C +ATOM 775 HD2 LYS 50 17.847 31.729 18.684 1.00 0.00 H +ATOM 776 HD3 LYS 50 18.722 30.709 17.525 1.00 0.00 H +ATOM 777 CE LYS 50 16.636 31.087 17.042 1.00 0.00 C +ATOM 778 HE2 LYS 50 15.680 30.851 17.523 1.00 0.00 H +ATOM 779 HE3 LYS 50 16.620 32.152 16.793 1.00 0.00 H +ATOM 780 NZ LYS 50 16.785 30.318 15.786 1.00 0.00 N +ATOM 781 HZ1 LYS 50 17.027 29.345 15.942 1.00 0.00 H +ATOM 782 HZ2 LYS 50 15.966 30.404 15.186 1.00 0.00 H +ATOM 783 HZ3 LYS 50 17.558 30.688 15.237 1.00 0.00 H +ATOM 784 C LYS 50 20.929 28.907 20.853 1.00 0.00 C +ATOM 785 O LYS 50 20.644 29.476 21.914 1.00 0.00 O +ATOM 786 N THR 51 22.073 28.246 20.666 1.00 0.00 N +ATOM 787 H THR 51 22.280 27.904 19.746 1.00 0.00 H +ATOM 788 CA THR 51 22.978 27.855 21.776 1.00 0.00 C +ATOM 789 HA THR 51 22.713 28.424 22.656 1.00 0.00 H +ATOM 790 CB THR 51 22.769 26.349 22.149 1.00 0.00 C +ATOM 791 HB THR 51 22.913 25.751 21.244 1.00 0.00 H +ATOM 792 CG2 THR 51 23.726 25.829 23.195 1.00 0.00 C +ATOM 793 HG21 THR 51 23.724 26.423 24.104 1.00 0.00 H +ATOM 794 HG22 THR 51 23.491 24.809 23.488 1.00 0.00 H +ATOM 795 HG23 THR 51 24.752 25.794 22.838 1.00 0.00 H +ATOM 796 OG1 THR 51 21.477 26.147 22.676 1.00 0.00 O +ATOM 797 HG1 THR 51 20.828 26.213 21.948 1.00 0.00 H +ATOM 798 C THR 51 24.498 28.160 21.552 1.00 0.00 C +ATOM 799 O THR 51 25.031 27.978 20.458 1.00 0.00 O +ATOM 800 N PHE 52 25.195 28.618 22.604 1.00 0.00 N +ATOM 801 H PHE 52 24.659 28.844 23.435 1.00 0.00 H +ATOM 802 CA PHE 52 26.648 28.754 22.682 1.00 0.00 C +ATOM 803 HA PHE 52 27.066 28.878 21.704 1.00 0.00 H +ATOM 804 CB PHE 52 27.049 29.989 23.564 1.00 0.00 C +ATOM 805 HB2 PHE 52 26.439 29.970 24.449 1.00 0.00 H +ATOM 806 HB3 PHE 52 28.080 29.863 23.877 1.00 0.00 H +ATOM 807 CG PHE 52 26.956 31.369 22.935 1.00 0.00 C +ATOM 808 CD1 PHE 52 26.137 32.360 23.496 1.00 0.00 C +ATOM 809 HD1 PHE 52 25.515 32.134 24.347 1.00 0.00 H +ATOM 810 CE1 PHE 52 26.022 33.613 22.875 1.00 0.00 C +ATOM 811 HE1 PHE 52 25.306 34.345 23.243 1.00 0.00 H +ATOM 812 CZ PHE 52 26.749 33.887 21.707 1.00 0.00 C +ATOM 813 HZ PHE 52 26.610 34.820 21.179 1.00 0.00 H +ATOM 814 CE2 PHE 52 27.660 32.942 21.218 1.00 0.00 C +ATOM 815 HE2 PHE 52 28.252 33.169 20.337 1.00 0.00 H +ATOM 816 CD2 PHE 52 27.757 31.680 21.826 1.00 0.00 C +ATOM 817 HD2 PHE 52 28.421 30.934 21.415 1.00 0.00 H +ATOM 818 C PHE 52 27.299 27.528 23.345 1.00 0.00 C +ATOM 819 O PHE 52 26.801 27.060 24.382 1.00 0.00 O +ATOM 820 N THR 53 28.455 27.080 22.828 1.00 0.00 N +ATOM 821 H THR 53 28.794 27.502 21.960 1.00 0.00 H +ATOM 822 CA THR 53 29.257 25.944 23.360 1.00 0.00 C +ATOM 823 HA THR 53 29.018 25.811 24.412 1.00 0.00 H +ATOM 824 CB THR 53 28.922 24.628 22.631 1.00 0.00 C +ATOM 825 HB THR 53 29.523 23.828 23.066 1.00 0.00 H +ATOM 826 CG2 THR 53 27.455 24.219 22.728 1.00 0.00 C +ATOM 827 HG21 THR 53 26.839 24.900 22.141 1.00 0.00 H +ATOM 828 HG22 THR 53 27.330 23.206 22.345 1.00 0.00 H +ATOM 829 HG23 THR 53 27.136 24.241 23.767 1.00 0.00 H +ATOM 830 OG1 THR 53 29.241 24.729 21.261 1.00 0.00 O +ATOM 831 HG1 THR 53 28.872 23.960 20.816 1.00 0.00 H +ATOM 832 C THR 53 30.775 26.169 23.265 1.00 0.00 C +ATOM 833 O THR 53 31.247 27.039 22.536 1.00 0.00 O +ATOM 834 N THR 54 31.550 25.363 23.995 1.00 0.00 N +ATOM 835 H THR 54 31.108 24.674 24.581 1.00 0.00 H +ATOM 836 CA THR 54 33.026 25.280 23.900 1.00 0.00 C +ATOM 837 HA THR 54 33.389 26.087 23.264 1.00 0.00 H +ATOM 838 CB THR 54 33.679 25.465 25.287 1.00 0.00 C +ATOM 839 HB THR 54 33.366 24.653 25.943 1.00 0.00 H +ATOM 840 CG2 THR 54 35.209 25.527 25.270 1.00 0.00 C +ATOM 841 HG21 THR 54 35.551 26.282 24.560 1.00 0.00 H +ATOM 842 HG22 THR 54 35.586 25.776 26.261 1.00 0.00 H +ATOM 843 HG23 THR 54 35.625 24.558 24.996 1.00 0.00 H +ATOM 844 OG1 THR 54 33.257 26.688 25.848 1.00 0.00 O +ATOM 845 HG1 THR 54 33.703 26.791 26.690 1.00 0.00 H +ATOM 846 C THR 54 33.453 23.948 23.240 1.00 0.00 C +ATOM 847 O THR 54 32.725 22.957 23.330 1.00 0.00 O +ATOM 848 N GLN 55 34.608 23.941 22.569 1.00 0.00 N +ATOM 849 H GLN 55 35.143 24.792 22.563 1.00 0.00 H +ATOM 850 CA GLN 55 35.230 22.769 21.928 1.00 0.00 C +ATOM 851 HA GLN 55 34.472 22.294 21.307 1.00 0.00 H +ATOM 852 CB GLN 55 36.356 23.273 20.997 1.00 0.00 C +ATOM 853 HB2 GLN 55 36.747 22.431 20.418 1.00 0.00 H +ATOM 854 HB3 GLN 55 35.915 23.976 20.284 1.00 0.00 H +ATOM 855 CG GLN 55 37.529 23.975 21.718 1.00 0.00 C +ATOM 856 HG2 GLN 55 37.135 24.635 22.490 1.00 0.00 H +ATOM 857 HG3 GLN 55 38.153 23.228 22.202 1.00 0.00 H +ATOM 858 CD GLN 55 38.400 24.813 20.772 1.00 0.00 C +ATOM 859 OE1 GLN 55 38.699 24.456 19.644 1.00 0.00 O +ATOM 860 NE2 GLN 55 38.838 25.984 21.186 1.00 0.00 N +ATOM 861 HE21 GLN 55 39.398 26.495 20.531 1.00 0.00 H +ATOM 862 HE22 GLN 55 38.530 26.390 22.059 1.00 0.00 H +ATOM 863 C GLN 55 35.729 21.702 22.920 1.00 0.00 C +ATOM 864 O GLN 55 35.936 21.998 24.098 1.00 0.00 O +ATOM 865 N GLU 56 35.911 20.461 22.436 1.00 0.00 N +ATOM 866 H GLU 56 35.764 20.328 21.453 1.00 0.00 H +ATOM 867 CA GLU 56 36.591 19.326 23.126 1.00 0.00 C +ATOM 868 HA GLU 56 36.581 19.527 24.209 1.00 0.00 H +ATOM 869 CB GLU 56 35.802 18.011 22.873 1.00 0.00 C +ATOM 870 HB2 GLU 56 34.794 18.115 23.271 1.00 0.00 H +ATOM 871 HB3 GLU 56 35.670 17.896 21.805 1.00 0.00 H +ATOM 872 CG GLU 56 36.406 16.708 23.419 1.00 0.00 C +ATOM 873 HG2 GLU 56 36.588 16.049 22.597 1.00 0.00 H +ATOM 874 HG3 GLU 56 37.378 16.911 23.804 1.00 0.00 H +ATOM 875 CD GLU 56 35.639 15.935 24.519 1.00 0.00 C +ATOM 876 OE1 GLU 56 36.261 15.255 25.395 1.00 0.00 O +ATOM 877 OE2 GLU 56 34.388 15.901 24.484 1.00 0.00 O +ATOM 878 C GLU 56 38.064 19.234 22.739 1.00 0.00 C +ATOM 879 O GLU 56 38.897 19.678 23.554 1.00 0.00 O +ATOM 880 OXT GLU 56 38.365 18.739 21.612 1.00 0.00 O +HETATM 881 ZN ZN1 57 26.696 32.427 29.378 1.00 0.00 Zn +HETATM 882 N AN1 58 28.269 33.325 30.318 1.00 0.00 N +HETATM 883 C AN1 58 30.569 34.237 31.119 1.00 0.00 C +HETATM 884 C1 AN1 58 29.262 33.721 30.709 1.00 0.00 C +HETATM 885 H AN1 58 30.559 34.480 32.185 1.00 0.00 H +HETATM 886 H1 AN1 58 30.794 35.142 30.544 1.00 0.00 H +HETATM 887 H2 AN1 58 31.328 33.474 30.919 1.00 0.00 H +HETATM 888 N1 AZI 59 30.711 28.496 29.887 1.00 0.00 N +HETATM 889 N2 AZI 59 30.239 29.556 30.281 1.00 0.00 N +HETATM 890 N3 AZI 59 29.793 30.642 30.720 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 881 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 137 134 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 140 142 +CONECT 140 139 +CONECT 141 139 +CONECT 142 139 145 143 144 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 142 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 194 189 +CONECT 188 187 +CONECT 189 187 192 190 191 +CONECT 190 189 +CONECT 191 189 +CONECT 192 193 189 +CONECT 193 192 +CONECT 194 196 187 195 +CONECT 195 194 +CONECT 196 197 198 194 +CONECT 197 196 +CONECT 198 205 196 200 199 +CONECT 199 198 +CONECT 200 201 198 202 203 +CONECT 201 200 +CONECT 202 200 +CONECT 203 200 204 +CONECT 204 203 +CONECT 205 206 207 198 +CONECT 206 205 +CONECT 207 209 205 208 +CONECT 208 207 +CONECT 209 210 227 211 207 +CONECT 210 209 +CONECT 211 214 209 212 213 +CONECT 212 211 +CONECT 213 211 +CONECT 214 216 215 217 211 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 214 219 220 +CONECT 218 217 +CONECT 219 217 +CONECT 220 217 222 223 221 +CONECT 221 220 +CONECT 222 220 +CONECT 223 226 220 225 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 223 +CONECT 227 228 209 229 +CONECT 228 227 +CONECT 229 227 231 230 +CONECT 230 229 +CONECT 231 234 229 232 233 +CONECT 232 231 +CONECT 233 231 +CONECT 234 235 236 231 +CONECT 235 234 +CONECT 236 238 234 237 +CONECT 237 236 +CONECT 238 240 239 250 236 +CONECT 239 238 +CONECT 240 246 241 242 238 +CONECT 241 240 +CONECT 242 244 240 243 245 +CONECT 243 242 +CONECT 244 242 +CONECT 245 242 +CONECT 246 248 247 249 240 +CONECT 247 246 +CONECT 248 246 +CONECT 249 246 +CONECT 250 238 252 251 +CONECT 251 250 +CONECT 252 262 253 250 +CONECT 253 254 252 263 256 +CONECT 254 255 269 253 +CONECT 255 254 +CONECT 256 253 257 264 265 +CONECT 257 258 259 256 +CONECT 258 261 267 257 +CONECT 259 260 257 266 +CONECT 260 261 268 259 +CONECT 261 881 258 260 +CONECT 262 252 +CONECT 263 253 +CONECT 264 256 +CONECT 265 256 +CONECT 266 259 +CONECT 267 258 +CONECT 268 260 +CONECT 269 271 254 270 +CONECT 270 269 +CONECT 271 272 273 281 269 +CONECT 272 271 +CONECT 273 274 275 271 279 +CONECT 274 273 +CONECT 275 278 277 273 276 +CONECT 276 275 +CONECT 277 275 +CONECT 278 275 +CONECT 279 273 280 +CONECT 280 279 +CONECT 281 283 271 282 +CONECT 282 281 +CONECT 283 293 284 281 +CONECT 284 285 287 283 294 +CONECT 285 286 300 284 +CONECT 286 285 +CONECT 287 295 296 284 288 +CONECT 288 287 289 290 +CONECT 289 298 288 292 +CONECT 290 288 297 291 +CONECT 291 292 290 299 +CONECT 292 289 881 291 +CONECT 293 283 +CONECT 294 284 +CONECT 295 287 +CONECT 296 287 +CONECT 297 290 +CONECT 298 289 +CONECT 299 291 +CONECT 300 302 285 301 +CONECT 301 300 +CONECT 302 313 303 300 304 +CONECT 303 302 +CONECT 304 302 307 306 305 +CONECT 305 304 +CONECT 306 304 +CONECT 307 309 310 304 308 +CONECT 308 307 +CONECT 309 307 +CONECT 310 311 307 312 +CONECT 311 310 +CONECT 312 310 +CONECT 313 315 314 302 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 323 319 318 315 +CONECT 318 317 +CONECT 319 321 320 317 322 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 325 324 317 +CONECT 324 323 +CONECT 325 327 326 323 +CONECT 326 325 +CONECT 327 339 329 328 325 +CONECT 328 327 +CONECT 329 330 335 327 331 +CONECT 330 329 +CONECT 331 329 333 334 332 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 336 337 329 338 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 340 341 327 +CONECT 340 339 +CONECT 341 343 339 342 +CONECT 342 341 +CONECT 343 345 344 351 341 +CONECT 344 343 +CONECT 345 348 346 347 343 +CONECT 346 345 +CONECT 347 345 +CONECT 348 350 349 345 +CONECT 349 348 +CONECT 350 348 +CONECT 351 353 343 352 +CONECT 352 351 +CONECT 353 354 355 351 +CONECT 354 353 +CONECT 355 357 353 375 356 +CONECT 356 355 +CONECT 357 359 358 360 355 +CONECT 358 357 +CONECT 359 357 +CONECT 360 361 357 374 +CONECT 361 362 363 360 +CONECT 362 361 +CONECT 363 361 364 365 +CONECT 364 363 +CONECT 365 363 374 366 +CONECT 366 365 367 368 +CONECT 367 366 +CONECT 368 366 370 369 +CONECT 369 368 +CONECT 370 372 368 371 +CONECT 371 370 +CONECT 372 374 373 370 +CONECT 373 372 +CONECT 374 360 365 372 +CONECT 375 377 355 376 +CONECT 376 375 +CONECT 377 378 379 375 +CONECT 378 377 +CONECT 379 381 377 380 385 +CONECT 380 379 +CONECT 381 384 382 383 379 +CONECT 382 381 +CONECT 383 381 +CONECT 384 381 +CONECT 385 379 386 387 +CONECT 386 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 390 391 400 +CONECT 390 389 +CONECT 391 394 392 389 393 +CONECT 392 391 +CONECT 393 391 +CONECT 394 395 396 397 391 +CONECT 395 394 +CONECT 396 394 +CONECT 397 399 394 398 +CONECT 398 397 +CONECT 399 397 +CONECT 400 389 402 401 +CONECT 401 400 +CONECT 402 403 400 404 +CONECT 403 402 +CONECT 404 402 406 410 405 +CONECT 405 404 +CONECT 406 407 409 404 408 +CONECT 407 406 +CONECT 408 406 +CONECT 409 406 +CONECT 410 412 404 411 +CONECT 411 410 +CONECT 412 413 414 410 +CONECT 413 412 +CONECT 414 416 412 415 425 +CONECT 415 414 +CONECT 416 417 418 419 414 +CONECT 417 416 +CONECT 418 416 +CONECT 419 422 416 421 420 +CONECT 420 419 +CONECT 421 419 +CONECT 422 424 423 419 +CONECT 423 422 +CONECT 424 422 +CONECT 425 414 427 426 +CONECT 426 425 +CONECT 427 428 425 429 +CONECT 428 427 +CONECT 429 427 431 430 447 +CONECT 430 429 +CONECT 431 434 432 433 429 +CONECT 432 431 +CONECT 433 431 +CONECT 434 436 437 435 431 +CONECT 435 434 +CONECT 436 434 +CONECT 437 440 438 439 434 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 441 442 437 +CONECT 441 440 +CONECT 442 440 +CONECT 443 445 444 446 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 +CONECT 447 429 449 448 +CONECT 448 447 +CONECT 449 450 447 451 +CONECT 450 449 +CONECT 451 449 453 452 467 +CONECT 452 451 +CONECT 453 456 454 451 455 +CONECT 454 453 +CONECT 455 453 +CONECT 456 457 465 453 +CONECT 457 459 458 456 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 462 459 463 +CONECT 462 461 +CONECT 463 461 464 465 +CONECT 464 463 +CONECT 465 463 456 466 +CONECT 466 465 +CONECT 467 451 469 468 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 473 469 481 472 +CONECT 472 471 +CONECT 473 474 479 475 471 +CONECT 474 473 +CONECT 475 473 477 478 476 +CONECT 476 475 +CONECT 477 475 +CONECT 478 475 +CONECT 479 480 473 +CONECT 480 479 +CONECT 481 483 471 482 +CONECT 482 481 +CONECT 483 484 485 481 +CONECT 484 483 +CONECT 485 487 483 486 503 +CONECT 486 485 +CONECT 487 490 488 489 485 +CONECT 488 487 +CONECT 489 487 +CONECT 490 493 492 491 487 +CONECT 491 490 +CONECT 492 490 +CONECT 493 496 494 495 490 +CONECT 494 493 +CONECT 495 493 +CONECT 496 498 497 499 493 +CONECT 497 496 +CONECT 498 496 +CONECT 499 501 496 502 500 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 485 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 508 513 +CONECT 508 507 +CONECT 509 512 510 507 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 507 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 534 518 +CONECT 518 517 +CONECT 519 521 520 517 522 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 525 523 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 526 522 528 527 +CONECT 526 525 +CONECT 527 525 +CONECT 528 530 525 531 529 +CONECT 529 528 +CONECT 530 528 +CONECT 531 533 528 532 +CONECT 532 531 +CONECT 533 531 +CONECT 534 536 517 535 +CONECT 535 534 +CONECT 536 537 538 534 +CONECT 537 536 +CONECT 538 540 536 544 539 +CONECT 539 538 +CONECT 540 541 543 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 +CONECT 544 538 546 545 +CONECT 545 544 +CONECT 546 547 544 548 +CONECT 547 546 +CONECT 548 550 546 549 558 +CONECT 549 548 +CONECT 550 553 551 552 548 +CONECT 551 550 +CONECT 552 550 +CONECT 553 555 554 550 +CONECT 554 553 +CONECT 555 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 548 560 559 +CONECT 559 558 +CONECT 560 561 558 562 +CONECT 561 560 +CONECT 562 560 564 563 570 +CONECT 563 562 +CONECT 564 567 565 562 566 +CONECT 565 564 +CONECT 566 564 +CONECT 567 569 568 564 +CONECT 568 567 +CONECT 569 567 +CONECT 570 562 572 571 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 592 576 575 +CONECT 575 574 +CONECT 576 579 574 578 577 +CONECT 577 576 +CONECT 578 576 +CONECT 579 580 581 582 576 +CONECT 580 579 +CONECT 581 579 +CONECT 582 585 584 579 583 +CONECT 583 582 +CONECT 584 582 +CONECT 585 588 587 586 582 +CONECT 586 585 +CONECT 587 585 +CONECT 588 590 591 589 585 +CONECT 589 588 +CONECT 590 588 +CONECT 591 588 +CONECT 592 594 593 574 +CONECT 593 592 +CONECT 594 596 595 592 +CONECT 595 594 +CONECT 596 599 594 597 598 +CONECT 597 596 +CONECT 598 596 +CONECT 599 601 600 596 +CONECT 600 599 +CONECT 601 603 602 599 +CONECT 602 601 +CONECT 603 623 604 605 601 +CONECT 604 603 +CONECT 605 606 603 607 608 +CONECT 606 605 +CONECT 607 605 +CONECT 608 609 605 610 611 +CONECT 609 608 +CONECT 610 608 +CONECT 611 608 613 614 612 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 616 615 +CONECT 615 614 +CONECT 616 617 614 620 +CONECT 617 618 619 616 +CONECT 618 617 +CONECT 619 617 +CONECT 620 616 622 621 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 603 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 629 635 628 625 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 632 +CONECT 635 637 636 627 +CONECT 636 635 +CONECT 637 639 638 635 +CONECT 638 637 +CONECT 639 642 640 641 637 +CONECT 640 639 +CONECT 641 639 +CONECT 642 644 643 639 +CONECT 643 642 +CONECT 644 646 645 642 +CONECT 645 644 +CONECT 646 648 647 657 644 +CONECT 647 646 +CONECT 648 650 651 649 646 +CONECT 649 648 +CONECT 650 648 +CONECT 651 653 648 654 652 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 655 656 +CONECT 655 654 +CONECT 656 654 +CONECT 657 659 646 658 +CONECT 658 657 +CONECT 659 660 661 657 +CONECT 660 659 +CONECT 661 681 659 662 663 +CONECT 662 661 +CONECT 663 661 666 664 665 +CONECT 664 663 +CONECT 665 663 +CONECT 666 668 667 663 669 +CONECT 667 666 +CONECT 668 666 +CONECT 669 666 672 670 671 +CONECT 670 669 +CONECT 671 669 +CONECT 672 673 674 669 +CONECT 673 672 +CONECT 674 678 675 672 +CONECT 675 677 676 674 +CONECT 676 675 +CONECT 677 675 +CONECT 678 679 680 674 +CONECT 679 678 +CONECT 680 678 +CONECT 681 682 683 661 +CONECT 682 681 +CONECT 683 685 681 684 +CONECT 684 683 +CONECT 685 686 687 695 683 +CONECT 686 685 +CONECT 687 689 693 685 688 +CONECT 688 687 +CONECT 689 690 691 692 687 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 +CONECT 693 694 687 +CONECT 694 693 +CONECT 695 697 685 696 +CONECT 696 695 +CONECT 697 698 699 695 +CONECT 698 697 +CONECT 699 714 701 697 700 +CONECT 700 699 +CONECT 701 707 702 699 703 +CONECT 702 701 +CONECT 703 701 705 704 706 +CONECT 704 703 +CONECT 705 703 +CONECT 706 703 +CONECT 707 710 709 708 701 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 713 711 707 +CONECT 711 710 +CONECT 712 710 +CONECT 713 710 +CONECT 714 715 716 699 +CONECT 715 714 +CONECT 716 718 714 717 +CONECT 717 716 +CONECT 718 719 726 720 716 +CONECT 719 718 +CONECT 720 723 718 721 722 +CONECT 721 720 +CONECT 722 720 +CONECT 723 725 720 724 +CONECT 724 723 +CONECT 725 723 +CONECT 726 728 718 727 +CONECT 727 726 +CONECT 728 729 730 726 +CONECT 729 728 +CONECT 730 732 728 738 731 +CONECT 731 730 +CONECT 732 734 735 733 730 +CONECT 733 732 +CONECT 734 732 +CONECT 735 736 732 737 +CONECT 736 735 +CONECT 737 735 +CONECT 738 740 730 739 +CONECT 739 738 +CONECT 740 741 742 738 +CONECT 741 740 +CONECT 742 744 743 740 748 +CONECT 743 742 +CONECT 744 747 746 745 742 +CONECT 745 744 +CONECT 746 744 +CONECT 747 744 +CONECT 748 742 749 750 +CONECT 749 748 +CONECT 750 748 751 752 +CONECT 751 750 +CONECT 752 750 753 754 762 +CONECT 753 752 +CONECT 754 756 752 760 755 +CONECT 755 754 +CONECT 756 757 759 758 754 +CONECT 757 756 +CONECT 758 756 +CONECT 759 756 +CONECT 760 761 754 +CONECT 761 760 +CONECT 762 752 764 763 +CONECT 763 762 +CONECT 764 765 766 762 +CONECT 765 764 +CONECT 766 767 764 768 784 +CONECT 767 766 +CONECT 768 771 766 770 769 +CONECT 769 768 +CONECT 770 768 +CONECT 771 774 772 773 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 777 776 775 771 +CONECT 775 774 +CONECT 776 774 +CONECT 777 780 779 778 774 +CONECT 778 777 +CONECT 779 777 +CONECT 780 782 783 781 777 +CONECT 781 780 +CONECT 782 780 +CONECT 783 780 +CONECT 784 766 786 785 +CONECT 785 784 +CONECT 786 787 784 788 +CONECT 787 786 +CONECT 788 786 798 790 789 +CONECT 789 788 +CONECT 790 791 788 796 792 +CONECT 791 790 +CONECT 792 790 795 794 793 +CONECT 793 792 +CONECT 794 792 +CONECT 795 792 +CONECT 796 797 790 +CONECT 797 796 +CONECT 798 799 788 800 +CONECT 799 798 +CONECT 800 798 802 801 +CONECT 801 800 +CONECT 802 803 800 818 804 +CONECT 803 802 +CONECT 804 802 807 806 805 +CONECT 805 804 +CONECT 806 804 +CONECT 807 816 808 804 +CONECT 808 810 807 809 +CONECT 809 808 +CONECT 810 812 811 808 +CONECT 811 810 +CONECT 812 813 814 810 +CONECT 813 812 +CONECT 814 815 812 816 +CONECT 815 814 +CONECT 816 814 817 807 +CONECT 817 816 +CONECT 818 802 820 819 +CONECT 819 818 +CONECT 820 821 818 822 +CONECT 821 820 +CONECT 822 824 820 832 823 +CONECT 823 822 +CONECT 824 830 826 825 822 +CONECT 825 824 +CONECT 826 827 828 824 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 +CONECT 830 831 824 +CONECT 831 830 +CONECT 832 833 822 834 +CONECT 833 832 +CONECT 834 832 836 835 +CONECT 835 834 +CONECT 836 846 837 834 838 +CONECT 837 836 +CONECT 838 836 840 844 839 +CONECT 839 838 +CONECT 840 841 843 838 842 +CONECT 841 840 +CONECT 842 840 +CONECT 843 840 +CONECT 844 838 845 +CONECT 845 844 +CONECT 846 848 847 836 +CONECT 847 846 +CONECT 848 850 849 846 +CONECT 849 848 +CONECT 850 852 851 848 863 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 858 852 857 856 +CONECT 856 855 +CONECT 857 855 +CONECT 858 859 860 855 +CONECT 859 858 +CONECT 860 861 858 862 +CONECT 861 860 +CONECT 862 860 +CONECT 863 850 865 864 +CONECT 864 863 +CONECT 865 866 863 867 +CONECT 866 865 +CONECT 867 865 878 869 868 +CONECT 868 867 +CONECT 869 871 867 870 872 +CONECT 870 869 +CONECT 871 869 +CONECT 872 873 869 874 875 +CONECT 873 872 +CONECT 874 872 +CONECT 875 872 877 876 +CONECT 876 875 +CONECT 877 875 +CONECT 878 880 867 879 +CONECT 879 878 +CONECT 880 878 +CONECT 881 87 292 882 261 +CONECT 882 881 884 +CONECT 883 886 884 887 885 +CONECT 884 882 883 +CONECT 885 883 +CONECT 886 883 +CONECT 887 883 +CONECT 888 889 +CONECT 889 888 890 +CONECT 890 889 +MASTER 0 0 0 0 0 0 0 0 890 0 890 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_4_front_0.pdb b/tests/nsga2/intermediate_molecules/min_iter_4_front_0.pdb new file mode 100644 index 0000000..c2d6518 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_4_front_0.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.331 51.38249999999948 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.971 23.610 1.00 0.00 N +ATOM 2 H1 MET 1 15.141 38.355 24.553 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.345 23.090 1.00 0.00 H +ATOM 4 H3 MET 1 16.014 38.281 23.181 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.500 23.668 1.00 0.00 C +ATOM 6 HA MET 1 14.171 36.197 24.096 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.872 22.269 1.00 0.00 C +ATOM 8 HB2 MET 1 14.392 36.151 21.668 1.00 0.00 H +ATOM 9 HB3 MET 1 16.153 36.270 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.371 34.332 22.296 1.00 0.00 C +ATOM 11 HG2 MET 1 16.259 34.062 22.867 1.00 0.00 H +ATOM 12 HG3 MET 1 14.494 33.923 22.804 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.525 20.666 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.569 20.066 1.00 0.00 C +ATOM 15 HE1 MET 1 13.461 34.598 20.015 1.00 0.00 H +ATOM 16 HE2 MET 1 13.777 33.132 19.069 1.00 0.00 H +ATOM 17 HE3 MET 1 13.174 32.990 20.731 1.00 0.00 H +ATOM 18 C MET 1 16.221 36.029 24.598 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.397 24.423 1.00 0.00 O +ATOM 20 N GLN 2 15.881 35.189 25.579 1.00 0.00 N +ATOM 21 H GLN 2 14.910 34.997 25.765 1.00 0.00 H +ATOM 22 CA GLN 2 16.846 34.478 26.432 1.00 0.00 C +ATOM 23 HA GLN 2 17.652 35.157 26.726 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.072 27.724 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.138 33.651 27.491 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.661 33.315 28.273 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.253 28.684 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.469 36.090 28.161 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.204 34.973 29.418 1.00 0.00 H +ATOM 30 CD GLN 2 17.129 35.580 29.525 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.164 34.935 29.495 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.031 36.470 30.481 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.772 36.536 31.097 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.109 36.732 30.769 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.304 25.672 1.00 0.00 C +ATOM 36 O GLN 2 17.101 32.148 25.833 1.00 0.00 O +ATOM 37 N TYR 3 18.476 33.620 24.822 1.00 0.00 N +ATOM 38 H TYR 3 18.753 34.594 24.753 1.00 0.00 H +ATOM 39 CA TYR 3 19.257 32.618 24.101 1.00 0.00 C +ATOM 40 HA TYR 3 18.571 31.964 23.563 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.286 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.865 33.945 23.646 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.482 22.671 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.069 21.936 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.528 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.821 32.423 20.552 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.146 34.202 19.540 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.115 33.734 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.845 35.572 19.674 1.00 0.00 C +ATOM 50 OH TYR 3 18.515 36.305 18.581 1.00 0.00 O +ATOM 51 HH TYR 3 18.774 35.870 17.765 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.190 20.937 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.729 37.250 21.020 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.323 35.442 22.065 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.447 35.936 23.020 1.00 0.00 H +ATOM 56 C TYR 3 20.090 31.765 25.077 1.00 0.00 C +ATOM 57 O TYR 3 20.461 32.246 26.149 1.00 0.00 O +ATOM 58 N LYS 4 20.401 30.506 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.251 30.222 23.770 1.00 0.00 H +ATOM 60 CA LYS 4 21.012 29.502 25.631 1.00 0.00 C +ATOM 61 HA LYS 4 20.728 29.716 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.477 28.101 25.270 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.521 27.983 24.189 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.144 27.345 25.695 1.00 0.00 H +ATOM 65 CG LYS 4 19.051 27.747 25.735 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.886 26.697 25.494 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.996 27.852 26.817 1.00 0.00 H +ATOM 68 CD LYS 4 17.924 28.566 25.082 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.889 29.561 25.522 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.146 28.677 24.019 1.00 0.00 H +ATOM 71 CE LYS 4 16.545 27.894 25.197 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.511 24.666 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.594 26.934 24.678 1.00 0.00 H +ATOM 74 NZ LYS 4 16.096 27.673 26.597 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.986 28.550 27.087 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.208 27.171 26.603 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.759 27.086 27.088 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.617 1.00 0.00 C +ATOM 79 O LYS 4 23.197 29.888 24.646 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.028 26.695 1.00 0.00 N +HETATM 81 CA HX1 5 24.626 28.831 26.818 1.00 0.00 C +HETATM 82 C HX1 5 24.900 27.673 27.781 1.00 0.00 C +HETATM 83 O HX1 5 24.403 27.682 28.908 1.00 0.00 O +HETATM 84 CB HX1 5 25.263 30.146 27.306 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.390 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.070 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.386 27.859 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.096 27.752 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.937 29.837 27.334 1.00 0.00 N +HETATM 90 H HX1 5 22.597 28.839 27.518 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.840 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.382 28.291 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.939 30.946 26.638 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.281 26.698 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.530 31.749 28.082 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.838 29.357 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.635 26.658 27.325 1.00 0.00 N +ATOM 98 H ILE 6 26.017 26.713 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.005 25.472 28.115 1.00 0.00 C +ATOM 100 HA ILE 6 25.305 25.371 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.849 24.199 27.245 1.00 0.00 C +ATOM 102 HB ILE 6 26.399 24.347 26.315 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.408 22.939 27.933 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.891 22.758 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.284 22.071 27.286 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.479 23.047 28.114 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.343 24.015 26.915 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.790 23.879 27.844 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.966 24.918 26.434 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.005 22.849 25.979 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.174 21.896 26.480 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.950 22.908 25.704 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.610 22.906 25.075 1.00 0.00 H +ATOM 114 C ILE 6 27.394 25.667 28.753 1.00 0.00 C +ATOM 115 O ILE 6 28.229 26.397 28.221 1.00 0.00 O +ATOM 116 N VAL 7 27.601 25.080 29.936 1.00 0.00 N +ATOM 117 H VAL 7 26.870 24.477 30.295 1.00 0.00 H +ATOM 118 CA VAL 7 28.779 25.286 30.801 1.00 0.00 C +ATOM 119 HA VAL 7 28.879 26.361 30.956 1.00 0.00 H +ATOM 120 CB VAL 7 28.501 24.640 32.176 1.00 0.00 C +ATOM 121 HB VAL 7 27.502 24.948 32.483 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.525 23.106 32.131 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.535 22.744 31.923 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.192 22.714 33.086 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.858 22.745 31.347 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.450 25.110 33.283 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.290 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.078 24.777 34.249 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.448 24.701 33.140 1.00 0.00 H +ATOM 130 C VAL 7 30.113 24.804 30.200 1.00 0.00 C +ATOM 131 O VAL 7 30.155 23.918 29.349 1.00 0.00 O +ATOM 132 N THR 8 31.216 25.379 30.688 1.00 0.00 N +ATOM 133 H THR 8 31.111 26.090 31.396 1.00 0.00 H +ATOM 134 CA THR 8 32.599 24.973 30.394 1.00 0.00 C +ATOM 135 HA THR 8 32.693 24.829 29.317 1.00 0.00 H +ATOM 136 CB THR 8 33.573 26.088 30.820 1.00 0.00 C +ATOM 137 HB THR 8 34.598 25.756 30.643 1.00 0.00 H +ATOM 138 CG2 THR 8 33.360 27.395 30.062 1.00 0.00 C +ATOM 139 HG21 THR 8 32.387 27.825 30.304 1.00 0.00 H +ATOM 140 HG22 THR 8 34.136 28.111 30.331 1.00 0.00 H +ATOM 141 HG23 THR 8 33.406 27.215 28.989 1.00 0.00 H +ATOM 142 OG1 THR 8 33.423 26.394 32.187 1.00 0.00 O +ATOM 143 HG1 THR 8 33.805 27.264 32.325 1.00 0.00 H +ATOM 144 C THR 8 33.011 23.656 31.078 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.249 32.104 1.00 0.00 O +ATOM 146 N GLY 9 34.050 23.008 30.534 1.00 0.00 N +ATOM 147 H GLY 9 34.405 23.337 29.651 1.00 0.00 H +ATOM 148 CA GLY 9 34.626 21.773 31.078 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.617 21.618 30.655 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.880 32.158 1.00 0.00 H +ATOM 151 C GLY 9 33.783 20.523 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.022 20.484 29.825 1.00 0.00 O +ATOM 153 N LYS 10 33.951 19.480 31.615 1.00 0.00 N +ATOM 154 H LYS 10 34.670 19.560 32.316 1.00 0.00 H +ATOM 155 CA LYS 10 33.230 18.191 31.479 1.00 0.00 C +ATOM 156 HA LYS 10 32.289 18.403 30.967 1.00 0.00 H +ATOM 157 CB LYS 10 34.057 17.246 30.577 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.677 17.847 29.907 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.724 16.640 31.194 1.00 0.00 H +ATOM 160 CG LYS 10 33.192 16.330 29.692 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.593 15.666 30.313 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.519 16.953 29.100 1.00 0.00 H +ATOM 163 CD LYS 10 34.058 15.492 28.736 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.721 16.156 28.178 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.661 14.791 29.314 1.00 0.00 H +ATOM 166 CE LYS 10 33.179 14.718 27.746 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.965 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.471 15.413 27.288 1.00 0.00 H +ATOM 169 NZ LYS 10 33.977 14.072 26.676 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.736 13.512 27.043 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.382 13.524 26.065 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.427 14.774 26.073 1.00 0.00 H +ATOM 173 C LYS 10 32.821 17.544 32.814 1.00 0.00 C +ATOM 174 O LYS 10 32.336 16.416 32.832 1.00 0.00 O +ATOM 175 N SER 11 33.037 18.243 33.935 1.00 0.00 N +ATOM 176 H SER 11 33.494 19.132 33.842 1.00 0.00 H +ATOM 177 CA SER 11 32.566 17.848 35.279 1.00 0.00 C +ATOM 178 HA SER 11 32.499 16.758 35.340 1.00 0.00 H +ATOM 179 CB SER 11 33.553 18.325 36.353 1.00 0.00 C +ATOM 180 HB2 SER 11 33.585 19.415 36.355 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.980 37.332 1.00 0.00 H +ATOM 182 OG SER 11 34.850 17.821 36.094 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.425 36.456 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.420 35.589 1.00 0.00 C +ATOM 185 O SER 11 30.351 17.750 36.199 1.00 0.00 O +ATOM 186 N CYS 12 30.919 19.655 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.630 20.134 34.627 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.270 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.870 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.351 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.324 22.215 34.523 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.251 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.149 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.145 23.412 37.057 1.00 0.00 H +ATOM 195 C CYS 12 28.853 19.936 33.838 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.667 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.513 19.990 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.060 20.142 34.736 1.00 0.00 H +ATOM 199 CA LYS 13 26.667 19.722 32.662 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.862 31.773 1.00 0.00 H +ATOM 201 CB LYS 13 26.223 18.247 32.706 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.032 17.655 33.143 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.346 18.144 33.358 1.00 0.00 H +ATOM 204 CG LYS 13 25.915 17.636 31.324 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.036 18.108 30.884 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.767 17.822 30.669 1.00 0.00 H +ATOM 207 CD LYS 13 25.684 16.116 31.406 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.690 15.716 30.391 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.518 15.663 31.947 1.00 0.00 H +ATOM 210 CE LYS 13 24.346 15.744 32.064 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.165 16.386 32.929 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.553 15.951 31.340 1.00 0.00 H +ATOM 213 NZ LYS 13 24.304 14.308 32.452 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.875 14.098 33.271 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.357 13.998 32.643 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.687 13.729 31.706 1.00 0.00 H +ATOM 217 C LYS 13 25.488 20.707 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.584 20.487 31.712 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.786 33.298 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.945 33.874 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.754 33.376 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.445 22.193 33.447 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.483 23.331 34.294 1.00 0.00 H +ATOM 224 C GLY 14 24.286 23.716 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.214 23.892 31.407 1.00 0.00 O +ATOM 226 N VAL 15 23.145 24.399 32.111 1.00 0.00 N +ATOM 227 H VAL 15 22.435 24.245 32.812 1.00 0.00 H +ATOM 228 CA VAL 15 22.778 25.387 31.071 1.00 0.00 C +ATOM 229 HA VAL 15 23.675 25.626 30.492 1.00 0.00 H +ATOM 230 CB VAL 15 21.760 24.738 30.089 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.856 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.449 24.318 30.766 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.938 25.178 31.211 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.793 23.856 30.028 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.579 31.548 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.416 25.668 28.927 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.331 26.008 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.820 25.120 28.196 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.841 26.533 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.282 26.685 31.729 1.00 0.00 C +ATOM 241 O VAL 15 21.714 26.632 32.818 1.00 0.00 O +HETATM 242 N HY1 16 22.496 27.830 31.091 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.109 31.450 1.00 0.00 C +HETATM 244 C HY1 16 21.616 29.886 30.135 1.00 0.00 C +HETATM 245 O HY1 16 21.780 29.350 29.023 1.00 0.00 O +HETATM 246 CB HY1 16 22.864 29.868 32.413 1.00 0.00 C +HETATM 247 CG HY1 16 24.212 30.223 31.813 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.549 31.404 31.207 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.321 29.396 31.740 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.303 30.091 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.880 31.315 30.788 1.00 0.00 N +HETATM 252 H HY1 16 22.997 27.783 30.210 1.00 0.00 H +HETATM 253 HA HY1 16 20.968 28.987 31.945 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.396 30.793 32.773 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.026 29.256 33.296 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.399 28.458 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.907 32.258 31.095 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.728 30.996 1.00 0.00 H +ATOM 259 N THR 17 21.166 31.142 30.265 1.00 0.00 N +ATOM 260 H THR 17 21.050 31.473 31.216 1.00 0.00 H +ATOM 261 CA THR 17 20.736 32.026 29.172 1.00 0.00 C +ATOM 262 HA THR 17 21.120 31.634 28.284 1.00 0.00 H +ATOM 263 CB THR 17 19.152 32.017 29.049 1.00 0.00 C +ATOM 264 HB THR 17 18.937 32.609 28.167 1.00 0.00 H +ATOM 265 CG2 THR 17 18.596 30.675 28.723 1.00 0.00 C +ATOM 266 HG21 THR 17 18.786 29.900 29.421 1.00 0.00 H +ATOM 267 HG22 THR 17 17.506 30.690 28.630 1.00 0.00 H +ATOM 268 HG23 THR 17 18.925 30.322 27.780 1.00 0.00 H +ATOM 269 OG1 THR 17 18.479 32.473 30.205 1.00 0.00 O +ATOM 270 HG1 THR 17 18.568 33.453 30.221 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.458 29.233 1.00 0.00 C +ATOM 272 O THR 17 21.702 33.916 30.265 1.00 0.00 O +HETATM 273 N HY2 18 21.139 34.162 28.101 1.00 0.00 N +HETATM 274 CA HY2 18 21.450 35.620 27.971 1.00 0.00 C +HETATM 275 C HY2 18 20.329 36.290 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.985 35.837 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.774 35.820 27.259 1.00 0.00 C +HETATM 278 CG HY2 18 24.005 35.327 28.003 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.420 34.030 28.155 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.943 36.119 28.644 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.315 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.707 27.237 1.00 0.00 H +HETATM 284 HA HY2 18 21.503 36.046 29.014 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.748 35.296 26.297 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.910 36.879 27.057 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.955 37.127 28.681 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.926 33.165 27.774 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.761 35.647 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.807 37.387 27.748 1.00 0.00 N +ATOM 291 H GLU 19 20.142 37.684 28.644 1.00 0.00 H +ATOM 292 CA GLU 19 18.798 38.219 27.101 1.00 0.00 C +ATOM 293 HA GLU 19 18.058 37.555 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.065 39.079 28.156 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.754 38.431 28.967 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.775 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.833 39.851 27.657 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.550 28.422 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.089 40.412 26.764 1.00 0.00 H +ATOM 300 CD GLU 19 15.654 38.901 27.366 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.588 38.373 26.224 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.813 38.691 28.275 1.00 0.00 O +ATOM 303 C GLU 19 19.405 39.113 25.992 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.857 26.273 1.00 0.00 O +ATOM 305 N ALA 20 18.878 39.052 24.762 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.354 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.961 23.686 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.963 24.094 1.00 0.00 H +ATOM 309 CB ALA 20 20.592 39.489 23.094 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.465 38.517 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.951 40.206 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.351 39.401 23.870 1.00 0.00 H +ATOM 313 C ALA 20 18.191 40.036 22.579 1.00 0.00 C +ATOM 314 O ALA 20 17.360 39.133 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.087 21.745 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.824 21.920 1.00 0.00 H +ATOM 317 CA VAL 21 17.460 41.147 20.465 1.00 0.00 C +ATOM 318 HA VAL 21 16.471 40.723 20.625 1.00 0.00 H +ATOM 319 CB VAL 21 17.274 42.597 19.972 1.00 0.00 C +ATOM 320 HB VAL 21 16.616 42.570 19.108 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.597 43.470 21.033 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.255 43.626 21.888 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.349 44.439 20.598 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.674 42.997 21.365 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.583 43.276 19.536 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.004 42.764 18.670 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.380 44.306 19.239 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.315 43.278 20.344 1.00 0.00 H +ATOM 329 C VAL 21 18.121 40.330 19.353 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.986 18.375 1.00 0.00 O +ATOM 331 N ASP 22 19.414 40.050 19.506 1.00 0.00 N +ATOM 332 H ASP 22 19.863 40.329 20.361 1.00 0.00 H +ATOM 333 CA ASP 22 20.295 39.463 18.502 1.00 0.00 C +ATOM 334 HA ASP 22 19.714 38.825 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.941 40.588 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.174 41.079 17.075 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.377 41.324 18.356 1.00 0.00 H +ATOM 338 CG ASP 22 22.025 40.044 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.147 40.586 16.800 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.762 39.018 16.087 1.00 0.00 O +ATOM 341 C ASP 22 21.366 38.597 19.178 1.00 0.00 C +ATOM 342 O ASP 22 21.825 38.880 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.789 37.545 18.492 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.489 17.520 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.608 18.984 1.00 0.00 C +ATOM 346 HA TRP 23 22.545 36.357 20.016 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.348 18.138 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.975 18.216 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.840 35.604 17.094 1.00 0.00 H +ATOM 350 CG TRP 23 23.573 34.244 18.531 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.517 33.704 17.733 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.739 34.020 16.723 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.129 32.678 18.412 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.903 32.155 18.035 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.589 32.475 19.659 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.825 31.536 20.665 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.540 30.741 20.523 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.682 21.888 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.012 22.701 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.765 22.099 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.900 23.082 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.005 33.658 21.055 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.310 34.465 21.213 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.637 33.527 19.797 1.00 0.00 C +ATOM 365 C TRP 23 24.210 37.185 18.982 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.925 1.00 0.00 O +ATOM 367 N ALA 24 24.557 38.022 17.997 1.00 0.00 N +ATOM 368 H ALA 24 23.880 38.262 17.279 1.00 0.00 H +ATOM 369 CA ALA 24 25.846 38.717 17.976 1.00 0.00 C +ATOM 370 HA ALA 24 26.618 38.001 18.267 1.00 0.00 H +ATOM 371 CB ALA 24 26.158 39.140 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.444 39.882 16.189 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.160 39.562 16.482 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.110 38.274 15.877 1.00 0.00 H +ATOM 375 C ALA 24 25.929 39.882 18.994 1.00 0.00 C +ATOM 376 O ALA 24 27.022 40.384 19.270 1.00 0.00 O +ATOM 377 N GLU 25 24.812 40.285 19.610 1.00 0.00 N +ATOM 378 H GLU 25 23.932 39.945 19.243 1.00 0.00 H +ATOM 379 CA GLU 25 24.791 41.075 20.852 1.00 0.00 C +ATOM 380 HA GLU 25 25.642 41.755 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.512 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.646 41.279 20.820 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.451 42.386 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.432 43.037 19.875 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.632 42.630 18.884 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.410 43.424 19.863 1.00 0.00 H +ATOM 387 CD GLU 25 24.381 44.197 20.185 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.918 45.196 20.744 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.601 44.048 19.836 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.102 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.517 23.016 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.005 22.132 1.00 0.00 N +ATOM 393 H ALA 26 23.666 38.775 21.366 1.00 0.00 H +ATOM 394 CA ALA 26 24.460 38.029 23.217 1.00 0.00 C +ATOM 395 HA ALA 26 24.199 38.524 24.148 1.00 0.00 H +ATOM 396 CB ALA 26 23.491 36.862 23.015 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.771 36.287 22.133 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.204 23.883 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.230 22.894 1.00 0.00 H +ATOM 400 C ALA 26 25.918 37.533 23.365 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.227 24.482 1.00 0.00 O +ATOM 402 N GLU 27 26.710 37.510 22.283 1.00 0.00 N +ATOM 403 H GLU 27 26.268 37.638 21.376 1.00 0.00 H +ATOM 404 CA GLU 27 28.167 37.303 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.369 36.351 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.763 37.247 20.913 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.152 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.735 38.251 20.486 1.00 0.00 H +ATOM 409 CG GLU 27 30.208 36.724 20.921 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.145 21.771 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.190 35.641 21.055 1.00 0.00 H +ATOM 412 CD GLU 27 30.982 37.089 19.641 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.725 38.106 19.697 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.344 18.641 1.00 0.00 O +ATOM 415 C GLU 27 28.849 38.396 23.183 1.00 0.00 C +ATOM 416 O GLU 27 29.572 38.094 24.134 1.00 0.00 O +ATOM 417 N LYS 28 28.547 39.673 22.914 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.853 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.817 23.666 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.667 1.00 0.00 H +ATOM 421 CB LYS 28 28.699 42.145 22.993 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.278 23.048 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.170 42.963 23.542 1.00 0.00 H +ATOM 424 CG LYS 28 29.137 42.221 21.519 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.207 42.027 21.443 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.604 41.462 20.949 1.00 0.00 H +ATOM 427 CD LYS 28 28.837 43.604 20.920 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.819 43.907 21.172 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.521 44.332 21.364 1.00 0.00 H +ATOM 430 CE LYS 28 29.006 43.629 19.396 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.103 44.670 19.084 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.926 43.113 19.127 1.00 0.00 H +ATOM 433 NZ LYS 28 27.841 43.021 18.708 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.981 43.489 19.017 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.904 43.103 17.704 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.722 42.040 18.958 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.782 25.132 1.00 0.00 C +ATOM 438 O LYS 28 29.482 40.969 26.019 1.00 0.00 O +ATOM 439 N PHE 29 27.393 40.452 25.417 1.00 0.00 N +ATOM 440 H PHE 29 26.740 40.365 24.642 1.00 0.00 H +ATOM 441 CA PHE 29 26.903 40.286 26.793 1.00 0.00 C +ATOM 442 HA PHE 29 27.228 41.146 27.379 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.264 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.038 39.343 26.310 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.022 40.230 27.832 1.00 0.00 H +ATOM 446 CG PHE 29 24.678 41.443 26.116 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.465 41.235 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.015 40.254 25.407 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.830 42.300 24.767 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.907 42.126 24.234 1.00 0.00 H +ATOM 451 CZ PHE 29 23.399 43.584 24.790 1.00 0.00 C +ATOM 452 HZ PHE 29 22.919 44.396 24.265 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.591 43.806 25.498 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.027 44.796 25.527 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.226 42.742 26.165 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.139 42.936 26.704 1.00 0.00 H +ATOM 457 C PHE 29 27.484 39.050 27.507 1.00 0.00 C +ATOM 458 O PHE 29 27.589 39.038 28.735 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.768 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.042 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.683 36.892 27.316 1.00 0.00 C +ATOM 462 HA THR 30 28.208 36.545 28.226 1.00 0.00 H +ATOM 463 CB THR 30 28.692 35.717 26.333 1.00 0.00 C +ATOM 464 HB THR 30 29.073 36.025 25.356 1.00 0.00 H +ATOM 465 CG2 THR 30 29.496 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.137 34.212 27.801 1.00 0.00 H +ATOM 467 HG22 THR 30 29.369 33.689 26.123 1.00 0.00 H +ATOM 468 HG23 THR 30 30.559 34.746 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.365 35.280 26.189 1.00 0.00 O +ATOM 470 HG1 THR 30 26.960 35.883 25.542 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.982 28.769 1.00 0.00 O +ATOM 473 N LYS 31 30.746 38.122 26.832 1.00 0.00 N +ATOM 474 H LYS 31 30.287 38.320 25.947 1.00 0.00 H +ATOM 475 CA LYS 31 32.078 38.702 27.069 1.00 0.00 C +ATOM 476 HA LYS 31 32.749 37.905 27.376 1.00 0.00 H +ATOM 477 CB LYS 31 32.616 39.317 25.766 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.011 25.348 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.529 39.865 25.987 1.00 0.00 H +ATOM 480 CG LYS 31 32.930 38.210 24.744 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.684 37.553 25.176 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.044 37.629 24.525 1.00 0.00 H +ATOM 483 CD LYS 31 33.459 38.818 23.435 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.384 22.952 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.299 39.497 23.642 1.00 0.00 H +ATOM 486 CE LYS 31 33.923 37.725 22.467 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.107 37.055 22.246 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.217 38.195 21.540 1.00 0.00 H +ATOM 489 NZ LYS 31 35.077 36.976 23.015 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.822 36.247 23.679 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.553 36.469 22.265 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.760 37.567 23.503 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.188 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.780 28.917 1.00 0.00 O +ATOM 495 N ALA 32 31.031 40.509 28.373 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.873 41.412 29.515 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.138 29.505 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.375 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.495 29.375 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.875 30.215 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.557 42.757 28.446 1.00 0.00 H +ATOM 503 C ALA 32 30.963 40.638 30.838 1.00 0.00 C +ATOM 504 O ALA 32 31.881 40.886 31.616 1.00 0.00 O +ATOM 505 N LYN 33 30.117 39.613 31.030 1.00 0.00 N +ATOM 506 H LYN 33 29.390 39.457 30.346 1.00 0.00 H +ATOM 507 CA LYN 33 30.156 38.755 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.022 39.383 33.110 1.00 0.00 H +ATOM 509 CB LYN 33 29.008 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.061 37.156 31.262 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.141 37.038 33.024 1.00 0.00 H +ATOM 512 CG LYN 33 27.610 38.358 32.315 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.564 38.982 33.207 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.412 38.981 31.444 1.00 0.00 H +ATOM 515 CD LYN 33 26.535 37.267 32.412 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.691 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.632 36.748 33.365 1.00 0.00 H +ATOM 518 CE LYN 33 25.122 37.835 32.288 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.934 38.514 33.114 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.035 38.378 31.349 1.00 0.00 H +ATOM 521 NZ LYN 33 24.115 36.761 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.184 37.154 32.261 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.253 36.113 31.547 1.00 0.00 H +ATOM 524 C LYN 33 31.510 38.042 32.391 1.00 0.00 C +ATOM 525 O LYN 33 32.008 37.922 33.505 1.00 0.00 O +ATOM 526 N ALA 34 32.143 37.585 31.305 1.00 0.00 N +ATOM 527 H ALA 34 31.696 37.677 30.400 1.00 0.00 H +ATOM 528 CA ALA 34 33.470 36.966 31.389 1.00 0.00 C +ATOM 529 HA ALA 34 33.428 36.160 32.125 1.00 0.00 H +ATOM 530 CB ALA 34 33.816 36.355 30.029 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.962 37.145 29.294 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.776 30.132 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.693 29.698 1.00 0.00 H +ATOM 534 C ALA 34 34.573 37.946 31.865 1.00 0.00 C +ATOM 535 O ALA 34 35.469 37.540 32.604 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.224 31.488 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.504 30.885 1.00 0.00 H +ATOM 538 CA ASN 35 35.368 40.286 32.000 1.00 0.00 C +ATOM 539 HA ASN 35 36.366 39.870 32.113 1.00 0.00 H +ATOM 540 CB ASN 35 35.476 41.416 30.969 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.486 41.702 30.624 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.287 31.449 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.031 29.800 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.581 41.002 29.898 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.705 28.668 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.448 27.895 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.600 28.628 1.00 0.00 H +ATOM 548 C ASN 35 34.981 40.786 33.404 1.00 0.00 C +ATOM 549 O ASN 35 35.867 41.207 34.150 1.00 0.00 O +ATOM 550 N ASP 36 33.718 40.635 33.831 1.00 0.00 N +ATOM 551 H ASP 36 32.984 40.413 33.166 1.00 0.00 H +ATOM 552 CA ASP 36 33.339 40.772 35.249 1.00 0.00 C +ATOM 553 HA ASP 36 33.668 41.747 35.602 1.00 0.00 H +ATOM 554 CB ASP 36 31.819 40.767 35.440 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.448 39.783 35.230 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.607 40.875 36.498 1.00 0.00 H +ATOM 557 CG ASP 36 30.981 41.783 34.657 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.512 42.876 34.366 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.778 41.516 34.402 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.708 36.125 1.00 0.00 C +ATOM 561 O ASP 36 34.482 40.004 37.236 1.00 0.00 O +ATOM 562 N PHE 37 34.227 38.480 35.608 1.00 0.00 N +ATOM 563 H PHE 37 33.751 38.279 34.737 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.459 36.179 1.00 0.00 C +ATOM 565 HA PHE 37 35.118 37.611 37.257 1.00 0.00 H +ATOM 566 CB PHE 37 34.574 36.041 35.932 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.663 35.826 34.870 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.334 36.446 1.00 0.00 H +ATOM 569 CG PHE 37 33.150 35.763 36.385 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.139 35.558 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.374 35.619 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.312 35.834 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.039 35.198 35.094 1.00 0.00 H +ATOM 574 CZ PHE 37 30.507 35.235 37.199 1.00 0.00 C +ATOM 575 HZ PHE 37 29.492 35.053 37.510 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.515 35.404 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.270 35.352 39.212 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.834 35.668 37.752 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.601 35.814 38.491 1.00 0.00 H +ATOM 580 C PHE 37 36.607 37.580 35.742 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.679 36.016 1.00 0.00 O +ATOM 582 N GLY 38 36.998 38.676 35.079 1.00 0.00 N +ATOM 583 H GLY 38 36.291 39.378 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.389 39.091 34.839 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.499 40.111 35.207 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.054 38.469 35.438 1.00 0.00 H +ATOM 587 C GLY 38 38.925 39.060 33.393 1.00 0.00 C +ATOM 588 O GLY 38 39.874 39.792 33.112 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.227 32.486 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.727 32.761 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.052 31.090 1.00 0.00 C +ATOM 592 HA ARG 39 38.944 39.045 30.646 1.00 0.00 H +ATOM 593 CB ARG 39 40.304 37.440 31.075 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.635 37.431 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.987 38.106 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.522 36.013 31.628 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.039 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.753 31.461 1.00 0.00 H +ATOM 599 CD ARG 39 40.222 35.826 33.132 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.861 36.507 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.182 36.080 33.342 1.00 0.00 H +ATOM 602 NE ARG 39 40.446 34.443 33.599 1.00 0.00 N +ATOM 603 HE ARG 39 41.205 34.297 34.244 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.303 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.469 32.493 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.428 34.360 32.093 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.296 32.621 32.084 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.954 32.226 33.819 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.694 32.095 34.491 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.336 31.450 33.602 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.225 30.193 1.00 0.00 C +ATOM 612 O ARG 39 37.522 36.137 30.605 1.00 0.00 O +ATOM 613 N ASP 40 37.650 37.678 28.959 1.00 0.00 N +ATOM 614 H ASP 40 38.029 38.573 28.674 1.00 0.00 H +ATOM 615 CA ASP 40 36.889 36.892 27.966 1.00 0.00 C +ATOM 616 HA ASP 40 36.166 36.309 28.530 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.733 26.970 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.444 37.038 26.402 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.369 38.350 27.538 1.00 0.00 H +ATOM 620 CG ASP 40 36.824 38.628 25.969 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.257 39.725 26.392 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.837 38.322 24.743 1.00 0.00 O +ATOM 623 C ASP 40 37.720 35.861 27.181 1.00 0.00 C +ATOM 624 O ASP 40 38.885 36.078 26.862 1.00 0.00 O +ATOM 625 N GLY 41 37.056 34.760 26.814 1.00 0.00 N +ATOM 626 H GLY 41 36.099 34.682 27.117 1.00 0.00 H +ATOM 627 CA GLY 41 37.471 33.828 25.758 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.459 34.099 25.383 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.531 32.823 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.482 33.818 24.581 1.00 0.00 C +ATOM 631 O GLY 41 35.578 34.655 24.504 1.00 0.00 O +ATOM 632 N GLU 42 36.638 32.853 23.674 1.00 0.00 N +ATOM 633 H GLU 42 37.348 32.156 23.828 1.00 0.00 H +ATOM 634 CA GLU 42 35.799 32.668 22.476 1.00 0.00 C +ATOM 635 HA GLU 42 35.112 33.509 22.376 1.00 0.00 H +ATOM 636 CB GLU 42 36.683 32.630 21.214 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.158 31.650 21.168 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.035 32.711 20.341 1.00 0.00 H +ATOM 639 CG GLU 42 37.803 33.694 21.111 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.575 33.457 21.850 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.277 33.620 20.129 1.00 0.00 H +ATOM 642 CD GLU 42 37.343 35.144 21.318 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.154 35.459 21.111 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.167 36.006 21.711 1.00 0.00 O +ATOM 645 C GLU 42 34.948 31.386 22.578 1.00 0.00 C +ATOM 646 O GLU 42 35.393 30.398 23.170 1.00 0.00 O +ATOM 647 N ALA 43 33.745 31.391 21.989 1.00 0.00 N +ATOM 648 H ALA 43 33.480 32.196 21.440 1.00 0.00 H +ATOM 649 CA ALA 43 32.756 30.306 22.060 1.00 0.00 C +ATOM 650 HA ALA 43 33.248 29.388 22.388 1.00 0.00 H +ATOM 651 CB ALA 43 31.692 30.672 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.181 31.592 22.812 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.959 29.866 23.177 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.164 30.811 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.110 30.017 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.882 30.932 19.898 1.00 0.00 O +ATOM 657 N THR 44 31.798 28.746 20.423 1.00 0.00 N +ATOM 658 H THR 44 31.919 28.067 21.168 1.00 0.00 H +ATOM 659 CA THR 44 31.131 28.283 19.194 1.00 0.00 C +ATOM 660 HA THR 44 31.425 28.947 18.381 1.00 0.00 H +ATOM 661 CB THR 44 31.610 26.868 18.823 1.00 0.00 C +ATOM 662 HB THR 44 31.430 26.188 19.657 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.281 17.554 1.00 0.00 C +ATOM 664 HG21 THR 44 31.071 26.989 16.727 1.00 0.00 H +ATOM 665 HG22 THR 44 31.502 25.358 17.280 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.037 17.727 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.927 18.561 1.00 0.00 O +ATOM 668 HG1 THR 44 33.234 26.124 18.092 1.00 0.00 H +ATOM 669 C THR 44 29.605 28.381 19.326 1.00 0.00 C +ATOM 670 O THR 44 29.072 28.429 20.436 1.00 0.00 O +ATOM 671 N ILE 45 28.899 28.459 18.193 1.00 0.00 N +ATOM 672 H ILE 45 29.373 28.324 17.314 1.00 0.00 H +ATOM 673 CA ILE 45 27.479 28.840 18.123 1.00 0.00 C +ATOM 674 HA ILE 45 27.060 28.756 19.126 1.00 0.00 H +ATOM 675 CB ILE 45 27.332 30.316 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.271 30.529 17.778 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.069 31.232 18.677 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.151 31.108 18.586 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.833 32.282 18.498 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.768 30.969 19.687 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.759 30.692 16.252 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.018 31.752 16.233 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.657 30.140 15.968 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.506 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.730 30.935 15.529 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.975 31.017 14.269 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.530 29.452 14.955 1.00 0.00 H +ATOM 688 C ILE 45 26.629 27.925 17.243 1.00 0.00 C +ATOM 689 O ILE 45 27.122 27.343 16.276 1.00 0.00 O +ATOM 690 N ASP 46 25.329 27.880 17.545 1.00 0.00 N +ATOM 691 H ASP 46 25.032 28.297 18.421 1.00 0.00 H +ATOM 692 CA ASP 46 24.280 27.260 16.735 1.00 0.00 C +ATOM 693 HA ASP 46 24.584 27.263 15.684 1.00 0.00 H +ATOM 694 CB ASP 46 24.077 25.807 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.221 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.955 25.788 18.267 1.00 0.00 H +ATOM 697 CG ASP 46 22.841 25.170 16.544 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.475 17.281 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.561 25.439 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.957 28.050 16.850 1.00 0.00 C +ATOM 701 O ASP 46 22.507 28.363 17.955 1.00 0.00 O +ATOM 702 N ASP 47 22.309 28.333 15.716 1.00 0.00 N +ATOM 703 H ASP 47 22.678 27.944 14.861 1.00 0.00 H +ATOM 704 CA ASP 47 20.969 28.925 15.674 1.00 0.00 C +ATOM 705 HA ASP 47 20.875 29.653 16.485 1.00 0.00 H +ATOM 706 CB ASP 47 20.776 29.674 14.345 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.520 30.467 14.253 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.912 28.978 13.514 1.00 0.00 H +ATOM 709 CG ASP 47 19.366 30.275 14.271 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.485 29.674 13.613 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.064 31.235 15.016 1.00 0.00 O +ATOM 712 C ASP 47 19.852 27.876 15.878 1.00 0.00 C +ATOM 713 O ASP 47 18.842 28.184 16.513 1.00 0.00 O +ATOM 714 N ALA 48 20.002 26.636 15.396 1.00 0.00 N +ATOM 715 H ALA 48 20.917 26.342 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.934 25.626 15.412 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.054 14.931 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.425 14.583 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.276 23.967 15.053 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.686 14.514 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.674 24.756 13.580 1.00 0.00 H +ATOM 722 C ALA 48 18.524 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.929 17.099 1.00 0.00 O +ATOM 724 N THR 49 19.475 25.245 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.436 25.295 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.265 25.120 19.229 1.00 0.00 C +ATOM 727 HA THR 49 18.215 24.872 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.099 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.818 23.859 20.868 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.628 19.137 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.666 18.098 1.00 0.00 H +ATOM 732 HG22 THR 49 20.434 21.857 19.654 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.165 1.00 0.00 H +ATOM 734 OG1 THR 49 21.478 24.244 19.774 1.00 0.00 O +ATOM 735 HG1 THR 49 21.730 24.270 18.816 1.00 0.00 H +ATOM 736 C THR 49 19.505 26.429 19.997 1.00 0.00 C +ATOM 737 O THR 49 19.426 26.431 21.226 1.00 0.00 O +ATOM 738 N LYS 50 19.766 27.551 19.307 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.297 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.906 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.354 29.538 19.086 1.00 0.00 H +ATOM 742 CB LYS 50 18.564 29.472 20.292 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.160 28.830 21.074 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.701 30.459 20.736 1.00 0.00 H +ATOM 745 CG LYS 50 17.492 29.593 19.188 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.426 28.657 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.740 19.683 1.00 0.00 H +ATOM 748 CD LYS 50 17.704 30.775 18.223 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.703 31.695 18.813 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.688 17.723 1.00 0.00 H +ATOM 751 CE LYS 50 16.571 30.869 17.187 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.603 17.664 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.507 31.899 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.997 16.018 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.231 29.102 16.282 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.013 29.838 15.434 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.544 30.418 15.421 1.00 0.00 H +ATOM 758 C LYS 50 20.986 28.948 21.020 1.00 0.00 C +ATOM 759 O LYS 50 20.693 29.519 22.082 1.00 0.00 O +ATOM 760 N THR 51 22.146 28.292 20.857 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.962 19.926 1.00 0.00 H +ATOM 762 CA THR 51 23.055 27.904 21.959 1.00 0.00 C +ATOM 763 HA THR 51 22.763 28.429 22.858 1.00 0.00 H +ATOM 764 CB THR 51 22.885 26.404 22.277 1.00 0.00 C +ATOM 765 HB THR 51 22.979 25.814 21.354 1.00 0.00 H +ATOM 766 CG2 THR 51 23.850 25.861 23.317 1.00 0.00 C +ATOM 767 HG21 THR 51 23.812 26.474 24.218 1.00 0.00 H +ATOM 768 HG22 THR 51 23.577 24.841 23.588 1.00 0.00 H +ATOM 769 HG23 THR 51 24.876 25.835 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.633 26.168 22.876 1.00 0.00 O +ATOM 771 HG1 THR 51 20.954 26.250 22.182 1.00 0.00 H +ATOM 772 C THR 51 24.556 28.224 21.725 1.00 0.00 C +ATOM 773 O THR 51 25.085 28.000 20.641 1.00 0.00 O +ATOM 774 N PHE 52 25.248 28.694 22.772 1.00 0.00 N +ATOM 775 H PHE 52 24.712 28.952 23.592 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.779 22.880 1.00 0.00 C +ATOM 777 HA PHE 52 27.145 28.937 21.899 1.00 0.00 H +ATOM 778 CB PHE 52 27.149 29.952 23.820 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.476 29.958 24.659 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.735 24.193 1.00 0.00 H +ATOM 781 CG PHE 52 27.217 31.347 23.228 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.428 32.382 23.752 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.751 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.443 33.652 23.161 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.777 34.431 23.515 1.00 0.00 H +ATOM 786 CZ PHE 52 27.281 33.893 22.066 1.00 0.00 C +ATOM 787 HZ PHE 52 27.244 34.837 21.559 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.160 32.902 21.616 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.836 33.108 20.791 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.628 22.199 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.778 30.857 21.828 1.00 0.00 H +ATOM 792 C PHE 52 27.331 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.809 27.010 24.505 1.00 0.00 O +ATOM 794 N THR 53 28.487 27.066 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.851 27.522 22.147 1.00 0.00 H +ATOM 796 CA THR 53 29.281 25.929 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.048 25.798 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.936 24.611 22.782 1.00 0.00 C +ATOM 799 HB THR 53 29.512 23.804 23.241 1.00 0.00 H +ATOM 800 CG2 THR 53 27.461 24.225 22.862 1.00 0.00 C +ATOM 801 HG21 THR 53 26.865 24.906 22.254 1.00 0.00 H +ATOM 802 HG22 THR 53 27.326 23.209 22.494 1.00 0.00 H +ATOM 803 HG23 THR 53 27.124 24.270 23.898 1.00 0.00 H +ATOM 804 OG1 THR 53 29.273 24.680 21.420 1.00 0.00 O +ATOM 805 HG1 THR 53 28.756 24.016 20.955 1.00 0.00 H +ATOM 806 C THR 53 30.804 26.149 23.413 1.00 0.00 C +ATOM 807 O THR 53 31.287 27.022 22.688 1.00 0.00 O +ATOM 808 N THR 54 31.571 25.328 24.145 1.00 0.00 N +ATOM 809 H THR 54 31.111 24.655 24.737 1.00 0.00 H +ATOM 810 CA THR 54 33.043 25.241 24.080 1.00 0.00 C +ATOM 811 HA THR 54 33.416 26.036 23.436 1.00 0.00 H +ATOM 812 CB THR 54 33.668 25.452 25.473 1.00 0.00 C +ATOM 813 HB THR 54 33.373 24.632 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.195 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.517 26.335 24.770 1.00 0.00 H +ATOM 816 HG22 THR 54 35.553 25.813 26.470 1.00 0.00 H +ATOM 817 HG23 THR 54 35.642 24.609 25.193 1.00 0.00 H +ATOM 818 OG1 THR 54 33.203 26.662 26.026 1.00 0.00 O +ATOM 819 HG1 THR 54 33.876 26.992 26.625 1.00 0.00 H +ATOM 820 C THR 54 33.479 23.896 23.474 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.895 23.605 1.00 0.00 O +ATOM 822 N GLN 55 34.635 23.879 22.803 1.00 0.00 N +ATOM 823 H GLN 55 35.156 24.739 22.761 1.00 0.00 H +ATOM 824 CA GLN 55 35.264 22.693 22.195 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.165 21.639 1.00 0.00 H +ATOM 826 CB GLN 55 36.319 23.163 21.173 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.730 22.295 20.657 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.804 23.775 20.430 1.00 0.00 H +ATOM 829 CG GLN 55 37.482 23.993 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.096 24.713 22.482 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.177 23.334 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.249 24.773 20.686 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.326 24.397 19.523 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.831 25.902 21.034 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.408 26.355 20.331 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.724 26.275 21.962 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.679 23.225 1.00 0.00 C +ATOM 838 O GLN 55 36.112 22.047 24.363 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.413 22.804 1.00 0.00 N +ATOM 840 H GLU 56 35.794 20.234 21.832 1.00 0.00 H +ATOM 841 CA GLU 56 36.491 19.249 23.573 1.00 0.00 C +ATOM 842 HA GLU 56 36.152 19.337 24.602 1.00 0.00 H +ATOM 843 CB GLU 56 35.885 17.954 22.967 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.804 17.985 23.074 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.993 21.896 1.00 0.00 H +ATOM 846 CG GLU 56 36.403 16.582 23.463 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.459 15.931 22.591 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.423 16.669 23.812 1.00 0.00 H +ATOM 849 CD GLU 56 35.548 15.855 24.520 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.094 15.347 25.534 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.325 15.660 24.312 1.00 0.00 O +ATOM 852 C GLU 56 38.030 19.202 23.644 1.00 0.00 C +ATOM 853 O GLU 56 38.535 19.186 24.795 1.00 0.00 O +ATOM 854 OXT GLU 56 38.680 19.141 22.578 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.717 32.457 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.342 33.248 30.282 1.00 0.00 N +HETATM 857 C AN1 58 30.690 33.885 31.200 1.00 0.00 C +HETATM 858 C1 AN1 58 29.362 33.529 30.704 1.00 0.00 C +HETATM 859 H AN1 58 30.622 34.282 32.217 1.00 0.00 H +HETATM 860 H1 AN1 58 31.134 34.634 30.540 1.00 0.00 H +HETATM 861 H2 AN1 58 31.317 32.983 31.203 1.00 0.00 H +HETATM 862 N1 AZI 59 31.272 30.355 29.425 1.00 0.00 N +HETATM 863 N2 AZI 59 30.474 30.251 30.345 1.00 0.00 N +HETATM 864 N3 AZI 59 29.631 30.164 31.291 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 148 144 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 643 639 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_4_front_1.pdb b/tests/nsga2/intermediate_molecules/min_iter_4_front_1.pdb new file mode 100644 index 0000000..c2d6518 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_4_front_1.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.331 51.38249999999948 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.971 23.610 1.00 0.00 N +ATOM 2 H1 MET 1 15.141 38.355 24.553 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.345 23.090 1.00 0.00 H +ATOM 4 H3 MET 1 16.014 38.281 23.181 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.500 23.668 1.00 0.00 C +ATOM 6 HA MET 1 14.171 36.197 24.096 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.872 22.269 1.00 0.00 C +ATOM 8 HB2 MET 1 14.392 36.151 21.668 1.00 0.00 H +ATOM 9 HB3 MET 1 16.153 36.270 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.371 34.332 22.296 1.00 0.00 C +ATOM 11 HG2 MET 1 16.259 34.062 22.867 1.00 0.00 H +ATOM 12 HG3 MET 1 14.494 33.923 22.804 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.525 20.666 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.569 20.066 1.00 0.00 C +ATOM 15 HE1 MET 1 13.461 34.598 20.015 1.00 0.00 H +ATOM 16 HE2 MET 1 13.777 33.132 19.069 1.00 0.00 H +ATOM 17 HE3 MET 1 13.174 32.990 20.731 1.00 0.00 H +ATOM 18 C MET 1 16.221 36.029 24.598 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.397 24.423 1.00 0.00 O +ATOM 20 N GLN 2 15.881 35.189 25.579 1.00 0.00 N +ATOM 21 H GLN 2 14.910 34.997 25.765 1.00 0.00 H +ATOM 22 CA GLN 2 16.846 34.478 26.432 1.00 0.00 C +ATOM 23 HA GLN 2 17.652 35.157 26.726 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.072 27.724 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.138 33.651 27.491 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.661 33.315 28.273 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.253 28.684 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.469 36.090 28.161 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.204 34.973 29.418 1.00 0.00 H +ATOM 30 CD GLN 2 17.129 35.580 29.525 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.164 34.935 29.495 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.031 36.470 30.481 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.772 36.536 31.097 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.109 36.732 30.769 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.304 25.672 1.00 0.00 C +ATOM 36 O GLN 2 17.101 32.148 25.833 1.00 0.00 O +ATOM 37 N TYR 3 18.476 33.620 24.822 1.00 0.00 N +ATOM 38 H TYR 3 18.753 34.594 24.753 1.00 0.00 H +ATOM 39 CA TYR 3 19.257 32.618 24.101 1.00 0.00 C +ATOM 40 HA TYR 3 18.571 31.964 23.563 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.286 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.865 33.945 23.646 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.482 22.671 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.069 21.936 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.528 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.821 32.423 20.552 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.146 34.202 19.540 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.115 33.734 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.845 35.572 19.674 1.00 0.00 C +ATOM 50 OH TYR 3 18.515 36.305 18.581 1.00 0.00 O +ATOM 51 HH TYR 3 18.774 35.870 17.765 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.190 20.937 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.729 37.250 21.020 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.323 35.442 22.065 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.447 35.936 23.020 1.00 0.00 H +ATOM 56 C TYR 3 20.090 31.765 25.077 1.00 0.00 C +ATOM 57 O TYR 3 20.461 32.246 26.149 1.00 0.00 O +ATOM 58 N LYS 4 20.401 30.506 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.251 30.222 23.770 1.00 0.00 H +ATOM 60 CA LYS 4 21.012 29.502 25.631 1.00 0.00 C +ATOM 61 HA LYS 4 20.728 29.716 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.477 28.101 25.270 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.521 27.983 24.189 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.144 27.345 25.695 1.00 0.00 H +ATOM 65 CG LYS 4 19.051 27.747 25.735 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.886 26.697 25.494 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.996 27.852 26.817 1.00 0.00 H +ATOM 68 CD LYS 4 17.924 28.566 25.082 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.889 29.561 25.522 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.146 28.677 24.019 1.00 0.00 H +ATOM 71 CE LYS 4 16.545 27.894 25.197 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.511 24.666 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.594 26.934 24.678 1.00 0.00 H +ATOM 74 NZ LYS 4 16.096 27.673 26.597 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.986 28.550 27.087 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.208 27.171 26.603 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.759 27.086 27.088 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.617 1.00 0.00 C +ATOM 79 O LYS 4 23.197 29.888 24.646 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.028 26.695 1.00 0.00 N +HETATM 81 CA HX1 5 24.626 28.831 26.818 1.00 0.00 C +HETATM 82 C HX1 5 24.900 27.673 27.781 1.00 0.00 C +HETATM 83 O HX1 5 24.403 27.682 28.908 1.00 0.00 O +HETATM 84 CB HX1 5 25.263 30.146 27.306 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.390 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.070 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.386 27.859 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.096 27.752 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.937 29.837 27.334 1.00 0.00 N +HETATM 90 H HX1 5 22.597 28.839 27.518 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.840 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.382 28.291 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.939 30.946 26.638 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.281 26.698 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.530 31.749 28.082 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.838 29.357 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.635 26.658 27.325 1.00 0.00 N +ATOM 98 H ILE 6 26.017 26.713 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.005 25.472 28.115 1.00 0.00 C +ATOM 100 HA ILE 6 25.305 25.371 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.849 24.199 27.245 1.00 0.00 C +ATOM 102 HB ILE 6 26.399 24.347 26.315 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.408 22.939 27.933 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.891 22.758 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.284 22.071 27.286 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.479 23.047 28.114 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.343 24.015 26.915 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.790 23.879 27.844 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.966 24.918 26.434 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.005 22.849 25.979 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.174 21.896 26.480 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.950 22.908 25.704 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.610 22.906 25.075 1.00 0.00 H +ATOM 114 C ILE 6 27.394 25.667 28.753 1.00 0.00 C +ATOM 115 O ILE 6 28.229 26.397 28.221 1.00 0.00 O +ATOM 116 N VAL 7 27.601 25.080 29.936 1.00 0.00 N +ATOM 117 H VAL 7 26.870 24.477 30.295 1.00 0.00 H +ATOM 118 CA VAL 7 28.779 25.286 30.801 1.00 0.00 C +ATOM 119 HA VAL 7 28.879 26.361 30.956 1.00 0.00 H +ATOM 120 CB VAL 7 28.501 24.640 32.176 1.00 0.00 C +ATOM 121 HB VAL 7 27.502 24.948 32.483 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.525 23.106 32.131 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.535 22.744 31.923 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.192 22.714 33.086 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.858 22.745 31.347 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.450 25.110 33.283 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.290 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.078 24.777 34.249 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.448 24.701 33.140 1.00 0.00 H +ATOM 130 C VAL 7 30.113 24.804 30.200 1.00 0.00 C +ATOM 131 O VAL 7 30.155 23.918 29.349 1.00 0.00 O +ATOM 132 N THR 8 31.216 25.379 30.688 1.00 0.00 N +ATOM 133 H THR 8 31.111 26.090 31.396 1.00 0.00 H +ATOM 134 CA THR 8 32.599 24.973 30.394 1.00 0.00 C +ATOM 135 HA THR 8 32.693 24.829 29.317 1.00 0.00 H +ATOM 136 CB THR 8 33.573 26.088 30.820 1.00 0.00 C +ATOM 137 HB THR 8 34.598 25.756 30.643 1.00 0.00 H +ATOM 138 CG2 THR 8 33.360 27.395 30.062 1.00 0.00 C +ATOM 139 HG21 THR 8 32.387 27.825 30.304 1.00 0.00 H +ATOM 140 HG22 THR 8 34.136 28.111 30.331 1.00 0.00 H +ATOM 141 HG23 THR 8 33.406 27.215 28.989 1.00 0.00 H +ATOM 142 OG1 THR 8 33.423 26.394 32.187 1.00 0.00 O +ATOM 143 HG1 THR 8 33.805 27.264 32.325 1.00 0.00 H +ATOM 144 C THR 8 33.011 23.656 31.078 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.249 32.104 1.00 0.00 O +ATOM 146 N GLY 9 34.050 23.008 30.534 1.00 0.00 N +ATOM 147 H GLY 9 34.405 23.337 29.651 1.00 0.00 H +ATOM 148 CA GLY 9 34.626 21.773 31.078 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.617 21.618 30.655 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.880 32.158 1.00 0.00 H +ATOM 151 C GLY 9 33.783 20.523 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.022 20.484 29.825 1.00 0.00 O +ATOM 153 N LYS 10 33.951 19.480 31.615 1.00 0.00 N +ATOM 154 H LYS 10 34.670 19.560 32.316 1.00 0.00 H +ATOM 155 CA LYS 10 33.230 18.191 31.479 1.00 0.00 C +ATOM 156 HA LYS 10 32.289 18.403 30.967 1.00 0.00 H +ATOM 157 CB LYS 10 34.057 17.246 30.577 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.677 17.847 29.907 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.724 16.640 31.194 1.00 0.00 H +ATOM 160 CG LYS 10 33.192 16.330 29.692 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.593 15.666 30.313 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.519 16.953 29.100 1.00 0.00 H +ATOM 163 CD LYS 10 34.058 15.492 28.736 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.721 16.156 28.178 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.661 14.791 29.314 1.00 0.00 H +ATOM 166 CE LYS 10 33.179 14.718 27.746 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.965 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.471 15.413 27.288 1.00 0.00 H +ATOM 169 NZ LYS 10 33.977 14.072 26.676 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.736 13.512 27.043 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.382 13.524 26.065 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.427 14.774 26.073 1.00 0.00 H +ATOM 173 C LYS 10 32.821 17.544 32.814 1.00 0.00 C +ATOM 174 O LYS 10 32.336 16.416 32.832 1.00 0.00 O +ATOM 175 N SER 11 33.037 18.243 33.935 1.00 0.00 N +ATOM 176 H SER 11 33.494 19.132 33.842 1.00 0.00 H +ATOM 177 CA SER 11 32.566 17.848 35.279 1.00 0.00 C +ATOM 178 HA SER 11 32.499 16.758 35.340 1.00 0.00 H +ATOM 179 CB SER 11 33.553 18.325 36.353 1.00 0.00 C +ATOM 180 HB2 SER 11 33.585 19.415 36.355 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.980 37.332 1.00 0.00 H +ATOM 182 OG SER 11 34.850 17.821 36.094 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.425 36.456 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.420 35.589 1.00 0.00 C +ATOM 185 O SER 11 30.351 17.750 36.199 1.00 0.00 O +ATOM 186 N CYS 12 30.919 19.655 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.630 20.134 34.627 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.270 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.870 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.351 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.324 22.215 34.523 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.251 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.149 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.145 23.412 37.057 1.00 0.00 H +ATOM 195 C CYS 12 28.853 19.936 33.838 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.667 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.513 19.990 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.060 20.142 34.736 1.00 0.00 H +ATOM 199 CA LYS 13 26.667 19.722 32.662 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.862 31.773 1.00 0.00 H +ATOM 201 CB LYS 13 26.223 18.247 32.706 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.032 17.655 33.143 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.346 18.144 33.358 1.00 0.00 H +ATOM 204 CG LYS 13 25.915 17.636 31.324 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.036 18.108 30.884 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.767 17.822 30.669 1.00 0.00 H +ATOM 207 CD LYS 13 25.684 16.116 31.406 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.690 15.716 30.391 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.518 15.663 31.947 1.00 0.00 H +ATOM 210 CE LYS 13 24.346 15.744 32.064 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.165 16.386 32.929 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.553 15.951 31.340 1.00 0.00 H +ATOM 213 NZ LYS 13 24.304 14.308 32.452 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.875 14.098 33.271 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.357 13.998 32.643 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.687 13.729 31.706 1.00 0.00 H +ATOM 217 C LYS 13 25.488 20.707 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.584 20.487 31.712 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.786 33.298 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.945 33.874 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.754 33.376 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.445 22.193 33.447 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.483 23.331 34.294 1.00 0.00 H +ATOM 224 C GLY 14 24.286 23.716 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.214 23.892 31.407 1.00 0.00 O +ATOM 226 N VAL 15 23.145 24.399 32.111 1.00 0.00 N +ATOM 227 H VAL 15 22.435 24.245 32.812 1.00 0.00 H +ATOM 228 CA VAL 15 22.778 25.387 31.071 1.00 0.00 C +ATOM 229 HA VAL 15 23.675 25.626 30.492 1.00 0.00 H +ATOM 230 CB VAL 15 21.760 24.738 30.089 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.856 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.449 24.318 30.766 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.938 25.178 31.211 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.793 23.856 30.028 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.579 31.548 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.416 25.668 28.927 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.331 26.008 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.820 25.120 28.196 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.841 26.533 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.282 26.685 31.729 1.00 0.00 C +ATOM 241 O VAL 15 21.714 26.632 32.818 1.00 0.00 O +HETATM 242 N HY1 16 22.496 27.830 31.091 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.109 31.450 1.00 0.00 C +HETATM 244 C HY1 16 21.616 29.886 30.135 1.00 0.00 C +HETATM 245 O HY1 16 21.780 29.350 29.023 1.00 0.00 O +HETATM 246 CB HY1 16 22.864 29.868 32.413 1.00 0.00 C +HETATM 247 CG HY1 16 24.212 30.223 31.813 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.549 31.404 31.207 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.321 29.396 31.740 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.303 30.091 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.880 31.315 30.788 1.00 0.00 N +HETATM 252 H HY1 16 22.997 27.783 30.210 1.00 0.00 H +HETATM 253 HA HY1 16 20.968 28.987 31.945 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.396 30.793 32.773 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.026 29.256 33.296 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.399 28.458 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.907 32.258 31.095 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.728 30.996 1.00 0.00 H +ATOM 259 N THR 17 21.166 31.142 30.265 1.00 0.00 N +ATOM 260 H THR 17 21.050 31.473 31.216 1.00 0.00 H +ATOM 261 CA THR 17 20.736 32.026 29.172 1.00 0.00 C +ATOM 262 HA THR 17 21.120 31.634 28.284 1.00 0.00 H +ATOM 263 CB THR 17 19.152 32.017 29.049 1.00 0.00 C +ATOM 264 HB THR 17 18.937 32.609 28.167 1.00 0.00 H +ATOM 265 CG2 THR 17 18.596 30.675 28.723 1.00 0.00 C +ATOM 266 HG21 THR 17 18.786 29.900 29.421 1.00 0.00 H +ATOM 267 HG22 THR 17 17.506 30.690 28.630 1.00 0.00 H +ATOM 268 HG23 THR 17 18.925 30.322 27.780 1.00 0.00 H +ATOM 269 OG1 THR 17 18.479 32.473 30.205 1.00 0.00 O +ATOM 270 HG1 THR 17 18.568 33.453 30.221 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.458 29.233 1.00 0.00 C +ATOM 272 O THR 17 21.702 33.916 30.265 1.00 0.00 O +HETATM 273 N HY2 18 21.139 34.162 28.101 1.00 0.00 N +HETATM 274 CA HY2 18 21.450 35.620 27.971 1.00 0.00 C +HETATM 275 C HY2 18 20.329 36.290 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.985 35.837 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.774 35.820 27.259 1.00 0.00 C +HETATM 278 CG HY2 18 24.005 35.327 28.003 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.420 34.030 28.155 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.943 36.119 28.644 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.315 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.707 27.237 1.00 0.00 H +HETATM 284 HA HY2 18 21.503 36.046 29.014 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.748 35.296 26.297 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.910 36.879 27.057 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.955 37.127 28.681 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.926 33.165 27.774 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.761 35.647 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.807 37.387 27.748 1.00 0.00 N +ATOM 291 H GLU 19 20.142 37.684 28.644 1.00 0.00 H +ATOM 292 CA GLU 19 18.798 38.219 27.101 1.00 0.00 C +ATOM 293 HA GLU 19 18.058 37.555 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.065 39.079 28.156 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.754 38.431 28.967 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.775 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.833 39.851 27.657 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.550 28.422 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.089 40.412 26.764 1.00 0.00 H +ATOM 300 CD GLU 19 15.654 38.901 27.366 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.588 38.373 26.224 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.813 38.691 28.275 1.00 0.00 O +ATOM 303 C GLU 19 19.405 39.113 25.992 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.857 26.273 1.00 0.00 O +ATOM 305 N ALA 20 18.878 39.052 24.762 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.354 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.961 23.686 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.963 24.094 1.00 0.00 H +ATOM 309 CB ALA 20 20.592 39.489 23.094 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.465 38.517 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.951 40.206 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.351 39.401 23.870 1.00 0.00 H +ATOM 313 C ALA 20 18.191 40.036 22.579 1.00 0.00 C +ATOM 314 O ALA 20 17.360 39.133 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.087 21.745 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.824 21.920 1.00 0.00 H +ATOM 317 CA VAL 21 17.460 41.147 20.465 1.00 0.00 C +ATOM 318 HA VAL 21 16.471 40.723 20.625 1.00 0.00 H +ATOM 319 CB VAL 21 17.274 42.597 19.972 1.00 0.00 C +ATOM 320 HB VAL 21 16.616 42.570 19.108 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.597 43.470 21.033 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.255 43.626 21.888 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.349 44.439 20.598 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.674 42.997 21.365 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.583 43.276 19.536 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.004 42.764 18.670 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.380 44.306 19.239 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.315 43.278 20.344 1.00 0.00 H +ATOM 329 C VAL 21 18.121 40.330 19.353 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.986 18.375 1.00 0.00 O +ATOM 331 N ASP 22 19.414 40.050 19.506 1.00 0.00 N +ATOM 332 H ASP 22 19.863 40.329 20.361 1.00 0.00 H +ATOM 333 CA ASP 22 20.295 39.463 18.502 1.00 0.00 C +ATOM 334 HA ASP 22 19.714 38.825 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.941 40.588 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.174 41.079 17.075 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.377 41.324 18.356 1.00 0.00 H +ATOM 338 CG ASP 22 22.025 40.044 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.147 40.586 16.800 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.762 39.018 16.087 1.00 0.00 O +ATOM 341 C ASP 22 21.366 38.597 19.178 1.00 0.00 C +ATOM 342 O ASP 22 21.825 38.880 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.789 37.545 18.492 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.489 17.520 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.608 18.984 1.00 0.00 C +ATOM 346 HA TRP 23 22.545 36.357 20.016 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.348 18.138 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.975 18.216 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.840 35.604 17.094 1.00 0.00 H +ATOM 350 CG TRP 23 23.573 34.244 18.531 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.517 33.704 17.733 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.739 34.020 16.723 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.129 32.678 18.412 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.903 32.155 18.035 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.589 32.475 19.659 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.825 31.536 20.665 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.540 30.741 20.523 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.682 21.888 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.012 22.701 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.765 22.099 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.900 23.082 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.005 33.658 21.055 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.310 34.465 21.213 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.637 33.527 19.797 1.00 0.00 C +ATOM 365 C TRP 23 24.210 37.185 18.982 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.925 1.00 0.00 O +ATOM 367 N ALA 24 24.557 38.022 17.997 1.00 0.00 N +ATOM 368 H ALA 24 23.880 38.262 17.279 1.00 0.00 H +ATOM 369 CA ALA 24 25.846 38.717 17.976 1.00 0.00 C +ATOM 370 HA ALA 24 26.618 38.001 18.267 1.00 0.00 H +ATOM 371 CB ALA 24 26.158 39.140 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.444 39.882 16.189 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.160 39.562 16.482 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.110 38.274 15.877 1.00 0.00 H +ATOM 375 C ALA 24 25.929 39.882 18.994 1.00 0.00 C +ATOM 376 O ALA 24 27.022 40.384 19.270 1.00 0.00 O +ATOM 377 N GLU 25 24.812 40.285 19.610 1.00 0.00 N +ATOM 378 H GLU 25 23.932 39.945 19.243 1.00 0.00 H +ATOM 379 CA GLU 25 24.791 41.075 20.852 1.00 0.00 C +ATOM 380 HA GLU 25 25.642 41.755 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.512 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.646 41.279 20.820 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.451 42.386 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.432 43.037 19.875 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.632 42.630 18.884 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.410 43.424 19.863 1.00 0.00 H +ATOM 387 CD GLU 25 24.381 44.197 20.185 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.918 45.196 20.744 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.601 44.048 19.836 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.102 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.517 23.016 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.005 22.132 1.00 0.00 N +ATOM 393 H ALA 26 23.666 38.775 21.366 1.00 0.00 H +ATOM 394 CA ALA 26 24.460 38.029 23.217 1.00 0.00 C +ATOM 395 HA ALA 26 24.199 38.524 24.148 1.00 0.00 H +ATOM 396 CB ALA 26 23.491 36.862 23.015 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.771 36.287 22.133 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.204 23.883 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.230 22.894 1.00 0.00 H +ATOM 400 C ALA 26 25.918 37.533 23.365 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.227 24.482 1.00 0.00 O +ATOM 402 N GLU 27 26.710 37.510 22.283 1.00 0.00 N +ATOM 403 H GLU 27 26.268 37.638 21.376 1.00 0.00 H +ATOM 404 CA GLU 27 28.167 37.303 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.369 36.351 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.763 37.247 20.913 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.152 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.735 38.251 20.486 1.00 0.00 H +ATOM 409 CG GLU 27 30.208 36.724 20.921 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.145 21.771 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.190 35.641 21.055 1.00 0.00 H +ATOM 412 CD GLU 27 30.982 37.089 19.641 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.725 38.106 19.697 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.344 18.641 1.00 0.00 O +ATOM 415 C GLU 27 28.849 38.396 23.183 1.00 0.00 C +ATOM 416 O GLU 27 29.572 38.094 24.134 1.00 0.00 O +ATOM 417 N LYS 28 28.547 39.673 22.914 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.853 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.817 23.666 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.667 1.00 0.00 H +ATOM 421 CB LYS 28 28.699 42.145 22.993 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.278 23.048 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.170 42.963 23.542 1.00 0.00 H +ATOM 424 CG LYS 28 29.137 42.221 21.519 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.207 42.027 21.443 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.604 41.462 20.949 1.00 0.00 H +ATOM 427 CD LYS 28 28.837 43.604 20.920 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.819 43.907 21.172 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.521 44.332 21.364 1.00 0.00 H +ATOM 430 CE LYS 28 29.006 43.629 19.396 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.103 44.670 19.084 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.926 43.113 19.127 1.00 0.00 H +ATOM 433 NZ LYS 28 27.841 43.021 18.708 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.981 43.489 19.017 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.904 43.103 17.704 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.722 42.040 18.958 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.782 25.132 1.00 0.00 C +ATOM 438 O LYS 28 29.482 40.969 26.019 1.00 0.00 O +ATOM 439 N PHE 29 27.393 40.452 25.417 1.00 0.00 N +ATOM 440 H PHE 29 26.740 40.365 24.642 1.00 0.00 H +ATOM 441 CA PHE 29 26.903 40.286 26.793 1.00 0.00 C +ATOM 442 HA PHE 29 27.228 41.146 27.379 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.264 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.038 39.343 26.310 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.022 40.230 27.832 1.00 0.00 H +ATOM 446 CG PHE 29 24.678 41.443 26.116 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.465 41.235 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.015 40.254 25.407 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.830 42.300 24.767 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.907 42.126 24.234 1.00 0.00 H +ATOM 451 CZ PHE 29 23.399 43.584 24.790 1.00 0.00 C +ATOM 452 HZ PHE 29 22.919 44.396 24.265 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.591 43.806 25.498 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.027 44.796 25.527 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.226 42.742 26.165 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.139 42.936 26.704 1.00 0.00 H +ATOM 457 C PHE 29 27.484 39.050 27.507 1.00 0.00 C +ATOM 458 O PHE 29 27.589 39.038 28.735 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.768 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.042 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.683 36.892 27.316 1.00 0.00 C +ATOM 462 HA THR 30 28.208 36.545 28.226 1.00 0.00 H +ATOM 463 CB THR 30 28.692 35.717 26.333 1.00 0.00 C +ATOM 464 HB THR 30 29.073 36.025 25.356 1.00 0.00 H +ATOM 465 CG2 THR 30 29.496 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.137 34.212 27.801 1.00 0.00 H +ATOM 467 HG22 THR 30 29.369 33.689 26.123 1.00 0.00 H +ATOM 468 HG23 THR 30 30.559 34.746 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.365 35.280 26.189 1.00 0.00 O +ATOM 470 HG1 THR 30 26.960 35.883 25.542 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.982 28.769 1.00 0.00 O +ATOM 473 N LYS 31 30.746 38.122 26.832 1.00 0.00 N +ATOM 474 H LYS 31 30.287 38.320 25.947 1.00 0.00 H +ATOM 475 CA LYS 31 32.078 38.702 27.069 1.00 0.00 C +ATOM 476 HA LYS 31 32.749 37.905 27.376 1.00 0.00 H +ATOM 477 CB LYS 31 32.616 39.317 25.766 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.011 25.348 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.529 39.865 25.987 1.00 0.00 H +ATOM 480 CG LYS 31 32.930 38.210 24.744 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.684 37.553 25.176 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.044 37.629 24.525 1.00 0.00 H +ATOM 483 CD LYS 31 33.459 38.818 23.435 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.384 22.952 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.299 39.497 23.642 1.00 0.00 H +ATOM 486 CE LYS 31 33.923 37.725 22.467 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.107 37.055 22.246 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.217 38.195 21.540 1.00 0.00 H +ATOM 489 NZ LYS 31 35.077 36.976 23.015 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.822 36.247 23.679 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.553 36.469 22.265 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.760 37.567 23.503 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.188 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.780 28.917 1.00 0.00 O +ATOM 495 N ALA 32 31.031 40.509 28.373 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.873 41.412 29.515 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.138 29.505 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.375 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.495 29.375 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.875 30.215 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.557 42.757 28.446 1.00 0.00 H +ATOM 503 C ALA 32 30.963 40.638 30.838 1.00 0.00 C +ATOM 504 O ALA 32 31.881 40.886 31.616 1.00 0.00 O +ATOM 505 N LYN 33 30.117 39.613 31.030 1.00 0.00 N +ATOM 506 H LYN 33 29.390 39.457 30.346 1.00 0.00 H +ATOM 507 CA LYN 33 30.156 38.755 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.022 39.383 33.110 1.00 0.00 H +ATOM 509 CB LYN 33 29.008 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.061 37.156 31.262 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.141 37.038 33.024 1.00 0.00 H +ATOM 512 CG LYN 33 27.610 38.358 32.315 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.564 38.982 33.207 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.412 38.981 31.444 1.00 0.00 H +ATOM 515 CD LYN 33 26.535 37.267 32.412 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.691 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.632 36.748 33.365 1.00 0.00 H +ATOM 518 CE LYN 33 25.122 37.835 32.288 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.934 38.514 33.114 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.035 38.378 31.349 1.00 0.00 H +ATOM 521 NZ LYN 33 24.115 36.761 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.184 37.154 32.261 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.253 36.113 31.547 1.00 0.00 H +ATOM 524 C LYN 33 31.510 38.042 32.391 1.00 0.00 C +ATOM 525 O LYN 33 32.008 37.922 33.505 1.00 0.00 O +ATOM 526 N ALA 34 32.143 37.585 31.305 1.00 0.00 N +ATOM 527 H ALA 34 31.696 37.677 30.400 1.00 0.00 H +ATOM 528 CA ALA 34 33.470 36.966 31.389 1.00 0.00 C +ATOM 529 HA ALA 34 33.428 36.160 32.125 1.00 0.00 H +ATOM 530 CB ALA 34 33.816 36.355 30.029 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.962 37.145 29.294 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.776 30.132 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.693 29.698 1.00 0.00 H +ATOM 534 C ALA 34 34.573 37.946 31.865 1.00 0.00 C +ATOM 535 O ALA 34 35.469 37.540 32.604 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.224 31.488 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.504 30.885 1.00 0.00 H +ATOM 538 CA ASN 35 35.368 40.286 32.000 1.00 0.00 C +ATOM 539 HA ASN 35 36.366 39.870 32.113 1.00 0.00 H +ATOM 540 CB ASN 35 35.476 41.416 30.969 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.486 41.702 30.624 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.287 31.449 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.031 29.800 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.581 41.002 29.898 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.705 28.668 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.448 27.895 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.600 28.628 1.00 0.00 H +ATOM 548 C ASN 35 34.981 40.786 33.404 1.00 0.00 C +ATOM 549 O ASN 35 35.867 41.207 34.150 1.00 0.00 O +ATOM 550 N ASP 36 33.718 40.635 33.831 1.00 0.00 N +ATOM 551 H ASP 36 32.984 40.413 33.166 1.00 0.00 H +ATOM 552 CA ASP 36 33.339 40.772 35.249 1.00 0.00 C +ATOM 553 HA ASP 36 33.668 41.747 35.602 1.00 0.00 H +ATOM 554 CB ASP 36 31.819 40.767 35.440 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.448 39.783 35.230 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.607 40.875 36.498 1.00 0.00 H +ATOM 557 CG ASP 36 30.981 41.783 34.657 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.512 42.876 34.366 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.778 41.516 34.402 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.708 36.125 1.00 0.00 C +ATOM 561 O ASP 36 34.482 40.004 37.236 1.00 0.00 O +ATOM 562 N PHE 37 34.227 38.480 35.608 1.00 0.00 N +ATOM 563 H PHE 37 33.751 38.279 34.737 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.459 36.179 1.00 0.00 C +ATOM 565 HA PHE 37 35.118 37.611 37.257 1.00 0.00 H +ATOM 566 CB PHE 37 34.574 36.041 35.932 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.663 35.826 34.870 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.334 36.446 1.00 0.00 H +ATOM 569 CG PHE 37 33.150 35.763 36.385 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.139 35.558 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.374 35.619 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.312 35.834 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.039 35.198 35.094 1.00 0.00 H +ATOM 574 CZ PHE 37 30.507 35.235 37.199 1.00 0.00 C +ATOM 575 HZ PHE 37 29.492 35.053 37.510 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.515 35.404 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.270 35.352 39.212 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.834 35.668 37.752 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.601 35.814 38.491 1.00 0.00 H +ATOM 580 C PHE 37 36.607 37.580 35.742 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.679 36.016 1.00 0.00 O +ATOM 582 N GLY 38 36.998 38.676 35.079 1.00 0.00 N +ATOM 583 H GLY 38 36.291 39.378 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.389 39.091 34.839 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.499 40.111 35.207 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.054 38.469 35.438 1.00 0.00 H +ATOM 587 C GLY 38 38.925 39.060 33.393 1.00 0.00 C +ATOM 588 O GLY 38 39.874 39.792 33.112 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.227 32.486 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.727 32.761 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.052 31.090 1.00 0.00 C +ATOM 592 HA ARG 39 38.944 39.045 30.646 1.00 0.00 H +ATOM 593 CB ARG 39 40.304 37.440 31.075 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.635 37.431 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.987 38.106 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.522 36.013 31.628 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.039 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.753 31.461 1.00 0.00 H +ATOM 599 CD ARG 39 40.222 35.826 33.132 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.861 36.507 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.182 36.080 33.342 1.00 0.00 H +ATOM 602 NE ARG 39 40.446 34.443 33.599 1.00 0.00 N +ATOM 603 HE ARG 39 41.205 34.297 34.244 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.303 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.469 32.493 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.428 34.360 32.093 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.296 32.621 32.084 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.954 32.226 33.819 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.694 32.095 34.491 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.336 31.450 33.602 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.225 30.193 1.00 0.00 C +ATOM 612 O ARG 39 37.522 36.137 30.605 1.00 0.00 O +ATOM 613 N ASP 40 37.650 37.678 28.959 1.00 0.00 N +ATOM 614 H ASP 40 38.029 38.573 28.674 1.00 0.00 H +ATOM 615 CA ASP 40 36.889 36.892 27.966 1.00 0.00 C +ATOM 616 HA ASP 40 36.166 36.309 28.530 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.733 26.970 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.444 37.038 26.402 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.369 38.350 27.538 1.00 0.00 H +ATOM 620 CG ASP 40 36.824 38.628 25.969 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.257 39.725 26.392 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.837 38.322 24.743 1.00 0.00 O +ATOM 623 C ASP 40 37.720 35.861 27.181 1.00 0.00 C +ATOM 624 O ASP 40 38.885 36.078 26.862 1.00 0.00 O +ATOM 625 N GLY 41 37.056 34.760 26.814 1.00 0.00 N +ATOM 626 H GLY 41 36.099 34.682 27.117 1.00 0.00 H +ATOM 627 CA GLY 41 37.471 33.828 25.758 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.459 34.099 25.383 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.531 32.823 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.482 33.818 24.581 1.00 0.00 C +ATOM 631 O GLY 41 35.578 34.655 24.504 1.00 0.00 O +ATOM 632 N GLU 42 36.638 32.853 23.674 1.00 0.00 N +ATOM 633 H GLU 42 37.348 32.156 23.828 1.00 0.00 H +ATOM 634 CA GLU 42 35.799 32.668 22.476 1.00 0.00 C +ATOM 635 HA GLU 42 35.112 33.509 22.376 1.00 0.00 H +ATOM 636 CB GLU 42 36.683 32.630 21.214 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.158 31.650 21.168 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.035 32.711 20.341 1.00 0.00 H +ATOM 639 CG GLU 42 37.803 33.694 21.111 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.575 33.457 21.850 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.277 33.620 20.129 1.00 0.00 H +ATOM 642 CD GLU 42 37.343 35.144 21.318 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.154 35.459 21.111 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.167 36.006 21.711 1.00 0.00 O +ATOM 645 C GLU 42 34.948 31.386 22.578 1.00 0.00 C +ATOM 646 O GLU 42 35.393 30.398 23.170 1.00 0.00 O +ATOM 647 N ALA 43 33.745 31.391 21.989 1.00 0.00 N +ATOM 648 H ALA 43 33.480 32.196 21.440 1.00 0.00 H +ATOM 649 CA ALA 43 32.756 30.306 22.060 1.00 0.00 C +ATOM 650 HA ALA 43 33.248 29.388 22.388 1.00 0.00 H +ATOM 651 CB ALA 43 31.692 30.672 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.181 31.592 22.812 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.959 29.866 23.177 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.164 30.811 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.110 30.017 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.882 30.932 19.898 1.00 0.00 O +ATOM 657 N THR 44 31.798 28.746 20.423 1.00 0.00 N +ATOM 658 H THR 44 31.919 28.067 21.168 1.00 0.00 H +ATOM 659 CA THR 44 31.131 28.283 19.194 1.00 0.00 C +ATOM 660 HA THR 44 31.425 28.947 18.381 1.00 0.00 H +ATOM 661 CB THR 44 31.610 26.868 18.823 1.00 0.00 C +ATOM 662 HB THR 44 31.430 26.188 19.657 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.281 17.554 1.00 0.00 C +ATOM 664 HG21 THR 44 31.071 26.989 16.727 1.00 0.00 H +ATOM 665 HG22 THR 44 31.502 25.358 17.280 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.037 17.727 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.927 18.561 1.00 0.00 O +ATOM 668 HG1 THR 44 33.234 26.124 18.092 1.00 0.00 H +ATOM 669 C THR 44 29.605 28.381 19.326 1.00 0.00 C +ATOM 670 O THR 44 29.072 28.429 20.436 1.00 0.00 O +ATOM 671 N ILE 45 28.899 28.459 18.193 1.00 0.00 N +ATOM 672 H ILE 45 29.373 28.324 17.314 1.00 0.00 H +ATOM 673 CA ILE 45 27.479 28.840 18.123 1.00 0.00 C +ATOM 674 HA ILE 45 27.060 28.756 19.126 1.00 0.00 H +ATOM 675 CB ILE 45 27.332 30.316 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.271 30.529 17.778 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.069 31.232 18.677 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.151 31.108 18.586 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.833 32.282 18.498 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.768 30.969 19.687 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.759 30.692 16.252 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.018 31.752 16.233 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.657 30.140 15.968 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.506 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.730 30.935 15.529 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.975 31.017 14.269 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.530 29.452 14.955 1.00 0.00 H +ATOM 688 C ILE 45 26.629 27.925 17.243 1.00 0.00 C +ATOM 689 O ILE 45 27.122 27.343 16.276 1.00 0.00 O +ATOM 690 N ASP 46 25.329 27.880 17.545 1.00 0.00 N +ATOM 691 H ASP 46 25.032 28.297 18.421 1.00 0.00 H +ATOM 692 CA ASP 46 24.280 27.260 16.735 1.00 0.00 C +ATOM 693 HA ASP 46 24.584 27.263 15.684 1.00 0.00 H +ATOM 694 CB ASP 46 24.077 25.807 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.221 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.955 25.788 18.267 1.00 0.00 H +ATOM 697 CG ASP 46 22.841 25.170 16.544 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.475 17.281 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.561 25.439 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.957 28.050 16.850 1.00 0.00 C +ATOM 701 O ASP 46 22.507 28.363 17.955 1.00 0.00 O +ATOM 702 N ASP 47 22.309 28.333 15.716 1.00 0.00 N +ATOM 703 H ASP 47 22.678 27.944 14.861 1.00 0.00 H +ATOM 704 CA ASP 47 20.969 28.925 15.674 1.00 0.00 C +ATOM 705 HA ASP 47 20.875 29.653 16.485 1.00 0.00 H +ATOM 706 CB ASP 47 20.776 29.674 14.345 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.520 30.467 14.253 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.912 28.978 13.514 1.00 0.00 H +ATOM 709 CG ASP 47 19.366 30.275 14.271 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.485 29.674 13.613 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.064 31.235 15.016 1.00 0.00 O +ATOM 712 C ASP 47 19.852 27.876 15.878 1.00 0.00 C +ATOM 713 O ASP 47 18.842 28.184 16.513 1.00 0.00 O +ATOM 714 N ALA 48 20.002 26.636 15.396 1.00 0.00 N +ATOM 715 H ALA 48 20.917 26.342 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.934 25.626 15.412 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.054 14.931 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.425 14.583 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.276 23.967 15.053 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.686 14.514 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.674 24.756 13.580 1.00 0.00 H +ATOM 722 C ALA 48 18.524 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.929 17.099 1.00 0.00 O +ATOM 724 N THR 49 19.475 25.245 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.436 25.295 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.265 25.120 19.229 1.00 0.00 C +ATOM 727 HA THR 49 18.215 24.872 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.099 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.818 23.859 20.868 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.628 19.137 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.666 18.098 1.00 0.00 H +ATOM 732 HG22 THR 49 20.434 21.857 19.654 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.165 1.00 0.00 H +ATOM 734 OG1 THR 49 21.478 24.244 19.774 1.00 0.00 O +ATOM 735 HG1 THR 49 21.730 24.270 18.816 1.00 0.00 H +ATOM 736 C THR 49 19.505 26.429 19.997 1.00 0.00 C +ATOM 737 O THR 49 19.426 26.431 21.226 1.00 0.00 O +ATOM 738 N LYS 50 19.766 27.551 19.307 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.297 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.906 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.354 29.538 19.086 1.00 0.00 H +ATOM 742 CB LYS 50 18.564 29.472 20.292 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.160 28.830 21.074 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.701 30.459 20.736 1.00 0.00 H +ATOM 745 CG LYS 50 17.492 29.593 19.188 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.426 28.657 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.740 19.683 1.00 0.00 H +ATOM 748 CD LYS 50 17.704 30.775 18.223 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.703 31.695 18.813 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.688 17.723 1.00 0.00 H +ATOM 751 CE LYS 50 16.571 30.869 17.187 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.603 17.664 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.507 31.899 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.997 16.018 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.231 29.102 16.282 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.013 29.838 15.434 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.544 30.418 15.421 1.00 0.00 H +ATOM 758 C LYS 50 20.986 28.948 21.020 1.00 0.00 C +ATOM 759 O LYS 50 20.693 29.519 22.082 1.00 0.00 O +ATOM 760 N THR 51 22.146 28.292 20.857 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.962 19.926 1.00 0.00 H +ATOM 762 CA THR 51 23.055 27.904 21.959 1.00 0.00 C +ATOM 763 HA THR 51 22.763 28.429 22.858 1.00 0.00 H +ATOM 764 CB THR 51 22.885 26.404 22.277 1.00 0.00 C +ATOM 765 HB THR 51 22.979 25.814 21.354 1.00 0.00 H +ATOM 766 CG2 THR 51 23.850 25.861 23.317 1.00 0.00 C +ATOM 767 HG21 THR 51 23.812 26.474 24.218 1.00 0.00 H +ATOM 768 HG22 THR 51 23.577 24.841 23.588 1.00 0.00 H +ATOM 769 HG23 THR 51 24.876 25.835 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.633 26.168 22.876 1.00 0.00 O +ATOM 771 HG1 THR 51 20.954 26.250 22.182 1.00 0.00 H +ATOM 772 C THR 51 24.556 28.224 21.725 1.00 0.00 C +ATOM 773 O THR 51 25.085 28.000 20.641 1.00 0.00 O +ATOM 774 N PHE 52 25.248 28.694 22.772 1.00 0.00 N +ATOM 775 H PHE 52 24.712 28.952 23.592 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.779 22.880 1.00 0.00 C +ATOM 777 HA PHE 52 27.145 28.937 21.899 1.00 0.00 H +ATOM 778 CB PHE 52 27.149 29.952 23.820 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.476 29.958 24.659 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.735 24.193 1.00 0.00 H +ATOM 781 CG PHE 52 27.217 31.347 23.228 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.428 32.382 23.752 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.751 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.443 33.652 23.161 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.777 34.431 23.515 1.00 0.00 H +ATOM 786 CZ PHE 52 27.281 33.893 22.066 1.00 0.00 C +ATOM 787 HZ PHE 52 27.244 34.837 21.559 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.160 32.902 21.616 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.836 33.108 20.791 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.628 22.199 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.778 30.857 21.828 1.00 0.00 H +ATOM 792 C PHE 52 27.331 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.809 27.010 24.505 1.00 0.00 O +ATOM 794 N THR 53 28.487 27.066 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.851 27.522 22.147 1.00 0.00 H +ATOM 796 CA THR 53 29.281 25.929 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.048 25.798 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.936 24.611 22.782 1.00 0.00 C +ATOM 799 HB THR 53 29.512 23.804 23.241 1.00 0.00 H +ATOM 800 CG2 THR 53 27.461 24.225 22.862 1.00 0.00 C +ATOM 801 HG21 THR 53 26.865 24.906 22.254 1.00 0.00 H +ATOM 802 HG22 THR 53 27.326 23.209 22.494 1.00 0.00 H +ATOM 803 HG23 THR 53 27.124 24.270 23.898 1.00 0.00 H +ATOM 804 OG1 THR 53 29.273 24.680 21.420 1.00 0.00 O +ATOM 805 HG1 THR 53 28.756 24.016 20.955 1.00 0.00 H +ATOM 806 C THR 53 30.804 26.149 23.413 1.00 0.00 C +ATOM 807 O THR 53 31.287 27.022 22.688 1.00 0.00 O +ATOM 808 N THR 54 31.571 25.328 24.145 1.00 0.00 N +ATOM 809 H THR 54 31.111 24.655 24.737 1.00 0.00 H +ATOM 810 CA THR 54 33.043 25.241 24.080 1.00 0.00 C +ATOM 811 HA THR 54 33.416 26.036 23.436 1.00 0.00 H +ATOM 812 CB THR 54 33.668 25.452 25.473 1.00 0.00 C +ATOM 813 HB THR 54 33.373 24.632 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.195 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.517 26.335 24.770 1.00 0.00 H +ATOM 816 HG22 THR 54 35.553 25.813 26.470 1.00 0.00 H +ATOM 817 HG23 THR 54 35.642 24.609 25.193 1.00 0.00 H +ATOM 818 OG1 THR 54 33.203 26.662 26.026 1.00 0.00 O +ATOM 819 HG1 THR 54 33.876 26.992 26.625 1.00 0.00 H +ATOM 820 C THR 54 33.479 23.896 23.474 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.895 23.605 1.00 0.00 O +ATOM 822 N GLN 55 34.635 23.879 22.803 1.00 0.00 N +ATOM 823 H GLN 55 35.156 24.739 22.761 1.00 0.00 H +ATOM 824 CA GLN 55 35.264 22.693 22.195 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.165 21.639 1.00 0.00 H +ATOM 826 CB GLN 55 36.319 23.163 21.173 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.730 22.295 20.657 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.804 23.775 20.430 1.00 0.00 H +ATOM 829 CG GLN 55 37.482 23.993 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.096 24.713 22.482 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.177 23.334 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.249 24.773 20.686 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.326 24.397 19.523 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.831 25.902 21.034 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.408 26.355 20.331 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.724 26.275 21.962 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.679 23.225 1.00 0.00 C +ATOM 838 O GLN 55 36.112 22.047 24.363 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.413 22.804 1.00 0.00 N +ATOM 840 H GLU 56 35.794 20.234 21.832 1.00 0.00 H +ATOM 841 CA GLU 56 36.491 19.249 23.573 1.00 0.00 C +ATOM 842 HA GLU 56 36.152 19.337 24.602 1.00 0.00 H +ATOM 843 CB GLU 56 35.885 17.954 22.967 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.804 17.985 23.074 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.993 21.896 1.00 0.00 H +ATOM 846 CG GLU 56 36.403 16.582 23.463 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.459 15.931 22.591 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.423 16.669 23.812 1.00 0.00 H +ATOM 849 CD GLU 56 35.548 15.855 24.520 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.094 15.347 25.534 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.325 15.660 24.312 1.00 0.00 O +ATOM 852 C GLU 56 38.030 19.202 23.644 1.00 0.00 C +ATOM 853 O GLU 56 38.535 19.186 24.795 1.00 0.00 O +ATOM 854 OXT GLU 56 38.680 19.141 22.578 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.717 32.457 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.342 33.248 30.282 1.00 0.00 N +HETATM 857 C AN1 58 30.690 33.885 31.200 1.00 0.00 C +HETATM 858 C1 AN1 58 29.362 33.529 30.704 1.00 0.00 C +HETATM 859 H AN1 58 30.622 34.282 32.217 1.00 0.00 H +HETATM 860 H1 AN1 58 31.134 34.634 30.540 1.00 0.00 H +HETATM 861 H2 AN1 58 31.317 32.983 31.203 1.00 0.00 H +HETATM 862 N1 AZI 59 31.272 30.355 29.425 1.00 0.00 N +HETATM 863 N2 AZI 59 30.474 30.251 30.345 1.00 0.00 N +HETATM 864 N3 AZI 59 29.631 30.164 31.291 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 148 144 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 643 639 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_4_front_2.pdb b/tests/nsga2/intermediate_molecules/min_iter_4_front_2.pdb new file mode 100644 index 0000000..93ef165 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_4_front_2.pdb @@ -0,0 +1,1785 @@ +COMPND fitness: -6.2239 90.03083333333325 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 50.124 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.128 37.937 23.379 1.00 0.00 N +ATOM 2 H1 MET 1 15.115 38.352 24.304 1.00 0.00 H +ATOM 3 H2 MET 1 14.353 38.281 22.845 1.00 0.00 H +ATOM 4 H3 MET 1 15.989 38.231 22.950 1.00 0.00 H +ATOM 5 CA MET 1 15.114 36.469 23.492 1.00 0.00 C +ATOM 6 HA MET 1 14.154 36.172 23.930 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.810 22.104 1.00 0.00 C +ATOM 8 HB2 MET 1 14.395 36.081 21.502 1.00 0.00 H +ATOM 9 HB3 MET 1 16.151 36.200 21.624 1.00 0.00 H +ATOM 10 CG MET 1 15.368 34.269 22.154 1.00 0.00 C +ATOM 11 HG2 MET 1 16.256 34.008 22.740 1.00 0.00 H +ATOM 12 HG3 MET 1 14.490 33.864 22.670 1.00 0.00 H +ATOM 13 SD MET 1 15.523 33.454 20.540 1.00 0.00 S +ATOM 14 CE MET 1 13.825 33.570 19.902 1.00 0.00 C +ATOM 15 HE1 MET 1 13.514 34.612 19.846 1.00 0.00 H +ATOM 16 HE2 MET 1 13.786 33.136 18.902 1.00 0.00 H +ATOM 17 HE3 MET 1 13.144 33.019 20.553 1.00 0.00 H +ATOM 18 C MET 1 16.215 36.013 24.449 1.00 0.00 C +ATOM 19 O MET 1 17.372 36.346 24.223 1.00 0.00 O +ATOM 20 N GLN 2 15.871 35.224 25.474 1.00 0.00 N +ATOM 21 H GLN 2 14.897 35.087 25.675 1.00 0.00 H +ATOM 22 CA GLN 2 16.831 34.496 26.306 1.00 0.00 C +ATOM 23 HA GLN 2 17.643 35.162 26.593 1.00 0.00 H +ATOM 24 CB GLN 2 16.127 34.008 27.587 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.159 33.579 27.318 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.708 33.210 28.060 1.00 0.00 H +ATOM 27 CG GLN 2 15.903 35.114 28.632 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.477 35.983 28.143 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.171 34.756 29.353 1.00 0.00 H +ATOM 30 CD GLN 2 17.153 35.508 29.416 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.264 35.044 29.192 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.019 36.331 30.429 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.839 36.559 30.955 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.114 36.721 30.646 1.00 0.00 H +ATOM 35 C GLN 2 17.469 33.325 25.522 1.00 0.00 C +ATOM 36 O GLN 2 17.052 32.167 25.651 1.00 0.00 O +ATOM 37 N TYR 3 18.463 33.623 24.678 1.00 0.00 N +ATOM 38 H TYR 3 18.765 34.592 24.628 1.00 0.00 H +ATOM 39 CA TYR 3 19.234 32.609 23.954 1.00 0.00 C +ATOM 40 HA TYR 3 18.545 31.959 23.422 1.00 0.00 H +ATOM 41 CB TYR 3 20.170 33.262 22.941 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.877 33.900 23.476 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.723 32.438 22.497 1.00 0.00 H +ATOM 44 CG TYR 3 19.600 34.062 21.781 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.519 33.459 20.512 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.802 32.423 20.390 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.149 34.213 19.385 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.118 33.754 18.409 1.00 0.00 H +ATOM 49 CZ TYR 3 18.855 35.585 19.528 1.00 0.00 C +ATOM 50 OH TYR 3 18.517 36.324 18.441 1.00 0.00 O +ATOM 51 HH TYR 3 18.718 35.875 17.614 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.941 36.195 20.795 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.739 37.253 20.885 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.327 35.436 21.918 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.448 35.924 22.876 1.00 0.00 H +ATOM 56 C TYR 3 20.072 31.754 24.926 1.00 0.00 C +ATOM 57 O TYR 3 20.489 32.242 25.980 1.00 0.00 O +ATOM 58 N LYS 4 20.339 30.479 24.600 1.00 0.00 N +ATOM 59 H LYS 4 20.151 30.180 23.644 1.00 0.00 H +ATOM 60 CA LYS 4 20.960 29.479 25.496 1.00 0.00 C +ATOM 61 HA LYS 4 20.692 29.716 26.523 1.00 0.00 H +ATOM 62 CB LYS 4 20.389 28.078 25.169 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.359 27.961 24.086 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.082 27.325 25.544 1.00 0.00 H +ATOM 65 CG LYS 4 18.993 27.726 25.738 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.817 26.675 25.502 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.009 27.823 26.824 1.00 0.00 H +ATOM 68 CD LYS 4 17.809 28.534 25.173 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.798 29.537 25.609 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.962 28.643 24.097 1.00 0.00 H +ATOM 71 CE LYS 4 16.441 27.842 25.378 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.715 28.351 24.738 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.517 26.807 25.026 1.00 0.00 H +ATOM 74 NZ LYS 4 15.935 27.871 26.782 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.755 28.812 27.098 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.064 27.350 26.889 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.572 27.463 27.463 1.00 0.00 H +ATOM 78 C LYS 4 22.499 29.490 25.466 1.00 0.00 C +ATOM 79 O LYS 4 23.140 29.867 24.490 1.00 0.00 O +HETATM 80 N HX1 5 23.130 29.035 26.548 1.00 0.00 N +HETATM 81 CA HX1 5 24.591 28.856 26.679 1.00 0.00 C +HETATM 82 C HX1 5 24.878 27.688 27.631 1.00 0.00 C +HETATM 83 O HX1 5 24.428 27.708 28.777 1.00 0.00 O +HETATM 84 CB HX1 5 25.222 30.175 27.180 1.00 0.00 C +HETATM 85 CG HX1 5 26.737 30.247 27.288 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.646 29.286 26.930 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.420 31.336 27.850 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.719 30.994 27.776 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.886 29.754 27.285 1.00 0.00 N +HETATM 90 H HX1 5 22.559 28.844 27.370 1.00 0.00 H +HETATM 91 HA HX1 5 25.018 28.612 25.702 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.806 30.413 28.160 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.913 30.973 26.501 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.458 28.305 26.513 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.519 31.581 28.203 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.738 29.194 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.579 26.661 27.147 1.00 0.00 N +ATOM 98 H ILE 6 25.921 26.711 26.193 1.00 0.00 H +ATOM 99 CA ILE 6 25.970 25.469 27.917 1.00 0.00 C +ATOM 100 HA ILE 6 25.283 25.357 28.755 1.00 0.00 H +ATOM 101 CB ILE 6 25.813 24.203 27.035 1.00 0.00 C +ATOM 102 HB ILE 6 26.347 24.367 26.099 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.392 22.937 27.698 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.889 22.736 28.645 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.267 22.079 27.038 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.465 23.049 27.864 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.304 24.011 26.726 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.764 23.868 27.661 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.914 24.914 26.252 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.964 22.843 25.793 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.140 21.891 26.293 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.908 22.895 25.523 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.564 22.899 24.885 1.00 0.00 H +ATOM 114 C ILE 6 27.370 25.661 28.537 1.00 0.00 C +ATOM 115 O ILE 6 28.186 26.422 28.017 1.00 0.00 O +ATOM 116 N VAL 7 27.605 25.035 29.694 1.00 0.00 N +ATOM 117 H VAL 7 26.884 24.405 30.032 1.00 0.00 H +ATOM 118 CA VAL 7 28.769 25.251 30.572 1.00 0.00 C +ATOM 119 HA VAL 7 28.849 26.325 30.732 1.00 0.00 H +ATOM 120 CB VAL 7 28.470 24.592 31.936 1.00 0.00 C +ATOM 121 HB VAL 7 27.460 24.891 32.229 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.498 23.060 31.893 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.507 22.695 31.701 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.158 22.662 32.842 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.845 22.689 31.104 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.397 25.060 33.063 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.408 26.149 33.096 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.024 24.680 34.015 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.403 24.676 32.902 1.00 0.00 H +ATOM 130 C VAL 7 30.119 24.780 29.995 1.00 0.00 C +ATOM 131 O VAL 7 30.207 23.763 29.310 1.00 0.00 O +ATOM 132 N ARG 8 31.201 25.497 30.343 1.00 0.00 N +ATOM 133 H ARG 8 31.031 26.423 30.713 1.00 0.00 H +ATOM 134 CA ARG 8 32.608 25.082 30.154 1.00 0.00 C +ATOM 135 HA ARG 8 32.717 24.857 29.094 1.00 0.00 H +ATOM 136 CB ARG 8 33.575 26.241 30.501 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.546 25.995 30.072 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.247 27.151 30.004 1.00 0.00 H +ATOM 139 CG ARG 8 33.814 26.544 32.001 1.00 0.00 C +ATOM 140 HG2 ARG 8 34.126 25.632 32.506 1.00 0.00 H +ATOM 141 HG3 ARG 8 34.652 27.235 32.093 1.00 0.00 H +ATOM 142 CD ARG 8 32.636 27.142 32.778 1.00 0.00 C +ATOM 143 HD2 ARG 8 31.766 26.524 32.631 1.00 0.00 H +ATOM 144 HD3 ARG 8 32.851 27.100 33.836 1.00 0.00 H +ATOM 145 NE ARG 8 32.321 28.531 32.389 1.00 0.00 N +ATOM 146 HE ARG 8 31.868 28.645 31.483 1.00 0.00 H +ATOM 147 CZ ARG 8 32.417 29.619 33.139 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.818 30.717 32.782 1.00 0.00 N +ATOM 149 HH11 ARG 8 31.188 30.675 31.981 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.731 31.448 33.453 1.00 0.00 H +ATOM 151 NH2 ARG 8 33.086 29.637 34.256 1.00 0.00 N +ATOM 152 HH21 ARG 8 33.619 28.829 34.514 1.00 0.00 H +ATOM 153 HH22 ARG 8 33.065 30.431 34.886 1.00 0.00 H +ATOM 154 C ARG 8 32.993 23.796 30.906 1.00 0.00 C +ATOM 155 O ARG 8 32.490 23.532 31.997 1.00 0.00 O +ATOM 156 N GLY 9 33.997 23.086 30.385 1.00 0.00 N +ATOM 157 H GLY 9 34.336 23.350 29.474 1.00 0.00 H +ATOM 158 CA GLY 9 34.544 21.859 30.982 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.546 21.680 30.585 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.627 21.989 32.066 1.00 0.00 H +ATOM 161 C GLY 9 33.690 20.615 30.703 1.00 0.00 C +ATOM 162 O GLY 9 32.893 20.602 29.772 1.00 0.00 O +ATOM 163 N LYS 10 33.877 19.558 31.507 1.00 0.00 N +ATOM 164 H LYS 10 34.624 19.619 32.176 1.00 0.00 H +ATOM 165 CA LYS 10 33.145 18.277 31.372 1.00 0.00 C +ATOM 166 HA LYS 10 32.234 18.481 30.799 1.00 0.00 H +ATOM 167 CB LYS 10 34.004 17.293 30.544 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.660 17.868 29.891 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.633 16.707 31.215 1.00 0.00 H +ATOM 170 CG LYS 10 33.182 16.351 29.644 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.576 15.685 30.259 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.517 16.953 29.025 1.00 0.00 H +ATOM 173 CD LYS 10 34.095 15.518 28.728 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.765 16.189 28.186 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.693 14.843 29.337 1.00 0.00 H +ATOM 176 CE LYS 10 33.287 14.702 27.711 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.727 13.931 28.247 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.567 15.368 27.228 1.00 0.00 H +ATOM 179 NZ LYS 10 34.153 14.097 26.667 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.950 13.593 27.047 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.637 13.513 26.029 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.558 14.828 26.065 1.00 0.00 H +ATOM 183 C LYS 10 32.647 17.678 32.701 1.00 0.00 C +ATOM 184 O LYS 10 31.863 16.738 32.687 1.00 0.00 O +ATOM 185 N SER 11 33.082 18.223 33.848 1.00 0.00 N +ATOM 186 H SER 11 33.752 18.967 33.790 1.00 0.00 H +ATOM 187 CA SER 11 32.570 17.839 35.182 1.00 0.00 C +ATOM 188 HA SER 11 32.446 16.755 35.225 1.00 0.00 H +ATOM 189 CB SER 11 33.539 18.260 36.295 1.00 0.00 C +ATOM 190 HB2 SER 11 33.665 19.345 36.284 1.00 0.00 H +ATOM 191 HB3 SER 11 33.107 17.977 37.259 1.00 0.00 H +ATOM 192 OG SER 11 34.809 17.642 36.180 1.00 0.00 O +ATOM 193 HG SER 11 35.427 18.251 35.756 1.00 0.00 H +ATOM 194 C SER 11 31.199 18.462 35.496 1.00 0.00 C +ATOM 195 O SER 11 30.406 17.878 36.230 1.00 0.00 O +ATOM 196 N CYS 12 30.923 19.656 34.964 1.00 0.00 N +ATOM 197 H CYS 12 31.599 20.053 34.332 1.00 0.00 H +ATOM 198 CA CYS 12 29.611 20.301 35.006 1.00 0.00 C +ATOM 199 HA CYS 12 29.036 19.906 35.847 1.00 0.00 H +ATOM 200 CB CYS 12 29.796 21.821 35.196 1.00 0.00 C +ATOM 201 HB2 CYS 12 30.330 22.228 34.334 1.00 0.00 H +ATOM 202 HB3 CYS 12 28.812 22.284 35.254 1.00 0.00 H +ATOM 203 SG CYS 12 30.722 22.206 36.721 1.00 0.00 S +ATOM 204 HG CYS 12 29.845 23.085 37.226 1.00 0.00 H +ATOM 205 C CYS 12 28.846 19.994 33.710 1.00 0.00 C +ATOM 206 O CYS 12 29.461 19.846 32.657 1.00 0.00 O +ATOM 207 N LYS 13 27.505 19.956 33.760 1.00 0.00 N +ATOM 208 H LYS 13 27.067 20.025 34.666 1.00 0.00 H +ATOM 209 CA LYS 13 26.638 19.689 32.587 1.00 0.00 C +ATOM 210 HA LYS 13 27.243 19.869 31.686 1.00 0.00 H +ATOM 211 CB LYS 13 26.243 18.193 32.591 1.00 0.00 C +ATOM 212 HB2 LYS 13 27.073 17.620 33.007 1.00 0.00 H +ATOM 213 HB3 LYS 13 25.379 18.062 33.237 1.00 0.00 H +ATOM 214 CG LYS 13 25.952 17.630 31.186 1.00 0.00 C +ATOM 215 HG2 LYS 13 25.065 18.101 30.761 1.00 0.00 H +ATOM 216 HG3 LYS 13 26.801 17.853 30.536 1.00 0.00 H +ATOM 217 CD LYS 13 25.755 16.105 31.210 1.00 0.00 C +ATOM 218 HD2 LYS 13 25.746 15.739 30.181 1.00 0.00 H +ATOM 219 HD3 LYS 13 26.602 15.645 31.726 1.00 0.00 H +ATOM 220 CE LYS 13 24.441 15.690 31.887 1.00 0.00 C +ATOM 221 HE2 LYS 13 24.310 16.264 32.808 1.00 0.00 H +ATOM 222 HE3 LYS 13 23.614 15.945 31.214 1.00 0.00 H +ATOM 223 NZ LYS 13 24.411 14.238 32.200 1.00 0.00 N +ATOM 224 HZ1 LYS 13 25.113 13.979 32.890 1.00 0.00 H +ATOM 225 HZ2 LYS 13 23.525 13.972 32.618 1.00 0.00 H +ATOM 226 HZ3 LYS 13 24.608 13.675 31.375 1.00 0.00 H +ATOM 227 C LYS 13 25.442 20.651 32.462 1.00 0.00 C +ATOM 228 O LYS 13 24.474 20.361 31.772 1.00 0.00 O +ATOM 229 N GLY 14 25.489 21.778 33.176 1.00 0.00 N +ATOM 230 H GLY 14 26.334 21.976 33.674 1.00 0.00 H +ATOM 231 CA GLY 14 24.400 22.746 33.252 1.00 0.00 C +ATOM 232 HA2 GLY 14 23.453 22.214 33.347 1.00 0.00 H +ATOM 233 HA3 GLY 14 24.522 23.365 34.139 1.00 0.00 H +ATOM 234 C GLY 14 24.283 23.694 32.040 1.00 0.00 C +ATOM 235 O GLY 14 25.205 23.839 31.229 1.00 0.00 O +ATOM 236 N VAL 15 23.147 24.397 31.969 1.00 0.00 N +ATOM 237 H VAL 15 22.465 24.249 32.702 1.00 0.00 H +ATOM 238 CA VAL 15 22.785 25.364 30.936 1.00 0.00 C +ATOM 239 HA VAL 15 23.676 25.622 30.371 1.00 0.00 H +ATOM 240 CB VAL 15 21.782 24.726 29.948 1.00 0.00 C +ATOM 241 HB VAL 15 22.261 23.828 29.523 1.00 0.00 H +ATOM 242 CG1 VAL 15 20.463 24.268 30.608 1.00 0.00 C +ATOM 243 HG11 VAL 15 19.940 25.116 31.035 1.00 0.00 H +ATOM 244 HG12 VAL 15 19.832 23.789 29.857 1.00 0.00 H +ATOM 245 HG13 VAL 15 20.672 23.536 31.384 1.00 0.00 H +ATOM 246 CG2 VAL 15 21.431 25.652 28.775 1.00 0.00 C +ATOM 247 HG21 VAL 15 22.344 26.000 28.296 1.00 0.00 H +ATOM 248 HG22 VAL 15 20.849 25.095 28.039 1.00 0.00 H +ATOM 249 HG23 VAL 15 20.845 26.497 29.121 1.00 0.00 H +ATOM 250 C VAL 15 22.255 26.634 31.587 1.00 0.00 C +ATOM 251 O VAL 15 21.634 26.597 32.639 1.00 0.00 O +HETATM 252 N HY1 16 22.503 27.793 30.973 1.00 0.00 N +HETATM 253 CA HY1 16 21.907 29.109 31.309 1.00 0.00 C +HETATM 254 C HY1 16 21.626 29.889 30.030 1.00 0.00 C +HETATM 255 O HY1 16 21.803 29.384 28.934 1.00 0.00 O +HETATM 256 CB HY1 16 22.834 29.825 32.330 1.00 0.00 C +HETATM 257 CG HY1 16 24.188 30.197 31.783 1.00 0.00 C +HETATM 258 CD2 HY1 16 24.521 31.376 31.162 1.00 0.00 C +HETATM 259 ND1 HY1 16 25.320 29.420 31.809 1.00 0.00 N +HETATM 260 CE1 HY1 16 26.313 30.124 31.227 1.00 0.00 C +HETATM 261 NE2 HY1 16 25.875 31.326 30.803 1.00 0.00 N +HETATM 262 H HY1 16 23.045 27.766 30.100 1.00 0.00 H +HETATM 263 HA HY1 16 20.949 28.916 31.823 1.00 0.00 H +HETATM 264 HB2 HY1 16 22.325 30.741 32.671 1.00 0.00 H +HETATM 265 HB3 HY1 16 22.960 29.204 33.207 1.00 0.00 H +HETATM 266 HD1 HY1 16 25.420 28.523 32.269 1.00 0.00 H +HETATM 267 HD2 HY1 16 23.853 32.210 30.983 1.00 0.00 H +HETATM 268 HE1 HY1 16 27.347 29.785 31.131 1.00 0.00 H +ATOM 269 N THR 17 21.180 31.133 30.157 1.00 0.00 N +ATOM 270 H THR 17 21.010 31.533 31.074 1.00 0.00 H +ATOM 271 CA THR 17 20.738 32.013 29.045 1.00 0.00 C +ATOM 272 HA THR 17 21.170 31.561 28.112 1.00 0.00 H +ATOM 273 CB THR 17 19.231 32.020 28.904 1.00 0.00 C +ATOM 274 HB THR 17 18.946 32.674 28.050 1.00 0.00 H +ATOM 275 CG2 THR 17 18.569 30.688 28.614 1.00 0.00 C +ATOM 276 HG21 THR 17 18.780 29.952 29.396 1.00 0.00 H +ATOM 277 HG22 THR 17 17.520 30.750 28.519 1.00 0.00 H +ATOM 278 HG23 THR 17 18.943 30.252 27.683 1.00 0.00 H +ATOM 279 OG1 THR 17 18.633 32.525 30.065 1.00 0.00 O +ATOM 280 HG1 THR 17 18.590 33.499 29.935 1.00 0.00 H +ATOM 281 C THR 17 21.325 33.419 29.080 1.00 0.00 C +ATOM 282 O THR 17 21.830 33.841 30.105 1.00 0.00 O +HETATM 283 N HY2 18 21.199 34.131 27.962 1.00 0.00 N +HETATM 284 CA HY2 18 21.498 35.567 27.862 1.00 0.00 C +HETATM 285 C HY2 18 20.379 36.266 27.075 1.00 0.00 C +HETATM 286 O HY2 18 20.033 35.823 25.984 1.00 0.00 O +HETATM 287 CB HY2 18 22.831 35.804 27.169 1.00 0.00 C +HETATM 288 CG HY2 18 24.029 35.337 27.962 1.00 0.00 C +HETATM 289 CD2 HY2 18 24.563 34.072 27.954 1.00 0.00 C +HETATM 290 ND1 HY2 18 24.707 36.053 28.927 1.00 0.00 N +HETATM 291 CE1 HY2 18 25.640 35.241 29.456 1.00 0.00 C +HETATM 292 NE2 HY2 18 25.591 34.016 28.902 1.00 0.00 N +HETATM 293 H HY2 18 20.786 33.675 27.148 1.00 0.00 H +HETATM 294 HA HY2 18 21.526 36.010 28.879 1.00 0.00 H +HETATM 295 HB2 HY2 18 22.841 35.309 26.183 1.00 0.00 H +HETATM 296 HB3 HY2 18 22.951 36.890 26.989 1.00 0.00 H +HETATM 297 HD1 HY2 18 24.548 37.015 29.189 1.00 0.00 H +HETATM 298 HD2 HY2 18 24.231 33.250 27.332 1.00 0.00 H +HETATM 299 HE1 HY2 18 26.337 35.534 30.234 1.00 0.00 H +ATOM 300 N GLU 19 19.854 37.365 27.613 1.00 0.00 N +ATOM 301 H GLU 19 20.181 37.657 28.514 1.00 0.00 H +ATOM 302 CA GLU 19 18.861 38.214 26.953 1.00 0.00 C +ATOM 303 HA GLU 19 18.118 37.567 26.510 1.00 0.00 H +ATOM 304 CB GLU 19 18.201 39.105 28.007 1.00 0.00 C +ATOM 305 HB2 GLU 19 17.888 38.497 28.852 1.00 0.00 H +ATOM 306 HB3 GLU 19 18.937 39.829 28.382 1.00 0.00 H +ATOM 307 CG GLU 19 16.971 39.870 27.494 1.00 0.00 C +ATOM 308 HG2 GLU 19 16.593 40.510 28.305 1.00 0.00 H +ATOM 309 HG3 GLU 19 17.267 40.530 26.668 1.00 0.00 H +ATOM 310 CD GLU 19 15.891 38.899 27.051 1.00 0.00 C +ATOM 311 OE1 GLU 19 15.841 38.587 25.838 1.00 0.00 O +ATOM 312 OE2 GLU 19 15.168 38.381 27.921 1.00 0.00 O +ATOM 313 C GLU 19 19.511 39.051 25.841 1.00 0.00 C +ATOM 314 O GLU 19 20.557 39.666 26.070 1.00 0.00 O +ATOM 315 N ALA 20 18.896 39.088 24.651 1.00 0.00 N +ATOM 316 H ALA 20 18.064 38.515 24.532 1.00 0.00 H +ATOM 317 CA ALA 20 19.271 39.983 23.548 1.00 0.00 C +ATOM 318 HA ALA 20 19.436 40.983 23.947 1.00 0.00 H +ATOM 319 CB ALA 20 20.578 39.484 22.920 1.00 0.00 C +ATOM 320 HB1 ALA 20 20.424 38.505 22.460 1.00 0.00 H +ATOM 321 HB2 ALA 20 20.915 40.186 22.161 1.00 0.00 H +ATOM 322 HB3 ALA 20 21.364 39.400 23.667 1.00 0.00 H +ATOM 323 C ALA 20 18.183 40.055 22.465 1.00 0.00 C +ATOM 324 O ALA 20 17.362 39.144 22.322 1.00 0.00 O +ATOM 325 N VAL 21 18.199 41.109 21.636 1.00 0.00 N +ATOM 326 H VAL 21 18.866 41.851 21.810 1.00 0.00 H +ATOM 327 CA VAL 21 17.428 41.159 20.367 1.00 0.00 C +ATOM 328 HA VAL 21 16.429 40.760 20.548 1.00 0.00 H +ATOM 329 CB VAL 21 17.259 42.610 19.852 1.00 0.00 C +ATOM 330 HB VAL 21 16.584 42.573 18.993 1.00 0.00 H +ATOM 331 CG1 VAL 21 16.606 43.510 20.912 1.00 0.00 C +ATOM 332 HG11 VAL 21 17.283 43.665 21.747 1.00 0.00 H +ATOM 333 HG12 VAL 21 16.368 44.469 20.461 1.00 0.00 H +ATOM 334 HG13 VAL 21 15.686 43.051 21.264 1.00 0.00 H +ATOM 335 CG2 VAL 21 18.574 43.260 19.386 1.00 0.00 C +ATOM 336 HG21 VAL 21 18.969 42.728 18.522 1.00 0.00 H +ATOM 337 HG22 VAL 21 18.382 44.286 19.080 1.00 0.00 H +ATOM 338 HG23 VAL 21 19.313 43.256 20.184 1.00 0.00 H +ATOM 339 C VAL 21 18.056 40.311 19.265 1.00 0.00 C +ATOM 340 O VAL 21 17.372 39.908 18.335 1.00 0.00 O +ATOM 341 N ASP 22 19.356 40.045 19.380 1.00 0.00 N +ATOM 342 H ASP 22 19.840 40.370 20.200 1.00 0.00 H +ATOM 343 CA ASP 22 20.203 39.414 18.367 1.00 0.00 C +ATOM 344 HA ASP 22 19.591 38.740 17.749 1.00 0.00 H +ATOM 345 CB ASP 22 20.808 40.497 17.447 1.00 0.00 C +ATOM 346 HB2 ASP 22 20.011 40.913 16.813 1.00 0.00 H +ATOM 347 HB3 ASP 22 21.216 41.310 18.079 1.00 0.00 H +ATOM 348 CG ASP 22 21.904 39.924 16.576 1.00 0.00 C +ATOM 349 OD1 ASP 22 23.061 40.332 16.776 1.00 0.00 O +ATOM 350 OD2 ASP 22 21.645 38.936 15.850 1.00 0.00 O +ATOM 351 C ASP 22 21.312 38.577 19.024 1.00 0.00 C +ATOM 352 O ASP 22 21.786 38.862 20.125 1.00 0.00 O +ATOM 353 N TRP 23 21.758 37.546 18.320 1.00 0.00 N +ATOM 354 H TRP 23 21.457 37.488 17.356 1.00 0.00 H +ATOM 355 CA TRP 23 22.777 36.618 18.774 1.00 0.00 C +ATOM 356 HA TRP 23 22.545 36.338 19.799 1.00 0.00 H +ATOM 357 CB TRP 23 22.654 35.377 17.900 1.00 0.00 C +ATOM 358 HB2 TRP 23 21.626 35.019 17.952 1.00 0.00 H +ATOM 359 HB3 TRP 23 22.841 35.665 16.862 1.00 0.00 H +ATOM 360 CG TRP 23 23.539 34.241 18.269 1.00 0.00 C +ATOM 361 CD1 TRP 23 24.465 33.691 17.461 1.00 0.00 C +ATOM 362 HD1 TRP 23 24.709 34.023 16.459 1.00 0.00 H +ATOM 363 NE1 TRP 23 25.028 32.616 18.105 1.00 0.00 N +ATOM 364 HE1 TRP 23 25.775 32.071 17.710 1.00 0.00 H +ATOM 365 CE2 TRP 23 24.471 32.396 19.344 1.00 0.00 C +ATOM 366 CZ2 TRP 23 24.645 31.401 20.312 1.00 0.00 C +ATOM 367 HZ2 TRP 23 25.308 30.566 20.135 1.00 0.00 H +ATOM 368 CH2 TRP 23 23.967 31.535 21.529 1.00 0.00 C +ATOM 369 HH2 TRP 23 24.088 30.820 22.312 1.00 0.00 H +ATOM 370 CZ3 TRP 23 23.194 32.666 21.795 1.00 0.00 C +ATOM 371 HZ3 TRP 23 22.789 32.798 22.788 1.00 0.00 H +ATOM 372 CE3 TRP 23 22.960 33.611 20.781 1.00 0.00 C +ATOM 373 HE3 TRP 23 22.305 34.442 20.972 1.00 0.00 H +ATOM 374 CD2 TRP 23 23.577 33.487 19.517 1.00 0.00 C +ATOM 375 C TRP 23 24.201 37.200 18.775 1.00 0.00 C +ATOM 376 O TRP 23 24.979 36.883 19.677 1.00 0.00 O +ATOM 377 N ALA 24 24.536 38.109 17.850 1.00 0.00 N +ATOM 378 H ALA 24 23.837 38.430 17.182 1.00 0.00 H +ATOM 379 CA ALA 24 25.826 38.805 17.840 1.00 0.00 C +ATOM 380 HA ALA 24 26.592 38.098 18.148 1.00 0.00 H +ATOM 381 CB ALA 24 26.163 39.206 16.400 1.00 0.00 C +ATOM 382 HB1 ALA 24 25.465 39.956 16.034 1.00 0.00 H +ATOM 383 HB2 ALA 24 27.173 39.612 16.353 1.00 0.00 H +ATOM 384 HB3 ALA 24 26.113 38.333 15.751 1.00 0.00 H +ATOM 385 C ALA 24 25.896 39.988 18.834 1.00 0.00 C +ATOM 386 O ALA 24 26.984 40.488 19.139 1.00 0.00 O +ATOM 387 N GLU 25 24.765 40.408 19.414 1.00 0.00 N +ATOM 388 H GLU 25 23.891 40.105 18.996 1.00 0.00 H +ATOM 389 CA GLU 25 24.725 41.188 20.666 1.00 0.00 C +ATOM 390 HA GLU 25 25.581 41.863 20.687 1.00 0.00 H +ATOM 391 CB GLU 25 23.451 42.045 20.730 1.00 0.00 C +ATOM 392 HB2 GLU 25 22.582 41.422 20.516 1.00 0.00 H +ATOM 393 HB3 GLU 25 23.342 42.425 21.740 1.00 0.00 H +ATOM 394 CG GLU 25 23.468 43.249 19.777 1.00 0.00 C +ATOM 395 HG2 GLU 25 23.540 42.881 18.748 1.00 0.00 H +ATOM 396 HG3 GLU 25 22.512 43.776 19.855 1.00 0.00 H +ATOM 397 CD GLU 25 24.619 44.199 20.081 1.00 0.00 C +ATOM 398 OE1 GLU 25 24.524 44.975 21.065 1.00 0.00 O +ATOM 399 OE2 GLU 25 25.648 44.107 19.362 1.00 0.00 O +ATOM 400 C GLU 25 24.874 40.287 21.906 1.00 0.00 C +ATOM 401 O GLU 25 25.688 40.579 22.784 1.00 0.00 O +ATOM 402 N ALA 26 24.201 39.125 21.956 1.00 0.00 N +ATOM 403 H ALA 26 23.518 38.919 21.232 1.00 0.00 H +ATOM 404 CA ALA 26 24.463 38.107 22.990 1.00 0.00 C +ATOM 405 HA ALA 26 24.293 38.571 23.963 1.00 0.00 H +ATOM 406 CB ALA 26 23.482 36.944 22.834 1.00 0.00 C +ATOM 407 HB1 ALA 26 23.667 36.421 21.901 1.00 0.00 H +ATOM 408 HB2 ALA 26 23.605 36.247 23.660 1.00 0.00 H +ATOM 409 HB3 ALA 26 22.458 37.314 22.841 1.00 0.00 H +ATOM 410 C ALA 26 25.930 37.609 22.973 1.00 0.00 C +ATOM 411 O ALA 26 26.453 37.180 24.015 1.00 0.00 O +ATOM 412 N GLU 27 26.614 37.710 21.825 1.00 0.00 N +ATOM 413 H GLU 27 26.089 37.904 20.980 1.00 0.00 H +ATOM 414 CA GLU 27 28.052 37.490 21.713 1.00 0.00 C +ATOM 415 HA GLU 27 28.210 36.457 21.940 1.00 0.00 H +ATOM 416 CB GLU 27 28.583 37.614 20.270 1.00 0.00 C +ATOM 417 HB2 GLU 27 27.924 37.058 19.610 1.00 0.00 H +ATOM 418 HB3 GLU 27 28.620 38.658 19.970 1.00 0.00 H +ATOM 419 CG GLU 27 29.988 36.996 20.197 1.00 0.00 C +ATOM 420 HG2 GLU 27 30.676 37.588 20.819 1.00 0.00 H +ATOM 421 HG3 GLU 27 29.956 35.983 20.634 1.00 0.00 H +ATOM 422 CD GLU 27 30.513 36.934 18.769 1.00 0.00 C +ATOM 423 OE1 GLU 27 30.943 38.000 18.278 1.00 0.00 O +ATOM 424 OE2 GLU 27 30.501 35.827 18.191 1.00 0.00 O +ATOM 425 C GLU 27 28.828 38.374 22.706 1.00 0.00 C +ATOM 426 O GLU 27 29.568 37.849 23.548 1.00 0.00 O +ATOM 427 N LYS 28 28.541 39.682 22.661 1.00 0.00 N +ATOM 428 H LYS 28 27.831 39.957 21.987 1.00 0.00 H +ATOM 429 CA LYS 28 29.121 40.758 23.481 1.00 0.00 C +ATOM 430 HA LYS 28 30.206 40.658 23.479 1.00 0.00 H +ATOM 431 CB LYS 28 28.761 42.131 22.873 1.00 0.00 C +ATOM 432 HB2 LYS 28 27.685 42.299 22.951 1.00 0.00 H +ATOM 433 HB3 LYS 28 29.264 42.909 23.451 1.00 0.00 H +ATOM 434 CG LYS 28 29.172 42.274 21.396 1.00 0.00 C +ATOM 435 HG2 LYS 28 30.244 42.100 21.301 1.00 0.00 H +ATOM 436 HG3 LYS 28 28.646 41.528 20.802 1.00 0.00 H +ATOM 437 CD LYS 28 28.833 43.668 20.845 1.00 0.00 C +ATOM 438 HD2 LYS 28 27.793 43.910 21.048 1.00 0.00 H +ATOM 439 HD3 LYS 28 29.453 44.406 21.356 1.00 0.00 H +ATOM 440 CE LYS 28 29.082 43.754 19.331 1.00 0.00 C +ATOM 441 HE2 LYS 28 29.159 44.812 19.054 1.00 0.00 H +ATOM 442 HE3 LYS 28 30.045 43.295 19.106 1.00 0.00 H +ATOM 443 NZ LYS 28 27.999 43.108 18.548 1.00 0.00 N +ATOM 444 HZ1 LYS 28 27.111 43.575 18.756 1.00 0.00 H +ATOM 445 HZ2 LYS 28 28.147 43.172 17.552 1.00 0.00 H +ATOM 446 HZ3 LYS 28 27.858 42.139 18.817 1.00 0.00 H +ATOM 447 C LYS 28 28.671 40.699 24.942 1.00 0.00 C +ATOM 448 O LYS 28 29.516 40.726 25.833 1.00 0.00 O +ATOM 449 N PHE 29 27.376 40.527 25.225 1.00 0.00 N +ATOM 450 H PHE 29 26.709 40.552 24.455 1.00 0.00 H +ATOM 451 CA PHE 29 26.873 40.474 26.615 1.00 0.00 C +ATOM 452 HA PHE 29 27.188 41.382 27.129 1.00 0.00 H +ATOM 453 CB PHE 29 25.335 40.437 26.615 1.00 0.00 C +ATOM 454 HB2 PHE 29 25.018 39.493 26.171 1.00 0.00 H +ATOM 455 HB3 PHE 29 24.990 40.451 27.649 1.00 0.00 H +ATOM 456 CG PHE 29 24.643 41.578 25.884 1.00 0.00 C +ATOM 457 CD1 PHE 29 23.461 41.323 25.164 1.00 0.00 C +ATOM 458 HD1 PHE 29 23.037 40.333 25.146 1.00 0.00 H +ATOM 459 CE1 PHE 29 22.822 42.359 24.462 1.00 0.00 C +ATOM 460 HE1 PHE 29 21.922 42.155 23.902 1.00 0.00 H +ATOM 461 CZ PHE 29 23.361 43.658 24.478 1.00 0.00 C +ATOM 462 HZ PHE 29 22.885 44.450 23.917 1.00 0.00 H +ATOM 463 CE2 PHE 29 24.520 43.928 25.225 1.00 0.00 C +ATOM 464 HE2 PHE 29 24.924 44.927 25.252 1.00 0.00 H +ATOM 465 CD2 PHE 29 25.155 42.893 25.932 1.00 0.00 C +ATOM 466 HD2 PHE 29 26.038 43.124 26.504 1.00 0.00 H +ATOM 467 C PHE 29 27.437 39.300 27.430 1.00 0.00 C +ATOM 468 O PHE 29 27.531 39.370 28.654 1.00 0.00 O +ATOM 469 N THR 30 27.865 38.222 26.770 1.00 0.00 N +ATOM 470 H THR 30 27.724 38.182 25.766 1.00 0.00 H +ATOM 471 CA THR 30 28.618 37.144 27.427 1.00 0.00 C +ATOM 472 HA THR 30 28.163 36.900 28.387 1.00 0.00 H +ATOM 473 CB THR 30 28.621 35.900 26.536 1.00 0.00 C +ATOM 474 HB THR 30 29.132 36.191 25.639 1.00 0.00 H +ATOM 475 CG2 THR 30 29.346 34.706 27.138 1.00 0.00 C +ATOM 476 HG21 THR 30 28.984 34.522 28.133 1.00 0.00 H +ATOM 477 HG22 THR 30 29.193 33.814 26.546 1.00 0.00 H +ATOM 478 HG23 THR 30 30.428 34.887 27.191 1.00 0.00 H +ATOM 479 OG1 THR 30 27.298 35.471 26.245 1.00 0.00 O +ATOM 480 HG1 THR 30 26.888 36.131 25.657 1.00 0.00 H +ATOM 481 C THR 30 30.081 37.537 27.695 1.00 0.00 C +ATOM 482 O THR 30 30.624 37.146 28.731 1.00 0.00 O +ATOM 483 N LYS 31 30.720 38.306 26.804 1.00 0.00 N +ATOM 484 H LYS 31 30.198 38.651 26.014 1.00 0.00 H +ATOM 485 CA LYS 31 32.070 38.835 27.005 1.00 0.00 C +ATOM 486 HA LYS 31 32.733 38.032 27.315 1.00 0.00 H +ATOM 487 CB LYS 31 32.647 39.415 25.683 1.00 0.00 C +ATOM 488 HB2 LYS 31 31.948 40.110 25.246 1.00 0.00 H +ATOM 489 HB3 LYS 31 33.566 39.953 25.914 1.00 0.00 H +ATOM 490 CG LYS 31 32.996 38.312 24.666 1.00 0.00 C +ATOM 491 HG2 LYS 31 33.730 37.640 25.106 1.00 0.00 H +ATOM 492 HG3 LYS 31 32.107 37.731 24.423 1.00 0.00 H +ATOM 493 CD LYS 31 33.567 38.923 23.384 1.00 0.00 C +ATOM 494 HD2 LYS 31 32.778 39.479 22.879 1.00 0.00 H +ATOM 495 HD3 LYS 31 34.355 39.629 23.638 1.00 0.00 H +ATOM 496 CE LYS 31 34.151 37.892 22.391 1.00 0.00 C +ATOM 497 HE2 LYS 31 33.409 37.129 22.159 1.00 0.00 H +ATOM 498 HE3 LYS 31 34.379 38.403 21.457 1.00 0.00 H +ATOM 499 NZ LYS 31 35.390 37.255 22.898 1.00 0.00 N +ATOM 500 HZ1 LYS 31 35.201 36.470 23.500 1.00 0.00 H +ATOM 501 HZ2 LYS 31 35.932 36.859 22.126 1.00 0.00 H +ATOM 502 HZ3 LYS 31 35.985 37.896 23.428 1.00 0.00 H +ATOM 503 C LYS 31 32.129 39.879 28.130 1.00 0.00 C +ATOM 504 O LYS 31 33.139 39.914 28.834 1.00 0.00 O +ATOM 505 N ALA 32 31.036 40.609 28.382 1.00 0.00 N +ATOM 506 H ALA 32 30.297 40.611 27.689 1.00 0.00 H +ATOM 507 CA ALA 32 30.856 41.387 29.608 1.00 0.00 C +ATOM 508 HA ALA 32 31.679 42.095 29.692 1.00 0.00 H +ATOM 509 CB ALA 32 29.558 42.200 29.527 1.00 0.00 C +ATOM 510 HB1 ALA 32 28.691 41.544 29.473 1.00 0.00 H +ATOM 511 HB2 ALA 32 29.463 42.823 30.421 1.00 0.00 H +ATOM 512 HB3 ALA 32 29.578 42.846 28.650 1.00 0.00 H +ATOM 513 C ALA 32 30.927 40.489 30.858 1.00 0.00 C +ATOM 514 O ALA 32 31.924 40.546 31.574 1.00 0.00 O +ATOM 515 N LYN 33 29.996 39.531 31.025 1.00 0.00 N +ATOM 516 H LYN 33 29.190 39.542 30.415 1.00 0.00 H +ATOM 517 CA LYN 33 30.009 38.573 32.151 1.00 0.00 C +ATOM 518 HA LYN 33 29.910 39.148 33.071 1.00 0.00 H +ATOM 519 CB LYN 33 28.774 37.649 32.038 1.00 0.00 C +ATOM 520 HB2 LYN 33 27.879 38.255 31.901 1.00 0.00 H +ATOM 521 HB3 LYN 33 28.890 37.020 31.159 1.00 0.00 H +ATOM 522 CG LYN 33 28.554 36.757 33.275 1.00 0.00 C +ATOM 523 HG2 LYN 33 29.439 36.152 33.441 1.00 0.00 H +ATOM 524 HG3 LYN 33 28.421 37.387 34.152 1.00 0.00 H +ATOM 525 CD LYN 33 27.373 35.776 33.182 1.00 0.00 C +ATOM 526 HD2 LYN 33 27.409 35.248 32.236 1.00 0.00 H +ATOM 527 HD3 LYN 33 27.480 35.041 33.977 1.00 0.00 H +ATOM 528 CE LYN 33 26.005 36.448 33.325 1.00 0.00 C +ATOM 529 HE2 LYN 33 26.005 37.059 34.229 1.00 0.00 H +ATOM 530 HE3 LYN 33 25.827 37.088 32.462 1.00 0.00 H +ATOM 531 NZ LYN 33 24.926 35.449 33.420 1.00 0.00 N +ATOM 532 HZ2 LYN 33 24.037 35.924 33.515 1.00 0.00 H +ATOM 533 HZ3 LYN 33 24.894 34.884 32.590 1.00 0.00 H +ATOM 534 C LYN 33 31.326 37.768 32.264 1.00 0.00 C +ATOM 535 O LYN 33 31.650 37.212 33.313 1.00 0.00 O +ATOM 536 N ALA 34 32.102 37.650 31.186 1.00 0.00 N +ATOM 537 H ALA 34 31.786 38.093 30.336 1.00 0.00 H +ATOM 538 CA ALA 34 33.415 37.025 31.197 1.00 0.00 C +ATOM 539 HA ALA 34 33.379 36.199 31.902 1.00 0.00 H +ATOM 540 CB ALA 34 33.660 36.419 29.822 1.00 0.00 C +ATOM 541 HB1 ALA 34 33.759 37.224 29.100 1.00 0.00 H +ATOM 542 HB2 ALA 34 34.569 35.830 29.857 1.00 0.00 H +ATOM 543 HB3 ALA 34 32.833 35.773 29.533 1.00 0.00 H +ATOM 544 C ALA 34 34.561 37.964 31.644 1.00 0.00 C +ATOM 545 O ALA 34 35.485 37.474 32.295 1.00 0.00 O +ATOM 546 N ASN 35 34.515 39.269 31.348 1.00 0.00 N +ATOM 547 H ASN 35 33.732 39.616 30.804 1.00 0.00 H +ATOM 548 CA ASN 35 35.446 40.284 31.873 1.00 0.00 C +ATOM 549 HA ASN 35 36.435 39.832 31.976 1.00 0.00 H +ATOM 550 CB ASN 35 35.582 41.433 30.859 1.00 0.00 C +ATOM 551 HB2 ASN 35 34.603 41.733 30.493 1.00 0.00 H +ATOM 552 HB3 ASN 35 36.033 42.295 31.352 1.00 0.00 H +ATOM 553 CG ASN 35 36.493 41.030 29.719 1.00 0.00 C +ATOM 554 OD1 ASN 35 37.698 40.971 29.868 1.00 0.00 O +ATOM 555 ND2 ASN 35 35.956 40.693 28.578 1.00 0.00 N +ATOM 556 HD21 ASN 35 36.601 40.354 27.860 1.00 0.00 H +ATOM 557 HD22 ASN 35 34.954 40.631 28.488 1.00 0.00 H +ATOM 558 C ASN 35 35.078 40.777 33.276 1.00 0.00 C +ATOM 559 O ASN 35 35.967 41.126 34.052 1.00 0.00 O +ATOM 560 N ASP 36 33.802 40.685 33.673 1.00 0.00 N +ATOM 561 H ASP 36 33.078 40.563 32.970 1.00 0.00 H +ATOM 562 CA ASP 36 33.357 40.843 35.067 1.00 0.00 C +ATOM 563 HA ASP 36 33.630 41.847 35.410 1.00 0.00 H +ATOM 564 CB ASP 36 31.839 40.739 35.150 1.00 0.00 C +ATOM 565 HB2 ASP 36 31.563 39.728 34.867 1.00 0.00 H +ATOM 566 HB3 ASP 36 31.542 40.818 36.195 1.00 0.00 H +ATOM 567 CG ASP 36 30.985 41.711 34.324 1.00 0.00 C +ATOM 568 OD1 ASP 36 31.462 42.836 34.035 1.00 0.00 O +ATOM 569 OD2 ASP 36 29.825 41.345 33.996 1.00 0.00 O +ATOM 570 C ASP 36 34.066 39.828 35.995 1.00 0.00 C +ATOM 571 O ASP 36 34.498 40.176 37.098 1.00 0.00 O +ATOM 572 N LYS 37 34.277 38.580 35.528 1.00 0.00 N +ATOM 573 H LYS 37 33.863 38.350 34.636 1.00 0.00 H +ATOM 574 CA LYS 37 35.150 37.580 36.183 1.00 0.00 C +ATOM 575 HA LYS 37 35.130 37.789 37.253 1.00 0.00 H +ATOM 576 CB LYS 37 34.565 36.152 36.027 1.00 0.00 C +ATOM 577 HB2 LYS 37 35.078 35.490 36.724 1.00 0.00 H +ATOM 578 HB3 LYS 37 33.508 36.149 36.288 1.00 0.00 H +ATOM 579 CG LYS 37 34.759 35.601 34.608 1.00 0.00 C +ATOM 580 HG2 LYS 37 34.139 36.177 33.928 1.00 0.00 H +ATOM 581 HG3 LYS 37 35.798 35.735 34.318 1.00 0.00 H +ATOM 582 CD LYS 37 34.436 34.122 34.422 1.00 0.00 C +ATOM 583 HD2 LYS 37 34.578 33.610 35.373 1.00 0.00 H +ATOM 584 HD3 LYS 37 33.395 34.014 34.154 1.00 0.00 H +ATOM 585 CE LYS 37 35.328 33.472 33.330 1.00 0.00 C +ATOM 586 HE2 LYS 37 36.315 33.292 33.762 1.00 0.00 H +ATOM 587 HE3 LYS 37 34.983 32.454 33.128 1.00 0.00 H +ATOM 588 NZ LYS 37 35.470 34.267 32.074 1.00 0.00 N +ATOM 589 HZ1 LYS 37 35.901 35.166 32.277 1.00 0.00 H +ATOM 590 HZ2 LYS 37 36.069 33.816 31.389 1.00 0.00 H +ATOM 591 HZ3 LYS 37 34.567 34.433 31.674 1.00 0.00 H +ATOM 592 C LYS 37 36.641 37.666 35.797 1.00 0.00 C +ATOM 593 O LYS 37 37.388 36.717 36.024 1.00 0.00 O +ATOM 594 N GLY 38 37.093 38.753 35.163 1.00 0.00 N +ATOM 595 H GLY 38 36.427 39.500 35.014 1.00 0.00 H +ATOM 596 CA GLY 38 38.497 39.081 34.900 1.00 0.00 C +ATOM 597 HA2 GLY 38 38.673 40.099 35.250 1.00 0.00 H +ATOM 598 HA3 GLY 38 39.136 38.422 35.493 1.00 0.00 H +ATOM 599 C GLY 38 38.992 39.003 33.451 1.00 0.00 C +ATOM 600 O GLY 38 39.908 39.749 33.113 1.00 0.00 O +ATOM 601 N ARG 39 38.439 38.123 32.592 1.00 0.00 N +ATOM 602 H ARG 39 37.620 37.630 32.924 1.00 0.00 H +ATOM 603 CA ARG 39 38.850 37.918 31.183 1.00 0.00 C +ATOM 604 HA ARG 39 38.819 38.900 30.702 1.00 0.00 H +ATOM 605 CB ARG 39 40.315 37.408 31.055 1.00 0.00 C +ATOM 606 HB2 ARG 39 40.570 37.429 29.993 1.00 0.00 H +ATOM 607 HB3 ARG 39 40.992 38.115 31.533 1.00 0.00 H +ATOM 608 CG ARG 39 40.642 35.990 31.575 1.00 0.00 C +ATOM 609 HG2 ARG 39 40.011 35.274 31.049 1.00 0.00 H +ATOM 610 HG3 ARG 39 41.676 35.759 31.313 1.00 0.00 H +ATOM 611 CD ARG 39 40.486 35.825 33.102 1.00 0.00 C +ATOM 612 HD2 ARG 39 41.184 36.504 33.600 1.00 0.00 H +ATOM 613 HD3 ARG 39 39.476 36.100 33.403 1.00 0.00 H +ATOM 614 NE ARG 39 40.739 34.451 33.582 1.00 0.00 N +ATOM 615 HE ARG 39 41.505 34.326 34.228 1.00 0.00 H +ATOM 616 CZ ARG 39 39.961 33.401 33.419 1.00 0.00 C +ATOM 617 NH1 ARG 39 38.912 33.425 32.650 1.00 0.00 N +ATOM 618 HH11 ARG 39 38.753 34.219 32.059 1.00 0.00 H +ATOM 619 HH12 ARG 39 38.395 32.553 32.564 1.00 0.00 H +ATOM 620 NH2 ARG 39 40.208 32.279 34.029 1.00 0.00 N +ATOM 621 HH21 ARG 39 41.021 32.194 34.618 1.00 0.00 H +ATOM 622 HH22 ARG 39 39.586 31.492 33.869 1.00 0.00 H +ATOM 623 C ARG 39 37.906 37.010 30.382 1.00 0.00 C +ATOM 624 O ARG 39 37.450 35.970 30.889 1.00 0.00 O +ATOM 625 N ASP 40 37.643 37.373 29.123 1.00 0.00 N +ATOM 626 H ASP 40 38.049 38.236 28.768 1.00 0.00 H +ATOM 627 CA ASP 40 36.914 36.559 28.147 1.00 0.00 C +ATOM 628 HA ASP 40 36.250 35.909 28.701 1.00 0.00 H +ATOM 629 CB ASP 40 36.024 37.438 27.250 1.00 0.00 C +ATOM 630 HB2 ASP 40 35.359 36.797 26.672 1.00 0.00 H +ATOM 631 HB3 ASP 40 35.373 38.034 27.885 1.00 0.00 H +ATOM 632 CG ASP 40 36.757 38.385 26.309 1.00 0.00 C +ATOM 633 OD1 ASP 40 37.565 39.185 26.826 1.00 0.00 O +ATOM 634 OD2 ASP 40 36.426 38.367 25.105 1.00 0.00 O +ATOM 635 C ASP 40 37.774 35.579 27.330 1.00 0.00 C +ATOM 636 O ASP 40 38.983 35.480 27.496 1.00 0.00 O +ATOM 637 N GLY 41 37.089 34.803 26.488 1.00 0.00 N +ATOM 638 H GLY 41 36.101 34.991 26.421 1.00 0.00 H +ATOM 639 CA GLY 41 37.618 33.880 25.478 1.00 0.00 C +ATOM 640 HA2 GLY 41 38.494 34.335 24.987 1.00 0.00 H +ATOM 641 HA3 GLY 41 37.896 32.927 25.956 1.00 0.00 H +ATOM 642 C GLY 41 36.528 33.613 24.424 1.00 0.00 C +ATOM 643 O GLY 41 35.445 34.207 24.475 1.00 0.00 O +ATOM 644 N GLU 42 36.788 32.709 23.482 1.00 0.00 N +ATOM 645 H GLU 42 37.670 32.237 23.523 1.00 0.00 H +ATOM 646 CA GLU 42 35.905 32.412 22.347 1.00 0.00 C +ATOM 647 HA GLU 42 35.125 33.167 22.344 1.00 0.00 H +ATOM 648 CB GLU 42 36.664 32.525 21.011 1.00 0.00 C +ATOM 649 HB2 GLU 42 37.366 31.695 20.944 1.00 0.00 H +ATOM 650 HB3 GLU 42 35.944 32.414 20.201 1.00 0.00 H +ATOM 651 CG GLU 42 37.443 33.834 20.782 1.00 0.00 C +ATOM 652 HG2 GLU 42 38.311 33.827 21.446 1.00 0.00 H +ATOM 653 HG3 GLU 42 37.826 33.837 19.759 1.00 0.00 H +ATOM 654 CD GLU 42 36.645 35.123 21.033 1.00 0.00 C +ATOM 655 OE1 GLU 42 35.399 35.099 21.148 1.00 0.00 O +ATOM 656 OE2 GLU 42 37.273 36.191 21.218 1.00 0.00 O +ATOM 657 C GLU 42 35.155 31.079 22.449 1.00 0.00 C +ATOM 658 O GLU 42 35.545 30.177 23.201 1.00 0.00 O +ATOM 659 N ARG 43 34.045 30.983 21.696 1.00 0.00 N +ATOM 660 H ARG 43 33.859 31.729 21.028 1.00 0.00 H +ATOM 661 CA ARG 43 33.015 29.940 21.796 1.00 0.00 C +ATOM 662 HA ARG 43 33.495 28.981 22.001 1.00 0.00 H +ATOM 663 CB ARG 43 32.087 30.275 22.974 1.00 0.00 C +ATOM 664 HB2 ARG 43 31.317 29.508 23.057 1.00 0.00 H +ATOM 665 HB3 ARG 43 32.669 30.262 23.897 1.00 0.00 H +ATOM 666 CG ARG 43 31.391 31.637 22.844 1.00 0.00 C +ATOM 667 HG2 ARG 43 32.110 32.434 22.660 1.00 0.00 H +ATOM 668 HG3 ARG 43 30.694 31.612 22.010 1.00 0.00 H +ATOM 669 CD ARG 43 30.634 31.967 24.121 1.00 0.00 C +ATOM 670 HD2 ARG 43 30.147 31.059 24.480 1.00 0.00 H +ATOM 671 HD3 ARG 43 31.339 32.284 24.887 1.00 0.00 H +ATOM 672 NE ARG 43 29.619 32.996 23.893 1.00 0.00 N +ATOM 673 HE ARG 43 28.685 32.661 23.712 1.00 0.00 H +ATOM 674 CZ ARG 43 29.781 34.291 23.756 1.00 0.00 C +ATOM 675 NH1 ARG 43 30.924 34.915 23.764 1.00 0.00 N +ATOM 676 HH11 ARG 43 31.776 34.380 23.737 1.00 0.00 H +ATOM 677 HH12 ARG 43 30.928 35.903 23.564 1.00 0.00 H +ATOM 678 NH2 ARG 43 28.724 35.010 23.622 1.00 0.00 N +ATOM 679 HH21 ARG 43 27.818 34.575 23.525 1.00 0.00 H +ATOM 680 HH22 ARG 43 28.806 36.015 23.611 1.00 0.00 H +ATOM 681 C ARG 43 32.226 29.788 20.491 1.00 0.00 C +ATOM 682 O ARG 43 32.016 30.775 19.792 1.00 0.00 O +ATOM 683 N THR 44 31.769 28.574 20.199 1.00 0.00 N +ATOM 684 H THR 44 31.893 27.856 20.903 1.00 0.00 H +ATOM 685 CA THR 44 31.059 28.197 18.965 1.00 0.00 C +ATOM 686 HA THR 44 31.367 28.878 18.171 1.00 0.00 H +ATOM 687 CB THR 44 31.491 26.779 18.541 1.00 0.00 C +ATOM 688 HB THR 44 31.284 26.073 19.347 1.00 0.00 H +ATOM 689 CG2 THR 44 30.877 26.255 17.242 1.00 0.00 C +ATOM 690 HG21 THR 44 30.980 26.998 16.449 1.00 0.00 H +ATOM 691 HG22 THR 44 31.383 25.337 16.935 1.00 0.00 H +ATOM 692 HG23 THR 44 29.824 26.016 17.397 1.00 0.00 H +ATOM 693 OG1 THR 44 32.880 26.818 18.313 1.00 0.00 O +ATOM 694 HG1 THR 44 33.143 26.013 17.857 1.00 0.00 H +ATOM 695 C THR 44 29.537 28.364 19.112 1.00 0.00 C +ATOM 696 O THR 44 29.024 28.513 20.225 1.00 0.00 O +ATOM 697 N ILE 45 28.813 28.404 17.984 1.00 0.00 N +ATOM 698 H ILE 45 29.281 28.200 17.114 1.00 0.00 H +ATOM 699 CA ILE 45 27.405 28.808 17.888 1.00 0.00 C +ATOM 700 HA ILE 45 26.992 28.796 18.898 1.00 0.00 H +ATOM 701 CB ILE 45 27.300 30.258 17.349 1.00 0.00 C +ATOM 702 HB ILE 45 26.234 30.493 17.386 1.00 0.00 H +ATOM 703 CG2 ILE 45 28.017 31.233 18.293 1.00 0.00 C +ATOM 704 HG21 ILE 45 29.094 31.074 18.238 1.00 0.00 H +ATOM 705 HG22 ILE 45 27.806 32.268 18.025 1.00 0.00 H +ATOM 706 HG23 ILE 45 27.671 31.042 19.300 1.00 0.00 H +ATOM 707 CG1 ILE 45 27.759 30.525 15.895 1.00 0.00 C +ATOM 708 HG12 ILE 45 28.047 31.568 15.812 1.00 0.00 H +ATOM 709 HG13 ILE 45 28.654 29.949 15.680 1.00 0.00 H +ATOM 710 CD1 ILE 45 26.691 30.279 14.822 1.00 0.00 C +ATOM 711 HD11 ILE 45 25.759 30.773 15.114 1.00 0.00 H +ATOM 712 HD12 ILE 45 27.018 30.695 13.866 1.00 0.00 H +ATOM 713 HD13 ILE 45 26.512 29.212 14.695 1.00 0.00 H +ATOM 714 C ILE 45 26.527 27.858 17.072 1.00 0.00 C +ATOM 715 O ILE 45 27.017 27.114 16.226 1.00 0.00 O +ATOM 716 N ASP 46 25.216 27.950 17.304 1.00 0.00 N +ATOM 717 H ASP 46 24.910 28.475 18.111 1.00 0.00 H +ATOM 718 CA ASP 46 24.153 27.357 16.483 1.00 0.00 C +ATOM 719 HA ASP 46 24.474 27.365 15.437 1.00 0.00 H +ATOM 720 CB ASP 46 23.935 25.904 16.910 1.00 0.00 C +ATOM 721 HB2 ASP 46 24.821 25.306 16.686 1.00 0.00 H +ATOM 722 HB3 ASP 46 23.790 25.882 17.995 1.00 0.00 H +ATOM 723 CG ASP 46 22.728 25.281 16.224 1.00 0.00 C +ATOM 724 OD1 ASP 46 21.961 24.603 16.947 1.00 0.00 O +ATOM 725 OD2 ASP 46 22.511 25.554 15.040 1.00 0.00 O +ATOM 726 C ASP 46 22.834 28.159 16.594 1.00 0.00 C +ATOM 727 O ASP 46 22.399 28.488 17.698 1.00 0.00 O +ATOM 728 N ASP 47 22.184 28.437 15.458 1.00 0.00 N +ATOM 729 H ASP 47 22.559 28.038 14.608 1.00 0.00 H +ATOM 730 CA ASP 47 20.840 29.039 15.391 1.00 0.00 C +ATOM 731 HA ASP 47 20.745 29.781 16.186 1.00 0.00 H +ATOM 732 CB ASP 47 20.651 29.780 14.049 1.00 0.00 C +ATOM 733 HB2 ASP 47 21.371 30.599 13.994 1.00 0.00 H +ATOM 734 HB3 ASP 47 20.869 29.092 13.229 1.00 0.00 H +ATOM 735 CG ASP 47 19.236 30.338 13.866 1.00 0.00 C +ATOM 736 OD1 ASP 47 18.366 29.642 13.294 1.00 0.00 O +ATOM 737 OD2 ASP 47 18.910 31.439 14.376 1.00 0.00 O +ATOM 738 C ASP 47 19.712 28.006 15.601 1.00 0.00 C +ATOM 739 O ASP 47 18.680 28.354 16.177 1.00 0.00 O +ATOM 740 N ALA 48 19.891 26.748 15.189 1.00 0.00 N +ATOM 741 H ALA 48 20.815 26.444 14.883 1.00 0.00 H +ATOM 742 CA ALA 48 18.830 25.738 15.223 1.00 0.00 C +ATOM 743 HA ALA 48 17.947 26.136 14.721 1.00 0.00 H +ATOM 744 CB ALA 48 19.314 24.506 14.451 1.00 0.00 C +ATOM 745 HB1 ALA 48 20.173 24.065 14.961 1.00 0.00 H +ATOM 746 HB2 ALA 48 18.518 23.764 14.391 1.00 0.00 H +ATOM 747 HB3 ALA 48 19.617 24.791 13.444 1.00 0.00 H +ATOM 748 C ALA 48 18.413 25.386 16.665 1.00 0.00 C +ATOM 749 O ALA 48 17.226 25.293 16.965 1.00 0.00 O +ATOM 750 N THR 49 19.383 25.251 17.569 1.00 0.00 N +ATOM 751 H THR 49 20.338 25.173 17.219 1.00 0.00 H +ATOM 752 CA THR 49 19.192 25.102 19.021 1.00 0.00 C +ATOM 753 HA THR 49 18.164 24.774 19.188 1.00 0.00 H +ATOM 754 CB THR 49 20.126 24.025 19.584 1.00 0.00 C +ATOM 755 HB THR 49 19.898 23.910 20.645 1.00 0.00 H +ATOM 756 CG2 THR 49 19.960 22.658 18.926 1.00 0.00 C +ATOM 757 HG21 THR 49 20.258 22.695 17.880 1.00 0.00 H +ATOM 758 HG22 THR 49 20.593 21.942 19.444 1.00 0.00 H +ATOM 759 HG23 THR 49 18.922 22.334 18.992 1.00 0.00 H +ATOM 760 OG1 THR 49 21.483 24.396 19.468 1.00 0.00 O +ATOM 761 HG1 THR 49 21.694 24.365 18.500 1.00 0.00 H +ATOM 762 C THR 49 19.397 26.401 19.808 1.00 0.00 C +ATOM 763 O THR 49 19.269 26.396 21.031 1.00 0.00 O +ATOM 764 N LYS 50 19.705 27.522 19.134 1.00 0.00 N +ATOM 765 H LYS 50 19.806 27.421 18.131 1.00 0.00 H +ATOM 766 CA LYS 50 19.900 28.882 19.702 1.00 0.00 C +ATOM 767 HA LYS 50 20.324 29.504 18.914 1.00 0.00 H +ATOM 768 CB LYS 50 18.514 29.466 20.090 1.00 0.00 C +ATOM 769 HB2 LYS 50 18.082 28.812 20.847 1.00 0.00 H +ATOM 770 HB3 LYS 50 18.662 30.440 20.569 1.00 0.00 H +ATOM 771 CG LYS 50 17.483 29.640 18.962 1.00 0.00 C +ATOM 772 HG2 LYS 50 17.406 28.724 18.377 1.00 0.00 H +ATOM 773 HG3 LYS 50 16.511 29.807 19.436 1.00 0.00 H +ATOM 774 CD LYS 50 17.771 30.842 18.048 1.00 0.00 C +ATOM 775 HD2 LYS 50 17.847 31.729 18.684 1.00 0.00 H +ATOM 776 HD3 LYS 50 18.722 30.709 17.525 1.00 0.00 H +ATOM 777 CE LYS 50 16.636 31.087 17.042 1.00 0.00 C +ATOM 778 HE2 LYS 50 15.680 30.851 17.523 1.00 0.00 H +ATOM 779 HE3 LYS 50 16.620 32.152 16.793 1.00 0.00 H +ATOM 780 NZ LYS 50 16.785 30.318 15.786 1.00 0.00 N +ATOM 781 HZ1 LYS 50 17.027 29.345 15.942 1.00 0.00 H +ATOM 782 HZ2 LYS 50 15.966 30.404 15.186 1.00 0.00 H +ATOM 783 HZ3 LYS 50 17.558 30.688 15.237 1.00 0.00 H +ATOM 784 C LYS 50 20.929 28.907 20.853 1.00 0.00 C +ATOM 785 O LYS 50 20.644 29.476 21.914 1.00 0.00 O +ATOM 786 N THR 51 22.073 28.246 20.666 1.00 0.00 N +ATOM 787 H THR 51 22.280 27.904 19.746 1.00 0.00 H +ATOM 788 CA THR 51 22.978 27.855 21.776 1.00 0.00 C +ATOM 789 HA THR 51 22.713 28.424 22.656 1.00 0.00 H +ATOM 790 CB THR 51 22.769 26.349 22.149 1.00 0.00 C +ATOM 791 HB THR 51 22.913 25.751 21.244 1.00 0.00 H +ATOM 792 CG2 THR 51 23.726 25.829 23.195 1.00 0.00 C +ATOM 793 HG21 THR 51 23.724 26.423 24.104 1.00 0.00 H +ATOM 794 HG22 THR 51 23.491 24.809 23.488 1.00 0.00 H +ATOM 795 HG23 THR 51 24.752 25.794 22.838 1.00 0.00 H +ATOM 796 OG1 THR 51 21.477 26.147 22.676 1.00 0.00 O +ATOM 797 HG1 THR 51 20.828 26.213 21.948 1.00 0.00 H +ATOM 798 C THR 51 24.498 28.160 21.552 1.00 0.00 C +ATOM 799 O THR 51 25.031 27.978 20.458 1.00 0.00 O +ATOM 800 N PHE 52 25.195 28.618 22.604 1.00 0.00 N +ATOM 801 H PHE 52 24.659 28.844 23.435 1.00 0.00 H +ATOM 802 CA PHE 52 26.648 28.754 22.682 1.00 0.00 C +ATOM 803 HA PHE 52 27.066 28.878 21.704 1.00 0.00 H +ATOM 804 CB PHE 52 27.049 29.989 23.564 1.00 0.00 C +ATOM 805 HB2 PHE 52 26.439 29.970 24.449 1.00 0.00 H +ATOM 806 HB3 PHE 52 28.080 29.863 23.877 1.00 0.00 H +ATOM 807 CG PHE 52 26.956 31.369 22.935 1.00 0.00 C +ATOM 808 CD1 PHE 52 26.137 32.360 23.496 1.00 0.00 C +ATOM 809 HD1 PHE 52 25.515 32.134 24.347 1.00 0.00 H +ATOM 810 CE1 PHE 52 26.022 33.613 22.875 1.00 0.00 C +ATOM 811 HE1 PHE 52 25.306 34.345 23.243 1.00 0.00 H +ATOM 812 CZ PHE 52 26.749 33.887 21.707 1.00 0.00 C +ATOM 813 HZ PHE 52 26.610 34.820 21.179 1.00 0.00 H +ATOM 814 CE2 PHE 52 27.660 32.942 21.218 1.00 0.00 C +ATOM 815 HE2 PHE 52 28.252 33.169 20.337 1.00 0.00 H +ATOM 816 CD2 PHE 52 27.757 31.680 21.826 1.00 0.00 C +ATOM 817 HD2 PHE 52 28.421 30.934 21.415 1.00 0.00 H +ATOM 818 C PHE 52 27.299 27.528 23.345 1.00 0.00 C +ATOM 819 O PHE 52 26.801 27.060 24.382 1.00 0.00 O +ATOM 820 N THR 53 28.455 27.080 22.828 1.00 0.00 N +ATOM 821 H THR 53 28.794 27.502 21.960 1.00 0.00 H +ATOM 822 CA THR 53 29.257 25.944 23.360 1.00 0.00 C +ATOM 823 HA THR 53 29.018 25.811 24.412 1.00 0.00 H +ATOM 824 CB THR 53 28.922 24.628 22.631 1.00 0.00 C +ATOM 825 HB THR 53 29.523 23.828 23.066 1.00 0.00 H +ATOM 826 CG2 THR 53 27.455 24.219 22.728 1.00 0.00 C +ATOM 827 HG21 THR 53 26.839 24.900 22.141 1.00 0.00 H +ATOM 828 HG22 THR 53 27.330 23.206 22.345 1.00 0.00 H +ATOM 829 HG23 THR 53 27.136 24.241 23.767 1.00 0.00 H +ATOM 830 OG1 THR 53 29.241 24.729 21.261 1.00 0.00 O +ATOM 831 HG1 THR 53 28.872 23.960 20.816 1.00 0.00 H +ATOM 832 C THR 53 30.775 26.169 23.265 1.00 0.00 C +ATOM 833 O THR 53 31.247 27.039 22.536 1.00 0.00 O +ATOM 834 N THR 54 31.550 25.363 23.995 1.00 0.00 N +ATOM 835 H THR 54 31.108 24.674 24.581 1.00 0.00 H +ATOM 836 CA THR 54 33.026 25.280 23.900 1.00 0.00 C +ATOM 837 HA THR 54 33.389 26.087 23.264 1.00 0.00 H +ATOM 838 CB THR 54 33.679 25.465 25.287 1.00 0.00 C +ATOM 839 HB THR 54 33.366 24.653 25.943 1.00 0.00 H +ATOM 840 CG2 THR 54 35.209 25.527 25.270 1.00 0.00 C +ATOM 841 HG21 THR 54 35.551 26.282 24.560 1.00 0.00 H +ATOM 842 HG22 THR 54 35.586 25.776 26.261 1.00 0.00 H +ATOM 843 HG23 THR 54 35.625 24.558 24.996 1.00 0.00 H +ATOM 844 OG1 THR 54 33.257 26.688 25.848 1.00 0.00 O +ATOM 845 HG1 THR 54 33.703 26.791 26.690 1.00 0.00 H +ATOM 846 C THR 54 33.453 23.948 23.240 1.00 0.00 C +ATOM 847 O THR 54 32.725 22.957 23.330 1.00 0.00 O +ATOM 848 N GLN 55 34.608 23.941 22.569 1.00 0.00 N +ATOM 849 H GLN 55 35.143 24.792 22.563 1.00 0.00 H +ATOM 850 CA GLN 55 35.230 22.769 21.928 1.00 0.00 C +ATOM 851 HA GLN 55 34.472 22.294 21.307 1.00 0.00 H +ATOM 852 CB GLN 55 36.356 23.273 20.997 1.00 0.00 C +ATOM 853 HB2 GLN 55 36.747 22.431 20.418 1.00 0.00 H +ATOM 854 HB3 GLN 55 35.915 23.976 20.284 1.00 0.00 H +ATOM 855 CG GLN 55 37.529 23.975 21.718 1.00 0.00 C +ATOM 856 HG2 GLN 55 37.135 24.635 22.490 1.00 0.00 H +ATOM 857 HG3 GLN 55 38.153 23.228 22.202 1.00 0.00 H +ATOM 858 CD GLN 55 38.400 24.813 20.772 1.00 0.00 C +ATOM 859 OE1 GLN 55 38.699 24.456 19.644 1.00 0.00 O +ATOM 860 NE2 GLN 55 38.838 25.984 21.186 1.00 0.00 N +ATOM 861 HE21 GLN 55 39.398 26.495 20.531 1.00 0.00 H +ATOM 862 HE22 GLN 55 38.530 26.390 22.059 1.00 0.00 H +ATOM 863 C GLN 55 35.729 21.702 22.920 1.00 0.00 C +ATOM 864 O GLN 55 35.936 21.998 24.098 1.00 0.00 O +ATOM 865 N GLU 56 35.911 20.461 22.436 1.00 0.00 N +ATOM 866 H GLU 56 35.764 20.328 21.453 1.00 0.00 H +ATOM 867 CA GLU 56 36.591 19.326 23.126 1.00 0.00 C +ATOM 868 HA GLU 56 36.581 19.527 24.209 1.00 0.00 H +ATOM 869 CB GLU 56 35.802 18.011 22.873 1.00 0.00 C +ATOM 870 HB2 GLU 56 34.794 18.115 23.271 1.00 0.00 H +ATOM 871 HB3 GLU 56 35.670 17.896 21.805 1.00 0.00 H +ATOM 872 CG GLU 56 36.406 16.708 23.419 1.00 0.00 C +ATOM 873 HG2 GLU 56 36.588 16.049 22.597 1.00 0.00 H +ATOM 874 HG3 GLU 56 37.378 16.911 23.804 1.00 0.00 H +ATOM 875 CD GLU 56 35.639 15.935 24.519 1.00 0.00 C +ATOM 876 OE1 GLU 56 36.261 15.255 25.395 1.00 0.00 O +ATOM 877 OE2 GLU 56 34.388 15.901 24.484 1.00 0.00 O +ATOM 878 C GLU 56 38.064 19.234 22.739 1.00 0.00 C +ATOM 879 O GLU 56 38.897 19.678 23.554 1.00 0.00 O +ATOM 880 OXT GLU 56 38.365 18.739 21.612 1.00 0.00 O +HETATM 881 ZN ZN1 57 26.696 32.427 29.378 1.00 0.00 Zn +HETATM 882 N AN1 58 28.269 33.325 30.318 1.00 0.00 N +HETATM 883 C AN1 58 30.569 34.237 31.119 1.00 0.00 C +HETATM 884 C1 AN1 58 29.262 33.721 30.709 1.00 0.00 C +HETATM 885 H AN1 58 30.559 34.480 32.185 1.00 0.00 H +HETATM 886 H1 AN1 58 30.794 35.142 30.544 1.00 0.00 H +HETATM 887 H2 AN1 58 31.328 33.474 30.919 1.00 0.00 H +HETATM 888 N1 AZI 59 30.711 28.496 29.887 1.00 0.00 N +HETATM 889 N2 AZI 59 30.239 29.556 30.281 1.00 0.00 N +HETATM 890 N3 AZI 59 29.793 30.642 30.720 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 881 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 137 134 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 140 142 +CONECT 140 139 +CONECT 141 139 +CONECT 142 139 145 143 144 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 142 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 194 189 +CONECT 188 187 +CONECT 189 187 192 190 191 +CONECT 190 189 +CONECT 191 189 +CONECT 192 193 189 +CONECT 193 192 +CONECT 194 196 187 195 +CONECT 195 194 +CONECT 196 197 198 194 +CONECT 197 196 +CONECT 198 205 196 200 199 +CONECT 199 198 +CONECT 200 201 198 202 203 +CONECT 201 200 +CONECT 202 200 +CONECT 203 200 204 +CONECT 204 203 +CONECT 205 206 207 198 +CONECT 206 205 +CONECT 207 209 205 208 +CONECT 208 207 +CONECT 209 210 227 211 207 +CONECT 210 209 +CONECT 211 214 209 212 213 +CONECT 212 211 +CONECT 213 211 +CONECT 214 216 215 217 211 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 214 219 220 +CONECT 218 217 +CONECT 219 217 +CONECT 220 217 222 223 221 +CONECT 221 220 +CONECT 222 220 +CONECT 223 226 220 225 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 223 +CONECT 227 228 209 229 +CONECT 228 227 +CONECT 229 227 231 230 +CONECT 230 229 +CONECT 231 234 229 232 233 +CONECT 232 231 +CONECT 233 231 +CONECT 234 235 236 231 +CONECT 235 234 +CONECT 236 238 234 237 +CONECT 237 236 +CONECT 238 240 239 250 236 +CONECT 239 238 +CONECT 240 246 241 242 238 +CONECT 241 240 +CONECT 242 244 240 243 245 +CONECT 243 242 +CONECT 244 242 +CONECT 245 242 +CONECT 246 248 247 249 240 +CONECT 247 246 +CONECT 248 246 +CONECT 249 246 +CONECT 250 238 252 251 +CONECT 251 250 +CONECT 252 262 253 250 +CONECT 253 254 252 263 256 +CONECT 254 255 269 253 +CONECT 255 254 +CONECT 256 253 257 264 265 +CONECT 257 258 259 256 +CONECT 258 261 267 257 +CONECT 259 260 257 266 +CONECT 260 261 268 259 +CONECT 261 881 258 260 +CONECT 262 252 +CONECT 263 253 +CONECT 264 256 +CONECT 265 256 +CONECT 266 259 +CONECT 267 258 +CONECT 268 260 +CONECT 269 271 254 270 +CONECT 270 269 +CONECT 271 272 273 281 269 +CONECT 272 271 +CONECT 273 274 275 271 279 +CONECT 274 273 +CONECT 275 278 277 273 276 +CONECT 276 275 +CONECT 277 275 +CONECT 278 275 +CONECT 279 273 280 +CONECT 280 279 +CONECT 281 283 271 282 +CONECT 282 281 +CONECT 283 293 284 281 +CONECT 284 285 287 283 294 +CONECT 285 286 300 284 +CONECT 286 285 +CONECT 287 295 296 284 288 +CONECT 288 287 289 290 +CONECT 289 298 288 292 +CONECT 290 288 297 291 +CONECT 291 292 290 299 +CONECT 292 289 881 291 +CONECT 293 283 +CONECT 294 284 +CONECT 295 287 +CONECT 296 287 +CONECT 297 290 +CONECT 298 289 +CONECT 299 291 +CONECT 300 302 285 301 +CONECT 301 300 +CONECT 302 313 303 300 304 +CONECT 303 302 +CONECT 304 302 307 306 305 +CONECT 305 304 +CONECT 306 304 +CONECT 307 309 310 304 308 +CONECT 308 307 +CONECT 309 307 +CONECT 310 311 307 312 +CONECT 311 310 +CONECT 312 310 +CONECT 313 315 314 302 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 323 319 318 315 +CONECT 318 317 +CONECT 319 321 320 317 322 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 325 324 317 +CONECT 324 323 +CONECT 325 327 326 323 +CONECT 326 325 +CONECT 327 339 329 328 325 +CONECT 328 327 +CONECT 329 330 335 327 331 +CONECT 330 329 +CONECT 331 329 333 334 332 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 336 337 329 338 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 340 341 327 +CONECT 340 339 +CONECT 341 343 339 342 +CONECT 342 341 +CONECT 343 345 344 351 341 +CONECT 344 343 +CONECT 345 348 346 347 343 +CONECT 346 345 +CONECT 347 345 +CONECT 348 350 349 345 +CONECT 349 348 +CONECT 350 348 +CONECT 351 353 343 352 +CONECT 352 351 +CONECT 353 354 355 351 +CONECT 354 353 +CONECT 355 357 353 375 356 +CONECT 356 355 +CONECT 357 359 358 360 355 +CONECT 358 357 +CONECT 359 357 +CONECT 360 361 357 374 +CONECT 361 362 363 360 +CONECT 362 361 +CONECT 363 361 364 365 +CONECT 364 363 +CONECT 365 363 374 366 +CONECT 366 365 367 368 +CONECT 367 366 +CONECT 368 366 370 369 +CONECT 369 368 +CONECT 370 372 368 371 +CONECT 371 370 +CONECT 372 374 373 370 +CONECT 373 372 +CONECT 374 360 365 372 +CONECT 375 377 355 376 +CONECT 376 375 +CONECT 377 378 379 375 +CONECT 378 377 +CONECT 379 381 377 380 385 +CONECT 380 379 +CONECT 381 384 382 383 379 +CONECT 382 381 +CONECT 383 381 +CONECT 384 381 +CONECT 385 379 386 387 +CONECT 386 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 390 391 400 +CONECT 390 389 +CONECT 391 394 392 389 393 +CONECT 392 391 +CONECT 393 391 +CONECT 394 395 396 397 391 +CONECT 395 394 +CONECT 396 394 +CONECT 397 399 394 398 +CONECT 398 397 +CONECT 399 397 +CONECT 400 389 402 401 +CONECT 401 400 +CONECT 402 403 400 404 +CONECT 403 402 +CONECT 404 402 406 410 405 +CONECT 405 404 +CONECT 406 407 409 404 408 +CONECT 407 406 +CONECT 408 406 +CONECT 409 406 +CONECT 410 412 404 411 +CONECT 411 410 +CONECT 412 413 414 410 +CONECT 413 412 +CONECT 414 416 412 415 425 +CONECT 415 414 +CONECT 416 417 418 419 414 +CONECT 417 416 +CONECT 418 416 +CONECT 419 422 416 421 420 +CONECT 420 419 +CONECT 421 419 +CONECT 422 424 423 419 +CONECT 423 422 +CONECT 424 422 +CONECT 425 414 427 426 +CONECT 426 425 +CONECT 427 428 425 429 +CONECT 428 427 +CONECT 429 427 431 430 447 +CONECT 430 429 +CONECT 431 434 432 433 429 +CONECT 432 431 +CONECT 433 431 +CONECT 434 436 437 435 431 +CONECT 435 434 +CONECT 436 434 +CONECT 437 440 438 439 434 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 441 442 437 +CONECT 441 440 +CONECT 442 440 +CONECT 443 445 444 446 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 +CONECT 447 429 449 448 +CONECT 448 447 +CONECT 449 450 447 451 +CONECT 450 449 +CONECT 451 449 453 452 467 +CONECT 452 451 +CONECT 453 456 454 451 455 +CONECT 454 453 +CONECT 455 453 +CONECT 456 457 465 453 +CONECT 457 459 458 456 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 462 459 463 +CONECT 462 461 +CONECT 463 461 464 465 +CONECT 464 463 +CONECT 465 463 456 466 +CONECT 466 465 +CONECT 467 451 469 468 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 473 469 481 472 +CONECT 472 471 +CONECT 473 474 479 475 471 +CONECT 474 473 +CONECT 475 473 477 478 476 +CONECT 476 475 +CONECT 477 475 +CONECT 478 475 +CONECT 479 480 473 +CONECT 480 479 +CONECT 481 483 471 482 +CONECT 482 481 +CONECT 483 484 485 481 +CONECT 484 483 +CONECT 485 487 483 486 503 +CONECT 486 485 +CONECT 487 490 488 489 485 +CONECT 488 487 +CONECT 489 487 +CONECT 490 493 492 491 487 +CONECT 491 490 +CONECT 492 490 +CONECT 493 496 494 495 490 +CONECT 494 493 +CONECT 495 493 +CONECT 496 498 497 499 493 +CONECT 497 496 +CONECT 498 496 +CONECT 499 501 496 502 500 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 485 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 508 513 +CONECT 508 507 +CONECT 509 512 510 507 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 507 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 534 518 +CONECT 518 517 +CONECT 519 521 520 517 522 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 525 523 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 526 522 528 527 +CONECT 526 525 +CONECT 527 525 +CONECT 528 530 525 531 529 +CONECT 529 528 +CONECT 530 528 +CONECT 531 533 528 532 +CONECT 532 531 +CONECT 533 531 +CONECT 534 536 517 535 +CONECT 535 534 +CONECT 536 537 538 534 +CONECT 537 536 +CONECT 538 540 536 544 539 +CONECT 539 538 +CONECT 540 541 543 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 +CONECT 544 538 546 545 +CONECT 545 544 +CONECT 546 547 544 548 +CONECT 547 546 +CONECT 548 550 546 549 558 +CONECT 549 548 +CONECT 550 553 551 552 548 +CONECT 551 550 +CONECT 552 550 +CONECT 553 555 554 550 +CONECT 554 553 +CONECT 555 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 548 560 559 +CONECT 559 558 +CONECT 560 561 558 562 +CONECT 561 560 +CONECT 562 560 564 563 570 +CONECT 563 562 +CONECT 564 567 565 562 566 +CONECT 565 564 +CONECT 566 564 +CONECT 567 569 568 564 +CONECT 568 567 +CONECT 569 567 +CONECT 570 562 572 571 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 592 576 575 +CONECT 575 574 +CONECT 576 579 574 578 577 +CONECT 577 576 +CONECT 578 576 +CONECT 579 580 581 582 576 +CONECT 580 579 +CONECT 581 579 +CONECT 582 585 584 579 583 +CONECT 583 582 +CONECT 584 582 +CONECT 585 588 587 586 582 +CONECT 586 585 +CONECT 587 585 +CONECT 588 590 591 589 585 +CONECT 589 588 +CONECT 590 588 +CONECT 591 588 +CONECT 592 594 593 574 +CONECT 593 592 +CONECT 594 596 595 592 +CONECT 595 594 +CONECT 596 599 594 597 598 +CONECT 597 596 +CONECT 598 596 +CONECT 599 601 600 596 +CONECT 600 599 +CONECT 601 603 602 599 +CONECT 602 601 +CONECT 603 623 604 605 601 +CONECT 604 603 +CONECT 605 606 603 607 608 +CONECT 606 605 +CONECT 607 605 +CONECT 608 609 605 610 611 +CONECT 609 608 +CONECT 610 608 +CONECT 611 608 613 614 612 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 616 615 +CONECT 615 614 +CONECT 616 617 614 620 +CONECT 617 618 619 616 +CONECT 618 617 +CONECT 619 617 +CONECT 620 616 622 621 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 603 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 629 635 628 625 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 632 +CONECT 635 637 636 627 +CONECT 636 635 +CONECT 637 639 638 635 +CONECT 638 637 +CONECT 639 642 640 641 637 +CONECT 640 639 +CONECT 641 639 +CONECT 642 644 643 639 +CONECT 643 642 +CONECT 644 646 645 642 +CONECT 645 644 +CONECT 646 648 647 657 644 +CONECT 647 646 +CONECT 648 650 651 649 646 +CONECT 649 648 +CONECT 650 648 +CONECT 651 653 648 654 652 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 655 656 +CONECT 655 654 +CONECT 656 654 +CONECT 657 659 646 658 +CONECT 658 657 +CONECT 659 660 661 657 +CONECT 660 659 +CONECT 661 681 659 662 663 +CONECT 662 661 +CONECT 663 661 666 664 665 +CONECT 664 663 +CONECT 665 663 +CONECT 666 668 667 663 669 +CONECT 667 666 +CONECT 668 666 +CONECT 669 666 672 670 671 +CONECT 670 669 +CONECT 671 669 +CONECT 672 673 674 669 +CONECT 673 672 +CONECT 674 678 675 672 +CONECT 675 677 676 674 +CONECT 676 675 +CONECT 677 675 +CONECT 678 679 680 674 +CONECT 679 678 +CONECT 680 678 +CONECT 681 682 683 661 +CONECT 682 681 +CONECT 683 685 681 684 +CONECT 684 683 +CONECT 685 686 687 695 683 +CONECT 686 685 +CONECT 687 689 693 685 688 +CONECT 688 687 +CONECT 689 690 691 692 687 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 +CONECT 693 694 687 +CONECT 694 693 +CONECT 695 697 685 696 +CONECT 696 695 +CONECT 697 698 699 695 +CONECT 698 697 +CONECT 699 714 701 697 700 +CONECT 700 699 +CONECT 701 707 702 699 703 +CONECT 702 701 +CONECT 703 701 705 704 706 +CONECT 704 703 +CONECT 705 703 +CONECT 706 703 +CONECT 707 710 709 708 701 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 713 711 707 +CONECT 711 710 +CONECT 712 710 +CONECT 713 710 +CONECT 714 715 716 699 +CONECT 715 714 +CONECT 716 718 714 717 +CONECT 717 716 +CONECT 718 719 726 720 716 +CONECT 719 718 +CONECT 720 723 718 721 722 +CONECT 721 720 +CONECT 722 720 +CONECT 723 725 720 724 +CONECT 724 723 +CONECT 725 723 +CONECT 726 728 718 727 +CONECT 727 726 +CONECT 728 729 730 726 +CONECT 729 728 +CONECT 730 732 728 738 731 +CONECT 731 730 +CONECT 732 734 735 733 730 +CONECT 733 732 +CONECT 734 732 +CONECT 735 736 732 737 +CONECT 736 735 +CONECT 737 735 +CONECT 738 740 730 739 +CONECT 739 738 +CONECT 740 741 742 738 +CONECT 741 740 +CONECT 742 744 743 740 748 +CONECT 743 742 +CONECT 744 747 746 745 742 +CONECT 745 744 +CONECT 746 744 +CONECT 747 744 +CONECT 748 742 749 750 +CONECT 749 748 +CONECT 750 748 751 752 +CONECT 751 750 +CONECT 752 750 753 754 762 +CONECT 753 752 +CONECT 754 756 752 760 755 +CONECT 755 754 +CONECT 756 757 759 758 754 +CONECT 757 756 +CONECT 758 756 +CONECT 759 756 +CONECT 760 761 754 +CONECT 761 760 +CONECT 762 752 764 763 +CONECT 763 762 +CONECT 764 765 766 762 +CONECT 765 764 +CONECT 766 767 764 768 784 +CONECT 767 766 +CONECT 768 771 766 770 769 +CONECT 769 768 +CONECT 770 768 +CONECT 771 774 772 773 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 777 776 775 771 +CONECT 775 774 +CONECT 776 774 +CONECT 777 780 779 778 774 +CONECT 778 777 +CONECT 779 777 +CONECT 780 782 783 781 777 +CONECT 781 780 +CONECT 782 780 +CONECT 783 780 +CONECT 784 766 786 785 +CONECT 785 784 +CONECT 786 787 784 788 +CONECT 787 786 +CONECT 788 786 798 790 789 +CONECT 789 788 +CONECT 790 791 788 796 792 +CONECT 791 790 +CONECT 792 790 795 794 793 +CONECT 793 792 +CONECT 794 792 +CONECT 795 792 +CONECT 796 797 790 +CONECT 797 796 +CONECT 798 799 788 800 +CONECT 799 798 +CONECT 800 798 802 801 +CONECT 801 800 +CONECT 802 803 800 818 804 +CONECT 803 802 +CONECT 804 802 807 806 805 +CONECT 805 804 +CONECT 806 804 +CONECT 807 816 808 804 +CONECT 808 810 807 809 +CONECT 809 808 +CONECT 810 812 811 808 +CONECT 811 810 +CONECT 812 813 814 810 +CONECT 813 812 +CONECT 814 815 812 816 +CONECT 815 814 +CONECT 816 814 817 807 +CONECT 817 816 +CONECT 818 802 820 819 +CONECT 819 818 +CONECT 820 821 818 822 +CONECT 821 820 +CONECT 822 824 820 832 823 +CONECT 823 822 +CONECT 824 830 826 825 822 +CONECT 825 824 +CONECT 826 827 828 824 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 +CONECT 830 831 824 +CONECT 831 830 +CONECT 832 833 822 834 +CONECT 833 832 +CONECT 834 832 836 835 +CONECT 835 834 +CONECT 836 846 837 834 838 +CONECT 837 836 +CONECT 838 836 840 844 839 +CONECT 839 838 +CONECT 840 841 843 838 842 +CONECT 841 840 +CONECT 842 840 +CONECT 843 840 +CONECT 844 838 845 +CONECT 845 844 +CONECT 846 848 847 836 +CONECT 847 846 +CONECT 848 850 849 846 +CONECT 849 848 +CONECT 850 852 851 848 863 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 858 852 857 856 +CONECT 856 855 +CONECT 857 855 +CONECT 858 859 860 855 +CONECT 859 858 +CONECT 860 861 858 862 +CONECT 861 860 +CONECT 862 860 +CONECT 863 850 865 864 +CONECT 864 863 +CONECT 865 866 863 867 +CONECT 866 865 +CONECT 867 865 878 869 868 +CONECT 868 867 +CONECT 869 871 867 870 872 +CONECT 870 869 +CONECT 871 869 +CONECT 872 873 869 874 875 +CONECT 873 872 +CONECT 874 872 +CONECT 875 872 877 876 +CONECT 876 875 +CONECT 877 875 +CONECT 878 880 867 879 +CONECT 879 878 +CONECT 880 878 +CONECT 881 87 292 882 261 +CONECT 882 881 884 +CONECT 883 886 884 887 885 +CONECT 884 882 883 +CONECT 885 883 +CONECT 886 883 +CONECT 887 883 +CONECT 888 889 +CONECT 889 888 890 +CONECT 890 889 +MASTER 0 0 0 0 0 0 0 0 890 0 890 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_4_front_38.pdb b/tests/nsga2/intermediate_molecules/min_iter_4_front_38.pdb new file mode 100644 index 0000000..04d4862 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_4_front_38.pdb @@ -0,0 +1,1819 @@ +COMPND fitness: -8.6377 60.54000000000042 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 58.230 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.023 37.894 23.481 1.00 0.00 N +ATOM 2 H1 MET 1 15.031 38.292 24.419 1.00 0.00 H +ATOM 3 H2 MET 1 14.184 38.187 23.003 1.00 0.00 H +ATOM 4 H3 MET 1 15.854 38.249 23.017 1.00 0.00 H +ATOM 5 CA MET 1 15.091 36.427 23.581 1.00 0.00 C +ATOM 6 HA MET 1 14.167 36.075 24.031 1.00 0.00 H +ATOM 7 CB MET 1 15.237 35.783 22.192 1.00 0.00 C +ATOM 8 HB2 MET 1 14.358 36.036 21.596 1.00 0.00 H +ATOM 9 HB3 MET 1 16.118 36.198 21.691 1.00 0.00 H +ATOM 10 CG MET 1 15.388 34.252 22.245 1.00 0.00 C +ATOM 11 HG2 MET 1 16.290 34.012 22.808 1.00 0.00 H +ATOM 12 HG3 MET 1 14.536 33.827 22.774 1.00 0.00 H +ATOM 13 SD MET 1 15.536 33.423 20.631 1.00 0.00 S +ATOM 14 CE MET 1 13.841 33.570 20.001 1.00 0.00 C +ATOM 15 HE1 MET 1 13.556 34.619 19.924 1.00 0.00 H +ATOM 16 HE2 MET 1 13.784 33.117 19.011 1.00 0.00 H +ATOM 17 HE3 MET 1 13.151 33.052 20.669 1.00 0.00 H +ATOM 18 C MET 1 16.235 36.020 24.497 1.00 0.00 C +ATOM 19 O MET 1 17.383 36.380 24.260 1.00 0.00 O +ATOM 20 N GLN 2 15.938 35.188 25.498 1.00 0.00 N +ATOM 21 H GLN 2 14.971 34.957 25.669 1.00 0.00 H +ATOM 22 CA GLN 2 16.932 34.498 26.333 1.00 0.00 C +ATOM 23 HA GLN 2 17.687 35.215 26.660 1.00 0.00 H +ATOM 24 CB GLN 2 16.209 33.943 27.579 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.287 33.458 27.254 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.811 33.171 28.048 1.00 0.00 H +ATOM 27 CG GLN 2 15.861 35.020 28.629 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.488 35.909 28.131 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.056 34.636 29.260 1.00 0.00 H +ATOM 30 CD GLN 2 17.025 35.443 29.523 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.185 35.106 29.309 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.767 36.182 30.583 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.533 36.436 31.175 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.848 36.586 30.697 1.00 0.00 H +ATOM 35 C GLN 2 17.645 33.388 25.534 1.00 0.00 C +ATOM 36 O GLN 2 17.256 32.220 25.591 1.00 0.00 O +ATOM 37 N TYR 3 18.687 33.745 24.775 1.00 0.00 N +ATOM 38 H TYR 3 18.965 34.723 24.789 1.00 0.00 H +ATOM 39 CA TYR 3 19.555 32.800 24.053 1.00 0.00 C +ATOM 40 HA TYR 3 18.943 32.202 23.374 1.00 0.00 H +ATOM 41 CB TYR 3 20.598 33.559 23.215 1.00 0.00 C +ATOM 42 HB2 TYR 3 21.078 34.317 23.834 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.375 32.858 22.909 1.00 0.00 H +ATOM 44 CG TYR 3 20.039 34.208 21.963 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.998 33.472 20.761 1.00 0.00 C +ATOM 46 HD1 TYR 3 20.369 32.456 20.738 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.498 34.061 19.585 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.491 33.503 18.660 1.00 0.00 H +ATOM 49 CZ TYR 3 19.029 35.392 19.611 1.00 0.00 C +ATOM 50 OH TYR 3 18.552 35.960 18.473 1.00 0.00 O +ATOM 51 HH TYR 3 18.603 35.354 17.732 1.00 0.00 H +ATOM 52 CE2 TYR 3 19.063 36.128 20.813 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.706 37.148 20.823 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.573 35.537 21.986 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.608 36.108 22.906 1.00 0.00 H +ATOM 56 C TYR 3 20.248 31.845 25.033 1.00 0.00 C +ATOM 57 O TYR 3 20.685 32.264 26.106 1.00 0.00 O +ATOM 58 N LYS 4 20.340 30.556 24.692 1.00 0.00 N +ATOM 59 H LYS 4 20.129 30.301 23.730 1.00 0.00 H +ATOM 60 CA LYS 4 20.870 29.502 25.568 1.00 0.00 C +ATOM 61 HA LYS 4 20.589 29.722 26.594 1.00 0.00 H +ATOM 62 CB LYS 4 20.256 28.137 25.182 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.229 28.055 24.096 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.912 27.343 25.544 1.00 0.00 H +ATOM 65 CG LYS 4 18.844 27.837 25.733 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.594 26.814 25.445 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.868 27.879 26.822 1.00 0.00 H +ATOM 68 CD LYS 4 17.732 28.765 25.211 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.855 29.758 25.642 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.845 28.854 24.128 1.00 0.00 H +ATOM 71 CE LYS 4 16.303 28.256 25.490 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.611 28.845 24.883 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.227 27.221 25.146 1.00 0.00 H +ATOM 74 NZ LYS 4 15.885 28.351 26.914 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.888 29.303 27.259 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.923 28.017 27.023 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.456 27.790 27.526 1.00 0.00 H +ATOM 78 C LYS 4 22.405 29.472 25.556 1.00 0.00 C +ATOM 79 O LYS 4 23.061 29.874 24.599 1.00 0.00 O +HETATM 80 N HX1 5 23.001 28.976 26.634 1.00 0.00 N +HETATM 81 CA HX1 5 24.455 28.837 26.775 1.00 0.00 C +HETATM 82 C HX1 5 24.789 27.634 27.660 1.00 0.00 C +HETATM 83 O HX1 5 24.335 27.562 28.808 1.00 0.00 O +HETATM 84 CB HX1 5 25.031 30.148 27.334 1.00 0.00 C +HETATM 85 CG HX1 5 26.538 30.209 27.470 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.450 29.325 26.959 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.211 31.181 28.221 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.506 30.842 28.126 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.675 29.712 27.423 1.00 0.00 N +HETATM 90 H HX1 5 22.422 28.791 27.450 1.00 0.00 H +HETATM 91 HA HX1 5 24.897 28.670 25.791 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.590 30.338 28.315 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.725 30.964 26.679 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.265 28.439 26.367 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.294 31.335 28.679 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.512 29.133 27.423 1.00 0.00 H +ATOM 97 N ILE 6 25.553 26.687 27.103 1.00 0.00 N +ATOM 98 H ILE 6 25.860 26.820 26.140 1.00 0.00 H +ATOM 99 CA ILE 6 26.053 25.480 27.773 1.00 0.00 C +ATOM 100 HA ILE 6 25.487 25.350 28.698 1.00 0.00 H +ATOM 101 CB ILE 6 25.775 24.227 26.903 1.00 0.00 C +ATOM 102 HB ILE 6 26.211 24.392 25.915 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.398 22.945 27.494 1.00 0.00 C +ATOM 104 HG21 ILE 6 26.001 22.755 28.494 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.175 22.090 26.856 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.485 23.023 27.529 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.239 24.061 26.759 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.800 23.944 27.752 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.821 24.964 26.310 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.785 22.881 25.889 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.964 21.937 26.408 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.714 22.975 25.701 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.321 22.892 24.937 1.00 0.00 H +ATOM 114 C ILE 6 27.522 25.671 28.210 1.00 0.00 C +ATOM 115 O ILE 6 28.273 26.491 27.680 1.00 0.00 O +ATOM 116 N VAL 7 27.870 24.954 29.270 1.00 0.00 N +ATOM 117 H VAL 7 27.214 24.234 29.536 1.00 0.00 H +ATOM 118 CA VAL 7 28.880 25.283 30.283 1.00 0.00 C +ATOM 119 HA VAL 7 28.902 26.368 30.378 1.00 0.00 H +ATOM 120 CB VAL 7 28.316 24.707 31.597 1.00 0.00 C +ATOM 121 HB VAL 7 27.286 25.053 31.693 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.317 23.175 31.642 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.336 22.787 31.583 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.862 22.843 32.571 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.740 22.771 30.810 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.045 25.229 32.817 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.029 26.318 32.819 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.558 24.874 33.725 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.062 24.859 32.782 1.00 0.00 H +ATOM 130 C VAL 7 30.322 24.815 29.967 1.00 0.00 C +ATOM 131 O VAL 7 30.512 23.771 29.342 1.00 0.00 O +ATOM 132 N ARG 8 31.363 25.547 30.427 1.00 0.00 N +ATOM 133 H ARG 8 31.169 26.465 30.808 1.00 0.00 H +ATOM 134 CA ARG 8 32.770 25.046 30.373 1.00 0.00 C +ATOM 135 HA ARG 8 32.887 24.637 29.359 1.00 0.00 H +ATOM 136 CB ARG 8 33.844 26.151 30.558 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.674 25.906 29.876 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.435 27.096 30.214 1.00 0.00 H +ATOM 139 CG ARG 8 34.419 26.296 31.981 1.00 0.00 C +ATOM 140 HG2 ARG 8 33.640 26.276 32.712 1.00 0.00 H +ATOM 141 HG3 ARG 8 35.099 25.463 32.178 1.00 0.00 H +ATOM 142 CD ARG 8 35.210 27.586 32.197 1.00 0.00 C +ATOM 143 HD2 ARG 8 35.722 27.511 33.189 1.00 0.00 H +ATOM 144 HD3 ARG 8 36.011 27.669 31.407 1.00 0.00 H +ATOM 145 NE ARG 8 34.351 28.769 32.290 1.00 0.00 N +ATOM 146 HE ARG 8 33.380 28.725 32.027 1.00 0.00 H +ATOM 147 CZ ARG 8 34.758 29.939 32.729 1.00 0.00 C +ATOM 148 NH1 ARG 8 33.881 30.880 32.889 1.00 0.00 N +ATOM 149 HH11 ARG 8 32.893 30.650 32.985 1.00 0.00 H +ATOM 150 HH12 ARG 8 34.101 31.822 33.160 1.00 0.00 H +ATOM 151 NH2 ARG 8 35.998 30.297 32.900 1.00 0.00 N +ATOM 152 HH21 ARG 8 36.679 29.649 32.569 1.00 0.00 H +ATOM 153 HH22 ARG 8 36.246 31.284 32.924 1.00 0.00 H +ATOM 154 C ARG 8 33.032 23.874 31.325 1.00 0.00 C +ATOM 155 O ARG 8 32.495 23.842 32.438 1.00 0.00 O +ATOM 156 N GLY 9 33.996 23.029 30.946 1.00 0.00 N +ATOM 157 H GLY 9 34.387 23.169 30.023 1.00 0.00 H +ATOM 158 CA GLY 9 34.398 21.818 31.656 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.429 21.574 31.386 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.352 21.988 32.736 1.00 0.00 H +ATOM 161 C GLY 9 33.502 20.624 31.304 1.00 0.00 C +ATOM 162 O GLY 9 32.440 20.781 30.707 1.00 0.00 O +ATOM 163 N LYS 10 33.939 19.418 31.693 1.00 0.00 N +ATOM 164 H LYS 10 34.878 19.355 32.062 1.00 0.00 H +ATOM 165 CA LYS 10 33.175 18.163 31.539 1.00 0.00 C +ATOM 166 HA LYS 10 32.267 18.388 30.974 1.00 0.00 H +ATOM 167 CB LYS 10 34.009 17.178 30.697 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.674 17.752 30.050 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.630 16.564 31.347 1.00 0.00 H +ATOM 170 CG LYS 10 33.157 16.281 29.785 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.562 15.599 30.390 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.483 16.911 29.207 1.00 0.00 H +ATOM 173 CD LYS 10 34.044 15.489 28.815 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.709 16.183 28.298 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.648 14.775 29.373 1.00 0.00 H +ATOM 176 CE LYS 10 33.207 14.748 27.768 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.627 13.967 28.265 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.513 15.465 27.321 1.00 0.00 H +ATOM 179 NZ LYS 10 34.072 14.179 26.706 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.778 13.564 27.081 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.544 13.711 25.985 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.597 14.939 26.247 1.00 0.00 H +ATOM 183 C LYS 10 32.677 17.588 32.882 1.00 0.00 C +ATOM 184 O LYS 10 31.971 16.590 32.914 1.00 0.00 O +ATOM 185 N ILE 11 33.056 18.232 33.992 1.00 0.00 N +ATOM 186 H ILE 11 33.659 19.026 33.866 1.00 0.00 H +ATOM 187 CA ILE 11 32.651 17.907 35.382 1.00 0.00 C +ATOM 188 HA ILE 11 32.486 16.828 35.456 1.00 0.00 H +ATOM 189 CB ILE 11 33.782 18.291 36.369 1.00 0.00 C +ATOM 190 HB ILE 11 33.419 18.074 37.374 1.00 0.00 H +ATOM 191 CG2 ILE 11 35.016 17.406 36.136 1.00 0.00 C +ATOM 192 HG21 ILE 11 35.481 17.632 35.178 1.00 0.00 H +ATOM 193 HG22 ILE 11 35.741 17.567 36.930 1.00 0.00 H +ATOM 194 HG23 ILE 11 34.721 16.358 36.157 1.00 0.00 H +ATOM 195 CG1 ILE 11 34.118 19.802 36.301 1.00 0.00 C +ATOM 196 HG12 ILE 11 34.608 20.029 35.353 1.00 0.00 H +ATOM 197 HG13 ILE 11 33.196 20.383 36.349 1.00 0.00 H +ATOM 198 CD1 ILE 11 35.014 20.289 37.443 1.00 0.00 C +ATOM 199 HD11 ILE 11 35.994 19.821 37.385 1.00 0.00 H +ATOM 200 HD12 ILE 11 35.138 21.369 37.362 1.00 0.00 H +ATOM 201 HD13 ILE 11 34.550 20.057 38.402 1.00 0.00 H +ATOM 202 C ILE 11 31.328 18.569 35.823 1.00 0.00 C +ATOM 203 O ILE 11 30.798 18.219 36.873 1.00 0.00 O +ATOM 204 N ARG 12 30.820 19.529 35.042 1.00 0.00 N +ATOM 205 H ARG 12 31.278 19.702 34.158 1.00 0.00 H +ATOM 206 CA ARG 12 29.534 20.208 35.245 1.00 0.00 C +ATOM 207 HA ARG 12 28.934 19.608 35.925 1.00 0.00 H +ATOM 208 CB ARG 12 29.736 21.588 35.902 1.00 0.00 C +ATOM 209 HB2 ARG 12 28.762 22.047 36.063 1.00 0.00 H +ATOM 210 HB3 ARG 12 30.192 21.453 36.883 1.00 0.00 H +ATOM 211 CG ARG 12 30.611 22.587 35.105 1.00 0.00 C +ATOM 212 HG2 ARG 12 31.610 22.179 34.948 1.00 0.00 H +ATOM 213 HG3 ARG 12 30.164 22.773 34.130 1.00 0.00 H +ATOM 214 CD ARG 12 30.767 23.952 35.814 1.00 0.00 C +ATOM 215 HD2 ARG 12 29.765 24.306 36.099 1.00 0.00 H +ATOM 216 HD3 ARG 12 31.359 23.819 36.734 1.00 0.00 H +ATOM 217 NE ARG 12 31.400 24.948 34.931 1.00 0.00 N +ATOM 218 HE ARG 12 31.866 24.594 34.104 1.00 0.00 H +ATOM 219 CZ ARG 12 31.184 26.243 34.951 1.00 0.00 C +ATOM 220 NH1 ARG 12 31.497 26.929 33.903 1.00 0.00 N +ATOM 221 HH11 ARG 12 31.810 26.554 33.042 1.00 0.00 H +ATOM 222 HH12 ARG 12 31.350 27.924 33.941 1.00 0.00 H +ATOM 223 NH2 ARG 12 30.679 26.915 35.950 1.00 0.00 N +ATOM 224 HH21 ARG 12 30.450 26.438 36.806 1.00 0.00 H +ATOM 225 HH22 ARG 12 30.627 27.929 35.864 1.00 0.00 H +ATOM 226 C ARG 12 28.804 20.259 33.911 1.00 0.00 C +ATOM 227 O ARG 12 29.451 20.417 32.881 1.00 0.00 O +ATOM 228 N LYS 13 27.480 20.077 33.923 1.00 0.00 N +ATOM 229 H LYS 13 27.050 19.916 34.826 1.00 0.00 H +ATOM 230 CA LYS 13 26.656 19.816 32.719 1.00 0.00 C +ATOM 231 HA LYS 13 27.232 20.091 31.832 1.00 0.00 H +ATOM 232 CB LYS 13 26.383 18.298 32.660 1.00 0.00 C +ATOM 233 HB2 LYS 13 27.285 17.780 32.997 1.00 0.00 H +ATOM 234 HB3 LYS 13 25.578 18.062 33.363 1.00 0.00 H +ATOM 235 CG LYS 13 26.045 17.746 31.257 1.00 0.00 C +ATOM 236 HG2 LYS 13 25.140 18.217 30.867 1.00 0.00 H +ATOM 237 HG3 LYS 13 26.877 17.978 30.585 1.00 0.00 H +ATOM 238 CD LYS 13 25.854 16.218 31.298 1.00 0.00 C +ATOM 239 HD2 LYS 13 25.820 15.843 30.277 1.00 0.00 H +ATOM 240 HD3 LYS 13 26.722 15.775 31.791 1.00 0.00 H +ATOM 241 CE LYS 13 24.561 15.813 32.027 1.00 0.00 C +ATOM 242 HE2 LYS 13 24.372 16.531 32.830 1.00 0.00 H +ATOM 243 HE3 LYS 13 23.717 15.868 31.330 1.00 0.00 H +ATOM 244 NZ LYS 13 24.668 14.461 32.629 1.00 0.00 N +ATOM 245 HZ1 LYS 13 25.518 14.384 33.174 1.00 0.00 H +ATOM 246 HZ2 LYS 13 23.932 14.309 33.317 1.00 0.00 H +ATOM 247 HZ3 LYS 13 24.624 13.709 31.952 1.00 0.00 H +ATOM 248 C LYS 13 25.379 20.680 32.662 1.00 0.00 C +ATOM 249 O LYS 13 24.388 20.330 32.023 1.00 0.00 O +ATOM 250 N GLY 14 25.390 21.796 33.400 1.00 0.00 N +ATOM 251 H GLY 14 26.246 22.035 33.878 1.00 0.00 H +ATOM 252 CA GLY 14 24.280 22.747 33.473 1.00 0.00 C +ATOM 253 HA2 GLY 14 23.348 22.197 33.614 1.00 0.00 H +ATOM 254 HA3 GLY 14 24.418 23.397 34.337 1.00 0.00 H +ATOM 255 C GLY 14 24.128 23.626 32.229 1.00 0.00 C +ATOM 256 O GLY 14 24.998 23.699 31.363 1.00 0.00 O +ATOM 257 N VAL 15 23.006 24.337 32.183 1.00 0.00 N +ATOM 258 H VAL 15 22.356 24.242 32.949 1.00 0.00 H +ATOM 259 CA VAL 15 22.625 25.269 31.109 1.00 0.00 C +ATOM 260 HA VAL 15 23.533 25.571 30.584 1.00 0.00 H +ATOM 261 CB VAL 15 21.699 24.575 30.080 1.00 0.00 C +ATOM 262 HB VAL 15 22.226 23.703 29.700 1.00 0.00 H +ATOM 263 CG1 VAL 15 20.372 24.109 30.694 1.00 0.00 C +ATOM 264 HG11 VAL 15 19.795 24.957 31.071 1.00 0.00 H +ATOM 265 HG12 VAL 15 19.787 23.585 29.936 1.00 0.00 H +ATOM 266 HG13 VAL 15 20.563 23.410 31.511 1.00 0.00 H +ATOM 267 CG2 VAL 15 21.379 25.483 28.885 1.00 0.00 C +ATOM 268 HG21 VAL 15 22.302 25.862 28.445 1.00 0.00 H +ATOM 269 HG22 VAL 15 20.852 24.902 28.127 1.00 0.00 H +ATOM 270 HG23 VAL 15 20.744 26.318 29.186 1.00 0.00 H +ATOM 271 C VAL 15 22.002 26.523 31.716 1.00 0.00 C +ATOM 272 O VAL 15 21.361 26.461 32.765 1.00 0.00 O +HETATM 273 N HY1 16 22.211 27.669 31.079 1.00 0.00 N +HETATM 274 CA HY1 16 21.615 28.952 31.457 1.00 0.00 C +HETATM 275 C HY1 16 21.470 29.832 30.196 1.00 0.00 C +HETATM 276 O HY1 16 21.720 29.350 29.083 1.00 0.00 O +HETATM 277 CB HY1 16 22.465 29.589 32.569 1.00 0.00 C +HETATM 278 CG HY1 16 23.891 29.860 32.143 1.00 0.00 C +HETATM 279 CD2 HY1 16 24.317 31.011 31.555 1.00 0.00 C +HETATM 280 ND1 HY1 16 24.948 28.966 32.110 1.00 0.00 N +HETATM 281 CE1 HY1 16 25.985 29.583 31.514 1.00 0.00 C +HETATM 282 NE2 HY1 16 25.634 30.826 31.151 1.00 0.00 N +HETATM 283 H HY1 16 22.755 27.649 30.220 1.00 0.00 H +HETATM 284 HA HY1 16 20.616 28.773 31.854 1.00 0.00 H +HETATM 285 HB2 HY1 16 22.004 30.524 32.886 1.00 0.00 H +HETATM 286 HB3 HY1 16 22.473 28.931 33.435 1.00 0.00 H +HETATM 287 HD1 HY1 16 24.946 28.021 32.495 1.00 0.00 H +HETATM 288 HD2 HY1 16 23.723 31.892 31.381 1.00 0.00 H +HETATM 289 HE1 HY1 16 26.970 29.151 31.359 1.00 0.00 H +ATOM 290 N THR 17 21.045 31.098 30.314 1.00 0.00 N +ATOM 291 H THR 17 20.837 31.487 31.225 1.00 0.00 H +ATOM 292 CA THR 17 20.674 31.937 29.170 1.00 0.00 C +ATOM 293 HA THR 17 21.122 31.522 28.276 1.00 0.00 H +ATOM 294 CB THR 17 19.158 31.970 28.996 1.00 0.00 C +ATOM 295 HB THR 17 18.914 32.636 28.169 1.00 0.00 H +ATOM 296 CG2 THR 17 18.507 30.601 28.730 1.00 0.00 C +ATOM 297 HG21 THR 17 18.684 29.925 29.565 1.00 0.00 H +ATOM 298 HG22 THR 17 17.431 30.727 28.608 1.00 0.00 H +ATOM 299 HG23 THR 17 18.909 30.163 27.822 1.00 0.00 H +ATOM 300 OG1 THR 17 18.545 32.490 30.158 1.00 0.00 O +ATOM 301 HG1 THR 17 18.497 33.455 30.031 1.00 0.00 H +ATOM 302 C THR 17 21.180 33.371 29.303 1.00 0.00 C +ATOM 303 O THR 17 21.540 33.816 30.396 1.00 0.00 O +HETATM 304 N HY2 18 21.171 34.107 28.183 1.00 0.00 N +HETATM 305 CA HY2 18 21.498 35.536 28.089 1.00 0.00 C +HETATM 306 C HY2 18 20.492 36.271 27.203 1.00 0.00 C +HETATM 307 O HY2 18 20.219 35.844 26.081 1.00 0.00 O +HETATM 308 CB HY2 18 22.938 35.721 27.585 1.00 0.00 C +HETATM 309 CG HY2 18 23.933 35.087 28.542 1.00 0.00 C +HETATM 310 CD2 HY2 18 24.630 33.923 28.352 1.00 0.00 C +HETATM 311 ND1 HY2 18 24.085 35.418 29.870 1.00 0.00 N +HETATM 312 CE1 HY2 18 24.825 34.466 30.454 1.00 0.00 C +HETATM 313 NE2 HY2 18 25.202 33.534 29.567 1.00 0.00 N +HETATM 314 H HY2 18 20.857 33.648 27.329 1.00 0.00 H +HETATM 315 HA HY2 18 21.447 35.973 29.085 1.00 0.00 H +HETATM 316 HB2 HY2 18 23.047 35.274 26.592 1.00 0.00 H +HETATM 317 HB3 HY2 18 23.155 36.786 27.492 1.00 0.00 H +HETATM 318 HD1 HY2 18 23.642 36.188 30.351 1.00 0.00 H +HETATM 319 HD2 HY2 18 24.646 33.351 27.443 1.00 0.00 H +HETATM 320 HE1 HY2 18 25.077 34.456 31.502 1.00 0.00 H +ATOM 321 N GLU 19 19.933 37.368 27.719 1.00 0.00 N +ATOM 322 H GLU 19 20.219 37.675 28.639 1.00 0.00 H +ATOM 323 CA GLU 19 18.908 38.182 27.051 1.00 0.00 C +ATOM 324 HA GLU 19 18.170 37.510 26.600 1.00 0.00 H +ATOM 325 CB GLU 19 18.203 39.035 28.129 1.00 0.00 C +ATOM 326 HB2 GLU 19 17.865 38.372 28.932 1.00 0.00 H +ATOM 327 HB3 GLU 19 18.925 39.725 28.561 1.00 0.00 H +ATOM 328 CG GLU 19 16.995 39.841 27.638 1.00 0.00 C +ATOM 329 HG2 GLU 19 16.553 40.368 28.483 1.00 0.00 H +ATOM 330 HG3 GLU 19 17.328 40.583 26.915 1.00 0.00 H +ATOM 331 CD GLU 19 15.947 38.924 26.995 1.00 0.00 C +ATOM 332 OE1 GLU 19 16.027 38.727 25.761 1.00 0.00 O +ATOM 333 OE2 GLU 19 15.108 38.347 27.720 1.00 0.00 O +ATOM 334 C GLU 19 19.509 39.052 25.942 1.00 0.00 C +ATOM 335 O GLU 19 20.499 39.742 26.173 1.00 0.00 O +ATOM 336 N ALA 20 18.918 39.025 24.746 1.00 0.00 N +ATOM 337 H ALA 20 18.106 38.434 24.626 1.00 0.00 H +ATOM 338 CA ALA 20 19.296 39.884 23.617 1.00 0.00 C +ATOM 339 HA ALA 20 19.430 40.905 23.995 1.00 0.00 H +ATOM 340 CB ALA 20 20.636 39.403 23.031 1.00 0.00 C +ATOM 341 HB1 ALA 20 20.511 38.417 22.593 1.00 0.00 H +ATOM 342 HB2 ALA 20 20.977 40.099 22.267 1.00 0.00 H +ATOM 343 HB3 ALA 20 21.397 39.358 23.807 1.00 0.00 H +ATOM 344 C ALA 20 18.227 39.924 22.501 1.00 0.00 C +ATOM 345 O ALA 20 17.354 39.055 22.410 1.00 0.00 O +ATOM 346 N VAL 21 18.350 40.904 21.604 1.00 0.00 N +ATOM 347 H VAL 21 19.047 41.606 21.753 1.00 0.00 H +ATOM 348 CA VAL 21 17.624 40.946 20.322 1.00 0.00 C +ATOM 349 HA VAL 21 16.630 40.506 20.449 1.00 0.00 H +ATOM 350 CB VAL 21 17.427 42.389 19.807 1.00 0.00 C +ATOM 351 HB VAL 21 16.798 42.355 18.923 1.00 0.00 H +ATOM 352 CG1 VAL 21 16.710 43.248 20.843 1.00 0.00 C +ATOM 353 HG11 VAL 21 17.331 43.410 21.732 1.00 0.00 H +ATOM 354 HG12 VAL 21 16.462 44.223 20.414 1.00 0.00 H +ATOM 355 HG13 VAL 21 15.775 42.769 21.155 1.00 0.00 H +ATOM 356 CG2 VAL 21 18.740 43.079 19.422 1.00 0.00 C +ATOM 357 HG21 VAL 21 19.223 42.555 18.594 1.00 0.00 H +ATOM 358 HG22 VAL 21 18.542 44.101 19.085 1.00 0.00 H +ATOM 359 HG23 VAL 21 19.435 43.121 20.266 1.00 0.00 H +ATOM 360 C VAL 21 18.314 40.093 19.222 1.00 0.00 C +ATOM 361 O VAL 21 17.710 39.857 18.171 1.00 0.00 O +ATOM 362 N ASP 22 19.566 39.676 19.443 1.00 0.00 N +ATOM 363 H ASP 22 19.965 39.914 20.332 1.00 0.00 H +ATOM 364 CA ASP 22 20.442 39.012 18.480 1.00 0.00 C +ATOM 365 HA ASP 22 19.843 38.307 17.885 1.00 0.00 H +ATOM 366 CB ASP 22 21.058 40.079 17.578 1.00 0.00 C +ATOM 367 HB2 ASP 22 20.259 40.715 17.194 1.00 0.00 H +ATOM 368 HB3 ASP 22 21.756 40.678 18.156 1.00 0.00 H +ATOM 369 CG ASP 22 21.831 39.502 16.363 1.00 0.00 C +ATOM 370 OD1 ASP 22 22.061 40.271 15.411 1.00 0.00 O +ATOM 371 OD2 ASP 22 22.119 38.268 16.335 1.00 0.00 O +ATOM 372 C ASP 22 21.513 38.201 19.242 1.00 0.00 C +ATOM 373 O ASP 22 22.031 38.649 20.272 1.00 0.00 O +ATOM 374 N TRP 23 21.909 37.031 18.735 1.00 0.00 N +ATOM 375 H TRP 23 21.638 36.851 17.773 1.00 0.00 H +ATOM 376 CA TRP 23 23.040 36.270 19.275 1.00 0.00 C +ATOM 377 HA TRP 23 22.833 36.116 20.324 1.00 0.00 H +ATOM 378 CB TRP 23 23.117 34.888 18.598 1.00 0.00 C +ATOM 379 HB2 TRP 23 23.874 34.310 19.120 1.00 0.00 H +ATOM 380 HB3 TRP 23 22.165 34.377 18.755 1.00 0.00 H +ATOM 381 CG TRP 23 23.449 34.862 17.135 1.00 0.00 C +ATOM 382 CD1 TRP 23 22.570 34.627 16.135 1.00 0.00 C +ATOM 383 HD1 TRP 23 21.516 34.414 16.262 1.00 0.00 H +ATOM 384 NE1 TRP 23 23.221 34.705 14.920 1.00 0.00 N +ATOM 385 HE1 TRP 23 22.760 34.582 14.028 1.00 0.00 H +ATOM 386 CE2 TRP 23 24.561 34.990 15.077 1.00 0.00 C +ATOM 387 CZ2 TRP 23 25.614 35.177 14.167 1.00 0.00 C +ATOM 388 HZ2 TRP 23 25.433 35.117 13.103 1.00 0.00 H +ATOM 389 CH2 TRP 23 26.902 35.456 14.657 1.00 0.00 C +ATOM 390 HH2 TRP 23 27.718 35.616 13.968 1.00 0.00 H +ATOM 391 CZ3 TRP 23 27.123 35.527 16.044 1.00 0.00 C +ATOM 392 HZ3 TRP 23 28.116 35.739 16.421 1.00 0.00 H +ATOM 393 CE3 TRP 23 26.061 35.320 16.947 1.00 0.00 C +ATOM 394 HE3 TRP 23 26.258 35.366 18.006 1.00 0.00 H +ATOM 395 CD2 TRP 23 24.746 35.068 16.490 1.00 0.00 C +ATOM 396 C TRP 23 24.353 37.048 19.161 1.00 0.00 C +ATOM 397 O TRP 23 25.202 36.925 20.040 1.00 0.00 O +ATOM 398 N ALA 24 24.513 37.913 18.151 1.00 0.00 N +ATOM 399 H ALA 24 23.791 37.953 17.427 1.00 0.00 H +ATOM 400 CA ALA 24 25.713 38.743 17.966 1.00 0.00 C +ATOM 401 HA ALA 24 26.589 38.100 18.116 1.00 0.00 H +ATOM 402 CB ALA 24 25.741 39.218 16.508 1.00 0.00 C +ATOM 403 HB1 ALA 24 24.898 39.872 16.308 1.00 0.00 H +ATOM 404 HB2 ALA 24 26.664 39.753 16.313 1.00 0.00 H +ATOM 405 HB3 ALA 24 25.686 38.361 15.838 1.00 0.00 H +ATOM 406 C ALA 24 25.841 39.914 18.967 1.00 0.00 C +ATOM 407 O ALA 24 26.920 40.505 19.096 1.00 0.00 O +ATOM 408 N GLU 25 24.772 40.231 19.705 1.00 0.00 N +ATOM 409 H GLU 25 23.914 39.733 19.521 1.00 0.00 H +ATOM 410 CA GLU 25 24.831 41.042 20.925 1.00 0.00 C +ATOM 411 HA GLU 25 25.721 41.677 20.911 1.00 0.00 H +ATOM 412 CB GLU 25 23.600 41.965 21.017 1.00 0.00 C +ATOM 413 HB2 GLU 25 22.700 41.386 20.828 1.00 0.00 H +ATOM 414 HB3 GLU 25 23.533 42.367 22.029 1.00 0.00 H +ATOM 415 CG GLU 25 23.657 43.147 20.037 1.00 0.00 C +ATOM 416 HG2 GLU 25 23.655 42.758 19.018 1.00 0.00 H +ATOM 417 HG3 GLU 25 22.763 43.759 20.160 1.00 0.00 H +ATOM 418 CD GLU 25 24.906 44.025 20.251 1.00 0.00 C +ATOM 419 OE1 GLU 25 25.126 44.521 21.384 1.00 0.00 O +ATOM 420 OE2 GLU 25 25.705 44.142 19.291 1.00 0.00 O +ATOM 421 C GLU 25 24.966 40.157 22.190 1.00 0.00 C +ATOM 422 O GLU 25 25.737 40.502 23.079 1.00 0.00 O +ATOM 423 N ALA 26 24.307 38.990 22.234 1.00 0.00 N +ATOM 424 H ALA 26 23.640 38.753 21.501 1.00 0.00 H +ATOM 425 CA ALA 26 24.488 38.023 23.322 1.00 0.00 C +ATOM 426 HA ALA 26 24.289 38.521 24.266 1.00 0.00 H +ATOM 427 CB ALA 26 23.562 36.834 23.133 1.00 0.00 C +ATOM 428 HB1 ALA 26 23.873 36.249 22.261 1.00 0.00 H +ATOM 429 HB2 ALA 26 23.595 36.188 24.016 1.00 0.00 H +ATOM 430 HB3 ALA 26 22.560 37.229 22.991 1.00 0.00 H +ATOM 431 C ALA 26 25.951 37.544 23.451 1.00 0.00 C +ATOM 432 O ALA 26 26.383 37.205 24.546 1.00 0.00 O +ATOM 433 N GLU 27 26.716 37.580 22.359 1.00 0.00 N +ATOM 434 H GLU 27 26.253 37.649 21.473 1.00 0.00 H +ATOM 435 CA GLU 27 28.181 37.359 22.355 1.00 0.00 C +ATOM 436 HA GLU 27 28.346 36.428 22.886 1.00 0.00 H +ATOM 437 CB GLU 27 28.702 37.292 20.894 1.00 0.00 C +ATOM 438 HB2 GLU 27 28.144 36.514 20.363 1.00 0.00 H +ATOM 439 HB3 GLU 27 28.488 38.276 20.408 1.00 0.00 H +ATOM 440 CG GLU 27 30.194 36.914 20.791 1.00 0.00 C +ATOM 441 HG2 GLU 27 30.798 37.373 21.568 1.00 0.00 H +ATOM 442 HG3 GLU 27 30.240 35.843 20.862 1.00 0.00 H +ATOM 443 CD GLU 27 30.769 37.259 19.424 1.00 0.00 C +ATOM 444 OE1 GLU 27 31.493 38.291 19.268 1.00 0.00 O +ATOM 445 OE2 GLU 27 30.578 36.467 18.446 1.00 0.00 O +ATOM 446 C GLU 27 28.933 38.479 23.123 1.00 0.00 C +ATOM 447 O GLU 27 29.789 38.191 23.962 1.00 0.00 O +ATOM 448 N LYS 28 28.591 39.749 22.854 1.00 0.00 N +ATOM 449 H LYS 28 27.866 39.903 22.160 1.00 0.00 H +ATOM 450 CA LYS 28 29.177 40.912 23.543 1.00 0.00 C +ATOM 451 HA LYS 28 30.258 40.826 23.486 1.00 0.00 H +ATOM 452 CB LYS 28 28.749 42.221 22.870 1.00 0.00 C +ATOM 453 HB2 LYS 28 27.660 42.333 22.922 1.00 0.00 H +ATOM 454 HB3 LYS 28 29.200 43.046 23.424 1.00 0.00 H +ATOM 455 CG LYS 28 29.188 42.308 21.401 1.00 0.00 C +ATOM 456 HG2 LYS 28 30.254 42.094 21.331 1.00 0.00 H +ATOM 457 HG3 LYS 28 28.641 41.564 20.826 1.00 0.00 H +ATOM 458 CD LYS 28 28.915 43.706 20.821 1.00 0.00 C +ATOM 459 HD2 LYS 28 27.883 43.999 21.023 1.00 0.00 H +ATOM 460 HD3 LYS 28 29.570 44.425 21.318 1.00 0.00 H +ATOM 461 CE LYS 28 29.175 43.759 19.309 1.00 0.00 C +ATOM 462 HE2 LYS 28 29.270 44.808 19.021 1.00 0.00 H +ATOM 463 HE3 LYS 28 30.126 43.269 19.095 1.00 0.00 H +ATOM 464 NZ LYS 28 28.069 43.129 18.542 1.00 0.00 N +ATOM 465 HZ1 LYS 28 27.190 43.612 18.760 1.00 0.00 H +ATOM 466 HZ2 LYS 28 28.198 43.199 17.544 1.00 0.00 H +ATOM 467 HZ3 LYS 28 27.908 42.160 18.810 1.00 0.00 H +ATOM 468 C LYS 28 28.807 40.932 25.020 1.00 0.00 C +ATOM 469 O LYS 28 29.677 41.059 25.882 1.00 0.00 O +ATOM 470 N PHE 29 27.534 40.696 25.351 1.00 0.00 N +ATOM 471 H PHE 29 26.850 40.637 24.596 1.00 0.00 H +ATOM 472 CA PHE 29 27.085 40.521 26.735 1.00 0.00 C +ATOM 473 HA PHE 29 27.340 41.399 27.305 1.00 0.00 H +ATOM 474 CB PHE 29 25.548 40.408 26.768 1.00 0.00 C +ATOM 475 HB2 PHE 29 25.256 39.470 26.292 1.00 0.00 H +ATOM 476 HB3 PHE 29 25.213 40.377 27.812 1.00 0.00 H +ATOM 477 CG PHE 29 24.780 41.539 26.098 1.00 0.00 C +ATOM 478 CD1 PHE 29 23.555 41.271 25.445 1.00 0.00 C +ATOM 479 HD1 PHE 29 23.147 40.268 25.447 1.00 0.00 H +ATOM 480 CE1 PHE 29 22.861 42.291 24.763 1.00 0.00 C +ATOM 481 HE1 PHE 29 21.944 42.064 24.247 1.00 0.00 H +ATOM 482 CZ PHE 29 23.389 43.595 24.738 1.00 0.00 C +ATOM 483 HZ PHE 29 22.888 44.372 24.182 1.00 0.00 H +ATOM 484 CE2 PHE 29 24.584 43.890 25.421 1.00 0.00 C +ATOM 485 HE2 PHE 29 24.989 44.890 25.404 1.00 0.00 H +ATOM 486 CD2 PHE 29 25.267 42.867 26.102 1.00 0.00 C +ATOM 487 HD2 PHE 29 26.187 43.110 26.606 1.00 0.00 H +ATOM 488 C PHE 29 27.757 39.285 27.408 1.00 0.00 C +ATOM 489 O PHE 29 27.951 39.315 28.627 1.00 0.00 O +ATOM 490 N THR 30 28.107 38.240 26.637 1.00 0.00 N +ATOM 491 H THR 30 27.892 38.272 25.643 1.00 0.00 H +ATOM 492 CA THR 30 28.857 37.078 27.134 1.00 0.00 C +ATOM 493 HA THR 30 28.490 36.842 28.093 1.00 0.00 H +ATOM 494 CB THR 30 28.711 35.822 26.164 1.00 0.00 C +ATOM 495 HB THR 30 29.084 36.150 25.197 1.00 0.00 H +ATOM 496 CG2 THR 30 29.631 34.697 26.551 1.00 0.00 C +ATOM 497 HG21 THR 30 29.536 34.335 27.563 1.00 0.00 H +ATOM 498 HG22 THR 30 29.500 33.826 25.902 1.00 0.00 H +ATOM 499 HG23 THR 30 30.652 35.020 26.392 1.00 0.00 H +ATOM 500 OG1 THR 30 27.374 35.342 26.118 1.00 0.00 O +ATOM 501 HG1 THR 30 26.854 36.062 25.695 1.00 0.00 H +ATOM 502 C THR 30 30.333 37.426 27.434 1.00 0.00 C +ATOM 503 O THR 30 30.859 36.996 28.446 1.00 0.00 O +ATOM 504 N LYS 31 30.983 38.324 26.709 1.00 0.00 N +ATOM 505 H LYS 31 30.520 38.707 25.896 1.00 0.00 H +ATOM 506 CA LYS 31 32.334 38.846 27.017 1.00 0.00 C +ATOM 507 HA LYS 31 32.976 38.020 27.293 1.00 0.00 H +ATOM 508 CB LYS 31 32.929 39.457 25.738 1.00 0.00 C +ATOM 509 HB2 LYS 31 32.236 40.194 25.323 1.00 0.00 H +ATOM 510 HB3 LYS 31 33.866 39.957 25.981 1.00 0.00 H +ATOM 511 CG LYS 31 33.218 38.364 24.689 1.00 0.00 C +ATOM 512 HG2 LYS 31 33.914 37.648 25.108 1.00 0.00 H +ATOM 513 HG3 LYS 31 32.316 37.824 24.417 1.00 0.00 H +ATOM 514 CD LYS 31 33.830 38.948 23.404 1.00 0.00 C +ATOM 515 HD2 LYS 31 33.075 39.546 22.894 1.00 0.00 H +ATOM 516 HD3 LYS 31 34.661 39.600 23.666 1.00 0.00 H +ATOM 517 CE LYS 31 34.328 37.865 22.434 1.00 0.00 C +ATOM 518 HE2 LYS 31 33.520 37.165 22.206 1.00 0.00 H +ATOM 519 HE3 LYS 31 34.607 38.350 21.493 1.00 0.00 H +ATOM 520 NZ LYS 31 35.504 37.125 22.957 1.00 0.00 N +ATOM 521 HZ1 LYS 31 35.242 36.342 23.541 1.00 0.00 H +ATOM 522 HZ2 LYS 31 36.052 36.717 22.188 1.00 0.00 H +ATOM 523 HZ3 LYS 31 36.122 37.714 23.520 1.00 0.00 H +ATOM 524 C LYS 31 32.336 39.792 28.211 1.00 0.00 C +ATOM 525 O LYS 31 33.319 39.773 28.948 1.00 0.00 O +ATOM 526 N ALA 32 31.249 40.543 28.451 1.00 0.00 N +ATOM 527 H ALA 32 30.508 40.566 27.750 1.00 0.00 H +ATOM 528 CA ALA 32 31.118 41.397 29.645 1.00 0.00 C +ATOM 529 HA ALA 32 31.926 42.131 29.633 1.00 0.00 H +ATOM 530 CB ALA 32 29.795 42.170 29.564 1.00 0.00 C +ATOM 531 HB1 ALA 32 28.949 41.487 29.563 1.00 0.00 H +ATOM 532 HB2 ALA 32 29.702 42.832 30.422 1.00 0.00 H +ATOM 533 HB3 ALA 32 29.768 42.771 28.655 1.00 0.00 H +ATOM 534 C ALA 32 31.262 40.605 30.958 1.00 0.00 C +ATOM 535 O ALA 32 32.275 40.728 31.646 1.00 0.00 O +ATOM 536 N MET 33 30.321 39.695 31.253 1.00 0.00 N +ATOM 537 H MET 33 29.518 39.622 30.641 1.00 0.00 H +ATOM 538 CA MET 33 30.335 38.881 32.484 1.00 0.00 C +ATOM 539 HA MET 33 30.364 39.562 33.335 1.00 0.00 H +ATOM 540 CB MET 33 29.031 38.072 32.588 1.00 0.00 C +ATOM 541 HB2 MET 33 29.063 37.468 33.493 1.00 0.00 H +ATOM 542 HB3 MET 33 28.176 38.744 32.653 1.00 0.00 H +ATOM 543 CG MET 33 28.863 37.159 31.375 1.00 0.00 C +ATOM 544 HG2 MET 33 28.517 37.760 30.535 1.00 0.00 H +ATOM 545 HG3 MET 33 29.830 36.736 31.101 1.00 0.00 H +ATOM 546 SD MET 33 27.726 35.781 31.569 1.00 0.00 S +ATOM 547 CE MET 33 27.783 35.334 29.824 1.00 0.00 C +ATOM 548 HE1 MET 33 28.808 35.428 29.472 1.00 0.00 H +ATOM 549 HE2 MET 33 27.482 34.313 29.665 1.00 0.00 H +ATOM 550 HE3 MET 33 27.111 35.986 29.261 1.00 0.00 H +ATOM 551 C MET 33 31.550 37.938 32.624 1.00 0.00 C +ATOM 552 O MET 33 31.764 37.358 33.689 1.00 0.00 O +ATOM 553 N ALA 34 32.330 37.727 31.558 1.00 0.00 N +ATOM 554 H ALA 34 32.096 38.206 30.701 1.00 0.00 H +ATOM 555 CA ALA 34 33.608 37.029 31.625 1.00 0.00 C +ATOM 556 HA ALA 34 33.547 36.247 32.386 1.00 0.00 H +ATOM 557 CB ALA 34 33.858 36.351 30.274 1.00 0.00 C +ATOM 558 HB1 ALA 34 34.003 37.107 29.503 1.00 0.00 H +ATOM 559 HB2 ALA 34 34.746 35.725 30.350 1.00 0.00 H +ATOM 560 HB3 ALA 34 33.005 35.727 30.009 1.00 0.00 H +ATOM 561 C ALA 34 34.759 37.969 32.049 1.00 0.00 C +ATOM 562 O ALA 34 35.585 37.581 32.874 1.00 0.00 O +ATOM 563 N ASN 35 34.773 39.218 31.569 1.00 0.00 N +ATOM 564 H ASN 35 34.038 39.507 30.932 1.00 0.00 H +ATOM 565 CA ASN 35 35.679 40.259 32.067 1.00 0.00 C +ATOM 566 HA ASN 35 36.687 39.846 32.122 1.00 0.00 H +ATOM 567 CB ASN 35 35.717 41.431 31.075 1.00 0.00 C +ATOM 568 HB2 ASN 35 34.711 41.694 30.749 1.00 0.00 H +ATOM 569 HB3 ASN 35 36.151 42.302 31.567 1.00 0.00 H +ATOM 570 CG ASN 35 36.597 41.101 29.885 1.00 0.00 C +ATOM 571 OD1 ASN 35 37.812 41.161 29.954 1.00 0.00 O +ATOM 572 ND2 ASN 35 36.031 40.697 28.778 1.00 0.00 N +ATOM 573 HD21 ASN 35 36.652 40.349 28.044 1.00 0.00 H +ATOM 574 HD22 ASN 35 35.033 40.536 28.756 1.00 0.00 H +ATOM 575 C ASN 35 35.343 40.707 33.503 1.00 0.00 C +ATOM 576 O ASN 35 36.267 40.967 34.270 1.00 0.00 O +ATOM 577 N ASP 36 34.071 40.666 33.920 1.00 0.00 N +ATOM 578 H ASP 36 33.338 40.591 33.220 1.00 0.00 H +ATOM 579 CA ASP 36 33.671 40.819 35.334 1.00 0.00 C +ATOM 580 HA ASP 36 34.038 41.780 35.697 1.00 0.00 H +ATOM 581 CB ASP 36 32.140 40.827 35.455 1.00 0.00 C +ATOM 582 HB2 ASP 36 31.753 39.893 35.051 1.00 0.00 H +ATOM 583 HB3 ASP 36 31.874 40.845 36.513 1.00 0.00 H +ATOM 584 CG ASP 36 31.443 42.015 34.776 1.00 0.00 C +ATOM 585 OD1 ASP 36 31.985 43.141 34.862 1.00 0.00 O +ATOM 586 OD2 ASP 36 30.343 41.790 34.216 1.00 0.00 O +ATOM 587 C ASP 36 34.265 39.723 36.248 1.00 0.00 C +ATOM 588 O ASP 36 34.526 39.967 37.426 1.00 0.00 O +ATOM 589 N LEU 37 34.516 38.519 35.709 1.00 0.00 N +ATOM 590 H LEU 37 34.242 38.377 34.747 1.00 0.00 H +ATOM 591 CA LEU 37 35.267 37.441 36.376 1.00 0.00 C +ATOM 592 HA LEU 37 35.087 37.525 37.448 1.00 0.00 H +ATOM 593 CB LEU 37 34.678 36.095 35.896 1.00 0.00 C +ATOM 594 HB2 LEU 37 33.602 36.106 36.076 1.00 0.00 H +ATOM 595 HB3 LEU 37 34.831 36.020 34.821 1.00 0.00 H +ATOM 596 CG LEU 37 35.262 34.826 36.549 1.00 0.00 C +ATOM 597 HG LEU 37 36.333 34.766 36.357 1.00 0.00 H +ATOM 598 CD1 LEU 37 35.018 34.770 38.060 1.00 0.00 C +ATOM 599 HD11 LEU 37 33.953 34.849 38.274 1.00 0.00 H +ATOM 600 HD12 LEU 37 35.402 33.833 38.463 1.00 0.00 H +ATOM 601 HD13 LEU 37 35.547 35.590 38.545 1.00 0.00 H +ATOM 602 CD2 LEU 37 34.616 33.584 35.924 1.00 0.00 C +ATOM 603 HD21 LEU 37 34.797 33.584 34.851 1.00 0.00 H +ATOM 604 HD22 LEU 37 35.055 32.685 36.358 1.00 0.00 H +ATOM 605 HD23 LEU 37 33.543 33.587 36.114 1.00 0.00 H +ATOM 606 C LEU 37 36.799 37.552 36.179 1.00 0.00 C +ATOM 607 O LEU 37 37.561 36.943 36.929 1.00 0.00 O +ATOM 608 N GLY 38 37.257 38.335 35.192 1.00 0.00 N +ATOM 609 H GLY 38 36.560 38.824 34.647 1.00 0.00 H +ATOM 610 CA GLY 38 38.652 38.750 34.997 1.00 0.00 C +ATOM 611 HA2 GLY 38 38.790 39.723 35.474 1.00 0.00 H +ATOM 612 HA3 GLY 38 39.314 38.041 35.493 1.00 0.00 H +ATOM 613 C GLY 38 39.116 38.869 33.535 1.00 0.00 C +ATOM 614 O GLY 38 39.924 39.746 33.227 1.00 0.00 O +ATOM 615 N ARG 39 38.624 38.009 32.629 1.00 0.00 N +ATOM 616 H ARG 39 37.900 37.373 32.945 1.00 0.00 H +ATOM 617 CA ARG 39 38.916 38.025 31.177 1.00 0.00 C +ATOM 618 HA ARG 39 38.800 39.051 30.823 1.00 0.00 H +ATOM 619 CB ARG 39 40.371 37.588 30.882 1.00 0.00 C +ATOM 620 HB2 ARG 39 40.562 37.740 29.819 1.00 0.00 H +ATOM 621 HB3 ARG 39 41.051 38.240 31.429 1.00 0.00 H +ATOM 622 CG ARG 39 40.697 36.124 31.230 1.00 0.00 C +ATOM 623 HG2 ARG 39 40.371 35.923 32.251 1.00 0.00 H +ATOM 624 HG3 ARG 39 40.153 35.455 30.561 1.00 0.00 H +ATOM 625 CD ARG 39 42.202 35.814 31.143 1.00 0.00 C +ATOM 626 HD2 ARG 39 42.735 36.490 31.816 1.00 0.00 H +ATOM 627 HD3 ARG 39 42.353 34.790 31.494 1.00 0.00 H +ATOM 628 NE ARG 39 42.752 35.939 29.773 1.00 0.00 N +ATOM 629 HE ARG 39 42.104 36.170 29.033 1.00 0.00 H +ATOM 630 CZ ARG 39 44.003 35.696 29.403 1.00 0.00 C +ATOM 631 NH1 ARG 39 44.928 35.315 30.239 1.00 0.00 N +ATOM 632 HH11 ARG 39 44.711 35.228 31.213 1.00 0.00 H +ATOM 633 HH12 ARG 39 45.878 35.204 29.914 1.00 0.00 H +ATOM 634 NH2 ARG 39 44.379 35.837 28.169 1.00 0.00 N +ATOM 635 HH21 ARG 39 43.786 36.294 27.478 1.00 0.00 H +ATOM 636 HH22 ARG 39 45.288 35.517 27.883 1.00 0.00 H +ATOM 637 C ARG 39 37.926 37.164 30.381 1.00 0.00 C +ATOM 638 O ARG 39 37.455 36.144 30.885 1.00 0.00 O +ATOM 639 N ASP 40 37.649 37.538 29.135 1.00 0.00 N +ATOM 640 H ASP 40 38.061 38.386 28.762 1.00 0.00 H +ATOM 641 CA ASP 40 36.886 36.702 28.202 1.00 0.00 C +ATOM 642 HA ASP 40 36.192 36.106 28.780 1.00 0.00 H +ATOM 643 CB ASP 40 36.032 37.563 27.258 1.00 0.00 C +ATOM 644 HB2 ASP 40 35.395 36.906 26.669 1.00 0.00 H +ATOM 645 HB3 ASP 40 35.362 38.175 27.856 1.00 0.00 H +ATOM 646 CG ASP 40 36.825 38.479 26.324 1.00 0.00 C +ATOM 647 OD1 ASP 40 37.538 39.364 26.846 1.00 0.00 O +ATOM 648 OD2 ASP 40 36.642 38.337 25.092 1.00 0.00 O +ATOM 649 C ASP 40 37.739 35.680 27.425 1.00 0.00 C +ATOM 650 O ASP 40 38.965 35.639 27.514 1.00 0.00 O +ATOM 651 N GLY 41 37.034 34.838 26.663 1.00 0.00 N +ATOM 652 H GLY 41 36.037 35.000 26.640 1.00 0.00 H +ATOM 653 CA GLY 41 37.551 33.939 25.628 1.00 0.00 C +ATOM 654 HA2 GLY 41 38.486 34.340 25.221 1.00 0.00 H +ATOM 655 HA3 GLY 41 37.728 32.949 26.061 1.00 0.00 H +ATOM 656 C GLY 41 36.521 33.822 24.491 1.00 0.00 C +ATOM 657 O GLY 41 35.528 34.563 24.453 1.00 0.00 O +ATOM 658 N GLU 42 36.725 32.872 23.576 1.00 0.00 N +ATOM 659 H GLU 42 37.515 32.257 23.691 1.00 0.00 H +ATOM 660 CA GLU 42 35.862 32.642 22.410 1.00 0.00 C +ATOM 661 HA GLU 42 35.176 33.479 22.316 1.00 0.00 H +ATOM 662 CB GLU 42 36.704 32.580 21.122 1.00 0.00 C +ATOM 663 HB2 GLU 42 37.313 31.676 21.146 1.00 0.00 H +ATOM 664 HB3 GLU 42 36.027 32.500 20.272 1.00 0.00 H +ATOM 665 CG GLU 42 37.639 33.783 20.884 1.00 0.00 C +ATOM 666 HG2 GLU 42 38.464 33.721 21.600 1.00 0.00 H +ATOM 667 HG3 GLU 42 38.071 33.697 19.884 1.00 0.00 H +ATOM 668 CD GLU 42 36.963 35.155 21.026 1.00 0.00 C +ATOM 669 OE1 GLU 42 35.727 35.264 20.884 1.00 0.00 O +ATOM 670 OE2 GLU 42 37.655 36.139 21.365 1.00 0.00 O +ATOM 671 C GLU 42 34.966 31.400 22.555 1.00 0.00 C +ATOM 672 O GLU 42 35.236 30.523 23.379 1.00 0.00 O +ATOM 673 N ARG 43 33.871 31.345 21.777 1.00 0.00 N +ATOM 674 H ARG 43 33.739 32.075 21.085 1.00 0.00 H +ATOM 675 CA ARG 43 32.808 30.323 21.876 1.00 0.00 C +ATOM 676 HA ARG 43 33.240 29.391 22.245 1.00 0.00 H +ATOM 677 CB ARG 43 31.717 30.792 22.852 1.00 0.00 C +ATOM 678 HB2 ARG 43 31.330 31.761 22.525 1.00 0.00 H +ATOM 679 HB3 ARG 43 30.894 30.076 22.837 1.00 0.00 H +ATOM 680 CG ARG 43 32.240 30.911 24.289 1.00 0.00 C +ATOM 681 HG2 ARG 43 32.696 29.965 24.582 1.00 0.00 H +ATOM 682 HG3 ARG 43 32.987 31.703 24.340 1.00 0.00 H +ATOM 683 CD ARG 43 31.115 31.262 25.264 1.00 0.00 C +ATOM 684 HD2 ARG 43 30.603 32.155 24.894 1.00 0.00 H +ATOM 685 HD3 ARG 43 30.387 30.446 25.295 1.00 0.00 H +ATOM 686 NE ARG 43 31.650 31.541 26.607 1.00 0.00 N +ATOM 687 HE ARG 43 31.860 32.502 26.805 1.00 0.00 H +ATOM 688 CZ ARG 43 31.874 30.665 27.566 1.00 0.00 C +ATOM 689 NH1 ARG 43 31.717 29.381 27.411 1.00 0.00 N +ATOM 690 HH11 ARG 43 31.664 29.009 26.475 1.00 0.00 H +ATOM 691 HH12 ARG 43 31.918 28.778 28.198 1.00 0.00 H +ATOM 692 NH2 ARG 43 32.245 31.074 28.740 1.00 0.00 N +ATOM 693 HH21 ARG 43 32.515 32.028 28.883 1.00 0.00 H +ATOM 694 HH22 ARG 43 32.317 30.381 29.488 1.00 0.00 H +ATOM 695 C ARG 43 32.166 30.026 20.520 1.00 0.00 C +ATOM 696 O ARG 43 31.992 30.936 19.715 1.00 0.00 O +ATOM 697 N THR 44 31.771 28.773 20.309 1.00 0.00 N +ATOM 698 H THR 44 31.934 28.099 21.040 1.00 0.00 H +ATOM 699 CA THR 44 30.992 28.332 19.132 1.00 0.00 C +ATOM 700 HA THR 44 31.270 28.970 18.289 1.00 0.00 H +ATOM 701 CB THR 44 31.360 26.883 18.761 1.00 0.00 C +ATOM 702 HB THR 44 31.085 26.214 19.575 1.00 0.00 H +ATOM 703 CG2 THR 44 30.724 26.381 17.462 1.00 0.00 C +ATOM 704 HG21 THR 44 30.873 27.108 16.660 1.00 0.00 H +ATOM 705 HG22 THR 44 31.170 25.429 17.170 1.00 0.00 H +ATOM 706 HG23 THR 44 29.656 26.210 17.610 1.00 0.00 H +ATOM 707 OG1 THR 44 32.751 26.805 18.555 1.00 0.00 O +ATOM 708 HG1 THR 44 32.911 26.105 17.915 1.00 0.00 H +ATOM 709 C THR 44 29.490 28.513 19.374 1.00 0.00 C +ATOM 710 O THR 44 29.046 28.595 20.522 1.00 0.00 O +ATOM 711 N ILE 45 28.707 28.596 18.296 1.00 0.00 N +ATOM 712 H ILE 45 29.129 28.473 17.388 1.00 0.00 H +ATOM 713 CA ILE 45 27.254 28.819 18.299 1.00 0.00 C +ATOM 714 HA ILE 45 26.875 28.630 19.303 1.00 0.00 H +ATOM 715 CB ILE 45 26.898 30.278 17.907 1.00 0.00 C +ATOM 716 HB ILE 45 25.811 30.333 17.833 1.00 0.00 H +ATOM 717 CG2 ILE 45 27.323 31.239 19.023 1.00 0.00 C +ATOM 718 HG21 ILE 45 28.412 31.290 19.094 1.00 0.00 H +ATOM 719 HG22 ILE 45 26.930 32.238 18.831 1.00 0.00 H +ATOM 720 HG23 ILE 45 26.911 30.893 19.971 1.00 0.00 H +ATOM 721 CG1 ILE 45 27.477 30.675 16.528 1.00 0.00 C +ATOM 722 HG12 ILE 45 28.569 30.700 16.582 1.00 0.00 H +ATOM 723 HG13 ILE 45 27.192 29.926 15.784 1.00 0.00 H +ATOM 724 CD1 ILE 45 26.974 32.034 16.019 1.00 0.00 C +ATOM 725 HD11 ILE 45 27.354 32.831 16.657 1.00 0.00 H +ATOM 726 HD12 ILE 45 27.330 32.207 15.002 1.00 0.00 H +ATOM 727 HD13 ILE 45 25.883 32.053 16.018 1.00 0.00 H +ATOM 728 C ILE 45 26.510 27.839 17.378 1.00 0.00 C +ATOM 729 O ILE 45 27.052 27.374 16.373 1.00 0.00 O +ATOM 730 N ASP 46 25.231 27.626 17.677 1.00 0.00 N +ATOM 731 H ASP 46 24.887 27.973 18.569 1.00 0.00 H +ATOM 732 CA ASP 46 24.240 27.063 16.767 1.00 0.00 C +ATOM 733 HA ASP 46 24.589 27.190 15.737 1.00 0.00 H +ATOM 734 CB ASP 46 24.016 25.578 17.089 1.00 0.00 C +ATOM 735 HB2 ASP 46 24.866 24.981 16.795 1.00 0.00 H +ATOM 736 HB3 ASP 46 23.881 25.490 18.158 1.00 0.00 H +ATOM 737 CG ASP 46 22.735 25.043 16.421 1.00 0.00 C +ATOM 738 OD1 ASP 46 21.940 24.401 17.146 1.00 0.00 O +ATOM 739 OD2 ASP 46 22.461 25.332 15.229 1.00 0.00 O +ATOM 740 C ASP 46 22.920 27.863 16.912 1.00 0.00 C +ATOM 741 O ASP 46 22.421 28.059 18.026 1.00 0.00 O +ATOM 742 N ASP 47 22.324 28.283 15.789 1.00 0.00 N +ATOM 743 H ASP 47 22.743 27.989 14.922 1.00 0.00 H +ATOM 744 CA ASP 47 21.034 28.977 15.762 1.00 0.00 C +ATOM 745 HA ASP 47 21.006 29.670 16.609 1.00 0.00 H +ATOM 746 CB ASP 47 20.894 29.841 14.508 1.00 0.00 C +ATOM 747 HB2 ASP 47 21.719 30.534 14.477 1.00 0.00 H +ATOM 748 HB3 ASP 47 20.907 29.218 13.620 1.00 0.00 H +ATOM 749 CG ASP 47 19.618 30.668 14.591 1.00 0.00 C +ATOM 750 OD1 ASP 47 18.610 30.348 13.901 1.00 0.00 O +ATOM 751 OD2 ASP 47 19.504 31.530 15.507 1.00 0.00 O +ATOM 752 C ASP 47 19.834 28.019 15.906 1.00 0.00 C +ATOM 753 O ASP 47 18.799 28.407 16.466 1.00 0.00 O +ATOM 754 N ALA 48 19.935 26.757 15.456 1.00 0.00 N +ATOM 755 H ALA 48 20.842 26.414 15.130 1.00 0.00 H +ATOM 756 CA ALA 48 18.818 25.814 15.507 1.00 0.00 C +ATOM 757 HA ALA 48 17.952 26.262 15.020 1.00 0.00 H +ATOM 758 CB ALA 48 19.205 24.545 14.739 1.00 0.00 C +ATOM 759 HB1 ALA 48 20.054 24.058 15.220 1.00 0.00 H +ATOM 760 HB2 ALA 48 18.369 23.849 14.718 1.00 0.00 H +ATOM 761 HB3 ALA 48 19.485 24.794 13.717 1.00 0.00 H +ATOM 762 C ALA 48 18.413 25.512 16.960 1.00 0.00 C +ATOM 763 O ALA 48 17.237 25.605 17.327 1.00 0.00 O +ATOM 764 N THR 49 19.388 25.224 17.823 1.00 0.00 N +ATOM 765 H THR 49 20.312 25.021 17.430 1.00 0.00 H +ATOM 766 CA THR 49 19.231 25.120 19.280 1.00 0.00 C +ATOM 767 HA THR 49 18.209 24.795 19.479 1.00 0.00 H +ATOM 768 CB THR 49 20.203 24.077 19.841 1.00 0.00 C +ATOM 769 HB THR 49 20.020 23.991 20.903 1.00 0.00 H +ATOM 770 CG2 THR 49 20.008 22.684 19.259 1.00 0.00 C +ATOM 771 HG21 THR 49 20.238 22.651 18.198 1.00 0.00 H +ATOM 772 HG22 THR 49 20.697 22.027 19.776 1.00 0.00 H +ATOM 773 HG23 THR 49 18.990 22.331 19.405 1.00 0.00 H +ATOM 774 OG1 THR 49 21.552 24.416 19.645 1.00 0.00 O +ATOM 775 HG1 THR 49 21.695 24.343 18.665 1.00 0.00 H +ATOM 776 C THR 49 19.398 26.445 20.037 1.00 0.00 C +ATOM 777 O THR 49 19.292 26.458 21.267 1.00 0.00 O +ATOM 778 N LYS 50 19.626 27.560 19.325 1.00 0.00 N +ATOM 779 H LYS 50 19.673 27.451 18.322 1.00 0.00 H +ATOM 780 CA LYS 50 19.805 28.927 19.867 1.00 0.00 C +ATOM 781 HA LYS 50 20.206 29.533 19.057 1.00 0.00 H +ATOM 782 CB LYS 50 18.441 29.510 20.311 1.00 0.00 C +ATOM 783 HB2 LYS 50 18.011 28.834 21.058 1.00 0.00 H +ATOM 784 HB3 LYS 50 18.608 30.472 20.802 1.00 0.00 H +ATOM 785 CG LYS 50 17.405 29.715 19.193 1.00 0.00 C +ATOM 786 HG2 LYS 50 17.355 28.829 18.554 1.00 0.00 H +ATOM 787 HG3 LYS 50 16.428 29.846 19.670 1.00 0.00 H +ATOM 788 CD LYS 50 17.702 30.977 18.351 1.00 0.00 C +ATOM 789 HD2 LYS 50 17.672 31.841 19.020 1.00 0.00 H +ATOM 790 HD3 LYS 50 18.705 30.903 17.908 1.00 0.00 H +ATOM 791 CE LYS 50 16.639 31.185 17.261 1.00 0.00 C +ATOM 792 HE2 LYS 50 15.655 30.886 17.644 1.00 0.00 H +ATOM 793 HE3 LYS 50 16.621 32.249 16.996 1.00 0.00 H +ATOM 794 NZ LYS 50 16.972 30.415 16.043 1.00 0.00 N +ATOM 795 HZ1 LYS 50 17.311 29.474 16.238 1.00 0.00 H +ATOM 796 HZ2 LYS 50 16.248 30.393 15.343 1.00 0.00 H +ATOM 797 HZ3 LYS 50 17.778 30.828 15.556 1.00 0.00 H +ATOM 798 C LYS 50 20.873 28.985 20.986 1.00 0.00 C +ATOM 799 O LYS 50 20.663 29.651 22.001 1.00 0.00 O +ATOM 800 N THR 51 21.977 28.244 20.840 1.00 0.00 N +ATOM 801 H THR 51 22.140 27.819 19.929 1.00 0.00 H +ATOM 802 CA THR 51 22.902 27.889 21.935 1.00 0.00 C +ATOM 803 HA THR 51 22.617 28.448 22.812 1.00 0.00 H +ATOM 804 CB THR 51 22.743 26.395 22.302 1.00 0.00 C +ATOM 805 HB THR 51 22.858 25.788 21.401 1.00 0.00 H +ATOM 806 CG2 THR 51 23.750 25.901 23.335 1.00 0.00 C +ATOM 807 HG21 THR 51 23.746 26.527 24.219 1.00 0.00 H +ATOM 808 HG22 THR 51 23.513 24.885 23.640 1.00 0.00 H +ATOM 809 HG23 THR 51 24.756 25.876 22.930 1.00 0.00 H +ATOM 810 OG1 THR 51 21.487 26.171 22.903 1.00 0.00 O +ATOM 811 HG1 THR 51 20.815 26.253 22.204 1.00 0.00 H +ATOM 812 C THR 51 24.376 28.226 21.660 1.00 0.00 C +ATOM 813 O THR 51 24.920 27.898 20.610 1.00 0.00 O +ATOM 814 N PHE 52 25.059 28.829 22.643 1.00 0.00 N +ATOM 815 H PHE 52 24.526 29.156 23.439 1.00 0.00 H +ATOM 816 CA PHE 52 26.530 28.907 22.739 1.00 0.00 C +ATOM 817 HA PHE 52 26.946 28.973 21.734 1.00 0.00 H +ATOM 818 CB PHE 52 26.945 30.161 23.528 1.00 0.00 C +ATOM 819 HB2 PHE 52 26.372 30.190 24.453 1.00 0.00 H +ATOM 820 HB3 PHE 52 27.994 30.055 23.805 1.00 0.00 H +ATOM 821 CG PHE 52 26.785 31.489 22.816 1.00 0.00 C +ATOM 822 CD1 PHE 52 25.537 32.141 22.788 1.00 0.00 C +ATOM 823 HD1 PHE 52 24.675 31.687 23.253 1.00 0.00 H +ATOM 824 CE1 PHE 52 25.405 33.382 22.139 1.00 0.00 C +ATOM 825 HE1 PHE 52 24.445 33.873 22.100 1.00 0.00 H +ATOM 826 CZ PHE 52 26.521 33.978 21.527 1.00 0.00 C +ATOM 827 HZ PHE 52 26.418 34.921 21.011 1.00 0.00 H +ATOM 828 CE2 PHE 52 27.770 33.336 21.559 1.00 0.00 C +ATOM 829 HE2 PHE 52 28.618 33.783 21.060 1.00 0.00 H +ATOM 830 CD2 PHE 52 27.900 32.091 22.201 1.00 0.00 C +ATOM 831 HD2 PHE 52 28.853 31.586 22.189 1.00 0.00 H +ATOM 832 C PHE 52 27.145 27.678 23.443 1.00 0.00 C +ATOM 833 O PHE 52 26.579 27.194 24.428 1.00 0.00 O +ATOM 834 N THR 53 28.345 27.250 23.032 1.00 0.00 N +ATOM 835 H THR 53 28.732 27.682 22.198 1.00 0.00 H +ATOM 836 CA THR 53 29.110 26.108 23.601 1.00 0.00 C +ATOM 837 HA THR 53 28.744 25.897 24.607 1.00 0.00 H +ATOM 838 CB THR 53 28.895 24.833 22.751 1.00 0.00 C +ATOM 839 HB THR 53 29.452 24.012 23.202 1.00 0.00 H +ATOM 840 CG2 THR 53 27.438 24.389 22.660 1.00 0.00 C +ATOM 841 HG21 THR 53 26.866 25.092 22.055 1.00 0.00 H +ATOM 842 HG22 THR 53 27.391 23.399 22.206 1.00 0.00 H +ATOM 843 HG23 THR 53 27.012 24.329 23.662 1.00 0.00 H +ATOM 844 OG1 THR 53 29.377 25.037 21.446 1.00 0.00 O +ATOM 845 HG1 THR 53 29.167 24.249 20.935 1.00 0.00 H +ATOM 846 C THR 53 30.624 26.402 23.742 1.00 0.00 C +ATOM 847 O THR 53 31.056 27.555 23.665 1.00 0.00 O +ATOM 848 N LYN 54 31.442 25.370 24.000 1.00 0.00 N +ATOM 849 H LYN 54 31.019 24.457 24.057 1.00 0.00 H +ATOM 850 CA LYN 54 32.897 25.350 23.807 1.00 0.00 C +ATOM 851 HA LYN 54 33.175 26.203 23.190 1.00 0.00 H +ATOM 852 CB LYN 54 33.644 25.488 25.152 1.00 0.00 C +ATOM 853 HB2 LYN 54 34.695 25.653 24.919 1.00 0.00 H +ATOM 854 HB3 LYN 54 33.295 26.378 25.675 1.00 0.00 H +ATOM 855 CG LYN 54 33.535 24.272 26.090 1.00 0.00 C +ATOM 856 HG2 LYN 54 32.630 24.360 26.691 1.00 0.00 H +ATOM 857 HG3 LYN 54 33.454 23.357 25.509 1.00 0.00 H +ATOM 858 CD LYN 54 34.768 24.152 26.998 1.00 0.00 C +ATOM 859 HD2 LYN 54 35.666 24.143 26.376 1.00 0.00 H +ATOM 860 HD3 LYN 54 34.813 25.007 27.673 1.00 0.00 H +ATOM 861 CE LYN 54 34.714 22.856 27.798 1.00 0.00 C +ATOM 862 HE2 LYN 54 33.879 22.909 28.492 1.00 0.00 H +ATOM 863 HE3 LYN 54 34.574 22.017 27.119 1.00 0.00 H +ATOM 864 NZ LYN 54 35.959 22.655 28.561 1.00 0.00 N +ATOM 865 HZ2 LYN 54 36.014 21.746 29.002 1.00 0.00 H +ATOM 866 HZ3 LYN 54 36.309 23.452 29.090 1.00 0.00 H +ATOM 867 C LYN 54 33.331 24.083 23.032 1.00 0.00 C +ATOM 868 O LYN 54 32.520 23.188 22.798 1.00 0.00 O +ATOM 869 N ASH 55 34.607 24.006 22.655 1.00 0.00 N +ATOM 870 H ASH 55 35.235 24.743 22.949 1.00 0.00 H +ATOM 871 CA ASH 55 35.245 22.818 22.062 1.00 0.00 C +ATOM 872 HA ASH 55 34.530 22.352 21.388 1.00 0.00 H +ATOM 873 CB ASH 55 36.458 23.263 21.212 1.00 0.00 C +ATOM 874 HB2 ASH 55 36.989 22.397 20.840 1.00 0.00 H +ATOM 875 HB3 ASH 55 36.090 23.787 20.334 1.00 0.00 H +ATOM 876 CG ASH 55 37.466 24.177 21.906 1.00 0.00 C +ATOM 877 OD1 ASH 55 37.235 24.894 22.872 1.00 0.00 O +ATOM 878 OD2 ASH 55 38.675 24.244 21.312 1.00 0.00 O +ATOM 879 HD2 ASH 55 39.183 24.875 21.825 1.00 0.00 H +ATOM 880 C ASH 55 35.617 21.725 23.093 1.00 0.00 C +ATOM 881 O ASH 55 35.389 21.890 24.291 1.00 0.00 O +ATOM 882 N GLU 56 36.168 20.603 22.606 1.00 0.00 N +ATOM 883 H GLU 56 36.363 20.571 21.617 1.00 0.00 H +ATOM 884 CA GLU 56 36.721 19.457 23.364 1.00 0.00 C +ATOM 885 HA GLU 56 36.608 19.641 24.435 1.00 0.00 H +ATOM 886 CB GLU 56 35.926 18.187 22.979 1.00 0.00 C +ATOM 887 HB2 GLU 56 34.867 18.360 23.145 1.00 0.00 H +ATOM 888 HB3 GLU 56 36.043 18.052 21.902 1.00 0.00 H +ATOM 889 CG GLU 56 36.342 16.868 23.662 1.00 0.00 C +ATOM 890 HG2 GLU 56 36.211 16.073 22.928 1.00 0.00 H +ATOM 891 HG3 GLU 56 37.405 16.881 23.874 1.00 0.00 H +ATOM 892 CD GLU 56 35.566 16.467 24.930 1.00 0.00 C +ATOM 893 OE1 GLU 56 36.075 15.627 25.717 1.00 0.00 O +ATOM 894 OE2 GLU 56 34.388 16.862 25.118 1.00 0.00 O +ATOM 895 C GLU 56 38.236 19.296 23.101 1.00 0.00 C +ATOM 896 O GLU 56 38.981 19.184 24.100 1.00 0.00 O +ATOM 897 OXT GLU 56 38.641 19.353 21.912 1.00 0.00 O +HETATM 898 ZN ZN1 57 26.481 32.007 29.869 1.00 0.00 Zn +HETATM 899 N AN1 58 28.178 32.408 30.980 1.00 0.00 N +HETATM 900 C AN1 58 30.463 33.089 32.031 1.00 0.00 C +HETATM 901 C1 AN1 58 29.210 32.642 31.443 1.00 0.00 C +HETATM 902 H AN1 58 30.315 33.475 33.056 1.00 0.00 H +HETATM 903 H1 AN1 58 30.922 33.875 31.415 1.00 0.00 H +HETATM 904 H2 AN1 58 31.115 32.221 32.084 1.00 0.00 H +HETATM 905 N1 AZI 59 31.873 28.965 30.695 1.00 0.00 N +HETATM 906 N2 AZI 59 30.632 28.938 30.595 1.00 0.00 N +HETATM 907 N3 AZI 59 29.373 28.899 30.435 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 898 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 105 101 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 118 132 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 137 138 134 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 142 140 +CONECT 140 139 +CONECT 141 139 +CONECT 142 144 139 145 143 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 142 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 147 149 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 147 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 202 189 +CONECT 188 187 +CONECT 189 187 191 195 190 +CONECT 190 189 +CONECT 191 192 194 189 193 +CONECT 192 191 +CONECT 193 191 +CONECT 194 191 +CONECT 195 196 197 189 198 +CONECT 196 195 +CONECT 197 195 +CONECT 198 195 200 199 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 226 204 208 207 +CONECT 207 206 +CONECT 208 211 206 209 210 +CONECT 209 208 +CONECT 210 208 +CONECT 211 213 212 214 208 +CONECT 212 211 +CONECT 213 211 +CONECT 214 217 211 215 216 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 219 214 +CONECT 218 217 +CONECT 219 220 217 223 +CONECT 220 221 222 219 +CONECT 221 220 +CONECT 222 220 +CONECT 223 219 225 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 227 228 206 +CONECT 227 226 +CONECT 228 230 226 229 +CONECT 229 228 +CONECT 230 231 232 248 228 +CONECT 231 230 +CONECT 232 235 230 233 234 +CONECT 233 232 +CONECT 234 232 +CONECT 235 237 236 238 232 +CONECT 236 235 +CONECT 237 235 +CONECT 238 239 235 240 241 +CONECT 239 238 +CONECT 240 238 +CONECT 241 238 243 244 242 +CONECT 242 241 +CONECT 243 241 +CONECT 244 247 241 245 246 +CONECT 245 244 +CONECT 246 244 +CONECT 247 244 +CONECT 248 249 230 250 +CONECT 249 248 +CONECT 250 248 252 251 +CONECT 251 250 +CONECT 252 255 250 253 254 +CONECT 253 252 +CONECT 254 252 +CONECT 255 256 257 252 +CONECT 256 255 +CONECT 257 259 255 258 +CONECT 258 257 +CONECT 259 261 260 271 257 +CONECT 260 259 +CONECT 261 267 262 263 259 +CONECT 262 261 +CONECT 263 265 261 264 266 +CONECT 264 263 +CONECT 265 263 +CONECT 266 263 +CONECT 267 269 268 270 261 +CONECT 268 267 +CONECT 269 267 +CONECT 270 267 +CONECT 271 273 259 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 273 284 277 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 274 278 285 286 +CONECT 278 279 280 277 +CONECT 279 282 288 278 +CONECT 280 281 278 287 +CONECT 281 282 289 280 +CONECT 282 898 281 279 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 293 294 302 290 +CONECT 293 292 +CONECT 294 295 296 292 300 +CONECT 295 294 +CONECT 296 299 298 294 297 +CONECT 297 296 +CONECT 298 296 +CONECT 299 296 +CONECT 300 294 301 +CONECT 301 300 +CONECT 302 304 292 303 +CONECT 303 302 +CONECT 304 314 305 302 +CONECT 305 306 308 304 315 +CONECT 306 307 321 305 +CONECT 307 306 +CONECT 308 316 317 305 309 +CONECT 309 308 310 311 +CONECT 310 319 309 313 +CONECT 311 309 318 312 +CONECT 312 313 311 320 +CONECT 313 310 898 312 +CONECT 314 304 +CONECT 315 305 +CONECT 316 308 +CONECT 317 308 +CONECT 318 311 +CONECT 319 310 +CONECT 320 312 +CONECT 321 323 306 322 +CONECT 322 321 +CONECT 323 334 324 321 325 +CONECT 324 323 +CONECT 325 323 328 327 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 330 331 325 329 +CONECT 329 328 +CONECT 330 328 +CONECT 331 332 328 333 +CONECT 332 331 +CONECT 333 331 +CONECT 334 336 335 323 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 344 340 339 336 +CONECT 339 338 +CONECT 340 342 341 338 343 +CONECT 341 340 +CONECT 342 340 +CONECT 343 340 +CONECT 344 346 345 338 +CONECT 345 344 +CONECT 346 348 347 344 +CONECT 347 346 +CONECT 348 360 350 349 346 +CONECT 349 348 +CONECT 350 351 356 348 352 +CONECT 351 350 +CONECT 352 350 354 355 353 +CONECT 353 352 +CONECT 354 352 +CONECT 355 352 +CONECT 356 357 358 350 359 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 +CONECT 360 361 362 348 +CONECT 361 360 +CONECT 362 364 360 363 +CONECT 363 362 +CONECT 364 366 365 372 362 +CONECT 365 364 +CONECT 366 369 367 368 364 +CONECT 367 366 +CONECT 368 366 +CONECT 369 370 371 366 +CONECT 370 369 +CONECT 371 369 +CONECT 372 364 374 373 +CONECT 373 372 +CONECT 374 375 372 376 +CONECT 375 374 +CONECT 376 378 374 396 377 +CONECT 377 376 +CONECT 378 381 380 379 376 +CONECT 379 378 +CONECT 380 378 +CONECT 381 382 395 378 +CONECT 382 384 383 381 +CONECT 383 382 +CONECT 384 385 386 382 +CONECT 385 384 +CONECT 386 387 384 395 +CONECT 387 388 389 386 +CONECT 388 387 +CONECT 389 390 387 391 +CONECT 390 389 +CONECT 391 389 392 393 +CONECT 392 391 +CONECT 393 391 395 394 +CONECT 394 393 +CONECT 395 386 393 381 +CONECT 396 398 376 397 +CONECT 397 396 +CONECT 398 399 400 396 +CONECT 399 398 +CONECT 400 402 401 398 406 +CONECT 401 400 +CONECT 402 405 403 404 400 +CONECT 403 402 +CONECT 404 402 +CONECT 405 402 +CONECT 406 400 407 408 +CONECT 407 406 +CONECT 408 406 409 410 +CONECT 409 408 +CONECT 410 408 411 412 421 +CONECT 411 410 +CONECT 412 415 413 410 414 +CONECT 413 412 +CONECT 414 412 +CONECT 415 416 417 418 412 +CONECT 416 415 +CONECT 417 415 +CONECT 418 420 415 419 +CONECT 419 418 +CONECT 420 418 +CONECT 421 410 423 422 +CONECT 422 421 +CONECT 423 424 421 425 +CONECT 424 423 +CONECT 425 423 427 431 426 +CONECT 426 425 +CONECT 427 428 430 425 429 +CONECT 428 427 +CONECT 429 427 +CONECT 430 427 +CONECT 431 433 425 432 +CONECT 432 431 +CONECT 433 434 435 431 +CONECT 434 433 +CONECT 435 437 433 436 446 +CONECT 436 435 +CONECT 437 438 439 440 435 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 442 437 441 +CONECT 441 440 +CONECT 442 440 +CONECT 443 445 444 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 435 448 447 +CONECT 447 446 +CONECT 448 449 446 450 +CONECT 449 448 +CONECT 450 448 452 451 468 +CONECT 451 450 +CONECT 452 455 453 454 450 +CONECT 453 452 +CONECT 454 452 +CONECT 455 458 457 456 452 +CONECT 456 455 +CONECT 457 455 +CONECT 458 461 459 460 455 +CONECT 459 458 +CONECT 460 458 +CONECT 461 464 462 463 458 +CONECT 462 461 +CONECT 463 461 +CONECT 464 466 465 467 461 +CONECT 465 464 +CONECT 466 464 +CONECT 467 464 +CONECT 468 450 470 469 +CONECT 469 468 +CONECT 470 471 468 472 +CONECT 471 470 +CONECT 472 470 474 473 488 +CONECT 473 472 +CONECT 474 477 475 472 476 +CONECT 475 474 +CONECT 476 474 +CONECT 477 478 486 474 +CONECT 478 480 479 477 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 483 480 484 +CONECT 483 482 +CONECT 484 482 485 486 +CONECT 485 484 +CONECT 486 484 477 487 +CONECT 487 486 +CONECT 488 490 472 489 +CONECT 489 488 +CONECT 490 491 492 488 +CONECT 491 490 +CONECT 492 494 490 502 493 +CONECT 493 492 +CONECT 494 495 500 496 492 +CONECT 495 494 +CONECT 496 498 494 499 497 +CONECT 497 496 +CONECT 498 496 +CONECT 499 496 +CONECT 500 501 494 +CONECT 501 500 +CONECT 502 504 492 503 +CONECT 503 502 +CONECT 504 505 506 502 +CONECT 505 504 +CONECT 506 508 504 507 524 +CONECT 507 506 +CONECT 508 511 509 510 506 +CONECT 509 508 +CONECT 510 508 +CONECT 511 514 513 512 508 +CONECT 512 511 +CONECT 513 511 +CONECT 514 517 515 516 511 +CONECT 515 514 +CONECT 516 514 +CONECT 517 519 518 520 514 +CONECT 518 517 +CONECT 519 517 +CONECT 520 522 517 523 521 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 506 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 530 529 534 +CONECT 529 528 +CONECT 530 533 531 528 532 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 536 540 551 539 +CONECT 539 538 +CONECT 540 543 538 542 541 +CONECT 541 540 +CONECT 542 540 +CONECT 543 544 545 546 540 +CONECT 544 543 +CONECT 545 543 +CONECT 546 547 543 +CONECT 547 550 548 549 546 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 553 538 552 +CONECT 552 551 +CONECT 553 554 555 551 +CONECT 554 553 +CONECT 555 557 553 561 556 +CONECT 556 555 +CONECT 557 558 560 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 557 +CONECT 561 563 555 562 +CONECT 562 561 +CONECT 563 564 561 565 +CONECT 564 563 +CONECT 565 567 563 566 575 +CONECT 566 565 +CONECT 567 570 568 569 565 +CONECT 568 567 +CONECT 569 567 +CONECT 570 572 571 567 +CONECT 571 570 +CONECT 572 573 574 570 +CONECT 573 572 +CONECT 574 572 +CONECT 575 565 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 581 580 587 +CONECT 580 579 +CONECT 581 584 582 579 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 586 585 581 +CONECT 585 584 +CONECT 586 584 +CONECT 587 579 589 588 +CONECT 588 587 +CONECT 589 590 587 591 +CONECT 590 589 +CONECT 591 589 593 606 592 +CONECT 592 591 +CONECT 593 595 594 591 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 593 602 597 598 +CONECT 597 596 +CONECT 598 596 599 600 601 +CONECT 599 598 +CONECT 600 598 +CONECT 601 598 +CONECT 602 603 605 604 596 +CONECT 603 602 +CONECT 604 602 +CONECT 605 602 +CONECT 606 608 591 607 +CONECT 607 606 +CONECT 608 609 610 606 +CONECT 609 608 +CONECT 610 613 608 611 612 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 610 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 637 618 619 615 +CONECT 618 617 +CONECT 619 620 617 622 621 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 619 625 623 +CONECT 623 622 +CONECT 624 622 +CONECT 625 628 622 627 626 +CONECT 626 625 +CONECT 627 625 +CONECT 628 629 630 625 +CONECT 629 628 +CONECT 630 634 628 631 +CONECT 631 630 633 632 +CONECT 632 631 +CONECT 633 631 +CONECT 634 635 636 630 +CONECT 635 634 +CONECT 636 634 +CONECT 637 639 638 617 +CONECT 638 637 +CONECT 639 641 640 637 +CONECT 640 639 +CONECT 641 643 649 642 639 +CONECT 642 641 +CONECT 643 646 644 645 641 +CONECT 644 643 +CONECT 645 643 +CONECT 646 648 647 643 +CONECT 647 646 +CONECT 648 646 +CONECT 649 651 650 641 +CONECT 650 649 +CONECT 651 653 652 649 +CONECT 652 651 +CONECT 653 656 654 655 651 +CONECT 654 653 +CONECT 655 653 +CONECT 656 658 657 653 +CONECT 657 656 +CONECT 658 660 659 656 +CONECT 659 658 +CONECT 660 662 661 671 658 +CONECT 661 660 +CONECT 662 664 665 663 660 +CONECT 663 662 +CONECT 664 662 +CONECT 665 667 668 662 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 665 669 670 +CONECT 669 668 +CONECT 670 668 +CONECT 671 673 660 672 +CONECT 672 671 +CONECT 673 674 675 671 +CONECT 674 673 +CONECT 675 695 673 676 677 +CONECT 676 675 +CONECT 677 675 678 679 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 682 681 683 +CONECT 681 680 +CONECT 682 680 +CONECT 683 680 684 685 686 +CONECT 684 683 +CONECT 685 683 +CONECT 686 683 687 688 +CONECT 687 686 +CONECT 688 686 689 692 +CONECT 689 690 688 691 +CONECT 690 689 +CONECT 691 689 +CONECT 692 688 693 694 +CONECT 693 692 +CONECT 694 692 +CONECT 695 696 697 675 +CONECT 696 695 +CONECT 697 699 695 698 +CONECT 698 697 +CONECT 699 700 701 709 697 +CONECT 700 699 +CONECT 701 703 707 699 702 +CONECT 702 701 +CONECT 703 704 705 706 701 +CONECT 704 703 +CONECT 705 703 +CONECT 706 703 +CONECT 707 708 701 +CONECT 708 707 +CONECT 709 711 699 710 +CONECT 710 709 +CONECT 711 712 713 709 +CONECT 712 711 +CONECT 713 728 715 711 714 +CONECT 714 713 +CONECT 715 721 716 713 717 +CONECT 716 715 +CONECT 717 715 719 718 720 +CONECT 718 717 +CONECT 719 717 +CONECT 720 717 +CONECT 721 723 724 722 715 +CONECT 722 721 +CONECT 723 721 +CONECT 724 726 727 721 725 +CONECT 725 724 +CONECT 726 724 +CONECT 727 724 +CONECT 728 729 730 713 +CONECT 729 728 +CONECT 730 732 728 731 +CONECT 731 730 +CONECT 732 733 740 734 730 +CONECT 733 732 +CONECT 734 737 732 735 736 +CONECT 735 734 +CONECT 736 734 +CONECT 737 739 734 738 +CONECT 738 737 +CONECT 739 737 +CONECT 740 742 732 741 +CONECT 741 740 +CONECT 742 743 744 740 +CONECT 743 742 +CONECT 744 746 742 752 745 +CONECT 745 744 +CONECT 746 748 747 749 744 +CONECT 747 746 +CONECT 748 746 +CONECT 749 750 746 751 +CONECT 750 749 +CONECT 751 749 +CONECT 752 754 744 753 +CONECT 753 752 +CONECT 754 755 756 752 +CONECT 755 754 +CONECT 756 758 757 754 762 +CONECT 757 756 +CONECT 758 761 760 759 756 +CONECT 759 758 +CONECT 760 758 +CONECT 761 758 +CONECT 762 756 763 764 +CONECT 763 762 +CONECT 764 762 765 766 +CONECT 765 764 +CONECT 766 764 767 768 776 +CONECT 767 766 +CONECT 768 770 766 774 769 +CONECT 769 768 +CONECT 770 771 773 772 768 +CONECT 771 770 +CONECT 772 770 +CONECT 773 770 +CONECT 774 775 768 +CONECT 775 774 +CONECT 776 766 778 777 +CONECT 777 776 +CONECT 778 779 780 776 +CONECT 779 778 +CONECT 780 781 778 782 798 +CONECT 781 780 +CONECT 782 785 780 784 783 +CONECT 783 782 +CONECT 784 782 +CONECT 785 788 786 787 782 +CONECT 786 785 +CONECT 787 785 +CONECT 788 791 790 789 785 +CONECT 789 788 +CONECT 790 788 +CONECT 791 794 793 792 788 +CONECT 792 791 +CONECT 793 791 +CONECT 794 796 797 795 791 +CONECT 795 794 +CONECT 796 794 +CONECT 797 794 +CONECT 798 780 800 799 +CONECT 799 798 +CONECT 800 801 798 802 +CONECT 801 800 +CONECT 802 800 812 804 803 +CONECT 803 802 +CONECT 804 805 802 810 806 +CONECT 805 804 +CONECT 806 804 809 808 807 +CONECT 807 806 +CONECT 808 806 +CONECT 809 806 +CONECT 810 811 804 +CONECT 811 810 +CONECT 812 813 802 814 +CONECT 813 812 +CONECT 814 812 816 815 +CONECT 815 814 +CONECT 816 817 814 832 818 +CONECT 817 816 +CONECT 818 816 821 820 819 +CONECT 819 818 +CONECT 820 818 +CONECT 821 830 822 818 +CONECT 822 824 821 823 +CONECT 823 822 +CONECT 824 826 825 822 +CONECT 825 824 +CONECT 826 827 828 824 +CONECT 827 826 +CONECT 828 829 826 830 +CONECT 829 828 +CONECT 830 828 831 821 +CONECT 831 830 +CONECT 832 816 834 833 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 838 834 846 837 +CONECT 837 836 +CONECT 838 844 840 839 836 +CONECT 839 838 +CONECT 840 841 842 838 843 +CONECT 841 840 +CONECT 842 840 +CONECT 843 840 +CONECT 844 845 838 +CONECT 845 844 +CONECT 846 836 847 848 +CONECT 847 846 +CONECT 848 846 850 849 +CONECT 849 848 +CONECT 850 867 851 848 852 +CONECT 851 850 +CONECT 852 850 853 854 855 +CONECT 853 852 +CONECT 854 852 +CONECT 855 852 857 856 858 +CONECT 856 855 +CONECT 857 855 +CONECT 858 855 859 860 861 +CONECT 859 858 +CONECT 860 858 +CONECT 861 858 863 862 864 +CONECT 862 861 +CONECT 863 861 +CONECT 864 861 865 866 +CONECT 865 864 +CONECT 866 864 +CONECT 867 869 868 850 +CONECT 868 867 +CONECT 869 871 870 867 +CONECT 870 869 +CONECT 871 873 872 869 880 +CONECT 872 871 +CONECT 873 875 874 876 871 +CONECT 874 873 +CONECT 875 873 +CONECT 876 873 878 877 +CONECT 877 876 +CONECT 878 879 876 +CONECT 879 878 +CONECT 880 871 882 881 +CONECT 881 880 +CONECT 882 883 880 884 +CONECT 883 882 +CONECT 884 882 886 895 885 +CONECT 885 884 +CONECT 886 888 887 884 889 +CONECT 887 886 +CONECT 888 886 +CONECT 889 890 886 891 892 +CONECT 890 889 +CONECT 891 889 +CONECT 892 889 894 893 +CONECT 893 892 +CONECT 894 892 +CONECT 895 897 884 896 +CONECT 896 895 +CONECT 897 895 +CONECT 898 87 313 899 282 +CONECT 899 898 901 +CONECT 900 903 901 904 902 +CONECT 901 899 900 +CONECT 902 900 +CONECT 903 900 +CONECT 904 900 +CONECT 905 906 +CONECT 906 907 905 +CONECT 907 906 +MASTER 0 0 0 0 0 0 0 0 907 0 907 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_4_front_4.pdb b/tests/nsga2/intermediate_molecules/min_iter_4_front_4.pdb new file mode 100644 index 0000000..055a3e7 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_4_front_4.pdb @@ -0,0 +1,1759 @@ +COMPND fitness: -3.1818 51.504999999999654 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.143 37.985 23.610 1.00 0.00 N +ATOM 2 H1 MET 1 15.124 38.373 24.555 1.00 0.00 H +ATOM 3 H2 MET 1 14.367 38.361 23.081 1.00 0.00 H +ATOM 4 H3 MET 1 16.013 38.294 23.187 1.00 0.00 H +ATOM 5 CA MET 1 15.112 36.512 23.675 1.00 0.00 C +ATOM 6 HA MET 1 14.160 36.216 24.101 1.00 0.00 H +ATOM 7 CB MET 1 15.250 35.885 22.281 1.00 0.00 C +ATOM 8 HB2 MET 1 14.380 36.161 21.670 1.00 0.00 H +ATOM 9 HB3 MET 1 16.147 36.282 21.783 1.00 0.00 H +ATOM 10 CG MET 1 15.360 34.343 22.311 1.00 0.00 C +ATOM 11 HG2 MET 1 16.249 34.076 22.883 1.00 0.00 H +ATOM 12 HG3 MET 1 14.486 33.935 22.815 1.00 0.00 H +ATOM 13 SD MET 1 15.524 33.527 20.684 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.579 20.074 1.00 0.00 C +ATOM 15 HE1 MET 1 13.468 34.610 20.016 1.00 0.00 H +ATOM 16 HE2 MET 1 13.779 33.136 19.079 1.00 0.00 H +ATOM 17 HE3 MET 1 13.164 33.009 20.739 1.00 0.00 H +ATOM 18 C MET 1 16.212 36.041 24.609 1.00 0.00 C +ATOM 19 O MET 1 17.363 36.415 24.425 1.00 0.00 O +ATOM 20 N GLN 2 15.870 35.214 25.595 1.00 0.00 N +ATOM 21 H GLN 2 14.892 35.031 25.773 1.00 0.00 H +ATOM 22 CA GLN 2 16.834 34.496 26.433 1.00 0.00 C +ATOM 23 HA GLN 2 17.639 35.169 26.726 1.00 0.00 H +ATOM 24 CB GLN 2 16.108 34.100 27.730 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.114 33.685 27.517 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.665 33.336 28.285 1.00 0.00 H +ATOM 27 CG GLN 2 15.906 35.258 28.690 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.472 36.127 28.192 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.177 34.968 29.445 1.00 0.00 H +ATOM 30 CD GLN 2 17.138 35.583 29.549 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.175 34.951 29.507 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.006 36.468 30.472 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.820 36.539 31.068 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.095 36.763 30.763 1.00 0.00 H +ATOM 35 C GLN 2 17.474 33.325 25.682 1.00 0.00 C +ATOM 36 O GLN 2 17.083 32.171 25.841 1.00 0.00 O +ATOM 37 N TYR 3 18.434 33.639 24.817 1.00 0.00 N +ATOM 38 H TYR 3 18.730 34.609 24.752 1.00 0.00 H +ATOM 39 CA TYR 3 19.211 32.639 24.095 1.00 0.00 C +ATOM 40 HA TYR 3 18.530 31.988 23.538 1.00 0.00 H +ATOM 41 CB TYR 3 20.157 33.301 23.092 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.840 33.964 23.635 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.751 32.494 22.652 1.00 0.00 H +ATOM 44 CG TYR 3 19.582 34.088 21.924 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.493 33.474 20.656 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.784 32.437 20.544 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.117 34.222 19.526 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.088 33.753 18.560 1.00 0.00 H +ATOM 49 CZ TYR 3 18.823 35.592 19.664 1.00 0.00 C +ATOM 50 OH TYR 3 18.501 36.326 18.572 1.00 0.00 O +ATOM 51 HH TYR 3 18.773 35.900 17.756 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.910 36.214 20.925 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.718 37.268 21.009 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.296 35.464 22.053 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.425 35.954 23.011 1.00 0.00 H +ATOM 56 C TYR 3 20.049 31.781 25.057 1.00 0.00 C +ATOM 57 O TYR 3 20.427 32.254 26.126 1.00 0.00 O +ATOM 58 N LYS 4 20.332 30.515 24.723 1.00 0.00 N +ATOM 59 H LYS 4 20.178 30.231 23.759 1.00 0.00 H +ATOM 60 CA LYS 4 20.951 29.510 25.613 1.00 0.00 C +ATOM 61 HA LYS 4 20.669 29.723 26.642 1.00 0.00 H +ATOM 62 CB LYS 4 20.428 28.102 25.249 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.474 27.988 24.171 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.104 27.360 25.675 1.00 0.00 H +ATOM 65 CG LYS 4 19.006 27.743 25.721 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.848 26.695 25.477 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.953 27.845 26.805 1.00 0.00 H +ATOM 68 CD LYS 4 17.876 28.560 25.074 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.833 29.552 25.522 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.097 28.676 24.012 1.00 0.00 H +ATOM 71 CE LYS 4 16.501 27.876 25.184 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.766 28.488 24.651 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.558 26.917 24.664 1.00 0.00 H +ATOM 74 NZ LYS 4 16.049 27.649 26.581 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.916 28.524 27.069 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.173 27.126 26.582 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.720 27.077 27.078 1.00 0.00 H +ATOM 78 C LYS 4 22.496 29.539 25.589 1.00 0.00 C +ATOM 79 O LYS 4 23.126 29.914 24.608 1.00 0.00 O +HETATM 80 N HX1 5 23.123 29.070 26.663 1.00 0.00 N +HETATM 81 CA HX1 5 24.574 28.879 26.771 1.00 0.00 C +HETATM 82 C HX1 5 24.845 27.683 27.682 1.00 0.00 C +HETATM 83 O HX1 5 24.411 27.675 28.838 1.00 0.00 O +HETATM 84 CB HX1 5 25.214 30.176 27.295 1.00 0.00 C +HETATM 85 CG HX1 5 26.729 30.252 27.370 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.639 29.290 27.013 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.408 31.375 27.858 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.709 31.060 27.740 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.883 29.809 27.277 1.00 0.00 N +HETATM 90 H HX1 5 22.554 28.878 27.485 1.00 0.00 H +HETATM 91 HA HX1 5 24.981 28.660 25.785 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.821 30.385 28.290 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.892 30.999 26.656 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.452 28.305 26.605 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.521 31.696 28.068 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.771 29.314 27.221 1.00 0.00 H +ATOM 97 N ILE 6 25.508 26.655 27.149 1.00 0.00 N +ATOM 98 H ILE 6 25.851 26.725 26.196 1.00 0.00 H +ATOM 99 CA ILE 6 25.910 25.449 27.896 1.00 0.00 C +ATOM 100 HA ILE 6 25.251 25.340 28.757 1.00 0.00 H +ATOM 101 CB ILE 6 25.717 24.186 27.023 1.00 0.00 C +ATOM 102 HB ILE 6 26.220 24.342 26.069 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.319 22.930 27.682 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.850 22.744 28.651 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.175 22.061 27.043 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.396 23.046 27.816 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.198 23.997 26.770 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.690 23.877 27.728 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.801 24.894 26.294 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.821 22.812 25.875 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.007 21.871 26.393 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.757 22.869 25.640 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.394 22.845 24.949 1.00 0.00 H +ATOM 114 C ILE 6 27.326 25.634 28.459 1.00 0.00 C +ATOM 115 O ILE 6 28.161 26.314 27.861 1.00 0.00 O +ATOM 116 N VAL 7 27.557 25.095 29.654 1.00 0.00 N +ATOM 117 H VAL 7 26.835 24.519 30.061 1.00 0.00 H +ATOM 118 CA VAL 7 28.720 25.390 30.497 1.00 0.00 C +ATOM 119 HA VAL 7 28.796 26.475 30.566 1.00 0.00 H +ATOM 120 CB VAL 7 28.425 24.856 31.917 1.00 0.00 C +ATOM 121 HB VAL 7 27.435 25.203 32.194 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.421 23.317 31.980 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.414 22.922 31.766 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.110 22.997 32.971 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.729 22.909 31.249 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.393 25.385 32.961 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.448 26.475 32.898 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.032 25.119 33.955 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.379 24.964 32.804 1.00 0.00 H +ATOM 130 C VAL 7 30.074 24.888 29.945 1.00 0.00 C +ATOM 131 O VAL 7 30.145 23.881 29.242 1.00 0.00 O +ATOM 132 N THR 8 31.160 25.572 30.325 1.00 0.00 N +ATOM 133 H THR 8 31.019 26.412 30.868 1.00 0.00 H +ATOM 134 CA THR 8 32.548 25.150 30.087 1.00 0.00 C +ATOM 135 HA THR 8 32.676 24.942 29.037 1.00 0.00 H +ATOM 136 CB THR 8 33.531 26.286 30.476 1.00 0.00 C +ATOM 137 HB THR 8 34.535 25.882 30.405 1.00 0.00 H +ATOM 138 CG2 THR 8 33.404 27.516 29.587 1.00 0.00 C +ATOM 139 HG21 THR 8 32.400 27.938 29.641 1.00 0.00 H +ATOM 140 HG22 THR 8 34.152 28.242 29.933 1.00 0.00 H +ATOM 141 HG23 THR 8 33.640 27.211 28.573 1.00 0.00 H +ATOM 142 OG1 THR 8 33.299 26.697 31.802 1.00 0.00 O +ATOM 143 HG1 THR 8 32.870 27.557 31.750 1.00 0.00 H +ATOM 144 C THR 8 32.947 23.867 30.855 1.00 0.00 C +ATOM 145 O THR 8 32.455 23.604 31.955 1.00 0.00 O +ATOM 146 N GLY 9 33.916 23.113 30.319 1.00 0.00 N +ATOM 147 H GLY 9 34.228 23.350 29.390 1.00 0.00 H +ATOM 148 CA GLY 9 34.483 21.905 30.944 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.467 21.720 30.517 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.591 22.078 32.015 1.00 0.00 H +ATOM 151 C GLY 9 33.617 20.656 30.725 1.00 0.00 C +ATOM 152 O GLY 9 32.761 20.625 29.849 1.00 0.00 O +ATOM 153 N LYS 10 33.857 19.605 31.523 1.00 0.00 N +ATOM 154 H LYS 10 34.648 19.678 32.142 1.00 0.00 H +ATOM 155 CA LYS 10 33.155 18.302 31.416 1.00 0.00 C +ATOM 156 HA LYS 10 32.232 18.487 30.864 1.00 0.00 H +ATOM 157 CB LYS 10 34.014 17.333 30.575 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.643 17.913 29.898 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.668 16.764 31.234 1.00 0.00 H +ATOM 160 CG LYS 10 33.172 16.374 29.715 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.598 15.707 30.358 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.475 16.966 29.120 1.00 0.00 H +ATOM 163 CD LYS 10 34.048 15.544 28.762 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.695 16.213 28.192 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.666 14.856 29.341 1.00 0.00 H +ATOM 166 CE LYS 10 33.168 14.751 27.787 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.998 28.344 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.452 15.437 27.326 1.00 0.00 H +ATOM 169 NZ LYS 10 33.963 14.103 26.716 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.727 13.547 27.077 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.367 13.556 26.105 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.408 14.809 26.111 1.00 0.00 H +ATOM 173 C LYS 10 32.705 17.689 32.753 1.00 0.00 C +ATOM 174 O LYS 10 31.954 16.719 32.762 1.00 0.00 O +ATOM 175 N SER 11 33.135 18.250 33.890 1.00 0.00 N +ATOM 176 H SER 11 33.861 18.944 33.825 1.00 0.00 H +ATOM 177 CA SER 11 32.715 17.837 35.249 1.00 0.00 C +ATOM 178 HA SER 11 32.578 16.753 35.268 1.00 0.00 H +ATOM 179 CB SER 11 33.803 18.197 36.271 1.00 0.00 C +ATOM 180 HB2 SER 11 33.797 19.276 36.438 1.00 0.00 H +ATOM 181 HB3 SER 11 33.596 17.691 37.215 1.00 0.00 H +ATOM 182 OG SER 11 35.079 17.815 35.795 1.00 0.00 O +ATOM 183 HG SER 11 35.730 17.919 36.496 1.00 0.00 H +ATOM 184 C SER 11 31.392 18.467 35.712 1.00 0.00 C +ATOM 185 O SER 11 30.952 18.228 36.831 1.00 0.00 O +ATOM 186 N ARG 12 30.783 19.321 34.884 1.00 0.00 N +ATOM 187 H ARG 12 31.191 19.425 33.963 1.00 0.00 H +ATOM 188 CA ARG 12 29.513 20.030 35.101 1.00 0.00 C +ATOM 189 HA ARG 12 28.908 19.448 35.793 1.00 0.00 H +ATOM 190 CB ARG 12 29.760 21.416 35.732 1.00 0.00 C +ATOM 191 HB2 ARG 12 28.806 21.937 35.834 1.00 0.00 H +ATOM 192 HB3 ARG 12 30.170 21.277 36.733 1.00 0.00 H +ATOM 193 CG ARG 12 30.730 22.314 34.928 1.00 0.00 C +ATOM 194 HG2 ARG 12 31.681 21.799 34.797 1.00 0.00 H +ATOM 195 HG3 ARG 12 30.310 22.519 33.949 1.00 0.00 H +ATOM 196 CD ARG 12 31.027 23.653 35.632 1.00 0.00 C +ATOM 197 HD2 ARG 12 30.082 24.209 35.755 1.00 0.00 H +ATOM 198 HD3 ARG 12 31.401 23.450 36.644 1.00 0.00 H +ATOM 199 NE ARG 12 32.012 24.458 34.883 1.00 0.00 N +ATOM 200 HE ARG 12 31.646 25.091 34.199 1.00 0.00 H +ATOM 201 CZ ARG 12 33.324 24.344 34.917 1.00 0.00 C +ATOM 202 NH1 ARG 12 33.924 23.512 35.719 1.00 0.00 N +ATOM 203 HH11 ARG 12 33.393 22.968 36.366 1.00 0.00 H +ATOM 204 HH12 ARG 12 34.928 23.374 35.636 1.00 0.00 H +ATOM 205 NH2 ARG 12 34.077 25.065 34.140 1.00 0.00 N +ATOM 206 HH21 ARG 12 33.667 25.594 33.377 1.00 0.00 H +ATOM 207 HH22 ARG 12 35.081 25.079 34.263 1.00 0.00 H +ATOM 208 C ARG 12 28.766 20.089 33.766 1.00 0.00 C +ATOM 209 O ARG 12 29.411 20.178 32.729 1.00 0.00 O +ATOM 210 N LYS 13 27.435 19.982 33.794 1.00 0.00 N +ATOM 211 H LYS 13 27.000 19.895 34.699 1.00 0.00 H +ATOM 212 CA LYS 13 26.597 19.734 32.598 1.00 0.00 C +ATOM 213 HA LYS 13 27.212 19.876 31.708 1.00 0.00 H +ATOM 214 CB LYS 13 26.152 18.255 32.639 1.00 0.00 C +ATOM 215 HB2 LYS 13 26.965 17.664 33.074 1.00 0.00 H +ATOM 216 HB3 LYS 13 25.278 18.158 33.291 1.00 0.00 H +ATOM 217 CG LYS 13 25.841 17.640 31.259 1.00 0.00 C +ATOM 218 HG2 LYS 13 24.958 18.111 30.821 1.00 0.00 H +ATOM 219 HG3 LYS 13 26.695 17.821 30.598 1.00 0.00 H +ATOM 220 CD LYS 13 25.621 16.115 31.353 1.00 0.00 C +ATOM 221 HD2 LYS 13 25.625 15.709 30.340 1.00 0.00 H +ATOM 222 HD3 LYS 13 26.454 15.670 31.901 1.00 0.00 H +ATOM 223 CE LYS 13 24.285 15.736 32.014 1.00 0.00 C +ATOM 224 HE2 LYS 13 24.108 16.376 32.881 1.00 0.00 H +ATOM 225 HE3 LYS 13 23.493 15.943 31.289 1.00 0.00 H +ATOM 226 NZ LYS 13 24.253 14.301 32.411 1.00 0.00 N +ATOM 227 HZ1 LYS 13 24.811 14.107 33.240 1.00 0.00 H +ATOM 228 HZ2 LYS 13 23.309 13.983 32.588 1.00 0.00 H +ATOM 229 HZ3 LYS 13 24.653 13.716 31.680 1.00 0.00 H +ATOM 230 C LYS 13 25.427 20.720 32.443 1.00 0.00 C +ATOM 231 O LYS 13 24.549 20.527 31.611 1.00 0.00 O +ATOM 232 N GLY 14 25.402 21.765 33.275 1.00 0.00 N +ATOM 233 H GLY 14 26.181 21.891 33.896 1.00 0.00 H +ATOM 234 CA GLY 14 24.303 22.731 33.349 1.00 0.00 C +ATOM 235 HA2 GLY 14 23.362 22.177 33.402 1.00 0.00 H +ATOM 236 HA3 GLY 14 24.394 23.307 34.272 1.00 0.00 H +ATOM 237 C GLY 14 24.229 23.712 32.165 1.00 0.00 C +ATOM 238 O GLY 14 25.167 23.864 31.379 1.00 0.00 O +ATOM 239 N VAL 15 23.105 24.424 32.073 1.00 0.00 N +ATOM 240 H VAL 15 22.394 24.283 32.775 1.00 0.00 H +ATOM 241 CA VAL 15 22.766 25.401 31.036 1.00 0.00 C +ATOM 242 HA VAL 15 23.655 25.640 30.454 1.00 0.00 H +ATOM 243 CB VAL 15 21.745 24.766 30.065 1.00 0.00 C +ATOM 244 HB VAL 15 22.195 23.865 29.647 1.00 0.00 H +ATOM 245 CG1 VAL 15 20.425 24.344 30.732 1.00 0.00 C +ATOM 246 HG11 VAL 15 19.919 25.204 31.178 1.00 0.00 H +ATOM 247 HG12 VAL 15 19.764 23.887 29.989 1.00 0.00 H +ATOM 248 HG13 VAL 15 20.614 23.598 31.511 1.00 0.00 H +ATOM 249 CG2 VAL 15 21.404 25.692 28.894 1.00 0.00 C +ATOM 250 HG21 VAL 15 22.323 26.024 28.411 1.00 0.00 H +ATOM 251 HG22 VAL 15 20.807 25.143 28.161 1.00 0.00 H +ATOM 252 HG23 VAL 15 20.832 26.553 29.242 1.00 0.00 H +ATOM 253 C VAL 15 22.266 26.694 31.700 1.00 0.00 C +ATOM 254 O VAL 15 21.705 26.652 32.791 1.00 0.00 O +HETATM 255 N HY1 16 22.495 27.833 31.062 1.00 0.00 N +HETATM 256 CA HY1 16 21.933 29.135 31.414 1.00 0.00 C +HETATM 257 C HY1 16 21.625 29.887 30.105 1.00 0.00 C +HETATM 258 O HY1 16 21.763 29.347 28.995 1.00 0.00 O +HETATM 259 CB HY1 16 22.878 29.886 32.385 1.00 0.00 C +HETATM 260 CG HY1 16 24.227 30.216 31.792 1.00 0.00 C +HETATM 261 CD2 HY1 16 24.567 31.405 31.207 1.00 0.00 C +HETATM 262 ND1 HY1 16 25.326 29.385 31.707 1.00 0.00 N +HETATM 263 CE1 HY1 16 26.315 30.087 31.127 1.00 0.00 C +HETATM 264 NE2 HY1 16 25.895 31.319 30.785 1.00 0.00 N +HETATM 265 H HY1 16 22.989 27.791 30.182 1.00 0.00 H +HETATM 266 HA HY1 16 20.963 29.030 31.902 1.00 0.00 H +HETATM 267 HB2 HY1 16 22.424 30.806 32.757 1.00 0.00 H +HETATM 268 HB3 HY1 16 23.026 29.261 33.277 1.00 0.00 H +HETATM 269 HD1 HY1 16 25.395 28.443 32.070 1.00 0.00 H +HETATM 270 HD2 HY1 16 23.925 32.270 31.110 1.00 0.00 H +HETATM 271 HE1 HY1 16 27.333 29.725 30.986 1.00 0.00 H +ATOM 272 N THR 17 21.170 31.128 30.268 1.00 0.00 N +ATOM 273 H THR 17 21.079 31.413 31.222 1.00 0.00 H +ATOM 274 CA THR 17 20.676 32.024 29.187 1.00 0.00 C +ATOM 275 HA THR 17 21.058 31.616 28.265 1.00 0.00 H +ATOM 276 CB THR 17 19.161 32.036 29.034 1.00 0.00 C +ATOM 277 HB THR 17 18.927 32.546 28.106 1.00 0.00 H +ATOM 278 CG2 THR 17 18.561 30.663 28.729 1.00 0.00 C +ATOM 279 HG21 THR 17 18.791 29.938 29.493 1.00 0.00 H +ATOM 280 HG22 THR 17 17.496 30.766 28.657 1.00 0.00 H +ATOM 281 HG23 THR 17 18.946 30.376 27.783 1.00 0.00 H +ATOM 282 OG1 THR 17 18.410 32.476 30.140 1.00 0.00 O +ATOM 283 HG1 THR 17 18.585 33.427 30.238 1.00 0.00 H +ATOM 284 C THR 17 21.222 33.465 29.200 1.00 0.00 C +ATOM 285 O THR 17 21.705 33.940 30.240 1.00 0.00 O +HETATM 286 N HY2 18 21.132 34.182 28.066 1.00 0.00 N +HETATM 287 CA HY2 18 21.431 35.612 28.001 1.00 0.00 C +HETATM 288 C HY2 18 20.328 36.310 27.213 1.00 0.00 C +HETATM 289 O HY2 18 19.975 35.851 26.125 1.00 0.00 O +HETATM 290 CB HY2 18 22.791 35.839 27.262 1.00 0.00 C +HETATM 291 CG HY2 18 24.006 35.348 28.021 1.00 0.00 C +HETATM 292 CD2 HY2 18 24.413 34.051 28.184 1.00 0.00 C +HETATM 293 ND1 HY2 18 24.960 36.137 28.624 1.00 0.00 N +HETATM 294 CE1 HY2 18 25.899 35.329 29.142 1.00 0.00 C +HETATM 295 NE2 HY2 18 25.606 34.045 28.910 1.00 0.00 N +HETATM 296 H HY2 18 20.782 33.736 27.218 1.00 0.00 H +HETATM 297 HA HY2 18 21.489 36.045 28.993 1.00 0.00 H +HETATM 298 HB2 HY2 18 22.749 35.327 26.310 1.00 0.00 H +HETATM 299 HB3 HY2 18 22.908 36.902 27.077 1.00 0.00 H +HETATM 300 HD1 HY2 18 24.991 37.149 28.638 1.00 0.00 H +HETATM 301 HD2 HY2 18 23.902 33.177 27.820 1.00 0.00 H +HETATM 302 HE1 HY2 18 26.787 35.668 29.652 1.00 0.00 H +ATOM 303 N GLU 19 19.791 37.399 27.752 1.00 0.00 N +ATOM 304 H GLU 19 20.124 37.705 28.652 1.00 0.00 H +ATOM 305 CA GLU 19 18.776 38.224 27.087 1.00 0.00 C +ATOM 306 HA GLU 19 18.046 37.565 26.625 1.00 0.00 H +ATOM 307 CB GLU 19 18.055 39.081 28.151 1.00 0.00 C +ATOM 308 HB2 GLU 19 17.742 38.439 28.965 1.00 0.00 H +ATOM 309 HB3 GLU 19 18.766 39.793 28.561 1.00 0.00 H +ATOM 310 CG GLU 19 16.818 39.843 27.647 1.00 0.00 C +ATOM 311 HG2 GLU 19 16.532 40.560 28.420 1.00 0.00 H +ATOM 312 HG3 GLU 19 17.067 40.405 26.749 1.00 0.00 H +ATOM 313 CD GLU 19 15.633 38.901 27.372 1.00 0.00 C +ATOM 314 OE1 GLU 19 15.556 38.375 26.231 1.00 0.00 O +ATOM 315 OE2 GLU 19 14.808 38.684 28.292 1.00 0.00 O +ATOM 316 C GLU 19 19.396 39.117 26.000 1.00 0.00 C +ATOM 317 O GLU 19 20.331 39.868 26.280 1.00 0.00 O +ATOM 318 N ALA 20 18.875 39.060 24.771 1.00 0.00 N +ATOM 319 H ALA 20 18.171 38.356 24.577 1.00 0.00 H +ATOM 320 CA ALA 20 19.256 39.967 23.684 1.00 0.00 C +ATOM 321 HA ALA 20 19.395 40.969 24.097 1.00 0.00 H +ATOM 322 CB ALA 20 20.591 39.496 23.094 1.00 0.00 C +ATOM 323 HB1 ALA 20 20.461 38.526 22.614 1.00 0.00 H +ATOM 324 HB2 ALA 20 20.949 40.215 22.359 1.00 0.00 H +ATOM 325 HB3 ALA 20 21.344 39.405 23.875 1.00 0.00 H +ATOM 326 C ALA 20 18.185 40.047 22.577 1.00 0.00 C +ATOM 327 O ALA 20 17.354 39.145 22.442 1.00 0.00 O +ATOM 328 N VAL 21 18.221 41.099 21.748 1.00 0.00 N +ATOM 329 H VAL 21 18.893 41.832 21.925 1.00 0.00 H +ATOM 330 CA VAL 21 17.459 41.162 20.475 1.00 0.00 C +ATOM 331 HA VAL 21 16.468 40.737 20.630 1.00 0.00 H +ATOM 332 CB VAL 21 17.270 42.614 19.983 1.00 0.00 C +ATOM 333 HB VAL 21 16.610 42.587 19.116 1.00 0.00 H +ATOM 334 CG1 VAL 21 16.590 43.481 21.047 1.00 0.00 C +ATOM 335 HG11 VAL 21 17.248 43.634 21.902 1.00 0.00 H +ATOM 336 HG12 VAL 21 16.341 44.452 20.615 1.00 0.00 H +ATOM 337 HG13 VAL 21 15.667 43.006 21.376 1.00 0.00 H +ATOM 338 CG2 VAL 21 18.578 43.295 19.550 1.00 0.00 C +ATOM 339 HG21 VAL 21 19.000 42.786 18.683 1.00 0.00 H +ATOM 340 HG22 VAL 21 18.373 44.324 19.255 1.00 0.00 H +ATOM 341 HG23 VAL 21 19.307 43.296 20.359 1.00 0.00 H +ATOM 342 C VAL 21 18.117 40.348 19.356 1.00 0.00 C +ATOM 343 O VAL 21 17.464 40.001 18.377 1.00 0.00 O +ATOM 344 N ASP 22 19.412 40.069 19.505 1.00 0.00 N +ATOM 345 H ASP 22 19.862 40.351 20.359 1.00 0.00 H +ATOM 346 CA ASP 22 20.289 39.480 18.502 1.00 0.00 C +ATOM 347 HA ASP 22 19.707 38.841 17.834 1.00 0.00 H +ATOM 348 CB ASP 22 20.936 40.601 17.673 1.00 0.00 C +ATOM 349 HB2 ASP 22 20.164 41.110 17.093 1.00 0.00 H +ATOM 350 HB3 ASP 22 21.395 41.325 18.350 1.00 0.00 H +ATOM 351 CG ASP 22 21.996 40.060 16.717 1.00 0.00 C +ATOM 352 OD1 ASP 22 23.093 40.648 16.681 1.00 0.00 O +ATOM 353 OD2 ASP 22 21.733 39.004 16.097 1.00 0.00 O +ATOM 354 C ASP 22 21.360 38.615 19.181 1.00 0.00 C +ATOM 355 O ASP 22 21.825 38.905 20.286 1.00 0.00 O +ATOM 356 N TRP 23 21.774 37.554 18.504 1.00 0.00 N +ATOM 357 H TRP 23 21.492 37.490 17.531 1.00 0.00 H +ATOM 358 CA TRP 23 22.767 36.618 19.006 1.00 0.00 C +ATOM 359 HA TRP 23 22.525 36.373 20.039 1.00 0.00 H +ATOM 360 CB TRP 23 22.646 35.352 18.169 1.00 0.00 C +ATOM 361 HB2 TRP 23 21.628 34.972 18.255 1.00 0.00 H +ATOM 362 HB3 TRP 23 22.822 35.600 17.122 1.00 0.00 H +ATOM 363 CG TRP 23 23.564 34.260 18.574 1.00 0.00 C +ATOM 364 CD1 TRP 23 24.539 33.738 17.789 1.00 0.00 C +ATOM 365 HD1 TRP 23 24.773 34.070 16.785 1.00 0.00 H +ATOM 366 NE1 TRP 23 25.153 32.722 18.467 1.00 0.00 N +ATOM 367 HE1 TRP 23 25.951 32.221 18.108 1.00 0.00 H +ATOM 368 CE2 TRP 23 24.593 32.496 19.714 1.00 0.00 C +ATOM 369 CZ2 TRP 23 24.828 31.562 20.706 1.00 0.00 C +ATOM 370 HZ2 TRP 23 25.556 30.774 20.575 1.00 0.00 H +ATOM 371 CH2 TRP 23 24.140 31.692 21.930 1.00 0.00 C +ATOM 372 HH2 TRP 23 24.335 31.027 22.741 1.00 0.00 H +ATOM 373 CZ3 TRP 23 23.269 32.767 22.129 1.00 0.00 C +ATOM 374 HZ3 TRP 23 22.829 32.889 23.111 1.00 0.00 H +ATOM 375 CE3 TRP 23 22.980 33.658 21.094 1.00 0.00 C +ATOM 376 HE3 TRP 23 22.278 34.461 21.241 1.00 0.00 H +ATOM 377 CD2 TRP 23 23.629 33.540 19.831 1.00 0.00 C +ATOM 378 C TRP 23 24.191 37.194 19.002 1.00 0.00 C +ATOM 379 O TRP 23 24.946 36.973 19.951 1.00 0.00 O +ATOM 380 N ALA 24 24.541 38.018 18.009 1.00 0.00 N +ATOM 381 H ALA 24 23.871 38.237 17.277 1.00 0.00 H +ATOM 382 CA ALA 24 25.829 38.715 17.984 1.00 0.00 C +ATOM 383 HA ALA 24 26.603 37.999 18.268 1.00 0.00 H +ATOM 384 CB ALA 24 26.130 39.149 16.545 1.00 0.00 C +ATOM 385 HB1 ALA 24 25.409 39.889 16.210 1.00 0.00 H +ATOM 386 HB2 ALA 24 27.130 39.576 16.491 1.00 0.00 H +ATOM 387 HB3 ALA 24 26.083 38.285 15.882 1.00 0.00 H +ATOM 388 C ALA 24 25.913 39.875 19.007 1.00 0.00 C +ATOM 389 O ALA 24 27.004 40.380 19.281 1.00 0.00 O +ATOM 390 N GLU 25 24.798 40.276 19.630 1.00 0.00 N +ATOM 391 H GLU 25 23.917 39.918 19.285 1.00 0.00 H +ATOM 392 CA GLU 25 24.787 41.074 20.867 1.00 0.00 C +ATOM 393 HA GLU 25 25.643 41.748 20.875 1.00 0.00 H +ATOM 394 CB GLU 25 23.515 41.935 20.943 1.00 0.00 C +ATOM 395 HB2 GLU 25 22.645 41.291 20.846 1.00 0.00 H +ATOM 396 HB3 GLU 25 23.462 42.403 21.924 1.00 0.00 H +ATOM 397 CG GLU 25 23.430 43.036 19.878 1.00 0.00 C +ATOM 398 HG2 GLU 25 23.642 42.620 18.894 1.00 0.00 H +ATOM 399 HG3 GLU 25 22.406 43.412 19.855 1.00 0.00 H +ATOM 400 CD GLU 25 24.383 44.195 20.176 1.00 0.00 C +ATOM 401 OE1 GLU 25 23.887 45.221 20.706 1.00 0.00 O +ATOM 402 OE2 GLU 25 25.589 44.053 19.865 1.00 0.00 O +ATOM 403 C GLU 25 24.926 40.185 22.120 1.00 0.00 C +ATOM 404 O GLU 25 25.682 40.523 23.033 1.00 0.00 O +ATOM 405 N ALA 26 24.283 39.009 22.156 1.00 0.00 N +ATOM 406 H ALA 26 23.666 38.773 21.386 1.00 0.00 H +ATOM 407 CA ALA 26 24.457 38.032 23.240 1.00 0.00 C +ATOM 408 HA ALA 26 24.199 38.527 24.174 1.00 0.00 H +ATOM 409 CB ALA 26 23.483 36.865 23.038 1.00 0.00 C +ATOM 410 HB1 ALA 26 23.764 36.292 22.156 1.00 0.00 H +ATOM 411 HB2 ALA 26 23.517 36.208 23.906 1.00 0.00 H +ATOM 412 HB3 ALA 26 22.467 37.238 22.916 1.00 0.00 H +ATOM 413 C ALA 26 25.913 37.533 23.381 1.00 0.00 C +ATOM 414 O ALA 26 26.342 37.219 24.495 1.00 0.00 O +ATOM 415 N GLU 27 26.696 37.513 22.296 1.00 0.00 N +ATOM 416 H GLU 27 26.247 37.646 21.393 1.00 0.00 H +ATOM 417 CA GLU 27 28.153 37.298 22.324 1.00 0.00 C +ATOM 418 HA GLU 27 28.361 36.338 22.799 1.00 0.00 H +ATOM 419 CB GLU 27 28.694 37.255 20.879 1.00 0.00 C +ATOM 420 HB2 GLU 27 28.051 36.617 20.269 1.00 0.00 H +ATOM 421 HB3 GLU 27 28.655 38.262 20.462 1.00 0.00 H +ATOM 422 CG GLU 27 30.131 36.716 20.800 1.00 0.00 C +ATOM 423 HG2 GLU 27 30.747 37.222 21.545 1.00 0.00 H +ATOM 424 HG3 GLU 27 30.124 35.652 21.043 1.00 0.00 H +ATOM 425 CD GLU 27 30.754 36.949 19.410 1.00 0.00 C +ATOM 426 OE1 GLU 27 31.211 38.094 19.177 1.00 0.00 O +ATOM 427 OE2 GLU 27 30.788 35.992 18.599 1.00 0.00 O +ATOM 428 C GLU 27 28.860 38.378 23.161 1.00 0.00 C +ATOM 429 O GLU 27 29.592 38.066 24.105 1.00 0.00 O +ATOM 430 N LYS 28 28.562 39.657 22.902 1.00 0.00 N +ATOM 431 H LYS 28 27.890 39.843 22.167 1.00 0.00 H +ATOM 432 CA LYS 28 29.110 40.795 23.659 1.00 0.00 C +ATOM 433 HA LYS 28 30.198 40.718 23.660 1.00 0.00 H +ATOM 434 CB LYS 28 28.720 42.129 22.993 1.00 0.00 C +ATOM 435 HB2 LYS 28 27.639 42.268 23.053 1.00 0.00 H +ATOM 436 HB3 LYS 28 29.199 42.942 23.542 1.00 0.00 H +ATOM 437 CG LYS 28 29.150 42.206 21.516 1.00 0.00 C +ATOM 438 HG2 LYS 28 30.220 42.003 21.435 1.00 0.00 H +ATOM 439 HG3 LYS 28 28.609 41.451 20.948 1.00 0.00 H +ATOM 440 CD LYS 28 28.859 43.592 20.921 1.00 0.00 C +ATOM 441 HD2 LYS 28 27.847 43.907 21.183 1.00 0.00 H +ATOM 442 HD3 LYS 28 29.557 44.311 21.354 1.00 0.00 H +ATOM 443 CE LYS 28 29.007 43.609 19.395 1.00 0.00 C +ATOM 444 HE2 LYS 28 29.103 44.648 19.076 1.00 0.00 H +ATOM 445 HE3 LYS 28 29.927 43.091 19.118 1.00 0.00 H +ATOM 446 NZ LYS 28 27.833 42.999 18.726 1.00 0.00 N +ATOM 447 HZ1 LYS 28 26.977 43.466 19.045 1.00 0.00 H +ATOM 448 HZ2 LYS 28 27.883 43.073 17.721 1.00 0.00 H +ATOM 449 HZ3 LYS 28 27.721 42.019 18.980 1.00 0.00 H +ATOM 450 C LYS 28 28.671 40.756 25.124 1.00 0.00 C +ATOM 451 O LYS 28 29.501 40.914 26.014 1.00 0.00 O +ATOM 452 N PHE 29 27.403 40.446 25.406 1.00 0.00 N +ATOM 453 H PHE 29 26.750 40.371 24.629 1.00 0.00 H +ATOM 454 CA PHE 29 26.909 40.272 26.780 1.00 0.00 C +ATOM 455 HA PHE 29 27.235 41.127 27.372 1.00 0.00 H +ATOM 456 CB PHE 29 25.370 40.257 26.782 1.00 0.00 C +ATOM 457 HB2 PHE 29 25.040 39.339 26.293 1.00 0.00 H +ATOM 458 HB3 PHE 29 25.026 40.219 27.817 1.00 0.00 H +ATOM 459 CG PHE 29 24.683 41.440 26.107 1.00 0.00 C +ATOM 460 CD1 PHE 29 23.464 41.237 25.430 1.00 0.00 C +ATOM 461 HD1 PHE 29 23.011 40.258 25.409 1.00 0.00 H +ATOM 462 CE1 PHE 29 22.827 42.305 24.774 1.00 0.00 C +ATOM 463 HE1 PHE 29 21.899 42.136 24.249 1.00 0.00 H +ATOM 464 CZ PHE 29 23.401 43.588 24.795 1.00 0.00 C +ATOM 465 HZ PHE 29 22.919 44.403 24.276 1.00 0.00 H +ATOM 466 CE2 PHE 29 24.600 43.805 25.495 1.00 0.00 C +ATOM 467 HE2 PHE 29 25.038 44.793 25.522 1.00 0.00 H +ATOM 468 CD2 PHE 29 25.236 42.738 26.153 1.00 0.00 C +ATOM 469 HD2 PHE 29 26.155 42.927 26.685 1.00 0.00 H +ATOM 470 C PHE 29 27.482 39.027 27.486 1.00 0.00 C +ATOM 471 O PHE 29 27.521 38.980 28.716 1.00 0.00 O +ATOM 472 N THR 30 27.960 38.026 26.741 1.00 0.00 N +ATOM 473 H THR 30 27.829 38.068 25.735 1.00 0.00 H +ATOM 474 CA THR 30 28.722 36.892 27.292 1.00 0.00 C +ATOM 475 HA THR 30 28.251 36.565 28.215 1.00 0.00 H +ATOM 476 CB THR 30 28.706 35.706 26.317 1.00 0.00 C +ATOM 477 HB THR 30 29.093 36.002 25.344 1.00 0.00 H +ATOM 478 CG2 THR 30 29.499 34.501 26.817 1.00 0.00 C +ATOM 479 HG21 THR 30 29.141 34.214 27.798 1.00 0.00 H +ATOM 480 HG22 THR 30 29.360 33.670 26.127 1.00 0.00 H +ATOM 481 HG23 THR 30 30.563 34.723 26.869 1.00 0.00 H +ATOM 482 OG1 THR 30 27.376 35.267 26.186 1.00 0.00 O +ATOM 483 HG1 THR 30 26.955 35.881 25.563 1.00 0.00 H +ATOM 484 C THR 30 30.150 37.299 27.655 1.00 0.00 C +ATOM 485 O THR 30 30.624 36.982 28.749 1.00 0.00 O +ATOM 486 N LYS 31 30.815 38.064 26.781 1.00 0.00 N +ATOM 487 H LYS 31 30.369 38.252 25.888 1.00 0.00 H +ATOM 488 CA LYS 31 32.152 38.634 27.020 1.00 0.00 C +ATOM 489 HA LYS 31 32.818 37.831 27.339 1.00 0.00 H +ATOM 490 CB LYS 31 32.706 39.226 25.717 1.00 0.00 C +ATOM 491 HB2 LYS 31 31.979 39.917 25.283 1.00 0.00 H +ATOM 492 HB3 LYS 31 33.613 39.789 25.949 1.00 0.00 H +ATOM 493 CG LYS 31 33.067 38.138 24.689 1.00 0.00 C +ATOM 494 HG2 LYS 31 33.816 37.480 25.124 1.00 0.00 H +ATOM 495 HG3 LYS 31 32.188 37.542 24.445 1.00 0.00 H +ATOM 496 CD LYS 31 33.619 38.762 23.398 1.00 0.00 C +ATOM 497 HD2 LYS 31 32.803 39.284 22.894 1.00 0.00 H +ATOM 498 HD3 LYS 31 34.390 39.495 23.648 1.00 0.00 H +ATOM 499 CE LYS 31 34.214 37.733 22.429 1.00 0.00 C +ATOM 500 HE2 LYS 31 33.486 36.945 22.216 1.00 0.00 H +ATOM 501 HE3 LYS 31 34.422 38.234 21.480 1.00 0.00 H +ATOM 502 NZ LYS 31 35.472 37.134 22.931 1.00 0.00 N +ATOM 503 HZ1 LYS 31 35.291 36.317 23.502 1.00 0.00 H +ATOM 504 HZ2 LYS 31 36.015 36.773 22.139 1.00 0.00 H +ATOM 505 HZ3 LYS 31 36.033 37.780 23.488 1.00 0.00 H +ATOM 506 C LYS 31 32.171 39.672 28.147 1.00 0.00 C +ATOM 507 O LYS 31 33.142 39.702 28.899 1.00 0.00 O +ATOM 508 N ALA 32 31.100 40.451 28.321 1.00 0.00 N +ATOM 509 H ALA 32 30.398 40.462 27.589 1.00 0.00 H +ATOM 510 CA ALA 32 30.931 41.365 29.453 1.00 0.00 C +ATOM 511 HA ALA 32 31.752 42.085 29.447 1.00 0.00 H +ATOM 512 CB ALA 32 29.618 42.142 29.287 1.00 0.00 C +ATOM 513 HB1 ALA 32 28.769 41.458 29.278 1.00 0.00 H +ATOM 514 HB2 ALA 32 29.501 42.841 30.118 1.00 0.00 H +ATOM 515 HB3 ALA 32 29.638 42.709 28.355 1.00 0.00 H +ATOM 516 C ALA 32 30.991 40.611 30.792 1.00 0.00 C +ATOM 517 O ALA 32 31.887 40.874 31.591 1.00 0.00 O +ATOM 518 N LYN 33 30.130 39.599 30.989 1.00 0.00 N +ATOM 519 H LYN 33 29.417 39.433 30.293 1.00 0.00 H +ATOM 520 CA LYN 33 30.139 38.766 32.203 1.00 0.00 C +ATOM 521 HA LYN 33 30.001 39.413 33.073 1.00 0.00 H +ATOM 522 CB LYN 33 28.987 37.743 32.169 1.00 0.00 C +ATOM 523 HB2 LYN 33 29.040 37.167 31.244 1.00 0.00 H +ATOM 524 HB3 LYN 33 29.118 37.055 33.007 1.00 0.00 H +ATOM 525 CG LYN 33 27.590 38.375 32.294 1.00 0.00 C +ATOM 526 HG2 LYN 33 27.545 39.000 33.186 1.00 0.00 H +ATOM 527 HG3 LYN 33 27.392 38.995 31.420 1.00 0.00 H +ATOM 528 CD LYN 33 26.522 37.277 32.395 1.00 0.00 C +ATOM 529 HD2 LYN 33 26.675 36.556 31.599 1.00 0.00 H +ATOM 530 HD3 LYN 33 26.628 36.757 33.347 1.00 0.00 H +ATOM 531 CE LYN 33 25.104 37.835 32.284 1.00 0.00 C +ATOM 532 HE2 LYN 33 24.914 38.506 33.118 1.00 0.00 H +ATOM 533 HE3 LYN 33 25.005 38.384 31.350 1.00 0.00 H +ATOM 534 NZ LYN 33 24.107 36.753 32.301 1.00 0.00 N +ATOM 535 HZ2 LYN 33 23.174 37.141 32.292 1.00 0.00 H +ATOM 536 HZ3 LYN 33 24.226 36.138 31.508 1.00 0.00 H +ATOM 537 C LYN 33 31.481 38.041 32.405 1.00 0.00 C +ATOM 538 O LYN 33 31.942 37.902 33.532 1.00 0.00 O +ATOM 539 N ALA 34 32.140 37.586 31.335 1.00 0.00 N +ATOM 540 H ALA 34 31.727 37.699 30.417 1.00 0.00 H +ATOM 541 CA ALA 34 33.461 36.962 31.455 1.00 0.00 C +ATOM 542 HA ALA 34 33.401 36.176 32.210 1.00 0.00 H +ATOM 543 CB ALA 34 33.817 36.311 30.120 1.00 0.00 C +ATOM 544 HB1 ALA 34 33.986 37.080 29.368 1.00 0.00 H +ATOM 545 HB2 ALA 34 34.719 35.716 30.257 1.00 0.00 H +ATOM 546 HB3 ALA 34 33.015 35.656 29.787 1.00 0.00 H +ATOM 547 C ALA 34 34.557 37.947 31.927 1.00 0.00 C +ATOM 548 O ALA 34 35.442 37.557 32.691 1.00 0.00 O +ATOM 549 N ASN 35 34.482 39.223 31.531 1.00 0.00 N +ATOM 550 H ASN 35 33.735 39.492 30.902 1.00 0.00 H +ATOM 551 CA ASN 35 35.346 40.291 32.051 1.00 0.00 C +ATOM 552 HA ASN 35 36.349 39.888 32.168 1.00 0.00 H +ATOM 553 CB ASN 35 35.438 41.431 31.030 1.00 0.00 C +ATOM 554 HB2 ASN 35 34.451 41.675 30.644 1.00 0.00 H +ATOM 555 HB3 ASN 35 35.833 42.319 31.524 1.00 0.00 H +ATOM 556 CG ASN 35 36.388 41.076 29.903 1.00 0.00 C +ATOM 557 OD1 ASN 35 37.597 41.133 30.044 1.00 0.00 O +ATOM 558 ND2 ASN 35 35.880 40.668 28.770 1.00 0.00 N +ATOM 559 HD21 ASN 35 36.541 40.390 28.044 1.00 0.00 H +ATOM 560 HD22 ASN 35 34.888 40.505 28.695 1.00 0.00 H +ATOM 561 C ASN 35 34.944 40.782 33.456 1.00 0.00 C +ATOM 562 O ASN 35 35.823 41.206 34.208 1.00 0.00 O +ATOM 563 N ASP 36 33.681 40.623 33.873 1.00 0.00 N +ATOM 564 H ASP 36 32.953 40.411 33.198 1.00 0.00 H +ATOM 565 CA ASP 36 33.299 40.753 35.289 1.00 0.00 C +ATOM 566 HA ASP 36 33.620 41.727 35.644 1.00 0.00 H +ATOM 567 CB ASP 36 31.771 40.726 35.477 1.00 0.00 C +ATOM 568 HB2 ASP 36 31.409 39.739 35.256 1.00 0.00 H +ATOM 569 HB3 ASP 36 31.566 40.838 36.535 1.00 0.00 H +ATOM 570 CG ASP 36 30.946 41.759 34.697 1.00 0.00 C +ATOM 571 OD1 ASP 36 31.473 42.854 34.397 1.00 0.00 O +ATOM 572 OD2 ASP 36 29.745 41.503 34.453 1.00 0.00 O +ATOM 573 C ASP 36 34.001 39.687 36.164 1.00 0.00 C +ATOM 574 O ASP 36 34.414 39.975 37.288 1.00 0.00 O +ATOM 575 N PHE 37 34.224 38.476 35.627 1.00 0.00 N +ATOM 576 H PHE 37 33.778 38.285 34.738 1.00 0.00 H +ATOM 577 CA PHE 37 35.119 37.457 36.204 1.00 0.00 C +ATOM 578 HA PHE 37 35.102 37.608 37.282 1.00 0.00 H +ATOM 579 CB PHE 37 34.584 36.039 35.941 1.00 0.00 C +ATOM 580 HB2 PHE 37 34.673 35.835 34.877 1.00 0.00 H +ATOM 581 HB3 PHE 37 35.235 35.333 36.451 1.00 0.00 H +ATOM 582 CG PHE 37 33.163 35.751 36.394 1.00 0.00 C +ATOM 583 CD1 PHE 37 32.154 35.533 35.443 1.00 0.00 C +ATOM 584 HD1 PHE 37 32.388 35.593 34.397 1.00 0.00 H +ATOM 585 CE1 PHE 37 30.832 35.284 35.846 1.00 0.00 C +ATOM 586 HE1 PHE 37 30.053 35.169 35.107 1.00 0.00 H +ATOM 587 CZ PHE 37 30.522 35.220 37.212 1.00 0.00 C +ATOM 588 HZ PHE 37 29.506 35.043 37.525 1.00 0.00 H +ATOM 589 CE2 PHE 37 31.529 35.401 38.173 1.00 0.00 C +ATOM 590 HE2 PHE 37 31.282 35.368 39.224 1.00 0.00 H +ATOM 591 CD2 PHE 37 32.847 35.666 37.762 1.00 0.00 C +ATOM 592 HD2 PHE 37 33.611 35.831 38.501 1.00 0.00 H +ATOM 593 C PHE 37 36.610 37.593 35.788 1.00 0.00 C +ATOM 594 O PHE 37 37.403 36.685 36.046 1.00 0.00 O +ATOM 595 N GLY 38 37.009 38.711 35.165 1.00 0.00 N +ATOM 596 H GLY 38 36.301 39.413 34.987 1.00 0.00 H +ATOM 597 CA GLY 38 38.402 39.132 34.947 1.00 0.00 C +ATOM 598 HA2 GLY 38 38.496 40.160 35.294 1.00 0.00 H +ATOM 599 HA3 GLY 38 39.060 38.525 35.570 1.00 0.00 H +ATOM 600 C GLY 38 38.960 39.077 33.512 1.00 0.00 C +ATOM 601 O GLY 38 39.924 39.793 33.233 1.00 0.00 O +ATOM 602 N ARG 39 38.411 38.239 32.614 1.00 0.00 N +ATOM 603 H ARG 39 37.570 37.746 32.897 1.00 0.00 H +ATOM 604 CA ARG 39 38.880 38.053 31.215 1.00 0.00 C +ATOM 605 HA ARG 39 38.893 39.037 30.743 1.00 0.00 H +ATOM 606 CB ARG 39 40.326 37.487 31.154 1.00 0.00 C +ATOM 607 HB2 ARG 39 40.634 37.506 30.107 1.00 0.00 H +ATOM 608 HB3 ARG 39 41.005 38.160 31.675 1.00 0.00 H +ATOM 609 CG ARG 39 40.587 36.054 31.667 1.00 0.00 C +ATOM 610 HG2 ARG 39 40.031 35.354 31.046 1.00 0.00 H +ATOM 611 HG3 ARG 39 41.646 35.833 31.521 1.00 0.00 H +ATOM 612 CD ARG 39 40.250 35.822 33.155 1.00 0.00 C +ATOM 613 HD2 ARG 39 40.874 36.485 33.760 1.00 0.00 H +ATOM 614 HD3 ARG 39 39.207 36.074 33.344 1.00 0.00 H +ATOM 615 NE ARG 39 40.449 34.422 33.582 1.00 0.00 N +ATOM 616 HE ARG 39 41.211 34.244 34.213 1.00 0.00 H +ATOM 617 CZ ARG 39 39.685 33.394 33.251 1.00 0.00 C +ATOM 618 NH1 ARG 39 38.675 33.509 32.434 1.00 0.00 N +ATOM 619 HH11 ARG 39 38.446 34.417 32.050 1.00 0.00 H +ATOM 620 HH12 ARG 39 38.287 32.681 31.992 1.00 0.00 H +ATOM 621 NH2 ARG 39 39.925 32.210 33.740 1.00 0.00 N +ATOM 622 HH21 ARG 39 40.672 32.054 34.398 1.00 0.00 H +ATOM 623 HH22 ARG 39 39.300 31.445 33.507 1.00 0.00 H +ATOM 624 C ARG 39 37.947 37.164 30.379 1.00 0.00 C +ATOM 625 O ARG 39 37.564 36.085 30.844 1.00 0.00 O +ATOM 626 N ASP 40 37.631 37.575 29.145 1.00 0.00 N +ATOM 627 H ASP 40 37.999 38.458 28.810 1.00 0.00 H +ATOM 628 CA ASP 40 36.870 36.764 28.180 1.00 0.00 C +ATOM 629 HA ASP 40 36.160 36.178 28.752 1.00 0.00 H +ATOM 630 CB ASP 40 36.028 37.628 27.214 1.00 0.00 C +ATOM 631 HB2 ASP 40 35.414 36.959 26.614 1.00 0.00 H +ATOM 632 HB3 ASP 40 35.330 38.215 27.807 1.00 0.00 H +ATOM 633 CG ASP 40 36.785 38.583 26.276 1.00 0.00 C +ATOM 634 OD1 ASP 40 37.479 39.492 26.781 1.00 0.00 O +ATOM 635 OD2 ASP 40 36.569 38.494 25.045 1.00 0.00 O +ATOM 636 C ASP 40 37.702 35.719 27.412 1.00 0.00 C +ATOM 637 O ASP 40 38.929 35.703 27.443 1.00 0.00 O +ATOM 638 N GLY 41 36.987 34.824 26.722 1.00 0.00 N +ATOM 639 H GLY 41 35.986 34.945 26.736 1.00 0.00 H +ATOM 640 CA GLY 41 37.491 33.909 25.694 1.00 0.00 C +ATOM 641 HA2 GLY 41 38.450 34.264 25.310 1.00 0.00 H +ATOM 642 HA3 GLY 41 37.626 32.915 26.126 1.00 0.00 H +ATOM 643 C GLY 41 36.490 33.825 24.530 1.00 0.00 C +ATOM 644 O GLY 41 35.608 34.679 24.411 1.00 0.00 O +ATOM 645 N GLU 42 36.598 32.789 23.694 1.00 0.00 N +ATOM 646 H GLU 42 37.307 32.099 23.872 1.00 0.00 H +ATOM 647 CA GLU 42 35.731 32.568 22.522 1.00 0.00 C +ATOM 648 HA GLU 42 35.013 33.385 22.459 1.00 0.00 H +ATOM 649 CB GLU 42 36.558 32.561 21.218 1.00 0.00 C +ATOM 650 HB2 GLU 42 37.196 31.676 21.230 1.00 0.00 H +ATOM 651 HB3 GLU 42 35.871 32.454 20.377 1.00 0.00 H +ATOM 652 CG GLU 42 37.461 33.787 20.960 1.00 0.00 C +ATOM 653 HG2 GLU 42 38.223 33.829 21.742 1.00 0.00 H +ATOM 654 HG3 GLU 42 37.980 33.632 20.011 1.00 0.00 H +ATOM 655 CD GLU 42 36.724 35.137 20.908 1.00 0.00 C +ATOM 656 OE1 GLU 42 35.483 35.176 21.031 1.00 0.00 O +ATOM 657 OE2 GLU 42 37.391 36.197 20.846 1.00 0.00 O +ATOM 658 C GLU 42 34.890 31.282 22.632 1.00 0.00 C +ATOM 659 O GLU 42 35.334 30.288 23.220 1.00 0.00 O +ATOM 660 N ALA 43 33.689 31.301 22.040 1.00 0.00 N +ATOM 661 H ALA 43 33.435 32.120 21.500 1.00 0.00 H +ATOM 662 CA ALA 43 32.685 30.234 22.101 1.00 0.00 C +ATOM 663 HA ALA 43 33.159 29.309 22.430 1.00 0.00 H +ATOM 664 CB ALA 43 31.621 30.621 23.139 1.00 0.00 C +ATOM 665 HB1 ALA 43 31.138 31.555 22.844 1.00 0.00 H +ATOM 666 HB2 ALA 43 30.866 29.838 23.204 1.00 0.00 H +ATOM 667 HB3 ALA 43 32.086 30.751 24.116 1.00 0.00 H +ATOM 668 C ALA 43 32.047 29.965 20.723 1.00 0.00 C +ATOM 669 O ALA 43 31.803 30.891 19.950 1.00 0.00 O +ATOM 670 N THR 44 31.754 28.697 20.429 1.00 0.00 N +ATOM 671 H THR 44 31.886 28.002 21.155 1.00 0.00 H +ATOM 672 CA THR 44 31.095 28.260 19.186 1.00 0.00 C +ATOM 673 HA THR 44 31.411 28.926 18.382 1.00 0.00 H +ATOM 674 CB THR 44 31.551 26.839 18.809 1.00 0.00 C +ATOM 675 HB THR 44 31.332 26.153 19.627 1.00 0.00 H +ATOM 676 CG2 THR 44 30.946 26.290 17.515 1.00 0.00 C +ATOM 677 HG21 THR 44 31.065 27.010 16.705 1.00 0.00 H +ATOM 678 HG22 THR 44 31.440 25.358 17.238 1.00 0.00 H +ATOM 679 HG23 THR 44 29.887 26.071 17.660 1.00 0.00 H +ATOM 680 OG1 THR 44 32.942 26.864 18.586 1.00 0.00 O +ATOM 681 HG1 THR 44 33.165 26.109 18.037 1.00 0.00 H +ATOM 682 C THR 44 29.572 28.381 19.304 1.00 0.00 C +ATOM 683 O THR 44 29.030 28.395 20.412 1.00 0.00 O +ATOM 684 N ILE 45 28.876 28.504 18.166 1.00 0.00 N +ATOM 685 H ILE 45 29.362 28.406 17.289 1.00 0.00 H +ATOM 686 CA ILE 45 27.461 28.894 18.096 1.00 0.00 C +ATOM 687 HA ILE 45 27.037 28.820 19.098 1.00 0.00 H +ATOM 688 CB ILE 45 27.326 30.368 17.651 1.00 0.00 C +ATOM 689 HB ILE 45 26.262 30.577 17.713 1.00 0.00 H +ATOM 690 CG2 ILE 45 28.061 31.286 18.642 1.00 0.00 C +ATOM 691 HG21 ILE 45 29.142 31.155 18.565 1.00 0.00 H +ATOM 692 HG22 ILE 45 27.838 32.337 18.468 1.00 0.00 H +ATOM 693 HG23 ILE 45 27.748 31.027 19.650 1.00 0.00 H +ATOM 694 CG1 ILE 45 27.760 30.675 16.198 1.00 0.00 C +ATOM 695 HG12 ILE 45 28.847 30.635 16.123 1.00 0.00 H +ATOM 696 HG13 ILE 45 27.346 29.927 15.524 1.00 0.00 H +ATOM 697 CD1 ILE 45 27.269 32.044 15.699 1.00 0.00 C +ATOM 698 HD11 ILE 45 27.702 32.852 16.288 1.00 0.00 H +ATOM 699 HD12 ILE 45 27.568 32.179 14.659 1.00 0.00 H +ATOM 700 HD13 ILE 45 26.182 32.091 15.757 1.00 0.00 H +ATOM 701 C ILE 45 26.606 27.983 17.209 1.00 0.00 C +ATOM 702 O ILE 45 27.086 27.449 16.212 1.00 0.00 O +ATOM 703 N ASP 46 25.319 27.893 17.544 1.00 0.00 N +ATOM 704 H ASP 46 25.030 28.275 18.437 1.00 0.00 H +ATOM 705 CA ASP 46 24.271 27.263 16.737 1.00 0.00 C +ATOM 706 HA ASP 46 24.569 27.261 15.686 1.00 0.00 H +ATOM 707 CB ASP 46 24.082 25.808 17.188 1.00 0.00 C +ATOM 708 HB2 ASP 46 24.964 25.230 16.919 1.00 0.00 H +ATOM 709 HB3 ASP 46 23.970 25.788 18.272 1.00 0.00 H +ATOM 710 CG ASP 46 22.847 25.164 16.551 1.00 0.00 C +ATOM 711 OD1 ASP 46 22.121 24.459 17.287 1.00 0.00 O +ATOM 712 OD2 ASP 46 22.564 25.434 15.363 1.00 0.00 O +ATOM 713 C ASP 46 22.942 28.040 16.854 1.00 0.00 C +ATOM 714 O ASP 46 22.481 28.333 17.959 1.00 0.00 O +ATOM 715 N ASP 47 22.303 28.334 15.719 1.00 0.00 N +ATOM 716 H ASP 47 22.690 27.972 14.860 1.00 0.00 H +ATOM 717 CA ASP 47 20.960 28.922 15.674 1.00 0.00 C +ATOM 718 HA ASP 47 20.867 29.653 16.484 1.00 0.00 H +ATOM 719 CB ASP 47 20.770 29.668 14.344 1.00 0.00 C +ATOM 720 HB2 ASP 47 21.505 30.467 14.270 1.00 0.00 H +ATOM 721 HB3 ASP 47 20.915 28.978 13.514 1.00 0.00 H +ATOM 722 CG ASP 47 19.357 30.272 14.273 1.00 0.00 C +ATOM 723 OD1 ASP 47 18.476 29.671 13.620 1.00 0.00 O +ATOM 724 OD2 ASP 47 19.059 31.234 15.015 1.00 0.00 O +ATOM 725 C ASP 47 19.843 27.873 15.876 1.00 0.00 C +ATOM 726 O ASP 47 18.829 28.182 16.505 1.00 0.00 O +ATOM 727 N ALA 48 20.002 26.635 15.397 1.00 0.00 N +ATOM 728 H ALA 48 20.918 26.350 15.053 1.00 0.00 H +ATOM 729 CA ALA 48 18.940 25.621 15.410 1.00 0.00 C +ATOM 730 HA ALA 48 18.054 26.044 14.932 1.00 0.00 H +ATOM 731 CB ALA 48 19.410 24.420 14.579 1.00 0.00 C +ATOM 732 HB1 ALA 48 20.283 23.961 15.047 1.00 0.00 H +ATOM 733 HB2 ALA 48 18.611 23.681 14.510 1.00 0.00 H +ATOM 734 HB3 ALA 48 19.678 24.752 13.576 1.00 0.00 H +ATOM 735 C ALA 48 18.530 25.204 16.836 1.00 0.00 C +ATOM 736 O ALA 48 17.357 24.917 17.091 1.00 0.00 O +ATOM 737 N THR 49 19.478 25.235 17.776 1.00 0.00 N +ATOM 738 H THR 49 20.442 25.294 17.450 1.00 0.00 H +ATOM 739 CA THR 49 19.259 25.108 19.224 1.00 0.00 C +ATOM 740 HA THR 49 18.214 24.847 19.390 1.00 0.00 H +ATOM 741 CB THR 49 20.096 23.965 19.823 1.00 0.00 C +ATOM 742 HB THR 49 19.809 23.853 20.868 1.00 0.00 H +ATOM 743 CG2 THR 49 19.864 22.618 19.134 1.00 0.00 C +ATOM 744 HG21 THR 49 20.201 22.658 18.097 1.00 0.00 H +ATOM 745 HG22 THR 49 20.426 21.844 19.656 1.00 0.00 H +ATOM 746 HG23 THR 49 18.803 22.371 19.159 1.00 0.00 H +ATOM 747 OG1 THR 49 21.474 24.242 19.784 1.00 0.00 O +ATOM 748 HG1 THR 49 21.744 24.259 18.832 1.00 0.00 H +ATOM 749 C THR 49 19.502 26.420 19.993 1.00 0.00 C +ATOM 750 O THR 49 19.436 26.422 21.225 1.00 0.00 O +ATOM 751 N LYS 50 19.754 27.548 19.304 1.00 0.00 N +ATOM 752 H LYS 50 19.767 27.466 18.294 1.00 0.00 H +ATOM 753 CA LYS 50 19.933 28.904 19.871 1.00 0.00 C +ATOM 754 HA LYS 50 20.345 29.539 19.085 1.00 0.00 H +ATOM 755 CB LYS 50 18.550 29.472 20.286 1.00 0.00 C +ATOM 756 HB2 LYS 50 18.148 28.822 21.067 1.00 0.00 H +ATOM 757 HB3 LYS 50 18.683 30.456 20.733 1.00 0.00 H +ATOM 758 CG LYS 50 17.477 29.587 19.183 1.00 0.00 C +ATOM 759 HG2 LYS 50 17.412 28.653 18.624 1.00 0.00 H +ATOM 760 HG3 LYS 50 16.516 29.737 19.679 1.00 0.00 H +ATOM 761 CD LYS 50 17.696 30.772 18.221 1.00 0.00 C +ATOM 762 HD2 LYS 50 17.689 31.691 18.811 1.00 0.00 H +ATOM 763 HD3 LYS 50 18.664 30.684 17.722 1.00 0.00 H +ATOM 764 CE LYS 50 16.561 30.863 17.183 1.00 0.00 C +ATOM 765 HE2 LYS 50 15.613 30.599 17.660 1.00 0.00 H +ATOM 766 HE3 LYS 50 16.499 31.897 16.833 1.00 0.00 H +ATOM 767 NZ LYS 50 16.816 29.992 16.015 1.00 0.00 N +ATOM 768 HZ1 LYS 50 17.225 29.100 16.279 1.00 0.00 H +ATOM 769 HZ2 LYS 50 16.009 29.832 15.431 1.00 0.00 H +ATOM 770 HZ3 LYS 50 17.539 30.414 15.421 1.00 0.00 H +ATOM 771 C LYS 50 20.970 28.951 21.017 1.00 0.00 C +ATOM 772 O LYS 50 20.682 29.512 22.077 1.00 0.00 O +ATOM 773 N THR 51 22.131 28.302 20.845 1.00 0.00 N +ATOM 774 H THR 51 22.339 27.968 19.903 1.00 0.00 H +ATOM 775 CA THR 51 23.053 27.907 21.937 1.00 0.00 C +ATOM 776 HA THR 51 22.762 28.449 22.830 1.00 0.00 H +ATOM 777 CB THR 51 22.870 26.407 22.254 1.00 0.00 C +ATOM 778 HB THR 51 22.978 25.828 21.339 1.00 0.00 H +ATOM 779 CG2 THR 51 23.853 25.855 23.296 1.00 0.00 C +ATOM 780 HG21 THR 51 23.832 26.468 24.189 1.00 0.00 H +ATOM 781 HG22 THR 51 23.578 24.838 23.563 1.00 0.00 H +ATOM 782 HG23 THR 51 24.863 25.826 22.898 1.00 0.00 H +ATOM 783 OG1 THR 51 21.621 26.148 22.865 1.00 0.00 O +ATOM 784 HG1 THR 51 20.921 26.263 22.202 1.00 0.00 H +ATOM 785 C THR 51 24.544 28.228 21.698 1.00 0.00 C +ATOM 786 O THR 51 25.084 27.988 20.620 1.00 0.00 O +ATOM 787 N PHE 52 25.238 28.707 22.747 1.00 0.00 N +ATOM 788 H PHE 52 24.707 28.976 23.559 1.00 0.00 H +ATOM 789 CA PHE 52 26.716 28.789 22.857 1.00 0.00 C +ATOM 790 HA PHE 52 27.140 28.941 21.862 1.00 0.00 H +ATOM 791 CB PHE 52 27.147 29.943 23.778 1.00 0.00 C +ATOM 792 HB2 PHE 52 26.473 29.956 24.634 1.00 0.00 H +ATOM 793 HB3 PHE 52 28.147 29.725 24.163 1.00 0.00 H +ATOM 794 CG PHE 52 27.225 31.342 23.209 1.00 0.00 C +ATOM 795 CD1 PHE 52 26.442 32.383 23.747 1.00 0.00 C +ATOM 796 HD1 PHE 52 25.773 32.191 24.563 1.00 0.00 H +ATOM 797 CE1 PHE 52 26.459 33.658 23.158 1.00 0.00 C +ATOM 798 HE1 PHE 52 25.803 34.434 23.518 1.00 0.00 H +ATOM 799 CZ PHE 52 27.293 33.897 22.055 1.00 0.00 C +ATOM 800 HZ PHE 52 27.255 34.841 21.550 1.00 0.00 H +ATOM 801 CE2 PHE 52 28.170 32.905 21.596 1.00 0.00 C +ATOM 802 HE2 PHE 52 28.842 33.114 20.775 1.00 0.00 H +ATOM 803 CD2 PHE 52 28.131 31.625 22.173 1.00 0.00 C +ATOM 804 HD2 PHE 52 28.777 30.853 21.793 1.00 0.00 H +ATOM 805 C PHE 52 27.312 27.504 23.461 1.00 0.00 C +ATOM 806 O PHE 52 26.769 27.002 24.452 1.00 0.00 O +ATOM 807 N THR 53 28.478 27.069 22.969 1.00 0.00 N +ATOM 808 H THR 53 28.846 27.530 22.138 1.00 0.00 H +ATOM 809 CA THR 53 29.266 25.932 23.499 1.00 0.00 C +ATOM 810 HA THR 53 29.009 25.788 24.548 1.00 0.00 H +ATOM 811 CB THR 53 28.936 24.619 22.755 1.00 0.00 C +ATOM 812 HB THR 53 29.500 23.807 23.219 1.00 0.00 H +ATOM 813 CG2 THR 53 27.462 24.234 22.788 1.00 0.00 C +ATOM 814 HG21 THR 53 26.881 24.922 22.172 1.00 0.00 H +ATOM 815 HG22 THR 53 27.335 23.219 22.405 1.00 0.00 H +ATOM 816 HG23 THR 53 27.097 24.266 23.815 1.00 0.00 H +ATOM 817 OG1 THR 53 29.318 24.703 21.403 1.00 0.00 O +ATOM 818 HG1 THR 53 28.790 24.067 20.912 1.00 0.00 H +ATOM 819 C THR 53 30.790 26.159 23.443 1.00 0.00 C +ATOM 820 O THR 53 31.282 27.102 22.823 1.00 0.00 O +ATOM 821 N THR 54 31.554 25.281 24.106 1.00 0.00 N +ATOM 822 H THR 54 31.091 24.549 24.623 1.00 0.00 H +ATOM 823 CA THR 54 33.029 25.192 24.040 1.00 0.00 C +ATOM 824 HA THR 54 33.396 25.977 23.380 1.00 0.00 H +ATOM 825 CB THR 54 33.662 25.402 25.430 1.00 0.00 C +ATOM 826 HB THR 54 33.369 24.575 26.079 1.00 0.00 H +ATOM 827 CG2 THR 54 35.187 25.519 25.423 1.00 0.00 C +ATOM 828 HG21 THR 54 35.503 26.288 24.716 1.00 0.00 H +ATOM 829 HG22 THR 54 35.531 25.780 26.424 1.00 0.00 H +ATOM 830 HG23 THR 54 35.635 24.563 25.155 1.00 0.00 H +ATOM 831 OG1 THR 54 33.191 26.599 26.010 1.00 0.00 O +ATOM 832 HG1 THR 54 33.471 27.330 25.451 1.00 0.00 H +ATOM 833 C THR 54 33.460 23.848 23.429 1.00 0.00 C +ATOM 834 O THR 54 32.747 22.851 23.553 1.00 0.00 O +ATOM 835 N GLN 55 34.613 23.837 22.755 1.00 0.00 N +ATOM 836 H GLN 55 35.135 24.697 22.711 1.00 0.00 H +ATOM 837 CA GLN 55 35.249 22.649 22.166 1.00 0.00 C +ATOM 838 HA GLN 55 34.484 22.117 21.600 1.00 0.00 H +ATOM 839 CB GLN 55 36.322 23.115 21.159 1.00 0.00 C +ATOM 840 HB2 GLN 55 36.756 22.242 20.673 1.00 0.00 H +ATOM 841 HB3 GLN 55 35.811 23.701 20.392 1.00 0.00 H +ATOM 842 CG GLN 55 37.456 23.975 21.751 1.00 0.00 C +ATOM 843 HG2 GLN 55 37.050 24.710 22.448 1.00 0.00 H +ATOM 844 HG3 GLN 55 38.149 23.338 22.304 1.00 0.00 H +ATOM 845 CD GLN 55 38.239 24.731 20.674 1.00 0.00 C +ATOM 846 OE1 GLN 55 38.376 24.300 19.537 1.00 0.00 O +ATOM 847 NE2 GLN 55 38.765 25.898 20.989 1.00 0.00 N +ATOM 848 HE21 GLN 55 39.353 26.343 20.289 1.00 0.00 H +ATOM 849 HE22 GLN 55 38.589 26.321 21.885 1.00 0.00 H +ATOM 850 C GLN 55 35.799 21.649 23.215 1.00 0.00 C +ATOM 851 O GLN 55 36.039 22.022 24.362 1.00 0.00 O +ATOM 852 N GLU 56 35.970 20.383 22.803 1.00 0.00 N +ATOM 853 H GLU 56 35.828 20.197 21.826 1.00 0.00 H +ATOM 854 CA GLU 56 36.484 19.235 23.593 1.00 0.00 C +ATOM 855 HA GLU 56 36.128 19.329 24.618 1.00 0.00 H +ATOM 856 CB GLU 56 35.902 17.932 22.988 1.00 0.00 C +ATOM 857 HB2 GLU 56 34.817 17.960 23.067 1.00 0.00 H +ATOM 858 HB3 GLU 56 36.130 17.955 21.922 1.00 0.00 H +ATOM 859 CG GLU 56 36.415 16.572 23.523 1.00 0.00 C +ATOM 860 HG2 GLU 56 36.456 15.892 22.671 1.00 0.00 H +ATOM 861 HG3 GLU 56 37.439 16.664 23.869 1.00 0.00 H +ATOM 862 CD GLU 56 35.553 15.892 24.605 1.00 0.00 C +ATOM 863 OE1 GLU 56 36.092 15.416 25.638 1.00 0.00 O +ATOM 864 OE2 GLU 56 34.328 15.697 24.407 1.00 0.00 O +ATOM 865 C GLU 56 38.023 19.208 23.699 1.00 0.00 C +ATOM 866 O GLU 56 38.504 19.229 24.856 1.00 0.00 O +ATOM 867 OXT GLU 56 38.696 19.129 22.645 1.00 0.00 O +HETATM 868 ZN ZN1 57 26.717 32.463 29.375 1.00 0.00 Zn +HETATM 869 N AN1 58 28.350 33.227 30.290 1.00 0.00 N +HETATM 870 C AN1 58 30.703 33.942 31.139 1.00 0.00 C +HETATM 871 C1 AN1 58 29.377 33.530 30.688 1.00 0.00 C +HETATM 872 H AN1 58 30.659 34.320 32.164 1.00 0.00 H +HETATM 873 H1 AN1 58 31.084 34.723 30.475 1.00 0.00 H +HETATM 874 H2 AN1 58 31.373 33.073 31.099 1.00 0.00 H +HETATM 875 N1 AZI 59 30.716 30.555 30.103 1.00 0.00 N +HETATM 876 N2 AZI 59 30.176 29.687 30.743 1.00 0.00 N +HETATM 877 N3 AZI 59 29.592 28.761 31.427 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 868 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 144 148 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 208 186 190 189 +CONECT 189 188 +CONECT 190 193 188 191 192 +CONECT 191 190 +CONECT 192 190 +CONECT 193 195 194 196 190 +CONECT 194 193 +CONECT 195 193 +CONECT 196 199 193 197 198 +CONECT 197 196 +CONECT 198 196 +CONECT 199 200 201 196 +CONECT 200 199 +CONECT 201 205 199 202 +CONECT 202 201 204 203 +CONECT 203 202 +CONECT 204 202 +CONECT 205 206 207 201 +CONECT 206 205 +CONECT 207 205 +CONECT 208 209 210 188 +CONECT 209 208 +CONECT 210 212 208 211 +CONECT 211 210 +CONECT 212 213 230 214 210 +CONECT 213 212 +CONECT 214 217 212 215 216 +CONECT 215 214 +CONECT 216 214 +CONECT 217 219 218 220 214 +CONECT 218 217 +CONECT 219 217 +CONECT 220 221 217 222 223 +CONECT 221 220 +CONECT 222 220 +CONECT 223 225 220 226 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 229 223 228 227 +CONECT 227 226 +CONECT 228 226 +CONECT 229 226 +CONECT 230 231 212 232 +CONECT 231 230 +CONECT 232 230 234 233 +CONECT 233 232 +CONECT 234 237 232 235 236 +CONECT 235 234 +CONECT 236 234 +CONECT 237 238 239 234 +CONECT 238 237 +CONECT 239 241 237 240 +CONECT 240 239 +CONECT 241 243 242 253 239 +CONECT 242 241 +CONECT 243 249 244 245 241 +CONECT 244 243 +CONECT 245 247 243 246 248 +CONECT 246 245 +CONECT 247 245 +CONECT 248 245 +CONECT 249 251 250 252 243 +CONECT 250 249 +CONECT 251 249 +CONECT 252 249 +CONECT 253 241 255 254 +CONECT 254 253 +CONECT 255 265 256 253 +CONECT 256 257 255 266 259 +CONECT 257 258 272 256 +CONECT 258 257 +CONECT 259 256 260 267 268 +CONECT 260 261 262 259 +CONECT 261 264 270 260 +CONECT 262 263 260 269 +CONECT 263 264 271 262 +CONECT 264 868 263 261 +CONECT 265 255 +CONECT 266 256 +CONECT 267 259 +CONECT 268 259 +CONECT 269 262 +CONECT 270 261 +CONECT 271 263 +CONECT 272 274 257 273 +CONECT 273 272 +CONECT 274 275 276 284 272 +CONECT 275 274 +CONECT 276 277 278 274 282 +CONECT 277 276 +CONECT 278 281 280 276 279 +CONECT 279 278 +CONECT 280 278 +CONECT 281 278 +CONECT 282 276 283 +CONECT 283 282 +CONECT 284 286 274 285 +CONECT 285 284 +CONECT 286 296 287 284 +CONECT 287 288 290 286 297 +CONECT 288 289 303 287 +CONECT 289 288 +CONECT 290 298 299 287 291 +CONECT 291 290 292 293 +CONECT 292 301 291 295 +CONECT 293 291 300 294 +CONECT 294 293 295 302 +CONECT 295 292 294 868 +CONECT 296 286 +CONECT 297 287 +CONECT 298 290 +CONECT 299 290 +CONECT 300 293 +CONECT 301 292 +CONECT 302 294 +CONECT 303 305 288 304 +CONECT 304 303 +CONECT 305 316 306 303 307 +CONECT 306 305 +CONECT 307 305 310 309 308 +CONECT 308 307 +CONECT 309 307 +CONECT 310 312 313 307 311 +CONECT 311 310 +CONECT 312 310 +CONECT 313 314 310 315 +CONECT 314 313 +CONECT 315 313 +CONECT 316 318 317 305 +CONECT 317 316 +CONECT 318 320 319 316 +CONECT 319 318 +CONECT 320 326 322 321 318 +CONECT 321 320 +CONECT 322 324 323 320 325 +CONECT 323 322 +CONECT 324 322 +CONECT 325 322 +CONECT 326 328 327 320 +CONECT 327 326 +CONECT 328 330 329 326 +CONECT 329 328 +CONECT 330 342 332 331 328 +CONECT 331 330 +CONECT 332 333 338 330 334 +CONECT 333 332 +CONECT 334 332 336 337 335 +CONECT 335 334 +CONECT 336 334 +CONECT 337 334 +CONECT 338 339 340 332 341 +CONECT 339 338 +CONECT 340 338 +CONECT 341 338 +CONECT 342 343 344 330 +CONECT 343 342 +CONECT 344 346 342 345 +CONECT 345 344 +CONECT 346 348 347 354 344 +CONECT 347 346 +CONECT 348 351 349 350 346 +CONECT 349 348 +CONECT 350 348 +CONECT 351 353 352 348 +CONECT 352 351 +CONECT 353 351 +CONECT 354 346 356 355 +CONECT 355 354 +CONECT 356 357 358 354 +CONECT 357 356 +CONECT 358 360 356 378 359 +CONECT 359 358 +CONECT 360 362 361 363 358 +CONECT 361 360 +CONECT 362 360 +CONECT 363 364 360 377 +CONECT 364 365 366 363 +CONECT 365 364 +CONECT 366 364 367 368 +CONECT 367 366 +CONECT 368 366 377 369 +CONECT 369 368 370 371 +CONECT 370 369 +CONECT 371 369 373 372 +CONECT 372 371 +CONECT 373 375 371 374 +CONECT 374 373 +CONECT 375 377 376 373 +CONECT 376 375 +CONECT 377 363 368 375 +CONECT 378 380 358 379 +CONECT 379 378 +CONECT 380 381 382 378 +CONECT 381 380 +CONECT 382 384 380 383 388 +CONECT 383 382 +CONECT 384 387 385 386 382 +CONECT 385 384 +CONECT 386 384 +CONECT 387 384 +CONECT 388 382 389 390 +CONECT 389 388 +CONECT 390 388 391 392 +CONECT 391 390 +CONECT 392 390 393 394 403 +CONECT 393 392 +CONECT 394 397 395 392 396 +CONECT 395 394 +CONECT 396 394 +CONECT 397 398 399 400 394 +CONECT 398 397 +CONECT 399 397 +CONECT 400 402 397 401 +CONECT 401 400 +CONECT 402 400 +CONECT 403 392 405 404 +CONECT 404 403 +CONECT 405 406 403 407 +CONECT 406 405 +CONECT 407 405 409 413 408 +CONECT 408 407 +CONECT 409 410 412 407 411 +CONECT 410 409 +CONECT 411 409 +CONECT 412 409 +CONECT 413 415 407 414 +CONECT 414 413 +CONECT 415 416 417 413 +CONECT 416 415 +CONECT 417 419 415 418 428 +CONECT 418 417 +CONECT 419 420 421 422 417 +CONECT 420 419 +CONECT 421 419 +CONECT 422 425 419 424 423 +CONECT 423 422 +CONECT 424 422 +CONECT 425 427 426 422 +CONECT 426 425 +CONECT 427 425 +CONECT 428 417 430 429 +CONECT 429 428 +CONECT 430 431 428 432 +CONECT 431 430 +CONECT 432 430 434 433 450 +CONECT 433 432 +CONECT 434 437 435 436 432 +CONECT 435 434 +CONECT 436 434 +CONECT 437 440 439 438 434 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 441 442 437 +CONECT 441 440 +CONECT 442 440 +CONECT 443 446 444 445 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 448 449 447 443 +CONECT 447 446 +CONECT 448 446 +CONECT 449 446 +CONECT 450 432 452 451 +CONECT 451 450 +CONECT 452 453 450 454 +CONECT 453 452 +CONECT 454 452 456 455 470 +CONECT 455 454 +CONECT 456 459 457 454 458 +CONECT 457 456 +CONECT 458 456 +CONECT 459 460 468 456 +CONECT 460 462 461 459 +CONECT 461 460 +CONECT 462 463 464 460 +CONECT 463 462 +CONECT 464 465 462 466 +CONECT 465 464 +CONECT 466 464 467 468 +CONECT 467 466 +CONECT 468 466 459 469 +CONECT 469 468 +CONECT 470 472 454 471 +CONECT 471 470 +CONECT 472 473 474 470 +CONECT 473 472 +CONECT 474 476 472 484 475 +CONECT 475 474 +CONECT 476 477 482 478 474 +CONECT 477 476 +CONECT 478 480 476 481 479 +CONECT 479 478 +CONECT 480 478 +CONECT 481 478 +CONECT 482 483 476 +CONECT 483 482 +CONECT 484 486 474 485 +CONECT 485 484 +CONECT 486 487 488 484 +CONECT 487 486 +CONECT 488 490 486 489 506 +CONECT 489 488 +CONECT 490 493 491 492 488 +CONECT 491 490 +CONECT 492 490 +CONECT 493 496 495 494 490 +CONECT 494 493 +CONECT 495 493 +CONECT 496 499 497 498 493 +CONECT 497 496 +CONECT 498 496 +CONECT 499 501 500 502 496 +CONECT 500 499 +CONECT 501 499 +CONECT 502 504 499 505 503 +CONECT 503 502 +CONECT 504 502 +CONECT 505 502 +CONECT 506 488 508 507 +CONECT 507 506 +CONECT 508 509 506 510 +CONECT 509 508 +CONECT 510 508 512 511 516 +CONECT 511 510 +CONECT 512 515 513 510 514 +CONECT 513 512 +CONECT 514 512 +CONECT 515 512 +CONECT 516 510 518 517 +CONECT 517 516 +CONECT 518 519 516 520 +CONECT 519 518 +CONECT 520 518 522 537 521 +CONECT 521 520 +CONECT 522 523 520 525 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 527 522 528 526 +CONECT 526 525 +CONECT 527 525 +CONECT 528 529 531 525 530 +CONECT 529 528 +CONECT 530 528 +CONECT 531 533 534 528 532 +CONECT 532 531 +CONECT 533 531 +CONECT 534 536 531 535 +CONECT 535 534 +CONECT 536 534 +CONECT 537 539 520 538 +CONECT 538 537 +CONECT 539 540 541 537 +CONECT 540 539 +CONECT 541 543 539 547 542 +CONECT 542 541 +CONECT 543 544 546 545 541 +CONECT 544 543 +CONECT 545 543 +CONECT 546 543 +CONECT 547 541 549 548 +CONECT 548 547 +CONECT 549 550 547 551 +CONECT 550 549 +CONECT 551 553 549 552 561 +CONECT 552 551 +CONECT 553 556 554 555 551 +CONECT 554 553 +CONECT 555 553 +CONECT 556 558 557 553 +CONECT 557 556 +CONECT 558 559 560 556 +CONECT 559 558 +CONECT 560 558 +CONECT 561 551 563 562 +CONECT 562 561 +CONECT 563 564 561 565 +CONECT 564 563 +CONECT 565 563 567 566 573 +CONECT 566 565 +CONECT 567 570 568 565 569 +CONECT 568 567 +CONECT 569 567 +CONECT 570 571 572 567 +CONECT 571 570 +CONECT 572 570 +CONECT 573 565 575 574 +CONECT 574 573 +CONECT 575 576 573 577 +CONECT 576 575 +CONECT 577 575 593 579 578 +CONECT 578 577 +CONECT 579 580 577 582 581 +CONECT 580 579 +CONECT 581 579 +CONECT 582 583 579 591 +CONECT 583 584 585 582 +CONECT 584 583 +CONECT 585 586 583 587 +CONECT 586 585 +CONECT 587 585 588 589 +CONECT 588 587 +CONECT 589 587 591 590 +CONECT 590 589 +CONECT 591 582 589 592 +CONECT 592 591 +CONECT 593 595 594 577 +CONECT 594 593 +CONECT 595 597 596 593 +CONECT 596 595 +CONECT 597 600 595 598 599 +CONECT 598 597 +CONECT 599 597 +CONECT 600 602 601 597 +CONECT 601 600 +CONECT 602 604 603 600 +CONECT 603 602 +CONECT 604 624 605 606 602 +CONECT 605 604 +CONECT 606 607 604 609 608 +CONECT 607 606 +CONECT 608 606 +CONECT 609 610 606 611 612 +CONECT 610 609 +CONECT 611 609 +CONECT 612 609 614 615 613 +CONECT 613 612 +CONECT 614 612 +CONECT 615 612 617 616 +CONECT 616 615 +CONECT 617 618 615 621 +CONECT 618 620 619 617 +CONECT 619 618 +CONECT 620 618 +CONECT 621 617 623 622 +CONECT 622 621 +CONECT 623 621 +CONECT 624 626 625 604 +CONECT 625 624 +CONECT 626 628 627 624 +CONECT 627 626 +CONECT 628 630 636 629 626 +CONECT 629 628 +CONECT 630 633 631 632 628 +CONECT 631 630 +CONECT 632 630 +CONECT 633 635 634 630 +CONECT 634 633 +CONECT 635 633 +CONECT 636 638 637 628 +CONECT 637 636 +CONECT 638 640 639 636 +CONECT 639 638 +CONECT 640 643 641 642 638 +CONECT 641 640 +CONECT 642 640 +CONECT 643 645 644 640 +CONECT 644 643 +CONECT 645 647 646 643 +CONECT 646 645 +CONECT 647 649 648 658 645 +CONECT 648 647 +CONECT 649 651 652 650 647 +CONECT 650 649 +CONECT 651 649 +CONECT 652 654 655 649 653 +CONECT 653 652 +CONECT 654 652 +CONECT 655 657 652 656 +CONECT 656 655 +CONECT 657 655 +CONECT 658 660 647 659 +CONECT 659 658 +CONECT 660 661 662 658 +CONECT 661 660 +CONECT 662 668 660 663 664 +CONECT 663 662 +CONECT 664 662 665 666 667 +CONECT 665 664 +CONECT 666 664 +CONECT 667 664 +CONECT 668 669 670 662 +CONECT 669 668 +CONECT 670 672 668 671 +CONECT 671 670 +CONECT 672 673 674 682 670 +CONECT 673 672 +CONECT 674 676 680 672 675 +CONECT 675 674 +CONECT 676 677 678 679 674 +CONECT 677 676 +CONECT 678 676 +CONECT 679 676 +CONECT 680 681 674 +CONECT 681 680 +CONECT 682 684 672 683 +CONECT 683 682 +CONECT 684 685 686 682 +CONECT 685 684 +CONECT 686 701 688 684 687 +CONECT 687 686 +CONECT 688 694 689 686 690 +CONECT 689 688 +CONECT 690 688 692 691 693 +CONECT 691 690 +CONECT 692 690 +CONECT 693 690 +CONECT 694 696 697 695 688 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 700 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 697 +CONECT 701 702 703 686 +CONECT 702 701 +CONECT 703 705 701 704 +CONECT 704 703 +CONECT 705 706 713 707 703 +CONECT 706 705 +CONECT 707 710 705 708 709 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 707 711 +CONECT 711 710 +CONECT 712 710 +CONECT 713 715 705 714 +CONECT 714 713 +CONECT 715 716 717 713 +CONECT 716 715 +CONECT 717 719 715 725 718 +CONECT 718 717 +CONECT 719 721 720 722 717 +CONECT 720 719 +CONECT 721 719 +CONECT 722 723 719 724 +CONECT 723 722 +CONECT 724 722 +CONECT 725 727 717 726 +CONECT 726 725 +CONECT 727 728 729 725 +CONECT 728 727 +CONECT 729 731 730 727 735 +CONECT 730 729 +CONECT 731 734 733 732 729 +CONECT 732 731 +CONECT 733 731 +CONECT 734 731 +CONECT 735 729 736 737 +CONECT 736 735 +CONECT 737 735 738 739 +CONECT 738 737 +CONECT 739 737 740 741 749 +CONECT 740 739 +CONECT 741 743 739 747 742 +CONECT 742 741 +CONECT 743 744 746 745 741 +CONECT 744 743 +CONECT 745 743 +CONECT 746 743 +CONECT 747 748 741 +CONECT 748 747 +CONECT 749 739 751 750 +CONECT 750 749 +CONECT 751 752 753 749 +CONECT 752 751 +CONECT 753 754 751 755 771 +CONECT 754 753 +CONECT 755 758 753 757 756 +CONECT 756 755 +CONECT 757 755 +CONECT 758 761 759 760 755 +CONECT 759 758 +CONECT 760 758 +CONECT 761 764 763 762 758 +CONECT 762 761 +CONECT 763 761 +CONECT 764 767 766 765 761 +CONECT 765 764 +CONECT 766 764 +CONECT 767 770 769 768 764 +CONECT 768 767 +CONECT 769 767 +CONECT 770 767 +CONECT 771 753 773 772 +CONECT 772 771 +CONECT 773 774 771 775 +CONECT 774 773 +CONECT 775 773 785 777 776 +CONECT 776 775 +CONECT 777 778 775 783 779 +CONECT 778 777 +CONECT 779 777 782 781 780 +CONECT 780 779 +CONECT 781 779 +CONECT 782 779 +CONECT 783 784 777 +CONECT 784 783 +CONECT 785 786 775 787 +CONECT 786 785 +CONECT 787 785 789 788 +CONECT 788 787 +CONECT 789 790 787 805 791 +CONECT 790 789 +CONECT 791 789 794 793 792 +CONECT 792 791 +CONECT 793 791 +CONECT 794 803 795 791 +CONECT 795 797 794 796 +CONECT 796 795 +CONECT 797 799 798 795 +CONECT 798 797 +CONECT 799 800 801 797 +CONECT 800 799 +CONECT 801 802 799 803 +CONECT 802 801 +CONECT 803 801 804 794 +CONECT 804 803 +CONECT 805 789 807 806 +CONECT 806 805 +CONECT 807 808 805 809 +CONECT 808 807 +CONECT 809 811 807 819 810 +CONECT 810 809 +CONECT 811 817 813 812 809 +CONECT 812 811 +CONECT 813 814 815 811 816 +CONECT 814 813 +CONECT 815 813 +CONECT 816 813 +CONECT 817 818 811 +CONECT 818 817 +CONECT 819 820 809 821 +CONECT 820 819 +CONECT 821 819 823 822 +CONECT 822 821 +CONECT 823 824 833 821 825 +CONECT 824 823 +CONECT 825 823 827 831 826 +CONECT 826 825 +CONECT 827 828 830 825 829 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 825 832 +CONECT 832 831 +CONECT 833 835 834 823 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 839 838 835 850 +CONECT 838 837 +CONECT 839 841 840 842 837 +CONECT 840 839 +CONECT 841 839 +CONECT 842 845 839 844 843 +CONECT 843 842 +CONECT 844 842 +CONECT 845 846 847 842 +CONECT 846 845 +CONECT 847 848 845 849 +CONECT 848 847 +CONECT 849 847 +CONECT 850 837 852 851 +CONECT 851 850 +CONECT 852 853 850 854 +CONECT 853 852 +CONECT 854 852 856 865 855 +CONECT 855 854 +CONECT 856 858 857 859 854 +CONECT 857 856 +CONECT 858 856 +CONECT 859 860 856 861 862 +CONECT 860 859 +CONECT 861 859 +CONECT 862 859 864 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 867 854 866 +CONECT 866 865 +CONECT 867 865 +CONECT 868 87 295 869 264 +CONECT 869 868 871 +CONECT 870 873 871 874 872 +CONECT 871 869 870 +CONECT 872 870 +CONECT 873 870 +CONECT 874 870 +CONECT 875 876 +CONECT 876 875 877 +CONECT 877 876 +MASTER 0 0 0 0 0 0 0 0 877 0 877 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_0.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_0.pdb new file mode 100644 index 0000000..833da76 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_0.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.304 51.40416666666647 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.973 23.612 1.00 0.00 N +ATOM 2 H1 MET 1 15.135 38.357 24.556 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.346 23.089 1.00 0.00 H +ATOM 4 H3 MET 1 16.016 38.284 23.187 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.505 23.669 1.00 0.00 C +ATOM 6 HA MET 1 14.170 36.198 24.097 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.876 22.273 1.00 0.00 C +ATOM 8 HB2 MET 1 14.391 36.152 21.672 1.00 0.00 H +ATOM 9 HB3 MET 1 16.152 36.273 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.373 34.334 22.298 1.00 0.00 C +ATOM 11 HG2 MET 1 16.260 34.066 22.868 1.00 0.00 H +ATOM 12 HG3 MET 1 14.495 33.925 22.807 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.526 20.668 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.572 20.068 1.00 0.00 C +ATOM 15 HE1 MET 1 13.463 34.602 20.016 1.00 0.00 H +ATOM 16 HE2 MET 1 13.776 33.133 19.073 1.00 0.00 H +ATOM 17 HE3 MET 1 13.173 32.997 20.735 1.00 0.00 H +ATOM 18 C MET 1 16.218 36.031 24.600 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.398 24.428 1.00 0.00 O +ATOM 20 N GLN 2 15.878 35.187 25.578 1.00 0.00 N +ATOM 21 H GLN 2 14.912 34.996 25.769 1.00 0.00 H +ATOM 22 CA GLN 2 16.850 34.477 26.430 1.00 0.00 C +ATOM 23 HA GLN 2 17.657 35.151 26.723 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.070 27.723 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.137 33.653 27.496 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.662 33.325 28.279 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.257 28.675 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.459 36.087 28.164 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.214 34.973 29.414 1.00 0.00 H +ATOM 30 CD GLN 2 17.128 35.581 29.524 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.143 34.924 29.512 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.039 36.476 30.468 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.764 36.535 31.087 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.097 36.723 30.761 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.301 25.666 1.00 0.00 C +ATOM 36 O GLN 2 17.102 32.148 25.829 1.00 0.00 O +ATOM 37 N TYR 3 18.478 33.617 24.821 1.00 0.00 N +ATOM 38 H TYR 3 18.752 34.594 24.754 1.00 0.00 H +ATOM 39 CA TYR 3 19.260 32.619 24.100 1.00 0.00 C +ATOM 40 HA TYR 3 18.568 31.967 23.564 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.285 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.866 33.942 23.645 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.481 22.672 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.068 21.937 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.530 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.822 32.423 20.550 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.147 34.204 19.542 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.116 33.738 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.844 35.573 19.676 1.00 0.00 C +ATOM 50 OH TYR 3 18.514 36.309 18.584 1.00 0.00 O +ATOM 51 HH TYR 3 18.772 35.874 17.768 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.189 20.940 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.728 37.250 21.025 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.324 35.441 22.067 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.446 35.934 23.023 1.00 0.00 H +ATOM 56 C TYR 3 20.089 31.764 25.076 1.00 0.00 C +ATOM 57 O TYR 3 20.459 32.245 26.150 1.00 0.00 O +ATOM 58 N LYS 4 20.399 30.504 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.250 30.220 23.771 1.00 0.00 H +ATOM 60 CA LYS 4 21.010 29.502 25.633 1.00 0.00 C +ATOM 61 HA LYS 4 20.726 29.715 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.476 28.101 25.273 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.522 27.982 24.192 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.145 27.345 25.699 1.00 0.00 H +ATOM 65 CG LYS 4 19.052 27.746 25.738 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.888 26.697 25.498 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.995 27.853 26.819 1.00 0.00 H +ATOM 68 CD LYS 4 17.923 28.564 25.084 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.886 29.557 25.526 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.149 28.678 24.022 1.00 0.00 H +ATOM 71 CE LYS 4 16.546 27.888 25.193 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.507 24.665 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.597 26.933 24.667 1.00 0.00 H +ATOM 74 NZ LYS 4 16.095 27.656 26.590 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.985 28.529 27.089 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.207 27.154 26.591 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.756 27.063 27.077 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.619 1.00 0.00 C +ATOM 79 O LYS 4 23.196 29.886 24.647 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.029 26.694 1.00 0.00 N +HETATM 81 CA HX1 5 24.625 28.832 26.820 1.00 0.00 C +HETATM 82 C HX1 5 24.899 27.672 27.782 1.00 0.00 C +HETATM 83 O HX1 5 24.405 27.683 28.909 1.00 0.00 O +HETATM 84 CB HX1 5 25.264 30.145 27.306 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.392 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.072 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.385 27.861 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.095 27.755 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.938 29.837 27.336 1.00 0.00 N +HETATM 90 H HX1 5 22.596 28.839 27.521 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.841 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.383 28.292 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.940 30.947 26.639 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.282 26.700 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.531 31.750 28.083 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.839 29.356 27.352 1.00 0.00 H +ATOM 97 N ILE 6 25.634 26.658 27.326 1.00 0.00 N +ATOM 98 H ILE 6 26.015 26.711 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.003 25.472 28.116 1.00 0.00 C +ATOM 100 HA ILE 6 25.303 25.370 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.851 24.199 27.246 1.00 0.00 C +ATOM 102 HB ILE 6 26.401 24.347 26.317 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.409 22.939 27.935 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.892 22.757 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.288 22.070 27.288 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.481 23.048 28.117 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.345 24.012 26.914 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.791 23.875 27.842 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.967 24.915 26.433 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.010 22.847 25.977 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.180 21.893 26.476 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.956 22.904 25.700 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.617 22.905 25.073 1.00 0.00 H +ATOM 114 C ILE 6 27.392 25.668 28.756 1.00 0.00 C +ATOM 115 O ILE 6 28.227 26.398 28.224 1.00 0.00 O +ATOM 116 N VAL 7 27.598 25.081 29.940 1.00 0.00 N +ATOM 117 H VAL 7 26.867 24.478 30.298 1.00 0.00 H +ATOM 118 CA VAL 7 28.776 25.287 30.804 1.00 0.00 C +ATOM 119 HA VAL 7 28.877 26.362 30.959 1.00 0.00 H +ATOM 120 CB VAL 7 28.499 24.641 32.179 1.00 0.00 C +ATOM 121 HB VAL 7 27.500 24.950 32.487 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.522 23.107 32.134 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.532 22.745 31.926 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.190 22.716 33.090 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.855 22.747 31.351 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.449 25.111 33.285 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.292 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.077 24.778 34.251 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.446 24.702 33.142 1.00 0.00 H +ATOM 130 C VAL 7 30.110 24.804 30.202 1.00 0.00 C +ATOM 131 O VAL 7 30.151 23.918 29.351 1.00 0.00 O +ATOM 132 N THR 8 31.213 25.378 30.689 1.00 0.00 N +ATOM 133 H THR 8 31.110 26.089 31.397 1.00 0.00 H +ATOM 134 CA THR 8 32.596 24.972 30.392 1.00 0.00 C +ATOM 135 HA THR 8 32.687 24.827 29.316 1.00 0.00 H +ATOM 136 CB THR 8 33.570 26.088 30.816 1.00 0.00 C +ATOM 137 HB THR 8 34.595 25.756 30.638 1.00 0.00 H +ATOM 138 CG2 THR 8 33.356 27.393 30.055 1.00 0.00 C +ATOM 139 HG21 THR 8 32.383 27.824 30.296 1.00 0.00 H +ATOM 140 HG22 THR 8 34.132 28.110 30.323 1.00 0.00 H +ATOM 141 HG23 THR 8 33.403 27.212 28.983 1.00 0.00 H +ATOM 142 OG1 THR 8 33.422 26.396 32.182 1.00 0.00 O +ATOM 143 HG1 THR 8 33.806 27.265 32.319 1.00 0.00 H +ATOM 144 C THR 8 33.009 23.656 31.077 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.250 32.105 1.00 0.00 O +ATOM 146 N GLY 9 34.047 23.007 30.532 1.00 0.00 N +ATOM 147 H GLY 9 34.399 23.335 29.647 1.00 0.00 H +ATOM 148 CA GLY 9 34.624 21.774 31.075 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.615 21.618 30.651 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.881 32.155 1.00 0.00 H +ATOM 151 C GLY 9 33.782 20.522 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.016 20.483 29.828 1.00 0.00 O +ATOM 153 N LYS 10 33.954 19.478 31.612 1.00 0.00 N +ATOM 154 H LYS 10 34.677 19.557 32.311 1.00 0.00 H +ATOM 155 CA LYS 10 33.235 18.188 31.477 1.00 0.00 C +ATOM 156 HA LYS 10 32.295 18.399 30.965 1.00 0.00 H +ATOM 157 CB LYS 10 34.063 17.245 30.575 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.682 17.846 29.905 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.730 16.638 31.191 1.00 0.00 H +ATOM 160 CG LYS 10 33.197 16.330 29.689 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.601 15.663 30.311 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.521 16.954 29.102 1.00 0.00 H +ATOM 163 CD LYS 10 34.060 15.496 28.727 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.718 16.162 28.166 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.669 14.795 29.300 1.00 0.00 H +ATOM 166 CE LYS 10 33.176 14.722 27.742 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.970 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.467 15.417 27.287 1.00 0.00 H +ATOM 169 NZ LYS 10 33.968 14.073 26.670 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.727 13.511 27.035 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.369 13.526 26.062 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.418 14.773 26.065 1.00 0.00 H +ATOM 173 C LYS 10 32.827 17.542 32.811 1.00 0.00 C +ATOM 174 O LYS 10 32.345 16.412 32.831 1.00 0.00 O +ATOM 175 N SER 11 33.039 18.242 33.932 1.00 0.00 N +ATOM 176 H SER 11 33.491 19.134 33.839 1.00 0.00 H +ATOM 177 CA SER 11 32.567 17.848 35.278 1.00 0.00 C +ATOM 178 HA SER 11 32.502 16.757 35.338 1.00 0.00 H +ATOM 179 CB SER 11 33.554 18.327 36.351 1.00 0.00 C +ATOM 180 HB2 SER 11 33.584 19.416 36.351 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.982 37.329 1.00 0.00 H +ATOM 182 OG SER 11 34.851 17.824 36.092 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.429 36.454 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.417 35.586 1.00 0.00 C +ATOM 185 O SER 11 30.350 17.745 36.192 1.00 0.00 O +ATOM 186 N CYS 12 30.920 19.653 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.631 20.135 34.631 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.268 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.868 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.352 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.323 22.214 34.524 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.249 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.147 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.147 23.411 37.056 1.00 0.00 H +ATOM 195 C CYS 12 28.852 19.934 33.837 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.664 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.512 19.988 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.061 20.142 34.737 1.00 0.00 H +ATOM 199 CA LYS 13 26.668 19.719 32.664 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.856 31.774 1.00 0.00 H +ATOM 201 CB LYS 13 26.222 18.245 32.710 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.030 17.652 33.147 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.343 18.143 33.363 1.00 0.00 H +ATOM 204 CG LYS 13 25.911 17.632 31.329 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.032 18.104 30.890 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.763 17.815 30.673 1.00 0.00 H +ATOM 207 CD LYS 13 25.679 16.113 31.416 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.682 15.711 30.401 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.513 15.660 31.956 1.00 0.00 H +ATOM 210 CE LYS 13 24.341 15.743 32.073 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.161 16.384 32.939 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.551 15.953 31.349 1.00 0.00 H +ATOM 213 NZ LYS 13 24.295 14.306 32.456 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.868 14.092 33.273 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.348 13.998 32.647 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.677 13.728 31.708 1.00 0.00 H +ATOM 217 C LYS 13 25.489 20.705 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.585 20.485 31.710 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.785 33.297 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.943 33.873 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.751 33.377 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.446 22.191 33.448 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.484 23.328 34.293 1.00 0.00 H +ATOM 224 C GLY 14 24.287 23.715 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.215 23.890 31.406 1.00 0.00 O +ATOM 226 N VAL 15 23.147 24.399 32.109 1.00 0.00 N +ATOM 227 H VAL 15 22.434 24.247 32.808 1.00 0.00 H +ATOM 228 CA VAL 15 22.780 25.390 31.070 1.00 0.00 C +ATOM 229 HA VAL 15 23.676 25.631 30.490 1.00 0.00 H +ATOM 230 CB VAL 15 21.762 24.738 30.086 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.858 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.449 24.323 30.767 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.939 25.182 31.209 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.794 23.862 30.026 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.583 31.546 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.419 25.672 28.928 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.336 26.009 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.822 25.122 28.195 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.846 26.536 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.285 26.687 31.731 1.00 0.00 C +ATOM 241 O VAL 15 21.718 26.631 32.821 1.00 0.00 O +HETATM 242 N HY1 16 22.498 27.830 31.091 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.110 31.451 1.00 0.00 C +HETATM 244 C HY1 16 21.620 29.885 30.134 1.00 0.00 C +HETATM 245 O HY1 16 21.778 29.349 29.016 1.00 0.00 O +HETATM 246 CB HY1 16 22.863 29.871 32.416 1.00 0.00 C +HETATM 247 CG HY1 16 24.211 30.225 31.815 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.548 31.406 31.209 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.320 29.397 31.739 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.302 30.092 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.879 31.314 30.787 1.00 0.00 N +HETATM 252 H HY1 16 22.998 27.783 30.212 1.00 0.00 H +HETATM 253 HA HY1 16 20.967 28.994 31.944 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.401 30.797 32.776 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.027 29.258 33.299 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.398 28.459 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.906 32.259 31.098 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.729 30.997 1.00 0.00 H +ATOM 259 N THR 17 21.169 31.140 30.273 1.00 0.00 N +ATOM 260 H THR 17 21.053 31.462 31.222 1.00 0.00 H +ATOM 261 CA THR 17 20.726 32.026 29.179 1.00 0.00 C +ATOM 262 HA THR 17 21.105 31.634 28.291 1.00 0.00 H +ATOM 263 CB THR 17 19.149 32.016 29.046 1.00 0.00 C +ATOM 264 HB THR 17 18.923 32.604 28.170 1.00 0.00 H +ATOM 265 CG2 THR 17 18.589 30.665 28.720 1.00 0.00 C +ATOM 266 HG21 THR 17 18.790 29.907 29.432 1.00 0.00 H +ATOM 267 HG22 THR 17 17.504 30.697 28.632 1.00 0.00 H +ATOM 268 HG23 THR 17 18.931 30.334 27.781 1.00 0.00 H +ATOM 269 OG1 THR 17 18.484 32.464 30.197 1.00 0.00 O +ATOM 270 HG1 THR 17 18.581 33.451 30.206 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.458 29.234 1.00 0.00 C +ATOM 272 O THR 17 21.706 33.922 30.266 1.00 0.00 O +HETATM 273 N HY2 18 21.133 34.157 28.097 1.00 0.00 N +HETATM 274 CA HY2 18 21.447 35.619 27.968 1.00 0.00 C +HETATM 275 C HY2 18 20.323 36.288 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.983 35.838 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.769 35.819 27.255 1.00 0.00 C +HETATM 278 CG HY2 18 23.998 35.326 28.000 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.419 34.029 28.151 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.941 36.119 28.642 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.317 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.707 27.234 1.00 0.00 H +HETATM 284 HA HY2 18 21.501 36.055 29.015 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.747 35.291 26.296 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.912 36.877 27.054 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.953 37.122 28.679 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.930 33.168 27.777 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.758 35.649 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.806 37.389 27.746 1.00 0.00 N +ATOM 291 H GLU 19 20.137 37.679 28.643 1.00 0.00 H +ATOM 292 CA GLU 19 18.797 38.219 27.105 1.00 0.00 C +ATOM 293 HA GLU 19 18.056 37.553 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.066 39.075 28.153 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.753 38.431 28.965 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.774 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.827 39.851 27.656 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.547 28.418 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.083 40.405 26.761 1.00 0.00 H +ATOM 300 CD GLU 19 15.649 38.897 27.370 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.578 38.371 26.227 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.813 38.685 28.283 1.00 0.00 O +ATOM 303 C GLU 19 19.403 39.112 25.991 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.858 26.275 1.00 0.00 O +ATOM 305 N ALA 20 18.876 39.050 24.758 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.353 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.964 23.687 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.962 24.097 1.00 0.00 H +ATOM 309 CB ALA 20 20.589 39.491 23.095 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.463 38.518 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.950 40.207 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.350 39.402 23.869 1.00 0.00 H +ATOM 313 C ALA 20 18.192 40.038 22.583 1.00 0.00 C +ATOM 314 O ALA 20 17.358 39.136 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.090 21.748 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.829 21.922 1.00 0.00 H +ATOM 317 CA VAL 21 17.459 41.151 20.464 1.00 0.00 C +ATOM 318 HA VAL 21 16.471 40.727 20.628 1.00 0.00 H +ATOM 319 CB VAL 21 17.272 42.602 19.975 1.00 0.00 C +ATOM 320 HB VAL 21 16.617 42.576 19.112 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.594 43.474 21.037 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.250 43.628 21.894 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.346 44.443 20.604 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.670 43.000 21.367 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.581 43.283 19.543 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.005 42.771 18.677 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.378 44.312 19.246 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.314 43.286 20.352 1.00 0.00 H +ATOM 329 C VAL 21 18.120 40.335 19.354 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.995 18.376 1.00 0.00 O +ATOM 331 N ASP 22 19.412 40.053 19.508 1.00 0.00 N +ATOM 332 H ASP 22 19.861 40.330 20.363 1.00 0.00 H +ATOM 333 CA ASP 22 20.292 39.467 18.503 1.00 0.00 C +ATOM 334 HA ASP 22 19.710 38.829 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.939 40.592 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.170 41.084 17.077 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.376 41.328 18.357 1.00 0.00 H +ATOM 338 CG ASP 22 22.019 40.045 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.149 40.566 16.817 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.744 39.033 16.072 1.00 0.00 O +ATOM 341 C ASP 22 21.365 38.599 19.176 1.00 0.00 C +ATOM 342 O ASP 22 21.822 38.878 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.790 37.551 18.485 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.496 17.513 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.613 18.977 1.00 0.00 C +ATOM 346 HA TRP 23 22.544 36.362 20.008 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.353 18.132 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.979 18.209 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.841 35.607 17.088 1.00 0.00 H +ATOM 350 CG TRP 23 23.572 34.246 18.526 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.514 33.704 17.727 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.735 34.018 16.716 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.125 32.677 18.407 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.897 32.152 18.028 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.587 32.476 19.654 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.823 31.538 20.660 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.537 30.742 20.518 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.687 21.884 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.018 22.698 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.769 22.095 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.905 23.078 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.006 33.662 21.051 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.312 34.470 21.209 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.636 33.530 19.792 1.00 0.00 C +ATOM 365 C TRP 23 24.211 37.188 18.977 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.920 1.00 0.00 O +ATOM 367 N ALA 24 24.560 38.026 17.993 1.00 0.00 N +ATOM 368 H ALA 24 23.883 38.270 17.276 1.00 0.00 H +ATOM 369 CA ALA 24 25.849 38.719 17.975 1.00 0.00 C +ATOM 370 HA ALA 24 26.620 38.003 18.265 1.00 0.00 H +ATOM 371 CB ALA 24 26.163 39.147 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.450 39.890 16.191 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.165 39.568 16.485 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.115 38.282 15.875 1.00 0.00 H +ATOM 375 C ALA 24 25.931 39.882 18.996 1.00 0.00 C +ATOM 376 O ALA 24 27.024 40.380 19.278 1.00 0.00 O +ATOM 377 N GLU 25 24.813 40.289 19.607 1.00 0.00 N +ATOM 378 H GLU 25 23.933 39.955 19.234 1.00 0.00 H +ATOM 379 CA GLU 25 24.789 41.076 20.851 1.00 0.00 C +ATOM 380 HA GLU 25 25.640 41.758 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.510 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.645 41.277 20.821 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.448 42.384 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.425 43.037 19.876 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.627 42.632 18.886 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.402 43.419 19.864 1.00 0.00 H +ATOM 387 CD GLU 25 24.366 44.203 20.189 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.896 45.204 20.734 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.592 44.053 19.851 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.098 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.518 23.014 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.004 22.127 1.00 0.00 N +ATOM 393 H ALA 26 23.667 38.776 21.363 1.00 0.00 H +ATOM 394 CA ALA 26 24.459 38.028 23.214 1.00 0.00 C +ATOM 395 HA ALA 26 24.198 38.523 24.144 1.00 0.00 H +ATOM 396 CB ALA 26 23.492 36.861 23.009 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.772 36.287 22.127 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.202 23.878 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.230 22.889 1.00 0.00 H +ATOM 400 C ALA 26 25.919 37.533 23.362 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.229 24.479 1.00 0.00 O +ATOM 402 N GLU 27 26.712 37.509 22.282 1.00 0.00 N +ATOM 403 H GLU 27 26.270 37.639 21.372 1.00 0.00 H +ATOM 404 CA GLU 27 28.168 37.305 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.370 36.352 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.768 37.249 20.914 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.159 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.737 38.253 20.487 1.00 0.00 H +ATOM 409 CG GLU 27 30.213 36.730 20.925 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.144 21.782 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.198 35.646 21.049 1.00 0.00 H +ATOM 412 CD GLU 27 30.995 37.107 19.653 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.754 38.110 19.728 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.384 18.638 1.00 0.00 O +ATOM 415 C GLU 27 28.847 38.398 23.184 1.00 0.00 C +ATOM 416 O GLU 27 29.569 38.095 24.137 1.00 0.00 O +ATOM 417 N LYS 28 28.546 39.674 22.913 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.854 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.819 23.667 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.668 1.00 0.00 H +ATOM 421 CB LYS 28 28.698 42.147 22.994 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.280 23.051 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.171 42.964 23.544 1.00 0.00 H +ATOM 424 CG LYS 28 29.135 42.222 21.520 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.205 42.027 21.442 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.600 41.464 20.951 1.00 0.00 H +ATOM 427 CD LYS 28 28.836 43.606 20.922 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.820 43.912 21.179 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.525 44.332 21.362 1.00 0.00 H +ATOM 430 CE LYS 28 28.996 43.630 19.397 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.091 44.670 19.083 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.914 43.114 19.123 1.00 0.00 H +ATOM 433 NZ LYS 28 27.828 43.021 18.717 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.970 43.488 19.030 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.885 43.102 17.711 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.711 42.039 18.969 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.783 25.133 1.00 0.00 C +ATOM 438 O LYS 28 29.480 40.969 26.020 1.00 0.00 O +ATOM 439 N PHE 29 27.392 40.453 25.418 1.00 0.00 N +ATOM 440 H PHE 29 26.739 40.365 24.641 1.00 0.00 H +ATOM 441 CA PHE 29 26.901 40.285 26.792 1.00 0.00 C +ATOM 442 HA PHE 29 27.227 41.146 27.380 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.262 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.036 39.343 26.309 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.020 40.229 27.831 1.00 0.00 H +ATOM 446 CG PHE 29 24.675 41.444 26.115 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.463 41.234 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.013 40.254 25.408 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.829 42.300 24.768 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.903 42.125 24.236 1.00 0.00 H +ATOM 451 CZ PHE 29 23.396 43.583 24.789 1.00 0.00 C +ATOM 452 HZ PHE 29 22.917 44.395 24.266 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.589 43.803 25.497 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.026 44.796 25.526 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.225 42.742 26.163 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.138 42.936 26.702 1.00 0.00 H +ATOM 457 C PHE 29 27.483 39.049 27.505 1.00 0.00 C +ATOM 458 O PHE 29 27.587 39.036 28.736 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.764 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.043 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.685 36.893 27.317 1.00 0.00 C +ATOM 462 HA THR 30 28.209 36.547 28.224 1.00 0.00 H +ATOM 463 CB THR 30 28.691 35.719 26.332 1.00 0.00 C +ATOM 464 HB THR 30 29.069 36.026 25.354 1.00 0.00 H +ATOM 465 CG2 THR 30 29.495 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.132 34.215 27.800 1.00 0.00 H +ATOM 467 HG22 THR 30 29.364 33.689 26.122 1.00 0.00 H +ATOM 468 HG23 THR 30 30.558 34.743 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.366 35.283 26.192 1.00 0.00 O +ATOM 470 HG1 THR 30 26.960 35.884 25.541 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.981 28.768 1.00 0.00 O +ATOM 473 N LYS 31 30.744 38.121 26.830 1.00 0.00 N +ATOM 474 H LYS 31 30.286 38.318 25.946 1.00 0.00 H +ATOM 475 CA LYS 31 32.077 38.701 27.066 1.00 0.00 C +ATOM 476 HA LYS 31 32.746 37.904 27.373 1.00 0.00 H +ATOM 477 CB LYS 31 32.614 39.318 25.767 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.010 25.345 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.526 39.864 25.985 1.00 0.00 H +ATOM 480 CG LYS 31 32.928 38.207 24.738 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.682 37.552 25.175 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.044 37.631 24.523 1.00 0.00 H +ATOM 483 CD LYS 31 33.460 38.815 23.434 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.383 22.946 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.300 39.496 23.639 1.00 0.00 H +ATOM 486 CE LYS 31 33.922 37.721 22.460 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.110 37.056 22.242 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.219 38.193 21.541 1.00 0.00 H +ATOM 489 NZ LYS 31 35.076 36.972 23.012 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.820 36.242 23.678 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.551 36.467 22.263 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.761 37.564 23.504 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.185 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.781 28.913 1.00 0.00 O +ATOM 495 N ALA 32 31.030 40.509 28.371 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.874 41.413 29.513 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.139 29.502 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.372 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.494 29.373 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.876 30.212 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.556 42.756 28.443 1.00 0.00 H +ATOM 503 C ALA 32 30.964 40.640 30.836 1.00 0.00 C +ATOM 504 O ALA 32 31.880 40.889 31.614 1.00 0.00 O +ATOM 505 N LYN 33 30.119 39.614 31.029 1.00 0.00 N +ATOM 506 H LYN 33 29.393 39.457 30.345 1.00 0.00 H +ATOM 507 CA LYN 33 30.159 38.756 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.026 39.385 33.109 1.00 0.00 H +ATOM 509 CB LYN 33 29.011 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.063 37.156 31.263 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.143 37.040 33.026 1.00 0.00 H +ATOM 512 CG LYN 33 27.613 38.360 32.313 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.566 38.985 33.205 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.415 38.982 31.441 1.00 0.00 H +ATOM 515 CD LYN 33 26.537 37.269 32.411 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.694 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.634 36.750 33.364 1.00 0.00 H +ATOM 518 CE LYN 33 25.125 37.836 32.286 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.936 38.516 33.109 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.037 38.375 31.345 1.00 0.00 H +ATOM 521 NZ LYN 33 24.119 36.762 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.186 37.155 32.262 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.255 36.114 31.546 1.00 0.00 H +ATOM 524 C LYN 33 31.513 38.043 32.390 1.00 0.00 C +ATOM 525 O LYN 33 32.010 37.922 33.504 1.00 0.00 O +ATOM 526 N ALA 34 32.145 37.587 31.303 1.00 0.00 N +ATOM 527 H ALA 34 31.697 37.679 30.398 1.00 0.00 H +ATOM 528 CA ALA 34 33.472 36.969 31.385 1.00 0.00 C +ATOM 529 HA ALA 34 33.431 36.162 32.122 1.00 0.00 H +ATOM 530 CB ALA 34 33.818 36.357 30.025 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.964 37.148 29.291 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.777 30.129 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.697 29.695 1.00 0.00 H +ATOM 534 C ALA 34 34.575 37.948 31.862 1.00 0.00 C +ATOM 535 O ALA 34 35.472 37.543 32.601 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.228 31.485 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.508 30.883 1.00 0.00 H +ATOM 538 CA ASN 35 35.366 40.292 31.998 1.00 0.00 C +ATOM 539 HA ASN 35 36.365 39.875 32.114 1.00 0.00 H +ATOM 540 CB ASN 35 35.477 41.419 30.965 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.487 41.705 30.621 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.289 31.446 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.032 29.798 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.582 41.001 29.896 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.708 28.665 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.450 27.893 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.606 28.624 1.00 0.00 H +ATOM 548 C ASN 35 34.980 40.792 33.401 1.00 0.00 C +ATOM 549 O ASN 35 35.862 41.217 34.149 1.00 0.00 O +ATOM 550 N ASP 36 33.716 40.637 33.828 1.00 0.00 N +ATOM 551 H ASP 36 32.980 40.415 33.164 1.00 0.00 H +ATOM 552 CA ASP 36 33.336 40.771 35.246 1.00 0.00 C +ATOM 553 HA ASP 36 33.662 41.747 35.601 1.00 0.00 H +ATOM 554 CB ASP 36 31.821 40.770 35.436 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.447 39.787 35.228 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.605 40.869 36.494 1.00 0.00 H +ATOM 557 CG ASP 36 30.980 41.782 34.656 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.511 42.875 34.375 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.773 41.517 34.399 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.709 36.121 1.00 0.00 C +ATOM 561 O ASP 36 34.483 40.005 37.231 1.00 0.00 O +ATOM 562 N PHE 37 34.225 38.482 35.605 1.00 0.00 N +ATOM 563 H PHE 37 33.748 38.284 34.733 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.460 36.169 1.00 0.00 C +ATOM 565 HA PHE 37 35.119 37.613 37.247 1.00 0.00 H +ATOM 566 CB PHE 37 34.572 36.046 35.924 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.659 35.830 34.863 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.338 36.433 1.00 0.00 H +ATOM 569 CG PHE 37 33.149 35.766 36.381 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.137 35.555 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.369 35.612 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.307 35.837 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.038 35.189 35.100 1.00 0.00 H +ATOM 574 CZ PHE 37 30.512 35.237 37.203 1.00 0.00 C +ATOM 575 HZ PHE 37 29.499 35.052 37.516 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.521 35.410 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.278 35.363 39.212 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.836 35.674 37.748 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.604 35.826 38.483 1.00 0.00 H +ATOM 580 C PHE 37 36.606 37.583 35.730 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.678 35.998 1.00 0.00 O +ATOM 582 N GLY 38 36.994 38.685 35.076 1.00 0.00 N +ATOM 583 H GLY 38 36.290 39.388 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.388 39.099 34.834 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.496 40.119 35.199 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.053 38.480 35.433 1.00 0.00 H +ATOM 587 C GLY 38 38.924 39.067 33.387 1.00 0.00 C +ATOM 588 O GLY 38 39.870 39.802 33.105 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.230 32.483 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.729 32.758 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.054 31.088 1.00 0.00 C +ATOM 592 HA ARG 39 38.947 39.047 30.642 1.00 0.00 H +ATOM 593 CB ARG 39 40.303 37.441 31.074 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.636 37.432 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.986 38.107 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.521 36.014 31.626 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.035 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.754 31.462 1.00 0.00 H +ATOM 599 CD ARG 39 40.216 35.825 33.129 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.853 36.510 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.175 36.078 33.336 1.00 0.00 H +ATOM 602 NE ARG 39 40.443 34.444 33.597 1.00 0.00 N +ATOM 603 HE ARG 39 41.200 34.298 34.242 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.298 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.466 32.486 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.428 34.356 32.087 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.300 32.617 32.077 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.956 32.225 33.814 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.695 32.096 34.487 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.340 31.449 33.597 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.227 30.190 1.00 0.00 C +ATOM 612 O ARG 39 37.524 36.138 30.601 1.00 0.00 O +ATOM 613 N ASP 40 37.649 37.680 28.957 1.00 0.00 N +ATOM 614 H ASP 40 38.027 38.575 28.671 1.00 0.00 H +ATOM 615 CA ASP 40 36.888 36.895 27.965 1.00 0.00 C +ATOM 616 HA ASP 40 36.165 36.313 28.528 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.736 26.967 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.446 37.041 26.398 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.370 38.354 27.534 1.00 0.00 H +ATOM 620 CG ASP 40 36.827 38.629 25.966 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.259 39.727 26.388 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.844 38.320 24.740 1.00 0.00 O +ATOM 623 C ASP 40 37.718 35.863 27.180 1.00 0.00 C +ATOM 624 O ASP 40 38.884 36.079 26.863 1.00 0.00 O +ATOM 625 N GLY 41 37.053 34.763 26.810 1.00 0.00 N +ATOM 626 H GLY 41 36.096 34.686 27.112 1.00 0.00 H +ATOM 627 CA GLY 41 37.470 33.830 25.756 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.458 34.102 25.380 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.530 32.826 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.480 33.816 24.578 1.00 0.00 C +ATOM 631 O GLY 41 35.572 34.650 24.502 1.00 0.00 O +ATOM 632 N GLU 42 36.641 32.855 23.669 1.00 0.00 N +ATOM 633 H GLU 42 37.356 32.161 23.819 1.00 0.00 H +ATOM 634 CA GLU 42 35.802 32.668 22.472 1.00 0.00 C +ATOM 635 HA GLU 42 35.115 33.509 22.372 1.00 0.00 H +ATOM 636 CB GLU 42 36.689 32.632 21.211 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.165 31.653 21.165 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.044 32.715 20.336 1.00 0.00 H +ATOM 639 CG GLU 42 37.807 33.696 21.110 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.580 33.458 21.845 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.278 33.628 20.127 1.00 0.00 H +ATOM 642 CD GLU 42 37.351 35.145 21.325 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.163 35.460 21.116 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.176 36.004 21.723 1.00 0.00 O +ATOM 645 C GLU 42 34.953 31.386 22.575 1.00 0.00 C +ATOM 646 O GLU 42 35.399 30.400 23.169 1.00 0.00 O +ATOM 647 N ALA 43 33.750 31.390 21.987 1.00 0.00 N +ATOM 648 H ALA 43 33.482 32.195 21.439 1.00 0.00 H +ATOM 649 CA ALA 43 32.763 30.304 22.059 1.00 0.00 C +ATOM 650 HA ALA 43 33.255 29.386 22.386 1.00 0.00 H +ATOM 651 CB ALA 43 31.699 30.668 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.186 31.588 22.813 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.966 29.860 23.179 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.172 30.808 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.115 30.014 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.888 30.928 19.897 1.00 0.00 O +ATOM 657 N THR 44 31.800 28.743 20.425 1.00 0.00 N +ATOM 658 H THR 44 31.921 28.066 21.171 1.00 0.00 H +ATOM 659 CA THR 44 31.132 28.280 19.197 1.00 0.00 C +ATOM 660 HA THR 44 31.427 28.942 18.384 1.00 0.00 H +ATOM 661 CB THR 44 31.609 26.864 18.827 1.00 0.00 C +ATOM 662 HB THR 44 31.426 26.183 19.661 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.277 17.557 1.00 0.00 C +ATOM 664 HG21 THR 44 31.074 26.985 16.731 1.00 0.00 H +ATOM 665 HG22 THR 44 31.501 25.353 17.284 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.035 17.728 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.918 18.568 1.00 0.00 O +ATOM 668 HG1 THR 44 33.233 26.114 18.102 1.00 0.00 H +ATOM 669 C THR 44 29.606 28.380 19.330 1.00 0.00 C +ATOM 670 O THR 44 29.074 28.429 20.439 1.00 0.00 O +ATOM 671 N ILE 45 28.902 28.457 18.195 1.00 0.00 N +ATOM 672 H ILE 45 29.375 28.320 17.316 1.00 0.00 H +ATOM 673 CA ILE 45 27.480 28.839 18.125 1.00 0.00 C +ATOM 674 HA ILE 45 27.062 28.755 19.129 1.00 0.00 H +ATOM 675 CB ILE 45 27.333 30.312 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.272 30.526 17.776 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.068 31.232 18.675 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.152 31.107 18.585 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.832 32.280 18.494 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.767 30.970 19.686 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.759 30.685 16.250 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.026 31.742 16.230 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.656 30.128 15.967 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.502 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.733 30.942 15.528 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.979 31.006 14.266 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.520 29.448 14.962 1.00 0.00 H +ATOM 688 C ILE 45 26.631 27.921 17.246 1.00 0.00 C +ATOM 689 O ILE 45 27.124 27.339 16.280 1.00 0.00 O +ATOM 690 N ASP 46 25.331 27.876 17.547 1.00 0.00 N +ATOM 691 H ASP 46 25.033 28.294 18.423 1.00 0.00 H +ATOM 692 CA ASP 46 24.283 27.257 16.737 1.00 0.00 C +ATOM 693 HA ASP 46 24.587 27.262 15.685 1.00 0.00 H +ATOM 694 CB ASP 46 24.078 25.805 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.217 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.957 25.786 18.268 1.00 0.00 H +ATOM 697 CG ASP 46 22.842 25.167 16.545 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.473 17.282 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.562 25.433 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.960 28.047 16.852 1.00 0.00 C +ATOM 701 O ASP 46 22.512 28.361 17.956 1.00 0.00 O +ATOM 702 N ASP 47 22.310 28.329 15.718 1.00 0.00 N +ATOM 703 H ASP 47 22.680 27.938 14.863 1.00 0.00 H +ATOM 704 CA ASP 47 20.971 28.922 15.676 1.00 0.00 C +ATOM 705 HA ASP 47 20.879 29.650 16.488 1.00 0.00 H +ATOM 706 CB ASP 47 20.780 29.672 14.348 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.524 30.465 14.258 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.918 28.977 13.517 1.00 0.00 H +ATOM 709 CG ASP 47 19.369 30.276 14.272 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.488 29.678 13.613 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.067 31.233 15.020 1.00 0.00 O +ATOM 712 C ASP 47 19.855 27.874 15.879 1.00 0.00 C +ATOM 713 O ASP 47 18.845 28.182 16.515 1.00 0.00 O +ATOM 714 N ALA 48 20.003 26.633 15.397 1.00 0.00 N +ATOM 715 H ALA 48 20.918 26.339 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.934 25.624 15.414 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.052 14.933 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.422 14.585 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.277 23.964 15.055 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.682 14.517 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.673 24.751 13.581 1.00 0.00 H +ATOM 722 C ALA 48 18.526 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.930 17.102 1.00 0.00 O +ATOM 724 N THR 49 19.478 25.244 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.438 25.291 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.267 25.119 19.230 1.00 0.00 C +ATOM 727 HA THR 49 18.217 24.871 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.101 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.822 23.860 20.869 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.626 19.138 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.664 18.100 1.00 0.00 H +ATOM 732 HG22 THR 49 20.432 21.855 19.655 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.166 1.00 0.00 H +ATOM 734 OG1 THR 49 21.479 24.241 19.772 1.00 0.00 O +ATOM 735 HG1 THR 49 21.731 24.265 18.814 1.00 0.00 H +ATOM 736 C THR 49 19.506 26.430 20.000 1.00 0.00 C +ATOM 737 O THR 49 19.425 26.431 21.224 1.00 0.00 O +ATOM 738 N LYS 50 19.768 27.552 19.311 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.294 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.905 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.356 29.539 19.085 1.00 0.00 H +ATOM 742 CB LYS 50 18.568 29.470 20.294 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.162 28.830 21.071 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.700 30.460 20.734 1.00 0.00 H +ATOM 745 CG LYS 50 17.490 29.595 19.184 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.427 28.653 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.736 19.684 1.00 0.00 H +ATOM 748 CD LYS 50 17.702 30.770 18.225 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.701 31.693 18.812 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.686 17.722 1.00 0.00 H +ATOM 751 CE LYS 50 16.567 30.866 17.186 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.595 17.663 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.503 31.892 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.995 16.015 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.233 29.097 16.281 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.015 29.834 15.433 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.545 30.416 15.422 1.00 0.00 H +ATOM 758 C LYS 50 20.985 28.947 21.017 1.00 0.00 C +ATOM 759 O LYS 50 20.690 29.519 22.087 1.00 0.00 O +ATOM 760 N THR 51 22.149 28.291 20.853 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.965 19.930 1.00 0.00 H +ATOM 762 CA THR 51 23.056 27.909 21.961 1.00 0.00 C +ATOM 763 HA THR 51 22.764 28.428 22.859 1.00 0.00 H +ATOM 764 CB THR 51 22.887 26.405 22.277 1.00 0.00 C +ATOM 765 HB THR 51 22.977 25.816 21.351 1.00 0.00 H +ATOM 766 CG2 THR 51 23.852 25.861 23.315 1.00 0.00 C +ATOM 767 HG21 THR 51 23.811 26.476 24.217 1.00 0.00 H +ATOM 768 HG22 THR 51 23.574 24.839 23.587 1.00 0.00 H +ATOM 769 HG23 THR 51 24.879 25.834 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.642 26.171 22.880 1.00 0.00 O +ATOM 771 HG1 THR 51 20.952 26.250 22.187 1.00 0.00 H +ATOM 772 C THR 51 24.558 28.226 21.727 1.00 0.00 C +ATOM 773 O THR 51 25.088 27.999 20.643 1.00 0.00 O +ATOM 774 N PHE 52 25.247 28.694 22.774 1.00 0.00 N +ATOM 775 H PHE 52 24.711 28.955 23.594 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.776 22.877 1.00 0.00 C +ATOM 777 HA PHE 52 27.143 28.936 21.901 1.00 0.00 H +ATOM 778 CB PHE 52 27.150 29.949 23.826 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.478 29.957 24.658 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.734 24.192 1.00 0.00 H +ATOM 781 CG PHE 52 27.216 31.350 23.227 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.432 32.382 23.751 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.753 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.448 33.649 23.160 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.778 34.433 23.517 1.00 0.00 H +ATOM 786 CZ PHE 52 27.282 33.889 22.068 1.00 0.00 C +ATOM 787 HZ PHE 52 27.247 34.834 21.561 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.159 32.900 21.619 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.839 33.106 20.790 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.629 22.200 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.776 30.856 21.829 1.00 0.00 H +ATOM 792 C PHE 52 27.330 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.807 27.009 24.507 1.00 0.00 O +ATOM 794 N THR 53 28.485 27.065 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.850 27.522 22.148 1.00 0.00 H +ATOM 796 CA THR 53 29.279 25.926 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.045 25.794 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.933 24.610 22.780 1.00 0.00 C +ATOM 799 HB THR 53 29.508 23.801 23.237 1.00 0.00 H +ATOM 800 CG2 THR 53 27.457 24.224 22.859 1.00 0.00 C +ATOM 801 HG21 THR 53 26.863 24.906 22.251 1.00 0.00 H +ATOM 802 HG22 THR 53 27.322 23.209 22.490 1.00 0.00 H +ATOM 803 HG23 THR 53 27.120 24.269 23.894 1.00 0.00 H +ATOM 804 OG1 THR 53 29.270 24.680 21.419 1.00 0.00 O +ATOM 805 HG1 THR 53 28.753 24.016 20.952 1.00 0.00 H +ATOM 806 C THR 53 30.801 26.146 23.414 1.00 0.00 C +ATOM 807 O THR 53 31.285 27.021 22.692 1.00 0.00 O +ATOM 808 N THR 54 31.568 25.322 24.142 1.00 0.00 N +ATOM 809 H THR 54 31.108 24.646 24.732 1.00 0.00 H +ATOM 810 CA THR 54 33.040 25.237 24.079 1.00 0.00 C +ATOM 811 HA THR 54 33.413 26.032 23.433 1.00 0.00 H +ATOM 812 CB THR 54 33.664 25.450 25.472 1.00 0.00 C +ATOM 813 HB THR 54 33.370 24.631 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.192 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.513 26.333 24.768 1.00 0.00 H +ATOM 816 HG22 THR 54 35.549 25.815 26.469 1.00 0.00 H +ATOM 817 HG23 THR 54 35.638 24.608 25.194 1.00 0.00 H +ATOM 818 OG1 THR 54 33.199 26.661 26.022 1.00 0.00 O +ATOM 819 HG1 THR 54 33.873 26.995 26.617 1.00 0.00 H +ATOM 820 C THR 54 33.478 23.891 23.475 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.890 23.606 1.00 0.00 O +ATOM 822 N GLN 55 34.634 23.874 22.804 1.00 0.00 N +ATOM 823 H GLN 55 35.155 24.736 22.760 1.00 0.00 H +ATOM 824 CA GLN 55 35.263 22.689 22.197 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.160 21.641 1.00 0.00 H +ATOM 826 CB GLN 55 36.318 23.157 21.174 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.731 22.289 20.660 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.803 23.768 20.429 1.00 0.00 H +ATOM 829 CG GLN 55 37.480 23.990 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.094 24.710 22.481 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.176 23.332 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.246 24.768 20.685 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.323 24.390 19.522 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.828 25.897 21.031 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.406 26.349 20.327 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.721 26.270 21.959 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.678 23.227 1.00 0.00 C +ATOM 838 O GLN 55 36.115 22.046 24.365 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.411 22.806 1.00 0.00 N +ATOM 840 H GLU 56 35.791 20.230 21.834 1.00 0.00 H +ATOM 841 CA GLU 56 36.494 19.248 23.574 1.00 0.00 C +ATOM 842 HA GLU 56 36.158 19.336 24.606 1.00 0.00 H +ATOM 843 CB GLU 56 35.887 17.954 22.970 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.807 17.983 23.079 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.991 21.899 1.00 0.00 H +ATOM 846 CG GLU 56 36.406 16.581 23.466 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.470 15.932 22.595 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.421 16.670 23.823 1.00 0.00 H +ATOM 849 CD GLU 56 35.546 15.853 24.519 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.084 15.362 25.545 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.329 15.640 24.294 1.00 0.00 O +ATOM 852 C GLU 56 38.033 19.203 23.640 1.00 0.00 C +ATOM 853 O GLU 56 38.543 19.194 24.791 1.00 0.00 O +ATOM 854 OXT GLU 56 38.679 19.135 22.573 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.719 32.459 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.328 33.244 30.277 1.00 0.00 N +HETATM 857 C AN1 58 30.687 33.879 31.201 1.00 0.00 C +HETATM 858 C1 AN1 58 29.381 33.532 30.714 1.00 0.00 C +HETATM 859 H AN1 58 30.624 34.272 32.222 1.00 0.00 H +HETATM 860 H1 AN1 58 31.138 34.632 30.547 1.00 0.00 H +HETATM 861 H2 AN1 58 31.318 32.977 31.202 1.00 0.00 H +HETATM 862 N1 AZI 59 31.274 30.374 29.434 1.00 0.00 N +HETATM 863 N2 AZI 59 30.476 30.257 30.351 1.00 0.00 N +HETATM 864 N3 AZI 59 29.630 30.157 31.295 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 148 144 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 639 643 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_1.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_1.pdb new file mode 100644 index 0000000..833da76 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_1.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.304 51.40416666666647 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.973 23.612 1.00 0.00 N +ATOM 2 H1 MET 1 15.135 38.357 24.556 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.346 23.089 1.00 0.00 H +ATOM 4 H3 MET 1 16.016 38.284 23.187 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.505 23.669 1.00 0.00 C +ATOM 6 HA MET 1 14.170 36.198 24.097 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.876 22.273 1.00 0.00 C +ATOM 8 HB2 MET 1 14.391 36.152 21.672 1.00 0.00 H +ATOM 9 HB3 MET 1 16.152 36.273 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.373 34.334 22.298 1.00 0.00 C +ATOM 11 HG2 MET 1 16.260 34.066 22.868 1.00 0.00 H +ATOM 12 HG3 MET 1 14.495 33.925 22.807 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.526 20.668 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.572 20.068 1.00 0.00 C +ATOM 15 HE1 MET 1 13.463 34.602 20.016 1.00 0.00 H +ATOM 16 HE2 MET 1 13.776 33.133 19.073 1.00 0.00 H +ATOM 17 HE3 MET 1 13.173 32.997 20.735 1.00 0.00 H +ATOM 18 C MET 1 16.218 36.031 24.600 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.398 24.428 1.00 0.00 O +ATOM 20 N GLN 2 15.878 35.187 25.578 1.00 0.00 N +ATOM 21 H GLN 2 14.912 34.996 25.769 1.00 0.00 H +ATOM 22 CA GLN 2 16.850 34.477 26.430 1.00 0.00 C +ATOM 23 HA GLN 2 17.657 35.151 26.723 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.070 27.723 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.137 33.653 27.496 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.662 33.325 28.279 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.257 28.675 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.459 36.087 28.164 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.214 34.973 29.414 1.00 0.00 H +ATOM 30 CD GLN 2 17.128 35.581 29.524 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.143 34.924 29.512 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.039 36.476 30.468 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.764 36.535 31.087 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.097 36.723 30.761 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.301 25.666 1.00 0.00 C +ATOM 36 O GLN 2 17.102 32.148 25.829 1.00 0.00 O +ATOM 37 N TYR 3 18.478 33.617 24.821 1.00 0.00 N +ATOM 38 H TYR 3 18.752 34.594 24.754 1.00 0.00 H +ATOM 39 CA TYR 3 19.260 32.619 24.100 1.00 0.00 C +ATOM 40 HA TYR 3 18.568 31.967 23.564 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.285 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.866 33.942 23.645 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.481 22.672 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.068 21.937 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.530 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.822 32.423 20.550 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.147 34.204 19.542 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.116 33.738 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.844 35.573 19.676 1.00 0.00 C +ATOM 50 OH TYR 3 18.514 36.309 18.584 1.00 0.00 O +ATOM 51 HH TYR 3 18.772 35.874 17.768 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.189 20.940 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.728 37.250 21.025 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.324 35.441 22.067 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.446 35.934 23.023 1.00 0.00 H +ATOM 56 C TYR 3 20.089 31.764 25.076 1.00 0.00 C +ATOM 57 O TYR 3 20.459 32.245 26.150 1.00 0.00 O +ATOM 58 N LYS 4 20.399 30.504 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.250 30.220 23.771 1.00 0.00 H +ATOM 60 CA LYS 4 21.010 29.502 25.633 1.00 0.00 C +ATOM 61 HA LYS 4 20.726 29.715 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.476 28.101 25.273 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.522 27.982 24.192 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.145 27.345 25.699 1.00 0.00 H +ATOM 65 CG LYS 4 19.052 27.746 25.738 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.888 26.697 25.498 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.995 27.853 26.819 1.00 0.00 H +ATOM 68 CD LYS 4 17.923 28.564 25.084 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.886 29.557 25.526 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.149 28.678 24.022 1.00 0.00 H +ATOM 71 CE LYS 4 16.546 27.888 25.193 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.507 24.665 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.597 26.933 24.667 1.00 0.00 H +ATOM 74 NZ LYS 4 16.095 27.656 26.590 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.985 28.529 27.089 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.207 27.154 26.591 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.756 27.063 27.077 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.619 1.00 0.00 C +ATOM 79 O LYS 4 23.196 29.886 24.647 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.029 26.694 1.00 0.00 N +HETATM 81 CA HX1 5 24.625 28.832 26.820 1.00 0.00 C +HETATM 82 C HX1 5 24.899 27.672 27.782 1.00 0.00 C +HETATM 83 O HX1 5 24.405 27.683 28.909 1.00 0.00 O +HETATM 84 CB HX1 5 25.264 30.145 27.306 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.392 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.072 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.385 27.861 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.095 27.755 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.938 29.837 27.336 1.00 0.00 N +HETATM 90 H HX1 5 22.596 28.839 27.521 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.841 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.383 28.292 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.940 30.947 26.639 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.282 26.700 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.531 31.750 28.083 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.839 29.356 27.352 1.00 0.00 H +ATOM 97 N ILE 6 25.634 26.658 27.326 1.00 0.00 N +ATOM 98 H ILE 6 26.015 26.711 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.003 25.472 28.116 1.00 0.00 C +ATOM 100 HA ILE 6 25.303 25.370 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.851 24.199 27.246 1.00 0.00 C +ATOM 102 HB ILE 6 26.401 24.347 26.317 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.409 22.939 27.935 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.892 22.757 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.288 22.070 27.288 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.481 23.048 28.117 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.345 24.012 26.914 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.791 23.875 27.842 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.967 24.915 26.433 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.010 22.847 25.977 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.180 21.893 26.476 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.956 22.904 25.700 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.617 22.905 25.073 1.00 0.00 H +ATOM 114 C ILE 6 27.392 25.668 28.756 1.00 0.00 C +ATOM 115 O ILE 6 28.227 26.398 28.224 1.00 0.00 O +ATOM 116 N VAL 7 27.598 25.081 29.940 1.00 0.00 N +ATOM 117 H VAL 7 26.867 24.478 30.298 1.00 0.00 H +ATOM 118 CA VAL 7 28.776 25.287 30.804 1.00 0.00 C +ATOM 119 HA VAL 7 28.877 26.362 30.959 1.00 0.00 H +ATOM 120 CB VAL 7 28.499 24.641 32.179 1.00 0.00 C +ATOM 121 HB VAL 7 27.500 24.950 32.487 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.522 23.107 32.134 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.532 22.745 31.926 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.190 22.716 33.090 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.855 22.747 31.351 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.449 25.111 33.285 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.292 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.077 24.778 34.251 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.446 24.702 33.142 1.00 0.00 H +ATOM 130 C VAL 7 30.110 24.804 30.202 1.00 0.00 C +ATOM 131 O VAL 7 30.151 23.918 29.351 1.00 0.00 O +ATOM 132 N THR 8 31.213 25.378 30.689 1.00 0.00 N +ATOM 133 H THR 8 31.110 26.089 31.397 1.00 0.00 H +ATOM 134 CA THR 8 32.596 24.972 30.392 1.00 0.00 C +ATOM 135 HA THR 8 32.687 24.827 29.316 1.00 0.00 H +ATOM 136 CB THR 8 33.570 26.088 30.816 1.00 0.00 C +ATOM 137 HB THR 8 34.595 25.756 30.638 1.00 0.00 H +ATOM 138 CG2 THR 8 33.356 27.393 30.055 1.00 0.00 C +ATOM 139 HG21 THR 8 32.383 27.824 30.296 1.00 0.00 H +ATOM 140 HG22 THR 8 34.132 28.110 30.323 1.00 0.00 H +ATOM 141 HG23 THR 8 33.403 27.212 28.983 1.00 0.00 H +ATOM 142 OG1 THR 8 33.422 26.396 32.182 1.00 0.00 O +ATOM 143 HG1 THR 8 33.806 27.265 32.319 1.00 0.00 H +ATOM 144 C THR 8 33.009 23.656 31.077 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.250 32.105 1.00 0.00 O +ATOM 146 N GLY 9 34.047 23.007 30.532 1.00 0.00 N +ATOM 147 H GLY 9 34.399 23.335 29.647 1.00 0.00 H +ATOM 148 CA GLY 9 34.624 21.774 31.075 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.615 21.618 30.651 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.881 32.155 1.00 0.00 H +ATOM 151 C GLY 9 33.782 20.522 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.016 20.483 29.828 1.00 0.00 O +ATOM 153 N LYS 10 33.954 19.478 31.612 1.00 0.00 N +ATOM 154 H LYS 10 34.677 19.557 32.311 1.00 0.00 H +ATOM 155 CA LYS 10 33.235 18.188 31.477 1.00 0.00 C +ATOM 156 HA LYS 10 32.295 18.399 30.965 1.00 0.00 H +ATOM 157 CB LYS 10 34.063 17.245 30.575 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.682 17.846 29.905 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.730 16.638 31.191 1.00 0.00 H +ATOM 160 CG LYS 10 33.197 16.330 29.689 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.601 15.663 30.311 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.521 16.954 29.102 1.00 0.00 H +ATOM 163 CD LYS 10 34.060 15.496 28.727 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.718 16.162 28.166 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.669 14.795 29.300 1.00 0.00 H +ATOM 166 CE LYS 10 33.176 14.722 27.742 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.970 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.467 15.417 27.287 1.00 0.00 H +ATOM 169 NZ LYS 10 33.968 14.073 26.670 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.727 13.511 27.035 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.369 13.526 26.062 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.418 14.773 26.065 1.00 0.00 H +ATOM 173 C LYS 10 32.827 17.542 32.811 1.00 0.00 C +ATOM 174 O LYS 10 32.345 16.412 32.831 1.00 0.00 O +ATOM 175 N SER 11 33.039 18.242 33.932 1.00 0.00 N +ATOM 176 H SER 11 33.491 19.134 33.839 1.00 0.00 H +ATOM 177 CA SER 11 32.567 17.848 35.278 1.00 0.00 C +ATOM 178 HA SER 11 32.502 16.757 35.338 1.00 0.00 H +ATOM 179 CB SER 11 33.554 18.327 36.351 1.00 0.00 C +ATOM 180 HB2 SER 11 33.584 19.416 36.351 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.982 37.329 1.00 0.00 H +ATOM 182 OG SER 11 34.851 17.824 36.092 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.429 36.454 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.417 35.586 1.00 0.00 C +ATOM 185 O SER 11 30.350 17.745 36.192 1.00 0.00 O +ATOM 186 N CYS 12 30.920 19.653 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.631 20.135 34.631 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.268 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.868 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.352 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.323 22.214 34.524 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.249 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.147 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.147 23.411 37.056 1.00 0.00 H +ATOM 195 C CYS 12 28.852 19.934 33.837 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.664 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.512 19.988 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.061 20.142 34.737 1.00 0.00 H +ATOM 199 CA LYS 13 26.668 19.719 32.664 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.856 31.774 1.00 0.00 H +ATOM 201 CB LYS 13 26.222 18.245 32.710 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.030 17.652 33.147 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.343 18.143 33.363 1.00 0.00 H +ATOM 204 CG LYS 13 25.911 17.632 31.329 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.032 18.104 30.890 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.763 17.815 30.673 1.00 0.00 H +ATOM 207 CD LYS 13 25.679 16.113 31.416 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.682 15.711 30.401 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.513 15.660 31.956 1.00 0.00 H +ATOM 210 CE LYS 13 24.341 15.743 32.073 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.161 16.384 32.939 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.551 15.953 31.349 1.00 0.00 H +ATOM 213 NZ LYS 13 24.295 14.306 32.456 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.868 14.092 33.273 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.348 13.998 32.647 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.677 13.728 31.708 1.00 0.00 H +ATOM 217 C LYS 13 25.489 20.705 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.585 20.485 31.710 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.785 33.297 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.943 33.873 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.751 33.377 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.446 22.191 33.448 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.484 23.328 34.293 1.00 0.00 H +ATOM 224 C GLY 14 24.287 23.715 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.215 23.890 31.406 1.00 0.00 O +ATOM 226 N VAL 15 23.147 24.399 32.109 1.00 0.00 N +ATOM 227 H VAL 15 22.434 24.247 32.808 1.00 0.00 H +ATOM 228 CA VAL 15 22.780 25.390 31.070 1.00 0.00 C +ATOM 229 HA VAL 15 23.676 25.631 30.490 1.00 0.00 H +ATOM 230 CB VAL 15 21.762 24.738 30.086 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.858 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.449 24.323 30.767 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.939 25.182 31.209 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.794 23.862 30.026 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.583 31.546 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.419 25.672 28.928 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.336 26.009 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.822 25.122 28.195 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.846 26.536 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.285 26.687 31.731 1.00 0.00 C +ATOM 241 O VAL 15 21.718 26.631 32.821 1.00 0.00 O +HETATM 242 N HY1 16 22.498 27.830 31.091 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.110 31.451 1.00 0.00 C +HETATM 244 C HY1 16 21.620 29.885 30.134 1.00 0.00 C +HETATM 245 O HY1 16 21.778 29.349 29.016 1.00 0.00 O +HETATM 246 CB HY1 16 22.863 29.871 32.416 1.00 0.00 C +HETATM 247 CG HY1 16 24.211 30.225 31.815 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.548 31.406 31.209 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.320 29.397 31.739 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.302 30.092 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.879 31.314 30.787 1.00 0.00 N +HETATM 252 H HY1 16 22.998 27.783 30.212 1.00 0.00 H +HETATM 253 HA HY1 16 20.967 28.994 31.944 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.401 30.797 32.776 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.027 29.258 33.299 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.398 28.459 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.906 32.259 31.098 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.729 30.997 1.00 0.00 H +ATOM 259 N THR 17 21.169 31.140 30.273 1.00 0.00 N +ATOM 260 H THR 17 21.053 31.462 31.222 1.00 0.00 H +ATOM 261 CA THR 17 20.726 32.026 29.179 1.00 0.00 C +ATOM 262 HA THR 17 21.105 31.634 28.291 1.00 0.00 H +ATOM 263 CB THR 17 19.149 32.016 29.046 1.00 0.00 C +ATOM 264 HB THR 17 18.923 32.604 28.170 1.00 0.00 H +ATOM 265 CG2 THR 17 18.589 30.665 28.720 1.00 0.00 C +ATOM 266 HG21 THR 17 18.790 29.907 29.432 1.00 0.00 H +ATOM 267 HG22 THR 17 17.504 30.697 28.632 1.00 0.00 H +ATOM 268 HG23 THR 17 18.931 30.334 27.781 1.00 0.00 H +ATOM 269 OG1 THR 17 18.484 32.464 30.197 1.00 0.00 O +ATOM 270 HG1 THR 17 18.581 33.451 30.206 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.458 29.234 1.00 0.00 C +ATOM 272 O THR 17 21.706 33.922 30.266 1.00 0.00 O +HETATM 273 N HY2 18 21.133 34.157 28.097 1.00 0.00 N +HETATM 274 CA HY2 18 21.447 35.619 27.968 1.00 0.00 C +HETATM 275 C HY2 18 20.323 36.288 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.983 35.838 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.769 35.819 27.255 1.00 0.00 C +HETATM 278 CG HY2 18 23.998 35.326 28.000 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.419 34.029 28.151 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.941 36.119 28.642 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.317 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.707 27.234 1.00 0.00 H +HETATM 284 HA HY2 18 21.501 36.055 29.015 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.747 35.291 26.296 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.912 36.877 27.054 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.953 37.122 28.679 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.930 33.168 27.777 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.758 35.649 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.806 37.389 27.746 1.00 0.00 N +ATOM 291 H GLU 19 20.137 37.679 28.643 1.00 0.00 H +ATOM 292 CA GLU 19 18.797 38.219 27.105 1.00 0.00 C +ATOM 293 HA GLU 19 18.056 37.553 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.066 39.075 28.153 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.753 38.431 28.965 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.774 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.827 39.851 27.656 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.547 28.418 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.083 40.405 26.761 1.00 0.00 H +ATOM 300 CD GLU 19 15.649 38.897 27.370 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.578 38.371 26.227 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.813 38.685 28.283 1.00 0.00 O +ATOM 303 C GLU 19 19.403 39.112 25.991 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.858 26.275 1.00 0.00 O +ATOM 305 N ALA 20 18.876 39.050 24.758 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.353 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.964 23.687 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.962 24.097 1.00 0.00 H +ATOM 309 CB ALA 20 20.589 39.491 23.095 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.463 38.518 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.950 40.207 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.350 39.402 23.869 1.00 0.00 H +ATOM 313 C ALA 20 18.192 40.038 22.583 1.00 0.00 C +ATOM 314 O ALA 20 17.358 39.136 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.090 21.748 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.829 21.922 1.00 0.00 H +ATOM 317 CA VAL 21 17.459 41.151 20.464 1.00 0.00 C +ATOM 318 HA VAL 21 16.471 40.727 20.628 1.00 0.00 H +ATOM 319 CB VAL 21 17.272 42.602 19.975 1.00 0.00 C +ATOM 320 HB VAL 21 16.617 42.576 19.112 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.594 43.474 21.037 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.250 43.628 21.894 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.346 44.443 20.604 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.670 43.000 21.367 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.581 43.283 19.543 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.005 42.771 18.677 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.378 44.312 19.246 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.314 43.286 20.352 1.00 0.00 H +ATOM 329 C VAL 21 18.120 40.335 19.354 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.995 18.376 1.00 0.00 O +ATOM 331 N ASP 22 19.412 40.053 19.508 1.00 0.00 N +ATOM 332 H ASP 22 19.861 40.330 20.363 1.00 0.00 H +ATOM 333 CA ASP 22 20.292 39.467 18.503 1.00 0.00 C +ATOM 334 HA ASP 22 19.710 38.829 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.939 40.592 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.170 41.084 17.077 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.376 41.328 18.357 1.00 0.00 H +ATOM 338 CG ASP 22 22.019 40.045 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.149 40.566 16.817 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.744 39.033 16.072 1.00 0.00 O +ATOM 341 C ASP 22 21.365 38.599 19.176 1.00 0.00 C +ATOM 342 O ASP 22 21.822 38.878 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.790 37.551 18.485 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.496 17.513 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.613 18.977 1.00 0.00 C +ATOM 346 HA TRP 23 22.544 36.362 20.008 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.353 18.132 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.979 18.209 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.841 35.607 17.088 1.00 0.00 H +ATOM 350 CG TRP 23 23.572 34.246 18.526 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.514 33.704 17.727 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.735 34.018 16.716 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.125 32.677 18.407 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.897 32.152 18.028 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.587 32.476 19.654 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.823 31.538 20.660 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.537 30.742 20.518 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.687 21.884 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.018 22.698 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.769 22.095 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.905 23.078 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.006 33.662 21.051 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.312 34.470 21.209 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.636 33.530 19.792 1.00 0.00 C +ATOM 365 C TRP 23 24.211 37.188 18.977 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.920 1.00 0.00 O +ATOM 367 N ALA 24 24.560 38.026 17.993 1.00 0.00 N +ATOM 368 H ALA 24 23.883 38.270 17.276 1.00 0.00 H +ATOM 369 CA ALA 24 25.849 38.719 17.975 1.00 0.00 C +ATOM 370 HA ALA 24 26.620 38.003 18.265 1.00 0.00 H +ATOM 371 CB ALA 24 26.163 39.147 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.450 39.890 16.191 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.165 39.568 16.485 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.115 38.282 15.875 1.00 0.00 H +ATOM 375 C ALA 24 25.931 39.882 18.996 1.00 0.00 C +ATOM 376 O ALA 24 27.024 40.380 19.278 1.00 0.00 O +ATOM 377 N GLU 25 24.813 40.289 19.607 1.00 0.00 N +ATOM 378 H GLU 25 23.933 39.955 19.234 1.00 0.00 H +ATOM 379 CA GLU 25 24.789 41.076 20.851 1.00 0.00 C +ATOM 380 HA GLU 25 25.640 41.758 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.510 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.645 41.277 20.821 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.448 42.384 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.425 43.037 19.876 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.627 42.632 18.886 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.402 43.419 19.864 1.00 0.00 H +ATOM 387 CD GLU 25 24.366 44.203 20.189 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.896 45.204 20.734 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.592 44.053 19.851 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.098 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.518 23.014 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.004 22.127 1.00 0.00 N +ATOM 393 H ALA 26 23.667 38.776 21.363 1.00 0.00 H +ATOM 394 CA ALA 26 24.459 38.028 23.214 1.00 0.00 C +ATOM 395 HA ALA 26 24.198 38.523 24.144 1.00 0.00 H +ATOM 396 CB ALA 26 23.492 36.861 23.009 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.772 36.287 22.127 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.202 23.878 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.230 22.889 1.00 0.00 H +ATOM 400 C ALA 26 25.919 37.533 23.362 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.229 24.479 1.00 0.00 O +ATOM 402 N GLU 27 26.712 37.509 22.282 1.00 0.00 N +ATOM 403 H GLU 27 26.270 37.639 21.372 1.00 0.00 H +ATOM 404 CA GLU 27 28.168 37.305 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.370 36.352 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.768 37.249 20.914 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.159 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.737 38.253 20.487 1.00 0.00 H +ATOM 409 CG GLU 27 30.213 36.730 20.925 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.144 21.782 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.198 35.646 21.049 1.00 0.00 H +ATOM 412 CD GLU 27 30.995 37.107 19.653 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.754 38.110 19.728 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.384 18.638 1.00 0.00 O +ATOM 415 C GLU 27 28.847 38.398 23.184 1.00 0.00 C +ATOM 416 O GLU 27 29.569 38.095 24.137 1.00 0.00 O +ATOM 417 N LYS 28 28.546 39.674 22.913 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.854 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.819 23.667 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.668 1.00 0.00 H +ATOM 421 CB LYS 28 28.698 42.147 22.994 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.280 23.051 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.171 42.964 23.544 1.00 0.00 H +ATOM 424 CG LYS 28 29.135 42.222 21.520 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.205 42.027 21.442 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.600 41.464 20.951 1.00 0.00 H +ATOM 427 CD LYS 28 28.836 43.606 20.922 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.820 43.912 21.179 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.525 44.332 21.362 1.00 0.00 H +ATOM 430 CE LYS 28 28.996 43.630 19.397 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.091 44.670 19.083 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.914 43.114 19.123 1.00 0.00 H +ATOM 433 NZ LYS 28 27.828 43.021 18.717 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.970 43.488 19.030 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.885 43.102 17.711 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.711 42.039 18.969 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.783 25.133 1.00 0.00 C +ATOM 438 O LYS 28 29.480 40.969 26.020 1.00 0.00 O +ATOM 439 N PHE 29 27.392 40.453 25.418 1.00 0.00 N +ATOM 440 H PHE 29 26.739 40.365 24.641 1.00 0.00 H +ATOM 441 CA PHE 29 26.901 40.285 26.792 1.00 0.00 C +ATOM 442 HA PHE 29 27.227 41.146 27.380 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.262 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.036 39.343 26.309 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.020 40.229 27.831 1.00 0.00 H +ATOM 446 CG PHE 29 24.675 41.444 26.115 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.463 41.234 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.013 40.254 25.408 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.829 42.300 24.768 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.903 42.125 24.236 1.00 0.00 H +ATOM 451 CZ PHE 29 23.396 43.583 24.789 1.00 0.00 C +ATOM 452 HZ PHE 29 22.917 44.395 24.266 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.589 43.803 25.497 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.026 44.796 25.526 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.225 42.742 26.163 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.138 42.936 26.702 1.00 0.00 H +ATOM 457 C PHE 29 27.483 39.049 27.505 1.00 0.00 C +ATOM 458 O PHE 29 27.587 39.036 28.736 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.764 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.043 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.685 36.893 27.317 1.00 0.00 C +ATOM 462 HA THR 30 28.209 36.547 28.224 1.00 0.00 H +ATOM 463 CB THR 30 28.691 35.719 26.332 1.00 0.00 C +ATOM 464 HB THR 30 29.069 36.026 25.354 1.00 0.00 H +ATOM 465 CG2 THR 30 29.495 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.132 34.215 27.800 1.00 0.00 H +ATOM 467 HG22 THR 30 29.364 33.689 26.122 1.00 0.00 H +ATOM 468 HG23 THR 30 30.558 34.743 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.366 35.283 26.192 1.00 0.00 O +ATOM 470 HG1 THR 30 26.960 35.884 25.541 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.981 28.768 1.00 0.00 O +ATOM 473 N LYS 31 30.744 38.121 26.830 1.00 0.00 N +ATOM 474 H LYS 31 30.286 38.318 25.946 1.00 0.00 H +ATOM 475 CA LYS 31 32.077 38.701 27.066 1.00 0.00 C +ATOM 476 HA LYS 31 32.746 37.904 27.373 1.00 0.00 H +ATOM 477 CB LYS 31 32.614 39.318 25.767 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.010 25.345 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.526 39.864 25.985 1.00 0.00 H +ATOM 480 CG LYS 31 32.928 38.207 24.738 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.682 37.552 25.175 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.044 37.631 24.523 1.00 0.00 H +ATOM 483 CD LYS 31 33.460 38.815 23.434 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.383 22.946 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.300 39.496 23.639 1.00 0.00 H +ATOM 486 CE LYS 31 33.922 37.721 22.460 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.110 37.056 22.242 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.219 38.193 21.541 1.00 0.00 H +ATOM 489 NZ LYS 31 35.076 36.972 23.012 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.820 36.242 23.678 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.551 36.467 22.263 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.761 37.564 23.504 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.185 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.781 28.913 1.00 0.00 O +ATOM 495 N ALA 32 31.030 40.509 28.371 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.874 41.413 29.513 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.139 29.502 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.372 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.494 29.373 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.876 30.212 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.556 42.756 28.443 1.00 0.00 H +ATOM 503 C ALA 32 30.964 40.640 30.836 1.00 0.00 C +ATOM 504 O ALA 32 31.880 40.889 31.614 1.00 0.00 O +ATOM 505 N LYN 33 30.119 39.614 31.029 1.00 0.00 N +ATOM 506 H LYN 33 29.393 39.457 30.345 1.00 0.00 H +ATOM 507 CA LYN 33 30.159 38.756 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.026 39.385 33.109 1.00 0.00 H +ATOM 509 CB LYN 33 29.011 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.063 37.156 31.263 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.143 37.040 33.026 1.00 0.00 H +ATOM 512 CG LYN 33 27.613 38.360 32.313 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.566 38.985 33.205 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.415 38.982 31.441 1.00 0.00 H +ATOM 515 CD LYN 33 26.537 37.269 32.411 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.694 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.634 36.750 33.364 1.00 0.00 H +ATOM 518 CE LYN 33 25.125 37.836 32.286 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.936 38.516 33.109 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.037 38.375 31.345 1.00 0.00 H +ATOM 521 NZ LYN 33 24.119 36.762 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.186 37.155 32.262 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.255 36.114 31.546 1.00 0.00 H +ATOM 524 C LYN 33 31.513 38.043 32.390 1.00 0.00 C +ATOM 525 O LYN 33 32.010 37.922 33.504 1.00 0.00 O +ATOM 526 N ALA 34 32.145 37.587 31.303 1.00 0.00 N +ATOM 527 H ALA 34 31.697 37.679 30.398 1.00 0.00 H +ATOM 528 CA ALA 34 33.472 36.969 31.385 1.00 0.00 C +ATOM 529 HA ALA 34 33.431 36.162 32.122 1.00 0.00 H +ATOM 530 CB ALA 34 33.818 36.357 30.025 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.964 37.148 29.291 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.777 30.129 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.697 29.695 1.00 0.00 H +ATOM 534 C ALA 34 34.575 37.948 31.862 1.00 0.00 C +ATOM 535 O ALA 34 35.472 37.543 32.601 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.228 31.485 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.508 30.883 1.00 0.00 H +ATOM 538 CA ASN 35 35.366 40.292 31.998 1.00 0.00 C +ATOM 539 HA ASN 35 36.365 39.875 32.114 1.00 0.00 H +ATOM 540 CB ASN 35 35.477 41.419 30.965 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.487 41.705 30.621 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.289 31.446 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.032 29.798 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.582 41.001 29.896 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.708 28.665 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.450 27.893 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.606 28.624 1.00 0.00 H +ATOM 548 C ASN 35 34.980 40.792 33.401 1.00 0.00 C +ATOM 549 O ASN 35 35.862 41.217 34.149 1.00 0.00 O +ATOM 550 N ASP 36 33.716 40.637 33.828 1.00 0.00 N +ATOM 551 H ASP 36 32.980 40.415 33.164 1.00 0.00 H +ATOM 552 CA ASP 36 33.336 40.771 35.246 1.00 0.00 C +ATOM 553 HA ASP 36 33.662 41.747 35.601 1.00 0.00 H +ATOM 554 CB ASP 36 31.821 40.770 35.436 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.447 39.787 35.228 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.605 40.869 36.494 1.00 0.00 H +ATOM 557 CG ASP 36 30.980 41.782 34.656 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.511 42.875 34.375 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.773 41.517 34.399 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.709 36.121 1.00 0.00 C +ATOM 561 O ASP 36 34.483 40.005 37.231 1.00 0.00 O +ATOM 562 N PHE 37 34.225 38.482 35.605 1.00 0.00 N +ATOM 563 H PHE 37 33.748 38.284 34.733 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.460 36.169 1.00 0.00 C +ATOM 565 HA PHE 37 35.119 37.613 37.247 1.00 0.00 H +ATOM 566 CB PHE 37 34.572 36.046 35.924 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.659 35.830 34.863 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.338 36.433 1.00 0.00 H +ATOM 569 CG PHE 37 33.149 35.766 36.381 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.137 35.555 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.369 35.612 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.307 35.837 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.038 35.189 35.100 1.00 0.00 H +ATOM 574 CZ PHE 37 30.512 35.237 37.203 1.00 0.00 C +ATOM 575 HZ PHE 37 29.499 35.052 37.516 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.521 35.410 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.278 35.363 39.212 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.836 35.674 37.748 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.604 35.826 38.483 1.00 0.00 H +ATOM 580 C PHE 37 36.606 37.583 35.730 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.678 35.998 1.00 0.00 O +ATOM 582 N GLY 38 36.994 38.685 35.076 1.00 0.00 N +ATOM 583 H GLY 38 36.290 39.388 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.388 39.099 34.834 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.496 40.119 35.199 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.053 38.480 35.433 1.00 0.00 H +ATOM 587 C GLY 38 38.924 39.067 33.387 1.00 0.00 C +ATOM 588 O GLY 38 39.870 39.802 33.105 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.230 32.483 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.729 32.758 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.054 31.088 1.00 0.00 C +ATOM 592 HA ARG 39 38.947 39.047 30.642 1.00 0.00 H +ATOM 593 CB ARG 39 40.303 37.441 31.074 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.636 37.432 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.986 38.107 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.521 36.014 31.626 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.035 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.754 31.462 1.00 0.00 H +ATOM 599 CD ARG 39 40.216 35.825 33.129 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.853 36.510 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.175 36.078 33.336 1.00 0.00 H +ATOM 602 NE ARG 39 40.443 34.444 33.597 1.00 0.00 N +ATOM 603 HE ARG 39 41.200 34.298 34.242 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.298 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.466 32.486 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.428 34.356 32.087 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.300 32.617 32.077 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.956 32.225 33.814 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.695 32.096 34.487 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.340 31.449 33.597 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.227 30.190 1.00 0.00 C +ATOM 612 O ARG 39 37.524 36.138 30.601 1.00 0.00 O +ATOM 613 N ASP 40 37.649 37.680 28.957 1.00 0.00 N +ATOM 614 H ASP 40 38.027 38.575 28.671 1.00 0.00 H +ATOM 615 CA ASP 40 36.888 36.895 27.965 1.00 0.00 C +ATOM 616 HA ASP 40 36.165 36.313 28.528 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.736 26.967 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.446 37.041 26.398 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.370 38.354 27.534 1.00 0.00 H +ATOM 620 CG ASP 40 36.827 38.629 25.966 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.259 39.727 26.388 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.844 38.320 24.740 1.00 0.00 O +ATOM 623 C ASP 40 37.718 35.863 27.180 1.00 0.00 C +ATOM 624 O ASP 40 38.884 36.079 26.863 1.00 0.00 O +ATOM 625 N GLY 41 37.053 34.763 26.810 1.00 0.00 N +ATOM 626 H GLY 41 36.096 34.686 27.112 1.00 0.00 H +ATOM 627 CA GLY 41 37.470 33.830 25.756 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.458 34.102 25.380 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.530 32.826 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.480 33.816 24.578 1.00 0.00 C +ATOM 631 O GLY 41 35.572 34.650 24.502 1.00 0.00 O +ATOM 632 N GLU 42 36.641 32.855 23.669 1.00 0.00 N +ATOM 633 H GLU 42 37.356 32.161 23.819 1.00 0.00 H +ATOM 634 CA GLU 42 35.802 32.668 22.472 1.00 0.00 C +ATOM 635 HA GLU 42 35.115 33.509 22.372 1.00 0.00 H +ATOM 636 CB GLU 42 36.689 32.632 21.211 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.165 31.653 21.165 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.044 32.715 20.336 1.00 0.00 H +ATOM 639 CG GLU 42 37.807 33.696 21.110 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.580 33.458 21.845 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.278 33.628 20.127 1.00 0.00 H +ATOM 642 CD GLU 42 37.351 35.145 21.325 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.163 35.460 21.116 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.176 36.004 21.723 1.00 0.00 O +ATOM 645 C GLU 42 34.953 31.386 22.575 1.00 0.00 C +ATOM 646 O GLU 42 35.399 30.400 23.169 1.00 0.00 O +ATOM 647 N ALA 43 33.750 31.390 21.987 1.00 0.00 N +ATOM 648 H ALA 43 33.482 32.195 21.439 1.00 0.00 H +ATOM 649 CA ALA 43 32.763 30.304 22.059 1.00 0.00 C +ATOM 650 HA ALA 43 33.255 29.386 22.386 1.00 0.00 H +ATOM 651 CB ALA 43 31.699 30.668 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.186 31.588 22.813 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.966 29.860 23.179 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.172 30.808 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.115 30.014 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.888 30.928 19.897 1.00 0.00 O +ATOM 657 N THR 44 31.800 28.743 20.425 1.00 0.00 N +ATOM 658 H THR 44 31.921 28.066 21.171 1.00 0.00 H +ATOM 659 CA THR 44 31.132 28.280 19.197 1.00 0.00 C +ATOM 660 HA THR 44 31.427 28.942 18.384 1.00 0.00 H +ATOM 661 CB THR 44 31.609 26.864 18.827 1.00 0.00 C +ATOM 662 HB THR 44 31.426 26.183 19.661 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.277 17.557 1.00 0.00 C +ATOM 664 HG21 THR 44 31.074 26.985 16.731 1.00 0.00 H +ATOM 665 HG22 THR 44 31.501 25.353 17.284 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.035 17.728 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.918 18.568 1.00 0.00 O +ATOM 668 HG1 THR 44 33.233 26.114 18.102 1.00 0.00 H +ATOM 669 C THR 44 29.606 28.380 19.330 1.00 0.00 C +ATOM 670 O THR 44 29.074 28.429 20.439 1.00 0.00 O +ATOM 671 N ILE 45 28.902 28.457 18.195 1.00 0.00 N +ATOM 672 H ILE 45 29.375 28.320 17.316 1.00 0.00 H +ATOM 673 CA ILE 45 27.480 28.839 18.125 1.00 0.00 C +ATOM 674 HA ILE 45 27.062 28.755 19.129 1.00 0.00 H +ATOM 675 CB ILE 45 27.333 30.312 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.272 30.526 17.776 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.068 31.232 18.675 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.152 31.107 18.585 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.832 32.280 18.494 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.767 30.970 19.686 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.759 30.685 16.250 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.026 31.742 16.230 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.656 30.128 15.967 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.502 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.733 30.942 15.528 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.979 31.006 14.266 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.520 29.448 14.962 1.00 0.00 H +ATOM 688 C ILE 45 26.631 27.921 17.246 1.00 0.00 C +ATOM 689 O ILE 45 27.124 27.339 16.280 1.00 0.00 O +ATOM 690 N ASP 46 25.331 27.876 17.547 1.00 0.00 N +ATOM 691 H ASP 46 25.033 28.294 18.423 1.00 0.00 H +ATOM 692 CA ASP 46 24.283 27.257 16.737 1.00 0.00 C +ATOM 693 HA ASP 46 24.587 27.262 15.685 1.00 0.00 H +ATOM 694 CB ASP 46 24.078 25.805 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.217 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.957 25.786 18.268 1.00 0.00 H +ATOM 697 CG ASP 46 22.842 25.167 16.545 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.473 17.282 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.562 25.433 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.960 28.047 16.852 1.00 0.00 C +ATOM 701 O ASP 46 22.512 28.361 17.956 1.00 0.00 O +ATOM 702 N ASP 47 22.310 28.329 15.718 1.00 0.00 N +ATOM 703 H ASP 47 22.680 27.938 14.863 1.00 0.00 H +ATOM 704 CA ASP 47 20.971 28.922 15.676 1.00 0.00 C +ATOM 705 HA ASP 47 20.879 29.650 16.488 1.00 0.00 H +ATOM 706 CB ASP 47 20.780 29.672 14.348 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.524 30.465 14.258 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.918 28.977 13.517 1.00 0.00 H +ATOM 709 CG ASP 47 19.369 30.276 14.272 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.488 29.678 13.613 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.067 31.233 15.020 1.00 0.00 O +ATOM 712 C ASP 47 19.855 27.874 15.879 1.00 0.00 C +ATOM 713 O ASP 47 18.845 28.182 16.515 1.00 0.00 O +ATOM 714 N ALA 48 20.003 26.633 15.397 1.00 0.00 N +ATOM 715 H ALA 48 20.918 26.339 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.934 25.624 15.414 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.052 14.933 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.422 14.585 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.277 23.964 15.055 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.682 14.517 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.673 24.751 13.581 1.00 0.00 H +ATOM 722 C ALA 48 18.526 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.930 17.102 1.00 0.00 O +ATOM 724 N THR 49 19.478 25.244 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.438 25.291 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.267 25.119 19.230 1.00 0.00 C +ATOM 727 HA THR 49 18.217 24.871 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.101 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.822 23.860 20.869 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.626 19.138 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.664 18.100 1.00 0.00 H +ATOM 732 HG22 THR 49 20.432 21.855 19.655 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.166 1.00 0.00 H +ATOM 734 OG1 THR 49 21.479 24.241 19.772 1.00 0.00 O +ATOM 735 HG1 THR 49 21.731 24.265 18.814 1.00 0.00 H +ATOM 736 C THR 49 19.506 26.430 20.000 1.00 0.00 C +ATOM 737 O THR 49 19.425 26.431 21.224 1.00 0.00 O +ATOM 738 N LYS 50 19.768 27.552 19.311 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.294 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.905 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.356 29.539 19.085 1.00 0.00 H +ATOM 742 CB LYS 50 18.568 29.470 20.294 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.162 28.830 21.071 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.700 30.460 20.734 1.00 0.00 H +ATOM 745 CG LYS 50 17.490 29.595 19.184 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.427 28.653 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.736 19.684 1.00 0.00 H +ATOM 748 CD LYS 50 17.702 30.770 18.225 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.701 31.693 18.812 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.686 17.722 1.00 0.00 H +ATOM 751 CE LYS 50 16.567 30.866 17.186 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.595 17.663 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.503 31.892 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.995 16.015 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.233 29.097 16.281 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.015 29.834 15.433 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.545 30.416 15.422 1.00 0.00 H +ATOM 758 C LYS 50 20.985 28.947 21.017 1.00 0.00 C +ATOM 759 O LYS 50 20.690 29.519 22.087 1.00 0.00 O +ATOM 760 N THR 51 22.149 28.291 20.853 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.965 19.930 1.00 0.00 H +ATOM 762 CA THR 51 23.056 27.909 21.961 1.00 0.00 C +ATOM 763 HA THR 51 22.764 28.428 22.859 1.00 0.00 H +ATOM 764 CB THR 51 22.887 26.405 22.277 1.00 0.00 C +ATOM 765 HB THR 51 22.977 25.816 21.351 1.00 0.00 H +ATOM 766 CG2 THR 51 23.852 25.861 23.315 1.00 0.00 C +ATOM 767 HG21 THR 51 23.811 26.476 24.217 1.00 0.00 H +ATOM 768 HG22 THR 51 23.574 24.839 23.587 1.00 0.00 H +ATOM 769 HG23 THR 51 24.879 25.834 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.642 26.171 22.880 1.00 0.00 O +ATOM 771 HG1 THR 51 20.952 26.250 22.187 1.00 0.00 H +ATOM 772 C THR 51 24.558 28.226 21.727 1.00 0.00 C +ATOM 773 O THR 51 25.088 27.999 20.643 1.00 0.00 O +ATOM 774 N PHE 52 25.247 28.694 22.774 1.00 0.00 N +ATOM 775 H PHE 52 24.711 28.955 23.594 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.776 22.877 1.00 0.00 C +ATOM 777 HA PHE 52 27.143 28.936 21.901 1.00 0.00 H +ATOM 778 CB PHE 52 27.150 29.949 23.826 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.478 29.957 24.658 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.734 24.192 1.00 0.00 H +ATOM 781 CG PHE 52 27.216 31.350 23.227 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.432 32.382 23.751 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.753 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.448 33.649 23.160 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.778 34.433 23.517 1.00 0.00 H +ATOM 786 CZ PHE 52 27.282 33.889 22.068 1.00 0.00 C +ATOM 787 HZ PHE 52 27.247 34.834 21.561 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.159 32.900 21.619 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.839 33.106 20.790 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.629 22.200 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.776 30.856 21.829 1.00 0.00 H +ATOM 792 C PHE 52 27.330 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.807 27.009 24.507 1.00 0.00 O +ATOM 794 N THR 53 28.485 27.065 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.850 27.522 22.148 1.00 0.00 H +ATOM 796 CA THR 53 29.279 25.926 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.045 25.794 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.933 24.610 22.780 1.00 0.00 C +ATOM 799 HB THR 53 29.508 23.801 23.237 1.00 0.00 H +ATOM 800 CG2 THR 53 27.457 24.224 22.859 1.00 0.00 C +ATOM 801 HG21 THR 53 26.863 24.906 22.251 1.00 0.00 H +ATOM 802 HG22 THR 53 27.322 23.209 22.490 1.00 0.00 H +ATOM 803 HG23 THR 53 27.120 24.269 23.894 1.00 0.00 H +ATOM 804 OG1 THR 53 29.270 24.680 21.419 1.00 0.00 O +ATOM 805 HG1 THR 53 28.753 24.016 20.952 1.00 0.00 H +ATOM 806 C THR 53 30.801 26.146 23.414 1.00 0.00 C +ATOM 807 O THR 53 31.285 27.021 22.692 1.00 0.00 O +ATOM 808 N THR 54 31.568 25.322 24.142 1.00 0.00 N +ATOM 809 H THR 54 31.108 24.646 24.732 1.00 0.00 H +ATOM 810 CA THR 54 33.040 25.237 24.079 1.00 0.00 C +ATOM 811 HA THR 54 33.413 26.032 23.433 1.00 0.00 H +ATOM 812 CB THR 54 33.664 25.450 25.472 1.00 0.00 C +ATOM 813 HB THR 54 33.370 24.631 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.192 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.513 26.333 24.768 1.00 0.00 H +ATOM 816 HG22 THR 54 35.549 25.815 26.469 1.00 0.00 H +ATOM 817 HG23 THR 54 35.638 24.608 25.194 1.00 0.00 H +ATOM 818 OG1 THR 54 33.199 26.661 26.022 1.00 0.00 O +ATOM 819 HG1 THR 54 33.873 26.995 26.617 1.00 0.00 H +ATOM 820 C THR 54 33.478 23.891 23.475 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.890 23.606 1.00 0.00 O +ATOM 822 N GLN 55 34.634 23.874 22.804 1.00 0.00 N +ATOM 823 H GLN 55 35.155 24.736 22.760 1.00 0.00 H +ATOM 824 CA GLN 55 35.263 22.689 22.197 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.160 21.641 1.00 0.00 H +ATOM 826 CB GLN 55 36.318 23.157 21.174 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.731 22.289 20.660 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.803 23.768 20.429 1.00 0.00 H +ATOM 829 CG GLN 55 37.480 23.990 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.094 24.710 22.481 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.176 23.332 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.246 24.768 20.685 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.323 24.390 19.522 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.828 25.897 21.031 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.406 26.349 20.327 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.721 26.270 21.959 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.678 23.227 1.00 0.00 C +ATOM 838 O GLN 55 36.115 22.046 24.365 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.411 22.806 1.00 0.00 N +ATOM 840 H GLU 56 35.791 20.230 21.834 1.00 0.00 H +ATOM 841 CA GLU 56 36.494 19.248 23.574 1.00 0.00 C +ATOM 842 HA GLU 56 36.158 19.336 24.606 1.00 0.00 H +ATOM 843 CB GLU 56 35.887 17.954 22.970 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.807 17.983 23.079 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.991 21.899 1.00 0.00 H +ATOM 846 CG GLU 56 36.406 16.581 23.466 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.470 15.932 22.595 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.421 16.670 23.823 1.00 0.00 H +ATOM 849 CD GLU 56 35.546 15.853 24.519 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.084 15.362 25.545 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.329 15.640 24.294 1.00 0.00 O +ATOM 852 C GLU 56 38.033 19.203 23.640 1.00 0.00 C +ATOM 853 O GLU 56 38.543 19.194 24.791 1.00 0.00 O +ATOM 854 OXT GLU 56 38.679 19.135 22.573 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.719 32.459 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.328 33.244 30.277 1.00 0.00 N +HETATM 857 C AN1 58 30.687 33.879 31.201 1.00 0.00 C +HETATM 858 C1 AN1 58 29.381 33.532 30.714 1.00 0.00 C +HETATM 859 H AN1 58 30.624 34.272 32.222 1.00 0.00 H +HETATM 860 H1 AN1 58 31.138 34.632 30.547 1.00 0.00 H +HETATM 861 H2 AN1 58 31.318 32.977 31.202 1.00 0.00 H +HETATM 862 N1 AZI 59 31.274 30.374 29.434 1.00 0.00 N +HETATM 863 N2 AZI 59 30.476 30.257 30.351 1.00 0.00 N +HETATM 864 N3 AZI 59 29.630 30.157 31.295 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 148 144 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 639 643 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_2.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_2.pdb new file mode 100644 index 0000000..925b319 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_2.pdb @@ -0,0 +1,1785 @@ +COMPND fitness: -6.2188 90.21749999999975 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 P1 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HX1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HX1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HX1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HX1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HX1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HX1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HX1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HX1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N ARG 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H ARG 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA ARG 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 CB ARG 8 32.132 -93.836 -4.510 1.00 0.00 C +ATOM 136 HB2 ARG 8 33.183 -94.106 -4.615 1.00 0.00 H +ATOM 137 HB3 ARG 8 31.914 -92.975 -5.142 1.00 0.00 H +ATOM 138 CG ARG 8 31.841 -93.485 -3.060 1.00 0.00 C +ATOM 139 HG2 ARG 8 31.934 -94.390 -2.458 1.00 0.00 H +ATOM 140 HG3 ARG 8 32.574 -92.751 -2.726 1.00 0.00 H +ATOM 141 CD ARG 8 30.442 -92.914 -2.901 1.00 0.00 C +ATOM 142 HD2 ARG 8 29.722 -93.620 -3.312 1.00 0.00 H +ATOM 143 HD3 ARG 8 30.238 -92.765 -1.841 1.00 0.00 H +ATOM 144 NE ARG 8 30.290 -91.636 -3.591 1.00 0.00 N +ATOM 145 HE ARG 8 29.906 -91.657 -4.525 1.00 0.00 H +ATOM 146 CZ ARG 8 30.622 -90.461 -3.067 1.00 0.00 C +ATOM 147 NH1 ARG 8 30.448 -89.350 -3.770 1.00 0.00 N +ATOM 148 HH11 ARG 8 30.063 -89.401 -4.703 1.00 0.00 H +ATOM 149 HH12 ARG 8 30.702 -88.457 -3.370 1.00 0.00 H +ATOM 150 NH2 ARG 8 31.126 -90.399 -1.843 1.00 0.00 N +ATOM 151 HH21 ARG 8 31.255 -91.247 -1.310 1.00 0.00 H +ATOM 152 HH22 ARG 8 31.377 -89.503 -1.447 1.00 0.00 H +ATOM 153 HA ARG 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 154 C ARG 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 155 O ARG 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 156 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 157 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 158 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 161 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 162 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 163 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 164 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 165 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 166 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 167 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 168 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 169 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 170 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 171 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 172 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 173 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 174 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 175 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 176 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 177 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 178 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 179 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 180 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 181 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 182 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 183 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 184 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 185 N SER 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 186 H SER 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 187 CA SER 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 188 CB SER 11 32.207-101.574 0.711 1.00 0.00 C +ATOM 189 HB2 SER 11 32.416-100.511 0.583 1.00 0.00 H +ATOM 190 HB3 SER 11 31.863-101.756 1.728 1.00 0.00 H +ATOM 191 OG SER 11 33.389-102.318 0.472 1.00 0.00 O +ATOM 192 HG SER 11 34.068-102.048 1.093 1.00 0.00 H +ATOM 193 HA SER 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 194 C SER 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 195 O SER 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 196 N CYS 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 197 H CYS 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 198 CA CYS 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 199 CB CYS 12 28.130 -98.237 -0.161 1.00 0.00 C +ATOM 200 HB2 CYS 12 28.781 -97.808 -0.923 1.00 0.00 H +ATOM 201 HB3 CYS 12 27.157 -97.746 -0.196 1.00 0.00 H +ATOM 202 SG CYS 12 28.866 -97.786 1.444 1.00 0.00 S +ATOM 203 HG CYS 12 28.829 -96.471 1.249 1.00 0.00 H +ATOM 204 HA CYS 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 205 C CYS 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 206 O CYS 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 207 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 208 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 209 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 210 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 211 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 212 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 213 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 214 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 215 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 216 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 217 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 218 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 219 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 220 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 221 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 222 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 223 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 224 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 225 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 226 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 227 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 228 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 229 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 230 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 231 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 232 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 233 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 234 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 235 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 236 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 237 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 238 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 239 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 240 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 241 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 242 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 243 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 244 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 245 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 246 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 247 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 248 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 249 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 250 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 251 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 252 N HY1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 253 CA HY1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 254 C HY1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 255 O HY1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 256 CB HY1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 257 CG HY1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 258 CD2 HY1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 259 ND1 HY1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 260 CE1 HY1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 261 NE2 HY1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 262 H HY1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 263 HA HY1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 264 HB2 HY1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 265 HB3 HY1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 266 HD1 HY1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 267 HD2 HY1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 268 HE1 HY1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 269 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 270 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 271 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 272 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 273 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 274 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 275 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 276 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 277 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 278 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 279 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 280 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 281 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 282 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 283 N HY2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 284 CA HY2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 285 C HY2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 286 O HY2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 287 CB HY2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 288 CG HY2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 289 CD2 HY2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 290 ND1 HY2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 291 CE1 HY2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 292 NE2 HY2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 293 H HY2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 294 HA HY2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 295 HB2 HY2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 296 HB3 HY2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 297 HD1 HY2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 298 HD2 HY2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 299 HE1 HY2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 300 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 301 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 302 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 303 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 304 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 305 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 306 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 307 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 308 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 309 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 310 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 311 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 312 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 313 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 314 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 315 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 316 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 317 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 318 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 319 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 320 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 321 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 322 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 323 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 324 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 325 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 326 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 327 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 328 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 329 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 330 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 331 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 332 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 333 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 334 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 335 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 336 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 337 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 338 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 339 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 340 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 341 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 342 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 343 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 344 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 345 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 346 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 347 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 348 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 349 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 350 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 351 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 352 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 353 N TRP 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 354 H TRP 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 355 CA TRP 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 356 CB TRP 23 21.411 -85.256 -16.822 1.00 0.00 C +ATOM 357 HB2 TRP 23 20.471 -85.768 -16.621 1.00 0.00 H +ATOM 358 HB3 TRP 23 21.494 -85.175 -17.905 1.00 0.00 H +ATOM 359 CG TRP 23 22.519 -86.148 -16.354 1.00 0.00 C +ATOM 360 CD1 TRP 23 23.651 -86.478 -17.042 1.00 0.00 C +ATOM 361 HD1 TRP 23 23.887 -86.129 -18.044 1.00 0.00 H +ATOM 362 NE1 TRP 23 24.435 -87.319 -16.290 1.00 0.00 N +ATOM 363 HE1 TRP 23 25.328 -87.711 -16.568 1.00 0.00 H +ATOM 364 CE2 TRP 23 23.809 -87.548 -15.088 1.00 0.00 C +ATOM 365 CZ2 TRP 23 24.208 -88.327 -14.004 1.00 0.00 C +ATOM 366 HZ2 TRP 23 25.139 -88.878 -14.005 1.00 0.00 H +ATOM 367 CH2 TRP 23 23.375 -88.374 -12.917 1.00 0.00 C +ATOM 368 HH2 TRP 23 23.669 -88.969 -12.061 1.00 0.00 H +ATOM 369 CZ3 TRP 23 22.163 -87.664 -12.899 1.00 0.00 C +ATOM 370 HZ3 TRP 23 21.536 -87.731 -12.021 1.00 0.00 H +ATOM 371 CE3 TRP 23 21.767 -86.890 -13.974 1.00 0.00 C +ATOM 372 HE3 TRP 23 20.836 -86.342 -13.975 1.00 0.00 H +ATOM 373 CD2 TRP 23 22.599 -86.826 -15.093 1.00 0.00 C +ATOM 374 HA TRP 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 375 C TRP 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 376 O TRP 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 377 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 378 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 379 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 380 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 381 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 382 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 383 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 384 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 385 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 386 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 387 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 388 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 389 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 390 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 391 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 392 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 393 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 394 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 395 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 396 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 397 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 398 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 399 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 400 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 401 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 402 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 403 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 404 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 405 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 406 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 407 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 408 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 409 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 410 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 411 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 412 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 413 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 414 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 415 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 416 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 417 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 418 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 419 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 420 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 421 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 422 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 423 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 424 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 425 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 426 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 427 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 428 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 429 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 430 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 431 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 432 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 433 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 434 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 435 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 436 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 437 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 438 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 439 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 440 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 441 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 442 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 443 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 444 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 445 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 446 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 447 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 448 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 449 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 450 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 451 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 452 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 453 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 454 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 455 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 456 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 457 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 458 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 459 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 460 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 461 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 462 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 463 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 464 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 465 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 466 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 467 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 468 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 469 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 470 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 471 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 472 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 473 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 474 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 475 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 476 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 477 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 478 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 479 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 480 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 481 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 482 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 483 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 484 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 485 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 486 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 487 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 488 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 489 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 490 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 491 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 492 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 493 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 494 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 495 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 496 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 497 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 498 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 499 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 500 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 501 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 502 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 503 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 504 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 505 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 506 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 507 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 508 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 509 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 510 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 511 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 512 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 513 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 514 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 515 N LYN 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 516 H LYN 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 517 CA LYN 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 518 CB LYN 33 27.315 -82.525 -3.272 1.00 0.00 C +ATOM 519 HB2 LYN 33 26.398 -81.939 -3.213 1.00 0.00 H +ATOM 520 HB3 LYN 33 27.388 -82.987 -4.256 1.00 0.00 H +ATOM 521 CG LYN 33 27.295 -83.606 -2.204 1.00 0.00 C +ATOM 522 HG2 LYN 33 28.222 -84.177 -2.270 1.00 0.00 H +ATOM 523 HG3 LYN 33 27.231 -83.128 -1.227 1.00 0.00 H +ATOM 524 CD LYN 33 26.111 -84.541 -2.388 1.00 0.00 C +ATOM 525 HD2 LYN 33 26.114 -84.908 -3.414 1.00 0.00 H +ATOM 526 HD3 LYN 33 26.222 -85.381 -1.702 1.00 0.00 H +ATOM 527 CE LYN 33 24.798 -83.829 -2.109 1.00 0.00 C +ATOM 528 HE2 LYN 33 24.821 -83.460 -1.084 1.00 0.00 H +ATOM 529 HE3 LYN 33 24.713 -82.987 -2.797 1.00 0.00 H +ATOM 530 NZ LYN 33 23.628 -84.733 -2.286 1.00 0.00 N +ATOM 531 HZ2 LYN 33 22.777 -84.224 -2.092 1.00 0.00 H +ATOM 532 HZ3 LYN 33 23.607 -85.075 -3.236 1.00 0.00 H +ATOM 533 HA LYN 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 534 C LYN 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 535 O LYN 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 536 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 537 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 538 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 539 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 540 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 541 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 542 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 543 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 544 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 545 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 546 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 547 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 548 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 549 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 550 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 551 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 552 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 553 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 554 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 555 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 556 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 557 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 558 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 559 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 560 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 561 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 562 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 563 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 564 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 565 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 566 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 567 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 568 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 569 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 570 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 571 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 572 N LYS 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 573 H LYS 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 574 CA LYS 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 575 CB LYS 37 33.048 -83.879 0.496 1.00 0.00 C +ATOM 576 HB2 LYS 37 33.471 -84.650 1.141 1.00 0.00 H +ATOM 577 HB3 LYS 37 31.965 -83.860 0.615 1.00 0.00 H +ATOM 578 CG LYS 37 33.393 -84.185 -0.952 1.00 0.00 C +ATOM 579 HG2 LYS 37 32.972 -83.401 -1.582 1.00 0.00 H +ATOM 580 HG3 LYS 37 34.478 -84.192 -1.057 1.00 0.00 H +ATOM 581 CD LYS 37 32.834 -85.533 -1.380 1.00 0.00 C +ATOM 582 HD2 LYS 37 33.256 -86.304 -0.735 1.00 0.00 H +ATOM 583 HD3 LYS 37 31.751 -85.513 -1.262 1.00 0.00 H +ATOM 584 CE LYS 37 33.180 -85.839 -2.828 1.00 0.00 C +ATOM 585 HE2 LYS 37 34.262 -85.779 -2.941 1.00 0.00 H +ATOM 586 HE3 LYS 37 32.849 -86.853 -3.051 1.00 0.00 H +ATOM 587 NZ LYS 37 32.529 -84.884 -3.768 1.00 0.00 N1+ +ATOM 588 HZ1 LYS 37 32.837 -83.945 -3.561 1.00 0.00 H +ATOM 589 HZ2 LYS 37 32.782 -85.121 -4.717 1.00 0.00 H +ATOM 590 HZ3 LYS 37 31.526 -84.940 -3.663 1.00 0.00 H +ATOM 591 HA LYS 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 592 C LYS 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 593 O LYS 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 594 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 595 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 596 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 597 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 598 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 599 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 600 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 601 N ARG 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 602 H ARG 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 603 CA ARG 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 604 CB ARG 39 38.868 -82.517 -4.462 1.00 0.00 C +ATOM 605 HB2 ARG 39 39.200 -82.458 -5.498 1.00 0.00 H +ATOM 606 HB3 ARG 39 39.426 -81.798 -3.861 1.00 0.00 H +ATOM 607 CG ARG 39 39.115 -83.920 -3.930 1.00 0.00 C +ATOM 608 HG2 ARG 39 38.452 -84.611 -4.452 1.00 0.00 H +ATOM 609 HG3 ARG 39 40.151 -84.191 -4.132 1.00 0.00 H +ATOM 610 CD ARG 39 38.853 -83.997 -2.436 1.00 0.00 C +ATOM 611 HD2 ARG 39 39.516 -83.301 -1.923 1.00 0.00 H +ATOM 612 HD3 ARG 39 37.817 -83.720 -2.242 1.00 0.00 H +ATOM 613 NE ARG 39 39.085 -85.339 -1.908 1.00 0.00 N +ATOM 614 HE ARG 39 39.993 -85.527 -1.508 1.00 0.00 H +ATOM 615 CZ ARG 39 38.183 -86.314 -1.923 1.00 0.00 C +ATOM 616 NH1 ARG 39 36.981 -86.099 -2.440 1.00 0.00 N +ATOM 617 HH11 ARG 39 36.755 -85.192 -2.822 1.00 0.00 H +ATOM 618 HH12 ARG 39 36.298 -86.842 -2.450 1.00 0.00 H +ATOM 619 NH2 ARG 39 38.485 -87.503 -1.419 1.00 0.00 N +ATOM 620 HH21 ARG 39 39.402 -87.663 -1.025 1.00 0.00 H +ATOM 621 HH22 ARG 39 37.797 -88.243 -1.432 1.00 0.00 H +ATOM 622 HA ARG 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 623 C ARG 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 624 O ARG 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 625 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 626 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 627 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 628 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 629 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 630 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 631 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 632 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 633 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 634 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 635 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 636 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 637 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 638 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 639 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 640 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 641 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 642 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 643 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 644 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 645 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 646 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 647 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 648 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 649 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 650 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 651 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 652 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 653 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 654 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 655 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 656 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 657 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 658 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 659 N ARG 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 660 H ARG 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 661 CA ARG 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 662 CB ARG 43 29.884 -89.033 -12.452 1.00 0.00 C +ATOM 663 HB2 ARG 43 29.195 -89.866 -12.312 1.00 0.00 H +ATOM 664 HB3 ARG 43 30.406 -88.833 -11.516 1.00 0.00 H +ATOM 665 CG ARG 43 29.106 -87.797 -12.871 1.00 0.00 C +ATOM 666 HG2 ARG 43 29.809 -86.976 -13.016 1.00 0.00 H +ATOM 667 HG3 ARG 43 28.598 -88.009 -13.812 1.00 0.00 H +ATOM 668 CD ARG 43 28.081 -87.406 -11.819 1.00 0.00 C +ATOM 669 HD2 ARG 43 27.386 -88.233 -11.676 1.00 0.00 H +ATOM 670 HD3 ARG 43 28.596 -87.199 -10.881 1.00 0.00 H +ATOM 671 NE ARG 43 27.323 -86.221 -12.207 1.00 0.00 N +ATOM 672 HE ARG 43 26.435 -86.368 -12.663 1.00 0.00 H +ATOM 673 CZ ARG 43 27.730 -84.973 -11.997 1.00 0.00 C +ATOM 674 NH1 ARG 43 28.892 -84.745 -11.401 1.00 0.00 N +ATOM 675 HH11 ARG 43 29.466 -85.523 -11.108 1.00 0.00 H +ATOM 676 HH12 ARG 43 29.198 -83.796 -11.243 1.00 0.00 H +ATOM 677 NH2 ARG 43 26.972 -83.955 -12.384 1.00 0.00 N +ATOM 678 HH21 ARG 43 26.087 -84.131 -12.838 1.00 0.00 H +ATOM 679 HH22 ARG 43 27.284 -83.008 -12.223 1.00 0.00 H +ATOM 680 HA ARG 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 681 C ARG 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 682 O ARG 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 683 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 684 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 685 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 686 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 687 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 688 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 689 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 690 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 691 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 692 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 693 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 694 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 695 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 696 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 697 N ILE 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 698 H ILE 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 699 CA ILE 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 700 CB ILE 45 25.264 -89.243 -17.471 1.00 0.00 C +ATOM 701 HB ILE 45 24.177 -89.166 -17.456 1.00 0.00 H +ATOM 702 CG2 ILE 45 25.843 -88.467 -16.298 1.00 0.00 C +ATOM 703 HG21 ILE 45 26.931 -88.545 -16.312 1.00 0.00 H +ATOM 704 HG22 ILE 45 25.553 -87.420 -16.375 1.00 0.00 H +ATOM 705 HG23 ILE 45 25.464 -88.881 -15.364 1.00 0.00 H +ATOM 706 CG1 ILE 45 25.812 -88.644 -18.767 1.00 0.00 C +ATOM 707 HG12 ILE 45 25.634 -87.570 -18.727 1.00 0.00 H +ATOM 708 HG13 ILE 45 26.886 -88.835 -18.784 1.00 0.00 H +ATOM 709 CD1 ILE 45 25.179 -89.214 -20.018 1.00 0.00 C +ATOM 710 HD11 ILE 45 24.105 -89.024 -20.003 1.00 0.00 H +ATOM 711 HD12 ILE 45 25.619 -88.741 -20.896 1.00 0.00 H +ATOM 712 HD13 ILE 45 25.357 -90.289 -20.058 1.00 0.00 H +ATOM 713 HA ILE 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 714 C ILE 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 715 O ILE 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 716 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 717 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 718 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 719 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 720 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 721 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 722 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 723 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 724 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 725 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 726 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 727 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 728 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 729 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 730 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 731 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 732 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 733 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 734 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 735 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 736 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 737 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 738 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 739 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 740 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 741 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 742 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 743 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 744 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 745 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 746 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 747 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 748 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 749 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 750 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 751 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 752 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 753 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 754 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 755 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 756 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 757 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 758 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 759 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 760 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 761 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 762 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 763 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 764 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 765 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 766 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 767 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 768 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 769 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 770 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 771 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 772 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 773 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 774 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 775 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 776 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 777 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 778 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 779 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 780 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 781 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 782 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 783 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 784 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 785 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 786 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 787 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 788 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 789 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 790 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 791 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 792 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 793 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 794 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 795 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 796 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 797 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 798 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 799 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 800 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 801 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 802 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 803 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 804 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 805 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 806 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 807 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 808 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 809 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 810 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 811 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 812 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 813 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 814 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 815 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 816 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 817 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 818 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 819 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 820 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 821 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 822 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 823 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 824 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 825 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 826 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 827 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 828 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 829 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 830 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 831 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 832 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 833 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 834 N THR 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 835 H THR 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 836 CA THR 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 837 CB THR 54 32.307 -94.492 -10.190 1.00 0.00 C +ATOM 838 HB THR 54 31.944 -95.343 -9.615 1.00 0.00 H +ATOM 839 CG2 THR 54 33.789 -94.670 -10.479 1.00 0.00 C +ATOM 840 HG21 THR 54 34.153 -93.819 -11.054 1.00 0.00 H +ATOM 841 HG22 THR 54 34.338 -94.734 -9.539 1.00 0.00 H +ATOM 842 HG23 THR 54 33.941 -95.586 -11.051 1.00 0.00 H +ATOM 843 OG1 THR 54 32.122 -93.285 -9.439 1.00 0.00 O +ATOM 844 HG1 THR 54 32.609 -93.345 -8.613 1.00 0.00 H +ATOM 845 HA THR 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 846 C THR 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 847 O THR 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 848 N GLN 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 849 H GLN 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 850 CA GLN 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 851 CB GLN 55 34.660 -96.376 -14.407 1.00 0.00 C +ATOM 852 HB2 GLN 55 34.997 -97.154 -15.093 1.00 0.00 H +ATOM 853 HB3 GLN 55 34.127 -95.606 -14.966 1.00 0.00 H +ATOM 854 CG GLN 55 35.862 -95.756 -13.713 1.00 0.00 C +ATOM 855 HG2 GLN 55 35.513 -94.985 -13.026 1.00 0.00 H +ATOM 856 HG3 GLN 55 36.382 -96.534 -13.153 1.00 0.00 H +ATOM 857 CD GLN 55 36.837 -95.128 -14.689 1.00 0.00 C +ATOM 858 OE1 GLN 55 36.898 -95.513 -15.856 1.00 0.00 O +ATOM 859 NE2 GLN 55 37.605 -94.154 -14.211 1.00 0.00 N +ATOM 860 HE21 GLN 55 38.274 -93.699 -14.816 1.00 0.00 H +ATOM 861 HE22 GLN 55 37.517 -93.873 -13.245 1.00 0.00 H +ATOM 862 HA GLN 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 863 C GLN 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 864 O GLN 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 865 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 866 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 867 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 868 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 869 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 870 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 871 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 872 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 873 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 874 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 875 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 876 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 877 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 878 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 879 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 880 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 881 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 Zn +ATOM 882 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 883 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 884 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 885 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 886 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 887 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +ATOM 888 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 889 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 890 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 17 15 13 16 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 65 60 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 68 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 65 69 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 881 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 104 106 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 111 112 113 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 153 132 154 135 +CONECT 135 136 137 138 134 +CONECT 136 135 +CONECT 137 135 +CONECT 138 135 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 142 143 144 +CONECT 142 141 +CONECT 143 141 +CONECT 144 141 145 146 +CONECT 145 144 +CONECT 146 144 147 150 +CONECT 147 146 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 146 151 152 +CONECT 151 150 +CONECT 152 150 +CONECT 153 134 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 165 169 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 170 175 +CONECT 174 173 +CONECT 175 173 +CONECT 176 178 179 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 182 181 176 180 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 193 194 188 +CONECT 188 189 190 191 187 +CONECT 189 188 +CONECT 190 188 +CONECT 191 188 192 +CONECT 192 191 +CONECT 193 187 +CONECT 194 196 187 195 +CONECT 195 194 +CONECT 196 197 198 194 +CONECT 197 196 +CONECT 198 205 196 204 199 +CONECT 199 200 201 202 198 +CONECT 200 199 +CONECT 201 199 +CONECT 202 199 203 +CONECT 203 202 +CONECT 204 198 +CONECT 205 206 207 198 +CONECT 206 205 +CONECT 207 209 205 208 +CONECT 208 207 +CONECT 209 210 211 227 207 +CONECT 210 209 +CONECT 211 214 209 212 213 +CONECT 212 211 +CONECT 213 211 +CONECT 214 216 215 217 211 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 214 220 219 +CONECT 218 217 +CONECT 219 217 +CONECT 220 222 217 223 221 +CONECT 221 220 +CONECT 222 220 +CONECT 223 226 220 224 225 +CONECT 224 223 +CONECT 225 223 +CONECT 226 223 +CONECT 227 228 209 229 +CONECT 228 227 +CONECT 229 227 231 230 +CONECT 230 229 +CONECT 231 234 229 232 233 +CONECT 232 231 +CONECT 233 231 +CONECT 234 235 236 231 +CONECT 235 234 +CONECT 236 238 234 237 +CONECT 237 236 +CONECT 238 240 239 250 236 +CONECT 239 238 +CONECT 240 246 241 242 238 +CONECT 241 240 +CONECT 242 240 245 244 243 +CONECT 243 242 +CONECT 244 242 +CONECT 245 242 +CONECT 246 248 249 247 240 +CONECT 247 246 +CONECT 248 246 +CONECT 249 246 +CONECT 250 252 238 251 +CONECT 251 250 +CONECT 252 262 253 250 +CONECT 253 254 252 263 256 +CONECT 254 255 269 253 +CONECT 255 254 +CONECT 256 253 257 264 265 +CONECT 257 258 259 256 +CONECT 258 261 267 257 +CONECT 259 260 257 266 +CONECT 260 261 268 259 +CONECT 261 881 260 258 +CONECT 262 252 +CONECT 263 253 +CONECT 264 256 +CONECT 265 256 +CONECT 266 259 +CONECT 267 258 +CONECT 268 260 +CONECT 269 271 254 270 +CONECT 270 269 +CONECT 271 272 273 281 269 +CONECT 272 271 +CONECT 273 274 275 271 279 +CONECT 274 273 +CONECT 275 276 277 273 278 +CONECT 276 275 +CONECT 277 275 +CONECT 278 275 +CONECT 279 273 280 +CONECT 280 279 +CONECT 281 283 271 282 +CONECT 282 281 +CONECT 283 293 284 281 +CONECT 284 285 287 283 294 +CONECT 285 286 300 284 +CONECT 286 285 +CONECT 287 295 296 284 288 +CONECT 288 287 289 290 +CONECT 289 298 288 292 +CONECT 290 288 297 291 +CONECT 291 292 290 299 +CONECT 292 289 291 881 +CONECT 293 283 +CONECT 294 284 +CONECT 295 287 +CONECT 296 287 +CONECT 297 290 +CONECT 298 289 +CONECT 299 291 +CONECT 300 302 285 301 +CONECT 301 300 +CONECT 302 313 303 300 304 +CONECT 303 302 +CONECT 304 302 307 306 305 +CONECT 305 304 +CONECT 306 304 +CONECT 307 309 310 304 308 +CONECT 308 307 +CONECT 309 307 +CONECT 310 311 307 312 +CONECT 311 310 +CONECT 312 310 +CONECT 313 315 314 302 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 323 319 318 315 +CONECT 318 317 +CONECT 319 322 321 317 320 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 325 324 317 +CONECT 324 323 +CONECT 325 327 326 323 +CONECT 326 325 +CONECT 327 339 329 328 325 +CONECT 328 327 +CONECT 329 330 335 327 331 +CONECT 330 329 +CONECT 331 329 332 334 333 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 338 337 329 336 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 340 341 327 +CONECT 340 339 +CONECT 341 343 339 342 +CONECT 342 341 +CONECT 343 345 344 351 341 +CONECT 344 343 +CONECT 345 348 346 347 343 +CONECT 346 345 +CONECT 347 345 +CONECT 348 349 350 345 +CONECT 349 348 +CONECT 350 348 +CONECT 351 343 353 352 +CONECT 352 351 +CONECT 353 354 351 355 +CONECT 354 353 +CONECT 355 353 375 374 356 +CONECT 356 357 358 359 355 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 360 373 +CONECT 360 359 361 362 +CONECT 361 360 +CONECT 362 360 363 364 +CONECT 363 362 +CONECT 364 362 365 373 +CONECT 365 364 366 367 +CONECT 366 365 +CONECT 367 365 368 369 +CONECT 368 367 +CONECT 369 367 370 371 +CONECT 370 369 +CONECT 371 369 372 373 +CONECT 372 371 +CONECT 373 359 364 371 +CONECT 374 355 +CONECT 375 377 355 376 +CONECT 376 375 +CONECT 377 378 379 375 +CONECT 378 377 +CONECT 379 381 377 380 385 +CONECT 380 379 +CONECT 381 383 382 384 379 +CONECT 382 381 +CONECT 383 381 +CONECT 384 381 +CONECT 385 379 386 387 +CONECT 386 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 391 390 400 +CONECT 390 389 +CONECT 391 394 389 392 393 +CONECT 392 391 +CONECT 393 391 +CONECT 394 395 397 396 391 +CONECT 395 394 +CONECT 396 394 +CONECT 397 399 394 398 +CONECT 398 397 +CONECT 399 397 +CONECT 400 389 402 401 +CONECT 401 400 +CONECT 402 403 400 404 +CONECT 403 402 +CONECT 404 402 406 410 405 +CONECT 405 404 +CONECT 406 407 408 404 409 +CONECT 407 406 +CONECT 408 406 +CONECT 409 406 +CONECT 410 412 404 411 +CONECT 411 410 +CONECT 412 413 414 410 +CONECT 413 412 +CONECT 414 416 412 415 425 +CONECT 415 414 +CONECT 416 417 418 419 414 +CONECT 417 416 +CONECT 418 416 +CONECT 419 422 416 421 420 +CONECT 420 419 +CONECT 421 419 +CONECT 422 423 424 419 +CONECT 423 422 +CONECT 424 422 +CONECT 425 414 427 426 +CONECT 426 425 +CONECT 427 428 425 429 +CONECT 428 427 +CONECT 429 427 431 430 447 +CONECT 430 429 +CONECT 431 434 432 433 429 +CONECT 432 431 +CONECT 433 431 +CONECT 434 437 436 435 431 +CONECT 435 434 +CONECT 436 434 +CONECT 437 440 438 434 439 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 442 441 437 +CONECT 441 440 +CONECT 442 440 +CONECT 443 446 445 444 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 +CONECT 447 429 449 448 +CONECT 448 447 +CONECT 449 450 447 451 +CONECT 450 449 +CONECT 451 449 453 452 467 +CONECT 452 451 +CONECT 453 456 454 451 455 +CONECT 454 453 +CONECT 455 453 +CONECT 456 457 465 453 +CONECT 457 459 458 456 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 462 459 463 +CONECT 462 461 +CONECT 463 461 464 465 +CONECT 464 463 +CONECT 465 463 456 466 +CONECT 466 465 +CONECT 467 451 469 468 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 473 469 481 472 +CONECT 472 471 +CONECT 473 474 479 475 471 +CONECT 474 473 +CONECT 475 476 473 477 478 +CONECT 476 475 +CONECT 477 475 +CONECT 478 475 +CONECT 479 480 473 +CONECT 480 479 +CONECT 481 483 471 482 +CONECT 482 481 +CONECT 483 484 485 481 +CONECT 484 483 +CONECT 485 487 483 486 503 +CONECT 486 485 +CONECT 487 490 488 489 485 +CONECT 488 487 +CONECT 489 487 +CONECT 490 493 492 491 487 +CONECT 491 490 +CONECT 492 490 +CONECT 493 496 494 495 490 +CONECT 494 493 +CONECT 495 493 +CONECT 496 498 499 497 493 +CONECT 497 496 +CONECT 498 496 +CONECT 499 501 496 500 502 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 485 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 508 513 +CONECT 508 507 +CONECT 509 511 512 507 510 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 507 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 534 533 518 +CONECT 518 519 520 521 517 +CONECT 519 518 +CONECT 520 518 +CONECT 521 518 522 523 524 +CONECT 522 521 +CONECT 523 521 +CONECT 524 521 525 526 527 +CONECT 525 524 +CONECT 526 524 +CONECT 527 524 528 529 530 +CONECT 528 527 +CONECT 529 527 +CONECT 530 527 531 532 +CONECT 531 530 +CONECT 532 530 +CONECT 533 517 +CONECT 534 536 517 535 +CONECT 535 534 +CONECT 536 537 538 534 +CONECT 537 536 +CONECT 538 540 536 544 539 +CONECT 539 538 +CONECT 540 541 542 543 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 +CONECT 544 546 538 545 +CONECT 545 544 +CONECT 546 547 548 544 +CONECT 547 546 +CONECT 548 550 546 549 558 +CONECT 549 548 +CONECT 550 553 551 552 548 +CONECT 551 550 +CONECT 552 550 +CONECT 553 555 554 550 +CONECT 554 553 +CONECT 555 557 556 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 548 560 559 +CONECT 559 558 +CONECT 560 561 558 562 +CONECT 561 560 +CONECT 562 560 563 564 570 +CONECT 563 562 +CONECT 564 565 562 567 566 +CONECT 565 564 +CONECT 566 564 +CONECT 567 568 569 564 +CONECT 568 567 +CONECT 569 567 +CONECT 570 562 572 571 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 592 591 575 +CONECT 575 576 577 578 574 +CONECT 576 575 +CONECT 577 575 +CONECT 578 575 579 580 581 +CONECT 579 578 +CONECT 580 578 +CONECT 581 578 582 583 584 +CONECT 582 581 +CONECT 583 581 +CONECT 584 581 585 586 587 +CONECT 585 584 +CONECT 586 584 +CONECT 587 584 588 589 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 574 +CONECT 592 594 574 593 +CONECT 593 592 +CONECT 594 595 596 592 +CONECT 595 594 +CONECT 596 599 598 594 597 +CONECT 597 596 +CONECT 598 596 +CONECT 599 601 600 596 +CONECT 600 599 +CONECT 601 603 602 599 +CONECT 602 601 +CONECT 603 623 622 601 604 +CONECT 604 605 606 607 603 +CONECT 605 604 +CONECT 606 604 +CONECT 607 604 608 609 610 +CONECT 608 607 +CONECT 609 607 +CONECT 610 607 611 612 613 +CONECT 611 610 +CONECT 612 610 +CONECT 613 610 614 615 +CONECT 614 613 +CONECT 615 613 616 619 +CONECT 616 615 617 618 +CONECT 617 616 +CONECT 618 616 +CONECT 619 615 620 621 +CONECT 620 619 +CONECT 621 619 +CONECT 622 603 +CONECT 623 625 624 603 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 629 635 628 625 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 632 +CONECT 635 636 637 627 +CONECT 636 635 +CONECT 637 639 635 638 +CONECT 638 637 +CONECT 639 642 640 641 637 +CONECT 640 639 +CONECT 641 639 +CONECT 642 644 643 639 +CONECT 643 642 +CONECT 644 646 645 642 +CONECT 645 644 +CONECT 646 648 647 657 644 +CONECT 647 646 +CONECT 648 650 651 649 646 +CONECT 649 648 +CONECT 650 648 +CONECT 651 653 654 648 652 +CONECT 652 651 +CONECT 653 651 +CONECT 654 655 651 656 +CONECT 655 654 +CONECT 656 654 +CONECT 657 659 646 658 +CONECT 658 657 +CONECT 659 660 661 657 +CONECT 660 659 +CONECT 661 681 659 680 662 +CONECT 662 663 664 665 661 +CONECT 663 662 +CONECT 664 662 +CONECT 665 662 666 667 668 +CONECT 666 665 +CONECT 667 665 +CONECT 668 665 669 670 671 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 672 673 +CONECT 672 671 +CONECT 673 671 674 677 +CONECT 674 673 675 676 +CONECT 675 674 +CONECT 676 674 +CONECT 677 673 678 679 +CONECT 678 677 +CONECT 679 677 +CONECT 680 661 +CONECT 681 682 683 661 +CONECT 682 681 +CONECT 683 685 681 684 +CONECT 684 683 +CONECT 685 686 687 695 683 +CONECT 686 685 +CONECT 687 689 693 685 688 +CONECT 688 687 +CONECT 689 692 691 690 687 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 +CONECT 693 687 694 +CONECT 694 693 +CONECT 695 697 685 696 +CONECT 696 695 +CONECT 697 698 699 695 +CONECT 698 697 +CONECT 699 714 697 713 700 +CONECT 700 701 702 706 699 +CONECT 701 700 +CONECT 702 700 703 704 705 +CONECT 703 702 +CONECT 704 702 +CONECT 705 702 +CONECT 706 700 707 708 709 +CONECT 707 706 +CONECT 708 706 +CONECT 709 706 710 711 712 +CONECT 710 709 +CONECT 711 709 +CONECT 712 709 +CONECT 713 699 +CONECT 714 715 716 699 +CONECT 715 714 +CONECT 716 718 714 717 +CONECT 717 716 +CONECT 718 719 726 720 716 +CONECT 719 718 +CONECT 720 723 718 721 722 +CONECT 721 720 +CONECT 722 720 +CONECT 723 725 724 720 +CONECT 724 723 +CONECT 725 723 +CONECT 726 728 718 727 +CONECT 727 726 +CONECT 728 729 730 726 +CONECT 729 728 +CONECT 730 732 728 738 731 +CONECT 731 730 +CONECT 732 734 735 733 730 +CONECT 733 732 +CONECT 734 732 +CONECT 735 736 732 737 +CONECT 736 735 +CONECT 737 735 +CONECT 738 740 730 739 +CONECT 739 738 +CONECT 740 741 742 738 +CONECT 741 740 +CONECT 742 744 743 740 748 +CONECT 743 742 +CONECT 744 747 745 746 742 +CONECT 745 744 +CONECT 746 744 +CONECT 747 744 +CONECT 748 742 749 750 +CONECT 749 748 +CONECT 750 748 751 752 +CONECT 751 750 +CONECT 752 750 753 754 762 +CONECT 753 752 +CONECT 754 756 752 760 755 +CONECT 755 754 +CONECT 756 758 759 757 754 +CONECT 757 756 +CONECT 758 756 +CONECT 759 756 +CONECT 760 761 754 +CONECT 761 760 +CONECT 762 752 764 763 +CONECT 763 762 +CONECT 764 765 766 762 +CONECT 765 764 +CONECT 766 767 764 768 784 +CONECT 767 766 +CONECT 768 771 766 770 769 +CONECT 769 768 +CONECT 770 768 +CONECT 771 774 772 773 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 777 776 775 771 +CONECT 775 774 +CONECT 776 774 +CONECT 777 780 779 778 774 +CONECT 778 777 +CONECT 779 777 +CONECT 780 782 781 783 777 +CONECT 781 780 +CONECT 782 780 +CONECT 783 780 +CONECT 784 766 786 785 +CONECT 785 784 +CONECT 786 787 784 788 +CONECT 787 786 +CONECT 788 786 798 790 789 +CONECT 789 788 +CONECT 790 791 788 796 792 +CONECT 791 790 +CONECT 792 790 793 794 795 +CONECT 793 792 +CONECT 794 792 +CONECT 795 792 +CONECT 796 797 790 +CONECT 797 796 +CONECT 798 799 788 800 +CONECT 799 798 +CONECT 800 798 802 801 +CONECT 801 800 +CONECT 802 803 800 804 818 +CONECT 803 802 +CONECT 804 807 802 806 805 +CONECT 805 804 +CONECT 806 804 +CONECT 807 816 808 804 +CONECT 808 810 807 809 +CONECT 809 808 +CONECT 810 812 811 808 +CONECT 811 810 +CONECT 812 813 814 810 +CONECT 813 812 +CONECT 814 815 812 816 +CONECT 815 814 +CONECT 816 814 817 807 +CONECT 817 816 +CONECT 818 802 820 819 +CONECT 819 818 +CONECT 820 821 818 822 +CONECT 821 820 +CONECT 822 820 824 832 823 +CONECT 823 822 +CONECT 824 830 826 825 822 +CONECT 825 824 +CONECT 826 827 829 824 828 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 +CONECT 830 831 824 +CONECT 831 830 +CONECT 832 833 822 834 +CONECT 833 832 +CONECT 834 832 836 835 +CONECT 835 834 +CONECT 836 846 845 834 837 +CONECT 837 838 839 843 836 +CONECT 838 837 +CONECT 839 837 840 841 842 +CONECT 840 839 +CONECT 841 839 +CONECT 842 839 +CONECT 843 837 844 +CONECT 844 843 +CONECT 845 836 +CONECT 846 848 847 836 +CONECT 847 846 +CONECT 848 850 849 846 +CONECT 849 848 +CONECT 850 862 848 863 851 +CONECT 851 852 853 854 850 +CONECT 852 851 +CONECT 853 851 +CONECT 854 851 855 856 857 +CONECT 855 854 +CONECT 856 854 +CONECT 857 854 858 859 +CONECT 858 857 +CONECT 859 857 860 861 +CONECT 860 859 +CONECT 861 859 +CONECT 862 850 +CONECT 863 850 865 864 +CONECT 864 863 +CONECT 865 866 863 867 +CONECT 866 865 +CONECT 867 869 865 878 868 +CONECT 868 867 +CONECT 869 871 870 872 867 +CONECT 870 869 +CONECT 871 869 +CONECT 872 873 869 874 875 +CONECT 873 872 +CONECT 874 872 +CONECT 875 872 876 877 +CONECT 876 875 +CONECT 877 875 +CONECT 878 880 867 879 +CONECT 879 878 +CONECT 880 878 +CONECT 881 87 292 882 261 +CONECT 882 881 884 +CONECT 883 886 884 887 885 +CONECT 884 882 883 +CONECT 885 883 +CONECT 886 883 +CONECT 887 883 +CONECT 888 889 +CONECT 889 888 890 +CONECT 890 889 +MASTER 0 0 0 0 0 0 0 0 890 0 890 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_20.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_20.pdb new file mode 100644 index 0000000..3e3a39f --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_20.pdb @@ -0,0 +1,1809 @@ +COMPND fitness: -6.0817 20.353333333334376 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 57.635 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.733 37.882 23.487 1.00 0.00 N +ATOM 2 H1 MET 1 14.720 38.282 24.421 1.00 0.00 H +ATOM 3 H2 MET 1 13.917 38.184 22.981 1.00 0.00 H +ATOM 4 H3 MET 1 15.578 38.225 23.048 1.00 0.00 H +ATOM 5 CA MET 1 14.792 36.416 23.590 1.00 0.00 C +ATOM 6 HA MET 1 13.860 36.073 24.043 1.00 0.00 H +ATOM 7 CB MET 1 14.935 35.769 22.200 1.00 0.00 C +ATOM 8 HB2 MET 1 14.056 36.020 21.608 1.00 0.00 H +ATOM 9 HB3 MET 1 15.812 36.185 21.703 1.00 0.00 H +ATOM 10 CG MET 1 15.084 34.237 22.253 1.00 0.00 C +ATOM 11 HG2 MET 1 15.984 33.994 22.819 1.00 0.00 H +ATOM 12 HG3 MET 1 14.229 33.815 22.784 1.00 0.00 H +ATOM 13 SD MET 1 15.224 33.412 20.642 1.00 0.00 S +ATOM 14 CE MET 1 13.528 33.568 20.007 1.00 0.00 C +ATOM 15 HE1 MET 1 13.252 34.619 19.925 1.00 0.00 H +ATOM 16 HE2 MET 1 13.470 33.110 19.019 1.00 0.00 H +ATOM 17 HE3 MET 1 12.834 33.058 20.677 1.00 0.00 H +ATOM 18 C MET 1 15.936 36.005 24.507 1.00 0.00 C +ATOM 19 O MET 1 17.078 36.384 24.271 1.00 0.00 O +ATOM 20 N GLN 2 15.645 35.165 25.501 1.00 0.00 N +ATOM 21 H GLN 2 14.682 34.927 25.672 1.00 0.00 H +ATOM 22 CA GLN 2 16.644 34.489 26.336 1.00 0.00 C +ATOM 23 HA GLN 2 17.396 35.209 26.661 1.00 0.00 H +ATOM 24 CB GLN 2 15.935 33.928 27.585 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.024 33.420 27.268 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.558 33.181 28.069 1.00 0.00 H +ATOM 27 CG GLN 2 15.561 35.011 28.619 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.143 35.874 28.111 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.784 34.607 29.268 1.00 0.00 H +ATOM 30 CD GLN 2 16.722 35.475 29.503 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.877 35.132 29.322 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.441 36.244 30.539 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.204 36.508 31.135 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.510 36.614 30.647 1.00 0.00 H +ATOM 35 C GLN 2 17.377 33.385 25.538 1.00 0.00 C +ATOM 36 O GLN 2 17.008 32.211 25.600 1.00 0.00 O +ATOM 37 N TYR 3 18.411 33.757 24.773 1.00 0.00 N +ATOM 38 H TYR 3 18.672 34.739 24.786 1.00 0.00 H +ATOM 39 CA TYR 3 19.290 32.821 24.056 1.00 0.00 C +ATOM 40 HA TYR 3 18.687 32.202 23.392 1.00 0.00 H +ATOM 41 CB TYR 3 20.314 33.591 23.210 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.781 34.366 23.822 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.106 32.902 22.911 1.00 0.00 H +ATOM 44 CG TYR 3 19.746 34.218 21.951 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.727 33.473 20.755 1.00 0.00 C +ATOM 46 HD1 TYR 3 20.111 32.461 20.742 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.227 34.046 19.571 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.233 33.479 18.651 1.00 0.00 H +ATOM 49 CZ TYR 3 18.735 35.368 19.584 1.00 0.00 C +ATOM 50 OH TYR 3 18.259 35.920 18.438 1.00 0.00 O +ATOM 51 HH TYR 3 18.372 35.323 17.696 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.746 36.113 20.783 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.372 37.126 20.782 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.256 35.539 21.964 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.271 36.115 22.881 1.00 0.00 H +ATOM 56 C TYR 3 20.018 31.899 25.043 1.00 0.00 C +ATOM 57 O TYR 3 20.478 32.355 26.091 1.00 0.00 O +ATOM 58 N LYS 4 20.122 30.602 24.736 1.00 0.00 N +ATOM 59 H LYS 4 19.879 30.316 23.790 1.00 0.00 H +ATOM 60 CA LYS 4 20.697 29.575 25.621 1.00 0.00 C +ATOM 61 HA LYS 4 20.441 29.816 26.648 1.00 0.00 H +ATOM 62 CB LYS 4 20.088 28.193 25.283 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.074 28.074 24.201 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.747 27.416 25.673 1.00 0.00 H +ATOM 65 CG LYS 4 18.667 27.898 25.823 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.435 26.863 25.567 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.670 27.976 26.910 1.00 0.00 H +ATOM 68 CD LYS 4 17.550 28.787 25.246 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.638 29.791 25.652 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.697 28.849 24.166 1.00 0.00 H +ATOM 71 CE LYS 4 16.121 28.258 25.489 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.439 28.816 24.841 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.075 27.212 25.171 1.00 0.00 H +ATOM 74 NZ LYS 4 15.648 28.384 26.896 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.624 29.346 27.209 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.690 28.033 26.984 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.209 27.851 27.541 1.00 0.00 H +ATOM 78 C LYS 4 22.232 29.571 25.565 1.00 0.00 C +ATOM 79 O LYS 4 22.854 29.936 24.571 1.00 0.00 O +HETATM 80 N HX1 5 22.870 29.128 26.642 1.00 0.00 N +HETATM 81 CA HX1 5 24.329 28.970 26.748 1.00 0.00 C +HETATM 82 C HX1 5 24.643 27.769 27.648 1.00 0.00 C +HETATM 83 O HX1 5 24.244 27.738 28.816 1.00 0.00 O +HETATM 84 CB HX1 5 24.952 30.290 27.252 1.00 0.00 C +HETATM 85 CG HX1 5 26.469 30.362 27.332 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.363 29.390 26.957 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.175 31.429 27.911 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.466 31.053 27.849 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.604 29.819 27.344 1.00 0.00 N +HETATM 90 H HX1 5 22.310 28.953 27.474 1.00 0.00 H +HETATM 91 HA HX1 5 24.742 28.771 25.757 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.550 30.512 28.241 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.620 31.090 26.587 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.157 28.428 26.510 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.281 31.619 28.276 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.424 29.221 27.483 1.00 0.00 H +ATOM 97 N ILE 6 25.307 26.763 27.077 1.00 0.00 N +ATOM 98 H ILE 6 25.595 26.868 26.108 1.00 0.00 H +ATOM 99 CA ILE 6 25.765 25.537 27.739 1.00 0.00 C +ATOM 100 HA ILE 6 25.204 25.422 28.669 1.00 0.00 H +ATOM 101 CB ILE 6 25.436 24.296 26.867 1.00 0.00 C +ATOM 102 HB ILE 6 25.850 24.459 25.873 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.032 22.983 27.418 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.637 22.772 28.412 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.788 22.152 26.759 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.120 23.033 27.448 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.895 24.171 26.756 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.472 24.073 27.756 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.490 25.081 26.313 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.388 22.996 25.911 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.540 22.055 26.442 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.319 23.119 25.730 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.912 22.966 24.955 1.00 0.00 H +ATOM 114 C ILE 6 27.247 25.665 28.145 1.00 0.00 C +ATOM 115 O ILE 6 28.018 26.445 27.588 1.00 0.00 O +ATOM 116 N VAL 7 27.582 24.926 29.196 1.00 0.00 N +ATOM 117 H VAL 7 26.882 24.256 29.481 1.00 0.00 H +ATOM 118 CA VAL 7 28.693 25.074 30.145 1.00 0.00 C +ATOM 119 HA VAL 7 28.730 26.129 30.427 1.00 0.00 H +ATOM 120 CB VAL 7 28.269 24.252 31.383 1.00 0.00 C +ATOM 121 HB VAL 7 27.375 24.724 31.800 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.921 22.783 31.084 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.772 22.277 30.631 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.655 22.280 32.005 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.065 22.703 30.419 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.319 24.238 32.489 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.739 25.230 32.636 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.842 23.896 33.399 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.109 23.538 32.226 1.00 0.00 H +ATOM 130 C VAL 7 30.116 24.724 29.656 1.00 0.00 C +ATOM 131 O VAL 7 30.321 23.777 28.892 1.00 0.00 O +ATOM 132 N ARG 8 31.114 25.464 30.176 1.00 0.00 N +ATOM 133 H ARG 8 30.841 26.310 30.657 1.00 0.00 H +ATOM 134 CA ARG 8 32.562 25.170 30.097 1.00 0.00 C +ATOM 135 HA ARG 8 32.796 25.020 29.044 1.00 0.00 H +ATOM 136 CB ARG 8 33.382 26.389 30.594 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.429 26.228 30.338 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.049 27.280 30.060 1.00 0.00 H +ATOM 139 CG ARG 8 33.292 26.662 32.117 1.00 0.00 C +ATOM 140 HG2 ARG 8 32.247 26.789 32.405 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.686 25.797 32.656 1.00 0.00 H +ATOM 142 CD ARG 8 34.100 27.882 32.598 1.00 0.00 C +ATOM 143 HD2 ARG 8 34.176 27.848 33.685 1.00 0.00 H +ATOM 144 HD3 ARG 8 35.110 27.811 32.195 1.00 0.00 H +ATOM 145 NE ARG 8 33.481 29.172 32.178 1.00 0.00 N +ATOM 146 HE ARG 8 33.844 29.587 31.325 1.00 0.00 H +ATOM 147 CZ ARG 8 32.373 29.703 32.657 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.806 29.364 33.755 1.00 0.00 N +ATOM 149 HH11 ARG 8 32.352 28.885 34.476 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.001 29.880 34.044 1.00 0.00 H +ATOM 151 NH2 ARG 8 31.748 30.634 31.987 1.00 0.00 N +ATOM 152 HH21 ARG 8 32.205 30.945 31.139 1.00 0.00 H +ATOM 153 HH22 ARG 8 30.748 30.522 31.964 1.00 0.00 H +ATOM 154 C ARG 8 32.972 23.881 30.836 1.00 0.00 C +ATOM 155 O ARG 8 32.549 23.638 31.967 1.00 0.00 O +ATOM 156 N GLY 9 33.890 23.108 30.255 1.00 0.00 N +ATOM 157 H GLY 9 34.198 23.350 29.326 1.00 0.00 H +ATOM 158 CA GLY 9 34.391 21.854 30.838 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.308 21.559 30.325 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.637 22.026 31.888 1.00 0.00 H +ATOM 161 C GLY 9 33.396 20.684 30.754 1.00 0.00 C +ATOM 162 O GLY 9 32.449 20.720 29.972 1.00 0.00 O +ATOM 163 N LYS 10 33.639 19.625 31.545 1.00 0.00 N +ATOM 164 H LYS 10 34.488 19.655 32.090 1.00 0.00 H +ATOM 165 CA LYS 10 32.906 18.337 31.474 1.00 0.00 C +ATOM 166 HA LYS 10 31.963 18.519 30.949 1.00 0.00 H +ATOM 167 CB LYS 10 33.740 17.356 30.619 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.365 17.937 29.938 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.403 16.783 31.269 1.00 0.00 H +ATOM 170 CG LYS 10 32.913 16.392 29.747 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.321 15.725 30.375 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.238 16.974 29.117 1.00 0.00 H +ATOM 173 CD LYS 10 33.859 15.570 28.853 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.548 16.251 28.351 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.435 14.886 29.473 1.00 0.00 H +ATOM 176 CE LYS 10 33.121 14.760 27.787 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.528 13.981 28.271 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.444 15.431 27.261 1.00 0.00 H +ATOM 179 NZ LYS 10 34.072 14.174 26.810 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.742 13.560 27.248 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.613 13.667 26.073 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.618 14.909 26.346 1.00 0.00 H +ATOM 183 C LYS 10 32.507 17.744 32.842 1.00 0.00 C +ATOM 184 O LYS 10 32.043 16.613 32.910 1.00 0.00 O +ATOM 185 N ILE 11 32.726 18.481 33.941 1.00 0.00 N +ATOM 186 H ILE 11 33.131 19.391 33.802 1.00 0.00 H +ATOM 187 CA ILE 11 32.393 18.074 35.332 1.00 0.00 C +ATOM 188 HA ILE 11 32.239 16.994 35.354 1.00 0.00 H +ATOM 189 CB ILE 11 33.556 18.396 36.299 1.00 0.00 C +ATOM 190 HB ILE 11 33.214 18.149 37.306 1.00 0.00 H +ATOM 191 CG2 ILE 11 34.762 17.492 36.001 1.00 0.00 C +ATOM 192 HG21 ILE 11 35.184 17.726 35.028 1.00 0.00 H +ATOM 193 HG22 ILE 11 35.525 17.626 36.764 1.00 0.00 H +ATOM 194 HG23 ILE 11 34.447 16.450 36.018 1.00 0.00 H +ATOM 195 CG1 ILE 11 33.922 19.899 36.281 1.00 0.00 C +ATOM 196 HG12 ILE 11 34.441 20.140 35.352 1.00 0.00 H +ATOM 197 HG13 ILE 11 33.009 20.495 36.322 1.00 0.00 H +ATOM 198 CD1 ILE 11 34.794 20.331 37.465 1.00 0.00 C +ATOM 199 HD11 ILE 11 35.761 19.829 37.430 1.00 0.00 H +ATOM 200 HD12 ILE 11 34.956 21.408 37.415 1.00 0.00 H +ATOM 201 HD13 ILE 11 34.288 20.093 38.402 1.00 0.00 H +ATOM 202 C ILE 11 31.078 18.677 35.871 1.00 0.00 C +ATOM 203 O ILE 11 30.598 18.265 36.924 1.00 0.00 O +ATOM 204 N ARG 12 30.502 19.644 35.152 1.00 0.00 N +ATOM 205 H ARG 12 30.918 19.878 34.255 1.00 0.00 H +ATOM 206 CA ARG 12 29.173 20.218 35.372 1.00 0.00 C +ATOM 207 HA ARG 12 28.595 19.556 36.008 1.00 0.00 H +ATOM 208 CB ARG 12 29.273 21.602 36.083 1.00 0.00 C +ATOM 209 HB2 ARG 12 28.289 22.053 36.075 1.00 0.00 H +ATOM 210 HB3 ARG 12 29.525 21.440 37.127 1.00 0.00 H +ATOM 211 CG ARG 12 30.283 22.581 35.505 1.00 0.00 C +ATOM 212 HG2 ARG 12 31.289 22.212 35.712 1.00 0.00 H +ATOM 213 HG3 ARG 12 30.227 22.593 34.426 1.00 0.00 H +ATOM 214 CD ARG 12 30.190 24.017 36.052 1.00 0.00 C +ATOM 215 HD2 ARG 12 30.509 23.998 37.086 1.00 0.00 H +ATOM 216 HD3 ARG 12 30.902 24.643 35.520 1.00 0.00 H +ATOM 217 NE ARG 12 28.857 24.665 35.907 1.00 0.00 N +ATOM 218 HE ARG 12 28.040 24.115 36.225 1.00 0.00 H +ATOM 219 CZ ARG 12 28.548 25.833 35.383 1.00 0.00 C +ATOM 220 NH1 ARG 12 29.423 26.658 34.869 1.00 0.00 N +ATOM 221 HH11 ARG 12 30.403 26.407 34.843 1.00 0.00 H +ATOM 222 HH12 ARG 12 29.115 27.513 34.414 1.00 0.00 H +ATOM 223 NH2 ARG 12 27.323 26.195 35.368 1.00 0.00 N +ATOM 224 HH21 ARG 12 26.614 25.556 35.771 1.00 0.00 H +ATOM 225 HH22 ARG 12 27.036 27.126 35.109 1.00 0.00 H +ATOM 226 C ARG 12 28.461 20.286 34.022 1.00 0.00 C +ATOM 227 O ARG 12 29.143 20.403 33.007 1.00 0.00 O +ATOM 228 N LYS 13 27.130 20.155 34.004 1.00 0.00 N +ATOM 229 H LYS 13 26.659 20.093 34.900 1.00 0.00 H +ATOM 230 CA LYS 13 26.345 19.829 32.783 1.00 0.00 C +ATOM 231 HA LYS 13 26.972 20.020 31.904 1.00 0.00 H +ATOM 232 CB LYS 13 26.021 18.312 32.799 1.00 0.00 C +ATOM 233 HB2 LYS 13 26.877 17.786 33.229 1.00 0.00 H +ATOM 234 HB3 LYS 13 25.159 18.146 33.449 1.00 0.00 H +ATOM 235 CG LYS 13 25.761 17.694 31.407 1.00 0.00 C +ATOM 236 HG2 LYS 13 24.874 18.132 30.949 1.00 0.00 H +ATOM 237 HG3 LYS 13 26.617 17.908 30.765 1.00 0.00 H +ATOM 238 CD LYS 13 25.580 16.165 31.479 1.00 0.00 C +ATOM 239 HD2 LYS 13 25.574 15.760 30.468 1.00 0.00 H +ATOM 240 HD3 LYS 13 26.429 15.736 32.015 1.00 0.00 H +ATOM 241 CE LYS 13 24.270 15.762 32.173 1.00 0.00 C +ATOM 242 HE2 LYS 13 24.118 16.413 33.037 1.00 0.00 H +ATOM 243 HE3 LYS 13 23.435 15.933 31.486 1.00 0.00 H +ATOM 244 NZ LYS 13 24.284 14.348 32.635 1.00 0.00 N +ATOM 245 HZ1 LYS 13 25.139 14.120 33.125 1.00 0.00 H +ATOM 246 HZ2 LYS 13 23.571 14.204 33.351 1.00 0.00 H +ATOM 247 HZ3 LYS 13 24.129 13.671 31.896 1.00 0.00 H +ATOM 248 C LYS 13 25.095 20.711 32.575 1.00 0.00 C +ATOM 249 O LYS 13 24.268 20.427 31.713 1.00 0.00 O +ATOM 250 N GLY 14 24.924 21.755 33.388 1.00 0.00 N +ATOM 251 H GLY 14 25.618 21.963 34.092 1.00 0.00 H +ATOM 252 CA GLY 14 23.761 22.636 33.327 1.00 0.00 C +ATOM 253 HA2 GLY 14 22.862 22.035 33.199 1.00 0.00 H +ATOM 254 HA3 GLY 14 23.649 23.171 34.265 1.00 0.00 H +ATOM 255 C GLY 14 23.799 23.677 32.204 1.00 0.00 C +ATOM 256 O GLY 14 24.756 23.814 31.437 1.00 0.00 O +ATOM 257 N VAL 15 22.713 24.445 32.139 1.00 0.00 N +ATOM 258 H VAL 15 22.005 24.307 32.849 1.00 0.00 H +ATOM 259 CA VAL 15 22.410 25.410 31.079 1.00 0.00 C +ATOM 260 HA VAL 15 23.331 25.644 30.549 1.00 0.00 H +ATOM 261 CB VAL 15 21.440 24.772 30.055 1.00 0.00 C +ATOM 262 HB VAL 15 21.934 23.889 29.642 1.00 0.00 H +ATOM 263 CG1 VAL 15 20.113 24.307 30.679 1.00 0.00 C +ATOM 264 HG11 VAL 15 19.568 25.147 31.104 1.00 0.00 H +ATOM 265 HG12 VAL 15 19.500 23.827 29.914 1.00 0.00 H +ATOM 266 HG13 VAL 15 20.302 23.566 31.456 1.00 0.00 H +ATOM 267 CG2 VAL 15 21.118 25.708 28.883 1.00 0.00 C +ATOM 268 HG21 VAL 15 22.041 26.075 28.436 1.00 0.00 H +ATOM 269 HG22 VAL 15 20.567 25.151 28.123 1.00 0.00 H +ATOM 270 HG23 VAL 15 20.507 26.545 29.214 1.00 0.00 H +ATOM 271 C VAL 15 21.879 26.704 31.693 1.00 0.00 C +ATOM 272 O VAL 15 21.217 26.687 32.729 1.00 0.00 O +HETATM 273 N HY1 16 22.181 27.843 31.069 1.00 0.00 N +HETATM 274 CA HY1 16 21.642 29.167 31.419 1.00 0.00 C +HETATM 275 C HY1 16 21.359 29.960 30.142 1.00 0.00 C +HETATM 276 O HY1 16 21.534 29.440 29.036 1.00 0.00 O +HETATM 277 CB HY1 16 22.607 29.888 32.385 1.00 0.00 C +HETATM 278 CG HY1 16 23.957 30.212 31.792 1.00 0.00 C +HETATM 279 CD2 HY1 16 24.370 31.432 31.323 1.00 0.00 C +HETATM 280 ND1 HY1 16 24.989 29.326 31.583 1.00 0.00 N +HETATM 281 CE1 HY1 16 26.006 30.011 31.032 1.00 0.00 C +HETATM 282 NE2 HY1 16 25.680 31.302 30.840 1.00 0.00 N +HETATM 283 H HY1 16 22.717 27.790 30.202 1.00 0.00 H +HETATM 284 HA HY1 16 20.690 29.029 31.943 1.00 0.00 H +HETATM 285 HB2 HY1 16 22.143 30.817 32.728 1.00 0.00 H +HETATM 286 HB3 HY1 16 22.751 29.274 33.274 1.00 0.00 H +HETATM 287 HD1 HY1 16 24.980 28.337 31.793 1.00 0.00 H +HETATM 288 HD2 HY1 16 23.782 32.341 31.320 1.00 0.00 H +HETATM 289 HE1 HY1 16 26.965 29.577 30.760 1.00 0.00 H +ATOM 290 N THR 17 20.918 31.210 30.268 1.00 0.00 N +ATOM 291 H THR 17 20.756 31.612 31.177 1.00 0.00 H +ATOM 292 CA THR 17 20.508 32.061 29.141 1.00 0.00 C +ATOM 293 HA THR 17 20.946 31.632 28.225 1.00 0.00 H +ATOM 294 CB THR 17 18.990 32.091 28.994 1.00 0.00 C +ATOM 295 HB THR 17 18.724 32.749 28.170 1.00 0.00 H +ATOM 296 CG2 THR 17 18.325 30.715 28.726 1.00 0.00 C +ATOM 297 HG21 THR 17 18.535 30.025 29.538 1.00 0.00 H +ATOM 298 HG22 THR 17 17.260 30.832 28.633 1.00 0.00 H +ATOM 299 HG23 THR 17 18.709 30.302 27.798 1.00 0.00 H +ATOM 300 OG1 THR 17 18.402 32.602 30.163 1.00 0.00 O +ATOM 301 HG1 THR 17 18.299 33.561 30.018 1.00 0.00 H +ATOM 302 C THR 17 21.065 33.480 29.240 1.00 0.00 C +ATOM 303 O THR 17 21.529 33.900 30.301 1.00 0.00 O +HETATM 304 N HY2 18 20.995 34.217 28.134 1.00 0.00 N +HETATM 305 CA HY2 18 21.280 35.652 28.047 1.00 0.00 C +HETATM 306 C HY2 18 20.166 36.342 27.251 1.00 0.00 C +HETATM 307 O HY2 18 19.832 35.890 26.156 1.00 0.00 O +HETATM 308 CB HY2 18 22.630 35.906 27.363 1.00 0.00 C +HETATM 309 CG HY2 18 23.819 35.419 28.161 1.00 0.00 C +HETATM 310 CD2 HY2 18 24.360 34.159 28.123 1.00 0.00 C +HETATM 311 ND1 HY2 18 24.511 36.125 29.124 1.00 0.00 N +HETATM 312 CE1 HY2 18 25.453 35.310 29.632 1.00 0.00 C +HETATM 313 NE2 HY2 18 25.397 34.094 29.059 1.00 0.00 N +HETATM 314 H HY2 18 20.638 33.771 27.299 1.00 0.00 H +HETATM 315 HA HY2 18 21.306 36.086 29.054 1.00 0.00 H +HETATM 316 HB2 HY2 18 22.636 35.423 26.383 1.00 0.00 H +HETATM 317 HB3 HY2 18 22.742 36.983 27.200 1.00 0.00 H +HETATM 318 HD1 HY2 18 24.354 37.089 29.396 1.00 0.00 H +HETATM 319 HD2 HY2 18 24.024 33.349 27.490 1.00 0.00 H +HETATM 320 HE1 HY2 18 26.158 35.595 30.403 1.00 0.00 H +ATOM 321 N GLU 19 19.612 37.430 27.783 1.00 0.00 N +ATOM 322 H GLU 19 19.937 37.755 28.675 1.00 0.00 H +ATOM 323 CA GLU 19 18.582 38.225 27.112 1.00 0.00 C +ATOM 324 HA GLU 19 17.856 37.548 26.670 1.00 0.00 H +ATOM 325 CB GLU 19 17.874 39.101 28.161 1.00 0.00 C +ATOM 326 HB2 GLU 19 17.541 38.465 28.981 1.00 0.00 H +ATOM 327 HB3 GLU 19 18.590 39.817 28.573 1.00 0.00 H +ATOM 328 CG GLU 19 16.656 39.877 27.634 1.00 0.00 C +ATOM 329 HG2 GLU 19 16.203 40.426 28.464 1.00 0.00 H +ATOM 330 HG3 GLU 19 16.991 40.608 26.895 1.00 0.00 H +ATOM 331 CD GLU 19 15.632 38.930 27.011 1.00 0.00 C +ATOM 332 OE1 GLU 19 15.691 38.740 25.776 1.00 0.00 O +ATOM 333 OE2 GLU 19 14.841 38.316 27.754 1.00 0.00 O +ATOM 334 C GLU 19 19.192 39.075 25.981 1.00 0.00 C +ATOM 335 O GLU 19 20.197 39.753 26.201 1.00 0.00 O +ATOM 336 N ALA 20 18.600 39.044 24.779 1.00 0.00 N +ATOM 337 H ALA 20 17.776 38.459 24.672 1.00 0.00 H +ATOM 338 CA ALA 20 18.990 39.887 23.646 1.00 0.00 C +ATOM 339 HA ALA 20 19.135 40.904 24.009 1.00 0.00 H +ATOM 340 CB ALA 20 20.320 39.383 23.066 1.00 0.00 C +ATOM 341 HB1 ALA 20 20.186 38.392 22.628 1.00 0.00 H +ATOM 342 HB2 ALA 20 20.677 40.066 22.297 1.00 0.00 H +ATOM 343 HB3 ALA 20 21.085 39.326 23.841 1.00 0.00 H +ATOM 344 C ALA 20 17.927 39.917 22.536 1.00 0.00 C +ATOM 345 O ALA 20 17.055 39.047 22.435 1.00 0.00 O +ATOM 346 N VAL 21 18.035 40.901 21.633 1.00 0.00 N +ATOM 347 H VAL 21 18.745 41.608 21.782 1.00 0.00 H +ATOM 348 CA VAL 21 17.314 40.928 20.337 1.00 0.00 C +ATOM 349 HA VAL 21 16.317 40.507 20.490 1.00 0.00 H +ATOM 350 CB VAL 21 17.119 42.380 19.833 1.00 0.00 C +ATOM 351 HB VAL 21 16.488 42.339 18.945 1.00 0.00 H +ATOM 352 CG1 VAL 21 16.394 43.247 20.872 1.00 0.00 C +ATOM 353 HG11 VAL 21 17.021 43.404 21.748 1.00 0.00 H +ATOM 354 HG12 VAL 21 16.153 44.212 20.432 1.00 0.00 H +ATOM 355 HG13 VAL 21 15.468 42.763 21.177 1.00 0.00 H +ATOM 356 CG2 VAL 21 18.437 43.072 19.442 1.00 0.00 C +ATOM 357 HG21 VAL 21 18.913 42.541 18.620 1.00 0.00 H +ATOM 358 HG22 VAL 21 18.230 44.085 19.104 1.00 0.00 H +ATOM 359 HG23 VAL 21 19.121 43.114 20.287 1.00 0.00 H +ATOM 360 C VAL 21 17.988 40.086 19.252 1.00 0.00 C +ATOM 361 O VAL 21 17.389 39.831 18.217 1.00 0.00 O +ATOM 362 N ASP 22 19.241 39.672 19.477 1.00 0.00 N +ATOM 363 H ASP 22 19.667 39.908 20.356 1.00 0.00 H +ATOM 364 CA ASP 22 20.117 39.000 18.509 1.00 0.00 C +ATOM 365 HA ASP 22 19.524 38.299 17.911 1.00 0.00 H +ATOM 366 CB ASP 22 20.737 40.055 17.575 1.00 0.00 C +ATOM 367 HB2 ASP 22 19.920 40.721 17.221 1.00 0.00 H +ATOM 368 HB3 ASP 22 21.431 40.686 18.183 1.00 0.00 H +ATOM 369 CG ASP 22 21.480 39.501 16.369 1.00 0.00 C +ATOM 370 OD1 ASP 22 21.691 40.281 15.410 1.00 0.00 O +ATOM 371 OD2 ASP 22 21.802 38.307 16.347 1.00 0.00 O +ATOM 372 C ASP 22 21.200 38.191 19.255 1.00 0.00 C +ATOM 373 O ASP 22 21.720 38.644 20.293 1.00 0.00 O +ATOM 374 N TRP 23 21.603 37.034 18.736 1.00 0.00 N +ATOM 375 H TRP 23 21.334 36.859 17.772 1.00 0.00 H +ATOM 376 CA TRP 23 22.738 36.278 19.255 1.00 0.00 C +ATOM 377 HA TRP 23 22.545 36.075 20.305 1.00 0.00 H +ATOM 378 CB TRP 23 22.860 34.923 18.525 1.00 0.00 C +ATOM 379 HB2 TRP 23 23.626 34.343 19.031 1.00 0.00 H +ATOM 380 HB3 TRP 23 21.920 34.390 18.639 1.00 0.00 H +ATOM 381 CG TRP 23 23.219 34.986 17.072 1.00 0.00 C +ATOM 382 CD1 TRP 23 22.358 34.801 16.042 1.00 0.00 C +ATOM 383 HD1 TRP 23 21.307 34.559 16.141 1.00 0.00 H +ATOM 384 NE1 TRP 23 23.019 34.998 14.846 1.00 0.00 N +ATOM 385 HE1 TRP 23 22.568 34.926 13.942 1.00 0.00 H +ATOM 386 CE2 TRP 23 24.340 35.337 15.041 1.00 0.00 C +ATOM 387 CZ2 TRP 23 25.385 35.682 14.167 1.00 0.00 C +ATOM 388 HZ2 TRP 23 25.205 35.732 13.103 1.00 0.00 H +ATOM 389 CH2 TRP 23 26.662 35.947 14.697 1.00 0.00 C +ATOM 390 HH2 TRP 23 27.478 36.209 14.036 1.00 0.00 H +ATOM 391 CZ3 TRP 23 26.882 35.845 16.083 1.00 0.00 C +ATOM 392 HZ3 TRP 23 27.865 36.041 16.487 1.00 0.00 H +ATOM 393 CE3 TRP 23 25.824 35.501 16.947 1.00 0.00 C +ATOM 394 HE3 TRP 23 26.011 35.438 18.006 1.00 0.00 H +ATOM 395 CD2 TRP 23 24.517 35.267 16.456 1.00 0.00 C +ATOM 396 C TRP 23 24.045 37.086 19.160 1.00 0.00 C +ATOM 397 O TRP 23 24.898 36.957 20.032 1.00 0.00 O +ATOM 398 N ALA 24 24.180 37.975 18.162 1.00 0.00 N +ATOM 399 H ALA 24 23.458 38.004 17.443 1.00 0.00 H +ATOM 400 CA ALA 24 25.368 38.813 17.979 1.00 0.00 C +ATOM 401 HA ALA 24 26.250 38.178 18.076 1.00 0.00 H +ATOM 402 CB ALA 24 25.346 39.355 16.545 1.00 0.00 C +ATOM 403 HB1 ALA 24 24.496 40.021 16.403 1.00 0.00 H +ATOM 404 HB2 ALA 24 26.263 39.903 16.336 1.00 0.00 H +ATOM 405 HB3 ALA 24 25.265 38.531 15.837 1.00 0.00 H +ATOM 406 C ALA 24 25.514 39.938 19.029 1.00 0.00 C +ATOM 407 O ALA 24 26.606 40.502 19.180 1.00 0.00 O +ATOM 408 N GLU 25 24.454 40.244 19.780 1.00 0.00 N +ATOM 409 H GLU 25 23.591 39.758 19.581 1.00 0.00 H +ATOM 410 CA GLU 25 24.520 41.026 21.025 1.00 0.00 C +ATOM 411 HA GLU 25 25.414 41.652 21.017 1.00 0.00 H +ATOM 412 CB GLU 25 23.296 41.956 21.127 1.00 0.00 C +ATOM 413 HB2 GLU 25 22.391 41.374 20.947 1.00 0.00 H +ATOM 414 HB3 GLU 25 23.243 42.348 22.140 1.00 0.00 H +ATOM 415 CG GLU 25 23.345 43.143 20.156 1.00 0.00 C +ATOM 416 HG2 GLU 25 23.341 42.753 19.131 1.00 0.00 H +ATOM 417 HG3 GLU 25 22.430 43.740 20.270 1.00 0.00 H +ATOM 418 CD GLU 25 24.577 44.030 20.374 1.00 0.00 C +ATOM 419 OE1 GLU 25 24.749 44.582 21.487 1.00 0.00 O +ATOM 420 OE2 GLU 25 25.405 44.097 19.435 1.00 0.00 O +ATOM 421 C GLU 25 24.640 40.109 22.257 1.00 0.00 C +ATOM 422 O GLU 25 25.417 40.418 23.158 1.00 0.00 O +ATOM 423 N ALA 26 23.983 38.945 22.291 1.00 0.00 N +ATOM 424 H ALA 26 23.327 38.720 21.542 1.00 0.00 H +ATOM 425 CA ALA 26 24.163 37.958 23.368 1.00 0.00 C +ATOM 426 HA ALA 26 23.931 38.449 24.314 1.00 0.00 H +ATOM 427 CB ALA 26 23.214 36.795 23.146 1.00 0.00 C +ATOM 428 HB1 ALA 26 23.527 36.237 22.262 1.00 0.00 H +ATOM 429 HB2 ALA 26 23.236 36.122 24.006 1.00 0.00 H +ATOM 430 HB3 ALA 26 22.198 37.172 23.004 1.00 0.00 H +ATOM 431 C ALA 26 25.614 37.449 23.491 1.00 0.00 C +ATOM 432 O ALA 26 26.020 37.084 24.593 1.00 0.00 O +ATOM 433 N GLU 27 26.387 37.470 22.400 1.00 0.00 N +ATOM 434 H GLU 27 25.912 37.567 21.509 1.00 0.00 H +ATOM 435 CA GLU 27 27.839 37.253 22.409 1.00 0.00 C +ATOM 436 HA GLU 27 28.019 36.294 22.873 1.00 0.00 H +ATOM 437 CB GLU 27 28.357 37.233 20.929 1.00 0.00 C +ATOM 438 HB2 GLU 27 27.775 36.503 20.372 1.00 0.00 H +ATOM 439 HB3 GLU 27 28.193 38.208 20.478 1.00 0.00 H +ATOM 440 CG GLU 27 29.831 36.834 20.783 1.00 0.00 C +ATOM 441 HG2 GLU 27 30.441 37.292 21.584 1.00 0.00 H +ATOM 442 HG3 GLU 27 29.892 35.745 20.925 1.00 0.00 H +ATOM 443 CD GLU 27 30.429 37.180 19.420 1.00 0.00 C +ATOM 444 OE1 GLU 27 30.994 38.286 19.282 1.00 0.00 O +ATOM 445 OE2 GLU 27 30.360 36.357 18.485 1.00 0.00 O +ATOM 446 C GLU 27 28.589 38.321 23.218 1.00 0.00 C +ATOM 447 O GLU 27 29.374 37.999 24.102 1.00 0.00 O +ATOM 448 N LYS 28 28.267 39.596 22.980 1.00 0.00 N +ATOM 449 H LYS 28 27.567 39.775 22.267 1.00 0.00 H +ATOM 450 CA LYS 28 28.829 40.742 23.719 1.00 0.00 C +ATOM 451 HA LYS 28 29.916 40.662 23.685 1.00 0.00 H +ATOM 452 CB LYS 28 28.419 42.071 23.060 1.00 0.00 C +ATOM 453 HB2 LYS 28 27.337 42.201 23.126 1.00 0.00 H +ATOM 454 HB3 LYS 28 28.894 42.872 23.622 1.00 0.00 H +ATOM 455 CG LYS 28 28.850 42.179 21.585 1.00 0.00 C +ATOM 456 HG2 LYS 28 29.918 41.970 21.513 1.00 0.00 H +ATOM 457 HG3 LYS 28 28.309 41.440 20.996 1.00 0.00 H +ATOM 458 CD LYS 28 28.572 43.582 21.017 1.00 0.00 C +ATOM 459 HD2 LYS 28 27.535 43.863 21.207 1.00 0.00 H +ATOM 460 HD3 LYS 28 29.210 44.300 21.537 1.00 0.00 H +ATOM 461 CE LYS 28 28.856 43.666 19.508 1.00 0.00 C +ATOM 462 HE2 LYS 28 28.968 44.722 19.237 1.00 0.00 H +ATOM 463 HE3 LYS 28 29.806 43.171 19.294 1.00 0.00 H +ATOM 464 NZ LYS 28 27.761 43.060 18.708 1.00 0.00 N +ATOM 465 HZ1 LYS 28 26.880 43.544 18.909 1.00 0.00 H +ATOM 466 HZ2 LYS 28 27.911 43.131 17.714 1.00 0.00 H +ATOM 467 HZ3 LYS 28 27.588 42.091 18.963 1.00 0.00 H +ATOM 468 C LYS 28 28.419 40.712 25.190 1.00 0.00 C +ATOM 469 O LYS 28 29.266 40.863 26.067 1.00 0.00 O +ATOM 470 N PHE 29 27.156 40.428 25.492 1.00 0.00 N +ATOM 471 H PHE 29 26.486 40.366 24.725 1.00 0.00 H +ATOM 472 CA PHE 29 26.664 40.284 26.870 1.00 0.00 C +ATOM 473 HA PHE 29 26.957 41.158 27.435 1.00 0.00 H +ATOM 474 CB PHE 29 25.127 40.248 26.870 1.00 0.00 C +ATOM 475 HB2 PHE 29 24.809 39.317 26.405 1.00 0.00 H +ATOM 476 HB3 PHE 29 24.776 40.238 27.908 1.00 0.00 H +ATOM 477 CG PHE 29 24.438 41.410 26.173 1.00 0.00 C +ATOM 478 CD1 PHE 29 23.210 41.197 25.509 1.00 0.00 C +ATOM 479 HD1 PHE 29 22.752 40.217 25.521 1.00 0.00 H +ATOM 480 CE1 PHE 29 22.579 42.248 24.814 1.00 0.00 C +ATOM 481 HE1 PHE 29 21.657 42.062 24.297 1.00 0.00 H +ATOM 482 CZ PHE 29 23.176 43.521 24.778 1.00 0.00 C +ATOM 483 HZ PHE 29 22.721 44.314 24.211 1.00 0.00 H +ATOM 484 CE2 PHE 29 24.380 43.758 25.464 1.00 0.00 C +ATOM 485 HE2 PHE 29 24.834 44.726 25.438 1.00 0.00 H +ATOM 486 CD2 PHE 29 25.002 42.710 26.164 1.00 0.00 C +ATOM 487 HD2 PHE 29 25.928 42.910 26.675 1.00 0.00 H +ATOM 488 C PHE 29 27.250 39.031 27.593 1.00 0.00 C +ATOM 489 O PHE 29 27.395 39.054 28.815 1.00 0.00 O +ATOM 490 N THR 30 27.623 37.977 26.858 1.00 0.00 N +ATOM 491 H THR 30 27.437 37.985 25.867 1.00 0.00 H +ATOM 492 CA THR 30 28.385 36.844 27.391 1.00 0.00 C +ATOM 493 HA THR 30 27.994 36.502 28.330 1.00 0.00 H +ATOM 494 CB THR 30 28.354 35.594 26.358 1.00 0.00 C +ATOM 495 HB THR 30 28.830 35.927 25.456 1.00 0.00 H +ATOM 496 CG2 THR 30 29.230 34.457 26.845 1.00 0.00 C +ATOM 497 HG21 THR 30 28.996 34.103 27.844 1.00 0.00 H +ATOM 498 HG22 THR 30 29.220 33.577 26.162 1.00 0.00 H +ATOM 499 HG23 THR 30 30.258 34.822 26.819 1.00 0.00 H +ATOM 500 OG1 THR 30 27.044 35.136 26.088 1.00 0.00 O +ATOM 501 HG1 THR 30 26.523 35.869 25.673 1.00 0.00 H +ATOM 502 C THR 30 29.850 37.261 27.705 1.00 0.00 C +ATOM 503 O THR 30 30.327 36.960 28.794 1.00 0.00 O +ATOM 504 N LYS 31 30.511 38.049 26.849 1.00 0.00 N +ATOM 505 H LYS 31 30.048 38.334 25.987 1.00 0.00 H +ATOM 506 CA LYS 31 31.851 38.598 27.107 1.00 0.00 C +ATOM 507 HA LYS 31 32.542 37.804 27.392 1.00 0.00 H +ATOM 508 CB LYS 31 32.396 39.237 25.806 1.00 0.00 C +ATOM 509 HB2 LYS 31 31.662 39.937 25.425 1.00 0.00 H +ATOM 510 HB3 LYS 31 33.307 39.778 26.044 1.00 0.00 H +ATOM 511 CG LYS 31 32.730 38.178 24.738 1.00 0.00 C +ATOM 512 HG2 LYS 31 33.486 37.507 25.134 1.00 0.00 H +ATOM 513 HG3 LYS 31 31.860 37.581 24.481 1.00 0.00 H +ATOM 514 CD LYS 31 33.272 38.860 23.469 1.00 0.00 C +ATOM 515 HD2 LYS 31 32.459 39.402 22.986 1.00 0.00 H +ATOM 516 HD3 LYS 31 34.038 39.577 23.751 1.00 0.00 H +ATOM 517 CE LYS 31 33.869 37.870 22.450 1.00 0.00 C +ATOM 518 HE2 LYS 31 33.131 37.110 22.193 1.00 0.00 H +ATOM 519 HE3 LYS 31 34.100 38.419 21.536 1.00 0.00 H +ATOM 520 NZ LYS 31 35.103 37.221 22.953 1.00 0.00 N +ATOM 521 HZ1 LYS 31 34.891 36.470 23.583 1.00 0.00 H +ATOM 522 HZ2 LYS 31 35.649 36.813 22.186 1.00 0.00 H +ATOM 523 HZ3 LYS 31 35.698 37.867 23.482 1.00 0.00 H +ATOM 524 C LYS 31 31.880 39.595 28.276 1.00 0.00 C +ATOM 525 O LYS 31 32.864 39.599 29.014 1.00 0.00 O +ATOM 526 N ALA 32 30.807 40.353 28.512 1.00 0.00 N +ATOM 527 H ALA 32 30.072 40.386 27.814 1.00 0.00 H +ATOM 528 CA ALA 32 30.673 41.190 29.709 1.00 0.00 C +ATOM 529 HA ALA 32 31.506 41.898 29.734 1.00 0.00 H +ATOM 530 CB ALA 32 29.369 41.991 29.627 1.00 0.00 C +ATOM 531 HB1 ALA 32 28.510 41.322 29.592 1.00 0.00 H +ATOM 532 HB2 ALA 32 29.277 42.633 30.508 1.00 0.00 H +ATOM 533 HB3 ALA 32 29.375 42.618 28.734 1.00 0.00 H +ATOM 534 C ALA 32 30.765 40.348 30.999 1.00 0.00 C +ATOM 535 O ALA 32 31.725 40.484 31.755 1.00 0.00 O +ATOM 536 N MET 33 29.870 39.362 31.156 1.00 0.00 N +ATOM 537 H MET 33 29.126 39.299 30.476 1.00 0.00 H +ATOM 538 CA MET 33 29.833 38.448 32.312 1.00 0.00 C +ATOM 539 HA MET 33 29.673 39.044 33.214 1.00 0.00 H +ATOM 540 CB MET 33 28.622 37.510 32.121 1.00 0.00 C +ATOM 541 HB2 MET 33 27.719 38.114 32.031 1.00 0.00 H +ATOM 542 HB3 MET 33 28.753 36.964 31.185 1.00 0.00 H +ATOM 543 CG MET 33 28.398 36.479 33.239 1.00 0.00 C +ATOM 544 HG2 MET 33 27.620 35.786 32.916 1.00 0.00 H +ATOM 545 HG3 MET 33 29.307 35.898 33.385 1.00 0.00 H +ATOM 546 SD MET 33 27.885 37.174 34.830 1.00 0.00 S +ATOM 547 CE MET 33 28.157 35.737 35.901 1.00 0.00 C +ATOM 548 HE1 MET 33 29.207 35.443 35.856 1.00 0.00 H +ATOM 549 HE2 MET 33 27.903 36.000 36.929 1.00 0.00 H +ATOM 550 HE3 MET 33 27.528 34.909 35.574 1.00 0.00 H +ATOM 551 C MET 33 31.145 37.655 32.520 1.00 0.00 C +ATOM 552 O MET 33 31.422 37.182 33.621 1.00 0.00 O +ATOM 553 N ALA 34 31.963 37.477 31.475 1.00 0.00 N +ATOM 554 H ALA 34 31.688 37.863 30.583 1.00 0.00 H +ATOM 555 CA ALA 34 33.300 36.894 31.597 1.00 0.00 C +ATOM 556 HA ALA 34 33.275 36.104 32.349 1.00 0.00 H +ATOM 557 CB ALA 34 33.665 36.250 30.259 1.00 0.00 C +ATOM 558 HB1 ALA 34 33.797 37.022 29.502 1.00 0.00 H +ATOM 559 HB2 ALA 34 34.587 35.685 30.384 1.00 0.00 H +ATOM 560 HB3 ALA 34 32.889 35.561 29.933 1.00 0.00 H +ATOM 561 C ALA 34 34.369 37.911 32.057 1.00 0.00 C +ATOM 562 O ALA 34 35.211 37.576 32.889 1.00 0.00 O +ATOM 563 N ASN 35 34.329 39.162 31.585 1.00 0.00 N +ATOM 564 H ASN 35 33.590 39.415 30.938 1.00 0.00 H +ATOM 565 CA ASN 35 35.222 40.229 32.061 1.00 0.00 C +ATOM 566 HA ASN 35 36.237 39.834 32.100 1.00 0.00 H +ATOM 567 CB ASN 35 35.227 41.396 31.063 1.00 0.00 C +ATOM 568 HB2 ASN 35 34.213 41.630 30.741 1.00 0.00 H +ATOM 569 HB3 ASN 35 35.645 42.279 31.546 1.00 0.00 H +ATOM 570 CG ASN 35 36.110 41.076 29.874 1.00 0.00 C +ATOM 571 OD1 ASN 35 37.326 41.135 29.941 1.00 0.00 O +ATOM 572 ND2 ASN 35 35.541 40.681 28.767 1.00 0.00 N +ATOM 573 HD21 ASN 35 36.166 40.338 28.035 1.00 0.00 H +ATOM 574 HD22 ASN 35 34.550 40.487 28.755 1.00 0.00 H +ATOM 575 C ASN 35 34.910 40.687 33.495 1.00 0.00 C +ATOM 576 O ASN 35 35.843 40.992 34.234 1.00 0.00 O +ATOM 577 N ASP 36 33.649 40.623 33.934 1.00 0.00 N +ATOM 578 H ASP 36 32.907 40.478 33.255 1.00 0.00 H +ATOM 579 CA ASP 36 33.266 40.781 35.349 1.00 0.00 C +ATOM 580 HA ASP 36 33.621 41.751 35.703 1.00 0.00 H +ATOM 581 CB ASP 36 31.735 40.759 35.471 1.00 0.00 C +ATOM 582 HB2 ASP 36 31.354 39.839 35.018 1.00 0.00 H +ATOM 583 HB3 ASP 36 31.472 40.735 36.531 1.00 0.00 H +ATOM 584 CG ASP 36 31.041 41.977 34.846 1.00 0.00 C +ATOM 585 OD1 ASP 36 31.535 43.109 35.068 1.00 0.00 O +ATOM 586 OD2 ASP 36 29.990 41.771 34.196 1.00 0.00 O +ATOM 587 C ASP 36 33.904 39.703 36.255 1.00 0.00 C +ATOM 588 O ASP 36 34.233 39.975 37.411 1.00 0.00 O +ATOM 589 N LEU 37 34.128 38.488 35.730 1.00 0.00 N +ATOM 590 H LEU 37 33.800 38.324 34.789 1.00 0.00 H +ATOM 591 CA LEU 37 34.906 37.425 36.387 1.00 0.00 C +ATOM 592 HA LEU 37 34.730 37.506 37.459 1.00 0.00 H +ATOM 593 CB LEU 37 34.348 36.068 35.906 1.00 0.00 C +ATOM 594 HB2 LEU 37 33.271 36.057 36.087 1.00 0.00 H +ATOM 595 HB3 LEU 37 34.501 35.996 34.829 1.00 0.00 H +ATOM 596 CG LEU 37 34.965 34.816 36.561 1.00 0.00 C +ATOM 597 HG LEU 37 36.033 34.779 36.354 1.00 0.00 H +ATOM 598 CD1 LEU 37 34.742 34.773 38.076 1.00 0.00 C +ATOM 599 HD11 LEU 37 33.678 34.851 38.302 1.00 0.00 H +ATOM 600 HD12 LEU 37 35.133 33.839 38.480 1.00 0.00 H +ATOM 601 HD13 LEU 37 35.274 35.599 38.547 1.00 0.00 H +ATOM 602 CD2 LEU 37 34.327 33.560 35.961 1.00 0.00 C +ATOM 603 HD21 LEU 37 34.493 33.548 34.884 1.00 0.00 H +ATOM 604 HD22 LEU 37 34.784 32.673 36.397 1.00 0.00 H +ATOM 605 HD23 LEU 37 33.255 33.554 36.161 1.00 0.00 H +ATOM 606 C LEU 37 36.435 37.569 36.178 1.00 0.00 C +ATOM 607 O LEU 37 37.219 37.038 36.968 1.00 0.00 O +ATOM 608 N GLY 38 36.865 38.302 35.143 1.00 0.00 N +ATOM 609 H GLY 38 36.149 38.688 34.540 1.00 0.00 H +ATOM 610 CA GLY 38 38.233 38.806 34.963 1.00 0.00 C +ATOM 611 HA2 GLY 38 38.289 39.801 35.406 1.00 0.00 H +ATOM 612 HA3 GLY 38 38.924 38.163 35.504 1.00 0.00 H +ATOM 613 C GLY 38 38.748 38.902 33.515 1.00 0.00 C +ATOM 614 O GLY 38 39.668 39.683 33.269 1.00 0.00 O +ATOM 615 N ARG 39 38.215 38.111 32.568 1.00 0.00 N +ATOM 616 H ARG 39 37.431 37.525 32.842 1.00 0.00 H +ATOM 617 CA ARG 39 38.619 38.063 31.138 1.00 0.00 C +ATOM 618 HA ARG 39 38.617 39.078 30.734 1.00 0.00 H +ATOM 619 CB ARG 39 40.041 37.460 31.036 1.00 0.00 C +ATOM 620 HB2 ARG 39 40.711 38.038 31.673 1.00 0.00 H +ATOM 621 HB3 ARG 39 40.023 36.432 31.406 1.00 0.00 H +ATOM 622 CG ARG 39 40.620 37.466 29.610 1.00 0.00 C +ATOM 623 HG2 ARG 39 40.041 36.780 28.991 1.00 0.00 H +ATOM 624 HG3 ARG 39 40.544 38.468 29.184 1.00 0.00 H +ATOM 625 CD ARG 39 42.088 37.005 29.572 1.00 0.00 C +ATOM 626 HD2 ARG 39 42.175 36.033 30.059 1.00 0.00 H +ATOM 627 HD3 ARG 39 42.368 36.866 28.525 1.00 0.00 H +ATOM 628 NE ARG 39 43.014 37.994 30.173 1.00 0.00 N +ATOM 629 HE ARG 39 43.212 38.804 29.608 1.00 0.00 H +ATOM 630 CZ ARG 39 43.635 37.927 31.340 1.00 0.00 C +ATOM 631 NH1 ARG 39 43.485 36.925 32.163 1.00 0.00 N +ATOM 632 HH11 ARG 39 42.923 36.146 31.873 1.00 0.00 H +ATOM 633 HH12 ARG 39 43.957 36.916 33.047 1.00 0.00 H +ATOM 634 NH2 ARG 39 44.433 38.889 31.712 1.00 0.00 N +ATOM 635 HH21 ARG 39 44.574 39.684 31.115 1.00 0.00 H +ATOM 636 HH22 ARG 39 44.954 38.829 32.570 1.00 0.00 H +ATOM 637 C ARG 39 37.631 37.219 30.320 1.00 0.00 C +ATOM 638 O ARG 39 37.150 36.211 30.827 1.00 0.00 O +ATOM 639 N ASP 40 37.358 37.580 29.063 1.00 0.00 N +ATOM 640 H ASP 40 37.762 38.425 28.678 1.00 0.00 H +ATOM 641 CA ASP 40 36.558 36.749 28.149 1.00 0.00 C +ATOM 642 HA ASP 40 35.894 36.146 28.755 1.00 0.00 H +ATOM 643 CB ASP 40 35.659 37.597 27.240 1.00 0.00 C +ATOM 644 HB2 ASP 40 35.047 36.917 26.651 1.00 0.00 H +ATOM 645 HB3 ASP 40 34.976 38.167 27.864 1.00 0.00 H +ATOM 646 CG ASP 40 36.390 38.566 26.306 1.00 0.00 C +ATOM 647 OD1 ASP 40 37.088 39.468 26.822 1.00 0.00 O +ATOM 648 OD2 ASP 40 36.149 38.468 25.082 1.00 0.00 O +ATOM 649 C ASP 40 37.358 35.741 27.308 1.00 0.00 C +ATOM 650 O ASP 40 38.512 35.966 26.956 1.00 0.00 O +ATOM 651 N GLY 41 36.679 34.649 26.933 1.00 0.00 N +ATOM 652 H GLY 41 35.753 34.538 27.313 1.00 0.00 H +ATOM 653 CA GLY 41 37.082 33.700 25.887 1.00 0.00 C +ATOM 654 HA2 GLY 41 37.989 34.064 25.391 1.00 0.00 H +ATOM 655 HA3 GLY 41 37.301 32.728 26.340 1.00 0.00 H +ATOM 656 C GLY 41 35.990 33.507 24.822 1.00 0.00 C +ATOM 657 O GLY 41 34.843 33.946 24.979 1.00 0.00 O +ATOM 658 N GLU 42 36.336 32.855 23.713 1.00 0.00 N +ATOM 659 H GLU 42 37.272 32.491 23.648 1.00 0.00 H +ATOM 660 CA GLU 42 35.429 32.621 22.578 1.00 0.00 C +ATOM 661 HA GLU 42 34.762 33.478 22.520 1.00 0.00 H +ATOM 662 CB GLU 42 36.221 32.536 21.258 1.00 0.00 C +ATOM 663 HB2 GLU 42 36.853 31.648 21.285 1.00 0.00 H +ATOM 664 HB3 GLU 42 35.512 32.415 20.439 1.00 0.00 H +ATOM 665 CG GLU 42 37.112 33.755 20.944 1.00 0.00 C +ATOM 666 HG2 GLU 42 37.959 33.742 21.635 1.00 0.00 H +ATOM 667 HG3 GLU 42 37.514 33.642 19.934 1.00 0.00 H +ATOM 668 CD GLU 42 36.398 35.112 21.057 1.00 0.00 C +ATOM 669 OE1 GLU 42 35.150 35.169 21.023 1.00 0.00 O +ATOM 670 OE2 GLU 42 37.076 36.139 21.273 1.00 0.00 O +ATOM 671 C GLU 42 34.501 31.409 22.755 1.00 0.00 C +ATOM 672 O GLU 42 34.764 30.521 23.563 1.00 0.00 O +ATOM 673 N HIP 43 33.379 31.397 22.018 1.00 0.00 N +ATOM 674 H HIP 43 33.252 32.121 21.320 1.00 0.00 H +ATOM 675 CA HIP 43 32.319 30.381 22.119 1.00 0.00 C +ATOM 676 HA HIP 43 32.743 29.457 22.517 1.00 0.00 H +ATOM 677 CB HIP 43 31.209 30.850 23.078 1.00 0.00 C +ATOM 678 HB2 HIP 43 30.752 31.756 22.679 1.00 0.00 H +ATOM 679 HB3 HIP 43 30.430 30.087 23.120 1.00 0.00 H +ATOM 680 CG HIP 43 31.678 31.129 24.480 1.00 0.00 C +ATOM 681 ND1 HIP 43 32.341 32.266 24.910 1.00 0.00 N +ATOM 682 HD1 HIP 43 32.668 33.029 24.329 1.00 0.00 H +ATOM 683 CE1 HIP 43 32.729 32.058 26.178 1.00 0.00 C +ATOM 684 HE1 HIP 43 33.376 32.711 26.761 1.00 0.00 H +ATOM 685 NE2 HIP 43 32.313 30.841 26.571 1.00 0.00 N +ATOM 686 HE2 HIP 43 32.568 30.435 27.479 1.00 0.00 H +ATOM 687 CD2 HIP 43 31.667 30.230 25.511 1.00 0.00 C +ATOM 688 HD2 HIP 43 31.310 29.208 25.458 1.00 0.00 H +ATOM 689 C HIP 43 31.718 30.065 20.746 1.00 0.00 C +ATOM 690 O HIP 43 31.453 30.988 19.980 1.00 0.00 O +ATOM 691 N THR 44 31.464 28.789 20.464 1.00 0.00 N +ATOM 692 H THR 44 31.685 28.097 21.164 1.00 0.00 H +ATOM 693 CA THR 44 30.720 28.342 19.270 1.00 0.00 C +ATOM 694 HA THR 44 31.006 28.970 18.427 1.00 0.00 H +ATOM 695 CB THR 44 31.086 26.885 18.921 1.00 0.00 C +ATOM 696 HB THR 44 30.777 26.222 19.732 1.00 0.00 H +ATOM 697 CG2 THR 44 30.487 26.380 17.607 1.00 0.00 C +ATOM 698 HG21 THR 44 30.648 27.112 16.815 1.00 0.00 H +ATOM 699 HG22 THR 44 30.951 25.437 17.318 1.00 0.00 H +ATOM 700 HG23 THR 44 29.419 26.199 17.729 1.00 0.00 H +ATOM 701 OG1 THR 44 32.485 26.786 18.775 1.00 0.00 O +ATOM 702 HG1 THR 44 32.696 25.894 18.479 1.00 0.00 H +ATOM 703 C THR 44 29.212 28.529 19.485 1.00 0.00 C +ATOM 704 O THR 44 28.769 28.657 20.629 1.00 0.00 O +ATOM 705 N LYN 45 28.412 28.565 18.413 1.00 0.00 N +ATOM 706 H LYN 45 28.810 28.412 17.498 1.00 0.00 H +ATOM 707 CA LYN 45 26.958 28.740 18.464 1.00 0.00 C +ATOM 708 HA LYN 45 26.621 28.492 19.466 1.00 0.00 H +ATOM 709 CB LYN 45 26.604 30.219 18.200 1.00 0.00 C +ATOM 710 HB2 LYN 45 25.543 30.367 18.414 1.00 0.00 H +ATOM 711 HB3 LYN 45 27.173 30.857 18.882 1.00 0.00 H +ATOM 712 CG LYN 45 26.889 30.652 16.744 1.00 0.00 C +ATOM 713 HG2 LYN 45 27.967 30.605 16.560 1.00 0.00 H +ATOM 714 HG3 LYN 45 26.388 29.969 16.056 1.00 0.00 H +ATOM 715 CD LYN 45 26.383 32.079 16.468 1.00 0.00 C +ATOM 716 HD2 LYN 45 25.317 32.130 16.691 1.00 0.00 H +ATOM 717 HD3 LYN 45 26.913 32.768 17.130 1.00 0.00 H +ATOM 718 CE LYN 45 26.622 32.505 15.008 1.00 0.00 C +ATOM 719 HE2 LYN 45 26.366 33.555 14.879 1.00 0.00 H +ATOM 720 HE3 LYN 45 27.677 32.382 14.764 1.00 0.00 H +ATOM 721 NZ LYN 45 25.857 31.685 14.060 1.00 0.00 N +ATOM 722 HZ2 LYN 45 25.483 32.266 13.322 1.00 0.00 H +ATOM 723 HZ3 LYN 45 26.480 31.005 13.670 1.00 0.00 H +ATOM 724 C LYN 45 26.207 27.816 17.500 1.00 0.00 C +ATOM 725 O LYN 45 26.778 27.341 16.520 1.00 0.00 O +ATOM 726 N ASP 46 24.909 27.652 17.739 1.00 0.00 N +ATOM 727 H ASP 46 24.545 28.007 18.619 1.00 0.00 H +ATOM 728 CA ASP 46 23.921 27.098 16.811 1.00 0.00 C +ATOM 729 HA ASP 46 24.296 27.215 15.789 1.00 0.00 H +ATOM 730 CB ASP 46 23.692 25.607 17.113 1.00 0.00 C +ATOM 731 HB2 ASP 46 24.555 25.009 16.812 1.00 0.00 H +ATOM 732 HB3 ASP 46 23.583 25.513 18.196 1.00 0.00 H +ATOM 733 CG ASP 46 22.439 25.081 16.434 1.00 0.00 C +ATOM 734 OD1 ASP 46 21.617 24.468 17.140 1.00 0.00 O +ATOM 735 OD2 ASP 46 22.242 25.329 15.229 1.00 0.00 O +ATOM 736 C ASP 46 22.601 27.871 16.961 1.00 0.00 C +ATOM 737 O ASP 46 22.092 28.040 18.070 1.00 0.00 O +ATOM 738 N ASP 47 22.014 28.307 15.840 1.00 0.00 N +ATOM 739 H ASP 47 22.476 28.086 14.971 1.00 0.00 H +ATOM 740 CA ASP 47 20.704 28.998 15.797 1.00 0.00 C +ATOM 741 HA ASP 47 20.681 29.711 16.619 1.00 0.00 H +ATOM 742 CB ASP 47 20.554 29.855 14.548 1.00 0.00 C +ATOM 743 HB2 ASP 47 21.374 30.558 14.563 1.00 0.00 H +ATOM 744 HB3 ASP 47 20.617 29.245 13.628 1.00 0.00 H +ATOM 745 CG ASP 47 19.301 30.681 14.637 1.00 0.00 C +ATOM 746 OD1 ASP 47 18.288 30.429 13.954 1.00 0.00 O +ATOM 747 OD2 ASP 47 19.216 31.525 15.549 1.00 0.00 O +ATOM 748 C ASP 47 19.503 28.053 15.938 1.00 0.00 C +ATOM 749 O ASP 47 18.476 28.429 16.506 1.00 0.00 O +ATOM 750 N ALA 48 19.617 26.801 15.480 1.00 0.00 N +ATOM 751 H ALA 48 20.528 26.487 15.141 1.00 0.00 H +ATOM 752 CA ALA 48 18.502 25.844 15.504 1.00 0.00 C +ATOM 753 HA ALA 48 17.643 26.301 15.010 1.00 0.00 H +ATOM 754 CB ALA 48 18.894 24.582 14.731 1.00 0.00 C +ATOM 755 HB1 ALA 48 19.738 24.093 15.216 1.00 0.00 H +ATOM 756 HB2 ALA 48 18.050 23.901 14.714 1.00 0.00 H +ATOM 757 HB3 ALA 48 19.173 24.823 13.706 1.00 0.00 H +ATOM 758 C ALA 48 18.085 25.539 16.950 1.00 0.00 C +ATOM 759 O ALA 48 16.906 25.620 17.307 1.00 0.00 O +ATOM 760 N THR 49 19.054 25.249 17.820 1.00 0.00 N +ATOM 761 H THR 49 19.989 25.053 17.454 1.00 0.00 H +ATOM 762 CA THR 49 18.878 25.125 19.272 1.00 0.00 C +ATOM 763 HA THR 49 17.852 24.796 19.451 1.00 0.00 H +ATOM 764 CB THR 49 19.831 24.062 19.831 1.00 0.00 C +ATOM 765 HB THR 49 19.641 23.980 20.898 1.00 0.00 H +ATOM 766 CG2 THR 49 19.649 22.679 19.218 1.00 0.00 C +ATOM 767 HG21 THR 49 19.902 22.678 18.156 1.00 0.00 H +ATOM 768 HG22 THR 49 20.317 22.000 19.737 1.00 0.00 H +ATOM 769 HG23 THR 49 18.620 22.344 19.337 1.00 0.00 H +ATOM 770 OG1 THR 49 21.178 24.417 19.659 1.00 0.00 O +ATOM 771 HG1 THR 49 21.380 24.348 18.691 1.00 0.00 H +ATOM 772 C THR 49 19.059 26.435 20.049 1.00 0.00 C +ATOM 773 O THR 49 18.993 26.431 21.279 1.00 0.00 O +ATOM 774 N LYS 50 19.283 27.560 19.358 1.00 0.00 N +ATOM 775 H LYS 50 19.336 27.455 18.356 1.00 0.00 H +ATOM 776 CA LYS 50 19.471 28.925 19.906 1.00 0.00 C +ATOM 777 HA LYS 50 19.876 29.539 19.099 1.00 0.00 H +ATOM 778 CB LYS 50 18.098 29.510 20.336 1.00 0.00 C +ATOM 779 HB2 LYS 50 17.671 28.839 21.079 1.00 0.00 H +ATOM 780 HB3 LYS 50 18.255 30.478 20.825 1.00 0.00 H +ATOM 781 CG LYS 50 17.066 29.713 19.213 1.00 0.00 C +ATOM 782 HG2 LYS 50 17.013 28.826 18.576 1.00 0.00 H +ATOM 783 HG3 LYS 50 16.080 29.849 19.676 1.00 0.00 H +ATOM 784 CD LYS 50 17.370 30.963 18.360 1.00 0.00 C +ATOM 785 HD2 LYS 50 17.354 31.835 19.020 1.00 0.00 H +ATOM 786 HD3 LYS 50 18.379 30.874 17.929 1.00 0.00 H +ATOM 787 CE LYS 50 16.323 31.169 17.249 1.00 0.00 C +ATOM 788 HE2 LYS 50 15.339 30.855 17.621 1.00 0.00 H +ATOM 789 HE3 LYS 50 16.289 32.236 16.986 1.00 0.00 H +ATOM 790 NZ LYS 50 16.654 30.389 16.037 1.00 0.00 N +ATOM 791 HZ1 LYS 50 16.994 29.455 16.256 1.00 0.00 H +ATOM 792 HZ2 LYS 50 15.928 30.352 15.337 1.00 0.00 H +ATOM 793 HZ3 LYS 50 17.459 30.798 15.540 1.00 0.00 H +ATOM 794 C LYS 50 20.524 28.976 21.035 1.00 0.00 C +ATOM 795 O LYS 50 20.294 29.624 22.060 1.00 0.00 O +ATOM 796 N THR 51 21.628 28.241 20.873 1.00 0.00 N +ATOM 797 H THR 51 21.784 27.837 19.953 1.00 0.00 H +ATOM 798 CA THR 51 22.556 27.875 21.961 1.00 0.00 C +ATOM 799 HA THR 51 22.300 28.460 22.830 1.00 0.00 H +ATOM 800 CB THR 51 22.372 26.372 22.355 1.00 0.00 C +ATOM 801 HB THR 51 22.498 25.763 21.460 1.00 0.00 H +ATOM 802 CG2 THR 51 23.390 25.877 23.378 1.00 0.00 C +ATOM 803 HG21 THR 51 23.422 26.504 24.267 1.00 0.00 H +ATOM 804 HG22 THR 51 23.170 24.851 23.686 1.00 0.00 H +ATOM 805 HG23 THR 51 24.376 25.854 22.923 1.00 0.00 H +ATOM 806 OG1 THR 51 21.093 26.132 22.903 1.00 0.00 O +ATOM 807 HG1 THR 51 20.417 26.262 22.204 1.00 0.00 H +ATOM 808 C THR 51 24.037 28.183 21.669 1.00 0.00 C +ATOM 809 O THR 51 24.561 27.811 20.623 1.00 0.00 O +ATOM 810 N PHE 52 24.752 28.784 22.628 1.00 0.00 N +ATOM 811 H PHE 52 24.244 29.166 23.421 1.00 0.00 H +ATOM 812 CA PHE 52 26.223 28.846 22.669 1.00 0.00 C +ATOM 813 HA PHE 52 26.607 28.826 21.653 1.00 0.00 H +ATOM 814 CB PHE 52 26.686 30.162 23.322 1.00 0.00 C +ATOM 815 HB2 PHE 52 26.168 30.282 24.273 1.00 0.00 H +ATOM 816 HB3 PHE 52 27.752 30.081 23.540 1.00 0.00 H +ATOM 817 CG PHE 52 26.482 31.405 22.478 1.00 0.00 C +ATOM 818 CD1 PHE 52 25.300 32.163 22.591 1.00 0.00 C +ATOM 819 HD1 PHE 52 24.508 31.840 23.249 1.00 0.00 H +ATOM 820 CE1 PHE 52 25.145 33.345 21.841 1.00 0.00 C +ATOM 821 HE1 PHE 52 24.238 33.926 21.923 1.00 0.00 H +ATOM 822 CZ PHE 52 26.172 33.772 20.979 1.00 0.00 C +ATOM 823 HZ PHE 52 26.053 34.675 20.401 1.00 0.00 H +ATOM 824 CE2 PHE 52 27.349 33.014 20.858 1.00 0.00 C +ATOM 825 HE2 PHE 52 28.134 33.340 20.187 1.00 0.00 H +ATOM 826 CD2 PHE 52 27.500 31.828 21.600 1.00 0.00 C +ATOM 827 HD2 PHE 52 28.399 31.242 21.486 1.00 0.00 H +ATOM 828 C PHE 52 26.848 27.665 23.436 1.00 0.00 C +ATOM 829 O PHE 52 26.286 27.209 24.436 1.00 0.00 O +ATOM 830 N THR 53 28.049 27.232 23.036 1.00 0.00 N +ATOM 831 H THR 53 28.443 27.667 22.204 1.00 0.00 H +ATOM 832 CA THR 53 28.822 26.103 23.614 1.00 0.00 C +ATOM 833 HA THR 53 28.487 25.932 24.637 1.00 0.00 H +ATOM 834 CB THR 53 28.586 24.803 22.814 1.00 0.00 C +ATOM 835 HB THR 53 29.132 23.991 23.298 1.00 0.00 H +ATOM 836 CG2 THR 53 27.124 24.375 22.725 1.00 0.00 C +ATOM 837 HG21 THR 53 26.562 25.073 22.105 1.00 0.00 H +ATOM 838 HG22 THR 53 27.063 23.377 22.291 1.00 0.00 H +ATOM 839 HG23 THR 53 26.693 24.343 23.723 1.00 0.00 H +ATOM 840 OG1 THR 53 29.075 24.942 21.501 1.00 0.00 O +ATOM 841 HG1 THR 53 28.760 24.185 20.996 1.00 0.00 H +ATOM 842 C THR 53 30.345 26.384 23.676 1.00 0.00 C +ATOM 843 O THR 53 30.805 27.476 23.336 1.00 0.00 O +ATOM 844 N SER 54 31.135 25.399 24.132 1.00 0.00 N +ATOM 845 H SER 54 30.695 24.526 24.387 1.00 0.00 H +ATOM 846 CA SER 54 32.609 25.376 24.066 1.00 0.00 C +ATOM 847 HA SER 54 32.940 26.180 23.411 1.00 0.00 H +ATOM 848 CB SER 54 33.218 25.621 25.450 1.00 0.00 C +ATOM 849 HB2 SER 54 32.854 26.578 25.834 1.00 0.00 H +ATOM 850 HB3 SER 54 32.915 24.830 26.140 1.00 0.00 H +ATOM 851 OG SER 54 34.632 25.663 25.380 1.00 0.00 O +ATOM 852 HG SER 54 34.988 24.765 25.419 1.00 0.00 H +ATOM 853 C SER 54 33.118 24.047 23.466 1.00 0.00 C +ATOM 854 O SER 54 32.462 23.014 23.608 1.00 0.00 O +ATOM 855 N LYS 55 34.277 24.083 22.808 1.00 0.00 N +ATOM 856 H LYS 55 34.800 24.947 22.823 1.00 0.00 H +ATOM 857 CA LYS 55 34.903 22.922 22.142 1.00 0.00 C +ATOM 858 HA LYS 55 34.129 22.400 21.578 1.00 0.00 H +ATOM 859 CB LYS 55 35.960 23.406 21.125 1.00 0.00 C +ATOM 860 HB2 LYS 55 36.273 22.557 20.512 1.00 0.00 H +ATOM 861 HB3 LYS 55 35.499 24.139 20.452 1.00 0.00 H +ATOM 862 CG LYS 55 37.216 24.028 21.782 1.00 0.00 C +ATOM 863 HG2 LYS 55 36.916 24.871 22.420 1.00 0.00 H +ATOM 864 HG3 LYS 55 37.711 23.284 22.412 1.00 0.00 H +ATOM 865 CD LYS 55 38.250 24.519 20.755 1.00 0.00 C +ATOM 866 HD2 LYS 55 37.778 25.284 20.123 1.00 0.00 H +ATOM 867 HD3 LYS 55 39.073 24.994 21.297 1.00 0.00 H +ATOM 868 CE LYS 55 38.841 23.412 19.864 1.00 0.00 C +ATOM 869 HE2 LYS 55 38.060 23.011 19.190 1.00 0.00 H +ATOM 870 HE3 LYS 55 39.595 23.920 19.268 1.00 0.00 H +ATOM 871 NZ LYS 55 39.563 22.352 20.623 1.00 0.00 N +ATOM 872 HZ1 LYS 55 38.957 21.593 20.936 1.00 0.00 H +ATOM 873 HZ2 LYS 55 40.251 21.913 20.019 1.00 0.00 H +ATOM 874 HZ3 LYS 55 40.043 22.702 21.436 1.00 0.00 H +ATOM 875 C LYS 55 35.494 21.899 23.117 1.00 0.00 C +ATOM 876 O LYS 55 35.822 22.221 24.260 1.00 0.00 O +ATOM 877 N GLU 56 35.661 20.698 22.571 1.00 0.00 N +ATOM 878 H GLU 56 35.339 20.591 21.624 1.00 0.00 H +ATOM 879 CA GLU 56 36.598 19.626 23.007 1.00 0.00 C +ATOM 880 HA GLU 56 36.765 19.745 24.072 1.00 0.00 H +ATOM 881 CB GLU 56 35.909 18.252 22.784 1.00 0.00 C +ATOM 882 HB2 GLU 56 34.839 18.355 22.952 1.00 0.00 H +ATOM 883 HB3 GLU 56 36.004 17.992 21.734 1.00 0.00 H +ATOM 884 CG GLU 56 36.418 17.051 23.629 1.00 0.00 C +ATOM 885 HG2 GLU 56 36.542 16.191 22.977 1.00 0.00 H +ATOM 886 HG3 GLU 56 37.404 17.277 24.015 1.00 0.00 H +ATOM 887 CD GLU 56 35.536 16.591 24.820 1.00 0.00 C +ATOM 888 OE1 GLU 56 35.979 15.637 25.511 1.00 0.00 O +ATOM 889 OE2 GLU 56 34.424 17.121 25.072 1.00 0.00 O +ATOM 890 C GLU 56 37.964 19.767 22.349 1.00 0.00 C +ATOM 891 O GLU 56 39.026 19.507 22.987 1.00 0.00 O +ATOM 892 OXT GLU 56 37.984 20.224 21.176 1.00 0.00 O +HETATM 893 ZN ZN1 57 26.505 32.486 29.471 1.00 0.00 Zn +HETATM 894 N AN1 58 28.231 33.196 30.369 1.00 0.00 N +HETATM 895 C AN1 58 30.581 34.110 31.019 1.00 0.00 C +HETATM 896 C1 AN1 58 29.253 33.582 30.683 1.00 0.00 C +HETATM 897 H AN1 58 30.653 34.342 32.086 1.00 0.00 H +HETATM 898 H1 AN1 58 30.760 35.025 30.448 1.00 0.00 H +HETATM 899 H2 AN1 58 31.360 33.384 30.760 1.00 0.00 H +HETATM 900 N1 AZI 59 30.168 28.689 29.579 1.00 0.00 N +HETATM 901 N2 AZI 59 29.655 28.930 30.696 1.00 0.00 N +HETATM 902 N3 AZI 59 29.177 29.187 31.800 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 893 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 105 101 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 118 132 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 140 142 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 139 145 144 143 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 142 147 +CONECT 146 145 +CONECT 147 151 145 148 +CONECT 148 147 150 149 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 153 147 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 202 189 +CONECT 188 187 +CONECT 189 187 191 195 190 +CONECT 190 189 +CONECT 191 192 194 189 193 +CONECT 192 191 +CONECT 193 191 +CONECT 194 191 +CONECT 195 196 189 197 198 +CONECT 196 195 +CONECT 197 195 +CONECT 198 195 200 199 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 226 204 207 208 +CONECT 207 206 +CONECT 208 206 211 209 210 +CONECT 209 208 +CONECT 210 208 +CONECT 211 213 212 214 208 +CONECT 212 211 +CONECT 213 211 +CONECT 214 211 216 217 215 +CONECT 215 214 +CONECT 216 214 +CONECT 217 219 214 218 +CONECT 218 217 +CONECT 219 220 223 217 +CONECT 220 222 221 219 +CONECT 221 220 +CONECT 222 220 +CONECT 223 225 219 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 227 228 206 +CONECT 227 226 +CONECT 228 230 226 229 +CONECT 229 228 +CONECT 230 231 248 232 228 +CONECT 231 230 +CONECT 232 235 230 233 234 +CONECT 233 232 +CONECT 234 232 +CONECT 235 237 236 238 232 +CONECT 236 235 +CONECT 237 235 +CONECT 238 239 235 240 241 +CONECT 239 238 +CONECT 240 238 +CONECT 241 238 243 244 242 +CONECT 242 241 +CONECT 243 241 +CONECT 244 247 241 245 246 +CONECT 245 244 +CONECT 246 244 +CONECT 247 244 +CONECT 248 249 230 250 +CONECT 249 248 +CONECT 250 248 252 251 +CONECT 251 250 +CONECT 252 255 253 250 254 +CONECT 253 252 +CONECT 254 252 +CONECT 255 256 257 252 +CONECT 256 255 +CONECT 257 259 255 258 +CONECT 258 257 +CONECT 259 261 260 271 257 +CONECT 260 259 +CONECT 261 267 262 263 259 +CONECT 262 261 +CONECT 263 265 261 264 266 +CONECT 264 263 +CONECT 265 263 +CONECT 266 263 +CONECT 267 269 268 270 261 +CONECT 268 267 +CONECT 269 267 +CONECT 270 267 +CONECT 271 273 259 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 273 284 277 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 274 278 285 286 +CONECT 278 279 280 277 +CONECT 279 282 288 278 +CONECT 280 281 278 287 +CONECT 281 289 282 280 +CONECT 282 893 281 279 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 293 294 302 290 +CONECT 293 292 +CONECT 294 295 296 292 300 +CONECT 295 294 +CONECT 296 299 298 294 297 +CONECT 297 296 +CONECT 298 296 +CONECT 299 296 +CONECT 300 294 301 +CONECT 301 300 +CONECT 302 304 292 303 +CONECT 303 302 +CONECT 304 314 305 302 +CONECT 305 306 308 304 315 +CONECT 306 307 321 305 +CONECT 307 306 +CONECT 308 316 317 305 309 +CONECT 309 308 310 311 +CONECT 310 319 309 313 +CONECT 311 309 318 312 +CONECT 312 313 311 320 +CONECT 313 310 893 312 +CONECT 314 304 +CONECT 315 305 +CONECT 316 308 +CONECT 317 308 +CONECT 318 311 +CONECT 319 310 +CONECT 320 312 +CONECT 321 323 306 322 +CONECT 322 321 +CONECT 323 334 324 321 325 +CONECT 324 323 +CONECT 325 323 328 327 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 330 331 325 329 +CONECT 329 328 +CONECT 330 328 +CONECT 331 332 328 333 +CONECT 332 331 +CONECT 333 331 +CONECT 334 336 335 323 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 344 340 339 336 +CONECT 339 338 +CONECT 340 342 341 338 343 +CONECT 341 340 +CONECT 342 340 +CONECT 343 340 +CONECT 344 346 345 338 +CONECT 345 344 +CONECT 346 348 347 344 +CONECT 347 346 +CONECT 348 360 350 349 346 +CONECT 349 348 +CONECT 350 351 356 348 352 +CONECT 351 350 +CONECT 352 350 354 355 353 +CONECT 353 352 +CONECT 354 352 +CONECT 355 352 +CONECT 356 357 358 350 359 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 +CONECT 360 361 362 348 +CONECT 361 360 +CONECT 362 364 360 363 +CONECT 363 362 +CONECT 364 366 365 372 362 +CONECT 365 364 +CONECT 366 369 367 368 364 +CONECT 367 366 +CONECT 368 366 +CONECT 369 370 371 366 +CONECT 370 369 +CONECT 371 369 +CONECT 372 364 374 373 +CONECT 373 372 +CONECT 374 375 376 372 +CONECT 375 374 +CONECT 376 378 374 396 377 +CONECT 377 376 +CONECT 378 381 380 379 376 +CONECT 379 378 +CONECT 380 378 +CONECT 381 382 395 378 +CONECT 382 384 383 381 +CONECT 383 382 +CONECT 384 385 386 382 +CONECT 385 384 +CONECT 386 387 384 395 +CONECT 387 388 389 386 +CONECT 388 387 +CONECT 389 390 387 391 +CONECT 390 389 +CONECT 391 389 392 393 +CONECT 392 391 +CONECT 393 391 395 394 +CONECT 394 393 +CONECT 395 386 393 381 +CONECT 396 398 376 397 +CONECT 397 396 +CONECT 398 399 400 396 +CONECT 399 398 +CONECT 400 402 401 398 406 +CONECT 401 400 +CONECT 402 405 404 403 400 +CONECT 403 402 +CONECT 404 402 +CONECT 405 402 +CONECT 406 400 407 408 +CONECT 407 406 +CONECT 408 406 409 410 +CONECT 409 408 +CONECT 410 408 411 412 421 +CONECT 411 410 +CONECT 412 415 413 410 414 +CONECT 413 412 +CONECT 414 412 +CONECT 415 416 417 418 412 +CONECT 416 415 +CONECT 417 415 +CONECT 418 420 415 419 +CONECT 419 418 +CONECT 420 418 +CONECT 421 410 423 422 +CONECT 422 421 +CONECT 423 424 421 425 +CONECT 424 423 +CONECT 425 423 427 431 426 +CONECT 426 425 +CONECT 427 428 430 425 429 +CONECT 428 427 +CONECT 429 427 +CONECT 430 427 +CONECT 431 433 425 432 +CONECT 432 431 +CONECT 433 434 435 431 +CONECT 434 433 +CONECT 435 437 433 436 446 +CONECT 436 435 +CONECT 437 438 439 440 435 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 442 437 441 +CONECT 441 440 +CONECT 442 440 +CONECT 443 445 444 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 435 448 447 +CONECT 447 446 +CONECT 448 449 446 450 +CONECT 449 448 +CONECT 450 448 452 451 468 +CONECT 451 450 +CONECT 452 455 453 454 450 +CONECT 453 452 +CONECT 454 452 +CONECT 455 457 458 456 452 +CONECT 456 455 +CONECT 457 455 +CONECT 458 461 459 460 455 +CONECT 459 458 +CONECT 460 458 +CONECT 461 464 462 463 458 +CONECT 462 461 +CONECT 463 461 +CONECT 464 466 465 467 461 +CONECT 465 464 +CONECT 466 464 +CONECT 467 464 +CONECT 468 450 470 469 +CONECT 469 468 +CONECT 470 471 468 472 +CONECT 471 470 +CONECT 472 470 474 473 488 +CONECT 473 472 +CONECT 474 477 475 472 476 +CONECT 475 474 +CONECT 476 474 +CONECT 477 478 486 474 +CONECT 478 480 479 477 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 483 480 484 +CONECT 483 482 +CONECT 484 482 485 486 +CONECT 485 484 +CONECT 486 484 477 487 +CONECT 487 486 +CONECT 488 490 472 489 +CONECT 489 488 +CONECT 490 491 492 488 +CONECT 491 490 +CONECT 492 494 490 502 493 +CONECT 493 492 +CONECT 494 495 500 496 492 +CONECT 495 494 +CONECT 496 498 494 499 497 +CONECT 497 496 +CONECT 498 496 +CONECT 499 496 +CONECT 500 501 494 +CONECT 501 500 +CONECT 502 504 492 503 +CONECT 503 502 +CONECT 504 505 506 502 +CONECT 505 504 +CONECT 506 508 504 507 524 +CONECT 507 506 +CONECT 508 511 509 510 506 +CONECT 509 508 +CONECT 510 508 +CONECT 511 514 513 512 508 +CONECT 512 511 +CONECT 513 511 +CONECT 514 517 515 516 511 +CONECT 515 514 +CONECT 516 514 +CONECT 517 519 518 520 514 +CONECT 518 517 +CONECT 519 517 +CONECT 520 522 517 523 521 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 506 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 530 529 534 +CONECT 529 528 +CONECT 530 533 531 528 532 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 536 540 551 539 +CONECT 539 538 +CONECT 540 542 541 538 543 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 544 545 546 +CONECT 544 543 +CONECT 545 543 +CONECT 546 543 547 +CONECT 547 546 550 548 549 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 553 538 552 +CONECT 552 551 +CONECT 553 554 555 551 +CONECT 554 553 +CONECT 555 557 553 561 556 +CONECT 556 555 +CONECT 557 558 560 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 557 +CONECT 561 563 555 562 +CONECT 562 561 +CONECT 563 564 561 565 +CONECT 564 563 +CONECT 565 567 563 566 575 +CONECT 566 565 +CONECT 567 570 568 569 565 +CONECT 568 567 +CONECT 569 567 +CONECT 570 572 571 567 +CONECT 571 570 +CONECT 572 573 574 570 +CONECT 573 572 +CONECT 574 572 +CONECT 575 565 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 581 580 587 +CONECT 580 579 +CONECT 581 584 582 579 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 586 585 581 +CONECT 585 584 +CONECT 586 584 +CONECT 587 579 589 588 +CONECT 588 587 +CONECT 589 590 587 591 +CONECT 590 589 +CONECT 591 589 593 606 592 +CONECT 592 591 +CONECT 593 595 594 591 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 593 602 597 598 +CONECT 597 596 +CONECT 598 596 599 600 601 +CONECT 599 598 +CONECT 600 598 +CONECT 601 598 +CONECT 602 603 605 604 596 +CONECT 603 602 +CONECT 604 602 +CONECT 605 602 +CONECT 606 608 591 607 +CONECT 607 606 +CONECT 608 609 610 606 +CONECT 609 608 +CONECT 610 613 608 611 612 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 610 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 637 618 619 615 +CONECT 618 617 +CONECT 619 622 617 621 620 +CONECT 620 619 +CONECT 621 619 +CONECT 622 623 624 625 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 627 622 626 628 +CONECT 626 625 +CONECT 627 625 +CONECT 628 625 629 630 +CONECT 629 628 +CONECT 630 628 634 631 +CONECT 631 630 632 633 +CONECT 632 631 +CONECT 633 631 +CONECT 634 635 630 636 +CONECT 635 634 +CONECT 636 634 +CONECT 637 639 638 617 +CONECT 638 637 +CONECT 639 641 640 637 +CONECT 640 639 +CONECT 641 643 649 642 639 +CONECT 642 641 +CONECT 643 646 644 645 641 +CONECT 644 643 +CONECT 645 643 +CONECT 646 648 647 643 +CONECT 647 646 +CONECT 648 646 +CONECT 649 651 650 641 +CONECT 650 649 +CONECT 651 653 649 652 +CONECT 652 651 +CONECT 653 656 654 655 651 +CONECT 654 653 +CONECT 655 653 +CONECT 656 658 657 653 +CONECT 657 656 +CONECT 658 660 659 656 +CONECT 659 658 +CONECT 660 662 661 671 658 +CONECT 661 660 +CONECT 662 664 665 663 660 +CONECT 663 662 +CONECT 664 662 +CONECT 665 667 668 662 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 665 669 670 +CONECT 669 668 +CONECT 670 668 +CONECT 671 673 660 672 +CONECT 672 671 +CONECT 673 674 675 671 +CONECT 674 673 +CONECT 675 689 673 676 677 +CONECT 676 675 +CONECT 677 675 678 679 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 681 687 +CONECT 681 682 680 683 +CONECT 682 681 +CONECT 683 681 685 684 +CONECT 684 683 +CONECT 685 687 683 686 +CONECT 686 685 +CONECT 687 680 688 685 +CONECT 688 687 +CONECT 689 690 691 675 +CONECT 690 689 +CONECT 691 693 689 692 +CONECT 692 691 +CONECT 693 694 695 703 691 +CONECT 694 693 +CONECT 695 697 701 693 696 +CONECT 696 695 +CONECT 697 698 699 700 695 +CONECT 698 697 +CONECT 699 697 +CONECT 700 697 +CONECT 701 702 695 +CONECT 702 701 +CONECT 703 705 693 704 +CONECT 704 703 +CONECT 705 706 707 703 +CONECT 706 705 +CONECT 707 724 709 705 708 +CONECT 708 707 +CONECT 709 712 710 707 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 715 713 709 +CONECT 713 712 +CONECT 714 712 +CONECT 715 718 716 712 717 +CONECT 716 715 +CONECT 717 715 +CONECT 718 721 720 719 715 +CONECT 719 718 +CONECT 720 718 +CONECT 721 722 723 718 +CONECT 722 721 +CONECT 723 721 +CONECT 724 725 726 707 +CONECT 725 724 +CONECT 726 728 724 727 +CONECT 727 726 +CONECT 728 729 736 730 726 +CONECT 729 728 +CONECT 730 733 728 731 732 +CONECT 731 730 +CONECT 732 730 +CONECT 733 735 730 734 +CONECT 734 733 +CONECT 735 733 +CONECT 736 738 728 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 742 738 748 741 +CONECT 741 740 +CONECT 742 744 743 745 740 +CONECT 743 742 +CONECT 744 742 +CONECT 745 746 742 747 +CONECT 746 745 +CONECT 747 745 +CONECT 748 750 740 749 +CONECT 749 748 +CONECT 750 751 752 748 +CONECT 751 750 +CONECT 752 754 753 750 758 +CONECT 753 752 +CONECT 754 757 756 755 752 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 752 759 760 +CONECT 759 758 +CONECT 760 758 761 762 +CONECT 761 760 +CONECT 762 760 763 764 772 +CONECT 763 762 +CONECT 764 766 762 770 765 +CONECT 765 764 +CONECT 766 767 769 768 764 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 762 774 773 +CONECT 773 772 +CONECT 774 775 776 772 +CONECT 775 774 +CONECT 776 777 774 778 794 +CONECT 777 776 +CONECT 778 781 776 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 784 782 783 778 +CONECT 782 781 +CONECT 783 781 +CONECT 784 787 786 785 781 +CONECT 785 784 +CONECT 786 784 +CONECT 787 790 789 788 784 +CONECT 788 787 +CONECT 789 787 +CONECT 790 792 793 791 787 +CONECT 791 790 +CONECT 792 790 +CONECT 793 790 +CONECT 794 776 796 795 +CONECT 795 794 +CONECT 796 797 794 798 +CONECT 797 796 +CONECT 798 796 808 800 799 +CONECT 799 798 +CONECT 800 801 798 806 802 +CONECT 801 800 +CONECT 802 800 805 804 803 +CONECT 803 802 +CONECT 804 802 +CONECT 805 802 +CONECT 806 807 800 +CONECT 807 806 +CONECT 808 809 798 810 +CONECT 809 808 +CONECT 810 808 812 811 +CONECT 811 810 +CONECT 812 813 810 814 828 +CONECT 813 812 +CONECT 814 817 812 816 815 +CONECT 815 814 +CONECT 816 814 +CONECT 817 826 818 814 +CONECT 818 820 817 819 +CONECT 819 818 +CONECT 820 822 821 818 +CONECT 821 820 +CONECT 822 823 824 820 +CONECT 823 822 +CONECT 824 825 822 826 +CONECT 825 824 +CONECT 826 824 827 817 +CONECT 827 826 +CONECT 828 812 830 829 +CONECT 829 828 +CONECT 830 831 828 832 +CONECT 831 830 +CONECT 832 834 830 842 833 +CONECT 833 832 +CONECT 834 840 836 835 832 +CONECT 835 834 +CONECT 836 837 838 834 839 +CONECT 837 836 +CONECT 838 836 +CONECT 839 836 +CONECT 840 841 834 +CONECT 841 840 +CONECT 842 843 832 844 +CONECT 843 842 +CONECT 844 842 846 845 +CONECT 845 844 +CONECT 846 847 853 844 848 +CONECT 847 846 +CONECT 848 846 851 849 850 +CONECT 849 848 +CONECT 850 848 +CONECT 851 852 848 +CONECT 852 851 +CONECT 853 855 854 846 +CONECT 854 853 +CONECT 855 857 856 853 +CONECT 856 855 +CONECT 857 859 858 855 875 +CONECT 858 857 +CONECT 859 861 860 862 857 +CONECT 860 859 +CONECT 861 859 +CONECT 862 865 859 864 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 868 866 867 862 +CONECT 866 865 +CONECT 867 865 +CONECT 868 869 870 871 865 +CONECT 869 868 +CONECT 870 868 +CONECT 871 868 873 872 874 +CONECT 872 871 +CONECT 873 871 +CONECT 874 871 +CONECT 875 857 877 876 +CONECT 876 875 +CONECT 877 878 879 875 +CONECT 878 877 +CONECT 879 890 877 881 880 +CONECT 880 879 +CONECT 881 883 882 879 884 +CONECT 882 881 +CONECT 883 881 +CONECT 884 881 885 886 887 +CONECT 885 884 +CONECT 886 884 +CONECT 887 884 889 888 +CONECT 888 887 +CONECT 889 887 +CONECT 890 892 891 879 +CONECT 891 890 +CONECT 892 890 +CONECT 893 87 313 894 282 +CONECT 894 893 896 +CONECT 895 898 896 899 897 +CONECT 896 894 895 +CONECT 897 895 +CONECT 898 895 +CONECT 899 895 +CONECT 900 901 +CONECT 901 900 902 +CONECT 902 901 +MASTER 0 0 0 0 0 0 0 0 902 0 902 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_27.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_27.pdb new file mode 100644 index 0000000..7cf8756 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_27.pdb @@ -0,0 +1,1823 @@ +COMPND fitness: -8.6139 59.35000000000082 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 58.230 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.032 37.890 23.485 1.00 0.00 N +ATOM 2 H1 MET 1 15.052 38.285 24.420 1.00 0.00 H +ATOM 3 H2 MET 1 14.189 38.186 23.020 1.00 0.00 H +ATOM 4 H3 MET 1 15.854 38.244 23.012 1.00 0.00 H +ATOM 5 CA MET 1 15.102 36.424 23.580 1.00 0.00 C +ATOM 6 HA MET 1 14.171 36.074 24.029 1.00 0.00 H +ATOM 7 CB MET 1 15.247 35.782 22.188 1.00 0.00 C +ATOM 8 HB2 MET 1 14.372 36.039 21.593 1.00 0.00 H +ATOM 9 HB3 MET 1 16.129 36.194 21.695 1.00 0.00 H +ATOM 10 CG MET 1 15.389 34.250 22.238 1.00 0.00 C +ATOM 11 HG2 MET 1 16.285 34.002 22.810 1.00 0.00 H +ATOM 12 HG3 MET 1 14.529 33.829 22.763 1.00 0.00 H +ATOM 13 SD MET 1 15.540 33.426 20.626 1.00 0.00 S +ATOM 14 CE MET 1 13.842 33.558 19.997 1.00 0.00 C +ATOM 15 HE1 MET 1 13.543 34.604 19.936 1.00 0.00 H +ATOM 16 HE2 MET 1 13.791 33.118 19.000 1.00 0.00 H +ATOM 17 HE3 MET 1 13.161 33.021 20.657 1.00 0.00 H +ATOM 18 C MET 1 16.246 36.011 24.497 1.00 0.00 C +ATOM 19 O MET 1 17.391 36.382 24.261 1.00 0.00 O +ATOM 20 N GLN 2 15.948 35.181 25.499 1.00 0.00 N +ATOM 21 H GLN 2 14.983 34.949 25.670 1.00 0.00 H +ATOM 22 CA GLN 2 16.940 34.500 26.334 1.00 0.00 C +ATOM 23 HA GLN 2 17.700 35.213 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 16.220 33.957 27.585 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.294 33.475 27.271 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.818 33.188 28.065 1.00 0.00 H +ATOM 27 CG GLN 2 15.884 35.042 28.625 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.500 35.926 28.124 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.089 34.662 29.268 1.00 0.00 H +ATOM 30 CD GLN 2 17.056 35.448 29.523 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.205 35.070 29.330 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.801 36.187 30.577 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.571 36.413 31.183 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.870 36.549 30.727 1.00 0.00 H +ATOM 35 C GLN 2 17.663 33.387 25.540 1.00 0.00 C +ATOM 36 O GLN 2 17.283 32.215 25.606 1.00 0.00 O +ATOM 37 N TYR 3 18.698 33.750 24.774 1.00 0.00 N +ATOM 38 H TYR 3 18.966 34.730 24.779 1.00 0.00 H +ATOM 39 CA TYR 3 19.564 32.808 24.049 1.00 0.00 C +ATOM 40 HA TYR 3 18.952 32.213 23.371 1.00 0.00 H +ATOM 41 CB TYR 3 20.605 33.570 23.216 1.00 0.00 C +ATOM 42 HB2 TYR 3 21.080 34.333 23.836 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.389 32.873 22.915 1.00 0.00 H +ATOM 44 CG TYR 3 20.050 34.214 21.959 1.00 0.00 C +ATOM 45 CD1 TYR 3 20.021 33.476 20.760 1.00 0.00 C +ATOM 46 HD1 TYR 3 20.396 32.461 20.740 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.525 34.061 19.579 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.525 33.501 18.656 1.00 0.00 H +ATOM 49 CZ TYR 3 19.046 35.388 19.601 1.00 0.00 C +ATOM 50 OH TYR 3 18.572 35.950 18.459 1.00 0.00 O +ATOM 51 HH TYR 3 18.641 35.345 17.719 1.00 0.00 H +ATOM 52 CE2 TYR 3 19.071 36.127 20.803 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.708 37.144 20.808 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.577 35.541 21.979 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.603 36.114 22.898 1.00 0.00 H +ATOM 56 C TYR 3 20.260 31.852 25.027 1.00 0.00 C +ATOM 57 O TYR 3 20.703 32.270 26.099 1.00 0.00 O +ATOM 58 N LYS 4 20.345 30.561 24.688 1.00 0.00 N +ATOM 59 H LYS 4 20.129 30.306 23.726 1.00 0.00 H +ATOM 60 CA LYS 4 20.880 29.504 25.562 1.00 0.00 C +ATOM 61 HA LYS 4 20.598 29.722 26.588 1.00 0.00 H +ATOM 62 CB LYS 4 20.269 28.140 25.173 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.242 28.061 24.086 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.929 27.347 25.529 1.00 0.00 H +ATOM 65 CG LYS 4 18.858 27.834 25.724 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.611 26.813 25.430 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.884 27.869 26.813 1.00 0.00 H +ATOM 68 CD LYS 4 17.745 28.763 25.207 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.865 29.752 25.642 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.861 28.856 24.126 1.00 0.00 H +ATOM 71 CE LYS 4 16.317 28.247 25.480 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.622 28.836 24.873 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.245 27.212 25.131 1.00 0.00 H +ATOM 74 NZ LYS 4 15.897 28.335 26.906 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.903 29.285 27.256 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.934 28.005 27.014 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.466 27.767 27.514 1.00 0.00 H +ATOM 78 C LYS 4 22.412 29.477 25.548 1.00 0.00 C +ATOM 79 O LYS 4 23.071 29.880 24.592 1.00 0.00 O +HETATM 80 N HX1 5 23.007 28.981 26.627 1.00 0.00 N +HETATM 81 CA HX1 5 24.460 28.845 26.773 1.00 0.00 C +HETATM 82 C HX1 5 24.796 27.645 27.662 1.00 0.00 C +HETATM 83 O HX1 5 24.340 27.577 28.806 1.00 0.00 O +HETATM 84 CB HX1 5 25.033 30.159 27.327 1.00 0.00 C +HETATM 85 CG HX1 5 26.539 30.225 27.456 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.449 29.343 26.938 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.208 31.201 28.202 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.505 30.865 28.104 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.676 29.733 27.398 1.00 0.00 N +HETATM 90 H HX1 5 22.427 28.795 27.442 1.00 0.00 H +HETATM 91 HA HX1 5 24.902 28.675 25.791 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.596 30.348 28.308 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.718 30.974 26.672 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.261 28.453 26.352 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.295 31.359 28.650 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.513 29.152 27.398 1.00 0.00 H +ATOM 97 N ILE 6 25.558 26.698 27.109 1.00 0.00 N +ATOM 98 H ILE 6 25.865 26.827 26.149 1.00 0.00 H +ATOM 99 CA ILE 6 26.057 25.492 27.782 1.00 0.00 C +ATOM 100 HA ILE 6 25.496 25.370 28.711 1.00 0.00 H +ATOM 101 CB ILE 6 25.773 24.233 26.921 1.00 0.00 C +ATOM 102 HB ILE 6 26.209 24.391 25.935 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.391 22.952 27.518 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.997 22.767 28.520 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.163 22.095 26.887 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.478 23.022 27.549 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.237 24.070 26.781 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.798 23.960 27.775 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.823 24.973 26.329 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.780 22.889 25.915 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.952 21.947 26.440 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.710 22.986 25.724 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.318 22.891 24.965 1.00 0.00 H +ATOM 114 C ILE 6 27.527 25.680 28.217 1.00 0.00 C +ATOM 115 O ILE 6 28.274 26.510 27.697 1.00 0.00 O +ATOM 116 N VAL 7 27.881 24.955 29.269 1.00 0.00 N +ATOM 117 H VAL 7 27.230 24.228 29.521 1.00 0.00 H +ATOM 118 CA VAL 7 28.885 25.280 30.286 1.00 0.00 C +ATOM 119 HA VAL 7 28.899 26.361 30.388 1.00 0.00 H +ATOM 120 CB VAL 7 28.305 24.690 31.587 1.00 0.00 C +ATOM 121 HB VAL 7 27.270 25.027 31.680 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.310 23.156 31.623 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.329 22.770 31.575 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.844 22.812 32.544 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.743 22.754 30.783 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.019 25.200 32.822 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.992 26.289 32.841 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.523 24.825 33.718 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.038 24.839 32.791 1.00 0.00 H +ATOM 130 C VAL 7 30.328 24.809 29.982 1.00 0.00 C +ATOM 131 O VAL 7 30.510 23.762 29.361 1.00 0.00 O +ATOM 132 N ARG 8 31.371 25.540 30.441 1.00 0.00 N +ATOM 133 H ARG 8 31.173 26.468 30.803 1.00 0.00 H +ATOM 134 CA ARG 8 32.774 25.040 30.384 1.00 0.00 C +ATOM 135 HA ARG 8 32.898 24.643 29.381 1.00 0.00 H +ATOM 136 CB ARG 8 33.850 26.145 30.575 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.692 25.904 29.921 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.447 27.099 30.241 1.00 0.00 H +ATOM 139 CG ARG 8 34.419 26.268 32.010 1.00 0.00 C +ATOM 140 HG2 ARG 8 33.618 26.226 32.748 1.00 0.00 H +ATOM 141 HG3 ARG 8 35.098 25.425 32.208 1.00 0.00 H +ATOM 142 CD ARG 8 35.213 27.554 32.270 1.00 0.00 C +ATOM 143 HD2 ARG 8 35.684 27.477 33.250 1.00 0.00 H +ATOM 144 HD3 ARG 8 36.004 27.653 31.522 1.00 0.00 H +ATOM 145 NE ARG 8 34.359 28.760 32.312 1.00 0.00 N +ATOM 146 HE ARG 8 33.391 28.671 32.001 1.00 0.00 H +ATOM 147 CZ ARG 8 34.735 29.972 32.673 1.00 0.00 C +ATOM 148 NH1 ARG 8 33.845 30.908 32.793 1.00 0.00 N +ATOM 149 HH11 ARG 8 32.865 30.655 32.907 1.00 0.00 H +ATOM 150 HH12 ARG 8 34.087 31.826 33.086 1.00 0.00 H +ATOM 151 NH2 ARG 8 35.981 30.298 32.869 1.00 0.00 N +ATOM 152 HH21 ARG 8 36.689 29.608 32.684 1.00 0.00 H +ATOM 153 HH22 ARG 8 36.249 31.263 32.970 1.00 0.00 H +ATOM 154 C ARG 8 33.043 23.864 31.329 1.00 0.00 C +ATOM 155 O ARG 8 32.491 23.812 32.430 1.00 0.00 O +ATOM 156 N GLY 9 34.013 23.033 30.959 1.00 0.00 N +ATOM 157 H GLY 9 34.412 23.188 30.045 1.00 0.00 H +ATOM 158 CA GLY 9 34.418 21.812 31.656 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.456 21.582 31.396 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.350 21.969 32.737 1.00 0.00 H +ATOM 161 C GLY 9 33.531 20.622 31.270 1.00 0.00 C +ATOM 162 O GLY 9 32.501 20.784 30.623 1.00 0.00 O +ATOM 163 N LYS 10 33.938 19.421 31.695 1.00 0.00 N +ATOM 164 H LYS 10 34.858 19.357 32.104 1.00 0.00 H +ATOM 165 CA LYS 10 33.167 18.172 31.537 1.00 0.00 C +ATOM 166 HA LYS 10 32.265 18.405 30.967 1.00 0.00 H +ATOM 167 CB LYS 10 33.999 17.187 30.692 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.665 17.760 30.045 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.620 16.575 31.342 1.00 0.00 H +ATOM 170 CG LYS 10 33.147 16.289 29.780 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.542 15.614 30.385 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.485 16.919 29.185 1.00 0.00 H +ATOM 173 CD LYS 10 34.041 15.479 28.830 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.714 16.160 28.307 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.637 14.772 29.408 1.00 0.00 H +ATOM 176 CE LYS 10 33.215 14.724 27.785 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.612 13.962 28.284 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.537 15.436 27.307 1.00 0.00 H +ATOM 179 NZ LYS 10 34.087 14.125 26.749 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.788 13.515 27.142 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.564 13.643 26.033 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.617 14.870 26.275 1.00 0.00 H +ATOM 183 C LYS 10 32.663 17.597 32.874 1.00 0.00 C +ATOM 184 O LYS 10 31.941 16.610 32.901 1.00 0.00 O +ATOM 185 N ILE 11 33.052 18.229 33.989 1.00 0.00 N +ATOM 186 H ILE 11 33.666 19.015 33.863 1.00 0.00 H +ATOM 187 CA ILE 11 32.643 17.905 35.373 1.00 0.00 C +ATOM 188 HA ILE 11 32.482 16.826 35.453 1.00 0.00 H +ATOM 189 CB ILE 11 33.767 18.297 36.363 1.00 0.00 C +ATOM 190 HB ILE 11 33.403 18.086 37.372 1.00 0.00 H +ATOM 191 CG2 ILE 11 35.005 17.412 36.140 1.00 0.00 C +ATOM 192 HG21 ILE 11 35.472 17.631 35.181 1.00 0.00 H +ATOM 193 HG22 ILE 11 35.731 17.578 36.936 1.00 0.00 H +ATOM 194 HG23 ILE 11 34.712 16.362 36.168 1.00 0.00 H +ATOM 195 CG1 ILE 11 34.107 19.808 36.287 1.00 0.00 C +ATOM 196 HG12 ILE 11 34.600 20.029 35.340 1.00 0.00 H +ATOM 197 HG13 ILE 11 33.186 20.388 36.330 1.00 0.00 H +ATOM 198 CD1 ILE 11 34.999 20.303 37.429 1.00 0.00 C +ATOM 199 HD11 ILE 11 35.981 19.833 37.377 1.00 0.00 H +ATOM 200 HD12 ILE 11 35.125 21.383 37.341 1.00 0.00 H +ATOM 201 HD13 ILE 11 34.533 20.078 38.388 1.00 0.00 H +ATOM 202 C ILE 11 31.323 18.566 35.807 1.00 0.00 C +ATOM 203 O ILE 11 30.775 18.209 36.845 1.00 0.00 O +ATOM 204 N ARG 12 30.824 19.541 35.039 1.00 0.00 N +ATOM 205 H ARG 12 31.295 19.720 34.165 1.00 0.00 H +ATOM 206 CA ARG 12 29.542 20.230 35.236 1.00 0.00 C +ATOM 207 HA ARG 12 28.937 19.626 35.917 1.00 0.00 H +ATOM 208 CB ARG 12 29.747 21.620 35.881 1.00 0.00 C +ATOM 209 HB2 ARG 12 28.769 22.073 36.033 1.00 0.00 H +ATOM 210 HB3 ARG 12 30.186 21.478 36.870 1.00 0.00 H +ATOM 211 CG ARG 12 30.629 22.607 35.088 1.00 0.00 C +ATOM 212 HG2 ARG 12 31.619 22.171 34.941 1.00 0.00 H +ATOM 213 HG3 ARG 12 30.175 22.763 34.106 1.00 0.00 H +ATOM 214 CD ARG 12 30.771 23.969 35.806 1.00 0.00 C +ATOM 215 HD2 ARG 12 29.770 24.317 36.078 1.00 0.00 H +ATOM 216 HD3 ARG 12 31.366 23.832 36.716 1.00 0.00 H +ATOM 217 NE ARG 12 31.412 24.962 34.905 1.00 0.00 N +ATOM 218 HE ARG 12 31.855 24.588 34.067 1.00 0.00 H +ATOM 219 CZ ARG 12 31.217 26.273 34.896 1.00 0.00 C +ATOM 220 NH1 ARG 12 31.492 26.958 33.828 1.00 0.00 N +ATOM 221 HH11 ARG 12 31.764 26.509 32.982 1.00 0.00 H +ATOM 222 HH12 ARG 12 31.304 27.960 33.851 1.00 0.00 H +ATOM 223 NH2 ARG 12 30.725 26.938 35.900 1.00 0.00 N +ATOM 224 HH21 ARG 12 30.503 26.473 36.762 1.00 0.00 H +ATOM 225 HH22 ARG 12 30.636 27.941 35.812 1.00 0.00 H +ATOM 226 C ARG 12 28.807 20.265 33.898 1.00 0.00 C +ATOM 227 O ARG 12 29.457 20.414 32.873 1.00 0.00 O +ATOM 228 N LYS 13 27.485 20.085 33.906 1.00 0.00 N +ATOM 229 H LYS 13 27.062 19.931 34.808 1.00 0.00 H +ATOM 230 CA LYS 13 26.656 19.821 32.705 1.00 0.00 C +ATOM 231 HA LYS 13 27.237 20.100 31.819 1.00 0.00 H +ATOM 232 CB LYS 13 26.386 18.302 32.647 1.00 0.00 C +ATOM 233 HB2 LYS 13 27.289 17.788 32.983 1.00 0.00 H +ATOM 234 HB3 LYS 13 25.583 18.070 33.348 1.00 0.00 H +ATOM 235 CG LYS 13 26.051 17.755 31.243 1.00 0.00 C +ATOM 236 HG2 LYS 13 25.150 18.227 30.848 1.00 0.00 H +ATOM 237 HG3 LYS 13 26.886 17.982 30.573 1.00 0.00 H +ATOM 238 CD LYS 13 25.854 16.229 31.284 1.00 0.00 C +ATOM 239 HD2 LYS 13 25.822 15.851 30.262 1.00 0.00 H +ATOM 240 HD3 LYS 13 26.719 15.780 31.779 1.00 0.00 H +ATOM 241 CE LYS 13 24.557 15.828 32.008 1.00 0.00 C +ATOM 242 HE2 LYS 13 24.367 16.547 32.810 1.00 0.00 H +ATOM 243 HE3 LYS 13 23.717 15.886 31.307 1.00 0.00 H +ATOM 244 NZ LYS 13 24.655 14.473 32.605 1.00 0.00 N +ATOM 245 HZ1 LYS 13 25.496 14.393 33.164 1.00 0.00 H +ATOM 246 HZ2 LYS 13 23.911 14.319 33.283 1.00 0.00 H +ATOM 247 HZ3 LYS 13 24.624 13.727 31.923 1.00 0.00 H +ATOM 248 C LYS 13 25.382 20.686 32.653 1.00 0.00 C +ATOM 249 O LYS 13 24.396 20.338 32.008 1.00 0.00 O +ATOM 250 N GLY 14 25.390 21.797 33.396 1.00 0.00 N +ATOM 251 H GLY 14 26.240 22.034 33.878 1.00 0.00 H +ATOM 252 CA GLY 14 24.279 22.743 33.471 1.00 0.00 C +ATOM 253 HA2 GLY 14 23.346 22.193 33.609 1.00 0.00 H +ATOM 254 HA3 GLY 14 24.412 23.393 34.338 1.00 0.00 H +ATOM 255 C GLY 14 24.126 23.629 32.230 1.00 0.00 C +ATOM 256 O GLY 14 24.994 23.693 31.357 1.00 0.00 O +ATOM 257 N VAL 15 23.011 24.357 32.184 1.00 0.00 N +ATOM 258 H VAL 15 22.364 24.269 32.955 1.00 0.00 H +ATOM 259 CA VAL 15 22.635 25.283 31.111 1.00 0.00 C +ATOM 260 HA VAL 15 23.539 25.582 30.580 1.00 0.00 H +ATOM 261 CB VAL 15 21.704 24.588 30.090 1.00 0.00 C +ATOM 262 HB VAL 15 22.230 23.712 29.707 1.00 0.00 H +ATOM 263 CG1 VAL 15 20.378 24.115 30.710 1.00 0.00 C +ATOM 264 HG11 VAL 15 19.801 24.961 31.086 1.00 0.00 H +ATOM 265 HG12 VAL 15 19.795 23.590 29.951 1.00 0.00 H +ATOM 266 HG13 VAL 15 20.575 23.417 31.523 1.00 0.00 H +ATOM 267 CG2 VAL 15 21.376 25.492 28.895 1.00 0.00 C +ATOM 268 HG21 VAL 15 22.296 25.873 28.452 1.00 0.00 H +ATOM 269 HG22 VAL 15 20.850 24.907 28.139 1.00 0.00 H +ATOM 270 HG23 VAL 15 20.741 26.323 29.197 1.00 0.00 H +ATOM 271 C VAL 15 22.011 26.536 31.718 1.00 0.00 C +ATOM 272 O VAL 15 21.371 26.478 32.766 1.00 0.00 O +HETATM 273 N HY1 16 22.222 27.683 31.080 1.00 0.00 N +HETATM 274 CA HY1 16 21.629 28.974 31.445 1.00 0.00 C +HETATM 275 C HY1 16 21.488 29.839 30.179 1.00 0.00 C +HETATM 276 O HY1 16 21.727 29.351 29.071 1.00 0.00 O +HETATM 277 CB HY1 16 22.483 29.609 32.562 1.00 0.00 C +HETATM 278 CG HY1 16 23.901 29.876 32.132 1.00 0.00 C +HETATM 279 CD2 HY1 16 24.323 31.033 31.545 1.00 0.00 C +HETATM 280 ND1 HY1 16 24.957 28.985 32.101 1.00 0.00 N +HETATM 281 CE1 HY1 16 25.996 29.605 31.500 1.00 0.00 C +HETATM 282 NE2 HY1 16 25.638 30.855 31.136 1.00 0.00 N +HETATM 283 H HY1 16 22.768 27.657 30.220 1.00 0.00 H +HETATM 284 HA HY1 16 20.627 28.801 31.847 1.00 0.00 H +HETATM 285 HB2 HY1 16 22.021 30.550 32.882 1.00 0.00 H +HETATM 286 HB3 HY1 16 22.494 28.951 33.430 1.00 0.00 H +HETATM 287 HD1 HY1 16 24.957 28.043 32.480 1.00 0.00 H +HETATM 288 HD2 HY1 16 23.726 31.919 31.369 1.00 0.00 H +HETATM 289 HE1 HY1 16 26.987 29.172 31.342 1.00 0.00 H +ATOM 290 N THR 17 21.073 31.101 30.306 1.00 0.00 N +ATOM 291 H THR 17 20.872 31.482 31.218 1.00 0.00 H +ATOM 292 CA THR 17 20.682 31.961 29.172 1.00 0.00 C +ATOM 293 HA THR 17 21.137 31.542 28.268 1.00 0.00 H +ATOM 294 CB THR 17 19.170 31.983 28.991 1.00 0.00 C +ATOM 295 HB THR 17 18.926 32.625 28.144 1.00 0.00 H +ATOM 296 CG2 THR 17 18.520 30.613 28.727 1.00 0.00 C +ATOM 297 HG21 THR 17 18.703 29.936 29.556 1.00 0.00 H +ATOM 298 HG22 THR 17 17.456 30.731 28.604 1.00 0.00 H +ATOM 299 HG23 THR 17 18.927 30.182 27.819 1.00 0.00 H +ATOM 300 OG1 THR 17 18.550 32.501 30.146 1.00 0.00 O +ATOM 301 HG1 THR 17 18.532 33.469 30.028 1.00 0.00 H +ATOM 302 C THR 17 21.199 33.391 29.286 1.00 0.00 C +ATOM 303 O THR 17 21.574 33.833 30.372 1.00 0.00 O +HETATM 304 N HY2 18 21.178 34.119 28.163 1.00 0.00 N +HETATM 305 CA HY2 18 21.508 35.545 28.069 1.00 0.00 C +HETATM 306 C HY2 18 20.490 36.290 27.199 1.00 0.00 C +HETATM 307 O HY2 18 20.211 35.866 26.081 1.00 0.00 O +HETATM 308 CB HY2 18 22.941 35.728 27.554 1.00 0.00 C +HETATM 309 CG HY2 18 23.936 35.106 28.507 1.00 0.00 C +HETATM 310 CD2 HY2 18 24.623 33.940 28.336 1.00 0.00 C +HETATM 311 ND1 HY2 18 24.098 35.440 29.823 1.00 0.00 N +HETATM 312 CE1 HY2 18 24.834 34.496 30.413 1.00 0.00 C +HETATM 313 NE2 HY2 18 25.197 33.551 29.546 1.00 0.00 N +HETATM 314 H HY2 18 20.865 33.662 27.311 1.00 0.00 H +HETATM 315 HA HY2 18 21.463 35.986 29.066 1.00 0.00 H +HETATM 316 HB2 HY2 18 23.040 35.278 26.567 1.00 0.00 H +HETATM 317 HB3 HY2 18 23.158 36.790 27.444 1.00 0.00 H +HETATM 318 HD1 HY2 18 23.679 36.218 30.295 1.00 0.00 H +HETATM 319 HD2 HY2 18 24.635 33.364 27.440 1.00 0.00 H +HETATM 320 HE1 HY2 18 25.088 34.499 31.458 1.00 0.00 H +ATOM 321 N GLU 19 19.933 37.381 27.724 1.00 0.00 N +ATOM 322 H GLU 19 20.222 37.676 28.639 1.00 0.00 H +ATOM 323 CA GLU 19 18.906 38.188 27.062 1.00 0.00 C +ATOM 324 HA GLU 19 18.174 37.521 26.611 1.00 0.00 H +ATOM 325 CB GLU 19 18.207 39.045 28.134 1.00 0.00 C +ATOM 326 HB2 GLU 19 17.873 38.394 28.939 1.00 0.00 H +ATOM 327 HB3 GLU 19 18.932 39.745 28.560 1.00 0.00 H +ATOM 328 CG GLU 19 16.994 39.845 27.637 1.00 0.00 C +ATOM 329 HG2 GLU 19 16.561 40.388 28.483 1.00 0.00 H +ATOM 330 HG3 GLU 19 17.326 40.587 26.905 1.00 0.00 H +ATOM 331 CD GLU 19 15.945 38.925 27.015 1.00 0.00 C +ATOM 332 OE1 GLU 19 16.017 38.711 25.785 1.00 0.00 O +ATOM 333 OE2 GLU 19 15.115 38.361 27.754 1.00 0.00 O +ATOM 334 C GLU 19 19.508 39.062 25.946 1.00 0.00 C +ATOM 335 O GLU 19 20.496 39.763 26.180 1.00 0.00 O +ATOM 336 N ALA 20 18.922 39.028 24.741 1.00 0.00 N +ATOM 337 H ALA 20 18.112 38.424 24.628 1.00 0.00 H +ATOM 338 CA ALA 20 19.298 39.888 23.623 1.00 0.00 C +ATOM 339 HA ALA 20 19.428 40.903 23.993 1.00 0.00 H +ATOM 340 CB ALA 20 20.635 39.409 23.040 1.00 0.00 C +ATOM 341 HB1 ALA 20 20.517 38.417 22.599 1.00 0.00 H +ATOM 342 HB2 ALA 20 20.982 40.099 22.272 1.00 0.00 H +ATOM 343 HB3 ALA 20 21.399 39.361 23.814 1.00 0.00 H +ATOM 344 C ALA 20 18.232 39.912 22.513 1.00 0.00 C +ATOM 345 O ALA 20 17.358 39.044 22.412 1.00 0.00 O +ATOM 346 N VAL 21 18.340 40.897 21.608 1.00 0.00 N +ATOM 347 H VAL 21 19.048 41.608 21.757 1.00 0.00 H +ATOM 348 CA VAL 21 17.620 40.923 20.310 1.00 0.00 C +ATOM 349 HA VAL 21 16.625 40.503 20.459 1.00 0.00 H +ATOM 350 CB VAL 21 17.428 42.377 19.808 1.00 0.00 C +ATOM 351 HB VAL 21 16.787 42.339 18.922 1.00 0.00 H +ATOM 352 CG1 VAL 21 16.715 43.251 20.853 1.00 0.00 C +ATOM 353 HG11 VAL 21 17.349 43.407 21.717 1.00 0.00 H +ATOM 354 HG12 VAL 21 16.474 44.211 20.412 1.00 0.00 H +ATOM 355 HG13 VAL 21 15.794 42.771 21.164 1.00 0.00 H +ATOM 356 CG2 VAL 21 18.747 43.063 19.405 1.00 0.00 C +ATOM 357 HG21 VAL 21 19.207 42.531 18.575 1.00 0.00 H +ATOM 358 HG22 VAL 21 18.542 44.078 19.074 1.00 0.00 H +ATOM 359 HG23 VAL 21 19.438 43.093 20.241 1.00 0.00 H +ATOM 360 C VAL 21 18.303 40.081 19.228 1.00 0.00 C +ATOM 361 O VAL 21 17.710 39.833 18.191 1.00 0.00 O +ATOM 362 N ASP 22 19.547 39.668 19.459 1.00 0.00 N +ATOM 363 H ASP 22 19.965 39.897 20.343 1.00 0.00 H +ATOM 364 CA ASP 22 20.437 38.996 18.493 1.00 0.00 C +ATOM 365 HA ASP 22 19.841 38.294 17.893 1.00 0.00 H +ATOM 366 CB ASP 22 21.067 40.056 17.575 1.00 0.00 C +ATOM 367 HB2 ASP 22 20.246 40.726 17.206 1.00 0.00 H +ATOM 368 HB3 ASP 22 21.773 40.680 18.191 1.00 0.00 H +ATOM 369 CG ASP 22 21.815 39.503 16.372 1.00 0.00 C +ATOM 370 OD1 ASP 22 22.067 40.269 15.446 1.00 0.00 O +ATOM 371 OD2 ASP 22 22.107 38.275 16.330 1.00 0.00 O +ATOM 372 C ASP 22 21.508 38.185 19.258 1.00 0.00 C +ATOM 373 O ASP 22 22.023 38.632 20.289 1.00 0.00 O +ATOM 374 N TRP 23 21.909 37.023 18.740 1.00 0.00 N +ATOM 375 H TRP 23 21.648 36.853 17.784 1.00 0.00 H +ATOM 376 CA TRP 23 23.037 36.262 19.263 1.00 0.00 C +ATOM 377 HA TRP 23 22.839 36.062 20.312 1.00 0.00 H +ATOM 378 CB TRP 23 23.148 34.906 18.536 1.00 0.00 C +ATOM 379 HB2 TRP 23 23.912 34.315 19.043 1.00 0.00 H +ATOM 380 HB3 TRP 23 22.207 34.376 18.652 1.00 0.00 H +ATOM 381 CG TRP 23 23.502 34.968 17.080 1.00 0.00 C +ATOM 382 CD1 TRP 23 22.636 34.812 16.053 1.00 0.00 C +ATOM 383 HD1 TRP 23 21.580 34.592 16.155 1.00 0.00 H +ATOM 384 NE1 TRP 23 23.295 35.016 14.857 1.00 0.00 N +ATOM 385 HE1 TRP 23 22.839 34.976 13.956 1.00 0.00 H +ATOM 386 CE2 TRP 23 24.622 35.330 15.052 1.00 0.00 C +ATOM 387 CZ2 TRP 23 25.667 35.668 14.179 1.00 0.00 C +ATOM 388 HZ2 TRP 23 25.487 35.737 13.117 1.00 0.00 H +ATOM 389 CH2 TRP 23 26.949 35.906 14.707 1.00 0.00 C +ATOM 390 HH2 TRP 23 27.766 36.170 14.050 1.00 0.00 H +ATOM 391 CZ3 TRP 23 27.173 35.783 16.090 1.00 0.00 C +ATOM 392 HZ3 TRP 23 28.160 35.962 16.498 1.00 0.00 H +ATOM 393 CE3 TRP 23 26.113 35.449 16.955 1.00 0.00 C +ATOM 394 HE3 TRP 23 26.300 35.374 18.015 1.00 0.00 H +ATOM 395 CD2 TRP 23 24.802 35.240 16.464 1.00 0.00 C +ATOM 396 C TRP 23 24.351 37.060 19.175 1.00 0.00 C +ATOM 397 O TRP 23 25.200 36.931 20.058 1.00 0.00 O +ATOM 398 N ALA 24 24.502 37.947 18.180 1.00 0.00 N +ATOM 399 H ALA 24 23.785 37.982 17.454 1.00 0.00 H +ATOM 400 CA ALA 24 25.699 38.770 17.999 1.00 0.00 C +ATOM 401 HA ALA 24 26.577 38.137 18.113 1.00 0.00 H +ATOM 402 CB ALA 24 25.698 39.290 16.561 1.00 0.00 C +ATOM 403 HB1 ALA 24 24.864 39.968 16.399 1.00 0.00 H +ATOM 404 HB2 ALA 24 26.622 39.820 16.345 1.00 0.00 H +ATOM 405 HB3 ALA 24 25.607 38.464 15.859 1.00 0.00 H +ATOM 406 C ALA 24 25.845 39.927 19.019 1.00 0.00 C +ATOM 407 O ALA 24 26.930 40.500 19.164 1.00 0.00 O +ATOM 408 N GLU 25 24.772 40.254 19.740 1.00 0.00 N +ATOM 409 H GLU 25 23.907 39.773 19.535 1.00 0.00 H +ATOM 410 CA GLU 25 24.822 41.062 20.971 1.00 0.00 C +ATOM 411 HA GLU 25 25.716 41.687 20.960 1.00 0.00 H +ATOM 412 CB GLU 25 23.599 41.988 21.048 1.00 0.00 C +ATOM 413 HB2 GLU 25 22.694 41.407 20.870 1.00 0.00 H +ATOM 414 HB3 GLU 25 23.535 42.398 22.052 1.00 0.00 H +ATOM 415 CG GLU 25 23.663 43.158 20.057 1.00 0.00 C +ATOM 416 HG2 GLU 25 23.637 42.752 19.042 1.00 0.00 H +ATOM 417 HG3 GLU 25 22.769 43.773 20.176 1.00 0.00 H +ATOM 418 CD GLU 25 24.914 44.020 20.244 1.00 0.00 C +ATOM 419 OE1 GLU 25 25.151 44.519 21.370 1.00 0.00 O +ATOM 420 OE2 GLU 25 25.696 44.129 19.273 1.00 0.00 O +ATOM 421 C GLU 25 24.946 40.168 22.223 1.00 0.00 C +ATOM 422 O GLU 25 25.715 40.500 23.116 1.00 0.00 O +ATOM 423 N ALA 26 24.291 39.006 22.254 1.00 0.00 N +ATOM 424 H ALA 26 23.638 38.768 21.520 1.00 0.00 H +ATOM 425 CA ALA 26 24.483 38.019 23.343 1.00 0.00 C +ATOM 426 HA ALA 26 24.238 38.522 24.282 1.00 0.00 H +ATOM 427 CB ALA 26 23.540 36.841 23.140 1.00 0.00 C +ATOM 428 HB1 ALA 26 23.849 36.265 22.273 1.00 0.00 H +ATOM 429 HB2 ALA 26 23.569 36.192 24.016 1.00 0.00 H +ATOM 430 HB3 ALA 26 22.529 37.210 22.998 1.00 0.00 H +ATOM 431 C ALA 26 25.935 37.553 23.471 1.00 0.00 C +ATOM 432 O ALA 26 26.382 37.220 24.575 1.00 0.00 O +ATOM 433 N GLU 27 26.716 37.557 22.377 1.00 0.00 N +ATOM 434 H GLU 27 26.235 37.650 21.484 1.00 0.00 H +ATOM 435 CA GLU 27 28.155 37.345 22.376 1.00 0.00 C +ATOM 436 HA GLU 27 28.356 36.403 22.885 1.00 0.00 H +ATOM 437 CB GLU 27 28.651 37.248 20.894 1.00 0.00 C +ATOM 438 HB2 GLU 27 28.044 36.505 20.373 1.00 0.00 H +ATOM 439 HB3 GLU 27 28.517 38.201 20.425 1.00 0.00 H +ATOM 440 CG GLU 27 30.125 36.814 20.741 1.00 0.00 C +ATOM 441 HG2 GLU 27 30.731 37.258 21.583 1.00 0.00 H +ATOM 442 HG3 GLU 27 30.161 35.709 20.917 1.00 0.00 H +ATOM 443 CD GLU 27 30.707 37.156 19.408 1.00 0.00 C +ATOM 444 OE1 GLU 27 31.378 38.192 19.248 1.00 0.00 O +ATOM 445 OE2 GLU 27 30.514 36.370 18.461 1.00 0.00 O +ATOM 446 C GLU 27 28.927 38.461 23.114 1.00 0.00 C +ATOM 447 O GLU 27 29.762 38.176 23.966 1.00 0.00 O +ATOM 448 N LYS 28 28.590 39.723 22.848 1.00 0.00 N +ATOM 449 H LYS 28 27.859 39.892 22.163 1.00 0.00 H +ATOM 450 CA LYS 28 29.173 40.896 23.542 1.00 0.00 C +ATOM 451 HA LYS 28 30.261 40.813 23.489 1.00 0.00 H +ATOM 452 CB LYS 28 28.746 42.210 22.871 1.00 0.00 C +ATOM 453 HB2 LYS 28 27.665 42.311 22.908 1.00 0.00 H +ATOM 454 HB3 LYS 28 29.187 43.031 23.431 1.00 0.00 H +ATOM 455 CG LYS 28 29.208 42.308 21.408 1.00 0.00 C +ATOM 456 HG2 LYS 28 30.277 42.108 21.350 1.00 0.00 H +ATOM 457 HG3 LYS 28 28.680 41.563 20.815 1.00 0.00 H +ATOM 458 CD LYS 28 28.927 43.707 20.842 1.00 0.00 C +ATOM 459 HD2 LYS 28 27.891 43.991 21.036 1.00 0.00 H +ATOM 460 HD3 LYS 28 29.570 44.428 21.354 1.00 0.00 H +ATOM 461 CE LYS 28 29.198 43.782 19.334 1.00 0.00 C +ATOM 462 HE2 LYS 28 29.314 44.836 19.061 1.00 0.00 H +ATOM 463 HE3 LYS 28 30.144 43.284 19.119 1.00 0.00 H +ATOM 464 NZ LYS 28 28.093 43.178 18.549 1.00 0.00 N +ATOM 465 HZ1 LYS 28 27.217 43.662 18.773 1.00 0.00 H +ATOM 466 HZ2 LYS 28 28.226 43.270 17.553 1.00 0.00 H +ATOM 467 HZ3 LYS 28 27.924 42.207 18.800 1.00 0.00 H +ATOM 468 C LYS 28 28.804 40.912 25.032 1.00 0.00 C +ATOM 469 O LYS 28 29.680 41.040 25.876 1.00 0.00 O +ATOM 470 N PHE 29 27.536 40.685 25.345 1.00 0.00 N +ATOM 471 H PHE 29 26.846 40.633 24.603 1.00 0.00 H +ATOM 472 CA PHE 29 27.076 40.511 26.734 1.00 0.00 C +ATOM 473 HA PHE 29 27.360 41.389 27.309 1.00 0.00 H +ATOM 474 CB PHE 29 25.537 40.411 26.769 1.00 0.00 C +ATOM 475 HB2 PHE 29 25.250 39.476 26.299 1.00 0.00 H +ATOM 476 HB3 PHE 29 25.217 40.373 27.814 1.00 0.00 H +ATOM 477 CG PHE 29 24.778 41.545 26.102 1.00 0.00 C +ATOM 478 CD1 PHE 29 23.556 41.278 25.453 1.00 0.00 C +ATOM 479 HD1 PHE 29 23.143 40.282 25.454 1.00 0.00 H +ATOM 480 CE1 PHE 29 22.863 42.301 24.776 1.00 0.00 C +ATOM 481 HE1 PHE 29 21.940 42.078 24.260 1.00 0.00 H +ATOM 482 CZ PHE 29 23.389 43.607 24.751 1.00 0.00 C +ATOM 483 HZ PHE 29 22.885 44.385 24.198 1.00 0.00 H +ATOM 484 CE2 PHE 29 24.585 43.897 25.432 1.00 0.00 C +ATOM 485 HE2 PHE 29 24.986 44.895 25.418 1.00 0.00 H +ATOM 486 CD2 PHE 29 25.270 42.871 26.111 1.00 0.00 C +ATOM 487 HD2 PHE 29 26.188 43.112 26.618 1.00 0.00 H +ATOM 488 C PHE 29 27.743 39.283 27.412 1.00 0.00 C +ATOM 489 O PHE 29 27.945 39.300 28.630 1.00 0.00 O +ATOM 490 N THR 30 28.111 38.252 26.636 1.00 0.00 N +ATOM 491 H THR 30 27.888 38.273 25.654 1.00 0.00 H +ATOM 492 CA THR 30 28.862 37.094 27.131 1.00 0.00 C +ATOM 493 HA THR 30 28.457 36.846 28.085 1.00 0.00 H +ATOM 494 CB THR 30 28.725 35.842 26.172 1.00 0.00 C +ATOM 495 HB THR 30 29.050 36.156 25.197 1.00 0.00 H +ATOM 496 CG2 THR 30 29.648 34.709 26.555 1.00 0.00 C +ATOM 497 HG21 THR 30 29.528 34.340 27.548 1.00 0.00 H +ATOM 498 HG22 THR 30 29.506 33.862 25.906 1.00 0.00 H +ATOM 499 HG23 THR 30 30.682 34.993 26.432 1.00 0.00 H +ATOM 500 OG1 THR 30 27.395 35.353 26.177 1.00 0.00 O +ATOM 501 HG1 THR 30 26.892 36.037 25.693 1.00 0.00 H +ATOM 502 C THR 30 30.334 37.437 27.454 1.00 0.00 C +ATOM 503 O THR 30 30.855 36.981 28.470 1.00 0.00 O +ATOM 504 N LYS 31 30.980 38.333 26.716 1.00 0.00 N +ATOM 505 H LYS 31 30.513 38.694 25.898 1.00 0.00 H +ATOM 506 CA LYS 31 32.312 38.841 27.020 1.00 0.00 C +ATOM 507 HA LYS 31 32.964 38.016 27.304 1.00 0.00 H +ATOM 508 CB LYS 31 32.924 39.468 25.742 1.00 0.00 C +ATOM 509 HB2 LYS 31 32.242 40.195 25.331 1.00 0.00 H +ATOM 510 HB3 LYS 31 33.862 39.961 25.990 1.00 0.00 H +ATOM 511 CG LYS 31 33.213 38.368 24.701 1.00 0.00 C +ATOM 512 HG2 LYS 31 33.915 37.654 25.120 1.00 0.00 H +ATOM 513 HG3 LYS 31 32.308 37.825 24.443 1.00 0.00 H +ATOM 514 CD LYS 31 33.806 38.950 23.412 1.00 0.00 C +ATOM 515 HD2 LYS 31 33.043 39.539 22.907 1.00 0.00 H +ATOM 516 HD3 LYS 31 34.638 39.605 23.657 1.00 0.00 H +ATOM 517 CE LYS 31 34.300 37.858 22.440 1.00 0.00 C +ATOM 518 HE2 LYS 31 33.493 37.155 22.230 1.00 0.00 H +ATOM 519 HE3 LYS 31 34.562 38.338 21.495 1.00 0.00 H +ATOM 520 NZ LYS 31 35.488 37.130 22.956 1.00 0.00 N +ATOM 521 HZ1 LYS 31 35.237 36.355 23.553 1.00 0.00 H +ATOM 522 HZ2 LYS 31 36.028 36.722 22.186 1.00 0.00 H +ATOM 523 HZ3 LYS 31 36.105 37.731 23.509 1.00 0.00 H +ATOM 524 C LYS 31 32.328 39.801 28.223 1.00 0.00 C +ATOM 525 O LYS 31 33.313 39.775 28.962 1.00 0.00 O +ATOM 526 N ALA 32 31.241 40.540 28.463 1.00 0.00 N +ATOM 527 H ALA 32 30.507 40.561 27.764 1.00 0.00 H +ATOM 528 CA ALA 32 31.100 41.390 29.653 1.00 0.00 C +ATOM 529 HA ALA 32 31.906 42.124 29.651 1.00 0.00 H +ATOM 530 CB ALA 32 29.777 42.157 29.576 1.00 0.00 C +ATOM 531 HB1 ALA 32 28.929 41.474 29.579 1.00 0.00 H +ATOM 532 HB2 ALA 32 29.683 42.821 30.440 1.00 0.00 H +ATOM 533 HB3 ALA 32 29.747 42.759 28.670 1.00 0.00 H +ATOM 534 C ALA 32 31.246 40.592 30.971 1.00 0.00 C +ATOM 535 O ALA 32 32.258 40.717 31.659 1.00 0.00 O +ATOM 536 N MET 33 30.311 39.675 31.258 1.00 0.00 N +ATOM 537 H MET 33 29.508 39.605 30.647 1.00 0.00 H +ATOM 538 CA MET 33 30.327 38.860 32.488 1.00 0.00 C +ATOM 539 HA MET 33 30.350 39.535 33.337 1.00 0.00 H +ATOM 540 CB MET 33 29.031 38.045 32.583 1.00 0.00 C +ATOM 541 HB2 MET 33 29.059 37.434 33.489 1.00 0.00 H +ATOM 542 HB3 MET 33 28.170 38.712 32.651 1.00 0.00 H +ATOM 543 CG MET 33 28.869 37.134 31.367 1.00 0.00 C +ATOM 544 HG2 MET 33 28.535 37.740 30.527 1.00 0.00 H +ATOM 545 HG3 MET 33 29.833 36.707 31.103 1.00 0.00 H +ATOM 546 SD MET 33 27.725 35.757 31.556 1.00 0.00 S +ATOM 547 CE MET 33 27.793 35.316 29.808 1.00 0.00 C +ATOM 548 HE1 MET 33 28.819 35.418 29.460 1.00 0.00 H +ATOM 549 HE2 MET 33 27.493 34.298 29.633 1.00 0.00 H +ATOM 550 HE3 MET 33 27.119 35.969 29.252 1.00 0.00 H +ATOM 551 C MET 33 31.544 37.922 32.625 1.00 0.00 C +ATOM 552 O MET 33 31.765 37.346 33.688 1.00 0.00 O +ATOM 553 N ALA 34 32.323 37.709 31.559 1.00 0.00 N +ATOM 554 H ALA 34 32.082 38.183 30.704 1.00 0.00 H +ATOM 555 CA ALA 34 33.606 37.014 31.625 1.00 0.00 C +ATOM 556 HA ALA 34 33.543 36.232 32.380 1.00 0.00 H +ATOM 557 CB ALA 34 33.857 36.342 30.272 1.00 0.00 C +ATOM 558 HB1 ALA 34 33.999 37.099 29.502 1.00 0.00 H +ATOM 559 HB2 ALA 34 34.746 35.720 30.347 1.00 0.00 H +ATOM 560 HB3 ALA 34 33.007 35.713 30.003 1.00 0.00 H +ATOM 561 C ALA 34 34.748 37.957 32.050 1.00 0.00 C +ATOM 562 O ALA 34 35.576 37.572 32.872 1.00 0.00 O +ATOM 563 N ASN 35 34.763 39.207 31.573 1.00 0.00 N +ATOM 564 H ASN 35 34.027 39.494 30.936 1.00 0.00 H +ATOM 565 CA ASN 35 35.665 40.253 32.070 1.00 0.00 C +ATOM 566 HA ASN 35 36.674 39.839 32.125 1.00 0.00 H +ATOM 567 CB ASN 35 35.704 41.422 31.072 1.00 0.00 C +ATOM 568 HB2 ASN 35 34.698 41.679 30.747 1.00 0.00 H +ATOM 569 HB3 ASN 35 36.134 42.292 31.564 1.00 0.00 H +ATOM 570 CG ASN 35 36.587 41.087 29.886 1.00 0.00 C +ATOM 571 OD1 ASN 35 37.801 41.145 29.959 1.00 0.00 O +ATOM 572 ND2 ASN 35 36.022 40.684 28.778 1.00 0.00 N +ATOM 573 HD21 ASN 35 36.644 40.334 28.046 1.00 0.00 H +ATOM 574 HD22 ASN 35 35.024 40.526 28.754 1.00 0.00 H +ATOM 575 C ASN 35 35.329 40.700 33.505 1.00 0.00 C +ATOM 576 O ASN 35 36.252 40.963 34.271 1.00 0.00 O +ATOM 577 N ASP 36 34.058 40.655 33.922 1.00 0.00 N +ATOM 578 H ASP 36 33.325 40.577 33.225 1.00 0.00 H +ATOM 579 CA ASP 36 33.656 40.808 35.335 1.00 0.00 C +ATOM 580 HA ASP 36 34.016 41.774 35.697 1.00 0.00 H +ATOM 581 CB ASP 36 32.128 40.806 35.456 1.00 0.00 C +ATOM 582 HB2 ASP 36 31.752 39.865 35.060 1.00 0.00 H +ATOM 583 HB3 ASP 36 31.860 40.821 36.513 1.00 0.00 H +ATOM 584 CG ASP 36 31.416 41.978 34.772 1.00 0.00 C +ATOM 585 OD1 ASP 36 31.960 43.104 34.832 1.00 0.00 O +ATOM 586 OD2 ASP 36 30.303 41.747 34.242 1.00 0.00 O +ATOM 587 C ASP 36 34.264 39.720 36.251 1.00 0.00 C +ATOM 588 O ASP 36 34.544 39.977 37.422 1.00 0.00 O +ATOM 589 N LEU 37 34.501 38.511 35.719 1.00 0.00 N +ATOM 590 H LEU 37 34.210 38.361 34.764 1.00 0.00 H +ATOM 591 CA LEU 37 35.253 37.437 36.386 1.00 0.00 C +ATOM 592 HA LEU 37 35.075 37.522 37.457 1.00 0.00 H +ATOM 593 CB LEU 37 34.670 36.088 35.909 1.00 0.00 C +ATOM 594 HB2 LEU 37 33.593 36.096 36.090 1.00 0.00 H +ATOM 595 HB3 LEU 37 34.822 36.016 34.832 1.00 0.00 H +ATOM 596 CG LEU 37 35.261 34.821 36.560 1.00 0.00 C +ATOM 597 HG LEU 37 36.329 34.768 36.367 1.00 0.00 H +ATOM 598 CD1 LEU 37 35.016 34.764 38.070 1.00 0.00 C +ATOM 599 HD11 LEU 37 33.949 34.834 38.282 1.00 0.00 H +ATOM 600 HD12 LEU 37 35.406 33.829 38.472 1.00 0.00 H +ATOM 601 HD13 LEU 37 35.537 35.587 38.556 1.00 0.00 H +ATOM 602 CD2 LEU 37 34.622 33.578 35.933 1.00 0.00 C +ATOM 603 HD21 LEU 37 34.804 33.579 34.860 1.00 0.00 H +ATOM 604 HD22 LEU 37 35.063 32.681 36.367 1.00 0.00 H +ATOM 605 HD23 LEU 37 33.548 33.574 36.121 1.00 0.00 H +ATOM 606 C LEU 37 36.788 37.551 36.189 1.00 0.00 C +ATOM 607 O LEU 37 37.552 36.948 36.943 1.00 0.00 O +ATOM 608 N GLY 38 37.242 38.328 35.197 1.00 0.00 N +ATOM 609 H GLY 38 36.545 38.808 34.643 1.00 0.00 H +ATOM 610 CA GLY 38 38.636 38.748 35.002 1.00 0.00 C +ATOM 611 HA2 GLY 38 38.770 39.718 35.475 1.00 0.00 H +ATOM 612 HA3 GLY 38 39.298 38.044 35.500 1.00 0.00 H +ATOM 613 C GLY 38 39.102 38.862 33.540 1.00 0.00 C +ATOM 614 O GLY 38 39.916 39.733 33.234 1.00 0.00 O +ATOM 615 N ARG 39 38.612 38.004 32.631 1.00 0.00 N +ATOM 616 H ARG 39 37.884 37.375 32.947 1.00 0.00 H +ATOM 617 CA ARG 39 38.906 38.019 31.178 1.00 0.00 C +ATOM 618 HA ARG 39 38.796 39.046 30.826 1.00 0.00 H +ATOM 619 CB ARG 39 40.361 37.577 30.892 1.00 0.00 C +ATOM 620 HB2 ARG 39 40.557 37.723 29.830 1.00 0.00 H +ATOM 621 HB3 ARG 39 41.043 38.230 31.437 1.00 0.00 H +ATOM 622 CG ARG 39 40.684 36.114 31.249 1.00 0.00 C +ATOM 623 HG2 ARG 39 40.360 35.923 32.273 1.00 0.00 H +ATOM 624 HG3 ARG 39 40.136 35.442 30.587 1.00 0.00 H +ATOM 625 CD ARG 39 42.189 35.802 31.162 1.00 0.00 C +ATOM 626 HD2 ARG 39 42.722 36.477 31.836 1.00 0.00 H +ATOM 627 HD3 ARG 39 42.339 34.779 31.512 1.00 0.00 H +ATOM 628 NE ARG 39 42.738 35.927 29.792 1.00 0.00 N +ATOM 629 HE ARG 39 42.088 36.145 29.049 1.00 0.00 H +ATOM 630 CZ ARG 39 43.992 35.698 29.424 1.00 0.00 C +ATOM 631 NH1 ARG 39 44.920 35.331 30.264 1.00 0.00 N +ATOM 632 HH11 ARG 39 44.697 35.239 31.236 1.00 0.00 H +ATOM 633 HH12 ARG 39 45.871 35.229 29.942 1.00 0.00 H +ATOM 634 NH2 ARG 39 44.365 35.836 28.189 1.00 0.00 N +ATOM 635 HH21 ARG 39 43.770 36.293 27.499 1.00 0.00 H +ATOM 636 HH22 ARG 39 45.283 35.550 27.901 1.00 0.00 H +ATOM 637 C ARG 39 37.921 37.161 30.384 1.00 0.00 C +ATOM 638 O ARG 39 37.447 36.139 30.884 1.00 0.00 O +ATOM 639 N ASP 40 37.642 37.535 29.136 1.00 0.00 N +ATOM 640 H ASP 40 38.054 38.385 28.762 1.00 0.00 H +ATOM 641 CA ASP 40 36.892 36.696 28.199 1.00 0.00 C +ATOM 642 HA ASP 40 36.196 36.096 28.776 1.00 0.00 H +ATOM 643 CB ASP 40 36.037 37.547 27.245 1.00 0.00 C +ATOM 644 HB2 ASP 40 35.414 36.882 26.654 1.00 0.00 H +ATOM 645 HB3 ASP 40 35.352 38.146 27.840 1.00 0.00 H +ATOM 646 CG ASP 40 36.821 38.476 26.319 1.00 0.00 C +ATOM 647 OD1 ASP 40 37.532 39.356 26.848 1.00 0.00 O +ATOM 648 OD2 ASP 40 36.628 38.351 25.088 1.00 0.00 O +ATOM 649 C ASP 40 37.750 35.673 27.433 1.00 0.00 C +ATOM 650 O ASP 40 38.976 35.663 27.502 1.00 0.00 O +ATOM 651 N GLY 41 37.052 34.801 26.704 1.00 0.00 N +ATOM 652 H GLY 41 36.055 34.942 26.704 1.00 0.00 H +ATOM 653 CA GLY 41 37.568 33.918 25.655 1.00 0.00 C +ATOM 654 HA2 GLY 41 38.506 34.323 25.252 1.00 0.00 H +ATOM 655 HA3 GLY 41 37.738 32.918 26.074 1.00 0.00 H +ATOM 656 C GLY 41 36.536 33.820 24.514 1.00 0.00 C +ATOM 657 O GLY 41 35.564 34.580 24.473 1.00 0.00 O +ATOM 658 N GLU 42 36.716 32.865 23.606 1.00 0.00 N +ATOM 659 H GLU 42 37.486 32.235 23.726 1.00 0.00 H +ATOM 660 CA GLU 42 35.850 32.648 22.436 1.00 0.00 C +ATOM 661 HA GLU 42 35.176 33.496 22.353 1.00 0.00 H +ATOM 662 CB GLU 42 36.695 32.588 21.151 1.00 0.00 C +ATOM 663 HB2 GLU 42 37.302 31.684 21.176 1.00 0.00 H +ATOM 664 HB3 GLU 42 36.016 32.507 20.301 1.00 0.00 H +ATOM 665 CG GLU 42 37.629 33.792 20.913 1.00 0.00 C +ATOM 666 HG2 GLU 42 38.445 33.738 21.639 1.00 0.00 H +ATOM 667 HG3 GLU 42 38.070 33.698 19.919 1.00 0.00 H +ATOM 668 CD GLU 42 36.944 35.161 21.035 1.00 0.00 C +ATOM 669 OE1 GLU 42 35.707 35.261 20.892 1.00 0.00 O +ATOM 670 OE2 GLU 42 37.630 36.154 21.360 1.00 0.00 O +ATOM 671 C GLU 42 34.945 31.417 22.573 1.00 0.00 C +ATOM 672 O GLU 42 35.209 30.530 23.392 1.00 0.00 O +ATOM 673 N ARG 43 33.848 31.379 21.797 1.00 0.00 N +ATOM 674 H ARG 43 33.717 32.120 21.116 1.00 0.00 H +ATOM 675 CA ARG 43 32.787 30.356 21.880 1.00 0.00 C +ATOM 676 HA ARG 43 33.217 29.424 22.251 1.00 0.00 H +ATOM 677 CB ARG 43 31.686 30.812 22.855 1.00 0.00 C +ATOM 678 HB2 ARG 43 31.288 31.774 22.526 1.00 0.00 H +ATOM 679 HB3 ARG 43 30.873 30.086 22.837 1.00 0.00 H +ATOM 680 CG ARG 43 32.207 30.938 24.289 1.00 0.00 C +ATOM 681 HG2 ARG 43 32.674 29.997 24.585 1.00 0.00 H +ATOM 682 HG3 ARG 43 32.948 31.736 24.339 1.00 0.00 H +ATOM 683 CD ARG 43 31.080 31.275 25.259 1.00 0.00 C +ATOM 684 HD2 ARG 43 30.566 32.166 24.898 1.00 0.00 H +ATOM 685 HD3 ARG 43 30.362 30.458 25.286 1.00 0.00 H +ATOM 686 NE ARG 43 31.615 31.546 26.607 1.00 0.00 N +ATOM 687 HE ARG 43 31.821 32.510 26.817 1.00 0.00 H +ATOM 688 CZ ARG 43 31.856 30.660 27.557 1.00 0.00 C +ATOM 689 NH1 ARG 43 31.708 29.377 27.385 1.00 0.00 N +ATOM 690 HH11 ARG 43 31.648 29.018 26.443 1.00 0.00 H +ATOM 691 HH12 ARG 43 31.919 28.765 28.159 1.00 0.00 H +ATOM 692 NH2 ARG 43 32.232 31.060 28.732 1.00 0.00 N +ATOM 693 HH21 ARG 43 32.503 32.009 28.885 1.00 0.00 H +ATOM 694 HH22 ARG 43 32.314 30.364 29.472 1.00 0.00 H +ATOM 695 C ARG 43 32.154 30.062 20.523 1.00 0.00 C +ATOM 696 O ARG 43 31.906 30.987 19.756 1.00 0.00 O +ATOM 697 N THR 44 31.837 28.793 20.274 1.00 0.00 N +ATOM 698 H THR 44 32.076 28.107 20.970 1.00 0.00 H +ATOM 699 CA THR 44 31.031 28.355 19.124 1.00 0.00 C +ATOM 700 HA THR 44 31.273 28.993 18.275 1.00 0.00 H +ATOM 701 CB THR 44 31.380 26.905 18.742 1.00 0.00 C +ATOM 702 HB THR 44 31.125 26.236 19.568 1.00 0.00 H +ATOM 703 CG2 THR 44 30.704 26.404 17.463 1.00 0.00 C +ATOM 704 HG21 THR 44 30.828 27.131 16.659 1.00 0.00 H +ATOM 705 HG22 THR 44 31.143 25.453 17.159 1.00 0.00 H +ATOM 706 HG23 THR 44 29.642 26.231 17.645 1.00 0.00 H +ATOM 707 OG1 THR 44 32.764 26.825 18.500 1.00 0.00 O +ATOM 708 HG1 THR 44 32.904 26.123 17.859 1.00 0.00 H +ATOM 709 C THR 44 29.531 28.535 19.415 1.00 0.00 C +ATOM 710 O THR 44 29.130 28.613 20.579 1.00 0.00 O +ATOM 711 N LYN 45 28.704 28.619 18.370 1.00 0.00 N +ATOM 712 H LYN 45 29.094 28.480 17.453 1.00 0.00 H +ATOM 713 CA LYN 45 27.251 28.785 18.436 1.00 0.00 C +ATOM 714 HA LYN 45 26.927 28.554 19.447 1.00 0.00 H +ATOM 715 CB LYN 45 26.884 30.251 18.128 1.00 0.00 C +ATOM 716 HB2 LYN 45 25.823 30.387 18.339 1.00 0.00 H +ATOM 717 HB3 LYN 45 27.441 30.912 18.797 1.00 0.00 H +ATOM 718 CG LYN 45 27.163 30.650 16.664 1.00 0.00 C +ATOM 719 HG2 LYN 45 28.242 30.667 16.501 1.00 0.00 H +ATOM 720 HG3 LYN 45 26.719 29.915 15.993 1.00 0.00 H +ATOM 721 CD LYN 45 26.567 32.022 16.327 1.00 0.00 C +ATOM 722 HD2 LYN 45 25.488 31.993 16.466 1.00 0.00 H +ATOM 723 HD3 LYN 45 26.987 32.759 17.013 1.00 0.00 H +ATOM 724 CE LYN 45 26.886 32.454 14.888 1.00 0.00 C +ATOM 725 HE2 LYN 45 26.487 33.450 14.715 1.00 0.00 H +ATOM 726 HE3 LYN 45 27.965 32.494 14.756 1.00 0.00 H +ATOM 727 NZ LYN 45 26.335 31.550 13.862 1.00 0.00 N +ATOM 728 HZ2 LYN 45 25.908 32.146 13.161 1.00 0.00 H +ATOM 729 HZ3 LYN 45 27.128 31.103 13.420 1.00 0.00 H +ATOM 730 C LYN 45 26.511 27.832 17.493 1.00 0.00 C +ATOM 731 O LYN 45 27.087 27.329 16.528 1.00 0.00 O +ATOM 732 N ASP 46 25.211 27.672 17.728 1.00 0.00 N +ATOM 733 H ASP 46 24.853 28.039 18.604 1.00 0.00 H +ATOM 734 CA ASP 46 24.222 27.118 16.802 1.00 0.00 C +ATOM 735 HA ASP 46 24.598 27.224 15.783 1.00 0.00 H +ATOM 736 CB ASP 46 24.001 25.629 17.107 1.00 0.00 C +ATOM 737 HB2 ASP 46 24.889 25.044 16.827 1.00 0.00 H +ATOM 738 HB3 ASP 46 23.886 25.525 18.195 1.00 0.00 H +ATOM 739 CG ASP 46 22.757 25.070 16.433 1.00 0.00 C +ATOM 740 OD1 ASP 46 21.976 24.406 17.140 1.00 0.00 O +ATOM 741 OD2 ASP 46 22.516 25.380 15.252 1.00 0.00 O +ATOM 742 C ASP 46 22.904 27.895 16.930 1.00 0.00 C +ATOM 743 O ASP 46 22.392 28.082 18.032 1.00 0.00 O +ATOM 744 N ASP 47 22.338 28.327 15.803 1.00 0.00 N +ATOM 745 H ASP 47 22.776 28.072 14.928 1.00 0.00 H +ATOM 746 CA ASP 47 21.019 28.999 15.768 1.00 0.00 C +ATOM 747 HA ASP 47 20.987 29.699 16.598 1.00 0.00 H +ATOM 748 CB ASP 47 20.862 29.860 14.512 1.00 0.00 C +ATOM 749 HB2 ASP 47 21.700 30.559 14.471 1.00 0.00 H +ATOM 750 HB3 ASP 47 20.917 29.222 13.613 1.00 0.00 H +ATOM 751 CG ASP 47 19.589 30.662 14.574 1.00 0.00 C +ATOM 752 OD1 ASP 47 18.593 30.316 13.905 1.00 0.00 O +ATOM 753 OD2 ASP 47 19.478 31.525 15.473 1.00 0.00 O +ATOM 754 C ASP 47 19.834 28.036 15.908 1.00 0.00 C +ATOM 755 O ASP 47 18.801 28.406 16.470 1.00 0.00 O +ATOM 756 N ALA 48 19.957 26.781 15.455 1.00 0.00 N +ATOM 757 H ALA 48 20.866 26.448 15.124 1.00 0.00 H +ATOM 758 CA ALA 48 18.849 25.817 15.492 1.00 0.00 C +ATOM 759 HA ALA 48 17.992 26.261 14.980 1.00 0.00 H +ATOM 760 CB ALA 48 19.257 24.554 14.723 1.00 0.00 C +ATOM 761 HB1 ALA 48 20.103 24.075 15.211 1.00 0.00 H +ATOM 762 HB2 ALA 48 18.428 23.852 14.689 1.00 0.00 H +ATOM 763 HB3 ALA 48 19.547 24.808 13.704 1.00 0.00 H +ATOM 764 C ALA 48 18.424 25.511 16.936 1.00 0.00 C +ATOM 765 O ALA 48 17.244 25.599 17.285 1.00 0.00 O +ATOM 766 N THR 49 19.389 25.220 17.807 1.00 0.00 N +ATOM 767 H THR 49 20.322 25.056 17.430 1.00 0.00 H +ATOM 768 CA THR 49 19.223 25.108 19.264 1.00 0.00 C +ATOM 769 HA THR 49 18.200 24.763 19.456 1.00 0.00 H +ATOM 770 CB THR 49 20.198 24.068 19.837 1.00 0.00 C +ATOM 771 HB THR 49 19.997 23.976 20.899 1.00 0.00 H +ATOM 772 CG2 THR 49 20.026 22.677 19.239 1.00 0.00 C +ATOM 773 HG21 THR 49 20.266 22.672 18.179 1.00 0.00 H +ATOM 774 HG22 THR 49 20.705 22.000 19.745 1.00 0.00 H +ATOM 775 HG23 THR 49 19.004 22.317 19.365 1.00 0.00 H +ATOM 776 OG1 THR 49 21.539 24.448 19.664 1.00 0.00 O +ATOM 777 HG1 THR 49 21.718 24.367 18.695 1.00 0.00 H +ATOM 778 C THR 49 19.381 26.433 20.023 1.00 0.00 C +ATOM 779 O THR 49 19.280 26.441 21.251 1.00 0.00 O +ATOM 780 N LYS 50 19.611 27.555 19.324 1.00 0.00 N +ATOM 781 H LYS 50 19.676 27.452 18.320 1.00 0.00 H +ATOM 782 CA LYS 50 19.796 28.917 19.877 1.00 0.00 C +ATOM 783 HA LYS 50 20.201 29.534 19.074 1.00 0.00 H +ATOM 784 CB LYS 50 18.425 29.504 20.316 1.00 0.00 C +ATOM 785 HB2 LYS 50 17.996 28.831 21.057 1.00 0.00 H +ATOM 786 HB3 LYS 50 18.594 30.468 20.807 1.00 0.00 H +ATOM 787 CG LYS 50 17.395 29.716 19.189 1.00 0.00 C +ATOM 788 HG2 LYS 50 17.343 28.826 18.554 1.00 0.00 H +ATOM 789 HG3 LYS 50 16.416 29.854 19.666 1.00 0.00 H +ATOM 790 CD LYS 50 17.708 30.972 18.346 1.00 0.00 C +ATOM 791 HD2 LYS 50 17.690 31.840 19.012 1.00 0.00 H +ATOM 792 HD3 LYS 50 18.714 30.881 17.897 1.00 0.00 H +ATOM 793 CE LYS 50 16.643 31.191 17.257 1.00 0.00 C +ATOM 794 HE2 LYS 50 15.654 30.901 17.645 1.00 0.00 H +ATOM 795 HE3 LYS 50 16.639 32.254 16.982 1.00 0.00 H +ATOM 796 NZ LYS 50 16.958 30.399 16.045 1.00 0.00 N +ATOM 797 HZ1 LYS 50 17.297 29.462 16.245 1.00 0.00 H +ATOM 798 HZ2 LYS 50 16.233 30.366 15.352 1.00 0.00 H +ATOM 799 HZ3 LYS 50 17.756 30.796 15.535 1.00 0.00 H +ATOM 800 C LYS 50 20.856 28.969 20.997 1.00 0.00 C +ATOM 801 O LYS 50 20.649 29.646 22.009 1.00 0.00 O +ATOM 802 N THR 51 21.948 28.212 20.856 1.00 0.00 N +ATOM 803 H THR 51 22.112 27.788 19.950 1.00 0.00 H +ATOM 804 CA THR 51 22.869 27.859 21.952 1.00 0.00 C +ATOM 805 HA THR 51 22.602 28.430 22.829 1.00 0.00 H +ATOM 806 CB THR 51 22.706 26.366 22.334 1.00 0.00 C +ATOM 807 HB THR 51 22.843 25.755 21.440 1.00 0.00 H +ATOM 808 CG2 THR 51 23.711 25.883 23.368 1.00 0.00 C +ATOM 809 HG21 THR 51 23.714 26.508 24.253 1.00 0.00 H +ATOM 810 HG22 THR 51 23.483 24.869 23.680 1.00 0.00 H +ATOM 811 HG23 THR 51 24.719 25.856 22.969 1.00 0.00 H +ATOM 812 OG1 THR 51 21.442 26.137 22.912 1.00 0.00 O +ATOM 813 HG1 THR 51 20.785 26.227 22.200 1.00 0.00 H +ATOM 814 C THR 51 24.351 28.179 21.662 1.00 0.00 C +ATOM 815 O THR 51 24.871 27.833 20.608 1.00 0.00 O +ATOM 816 N PHE 52 25.060 28.782 22.625 1.00 0.00 N +ATOM 817 H PHE 52 24.550 29.130 23.427 1.00 0.00 H +ATOM 818 CA PHE 52 26.533 28.833 22.669 1.00 0.00 C +ATOM 819 HA PHE 52 26.920 28.806 21.657 1.00 0.00 H +ATOM 820 CB PHE 52 27.003 30.150 23.322 1.00 0.00 C +ATOM 821 HB2 PHE 52 26.487 30.274 24.273 1.00 0.00 H +ATOM 822 HB3 PHE 52 28.068 30.061 23.540 1.00 0.00 H +ATOM 823 CG PHE 52 26.808 31.394 22.478 1.00 0.00 C +ATOM 824 CD1 PHE 52 25.626 32.152 22.587 1.00 0.00 C +ATOM 825 HD1 PHE 52 24.830 31.827 23.241 1.00 0.00 H +ATOM 826 CE1 PHE 52 25.480 33.336 21.843 1.00 0.00 C +ATOM 827 HE1 PHE 52 24.573 33.920 21.921 1.00 0.00 H +ATOM 828 CZ PHE 52 26.513 33.766 20.992 1.00 0.00 C +ATOM 829 HZ PHE 52 26.402 34.674 20.419 1.00 0.00 H +ATOM 830 CE2 PHE 52 27.688 33.006 20.873 1.00 0.00 C +ATOM 831 HE2 PHE 52 28.479 33.334 20.208 1.00 0.00 H +ATOM 832 CD2 PHE 52 27.833 31.817 21.610 1.00 0.00 C +ATOM 833 HD2 PHE 52 28.735 31.231 21.503 1.00 0.00 H +ATOM 834 C PHE 52 27.154 27.653 23.446 1.00 0.00 C +ATOM 835 O PHE 52 26.578 27.192 24.437 1.00 0.00 O +ATOM 836 N THR 53 28.364 27.223 23.064 1.00 0.00 N +ATOM 837 H THR 53 28.759 27.646 22.225 1.00 0.00 H +ATOM 838 CA THR 53 29.123 26.091 23.655 1.00 0.00 C +ATOM 839 HA THR 53 28.745 25.892 24.655 1.00 0.00 H +ATOM 840 CB THR 53 28.918 24.812 22.812 1.00 0.00 C +ATOM 841 HB THR 53 29.482 23.997 23.266 1.00 0.00 H +ATOM 842 CG2 THR 53 27.465 24.353 22.722 1.00 0.00 C +ATOM 843 HG21 THR 53 26.883 25.053 22.121 1.00 0.00 H +ATOM 844 HG22 THR 53 27.429 23.363 22.264 1.00 0.00 H +ATOM 845 HG23 THR 53 27.045 24.286 23.725 1.00 0.00 H +ATOM 846 OG1 THR 53 29.402 25.012 21.504 1.00 0.00 O +ATOM 847 HG1 THR 53 29.192 24.221 20.995 1.00 0.00 H +ATOM 848 C THR 53 30.632 26.396 23.807 1.00 0.00 C +ATOM 849 O THR 53 31.056 27.552 23.770 1.00 0.00 O +ATOM 850 N LYN 54 31.458 25.368 24.042 1.00 0.00 N +ATOM 851 H LYN 54 31.042 24.453 24.078 1.00 0.00 H +ATOM 852 CA LYN 54 32.913 25.351 23.840 1.00 0.00 C +ATOM 853 HA LYN 54 33.182 26.210 23.226 1.00 0.00 H +ATOM 854 CB LYN 54 33.664 25.483 25.181 1.00 0.00 C +ATOM 855 HB2 LYN 54 34.713 25.642 24.946 1.00 0.00 H +ATOM 856 HB3 LYN 54 33.324 26.374 25.708 1.00 0.00 H +ATOM 857 CG LYN 54 33.550 24.266 26.114 1.00 0.00 C +ATOM 858 HG2 LYN 54 32.643 24.349 26.707 1.00 0.00 H +ATOM 859 HG3 LYN 54 33.472 23.354 25.530 1.00 0.00 H +ATOM 860 CD LYN 54 34.776 24.141 27.028 1.00 0.00 C +ATOM 861 HD2 LYN 54 35.677 24.137 26.415 1.00 0.00 H +ATOM 862 HD3 LYN 54 34.812 24.988 27.712 1.00 0.00 H +ATOM 863 CE LYN 54 34.715 22.837 27.818 1.00 0.00 C +ATOM 864 HE2 LYN 54 33.874 22.891 28.512 1.00 0.00 H +ATOM 865 HE3 LYN 54 34.566 22.001 27.128 1.00 0.00 H +ATOM 866 NZ LYN 54 35.954 22.621 28.583 1.00 0.00 N +ATOM 867 HZ2 LYN 54 35.996 21.715 29.019 1.00 0.00 H +ATOM 868 HZ3 LYN 54 36.316 23.409 29.104 1.00 0.00 H +ATOM 869 C LYN 54 33.344 24.088 23.060 1.00 0.00 C +ATOM 870 O LYN 54 32.535 23.186 22.842 1.00 0.00 O +ATOM 871 N ASH 55 34.615 24.016 22.664 1.00 0.00 N +ATOM 872 H ASH 55 35.245 24.756 22.951 1.00 0.00 H +ATOM 873 CA ASH 55 35.247 22.828 22.072 1.00 0.00 C +ATOM 874 HA ASH 55 34.525 22.358 21.405 1.00 0.00 H +ATOM 875 CB ASH 55 36.455 23.264 21.216 1.00 0.00 C +ATOM 876 HB2 ASH 55 36.979 22.395 20.845 1.00 0.00 H +ATOM 877 HB3 ASH 55 36.084 23.777 20.334 1.00 0.00 H +ATOM 878 CG ASH 55 37.470 24.180 21.891 1.00 0.00 C +ATOM 879 OD1 ASH 55 37.241 24.906 22.847 1.00 0.00 O +ATOM 880 OD2 ASH 55 38.676 24.238 21.290 1.00 0.00 O +ATOM 881 HD2 ASH 55 39.185 24.871 21.797 1.00 0.00 H +ATOM 882 C ASH 55 35.628 21.735 23.102 1.00 0.00 C +ATOM 883 O ASH 55 35.449 21.925 24.300 1.00 0.00 O +ATOM 884 N GLU 56 36.125 20.591 22.614 1.00 0.00 N +ATOM 885 H GLU 56 36.281 20.544 21.624 1.00 0.00 H +ATOM 886 CA GLU 56 36.691 19.446 23.366 1.00 0.00 C +ATOM 887 HA GLU 56 36.560 19.618 24.435 1.00 0.00 H +ATOM 888 CB GLU 56 35.918 18.170 22.961 1.00 0.00 C +ATOM 889 HB2 GLU 56 34.856 18.327 23.109 1.00 0.00 H +ATOM 890 HB3 GLU 56 36.052 18.047 21.886 1.00 0.00 H +ATOM 891 CG GLU 56 36.339 16.851 23.639 1.00 0.00 C +ATOM 892 HG2 GLU 56 36.223 16.062 22.899 1.00 0.00 H +ATOM 893 HG3 GLU 56 37.398 16.876 23.855 1.00 0.00 H +ATOM 894 CD GLU 56 35.563 16.428 24.902 1.00 0.00 C +ATOM 895 OE1 GLU 56 36.058 15.544 25.648 1.00 0.00 O +ATOM 896 OE2 GLU 56 34.409 16.864 25.124 1.00 0.00 O +ATOM 897 C GLU 56 38.210 19.309 23.118 1.00 0.00 C +ATOM 898 O GLU 56 38.945 19.183 24.123 1.00 0.00 O +ATOM 899 OXT GLU 56 38.625 19.395 21.934 1.00 0.00 O +HETATM 900 ZN ZN1 57 26.470 32.045 29.849 1.00 0.00 Zn +HETATM 901 N AN1 58 28.199 32.402 30.955 1.00 0.00 N +HETATM 902 C AN1 58 30.486 33.121 31.982 1.00 0.00 C +HETATM 903 C1 AN1 58 29.217 32.670 31.424 1.00 0.00 C +HETATM 904 H AN1 58 30.328 33.549 32.983 1.00 0.00 H +HETATM 905 H1 AN1 58 30.941 33.882 31.335 1.00 0.00 H +HETATM 906 H2 AN1 58 31.141 32.254 32.077 1.00 0.00 H +HETATM 907 N1 AZI 59 31.846 28.958 30.692 1.00 0.00 N +HETATM 908 N2 AZI 59 30.630 28.927 30.576 1.00 0.00 N +HETATM 909 N3 AZI 59 29.402 28.909 30.421 1.00 0.00 N +CONECT 1 4 3 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 900 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 105 101 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 118 132 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 137 138 134 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 142 140 +CONECT 140 139 +CONECT 141 139 +CONECT 142 144 139 145 143 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 142 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 147 149 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 202 189 +CONECT 188 187 +CONECT 189 187 191 195 190 +CONECT 190 189 +CONECT 191 192 194 189 193 +CONECT 192 191 +CONECT 193 191 +CONECT 194 191 +CONECT 195 196 197 189 198 +CONECT 196 195 +CONECT 197 195 +CONECT 198 195 200 199 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 226 204 208 207 +CONECT 207 206 +CONECT 208 211 206 209 210 +CONECT 209 208 +CONECT 210 208 +CONECT 211 213 212 214 208 +CONECT 212 211 +CONECT 213 211 +CONECT 214 217 211 215 216 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 219 214 +CONECT 218 217 +CONECT 219 220 217 223 +CONECT 220 221 222 219 +CONECT 221 220 +CONECT 222 220 +CONECT 223 219 225 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 227 228 206 +CONECT 227 226 +CONECT 228 230 226 229 +CONECT 229 228 +CONECT 230 231 232 248 228 +CONECT 231 230 +CONECT 232 235 230 233 234 +CONECT 233 232 +CONECT 234 232 +CONECT 235 237 236 238 232 +CONECT 236 235 +CONECT 237 235 +CONECT 238 239 235 240 241 +CONECT 239 238 +CONECT 240 238 +CONECT 241 238 243 244 242 +CONECT 242 241 +CONECT 243 241 +CONECT 244 247 241 245 246 +CONECT 245 244 +CONECT 246 244 +CONECT 247 244 +CONECT 248 249 230 250 +CONECT 249 248 +CONECT 250 248 252 251 +CONECT 251 250 +CONECT 252 255 250 253 254 +CONECT 253 252 +CONECT 254 252 +CONECT 255 256 257 252 +CONECT 256 255 +CONECT 257 259 255 258 +CONECT 258 257 +CONECT 259 261 260 271 257 +CONECT 260 259 +CONECT 261 267 262 263 259 +CONECT 262 261 +CONECT 263 265 261 264 266 +CONECT 264 263 +CONECT 265 263 +CONECT 266 263 +CONECT 267 269 268 270 261 +CONECT 268 267 +CONECT 269 267 +CONECT 270 267 +CONECT 271 273 259 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 273 284 277 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 274 278 285 286 +CONECT 278 279 280 277 +CONECT 279 282 288 278 +CONECT 280 281 278 287 +CONECT 281 282 289 280 +CONECT 282 900 281 279 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 293 294 302 290 +CONECT 293 292 +CONECT 294 295 296 292 300 +CONECT 295 294 +CONECT 296 299 298 294 297 +CONECT 297 296 +CONECT 298 296 +CONECT 299 296 +CONECT 300 294 301 +CONECT 301 300 +CONECT 302 304 292 303 +CONECT 303 302 +CONECT 304 314 305 302 +CONECT 305 306 308 304 315 +CONECT 306 307 321 305 +CONECT 307 306 +CONECT 308 316 317 305 309 +CONECT 309 308 310 311 +CONECT 310 319 309 313 +CONECT 311 309 318 312 +CONECT 312 313 311 320 +CONECT 313 310 900 312 +CONECT 314 304 +CONECT 315 305 +CONECT 316 308 +CONECT 317 308 +CONECT 318 311 +CONECT 319 310 +CONECT 320 312 +CONECT 321 323 306 322 +CONECT 322 321 +CONECT 323 334 324 321 325 +CONECT 324 323 +CONECT 325 323 328 327 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 330 331 325 329 +CONECT 329 328 +CONECT 330 328 +CONECT 331 332 328 333 +CONECT 332 331 +CONECT 333 331 +CONECT 334 336 335 323 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 344 340 339 336 +CONECT 339 338 +CONECT 340 342 341 338 343 +CONECT 341 340 +CONECT 342 340 +CONECT 343 340 +CONECT 344 346 345 338 +CONECT 345 344 +CONECT 346 348 347 344 +CONECT 347 346 +CONECT 348 360 350 349 346 +CONECT 349 348 +CONECT 350 351 356 348 352 +CONECT 351 350 +CONECT 352 350 354 355 353 +CONECT 353 352 +CONECT 354 352 +CONECT 355 352 +CONECT 356 357 358 350 359 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 +CONECT 360 361 362 348 +CONECT 361 360 +CONECT 362 364 360 363 +CONECT 363 362 +CONECT 364 366 365 372 362 +CONECT 365 364 +CONECT 366 369 367 368 364 +CONECT 367 366 +CONECT 368 366 +CONECT 369 370 371 366 +CONECT 370 369 +CONECT 371 369 +CONECT 372 364 374 373 +CONECT 373 372 +CONECT 374 375 372 376 +CONECT 375 374 +CONECT 376 378 374 396 377 +CONECT 377 376 +CONECT 378 381 380 379 376 +CONECT 379 378 +CONECT 380 378 +CONECT 381 382 395 378 +CONECT 382 384 383 381 +CONECT 383 382 +CONECT 384 385 386 382 +CONECT 385 384 +CONECT 386 387 384 395 +CONECT 387 388 389 386 +CONECT 388 387 +CONECT 389 390 387 391 +CONECT 390 389 +CONECT 391 389 392 393 +CONECT 392 391 +CONECT 393 391 395 394 +CONECT 394 393 +CONECT 395 386 393 381 +CONECT 396 398 376 397 +CONECT 397 396 +CONECT 398 399 400 396 +CONECT 399 398 +CONECT 400 402 401 398 406 +CONECT 401 400 +CONECT 402 405 404 403 400 +CONECT 403 402 +CONECT 404 402 +CONECT 405 402 +CONECT 406 400 407 408 +CONECT 407 406 +CONECT 408 406 409 410 +CONECT 409 408 +CONECT 410 408 411 412 421 +CONECT 411 410 +CONECT 412 415 413 410 414 +CONECT 413 412 +CONECT 414 412 +CONECT 415 416 417 418 412 +CONECT 416 415 +CONECT 417 415 +CONECT 418 420 415 419 +CONECT 419 418 +CONECT 420 418 +CONECT 421 410 423 422 +CONECT 422 421 +CONECT 423 424 421 425 +CONECT 424 423 +CONECT 425 423 427 431 426 +CONECT 426 425 +CONECT 427 428 430 425 429 +CONECT 428 427 +CONECT 429 427 +CONECT 430 427 +CONECT 431 433 425 432 +CONECT 432 431 +CONECT 433 434 435 431 +CONECT 434 433 +CONECT 435 437 433 436 446 +CONECT 436 435 +CONECT 437 438 439 440 435 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 437 442 441 +CONECT 441 440 +CONECT 442 440 +CONECT 443 445 444 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 435 448 447 +CONECT 447 446 +CONECT 448 449 446 450 +CONECT 449 448 +CONECT 450 448 452 451 468 +CONECT 451 450 +CONECT 452 455 453 454 450 +CONECT 453 452 +CONECT 454 452 +CONECT 455 457 458 456 452 +CONECT 456 455 +CONECT 457 455 +CONECT 458 461 459 460 455 +CONECT 459 458 +CONECT 460 458 +CONECT 461 464 462 463 458 +CONECT 462 461 +CONECT 463 461 +CONECT 464 466 465 467 461 +CONECT 465 464 +CONECT 466 464 +CONECT 467 464 +CONECT 468 450 470 469 +CONECT 469 468 +CONECT 470 471 468 472 +CONECT 471 470 +CONECT 472 470 474 473 488 +CONECT 473 472 +CONECT 474 477 475 472 476 +CONECT 475 474 +CONECT 476 474 +CONECT 477 478 486 474 +CONECT 478 480 479 477 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 483 480 484 +CONECT 483 482 +CONECT 484 482 485 486 +CONECT 485 484 +CONECT 486 484 477 487 +CONECT 487 486 +CONECT 488 490 472 489 +CONECT 489 488 +CONECT 490 491 492 488 +CONECT 491 490 +CONECT 492 494 490 502 493 +CONECT 493 492 +CONECT 494 495 500 496 492 +CONECT 495 494 +CONECT 496 498 494 499 497 +CONECT 497 496 +CONECT 498 496 +CONECT 499 496 +CONECT 500 501 494 +CONECT 501 500 +CONECT 502 504 492 503 +CONECT 503 502 +CONECT 504 505 506 502 +CONECT 505 504 +CONECT 506 508 504 507 524 +CONECT 507 506 +CONECT 508 511 509 510 506 +CONECT 509 508 +CONECT 510 508 +CONECT 511 514 513 512 508 +CONECT 512 511 +CONECT 513 511 +CONECT 514 517 515 516 511 +CONECT 515 514 +CONECT 516 514 +CONECT 517 519 518 520 514 +CONECT 518 517 +CONECT 519 517 +CONECT 520 522 517 523 521 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 506 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 530 529 534 +CONECT 529 528 +CONECT 530 533 531 528 532 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 536 540 551 539 +CONECT 539 538 +CONECT 540 543 538 542 541 +CONECT 541 540 +CONECT 542 540 +CONECT 543 544 545 546 540 +CONECT 544 543 +CONECT 545 543 +CONECT 546 547 543 +CONECT 547 550 548 549 546 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 553 538 552 +CONECT 552 551 +CONECT 553 554 555 551 +CONECT 554 553 +CONECT 555 557 553 561 556 +CONECT 556 555 +CONECT 557 558 560 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 557 +CONECT 561 563 555 562 +CONECT 562 561 +CONECT 563 564 561 565 +CONECT 564 563 +CONECT 565 567 563 566 575 +CONECT 566 565 +CONECT 567 570 568 569 565 +CONECT 568 567 +CONECT 569 567 +CONECT 570 572 571 567 +CONECT 571 570 +CONECT 572 573 574 570 +CONECT 573 572 +CONECT 574 572 +CONECT 575 565 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 581 580 587 +CONECT 580 579 +CONECT 581 584 582 579 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 586 585 581 +CONECT 585 584 +CONECT 586 584 +CONECT 587 579 589 588 +CONECT 588 587 +CONECT 589 590 587 591 +CONECT 590 589 +CONECT 591 589 593 606 592 +CONECT 592 591 +CONECT 593 595 594 591 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 593 602 597 598 +CONECT 597 596 +CONECT 598 596 599 600 601 +CONECT 599 598 +CONECT 600 598 +CONECT 601 598 +CONECT 602 603 605 604 596 +CONECT 603 602 +CONECT 604 602 +CONECT 605 602 +CONECT 606 608 591 607 +CONECT 607 606 +CONECT 608 609 610 606 +CONECT 609 608 +CONECT 610 613 608 611 612 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 610 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 637 618 619 615 +CONECT 618 617 +CONECT 619 620 617 622 621 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 619 625 623 +CONECT 623 622 +CONECT 624 622 +CONECT 625 628 622 627 626 +CONECT 626 625 +CONECT 627 625 +CONECT 628 629 630 625 +CONECT 629 628 +CONECT 630 634 628 631 +CONECT 631 630 633 632 +CONECT 632 631 +CONECT 633 631 +CONECT 634 635 636 630 +CONECT 635 634 +CONECT 636 634 +CONECT 637 639 638 617 +CONECT 638 637 +CONECT 639 641 640 637 +CONECT 640 639 +CONECT 641 643 649 642 639 +CONECT 642 641 +CONECT 643 646 644 645 641 +CONECT 644 643 +CONECT 645 643 +CONECT 646 648 647 643 +CONECT 647 646 +CONECT 648 646 +CONECT 649 651 650 641 +CONECT 650 649 +CONECT 651 653 652 649 +CONECT 652 651 +CONECT 653 656 654 655 651 +CONECT 654 653 +CONECT 655 653 +CONECT 656 658 657 653 +CONECT 657 656 +CONECT 658 660 659 656 +CONECT 659 658 +CONECT 660 662 661 671 658 +CONECT 661 660 +CONECT 662 664 665 663 660 +CONECT 663 662 +CONECT 664 662 +CONECT 665 667 668 662 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 669 665 670 +CONECT 669 668 +CONECT 670 668 +CONECT 671 673 660 672 +CONECT 672 671 +CONECT 673 674 675 671 +CONECT 674 673 +CONECT 675 695 673 676 677 +CONECT 676 675 +CONECT 677 675 678 679 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 682 681 683 +CONECT 681 680 +CONECT 682 680 +CONECT 683 680 684 685 686 +CONECT 684 683 +CONECT 685 683 +CONECT 686 683 687 688 +CONECT 687 686 +CONECT 688 686 689 692 +CONECT 689 690 688 691 +CONECT 690 689 +CONECT 691 689 +CONECT 692 688 693 694 +CONECT 693 692 +CONECT 694 692 +CONECT 695 696 697 675 +CONECT 696 695 +CONECT 697 699 695 698 +CONECT 698 697 +CONECT 699 700 701 709 697 +CONECT 700 699 +CONECT 701 703 707 699 702 +CONECT 702 701 +CONECT 703 704 705 706 701 +CONECT 704 703 +CONECT 705 703 +CONECT 706 703 +CONECT 707 708 701 +CONECT 708 707 +CONECT 709 711 699 710 +CONECT 710 709 +CONECT 711 712 713 709 +CONECT 712 711 +CONECT 713 730 715 711 714 +CONECT 714 713 +CONECT 715 718 716 713 717 +CONECT 716 715 +CONECT 717 715 +CONECT 718 720 721 719 715 +CONECT 719 718 +CONECT 720 718 +CONECT 721 724 722 718 723 +CONECT 722 721 +CONECT 723 721 +CONECT 724 727 725 726 721 +CONECT 725 724 +CONECT 726 724 +CONECT 727 728 729 724 +CONECT 728 727 +CONECT 729 727 +CONECT 730 731 732 713 +CONECT 731 730 +CONECT 732 734 730 733 +CONECT 733 732 +CONECT 734 735 742 736 732 +CONECT 735 734 +CONECT 736 739 734 737 738 +CONECT 737 736 +CONECT 738 736 +CONECT 739 741 736 740 +CONECT 740 739 +CONECT 741 739 +CONECT 742 744 734 743 +CONECT 743 742 +CONECT 744 745 746 742 +CONECT 745 744 +CONECT 746 748 744 754 747 +CONECT 747 746 +CONECT 748 750 749 751 746 +CONECT 749 748 +CONECT 750 748 +CONECT 751 752 748 753 +CONECT 752 751 +CONECT 753 751 +CONECT 754 756 746 755 +CONECT 755 754 +CONECT 756 757 758 754 +CONECT 757 756 +CONECT 758 760 759 756 764 +CONECT 759 758 +CONECT 760 763 762 761 758 +CONECT 761 760 +CONECT 762 760 +CONECT 763 760 +CONECT 764 758 765 766 +CONECT 765 764 +CONECT 766 764 767 768 +CONECT 767 766 +CONECT 768 766 769 770 778 +CONECT 769 768 +CONECT 770 772 768 776 771 +CONECT 771 770 +CONECT 772 773 775 774 770 +CONECT 773 772 +CONECT 774 772 +CONECT 775 772 +CONECT 776 777 770 +CONECT 777 776 +CONECT 778 768 780 779 +CONECT 779 778 +CONECT 780 781 782 778 +CONECT 781 780 +CONECT 782 783 780 784 800 +CONECT 783 782 +CONECT 784 787 782 786 785 +CONECT 785 784 +CONECT 786 784 +CONECT 787 790 788 789 784 +CONECT 788 787 +CONECT 789 787 +CONECT 790 793 792 791 787 +CONECT 791 790 +CONECT 792 790 +CONECT 793 796 795 794 790 +CONECT 794 793 +CONECT 795 793 +CONECT 796 798 799 797 793 +CONECT 797 796 +CONECT 798 796 +CONECT 799 796 +CONECT 800 782 802 801 +CONECT 801 800 +CONECT 802 803 800 804 +CONECT 803 802 +CONECT 804 802 814 806 805 +CONECT 805 804 +CONECT 806 807 804 812 808 +CONECT 807 806 +CONECT 808 806 811 810 809 +CONECT 809 808 +CONECT 810 808 +CONECT 811 808 +CONECT 812 813 806 +CONECT 813 812 +CONECT 814 815 804 816 +CONECT 815 814 +CONECT 816 814 818 817 +CONECT 817 816 +CONECT 818 819 816 820 834 +CONECT 819 818 +CONECT 820 823 818 822 821 +CONECT 821 820 +CONECT 822 820 +CONECT 823 832 824 820 +CONECT 824 826 823 825 +CONECT 825 824 +CONECT 826 828 827 824 +CONECT 827 826 +CONECT 828 829 830 826 +CONECT 829 828 +CONECT 830 831 828 832 +CONECT 831 830 +CONECT 832 830 833 823 +CONECT 833 832 +CONECT 834 818 836 835 +CONECT 835 834 +CONECT 836 837 834 838 +CONECT 837 836 +CONECT 838 840 836 848 839 +CONECT 839 838 +CONECT 840 846 842 841 838 +CONECT 841 840 +CONECT 842 843 844 840 845 +CONECT 843 842 +CONECT 844 842 +CONECT 845 842 +CONECT 846 847 840 +CONECT 847 846 +CONECT 848 838 849 850 +CONECT 849 848 +CONECT 850 848 852 851 +CONECT 851 850 +CONECT 852 869 853 850 854 +CONECT 853 852 +CONECT 854 852 855 856 857 +CONECT 855 854 +CONECT 856 854 +CONECT 857 854 859 858 860 +CONECT 858 857 +CONECT 859 857 +CONECT 860 857 861 862 863 +CONECT 861 860 +CONECT 862 860 +CONECT 863 860 865 864 866 +CONECT 864 863 +CONECT 865 863 +CONECT 866 863 867 868 +CONECT 867 866 +CONECT 868 866 +CONECT 869 871 870 852 +CONECT 870 869 +CONECT 871 873 872 869 +CONECT 872 871 +CONECT 873 875 874 871 882 +CONECT 874 873 +CONECT 875 877 876 878 873 +CONECT 876 875 +CONECT 877 875 +CONECT 878 875 880 879 +CONECT 879 878 +CONECT 880 881 878 +CONECT 881 880 +CONECT 882 873 884 883 +CONECT 883 882 +CONECT 884 885 882 886 +CONECT 885 884 +CONECT 886 884 888 897 887 +CONECT 887 886 +CONECT 888 890 889 886 891 +CONECT 889 888 +CONECT 890 888 +CONECT 891 892 888 893 894 +CONECT 892 891 +CONECT 893 891 +CONECT 894 891 896 895 +CONECT 895 894 +CONECT 896 894 +CONECT 897 899 886 898 +CONECT 898 897 +CONECT 899 897 +CONECT 900 87 313 901 282 +CONECT 901 900 903 +CONECT 902 905 903 906 904 +CONECT 903 901 902 +CONECT 904 902 +CONECT 905 902 +CONECT 906 902 +CONECT 907 908 +CONECT 908 909 907 +CONECT 909 908 +MASTER 0 0 0 0 0 0 0 0 909 0 909 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_3.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_3.pdb new file mode 100644 index 0000000..055a3e7 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_3.pdb @@ -0,0 +1,1759 @@ +COMPND fitness: -3.1818 51.504999999999654 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.143 37.985 23.610 1.00 0.00 N +ATOM 2 H1 MET 1 15.124 38.373 24.555 1.00 0.00 H +ATOM 3 H2 MET 1 14.367 38.361 23.081 1.00 0.00 H +ATOM 4 H3 MET 1 16.013 38.294 23.187 1.00 0.00 H +ATOM 5 CA MET 1 15.112 36.512 23.675 1.00 0.00 C +ATOM 6 HA MET 1 14.160 36.216 24.101 1.00 0.00 H +ATOM 7 CB MET 1 15.250 35.885 22.281 1.00 0.00 C +ATOM 8 HB2 MET 1 14.380 36.161 21.670 1.00 0.00 H +ATOM 9 HB3 MET 1 16.147 36.282 21.783 1.00 0.00 H +ATOM 10 CG MET 1 15.360 34.343 22.311 1.00 0.00 C +ATOM 11 HG2 MET 1 16.249 34.076 22.883 1.00 0.00 H +ATOM 12 HG3 MET 1 14.486 33.935 22.815 1.00 0.00 H +ATOM 13 SD MET 1 15.524 33.527 20.684 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.579 20.074 1.00 0.00 C +ATOM 15 HE1 MET 1 13.468 34.610 20.016 1.00 0.00 H +ATOM 16 HE2 MET 1 13.779 33.136 19.079 1.00 0.00 H +ATOM 17 HE3 MET 1 13.164 33.009 20.739 1.00 0.00 H +ATOM 18 C MET 1 16.212 36.041 24.609 1.00 0.00 C +ATOM 19 O MET 1 17.363 36.415 24.425 1.00 0.00 O +ATOM 20 N GLN 2 15.870 35.214 25.595 1.00 0.00 N +ATOM 21 H GLN 2 14.892 35.031 25.773 1.00 0.00 H +ATOM 22 CA GLN 2 16.834 34.496 26.433 1.00 0.00 C +ATOM 23 HA GLN 2 17.639 35.169 26.726 1.00 0.00 H +ATOM 24 CB GLN 2 16.108 34.100 27.730 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.114 33.685 27.517 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.665 33.336 28.285 1.00 0.00 H +ATOM 27 CG GLN 2 15.906 35.258 28.690 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.472 36.127 28.192 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.177 34.968 29.445 1.00 0.00 H +ATOM 30 CD GLN 2 17.138 35.583 29.549 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.175 34.951 29.507 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.006 36.468 30.472 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.820 36.539 31.068 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.095 36.763 30.763 1.00 0.00 H +ATOM 35 C GLN 2 17.474 33.325 25.682 1.00 0.00 C +ATOM 36 O GLN 2 17.083 32.171 25.841 1.00 0.00 O +ATOM 37 N TYR 3 18.434 33.639 24.817 1.00 0.00 N +ATOM 38 H TYR 3 18.730 34.609 24.752 1.00 0.00 H +ATOM 39 CA TYR 3 19.211 32.639 24.095 1.00 0.00 C +ATOM 40 HA TYR 3 18.530 31.988 23.538 1.00 0.00 H +ATOM 41 CB TYR 3 20.157 33.301 23.092 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.840 33.964 23.635 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.751 32.494 22.652 1.00 0.00 H +ATOM 44 CG TYR 3 19.582 34.088 21.924 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.493 33.474 20.656 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.784 32.437 20.544 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.117 34.222 19.526 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.088 33.753 18.560 1.00 0.00 H +ATOM 49 CZ TYR 3 18.823 35.592 19.664 1.00 0.00 C +ATOM 50 OH TYR 3 18.501 36.326 18.572 1.00 0.00 O +ATOM 51 HH TYR 3 18.773 35.900 17.756 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.910 36.214 20.925 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.718 37.268 21.009 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.296 35.464 22.053 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.425 35.954 23.011 1.00 0.00 H +ATOM 56 C TYR 3 20.049 31.781 25.057 1.00 0.00 C +ATOM 57 O TYR 3 20.427 32.254 26.126 1.00 0.00 O +ATOM 58 N LYS 4 20.332 30.515 24.723 1.00 0.00 N +ATOM 59 H LYS 4 20.178 30.231 23.759 1.00 0.00 H +ATOM 60 CA LYS 4 20.951 29.510 25.613 1.00 0.00 C +ATOM 61 HA LYS 4 20.669 29.723 26.642 1.00 0.00 H +ATOM 62 CB LYS 4 20.428 28.102 25.249 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.474 27.988 24.171 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.104 27.360 25.675 1.00 0.00 H +ATOM 65 CG LYS 4 19.006 27.743 25.721 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.848 26.695 25.477 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.953 27.845 26.805 1.00 0.00 H +ATOM 68 CD LYS 4 17.876 28.560 25.074 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.833 29.552 25.522 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.097 28.676 24.012 1.00 0.00 H +ATOM 71 CE LYS 4 16.501 27.876 25.184 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.766 28.488 24.651 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.558 26.917 24.664 1.00 0.00 H +ATOM 74 NZ LYS 4 16.049 27.649 26.581 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.916 28.524 27.069 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.173 27.126 26.582 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.720 27.077 27.078 1.00 0.00 H +ATOM 78 C LYS 4 22.496 29.539 25.589 1.00 0.00 C +ATOM 79 O LYS 4 23.126 29.914 24.608 1.00 0.00 O +HETATM 80 N HX1 5 23.123 29.070 26.663 1.00 0.00 N +HETATM 81 CA HX1 5 24.574 28.879 26.771 1.00 0.00 C +HETATM 82 C HX1 5 24.845 27.683 27.682 1.00 0.00 C +HETATM 83 O HX1 5 24.411 27.675 28.838 1.00 0.00 O +HETATM 84 CB HX1 5 25.214 30.176 27.295 1.00 0.00 C +HETATM 85 CG HX1 5 26.729 30.252 27.370 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.639 29.290 27.013 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.408 31.375 27.858 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.709 31.060 27.740 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.883 29.809 27.277 1.00 0.00 N +HETATM 90 H HX1 5 22.554 28.878 27.485 1.00 0.00 H +HETATM 91 HA HX1 5 24.981 28.660 25.785 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.821 30.385 28.290 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.892 30.999 26.656 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.452 28.305 26.605 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.521 31.696 28.068 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.771 29.314 27.221 1.00 0.00 H +ATOM 97 N ILE 6 25.508 26.655 27.149 1.00 0.00 N +ATOM 98 H ILE 6 25.851 26.725 26.196 1.00 0.00 H +ATOM 99 CA ILE 6 25.910 25.449 27.896 1.00 0.00 C +ATOM 100 HA ILE 6 25.251 25.340 28.757 1.00 0.00 H +ATOM 101 CB ILE 6 25.717 24.186 27.023 1.00 0.00 C +ATOM 102 HB ILE 6 26.220 24.342 26.069 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.319 22.930 27.682 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.850 22.744 28.651 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.175 22.061 27.043 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.396 23.046 27.816 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.198 23.997 26.770 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.690 23.877 27.728 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.801 24.894 26.294 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.821 22.812 25.875 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.007 21.871 26.393 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.757 22.869 25.640 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.394 22.845 24.949 1.00 0.00 H +ATOM 114 C ILE 6 27.326 25.634 28.459 1.00 0.00 C +ATOM 115 O ILE 6 28.161 26.314 27.861 1.00 0.00 O +ATOM 116 N VAL 7 27.557 25.095 29.654 1.00 0.00 N +ATOM 117 H VAL 7 26.835 24.519 30.061 1.00 0.00 H +ATOM 118 CA VAL 7 28.720 25.390 30.497 1.00 0.00 C +ATOM 119 HA VAL 7 28.796 26.475 30.566 1.00 0.00 H +ATOM 120 CB VAL 7 28.425 24.856 31.917 1.00 0.00 C +ATOM 121 HB VAL 7 27.435 25.203 32.194 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.421 23.317 31.980 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.414 22.922 31.766 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.110 22.997 32.971 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.729 22.909 31.249 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.393 25.385 32.961 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.448 26.475 32.898 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.032 25.119 33.955 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.379 24.964 32.804 1.00 0.00 H +ATOM 130 C VAL 7 30.074 24.888 29.945 1.00 0.00 C +ATOM 131 O VAL 7 30.145 23.881 29.242 1.00 0.00 O +ATOM 132 N THR 8 31.160 25.572 30.325 1.00 0.00 N +ATOM 133 H THR 8 31.019 26.412 30.868 1.00 0.00 H +ATOM 134 CA THR 8 32.548 25.150 30.087 1.00 0.00 C +ATOM 135 HA THR 8 32.676 24.942 29.037 1.00 0.00 H +ATOM 136 CB THR 8 33.531 26.286 30.476 1.00 0.00 C +ATOM 137 HB THR 8 34.535 25.882 30.405 1.00 0.00 H +ATOM 138 CG2 THR 8 33.404 27.516 29.587 1.00 0.00 C +ATOM 139 HG21 THR 8 32.400 27.938 29.641 1.00 0.00 H +ATOM 140 HG22 THR 8 34.152 28.242 29.933 1.00 0.00 H +ATOM 141 HG23 THR 8 33.640 27.211 28.573 1.00 0.00 H +ATOM 142 OG1 THR 8 33.299 26.697 31.802 1.00 0.00 O +ATOM 143 HG1 THR 8 32.870 27.557 31.750 1.00 0.00 H +ATOM 144 C THR 8 32.947 23.867 30.855 1.00 0.00 C +ATOM 145 O THR 8 32.455 23.604 31.955 1.00 0.00 O +ATOM 146 N GLY 9 33.916 23.113 30.319 1.00 0.00 N +ATOM 147 H GLY 9 34.228 23.350 29.390 1.00 0.00 H +ATOM 148 CA GLY 9 34.483 21.905 30.944 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.467 21.720 30.517 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.591 22.078 32.015 1.00 0.00 H +ATOM 151 C GLY 9 33.617 20.656 30.725 1.00 0.00 C +ATOM 152 O GLY 9 32.761 20.625 29.849 1.00 0.00 O +ATOM 153 N LYS 10 33.857 19.605 31.523 1.00 0.00 N +ATOM 154 H LYS 10 34.648 19.678 32.142 1.00 0.00 H +ATOM 155 CA LYS 10 33.155 18.302 31.416 1.00 0.00 C +ATOM 156 HA LYS 10 32.232 18.487 30.864 1.00 0.00 H +ATOM 157 CB LYS 10 34.014 17.333 30.575 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.643 17.913 29.898 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.668 16.764 31.234 1.00 0.00 H +ATOM 160 CG LYS 10 33.172 16.374 29.715 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.598 15.707 30.358 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.475 16.966 29.120 1.00 0.00 H +ATOM 163 CD LYS 10 34.048 15.544 28.762 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.695 16.213 28.192 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.666 14.856 29.341 1.00 0.00 H +ATOM 166 CE LYS 10 33.168 14.751 27.787 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.998 28.344 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.452 15.437 27.326 1.00 0.00 H +ATOM 169 NZ LYS 10 33.963 14.103 26.716 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.727 13.547 27.077 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.367 13.556 26.105 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.408 14.809 26.111 1.00 0.00 H +ATOM 173 C LYS 10 32.705 17.689 32.753 1.00 0.00 C +ATOM 174 O LYS 10 31.954 16.719 32.762 1.00 0.00 O +ATOM 175 N SER 11 33.135 18.250 33.890 1.00 0.00 N +ATOM 176 H SER 11 33.861 18.944 33.825 1.00 0.00 H +ATOM 177 CA SER 11 32.715 17.837 35.249 1.00 0.00 C +ATOM 178 HA SER 11 32.578 16.753 35.268 1.00 0.00 H +ATOM 179 CB SER 11 33.803 18.197 36.271 1.00 0.00 C +ATOM 180 HB2 SER 11 33.797 19.276 36.438 1.00 0.00 H +ATOM 181 HB3 SER 11 33.596 17.691 37.215 1.00 0.00 H +ATOM 182 OG SER 11 35.079 17.815 35.795 1.00 0.00 O +ATOM 183 HG SER 11 35.730 17.919 36.496 1.00 0.00 H +ATOM 184 C SER 11 31.392 18.467 35.712 1.00 0.00 C +ATOM 185 O SER 11 30.952 18.228 36.831 1.00 0.00 O +ATOM 186 N ARG 12 30.783 19.321 34.884 1.00 0.00 N +ATOM 187 H ARG 12 31.191 19.425 33.963 1.00 0.00 H +ATOM 188 CA ARG 12 29.513 20.030 35.101 1.00 0.00 C +ATOM 189 HA ARG 12 28.908 19.448 35.793 1.00 0.00 H +ATOM 190 CB ARG 12 29.760 21.416 35.732 1.00 0.00 C +ATOM 191 HB2 ARG 12 28.806 21.937 35.834 1.00 0.00 H +ATOM 192 HB3 ARG 12 30.170 21.277 36.733 1.00 0.00 H +ATOM 193 CG ARG 12 30.730 22.314 34.928 1.00 0.00 C +ATOM 194 HG2 ARG 12 31.681 21.799 34.797 1.00 0.00 H +ATOM 195 HG3 ARG 12 30.310 22.519 33.949 1.00 0.00 H +ATOM 196 CD ARG 12 31.027 23.653 35.632 1.00 0.00 C +ATOM 197 HD2 ARG 12 30.082 24.209 35.755 1.00 0.00 H +ATOM 198 HD3 ARG 12 31.401 23.450 36.644 1.00 0.00 H +ATOM 199 NE ARG 12 32.012 24.458 34.883 1.00 0.00 N +ATOM 200 HE ARG 12 31.646 25.091 34.199 1.00 0.00 H +ATOM 201 CZ ARG 12 33.324 24.344 34.917 1.00 0.00 C +ATOM 202 NH1 ARG 12 33.924 23.512 35.719 1.00 0.00 N +ATOM 203 HH11 ARG 12 33.393 22.968 36.366 1.00 0.00 H +ATOM 204 HH12 ARG 12 34.928 23.374 35.636 1.00 0.00 H +ATOM 205 NH2 ARG 12 34.077 25.065 34.140 1.00 0.00 N +ATOM 206 HH21 ARG 12 33.667 25.594 33.377 1.00 0.00 H +ATOM 207 HH22 ARG 12 35.081 25.079 34.263 1.00 0.00 H +ATOM 208 C ARG 12 28.766 20.089 33.766 1.00 0.00 C +ATOM 209 O ARG 12 29.411 20.178 32.729 1.00 0.00 O +ATOM 210 N LYS 13 27.435 19.982 33.794 1.00 0.00 N +ATOM 211 H LYS 13 27.000 19.895 34.699 1.00 0.00 H +ATOM 212 CA LYS 13 26.597 19.734 32.598 1.00 0.00 C +ATOM 213 HA LYS 13 27.212 19.876 31.708 1.00 0.00 H +ATOM 214 CB LYS 13 26.152 18.255 32.639 1.00 0.00 C +ATOM 215 HB2 LYS 13 26.965 17.664 33.074 1.00 0.00 H +ATOM 216 HB3 LYS 13 25.278 18.158 33.291 1.00 0.00 H +ATOM 217 CG LYS 13 25.841 17.640 31.259 1.00 0.00 C +ATOM 218 HG2 LYS 13 24.958 18.111 30.821 1.00 0.00 H +ATOM 219 HG3 LYS 13 26.695 17.821 30.598 1.00 0.00 H +ATOM 220 CD LYS 13 25.621 16.115 31.353 1.00 0.00 C +ATOM 221 HD2 LYS 13 25.625 15.709 30.340 1.00 0.00 H +ATOM 222 HD3 LYS 13 26.454 15.670 31.901 1.00 0.00 H +ATOM 223 CE LYS 13 24.285 15.736 32.014 1.00 0.00 C +ATOM 224 HE2 LYS 13 24.108 16.376 32.881 1.00 0.00 H +ATOM 225 HE3 LYS 13 23.493 15.943 31.289 1.00 0.00 H +ATOM 226 NZ LYS 13 24.253 14.301 32.411 1.00 0.00 N +ATOM 227 HZ1 LYS 13 24.811 14.107 33.240 1.00 0.00 H +ATOM 228 HZ2 LYS 13 23.309 13.983 32.588 1.00 0.00 H +ATOM 229 HZ3 LYS 13 24.653 13.716 31.680 1.00 0.00 H +ATOM 230 C LYS 13 25.427 20.720 32.443 1.00 0.00 C +ATOM 231 O LYS 13 24.549 20.527 31.611 1.00 0.00 O +ATOM 232 N GLY 14 25.402 21.765 33.275 1.00 0.00 N +ATOM 233 H GLY 14 26.181 21.891 33.896 1.00 0.00 H +ATOM 234 CA GLY 14 24.303 22.731 33.349 1.00 0.00 C +ATOM 235 HA2 GLY 14 23.362 22.177 33.402 1.00 0.00 H +ATOM 236 HA3 GLY 14 24.394 23.307 34.272 1.00 0.00 H +ATOM 237 C GLY 14 24.229 23.712 32.165 1.00 0.00 C +ATOM 238 O GLY 14 25.167 23.864 31.379 1.00 0.00 O +ATOM 239 N VAL 15 23.105 24.424 32.073 1.00 0.00 N +ATOM 240 H VAL 15 22.394 24.283 32.775 1.00 0.00 H +ATOM 241 CA VAL 15 22.766 25.401 31.036 1.00 0.00 C +ATOM 242 HA VAL 15 23.655 25.640 30.454 1.00 0.00 H +ATOM 243 CB VAL 15 21.745 24.766 30.065 1.00 0.00 C +ATOM 244 HB VAL 15 22.195 23.865 29.647 1.00 0.00 H +ATOM 245 CG1 VAL 15 20.425 24.344 30.732 1.00 0.00 C +ATOM 246 HG11 VAL 15 19.919 25.204 31.178 1.00 0.00 H +ATOM 247 HG12 VAL 15 19.764 23.887 29.989 1.00 0.00 H +ATOM 248 HG13 VAL 15 20.614 23.598 31.511 1.00 0.00 H +ATOM 249 CG2 VAL 15 21.404 25.692 28.894 1.00 0.00 C +ATOM 250 HG21 VAL 15 22.323 26.024 28.411 1.00 0.00 H +ATOM 251 HG22 VAL 15 20.807 25.143 28.161 1.00 0.00 H +ATOM 252 HG23 VAL 15 20.832 26.553 29.242 1.00 0.00 H +ATOM 253 C VAL 15 22.266 26.694 31.700 1.00 0.00 C +ATOM 254 O VAL 15 21.705 26.652 32.791 1.00 0.00 O +HETATM 255 N HY1 16 22.495 27.833 31.062 1.00 0.00 N +HETATM 256 CA HY1 16 21.933 29.135 31.414 1.00 0.00 C +HETATM 257 C HY1 16 21.625 29.887 30.105 1.00 0.00 C +HETATM 258 O HY1 16 21.763 29.347 28.995 1.00 0.00 O +HETATM 259 CB HY1 16 22.878 29.886 32.385 1.00 0.00 C +HETATM 260 CG HY1 16 24.227 30.216 31.792 1.00 0.00 C +HETATM 261 CD2 HY1 16 24.567 31.405 31.207 1.00 0.00 C +HETATM 262 ND1 HY1 16 25.326 29.385 31.707 1.00 0.00 N +HETATM 263 CE1 HY1 16 26.315 30.087 31.127 1.00 0.00 C +HETATM 264 NE2 HY1 16 25.895 31.319 30.785 1.00 0.00 N +HETATM 265 H HY1 16 22.989 27.791 30.182 1.00 0.00 H +HETATM 266 HA HY1 16 20.963 29.030 31.902 1.00 0.00 H +HETATM 267 HB2 HY1 16 22.424 30.806 32.757 1.00 0.00 H +HETATM 268 HB3 HY1 16 23.026 29.261 33.277 1.00 0.00 H +HETATM 269 HD1 HY1 16 25.395 28.443 32.070 1.00 0.00 H +HETATM 270 HD2 HY1 16 23.925 32.270 31.110 1.00 0.00 H +HETATM 271 HE1 HY1 16 27.333 29.725 30.986 1.00 0.00 H +ATOM 272 N THR 17 21.170 31.128 30.268 1.00 0.00 N +ATOM 273 H THR 17 21.079 31.413 31.222 1.00 0.00 H +ATOM 274 CA THR 17 20.676 32.024 29.187 1.00 0.00 C +ATOM 275 HA THR 17 21.058 31.616 28.265 1.00 0.00 H +ATOM 276 CB THR 17 19.161 32.036 29.034 1.00 0.00 C +ATOM 277 HB THR 17 18.927 32.546 28.106 1.00 0.00 H +ATOM 278 CG2 THR 17 18.561 30.663 28.729 1.00 0.00 C +ATOM 279 HG21 THR 17 18.791 29.938 29.493 1.00 0.00 H +ATOM 280 HG22 THR 17 17.496 30.766 28.657 1.00 0.00 H +ATOM 281 HG23 THR 17 18.946 30.376 27.783 1.00 0.00 H +ATOM 282 OG1 THR 17 18.410 32.476 30.140 1.00 0.00 O +ATOM 283 HG1 THR 17 18.585 33.427 30.238 1.00 0.00 H +ATOM 284 C THR 17 21.222 33.465 29.200 1.00 0.00 C +ATOM 285 O THR 17 21.705 33.940 30.240 1.00 0.00 O +HETATM 286 N HY2 18 21.132 34.182 28.066 1.00 0.00 N +HETATM 287 CA HY2 18 21.431 35.612 28.001 1.00 0.00 C +HETATM 288 C HY2 18 20.328 36.310 27.213 1.00 0.00 C +HETATM 289 O HY2 18 19.975 35.851 26.125 1.00 0.00 O +HETATM 290 CB HY2 18 22.791 35.839 27.262 1.00 0.00 C +HETATM 291 CG HY2 18 24.006 35.348 28.021 1.00 0.00 C +HETATM 292 CD2 HY2 18 24.413 34.051 28.184 1.00 0.00 C +HETATM 293 ND1 HY2 18 24.960 36.137 28.624 1.00 0.00 N +HETATM 294 CE1 HY2 18 25.899 35.329 29.142 1.00 0.00 C +HETATM 295 NE2 HY2 18 25.606 34.045 28.910 1.00 0.00 N +HETATM 296 H HY2 18 20.782 33.736 27.218 1.00 0.00 H +HETATM 297 HA HY2 18 21.489 36.045 28.993 1.00 0.00 H +HETATM 298 HB2 HY2 18 22.749 35.327 26.310 1.00 0.00 H +HETATM 299 HB3 HY2 18 22.908 36.902 27.077 1.00 0.00 H +HETATM 300 HD1 HY2 18 24.991 37.149 28.638 1.00 0.00 H +HETATM 301 HD2 HY2 18 23.902 33.177 27.820 1.00 0.00 H +HETATM 302 HE1 HY2 18 26.787 35.668 29.652 1.00 0.00 H +ATOM 303 N GLU 19 19.791 37.399 27.752 1.00 0.00 N +ATOM 304 H GLU 19 20.124 37.705 28.652 1.00 0.00 H +ATOM 305 CA GLU 19 18.776 38.224 27.087 1.00 0.00 C +ATOM 306 HA GLU 19 18.046 37.565 26.625 1.00 0.00 H +ATOM 307 CB GLU 19 18.055 39.081 28.151 1.00 0.00 C +ATOM 308 HB2 GLU 19 17.742 38.439 28.965 1.00 0.00 H +ATOM 309 HB3 GLU 19 18.766 39.793 28.561 1.00 0.00 H +ATOM 310 CG GLU 19 16.818 39.843 27.647 1.00 0.00 C +ATOM 311 HG2 GLU 19 16.532 40.560 28.420 1.00 0.00 H +ATOM 312 HG3 GLU 19 17.067 40.405 26.749 1.00 0.00 H +ATOM 313 CD GLU 19 15.633 38.901 27.372 1.00 0.00 C +ATOM 314 OE1 GLU 19 15.556 38.375 26.231 1.00 0.00 O +ATOM 315 OE2 GLU 19 14.808 38.684 28.292 1.00 0.00 O +ATOM 316 C GLU 19 19.396 39.117 26.000 1.00 0.00 C +ATOM 317 O GLU 19 20.331 39.868 26.280 1.00 0.00 O +ATOM 318 N ALA 20 18.875 39.060 24.771 1.00 0.00 N +ATOM 319 H ALA 20 18.171 38.356 24.577 1.00 0.00 H +ATOM 320 CA ALA 20 19.256 39.967 23.684 1.00 0.00 C +ATOM 321 HA ALA 20 19.395 40.969 24.097 1.00 0.00 H +ATOM 322 CB ALA 20 20.591 39.496 23.094 1.00 0.00 C +ATOM 323 HB1 ALA 20 20.461 38.526 22.614 1.00 0.00 H +ATOM 324 HB2 ALA 20 20.949 40.215 22.359 1.00 0.00 H +ATOM 325 HB3 ALA 20 21.344 39.405 23.875 1.00 0.00 H +ATOM 326 C ALA 20 18.185 40.047 22.577 1.00 0.00 C +ATOM 327 O ALA 20 17.354 39.145 22.442 1.00 0.00 O +ATOM 328 N VAL 21 18.221 41.099 21.748 1.00 0.00 N +ATOM 329 H VAL 21 18.893 41.832 21.925 1.00 0.00 H +ATOM 330 CA VAL 21 17.459 41.162 20.475 1.00 0.00 C +ATOM 331 HA VAL 21 16.468 40.737 20.630 1.00 0.00 H +ATOM 332 CB VAL 21 17.270 42.614 19.983 1.00 0.00 C +ATOM 333 HB VAL 21 16.610 42.587 19.116 1.00 0.00 H +ATOM 334 CG1 VAL 21 16.590 43.481 21.047 1.00 0.00 C +ATOM 335 HG11 VAL 21 17.248 43.634 21.902 1.00 0.00 H +ATOM 336 HG12 VAL 21 16.341 44.452 20.615 1.00 0.00 H +ATOM 337 HG13 VAL 21 15.667 43.006 21.376 1.00 0.00 H +ATOM 338 CG2 VAL 21 18.578 43.295 19.550 1.00 0.00 C +ATOM 339 HG21 VAL 21 19.000 42.786 18.683 1.00 0.00 H +ATOM 340 HG22 VAL 21 18.373 44.324 19.255 1.00 0.00 H +ATOM 341 HG23 VAL 21 19.307 43.296 20.359 1.00 0.00 H +ATOM 342 C VAL 21 18.117 40.348 19.356 1.00 0.00 C +ATOM 343 O VAL 21 17.464 40.001 18.377 1.00 0.00 O +ATOM 344 N ASP 22 19.412 40.069 19.505 1.00 0.00 N +ATOM 345 H ASP 22 19.862 40.351 20.359 1.00 0.00 H +ATOM 346 CA ASP 22 20.289 39.480 18.502 1.00 0.00 C +ATOM 347 HA ASP 22 19.707 38.841 17.834 1.00 0.00 H +ATOM 348 CB ASP 22 20.936 40.601 17.673 1.00 0.00 C +ATOM 349 HB2 ASP 22 20.164 41.110 17.093 1.00 0.00 H +ATOM 350 HB3 ASP 22 21.395 41.325 18.350 1.00 0.00 H +ATOM 351 CG ASP 22 21.996 40.060 16.717 1.00 0.00 C +ATOM 352 OD1 ASP 22 23.093 40.648 16.681 1.00 0.00 O +ATOM 353 OD2 ASP 22 21.733 39.004 16.097 1.00 0.00 O +ATOM 354 C ASP 22 21.360 38.615 19.181 1.00 0.00 C +ATOM 355 O ASP 22 21.825 38.905 20.286 1.00 0.00 O +ATOM 356 N TRP 23 21.774 37.554 18.504 1.00 0.00 N +ATOM 357 H TRP 23 21.492 37.490 17.531 1.00 0.00 H +ATOM 358 CA TRP 23 22.767 36.618 19.006 1.00 0.00 C +ATOM 359 HA TRP 23 22.525 36.373 20.039 1.00 0.00 H +ATOM 360 CB TRP 23 22.646 35.352 18.169 1.00 0.00 C +ATOM 361 HB2 TRP 23 21.628 34.972 18.255 1.00 0.00 H +ATOM 362 HB3 TRP 23 22.822 35.600 17.122 1.00 0.00 H +ATOM 363 CG TRP 23 23.564 34.260 18.574 1.00 0.00 C +ATOM 364 CD1 TRP 23 24.539 33.738 17.789 1.00 0.00 C +ATOM 365 HD1 TRP 23 24.773 34.070 16.785 1.00 0.00 H +ATOM 366 NE1 TRP 23 25.153 32.722 18.467 1.00 0.00 N +ATOM 367 HE1 TRP 23 25.951 32.221 18.108 1.00 0.00 H +ATOM 368 CE2 TRP 23 24.593 32.496 19.714 1.00 0.00 C +ATOM 369 CZ2 TRP 23 24.828 31.562 20.706 1.00 0.00 C +ATOM 370 HZ2 TRP 23 25.556 30.774 20.575 1.00 0.00 H +ATOM 371 CH2 TRP 23 24.140 31.692 21.930 1.00 0.00 C +ATOM 372 HH2 TRP 23 24.335 31.027 22.741 1.00 0.00 H +ATOM 373 CZ3 TRP 23 23.269 32.767 22.129 1.00 0.00 C +ATOM 374 HZ3 TRP 23 22.829 32.889 23.111 1.00 0.00 H +ATOM 375 CE3 TRP 23 22.980 33.658 21.094 1.00 0.00 C +ATOM 376 HE3 TRP 23 22.278 34.461 21.241 1.00 0.00 H +ATOM 377 CD2 TRP 23 23.629 33.540 19.831 1.00 0.00 C +ATOM 378 C TRP 23 24.191 37.194 19.002 1.00 0.00 C +ATOM 379 O TRP 23 24.946 36.973 19.951 1.00 0.00 O +ATOM 380 N ALA 24 24.541 38.018 18.009 1.00 0.00 N +ATOM 381 H ALA 24 23.871 38.237 17.277 1.00 0.00 H +ATOM 382 CA ALA 24 25.829 38.715 17.984 1.00 0.00 C +ATOM 383 HA ALA 24 26.603 37.999 18.268 1.00 0.00 H +ATOM 384 CB ALA 24 26.130 39.149 16.545 1.00 0.00 C +ATOM 385 HB1 ALA 24 25.409 39.889 16.210 1.00 0.00 H +ATOM 386 HB2 ALA 24 27.130 39.576 16.491 1.00 0.00 H +ATOM 387 HB3 ALA 24 26.083 38.285 15.882 1.00 0.00 H +ATOM 388 C ALA 24 25.913 39.875 19.007 1.00 0.00 C +ATOM 389 O ALA 24 27.004 40.380 19.281 1.00 0.00 O +ATOM 390 N GLU 25 24.798 40.276 19.630 1.00 0.00 N +ATOM 391 H GLU 25 23.917 39.918 19.285 1.00 0.00 H +ATOM 392 CA GLU 25 24.787 41.074 20.867 1.00 0.00 C +ATOM 393 HA GLU 25 25.643 41.748 20.875 1.00 0.00 H +ATOM 394 CB GLU 25 23.515 41.935 20.943 1.00 0.00 C +ATOM 395 HB2 GLU 25 22.645 41.291 20.846 1.00 0.00 H +ATOM 396 HB3 GLU 25 23.462 42.403 21.924 1.00 0.00 H +ATOM 397 CG GLU 25 23.430 43.036 19.878 1.00 0.00 C +ATOM 398 HG2 GLU 25 23.642 42.620 18.894 1.00 0.00 H +ATOM 399 HG3 GLU 25 22.406 43.412 19.855 1.00 0.00 H +ATOM 400 CD GLU 25 24.383 44.195 20.176 1.00 0.00 C +ATOM 401 OE1 GLU 25 23.887 45.221 20.706 1.00 0.00 O +ATOM 402 OE2 GLU 25 25.589 44.053 19.865 1.00 0.00 O +ATOM 403 C GLU 25 24.926 40.185 22.120 1.00 0.00 C +ATOM 404 O GLU 25 25.682 40.523 23.033 1.00 0.00 O +ATOM 405 N ALA 26 24.283 39.009 22.156 1.00 0.00 N +ATOM 406 H ALA 26 23.666 38.773 21.386 1.00 0.00 H +ATOM 407 CA ALA 26 24.457 38.032 23.240 1.00 0.00 C +ATOM 408 HA ALA 26 24.199 38.527 24.174 1.00 0.00 H +ATOM 409 CB ALA 26 23.483 36.865 23.038 1.00 0.00 C +ATOM 410 HB1 ALA 26 23.764 36.292 22.156 1.00 0.00 H +ATOM 411 HB2 ALA 26 23.517 36.208 23.906 1.00 0.00 H +ATOM 412 HB3 ALA 26 22.467 37.238 22.916 1.00 0.00 H +ATOM 413 C ALA 26 25.913 37.533 23.381 1.00 0.00 C +ATOM 414 O ALA 26 26.342 37.219 24.495 1.00 0.00 O +ATOM 415 N GLU 27 26.696 37.513 22.296 1.00 0.00 N +ATOM 416 H GLU 27 26.247 37.646 21.393 1.00 0.00 H +ATOM 417 CA GLU 27 28.153 37.298 22.324 1.00 0.00 C +ATOM 418 HA GLU 27 28.361 36.338 22.799 1.00 0.00 H +ATOM 419 CB GLU 27 28.694 37.255 20.879 1.00 0.00 C +ATOM 420 HB2 GLU 27 28.051 36.617 20.269 1.00 0.00 H +ATOM 421 HB3 GLU 27 28.655 38.262 20.462 1.00 0.00 H +ATOM 422 CG GLU 27 30.131 36.716 20.800 1.00 0.00 C +ATOM 423 HG2 GLU 27 30.747 37.222 21.545 1.00 0.00 H +ATOM 424 HG3 GLU 27 30.124 35.652 21.043 1.00 0.00 H +ATOM 425 CD GLU 27 30.754 36.949 19.410 1.00 0.00 C +ATOM 426 OE1 GLU 27 31.211 38.094 19.177 1.00 0.00 O +ATOM 427 OE2 GLU 27 30.788 35.992 18.599 1.00 0.00 O +ATOM 428 C GLU 27 28.860 38.378 23.161 1.00 0.00 C +ATOM 429 O GLU 27 29.592 38.066 24.105 1.00 0.00 O +ATOM 430 N LYS 28 28.562 39.657 22.902 1.00 0.00 N +ATOM 431 H LYS 28 27.890 39.843 22.167 1.00 0.00 H +ATOM 432 CA LYS 28 29.110 40.795 23.659 1.00 0.00 C +ATOM 433 HA LYS 28 30.198 40.718 23.660 1.00 0.00 H +ATOM 434 CB LYS 28 28.720 42.129 22.993 1.00 0.00 C +ATOM 435 HB2 LYS 28 27.639 42.268 23.053 1.00 0.00 H +ATOM 436 HB3 LYS 28 29.199 42.942 23.542 1.00 0.00 H +ATOM 437 CG LYS 28 29.150 42.206 21.516 1.00 0.00 C +ATOM 438 HG2 LYS 28 30.220 42.003 21.435 1.00 0.00 H +ATOM 439 HG3 LYS 28 28.609 41.451 20.948 1.00 0.00 H +ATOM 440 CD LYS 28 28.859 43.592 20.921 1.00 0.00 C +ATOM 441 HD2 LYS 28 27.847 43.907 21.183 1.00 0.00 H +ATOM 442 HD3 LYS 28 29.557 44.311 21.354 1.00 0.00 H +ATOM 443 CE LYS 28 29.007 43.609 19.395 1.00 0.00 C +ATOM 444 HE2 LYS 28 29.103 44.648 19.076 1.00 0.00 H +ATOM 445 HE3 LYS 28 29.927 43.091 19.118 1.00 0.00 H +ATOM 446 NZ LYS 28 27.833 42.999 18.726 1.00 0.00 N +ATOM 447 HZ1 LYS 28 26.977 43.466 19.045 1.00 0.00 H +ATOM 448 HZ2 LYS 28 27.883 43.073 17.721 1.00 0.00 H +ATOM 449 HZ3 LYS 28 27.721 42.019 18.980 1.00 0.00 H +ATOM 450 C LYS 28 28.671 40.756 25.124 1.00 0.00 C +ATOM 451 O LYS 28 29.501 40.914 26.014 1.00 0.00 O +ATOM 452 N PHE 29 27.403 40.446 25.406 1.00 0.00 N +ATOM 453 H PHE 29 26.750 40.371 24.629 1.00 0.00 H +ATOM 454 CA PHE 29 26.909 40.272 26.780 1.00 0.00 C +ATOM 455 HA PHE 29 27.235 41.127 27.372 1.00 0.00 H +ATOM 456 CB PHE 29 25.370 40.257 26.782 1.00 0.00 C +ATOM 457 HB2 PHE 29 25.040 39.339 26.293 1.00 0.00 H +ATOM 458 HB3 PHE 29 25.026 40.219 27.817 1.00 0.00 H +ATOM 459 CG PHE 29 24.683 41.440 26.107 1.00 0.00 C +ATOM 460 CD1 PHE 29 23.464 41.237 25.430 1.00 0.00 C +ATOM 461 HD1 PHE 29 23.011 40.258 25.409 1.00 0.00 H +ATOM 462 CE1 PHE 29 22.827 42.305 24.774 1.00 0.00 C +ATOM 463 HE1 PHE 29 21.899 42.136 24.249 1.00 0.00 H +ATOM 464 CZ PHE 29 23.401 43.588 24.795 1.00 0.00 C +ATOM 465 HZ PHE 29 22.919 44.403 24.276 1.00 0.00 H +ATOM 466 CE2 PHE 29 24.600 43.805 25.495 1.00 0.00 C +ATOM 467 HE2 PHE 29 25.038 44.793 25.522 1.00 0.00 H +ATOM 468 CD2 PHE 29 25.236 42.738 26.153 1.00 0.00 C +ATOM 469 HD2 PHE 29 26.155 42.927 26.685 1.00 0.00 H +ATOM 470 C PHE 29 27.482 39.027 27.486 1.00 0.00 C +ATOM 471 O PHE 29 27.521 38.980 28.716 1.00 0.00 O +ATOM 472 N THR 30 27.960 38.026 26.741 1.00 0.00 N +ATOM 473 H THR 30 27.829 38.068 25.735 1.00 0.00 H +ATOM 474 CA THR 30 28.722 36.892 27.292 1.00 0.00 C +ATOM 475 HA THR 30 28.251 36.565 28.215 1.00 0.00 H +ATOM 476 CB THR 30 28.706 35.706 26.317 1.00 0.00 C +ATOM 477 HB THR 30 29.093 36.002 25.344 1.00 0.00 H +ATOM 478 CG2 THR 30 29.499 34.501 26.817 1.00 0.00 C +ATOM 479 HG21 THR 30 29.141 34.214 27.798 1.00 0.00 H +ATOM 480 HG22 THR 30 29.360 33.670 26.127 1.00 0.00 H +ATOM 481 HG23 THR 30 30.563 34.723 26.869 1.00 0.00 H +ATOM 482 OG1 THR 30 27.376 35.267 26.186 1.00 0.00 O +ATOM 483 HG1 THR 30 26.955 35.881 25.563 1.00 0.00 H +ATOM 484 C THR 30 30.150 37.299 27.655 1.00 0.00 C +ATOM 485 O THR 30 30.624 36.982 28.749 1.00 0.00 O +ATOM 486 N LYS 31 30.815 38.064 26.781 1.00 0.00 N +ATOM 487 H LYS 31 30.369 38.252 25.888 1.00 0.00 H +ATOM 488 CA LYS 31 32.152 38.634 27.020 1.00 0.00 C +ATOM 489 HA LYS 31 32.818 37.831 27.339 1.00 0.00 H +ATOM 490 CB LYS 31 32.706 39.226 25.717 1.00 0.00 C +ATOM 491 HB2 LYS 31 31.979 39.917 25.283 1.00 0.00 H +ATOM 492 HB3 LYS 31 33.613 39.789 25.949 1.00 0.00 H +ATOM 493 CG LYS 31 33.067 38.138 24.689 1.00 0.00 C +ATOM 494 HG2 LYS 31 33.816 37.480 25.124 1.00 0.00 H +ATOM 495 HG3 LYS 31 32.188 37.542 24.445 1.00 0.00 H +ATOM 496 CD LYS 31 33.619 38.762 23.398 1.00 0.00 C +ATOM 497 HD2 LYS 31 32.803 39.284 22.894 1.00 0.00 H +ATOM 498 HD3 LYS 31 34.390 39.495 23.648 1.00 0.00 H +ATOM 499 CE LYS 31 34.214 37.733 22.429 1.00 0.00 C +ATOM 500 HE2 LYS 31 33.486 36.945 22.216 1.00 0.00 H +ATOM 501 HE3 LYS 31 34.422 38.234 21.480 1.00 0.00 H +ATOM 502 NZ LYS 31 35.472 37.134 22.931 1.00 0.00 N +ATOM 503 HZ1 LYS 31 35.291 36.317 23.502 1.00 0.00 H +ATOM 504 HZ2 LYS 31 36.015 36.773 22.139 1.00 0.00 H +ATOM 505 HZ3 LYS 31 36.033 37.780 23.488 1.00 0.00 H +ATOM 506 C LYS 31 32.171 39.672 28.147 1.00 0.00 C +ATOM 507 O LYS 31 33.142 39.702 28.899 1.00 0.00 O +ATOM 508 N ALA 32 31.100 40.451 28.321 1.00 0.00 N +ATOM 509 H ALA 32 30.398 40.462 27.589 1.00 0.00 H +ATOM 510 CA ALA 32 30.931 41.365 29.453 1.00 0.00 C +ATOM 511 HA ALA 32 31.752 42.085 29.447 1.00 0.00 H +ATOM 512 CB ALA 32 29.618 42.142 29.287 1.00 0.00 C +ATOM 513 HB1 ALA 32 28.769 41.458 29.278 1.00 0.00 H +ATOM 514 HB2 ALA 32 29.501 42.841 30.118 1.00 0.00 H +ATOM 515 HB3 ALA 32 29.638 42.709 28.355 1.00 0.00 H +ATOM 516 C ALA 32 30.991 40.611 30.792 1.00 0.00 C +ATOM 517 O ALA 32 31.887 40.874 31.591 1.00 0.00 O +ATOM 518 N LYN 33 30.130 39.599 30.989 1.00 0.00 N +ATOM 519 H LYN 33 29.417 39.433 30.293 1.00 0.00 H +ATOM 520 CA LYN 33 30.139 38.766 32.203 1.00 0.00 C +ATOM 521 HA LYN 33 30.001 39.413 33.073 1.00 0.00 H +ATOM 522 CB LYN 33 28.987 37.743 32.169 1.00 0.00 C +ATOM 523 HB2 LYN 33 29.040 37.167 31.244 1.00 0.00 H +ATOM 524 HB3 LYN 33 29.118 37.055 33.007 1.00 0.00 H +ATOM 525 CG LYN 33 27.590 38.375 32.294 1.00 0.00 C +ATOM 526 HG2 LYN 33 27.545 39.000 33.186 1.00 0.00 H +ATOM 527 HG3 LYN 33 27.392 38.995 31.420 1.00 0.00 H +ATOM 528 CD LYN 33 26.522 37.277 32.395 1.00 0.00 C +ATOM 529 HD2 LYN 33 26.675 36.556 31.599 1.00 0.00 H +ATOM 530 HD3 LYN 33 26.628 36.757 33.347 1.00 0.00 H +ATOM 531 CE LYN 33 25.104 37.835 32.284 1.00 0.00 C +ATOM 532 HE2 LYN 33 24.914 38.506 33.118 1.00 0.00 H +ATOM 533 HE3 LYN 33 25.005 38.384 31.350 1.00 0.00 H +ATOM 534 NZ LYN 33 24.107 36.753 32.301 1.00 0.00 N +ATOM 535 HZ2 LYN 33 23.174 37.141 32.292 1.00 0.00 H +ATOM 536 HZ3 LYN 33 24.226 36.138 31.508 1.00 0.00 H +ATOM 537 C LYN 33 31.481 38.041 32.405 1.00 0.00 C +ATOM 538 O LYN 33 31.942 37.902 33.532 1.00 0.00 O +ATOM 539 N ALA 34 32.140 37.586 31.335 1.00 0.00 N +ATOM 540 H ALA 34 31.727 37.699 30.417 1.00 0.00 H +ATOM 541 CA ALA 34 33.461 36.962 31.455 1.00 0.00 C +ATOM 542 HA ALA 34 33.401 36.176 32.210 1.00 0.00 H +ATOM 543 CB ALA 34 33.817 36.311 30.120 1.00 0.00 C +ATOM 544 HB1 ALA 34 33.986 37.080 29.368 1.00 0.00 H +ATOM 545 HB2 ALA 34 34.719 35.716 30.257 1.00 0.00 H +ATOM 546 HB3 ALA 34 33.015 35.656 29.787 1.00 0.00 H +ATOM 547 C ALA 34 34.557 37.947 31.927 1.00 0.00 C +ATOM 548 O ALA 34 35.442 37.557 32.691 1.00 0.00 O +ATOM 549 N ASN 35 34.482 39.223 31.531 1.00 0.00 N +ATOM 550 H ASN 35 33.735 39.492 30.902 1.00 0.00 H +ATOM 551 CA ASN 35 35.346 40.291 32.051 1.00 0.00 C +ATOM 552 HA ASN 35 36.349 39.888 32.168 1.00 0.00 H +ATOM 553 CB ASN 35 35.438 41.431 31.030 1.00 0.00 C +ATOM 554 HB2 ASN 35 34.451 41.675 30.644 1.00 0.00 H +ATOM 555 HB3 ASN 35 35.833 42.319 31.524 1.00 0.00 H +ATOM 556 CG ASN 35 36.388 41.076 29.903 1.00 0.00 C +ATOM 557 OD1 ASN 35 37.597 41.133 30.044 1.00 0.00 O +ATOM 558 ND2 ASN 35 35.880 40.668 28.770 1.00 0.00 N +ATOM 559 HD21 ASN 35 36.541 40.390 28.044 1.00 0.00 H +ATOM 560 HD22 ASN 35 34.888 40.505 28.695 1.00 0.00 H +ATOM 561 C ASN 35 34.944 40.782 33.456 1.00 0.00 C +ATOM 562 O ASN 35 35.823 41.206 34.208 1.00 0.00 O +ATOM 563 N ASP 36 33.681 40.623 33.873 1.00 0.00 N +ATOM 564 H ASP 36 32.953 40.411 33.198 1.00 0.00 H +ATOM 565 CA ASP 36 33.299 40.753 35.289 1.00 0.00 C +ATOM 566 HA ASP 36 33.620 41.727 35.644 1.00 0.00 H +ATOM 567 CB ASP 36 31.771 40.726 35.477 1.00 0.00 C +ATOM 568 HB2 ASP 36 31.409 39.739 35.256 1.00 0.00 H +ATOM 569 HB3 ASP 36 31.566 40.838 36.535 1.00 0.00 H +ATOM 570 CG ASP 36 30.946 41.759 34.697 1.00 0.00 C +ATOM 571 OD1 ASP 36 31.473 42.854 34.397 1.00 0.00 O +ATOM 572 OD2 ASP 36 29.745 41.503 34.453 1.00 0.00 O +ATOM 573 C ASP 36 34.001 39.687 36.164 1.00 0.00 C +ATOM 574 O ASP 36 34.414 39.975 37.288 1.00 0.00 O +ATOM 575 N PHE 37 34.224 38.476 35.627 1.00 0.00 N +ATOM 576 H PHE 37 33.778 38.285 34.738 1.00 0.00 H +ATOM 577 CA PHE 37 35.119 37.457 36.204 1.00 0.00 C +ATOM 578 HA PHE 37 35.102 37.608 37.282 1.00 0.00 H +ATOM 579 CB PHE 37 34.584 36.039 35.941 1.00 0.00 C +ATOM 580 HB2 PHE 37 34.673 35.835 34.877 1.00 0.00 H +ATOM 581 HB3 PHE 37 35.235 35.333 36.451 1.00 0.00 H +ATOM 582 CG PHE 37 33.163 35.751 36.394 1.00 0.00 C +ATOM 583 CD1 PHE 37 32.154 35.533 35.443 1.00 0.00 C +ATOM 584 HD1 PHE 37 32.388 35.593 34.397 1.00 0.00 H +ATOM 585 CE1 PHE 37 30.832 35.284 35.846 1.00 0.00 C +ATOM 586 HE1 PHE 37 30.053 35.169 35.107 1.00 0.00 H +ATOM 587 CZ PHE 37 30.522 35.220 37.212 1.00 0.00 C +ATOM 588 HZ PHE 37 29.506 35.043 37.525 1.00 0.00 H +ATOM 589 CE2 PHE 37 31.529 35.401 38.173 1.00 0.00 C +ATOM 590 HE2 PHE 37 31.282 35.368 39.224 1.00 0.00 H +ATOM 591 CD2 PHE 37 32.847 35.666 37.762 1.00 0.00 C +ATOM 592 HD2 PHE 37 33.611 35.831 38.501 1.00 0.00 H +ATOM 593 C PHE 37 36.610 37.593 35.788 1.00 0.00 C +ATOM 594 O PHE 37 37.403 36.685 36.046 1.00 0.00 O +ATOM 595 N GLY 38 37.009 38.711 35.165 1.00 0.00 N +ATOM 596 H GLY 38 36.301 39.413 34.987 1.00 0.00 H +ATOM 597 CA GLY 38 38.402 39.132 34.947 1.00 0.00 C +ATOM 598 HA2 GLY 38 38.496 40.160 35.294 1.00 0.00 H +ATOM 599 HA3 GLY 38 39.060 38.525 35.570 1.00 0.00 H +ATOM 600 C GLY 38 38.960 39.077 33.512 1.00 0.00 C +ATOM 601 O GLY 38 39.924 39.793 33.233 1.00 0.00 O +ATOM 602 N ARG 39 38.411 38.239 32.614 1.00 0.00 N +ATOM 603 H ARG 39 37.570 37.746 32.897 1.00 0.00 H +ATOM 604 CA ARG 39 38.880 38.053 31.215 1.00 0.00 C +ATOM 605 HA ARG 39 38.893 39.037 30.743 1.00 0.00 H +ATOM 606 CB ARG 39 40.326 37.487 31.154 1.00 0.00 C +ATOM 607 HB2 ARG 39 40.634 37.506 30.107 1.00 0.00 H +ATOM 608 HB3 ARG 39 41.005 38.160 31.675 1.00 0.00 H +ATOM 609 CG ARG 39 40.587 36.054 31.667 1.00 0.00 C +ATOM 610 HG2 ARG 39 40.031 35.354 31.046 1.00 0.00 H +ATOM 611 HG3 ARG 39 41.646 35.833 31.521 1.00 0.00 H +ATOM 612 CD ARG 39 40.250 35.822 33.155 1.00 0.00 C +ATOM 613 HD2 ARG 39 40.874 36.485 33.760 1.00 0.00 H +ATOM 614 HD3 ARG 39 39.207 36.074 33.344 1.00 0.00 H +ATOM 615 NE ARG 39 40.449 34.422 33.582 1.00 0.00 N +ATOM 616 HE ARG 39 41.211 34.244 34.213 1.00 0.00 H +ATOM 617 CZ ARG 39 39.685 33.394 33.251 1.00 0.00 C +ATOM 618 NH1 ARG 39 38.675 33.509 32.434 1.00 0.00 N +ATOM 619 HH11 ARG 39 38.446 34.417 32.050 1.00 0.00 H +ATOM 620 HH12 ARG 39 38.287 32.681 31.992 1.00 0.00 H +ATOM 621 NH2 ARG 39 39.925 32.210 33.740 1.00 0.00 N +ATOM 622 HH21 ARG 39 40.672 32.054 34.398 1.00 0.00 H +ATOM 623 HH22 ARG 39 39.300 31.445 33.507 1.00 0.00 H +ATOM 624 C ARG 39 37.947 37.164 30.379 1.00 0.00 C +ATOM 625 O ARG 39 37.564 36.085 30.844 1.00 0.00 O +ATOM 626 N ASP 40 37.631 37.575 29.145 1.00 0.00 N +ATOM 627 H ASP 40 37.999 38.458 28.810 1.00 0.00 H +ATOM 628 CA ASP 40 36.870 36.764 28.180 1.00 0.00 C +ATOM 629 HA ASP 40 36.160 36.178 28.752 1.00 0.00 H +ATOM 630 CB ASP 40 36.028 37.628 27.214 1.00 0.00 C +ATOM 631 HB2 ASP 40 35.414 36.959 26.614 1.00 0.00 H +ATOM 632 HB3 ASP 40 35.330 38.215 27.807 1.00 0.00 H +ATOM 633 CG ASP 40 36.785 38.583 26.276 1.00 0.00 C +ATOM 634 OD1 ASP 40 37.479 39.492 26.781 1.00 0.00 O +ATOM 635 OD2 ASP 40 36.569 38.494 25.045 1.00 0.00 O +ATOM 636 C ASP 40 37.702 35.719 27.412 1.00 0.00 C +ATOM 637 O ASP 40 38.929 35.703 27.443 1.00 0.00 O +ATOM 638 N GLY 41 36.987 34.824 26.722 1.00 0.00 N +ATOM 639 H GLY 41 35.986 34.945 26.736 1.00 0.00 H +ATOM 640 CA GLY 41 37.491 33.909 25.694 1.00 0.00 C +ATOM 641 HA2 GLY 41 38.450 34.264 25.310 1.00 0.00 H +ATOM 642 HA3 GLY 41 37.626 32.915 26.126 1.00 0.00 H +ATOM 643 C GLY 41 36.490 33.825 24.530 1.00 0.00 C +ATOM 644 O GLY 41 35.608 34.679 24.411 1.00 0.00 O +ATOM 645 N GLU 42 36.598 32.789 23.694 1.00 0.00 N +ATOM 646 H GLU 42 37.307 32.099 23.872 1.00 0.00 H +ATOM 647 CA GLU 42 35.731 32.568 22.522 1.00 0.00 C +ATOM 648 HA GLU 42 35.013 33.385 22.459 1.00 0.00 H +ATOM 649 CB GLU 42 36.558 32.561 21.218 1.00 0.00 C +ATOM 650 HB2 GLU 42 37.196 31.676 21.230 1.00 0.00 H +ATOM 651 HB3 GLU 42 35.871 32.454 20.377 1.00 0.00 H +ATOM 652 CG GLU 42 37.461 33.787 20.960 1.00 0.00 C +ATOM 653 HG2 GLU 42 38.223 33.829 21.742 1.00 0.00 H +ATOM 654 HG3 GLU 42 37.980 33.632 20.011 1.00 0.00 H +ATOM 655 CD GLU 42 36.724 35.137 20.908 1.00 0.00 C +ATOM 656 OE1 GLU 42 35.483 35.176 21.031 1.00 0.00 O +ATOM 657 OE2 GLU 42 37.391 36.197 20.846 1.00 0.00 O +ATOM 658 C GLU 42 34.890 31.282 22.632 1.00 0.00 C +ATOM 659 O GLU 42 35.334 30.288 23.220 1.00 0.00 O +ATOM 660 N ALA 43 33.689 31.301 22.040 1.00 0.00 N +ATOM 661 H ALA 43 33.435 32.120 21.500 1.00 0.00 H +ATOM 662 CA ALA 43 32.685 30.234 22.101 1.00 0.00 C +ATOM 663 HA ALA 43 33.159 29.309 22.430 1.00 0.00 H +ATOM 664 CB ALA 43 31.621 30.621 23.139 1.00 0.00 C +ATOM 665 HB1 ALA 43 31.138 31.555 22.844 1.00 0.00 H +ATOM 666 HB2 ALA 43 30.866 29.838 23.204 1.00 0.00 H +ATOM 667 HB3 ALA 43 32.086 30.751 24.116 1.00 0.00 H +ATOM 668 C ALA 43 32.047 29.965 20.723 1.00 0.00 C +ATOM 669 O ALA 43 31.803 30.891 19.950 1.00 0.00 O +ATOM 670 N THR 44 31.754 28.697 20.429 1.00 0.00 N +ATOM 671 H THR 44 31.886 28.002 21.155 1.00 0.00 H +ATOM 672 CA THR 44 31.095 28.260 19.186 1.00 0.00 C +ATOM 673 HA THR 44 31.411 28.926 18.382 1.00 0.00 H +ATOM 674 CB THR 44 31.551 26.839 18.809 1.00 0.00 C +ATOM 675 HB THR 44 31.332 26.153 19.627 1.00 0.00 H +ATOM 676 CG2 THR 44 30.946 26.290 17.515 1.00 0.00 C +ATOM 677 HG21 THR 44 31.065 27.010 16.705 1.00 0.00 H +ATOM 678 HG22 THR 44 31.440 25.358 17.238 1.00 0.00 H +ATOM 679 HG23 THR 44 29.887 26.071 17.660 1.00 0.00 H +ATOM 680 OG1 THR 44 32.942 26.864 18.586 1.00 0.00 O +ATOM 681 HG1 THR 44 33.165 26.109 18.037 1.00 0.00 H +ATOM 682 C THR 44 29.572 28.381 19.304 1.00 0.00 C +ATOM 683 O THR 44 29.030 28.395 20.412 1.00 0.00 O +ATOM 684 N ILE 45 28.876 28.504 18.166 1.00 0.00 N +ATOM 685 H ILE 45 29.362 28.406 17.289 1.00 0.00 H +ATOM 686 CA ILE 45 27.461 28.894 18.096 1.00 0.00 C +ATOM 687 HA ILE 45 27.037 28.820 19.098 1.00 0.00 H +ATOM 688 CB ILE 45 27.326 30.368 17.651 1.00 0.00 C +ATOM 689 HB ILE 45 26.262 30.577 17.713 1.00 0.00 H +ATOM 690 CG2 ILE 45 28.061 31.286 18.642 1.00 0.00 C +ATOM 691 HG21 ILE 45 29.142 31.155 18.565 1.00 0.00 H +ATOM 692 HG22 ILE 45 27.838 32.337 18.468 1.00 0.00 H +ATOM 693 HG23 ILE 45 27.748 31.027 19.650 1.00 0.00 H +ATOM 694 CG1 ILE 45 27.760 30.675 16.198 1.00 0.00 C +ATOM 695 HG12 ILE 45 28.847 30.635 16.123 1.00 0.00 H +ATOM 696 HG13 ILE 45 27.346 29.927 15.524 1.00 0.00 H +ATOM 697 CD1 ILE 45 27.269 32.044 15.699 1.00 0.00 C +ATOM 698 HD11 ILE 45 27.702 32.852 16.288 1.00 0.00 H +ATOM 699 HD12 ILE 45 27.568 32.179 14.659 1.00 0.00 H +ATOM 700 HD13 ILE 45 26.182 32.091 15.757 1.00 0.00 H +ATOM 701 C ILE 45 26.606 27.983 17.209 1.00 0.00 C +ATOM 702 O ILE 45 27.086 27.449 16.212 1.00 0.00 O +ATOM 703 N ASP 46 25.319 27.893 17.544 1.00 0.00 N +ATOM 704 H ASP 46 25.030 28.275 18.437 1.00 0.00 H +ATOM 705 CA ASP 46 24.271 27.263 16.737 1.00 0.00 C +ATOM 706 HA ASP 46 24.569 27.261 15.686 1.00 0.00 H +ATOM 707 CB ASP 46 24.082 25.808 17.188 1.00 0.00 C +ATOM 708 HB2 ASP 46 24.964 25.230 16.919 1.00 0.00 H +ATOM 709 HB3 ASP 46 23.970 25.788 18.272 1.00 0.00 H +ATOM 710 CG ASP 46 22.847 25.164 16.551 1.00 0.00 C +ATOM 711 OD1 ASP 46 22.121 24.459 17.287 1.00 0.00 O +ATOM 712 OD2 ASP 46 22.564 25.434 15.363 1.00 0.00 O +ATOM 713 C ASP 46 22.942 28.040 16.854 1.00 0.00 C +ATOM 714 O ASP 46 22.481 28.333 17.959 1.00 0.00 O +ATOM 715 N ASP 47 22.303 28.334 15.719 1.00 0.00 N +ATOM 716 H ASP 47 22.690 27.972 14.860 1.00 0.00 H +ATOM 717 CA ASP 47 20.960 28.922 15.674 1.00 0.00 C +ATOM 718 HA ASP 47 20.867 29.653 16.484 1.00 0.00 H +ATOM 719 CB ASP 47 20.770 29.668 14.344 1.00 0.00 C +ATOM 720 HB2 ASP 47 21.505 30.467 14.270 1.00 0.00 H +ATOM 721 HB3 ASP 47 20.915 28.978 13.514 1.00 0.00 H +ATOM 722 CG ASP 47 19.357 30.272 14.273 1.00 0.00 C +ATOM 723 OD1 ASP 47 18.476 29.671 13.620 1.00 0.00 O +ATOM 724 OD2 ASP 47 19.059 31.234 15.015 1.00 0.00 O +ATOM 725 C ASP 47 19.843 27.873 15.876 1.00 0.00 C +ATOM 726 O ASP 47 18.829 28.182 16.505 1.00 0.00 O +ATOM 727 N ALA 48 20.002 26.635 15.397 1.00 0.00 N +ATOM 728 H ALA 48 20.918 26.350 15.053 1.00 0.00 H +ATOM 729 CA ALA 48 18.940 25.621 15.410 1.00 0.00 C +ATOM 730 HA ALA 48 18.054 26.044 14.932 1.00 0.00 H +ATOM 731 CB ALA 48 19.410 24.420 14.579 1.00 0.00 C +ATOM 732 HB1 ALA 48 20.283 23.961 15.047 1.00 0.00 H +ATOM 733 HB2 ALA 48 18.611 23.681 14.510 1.00 0.00 H +ATOM 734 HB3 ALA 48 19.678 24.752 13.576 1.00 0.00 H +ATOM 735 C ALA 48 18.530 25.204 16.836 1.00 0.00 C +ATOM 736 O ALA 48 17.357 24.917 17.091 1.00 0.00 O +ATOM 737 N THR 49 19.478 25.235 17.776 1.00 0.00 N +ATOM 738 H THR 49 20.442 25.294 17.450 1.00 0.00 H +ATOM 739 CA THR 49 19.259 25.108 19.224 1.00 0.00 C +ATOM 740 HA THR 49 18.214 24.847 19.390 1.00 0.00 H +ATOM 741 CB THR 49 20.096 23.965 19.823 1.00 0.00 C +ATOM 742 HB THR 49 19.809 23.853 20.868 1.00 0.00 H +ATOM 743 CG2 THR 49 19.864 22.618 19.134 1.00 0.00 C +ATOM 744 HG21 THR 49 20.201 22.658 18.097 1.00 0.00 H +ATOM 745 HG22 THR 49 20.426 21.844 19.656 1.00 0.00 H +ATOM 746 HG23 THR 49 18.803 22.371 19.159 1.00 0.00 H +ATOM 747 OG1 THR 49 21.474 24.242 19.784 1.00 0.00 O +ATOM 748 HG1 THR 49 21.744 24.259 18.832 1.00 0.00 H +ATOM 749 C THR 49 19.502 26.420 19.993 1.00 0.00 C +ATOM 750 O THR 49 19.436 26.422 21.225 1.00 0.00 O +ATOM 751 N LYS 50 19.754 27.548 19.304 1.00 0.00 N +ATOM 752 H LYS 50 19.767 27.466 18.294 1.00 0.00 H +ATOM 753 CA LYS 50 19.933 28.904 19.871 1.00 0.00 C +ATOM 754 HA LYS 50 20.345 29.539 19.085 1.00 0.00 H +ATOM 755 CB LYS 50 18.550 29.472 20.286 1.00 0.00 C +ATOM 756 HB2 LYS 50 18.148 28.822 21.067 1.00 0.00 H +ATOM 757 HB3 LYS 50 18.683 30.456 20.733 1.00 0.00 H +ATOM 758 CG LYS 50 17.477 29.587 19.183 1.00 0.00 C +ATOM 759 HG2 LYS 50 17.412 28.653 18.624 1.00 0.00 H +ATOM 760 HG3 LYS 50 16.516 29.737 19.679 1.00 0.00 H +ATOM 761 CD LYS 50 17.696 30.772 18.221 1.00 0.00 C +ATOM 762 HD2 LYS 50 17.689 31.691 18.811 1.00 0.00 H +ATOM 763 HD3 LYS 50 18.664 30.684 17.722 1.00 0.00 H +ATOM 764 CE LYS 50 16.561 30.863 17.183 1.00 0.00 C +ATOM 765 HE2 LYS 50 15.613 30.599 17.660 1.00 0.00 H +ATOM 766 HE3 LYS 50 16.499 31.897 16.833 1.00 0.00 H +ATOM 767 NZ LYS 50 16.816 29.992 16.015 1.00 0.00 N +ATOM 768 HZ1 LYS 50 17.225 29.100 16.279 1.00 0.00 H +ATOM 769 HZ2 LYS 50 16.009 29.832 15.431 1.00 0.00 H +ATOM 770 HZ3 LYS 50 17.539 30.414 15.421 1.00 0.00 H +ATOM 771 C LYS 50 20.970 28.951 21.017 1.00 0.00 C +ATOM 772 O LYS 50 20.682 29.512 22.077 1.00 0.00 O +ATOM 773 N THR 51 22.131 28.302 20.845 1.00 0.00 N +ATOM 774 H THR 51 22.339 27.968 19.903 1.00 0.00 H +ATOM 775 CA THR 51 23.053 27.907 21.937 1.00 0.00 C +ATOM 776 HA THR 51 22.762 28.449 22.830 1.00 0.00 H +ATOM 777 CB THR 51 22.870 26.407 22.254 1.00 0.00 C +ATOM 778 HB THR 51 22.978 25.828 21.339 1.00 0.00 H +ATOM 779 CG2 THR 51 23.853 25.855 23.296 1.00 0.00 C +ATOM 780 HG21 THR 51 23.832 26.468 24.189 1.00 0.00 H +ATOM 781 HG22 THR 51 23.578 24.838 23.563 1.00 0.00 H +ATOM 782 HG23 THR 51 24.863 25.826 22.898 1.00 0.00 H +ATOM 783 OG1 THR 51 21.621 26.148 22.865 1.00 0.00 O +ATOM 784 HG1 THR 51 20.921 26.263 22.202 1.00 0.00 H +ATOM 785 C THR 51 24.544 28.228 21.698 1.00 0.00 C +ATOM 786 O THR 51 25.084 27.988 20.620 1.00 0.00 O +ATOM 787 N PHE 52 25.238 28.707 22.747 1.00 0.00 N +ATOM 788 H PHE 52 24.707 28.976 23.559 1.00 0.00 H +ATOM 789 CA PHE 52 26.716 28.789 22.857 1.00 0.00 C +ATOM 790 HA PHE 52 27.140 28.941 21.862 1.00 0.00 H +ATOM 791 CB PHE 52 27.147 29.943 23.778 1.00 0.00 C +ATOM 792 HB2 PHE 52 26.473 29.956 24.634 1.00 0.00 H +ATOM 793 HB3 PHE 52 28.147 29.725 24.163 1.00 0.00 H +ATOM 794 CG PHE 52 27.225 31.342 23.209 1.00 0.00 C +ATOM 795 CD1 PHE 52 26.442 32.383 23.747 1.00 0.00 C +ATOM 796 HD1 PHE 52 25.773 32.191 24.563 1.00 0.00 H +ATOM 797 CE1 PHE 52 26.459 33.658 23.158 1.00 0.00 C +ATOM 798 HE1 PHE 52 25.803 34.434 23.518 1.00 0.00 H +ATOM 799 CZ PHE 52 27.293 33.897 22.055 1.00 0.00 C +ATOM 800 HZ PHE 52 27.255 34.841 21.550 1.00 0.00 H +ATOM 801 CE2 PHE 52 28.170 32.905 21.596 1.00 0.00 C +ATOM 802 HE2 PHE 52 28.842 33.114 20.775 1.00 0.00 H +ATOM 803 CD2 PHE 52 28.131 31.625 22.173 1.00 0.00 C +ATOM 804 HD2 PHE 52 28.777 30.853 21.793 1.00 0.00 H +ATOM 805 C PHE 52 27.312 27.504 23.461 1.00 0.00 C +ATOM 806 O PHE 52 26.769 27.002 24.452 1.00 0.00 O +ATOM 807 N THR 53 28.478 27.069 22.969 1.00 0.00 N +ATOM 808 H THR 53 28.846 27.530 22.138 1.00 0.00 H +ATOM 809 CA THR 53 29.266 25.932 23.499 1.00 0.00 C +ATOM 810 HA THR 53 29.009 25.788 24.548 1.00 0.00 H +ATOM 811 CB THR 53 28.936 24.619 22.755 1.00 0.00 C +ATOM 812 HB THR 53 29.500 23.807 23.219 1.00 0.00 H +ATOM 813 CG2 THR 53 27.462 24.234 22.788 1.00 0.00 C +ATOM 814 HG21 THR 53 26.881 24.922 22.172 1.00 0.00 H +ATOM 815 HG22 THR 53 27.335 23.219 22.405 1.00 0.00 H +ATOM 816 HG23 THR 53 27.097 24.266 23.815 1.00 0.00 H +ATOM 817 OG1 THR 53 29.318 24.703 21.403 1.00 0.00 O +ATOM 818 HG1 THR 53 28.790 24.067 20.912 1.00 0.00 H +ATOM 819 C THR 53 30.790 26.159 23.443 1.00 0.00 C +ATOM 820 O THR 53 31.282 27.102 22.823 1.00 0.00 O +ATOM 821 N THR 54 31.554 25.281 24.106 1.00 0.00 N +ATOM 822 H THR 54 31.091 24.549 24.623 1.00 0.00 H +ATOM 823 CA THR 54 33.029 25.192 24.040 1.00 0.00 C +ATOM 824 HA THR 54 33.396 25.977 23.380 1.00 0.00 H +ATOM 825 CB THR 54 33.662 25.402 25.430 1.00 0.00 C +ATOM 826 HB THR 54 33.369 24.575 26.079 1.00 0.00 H +ATOM 827 CG2 THR 54 35.187 25.519 25.423 1.00 0.00 C +ATOM 828 HG21 THR 54 35.503 26.288 24.716 1.00 0.00 H +ATOM 829 HG22 THR 54 35.531 25.780 26.424 1.00 0.00 H +ATOM 830 HG23 THR 54 35.635 24.563 25.155 1.00 0.00 H +ATOM 831 OG1 THR 54 33.191 26.599 26.010 1.00 0.00 O +ATOM 832 HG1 THR 54 33.471 27.330 25.451 1.00 0.00 H +ATOM 833 C THR 54 33.460 23.848 23.429 1.00 0.00 C +ATOM 834 O THR 54 32.747 22.851 23.553 1.00 0.00 O +ATOM 835 N GLN 55 34.613 23.837 22.755 1.00 0.00 N +ATOM 836 H GLN 55 35.135 24.697 22.711 1.00 0.00 H +ATOM 837 CA GLN 55 35.249 22.649 22.166 1.00 0.00 C +ATOM 838 HA GLN 55 34.484 22.117 21.600 1.00 0.00 H +ATOM 839 CB GLN 55 36.322 23.115 21.159 1.00 0.00 C +ATOM 840 HB2 GLN 55 36.756 22.242 20.673 1.00 0.00 H +ATOM 841 HB3 GLN 55 35.811 23.701 20.392 1.00 0.00 H +ATOM 842 CG GLN 55 37.456 23.975 21.751 1.00 0.00 C +ATOM 843 HG2 GLN 55 37.050 24.710 22.448 1.00 0.00 H +ATOM 844 HG3 GLN 55 38.149 23.338 22.304 1.00 0.00 H +ATOM 845 CD GLN 55 38.239 24.731 20.674 1.00 0.00 C +ATOM 846 OE1 GLN 55 38.376 24.300 19.537 1.00 0.00 O +ATOM 847 NE2 GLN 55 38.765 25.898 20.989 1.00 0.00 N +ATOM 848 HE21 GLN 55 39.353 26.343 20.289 1.00 0.00 H +ATOM 849 HE22 GLN 55 38.589 26.321 21.885 1.00 0.00 H +ATOM 850 C GLN 55 35.799 21.649 23.215 1.00 0.00 C +ATOM 851 O GLN 55 36.039 22.022 24.362 1.00 0.00 O +ATOM 852 N GLU 56 35.970 20.383 22.803 1.00 0.00 N +ATOM 853 H GLU 56 35.828 20.197 21.826 1.00 0.00 H +ATOM 854 CA GLU 56 36.484 19.235 23.593 1.00 0.00 C +ATOM 855 HA GLU 56 36.128 19.329 24.618 1.00 0.00 H +ATOM 856 CB GLU 56 35.902 17.932 22.988 1.00 0.00 C +ATOM 857 HB2 GLU 56 34.817 17.960 23.067 1.00 0.00 H +ATOM 858 HB3 GLU 56 36.130 17.955 21.922 1.00 0.00 H +ATOM 859 CG GLU 56 36.415 16.572 23.523 1.00 0.00 C +ATOM 860 HG2 GLU 56 36.456 15.892 22.671 1.00 0.00 H +ATOM 861 HG3 GLU 56 37.439 16.664 23.869 1.00 0.00 H +ATOM 862 CD GLU 56 35.553 15.892 24.605 1.00 0.00 C +ATOM 863 OE1 GLU 56 36.092 15.416 25.638 1.00 0.00 O +ATOM 864 OE2 GLU 56 34.328 15.697 24.407 1.00 0.00 O +ATOM 865 C GLU 56 38.023 19.208 23.699 1.00 0.00 C +ATOM 866 O GLU 56 38.504 19.229 24.856 1.00 0.00 O +ATOM 867 OXT GLU 56 38.696 19.129 22.645 1.00 0.00 O +HETATM 868 ZN ZN1 57 26.717 32.463 29.375 1.00 0.00 Zn +HETATM 869 N AN1 58 28.350 33.227 30.290 1.00 0.00 N +HETATM 870 C AN1 58 30.703 33.942 31.139 1.00 0.00 C +HETATM 871 C1 AN1 58 29.377 33.530 30.688 1.00 0.00 C +HETATM 872 H AN1 58 30.659 34.320 32.164 1.00 0.00 H +HETATM 873 H1 AN1 58 31.084 34.723 30.475 1.00 0.00 H +HETATM 874 H2 AN1 58 31.373 33.073 31.099 1.00 0.00 H +HETATM 875 N1 AZI 59 30.716 30.555 30.103 1.00 0.00 N +HETATM 876 N2 AZI 59 30.176 29.687 30.743 1.00 0.00 N +HETATM 877 N3 AZI 59 29.592 28.761 31.427 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 868 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 144 148 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 208 186 190 189 +CONECT 189 188 +CONECT 190 193 188 191 192 +CONECT 191 190 +CONECT 192 190 +CONECT 193 195 194 196 190 +CONECT 194 193 +CONECT 195 193 +CONECT 196 199 193 197 198 +CONECT 197 196 +CONECT 198 196 +CONECT 199 200 201 196 +CONECT 200 199 +CONECT 201 205 199 202 +CONECT 202 201 204 203 +CONECT 203 202 +CONECT 204 202 +CONECT 205 206 207 201 +CONECT 206 205 +CONECT 207 205 +CONECT 208 209 210 188 +CONECT 209 208 +CONECT 210 212 208 211 +CONECT 211 210 +CONECT 212 213 230 214 210 +CONECT 213 212 +CONECT 214 217 212 215 216 +CONECT 215 214 +CONECT 216 214 +CONECT 217 219 218 220 214 +CONECT 218 217 +CONECT 219 217 +CONECT 220 221 217 222 223 +CONECT 221 220 +CONECT 222 220 +CONECT 223 225 220 226 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 229 223 228 227 +CONECT 227 226 +CONECT 228 226 +CONECT 229 226 +CONECT 230 231 212 232 +CONECT 231 230 +CONECT 232 230 234 233 +CONECT 233 232 +CONECT 234 237 232 235 236 +CONECT 235 234 +CONECT 236 234 +CONECT 237 238 239 234 +CONECT 238 237 +CONECT 239 241 237 240 +CONECT 240 239 +CONECT 241 243 242 253 239 +CONECT 242 241 +CONECT 243 249 244 245 241 +CONECT 244 243 +CONECT 245 247 243 246 248 +CONECT 246 245 +CONECT 247 245 +CONECT 248 245 +CONECT 249 251 250 252 243 +CONECT 250 249 +CONECT 251 249 +CONECT 252 249 +CONECT 253 241 255 254 +CONECT 254 253 +CONECT 255 265 256 253 +CONECT 256 257 255 266 259 +CONECT 257 258 272 256 +CONECT 258 257 +CONECT 259 256 260 267 268 +CONECT 260 261 262 259 +CONECT 261 264 270 260 +CONECT 262 263 260 269 +CONECT 263 264 271 262 +CONECT 264 868 263 261 +CONECT 265 255 +CONECT 266 256 +CONECT 267 259 +CONECT 268 259 +CONECT 269 262 +CONECT 270 261 +CONECT 271 263 +CONECT 272 274 257 273 +CONECT 273 272 +CONECT 274 275 276 284 272 +CONECT 275 274 +CONECT 276 277 278 274 282 +CONECT 277 276 +CONECT 278 281 280 276 279 +CONECT 279 278 +CONECT 280 278 +CONECT 281 278 +CONECT 282 276 283 +CONECT 283 282 +CONECT 284 286 274 285 +CONECT 285 284 +CONECT 286 296 287 284 +CONECT 287 288 290 286 297 +CONECT 288 289 303 287 +CONECT 289 288 +CONECT 290 298 299 287 291 +CONECT 291 290 292 293 +CONECT 292 301 291 295 +CONECT 293 291 300 294 +CONECT 294 293 295 302 +CONECT 295 292 294 868 +CONECT 296 286 +CONECT 297 287 +CONECT 298 290 +CONECT 299 290 +CONECT 300 293 +CONECT 301 292 +CONECT 302 294 +CONECT 303 305 288 304 +CONECT 304 303 +CONECT 305 316 306 303 307 +CONECT 306 305 +CONECT 307 305 310 309 308 +CONECT 308 307 +CONECT 309 307 +CONECT 310 312 313 307 311 +CONECT 311 310 +CONECT 312 310 +CONECT 313 314 310 315 +CONECT 314 313 +CONECT 315 313 +CONECT 316 318 317 305 +CONECT 317 316 +CONECT 318 320 319 316 +CONECT 319 318 +CONECT 320 326 322 321 318 +CONECT 321 320 +CONECT 322 324 323 320 325 +CONECT 323 322 +CONECT 324 322 +CONECT 325 322 +CONECT 326 328 327 320 +CONECT 327 326 +CONECT 328 330 329 326 +CONECT 329 328 +CONECT 330 342 332 331 328 +CONECT 331 330 +CONECT 332 333 338 330 334 +CONECT 333 332 +CONECT 334 332 336 337 335 +CONECT 335 334 +CONECT 336 334 +CONECT 337 334 +CONECT 338 339 340 332 341 +CONECT 339 338 +CONECT 340 338 +CONECT 341 338 +CONECT 342 343 344 330 +CONECT 343 342 +CONECT 344 346 342 345 +CONECT 345 344 +CONECT 346 348 347 354 344 +CONECT 347 346 +CONECT 348 351 349 350 346 +CONECT 349 348 +CONECT 350 348 +CONECT 351 353 352 348 +CONECT 352 351 +CONECT 353 351 +CONECT 354 346 356 355 +CONECT 355 354 +CONECT 356 357 358 354 +CONECT 357 356 +CONECT 358 360 356 378 359 +CONECT 359 358 +CONECT 360 362 361 363 358 +CONECT 361 360 +CONECT 362 360 +CONECT 363 364 360 377 +CONECT 364 365 366 363 +CONECT 365 364 +CONECT 366 364 367 368 +CONECT 367 366 +CONECT 368 366 377 369 +CONECT 369 368 370 371 +CONECT 370 369 +CONECT 371 369 373 372 +CONECT 372 371 +CONECT 373 375 371 374 +CONECT 374 373 +CONECT 375 377 376 373 +CONECT 376 375 +CONECT 377 363 368 375 +CONECT 378 380 358 379 +CONECT 379 378 +CONECT 380 381 382 378 +CONECT 381 380 +CONECT 382 384 380 383 388 +CONECT 383 382 +CONECT 384 387 385 386 382 +CONECT 385 384 +CONECT 386 384 +CONECT 387 384 +CONECT 388 382 389 390 +CONECT 389 388 +CONECT 390 388 391 392 +CONECT 391 390 +CONECT 392 390 393 394 403 +CONECT 393 392 +CONECT 394 397 395 392 396 +CONECT 395 394 +CONECT 396 394 +CONECT 397 398 399 400 394 +CONECT 398 397 +CONECT 399 397 +CONECT 400 402 397 401 +CONECT 401 400 +CONECT 402 400 +CONECT 403 392 405 404 +CONECT 404 403 +CONECT 405 406 403 407 +CONECT 406 405 +CONECT 407 405 409 413 408 +CONECT 408 407 +CONECT 409 410 412 407 411 +CONECT 410 409 +CONECT 411 409 +CONECT 412 409 +CONECT 413 415 407 414 +CONECT 414 413 +CONECT 415 416 417 413 +CONECT 416 415 +CONECT 417 419 415 418 428 +CONECT 418 417 +CONECT 419 420 421 422 417 +CONECT 420 419 +CONECT 421 419 +CONECT 422 425 419 424 423 +CONECT 423 422 +CONECT 424 422 +CONECT 425 427 426 422 +CONECT 426 425 +CONECT 427 425 +CONECT 428 417 430 429 +CONECT 429 428 +CONECT 430 431 428 432 +CONECT 431 430 +CONECT 432 430 434 433 450 +CONECT 433 432 +CONECT 434 437 435 436 432 +CONECT 435 434 +CONECT 436 434 +CONECT 437 440 439 438 434 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 441 442 437 +CONECT 441 440 +CONECT 442 440 +CONECT 443 446 444 445 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 448 449 447 443 +CONECT 447 446 +CONECT 448 446 +CONECT 449 446 +CONECT 450 432 452 451 +CONECT 451 450 +CONECT 452 453 450 454 +CONECT 453 452 +CONECT 454 452 456 455 470 +CONECT 455 454 +CONECT 456 459 457 454 458 +CONECT 457 456 +CONECT 458 456 +CONECT 459 460 468 456 +CONECT 460 462 461 459 +CONECT 461 460 +CONECT 462 463 464 460 +CONECT 463 462 +CONECT 464 465 462 466 +CONECT 465 464 +CONECT 466 464 467 468 +CONECT 467 466 +CONECT 468 466 459 469 +CONECT 469 468 +CONECT 470 472 454 471 +CONECT 471 470 +CONECT 472 473 474 470 +CONECT 473 472 +CONECT 474 476 472 484 475 +CONECT 475 474 +CONECT 476 477 482 478 474 +CONECT 477 476 +CONECT 478 480 476 481 479 +CONECT 479 478 +CONECT 480 478 +CONECT 481 478 +CONECT 482 483 476 +CONECT 483 482 +CONECT 484 486 474 485 +CONECT 485 484 +CONECT 486 487 488 484 +CONECT 487 486 +CONECT 488 490 486 489 506 +CONECT 489 488 +CONECT 490 493 491 492 488 +CONECT 491 490 +CONECT 492 490 +CONECT 493 496 495 494 490 +CONECT 494 493 +CONECT 495 493 +CONECT 496 499 497 498 493 +CONECT 497 496 +CONECT 498 496 +CONECT 499 501 500 502 496 +CONECT 500 499 +CONECT 501 499 +CONECT 502 504 499 505 503 +CONECT 503 502 +CONECT 504 502 +CONECT 505 502 +CONECT 506 488 508 507 +CONECT 507 506 +CONECT 508 509 506 510 +CONECT 509 508 +CONECT 510 508 512 511 516 +CONECT 511 510 +CONECT 512 515 513 510 514 +CONECT 513 512 +CONECT 514 512 +CONECT 515 512 +CONECT 516 510 518 517 +CONECT 517 516 +CONECT 518 519 516 520 +CONECT 519 518 +CONECT 520 518 522 537 521 +CONECT 521 520 +CONECT 522 523 520 525 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 527 522 528 526 +CONECT 526 525 +CONECT 527 525 +CONECT 528 529 531 525 530 +CONECT 529 528 +CONECT 530 528 +CONECT 531 533 534 528 532 +CONECT 532 531 +CONECT 533 531 +CONECT 534 536 531 535 +CONECT 535 534 +CONECT 536 534 +CONECT 537 539 520 538 +CONECT 538 537 +CONECT 539 540 541 537 +CONECT 540 539 +CONECT 541 543 539 547 542 +CONECT 542 541 +CONECT 543 544 546 545 541 +CONECT 544 543 +CONECT 545 543 +CONECT 546 543 +CONECT 547 541 549 548 +CONECT 548 547 +CONECT 549 550 547 551 +CONECT 550 549 +CONECT 551 553 549 552 561 +CONECT 552 551 +CONECT 553 556 554 555 551 +CONECT 554 553 +CONECT 555 553 +CONECT 556 558 557 553 +CONECT 557 556 +CONECT 558 559 560 556 +CONECT 559 558 +CONECT 560 558 +CONECT 561 551 563 562 +CONECT 562 561 +CONECT 563 564 561 565 +CONECT 564 563 +CONECT 565 563 567 566 573 +CONECT 566 565 +CONECT 567 570 568 565 569 +CONECT 568 567 +CONECT 569 567 +CONECT 570 571 572 567 +CONECT 571 570 +CONECT 572 570 +CONECT 573 565 575 574 +CONECT 574 573 +CONECT 575 576 573 577 +CONECT 576 575 +CONECT 577 575 593 579 578 +CONECT 578 577 +CONECT 579 580 577 582 581 +CONECT 580 579 +CONECT 581 579 +CONECT 582 583 579 591 +CONECT 583 584 585 582 +CONECT 584 583 +CONECT 585 586 583 587 +CONECT 586 585 +CONECT 587 585 588 589 +CONECT 588 587 +CONECT 589 587 591 590 +CONECT 590 589 +CONECT 591 582 589 592 +CONECT 592 591 +CONECT 593 595 594 577 +CONECT 594 593 +CONECT 595 597 596 593 +CONECT 596 595 +CONECT 597 600 595 598 599 +CONECT 598 597 +CONECT 599 597 +CONECT 600 602 601 597 +CONECT 601 600 +CONECT 602 604 603 600 +CONECT 603 602 +CONECT 604 624 605 606 602 +CONECT 605 604 +CONECT 606 607 604 609 608 +CONECT 607 606 +CONECT 608 606 +CONECT 609 610 606 611 612 +CONECT 610 609 +CONECT 611 609 +CONECT 612 609 614 615 613 +CONECT 613 612 +CONECT 614 612 +CONECT 615 612 617 616 +CONECT 616 615 +CONECT 617 618 615 621 +CONECT 618 620 619 617 +CONECT 619 618 +CONECT 620 618 +CONECT 621 617 623 622 +CONECT 622 621 +CONECT 623 621 +CONECT 624 626 625 604 +CONECT 625 624 +CONECT 626 628 627 624 +CONECT 627 626 +CONECT 628 630 636 629 626 +CONECT 629 628 +CONECT 630 633 631 632 628 +CONECT 631 630 +CONECT 632 630 +CONECT 633 635 634 630 +CONECT 634 633 +CONECT 635 633 +CONECT 636 638 637 628 +CONECT 637 636 +CONECT 638 640 639 636 +CONECT 639 638 +CONECT 640 643 641 642 638 +CONECT 641 640 +CONECT 642 640 +CONECT 643 645 644 640 +CONECT 644 643 +CONECT 645 647 646 643 +CONECT 646 645 +CONECT 647 649 648 658 645 +CONECT 648 647 +CONECT 649 651 652 650 647 +CONECT 650 649 +CONECT 651 649 +CONECT 652 654 655 649 653 +CONECT 653 652 +CONECT 654 652 +CONECT 655 657 652 656 +CONECT 656 655 +CONECT 657 655 +CONECT 658 660 647 659 +CONECT 659 658 +CONECT 660 661 662 658 +CONECT 661 660 +CONECT 662 668 660 663 664 +CONECT 663 662 +CONECT 664 662 665 666 667 +CONECT 665 664 +CONECT 666 664 +CONECT 667 664 +CONECT 668 669 670 662 +CONECT 669 668 +CONECT 670 672 668 671 +CONECT 671 670 +CONECT 672 673 674 682 670 +CONECT 673 672 +CONECT 674 676 680 672 675 +CONECT 675 674 +CONECT 676 677 678 679 674 +CONECT 677 676 +CONECT 678 676 +CONECT 679 676 +CONECT 680 681 674 +CONECT 681 680 +CONECT 682 684 672 683 +CONECT 683 682 +CONECT 684 685 686 682 +CONECT 685 684 +CONECT 686 701 688 684 687 +CONECT 687 686 +CONECT 688 694 689 686 690 +CONECT 689 688 +CONECT 690 688 692 691 693 +CONECT 691 690 +CONECT 692 690 +CONECT 693 690 +CONECT 694 696 697 695 688 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 700 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 697 +CONECT 701 702 703 686 +CONECT 702 701 +CONECT 703 705 701 704 +CONECT 704 703 +CONECT 705 706 713 707 703 +CONECT 706 705 +CONECT 707 710 705 708 709 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 707 711 +CONECT 711 710 +CONECT 712 710 +CONECT 713 715 705 714 +CONECT 714 713 +CONECT 715 716 717 713 +CONECT 716 715 +CONECT 717 719 715 725 718 +CONECT 718 717 +CONECT 719 721 720 722 717 +CONECT 720 719 +CONECT 721 719 +CONECT 722 723 719 724 +CONECT 723 722 +CONECT 724 722 +CONECT 725 727 717 726 +CONECT 726 725 +CONECT 727 728 729 725 +CONECT 728 727 +CONECT 729 731 730 727 735 +CONECT 730 729 +CONECT 731 734 733 732 729 +CONECT 732 731 +CONECT 733 731 +CONECT 734 731 +CONECT 735 729 736 737 +CONECT 736 735 +CONECT 737 735 738 739 +CONECT 738 737 +CONECT 739 737 740 741 749 +CONECT 740 739 +CONECT 741 743 739 747 742 +CONECT 742 741 +CONECT 743 744 746 745 741 +CONECT 744 743 +CONECT 745 743 +CONECT 746 743 +CONECT 747 748 741 +CONECT 748 747 +CONECT 749 739 751 750 +CONECT 750 749 +CONECT 751 752 753 749 +CONECT 752 751 +CONECT 753 754 751 755 771 +CONECT 754 753 +CONECT 755 758 753 757 756 +CONECT 756 755 +CONECT 757 755 +CONECT 758 761 759 760 755 +CONECT 759 758 +CONECT 760 758 +CONECT 761 764 763 762 758 +CONECT 762 761 +CONECT 763 761 +CONECT 764 767 766 765 761 +CONECT 765 764 +CONECT 766 764 +CONECT 767 770 769 768 764 +CONECT 768 767 +CONECT 769 767 +CONECT 770 767 +CONECT 771 753 773 772 +CONECT 772 771 +CONECT 773 774 771 775 +CONECT 774 773 +CONECT 775 773 785 777 776 +CONECT 776 775 +CONECT 777 778 775 783 779 +CONECT 778 777 +CONECT 779 777 782 781 780 +CONECT 780 779 +CONECT 781 779 +CONECT 782 779 +CONECT 783 784 777 +CONECT 784 783 +CONECT 785 786 775 787 +CONECT 786 785 +CONECT 787 785 789 788 +CONECT 788 787 +CONECT 789 790 787 805 791 +CONECT 790 789 +CONECT 791 789 794 793 792 +CONECT 792 791 +CONECT 793 791 +CONECT 794 803 795 791 +CONECT 795 797 794 796 +CONECT 796 795 +CONECT 797 799 798 795 +CONECT 798 797 +CONECT 799 800 801 797 +CONECT 800 799 +CONECT 801 802 799 803 +CONECT 802 801 +CONECT 803 801 804 794 +CONECT 804 803 +CONECT 805 789 807 806 +CONECT 806 805 +CONECT 807 808 805 809 +CONECT 808 807 +CONECT 809 811 807 819 810 +CONECT 810 809 +CONECT 811 817 813 812 809 +CONECT 812 811 +CONECT 813 814 815 811 816 +CONECT 814 813 +CONECT 815 813 +CONECT 816 813 +CONECT 817 818 811 +CONECT 818 817 +CONECT 819 820 809 821 +CONECT 820 819 +CONECT 821 819 823 822 +CONECT 822 821 +CONECT 823 824 833 821 825 +CONECT 824 823 +CONECT 825 823 827 831 826 +CONECT 826 825 +CONECT 827 828 830 825 829 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 825 832 +CONECT 832 831 +CONECT 833 835 834 823 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 839 838 835 850 +CONECT 838 837 +CONECT 839 841 840 842 837 +CONECT 840 839 +CONECT 841 839 +CONECT 842 845 839 844 843 +CONECT 843 842 +CONECT 844 842 +CONECT 845 846 847 842 +CONECT 846 845 +CONECT 847 848 845 849 +CONECT 848 847 +CONECT 849 847 +CONECT 850 837 852 851 +CONECT 851 850 +CONECT 852 853 850 854 +CONECT 853 852 +CONECT 854 852 856 865 855 +CONECT 855 854 +CONECT 856 858 857 859 854 +CONECT 857 856 +CONECT 858 856 +CONECT 859 860 856 861 862 +CONECT 860 859 +CONECT 861 859 +CONECT 862 859 864 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 867 854 866 +CONECT 866 865 +CONECT 867 865 +CONECT 868 87 295 869 264 +CONECT 869 868 871 +CONECT 870 873 871 874 872 +CONECT 871 869 870 +CONECT 872 870 +CONECT 873 870 +CONECT 874 870 +CONECT 875 876 +CONECT 876 875 877 +CONECT 877 876 +MASTER 0 0 0 0 0 0 0 0 877 0 877 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_30.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_30.pdb new file mode 100644 index 0000000..3ca9546 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_30.pdb @@ -0,0 +1,1841 @@ +COMPND fitness: -8.3687 44.379166666667516 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 55.366 58.077 50.629 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.810 37.896 23.156 1.00 0.00 N +ATOM 2 H1 MET 1 14.781 38.325 24.075 1.00 0.00 H +ATOM 3 H2 MET 1 14.030 38.225 22.611 1.00 0.00 H +ATOM 4 H3 MET 1 15.675 38.203 22.728 1.00 0.00 H +ATOM 5 CA MET 1 14.805 36.429 23.282 1.00 0.00 C +ATOM 6 HA MET 1 13.866 36.129 23.745 1.00 0.00 H +ATOM 7 CB MET 1 14.920 35.755 21.903 1.00 0.00 C +ATOM 8 HB2 MET 1 14.048 36.039 21.310 1.00 0.00 H +ATOM 9 HB3 MET 1 15.816 36.128 21.393 1.00 0.00 H +ATOM 10 CG MET 1 15.000 34.220 21.975 1.00 0.00 C +ATOM 11 HG2 MET 1 15.888 33.950 22.548 1.00 0.00 H +ATOM 12 HG3 MET 1 14.121 33.844 22.502 1.00 0.00 H +ATOM 13 SD MET 1 15.126 33.370 20.368 1.00 0.00 S +ATOM 14 CE MET 1 13.439 33.556 19.722 1.00 0.00 C +ATOM 15 HE1 MET 1 13.184 34.612 19.632 1.00 0.00 H +ATOM 16 HE2 MET 1 13.380 33.096 18.736 1.00 0.00 H +ATOM 17 HE3 MET 1 12.727 33.063 20.386 1.00 0.00 H +ATOM 18 C MET 1 15.933 36.001 24.207 1.00 0.00 C +ATOM 19 O MET 1 17.087 36.357 23.995 1.00 0.00 O +ATOM 20 N GLN 2 15.622 35.173 25.206 1.00 0.00 N +ATOM 21 H GLN 2 14.653 34.977 25.411 1.00 0.00 H +ATOM 22 CA GLN 2 16.610 34.463 26.028 1.00 0.00 C +ATOM 23 HA GLN 2 17.371 35.162 26.387 1.00 0.00 H +ATOM 24 CB GLN 2 15.875 33.910 27.271 1.00 0.00 C +ATOM 25 HB2 GLN 2 14.938 33.443 26.967 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.454 33.148 27.774 1.00 0.00 H +ATOM 27 CG GLN 2 15.544 34.974 28.319 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.024 35.790 27.864 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.857 34.559 29.026 1.00 0.00 H +ATOM 30 CD GLN 2 16.711 35.440 29.166 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.819 34.968 29.050 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.514 36.329 30.094 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.267 36.567 30.713 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.590 36.676 30.209 1.00 0.00 H +ATOM 35 C GLN 2 17.321 33.350 25.230 1.00 0.00 C +ATOM 36 O GLN 2 16.925 32.184 25.299 1.00 0.00 O +ATOM 37 N TYR 3 18.372 33.716 24.495 1.00 0.00 N +ATOM 38 H TYR 3 18.637 34.699 24.501 1.00 0.00 H +ATOM 39 CA TYR 3 19.222 32.769 23.770 1.00 0.00 C +ATOM 40 HA TYR 3 18.596 32.181 23.093 1.00 0.00 H +ATOM 41 CB TYR 3 20.262 33.523 22.930 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.756 34.272 23.548 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.025 32.816 22.607 1.00 0.00 H +ATOM 44 CG TYR 3 19.693 34.191 21.693 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.621 33.470 20.485 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.975 32.449 20.444 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.105 34.077 19.324 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.069 33.528 18.395 1.00 0.00 H +ATOM 49 CZ TYR 3 18.652 35.411 19.375 1.00 0.00 C +ATOM 50 OH TYR 3 18.162 36.004 18.258 1.00 0.00 O +ATOM 51 HH TYR 3 18.302 35.468 17.477 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.722 36.135 20.583 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.382 37.161 20.607 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.248 35.526 21.738 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.310 36.088 22.662 1.00 0.00 H +ATOM 56 C TYR 3 19.905 31.811 24.757 1.00 0.00 C +ATOM 57 O TYR 3 20.348 32.238 25.826 1.00 0.00 O +ATOM 58 N LYS 4 19.988 30.523 24.416 1.00 0.00 N +ATOM 59 H LYS 4 19.772 30.263 23.457 1.00 0.00 H +ATOM 60 CA LYS 4 20.543 29.473 25.284 1.00 0.00 C +ATOM 61 HA LYS 4 20.253 29.669 26.308 1.00 0.00 H +ATOM 62 CB LYS 4 19.975 28.099 24.879 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.921 28.051 23.793 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.673 27.321 25.199 1.00 0.00 H +ATOM 65 CG LYS 4 18.596 27.724 25.458 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.385 26.703 25.139 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.647 27.730 26.546 1.00 0.00 H +ATOM 68 CD LYS 4 17.433 28.618 24.998 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.440 29.557 25.550 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.580 28.854 23.943 1.00 0.00 H +ATOM 71 CE LYS 4 16.058 27.935 25.121 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.318 28.555 24.608 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.105 26.983 24.586 1.00 0.00 H +ATOM 74 NZ LYS 4 15.591 27.684 26.511 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.322 28.531 26.991 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.771 27.074 26.476 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.274 27.212 27.093 1.00 0.00 H +ATOM 78 C LYS 4 22.076 29.472 25.281 1.00 0.00 C +ATOM 79 O LYS 4 22.731 29.878 24.322 1.00 0.00 O +HETATM 80 N HX1 5 22.675 28.981 26.363 1.00 0.00 N +HETATM 81 CA HX1 5 24.131 28.838 26.502 1.00 0.00 C +HETATM 82 C HX1 5 24.458 27.630 27.385 1.00 0.00 C +HETATM 83 O HX1 5 24.012 27.555 28.533 1.00 0.00 O +HETATM 84 CB HX1 5 24.708 30.144 27.072 1.00 0.00 C +HETATM 85 CG HX1 5 26.213 30.207 27.214 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.124 29.319 26.712 1.00 0.00 C +HETATM 87 ND1 HX1 5 26.879 31.181 27.965 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.176 30.844 27.879 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.347 29.708 27.182 1.00 0.00 N +HETATM 90 H HX1 5 22.092 28.783 27.179 1.00 0.00 H +HETATM 91 HA HX1 5 24.573 28.672 25.516 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.265 30.334 28.055 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.413 30.965 26.417 1.00 0.00 H +HETATM 94 HD2 HX1 5 26.938 28.431 26.124 1.00 0.00 H +HETATM 95 HE1 HX1 5 28.958 31.330 28.445 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.180 29.125 27.205 1.00 0.00 H +ATOM 97 N ILE 6 25.208 26.678 26.825 1.00 0.00 N +ATOM 98 H ILE 6 25.507 26.806 25.863 1.00 0.00 H +ATOM 99 CA ILE 6 25.700 25.466 27.493 1.00 0.00 C +ATOM 100 HA ILE 6 25.128 25.337 28.412 1.00 0.00 H +ATOM 101 CB ILE 6 25.417 24.214 26.622 1.00 0.00 C +ATOM 102 HB ILE 6 25.856 24.377 25.637 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.034 22.933 27.216 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.628 22.739 28.211 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.817 22.081 26.573 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.121 23.009 27.262 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.881 24.055 26.476 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.441 23.945 27.470 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.470 24.958 26.023 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.422 22.874 25.611 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.602 21.932 26.133 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.350 22.970 25.428 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.955 22.882 24.656 1.00 0.00 H +ATOM 114 C ILE 6 27.163 25.654 27.940 1.00 0.00 C +ATOM 115 O ILE 6 27.928 26.454 27.399 1.00 0.00 O +ATOM 116 N VAL 7 27.502 24.961 29.020 1.00 0.00 N +ATOM 117 H VAL 7 26.856 24.235 29.286 1.00 0.00 H +ATOM 118 CA VAL 7 28.512 25.289 30.028 1.00 0.00 C +ATOM 119 HA VAL 7 28.532 26.370 30.128 1.00 0.00 H +ATOM 120 CB VAL 7 27.946 24.713 31.341 1.00 0.00 C +ATOM 121 HB VAL 7 26.916 25.052 31.444 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.946 23.181 31.389 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.963 22.795 31.331 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.492 22.839 32.315 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.374 22.770 30.560 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.683 25.226 32.558 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.692 26.315 32.554 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.186 24.885 33.464 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.692 24.834 32.535 1.00 0.00 H +ATOM 130 C VAL 7 29.955 24.827 29.718 1.00 0.00 C +ATOM 131 O VAL 7 30.144 23.805 29.062 1.00 0.00 O +ATOM 132 N ARG 8 30.991 25.543 30.213 1.00 0.00 N +ATOM 133 H ARG 8 30.789 26.458 30.603 1.00 0.00 H +ATOM 134 CA ARG 8 32.394 25.042 30.153 1.00 0.00 C +ATOM 135 HA ARG 8 32.522 24.644 29.143 1.00 0.00 H +ATOM 136 CB ARG 8 33.460 26.152 30.328 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.302 25.916 29.672 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.059 27.095 29.971 1.00 0.00 H +ATOM 139 CG ARG 8 34.052 26.304 31.749 1.00 0.00 C +ATOM 140 HG2 ARG 8 33.265 26.253 32.482 1.00 0.00 H +ATOM 141 HG3 ARG 8 34.726 25.464 31.934 1.00 0.00 H +ATOM 142 CD ARG 8 34.841 27.600 31.983 1.00 0.00 C +ATOM 143 HD2 ARG 8 35.302 27.517 32.981 1.00 0.00 H +ATOM 144 HD3 ARG 8 35.636 27.683 31.223 1.00 0.00 H +ATOM 145 NE ARG 8 33.974 28.785 31.963 1.00 0.00 N +ATOM 146 HE ARG 8 33.063 28.702 31.530 1.00 0.00 H +ATOM 147 CZ ARG 8 34.263 29.964 32.471 1.00 0.00 C +ATOM 148 NH1 ARG 8 33.342 30.877 32.517 1.00 0.00 N +ATOM 149 HH11 ARG 8 32.378 30.557 32.429 1.00 0.00 H +ATOM 150 HH12 ARG 8 33.525 31.725 33.019 1.00 0.00 H +ATOM 151 NH2 ARG 8 35.432 30.267 32.971 1.00 0.00 N +ATOM 152 HH21 ARG 8 36.155 29.576 33.011 1.00 0.00 H +ATOM 153 HH22 ARG 8 35.604 31.190 33.316 1.00 0.00 H +ATOM 154 C ARG 8 32.650 23.855 31.098 1.00 0.00 C +ATOM 155 O ARG 8 32.163 23.850 32.229 1.00 0.00 O +ATOM 156 N GLY 9 33.544 22.962 30.683 1.00 0.00 N +ATOM 157 H GLY 9 33.828 23.040 29.724 1.00 0.00 H +ATOM 158 CA GLY 9 33.999 21.775 31.414 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.033 21.561 31.137 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.969 21.975 32.484 1.00 0.00 H +ATOM 161 C GLY 9 33.135 20.544 31.121 1.00 0.00 C +ATOM 162 O GLY 9 32.019 20.668 30.627 1.00 0.00 O +ATOM 163 N LYS 10 33.656 19.355 31.465 1.00 0.00 N +ATOM 164 H LYS 10 34.611 19.323 31.807 1.00 0.00 H +ATOM 165 CA LYS 10 32.935 18.066 31.331 1.00 0.00 C +ATOM 166 HA LYS 10 31.981 18.264 30.836 1.00 0.00 H +ATOM 167 CB LYS 10 33.733 17.132 30.394 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.358 17.735 29.735 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.390 16.486 30.971 1.00 0.00 H +ATOM 170 CG LYS 10 32.832 16.275 29.492 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.240 15.592 30.094 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.147 16.930 28.958 1.00 0.00 H +ATOM 173 CD LYS 10 33.641 15.473 28.465 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.298 16.145 27.920 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.248 14.727 28.978 1.00 0.00 H +ATOM 176 CE LYS 10 32.710 14.801 27.454 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.105 14.062 27.971 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.034 15.552 27.039 1.00 0.00 H +ATOM 179 NZ LYS 10 33.459 14.162 26.352 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.152 13.505 26.677 1.00 0.00 H +ATOM 181 HZ2 LYS 10 32.816 13.703 25.710 1.00 0.00 H +ATOM 182 HZ3 LYS 10 33.976 14.870 25.813 1.00 0.00 H +ATOM 183 C LYS 10 32.541 17.443 32.683 1.00 0.00 C +ATOM 184 O LYS 10 32.191 16.270 32.761 1.00 0.00 O +ATOM 185 N ILE 11 32.636 18.241 33.751 1.00 0.00 N +ATOM 186 H ILE 11 32.979 19.168 33.577 1.00 0.00 H +ATOM 187 CA ILE 11 32.264 17.914 35.145 1.00 0.00 C +ATOM 188 HA ILE 11 32.109 16.835 35.228 1.00 0.00 H +ATOM 189 CB ILE 11 33.407 18.303 36.114 1.00 0.00 C +ATOM 190 HB ILE 11 33.061 18.086 37.126 1.00 0.00 H +ATOM 191 CG2 ILE 11 34.646 17.427 35.863 1.00 0.00 C +ATOM 192 HG21 ILE 11 35.089 17.649 34.893 1.00 0.00 H +ATOM 193 HG22 ILE 11 35.389 17.601 36.638 1.00 0.00 H +ATOM 194 HG23 ILE 11 34.363 16.375 35.894 1.00 0.00 H +ATOM 195 CG1 ILE 11 33.735 19.815 36.040 1.00 0.00 C +ATOM 196 HG12 ILE 11 34.228 20.041 35.093 1.00 0.00 H +ATOM 197 HG13 ILE 11 32.810 20.392 36.083 1.00 0.00 H +ATOM 198 CD1 ILE 11 34.626 20.311 37.185 1.00 0.00 C +ATOM 199 HD11 ILE 11 35.608 19.842 37.137 1.00 0.00 H +ATOM 200 HD12 ILE 11 34.751 21.392 37.100 1.00 0.00 H +ATOM 201 HD13 ILE 11 34.158 20.086 38.144 1.00 0.00 H +ATOM 202 C ILE 11 30.938 18.565 35.591 1.00 0.00 C +ATOM 203 O ILE 11 30.441 18.266 36.669 1.00 0.00 O +ATOM 204 N ARG 12 30.370 19.460 34.781 1.00 0.00 N +ATOM 205 H ARG 12 30.802 19.606 33.883 1.00 0.00 H +ATOM 206 CA ARG 12 29.082 20.128 34.990 1.00 0.00 C +ATOM 207 HA ARG 12 28.494 19.515 35.665 1.00 0.00 H +ATOM 208 CB ARG 12 29.277 21.501 35.652 1.00 0.00 C +ATOM 209 HB2 ARG 12 28.304 21.959 35.796 1.00 0.00 H +ATOM 210 HB3 ARG 12 29.706 21.355 36.639 1.00 0.00 H +ATOM 211 CG ARG 12 30.165 22.496 34.877 1.00 0.00 C +ATOM 212 HG2 ARG 12 31.152 22.068 34.717 1.00 0.00 H +ATOM 213 HG3 ARG 12 29.710 22.699 33.910 1.00 0.00 H +ATOM 214 CD ARG 12 30.343 23.833 35.626 1.00 0.00 C +ATOM 215 HD2 ARG 12 29.347 24.208 35.923 1.00 0.00 H +ATOM 216 HD3 ARG 12 30.924 23.670 36.549 1.00 0.00 H +ATOM 217 NE ARG 12 31.020 24.807 34.757 1.00 0.00 N +ATOM 218 HE ARG 12 31.495 24.429 33.946 1.00 0.00 H +ATOM 219 CZ ARG 12 30.849 26.117 34.770 1.00 0.00 C +ATOM 220 NH1 ARG 12 31.183 26.785 33.713 1.00 0.00 N +ATOM 221 HH11 ARG 12 31.469 26.304 32.892 1.00 0.00 H +ATOM 222 HH12 ARG 12 31.007 27.788 33.666 1.00 0.00 H +ATOM 223 NH2 ARG 12 30.345 26.820 35.739 1.00 0.00 N +ATOM 224 HH21 ARG 12 30.206 26.407 36.652 1.00 0.00 H +ATOM 225 HH22 ARG 12 30.268 27.832 35.639 1.00 0.00 H +ATOM 226 C ARG 12 28.342 20.173 33.654 1.00 0.00 C +ATOM 227 O ARG 12 28.991 20.349 32.630 1.00 0.00 O +ATOM 228 N LYS 13 27.025 19.950 33.663 1.00 0.00 N +ATOM 229 H LYS 13 26.595 19.795 34.566 1.00 0.00 H +ATOM 230 CA LYS 13 26.218 19.659 32.450 1.00 0.00 C +ATOM 231 HA LYS 13 26.820 19.893 31.575 1.00 0.00 H +ATOM 232 CB LYS 13 25.899 18.146 32.436 1.00 0.00 C +ATOM 233 HB2 LYS 13 26.763 17.619 32.862 1.00 0.00 H +ATOM 234 HB3 LYS 13 25.032 17.952 33.085 1.00 0.00 H +ATOM 235 CG LYS 13 25.649 17.554 31.026 1.00 0.00 C +ATOM 236 HG2 LYS 13 24.714 17.955 30.608 1.00 0.00 H +ATOM 237 HG3 LYS 13 26.482 17.864 30.386 1.00 0.00 H +ATOM 238 CD LYS 13 25.622 16.004 31.030 1.00 0.00 C +ATOM 239 HD2 LYS 13 25.691 15.661 29.990 1.00 0.00 H +ATOM 240 HD3 LYS 13 26.490 15.622 31.591 1.00 0.00 H +ATOM 241 CE LYS 13 24.323 15.436 31.638 1.00 0.00 C +ATOM 242 HE2 LYS 13 24.127 15.931 32.592 1.00 0.00 H +ATOM 243 HE3 LYS 13 23.476 15.633 30.959 1.00 0.00 H +ATOM 244 NZ LYS 13 24.441 13.975 31.897 1.00 0.00 N +ATOM 245 HZ1 LYS 13 24.985 13.753 32.724 1.00 0.00 H +ATOM 246 HZ2 LYS 13 23.537 13.547 32.040 1.00 0.00 H +ATOM 247 HZ3 LYS 13 24.859 13.466 31.116 1.00 0.00 H +ATOM 248 C LYS 13 24.972 20.564 32.337 1.00 0.00 C +ATOM 249 O LYS 13 24.016 20.241 31.647 1.00 0.00 O +ATOM 250 N GLY 14 24.970 21.681 33.072 1.00 0.00 N +ATOM 251 H GLY 14 25.796 21.891 33.611 1.00 0.00 H +ATOM 252 CA GLY 14 23.855 22.648 33.131 1.00 0.00 C +ATOM 253 HA2 GLY 14 22.923 22.083 33.238 1.00 0.00 H +ATOM 254 HA3 GLY 14 23.979 23.259 34.033 1.00 0.00 H +ATOM 255 C GLY 14 23.743 23.567 31.919 1.00 0.00 C +ATOM 256 O GLY 14 24.631 23.662 31.081 1.00 0.00 O +ATOM 257 N VAL 15 22.637 24.303 31.863 1.00 0.00 N +ATOM 258 H VAL 15 21.969 24.214 32.610 1.00 0.00 H +ATOM 259 CA VAL 15 22.262 25.252 30.792 1.00 0.00 C +ATOM 260 HA VAL 15 23.177 25.561 30.264 1.00 0.00 H +ATOM 261 CB VAL 15 21.336 24.559 29.761 1.00 0.00 C +ATOM 262 HB VAL 15 21.853 23.695 29.384 1.00 0.00 H +ATOM 263 CG1 VAL 15 20.007 24.099 30.366 1.00 0.00 C +ATOM 264 HG11 VAL 15 19.423 24.954 30.737 1.00 0.00 H +ATOM 265 HG12 VAL 15 19.423 23.580 29.605 1.00 0.00 H +ATOM 266 HG13 VAL 15 20.183 23.405 31.193 1.00 0.00 H +ATOM 267 CG2 VAL 15 21.024 25.480 28.579 1.00 0.00 C +ATOM 268 HG21 VAL 15 21.949 25.858 28.142 1.00 0.00 H +ATOM 269 HG22 VAL 15 20.490 24.914 27.818 1.00 0.00 H +ATOM 270 HG23 VAL 15 20.396 26.324 28.889 1.00 0.00 H +ATOM 271 C VAL 15 21.625 26.502 31.408 1.00 0.00 C +ATOM 272 O VAL 15 20.940 26.406 32.433 1.00 0.00 O +HETATM 273 N HY1 16 21.859 27.662 30.803 1.00 0.00 N +HETATM 274 CA HY1 16 21.283 28.927 31.185 1.00 0.00 C +HETATM 275 C HY1 16 21.137 29.800 29.910 1.00 0.00 C +HETATM 276 O HY1 16 21.407 29.318 28.797 1.00 0.00 O +HETATM 277 CB HY1 16 22.126 29.573 32.300 1.00 0.00 C +HETATM 278 CG HY1 16 23.550 29.847 31.869 1.00 0.00 C +HETATM 279 CD2 HY1 16 23.975 31.005 31.299 1.00 0.00 C +HETATM 280 ND1 HY1 16 24.602 28.944 31.803 1.00 0.00 N +HETATM 281 CE1 HY1 16 25.637 29.564 31.215 1.00 0.00 C +HETATM 282 NE2 HY1 16 25.289 30.815 30.889 1.00 0.00 N +HETATM 283 H HY1 16 22.430 27.630 29.967 1.00 0.00 H +HETATM 284 HA HY1 16 20.281 28.791 31.554 1.00 0.00 H +HETATM 285 HB2 HY1 16 21.681 30.513 32.631 1.00 0.00 H +HETATM 286 HB3 HY1 16 22.135 28.912 33.167 1.00 0.00 H +HETATM 287 HD1 HY1 16 24.582 27.989 32.150 1.00 0.00 H +HETATM 288 HD2 HY1 16 23.385 31.889 31.155 1.00 0.00 H +HETATM 289 HE1 HY1 16 26.619 29.136 31.055 1.00 0.00 H +ATOM 290 N THR 17 20.701 31.069 30.039 1.00 0.00 N +ATOM 291 H THR 17 20.516 31.385 30.989 1.00 0.00 H +ATOM 292 CA THR 17 20.334 31.937 28.911 1.00 0.00 C +ATOM 293 HA THR 17 20.744 31.511 28.039 1.00 0.00 H +ATOM 294 CB THR 17 18.812 31.963 28.723 1.00 0.00 C +ATOM 295 HB THR 17 18.561 32.513 27.830 1.00 0.00 H +ATOM 296 CG2 THR 17 18.217 30.618 28.451 1.00 0.00 C +ATOM 297 HG21 THR 17 18.330 29.925 29.227 1.00 0.00 H +ATOM 298 HG22 THR 17 17.158 30.642 28.317 1.00 0.00 H +ATOM 299 HG23 THR 17 18.570 30.150 27.584 1.00 0.00 H +ATOM 300 OG1 THR 17 18.091 32.406 29.852 1.00 0.00 O +ATOM 301 HG1 THR 17 18.179 33.368 29.792 1.00 0.00 H +ATOM 302 C THR 17 20.820 33.362 29.011 1.00 0.00 C +ATOM 303 O THR 17 21.176 33.805 30.101 1.00 0.00 O +HETATM 304 N HY2 18 20.786 34.099 27.886 1.00 0.00 N +HETATM 305 CA HY2 18 21.144 35.531 27.804 1.00 0.00 C +HETATM 306 C HY2 18 20.144 36.277 26.913 1.00 0.00 C +HETATM 307 O HY2 18 19.871 35.839 25.808 1.00 0.00 O +HETATM 308 CB HY2 18 22.597 35.692 27.307 1.00 0.00 C +HETATM 309 CG HY2 18 23.588 35.055 28.264 1.00 0.00 C +HETATM 310 CD2 HY2 18 24.278 33.882 28.072 1.00 0.00 C +HETATM 311 ND1 HY2 18 23.735 35.404 29.593 1.00 0.00 N +HETATM 312 CE1 HY2 18 24.473 34.452 30.175 1.00 0.00 C +HETATM 313 NE2 HY2 18 24.847 33.511 29.293 1.00 0.00 N +HETATM 314 H HY2 18 20.512 33.620 27.014 1.00 0.00 H +HETATM 315 HA HY2 18 21.073 35.950 28.813 1.00 0.00 H +HETATM 316 HB2 HY2 18 22.679 35.237 26.327 1.00 0.00 H +HETATM 317 HB3 HY2 18 22.810 36.744 27.207 1.00 0.00 H +HETATM 318 HD1 HY2 18 23.274 36.174 30.067 1.00 0.00 H +HETATM 319 HD2 HY2 18 24.291 33.309 27.157 1.00 0.00 H +HETATM 320 HE1 HY2 18 24.717 34.441 31.223 1.00 0.00 H +ATOM 321 N GLU 19 19.585 37.337 27.457 1.00 0.00 N +ATOM 322 H GLU 19 19.839 37.626 28.378 1.00 0.00 H +ATOM 323 CA GLU 19 18.579 38.174 26.787 1.00 0.00 C +ATOM 324 HA GLU 19 17.832 37.518 26.323 1.00 0.00 H +ATOM 325 CB GLU 19 17.878 39.049 27.855 1.00 0.00 C +ATOM 326 HB2 GLU 19 17.566 38.399 28.670 1.00 0.00 H +ATOM 327 HB3 GLU 19 18.587 39.758 28.257 1.00 0.00 H +ATOM 328 CG GLU 19 16.638 39.804 27.345 1.00 0.00 C +ATOM 329 HG2 GLU 19 16.213 40.368 28.177 1.00 0.00 H +ATOM 330 HG3 GLU 19 16.942 40.507 26.568 1.00 0.00 H +ATOM 331 CD GLU 19 15.618 38.829 26.801 1.00 0.00 C +ATOM 332 OE1 GLU 19 15.568 38.620 25.549 1.00 0.00 O +ATOM 333 OE2 GLU 19 14.888 38.181 27.604 1.00 0.00 O +ATOM 334 C GLU 19 19.197 39.056 25.675 1.00 0.00 C +ATOM 335 O GLU 19 20.188 39.740 25.920 1.00 0.00 O +ATOM 336 N ALA 20 18.597 39.040 24.482 1.00 0.00 N +ATOM 337 H ALA 20 17.799 38.435 24.339 1.00 0.00 H +ATOM 338 CA ALA 20 18.979 39.916 23.367 1.00 0.00 C +ATOM 339 HA ALA 20 19.120 40.924 23.755 1.00 0.00 H +ATOM 340 CB ALA 20 20.313 39.436 22.780 1.00 0.00 C +ATOM 341 HB1 ALA 20 20.185 38.453 22.335 1.00 0.00 H +ATOM 342 HB2 ALA 20 20.658 40.128 22.009 1.00 0.00 H +ATOM 343 HB3 ALA 20 21.082 39.378 23.542 1.00 0.00 H +ATOM 344 C ALA 20 17.931 39.961 22.260 1.00 0.00 C +ATOM 345 O ALA 20 17.081 39.064 22.134 1.00 0.00 O +ATOM 346 N VAL 21 18.001 40.972 21.366 1.00 0.00 N +ATOM 347 H VAL 21 18.685 41.703 21.535 1.00 0.00 H +ATOM 348 CA VAL 21 17.261 40.990 20.087 1.00 0.00 C +ATOM 349 HA VAL 21 16.266 40.573 20.257 1.00 0.00 H +ATOM 350 CB VAL 21 17.074 42.434 19.562 1.00 0.00 C +ATOM 351 HB VAL 21 16.433 42.379 18.683 1.00 0.00 H +ATOM 352 CG1 VAL 21 16.362 43.316 20.595 1.00 0.00 C +ATOM 353 HG11 VAL 21 16.997 43.491 21.462 1.00 0.00 H +ATOM 354 HG12 VAL 21 16.120 44.277 20.137 1.00 0.00 H +ATOM 355 HG13 VAL 21 15.432 42.844 20.914 1.00 0.00 H +ATOM 356 CG2 VAL 21 18.392 43.108 19.152 1.00 0.00 C +ATOM 357 HG21 VAL 21 18.853 42.557 18.329 1.00 0.00 H +ATOM 358 HG22 VAL 21 18.179 44.121 18.800 1.00 0.00 H +ATOM 359 HG23 VAL 21 19.084 43.158 19.995 1.00 0.00 H +ATOM 360 C VAL 21 17.909 40.128 19.005 1.00 0.00 C +ATOM 361 O VAL 21 17.275 39.814 17.997 1.00 0.00 O +ATOM 362 N ASP 22 19.178 39.723 19.195 1.00 0.00 N +ATOM 363 H ASP 22 19.624 39.965 20.072 1.00 0.00 H +ATOM 364 CA ASP 22 20.035 39.052 18.220 1.00 0.00 C +ATOM 365 HA ASP 22 19.439 38.351 17.611 1.00 0.00 H +ATOM 366 CB ASP 22 20.644 40.138 17.282 1.00 0.00 C +ATOM 367 HB2 ASP 22 19.813 40.755 16.904 1.00 0.00 H +ATOM 368 HB3 ASP 22 21.329 40.774 17.879 1.00 0.00 H +ATOM 369 CG ASP 22 21.387 39.586 16.056 1.00 0.00 C +ATOM 370 OD1 ASP 22 21.575 40.362 15.085 1.00 0.00 O +ATOM 371 OD2 ASP 22 21.776 38.385 16.042 1.00 0.00 O +ATOM 372 C ASP 22 21.124 38.248 18.951 1.00 0.00 C +ATOM 373 O ASP 22 21.658 38.680 19.984 1.00 0.00 O +ATOM 374 N TRP 23 21.536 37.077 18.431 1.00 0.00 N +ATOM 375 H TRP 23 21.261 36.904 17.472 1.00 0.00 H +ATOM 376 CA TRP 23 22.639 36.305 18.975 1.00 0.00 C +ATOM 377 HA TRP 23 22.436 36.147 20.031 1.00 0.00 H +ATOM 378 CB TRP 23 22.716 34.913 18.315 1.00 0.00 C +ATOM 379 HB2 TRP 23 23.468 34.331 18.849 1.00 0.00 H +ATOM 380 HB3 TRP 23 21.761 34.407 18.468 1.00 0.00 H +ATOM 381 CG TRP 23 23.056 34.865 16.856 1.00 0.00 C +ATOM 382 CD1 TRP 23 22.182 34.606 15.856 1.00 0.00 C +ATOM 383 HD1 TRP 23 21.129 34.392 15.985 1.00 0.00 H +ATOM 384 NE1 TRP 23 22.836 34.656 14.640 1.00 0.00 N +ATOM 385 HE1 TRP 23 22.377 34.495 13.756 1.00 0.00 H +ATOM 386 CE2 TRP 23 24.173 34.956 14.793 1.00 0.00 C +ATOM 387 CZ2 TRP 23 25.224 35.124 13.880 1.00 0.00 C +ATOM 388 HZ2 TRP 23 25.045 35.029 12.819 1.00 0.00 H +ATOM 389 CH2 TRP 23 26.512 35.408 14.367 1.00 0.00 C +ATOM 390 HH2 TRP 23 27.335 35.536 13.682 1.00 0.00 H +ATOM 391 CZ3 TRP 23 26.731 35.505 15.753 1.00 0.00 C +ATOM 392 HZ3 TRP 23 27.728 35.708 16.132 1.00 0.00 H +ATOM 393 CE3 TRP 23 25.668 35.319 16.658 1.00 0.00 C +ATOM 394 HE3 TRP 23 25.863 35.376 17.718 1.00 0.00 H +ATOM 395 CD2 TRP 23 24.354 35.062 16.205 1.00 0.00 C +ATOM 396 C TRP 23 23.973 37.058 18.875 1.00 0.00 C +ATOM 397 O TRP 23 24.805 36.934 19.776 1.00 0.00 O +ATOM 398 N ALA 24 24.163 37.902 17.855 1.00 0.00 N +ATOM 399 H ALA 24 23.453 37.960 17.119 1.00 0.00 H +ATOM 400 CA ALA 24 25.385 38.700 17.711 1.00 0.00 C +ATOM 401 HA ALA 24 26.245 38.053 17.911 1.00 0.00 H +ATOM 402 CB ALA 24 25.501 39.154 16.254 1.00 0.00 C +ATOM 403 HB1 ALA 24 24.697 39.838 16.001 1.00 0.00 H +ATOM 404 HB2 ALA 24 26.456 39.645 16.091 1.00 0.00 H +ATOM 405 HB3 ALA 24 25.447 38.292 15.591 1.00 0.00 H +ATOM 406 C ALA 24 25.479 39.883 18.706 1.00 0.00 C +ATOM 407 O ALA 24 26.549 40.471 18.877 1.00 0.00 O +ATOM 408 N GLU 25 24.381 40.226 19.382 1.00 0.00 N +ATOM 409 H GLU 25 23.524 39.737 19.167 1.00 0.00 H +ATOM 410 CA GLU 25 24.399 41.070 20.587 1.00 0.00 C +ATOM 411 HA GLU 25 25.243 41.761 20.550 1.00 0.00 H +ATOM 412 CB GLU 25 23.113 41.911 20.663 1.00 0.00 C +ATOM 413 HB2 GLU 25 22.262 41.238 20.653 1.00 0.00 H +ATOM 414 HB3 GLU 25 23.094 42.452 21.610 1.00 0.00 H +ATOM 415 CG GLU 25 22.938 42.922 19.518 1.00 0.00 C +ATOM 416 HG2 GLU 25 23.178 42.457 18.564 1.00 0.00 H +ATOM 417 HG3 GLU 25 21.886 43.210 19.485 1.00 0.00 H +ATOM 418 CD GLU 25 23.777 44.192 19.700 1.00 0.00 C +ATOM 419 OE1 GLU 25 23.167 45.262 19.904 1.00 0.00 O +ATOM 420 OE2 GLU 25 25.040 44.074 19.609 1.00 0.00 O +ATOM 421 C GLU 25 24.586 40.217 21.858 1.00 0.00 C +ATOM 422 O GLU 25 25.378 40.581 22.731 1.00 0.00 O +ATOM 423 N ALA 26 23.940 39.044 21.928 1.00 0.00 N +ATOM 424 H ALA 26 23.284 38.796 21.195 1.00 0.00 H +ATOM 425 CA ALA 26 24.138 38.089 23.021 1.00 0.00 C +ATOM 426 HA ALA 26 23.883 38.587 23.958 1.00 0.00 H +ATOM 427 CB ALA 26 23.191 36.896 22.844 1.00 0.00 C +ATOM 428 HB1 ALA 26 23.493 36.304 21.983 1.00 0.00 H +ATOM 429 HB2 ALA 26 23.226 36.262 23.732 1.00 0.00 H +ATOM 430 HB3 ALA 26 22.172 37.248 22.702 1.00 0.00 H +ATOM 431 C ALA 26 25.601 37.610 23.154 1.00 0.00 C +ATOM 432 O ALA 26 26.040 37.316 24.264 1.00 0.00 O +ATOM 433 N GLU 27 26.379 37.586 22.069 1.00 0.00 N +ATOM 434 H GLU 27 25.913 37.701 21.177 1.00 0.00 H +ATOM 435 CA GLU 27 27.832 37.366 22.073 1.00 0.00 C +ATOM 436 HA GLU 27 28.038 36.419 22.575 1.00 0.00 H +ATOM 437 CB GLU 27 28.342 37.268 20.622 1.00 0.00 C +ATOM 438 HB2 GLU 27 27.755 36.521 20.083 1.00 0.00 H +ATOM 439 HB3 GLU 27 28.196 38.236 20.132 1.00 0.00 H +ATOM 440 CG GLU 27 29.827 36.879 20.538 1.00 0.00 C +ATOM 441 HG2 GLU 27 30.407 37.464 21.249 1.00 0.00 H +ATOM 442 HG3 GLU 27 29.934 35.831 20.818 1.00 0.00 H +ATOM 443 CD GLU 27 30.387 37.124 19.127 1.00 0.00 C +ATOM 444 OE1 GLU 27 30.923 38.241 18.911 1.00 0.00 O +ATOM 445 OE2 GLU 27 30.274 36.204 18.285 1.00 0.00 O +ATOM 446 C GLU 27 28.571 38.479 22.846 1.00 0.00 C +ATOM 447 O GLU 27 29.373 38.190 23.740 1.00 0.00 O +ATOM 448 N LYS 28 28.237 39.753 22.584 1.00 0.00 N +ATOM 449 H LYS 28 27.510 39.926 21.897 1.00 0.00 H +ATOM 450 CA LYS 28 28.828 40.908 23.288 1.00 0.00 C +ATOM 451 HA LYS 28 29.915 40.822 23.258 1.00 0.00 H +ATOM 452 CB LYS 28 28.423 42.229 22.616 1.00 0.00 C +ATOM 453 HB2 LYS 28 27.343 42.364 22.694 1.00 0.00 H +ATOM 454 HB3 LYS 28 28.905 43.050 23.151 1.00 0.00 H +ATOM 455 CG LYS 28 28.823 42.299 21.135 1.00 0.00 C +ATOM 456 HG2 LYS 28 29.886 42.084 21.032 1.00 0.00 H +ATOM 457 HG3 LYS 28 28.259 41.554 20.578 1.00 0.00 H +ATOM 458 CD LYS 28 28.538 43.697 20.569 1.00 0.00 C +ATOM 459 HD2 LYS 28 27.558 44.045 20.900 1.00 0.00 H +ATOM 460 HD3 LYS 28 29.287 44.391 20.955 1.00 0.00 H +ATOM 461 CE LYS 28 28.580 43.720 19.038 1.00 0.00 C +ATOM 462 HE2 LYS 28 28.671 44.761 18.716 1.00 0.00 H +ATOM 463 HE3 LYS 28 29.464 43.178 18.695 1.00 0.00 H +ATOM 464 NZ LYS 28 27.343 43.138 18.463 1.00 0.00 N +ATOM 465 HZ1 LYS 28 26.515 43.604 18.853 1.00 0.00 H +ATOM 466 HZ2 LYS 28 27.315 43.239 17.460 1.00 0.00 H +ATOM 467 HZ3 LYS 28 27.245 42.151 18.698 1.00 0.00 H +ATOM 468 C LYS 28 28.434 40.926 24.766 1.00 0.00 C +ATOM 469 O LYS 28 29.293 41.065 25.637 1.00 0.00 O +ATOM 470 N PHE 29 27.159 40.680 25.068 1.00 0.00 N +ATOM 471 H PHE 29 26.486 40.609 24.310 1.00 0.00 H +ATOM 472 CA PHE 29 26.696 40.485 26.447 1.00 0.00 C +ATOM 473 HA PHE 29 26.983 41.351 27.036 1.00 0.00 H +ATOM 474 CB PHE 29 25.158 40.399 26.471 1.00 0.00 C +ATOM 475 HB2 PHE 29 24.860 39.466 25.989 1.00 0.00 H +ATOM 476 HB3 PHE 29 24.823 40.356 27.511 1.00 0.00 H +ATOM 477 CG PHE 29 24.407 41.543 25.797 1.00 0.00 C +ATOM 478 CD1 PHE 29 23.192 41.285 25.128 1.00 0.00 C +ATOM 479 HD1 PHE 29 22.779 40.286 25.115 1.00 0.00 H +ATOM 480 CE1 PHE 29 22.500 42.319 24.468 1.00 0.00 C +ATOM 481 HE1 PHE 29 21.573 42.104 23.954 1.00 0.00 H +ATOM 482 CZ PHE 29 23.012 43.627 24.483 1.00 0.00 C +ATOM 483 HZ PHE 29 22.487 44.422 23.972 1.00 0.00 H +ATOM 484 CE2 PHE 29 24.202 43.905 25.179 1.00 0.00 C +ATOM 485 HE2 PHE 29 24.589 44.917 25.212 1.00 0.00 H +ATOM 486 CD2 PHE 29 24.891 42.868 25.836 1.00 0.00 C +ATOM 487 HD2 PHE 29 25.799 43.104 26.367 1.00 0.00 H +ATOM 488 C PHE 29 27.361 39.269 27.118 1.00 0.00 C +ATOM 489 O PHE 29 27.558 39.267 28.337 1.00 0.00 O +ATOM 490 N THR 30 27.747 38.247 26.334 1.00 0.00 N +ATOM 491 H THR 30 27.504 38.268 25.347 1.00 0.00 H +ATOM 492 CA THR 30 28.501 37.093 26.825 1.00 0.00 C +ATOM 493 HA THR 30 28.076 36.836 27.771 1.00 0.00 H +ATOM 494 CB THR 30 28.366 35.887 25.881 1.00 0.00 C +ATOM 495 HB THR 30 28.702 36.170 24.881 1.00 0.00 H +ATOM 496 CG2 THR 30 29.257 34.723 26.265 1.00 0.00 C +ATOM 497 HG21 THR 30 29.090 34.366 27.247 1.00 0.00 H +ATOM 498 HG22 THR 30 29.084 33.886 25.633 1.00 0.00 H +ATOM 499 HG23 THR 30 30.305 34.920 26.193 1.00 0.00 H +ATOM 500 OG1 THR 30 27.050 35.383 25.925 1.00 0.00 O +ATOM 501 HG1 THR 30 26.605 36.046 25.375 1.00 0.00 H +ATOM 502 C THR 30 29.959 37.434 27.152 1.00 0.00 C +ATOM 503 O THR 30 30.494 36.992 28.166 1.00 0.00 O +ATOM 504 N LYS 31 30.609 38.324 26.407 1.00 0.00 N +ATOM 505 H LYS 31 30.146 38.633 25.568 1.00 0.00 H +ATOM 506 CA LYS 31 31.941 38.870 26.696 1.00 0.00 C +ATOM 507 HA LYS 31 32.583 38.047 26.983 1.00 0.00 H +ATOM 508 CB LYS 31 32.534 39.486 25.419 1.00 0.00 C +ATOM 509 HB2 LYS 31 31.836 40.213 24.997 1.00 0.00 H +ATOM 510 HB3 LYS 31 33.464 40.003 25.669 1.00 0.00 H +ATOM 511 CG LYS 31 32.848 38.400 24.370 1.00 0.00 C +ATOM 512 HG2 LYS 31 33.565 37.703 24.796 1.00 0.00 H +ATOM 513 HG3 LYS 31 31.949 37.844 24.112 1.00 0.00 H +ATOM 514 CD LYS 31 33.427 39.004 23.083 1.00 0.00 C +ATOM 515 HD2 LYS 31 32.650 39.590 22.591 1.00 0.00 H +ATOM 516 HD3 LYS 31 34.254 39.671 23.332 1.00 0.00 H +ATOM 517 CE LYS 31 33.930 37.938 22.098 1.00 0.00 C +ATOM 518 HE2 LYS 31 33.126 37.230 21.869 1.00 0.00 H +ATOM 519 HE3 LYS 31 34.207 38.431 21.161 1.00 0.00 H +ATOM 520 NZ LYS 31 35.111 37.211 22.624 1.00 0.00 N +ATOM 521 HZ1 LYS 31 34.845 36.469 23.248 1.00 0.00 H +ATOM 522 HZ2 LYS 31 35.636 36.757 21.867 1.00 0.00 H +ATOM 523 HZ3 LYS 31 35.747 37.813 23.153 1.00 0.00 H +ATOM 524 C LYS 31 31.938 39.839 27.871 1.00 0.00 C +ATOM 525 O LYS 31 32.922 39.852 28.608 1.00 0.00 O +ATOM 526 N ALA 32 30.835 40.568 28.106 1.00 0.00 N +ATOM 527 H ALA 32 30.101 40.566 27.397 1.00 0.00 H +ATOM 528 CA ALA 32 30.677 41.430 29.283 1.00 0.00 C +ATOM 529 HA ALA 32 31.472 42.177 29.269 1.00 0.00 H +ATOM 530 CB ALA 32 29.342 42.182 29.196 1.00 0.00 C +ATOM 531 HB1 ALA 32 28.507 41.488 29.223 1.00 0.00 H +ATOM 532 HB2 ALA 32 29.250 42.861 30.041 1.00 0.00 H +ATOM 533 HB3 ALA 32 29.293 42.760 28.274 1.00 0.00 H +ATOM 534 C ALA 32 30.832 40.648 30.605 1.00 0.00 C +ATOM 535 O ALA 32 31.829 40.819 31.297 1.00 0.00 O +ATOM 536 N MET 33 29.925 39.708 30.898 1.00 0.00 N +ATOM 537 H MET 33 29.126 39.595 30.286 1.00 0.00 H +ATOM 538 CA MET 33 29.975 38.900 32.136 1.00 0.00 C +ATOM 539 HA MET 33 29.996 39.584 32.977 1.00 0.00 H +ATOM 540 CB MET 33 28.700 38.060 32.282 1.00 0.00 C +ATOM 541 HB2 MET 33 28.755 37.473 33.199 1.00 0.00 H +ATOM 542 HB3 MET 33 27.831 38.713 32.342 1.00 0.00 H +ATOM 543 CG MET 33 28.545 37.125 31.088 1.00 0.00 C +ATOM 544 HG2 MET 33 28.241 37.722 30.228 1.00 0.00 H +ATOM 545 HG3 MET 33 29.508 36.671 30.854 1.00 0.00 H +ATOM 546 SD MET 33 27.368 35.782 31.289 1.00 0.00 S +ATOM 547 CE MET 33 27.421 35.320 29.548 1.00 0.00 C +ATOM 548 HE1 MET 33 28.445 35.408 29.190 1.00 0.00 H +ATOM 549 HE2 MET 33 27.112 34.299 29.392 1.00 0.00 H +ATOM 550 HE3 MET 33 26.748 35.971 28.989 1.00 0.00 H +ATOM 551 C MET 33 31.231 38.006 32.279 1.00 0.00 C +ATOM 552 O MET 33 31.502 37.489 33.359 1.00 0.00 O +ATOM 553 N ALA 34 31.989 37.791 31.206 1.00 0.00 N +ATOM 554 H ALA 34 31.723 38.220 30.337 1.00 0.00 H +ATOM 555 CA ALA 34 33.289 37.128 31.277 1.00 0.00 C +ATOM 556 HA ALA 34 33.259 36.380 32.069 1.00 0.00 H +ATOM 557 CB ALA 34 33.515 36.384 29.965 1.00 0.00 C +ATOM 558 HB1 ALA 34 33.628 37.095 29.149 1.00 0.00 H +ATOM 559 HB2 ALA 34 34.413 35.774 30.059 1.00 0.00 H +ATOM 560 HB3 ALA 34 32.667 35.732 29.756 1.00 0.00 H +ATOM 561 C ALA 34 34.427 38.109 31.632 1.00 0.00 C +ATOM 562 O ALA 34 35.323 37.754 32.391 1.00 0.00 O +ATOM 563 N ASN 35 34.377 39.363 31.183 1.00 0.00 N +ATOM 564 H ASN 35 33.612 39.639 30.581 1.00 0.00 H +ATOM 565 CA ASN 35 35.253 40.416 31.708 1.00 0.00 C +ATOM 566 HA ASN 35 36.262 40.013 31.792 1.00 0.00 H +ATOM 567 CB ASN 35 35.324 41.567 30.698 1.00 0.00 C +ATOM 568 HB2 ASN 35 34.330 41.833 30.343 1.00 0.00 H +ATOM 569 HB3 ASN 35 35.759 42.442 31.181 1.00 0.00 H +ATOM 570 CG ASN 35 36.226 41.188 29.535 1.00 0.00 C +ATOM 571 OD1 ASN 35 37.440 41.250 29.628 1.00 0.00 O +ATOM 572 ND2 ASN 35 35.679 40.742 28.434 1.00 0.00 N +ATOM 573 HD21 ASN 35 36.316 40.422 27.696 1.00 0.00 H +ATOM 574 HD22 ASN 35 34.684 40.585 28.391 1.00 0.00 H +ATOM 575 C ASN 35 34.867 40.849 33.132 1.00 0.00 C +ATOM 576 O ASN 35 35.759 41.190 33.910 1.00 0.00 O +ATOM 577 N ASP 36 33.594 40.704 33.536 1.00 0.00 N +ATOM 578 H ASP 36 32.879 40.601 32.821 1.00 0.00 H +ATOM 579 CA ASP 36 33.161 40.835 34.937 1.00 0.00 C +ATOM 580 HA ASP 36 33.474 41.814 35.299 1.00 0.00 H +ATOM 581 CB ASP 36 31.618 40.791 35.059 1.00 0.00 C +ATOM 582 HB2 ASP 36 31.283 39.805 34.752 1.00 0.00 H +ATOM 583 HB3 ASP 36 31.364 40.875 36.115 1.00 0.00 H +ATOM 584 CG ASP 36 30.808 41.855 34.299 1.00 0.00 C +ATOM 585 OD1 ASP 36 31.369 42.914 33.930 1.00 0.00 O +ATOM 586 OD2 ASP 36 29.584 41.632 34.102 1.00 0.00 O +ATOM 587 C ASP 36 33.810 39.782 35.867 1.00 0.00 C +ATOM 588 O ASP 36 34.101 40.094 37.024 1.00 0.00 O +ATOM 589 N LEU 37 34.093 38.548 35.389 1.00 0.00 N +ATOM 590 H LEU 37 33.780 38.321 34.454 1.00 0.00 H +ATOM 591 CA LEU 37 34.905 37.559 36.137 1.00 0.00 C +ATOM 592 HA LEU 37 34.756 37.775 37.197 1.00 0.00 H +ATOM 593 CB LEU 37 34.368 36.116 35.941 1.00 0.00 C +ATOM 594 HB2 LEU 37 34.670 35.527 36.806 1.00 0.00 H +ATOM 595 HB3 LEU 37 33.281 36.179 35.978 1.00 0.00 H +ATOM 596 CG LEU 37 34.765 35.325 34.674 1.00 0.00 C +ATOM 597 HG LEU 37 34.708 35.979 33.819 1.00 0.00 H +ATOM 598 CD1 LEU 37 36.159 34.688 34.730 1.00 0.00 C +ATOM 599 HD11 LEU 37 36.252 34.061 35.616 1.00 0.00 H +ATOM 600 HD12 LEU 37 36.338 34.095 33.834 1.00 0.00 H +ATOM 601 HD13 LEU 37 36.927 35.457 34.759 1.00 0.00 H +ATOM 602 CD2 LEU 37 33.785 34.176 34.413 1.00 0.00 C +ATOM 603 HD21 LEU 37 32.776 34.580 34.320 1.00 0.00 H +ATOM 604 HD22 LEU 37 34.051 33.686 33.479 1.00 0.00 H +ATOM 605 HD23 LEU 37 33.813 33.465 35.241 1.00 0.00 H +ATOM 606 C LEU 37 36.428 37.716 35.923 1.00 0.00 C +ATOM 607 O LEU 37 37.222 37.168 36.693 1.00 0.00 O +ATOM 608 N GLY 38 36.846 38.472 34.902 1.00 0.00 N +ATOM 609 H GLY 38 36.129 38.909 34.342 1.00 0.00 H +ATOM 610 CA GLY 38 38.217 38.958 34.708 1.00 0.00 C +ATOM 611 HA2 GLY 38 38.282 39.981 35.091 1.00 0.00 H +ATOM 612 HA3 GLY 38 38.907 38.340 35.287 1.00 0.00 H +ATOM 613 C GLY 38 38.735 38.974 33.259 1.00 0.00 C +ATOM 614 O GLY 38 39.662 39.725 32.979 1.00 0.00 O +ATOM 615 N ARG 39 38.206 38.155 32.340 1.00 0.00 N +ATOM 616 H ARG 39 37.404 37.619 32.634 1.00 0.00 H +ATOM 617 CA ARG 39 38.603 38.050 30.914 1.00 0.00 C +ATOM 618 HA ARG 39 38.582 39.053 30.484 1.00 0.00 H +ATOM 619 CB ARG 39 40.027 37.466 30.821 1.00 0.00 C +ATOM 620 HB2 ARG 39 40.701 38.039 31.455 1.00 0.00 H +ATOM 621 HB3 ARG 39 39.995 36.446 31.203 1.00 0.00 H +ATOM 622 CG ARG 39 40.598 37.481 29.395 1.00 0.00 C +ATOM 623 HG2 ARG 39 39.941 36.939 28.727 1.00 0.00 H +ATOM 624 HG3 ARG 39 40.661 38.514 29.050 1.00 0.00 H +ATOM 625 CD ARG 39 41.988 36.840 29.317 1.00 0.00 C +ATOM 626 HD2 ARG 39 42.341 36.892 28.287 1.00 0.00 H +ATOM 627 HD3 ARG 39 42.673 37.431 29.929 1.00 0.00 H +ATOM 628 NE ARG 39 41.998 35.438 29.788 1.00 0.00 N +ATOM 629 HE ARG 39 42.280 35.294 30.743 1.00 0.00 H +ATOM 630 CZ ARG 39 41.765 34.339 29.089 1.00 0.00 C +ATOM 631 NH1 ARG 39 41.348 34.331 27.856 1.00 0.00 N +ATOM 632 HH11 ARG 39 40.915 35.163 27.479 1.00 0.00 H +ATOM 633 HH12 ARG 39 41.218 33.449 27.385 1.00 0.00 H +ATOM 634 NH2 ARG 39 41.938 33.180 29.650 1.00 0.00 N +ATOM 635 HH21 ARG 39 42.075 33.144 30.652 1.00 0.00 H +ATOM 636 HH22 ARG 39 41.802 32.347 29.100 1.00 0.00 H +ATOM 637 C ARG 39 37.638 37.147 30.123 1.00 0.00 C +ATOM 638 O ARG 39 37.225 36.105 30.635 1.00 0.00 O +ATOM 639 N ASP 40 37.331 37.498 28.872 1.00 0.00 N +ATOM 640 H ASP 40 37.689 38.370 28.492 1.00 0.00 H +ATOM 641 CA ASP 40 36.560 36.646 27.954 1.00 0.00 C +ATOM 642 HA ASP 40 35.882 36.048 28.552 1.00 0.00 H +ATOM 643 CB ASP 40 35.679 37.510 27.036 1.00 0.00 C +ATOM 644 HB2 ASP 40 35.010 36.862 26.471 1.00 0.00 H +ATOM 645 HB3 ASP 40 35.045 38.138 27.655 1.00 0.00 H +ATOM 646 CG ASP 40 36.446 38.412 26.064 1.00 0.00 C +ATOM 647 OD1 ASP 40 37.214 39.273 26.564 1.00 0.00 O +ATOM 648 OD2 ASP 40 36.208 38.281 24.849 1.00 0.00 O +ATOM 649 C ASP 40 37.385 35.610 27.150 1.00 0.00 C +ATOM 650 O ASP 40 38.610 35.494 27.249 1.00 0.00 O +ATOM 651 N GLY 41 36.662 34.808 26.363 1.00 0.00 N +ATOM 652 H GLY 41 35.670 34.989 26.320 1.00 0.00 H +ATOM 653 CA GLY 41 37.158 33.813 25.412 1.00 0.00 C +ATOM 654 HA2 GLY 41 38.030 34.210 24.890 1.00 0.00 H +ATOM 655 HA3 GLY 41 37.431 32.901 25.942 1.00 0.00 H +ATOM 656 C GLY 41 36.065 33.484 24.376 1.00 0.00 C +ATOM 657 O GLY 41 34.916 33.916 24.516 1.00 0.00 O +ATOM 658 N GLU 42 36.424 32.735 23.335 1.00 0.00 N +ATOM 659 H GLU 42 37.367 32.385 23.294 1.00 0.00 H +ATOM 660 CA GLU 42 35.558 32.488 22.167 1.00 0.00 C +ATOM 661 HA GLU 42 34.843 33.303 22.111 1.00 0.00 H +ATOM 662 CB GLU 42 36.385 32.496 20.868 1.00 0.00 C +ATOM 663 HB2 GLU 42 37.028 31.616 20.856 1.00 0.00 H +ATOM 664 HB3 GLU 42 35.700 32.412 20.024 1.00 0.00 H +ATOM 665 CG GLU 42 37.265 33.743 20.651 1.00 0.00 C +ATOM 666 HG2 GLU 42 38.105 33.688 21.350 1.00 0.00 H +ATOM 667 HG3 GLU 42 37.682 33.701 19.641 1.00 0.00 H +ATOM 668 CD GLU 42 36.538 35.079 20.850 1.00 0.00 C +ATOM 669 OE1 GLU 42 35.290 35.137 20.795 1.00 0.00 O +ATOM 670 OE2 GLU 42 37.201 36.089 21.167 1.00 0.00 O +ATOM 671 C GLU 42 34.699 31.219 22.262 1.00 0.00 C +ATOM 672 O GLU 42 35.019 30.277 22.993 1.00 0.00 O +ATOM 673 N ARG 43 33.589 31.206 21.508 1.00 0.00 N +ATOM 674 H ARG 43 33.441 31.981 20.867 1.00 0.00 H +ATOM 675 CA ARG 43 32.511 30.199 21.581 1.00 0.00 C +ATOM 676 HA ARG 43 32.907 29.272 21.999 1.00 0.00 H +ATOM 677 CB ARG 43 31.395 30.717 22.507 1.00 0.00 C +ATOM 678 HB2 ARG 43 31.036 31.680 22.144 1.00 0.00 H +ATOM 679 HB3 ARG 43 30.558 30.020 22.496 1.00 0.00 H +ATOM 680 CG ARG 43 31.894 30.874 23.949 1.00 0.00 C +ATOM 681 HG2 ARG 43 32.329 29.935 24.287 1.00 0.00 H +ATOM 682 HG3 ARG 43 32.658 31.646 23.988 1.00 0.00 H +ATOM 683 CD ARG 43 30.780 31.283 24.907 1.00 0.00 C +ATOM 684 HD2 ARG 43 30.284 32.168 24.500 1.00 0.00 H +ATOM 685 HD3 ARG 43 30.035 30.486 24.967 1.00 0.00 H +ATOM 686 NE ARG 43 31.325 31.604 26.238 1.00 0.00 N +ATOM 687 HE ARG 43 31.542 32.570 26.395 1.00 0.00 H +ATOM 688 CZ ARG 43 31.574 30.770 27.229 1.00 0.00 C +ATOM 689 NH1 ARG 43 31.415 29.481 27.125 1.00 0.00 N +ATOM 690 HH11 ARG 43 31.350 29.072 26.209 1.00 0.00 H +ATOM 691 HH12 ARG 43 31.638 28.916 27.933 1.00 0.00 H +ATOM 692 NH2 ARG 43 31.958 31.223 28.383 1.00 0.00 N +ATOM 693 HH21 ARG 43 32.268 32.172 28.480 1.00 0.00 H +ATOM 694 HH22 ARG 43 32.079 30.544 29.137 1.00 0.00 H +ATOM 695 C ARG 43 31.951 29.870 20.198 1.00 0.00 C +ATOM 696 O ARG 43 31.948 30.724 19.318 1.00 0.00 O +ATOM 697 N THR 44 31.459 28.643 20.019 1.00 0.00 N +ATOM 698 H THR 44 31.399 28.048 20.837 1.00 0.00 H +ATOM 699 CA THR 44 30.694 28.234 18.824 1.00 0.00 C +ATOM 700 HA THR 44 30.974 28.883 17.990 1.00 0.00 H +ATOM 701 CB THR 44 31.052 26.787 18.420 1.00 0.00 C +ATOM 702 HB THR 44 30.938 26.133 19.286 1.00 0.00 H +ATOM 703 CG2 THR 44 30.224 26.224 17.261 1.00 0.00 C +ATOM 704 HG21 THR 44 30.244 26.908 16.410 1.00 0.00 H +ATOM 705 HG22 THR 44 30.619 25.255 16.954 1.00 0.00 H +ATOM 706 HG23 THR 44 29.191 26.069 17.579 1.00 0.00 H +ATOM 707 OG1 THR 44 32.387 26.717 17.944 1.00 0.00 O +ATOM 708 HG1 THR 44 32.304 26.255 17.101 1.00 0.00 H +ATOM 709 C THR 44 29.194 28.450 19.073 1.00 0.00 C +ATOM 710 O THR 44 28.754 28.500 20.224 1.00 0.00 O +ATOM 711 N ILE 45 28.401 28.604 18.007 1.00 0.00 N +ATOM 712 H ILE 45 28.816 28.533 17.092 1.00 0.00 H +ATOM 713 CA ILE 45 26.946 28.806 18.040 1.00 0.00 C +ATOM 714 HA ILE 45 26.591 28.637 19.057 1.00 0.00 H +ATOM 715 CB ILE 45 26.567 30.255 17.641 1.00 0.00 C +ATOM 716 HB ILE 45 25.479 30.306 17.595 1.00 0.00 H +ATOM 717 CG2 ILE 45 27.002 31.233 18.739 1.00 0.00 C +ATOM 718 HG21 ILE 45 28.090 31.292 18.796 1.00 0.00 H +ATOM 719 HG22 ILE 45 26.598 32.226 18.539 1.00 0.00 H +ATOM 720 HG23 ILE 45 26.601 30.895 19.694 1.00 0.00 H +ATOM 721 CG1 ILE 45 27.110 30.646 16.245 1.00 0.00 C +ATOM 722 HG12 ILE 45 28.199 30.699 16.276 1.00 0.00 H +ATOM 723 HG13 ILE 45 26.824 29.882 15.520 1.00 0.00 H +ATOM 724 CD1 ILE 45 26.575 31.989 15.735 1.00 0.00 C +ATOM 725 HD11 ILE 45 26.954 32.798 16.359 1.00 0.00 H +ATOM 726 HD12 ILE 45 26.917 32.152 14.713 1.00 0.00 H +ATOM 727 HD13 ILE 45 25.484 31.992 15.751 1.00 0.00 H +ATOM 728 C ILE 45 26.195 27.799 17.156 1.00 0.00 C +ATOM 729 O ILE 45 26.760 27.213 16.229 1.00 0.00 O +ATOM 730 N ASP 46 24.897 27.668 17.419 1.00 0.00 N +ATOM 731 H ASP 46 24.548 28.063 18.287 1.00 0.00 H +ATOM 732 CA ASP 46 23.892 27.103 16.524 1.00 0.00 C +ATOM 733 HA ASP 46 24.230 27.184 15.489 1.00 0.00 H +ATOM 734 CB ASP 46 23.668 25.620 16.848 1.00 0.00 C +ATOM 735 HB2 ASP 46 24.538 25.049 16.529 1.00 0.00 H +ATOM 736 HB3 ASP 46 23.534 25.507 17.926 1.00 0.00 H +ATOM 737 CG ASP 46 22.422 25.088 16.135 1.00 0.00 C +ATOM 738 OD1 ASP 46 21.596 24.436 16.815 1.00 0.00 O +ATOM 739 OD2 ASP 46 22.215 25.420 14.939 1.00 0.00 O +ATOM 740 C ASP 46 22.576 27.901 16.648 1.00 0.00 C +ATOM 741 O ASP 46 22.097 28.156 17.756 1.00 0.00 O +ATOM 742 N ASP 47 21.963 28.271 15.521 1.00 0.00 N +ATOM 743 H ASP 47 22.345 27.930 14.651 1.00 0.00 H +ATOM 744 CA ASP 47 20.663 28.944 15.502 1.00 0.00 C +ATOM 745 HA ASP 47 20.596 29.585 16.384 1.00 0.00 H +ATOM 746 CB ASP 47 20.567 29.848 14.270 1.00 0.00 C +ATOM 747 HB2 ASP 47 21.422 30.514 14.234 1.00 0.00 H +ATOM 748 HB3 ASP 47 20.566 29.235 13.377 1.00 0.00 H +ATOM 749 CG ASP 47 19.281 30.694 14.320 1.00 0.00 C +ATOM 750 OD1 ASP 47 18.339 30.393 13.566 1.00 0.00 O +ATOM 751 OD2 ASP 47 19.129 31.507 15.254 1.00 0.00 O +ATOM 752 C ASP 47 19.472 27.954 15.574 1.00 0.00 C +ATOM 753 O ASP 47 18.421 28.314 16.110 1.00 0.00 O +ATOM 754 N ALA 48 19.625 26.706 15.111 1.00 0.00 N +ATOM 755 H ALA 48 20.544 26.384 14.803 1.00 0.00 H +ATOM 756 CA ALA 48 18.530 25.722 15.102 1.00 0.00 C +ATOM 757 HA ALA 48 17.674 26.160 14.585 1.00 0.00 H +ATOM 758 CB ALA 48 18.995 24.492 14.312 1.00 0.00 C +ATOM 759 HB1 ALA 48 19.841 24.020 14.818 1.00 0.00 H +ATOM 760 HB2 ALA 48 18.180 23.771 14.228 1.00 0.00 H +ATOM 761 HB3 ALA 48 19.309 24.798 13.313 1.00 0.00 H +ATOM 762 C ALA 48 18.071 25.358 16.529 1.00 0.00 C +ATOM 763 O ALA 48 16.875 25.220 16.791 1.00 0.00 O +ATOM 764 N THR 49 19.018 25.267 17.466 1.00 0.00 N +ATOM 765 H THR 49 19.978 25.242 17.128 1.00 0.00 H +ATOM 766 CA THR 49 18.813 25.146 18.920 1.00 0.00 C +ATOM 767 HA THR 49 17.790 24.817 19.098 1.00 0.00 H +ATOM 768 CB THR 49 19.758 24.092 19.523 1.00 0.00 C +ATOM 769 HB THR 49 19.536 24.010 20.585 1.00 0.00 H +ATOM 770 CG2 THR 49 19.585 22.700 18.913 1.00 0.00 C +ATOM 771 HG21 THR 49 19.847 22.712 17.856 1.00 0.00 H +ATOM 772 HG22 THR 49 20.244 22.001 19.429 1.00 0.00 H +ATOM 773 HG23 THR 49 18.553 22.367 19.026 1.00 0.00 H +ATOM 774 OG1 THR 49 21.099 24.489 19.381 1.00 0.00 O +ATOM 775 HG1 THR 49 21.324 24.385 18.426 1.00 0.00 H +ATOM 776 C THR 49 18.982 26.474 19.675 1.00 0.00 C +ATOM 777 O THR 49 18.864 26.493 20.903 1.00 0.00 O +ATOM 778 N LYS 50 19.245 27.599 18.981 1.00 0.00 N +ATOM 779 H LYS 50 19.315 27.502 17.975 1.00 0.00 H +ATOM 780 CA LYS 50 19.432 28.954 19.545 1.00 0.00 C +ATOM 781 HA LYS 50 19.851 29.579 18.758 1.00 0.00 H +ATOM 782 CB LYS 50 18.064 29.549 19.970 1.00 0.00 C +ATOM 783 HB2 LYS 50 17.635 28.897 20.734 1.00 0.00 H +ATOM 784 HB3 LYS 50 18.224 30.526 20.431 1.00 0.00 H +ATOM 785 CG LYS 50 17.019 29.715 18.848 1.00 0.00 C +ATOM 786 HG2 LYS 50 16.975 28.815 18.232 1.00 0.00 H +ATOM 787 HG3 LYS 50 16.043 29.850 19.320 1.00 0.00 H +ATOM 788 CD LYS 50 17.290 30.952 17.972 1.00 0.00 C +ATOM 789 HD2 LYS 50 17.253 31.836 18.611 1.00 0.00 H +ATOM 790 HD3 LYS 50 18.290 30.888 17.533 1.00 0.00 H +ATOM 791 CE LYS 50 16.231 31.126 16.870 1.00 0.00 C +ATOM 792 HE2 LYS 50 15.249 30.833 17.256 1.00 0.00 H +ATOM 793 HE3 LYS 50 16.192 32.182 16.594 1.00 0.00 H +ATOM 794 NZ LYS 50 16.573 30.354 15.653 1.00 0.00 N +ATOM 795 HZ1 LYS 50 16.917 29.421 15.857 1.00 0.00 H +ATOM 796 HZ2 LYS 50 15.833 30.311 14.969 1.00 0.00 H +ATOM 797 HZ3 LYS 50 17.375 30.777 15.163 1.00 0.00 H +ATOM 798 C LYS 50 20.484 29.001 20.681 1.00 0.00 C +ATOM 799 O LYS 50 20.259 29.665 21.697 1.00 0.00 O +ATOM 800 N THR 51 21.593 28.266 20.548 1.00 0.00 N +ATOM 801 H THR 51 21.764 27.850 19.635 1.00 0.00 H +ATOM 802 CA THR 51 22.517 27.908 21.646 1.00 0.00 C +ATOM 803 HA THR 51 22.218 28.455 22.531 1.00 0.00 H +ATOM 804 CB THR 51 22.373 26.416 21.989 1.00 0.00 C +ATOM 805 HB THR 51 22.523 25.817 21.087 1.00 0.00 H +ATOM 806 CG2 THR 51 23.361 25.936 23.043 1.00 0.00 C +ATOM 807 HG21 THR 51 23.319 26.559 23.921 1.00 0.00 H +ATOM 808 HG22 THR 51 23.117 24.926 23.338 1.00 0.00 H +ATOM 809 HG23 THR 51 24.378 25.919 22.675 1.00 0.00 H +ATOM 810 OG1 THR 51 21.116 26.179 22.582 1.00 0.00 O +ATOM 811 HG1 THR 51 20.471 26.217 21.861 1.00 0.00 H +ATOM 812 C THR 51 23.992 28.258 21.374 1.00 0.00 C +ATOM 813 O THR 51 24.539 27.948 20.321 1.00 0.00 O +ATOM 814 N PHE 52 24.674 28.859 22.358 1.00 0.00 N +ATOM 815 H PHE 52 24.142 29.168 23.158 1.00 0.00 H +ATOM 816 CA PHE 52 26.146 28.939 22.451 1.00 0.00 C +ATOM 817 HA PHE 52 26.561 29.009 21.446 1.00 0.00 H +ATOM 818 CB PHE 52 26.561 30.187 23.250 1.00 0.00 C +ATOM 819 HB2 PHE 52 25.986 30.215 24.173 1.00 0.00 H +ATOM 820 HB3 PHE 52 27.608 30.079 23.530 1.00 0.00 H +ATOM 821 CG PHE 52 26.406 31.518 22.543 1.00 0.00 C +ATOM 822 CD1 PHE 52 25.157 32.166 22.504 1.00 0.00 C +ATOM 823 HD1 PHE 52 24.291 31.707 22.960 1.00 0.00 H +ATOM 824 CE1 PHE 52 25.028 33.406 21.854 1.00 0.00 C +ATOM 825 HE1 PHE 52 24.066 33.894 21.802 1.00 0.00 H +ATOM 826 CZ PHE 52 26.147 34.005 21.250 1.00 0.00 C +ATOM 827 HZ PHE 52 26.043 34.945 20.728 1.00 0.00 H +ATOM 828 CE2 PHE 52 27.398 33.366 21.295 1.00 0.00 C +ATOM 829 HE2 PHE 52 28.249 33.816 20.801 1.00 0.00 H +ATOM 830 CD2 PHE 52 27.527 32.123 21.940 1.00 0.00 C +ATOM 831 HD2 PHE 52 28.484 31.623 21.939 1.00 0.00 H +ATOM 832 C PHE 52 26.769 27.703 23.145 1.00 0.00 C +ATOM 833 O PHE 52 26.234 27.232 24.152 1.00 0.00 O +ATOM 834 N THR 53 27.952 27.267 22.699 1.00 0.00 N +ATOM 835 H THR 53 28.326 27.689 21.852 1.00 0.00 H +ATOM 836 CA THR 53 28.737 26.135 23.258 1.00 0.00 C +ATOM 837 HA THR 53 28.419 25.956 24.285 1.00 0.00 H +ATOM 838 CB THR 53 28.495 24.838 22.457 1.00 0.00 C +ATOM 839 HB THR 53 29.062 24.032 22.926 1.00 0.00 H +ATOM 840 CG2 THR 53 27.035 24.403 22.411 1.00 0.00 C +ATOM 841 HG21 THR 53 26.453 25.089 21.797 1.00 0.00 H +ATOM 842 HG22 THR 53 26.967 23.400 21.989 1.00 0.00 H +ATOM 843 HG23 THR 53 26.625 24.377 23.420 1.00 0.00 H +ATOM 844 OG1 THR 53 28.944 24.987 21.132 1.00 0.00 O +ATOM 845 HG1 THR 53 28.633 24.216 20.649 1.00 0.00 H +ATOM 846 C THR 53 30.254 26.418 23.296 1.00 0.00 C +ATOM 847 O THR 53 30.723 27.466 22.848 1.00 0.00 O +ATOM 848 N LYN 54 31.045 25.494 23.858 1.00 0.00 N +ATOM 849 H LYN 54 30.596 24.652 24.182 1.00 0.00 H +ATOM 850 CA LYN 54 32.502 25.405 23.658 1.00 0.00 C +ATOM 851 HA LYN 54 32.816 26.265 23.067 1.00 0.00 H +ATOM 852 CB LYN 54 33.254 25.490 25.002 1.00 0.00 C +ATOM 853 HB2 LYN 54 34.299 25.684 24.767 1.00 0.00 H +ATOM 854 HB3 LYN 54 32.894 26.346 25.573 1.00 0.00 H +ATOM 855 CG LYN 54 33.175 24.224 25.877 1.00 0.00 C +ATOM 856 HG2 LYN 54 32.259 24.249 26.468 1.00 0.00 H +ATOM 857 HG3 LYN 54 33.147 23.334 25.254 1.00 0.00 H +ATOM 858 CD LYN 54 34.396 24.110 26.793 1.00 0.00 C +ATOM 859 HD2 LYN 54 35.300 24.184 26.186 1.00 0.00 H +ATOM 860 HD3 LYN 54 34.395 24.932 27.509 1.00 0.00 H +ATOM 861 CE LYN 54 34.402 22.769 27.513 1.00 0.00 C +ATOM 862 HE2 LYN 54 33.567 22.732 28.205 1.00 0.00 H +ATOM 863 HE3 LYN 54 34.312 21.973 26.784 1.00 0.00 H +ATOM 864 NZ LYN 54 35.655 22.587 28.270 1.00 0.00 N +ATOM 865 HZ2 LYN 54 35.720 21.614 28.564 1.00 0.00 H +ATOM 866 HZ3 LYN 54 35.749 23.245 29.038 1.00 0.00 H +ATOM 867 C LYN 54 32.889 24.159 22.839 1.00 0.00 C +ATOM 868 O LYN 54 32.039 23.323 22.534 1.00 0.00 O +ATOM 869 N ARG 55 34.178 24.033 22.499 1.00 0.00 N +ATOM 870 H ARG 55 34.816 24.708 22.889 1.00 0.00 H +ATOM 871 CA ARG 55 34.769 22.908 21.751 1.00 0.00 C +ATOM 872 HA ARG 55 33.974 22.395 21.206 1.00 0.00 H +ATOM 873 CB ARG 55 35.791 23.459 20.738 1.00 0.00 C +ATOM 874 HB2 ARG 55 36.589 23.965 21.286 1.00 0.00 H +ATOM 875 HB3 ARG 55 36.230 22.625 20.191 1.00 0.00 H +ATOM 876 CG ARG 55 35.149 24.436 19.734 1.00 0.00 C +ATOM 877 HG2 ARG 55 34.383 23.909 19.160 1.00 0.00 H +ATOM 878 HG3 ARG 55 34.683 25.263 20.274 1.00 0.00 H +ATOM 879 CD ARG 55 36.197 25.018 18.777 1.00 0.00 C +ATOM 880 HD2 ARG 55 37.009 25.448 19.372 1.00 0.00 H +ATOM 881 HD3 ARG 55 36.600 24.208 18.158 1.00 0.00 H +ATOM 882 NE ARG 55 35.609 26.074 17.925 1.00 0.00 N +ATOM 883 HE ARG 55 34.626 26.279 18.049 1.00 0.00 H +ATOM 884 CZ ARG 55 36.261 26.813 17.045 1.00 0.00 C +ATOM 885 NH1 ARG 55 37.528 26.646 16.798 1.00 0.00 N +ATOM 886 HH11 ARG 55 38.045 25.902 17.225 1.00 0.00 H +ATOM 887 HH12 ARG 55 37.977 27.284 16.150 1.00 0.00 H +ATOM 888 NH2 ARG 55 35.666 27.762 16.387 1.00 0.00 N +ATOM 889 HH21 ARG 55 34.691 27.963 16.537 1.00 0.00 H +ATOM 890 HH22 ARG 55 36.213 28.287 15.715 1.00 0.00 H +ATOM 891 C ARG 55 35.397 21.855 22.681 1.00 0.00 C +ATOM 892 O ARG 55 35.642 22.153 23.849 1.00 0.00 O +ATOM 893 N GLU 56 35.638 20.654 22.140 1.00 0.00 N +ATOM 894 H GLU 56 35.420 20.544 21.167 1.00 0.00 H +ATOM 895 CA GLU 56 36.360 19.525 22.759 1.00 0.00 C +ATOM 896 HA GLU 56 36.457 19.716 23.823 1.00 0.00 H +ATOM 897 CB GLU 56 35.514 18.242 22.595 1.00 0.00 C +ATOM 898 HB2 GLU 56 34.490 18.465 22.861 1.00 0.00 H +ATOM 899 HB3 GLU 56 35.477 18.007 21.532 1.00 0.00 H +ATOM 900 CG GLU 56 36.004 16.993 23.363 1.00 0.00 C +ATOM 901 HG2 GLU 56 36.125 16.204 22.620 1.00 0.00 H +ATOM 902 HG3 GLU 56 36.996 17.206 23.755 1.00 0.00 H +ATOM 903 CD GLU 56 35.102 16.435 24.504 1.00 0.00 C +ATOM 904 OE1 GLU 56 35.457 15.392 25.104 1.00 0.00 O +ATOM 905 OE2 GLU 56 34.009 16.974 24.787 1.00 0.00 O +ATOM 906 C GLU 56 37.805 19.402 22.220 1.00 0.00 C +ATOM 907 O GLU 56 38.714 19.885 22.928 1.00 0.00 O +ATOM 908 OXT GLU 56 37.983 18.915 21.074 1.00 0.00 O +HETATM 909 ZN ZN1 57 26.140 31.996 29.611 1.00 0.00 Zn +HETATM 910 N AN1 58 27.830 32.401 30.731 1.00 0.00 N +HETATM 911 C AN1 58 30.087 33.113 31.820 1.00 0.00 C +HETATM 912 C1 AN1 58 28.816 32.693 31.235 1.00 0.00 C +HETATM 913 H AN1 58 29.906 33.496 32.829 1.00 0.00 H +HETATM 914 H1 AN1 58 30.537 33.907 31.215 1.00 0.00 H +HETATM 915 H2 AN1 58 30.760 32.252 31.893 1.00 0.00 H +HETATM 916 N1 AZI 59 31.570 29.091 30.304 1.00 0.00 N +HETATM 917 N2 AZI 59 30.346 28.966 30.237 1.00 0.00 N +HETATM 918 N3 AZI 59 29.098 28.869 30.181 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 65 69 +CONECT 69 68 +CONECT 70 68 +CONECT 71 73 72 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 909 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 105 101 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 118 132 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 137 138 134 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 142 140 +CONECT 140 139 +CONECT 141 139 +CONECT 142 144 139 145 143 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 142 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 202 189 +CONECT 188 187 +CONECT 189 187 191 195 190 +CONECT 190 189 +CONECT 191 192 194 189 193 +CONECT 192 191 +CONECT 193 191 +CONECT 194 191 +CONECT 195 196 197 189 198 +CONECT 196 195 +CONECT 197 195 +CONECT 198 195 200 199 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 +CONECT 202 204 187 203 +CONECT 203 202 +CONECT 204 205 206 202 +CONECT 205 204 +CONECT 206 226 204 208 207 +CONECT 207 206 +CONECT 208 211 206 209 210 +CONECT 209 208 +CONECT 210 208 +CONECT 211 213 212 214 208 +CONECT 212 211 +CONECT 213 211 +CONECT 214 217 211 215 216 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 219 214 +CONECT 218 217 +CONECT 219 220 217 223 +CONECT 220 221 222 219 +CONECT 221 220 +CONECT 222 220 +CONECT 223 219 225 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 227 228 206 +CONECT 227 226 +CONECT 228 230 226 229 +CONECT 229 228 +CONECT 230 231 248 232 228 +CONECT 231 230 +CONECT 232 235 230 233 234 +CONECT 233 232 +CONECT 234 232 +CONECT 235 237 236 238 232 +CONECT 236 235 +CONECT 237 235 +CONECT 238 239 235 240 241 +CONECT 239 238 +CONECT 240 238 +CONECT 241 243 238 244 242 +CONECT 242 241 +CONECT 243 241 +CONECT 244 247 241 246 245 +CONECT 245 244 +CONECT 246 244 +CONECT 247 244 +CONECT 248 249 230 250 +CONECT 249 248 +CONECT 250 248 252 251 +CONECT 251 250 +CONECT 252 255 250 253 254 +CONECT 253 252 +CONECT 254 252 +CONECT 255 256 257 252 +CONECT 256 255 +CONECT 257 259 255 258 +CONECT 258 257 +CONECT 259 261 260 271 257 +CONECT 260 259 +CONECT 261 267 262 263 259 +CONECT 262 261 +CONECT 263 265 261 264 266 +CONECT 264 263 +CONECT 265 263 +CONECT 266 263 +CONECT 267 269 268 270 261 +CONECT 268 267 +CONECT 269 267 +CONECT 270 267 +CONECT 271 259 273 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 273 284 277 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 274 278 285 286 +CONECT 278 279 280 277 +CONECT 279 282 288 278 +CONECT 280 281 278 287 +CONECT 281 282 289 280 +CONECT 282 909 281 279 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 293 294 302 290 +CONECT 293 292 +CONECT 294 295 296 292 300 +CONECT 295 294 +CONECT 296 299 298 294 297 +CONECT 297 296 +CONECT 298 296 +CONECT 299 296 +CONECT 300 294 301 +CONECT 301 300 +CONECT 302 304 292 303 +CONECT 303 302 +CONECT 304 314 305 302 +CONECT 305 306 308 304 315 +CONECT 306 307 321 305 +CONECT 307 306 +CONECT 308 316 317 305 309 +CONECT 309 308 310 311 +CONECT 310 319 309 313 +CONECT 311 309 318 312 +CONECT 312 313 311 320 +CONECT 313 310 909 312 +CONECT 314 304 +CONECT 315 305 +CONECT 316 308 +CONECT 317 308 +CONECT 318 311 +CONECT 319 310 +CONECT 320 312 +CONECT 321 323 306 322 +CONECT 322 321 +CONECT 323 334 324 321 325 +CONECT 324 323 +CONECT 325 323 328 327 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 330 331 325 329 +CONECT 329 328 +CONECT 330 328 +CONECT 331 332 328 333 +CONECT 332 331 +CONECT 333 331 +CONECT 334 336 335 323 +CONECT 335 334 +CONECT 336 338 337 334 +CONECT 337 336 +CONECT 338 344 340 339 336 +CONECT 339 338 +CONECT 340 342 341 338 343 +CONECT 341 340 +CONECT 342 340 +CONECT 343 340 +CONECT 344 346 345 338 +CONECT 345 344 +CONECT 346 348 347 344 +CONECT 347 346 +CONECT 348 360 350 349 346 +CONECT 349 348 +CONECT 350 351 356 348 352 +CONECT 351 350 +CONECT 352 350 354 355 353 +CONECT 353 352 +CONECT 354 352 +CONECT 355 352 +CONECT 356 357 358 350 359 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 +CONECT 360 361 362 348 +CONECT 361 360 +CONECT 362 364 360 363 +CONECT 363 362 +CONECT 364 366 365 372 362 +CONECT 365 364 +CONECT 366 369 367 368 364 +CONECT 367 366 +CONECT 368 366 +CONECT 369 370 371 366 +CONECT 370 369 +CONECT 371 369 +CONECT 372 364 374 373 +CONECT 373 372 +CONECT 374 375 372 376 +CONECT 375 374 +CONECT 376 378 374 396 377 +CONECT 377 376 +CONECT 378 381 380 379 376 +CONECT 379 378 +CONECT 380 378 +CONECT 381 382 395 378 +CONECT 382 384 383 381 +CONECT 383 382 +CONECT 384 385 386 382 +CONECT 385 384 +CONECT 386 387 384 395 +CONECT 387 388 389 386 +CONECT 388 387 +CONECT 389 390 387 391 +CONECT 390 389 +CONECT 391 389 392 393 +CONECT 392 391 +CONECT 393 391 395 394 +CONECT 394 393 +CONECT 395 386 393 381 +CONECT 396 398 376 397 +CONECT 397 396 +CONECT 398 399 400 396 +CONECT 399 398 +CONECT 400 402 398 401 406 +CONECT 401 400 +CONECT 402 405 403 404 400 +CONECT 403 402 +CONECT 404 402 +CONECT 405 402 +CONECT 406 400 407 408 +CONECT 407 406 +CONECT 408 406 409 410 +CONECT 409 408 +CONECT 410 408 411 412 421 +CONECT 411 410 +CONECT 412 415 410 413 414 +CONECT 413 412 +CONECT 414 412 +CONECT 415 416 417 418 412 +CONECT 416 415 +CONECT 417 415 +CONECT 418 415 420 419 +CONECT 419 418 +CONECT 420 418 +CONECT 421 410 423 422 +CONECT 422 421 +CONECT 423 424 421 425 +CONECT 424 423 +CONECT 425 423 427 431 426 +CONECT 426 425 +CONECT 427 428 430 425 429 +CONECT 428 427 +CONECT 429 427 +CONECT 430 427 +CONECT 431 433 425 432 +CONECT 432 431 +CONECT 433 434 435 431 +CONECT 434 433 +CONECT 435 437 433 436 446 +CONECT 436 435 +CONECT 437 438 439 440 435 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 437 442 441 +CONECT 441 440 +CONECT 442 440 +CONECT 443 445 444 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 435 448 447 +CONECT 447 446 +CONECT 448 449 446 450 +CONECT 449 448 +CONECT 450 448 452 451 468 +CONECT 451 450 +CONECT 452 455 453 454 450 +CONECT 453 452 +CONECT 454 452 +CONECT 455 458 457 456 452 +CONECT 456 455 +CONECT 457 455 +CONECT 458 461 459 460 455 +CONECT 459 458 +CONECT 460 458 +CONECT 461 464 463 462 458 +CONECT 462 461 +CONECT 463 461 +CONECT 464 466 467 465 461 +CONECT 465 464 +CONECT 466 464 +CONECT 467 464 +CONECT 468 450 470 469 +CONECT 469 468 +CONECT 470 471 468 472 +CONECT 471 470 +CONECT 472 470 474 473 488 +CONECT 473 472 +CONECT 474 477 475 472 476 +CONECT 475 474 +CONECT 476 474 +CONECT 477 478 486 474 +CONECT 478 480 479 477 +CONECT 479 478 +CONECT 480 481 482 478 +CONECT 481 480 +CONECT 482 483 480 484 +CONECT 483 482 +CONECT 484 482 485 486 +CONECT 485 484 +CONECT 486 484 477 487 +CONECT 487 486 +CONECT 488 490 472 489 +CONECT 489 488 +CONECT 490 491 492 488 +CONECT 491 490 +CONECT 492 494 490 502 493 +CONECT 493 492 +CONECT 494 495 500 496 492 +CONECT 495 494 +CONECT 496 498 494 499 497 +CONECT 497 496 +CONECT 498 496 +CONECT 499 496 +CONECT 500 501 494 +CONECT 501 500 +CONECT 502 504 492 503 +CONECT 503 502 +CONECT 504 505 506 502 +CONECT 505 504 +CONECT 506 508 504 507 524 +CONECT 507 506 +CONECT 508 511 509 510 506 +CONECT 509 508 +CONECT 510 508 +CONECT 511 514 513 512 508 +CONECT 512 511 +CONECT 513 511 +CONECT 514 517 515 516 511 +CONECT 515 514 +CONECT 516 514 +CONECT 517 519 518 520 514 +CONECT 518 517 +CONECT 519 517 +CONECT 520 522 517 523 521 +CONECT 521 520 +CONECT 522 520 +CONECT 523 520 +CONECT 524 506 526 525 +CONECT 525 524 +CONECT 526 527 524 528 +CONECT 527 526 +CONECT 528 526 530 529 534 +CONECT 529 528 +CONECT 530 533 531 528 532 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 536 551 540 539 +CONECT 539 538 +CONECT 540 543 538 542 541 +CONECT 541 540 +CONECT 542 540 +CONECT 543 544 545 546 540 +CONECT 544 543 +CONECT 545 543 +CONECT 546 547 543 +CONECT 547 550 548 549 546 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 +CONECT 551 553 538 552 +CONECT 552 551 +CONECT 553 554 555 551 +CONECT 554 553 +CONECT 555 557 553 561 556 +CONECT 556 555 +CONECT 557 558 560 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 557 +CONECT 561 563 555 562 +CONECT 562 561 +CONECT 563 564 561 565 +CONECT 564 563 +CONECT 565 567 563 566 575 +CONECT 566 565 +CONECT 567 570 568 569 565 +CONECT 568 567 +CONECT 569 567 +CONECT 570 572 571 567 +CONECT 571 570 +CONECT 572 573 574 570 +CONECT 573 572 +CONECT 574 572 +CONECT 575 565 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 581 580 587 +CONECT 580 579 +CONECT 581 584 582 579 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 585 586 581 +CONECT 585 584 +CONECT 586 584 +CONECT 587 579 589 588 +CONECT 588 587 +CONECT 589 590 587 591 +CONECT 590 589 +CONECT 591 589 606 593 592 +CONECT 592 591 +CONECT 593 596 595 591 594 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 602 598 593 +CONECT 597 596 +CONECT 598 600 596 601 599 +CONECT 599 598 +CONECT 600 598 +CONECT 601 598 +CONECT 602 604 603 596 605 +CONECT 603 602 +CONECT 604 602 +CONECT 605 602 +CONECT 606 608 591 607 +CONECT 607 606 +CONECT 608 609 610 606 +CONECT 609 608 +CONECT 610 613 608 611 612 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 610 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 637 618 619 615 +CONECT 618 617 +CONECT 619 622 617 621 620 +CONECT 620 619 +CONECT 621 619 +CONECT 622 623 624 625 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 622 628 627 +CONECT 626 625 +CONECT 627 625 +CONECT 628 630 625 629 +CONECT 629 628 +CONECT 630 631 634 628 +CONECT 631 633 632 630 +CONECT 632 631 +CONECT 633 631 +CONECT 634 630 636 635 +CONECT 635 634 +CONECT 636 634 +CONECT 637 639 638 617 +CONECT 638 637 +CONECT 639 641 640 637 +CONECT 640 639 +CONECT 641 643 649 642 639 +CONECT 642 641 +CONECT 643 646 644 645 641 +CONECT 644 643 +CONECT 645 643 +CONECT 646 648 647 643 +CONECT 647 646 +CONECT 648 646 +CONECT 649 651 650 641 +CONECT 650 649 +CONECT 651 653 652 649 +CONECT 652 651 +CONECT 653 656 654 655 651 +CONECT 654 653 +CONECT 655 653 +CONECT 656 658 657 653 +CONECT 657 656 +CONECT 658 660 659 656 +CONECT 659 658 +CONECT 660 662 661 671 658 +CONECT 661 660 +CONECT 662 664 665 663 660 +CONECT 663 662 +CONECT 664 662 +CONECT 665 667 668 662 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 665 669 670 +CONECT 669 668 +CONECT 670 668 +CONECT 671 673 660 672 +CONECT 672 671 +CONECT 673 674 675 671 +CONECT 674 673 +CONECT 675 695 673 676 677 +CONECT 676 675 +CONECT 677 675 678 679 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 682 681 683 +CONECT 681 680 +CONECT 682 680 +CONECT 683 680 684 685 686 +CONECT 684 683 +CONECT 685 683 +CONECT 686 683 687 688 +CONECT 687 686 +CONECT 688 686 689 692 +CONECT 689 690 688 691 +CONECT 690 689 +CONECT 691 689 +CONECT 692 688 693 694 +CONECT 693 692 +CONECT 694 692 +CONECT 695 696 697 675 +CONECT 696 695 +CONECT 697 699 695 698 +CONECT 698 697 +CONECT 699 700 701 709 697 +CONECT 700 699 +CONECT 701 703 707 699 702 +CONECT 702 701 +CONECT 703 704 705 706 701 +CONECT 704 703 +CONECT 705 703 +CONECT 706 703 +CONECT 707 708 701 +CONECT 708 707 +CONECT 709 711 699 710 +CONECT 710 709 +CONECT 711 712 713 709 +CONECT 712 711 +CONECT 713 728 715 711 714 +CONECT 714 713 +CONECT 715 721 716 713 717 +CONECT 716 715 +CONECT 717 715 719 718 720 +CONECT 718 717 +CONECT 719 717 +CONECT 720 717 +CONECT 721 723 724 722 715 +CONECT 722 721 +CONECT 723 721 +CONECT 724 726 727 721 725 +CONECT 725 724 +CONECT 726 724 +CONECT 727 724 +CONECT 728 729 730 713 +CONECT 729 728 +CONECT 730 732 728 731 +CONECT 731 730 +CONECT 732 733 740 734 730 +CONECT 733 732 +CONECT 734 737 732 735 736 +CONECT 735 734 +CONECT 736 734 +CONECT 737 739 738 734 +CONECT 738 737 +CONECT 739 737 +CONECT 740 742 732 741 +CONECT 741 740 +CONECT 742 743 744 740 +CONECT 743 742 +CONECT 744 746 742 752 745 +CONECT 745 744 +CONECT 746 748 747 749 744 +CONECT 747 746 +CONECT 748 746 +CONECT 749 750 746 751 +CONECT 750 749 +CONECT 751 749 +CONECT 752 754 744 753 +CONECT 753 752 +CONECT 754 755 756 752 +CONECT 755 754 +CONECT 756 758 757 754 762 +CONECT 757 756 +CONECT 758 761 760 759 756 +CONECT 759 758 +CONECT 760 758 +CONECT 761 758 +CONECT 762 756 763 764 +CONECT 763 762 +CONECT 764 762 765 766 +CONECT 765 764 +CONECT 766 764 767 768 776 +CONECT 767 766 +CONECT 768 770 766 774 769 +CONECT 769 768 +CONECT 770 771 773 772 768 +CONECT 771 770 +CONECT 772 770 +CONECT 773 770 +CONECT 774 775 768 +CONECT 775 774 +CONECT 776 766 778 777 +CONECT 777 776 +CONECT 778 779 780 776 +CONECT 779 778 +CONECT 780 781 778 782 798 +CONECT 781 780 +CONECT 782 785 780 784 783 +CONECT 783 782 +CONECT 784 782 +CONECT 785 788 786 787 782 +CONECT 786 785 +CONECT 787 785 +CONECT 788 791 790 789 785 +CONECT 789 788 +CONECT 790 788 +CONECT 791 794 793 792 788 +CONECT 792 791 +CONECT 793 791 +CONECT 794 796 797 795 791 +CONECT 795 794 +CONECT 796 794 +CONECT 797 794 +CONECT 798 780 800 799 +CONECT 799 798 +CONECT 800 801 798 802 +CONECT 801 800 +CONECT 802 800 812 804 803 +CONECT 803 802 +CONECT 804 805 802 810 806 +CONECT 805 804 +CONECT 806 804 809 808 807 +CONECT 807 806 +CONECT 808 806 +CONECT 809 806 +CONECT 810 811 804 +CONECT 811 810 +CONECT 812 813 802 814 +CONECT 813 812 +CONECT 814 812 816 815 +CONECT 815 814 +CONECT 816 817 814 832 818 +CONECT 817 816 +CONECT 818 816 821 820 819 +CONECT 819 818 +CONECT 820 818 +CONECT 821 830 822 818 +CONECT 822 824 821 823 +CONECT 823 822 +CONECT 824 826 825 822 +CONECT 825 824 +CONECT 826 827 828 824 +CONECT 827 826 +CONECT 828 829 826 830 +CONECT 829 828 +CONECT 830 828 831 821 +CONECT 831 830 +CONECT 832 816 834 833 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 838 834 846 837 +CONECT 837 836 +CONECT 838 844 840 839 836 +CONECT 839 838 +CONECT 840 841 842 838 843 +CONECT 841 840 +CONECT 842 840 +CONECT 843 840 +CONECT 844 845 838 +CONECT 845 844 +CONECT 846 847 836 848 +CONECT 847 846 +CONECT 848 846 850 849 +CONECT 849 848 +CONECT 850 867 851 848 852 +CONECT 851 850 +CONECT 852 850 853 854 855 +CONECT 853 852 +CONECT 854 852 +CONECT 855 852 857 856 858 +CONECT 856 855 +CONECT 857 855 +CONECT 858 855 859 860 861 +CONECT 859 858 +CONECT 860 858 +CONECT 861 863 858 862 864 +CONECT 862 861 +CONECT 863 861 +CONECT 864 861 865 866 +CONECT 865 864 +CONECT 866 864 +CONECT 867 869 868 850 +CONECT 868 867 +CONECT 869 871 867 870 +CONECT 870 869 +CONECT 871 873 872 869 891 +CONECT 872 871 +CONECT 873 876 875 874 871 +CONECT 874 873 +CONECT 875 873 +CONECT 876 879 877 878 873 +CONECT 877 876 +CONECT 878 876 +CONECT 879 882 881 880 876 +CONECT 880 879 +CONECT 881 879 +CONECT 882 884 883 879 +CONECT 883 882 +CONECT 884 888 885 882 +CONECT 885 887 884 886 +CONECT 886 885 +CONECT 887 885 +CONECT 888 890 889 884 +CONECT 889 888 +CONECT 890 888 +CONECT 891 871 893 892 +CONECT 892 891 +CONECT 893 894 891 895 +CONECT 894 893 +CONECT 895 893 906 897 896 +CONECT 896 895 +CONECT 897 899 895 898 900 +CONECT 898 897 +CONECT 899 897 +CONECT 900 897 901 902 903 +CONECT 901 900 +CONECT 902 900 +CONECT 903 900 905 904 +CONECT 904 903 +CONECT 905 903 +CONECT 906 908 895 907 +CONECT 907 906 +CONECT 908 906 +CONECT 909 87 313 910 282 +CONECT 910 909 912 +CONECT 911 914 912 915 913 +CONECT 912 910 911 +CONECT 913 911 +CONECT 914 911 +CONECT 915 911 +CONECT 916 917 +CONECT 917 918 916 +CONECT 918 917 +MASTER 0 0 0 0 0 0 0 0 918 0 918 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_4.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_4.pdb new file mode 100644 index 0000000..f0150b2 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_4.pdb @@ -0,0 +1,1785 @@ +COMPND fitness: -6.2188 90.21749999999975 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 50.124 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.128 37.937 23.379 1.00 0.00 N +ATOM 2 H1 MET 1 15.115 38.352 24.304 1.00 0.00 H +ATOM 3 H2 MET 1 14.353 38.281 22.845 1.00 0.00 H +ATOM 4 H3 MET 1 15.989 38.231 22.950 1.00 0.00 H +ATOM 5 CA MET 1 15.114 36.469 23.492 1.00 0.00 C +ATOM 6 HA MET 1 14.154 36.172 23.930 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.810 22.104 1.00 0.00 C +ATOM 8 HB2 MET 1 14.395 36.081 21.502 1.00 0.00 H +ATOM 9 HB3 MET 1 16.151 36.200 21.624 1.00 0.00 H +ATOM 10 CG MET 1 15.368 34.269 22.154 1.00 0.00 C +ATOM 11 HG2 MET 1 16.256 34.008 22.740 1.00 0.00 H +ATOM 12 HG3 MET 1 14.490 33.864 22.670 1.00 0.00 H +ATOM 13 SD MET 1 15.523 33.454 20.540 1.00 0.00 S +ATOM 14 CE MET 1 13.825 33.570 19.902 1.00 0.00 C +ATOM 15 HE1 MET 1 13.514 34.612 19.846 1.00 0.00 H +ATOM 16 HE2 MET 1 13.786 33.136 18.902 1.00 0.00 H +ATOM 17 HE3 MET 1 13.144 33.019 20.553 1.00 0.00 H +ATOM 18 C MET 1 16.215 36.013 24.449 1.00 0.00 C +ATOM 19 O MET 1 17.372 36.346 24.223 1.00 0.00 O +ATOM 20 N GLN 2 15.871 35.224 25.474 1.00 0.00 N +ATOM 21 H GLN 2 14.897 35.087 25.675 1.00 0.00 H +ATOM 22 CA GLN 2 16.831 34.496 26.306 1.00 0.00 C +ATOM 23 HA GLN 2 17.643 35.162 26.593 1.00 0.00 H +ATOM 24 CB GLN 2 16.127 34.008 27.587 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.159 33.579 27.318 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.708 33.210 28.060 1.00 0.00 H +ATOM 27 CG GLN 2 15.903 35.114 28.632 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.477 35.983 28.143 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.171 34.756 29.353 1.00 0.00 H +ATOM 30 CD GLN 2 17.153 35.508 29.416 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.264 35.044 29.192 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.019 36.330 30.429 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.839 36.559 30.955 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.114 36.721 30.646 1.00 0.00 H +ATOM 35 C GLN 2 17.469 33.325 25.522 1.00 0.00 C +ATOM 36 O GLN 2 17.052 32.167 25.651 1.00 0.00 O +ATOM 37 N TYR 3 18.463 33.623 24.679 1.00 0.00 N +ATOM 38 H TYR 3 18.765 34.592 24.628 1.00 0.00 H +ATOM 39 CA TYR 3 19.234 32.609 23.954 1.00 0.00 C +ATOM 40 HA TYR 3 18.545 31.959 23.422 1.00 0.00 H +ATOM 41 CB TYR 3 20.170 33.262 22.941 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.877 33.900 23.476 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.723 32.438 22.497 1.00 0.00 H +ATOM 44 CG TYR 3 19.600 34.062 21.781 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.519 33.459 20.512 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.802 32.423 20.390 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.149 34.213 19.385 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.118 33.754 18.409 1.00 0.00 H +ATOM 49 CZ TYR 3 18.855 35.585 19.528 1.00 0.00 C +ATOM 50 OH TYR 3 18.517 36.324 18.441 1.00 0.00 O +ATOM 51 HH TYR 3 18.718 35.875 17.614 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.941 36.195 20.795 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.739 37.253 20.885 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.327 35.436 21.917 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.448 35.924 22.876 1.00 0.00 H +ATOM 56 C TYR 3 20.072 31.754 24.926 1.00 0.00 C +ATOM 57 O TYR 3 20.489 32.242 25.980 1.00 0.00 O +ATOM 58 N LYS 4 20.339 30.479 24.600 1.00 0.00 N +ATOM 59 H LYS 4 20.151 30.180 23.644 1.00 0.00 H +ATOM 60 CA LYS 4 20.960 29.479 25.496 1.00 0.00 C +ATOM 61 HA LYS 4 20.692 29.716 26.523 1.00 0.00 H +ATOM 62 CB LYS 4 20.389 28.078 25.169 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.359 27.961 24.086 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.082 27.325 25.544 1.00 0.00 H +ATOM 65 CG LYS 4 18.993 27.726 25.738 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.817 26.675 25.502 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.009 27.823 26.824 1.00 0.00 H +ATOM 68 CD LYS 4 17.809 28.534 25.173 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.798 29.537 25.609 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.962 28.643 24.097 1.00 0.00 H +ATOM 71 CE LYS 4 16.441 27.842 25.378 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.715 28.351 24.738 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.517 26.807 25.026 1.00 0.00 H +ATOM 74 NZ LYS 4 15.935 27.871 26.782 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.755 28.812 27.098 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.064 27.350 26.889 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.572 27.463 27.463 1.00 0.00 H +ATOM 78 C LYS 4 22.499 29.490 25.466 1.00 0.00 C +ATOM 79 O LYS 4 23.140 29.867 24.490 1.00 0.00 O +HETATM 80 N HX1 5 23.130 29.035 26.548 1.00 0.00 N +HETATM 81 CA HX1 5 24.591 28.856 26.679 1.00 0.00 C +HETATM 82 C HX1 5 24.878 27.688 27.631 1.00 0.00 C +HETATM 83 O HX1 5 24.428 27.708 28.777 1.00 0.00 O +HETATM 84 CB HX1 5 25.222 30.175 27.180 1.00 0.00 C +HETATM 85 CG HX1 5 26.737 30.247 27.288 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.646 29.286 26.930 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.420 31.336 27.850 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.719 30.994 27.776 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.886 29.754 27.285 1.00 0.00 N +HETATM 90 H HX1 5 22.559 28.844 27.370 1.00 0.00 H +HETATM 91 HA HX1 5 25.018 28.612 25.702 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.806 30.413 28.160 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.913 30.973 26.501 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.458 28.305 26.513 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.519 31.581 28.203 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.738 29.194 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.579 26.661 27.147 1.00 0.00 N +ATOM 98 H ILE 6 25.921 26.711 26.193 1.00 0.00 H +ATOM 99 CA ILE 6 25.970 25.469 27.917 1.00 0.00 C +ATOM 100 HA ILE 6 25.283 25.357 28.755 1.00 0.00 H +ATOM 101 CB ILE 6 25.813 24.203 27.035 1.00 0.00 C +ATOM 102 HB ILE 6 26.347 24.367 26.099 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.392 22.937 27.698 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.889 22.736 28.645 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.267 22.079 27.038 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.465 23.049 27.864 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.304 24.011 26.726 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.764 23.868 27.661 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.914 24.914 26.252 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.964 22.843 25.793 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.140 21.891 26.293 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.908 22.895 25.523 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.563 22.899 24.885 1.00 0.00 H +ATOM 114 C ILE 6 27.370 25.661 28.537 1.00 0.00 C +ATOM 115 O ILE 6 28.186 26.422 28.017 1.00 0.00 O +ATOM 116 N VAL 7 27.605 25.035 29.694 1.00 0.00 N +ATOM 117 H VAL 7 26.884 24.405 30.032 1.00 0.00 H +ATOM 118 CA VAL 7 28.769 25.250 30.572 1.00 0.00 C +ATOM 119 HA VAL 7 28.849 26.324 30.732 1.00 0.00 H +ATOM 120 CB VAL 7 28.470 24.592 31.936 1.00 0.00 C +ATOM 121 HB VAL 7 27.460 24.891 32.229 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.498 23.060 31.893 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.507 22.695 31.701 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.158 22.662 32.842 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.845 22.689 31.104 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.397 25.060 33.063 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.408 26.149 33.096 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.024 24.680 34.015 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.403 24.676 32.902 1.00 0.00 H +ATOM 130 C VAL 7 30.119 24.780 29.995 1.00 0.00 C +ATOM 131 O VAL 7 30.207 23.763 29.310 1.00 0.00 O +ATOM 132 N ARG 8 31.201 25.497 30.343 1.00 0.00 N +ATOM 133 H ARG 8 31.031 26.423 30.713 1.00 0.00 H +ATOM 134 CA ARG 8 32.608 25.082 30.154 1.00 0.00 C +ATOM 135 HA ARG 8 32.717 24.857 29.094 1.00 0.00 H +ATOM 136 CB ARG 8 33.575 26.241 30.501 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.546 25.995 30.072 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.247 27.151 30.004 1.00 0.00 H +ATOM 139 CG ARG 8 33.814 26.544 32.001 1.00 0.00 C +ATOM 140 HG2 ARG 8 34.126 25.632 32.506 1.00 0.00 H +ATOM 141 HG3 ARG 8 34.652 27.235 32.093 1.00 0.00 H +ATOM 142 CD ARG 8 32.636 27.142 32.778 1.00 0.00 C +ATOM 143 HD2 ARG 8 31.766 26.524 32.631 1.00 0.00 H +ATOM 144 HD3 ARG 8 32.851 27.100 33.836 1.00 0.00 H +ATOM 145 NE ARG 8 32.321 28.531 32.389 1.00 0.00 N +ATOM 146 HE ARG 8 31.868 28.645 31.483 1.00 0.00 H +ATOM 147 CZ ARG 8 32.417 29.619 33.139 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.818 30.717 32.782 1.00 0.00 N +ATOM 149 HH11 ARG 8 31.188 30.675 31.981 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.731 31.448 33.453 1.00 0.00 H +ATOM 151 NH2 ARG 8 33.086 29.637 34.256 1.00 0.00 N +ATOM 152 HH21 ARG 8 33.619 28.829 34.514 1.00 0.00 H +ATOM 153 HH22 ARG 8 33.065 30.431 34.886 1.00 0.00 H +ATOM 154 C ARG 8 32.993 23.796 30.906 1.00 0.00 C +ATOM 155 O ARG 8 32.489 23.532 31.997 1.00 0.00 O +ATOM 156 N GLY 9 33.997 23.086 30.385 1.00 0.00 N +ATOM 157 H GLY 9 34.337 23.350 29.474 1.00 0.00 H +ATOM 158 CA GLY 9 34.544 21.859 30.982 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.546 21.680 30.585 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.627 21.989 32.066 1.00 0.00 H +ATOM 161 C GLY 9 33.690 20.615 30.703 1.00 0.00 C +ATOM 162 O GLY 9 32.893 20.602 29.772 1.00 0.00 O +ATOM 163 N LYS 10 33.877 19.558 31.507 1.00 0.00 N +ATOM 164 H LYS 10 34.624 19.619 32.176 1.00 0.00 H +ATOM 165 CA LYS 10 33.144 18.277 31.372 1.00 0.00 C +ATOM 166 HA LYS 10 32.234 18.481 30.799 1.00 0.00 H +ATOM 167 CB LYS 10 34.004 17.293 30.544 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.660 17.868 29.891 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.633 16.707 31.215 1.00 0.00 H +ATOM 170 CG LYS 10 33.182 16.351 29.644 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.576 15.685 30.259 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.517 16.953 29.025 1.00 0.00 H +ATOM 173 CD LYS 10 34.095 15.518 28.728 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.765 16.189 28.186 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.693 14.843 29.338 1.00 0.00 H +ATOM 176 CE LYS 10 33.287 14.702 27.711 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.727 13.931 28.247 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.567 15.368 27.228 1.00 0.00 H +ATOM 179 NZ LYS 10 34.154 14.097 26.668 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.950 13.593 27.047 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.637 13.513 26.029 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.558 14.828 26.065 1.00 0.00 H +ATOM 183 C LYS 10 32.647 17.678 32.701 1.00 0.00 C +ATOM 184 O LYS 10 31.863 16.738 32.687 1.00 0.00 O +ATOM 185 N SER 11 33.082 18.223 33.848 1.00 0.00 N +ATOM 186 H SER 11 33.752 18.967 33.790 1.00 0.00 H +ATOM 187 CA SER 11 32.570 17.839 35.182 1.00 0.00 C +ATOM 188 HA SER 11 32.446 16.755 35.225 1.00 0.00 H +ATOM 189 CB SER 11 33.539 18.260 36.295 1.00 0.00 C +ATOM 190 HB2 SER 11 33.665 19.345 36.284 1.00 0.00 H +ATOM 191 HB3 SER 11 33.107 17.977 37.258 1.00 0.00 H +ATOM 192 OG SER 11 34.809 17.642 36.180 1.00 0.00 O +ATOM 193 HG SER 11 35.427 18.251 35.756 1.00 0.00 H +ATOM 194 C SER 11 31.199 18.462 35.496 1.00 0.00 C +ATOM 195 O SER 11 30.406 17.878 36.230 1.00 0.00 O +ATOM 196 N CYS 12 30.923 19.656 34.964 1.00 0.00 N +ATOM 197 H CYS 12 31.599 20.053 34.332 1.00 0.00 H +ATOM 198 CA CYS 12 29.611 20.301 35.006 1.00 0.00 C +ATOM 199 HA CYS 12 29.036 19.906 35.847 1.00 0.00 H +ATOM 200 CB CYS 12 29.796 21.821 35.196 1.00 0.00 C +ATOM 201 HB2 CYS 12 30.330 22.228 34.334 1.00 0.00 H +ATOM 202 HB3 CYS 12 28.812 22.284 35.254 1.00 0.00 H +ATOM 203 SG CYS 12 30.722 22.206 36.721 1.00 0.00 S +ATOM 204 HG CYS 12 29.845 23.085 37.226 1.00 0.00 H +ATOM 205 C CYS 12 28.846 19.994 33.710 1.00 0.00 C +ATOM 206 O CYS 12 29.462 19.846 32.657 1.00 0.00 O +ATOM 207 N LYS 13 27.505 19.956 33.760 1.00 0.00 N +ATOM 208 H LYS 13 27.067 20.025 34.666 1.00 0.00 H +ATOM 209 CA LYS 13 26.638 19.689 32.587 1.00 0.00 C +ATOM 210 HA LYS 13 27.243 19.869 31.686 1.00 0.00 H +ATOM 211 CB LYS 13 26.243 18.193 32.591 1.00 0.00 C +ATOM 212 HB2 LYS 13 27.073 17.620 33.007 1.00 0.00 H +ATOM 213 HB3 LYS 13 25.379 18.062 33.237 1.00 0.00 H +ATOM 214 CG LYS 13 25.952 17.630 31.186 1.00 0.00 C +ATOM 215 HG2 LYS 13 25.065 18.101 30.760 1.00 0.00 H +ATOM 216 HG3 LYS 13 26.801 17.853 30.536 1.00 0.00 H +ATOM 217 CD LYS 13 25.755 16.105 31.210 1.00 0.00 C +ATOM 218 HD2 LYS 13 25.746 15.739 30.181 1.00 0.00 H +ATOM 219 HD3 LYS 13 26.602 15.645 31.726 1.00 0.00 H +ATOM 220 CE LYS 13 24.441 15.690 31.887 1.00 0.00 C +ATOM 221 HE2 LYS 13 24.310 16.264 32.808 1.00 0.00 H +ATOM 222 HE3 LYS 13 23.614 15.945 31.214 1.00 0.00 H +ATOM 223 NZ LYS 13 24.411 14.238 32.200 1.00 0.00 N +ATOM 224 HZ1 LYS 13 25.113 13.979 32.890 1.00 0.00 H +ATOM 225 HZ2 LYS 13 23.525 13.972 32.618 1.00 0.00 H +ATOM 226 HZ3 LYS 13 24.608 13.675 31.374 1.00 0.00 H +ATOM 227 C LYS 13 25.442 20.651 32.462 1.00 0.00 C +ATOM 228 O LYS 13 24.474 20.361 31.772 1.00 0.00 O +ATOM 229 N GLY 14 25.489 21.778 33.176 1.00 0.00 N +ATOM 230 H GLY 14 26.334 21.976 33.674 1.00 0.00 H +ATOM 231 CA GLY 14 24.400 22.746 33.252 1.00 0.00 C +ATOM 232 HA2 GLY 14 23.453 22.214 33.347 1.00 0.00 H +ATOM 233 HA3 GLY 14 24.522 23.365 34.139 1.00 0.00 H +ATOM 234 C GLY 14 24.283 23.694 32.040 1.00 0.00 C +ATOM 235 O GLY 14 25.205 23.839 31.229 1.00 0.00 O +ATOM 236 N VAL 15 23.147 24.397 31.969 1.00 0.00 N +ATOM 237 H VAL 15 22.465 24.249 32.703 1.00 0.00 H +ATOM 238 CA VAL 15 22.785 25.364 30.936 1.00 0.00 C +ATOM 239 HA VAL 15 23.676 25.622 30.371 1.00 0.00 H +ATOM 240 CB VAL 15 21.782 24.726 29.948 1.00 0.00 C +ATOM 241 HB VAL 15 22.261 23.828 29.523 1.00 0.00 H +ATOM 242 CG1 VAL 15 20.463 24.268 30.608 1.00 0.00 C +ATOM 243 HG11 VAL 15 19.940 25.116 31.035 1.00 0.00 H +ATOM 244 HG12 VAL 15 19.832 23.789 29.857 1.00 0.00 H +ATOM 245 HG13 VAL 15 20.672 23.536 31.384 1.00 0.00 H +ATOM 246 CG2 VAL 15 21.431 25.652 28.775 1.00 0.00 C +ATOM 247 HG21 VAL 15 22.344 26.000 28.296 1.00 0.00 H +ATOM 248 HG22 VAL 15 20.849 25.095 28.039 1.00 0.00 H +ATOM 249 HG23 VAL 15 20.845 26.497 29.121 1.00 0.00 H +ATOM 250 C VAL 15 22.255 26.634 31.587 1.00 0.00 C +ATOM 251 O VAL 15 21.634 26.597 32.639 1.00 0.00 O +HETATM 252 N HY1 16 22.503 27.793 30.973 1.00 0.00 N +HETATM 253 CA HY1 16 21.907 29.109 31.309 1.00 0.00 C +HETATM 254 C HY1 16 21.626 29.889 30.030 1.00 0.00 C +HETATM 255 O HY1 16 21.802 29.384 28.934 1.00 0.00 O +HETATM 256 CB HY1 16 22.834 29.825 32.330 1.00 0.00 C +HETATM 257 CG HY1 16 24.188 30.197 31.783 1.00 0.00 C +HETATM 258 CD2 HY1 16 24.521 31.376 31.162 1.00 0.00 C +HETATM 259 ND1 HY1 16 25.320 29.420 31.809 1.00 0.00 N +HETATM 260 CE1 HY1 16 26.313 30.124 31.227 1.00 0.00 C +HETATM 261 NE2 HY1 16 25.875 31.326 30.803 1.00 0.00 N +HETATM 262 H HY1 16 23.045 27.766 30.100 1.00 0.00 H +HETATM 263 HA HY1 16 20.949 28.916 31.823 1.00 0.00 H +HETATM 264 HB2 HY1 16 22.325 30.741 32.671 1.00 0.00 H +HETATM 265 HB3 HY1 16 22.960 29.204 33.207 1.00 0.00 H +HETATM 266 HD1 HY1 16 25.420 28.523 32.269 1.00 0.00 H +HETATM 267 HD2 HY1 16 23.853 32.210 30.983 1.00 0.00 H +HETATM 268 HE1 HY1 16 27.347 29.785 31.131 1.00 0.00 H +ATOM 269 N THR 17 21.180 31.133 30.157 1.00 0.00 N +ATOM 270 H THR 17 21.010 31.534 31.074 1.00 0.00 H +ATOM 271 CA THR 17 20.738 32.013 29.045 1.00 0.00 C +ATOM 272 HA THR 17 21.170 31.561 28.112 1.00 0.00 H +ATOM 273 CB THR 17 19.231 32.020 28.904 1.00 0.00 C +ATOM 274 HB THR 17 18.946 32.674 28.050 1.00 0.00 H +ATOM 275 CG2 THR 17 18.569 30.688 28.614 1.00 0.00 C +ATOM 276 HG21 THR 17 18.780 29.952 29.396 1.00 0.00 H +ATOM 277 HG22 THR 17 17.520 30.750 28.519 1.00 0.00 H +ATOM 278 HG23 THR 17 18.943 30.252 27.683 1.00 0.00 H +ATOM 279 OG1 THR 17 18.633 32.525 30.065 1.00 0.00 O +ATOM 280 HG1 THR 17 18.590 33.499 29.935 1.00 0.00 H +ATOM 281 C THR 17 21.325 33.419 29.080 1.00 0.00 C +ATOM 282 O THR 17 21.830 33.841 30.105 1.00 0.00 O +HETATM 283 N HY2 18 21.199 34.131 27.962 1.00 0.00 N +HETATM 284 CA HY2 18 21.498 35.567 27.862 1.00 0.00 C +HETATM 285 C HY2 18 20.379 36.266 27.075 1.00 0.00 C +HETATM 286 O HY2 18 20.033 35.823 25.984 1.00 0.00 O +HETATM 287 CB HY2 18 22.831 35.804 27.169 1.00 0.00 C +HETATM 288 CG HY2 18 24.029 35.337 27.962 1.00 0.00 C +HETATM 289 CD2 HY2 18 24.563 34.072 27.954 1.00 0.00 C +HETATM 290 ND1 HY2 18 24.707 36.053 28.927 1.00 0.00 N +HETATM 291 CE1 HY2 18 25.640 35.241 29.456 1.00 0.00 C +HETATM 292 NE2 HY2 18 25.591 34.016 28.902 1.00 0.00 N +HETATM 293 H HY2 18 20.786 33.675 27.148 1.00 0.00 H +HETATM 294 HA HY2 18 21.526 36.010 28.879 1.00 0.00 H +HETATM 295 HB2 HY2 18 22.841 35.309 26.183 1.00 0.00 H +HETATM 296 HB3 HY2 18 22.951 36.890 26.989 1.00 0.00 H +HETATM 297 HD1 HY2 18 24.548 37.015 29.189 1.00 0.00 H +HETATM 298 HD2 HY2 18 24.231 33.250 27.332 1.00 0.00 H +HETATM 299 HE1 HY2 18 26.337 35.534 30.234 1.00 0.00 H +ATOM 300 N GLU 19 19.854 37.365 27.613 1.00 0.00 N +ATOM 301 H GLU 19 20.181 37.657 28.514 1.00 0.00 H +ATOM 302 CA GLU 19 18.861 38.214 26.953 1.00 0.00 C +ATOM 303 HA GLU 19 18.118 37.567 26.510 1.00 0.00 H +ATOM 304 CB GLU 19 18.201 39.105 28.007 1.00 0.00 C +ATOM 305 HB2 GLU 19 17.888 38.498 28.852 1.00 0.00 H +ATOM 306 HB3 GLU 19 18.937 39.829 28.382 1.00 0.00 H +ATOM 307 CG GLU 19 16.971 39.870 27.494 1.00 0.00 C +ATOM 308 HG2 GLU 19 16.593 40.510 28.305 1.00 0.00 H +ATOM 309 HG3 GLU 19 17.267 40.530 26.669 1.00 0.00 H +ATOM 310 CD GLU 19 15.891 38.899 27.051 1.00 0.00 C +ATOM 311 OE1 GLU 19 15.841 38.587 25.838 1.00 0.00 O +ATOM 312 OE2 GLU 19 15.167 38.381 27.921 1.00 0.00 O +ATOM 313 C GLU 19 19.511 39.051 25.841 1.00 0.00 C +ATOM 314 O GLU 19 20.557 39.666 26.070 1.00 0.00 O +ATOM 315 N ALA 20 18.896 39.088 24.651 1.00 0.00 N +ATOM 316 H ALA 20 18.064 38.515 24.532 1.00 0.00 H +ATOM 317 CA ALA 20 19.271 39.983 23.548 1.00 0.00 C +ATOM 318 HA ALA 20 19.436 40.983 23.947 1.00 0.00 H +ATOM 319 CB ALA 20 20.578 39.484 22.920 1.00 0.00 C +ATOM 320 HB1 ALA 20 20.424 38.505 22.460 1.00 0.00 H +ATOM 321 HB2 ALA 20 20.915 40.186 22.161 1.00 0.00 H +ATOM 322 HB3 ALA 20 21.364 39.400 23.667 1.00 0.00 H +ATOM 323 C ALA 20 18.183 40.055 22.465 1.00 0.00 C +ATOM 324 O ALA 20 17.362 39.144 22.322 1.00 0.00 O +ATOM 325 N VAL 21 18.199 41.109 21.636 1.00 0.00 N +ATOM 326 H VAL 21 18.866 41.851 21.810 1.00 0.00 H +ATOM 327 CA VAL 21 17.428 41.159 20.367 1.00 0.00 C +ATOM 328 HA VAL 21 16.429 40.760 20.548 1.00 0.00 H +ATOM 329 CB VAL 21 17.259 42.610 19.852 1.00 0.00 C +ATOM 330 HB VAL 21 16.584 42.573 18.993 1.00 0.00 H +ATOM 331 CG1 VAL 21 16.606 43.510 20.912 1.00 0.00 C +ATOM 332 HG11 VAL 21 17.283 43.665 21.747 1.00 0.00 H +ATOM 333 HG12 VAL 21 16.368 44.469 20.461 1.00 0.00 H +ATOM 334 HG13 VAL 21 15.686 43.051 21.264 1.00 0.00 H +ATOM 335 CG2 VAL 21 18.574 43.260 19.386 1.00 0.00 C +ATOM 336 HG21 VAL 21 18.969 42.728 18.522 1.00 0.00 H +ATOM 337 HG22 VAL 21 18.382 44.286 19.080 1.00 0.00 H +ATOM 338 HG23 VAL 21 19.313 43.256 20.184 1.00 0.00 H +ATOM 339 C VAL 21 18.056 40.311 19.265 1.00 0.00 C +ATOM 340 O VAL 21 17.372 39.908 18.335 1.00 0.00 O +ATOM 341 N ASP 22 19.356 40.045 19.380 1.00 0.00 N +ATOM 342 H ASP 22 19.840 40.370 20.200 1.00 0.00 H +ATOM 343 CA ASP 22 20.203 39.414 18.367 1.00 0.00 C +ATOM 344 HA ASP 22 19.591 38.740 17.749 1.00 0.00 H +ATOM 345 CB ASP 22 20.808 40.497 17.447 1.00 0.00 C +ATOM 346 HB2 ASP 22 20.011 40.913 16.813 1.00 0.00 H +ATOM 347 HB3 ASP 22 21.216 41.310 18.079 1.00 0.00 H +ATOM 348 CG ASP 22 21.904 39.924 16.576 1.00 0.00 C +ATOM 349 OD1 ASP 22 23.061 40.332 16.776 1.00 0.00 O +ATOM 350 OD2 ASP 22 21.645 38.936 15.850 1.00 0.00 O +ATOM 351 C ASP 22 21.312 38.577 19.024 1.00 0.00 C +ATOM 352 O ASP 22 21.786 38.862 20.125 1.00 0.00 O +ATOM 353 N TRP 23 21.758 37.546 18.320 1.00 0.00 N +ATOM 354 H TRP 23 21.457 37.488 17.356 1.00 0.00 H +ATOM 355 CA TRP 23 22.777 36.618 18.774 1.00 0.00 C +ATOM 356 HA TRP 23 22.545 36.338 19.799 1.00 0.00 H +ATOM 357 CB TRP 23 22.654 35.377 17.900 1.00 0.00 C +ATOM 358 HB2 TRP 23 21.626 35.019 17.952 1.00 0.00 H +ATOM 359 HB3 TRP 23 22.841 35.665 16.862 1.00 0.00 H +ATOM 360 CG TRP 23 23.539 34.241 18.270 1.00 0.00 C +ATOM 361 CD1 TRP 23 24.465 33.691 17.461 1.00 0.00 C +ATOM 362 HD1 TRP 23 24.709 34.023 16.459 1.00 0.00 H +ATOM 363 NE1 TRP 23 25.028 32.616 18.105 1.00 0.00 N +ATOM 364 HE1 TRP 23 25.775 32.071 17.710 1.00 0.00 H +ATOM 365 CE2 TRP 23 24.471 32.396 19.344 1.00 0.00 C +ATOM 366 CZ2 TRP 23 24.645 31.401 20.312 1.00 0.00 C +ATOM 367 HZ2 TRP 23 25.308 30.566 20.135 1.00 0.00 H +ATOM 368 CH2 TRP 23 23.967 31.535 21.529 1.00 0.00 C +ATOM 369 HH2 TRP 23 24.088 30.820 22.312 1.00 0.00 H +ATOM 370 CZ3 TRP 23 23.194 32.666 21.795 1.00 0.00 C +ATOM 371 HZ3 TRP 23 22.789 32.798 22.788 1.00 0.00 H +ATOM 372 CE3 TRP 23 22.960 33.611 20.781 1.00 0.00 C +ATOM 373 HE3 TRP 23 22.305 34.442 20.972 1.00 0.00 H +ATOM 374 CD2 TRP 23 23.577 33.487 19.517 1.00 0.00 C +ATOM 375 C TRP 23 24.201 37.200 18.775 1.00 0.00 C +ATOM 376 O TRP 23 24.979 36.883 19.677 1.00 0.00 O +ATOM 377 N ALA 24 24.536 38.109 17.850 1.00 0.00 N +ATOM 378 H ALA 24 23.837 38.430 17.182 1.00 0.00 H +ATOM 379 CA ALA 24 25.826 38.805 17.840 1.00 0.00 C +ATOM 380 HA ALA 24 26.592 38.098 18.148 1.00 0.00 H +ATOM 381 CB ALA 24 26.163 39.206 16.400 1.00 0.00 C +ATOM 382 HB1 ALA 24 25.465 39.956 16.034 1.00 0.00 H +ATOM 383 HB2 ALA 24 27.173 39.612 16.353 1.00 0.00 H +ATOM 384 HB3 ALA 24 26.113 38.333 15.751 1.00 0.00 H +ATOM 385 C ALA 24 25.896 39.988 18.834 1.00 0.00 C +ATOM 386 O ALA 24 26.984 40.488 19.139 1.00 0.00 O +ATOM 387 N GLU 25 24.765 40.408 19.414 1.00 0.00 N +ATOM 388 H GLU 25 23.891 40.105 18.996 1.00 0.00 H +ATOM 389 CA GLU 25 24.725 41.188 20.666 1.00 0.00 C +ATOM 390 HA GLU 25 25.581 41.863 20.687 1.00 0.00 H +ATOM 391 CB GLU 25 23.451 42.045 20.730 1.00 0.00 C +ATOM 392 HB2 GLU 25 22.582 41.422 20.516 1.00 0.00 H +ATOM 393 HB3 GLU 25 23.342 42.425 21.740 1.00 0.00 H +ATOM 394 CG GLU 25 23.468 43.249 19.777 1.00 0.00 C +ATOM 395 HG2 GLU 25 23.540 42.880 18.748 1.00 0.00 H +ATOM 396 HG3 GLU 25 22.512 43.776 19.855 1.00 0.00 H +ATOM 397 CD GLU 25 24.619 44.199 20.080 1.00 0.00 C +ATOM 398 OE1 GLU 25 24.524 44.975 21.065 1.00 0.00 O +ATOM 399 OE2 GLU 25 25.648 44.107 19.362 1.00 0.00 O +ATOM 400 C GLU 25 24.874 40.287 21.906 1.00 0.00 C +ATOM 401 O GLU 25 25.688 40.579 22.784 1.00 0.00 O +ATOM 402 N ALA 26 24.201 39.125 21.956 1.00 0.00 N +ATOM 403 H ALA 26 23.518 38.919 21.232 1.00 0.00 H +ATOM 404 CA ALA 26 24.463 38.107 22.990 1.00 0.00 C +ATOM 405 HA ALA 26 24.293 38.571 23.963 1.00 0.00 H +ATOM 406 CB ALA 26 23.482 36.944 22.834 1.00 0.00 C +ATOM 407 HB1 ALA 26 23.667 36.421 21.901 1.00 0.00 H +ATOM 408 HB2 ALA 26 23.605 36.247 23.660 1.00 0.00 H +ATOM 409 HB3 ALA 26 22.458 37.314 22.841 1.00 0.00 H +ATOM 410 C ALA 26 25.930 37.609 22.973 1.00 0.00 C +ATOM 411 O ALA 26 26.453 37.180 24.015 1.00 0.00 O +ATOM 412 N GLU 27 26.614 37.710 21.825 1.00 0.00 N +ATOM 413 H GLU 27 26.089 37.904 20.980 1.00 0.00 H +ATOM 414 CA GLU 27 28.052 37.490 21.713 1.00 0.00 C +ATOM 415 HA GLU 27 28.210 36.457 21.940 1.00 0.00 H +ATOM 416 CB GLU 27 28.583 37.614 20.270 1.00 0.00 C +ATOM 417 HB2 GLU 27 27.924 37.058 19.610 1.00 0.00 H +ATOM 418 HB3 GLU 27 28.620 38.658 19.970 1.00 0.00 H +ATOM 419 CG GLU 27 29.988 36.996 20.197 1.00 0.00 C +ATOM 420 HG2 GLU 27 30.676 37.588 20.819 1.00 0.00 H +ATOM 421 HG3 GLU 27 29.956 35.983 20.634 1.00 0.00 H +ATOM 422 CD GLU 27 30.513 36.934 18.769 1.00 0.00 C +ATOM 423 OE1 GLU 27 30.943 38.000 18.278 1.00 0.00 O +ATOM 424 OE2 GLU 27 30.501 35.827 18.191 1.00 0.00 O +ATOM 425 C GLU 27 28.828 38.374 22.706 1.00 0.00 C +ATOM 426 O GLU 27 29.568 37.849 23.548 1.00 0.00 O +ATOM 427 N LYS 28 28.541 39.682 22.661 1.00 0.00 N +ATOM 428 H LYS 28 27.831 39.957 21.987 1.00 0.00 H +ATOM 429 CA LYS 28 29.121 40.758 23.481 1.00 0.00 C +ATOM 430 HA LYS 28 30.206 40.658 23.479 1.00 0.00 H +ATOM 431 CB LYS 28 28.761 42.131 22.873 1.00 0.00 C +ATOM 432 HB2 LYS 28 27.685 42.299 22.951 1.00 0.00 H +ATOM 433 HB3 LYS 28 29.264 42.909 23.451 1.00 0.00 H +ATOM 434 CG LYS 28 29.172 42.274 21.396 1.00 0.00 C +ATOM 435 HG2 LYS 28 30.244 42.100 21.301 1.00 0.00 H +ATOM 436 HG3 LYS 28 28.646 41.528 20.802 1.00 0.00 H +ATOM 437 CD LYS 28 28.833 43.668 20.845 1.00 0.00 C +ATOM 438 HD2 LYS 28 27.793 43.910 21.048 1.00 0.00 H +ATOM 439 HD3 LYS 28 29.453 44.406 21.356 1.00 0.00 H +ATOM 440 CE LYS 28 29.082 43.754 19.331 1.00 0.00 C +ATOM 441 HE2 LYS 28 29.159 44.812 19.054 1.00 0.00 H +ATOM 442 HE3 LYS 28 30.045 43.295 19.106 1.00 0.00 H +ATOM 443 NZ LYS 28 27.999 43.108 18.548 1.00 0.00 N +ATOM 444 HZ1 LYS 28 27.111 43.575 18.756 1.00 0.00 H +ATOM 445 HZ2 LYS 28 28.148 43.172 17.552 1.00 0.00 H +ATOM 446 HZ3 LYS 28 27.858 42.139 18.817 1.00 0.00 H +ATOM 447 C LYS 28 28.671 40.699 24.942 1.00 0.00 C +ATOM 448 O LYS 28 29.516 40.726 25.833 1.00 0.00 O +ATOM 449 N PHE 29 27.376 40.527 25.225 1.00 0.00 N +ATOM 450 H PHE 29 26.709 40.552 24.455 1.00 0.00 H +ATOM 451 CA PHE 29 26.873 40.474 26.615 1.00 0.00 C +ATOM 452 HA PHE 29 27.188 41.382 27.129 1.00 0.00 H +ATOM 453 CB PHE 29 25.335 40.437 26.615 1.00 0.00 C +ATOM 454 HB2 PHE 29 25.018 39.493 26.172 1.00 0.00 H +ATOM 455 HB3 PHE 29 24.990 40.451 27.649 1.00 0.00 H +ATOM 456 CG PHE 29 24.643 41.578 25.884 1.00 0.00 C +ATOM 457 CD1 PHE 29 23.461 41.323 25.164 1.00 0.00 C +ATOM 458 HD1 PHE 29 23.037 40.333 25.146 1.00 0.00 H +ATOM 459 CE1 PHE 29 22.822 42.359 24.462 1.00 0.00 C +ATOM 460 HE1 PHE 29 21.922 42.155 23.902 1.00 0.00 H +ATOM 461 CZ PHE 29 23.361 43.658 24.479 1.00 0.00 C +ATOM 462 HZ PHE 29 22.885 44.450 23.917 1.00 0.00 H +ATOM 463 CE2 PHE 29 24.520 43.928 25.225 1.00 0.00 C +ATOM 464 HE2 PHE 29 24.924 44.927 25.252 1.00 0.00 H +ATOM 465 CD2 PHE 29 25.155 42.893 25.932 1.00 0.00 C +ATOM 466 HD2 PHE 29 26.038 43.124 26.504 1.00 0.00 H +ATOM 467 C PHE 29 27.437 39.300 27.430 1.00 0.00 C +ATOM 468 O PHE 29 27.532 39.370 28.654 1.00 0.00 O +ATOM 469 N THR 30 27.865 38.222 26.770 1.00 0.00 N +ATOM 470 H THR 30 27.724 38.182 25.766 1.00 0.00 H +ATOM 471 CA THR 30 28.618 37.144 27.427 1.00 0.00 C +ATOM 472 HA THR 30 28.163 36.900 28.387 1.00 0.00 H +ATOM 473 CB THR 30 28.621 35.900 26.536 1.00 0.00 C +ATOM 474 HB THR 30 29.132 36.191 25.639 1.00 0.00 H +ATOM 475 CG2 THR 30 29.346 34.706 27.138 1.00 0.00 C +ATOM 476 HG21 THR 30 28.984 34.522 28.133 1.00 0.00 H +ATOM 477 HG22 THR 30 29.193 33.814 26.546 1.00 0.00 H +ATOM 478 HG23 THR 30 30.428 34.887 27.191 1.00 0.00 H +ATOM 479 OG1 THR 30 27.299 35.471 26.245 1.00 0.00 O +ATOM 480 HG1 THR 30 26.888 36.131 25.658 1.00 0.00 H +ATOM 481 C THR 30 30.081 37.537 27.695 1.00 0.00 C +ATOM 482 O THR 30 30.624 37.146 28.731 1.00 0.00 O +ATOM 483 N LYS 31 30.720 38.306 26.804 1.00 0.00 N +ATOM 484 H LYS 31 30.198 38.651 26.014 1.00 0.00 H +ATOM 485 CA LYS 31 32.070 38.835 27.005 1.00 0.00 C +ATOM 486 HA LYS 31 32.733 38.032 27.315 1.00 0.00 H +ATOM 487 CB LYS 31 32.647 39.415 25.683 1.00 0.00 C +ATOM 488 HB2 LYS 31 31.948 40.110 25.246 1.00 0.00 H +ATOM 489 HB3 LYS 31 33.566 39.953 25.914 1.00 0.00 H +ATOM 490 CG LYS 31 32.996 38.312 24.666 1.00 0.00 C +ATOM 491 HG2 LYS 31 33.730 37.640 25.106 1.00 0.00 H +ATOM 492 HG3 LYS 31 32.107 37.731 24.423 1.00 0.00 H +ATOM 493 CD LYS 31 33.567 38.923 23.384 1.00 0.00 C +ATOM 494 HD2 LYS 31 32.778 39.479 22.879 1.00 0.00 H +ATOM 495 HD3 LYS 31 34.355 39.629 23.638 1.00 0.00 H +ATOM 496 CE LYS 31 34.151 37.892 22.391 1.00 0.00 C +ATOM 497 HE2 LYS 31 33.409 37.129 22.159 1.00 0.00 H +ATOM 498 HE3 LYS 31 34.379 38.403 21.457 1.00 0.00 H +ATOM 499 NZ LYS 31 35.390 37.255 22.898 1.00 0.00 N +ATOM 500 HZ1 LYS 31 35.201 36.470 23.500 1.00 0.00 H +ATOM 501 HZ2 LYS 31 35.932 36.859 22.126 1.00 0.00 H +ATOM 502 HZ3 LYS 31 35.985 37.896 23.428 1.00 0.00 H +ATOM 503 C LYS 31 32.129 39.879 28.130 1.00 0.00 C +ATOM 504 O LYS 31 33.139 39.914 28.834 1.00 0.00 O +ATOM 505 N ALA 32 31.036 40.609 28.382 1.00 0.00 N +ATOM 506 H ALA 32 30.297 40.611 27.690 1.00 0.00 H +ATOM 507 CA ALA 32 30.856 41.387 29.608 1.00 0.00 C +ATOM 508 HA ALA 32 31.679 42.095 29.692 1.00 0.00 H +ATOM 509 CB ALA 32 29.558 42.200 29.527 1.00 0.00 C +ATOM 510 HB1 ALA 32 28.691 41.544 29.473 1.00 0.00 H +ATOM 511 HB2 ALA 32 29.463 42.823 30.421 1.00 0.00 H +ATOM 512 HB3 ALA 32 29.578 42.846 28.650 1.00 0.00 H +ATOM 513 C ALA 32 30.927 40.489 30.858 1.00 0.00 C +ATOM 514 O ALA 32 31.924 40.546 31.574 1.00 0.00 O +ATOM 515 N LYN 33 29.996 39.531 31.025 1.00 0.00 N +ATOM 516 H LYN 33 29.190 39.542 30.415 1.00 0.00 H +ATOM 517 CA LYN 33 30.009 38.573 32.151 1.00 0.00 C +ATOM 518 HA LYN 33 29.910 39.148 33.071 1.00 0.00 H +ATOM 519 CB LYN 33 28.774 37.649 32.038 1.00 0.00 C +ATOM 520 HB2 LYN 33 27.879 38.255 31.901 1.00 0.00 H +ATOM 521 HB3 LYN 33 28.890 37.020 31.159 1.00 0.00 H +ATOM 522 CG LYN 33 28.554 36.757 33.275 1.00 0.00 C +ATOM 523 HG2 LYN 33 29.439 36.152 33.441 1.00 0.00 H +ATOM 524 HG3 LYN 33 28.421 37.387 34.152 1.00 0.00 H +ATOM 525 CD LYN 33 27.373 35.776 33.182 1.00 0.00 C +ATOM 526 HD2 LYN 33 27.409 35.248 32.236 1.00 0.00 H +ATOM 527 HD3 LYN 33 27.480 35.041 33.977 1.00 0.00 H +ATOM 528 CE LYN 33 26.005 36.448 33.325 1.00 0.00 C +ATOM 529 HE2 LYN 33 26.005 37.059 34.229 1.00 0.00 H +ATOM 530 HE3 LYN 33 25.827 37.088 32.462 1.00 0.00 H +ATOM 531 NZ LYN 33 24.926 35.449 33.419 1.00 0.00 N +ATOM 532 HZ2 LYN 33 24.037 35.924 33.515 1.00 0.00 H +ATOM 533 HZ3 LYN 33 24.894 34.884 32.590 1.00 0.00 H +ATOM 534 C LYN 33 31.326 37.768 32.264 1.00 0.00 C +ATOM 535 O LYN 33 31.650 37.212 33.313 1.00 0.00 O +ATOM 536 N ALA 34 32.102 37.650 31.186 1.00 0.00 N +ATOM 537 H ALA 34 31.786 38.093 30.336 1.00 0.00 H +ATOM 538 CA ALA 34 33.415 37.025 31.197 1.00 0.00 C +ATOM 539 HA ALA 34 33.379 36.199 31.903 1.00 0.00 H +ATOM 540 CB ALA 34 33.660 36.419 29.822 1.00 0.00 C +ATOM 541 HB1 ALA 34 33.759 37.224 29.100 1.00 0.00 H +ATOM 542 HB2 ALA 34 34.569 35.830 29.857 1.00 0.00 H +ATOM 543 HB3 ALA 34 32.833 35.773 29.533 1.00 0.00 H +ATOM 544 C ALA 34 34.561 37.964 31.644 1.00 0.00 C +ATOM 545 O ALA 34 35.485 37.474 32.295 1.00 0.00 O +ATOM 546 N ASN 35 34.515 39.269 31.348 1.00 0.00 N +ATOM 547 H ASN 35 33.732 39.616 30.804 1.00 0.00 H +ATOM 548 CA ASN 35 35.446 40.284 31.873 1.00 0.00 C +ATOM 549 HA ASN 35 36.435 39.832 31.976 1.00 0.00 H +ATOM 550 CB ASN 35 35.582 41.433 30.859 1.00 0.00 C +ATOM 551 HB2 ASN 35 34.603 41.733 30.493 1.00 0.00 H +ATOM 552 HB3 ASN 35 36.033 42.295 31.352 1.00 0.00 H +ATOM 553 CG ASN 35 36.493 41.030 29.719 1.00 0.00 C +ATOM 554 OD1 ASN 35 37.698 40.971 29.868 1.00 0.00 O +ATOM 555 ND2 ASN 35 35.956 40.693 28.578 1.00 0.00 N +ATOM 556 HD21 ASN 35 36.601 40.354 27.860 1.00 0.00 H +ATOM 557 HD22 ASN 35 34.954 40.631 28.488 1.00 0.00 H +ATOM 558 C ASN 35 35.078 40.777 33.276 1.00 0.00 C +ATOM 559 O ASN 35 35.967 41.126 34.052 1.00 0.00 O +ATOM 560 N ASP 36 33.802 40.685 33.673 1.00 0.00 N +ATOM 561 H ASP 36 33.078 40.563 32.970 1.00 0.00 H +ATOM 562 CA ASP 36 33.357 40.843 35.067 1.00 0.00 C +ATOM 563 HA ASP 36 33.630 41.847 35.410 1.00 0.00 H +ATOM 564 CB ASP 36 31.839 40.739 35.150 1.00 0.00 C +ATOM 565 HB2 ASP 36 31.563 39.728 34.867 1.00 0.00 H +ATOM 566 HB3 ASP 36 31.542 40.818 36.195 1.00 0.00 H +ATOM 567 CG ASP 36 30.985 41.711 34.324 1.00 0.00 C +ATOM 568 OD1 ASP 36 31.462 42.836 34.035 1.00 0.00 O +ATOM 569 OD2 ASP 36 29.825 41.345 33.996 1.00 0.00 O +ATOM 570 C ASP 36 34.066 39.828 35.995 1.00 0.00 C +ATOM 571 O ASP 36 34.498 40.176 37.098 1.00 0.00 O +ATOM 572 N LYS 37 34.277 38.580 35.528 1.00 0.00 N +ATOM 573 H LYS 37 33.863 38.350 34.636 1.00 0.00 H +ATOM 574 CA LYS 37 35.150 37.580 36.183 1.00 0.00 C +ATOM 575 HA LYS 37 35.130 37.789 37.253 1.00 0.00 H +ATOM 576 CB LYS 37 34.565 36.152 36.027 1.00 0.00 C +ATOM 577 HB2 LYS 37 35.078 35.490 36.724 1.00 0.00 H +ATOM 578 HB3 LYS 37 33.508 36.149 36.288 1.00 0.00 H +ATOM 579 CG LYS 37 34.759 35.601 34.608 1.00 0.00 C +ATOM 580 HG2 LYS 37 34.139 36.177 33.928 1.00 0.00 H +ATOM 581 HG3 LYS 37 35.798 35.735 34.318 1.00 0.00 H +ATOM 582 CD LYS 37 34.436 34.122 34.422 1.00 0.00 C +ATOM 583 HD2 LYS 37 34.578 33.610 35.372 1.00 0.00 H +ATOM 584 HD3 LYS 37 33.395 34.014 34.154 1.00 0.00 H +ATOM 585 CE LYS 37 35.328 33.472 33.330 1.00 0.00 C +ATOM 586 HE2 LYS 37 36.315 33.292 33.762 1.00 0.00 H +ATOM 587 HE3 LYS 37 34.983 32.454 33.128 1.00 0.00 H +ATOM 588 NZ LYS 37 35.470 34.267 32.074 1.00 0.00 N +ATOM 589 HZ1 LYS 37 35.901 35.166 32.277 1.00 0.00 H +ATOM 590 HZ2 LYS 37 36.068 33.816 31.390 1.00 0.00 H +ATOM 591 HZ3 LYS 37 34.567 34.433 31.674 1.00 0.00 H +ATOM 592 C LYS 37 36.641 37.666 35.797 1.00 0.00 C +ATOM 593 O LYS 37 37.388 36.717 36.024 1.00 0.00 O +ATOM 594 N GLY 38 37.093 38.753 35.163 1.00 0.00 N +ATOM 595 H GLY 38 36.427 39.500 35.014 1.00 0.00 H +ATOM 596 CA GLY 38 38.497 39.081 34.900 1.00 0.00 C +ATOM 597 HA2 GLY 38 38.673 40.099 35.250 1.00 0.00 H +ATOM 598 HA3 GLY 38 39.136 38.422 35.493 1.00 0.00 H +ATOM 599 C GLY 38 38.992 39.003 33.451 1.00 0.00 C +ATOM 600 O GLY 38 39.908 39.749 33.113 1.00 0.00 O +ATOM 601 N ARG 39 38.439 38.123 32.592 1.00 0.00 N +ATOM 602 H ARG 39 37.620 37.630 32.924 1.00 0.00 H +ATOM 603 CA ARG 39 38.850 37.918 31.183 1.00 0.00 C +ATOM 604 HA ARG 39 38.819 38.901 30.702 1.00 0.00 H +ATOM 605 CB ARG 39 40.315 37.408 31.055 1.00 0.00 C +ATOM 606 HB2 ARG 39 40.570 37.429 29.993 1.00 0.00 H +ATOM 607 HB3 ARG 39 40.992 38.115 31.533 1.00 0.00 H +ATOM 608 CG ARG 39 40.642 35.990 31.575 1.00 0.00 C +ATOM 609 HG2 ARG 39 40.011 35.274 31.049 1.00 0.00 H +ATOM 610 HG3 ARG 39 41.676 35.760 31.313 1.00 0.00 H +ATOM 611 CD ARG 39 40.486 35.825 33.102 1.00 0.00 C +ATOM 612 HD2 ARG 39 41.184 36.504 33.600 1.00 0.00 H +ATOM 613 HD3 ARG 39 39.476 36.100 33.403 1.00 0.00 H +ATOM 614 NE ARG 39 40.739 34.451 33.582 1.00 0.00 N +ATOM 615 HE ARG 39 41.505 34.326 34.228 1.00 0.00 H +ATOM 616 CZ ARG 39 39.961 33.401 33.419 1.00 0.00 C +ATOM 617 NH1 ARG 39 38.912 33.425 32.650 1.00 0.00 N +ATOM 618 HH11 ARG 39 38.753 34.219 32.059 1.00 0.00 H +ATOM 619 HH12 ARG 39 38.395 32.553 32.564 1.00 0.00 H +ATOM 620 NH2 ARG 39 40.208 32.279 34.029 1.00 0.00 N +ATOM 621 HH21 ARG 39 41.021 32.194 34.618 1.00 0.00 H +ATOM 622 HH22 ARG 39 39.586 31.492 33.869 1.00 0.00 H +ATOM 623 C ARG 39 37.906 37.010 30.382 1.00 0.00 C +ATOM 624 O ARG 39 37.450 35.970 30.889 1.00 0.00 O +ATOM 625 N ASP 40 37.643 37.373 29.123 1.00 0.00 N +ATOM 626 H ASP 40 38.049 38.236 28.768 1.00 0.00 H +ATOM 627 CA ASP 40 36.914 36.559 28.147 1.00 0.00 C +ATOM 628 HA ASP 40 36.250 35.909 28.701 1.00 0.00 H +ATOM 629 CB ASP 40 36.024 37.438 27.250 1.00 0.00 C +ATOM 630 HB2 ASP 40 35.359 36.797 26.672 1.00 0.00 H +ATOM 631 HB3 ASP 40 35.373 38.034 27.885 1.00 0.00 H +ATOM 632 CG ASP 40 36.757 38.385 26.309 1.00 0.00 C +ATOM 633 OD1 ASP 40 37.565 39.185 26.826 1.00 0.00 O +ATOM 634 OD2 ASP 40 36.426 38.367 25.105 1.00 0.00 O +ATOM 635 C ASP 40 37.774 35.579 27.330 1.00 0.00 C +ATOM 636 O ASP 40 38.983 35.481 27.496 1.00 0.00 O +ATOM 637 N GLY 41 37.089 34.803 26.488 1.00 0.00 N +ATOM 638 H GLY 41 36.101 34.991 26.421 1.00 0.00 H +ATOM 639 CA GLY 41 37.619 33.880 25.478 1.00 0.00 C +ATOM 640 HA2 GLY 41 38.494 34.335 24.987 1.00 0.00 H +ATOM 641 HA3 GLY 41 37.896 32.927 25.956 1.00 0.00 H +ATOM 642 C GLY 41 36.528 33.613 24.424 1.00 0.00 C +ATOM 643 O GLY 41 35.445 34.207 24.475 1.00 0.00 O +ATOM 644 N GLU 42 36.788 32.709 23.482 1.00 0.00 N +ATOM 645 H GLU 42 37.670 32.237 23.523 1.00 0.00 H +ATOM 646 CA GLU 42 35.905 32.412 22.347 1.00 0.00 C +ATOM 647 HA GLU 42 35.125 33.167 22.344 1.00 0.00 H +ATOM 648 CB GLU 42 36.664 32.525 21.011 1.00 0.00 C +ATOM 649 HB2 GLU 42 37.366 31.695 20.944 1.00 0.00 H +ATOM 650 HB3 GLU 42 35.944 32.414 20.201 1.00 0.00 H +ATOM 651 CG GLU 42 37.443 33.834 20.782 1.00 0.00 C +ATOM 652 HG2 GLU 42 38.311 33.827 21.446 1.00 0.00 H +ATOM 653 HG3 GLU 42 37.826 33.837 19.759 1.00 0.00 H +ATOM 654 CD GLU 42 36.645 35.123 21.033 1.00 0.00 C +ATOM 655 OE1 GLU 42 35.399 35.099 21.148 1.00 0.00 O +ATOM 656 OE2 GLU 42 37.273 36.191 21.218 1.00 0.00 O +ATOM 657 C GLU 42 35.155 31.079 22.449 1.00 0.00 C +ATOM 658 O GLU 42 35.545 30.177 23.201 1.00 0.00 O +ATOM 659 N ARG 43 34.045 30.983 21.696 1.00 0.00 N +ATOM 660 H ARG 43 33.859 31.729 21.028 1.00 0.00 H +ATOM 661 CA ARG 43 33.015 29.940 21.796 1.00 0.00 C +ATOM 662 HA ARG 43 33.495 28.981 22.001 1.00 0.00 H +ATOM 663 CB ARG 43 32.087 30.275 22.974 1.00 0.00 C +ATOM 664 HB2 ARG 43 31.317 29.508 23.057 1.00 0.00 H +ATOM 665 HB3 ARG 43 32.669 30.262 23.897 1.00 0.00 H +ATOM 666 CG ARG 43 31.391 31.637 22.844 1.00 0.00 C +ATOM 667 HG2 ARG 43 32.110 32.434 22.660 1.00 0.00 H +ATOM 668 HG3 ARG 43 30.694 31.612 22.010 1.00 0.00 H +ATOM 669 CD ARG 43 30.634 31.967 24.121 1.00 0.00 C +ATOM 670 HD2 ARG 43 30.147 31.059 24.480 1.00 0.00 H +ATOM 671 HD3 ARG 43 31.339 32.284 24.887 1.00 0.00 H +ATOM 672 NE ARG 43 29.619 32.996 23.893 1.00 0.00 N +ATOM 673 HE ARG 43 28.685 32.661 23.712 1.00 0.00 H +ATOM 674 CZ ARG 43 29.781 34.291 23.756 1.00 0.00 C +ATOM 675 NH1 ARG 43 30.924 34.915 23.764 1.00 0.00 N +ATOM 676 HH11 ARG 43 31.776 34.380 23.737 1.00 0.00 H +ATOM 677 HH12 ARG 43 30.928 35.903 23.564 1.00 0.00 H +ATOM 678 NH2 ARG 43 28.724 35.010 23.622 1.00 0.00 N +ATOM 679 HH21 ARG 43 27.818 34.575 23.525 1.00 0.00 H +ATOM 680 HH22 ARG 43 28.806 36.015 23.611 1.00 0.00 H +ATOM 681 C ARG 43 32.226 29.788 20.491 1.00 0.00 C +ATOM 682 O ARG 43 32.016 30.775 19.792 1.00 0.00 O +ATOM 683 N THR 44 31.769 28.574 20.199 1.00 0.00 N +ATOM 684 H THR 44 31.893 27.856 20.903 1.00 0.00 H +ATOM 685 CA THR 44 31.059 28.197 18.965 1.00 0.00 C +ATOM 686 HA THR 44 31.367 28.878 18.171 1.00 0.00 H +ATOM 687 CB THR 44 31.491 26.780 18.541 1.00 0.00 C +ATOM 688 HB THR 44 31.284 26.073 19.347 1.00 0.00 H +ATOM 689 CG2 THR 44 30.877 26.255 17.242 1.00 0.00 C +ATOM 690 HG21 THR 44 30.980 26.998 16.449 1.00 0.00 H +ATOM 691 HG22 THR 44 31.383 25.337 16.935 1.00 0.00 H +ATOM 692 HG23 THR 44 29.824 26.016 17.397 1.00 0.00 H +ATOM 693 OG1 THR 44 32.880 26.818 18.313 1.00 0.00 O +ATOM 694 HG1 THR 44 33.143 26.013 17.857 1.00 0.00 H +ATOM 695 C THR 44 29.537 28.364 19.112 1.00 0.00 C +ATOM 696 O THR 44 29.024 28.513 20.225 1.00 0.00 O +ATOM 697 N ILE 45 28.813 28.404 17.984 1.00 0.00 N +ATOM 698 H ILE 45 29.281 28.200 17.114 1.00 0.00 H +ATOM 699 CA ILE 45 27.405 28.808 17.888 1.00 0.00 C +ATOM 700 HA ILE 45 26.992 28.796 18.898 1.00 0.00 H +ATOM 701 CB ILE 45 27.300 30.258 17.349 1.00 0.00 C +ATOM 702 HB ILE 45 26.234 30.494 17.386 1.00 0.00 H +ATOM 703 CG2 ILE 45 28.017 31.233 18.293 1.00 0.00 C +ATOM 704 HG21 ILE 45 29.094 31.074 18.238 1.00 0.00 H +ATOM 705 HG22 ILE 45 27.806 32.268 18.025 1.00 0.00 H +ATOM 706 HG23 ILE 45 27.671 31.042 19.300 1.00 0.00 H +ATOM 707 CG1 ILE 45 27.759 30.525 15.895 1.00 0.00 C +ATOM 708 HG12 ILE 45 28.047 31.568 15.812 1.00 0.00 H +ATOM 709 HG13 ILE 45 28.654 29.949 15.680 1.00 0.00 H +ATOM 710 CD1 ILE 45 26.691 30.279 14.822 1.00 0.00 C +ATOM 711 HD11 ILE 45 25.759 30.773 15.114 1.00 0.00 H +ATOM 712 HD12 ILE 45 27.018 30.695 13.866 1.00 0.00 H +ATOM 713 HD13 ILE 45 26.512 29.212 14.695 1.00 0.00 H +ATOM 714 C ILE 45 26.527 27.858 17.072 1.00 0.00 C +ATOM 715 O ILE 45 27.017 27.114 16.226 1.00 0.00 O +ATOM 716 N ASP 46 25.216 27.950 17.304 1.00 0.00 N +ATOM 717 H ASP 46 24.910 28.475 18.111 1.00 0.00 H +ATOM 718 CA ASP 46 24.153 27.357 16.483 1.00 0.00 C +ATOM 719 HA ASP 46 24.474 27.365 15.437 1.00 0.00 H +ATOM 720 CB ASP 46 23.935 25.904 16.910 1.00 0.00 C +ATOM 721 HB2 ASP 46 24.821 25.306 16.686 1.00 0.00 H +ATOM 722 HB3 ASP 46 23.790 25.882 17.995 1.00 0.00 H +ATOM 723 CG ASP 46 22.728 25.281 16.224 1.00 0.00 C +ATOM 724 OD1 ASP 46 21.961 24.603 16.947 1.00 0.00 O +ATOM 725 OD2 ASP 46 22.511 25.554 15.040 1.00 0.00 O +ATOM 726 C ASP 46 22.834 28.159 16.594 1.00 0.00 C +ATOM 727 O ASP 46 22.399 28.488 17.698 1.00 0.00 O +ATOM 728 N ASP 47 22.184 28.437 15.458 1.00 0.00 N +ATOM 729 H ASP 47 22.559 28.038 14.608 1.00 0.00 H +ATOM 730 CA ASP 47 20.840 29.039 15.391 1.00 0.00 C +ATOM 731 HA ASP 47 20.745 29.781 16.186 1.00 0.00 H +ATOM 732 CB ASP 47 20.651 29.780 14.049 1.00 0.00 C +ATOM 733 HB2 ASP 47 21.371 30.599 13.994 1.00 0.00 H +ATOM 734 HB3 ASP 47 20.869 29.092 13.229 1.00 0.00 H +ATOM 735 CG ASP 47 19.236 30.338 13.866 1.00 0.00 C +ATOM 736 OD1 ASP 47 18.366 29.642 13.294 1.00 0.00 O +ATOM 737 OD2 ASP 47 18.910 31.439 14.376 1.00 0.00 O +ATOM 738 C ASP 47 19.712 28.006 15.601 1.00 0.00 C +ATOM 739 O ASP 47 18.680 28.354 16.177 1.00 0.00 O +ATOM 740 N ALA 48 19.891 26.748 15.189 1.00 0.00 N +ATOM 741 H ALA 48 20.815 26.444 14.883 1.00 0.00 H +ATOM 742 CA ALA 48 18.830 25.738 15.223 1.00 0.00 C +ATOM 743 HA ALA 48 17.947 26.136 14.721 1.00 0.00 H +ATOM 744 CB ALA 48 19.314 24.506 14.451 1.00 0.00 C +ATOM 745 HB1 ALA 48 20.173 24.065 14.961 1.00 0.00 H +ATOM 746 HB2 ALA 48 18.518 23.764 14.391 1.00 0.00 H +ATOM 747 HB3 ALA 48 19.617 24.791 13.444 1.00 0.00 H +ATOM 748 C ALA 48 18.413 25.386 16.664 1.00 0.00 C +ATOM 749 O ALA 48 17.226 25.293 16.965 1.00 0.00 O +ATOM 750 N THR 49 19.383 25.251 17.569 1.00 0.00 N +ATOM 751 H THR 49 20.338 25.173 17.219 1.00 0.00 H +ATOM 752 CA THR 49 19.192 25.102 19.021 1.00 0.00 C +ATOM 753 HA THR 49 18.164 24.774 19.188 1.00 0.00 H +ATOM 754 CB THR 49 20.126 24.025 19.584 1.00 0.00 C +ATOM 755 HB THR 49 19.898 23.910 20.645 1.00 0.00 H +ATOM 756 CG2 THR 49 19.960 22.658 18.926 1.00 0.00 C +ATOM 757 HG21 THR 49 20.258 22.695 17.880 1.00 0.00 H +ATOM 758 HG22 THR 49 20.593 21.942 19.444 1.00 0.00 H +ATOM 759 HG23 THR 49 18.922 22.334 18.992 1.00 0.00 H +ATOM 760 OG1 THR 49 21.483 24.396 19.468 1.00 0.00 O +ATOM 761 HG1 THR 49 21.694 24.365 18.501 1.00 0.00 H +ATOM 762 C THR 49 19.397 26.401 19.808 1.00 0.00 C +ATOM 763 O THR 49 19.269 26.396 21.031 1.00 0.00 O +ATOM 764 N LYS 50 19.705 27.522 19.134 1.00 0.00 N +ATOM 765 H LYS 50 19.806 27.421 18.131 1.00 0.00 H +ATOM 766 CA LYS 50 19.900 28.882 19.702 1.00 0.00 C +ATOM 767 HA LYS 50 20.324 29.504 18.914 1.00 0.00 H +ATOM 768 CB LYS 50 18.514 29.466 20.090 1.00 0.00 C +ATOM 769 HB2 LYS 50 18.082 28.812 20.847 1.00 0.00 H +ATOM 770 HB3 LYS 50 18.662 30.440 20.569 1.00 0.00 H +ATOM 771 CG LYS 50 17.483 29.640 18.962 1.00 0.00 C +ATOM 772 HG2 LYS 50 17.406 28.724 18.377 1.00 0.00 H +ATOM 773 HG3 LYS 50 16.511 29.807 19.436 1.00 0.00 H +ATOM 774 CD LYS 50 17.771 30.842 18.048 1.00 0.00 C +ATOM 775 HD2 LYS 50 17.847 31.729 18.684 1.00 0.00 H +ATOM 776 HD3 LYS 50 18.722 30.709 17.525 1.00 0.00 H +ATOM 777 CE LYS 50 16.636 31.087 17.042 1.00 0.00 C +ATOM 778 HE2 LYS 50 15.680 30.851 17.523 1.00 0.00 H +ATOM 779 HE3 LYS 50 16.620 32.152 16.793 1.00 0.00 H +ATOM 780 NZ LYS 50 16.785 30.318 15.786 1.00 0.00 N +ATOM 781 HZ1 LYS 50 17.027 29.345 15.942 1.00 0.00 H +ATOM 782 HZ2 LYS 50 15.966 30.404 15.186 1.00 0.00 H +ATOM 783 HZ3 LYS 50 17.558 30.688 15.237 1.00 0.00 H +ATOM 784 C LYS 50 20.929 28.907 20.853 1.00 0.00 C +ATOM 785 O LYS 50 20.644 29.476 21.914 1.00 0.00 O +ATOM 786 N THR 51 22.073 28.246 20.666 1.00 0.00 N +ATOM 787 H THR 51 22.280 27.904 19.746 1.00 0.00 H +ATOM 788 CA THR 51 22.978 27.855 21.776 1.00 0.00 C +ATOM 789 HA THR 51 22.713 28.423 22.656 1.00 0.00 H +ATOM 790 CB THR 51 22.769 26.349 22.149 1.00 0.00 C +ATOM 791 HB THR 51 22.913 25.751 21.244 1.00 0.00 H +ATOM 792 CG2 THR 51 23.726 25.829 23.195 1.00 0.00 C +ATOM 793 HG21 THR 51 23.724 26.423 24.104 1.00 0.00 H +ATOM 794 HG22 THR 51 23.490 24.809 23.488 1.00 0.00 H +ATOM 795 HG23 THR 51 24.752 25.794 22.838 1.00 0.00 H +ATOM 796 OG1 THR 51 21.477 26.147 22.676 1.00 0.00 O +ATOM 797 HG1 THR 51 20.828 26.213 21.948 1.00 0.00 H +ATOM 798 C THR 51 24.498 28.160 21.552 1.00 0.00 C +ATOM 799 O THR 51 25.031 27.978 20.458 1.00 0.00 O +ATOM 800 N PHE 52 25.195 28.618 22.604 1.00 0.00 N +ATOM 801 H PHE 52 24.659 28.844 23.435 1.00 0.00 H +ATOM 802 CA PHE 52 26.648 28.754 22.682 1.00 0.00 C +ATOM 803 HA PHE 52 27.066 28.878 21.704 1.00 0.00 H +ATOM 804 CB PHE 52 27.049 29.989 23.564 1.00 0.00 C +ATOM 805 HB2 PHE 52 26.439 29.970 24.449 1.00 0.00 H +ATOM 806 HB3 PHE 52 28.080 29.863 23.877 1.00 0.00 H +ATOM 807 CG PHE 52 26.956 31.369 22.935 1.00 0.00 C +ATOM 808 CD1 PHE 52 26.137 32.360 23.496 1.00 0.00 C +ATOM 809 HD1 PHE 52 25.515 32.134 24.347 1.00 0.00 H +ATOM 810 CE1 PHE 52 26.022 33.613 22.875 1.00 0.00 C +ATOM 811 HE1 PHE 52 25.306 34.345 23.243 1.00 0.00 H +ATOM 812 CZ PHE 52 26.749 33.887 21.707 1.00 0.00 C +ATOM 813 HZ PHE 52 26.610 34.820 21.179 1.00 0.00 H +ATOM 814 CE2 PHE 52 27.660 32.942 21.218 1.00 0.00 C +ATOM 815 HE2 PHE 52 28.252 33.169 20.337 1.00 0.00 H +ATOM 816 CD2 PHE 52 27.757 31.680 21.826 1.00 0.00 C +ATOM 817 HD2 PHE 52 28.421 30.934 21.415 1.00 0.00 H +ATOM 818 C PHE 52 27.299 27.528 23.345 1.00 0.00 C +ATOM 819 O PHE 52 26.801 27.060 24.382 1.00 0.00 O +ATOM 820 N THR 53 28.455 27.080 22.828 1.00 0.00 N +ATOM 821 H THR 53 28.794 27.502 21.960 1.00 0.00 H +ATOM 822 CA THR 53 29.257 25.944 23.360 1.00 0.00 C +ATOM 823 HA THR 53 29.018 25.811 24.412 1.00 0.00 H +ATOM 824 CB THR 53 28.922 24.628 22.631 1.00 0.00 C +ATOM 825 HB THR 53 29.523 23.828 23.066 1.00 0.00 H +ATOM 826 CG2 THR 53 27.455 24.219 22.728 1.00 0.00 C +ATOM 827 HG21 THR 53 26.839 24.900 22.141 1.00 0.00 H +ATOM 828 HG22 THR 53 27.330 23.206 22.345 1.00 0.00 H +ATOM 829 HG23 THR 53 27.136 24.241 23.767 1.00 0.00 H +ATOM 830 OG1 THR 53 29.241 24.729 21.261 1.00 0.00 O +ATOM 831 HG1 THR 53 28.872 23.960 20.816 1.00 0.00 H +ATOM 832 C THR 53 30.775 26.169 23.265 1.00 0.00 C +ATOM 833 O THR 53 31.247 27.039 22.536 1.00 0.00 O +ATOM 834 N THR 54 31.550 25.363 23.995 1.00 0.00 N +ATOM 835 H THR 54 31.108 24.674 24.581 1.00 0.00 H +ATOM 836 CA THR 54 33.026 25.280 23.900 1.00 0.00 C +ATOM 837 HA THR 54 33.389 26.087 23.264 1.00 0.00 H +ATOM 838 CB THR 54 33.679 25.465 25.287 1.00 0.00 C +ATOM 839 HB THR 54 33.366 24.653 25.943 1.00 0.00 H +ATOM 840 CG2 THR 54 35.209 25.527 25.270 1.00 0.00 C +ATOM 841 HG21 THR 54 35.551 26.282 24.561 1.00 0.00 H +ATOM 842 HG22 THR 54 35.586 25.776 26.261 1.00 0.00 H +ATOM 843 HG23 THR 54 35.625 24.558 24.996 1.00 0.00 H +ATOM 844 OG1 THR 54 33.257 26.688 25.848 1.00 0.00 O +ATOM 845 HG1 THR 54 33.703 26.791 26.690 1.00 0.00 H +ATOM 846 C THR 54 33.453 23.948 23.240 1.00 0.00 C +ATOM 847 O THR 54 32.725 22.957 23.330 1.00 0.00 O +ATOM 848 N GLN 55 34.608 23.941 22.569 1.00 0.00 N +ATOM 849 H GLN 55 35.143 24.792 22.563 1.00 0.00 H +ATOM 850 CA GLN 55 35.230 22.769 21.928 1.00 0.00 C +ATOM 851 HA GLN 55 34.472 22.294 21.307 1.00 0.00 H +ATOM 852 CB GLN 55 36.356 23.273 20.997 1.00 0.00 C +ATOM 853 HB2 GLN 55 36.747 22.431 20.418 1.00 0.00 H +ATOM 854 HB3 GLN 55 35.915 23.976 20.284 1.00 0.00 H +ATOM 855 CG GLN 55 37.529 23.975 21.718 1.00 0.00 C +ATOM 856 HG2 GLN 55 37.135 24.635 22.490 1.00 0.00 H +ATOM 857 HG3 GLN 55 38.153 23.228 22.202 1.00 0.00 H +ATOM 858 CD GLN 55 38.400 24.813 20.772 1.00 0.00 C +ATOM 859 OE1 GLN 55 38.699 24.456 19.644 1.00 0.00 O +ATOM 860 NE2 GLN 55 38.838 25.984 21.186 1.00 0.00 N +ATOM 861 HE21 GLN 55 39.398 26.495 20.531 1.00 0.00 H +ATOM 862 HE22 GLN 55 38.530 26.390 22.059 1.00 0.00 H +ATOM 863 C GLN 55 35.729 21.702 22.920 1.00 0.00 C +ATOM 864 O GLN 55 35.936 21.998 24.098 1.00 0.00 O +ATOM 865 N GLU 56 35.911 20.461 22.436 1.00 0.00 N +ATOM 866 H GLU 56 35.764 20.328 21.453 1.00 0.00 H +ATOM 867 CA GLU 56 36.591 19.326 23.126 1.00 0.00 C +ATOM 868 HA GLU 56 36.581 19.527 24.209 1.00 0.00 H +ATOM 869 CB GLU 56 35.802 18.011 22.873 1.00 0.00 C +ATOM 870 HB2 GLU 56 34.794 18.115 23.271 1.00 0.00 H +ATOM 871 HB3 GLU 56 35.670 17.896 21.805 1.00 0.00 H +ATOM 872 CG GLU 56 36.406 16.708 23.419 1.00 0.00 C +ATOM 873 HG2 GLU 56 36.588 16.049 22.597 1.00 0.00 H +ATOM 874 HG3 GLU 56 37.378 16.911 23.804 1.00 0.00 H +ATOM 875 CD GLU 56 35.639 15.935 24.519 1.00 0.00 C +ATOM 876 OE1 GLU 56 36.261 15.255 25.395 1.00 0.00 O +ATOM 877 OE2 GLU 56 34.388 15.901 24.484 1.00 0.00 O +ATOM 878 C GLU 56 38.064 19.234 22.739 1.00 0.00 C +ATOM 879 O GLU 56 38.897 19.678 23.554 1.00 0.00 O +ATOM 880 OXT GLU 56 38.365 18.739 21.612 1.00 0.00 O +HETATM 881 ZN ZN1 57 26.696 32.427 29.378 1.00 0.00 Zn +HETATM 882 N AN1 58 28.269 33.325 30.318 1.00 0.00 N +HETATM 883 C AN1 58 30.569 34.237 31.119 1.00 0.00 C +HETATM 884 C1 AN1 58 29.262 33.721 30.709 1.00 0.00 C +HETATM 885 H AN1 58 30.559 34.480 32.185 1.00 0.00 H +HETATM 886 H1 AN1 58 30.794 35.142 30.544 1.00 0.00 H +HETATM 887 H2 AN1 58 31.328 33.474 30.919 1.00 0.00 H +HETATM 888 N1 AZI 59 30.711 28.496 29.886 1.00 0.00 N +HETATM 889 N2 AZI 59 30.239 29.555 30.281 1.00 0.00 N +HETATM 890 N3 AZI 59 29.793 30.641 30.720 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 881 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 137 134 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 140 142 +CONECT 140 139 +CONECT 141 139 +CONECT 142 139 145 143 144 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 142 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 194 189 +CONECT 188 187 +CONECT 189 187 192 190 191 +CONECT 190 189 +CONECT 191 189 +CONECT 192 193 189 +CONECT 193 192 +CONECT 194 196 187 195 +CONECT 195 194 +CONECT 196 197 198 194 +CONECT 197 196 +CONECT 198 205 196 200 199 +CONECT 199 198 +CONECT 200 201 198 202 203 +CONECT 201 200 +CONECT 202 200 +CONECT 203 200 204 +CONECT 204 203 +CONECT 205 206 207 198 +CONECT 206 205 +CONECT 207 209 205 208 +CONECT 208 207 +CONECT 209 210 227 211 207 +CONECT 210 209 +CONECT 211 214 209 212 213 +CONECT 212 211 +CONECT 213 211 +CONECT 214 216 215 217 211 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 214 219 220 +CONECT 218 217 +CONECT 219 217 +CONECT 220 217 222 223 221 +CONECT 221 220 +CONECT 222 220 +CONECT 223 226 220 225 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 223 +CONECT 227 228 209 229 +CONECT 228 227 +CONECT 229 227 231 230 +CONECT 230 229 +CONECT 231 234 229 232 233 +CONECT 232 231 +CONECT 233 231 +CONECT 234 235 236 231 +CONECT 235 234 +CONECT 236 238 234 237 +CONECT 237 236 +CONECT 238 240 239 250 236 +CONECT 239 238 +CONECT 240 246 241 242 238 +CONECT 241 240 +CONECT 242 244 240 243 245 +CONECT 243 242 +CONECT 244 242 +CONECT 245 242 +CONECT 246 248 247 249 240 +CONECT 247 246 +CONECT 248 246 +CONECT 249 246 +CONECT 250 238 252 251 +CONECT 251 250 +CONECT 252 262 253 250 +CONECT 253 254 252 263 256 +CONECT 254 255 269 253 +CONECT 255 254 +CONECT 256 253 257 264 265 +CONECT 257 258 259 256 +CONECT 258 261 267 257 +CONECT 259 260 257 266 +CONECT 260 261 268 259 +CONECT 261 881 258 260 +CONECT 262 252 +CONECT 263 253 +CONECT 264 256 +CONECT 265 256 +CONECT 266 259 +CONECT 267 258 +CONECT 268 260 +CONECT 269 271 254 270 +CONECT 270 269 +CONECT 271 272 273 281 269 +CONECT 272 271 +CONECT 273 274 275 271 279 +CONECT 274 273 +CONECT 275 278 277 273 276 +CONECT 276 275 +CONECT 277 275 +CONECT 278 275 +CONECT 279 273 280 +CONECT 280 279 +CONECT 281 283 271 282 +CONECT 282 281 +CONECT 283 293 284 281 +CONECT 284 285 287 283 294 +CONECT 285 286 300 284 +CONECT 286 285 +CONECT 287 295 296 284 288 +CONECT 288 287 289 290 +CONECT 289 298 288 292 +CONECT 290 288 297 291 +CONECT 291 292 290 299 +CONECT 292 289 881 291 +CONECT 293 283 +CONECT 294 284 +CONECT 295 287 +CONECT 296 287 +CONECT 297 290 +CONECT 298 289 +CONECT 299 291 +CONECT 300 302 285 301 +CONECT 301 300 +CONECT 302 313 303 300 304 +CONECT 303 302 +CONECT 304 302 307 306 305 +CONECT 305 304 +CONECT 306 304 +CONECT 307 309 310 304 308 +CONECT 308 307 +CONECT 309 307 +CONECT 310 311 307 312 +CONECT 311 310 +CONECT 312 310 +CONECT 313 315 314 302 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 323 319 318 315 +CONECT 318 317 +CONECT 319 321 320 317 322 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 325 324 317 +CONECT 324 323 +CONECT 325 327 326 323 +CONECT 326 325 +CONECT 327 339 329 328 325 +CONECT 328 327 +CONECT 329 330 335 327 331 +CONECT 330 329 +CONECT 331 329 333 334 332 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 336 337 329 338 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 340 341 327 +CONECT 340 339 +CONECT 341 343 339 342 +CONECT 342 341 +CONECT 343 345 344 351 341 +CONECT 344 343 +CONECT 345 348 346 347 343 +CONECT 346 345 +CONECT 347 345 +CONECT 348 350 349 345 +CONECT 349 348 +CONECT 350 348 +CONECT 351 353 343 352 +CONECT 352 351 +CONECT 353 354 355 351 +CONECT 354 353 +CONECT 355 357 353 375 356 +CONECT 356 355 +CONECT 357 359 358 360 355 +CONECT 358 357 +CONECT 359 357 +CONECT 360 361 357 374 +CONECT 361 362 363 360 +CONECT 362 361 +CONECT 363 361 364 365 +CONECT 364 363 +CONECT 365 363 374 366 +CONECT 366 365 367 368 +CONECT 367 366 +CONECT 368 366 370 369 +CONECT 369 368 +CONECT 370 372 368 371 +CONECT 371 370 +CONECT 372 374 373 370 +CONECT 373 372 +CONECT 374 360 365 372 +CONECT 375 377 355 376 +CONECT 376 375 +CONECT 377 378 379 375 +CONECT 378 377 +CONECT 379 381 377 380 385 +CONECT 380 379 +CONECT 381 384 382 383 379 +CONECT 382 381 +CONECT 383 381 +CONECT 384 381 +CONECT 385 379 386 387 +CONECT 386 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 390 391 400 +CONECT 390 389 +CONECT 391 394 392 389 393 +CONECT 392 391 +CONECT 393 391 +CONECT 394 395 396 397 391 +CONECT 395 394 +CONECT 396 394 +CONECT 397 399 394 398 +CONECT 398 397 +CONECT 399 397 +CONECT 400 389 402 401 +CONECT 401 400 +CONECT 402 403 400 404 +CONECT 403 402 +CONECT 404 402 406 410 405 +CONECT 405 404 +CONECT 406 407 409 404 408 +CONECT 407 406 +CONECT 408 406 +CONECT 409 406 +CONECT 410 412 404 411 +CONECT 411 410 +CONECT 412 413 414 410 +CONECT 413 412 +CONECT 414 416 412 415 425 +CONECT 415 414 +CONECT 416 417 418 419 414 +CONECT 417 416 +CONECT 418 416 +CONECT 419 422 416 421 420 +CONECT 420 419 +CONECT 421 419 +CONECT 422 424 423 419 +CONECT 423 422 +CONECT 424 422 +CONECT 425 414 427 426 +CONECT 426 425 +CONECT 427 428 425 429 +CONECT 428 427 +CONECT 429 427 431 430 447 +CONECT 430 429 +CONECT 431 434 432 433 429 +CONECT 432 431 +CONECT 433 431 +CONECT 434 436 437 435 431 +CONECT 435 434 +CONECT 436 434 +CONECT 437 440 438 439 434 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 441 442 437 +CONECT 441 440 +CONECT 442 440 +CONECT 443 445 444 446 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 +CONECT 447 429 449 448 +CONECT 448 447 +CONECT 449 450 447 451 +CONECT 450 449 +CONECT 451 449 453 452 467 +CONECT 452 451 +CONECT 453 456 454 451 455 +CONECT 454 453 +CONECT 455 453 +CONECT 456 457 465 453 +CONECT 457 459 458 456 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 462 459 463 +CONECT 462 461 +CONECT 463 461 464 465 +CONECT 464 463 +CONECT 465 463 456 466 +CONECT 466 465 +CONECT 467 451 469 468 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 473 469 481 472 +CONECT 472 471 +CONECT 473 474 479 475 471 +CONECT 474 473 +CONECT 475 473 477 478 476 +CONECT 476 475 +CONECT 477 475 +CONECT 478 475 +CONECT 479 480 473 +CONECT 480 479 +CONECT 481 483 471 482 +CONECT 482 481 +CONECT 483 484 485 481 +CONECT 484 483 +CONECT 485 487 483 486 503 +CONECT 486 485 +CONECT 487 490 488 489 485 +CONECT 488 487 +CONECT 489 487 +CONECT 490 493 492 491 487 +CONECT 491 490 +CONECT 492 490 +CONECT 493 496 494 495 490 +CONECT 494 493 +CONECT 495 493 +CONECT 496 498 497 499 493 +CONECT 497 496 +CONECT 498 496 +CONECT 499 501 496 502 500 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 485 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 508 513 +CONECT 508 507 +CONECT 509 512 510 507 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 507 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 534 518 +CONECT 518 517 +CONECT 519 521 520 517 522 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 525 523 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 526 522 528 527 +CONECT 526 525 +CONECT 527 525 +CONECT 528 530 525 531 529 +CONECT 529 528 +CONECT 530 528 +CONECT 531 533 528 532 +CONECT 532 531 +CONECT 533 531 +CONECT 534 536 517 535 +CONECT 535 534 +CONECT 536 537 538 534 +CONECT 537 536 +CONECT 538 540 536 544 539 +CONECT 539 538 +CONECT 540 541 543 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 +CONECT 544 538 546 545 +CONECT 545 544 +CONECT 546 547 544 548 +CONECT 547 546 +CONECT 548 550 546 549 558 +CONECT 549 548 +CONECT 550 553 551 552 548 +CONECT 551 550 +CONECT 552 550 +CONECT 553 555 554 550 +CONECT 554 553 +CONECT 555 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 548 560 559 +CONECT 559 558 +CONECT 560 561 558 562 +CONECT 561 560 +CONECT 562 560 564 563 570 +CONECT 563 562 +CONECT 564 567 565 562 566 +CONECT 565 564 +CONECT 566 564 +CONECT 567 569 568 564 +CONECT 568 567 +CONECT 569 567 +CONECT 570 562 572 571 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 592 576 575 +CONECT 575 574 +CONECT 576 579 574 578 577 +CONECT 577 576 +CONECT 578 576 +CONECT 579 580 581 582 576 +CONECT 580 579 +CONECT 581 579 +CONECT 582 585 584 579 583 +CONECT 583 582 +CONECT 584 582 +CONECT 585 588 587 586 582 +CONECT 586 585 +CONECT 587 585 +CONECT 588 590 591 589 585 +CONECT 589 588 +CONECT 590 588 +CONECT 591 588 +CONECT 592 594 593 574 +CONECT 593 592 +CONECT 594 596 595 592 +CONECT 595 594 +CONECT 596 599 594 597 598 +CONECT 597 596 +CONECT 598 596 +CONECT 599 601 600 596 +CONECT 600 599 +CONECT 601 603 602 599 +CONECT 602 601 +CONECT 603 623 604 605 601 +CONECT 604 603 +CONECT 605 606 603 607 608 +CONECT 606 605 +CONECT 607 605 +CONECT 608 609 605 610 611 +CONECT 609 608 +CONECT 610 608 +CONECT 611 608 613 614 612 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 616 615 +CONECT 615 614 +CONECT 616 617 614 620 +CONECT 617 618 619 616 +CONECT 618 617 +CONECT 619 617 +CONECT 620 616 622 621 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 603 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 629 635 628 625 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 632 +CONECT 635 637 636 627 +CONECT 636 635 +CONECT 637 639 638 635 +CONECT 638 637 +CONECT 639 642 640 641 637 +CONECT 640 639 +CONECT 641 639 +CONECT 642 644 643 639 +CONECT 643 642 +CONECT 644 646 645 642 +CONECT 645 644 +CONECT 646 648 647 657 644 +CONECT 647 646 +CONECT 648 650 651 649 646 +CONECT 649 648 +CONECT 650 648 +CONECT 651 653 648 654 652 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 655 656 +CONECT 655 654 +CONECT 656 654 +CONECT 657 659 646 658 +CONECT 658 657 +CONECT 659 660 661 657 +CONECT 660 659 +CONECT 661 681 659 662 663 +CONECT 662 661 +CONECT 663 661 666 664 665 +CONECT 664 663 +CONECT 665 663 +CONECT 666 668 667 663 669 +CONECT 667 666 +CONECT 668 666 +CONECT 669 666 672 670 671 +CONECT 670 669 +CONECT 671 669 +CONECT 672 673 674 669 +CONECT 673 672 +CONECT 674 678 675 672 +CONECT 675 677 676 674 +CONECT 676 675 +CONECT 677 675 +CONECT 678 679 680 674 +CONECT 679 678 +CONECT 680 678 +CONECT 681 682 683 661 +CONECT 682 681 +CONECT 683 685 681 684 +CONECT 684 683 +CONECT 685 686 687 695 683 +CONECT 686 685 +CONECT 687 689 693 685 688 +CONECT 688 687 +CONECT 689 690 691 692 687 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 +CONECT 693 694 687 +CONECT 694 693 +CONECT 695 697 685 696 +CONECT 696 695 +CONECT 697 698 699 695 +CONECT 698 697 +CONECT 699 714 701 697 700 +CONECT 700 699 +CONECT 701 707 702 699 703 +CONECT 702 701 +CONECT 703 701 705 704 706 +CONECT 704 703 +CONECT 705 703 +CONECT 706 703 +CONECT 707 710 709 708 701 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 713 711 707 +CONECT 711 710 +CONECT 712 710 +CONECT 713 710 +CONECT 714 715 716 699 +CONECT 715 714 +CONECT 716 718 714 717 +CONECT 717 716 +CONECT 718 719 726 720 716 +CONECT 719 718 +CONECT 720 723 718 721 722 +CONECT 721 720 +CONECT 722 720 +CONECT 723 725 720 724 +CONECT 724 723 +CONECT 725 723 +CONECT 726 728 718 727 +CONECT 727 726 +CONECT 728 729 730 726 +CONECT 729 728 +CONECT 730 732 728 738 731 +CONECT 731 730 +CONECT 732 734 735 733 730 +CONECT 733 732 +CONECT 734 732 +CONECT 735 736 732 737 +CONECT 736 735 +CONECT 737 735 +CONECT 738 740 730 739 +CONECT 739 738 +CONECT 740 741 742 738 +CONECT 741 740 +CONECT 742 744 743 740 748 +CONECT 743 742 +CONECT 744 747 746 745 742 +CONECT 745 744 +CONECT 746 744 +CONECT 747 744 +CONECT 748 742 749 750 +CONECT 749 748 +CONECT 750 748 751 752 +CONECT 751 750 +CONECT 752 750 753 754 762 +CONECT 753 752 +CONECT 754 756 752 760 755 +CONECT 755 754 +CONECT 756 757 759 758 754 +CONECT 757 756 +CONECT 758 756 +CONECT 759 756 +CONECT 760 761 754 +CONECT 761 760 +CONECT 762 752 764 763 +CONECT 763 762 +CONECT 764 765 766 762 +CONECT 765 764 +CONECT 766 767 764 768 784 +CONECT 767 766 +CONECT 768 771 766 770 769 +CONECT 769 768 +CONECT 770 768 +CONECT 771 774 772 773 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 777 776 775 771 +CONECT 775 774 +CONECT 776 774 +CONECT 777 780 779 778 774 +CONECT 778 777 +CONECT 779 777 +CONECT 780 782 783 781 777 +CONECT 781 780 +CONECT 782 780 +CONECT 783 780 +CONECT 784 766 786 785 +CONECT 785 784 +CONECT 786 787 784 788 +CONECT 787 786 +CONECT 788 786 798 790 789 +CONECT 789 788 +CONECT 790 791 788 796 792 +CONECT 791 790 +CONECT 792 790 795 794 793 +CONECT 793 792 +CONECT 794 792 +CONECT 795 792 +CONECT 796 797 790 +CONECT 797 796 +CONECT 798 799 788 800 +CONECT 799 798 +CONECT 800 798 802 801 +CONECT 801 800 +CONECT 802 803 800 818 804 +CONECT 803 802 +CONECT 804 802 807 806 805 +CONECT 805 804 +CONECT 806 804 +CONECT 807 816 808 804 +CONECT 808 810 807 809 +CONECT 809 808 +CONECT 810 812 811 808 +CONECT 811 810 +CONECT 812 813 814 810 +CONECT 813 812 +CONECT 814 815 812 816 +CONECT 815 814 +CONECT 816 814 817 807 +CONECT 817 816 +CONECT 818 802 820 819 +CONECT 819 818 +CONECT 820 821 818 822 +CONECT 821 820 +CONECT 822 824 820 832 823 +CONECT 823 822 +CONECT 824 830 826 825 822 +CONECT 825 824 +CONECT 826 827 828 824 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 +CONECT 830 831 824 +CONECT 831 830 +CONECT 832 833 822 834 +CONECT 833 832 +CONECT 834 832 836 835 +CONECT 835 834 +CONECT 836 846 837 834 838 +CONECT 837 836 +CONECT 838 836 840 844 839 +CONECT 839 838 +CONECT 840 841 843 838 842 +CONECT 841 840 +CONECT 842 840 +CONECT 843 840 +CONECT 844 838 845 +CONECT 845 844 +CONECT 846 848 847 836 +CONECT 847 846 +CONECT 848 850 849 846 +CONECT 849 848 +CONECT 850 852 851 848 863 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 858 852 857 856 +CONECT 856 855 +CONECT 857 855 +CONECT 858 859 860 855 +CONECT 859 858 +CONECT 860 861 858 862 +CONECT 861 860 +CONECT 862 860 +CONECT 863 850 865 864 +CONECT 864 863 +CONECT 865 866 863 867 +CONECT 866 865 +CONECT 867 865 878 869 868 +CONECT 868 867 +CONECT 869 871 867 870 872 +CONECT 870 869 +CONECT 871 869 +CONECT 872 873 869 874 875 +CONECT 873 872 +CONECT 874 872 +CONECT 875 872 877 876 +CONECT 876 875 +CONECT 877 875 +CONECT 878 880 867 879 +CONECT 879 878 +CONECT 880 878 +CONECT 881 87 292 882 261 +CONECT 882 881 884 +CONECT 883 886 884 887 885 +CONECT 884 882 883 +CONECT 885 883 +CONECT 886 883 +CONECT 887 883 +CONECT 888 889 +CONECT 889 888 890 +CONECT 890 889 +MASTER 0 0 0 0 0 0 0 0 890 0 890 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_5.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_5.pdb new file mode 100644 index 0000000..925b319 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_5.pdb @@ -0,0 +1,1785 @@ +COMPND fitness: -6.2188 90.21749999999975 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 P1 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HX1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HX1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HX1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HX1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HX1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HX1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HX1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HX1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N ARG 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H ARG 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA ARG 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 CB ARG 8 32.132 -93.836 -4.510 1.00 0.00 C +ATOM 136 HB2 ARG 8 33.183 -94.106 -4.615 1.00 0.00 H +ATOM 137 HB3 ARG 8 31.914 -92.975 -5.142 1.00 0.00 H +ATOM 138 CG ARG 8 31.841 -93.485 -3.060 1.00 0.00 C +ATOM 139 HG2 ARG 8 31.934 -94.390 -2.458 1.00 0.00 H +ATOM 140 HG3 ARG 8 32.574 -92.751 -2.726 1.00 0.00 H +ATOM 141 CD ARG 8 30.442 -92.914 -2.901 1.00 0.00 C +ATOM 142 HD2 ARG 8 29.722 -93.620 -3.312 1.00 0.00 H +ATOM 143 HD3 ARG 8 30.238 -92.765 -1.841 1.00 0.00 H +ATOM 144 NE ARG 8 30.290 -91.636 -3.591 1.00 0.00 N +ATOM 145 HE ARG 8 29.906 -91.657 -4.525 1.00 0.00 H +ATOM 146 CZ ARG 8 30.622 -90.461 -3.067 1.00 0.00 C +ATOM 147 NH1 ARG 8 30.448 -89.350 -3.770 1.00 0.00 N +ATOM 148 HH11 ARG 8 30.063 -89.401 -4.703 1.00 0.00 H +ATOM 149 HH12 ARG 8 30.702 -88.457 -3.370 1.00 0.00 H +ATOM 150 NH2 ARG 8 31.126 -90.399 -1.843 1.00 0.00 N +ATOM 151 HH21 ARG 8 31.255 -91.247 -1.310 1.00 0.00 H +ATOM 152 HH22 ARG 8 31.377 -89.503 -1.447 1.00 0.00 H +ATOM 153 HA ARG 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 154 C ARG 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 155 O ARG 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 156 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 157 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 158 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 161 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 162 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 163 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 164 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 165 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 166 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 167 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 168 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 169 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 170 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 171 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 172 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 173 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 174 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 175 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 176 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 177 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 178 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 179 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 180 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 181 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 182 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 183 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 184 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 185 N SER 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 186 H SER 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 187 CA SER 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 188 CB SER 11 32.207-101.574 0.711 1.00 0.00 C +ATOM 189 HB2 SER 11 32.416-100.511 0.583 1.00 0.00 H +ATOM 190 HB3 SER 11 31.863-101.756 1.728 1.00 0.00 H +ATOM 191 OG SER 11 33.389-102.318 0.472 1.00 0.00 O +ATOM 192 HG SER 11 34.068-102.048 1.093 1.00 0.00 H +ATOM 193 HA SER 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 194 C SER 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 195 O SER 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 196 N CYS 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 197 H CYS 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 198 CA CYS 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 199 CB CYS 12 28.130 -98.237 -0.161 1.00 0.00 C +ATOM 200 HB2 CYS 12 28.781 -97.808 -0.923 1.00 0.00 H +ATOM 201 HB3 CYS 12 27.157 -97.746 -0.196 1.00 0.00 H +ATOM 202 SG CYS 12 28.866 -97.786 1.444 1.00 0.00 S +ATOM 203 HG CYS 12 28.829 -96.471 1.249 1.00 0.00 H +ATOM 204 HA CYS 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 205 C CYS 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 206 O CYS 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 207 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 208 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 209 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 210 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 211 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 212 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 213 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 214 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 215 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 216 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 217 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 218 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 219 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 220 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 221 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 222 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 223 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 224 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 225 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 226 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 227 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 228 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 229 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 230 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 231 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 232 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 233 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 234 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 235 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 236 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 237 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 238 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 239 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 240 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 241 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 242 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 243 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 244 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 245 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 246 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 247 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 248 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 249 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 250 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 251 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 252 N HY1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 253 CA HY1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 254 C HY1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 255 O HY1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 256 CB HY1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 257 CG HY1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 258 CD2 HY1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 259 ND1 HY1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 260 CE1 HY1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 261 NE2 HY1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 262 H HY1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 263 HA HY1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 264 HB2 HY1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 265 HB3 HY1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 266 HD1 HY1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 267 HD2 HY1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 268 HE1 HY1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 269 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 270 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 271 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 272 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 273 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 274 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 275 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 276 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 277 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 278 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 279 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 280 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 281 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 282 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 283 N HY2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 284 CA HY2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 285 C HY2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 286 O HY2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 287 CB HY2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 288 CG HY2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 289 CD2 HY2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 290 ND1 HY2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 291 CE1 HY2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 292 NE2 HY2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 293 H HY2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 294 HA HY2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 295 HB2 HY2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 296 HB3 HY2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 297 HD1 HY2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 298 HD2 HY2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 299 HE1 HY2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 300 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 301 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 302 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 303 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 304 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 305 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 306 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 307 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 308 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 309 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 310 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 311 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 312 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 313 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 314 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 315 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 316 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 317 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 318 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 319 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 320 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 321 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 322 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 323 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 324 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 325 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 326 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 327 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 328 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 329 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 330 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 331 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 332 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 333 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 334 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 335 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 336 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 337 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 338 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 339 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 340 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 341 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 342 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 343 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 344 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 345 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 346 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 347 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 348 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 349 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 350 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 351 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 352 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 353 N TRP 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 354 H TRP 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 355 CA TRP 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 356 CB TRP 23 21.411 -85.256 -16.822 1.00 0.00 C +ATOM 357 HB2 TRP 23 20.471 -85.768 -16.621 1.00 0.00 H +ATOM 358 HB3 TRP 23 21.494 -85.175 -17.905 1.00 0.00 H +ATOM 359 CG TRP 23 22.519 -86.148 -16.354 1.00 0.00 C +ATOM 360 CD1 TRP 23 23.651 -86.478 -17.042 1.00 0.00 C +ATOM 361 HD1 TRP 23 23.887 -86.129 -18.044 1.00 0.00 H +ATOM 362 NE1 TRP 23 24.435 -87.319 -16.290 1.00 0.00 N +ATOM 363 HE1 TRP 23 25.328 -87.711 -16.568 1.00 0.00 H +ATOM 364 CE2 TRP 23 23.809 -87.548 -15.088 1.00 0.00 C +ATOM 365 CZ2 TRP 23 24.208 -88.327 -14.004 1.00 0.00 C +ATOM 366 HZ2 TRP 23 25.139 -88.878 -14.005 1.00 0.00 H +ATOM 367 CH2 TRP 23 23.375 -88.374 -12.917 1.00 0.00 C +ATOM 368 HH2 TRP 23 23.669 -88.969 -12.061 1.00 0.00 H +ATOM 369 CZ3 TRP 23 22.163 -87.664 -12.899 1.00 0.00 C +ATOM 370 HZ3 TRP 23 21.536 -87.731 -12.021 1.00 0.00 H +ATOM 371 CE3 TRP 23 21.767 -86.890 -13.974 1.00 0.00 C +ATOM 372 HE3 TRP 23 20.836 -86.342 -13.975 1.00 0.00 H +ATOM 373 CD2 TRP 23 22.599 -86.826 -15.093 1.00 0.00 C +ATOM 374 HA TRP 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 375 C TRP 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 376 O TRP 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 377 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 378 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 379 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 380 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 381 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 382 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 383 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 384 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 385 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 386 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 387 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 388 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 389 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 390 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 391 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 392 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 393 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 394 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 395 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 396 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 397 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 398 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 399 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 400 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 401 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 402 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 403 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 404 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 405 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 406 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 407 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 408 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 409 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 410 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 411 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 412 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 413 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 414 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 415 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 416 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 417 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 418 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 419 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 420 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 421 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 422 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 423 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 424 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 425 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 426 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 427 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 428 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 429 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 430 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 431 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 432 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 433 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 434 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 435 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 436 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 437 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 438 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 439 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 440 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 441 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 442 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 443 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 444 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 445 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 446 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 447 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 448 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 449 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 450 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 451 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 452 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 453 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 454 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 455 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 456 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 457 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 458 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 459 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 460 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 461 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 462 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 463 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 464 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 465 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 466 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 467 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 468 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 469 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 470 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 471 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 472 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 473 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 474 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 475 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 476 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 477 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 478 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 479 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 480 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 481 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 482 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 483 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 484 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 485 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 486 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 487 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 488 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 489 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 490 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 491 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 492 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 493 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 494 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 495 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 496 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 497 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 498 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 499 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 500 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 501 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 502 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 503 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 504 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 505 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 506 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 507 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 508 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 509 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 510 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 511 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 512 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 513 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 514 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 515 N LYN 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 516 H LYN 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 517 CA LYN 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 518 CB LYN 33 27.315 -82.525 -3.272 1.00 0.00 C +ATOM 519 HB2 LYN 33 26.398 -81.939 -3.213 1.00 0.00 H +ATOM 520 HB3 LYN 33 27.388 -82.987 -4.256 1.00 0.00 H +ATOM 521 CG LYN 33 27.295 -83.606 -2.204 1.00 0.00 C +ATOM 522 HG2 LYN 33 28.222 -84.177 -2.270 1.00 0.00 H +ATOM 523 HG3 LYN 33 27.231 -83.128 -1.227 1.00 0.00 H +ATOM 524 CD LYN 33 26.111 -84.541 -2.388 1.00 0.00 C +ATOM 525 HD2 LYN 33 26.114 -84.908 -3.414 1.00 0.00 H +ATOM 526 HD3 LYN 33 26.222 -85.381 -1.702 1.00 0.00 H +ATOM 527 CE LYN 33 24.798 -83.829 -2.109 1.00 0.00 C +ATOM 528 HE2 LYN 33 24.821 -83.460 -1.084 1.00 0.00 H +ATOM 529 HE3 LYN 33 24.713 -82.987 -2.797 1.00 0.00 H +ATOM 530 NZ LYN 33 23.628 -84.733 -2.286 1.00 0.00 N +ATOM 531 HZ2 LYN 33 22.777 -84.224 -2.092 1.00 0.00 H +ATOM 532 HZ3 LYN 33 23.607 -85.075 -3.236 1.00 0.00 H +ATOM 533 HA LYN 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 534 C LYN 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 535 O LYN 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 536 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 537 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 538 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 539 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 540 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 541 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 542 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 543 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 544 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 545 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 546 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 547 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 548 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 549 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 550 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 551 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 552 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 553 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 554 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 555 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 556 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 557 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 558 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 559 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 560 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 561 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 562 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 563 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 564 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 565 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 566 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 567 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 568 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 569 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 570 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 571 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 572 N LYS 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 573 H LYS 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 574 CA LYS 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 575 CB LYS 37 33.048 -83.879 0.496 1.00 0.00 C +ATOM 576 HB2 LYS 37 33.471 -84.650 1.141 1.00 0.00 H +ATOM 577 HB3 LYS 37 31.965 -83.860 0.615 1.00 0.00 H +ATOM 578 CG LYS 37 33.393 -84.185 -0.952 1.00 0.00 C +ATOM 579 HG2 LYS 37 32.972 -83.401 -1.582 1.00 0.00 H +ATOM 580 HG3 LYS 37 34.478 -84.192 -1.057 1.00 0.00 H +ATOM 581 CD LYS 37 32.834 -85.533 -1.380 1.00 0.00 C +ATOM 582 HD2 LYS 37 33.256 -86.304 -0.735 1.00 0.00 H +ATOM 583 HD3 LYS 37 31.751 -85.513 -1.262 1.00 0.00 H +ATOM 584 CE LYS 37 33.180 -85.839 -2.828 1.00 0.00 C +ATOM 585 HE2 LYS 37 34.262 -85.779 -2.941 1.00 0.00 H +ATOM 586 HE3 LYS 37 32.849 -86.853 -3.051 1.00 0.00 H +ATOM 587 NZ LYS 37 32.529 -84.884 -3.768 1.00 0.00 N1+ +ATOM 588 HZ1 LYS 37 32.837 -83.945 -3.561 1.00 0.00 H +ATOM 589 HZ2 LYS 37 32.782 -85.121 -4.717 1.00 0.00 H +ATOM 590 HZ3 LYS 37 31.526 -84.940 -3.663 1.00 0.00 H +ATOM 591 HA LYS 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 592 C LYS 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 593 O LYS 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 594 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 595 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 596 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 597 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 598 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 599 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 600 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 601 N ARG 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 602 H ARG 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 603 CA ARG 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 604 CB ARG 39 38.868 -82.517 -4.462 1.00 0.00 C +ATOM 605 HB2 ARG 39 39.200 -82.458 -5.498 1.00 0.00 H +ATOM 606 HB3 ARG 39 39.426 -81.798 -3.861 1.00 0.00 H +ATOM 607 CG ARG 39 39.115 -83.920 -3.930 1.00 0.00 C +ATOM 608 HG2 ARG 39 38.452 -84.611 -4.452 1.00 0.00 H +ATOM 609 HG3 ARG 39 40.151 -84.191 -4.132 1.00 0.00 H +ATOM 610 CD ARG 39 38.853 -83.997 -2.436 1.00 0.00 C +ATOM 611 HD2 ARG 39 39.516 -83.301 -1.923 1.00 0.00 H +ATOM 612 HD3 ARG 39 37.817 -83.720 -2.242 1.00 0.00 H +ATOM 613 NE ARG 39 39.085 -85.339 -1.908 1.00 0.00 N +ATOM 614 HE ARG 39 39.993 -85.527 -1.508 1.00 0.00 H +ATOM 615 CZ ARG 39 38.183 -86.314 -1.923 1.00 0.00 C +ATOM 616 NH1 ARG 39 36.981 -86.099 -2.440 1.00 0.00 N +ATOM 617 HH11 ARG 39 36.755 -85.192 -2.822 1.00 0.00 H +ATOM 618 HH12 ARG 39 36.298 -86.842 -2.450 1.00 0.00 H +ATOM 619 NH2 ARG 39 38.485 -87.503 -1.419 1.00 0.00 N +ATOM 620 HH21 ARG 39 39.402 -87.663 -1.025 1.00 0.00 H +ATOM 621 HH22 ARG 39 37.797 -88.243 -1.432 1.00 0.00 H +ATOM 622 HA ARG 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 623 C ARG 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 624 O ARG 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 625 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 626 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 627 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 628 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 629 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 630 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 631 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 632 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 633 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 634 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 635 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 636 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 637 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 638 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 639 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 640 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 641 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 642 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 643 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 644 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 645 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 646 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 647 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 648 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 649 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 650 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 651 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 652 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 653 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 654 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 655 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 656 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 657 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 658 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 659 N ARG 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 660 H ARG 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 661 CA ARG 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 662 CB ARG 43 29.884 -89.033 -12.452 1.00 0.00 C +ATOM 663 HB2 ARG 43 29.195 -89.866 -12.312 1.00 0.00 H +ATOM 664 HB3 ARG 43 30.406 -88.833 -11.516 1.00 0.00 H +ATOM 665 CG ARG 43 29.106 -87.797 -12.871 1.00 0.00 C +ATOM 666 HG2 ARG 43 29.809 -86.976 -13.016 1.00 0.00 H +ATOM 667 HG3 ARG 43 28.598 -88.009 -13.812 1.00 0.00 H +ATOM 668 CD ARG 43 28.081 -87.406 -11.819 1.00 0.00 C +ATOM 669 HD2 ARG 43 27.386 -88.233 -11.676 1.00 0.00 H +ATOM 670 HD3 ARG 43 28.596 -87.199 -10.881 1.00 0.00 H +ATOM 671 NE ARG 43 27.323 -86.221 -12.207 1.00 0.00 N +ATOM 672 HE ARG 43 26.435 -86.368 -12.663 1.00 0.00 H +ATOM 673 CZ ARG 43 27.730 -84.973 -11.997 1.00 0.00 C +ATOM 674 NH1 ARG 43 28.892 -84.745 -11.401 1.00 0.00 N +ATOM 675 HH11 ARG 43 29.466 -85.523 -11.108 1.00 0.00 H +ATOM 676 HH12 ARG 43 29.198 -83.796 -11.243 1.00 0.00 H +ATOM 677 NH2 ARG 43 26.972 -83.955 -12.384 1.00 0.00 N +ATOM 678 HH21 ARG 43 26.087 -84.131 -12.838 1.00 0.00 H +ATOM 679 HH22 ARG 43 27.284 -83.008 -12.223 1.00 0.00 H +ATOM 680 HA ARG 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 681 C ARG 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 682 O ARG 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 683 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 684 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 685 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 686 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 687 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 688 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 689 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 690 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 691 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 692 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 693 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 694 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 695 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 696 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 697 N ILE 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 698 H ILE 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 699 CA ILE 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 700 CB ILE 45 25.264 -89.243 -17.471 1.00 0.00 C +ATOM 701 HB ILE 45 24.177 -89.166 -17.456 1.00 0.00 H +ATOM 702 CG2 ILE 45 25.843 -88.467 -16.298 1.00 0.00 C +ATOM 703 HG21 ILE 45 26.931 -88.545 -16.312 1.00 0.00 H +ATOM 704 HG22 ILE 45 25.553 -87.420 -16.375 1.00 0.00 H +ATOM 705 HG23 ILE 45 25.464 -88.881 -15.364 1.00 0.00 H +ATOM 706 CG1 ILE 45 25.812 -88.644 -18.767 1.00 0.00 C +ATOM 707 HG12 ILE 45 25.634 -87.570 -18.727 1.00 0.00 H +ATOM 708 HG13 ILE 45 26.886 -88.835 -18.784 1.00 0.00 H +ATOM 709 CD1 ILE 45 25.179 -89.214 -20.018 1.00 0.00 C +ATOM 710 HD11 ILE 45 24.105 -89.024 -20.003 1.00 0.00 H +ATOM 711 HD12 ILE 45 25.619 -88.741 -20.896 1.00 0.00 H +ATOM 712 HD13 ILE 45 25.357 -90.289 -20.058 1.00 0.00 H +ATOM 713 HA ILE 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 714 C ILE 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 715 O ILE 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 716 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 717 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 718 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 719 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 720 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 721 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 722 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 723 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 724 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 725 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 726 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 727 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 728 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 729 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 730 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 731 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 732 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 733 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 734 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 735 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 736 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 737 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 738 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 739 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 740 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 741 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 742 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 743 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 744 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 745 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 746 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 747 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 748 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 749 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 750 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 751 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 752 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 753 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 754 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 755 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 756 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 757 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 758 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 759 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 760 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 761 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 762 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 763 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 764 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 765 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 766 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 767 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 768 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 769 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 770 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 771 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 772 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 773 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 774 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 775 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 776 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 777 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 778 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 779 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 780 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 781 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 782 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 783 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 784 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 785 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 786 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 787 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 788 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 789 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 790 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 791 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 792 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 793 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 794 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 795 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 796 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 797 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 798 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 799 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 800 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 801 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 802 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 803 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 804 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 805 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 806 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 807 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 808 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 809 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 810 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 811 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 812 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 813 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 814 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 815 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 816 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 817 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 818 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 819 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 820 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 821 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 822 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 823 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 824 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 825 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 826 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 827 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 828 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 829 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 830 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 831 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 832 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 833 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 834 N THR 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 835 H THR 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 836 CA THR 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 837 CB THR 54 32.307 -94.492 -10.190 1.00 0.00 C +ATOM 838 HB THR 54 31.944 -95.343 -9.615 1.00 0.00 H +ATOM 839 CG2 THR 54 33.789 -94.670 -10.479 1.00 0.00 C +ATOM 840 HG21 THR 54 34.153 -93.819 -11.054 1.00 0.00 H +ATOM 841 HG22 THR 54 34.338 -94.734 -9.539 1.00 0.00 H +ATOM 842 HG23 THR 54 33.941 -95.586 -11.051 1.00 0.00 H +ATOM 843 OG1 THR 54 32.122 -93.285 -9.439 1.00 0.00 O +ATOM 844 HG1 THR 54 32.609 -93.345 -8.613 1.00 0.00 H +ATOM 845 HA THR 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 846 C THR 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 847 O THR 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 848 N GLN 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 849 H GLN 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 850 CA GLN 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 851 CB GLN 55 34.660 -96.376 -14.407 1.00 0.00 C +ATOM 852 HB2 GLN 55 34.997 -97.154 -15.093 1.00 0.00 H +ATOM 853 HB3 GLN 55 34.127 -95.606 -14.966 1.00 0.00 H +ATOM 854 CG GLN 55 35.862 -95.756 -13.713 1.00 0.00 C +ATOM 855 HG2 GLN 55 35.513 -94.985 -13.026 1.00 0.00 H +ATOM 856 HG3 GLN 55 36.382 -96.534 -13.153 1.00 0.00 H +ATOM 857 CD GLN 55 36.837 -95.128 -14.689 1.00 0.00 C +ATOM 858 OE1 GLN 55 36.898 -95.513 -15.856 1.00 0.00 O +ATOM 859 NE2 GLN 55 37.605 -94.154 -14.211 1.00 0.00 N +ATOM 860 HE21 GLN 55 38.274 -93.699 -14.816 1.00 0.00 H +ATOM 861 HE22 GLN 55 37.517 -93.873 -13.245 1.00 0.00 H +ATOM 862 HA GLN 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 863 C GLN 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 864 O GLN 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 865 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 866 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 867 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 868 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 869 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 870 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 871 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 872 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 873 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 874 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 875 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 876 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 877 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 878 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 879 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 880 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 881 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 Zn +ATOM 882 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 883 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 884 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 885 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 886 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 887 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +ATOM 888 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 889 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 890 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 17 15 13 16 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 65 60 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 68 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 65 69 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 881 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 104 106 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 111 112 113 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 153 132 154 135 +CONECT 135 136 137 138 134 +CONECT 136 135 +CONECT 137 135 +CONECT 138 135 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 142 143 144 +CONECT 142 141 +CONECT 143 141 +CONECT 144 141 145 146 +CONECT 145 144 +CONECT 146 144 147 150 +CONECT 147 146 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 146 151 152 +CONECT 151 150 +CONECT 152 150 +CONECT 153 134 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 161 159 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 165 169 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 170 175 +CONECT 174 173 +CONECT 175 173 +CONECT 176 178 179 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 182 181 176 180 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 193 194 188 +CONECT 188 189 190 191 187 +CONECT 189 188 +CONECT 190 188 +CONECT 191 188 192 +CONECT 192 191 +CONECT 193 187 +CONECT 194 196 187 195 +CONECT 195 194 +CONECT 196 197 198 194 +CONECT 197 196 +CONECT 198 205 196 204 199 +CONECT 199 200 201 202 198 +CONECT 200 199 +CONECT 201 199 +CONECT 202 199 203 +CONECT 203 202 +CONECT 204 198 +CONECT 205 206 207 198 +CONECT 206 205 +CONECT 207 209 205 208 +CONECT 208 207 +CONECT 209 210 211 227 207 +CONECT 210 209 +CONECT 211 214 209 212 213 +CONECT 212 211 +CONECT 213 211 +CONECT 214 216 215 217 211 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 214 220 219 +CONECT 218 217 +CONECT 219 217 +CONECT 220 222 217 223 221 +CONECT 221 220 +CONECT 222 220 +CONECT 223 226 220 224 225 +CONECT 224 223 +CONECT 225 223 +CONECT 226 223 +CONECT 227 228 209 229 +CONECT 228 227 +CONECT 229 227 231 230 +CONECT 230 229 +CONECT 231 234 229 232 233 +CONECT 232 231 +CONECT 233 231 +CONECT 234 235 236 231 +CONECT 235 234 +CONECT 236 238 234 237 +CONECT 237 236 +CONECT 238 240 239 250 236 +CONECT 239 238 +CONECT 240 246 241 242 238 +CONECT 241 240 +CONECT 242 240 245 244 243 +CONECT 243 242 +CONECT 244 242 +CONECT 245 242 +CONECT 246 248 249 247 240 +CONECT 247 246 +CONECT 248 246 +CONECT 249 246 +CONECT 250 252 238 251 +CONECT 251 250 +CONECT 252 262 253 250 +CONECT 253 254 252 263 256 +CONECT 254 255 269 253 +CONECT 255 254 +CONECT 256 253 257 264 265 +CONECT 257 258 259 256 +CONECT 258 261 267 257 +CONECT 259 260 257 266 +CONECT 260 261 268 259 +CONECT 261 881 260 258 +CONECT 262 252 +CONECT 263 253 +CONECT 264 256 +CONECT 265 256 +CONECT 266 259 +CONECT 267 258 +CONECT 268 260 +CONECT 269 271 254 270 +CONECT 270 269 +CONECT 271 272 273 281 269 +CONECT 272 271 +CONECT 273 274 275 271 279 +CONECT 274 273 +CONECT 275 276 277 273 278 +CONECT 276 275 +CONECT 277 275 +CONECT 278 275 +CONECT 279 273 280 +CONECT 280 279 +CONECT 281 283 271 282 +CONECT 282 281 +CONECT 283 293 284 281 +CONECT 284 285 287 283 294 +CONECT 285 286 300 284 +CONECT 286 285 +CONECT 287 295 296 284 288 +CONECT 288 287 289 290 +CONECT 289 298 288 292 +CONECT 290 288 297 291 +CONECT 291 292 290 299 +CONECT 292 289 291 881 +CONECT 293 283 +CONECT 294 284 +CONECT 295 287 +CONECT 296 287 +CONECT 297 290 +CONECT 298 289 +CONECT 299 291 +CONECT 300 302 285 301 +CONECT 301 300 +CONECT 302 313 303 300 304 +CONECT 303 302 +CONECT 304 302 307 306 305 +CONECT 305 304 +CONECT 306 304 +CONECT 307 309 310 304 308 +CONECT 308 307 +CONECT 309 307 +CONECT 310 311 307 312 +CONECT 311 310 +CONECT 312 310 +CONECT 313 315 314 302 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 323 319 318 315 +CONECT 318 317 +CONECT 319 322 321 317 320 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 325 324 317 +CONECT 324 323 +CONECT 325 327 326 323 +CONECT 326 325 +CONECT 327 339 329 328 325 +CONECT 328 327 +CONECT 329 330 335 327 331 +CONECT 330 329 +CONECT 331 329 332 334 333 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 338 337 329 336 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 340 341 327 +CONECT 340 339 +CONECT 341 343 339 342 +CONECT 342 341 +CONECT 343 345 344 351 341 +CONECT 344 343 +CONECT 345 348 346 347 343 +CONECT 346 345 +CONECT 347 345 +CONECT 348 349 350 345 +CONECT 349 348 +CONECT 350 348 +CONECT 351 343 353 352 +CONECT 352 351 +CONECT 353 354 351 355 +CONECT 354 353 +CONECT 355 353 375 374 356 +CONECT 356 357 358 359 355 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 360 373 +CONECT 360 359 361 362 +CONECT 361 360 +CONECT 362 360 363 364 +CONECT 363 362 +CONECT 364 362 365 373 +CONECT 365 364 366 367 +CONECT 366 365 +CONECT 367 365 368 369 +CONECT 368 367 +CONECT 369 367 370 371 +CONECT 370 369 +CONECT 371 369 372 373 +CONECT 372 371 +CONECT 373 359 364 371 +CONECT 374 355 +CONECT 375 377 355 376 +CONECT 376 375 +CONECT 377 378 379 375 +CONECT 378 377 +CONECT 379 381 377 380 385 +CONECT 380 379 +CONECT 381 383 382 384 379 +CONECT 382 381 +CONECT 383 381 +CONECT 384 381 +CONECT 385 379 386 387 +CONECT 386 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 391 390 400 +CONECT 390 389 +CONECT 391 394 389 392 393 +CONECT 392 391 +CONECT 393 391 +CONECT 394 395 397 396 391 +CONECT 395 394 +CONECT 396 394 +CONECT 397 399 394 398 +CONECT 398 397 +CONECT 399 397 +CONECT 400 389 402 401 +CONECT 401 400 +CONECT 402 403 400 404 +CONECT 403 402 +CONECT 404 402 406 410 405 +CONECT 405 404 +CONECT 406 407 408 404 409 +CONECT 407 406 +CONECT 408 406 +CONECT 409 406 +CONECT 410 412 404 411 +CONECT 411 410 +CONECT 412 413 414 410 +CONECT 413 412 +CONECT 414 416 412 415 425 +CONECT 415 414 +CONECT 416 417 418 419 414 +CONECT 417 416 +CONECT 418 416 +CONECT 419 422 416 421 420 +CONECT 420 419 +CONECT 421 419 +CONECT 422 423 424 419 +CONECT 423 422 +CONECT 424 422 +CONECT 425 414 427 426 +CONECT 426 425 +CONECT 427 428 425 429 +CONECT 428 427 +CONECT 429 427 431 430 447 +CONECT 430 429 +CONECT 431 434 432 433 429 +CONECT 432 431 +CONECT 433 431 +CONECT 434 437 436 435 431 +CONECT 435 434 +CONECT 436 434 +CONECT 437 440 438 434 439 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 442 441 437 +CONECT 441 440 +CONECT 442 440 +CONECT 443 446 445 444 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 +CONECT 447 429 449 448 +CONECT 448 447 +CONECT 449 450 447 451 +CONECT 450 449 +CONECT 451 449 453 452 467 +CONECT 452 451 +CONECT 453 456 454 451 455 +CONECT 454 453 +CONECT 455 453 +CONECT 456 457 465 453 +CONECT 457 459 458 456 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 462 459 463 +CONECT 462 461 +CONECT 463 461 464 465 +CONECT 464 463 +CONECT 465 463 456 466 +CONECT 466 465 +CONECT 467 451 469 468 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 473 469 481 472 +CONECT 472 471 +CONECT 473 474 479 475 471 +CONECT 474 473 +CONECT 475 476 473 477 478 +CONECT 476 475 +CONECT 477 475 +CONECT 478 475 +CONECT 479 480 473 +CONECT 480 479 +CONECT 481 483 471 482 +CONECT 482 481 +CONECT 483 484 485 481 +CONECT 484 483 +CONECT 485 487 483 486 503 +CONECT 486 485 +CONECT 487 490 488 489 485 +CONECT 488 487 +CONECT 489 487 +CONECT 490 493 492 491 487 +CONECT 491 490 +CONECT 492 490 +CONECT 493 496 494 495 490 +CONECT 494 493 +CONECT 495 493 +CONECT 496 498 499 497 493 +CONECT 497 496 +CONECT 498 496 +CONECT 499 501 496 500 502 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 485 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 508 513 +CONECT 508 507 +CONECT 509 511 512 507 510 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 507 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 534 533 518 +CONECT 518 519 520 521 517 +CONECT 519 518 +CONECT 520 518 +CONECT 521 518 522 523 524 +CONECT 522 521 +CONECT 523 521 +CONECT 524 521 525 526 527 +CONECT 525 524 +CONECT 526 524 +CONECT 527 524 528 529 530 +CONECT 528 527 +CONECT 529 527 +CONECT 530 527 531 532 +CONECT 531 530 +CONECT 532 530 +CONECT 533 517 +CONECT 534 536 517 535 +CONECT 535 534 +CONECT 536 537 538 534 +CONECT 537 536 +CONECT 538 540 536 544 539 +CONECT 539 538 +CONECT 540 541 542 543 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 +CONECT 544 546 538 545 +CONECT 545 544 +CONECT 546 547 548 544 +CONECT 547 546 +CONECT 548 550 546 549 558 +CONECT 549 548 +CONECT 550 553 551 552 548 +CONECT 551 550 +CONECT 552 550 +CONECT 553 555 554 550 +CONECT 554 553 +CONECT 555 557 556 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 548 560 559 +CONECT 559 558 +CONECT 560 561 558 562 +CONECT 561 560 +CONECT 562 560 563 564 570 +CONECT 563 562 +CONECT 564 565 562 567 566 +CONECT 565 564 +CONECT 566 564 +CONECT 567 568 569 564 +CONECT 568 567 +CONECT 569 567 +CONECT 570 562 572 571 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 592 591 575 +CONECT 575 576 577 578 574 +CONECT 576 575 +CONECT 577 575 +CONECT 578 575 579 580 581 +CONECT 579 578 +CONECT 580 578 +CONECT 581 578 582 583 584 +CONECT 582 581 +CONECT 583 581 +CONECT 584 581 585 586 587 +CONECT 585 584 +CONECT 586 584 +CONECT 587 584 588 589 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 574 +CONECT 592 594 574 593 +CONECT 593 592 +CONECT 594 595 596 592 +CONECT 595 594 +CONECT 596 599 598 594 597 +CONECT 597 596 +CONECT 598 596 +CONECT 599 601 600 596 +CONECT 600 599 +CONECT 601 603 602 599 +CONECT 602 601 +CONECT 603 623 622 601 604 +CONECT 604 605 606 607 603 +CONECT 605 604 +CONECT 606 604 +CONECT 607 604 608 609 610 +CONECT 608 607 +CONECT 609 607 +CONECT 610 607 611 612 613 +CONECT 611 610 +CONECT 612 610 +CONECT 613 610 614 615 +CONECT 614 613 +CONECT 615 613 616 619 +CONECT 616 615 617 618 +CONECT 617 616 +CONECT 618 616 +CONECT 619 615 620 621 +CONECT 620 619 +CONECT 621 619 +CONECT 622 603 +CONECT 623 625 624 603 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 629 635 628 625 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 632 +CONECT 635 636 637 627 +CONECT 636 635 +CONECT 637 639 635 638 +CONECT 638 637 +CONECT 639 642 640 641 637 +CONECT 640 639 +CONECT 641 639 +CONECT 642 644 643 639 +CONECT 643 642 +CONECT 644 646 645 642 +CONECT 645 644 +CONECT 646 648 647 657 644 +CONECT 647 646 +CONECT 648 650 651 649 646 +CONECT 649 648 +CONECT 650 648 +CONECT 651 653 654 648 652 +CONECT 652 651 +CONECT 653 651 +CONECT 654 655 651 656 +CONECT 655 654 +CONECT 656 654 +CONECT 657 659 646 658 +CONECT 658 657 +CONECT 659 660 661 657 +CONECT 660 659 +CONECT 661 681 659 680 662 +CONECT 662 663 664 665 661 +CONECT 663 662 +CONECT 664 662 +CONECT 665 662 666 667 668 +CONECT 666 665 +CONECT 667 665 +CONECT 668 665 669 670 671 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 672 673 +CONECT 672 671 +CONECT 673 671 674 677 +CONECT 674 673 675 676 +CONECT 675 674 +CONECT 676 674 +CONECT 677 673 678 679 +CONECT 678 677 +CONECT 679 677 +CONECT 680 661 +CONECT 681 682 683 661 +CONECT 682 681 +CONECT 683 685 681 684 +CONECT 684 683 +CONECT 685 686 687 695 683 +CONECT 686 685 +CONECT 687 689 693 685 688 +CONECT 688 687 +CONECT 689 692 691 690 687 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 +CONECT 693 687 694 +CONECT 694 693 +CONECT 695 697 685 696 +CONECT 696 695 +CONECT 697 698 699 695 +CONECT 698 697 +CONECT 699 714 697 713 700 +CONECT 700 701 702 706 699 +CONECT 701 700 +CONECT 702 700 703 704 705 +CONECT 703 702 +CONECT 704 702 +CONECT 705 702 +CONECT 706 700 707 708 709 +CONECT 707 706 +CONECT 708 706 +CONECT 709 706 710 711 712 +CONECT 710 709 +CONECT 711 709 +CONECT 712 709 +CONECT 713 699 +CONECT 714 715 716 699 +CONECT 715 714 +CONECT 716 718 714 717 +CONECT 717 716 +CONECT 718 719 726 720 716 +CONECT 719 718 +CONECT 720 723 718 721 722 +CONECT 721 720 +CONECT 722 720 +CONECT 723 725 724 720 +CONECT 724 723 +CONECT 725 723 +CONECT 726 728 718 727 +CONECT 727 726 +CONECT 728 729 730 726 +CONECT 729 728 +CONECT 730 732 728 738 731 +CONECT 731 730 +CONECT 732 734 735 733 730 +CONECT 733 732 +CONECT 734 732 +CONECT 735 736 732 737 +CONECT 736 735 +CONECT 737 735 +CONECT 738 740 730 739 +CONECT 739 738 +CONECT 740 741 742 738 +CONECT 741 740 +CONECT 742 744 743 740 748 +CONECT 743 742 +CONECT 744 747 745 746 742 +CONECT 745 744 +CONECT 746 744 +CONECT 747 744 +CONECT 748 742 749 750 +CONECT 749 748 +CONECT 750 748 751 752 +CONECT 751 750 +CONECT 752 750 753 754 762 +CONECT 753 752 +CONECT 754 756 752 760 755 +CONECT 755 754 +CONECT 756 758 759 757 754 +CONECT 757 756 +CONECT 758 756 +CONECT 759 756 +CONECT 760 761 754 +CONECT 761 760 +CONECT 762 752 764 763 +CONECT 763 762 +CONECT 764 765 766 762 +CONECT 765 764 +CONECT 766 767 764 768 784 +CONECT 767 766 +CONECT 768 771 766 770 769 +CONECT 769 768 +CONECT 770 768 +CONECT 771 774 772 773 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 777 776 775 771 +CONECT 775 774 +CONECT 776 774 +CONECT 777 780 779 778 774 +CONECT 778 777 +CONECT 779 777 +CONECT 780 782 781 783 777 +CONECT 781 780 +CONECT 782 780 +CONECT 783 780 +CONECT 784 766 786 785 +CONECT 785 784 +CONECT 786 787 784 788 +CONECT 787 786 +CONECT 788 786 798 790 789 +CONECT 789 788 +CONECT 790 791 788 796 792 +CONECT 791 790 +CONECT 792 790 793 794 795 +CONECT 793 792 +CONECT 794 792 +CONECT 795 792 +CONECT 796 797 790 +CONECT 797 796 +CONECT 798 799 788 800 +CONECT 799 798 +CONECT 800 798 802 801 +CONECT 801 800 +CONECT 802 803 800 804 818 +CONECT 803 802 +CONECT 804 807 802 806 805 +CONECT 805 804 +CONECT 806 804 +CONECT 807 816 808 804 +CONECT 808 810 807 809 +CONECT 809 808 +CONECT 810 812 811 808 +CONECT 811 810 +CONECT 812 813 814 810 +CONECT 813 812 +CONECT 814 815 812 816 +CONECT 815 814 +CONECT 816 814 817 807 +CONECT 817 816 +CONECT 818 802 820 819 +CONECT 819 818 +CONECT 820 821 818 822 +CONECT 821 820 +CONECT 822 820 824 832 823 +CONECT 823 822 +CONECT 824 830 826 825 822 +CONECT 825 824 +CONECT 826 827 829 824 828 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 +CONECT 830 831 824 +CONECT 831 830 +CONECT 832 833 822 834 +CONECT 833 832 +CONECT 834 832 836 835 +CONECT 835 834 +CONECT 836 846 845 834 837 +CONECT 837 838 839 843 836 +CONECT 838 837 +CONECT 839 837 840 841 842 +CONECT 840 839 +CONECT 841 839 +CONECT 842 839 +CONECT 843 837 844 +CONECT 844 843 +CONECT 845 836 +CONECT 846 848 847 836 +CONECT 847 846 +CONECT 848 850 849 846 +CONECT 849 848 +CONECT 850 862 848 863 851 +CONECT 851 852 853 854 850 +CONECT 852 851 +CONECT 853 851 +CONECT 854 851 855 856 857 +CONECT 855 854 +CONECT 856 854 +CONECT 857 854 858 859 +CONECT 858 857 +CONECT 859 857 860 861 +CONECT 860 859 +CONECT 861 859 +CONECT 862 850 +CONECT 863 850 865 864 +CONECT 864 863 +CONECT 865 866 863 867 +CONECT 866 865 +CONECT 867 869 865 878 868 +CONECT 868 867 +CONECT 869 871 870 872 867 +CONECT 870 869 +CONECT 871 869 +CONECT 872 873 869 874 875 +CONECT 873 872 +CONECT 874 872 +CONECT 875 872 876 877 +CONECT 876 875 +CONECT 877 875 +CONECT 878 880 867 879 +CONECT 879 878 +CONECT 880 878 +CONECT 881 87 292 882 261 +CONECT 882 881 884 +CONECT 883 886 884 887 885 +CONECT 884 882 883 +CONECT 885 883 +CONECT 886 883 +CONECT 887 883 +CONECT 888 889 +CONECT 889 888 890 +CONECT 890 889 +MASTER 0 0 0 0 0 0 0 0 890 0 890 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_6.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_6.pdb new file mode 100644 index 0000000..833da76 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_6.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.304 51.40416666666647 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.153 37.973 23.612 1.00 0.00 N +ATOM 2 H1 MET 1 15.135 38.357 24.556 1.00 0.00 H +ATOM 3 H2 MET 1 14.375 38.346 23.089 1.00 0.00 H +ATOM 4 H3 MET 1 16.016 38.284 23.187 1.00 0.00 H +ATOM 5 CA MET 1 15.124 36.505 23.669 1.00 0.00 C +ATOM 6 HA MET 1 14.170 36.198 24.097 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.876 22.273 1.00 0.00 C +ATOM 8 HB2 MET 1 14.391 36.152 21.672 1.00 0.00 H +ATOM 9 HB3 MET 1 16.152 36.273 21.776 1.00 0.00 H +ATOM 10 CG MET 1 15.373 34.334 22.298 1.00 0.00 C +ATOM 11 HG2 MET 1 16.260 34.066 22.868 1.00 0.00 H +ATOM 12 HG3 MET 1 14.495 33.925 22.807 1.00 0.00 H +ATOM 13 SD MET 1 15.530 33.526 20.668 1.00 0.00 S +ATOM 14 CE MET 1 13.816 33.572 20.068 1.00 0.00 C +ATOM 15 HE1 MET 1 13.463 34.602 20.016 1.00 0.00 H +ATOM 16 HE2 MET 1 13.776 33.133 19.073 1.00 0.00 H +ATOM 17 HE3 MET 1 13.173 32.997 20.735 1.00 0.00 H +ATOM 18 C MET 1 16.218 36.031 24.600 1.00 0.00 C +ATOM 19 O MET 1 17.377 36.398 24.428 1.00 0.00 O +ATOM 20 N GLN 2 15.878 35.187 25.578 1.00 0.00 N +ATOM 21 H GLN 2 14.912 34.996 25.769 1.00 0.00 H +ATOM 22 CA GLN 2 16.850 34.477 26.430 1.00 0.00 C +ATOM 23 HA GLN 2 17.657 35.151 26.723 1.00 0.00 H +ATOM 24 CB GLN 2 16.115 34.070 27.723 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.137 33.653 27.496 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.662 33.325 28.279 1.00 0.00 H +ATOM 27 CG GLN 2 15.931 35.257 28.675 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.459 36.087 28.164 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.214 34.973 29.414 1.00 0.00 H +ATOM 30 CD GLN 2 17.128 35.581 29.524 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.143 34.924 29.512 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.039 36.476 30.468 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.764 36.535 31.087 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.097 36.723 30.761 1.00 0.00 H +ATOM 35 C GLN 2 17.499 33.301 25.666 1.00 0.00 C +ATOM 36 O GLN 2 17.102 32.148 25.829 1.00 0.00 O +ATOM 37 N TYR 3 18.478 33.617 24.821 1.00 0.00 N +ATOM 38 H TYR 3 18.752 34.594 24.754 1.00 0.00 H +ATOM 39 CA TYR 3 19.260 32.619 24.100 1.00 0.00 C +ATOM 40 HA TYR 3 18.568 31.967 23.564 1.00 0.00 H +ATOM 41 CB TYR 3 20.192 33.285 23.100 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.866 33.942 23.645 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.781 32.481 22.672 1.00 0.00 H +ATOM 44 CG TYR 3 19.610 34.068 21.937 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.530 33.458 20.670 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.822 32.423 20.550 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.147 34.204 19.542 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.116 33.738 18.567 1.00 0.00 H +ATOM 49 CZ TYR 3 18.844 35.573 19.676 1.00 0.00 C +ATOM 50 OH TYR 3 18.514 36.309 18.584 1.00 0.00 O +ATOM 51 HH TYR 3 18.772 35.874 17.768 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.930 36.189 20.940 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.728 37.250 21.025 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.324 35.441 22.067 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.446 35.934 23.023 1.00 0.00 H +ATOM 56 C TYR 3 20.089 31.764 25.076 1.00 0.00 C +ATOM 57 O TYR 3 20.459 32.245 26.150 1.00 0.00 O +ATOM 58 N LYS 4 20.399 30.504 24.735 1.00 0.00 N +ATOM 59 H LYS 4 20.250 30.220 23.771 1.00 0.00 H +ATOM 60 CA LYS 4 21.010 29.502 25.633 1.00 0.00 C +ATOM 61 HA LYS 4 20.726 29.715 26.656 1.00 0.00 H +ATOM 62 CB LYS 4 20.476 28.101 25.273 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.522 27.982 24.192 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.145 27.345 25.699 1.00 0.00 H +ATOM 65 CG LYS 4 19.052 27.746 25.738 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.888 26.697 25.498 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.995 27.853 26.819 1.00 0.00 H +ATOM 68 CD LYS 4 17.923 28.564 25.084 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.886 29.557 25.526 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.149 28.678 24.022 1.00 0.00 H +ATOM 71 CE LYS 4 16.546 27.888 25.193 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.815 28.507 24.665 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.597 26.933 24.667 1.00 0.00 H +ATOM 74 NZ LYS 4 16.095 27.656 26.590 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.985 28.529 27.089 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.207 27.154 26.591 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.756 27.063 27.077 1.00 0.00 H +ATOM 78 C LYS 4 22.551 29.511 25.619 1.00 0.00 C +ATOM 79 O LYS 4 23.196 29.886 24.647 1.00 0.00 O +HETATM 80 N HX1 5 23.171 29.029 26.694 1.00 0.00 N +HETATM 81 CA HX1 5 24.625 28.832 26.820 1.00 0.00 C +HETATM 82 C HX1 5 24.899 27.672 27.782 1.00 0.00 C +HETATM 83 O HX1 5 24.405 27.683 28.909 1.00 0.00 O +HETATM 84 CB HX1 5 25.264 30.145 27.306 1.00 0.00 C +HETATM 85 CG HX1 5 26.774 30.239 27.392 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.706 29.285 27.072 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.427 31.385 27.861 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.732 31.095 27.755 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.938 29.837 27.336 1.00 0.00 N +HETATM 90 H HX1 5 22.596 28.839 27.521 1.00 0.00 H +HETATM 91 HA HX1 5 25.040 28.578 25.841 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.857 30.383 28.292 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.940 30.947 26.639 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.545 28.282 26.700 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.531 31.750 28.083 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.839 29.356 27.352 1.00 0.00 H +ATOM 97 N ILE 6 25.634 26.658 27.326 1.00 0.00 N +ATOM 98 H ILE 6 26.015 26.711 26.385 1.00 0.00 H +ATOM 99 CA ILE 6 26.003 25.472 28.116 1.00 0.00 C +ATOM 100 HA ILE 6 25.303 25.370 28.945 1.00 0.00 H +ATOM 101 CB ILE 6 25.851 24.199 27.246 1.00 0.00 C +ATOM 102 HB ILE 6 26.401 24.347 26.317 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.409 22.939 27.935 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.892 22.757 28.878 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.288 22.070 27.288 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.481 23.048 28.117 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.345 24.012 26.914 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.791 23.875 27.842 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.967 24.915 26.433 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.010 22.847 25.977 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.180 21.893 26.476 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.956 22.904 25.700 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.617 22.905 25.073 1.00 0.00 H +ATOM 114 C ILE 6 27.392 25.668 28.756 1.00 0.00 C +ATOM 115 O ILE 6 28.227 26.398 28.224 1.00 0.00 O +ATOM 116 N VAL 7 27.598 25.081 29.940 1.00 0.00 N +ATOM 117 H VAL 7 26.867 24.478 30.298 1.00 0.00 H +ATOM 118 CA VAL 7 28.776 25.287 30.804 1.00 0.00 C +ATOM 119 HA VAL 7 28.877 26.362 30.959 1.00 0.00 H +ATOM 120 CB VAL 7 28.499 24.641 32.179 1.00 0.00 C +ATOM 121 HB VAL 7 27.500 24.950 32.487 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.522 23.107 32.134 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.532 22.745 31.926 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.190 22.716 33.090 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.855 22.747 31.351 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.449 25.111 33.285 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.505 26.198 33.292 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.077 24.778 34.251 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.446 24.702 33.142 1.00 0.00 H +ATOM 130 C VAL 7 30.110 24.804 30.202 1.00 0.00 C +ATOM 131 O VAL 7 30.151 23.918 29.351 1.00 0.00 O +ATOM 132 N THR 8 31.213 25.378 30.689 1.00 0.00 N +ATOM 133 H THR 8 31.110 26.089 31.397 1.00 0.00 H +ATOM 134 CA THR 8 32.596 24.972 30.392 1.00 0.00 C +ATOM 135 HA THR 8 32.687 24.827 29.316 1.00 0.00 H +ATOM 136 CB THR 8 33.570 26.088 30.816 1.00 0.00 C +ATOM 137 HB THR 8 34.595 25.756 30.638 1.00 0.00 H +ATOM 138 CG2 THR 8 33.356 27.393 30.055 1.00 0.00 C +ATOM 139 HG21 THR 8 32.383 27.824 30.296 1.00 0.00 H +ATOM 140 HG22 THR 8 34.132 28.110 30.323 1.00 0.00 H +ATOM 141 HG23 THR 8 33.403 27.212 28.983 1.00 0.00 H +ATOM 142 OG1 THR 8 33.422 26.396 32.182 1.00 0.00 O +ATOM 143 HG1 THR 8 33.806 27.265 32.319 1.00 0.00 H +ATOM 144 C THR 8 33.009 23.656 31.077 1.00 0.00 C +ATOM 145 O THR 8 32.460 23.250 32.105 1.00 0.00 O +ATOM 146 N GLY 9 34.047 23.007 30.532 1.00 0.00 N +ATOM 147 H GLY 9 34.399 23.335 29.647 1.00 0.00 H +ATOM 148 CA GLY 9 34.624 21.774 31.075 1.00 0.00 C +ATOM 149 HA2 GLY 9 35.615 21.618 30.651 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.731 21.881 32.155 1.00 0.00 H +ATOM 151 C GLY 9 33.782 20.522 30.787 1.00 0.00 C +ATOM 152 O GLY 9 33.016 20.483 29.828 1.00 0.00 O +ATOM 153 N LYS 10 33.954 19.478 31.612 1.00 0.00 N +ATOM 154 H LYS 10 34.677 19.557 32.311 1.00 0.00 H +ATOM 155 CA LYS 10 33.235 18.188 31.477 1.00 0.00 C +ATOM 156 HA LYS 10 32.295 18.399 30.965 1.00 0.00 H +ATOM 157 CB LYS 10 34.063 17.245 30.575 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.682 17.846 29.905 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.730 16.638 31.191 1.00 0.00 H +ATOM 160 CG LYS 10 33.197 16.330 29.689 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.601 15.663 30.311 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.521 16.954 29.102 1.00 0.00 H +ATOM 163 CD LYS 10 34.060 15.496 28.727 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.718 16.162 28.166 1.00 0.00 H +ATOM 165 HD3 LYS 10 34.669 14.795 29.300 1.00 0.00 H +ATOM 166 CE LYS 10 33.176 14.722 27.742 1.00 0.00 C +ATOM 167 HE2 LYS 10 32.606 13.970 28.293 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.467 15.417 27.287 1.00 0.00 H +ATOM 169 NZ LYS 10 33.968 14.073 26.670 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.727 13.511 27.035 1.00 0.00 H +ATOM 171 HZ2 LYS 10 33.369 13.526 26.062 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.418 14.773 26.065 1.00 0.00 H +ATOM 173 C LYS 10 32.827 17.542 32.811 1.00 0.00 C +ATOM 174 O LYS 10 32.345 16.412 32.831 1.00 0.00 O +ATOM 175 N SER 11 33.039 18.242 33.932 1.00 0.00 N +ATOM 176 H SER 11 33.491 19.134 33.839 1.00 0.00 H +ATOM 177 CA SER 11 32.567 17.848 35.278 1.00 0.00 C +ATOM 178 HA SER 11 32.502 16.757 35.338 1.00 0.00 H +ATOM 179 CB SER 11 33.554 18.327 36.351 1.00 0.00 C +ATOM 180 HB2 SER 11 33.584 19.416 36.351 1.00 0.00 H +ATOM 181 HB3 SER 11 33.218 17.982 37.329 1.00 0.00 H +ATOM 182 OG SER 11 34.851 17.824 36.092 1.00 0.00 O +ATOM 183 HG SER 11 35.507 18.429 36.454 1.00 0.00 H +ATOM 184 C SER 11 31.179 18.417 35.586 1.00 0.00 C +ATOM 185 O SER 11 30.350 17.745 36.192 1.00 0.00 O +ATOM 186 N CYS 12 30.920 19.653 35.153 1.00 0.00 N +ATOM 187 H CYS 12 31.631 20.135 34.631 1.00 0.00 H +ATOM 188 CA CYS 12 29.595 20.268 35.152 1.00 0.00 C +ATOM 189 HA CYS 12 29.010 19.868 35.983 1.00 0.00 H +ATOM 190 CB CYS 12 29.748 21.791 35.352 1.00 0.00 C +ATOM 191 HB2 CYS 12 30.323 22.214 34.524 1.00 0.00 H +ATOM 192 HB3 CYS 12 28.757 22.249 35.361 1.00 0.00 H +ATOM 193 SG CYS 12 30.576 22.147 36.926 1.00 0.00 S +ATOM 194 HG CYS 12 30.147 23.411 37.056 1.00 0.00 H +ATOM 195 C CYS 12 28.852 19.934 33.837 1.00 0.00 C +ATOM 196 O CYS 12 29.493 19.664 32.824 1.00 0.00 O +ATOM 197 N LYS 13 27.512 19.988 33.846 1.00 0.00 N +ATOM 198 H LYS 13 27.061 20.142 34.737 1.00 0.00 H +ATOM 199 CA LYS 13 26.668 19.719 32.664 1.00 0.00 C +ATOM 200 HA LYS 13 27.272 19.856 31.774 1.00 0.00 H +ATOM 201 CB LYS 13 26.222 18.245 32.710 1.00 0.00 C +ATOM 202 HB2 LYS 13 27.030 17.652 33.147 1.00 0.00 H +ATOM 203 HB3 LYS 13 25.343 18.143 33.363 1.00 0.00 H +ATOM 204 CG LYS 13 25.911 17.632 31.329 1.00 0.00 C +ATOM 205 HG2 LYS 13 25.032 18.104 30.890 1.00 0.00 H +ATOM 206 HG3 LYS 13 26.763 17.815 30.673 1.00 0.00 H +ATOM 207 CD LYS 13 25.679 16.113 31.416 1.00 0.00 C +ATOM 208 HD2 LYS 13 25.682 15.711 30.401 1.00 0.00 H +ATOM 209 HD3 LYS 13 26.513 15.660 31.956 1.00 0.00 H +ATOM 210 CE LYS 13 24.341 15.743 32.073 1.00 0.00 C +ATOM 211 HE2 LYS 13 24.161 16.384 32.939 1.00 0.00 H +ATOM 212 HE3 LYS 13 23.551 15.953 31.349 1.00 0.00 H +ATOM 213 NZ LYS 13 24.295 14.306 32.456 1.00 0.00 N +ATOM 214 HZ1 LYS 13 24.868 14.092 33.273 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.348 13.998 32.647 1.00 0.00 H +ATOM 216 HZ3 LYS 13 24.677 13.728 31.708 1.00 0.00 H +ATOM 217 C LYS 13 25.489 20.705 32.507 1.00 0.00 C +ATOM 218 O LYS 13 24.585 20.485 31.710 1.00 0.00 O +ATOM 219 N GLY 14 25.482 21.785 33.297 1.00 0.00 N +ATOM 220 H GLY 14 26.293 21.943 33.873 1.00 0.00 H +ATOM 221 CA GLY 14 24.378 22.751 33.377 1.00 0.00 C +ATOM 222 HA2 GLY 14 23.446 22.191 33.448 1.00 0.00 H +ATOM 223 HA3 GLY 14 24.484 23.328 34.293 1.00 0.00 H +ATOM 224 C GLY 14 24.287 23.715 32.195 1.00 0.00 C +ATOM 225 O GLY 14 25.215 23.890 31.406 1.00 0.00 O +ATOM 226 N VAL 15 23.147 24.399 32.109 1.00 0.00 N +ATOM 227 H VAL 15 22.434 24.247 32.808 1.00 0.00 H +ATOM 228 CA VAL 15 22.780 25.390 31.070 1.00 0.00 C +ATOM 229 HA VAL 15 23.676 25.631 30.490 1.00 0.00 H +ATOM 230 CB VAL 15 21.762 24.738 30.086 1.00 0.00 C +ATOM 231 HB VAL 15 22.219 23.858 29.682 1.00 0.00 H +ATOM 232 CG1 VAL 15 20.449 24.323 30.767 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.939 25.182 31.209 1.00 0.00 H +ATOM 234 HG12 VAL 15 19.794 23.862 30.026 1.00 0.00 H +ATOM 235 HG13 VAL 15 20.644 23.583 31.546 1.00 0.00 H +ATOM 236 CG2 VAL 15 21.419 25.672 28.928 1.00 0.00 C +ATOM 237 HG21 VAL 15 22.336 26.009 28.435 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.822 25.122 28.195 1.00 0.00 H +ATOM 239 HG23 VAL 15 20.846 26.536 29.269 1.00 0.00 H +ATOM 240 C VAL 15 22.285 26.687 31.731 1.00 0.00 C +ATOM 241 O VAL 15 21.718 26.631 32.821 1.00 0.00 O +HETATM 242 N HY1 16 22.498 27.830 31.091 1.00 0.00 N +HETATM 243 CA HY1 16 21.925 29.110 31.451 1.00 0.00 C +HETATM 244 C HY1 16 21.620 29.885 30.134 1.00 0.00 C +HETATM 245 O HY1 16 21.778 29.349 29.016 1.00 0.00 O +HETATM 246 CB HY1 16 22.863 29.871 32.416 1.00 0.00 C +HETATM 247 CG HY1 16 24.211 30.225 31.815 1.00 0.00 C +HETATM 248 CD2 HY1 16 24.548 31.406 31.209 1.00 0.00 C +HETATM 249 ND1 HY1 16 25.320 29.397 31.739 1.00 0.00 N +HETATM 250 CE1 HY1 16 26.302 30.092 31.143 1.00 0.00 C +HETATM 251 NE2 HY1 16 25.879 31.314 30.787 1.00 0.00 N +HETATM 252 H HY1 16 22.998 27.783 30.212 1.00 0.00 H +HETATM 253 HA HY1 16 20.967 28.994 31.944 1.00 0.00 H +HETATM 254 HB2 HY1 16 22.401 30.797 32.776 1.00 0.00 H +HETATM 255 HB3 HY1 16 23.027 29.258 33.299 1.00 0.00 H +HETATM 256 HD1 HY1 16 25.398 28.459 32.130 1.00 0.00 H +HETATM 257 HD2 HY1 16 23.906 32.259 31.098 1.00 0.00 H +HETATM 258 HE1 HY1 16 27.313 29.729 30.997 1.00 0.00 H +ATOM 259 N THR 17 21.169 31.140 30.273 1.00 0.00 N +ATOM 260 H THR 17 21.053 31.462 31.222 1.00 0.00 H +ATOM 261 CA THR 17 20.726 32.026 29.179 1.00 0.00 C +ATOM 262 HA THR 17 21.105 31.634 28.291 1.00 0.00 H +ATOM 263 CB THR 17 19.149 32.016 29.046 1.00 0.00 C +ATOM 264 HB THR 17 18.923 32.604 28.170 1.00 0.00 H +ATOM 265 CG2 THR 17 18.589 30.665 28.720 1.00 0.00 C +ATOM 266 HG21 THR 17 18.790 29.907 29.432 1.00 0.00 H +ATOM 267 HG22 THR 17 17.504 30.697 28.632 1.00 0.00 H +ATOM 268 HG23 THR 17 18.931 30.334 27.781 1.00 0.00 H +ATOM 269 OG1 THR 17 18.484 32.464 30.197 1.00 0.00 O +ATOM 270 HG1 THR 17 18.581 33.451 30.206 1.00 0.00 H +ATOM 271 C THR 17 21.249 33.458 29.234 1.00 0.00 C +ATOM 272 O THR 17 21.706 33.922 30.266 1.00 0.00 O +HETATM 273 N HY2 18 21.133 34.157 28.097 1.00 0.00 N +HETATM 274 CA HY2 18 21.447 35.619 27.968 1.00 0.00 C +HETATM 275 C HY2 18 20.323 36.288 27.216 1.00 0.00 C +HETATM 276 O HY2 18 19.983 35.838 26.129 1.00 0.00 O +HETATM 277 CB HY2 18 22.769 35.819 27.255 1.00 0.00 C +HETATM 278 CG HY2 18 23.998 35.326 28.000 1.00 0.00 C +HETATM 279 CD2 HY2 18 24.419 34.029 28.151 1.00 0.00 C +HETATM 280 ND1 HY2 18 24.941 36.119 28.642 1.00 0.00 N +HETATM 281 CE1 HY2 18 25.882 35.317 29.157 1.00 0.00 C +HETATM 282 NE2 HY2 18 25.603 34.030 28.899 1.00 0.00 N +HETATM 283 H HY2 18 20.783 33.707 27.234 1.00 0.00 H +HETATM 284 HA HY2 18 21.501 36.055 29.015 1.00 0.00 H +HETATM 285 HB2 HY2 18 22.747 35.291 26.296 1.00 0.00 H +HETATM 286 HB3 HY2 18 22.912 36.877 27.054 1.00 0.00 H +HETATM 287 HD1 HY2 18 24.953 37.122 28.679 1.00 0.00 H +HETATM 288 HD2 HY2 18 23.930 33.168 27.777 1.00 0.00 H +HETATM 289 HE1 HY2 18 26.758 35.649 29.684 1.00 0.00 H +ATOM 290 N GLU 19 19.806 37.389 27.746 1.00 0.00 N +ATOM 291 H GLU 19 20.137 37.679 28.643 1.00 0.00 H +ATOM 292 CA GLU 19 18.797 38.219 27.105 1.00 0.00 C +ATOM 293 HA GLU 19 18.056 37.553 26.623 1.00 0.00 H +ATOM 294 CB GLU 19 18.066 39.075 28.153 1.00 0.00 C +ATOM 295 HB2 GLU 19 17.753 38.431 28.965 1.00 0.00 H +ATOM 296 HB3 GLU 19 18.774 39.783 28.568 1.00 0.00 H +ATOM 297 CG GLU 19 16.827 39.851 27.656 1.00 0.00 C +ATOM 298 HG2 GLU 19 16.544 40.547 28.418 1.00 0.00 H +ATOM 299 HG3 GLU 19 17.083 40.405 26.761 1.00 0.00 H +ATOM 300 CD GLU 19 15.649 38.897 27.370 1.00 0.00 C +ATOM 301 OE1 GLU 19 15.578 38.371 26.227 1.00 0.00 O +ATOM 302 OE2 GLU 19 14.813 38.685 28.283 1.00 0.00 O +ATOM 303 C GLU 19 19.403 39.112 25.991 1.00 0.00 C +ATOM 304 O GLU 19 20.346 39.858 26.275 1.00 0.00 O +ATOM 305 N ALA 20 18.876 39.050 24.758 1.00 0.00 N +ATOM 306 H ALA 20 18.171 38.353 24.576 1.00 0.00 H +ATOM 307 CA ALA 20 19.261 39.964 23.687 1.00 0.00 C +ATOM 308 HA ALA 20 19.401 40.962 24.097 1.00 0.00 H +ATOM 309 CB ALA 20 20.589 39.491 23.095 1.00 0.00 C +ATOM 310 HB1 ALA 20 20.463 38.518 22.615 1.00 0.00 H +ATOM 311 HB2 ALA 20 20.950 40.207 22.354 1.00 0.00 H +ATOM 312 HB3 ALA 20 21.350 39.402 23.869 1.00 0.00 H +ATOM 313 C ALA 20 18.192 40.038 22.583 1.00 0.00 C +ATOM 314 O ALA 20 17.358 39.136 22.439 1.00 0.00 O +ATOM 315 N VAL 21 18.223 41.090 21.748 1.00 0.00 N +ATOM 316 H VAL 21 18.895 41.829 21.922 1.00 0.00 H +ATOM 317 CA VAL 21 17.459 41.151 20.464 1.00 0.00 C +ATOM 318 HA VAL 21 16.471 40.727 20.628 1.00 0.00 H +ATOM 319 CB VAL 21 17.272 42.602 19.975 1.00 0.00 C +ATOM 320 HB VAL 21 16.617 42.576 19.112 1.00 0.00 H +ATOM 321 CG1 VAL 21 16.594 43.474 21.037 1.00 0.00 C +ATOM 322 HG11 VAL 21 17.250 43.628 21.894 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.346 44.443 20.604 1.00 0.00 H +ATOM 324 HG13 VAL 21 15.670 43.000 21.367 1.00 0.00 H +ATOM 325 CG2 VAL 21 18.581 43.283 19.543 1.00 0.00 C +ATOM 326 HG21 VAL 21 19.005 42.771 18.677 1.00 0.00 H +ATOM 327 HG22 VAL 21 18.378 44.312 19.246 1.00 0.00 H +ATOM 328 HG23 VAL 21 19.314 43.286 20.352 1.00 0.00 H +ATOM 329 C VAL 21 18.120 40.335 19.354 1.00 0.00 C +ATOM 330 O VAL 21 17.471 39.995 18.376 1.00 0.00 O +ATOM 331 N ASP 22 19.412 40.053 19.508 1.00 0.00 N +ATOM 332 H ASP 22 19.861 40.330 20.363 1.00 0.00 H +ATOM 333 CA ASP 22 20.292 39.467 18.503 1.00 0.00 C +ATOM 334 HA ASP 22 19.710 38.829 17.831 1.00 0.00 H +ATOM 335 CB ASP 22 20.939 40.592 17.676 1.00 0.00 C +ATOM 336 HB2 ASP 22 20.170 41.084 17.077 1.00 0.00 H +ATOM 337 HB3 ASP 22 21.376 41.328 18.357 1.00 0.00 H +ATOM 338 CG ASP 22 22.019 40.045 16.749 1.00 0.00 C +ATOM 339 OD1 ASP 22 23.149 40.566 16.817 1.00 0.00 O +ATOM 340 OD2 ASP 22 21.744 39.033 16.072 1.00 0.00 O +ATOM 341 C ASP 22 21.365 38.599 19.176 1.00 0.00 C +ATOM 342 O ASP 22 21.822 38.878 20.287 1.00 0.00 O +ATOM 343 N TRP 23 21.790 37.551 18.485 1.00 0.00 N +ATOM 344 H TRP 23 21.507 37.496 17.513 1.00 0.00 H +ATOM 345 CA TRP 23 22.786 36.613 18.977 1.00 0.00 C +ATOM 346 HA TRP 23 22.544 36.362 20.008 1.00 0.00 H +ATOM 347 CB TRP 23 22.661 35.353 18.132 1.00 0.00 C +ATOM 348 HB2 TRP 23 21.641 34.979 18.209 1.00 0.00 H +ATOM 349 HB3 TRP 23 22.841 35.607 17.088 1.00 0.00 H +ATOM 350 CG TRP 23 23.572 34.246 18.526 1.00 0.00 C +ATOM 351 CD1 TRP 23 24.514 33.704 17.727 1.00 0.00 C +ATOM 352 HD1 TRP 23 24.735 34.018 16.716 1.00 0.00 H +ATOM 353 NE1 TRP 23 25.125 32.677 18.407 1.00 0.00 N +ATOM 354 HE1 TRP 23 25.897 32.152 18.028 1.00 0.00 H +ATOM 355 CE2 TRP 23 24.587 32.476 19.654 1.00 0.00 C +ATOM 356 CZ2 TRP 23 24.823 31.538 20.660 1.00 0.00 C +ATOM 357 HZ2 TRP 23 25.537 30.742 20.518 1.00 0.00 H +ATOM 358 CH2 TRP 23 24.150 31.687 21.884 1.00 0.00 C +ATOM 359 HH2 TRP 23 24.343 31.018 22.698 1.00 0.00 H +ATOM 360 CZ3 TRP 23 23.296 32.769 22.095 1.00 0.00 C +ATOM 361 HZ3 TRP 23 22.869 32.905 23.078 1.00 0.00 H +ATOM 362 CE3 TRP 23 23.006 33.662 21.051 1.00 0.00 C +ATOM 363 HE3 TRP 23 22.312 34.470 21.209 1.00 0.00 H +ATOM 364 CD2 TRP 23 23.636 33.530 19.792 1.00 0.00 C +ATOM 365 C TRP 23 24.211 37.188 18.977 1.00 0.00 C +ATOM 366 O TRP 23 24.970 36.952 19.920 1.00 0.00 O +ATOM 367 N ALA 24 24.560 38.026 17.993 1.00 0.00 N +ATOM 368 H ALA 24 23.883 38.270 17.276 1.00 0.00 H +ATOM 369 CA ALA 24 25.849 38.719 17.975 1.00 0.00 C +ATOM 370 HA ALA 24 26.620 38.003 18.265 1.00 0.00 H +ATOM 371 CB ALA 24 26.163 39.147 16.535 1.00 0.00 C +ATOM 372 HB1 ALA 24 25.450 39.890 16.191 1.00 0.00 H +ATOM 373 HB2 ALA 24 27.165 39.568 16.485 1.00 0.00 H +ATOM 374 HB3 ALA 24 26.115 38.282 15.875 1.00 0.00 H +ATOM 375 C ALA 24 25.931 39.882 18.996 1.00 0.00 C +ATOM 376 O ALA 24 27.024 40.380 19.278 1.00 0.00 O +ATOM 377 N GLU 25 24.813 40.289 19.607 1.00 0.00 N +ATOM 378 H GLU 25 23.933 39.955 19.234 1.00 0.00 H +ATOM 379 CA GLU 25 24.789 41.076 20.851 1.00 0.00 C +ATOM 380 HA GLU 25 25.640 41.758 20.867 1.00 0.00 H +ATOM 381 CB GLU 25 23.510 41.927 20.928 1.00 0.00 C +ATOM 382 HB2 GLU 25 22.645 41.277 20.821 1.00 0.00 H +ATOM 383 HB3 GLU 25 23.448 42.384 21.914 1.00 0.00 H +ATOM 384 CG GLU 25 23.425 43.037 19.876 1.00 0.00 C +ATOM 385 HG2 GLU 25 23.627 42.632 18.886 1.00 0.00 H +ATOM 386 HG3 GLU 25 22.402 43.419 19.864 1.00 0.00 H +ATOM 387 CD GLU 25 24.366 44.203 20.189 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.896 45.204 20.734 1.00 0.00 O +ATOM 389 OE2 GLU 25 25.592 44.053 19.851 1.00 0.00 O +ATOM 390 C GLU 25 24.930 40.183 22.098 1.00 0.00 C +ATOM 391 O GLU 25 25.687 40.518 23.014 1.00 0.00 O +ATOM 392 N ALA 26 24.290 39.004 22.127 1.00 0.00 N +ATOM 393 H ALA 26 23.667 38.776 21.363 1.00 0.00 H +ATOM 394 CA ALA 26 24.459 38.028 23.214 1.00 0.00 C +ATOM 395 HA ALA 26 24.198 38.523 24.144 1.00 0.00 H +ATOM 396 CB ALA 26 23.492 36.861 23.009 1.00 0.00 C +ATOM 397 HB1 ALA 26 23.772 36.287 22.127 1.00 0.00 H +ATOM 398 HB2 ALA 26 23.527 36.202 23.878 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.473 37.230 22.889 1.00 0.00 H +ATOM 400 C ALA 26 25.919 37.533 23.362 1.00 0.00 C +ATOM 401 O ALA 26 26.344 37.229 24.479 1.00 0.00 O +ATOM 402 N GLU 27 26.712 37.509 22.282 1.00 0.00 N +ATOM 403 H GLU 27 26.270 37.639 21.372 1.00 0.00 H +ATOM 404 CA GLU 27 28.168 37.305 22.342 1.00 0.00 C +ATOM 405 HA GLU 27 28.370 36.352 22.829 1.00 0.00 H +ATOM 406 CB GLU 27 28.768 37.249 20.914 1.00 0.00 C +ATOM 407 HB2 GLU 27 28.159 36.598 20.284 1.00 0.00 H +ATOM 408 HB3 GLU 27 28.737 38.253 20.487 1.00 0.00 H +ATOM 409 CG GLU 27 30.213 36.730 20.925 1.00 0.00 C +ATOM 410 HG2 GLU 27 30.743 37.144 21.782 1.00 0.00 H +ATOM 411 HG3 GLU 27 30.198 35.646 21.049 1.00 0.00 H +ATOM 412 CD GLU 27 30.995 37.107 19.653 1.00 0.00 C +ATOM 413 OE1 GLU 27 31.754 38.110 19.728 1.00 0.00 O +ATOM 414 OE2 GLU 27 30.871 36.384 18.638 1.00 0.00 O +ATOM 415 C GLU 27 28.847 38.398 23.184 1.00 0.00 C +ATOM 416 O GLU 27 29.569 38.095 24.137 1.00 0.00 O +ATOM 417 N LYS 28 28.546 39.674 22.913 1.00 0.00 N +ATOM 418 H LYS 28 27.872 39.854 22.182 1.00 0.00 H +ATOM 419 CA LYS 28 29.092 40.819 23.667 1.00 0.00 C +ATOM 420 HA LYS 28 30.180 40.742 23.668 1.00 0.00 H +ATOM 421 CB LYS 28 28.698 42.147 22.994 1.00 0.00 C +ATOM 422 HB2 LYS 28 27.618 42.280 23.051 1.00 0.00 H +ATOM 423 HB3 LYS 28 29.171 42.964 23.544 1.00 0.00 H +ATOM 424 CG LYS 28 29.135 42.222 21.520 1.00 0.00 C +ATOM 425 HG2 LYS 28 30.205 42.027 21.442 1.00 0.00 H +ATOM 426 HG3 LYS 28 28.600 41.464 20.951 1.00 0.00 H +ATOM 427 CD LYS 28 28.836 43.606 20.922 1.00 0.00 C +ATOM 428 HD2 LYS 28 27.820 43.912 21.179 1.00 0.00 H +ATOM 429 HD3 LYS 28 29.525 44.332 21.362 1.00 0.00 H +ATOM 430 CE LYS 28 28.996 43.630 19.397 1.00 0.00 C +ATOM 431 HE2 LYS 28 29.091 44.670 19.083 1.00 0.00 H +ATOM 432 HE3 LYS 28 29.914 43.114 19.123 1.00 0.00 H +ATOM 433 NZ LYS 28 27.828 43.021 18.717 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.970 43.488 19.030 1.00 0.00 H +ATOM 435 HZ2 LYS 28 27.885 43.102 17.711 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.711 42.039 18.969 1.00 0.00 H +ATOM 437 C LYS 28 28.654 40.783 25.133 1.00 0.00 C +ATOM 438 O LYS 28 29.480 40.969 26.020 1.00 0.00 O +ATOM 439 N PHE 29 27.392 40.453 25.418 1.00 0.00 N +ATOM 440 H PHE 29 26.739 40.365 24.641 1.00 0.00 H +ATOM 441 CA PHE 29 26.901 40.285 26.792 1.00 0.00 C +ATOM 442 HA PHE 29 27.227 41.146 27.380 1.00 0.00 H +ATOM 443 CB PHE 29 25.365 40.262 26.797 1.00 0.00 C +ATOM 444 HB2 PHE 29 25.036 39.343 26.309 1.00 0.00 H +ATOM 445 HB3 PHE 29 25.020 40.229 27.831 1.00 0.00 H +ATOM 446 CG PHE 29 24.675 41.444 26.115 1.00 0.00 C +ATOM 447 CD1 PHE 29 23.463 41.234 25.430 1.00 0.00 C +ATOM 448 HD1 PHE 29 23.013 40.254 25.408 1.00 0.00 H +ATOM 449 CE1 PHE 29 22.829 42.300 24.768 1.00 0.00 C +ATOM 450 HE1 PHE 29 21.903 42.125 24.236 1.00 0.00 H +ATOM 451 CZ PHE 29 23.396 43.583 24.789 1.00 0.00 C +ATOM 452 HZ PHE 29 22.917 44.395 24.266 1.00 0.00 H +ATOM 453 CE2 PHE 29 24.589 43.803 25.497 1.00 0.00 C +ATOM 454 HE2 PHE 29 25.026 44.796 25.526 1.00 0.00 H +ATOM 455 CD2 PHE 29 25.225 42.742 26.163 1.00 0.00 C +ATOM 456 HD2 PHE 29 26.138 42.936 26.702 1.00 0.00 H +ATOM 457 C PHE 29 27.483 39.049 27.505 1.00 0.00 C +ATOM 458 O PHE 29 27.587 39.036 28.736 1.00 0.00 O +ATOM 459 N THR 30 27.910 38.022 26.764 1.00 0.00 N +ATOM 460 H THR 30 27.732 38.043 25.768 1.00 0.00 H +ATOM 461 CA THR 30 28.685 36.893 27.317 1.00 0.00 C +ATOM 462 HA THR 30 28.209 36.547 28.224 1.00 0.00 H +ATOM 463 CB THR 30 28.691 35.719 26.332 1.00 0.00 C +ATOM 464 HB THR 30 29.069 36.026 25.354 1.00 0.00 H +ATOM 465 CG2 THR 30 29.495 34.515 26.822 1.00 0.00 C +ATOM 466 HG21 THR 30 29.132 34.215 27.800 1.00 0.00 H +ATOM 467 HG22 THR 30 29.364 33.689 26.122 1.00 0.00 H +ATOM 468 HG23 THR 30 30.558 34.743 26.888 1.00 0.00 H +ATOM 469 OG1 THR 30 27.366 35.283 26.192 1.00 0.00 O +ATOM 470 HG1 THR 30 26.960 35.884 25.541 1.00 0.00 H +ATOM 471 C THR 30 30.104 37.319 27.687 1.00 0.00 C +ATOM 472 O THR 30 30.591 36.981 28.768 1.00 0.00 O +ATOM 473 N LYS 31 30.744 38.121 26.830 1.00 0.00 N +ATOM 474 H LYS 31 30.286 38.318 25.946 1.00 0.00 H +ATOM 475 CA LYS 31 32.077 38.701 27.066 1.00 0.00 C +ATOM 476 HA LYS 31 32.746 37.904 27.373 1.00 0.00 H +ATOM 477 CB LYS 31 32.614 39.318 25.767 1.00 0.00 C +ATOM 478 HB2 LYS 31 31.884 40.010 25.345 1.00 0.00 H +ATOM 479 HB3 LYS 31 33.526 39.864 25.985 1.00 0.00 H +ATOM 480 CG LYS 31 32.928 38.207 24.738 1.00 0.00 C +ATOM 481 HG2 LYS 31 33.682 37.552 25.175 1.00 0.00 H +ATOM 482 HG3 LYS 31 32.044 37.631 24.523 1.00 0.00 H +ATOM 483 CD LYS 31 33.460 38.815 23.434 1.00 0.00 C +ATOM 484 HD2 LYS 31 32.649 39.383 22.946 1.00 0.00 H +ATOM 485 HD3 LYS 31 34.300 39.496 23.639 1.00 0.00 H +ATOM 486 CE LYS 31 33.922 37.721 22.460 1.00 0.00 C +ATOM 487 HE2 LYS 31 33.110 37.056 22.242 1.00 0.00 H +ATOM 488 HE3 LYS 31 34.219 38.193 21.541 1.00 0.00 H +ATOM 489 NZ LYS 31 35.076 36.972 23.012 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.820 36.242 23.678 1.00 0.00 H +ATOM 491 HZ2 LYS 31 35.551 36.467 22.263 1.00 0.00 H +ATOM 492 HZ3 LYS 31 35.761 37.564 23.504 1.00 0.00 H +ATOM 493 C LYS 31 32.103 39.738 28.185 1.00 0.00 C +ATOM 494 O LYS 31 33.090 39.781 28.913 1.00 0.00 O +ATOM 495 N ALA 32 31.030 40.509 28.371 1.00 0.00 N +ATOM 496 H ALA 32 30.314 40.508 27.657 1.00 0.00 H +ATOM 497 CA ALA 32 30.874 41.413 29.513 1.00 0.00 C +ATOM 498 HA ALA 32 31.690 42.139 29.502 1.00 0.00 H +ATOM 499 CB ALA 32 29.553 42.184 29.372 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.707 41.494 29.373 1.00 0.00 H +ATOM 501 HB2 ALA 32 29.448 42.876 30.212 1.00 0.00 H +ATOM 502 HB3 ALA 32 29.556 42.756 28.443 1.00 0.00 H +ATOM 503 C ALA 32 30.964 40.640 30.836 1.00 0.00 C +ATOM 504 O ALA 32 31.880 40.889 31.614 1.00 0.00 O +ATOM 505 N LYN 33 30.119 39.614 31.029 1.00 0.00 N +ATOM 506 H LYN 33 29.393 39.457 30.345 1.00 0.00 H +ATOM 507 CA LYN 33 30.159 38.756 32.224 1.00 0.00 C +ATOM 508 HA LYN 33 30.026 39.385 33.109 1.00 0.00 H +ATOM 509 CB LYN 33 29.011 37.728 32.189 1.00 0.00 C +ATOM 510 HB2 LYN 33 29.063 37.156 31.263 1.00 0.00 H +ATOM 511 HB3 LYN 33 29.143 37.040 33.026 1.00 0.00 H +ATOM 512 CG LYN 33 27.613 38.360 32.313 1.00 0.00 C +ATOM 513 HG2 LYN 33 27.566 38.985 33.205 1.00 0.00 H +ATOM 514 HG3 LYN 33 27.415 38.982 31.441 1.00 0.00 H +ATOM 515 CD LYN 33 26.537 37.269 32.411 1.00 0.00 C +ATOM 516 HD2 LYN 33 26.694 36.543 31.619 1.00 0.00 H +ATOM 517 HD3 LYN 33 26.634 36.750 33.364 1.00 0.00 H +ATOM 518 CE LYN 33 25.125 37.836 32.286 1.00 0.00 C +ATOM 519 HE2 LYN 33 24.936 38.516 33.109 1.00 0.00 H +ATOM 520 HE3 LYN 33 25.037 38.375 31.345 1.00 0.00 H +ATOM 521 NZ LYN 33 24.119 36.762 32.310 1.00 0.00 N +ATOM 522 HZ2 LYN 33 23.186 37.155 32.262 1.00 0.00 H +ATOM 523 HZ3 LYN 33 24.255 36.114 31.546 1.00 0.00 H +ATOM 524 C LYN 33 31.513 38.043 32.390 1.00 0.00 C +ATOM 525 O LYN 33 32.010 37.922 33.504 1.00 0.00 O +ATOM 526 N ALA 34 32.145 37.587 31.303 1.00 0.00 N +ATOM 527 H ALA 34 31.697 37.679 30.398 1.00 0.00 H +ATOM 528 CA ALA 34 33.472 36.969 31.385 1.00 0.00 C +ATOM 529 HA ALA 34 33.431 36.162 32.122 1.00 0.00 H +ATOM 530 CB ALA 34 33.818 36.357 30.025 1.00 0.00 C +ATOM 531 HB1 ALA 34 33.964 37.148 29.291 1.00 0.00 H +ATOM 532 HB2 ALA 34 34.734 35.777 30.129 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.019 35.697 29.695 1.00 0.00 H +ATOM 534 C ALA 34 34.575 37.948 31.862 1.00 0.00 C +ATOM 535 O ALA 34 35.472 37.543 32.601 1.00 0.00 O +ATOM 536 N ASN 35 34.489 39.228 31.485 1.00 0.00 N +ATOM 537 H ASN 35 33.728 39.508 30.883 1.00 0.00 H +ATOM 538 CA ASN 35 35.366 40.292 31.998 1.00 0.00 C +ATOM 539 HA ASN 35 36.365 39.875 32.114 1.00 0.00 H +ATOM 540 CB ASN 35 35.477 41.419 30.965 1.00 0.00 C +ATOM 541 HB2 ASN 35 34.487 41.705 30.621 1.00 0.00 H +ATOM 542 HB3 ASN 35 35.924 42.289 31.446 1.00 0.00 H +ATOM 543 CG ASN 35 36.367 41.032 29.798 1.00 0.00 C +ATOM 544 OD1 ASN 35 37.582 41.001 29.896 1.00 0.00 O +ATOM 545 ND2 ASN 35 35.801 40.708 28.665 1.00 0.00 N +ATOM 546 HD21 ASN 35 36.412 40.450 27.893 1.00 0.00 H +ATOM 547 HD22 ASN 35 34.798 40.606 28.624 1.00 0.00 H +ATOM 548 C ASN 35 34.980 40.792 33.401 1.00 0.00 C +ATOM 549 O ASN 35 35.862 41.217 34.149 1.00 0.00 O +ATOM 550 N ASP 36 33.716 40.637 33.828 1.00 0.00 N +ATOM 551 H ASP 36 32.980 40.415 33.164 1.00 0.00 H +ATOM 552 CA ASP 36 33.336 40.771 35.246 1.00 0.00 C +ATOM 553 HA ASP 36 33.662 41.747 35.601 1.00 0.00 H +ATOM 554 CB ASP 36 31.821 40.770 35.436 1.00 0.00 C +ATOM 555 HB2 ASP 36 31.447 39.787 35.228 1.00 0.00 H +ATOM 556 HB3 ASP 36 31.605 40.869 36.494 1.00 0.00 H +ATOM 557 CG ASP 36 30.980 41.782 34.656 1.00 0.00 C +ATOM 558 OD1 ASP 36 31.511 42.875 34.375 1.00 0.00 O +ATOM 559 OD2 ASP 36 29.773 41.517 34.399 1.00 0.00 O +ATOM 560 C ASP 36 34.037 39.709 36.121 1.00 0.00 C +ATOM 561 O ASP 36 34.483 40.005 37.231 1.00 0.00 O +ATOM 562 N PHE 37 34.225 38.482 35.605 1.00 0.00 N +ATOM 563 H PHE 37 33.748 38.284 34.733 1.00 0.00 H +ATOM 564 CA PHE 37 35.119 37.460 36.169 1.00 0.00 C +ATOM 565 HA PHE 37 35.119 37.613 37.247 1.00 0.00 H +ATOM 566 CB PHE 37 34.572 36.046 35.924 1.00 0.00 C +ATOM 567 HB2 PHE 37 34.659 35.830 34.863 1.00 0.00 H +ATOM 568 HB3 PHE 37 35.221 35.338 36.433 1.00 0.00 H +ATOM 569 CG PHE 37 33.149 35.766 36.381 1.00 0.00 C +ATOM 570 CD1 PHE 37 32.137 35.555 35.433 1.00 0.00 C +ATOM 571 HD1 PHE 37 32.369 35.612 34.388 1.00 0.00 H +ATOM 572 CE1 PHE 37 30.817 35.307 35.837 1.00 0.00 C +ATOM 573 HE1 PHE 37 30.038 35.189 35.100 1.00 0.00 H +ATOM 574 CZ PHE 37 30.512 35.237 37.203 1.00 0.00 C +ATOM 575 HZ PHE 37 29.499 35.052 37.516 1.00 0.00 H +ATOM 576 CE2 PHE 37 31.521 35.410 38.161 1.00 0.00 C +ATOM 577 HE2 PHE 37 31.278 35.363 39.212 1.00 0.00 H +ATOM 578 CD2 PHE 37 32.836 35.674 37.748 1.00 0.00 C +ATOM 579 HD2 PHE 37 33.604 35.826 38.483 1.00 0.00 H +ATOM 580 C PHE 37 36.606 37.583 35.730 1.00 0.00 C +ATOM 581 O PHE 37 37.404 36.678 35.998 1.00 0.00 O +ATOM 582 N GLY 38 36.994 38.685 35.076 1.00 0.00 N +ATOM 583 H GLY 38 36.290 39.388 34.898 1.00 0.00 H +ATOM 584 CA GLY 38 38.388 39.099 34.834 1.00 0.00 C +ATOM 585 HA2 GLY 38 38.496 40.119 35.199 1.00 0.00 H +ATOM 586 HA3 GLY 38 39.053 38.480 35.433 1.00 0.00 H +ATOM 587 C GLY 38 38.924 39.067 33.387 1.00 0.00 C +ATOM 588 O GLY 38 39.870 39.802 33.105 1.00 0.00 O +ATOM 589 N ARG 39 38.383 38.230 32.483 1.00 0.00 N +ATOM 590 H ARG 39 37.544 37.729 32.758 1.00 0.00 H +ATOM 591 CA ARG 39 38.875 38.054 31.088 1.00 0.00 C +ATOM 592 HA ARG 39 38.947 39.047 30.642 1.00 0.00 H +ATOM 593 CB ARG 39 40.303 37.441 31.074 1.00 0.00 C +ATOM 594 HB2 ARG 39 40.636 37.432 30.037 1.00 0.00 H +ATOM 595 HB3 ARG 39 40.986 38.107 31.599 1.00 0.00 H +ATOM 596 CG ARG 39 40.521 36.014 31.626 1.00 0.00 C +ATOM 597 HG2 ARG 39 39.928 35.317 31.035 1.00 0.00 H +ATOM 598 HG3 ARG 39 41.569 35.754 31.462 1.00 0.00 H +ATOM 599 CD ARG 39 40.216 35.825 33.129 1.00 0.00 C +ATOM 600 HD2 ARG 39 40.853 36.510 33.703 1.00 0.00 H +ATOM 601 HD3 ARG 39 39.175 36.078 33.336 1.00 0.00 H +ATOM 602 NE ARG 39 40.443 34.444 33.597 1.00 0.00 N +ATOM 603 HE ARG 39 41.200 34.298 34.242 1.00 0.00 H +ATOM 604 CZ ARG 39 39.697 33.392 33.298 1.00 0.00 C +ATOM 605 NH1 ARG 39 38.679 33.466 32.486 1.00 0.00 N +ATOM 606 HH11 ARG 39 38.428 34.356 32.087 1.00 0.00 H +ATOM 607 HH12 ARG 39 38.300 32.617 32.077 1.00 0.00 H +ATOM 608 NH2 ARG 39 39.956 32.225 33.814 1.00 0.00 N +ATOM 609 HH21 ARG 39 40.695 32.096 34.487 1.00 0.00 H +ATOM 610 HH22 ARG 39 39.340 31.449 33.597 1.00 0.00 H +ATOM 611 C ARG 39 37.939 37.227 30.190 1.00 0.00 C +ATOM 612 O ARG 39 37.524 36.138 30.601 1.00 0.00 O +ATOM 613 N ASP 40 37.649 37.680 28.957 1.00 0.00 N +ATOM 614 H ASP 40 38.027 38.575 28.671 1.00 0.00 H +ATOM 615 CA ASP 40 36.888 36.895 27.965 1.00 0.00 C +ATOM 616 HA ASP 40 36.165 36.313 28.528 1.00 0.00 H +ATOM 617 CB ASP 40 36.061 37.736 26.967 1.00 0.00 C +ATOM 618 HB2 ASP 40 35.446 37.041 26.398 1.00 0.00 H +ATOM 619 HB3 ASP 40 35.370 38.354 27.534 1.00 0.00 H +ATOM 620 CG ASP 40 36.827 38.629 25.966 1.00 0.00 C +ATOM 621 OD1 ASP 40 37.259 39.727 26.388 1.00 0.00 O +ATOM 622 OD2 ASP 40 36.844 38.320 24.740 1.00 0.00 O +ATOM 623 C ASP 40 37.718 35.863 27.180 1.00 0.00 C +ATOM 624 O ASP 40 38.884 36.079 26.863 1.00 0.00 O +ATOM 625 N GLY 41 37.053 34.763 26.810 1.00 0.00 N +ATOM 626 H GLY 41 36.096 34.686 27.112 1.00 0.00 H +ATOM 627 CA GLY 41 37.470 33.830 25.756 1.00 0.00 C +ATOM 628 HA2 GLY 41 38.458 34.102 25.380 1.00 0.00 H +ATOM 629 HA3 GLY 41 37.530 32.826 26.176 1.00 0.00 H +ATOM 630 C GLY 41 36.480 33.816 24.578 1.00 0.00 C +ATOM 631 O GLY 41 35.572 34.650 24.502 1.00 0.00 O +ATOM 632 N GLU 42 36.641 32.855 23.669 1.00 0.00 N +ATOM 633 H GLU 42 37.356 32.161 23.819 1.00 0.00 H +ATOM 634 CA GLU 42 35.802 32.668 22.472 1.00 0.00 C +ATOM 635 HA GLU 42 35.115 33.509 22.372 1.00 0.00 H +ATOM 636 CB GLU 42 36.689 32.632 21.211 1.00 0.00 C +ATOM 637 HB2 GLU 42 37.165 31.653 21.165 1.00 0.00 H +ATOM 638 HB3 GLU 42 36.044 32.715 20.336 1.00 0.00 H +ATOM 639 CG GLU 42 37.807 33.696 21.110 1.00 0.00 C +ATOM 640 HG2 GLU 42 38.580 33.458 21.845 1.00 0.00 H +ATOM 641 HG3 GLU 42 38.278 33.628 20.127 1.00 0.00 H +ATOM 642 CD GLU 42 37.351 35.145 21.325 1.00 0.00 C +ATOM 643 OE1 GLU 42 36.163 35.460 21.116 1.00 0.00 O +ATOM 644 OE2 GLU 42 38.176 36.004 21.723 1.00 0.00 O +ATOM 645 C GLU 42 34.953 31.386 22.575 1.00 0.00 C +ATOM 646 O GLU 42 35.399 30.400 23.169 1.00 0.00 O +ATOM 647 N ALA 43 33.750 31.390 21.987 1.00 0.00 N +ATOM 648 H ALA 43 33.482 32.195 21.439 1.00 0.00 H +ATOM 649 CA ALA 43 32.763 30.304 22.059 1.00 0.00 C +ATOM 650 HA ALA 43 33.255 29.386 22.386 1.00 0.00 H +ATOM 651 CB ALA 43 31.699 30.668 23.106 1.00 0.00 C +ATOM 652 HB1 ALA 43 31.186 31.588 22.813 1.00 0.00 H +ATOM 653 HB2 ALA 43 30.966 29.860 23.179 1.00 0.00 H +ATOM 654 HB3 ALA 43 32.172 30.808 24.079 1.00 0.00 H +ATOM 655 C ALA 43 32.115 30.014 20.690 1.00 0.00 C +ATOM 656 O ALA 43 31.888 30.928 19.897 1.00 0.00 O +ATOM 657 N THR 44 31.800 28.743 20.425 1.00 0.00 N +ATOM 658 H THR 44 31.921 28.066 21.171 1.00 0.00 H +ATOM 659 CA THR 44 31.132 28.280 19.197 1.00 0.00 C +ATOM 660 HA THR 44 31.427 28.942 18.384 1.00 0.00 H +ATOM 661 CB THR 44 31.609 26.864 18.827 1.00 0.00 C +ATOM 662 HB THR 44 31.426 26.183 19.661 1.00 0.00 H +ATOM 663 CG2 THR 44 30.989 26.277 17.557 1.00 0.00 C +ATOM 664 HG21 THR 44 31.074 26.985 16.731 1.00 0.00 H +ATOM 665 HG22 THR 44 31.501 25.353 17.284 1.00 0.00 H +ATOM 666 HG23 THR 44 29.941 26.035 17.728 1.00 0.00 H +ATOM 667 OG1 THR 44 32.994 26.918 18.568 1.00 0.00 O +ATOM 668 HG1 THR 44 33.233 26.114 18.102 1.00 0.00 H +ATOM 669 C THR 44 29.606 28.380 19.330 1.00 0.00 C +ATOM 670 O THR 44 29.074 28.429 20.439 1.00 0.00 O +ATOM 671 N ILE 45 28.902 28.457 18.195 1.00 0.00 N +ATOM 672 H ILE 45 29.375 28.320 17.316 1.00 0.00 H +ATOM 673 CA ILE 45 27.480 28.839 18.125 1.00 0.00 C +ATOM 674 HA ILE 45 27.062 28.755 19.129 1.00 0.00 H +ATOM 675 CB ILE 45 27.333 30.312 17.691 1.00 0.00 C +ATOM 676 HB ILE 45 26.272 30.526 17.776 1.00 0.00 H +ATOM 677 CG2 ILE 45 28.068 31.232 18.675 1.00 0.00 C +ATOM 678 HG21 ILE 45 29.152 31.107 18.585 1.00 0.00 H +ATOM 679 HG22 ILE 45 27.832 32.280 18.494 1.00 0.00 H +ATOM 680 HG23 ILE 45 27.767 30.970 19.686 1.00 0.00 H +ATOM 681 CG1 ILE 45 27.759 30.685 16.250 1.00 0.00 C +ATOM 682 HG12 ILE 45 28.026 31.742 16.230 1.00 0.00 H +ATOM 683 HG13 ILE 45 28.656 30.128 15.967 1.00 0.00 H +ATOM 684 CD1 ILE 45 26.673 30.502 15.184 1.00 0.00 C +ATOM 685 HD11 ILE 45 25.733 30.942 15.528 1.00 0.00 H +ATOM 686 HD12 ILE 45 26.979 31.006 14.266 1.00 0.00 H +ATOM 687 HD13 ILE 45 26.520 29.448 14.962 1.00 0.00 H +ATOM 688 C ILE 45 26.631 27.921 17.246 1.00 0.00 C +ATOM 689 O ILE 45 27.124 27.339 16.280 1.00 0.00 O +ATOM 690 N ASP 46 25.331 27.876 17.547 1.00 0.00 N +ATOM 691 H ASP 46 25.033 28.294 18.423 1.00 0.00 H +ATOM 692 CA ASP 46 24.283 27.257 16.737 1.00 0.00 C +ATOM 693 HA ASP 46 24.587 27.262 15.685 1.00 0.00 H +ATOM 694 CB ASP 46 24.078 25.805 17.182 1.00 0.00 C +ATOM 695 HB2 ASP 46 24.957 25.217 16.926 1.00 0.00 H +ATOM 696 HB3 ASP 46 23.957 25.786 18.268 1.00 0.00 H +ATOM 697 CG ASP 46 22.842 25.167 16.545 1.00 0.00 C +ATOM 698 OD1 ASP 46 22.106 24.473 17.282 1.00 0.00 O +ATOM 699 OD2 ASP 46 22.562 25.433 15.354 1.00 0.00 O +ATOM 700 C ASP 46 22.960 28.047 16.852 1.00 0.00 C +ATOM 701 O ASP 46 22.512 28.361 17.956 1.00 0.00 O +ATOM 702 N ASP 47 22.310 28.329 15.718 1.00 0.00 N +ATOM 703 H ASP 47 22.680 27.938 14.863 1.00 0.00 H +ATOM 704 CA ASP 47 20.971 28.922 15.676 1.00 0.00 C +ATOM 705 HA ASP 47 20.879 29.650 16.488 1.00 0.00 H +ATOM 706 CB ASP 47 20.780 29.672 14.348 1.00 0.00 C +ATOM 707 HB2 ASP 47 21.524 30.465 14.258 1.00 0.00 H +ATOM 708 HB3 ASP 47 20.918 28.977 13.517 1.00 0.00 H +ATOM 709 CG ASP 47 19.369 30.276 14.272 1.00 0.00 C +ATOM 710 OD1 ASP 47 18.488 29.678 13.613 1.00 0.00 O +ATOM 711 OD2 ASP 47 19.067 31.233 15.020 1.00 0.00 O +ATOM 712 C ASP 47 19.855 27.874 15.879 1.00 0.00 C +ATOM 713 O ASP 47 18.845 28.182 16.515 1.00 0.00 O +ATOM 714 N ALA 48 20.003 26.633 15.397 1.00 0.00 N +ATOM 715 H ALA 48 20.918 26.339 15.051 1.00 0.00 H +ATOM 716 CA ALA 48 18.934 25.624 15.414 1.00 0.00 C +ATOM 717 HA ALA 48 18.053 26.052 14.933 1.00 0.00 H +ATOM 718 CB ALA 48 19.403 24.422 14.585 1.00 0.00 C +ATOM 719 HB1 ALA 48 20.277 23.964 15.055 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.605 23.682 14.517 1.00 0.00 H +ATOM 721 HB3 ALA 48 19.673 24.751 13.581 1.00 0.00 H +ATOM 722 C ALA 48 18.526 25.214 16.838 1.00 0.00 C +ATOM 723 O ALA 48 17.354 24.930 17.102 1.00 0.00 O +ATOM 724 N THR 49 19.478 25.244 17.775 1.00 0.00 N +ATOM 725 H THR 49 20.438 25.291 17.442 1.00 0.00 H +ATOM 726 CA THR 49 19.267 25.119 19.230 1.00 0.00 C +ATOM 727 HA THR 49 18.217 24.871 19.400 1.00 0.00 H +ATOM 728 CB THR 49 20.101 23.973 19.823 1.00 0.00 C +ATOM 729 HB THR 49 19.822 23.860 20.869 1.00 0.00 H +ATOM 730 CG2 THR 49 19.866 22.626 19.138 1.00 0.00 C +ATOM 731 HG21 THR 49 20.198 22.664 18.100 1.00 0.00 H +ATOM 732 HG22 THR 49 20.432 21.855 19.655 1.00 0.00 H +ATOM 733 HG23 THR 49 18.806 22.375 19.166 1.00 0.00 H +ATOM 734 OG1 THR 49 21.479 24.241 19.772 1.00 0.00 O +ATOM 735 HG1 THR 49 21.731 24.265 18.814 1.00 0.00 H +ATOM 736 C THR 49 19.506 26.430 20.000 1.00 0.00 C +ATOM 737 O THR 49 19.425 26.431 21.224 1.00 0.00 O +ATOM 738 N LYS 50 19.768 27.552 19.311 1.00 0.00 N +ATOM 739 H LYS 50 19.775 27.469 18.294 1.00 0.00 H +ATOM 740 CA LYS 50 19.945 28.905 19.873 1.00 0.00 C +ATOM 741 HA LYS 50 20.356 29.539 19.085 1.00 0.00 H +ATOM 742 CB LYS 50 18.568 29.470 20.294 1.00 0.00 C +ATOM 743 HB2 LYS 50 18.162 28.830 21.071 1.00 0.00 H +ATOM 744 HB3 LYS 50 18.700 30.460 20.734 1.00 0.00 H +ATOM 745 CG LYS 50 17.490 29.595 19.184 1.00 0.00 C +ATOM 746 HG2 LYS 50 17.427 28.653 18.628 1.00 0.00 H +ATOM 747 HG3 LYS 50 16.528 29.736 19.684 1.00 0.00 H +ATOM 748 CD LYS 50 17.702 30.770 18.225 1.00 0.00 C +ATOM 749 HD2 LYS 50 17.701 31.693 18.812 1.00 0.00 H +ATOM 750 HD3 LYS 50 18.677 30.686 17.722 1.00 0.00 H +ATOM 751 CE LYS 50 16.567 30.866 17.186 1.00 0.00 C +ATOM 752 HE2 LYS 50 15.625 30.595 17.663 1.00 0.00 H +ATOM 753 HE3 LYS 50 16.503 31.892 16.837 1.00 0.00 H +ATOM 754 NZ LYS 50 16.823 29.995 16.015 1.00 0.00 N +ATOM 755 HZ1 LYS 50 17.233 29.097 16.281 1.00 0.00 H +ATOM 756 HZ2 LYS 50 16.015 29.834 15.433 1.00 0.00 H +ATOM 757 HZ3 LYS 50 17.545 30.416 15.422 1.00 0.00 H +ATOM 758 C LYS 50 20.985 28.947 21.017 1.00 0.00 C +ATOM 759 O LYS 50 20.690 29.519 22.087 1.00 0.00 O +ATOM 760 N THR 51 22.149 28.291 20.853 1.00 0.00 N +ATOM 761 H THR 51 22.356 27.965 19.930 1.00 0.00 H +ATOM 762 CA THR 51 23.056 27.909 21.961 1.00 0.00 C +ATOM 763 HA THR 51 22.764 28.428 22.859 1.00 0.00 H +ATOM 764 CB THR 51 22.887 26.405 22.277 1.00 0.00 C +ATOM 765 HB THR 51 22.977 25.816 21.351 1.00 0.00 H +ATOM 766 CG2 THR 51 23.852 25.861 23.315 1.00 0.00 C +ATOM 767 HG21 THR 51 23.811 26.476 24.217 1.00 0.00 H +ATOM 768 HG22 THR 51 23.574 24.839 23.587 1.00 0.00 H +ATOM 769 HG23 THR 51 24.879 25.834 22.955 1.00 0.00 H +ATOM 770 OG1 THR 51 21.642 26.171 22.880 1.00 0.00 O +ATOM 771 HG1 THR 51 20.952 26.250 22.187 1.00 0.00 H +ATOM 772 C THR 51 24.558 28.226 21.727 1.00 0.00 C +ATOM 773 O THR 51 25.088 27.999 20.643 1.00 0.00 O +ATOM 774 N PHE 52 25.247 28.694 22.774 1.00 0.00 N +ATOM 775 H PHE 52 24.711 28.955 23.594 1.00 0.00 H +ATOM 776 CA PHE 52 26.721 28.776 22.877 1.00 0.00 C +ATOM 777 HA PHE 52 27.143 28.936 21.901 1.00 0.00 H +ATOM 778 CB PHE 52 27.150 29.949 23.826 1.00 0.00 C +ATOM 779 HB2 PHE 52 26.478 29.957 24.658 1.00 0.00 H +ATOM 780 HB3 PHE 52 28.142 29.734 24.192 1.00 0.00 H +ATOM 781 CG PHE 52 27.216 31.350 23.227 1.00 0.00 C +ATOM 782 CD1 PHE 52 26.432 32.382 23.751 1.00 0.00 C +ATOM 783 HD1 PHE 52 25.753 32.191 24.567 1.00 0.00 H +ATOM 784 CE1 PHE 52 26.448 33.649 23.160 1.00 0.00 C +ATOM 785 HE1 PHE 52 25.778 34.433 23.517 1.00 0.00 H +ATOM 786 CZ PHE 52 27.282 33.889 22.068 1.00 0.00 C +ATOM 787 HZ PHE 52 27.247 34.834 21.561 1.00 0.00 H +ATOM 788 CE2 PHE 52 28.159 32.900 21.619 1.00 0.00 C +ATOM 789 HE2 PHE 52 28.839 33.106 20.790 1.00 0.00 H +ATOM 790 CD2 PHE 52 28.127 31.629 22.200 1.00 0.00 C +ATOM 791 HD2 PHE 52 28.776 30.856 21.829 1.00 0.00 H +ATOM 792 C PHE 52 27.330 27.510 23.496 1.00 0.00 C +ATOM 793 O PHE 52 26.807 27.009 24.507 1.00 0.00 O +ATOM 794 N THR 53 28.485 27.065 22.983 1.00 0.00 N +ATOM 795 H THR 53 28.850 27.522 22.148 1.00 0.00 H +ATOM 796 CA THR 53 29.279 25.926 23.504 1.00 0.00 C +ATOM 797 HA THR 53 29.045 25.794 24.563 1.00 0.00 H +ATOM 798 CB THR 53 28.933 24.610 22.780 1.00 0.00 C +ATOM 799 HB THR 53 29.508 23.801 23.237 1.00 0.00 H +ATOM 800 CG2 THR 53 27.457 24.224 22.859 1.00 0.00 C +ATOM 801 HG21 THR 53 26.863 24.906 22.251 1.00 0.00 H +ATOM 802 HG22 THR 53 27.322 23.209 22.490 1.00 0.00 H +ATOM 803 HG23 THR 53 27.120 24.269 23.894 1.00 0.00 H +ATOM 804 OG1 THR 53 29.270 24.680 21.419 1.00 0.00 O +ATOM 805 HG1 THR 53 28.753 24.016 20.952 1.00 0.00 H +ATOM 806 C THR 53 30.801 26.146 23.414 1.00 0.00 C +ATOM 807 O THR 53 31.285 27.021 22.692 1.00 0.00 O +ATOM 808 N THR 54 31.568 25.322 24.142 1.00 0.00 N +ATOM 809 H THR 54 31.108 24.646 24.732 1.00 0.00 H +ATOM 810 CA THR 54 33.040 25.237 24.079 1.00 0.00 C +ATOM 811 HA THR 54 33.413 26.032 23.433 1.00 0.00 H +ATOM 812 CB THR 54 33.664 25.450 25.472 1.00 0.00 C +ATOM 813 HB THR 54 33.370 24.631 26.132 1.00 0.00 H +ATOM 814 CG2 THR 54 35.192 25.563 25.471 1.00 0.00 C +ATOM 815 HG21 THR 54 35.513 26.333 24.768 1.00 0.00 H +ATOM 816 HG22 THR 54 35.549 25.815 26.469 1.00 0.00 H +ATOM 817 HG23 THR 54 35.638 24.608 25.194 1.00 0.00 H +ATOM 818 OG1 THR 54 33.199 26.661 26.022 1.00 0.00 O +ATOM 819 HG1 THR 54 33.873 26.995 26.617 1.00 0.00 H +ATOM 820 C THR 54 33.478 23.891 23.475 1.00 0.00 C +ATOM 821 O THR 54 32.772 22.890 23.606 1.00 0.00 O +ATOM 822 N GLN 55 34.634 23.874 22.804 1.00 0.00 N +ATOM 823 H GLN 55 35.155 24.736 22.760 1.00 0.00 H +ATOM 824 CA GLN 55 35.263 22.689 22.197 1.00 0.00 C +ATOM 825 HA GLN 55 34.489 22.160 21.641 1.00 0.00 H +ATOM 826 CB GLN 55 36.318 23.157 21.174 1.00 0.00 C +ATOM 827 HB2 GLN 55 36.731 22.289 20.660 1.00 0.00 H +ATOM 828 HB3 GLN 55 35.803 23.768 20.429 1.00 0.00 H +ATOM 829 CG GLN 55 37.480 23.990 21.758 1.00 0.00 C +ATOM 830 HG2 GLN 55 37.094 24.710 22.481 1.00 0.00 H +ATOM 831 HG3 GLN 55 38.176 23.332 22.280 1.00 0.00 H +ATOM 832 CD GLN 55 38.246 24.768 20.685 1.00 0.00 C +ATOM 833 OE1 GLN 55 38.323 24.390 19.522 1.00 0.00 O +ATOM 834 NE2 GLN 55 38.828 25.897 21.031 1.00 0.00 N +ATOM 835 HE21 GLN 55 39.406 26.349 20.327 1.00 0.00 H +ATOM 836 HE22 GLN 55 38.721 26.270 21.959 1.00 0.00 H +ATOM 837 C GLN 55 35.830 21.678 23.227 1.00 0.00 C +ATOM 838 O GLN 55 36.115 22.046 24.365 1.00 0.00 O +ATOM 839 N GLU 56 35.970 20.411 22.806 1.00 0.00 N +ATOM 840 H GLU 56 35.791 20.230 21.834 1.00 0.00 H +ATOM 841 CA GLU 56 36.494 19.248 23.574 1.00 0.00 C +ATOM 842 HA GLU 56 36.158 19.336 24.606 1.00 0.00 H +ATOM 843 CB GLU 56 35.887 17.954 22.970 1.00 0.00 C +ATOM 844 HB2 GLU 56 34.807 17.983 23.079 1.00 0.00 H +ATOM 845 HB3 GLU 56 36.081 17.991 21.899 1.00 0.00 H +ATOM 846 CG GLU 56 36.406 16.581 23.466 1.00 0.00 C +ATOM 847 HG2 GLU 56 36.470 15.932 22.595 1.00 0.00 H +ATOM 848 HG3 GLU 56 37.421 16.670 23.823 1.00 0.00 H +ATOM 849 CD GLU 56 35.546 15.853 24.519 1.00 0.00 C +ATOM 850 OE1 GLU 56 36.084 15.362 25.545 1.00 0.00 O +ATOM 851 OE2 GLU 56 34.329 15.640 24.294 1.00 0.00 O +ATOM 852 C GLU 56 38.033 19.203 23.640 1.00 0.00 C +ATOM 853 O GLU 56 38.543 19.194 24.791 1.00 0.00 O +ATOM 854 OXT GLU 56 38.679 19.135 22.573 1.00 0.00 O +HETATM 855 ZN ZN1 57 26.719 32.459 29.379 1.00 0.00 Zn +HETATM 856 N AN1 58 28.328 33.244 30.277 1.00 0.00 N +HETATM 857 C AN1 58 30.687 33.879 31.201 1.00 0.00 C +HETATM 858 C1 AN1 58 29.381 33.532 30.714 1.00 0.00 C +HETATM 859 H AN1 58 30.624 34.272 32.222 1.00 0.00 H +HETATM 860 H1 AN1 58 31.138 34.632 30.547 1.00 0.00 H +HETATM 861 H2 AN1 58 31.318 32.977 31.202 1.00 0.00 H +HETATM 862 N1 AZI 59 31.274 30.374 29.434 1.00 0.00 N +HETATM 863 N2 AZI 59 30.476 30.257 30.351 1.00 0.00 N +HETATM 864 N3 AZI 59 29.630 30.157 31.295 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 144 +CONECT 135 134 +CONECT 136 138 134 137 142 +CONECT 137 136 +CONECT 138 141 139 140 136 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 +CONECT 143 142 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 148 144 +CONECT 147 146 +CONECT 148 146 149 151 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 159 155 +CONECT 158 157 +CONECT 159 157 +CONECT 160 163 162 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 165 160 +CONECT 164 163 +CONECT 165 163 +CONECT 166 169 168 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 171 172 170 166 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 178 184 179 +CONECT 178 177 +CONECT 179 177 182 180 181 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 183 +CONECT 183 182 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 190 189 +CONECT 189 188 +CONECT 190 191 188 192 193 +CONECT 191 190 +CONECT 192 190 +CONECT 193 190 194 +CONECT 194 193 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 217 201 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 234 230 233 235 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 237 239 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 228 242 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 268 267 263 266 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 280 282 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 311 310 307 312 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 323 324 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 326 327 319 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 340 339 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 343 333 342 +CONECT 342 341 +CONECT 343 344 345 341 +CONECT 344 343 +CONECT 345 347 343 365 346 +CONECT 346 345 +CONECT 347 349 348 350 345 +CONECT 348 347 +CONECT 349 347 +CONECT 350 351 347 364 +CONECT 351 352 353 350 +CONECT 352 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 364 356 +CONECT 356 355 357 358 +CONECT 357 356 +CONECT 358 356 360 359 +CONECT 359 358 +CONECT 360 362 358 361 +CONECT 361 360 +CONECT 362 364 363 360 +CONECT 363 362 +CONECT 364 350 355 362 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 374 372 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 380 381 390 +CONECT 380 379 +CONECT 381 384 382 379 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 386 387 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 399 394 398 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 414 413 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 429 424 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 431 432 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 435 436 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 459 441 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 467 463 468 466 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 487 489 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 492 490 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 502 500 497 501 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 524 508 +CONECT 508 507 +CONECT 509 510 507 512 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 516 518 512 517 +CONECT 516 515 +CONECT 517 515 +CONECT 518 520 521 515 519 +CONECT 519 518 +CONECT 520 518 +CONECT 521 523 522 518 +CONECT 522 521 +CONECT 523 521 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 533 532 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 528 536 535 +CONECT 535 534 +CONECT 536 537 534 538 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 546 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 554 553 560 +CONECT 553 552 +CONECT 554 557 555 552 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 566 565 +CONECT 565 564 +CONECT 566 567 564 569 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 570 566 578 +CONECT 570 571 572 569 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 578 577 +CONECT 577 576 +CONECT 578 569 576 579 +CONECT 579 578 +CONECT 580 582 581 564 +CONECT 581 580 +CONECT 582 584 583 580 +CONECT 583 582 +CONECT 584 587 582 585 586 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 592 593 589 +CONECT 592 591 +CONECT 593 594 591 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 597 593 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 601 602 600 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 604 603 +CONECT 603 602 +CONECT 604 605 602 608 +CONECT 605 607 606 604 +CONECT 606 605 +CONECT 607 605 +CONECT 608 604 610 609 +CONECT 609 608 +CONECT 610 608 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 615 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 636 642 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 639 643 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 650 651 +CONECT 650 649 +CONECT 651 649 652 653 654 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 664 665 666 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 668 661 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 675 671 674 +CONECT 674 673 +CONECT 675 681 676 673 677 +CONECT 676 675 +CONECT 677 675 679 678 680 +CONECT 678 677 +CONECT 679 677 +CONECT 680 677 +CONECT 681 684 683 682 675 +CONECT 682 681 +CONECT 683 681 +CONECT 684 686 687 685 681 +CONECT 685 684 +CONECT 686 684 +CONECT 687 684 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 694 698 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 707 709 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 720 719 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 731 733 732 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 757 756 755 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 769 768 767 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 792 778 +CONECT 777 776 +CONECT 778 776 781 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 798 794 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 802 798 803 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 811 820 808 812 +CONECT 811 810 +CONECT 812 810 814 818 813 +CONECT 813 812 +CONECT 814 815 817 812 816 +CONECT 815 814 +CONECT 816 814 +CONECT 817 814 +CONECT 818 812 819 +CONECT 819 818 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 826 825 822 837 +CONECT 825 824 +CONECT 826 828 827 829 824 +CONECT 827 826 +CONECT 828 826 +CONECT 829 832 826 831 830 +CONECT 830 829 +CONECT 831 829 +CONECT 832 833 834 829 +CONECT 833 832 +CONECT 834 835 832 836 +CONECT 835 834 +CONECT 836 834 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 839 843 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 851 850 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/intermediate_molecules/min_iter_5_front_7.pdb b/tests/nsga2/intermediate_molecules/min_iter_5_front_7.pdb new file mode 100644 index 0000000..3b66752 --- /dev/null +++ b/tests/nsga2/intermediate_molecules/min_iter_5_front_7.pdb @@ -0,0 +1,1733 @@ +COMPND fitness: -0.304 51.40416666666647 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 P1 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HX1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HX1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HX1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HX1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HX1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HX1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HX1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HX1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N THR 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H THR 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA THR 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 CB THR 8 32.137 -93.828 -4.507 1.00 0.00 C +ATOM 136 HB THR 8 33.195 -94.062 -4.627 1.00 0.00 H +ATOM 137 CG2 THR 8 31.810 -92.554 -5.271 1.00 0.00 C +ATOM 138 HG21 THR 8 30.752 -92.319 -5.151 1.00 0.00 H +ATOM 139 HG22 THR 8 32.411 -91.731 -4.881 1.00 0.00 H +ATOM 140 HG23 THR 8 32.034 -92.697 -6.328 1.00 0.00 H +ATOM 141 OG1 THR 8 31.840 -93.626 -3.119 1.00 0.00 O +ATOM 142 HG1 THR 8 32.368 -92.900 -2.780 1.00 0.00 H +ATOM 143 HA THR 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 144 C THR 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 145 O THR 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 146 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 147 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 148 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 149 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 150 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 151 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 152 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 153 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 154 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 155 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 156 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 157 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 158 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 159 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 160 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 161 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 162 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 163 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 164 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 165 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 166 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 167 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 168 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 169 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 170 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 171 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 172 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 173 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 174 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 175 N SER 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 176 H SER 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 177 CA SER 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 178 CB SER 11 32.207-101.574 0.711 1.00 0.00 C +ATOM 179 HB2 SER 11 32.416-100.511 0.583 1.00 0.00 H +ATOM 180 HB3 SER 11 31.863-101.756 1.728 1.00 0.00 H +ATOM 181 OG SER 11 33.389-102.318 0.472 1.00 0.00 O +ATOM 182 HG SER 11 34.068-102.048 1.093 1.00 0.00 H +ATOM 183 HA SER 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 184 C SER 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 185 O SER 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 186 N CYS 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 187 H CYS 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 188 CA CYS 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 189 CB CYS 12 28.130 -98.237 -0.161 1.00 0.00 C +ATOM 190 HB2 CYS 12 28.781 -97.808 -0.923 1.00 0.00 H +ATOM 191 HB3 CYS 12 27.157 -97.746 -0.196 1.00 0.00 H +ATOM 192 SG CYS 12 28.866 -97.786 1.444 1.00 0.00 S +ATOM 193 HG CYS 12 28.829 -96.471 1.249 1.00 0.00 H +ATOM 194 HA CYS 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 195 C CYS 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 196 O CYS 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 197 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 198 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 199 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 200 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 201 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 202 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 203 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 204 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 205 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 206 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 207 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 208 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 209 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 210 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 211 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 212 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 213 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 214 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 215 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 216 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 217 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 218 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 219 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 220 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 221 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 222 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 223 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 224 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 225 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 226 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 227 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 228 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 229 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 230 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 231 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 232 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 233 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 234 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 235 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 236 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 237 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 238 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 239 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 240 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 241 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 242 N HY1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 243 CA HY1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 244 C HY1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 245 O HY1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 246 CB HY1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 247 CG HY1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 248 CD2 HY1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 249 ND1 HY1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 250 CE1 HY1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 251 NE2 HY1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 252 H HY1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 253 HA HY1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 254 HB2 HY1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 255 HB3 HY1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 256 HD1 HY1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 257 HD2 HY1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 258 HE1 HY1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 259 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 260 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 261 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 262 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 263 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 264 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 265 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 266 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 267 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 268 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 269 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 270 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 271 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 272 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 273 N HY2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 274 CA HY2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 275 C HY2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 276 O HY2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 277 CB HY2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 278 CG HY2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 279 CD2 HY2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 280 ND1 HY2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 281 CE1 HY2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 282 NE2 HY2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 283 H HY2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 284 HA HY2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 285 HB2 HY2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 286 HB3 HY2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 287 HD1 HY2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 288 HD2 HY2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 289 HE1 HY2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 290 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 291 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 292 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 293 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 294 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 295 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 296 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 297 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 298 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 299 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 300 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 301 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 302 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 303 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 304 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 305 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 306 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 307 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 308 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 309 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 310 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 311 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 312 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 313 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 314 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 315 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 316 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 317 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 318 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 319 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 320 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 321 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 322 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 323 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 324 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 325 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 326 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 327 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 328 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 329 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 330 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 331 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 332 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 333 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 334 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 335 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 336 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 337 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 338 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 339 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 340 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 341 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 342 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 343 N TRP 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 344 H TRP 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 345 CA TRP 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 346 CB TRP 23 21.411 -85.256 -16.822 1.00 0.00 C +ATOM 347 HB2 TRP 23 20.471 -85.768 -16.621 1.00 0.00 H +ATOM 348 HB3 TRP 23 21.494 -85.175 -17.905 1.00 0.00 H +ATOM 349 CG TRP 23 22.519 -86.148 -16.354 1.00 0.00 C +ATOM 350 CD1 TRP 23 23.651 -86.478 -17.042 1.00 0.00 C +ATOM 351 HD1 TRP 23 23.887 -86.129 -18.044 1.00 0.00 H +ATOM 352 NE1 TRP 23 24.435 -87.319 -16.290 1.00 0.00 N +ATOM 353 HE1 TRP 23 25.328 -87.711 -16.568 1.00 0.00 H +ATOM 354 CE2 TRP 23 23.809 -87.548 -15.088 1.00 0.00 C +ATOM 355 CZ2 TRP 23 24.208 -88.327 -14.004 1.00 0.00 C +ATOM 356 HZ2 TRP 23 25.139 -88.878 -14.005 1.00 0.00 H +ATOM 357 CH2 TRP 23 23.375 -88.374 -12.917 1.00 0.00 C +ATOM 358 HH2 TRP 23 23.669 -88.969 -12.061 1.00 0.00 H +ATOM 359 CZ3 TRP 23 22.163 -87.664 -12.899 1.00 0.00 C +ATOM 360 HZ3 TRP 23 21.536 -87.731 -12.021 1.00 0.00 H +ATOM 361 CE3 TRP 23 21.767 -86.890 -13.974 1.00 0.00 C +ATOM 362 HE3 TRP 23 20.836 -86.342 -13.975 1.00 0.00 H +ATOM 363 CD2 TRP 23 22.599 -86.826 -15.093 1.00 0.00 C +ATOM 364 HA TRP 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 365 C TRP 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 366 O TRP 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 367 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 368 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 369 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 370 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 371 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 372 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 373 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 374 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 375 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 376 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 377 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 378 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 379 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 380 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 381 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 382 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 383 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 384 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 385 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 386 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 387 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 388 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 389 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 390 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 391 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 392 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 393 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 394 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 395 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 396 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 397 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 398 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 399 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 400 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 401 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 402 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 403 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 404 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 405 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 406 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 407 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 408 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 409 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 410 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 411 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 412 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 413 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 414 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 415 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 416 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 417 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 418 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 419 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 420 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 421 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 422 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 423 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 424 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 425 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 426 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 427 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 428 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 429 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 430 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 431 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 432 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 433 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 434 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 435 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 436 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 437 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 438 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 439 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 440 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 441 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 442 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 443 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 444 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 445 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 446 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 447 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 448 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 449 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 450 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 451 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 452 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 453 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 454 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 455 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 456 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 457 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 458 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 459 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 460 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 461 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 462 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 463 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 464 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 465 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 466 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 467 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 468 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 469 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 470 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 471 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 472 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 473 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 474 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 475 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 476 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 477 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 478 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 479 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 480 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 481 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 482 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 483 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 484 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 485 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 486 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 487 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 488 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 489 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 490 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 491 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 492 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 493 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 494 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 495 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 496 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 497 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 498 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 499 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 500 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 501 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 502 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 503 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 504 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 505 N LYN 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 506 H LYN 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 507 CA LYN 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 508 CB LYN 33 27.315 -82.525 -3.272 1.00 0.00 C +ATOM 509 HB2 LYN 33 27.425 -83.036 -4.229 1.00 0.00 H +ATOM 510 HB3 LYN 33 27.414 -83.247 -2.462 1.00 0.00 H +ATOM 511 CG LYN 33 25.946 -81.869 -3.202 1.00 0.00 C +ATOM 512 HG2 LYN 33 25.855 -81.355 -2.244 1.00 0.00 H +ATOM 513 HG3 LYN 33 25.867 -81.143 -4.012 1.00 0.00 H +ATOM 514 CD LYN 33 24.835 -82.898 -3.332 1.00 0.00 C +ATOM 515 HD2 LYN 33 24.944 -83.409 -4.289 1.00 0.00 H +ATOM 516 HD3 LYN 33 24.933 -83.620 -2.522 1.00 0.00 H +ATOM 517 CE LYN 33 23.466 -82.242 -3.262 1.00 0.00 C +ATOM 518 HE2 LYN 33 23.381 -81.728 -2.305 1.00 0.00 H +ATOM 519 HE3 LYN 33 23.393 -81.515 -4.072 1.00 0.00 H +ATOM 520 NZ LYN 33 22.365 -83.238 -3.389 1.00 0.00 N +ATOM 521 HZ2 LYN 33 21.474 -82.764 -3.338 1.00 0.00 H +ATOM 522 HZ3 LYN 33 22.443 -83.714 -4.276 1.00 0.00 H +ATOM 523 HA LYN 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 524 C LYN 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 525 O LYN 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 526 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 527 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 528 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 529 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 530 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 531 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 532 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 533 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 534 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 535 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 536 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 537 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 538 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 539 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 540 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 541 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 542 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 543 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 544 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 545 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 546 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 547 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 548 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 549 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 550 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 551 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 552 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 553 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 554 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 555 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 556 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 557 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 558 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 559 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 560 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 561 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 562 N PHE 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 563 H PHE 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 564 CA PHE 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 565 CB PHE 37 33.048 -83.879 0.496 1.00 0.00 C +ATOM 566 HB2 PHE 37 33.185 -83.964 -0.582 1.00 0.00 H +ATOM 567 HB3 PHE 37 33.573 -84.694 0.994 1.00 0.00 H +ATOM 568 CG PHE 37 31.585 -84.086 0.761 1.00 0.00 C +ATOM 569 CD1 PHE 37 30.636 -83.692 -0.167 1.00 0.00 C +ATOM 570 HD1 PHE 37 30.960 -83.226 -1.099 1.00 0.00 H +ATOM 571 CE1 PHE 37 29.289 -83.884 0.077 1.00 0.00 C +ATOM 572 HE1 PHE 37 28.554 -83.569 -0.664 1.00 0.00 H +ATOM 573 CZ PHE 37 28.876 -84.472 1.252 1.00 0.00 C +ATOM 574 HZ PHE 37 27.814 -84.622 1.446 1.00 0.00 H +ATOM 575 CE2 PHE 37 29.809 -84.868 2.183 1.00 0.00 C +ATOM 576 HE2 PHE 37 29.487 -85.333 3.115 1.00 0.00 H +ATOM 577 CD2 PHE 37 31.155 -84.676 1.936 1.00 0.00 C +ATOM 578 HD2 PHE 37 31.895 -84.991 2.672 1.00 0.00 H +ATOM 579 HA PHE 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 580 C PHE 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 581 O PHE 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 582 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 583 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 584 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 585 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 586 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 587 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 588 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 589 N ARG 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 590 H ARG 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 591 CA ARG 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 592 CB ARG 39 38.868 -82.517 -4.462 1.00 0.00 C +ATOM 593 HB2 ARG 39 39.200 -82.458 -5.498 1.00 0.00 H +ATOM 594 HB3 ARG 39 39.426 -81.798 -3.861 1.00 0.00 H +ATOM 595 CG ARG 39 39.115 -83.920 -3.930 1.00 0.00 C +ATOM 596 HG2 ARG 39 38.452 -84.611 -4.452 1.00 0.00 H +ATOM 597 HG3 ARG 39 40.151 -84.191 -4.132 1.00 0.00 H +ATOM 598 CD ARG 39 38.853 -83.997 -2.436 1.00 0.00 C +ATOM 599 HD2 ARG 39 39.516 -83.301 -1.923 1.00 0.00 H +ATOM 600 HD3 ARG 39 37.817 -83.720 -2.242 1.00 0.00 H +ATOM 601 NE ARG 39 39.085 -85.339 -1.908 1.00 0.00 N +ATOM 602 HE ARG 39 39.993 -85.527 -1.508 1.00 0.00 H +ATOM 603 CZ ARG 39 38.183 -86.314 -1.923 1.00 0.00 C +ATOM 604 NH1 ARG 39 36.981 -86.099 -2.440 1.00 0.00 N +ATOM 605 HH11 ARG 39 36.755 -85.192 -2.822 1.00 0.00 H +ATOM 606 HH12 ARG 39 36.298 -86.842 -2.450 1.00 0.00 H +ATOM 607 NH2 ARG 39 38.485 -87.503 -1.419 1.00 0.00 N +ATOM 608 HH21 ARG 39 39.402 -87.663 -1.025 1.00 0.00 H +ATOM 609 HH22 ARG 39 37.797 -88.243 -1.432 1.00 0.00 H +ATOM 610 HA ARG 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 611 C ARG 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 612 O ARG 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 613 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 614 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 615 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 616 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 617 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 618 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 619 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 620 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 621 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 622 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 623 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 624 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 625 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 626 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 627 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 628 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 629 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 630 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 631 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 632 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 633 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 634 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 635 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 636 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 637 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 638 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 639 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 640 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 641 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 642 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 643 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 644 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 645 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 646 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 647 N ALA 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 648 H ALA 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 649 CA ALA 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 650 CB ALA 43 29.880 -89.031 -12.448 1.00 0.00 C +ATOM 651 HB1 ALA 43 30.340 -88.939 -11.464 1.00 0.00 H +ATOM 652 HB2 ALA 43 29.473 -88.066 -12.750 1.00 0.00 H +ATOM 653 HB3 ALA 43 29.077 -89.766 -12.405 1.00 0.00 H +ATOM 654 HA ALA 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 655 C ALA 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 656 O ALA 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 657 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 658 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 659 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 660 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 661 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 662 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 663 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 664 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 665 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 666 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 667 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 668 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 669 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 670 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 671 N ILE 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 672 H ILE 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 673 CA ILE 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 674 CB ILE 45 25.264 -89.243 -17.471 1.00 0.00 C +ATOM 675 HB ILE 45 24.177 -89.166 -17.456 1.00 0.00 H +ATOM 676 CG2 ILE 45 25.843 -88.467 -16.298 1.00 0.00 C +ATOM 677 HG21 ILE 45 26.931 -88.545 -16.312 1.00 0.00 H +ATOM 678 HG22 ILE 45 25.553 -87.420 -16.375 1.00 0.00 H +ATOM 679 HG23 ILE 45 25.464 -88.881 -15.364 1.00 0.00 H +ATOM 680 CG1 ILE 45 25.812 -88.644 -18.767 1.00 0.00 C +ATOM 681 HG12 ILE 45 25.634 -87.570 -18.727 1.00 0.00 H +ATOM 682 HG13 ILE 45 26.886 -88.835 -18.784 1.00 0.00 H +ATOM 683 CD1 ILE 45 25.179 -89.214 -20.018 1.00 0.00 C +ATOM 684 HD11 ILE 45 24.105 -89.024 -20.003 1.00 0.00 H +ATOM 685 HD12 ILE 45 25.619 -88.741 -20.896 1.00 0.00 H +ATOM 686 HD13 ILE 45 25.357 -90.289 -20.058 1.00 0.00 H +ATOM 687 HA ILE 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 688 C ILE 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 689 O ILE 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 690 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 691 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 692 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 693 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 694 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 695 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 696 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 697 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 698 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 699 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 700 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 701 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 702 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 703 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 704 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 705 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 706 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 707 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 708 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 709 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 710 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 711 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 712 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 713 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 714 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 715 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 716 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 717 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 718 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 719 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 720 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 721 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 722 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 723 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 724 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 725 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 726 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 727 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 728 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 729 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 730 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 731 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 732 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 733 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 734 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 735 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 736 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 737 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 738 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 739 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 740 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 741 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 742 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 743 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 744 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 745 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 746 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 747 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 748 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 749 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 750 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 751 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 752 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 753 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 754 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 755 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 756 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 757 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 758 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 759 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 760 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 761 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 762 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 763 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 764 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 765 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 766 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 767 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 768 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 769 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 770 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 771 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 772 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 773 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 774 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 775 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 776 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 777 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 778 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 779 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 780 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 781 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 782 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 783 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 784 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 785 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 786 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 787 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 788 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 789 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 790 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 791 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 792 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 793 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 794 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 795 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 796 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 797 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 798 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 799 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 800 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 801 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 802 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 803 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 804 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 805 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 806 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 807 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 808 N THR 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 809 H THR 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 810 CA THR 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 811 CB THR 54 32.307 -94.492 -10.190 1.00 0.00 C +ATOM 812 HB THR 54 31.944 -95.343 -9.615 1.00 0.00 H +ATOM 813 CG2 THR 54 33.789 -94.670 -10.479 1.00 0.00 C +ATOM 814 HG21 THR 54 34.153 -93.819 -11.054 1.00 0.00 H +ATOM 815 HG22 THR 54 34.338 -94.734 -9.539 1.00 0.00 H +ATOM 816 HG23 THR 54 33.941 -95.586 -11.051 1.00 0.00 H +ATOM 817 OG1 THR 54 32.122 -93.285 -9.439 1.00 0.00 O +ATOM 818 HG1 THR 54 32.609 -93.345 -8.613 1.00 0.00 H +ATOM 819 HA THR 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 820 C THR 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 821 O THR 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 822 N GLN 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 823 H GLN 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 824 CA GLN 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 825 CB GLN 55 34.660 -96.376 -14.407 1.00 0.00 C +ATOM 826 HB2 GLN 55 34.997 -97.154 -15.093 1.00 0.00 H +ATOM 827 HB3 GLN 55 34.127 -95.606 -14.966 1.00 0.00 H +ATOM 828 CG GLN 55 35.862 -95.756 -13.713 1.00 0.00 C +ATOM 829 HG2 GLN 55 35.513 -94.985 -13.026 1.00 0.00 H +ATOM 830 HG3 GLN 55 36.382 -96.534 -13.153 1.00 0.00 H +ATOM 831 CD GLN 55 36.837 -95.128 -14.689 1.00 0.00 C +ATOM 832 OE1 GLN 55 36.898 -95.513 -15.856 1.00 0.00 O +ATOM 833 NE2 GLN 55 37.605 -94.154 -14.211 1.00 0.00 N +ATOM 834 HE21 GLN 55 38.274 -93.699 -14.816 1.00 0.00 H +ATOM 835 HE22 GLN 55 37.517 -93.873 -13.245 1.00 0.00 H +ATOM 836 HA GLN 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 837 C GLN 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 838 O GLN 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 839 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 840 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 841 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 842 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 843 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 844 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 845 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 846 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 847 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 848 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 849 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 850 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 851 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 852 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 853 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 854 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 855 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 Zn +ATOM 856 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 857 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 858 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 859 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 860 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 861 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +ATOM 862 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 863 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 864 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 17 15 13 16 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 65 60 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 68 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 65 69 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 855 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 104 106 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 111 112 113 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 143 132 144 135 +CONECT 135 136 137 141 134 +CONECT 136 135 +CONECT 137 135 138 139 140 +CONECT 138 137 +CONECT 139 137 +CONECT 140 137 +CONECT 141 135 142 +CONECT 142 141 +CONECT 143 134 +CONECT 144 134 146 145 +CONECT 145 144 +CONECT 146 147 144 148 +CONECT 147 146 +CONECT 148 146 151 149 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 152 148 153 +CONECT 152 151 +CONECT 153 151 155 154 +CONECT 154 153 +CONECT 155 157 156 153 173 +CONECT 156 155 +CONECT 157 160 158 155 159 +CONECT 158 157 +CONECT 159 157 +CONECT 160 162 163 161 157 +CONECT 161 160 +CONECT 162 160 +CONECT 163 166 164 160 165 +CONECT 164 163 +CONECT 165 163 +CONECT 166 168 169 167 163 +CONECT 167 166 +CONECT 168 166 +CONECT 169 172 171 166 170 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 +CONECT 173 155 174 175 +CONECT 174 173 +CONECT 175 173 176 177 +CONECT 176 175 +CONECT 177 175 183 184 178 +CONECT 178 179 180 181 177 +CONECT 179 178 +CONECT 180 178 +CONECT 181 178 182 +CONECT 182 181 +CONECT 183 177 +CONECT 184 186 177 185 +CONECT 185 184 +CONECT 186 187 188 184 +CONECT 187 186 +CONECT 188 195 186 194 189 +CONECT 189 190 191 192 188 +CONECT 190 189 +CONECT 191 189 +CONECT 192 189 193 +CONECT 193 192 +CONECT 194 188 +CONECT 195 196 197 188 +CONECT 196 195 +CONECT 197 199 195 198 +CONECT 198 197 +CONECT 199 200 201 217 197 +CONECT 200 199 +CONECT 201 204 199 202 203 +CONECT 202 201 +CONECT 203 201 +CONECT 204 206 205 207 201 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 204 210 209 +CONECT 208 207 +CONECT 209 207 +CONECT 210 212 207 213 211 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 214 215 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 +CONECT 217 218 199 219 +CONECT 218 217 +CONECT 219 217 221 220 +CONECT 220 219 +CONECT 221 224 219 222 223 +CONECT 222 221 +CONECT 223 221 +CONECT 224 225 226 221 +CONECT 225 224 +CONECT 226 228 224 227 +CONECT 227 226 +CONECT 228 230 229 240 226 +CONECT 229 228 +CONECT 230 236 231 232 228 +CONECT 231 230 +CONECT 232 230 235 234 233 +CONECT 233 232 +CONECT 234 232 +CONECT 235 232 +CONECT 236 238 239 237 230 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 242 228 241 +CONECT 241 240 +CONECT 242 252 243 240 +CONECT 243 244 242 253 246 +CONECT 244 245 259 243 +CONECT 245 244 +CONECT 246 243 247 254 255 +CONECT 247 248 249 246 +CONECT 248 251 257 247 +CONECT 249 250 247 256 +CONECT 250 251 258 249 +CONECT 251 855 250 248 +CONECT 252 242 +CONECT 253 243 +CONECT 254 246 +CONECT 255 246 +CONECT 256 249 +CONECT 257 248 +CONECT 258 250 +CONECT 259 261 244 260 +CONECT 260 259 +CONECT 261 262 263 271 259 +CONECT 262 261 +CONECT 263 264 265 261 269 +CONECT 264 263 +CONECT 265 266 267 263 268 +CONECT 266 265 +CONECT 267 265 +CONECT 268 265 +CONECT 269 263 270 +CONECT 270 269 +CONECT 271 273 261 272 +CONECT 272 271 +CONECT 273 283 274 271 +CONECT 274 275 277 273 284 +CONECT 275 276 290 274 +CONECT 276 275 +CONECT 277 285 286 274 278 +CONECT 278 277 279 280 +CONECT 279 288 278 282 +CONECT 280 278 287 281 +CONECT 281 282 280 289 +CONECT 282 279 281 855 +CONECT 283 273 +CONECT 284 274 +CONECT 285 277 +CONECT 286 277 +CONECT 287 280 +CONECT 288 279 +CONECT 289 281 +CONECT 290 292 275 291 +CONECT 291 290 +CONECT 292 303 293 290 294 +CONECT 293 292 +CONECT 294 292 297 296 295 +CONECT 295 294 +CONECT 296 294 +CONECT 297 299 300 294 298 +CONECT 298 297 +CONECT 299 297 +CONECT 300 301 297 302 +CONECT 301 300 +CONECT 302 300 +CONECT 303 305 304 292 +CONECT 304 303 +CONECT 305 307 306 303 +CONECT 306 305 +CONECT 307 313 309 308 305 +CONECT 308 307 +CONECT 309 312 311 307 310 +CONECT 310 309 +CONECT 311 309 +CONECT 312 309 +CONECT 313 315 314 307 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 329 319 318 315 +CONECT 318 317 +CONECT 319 320 325 317 321 +CONECT 320 319 +CONECT 321 319 322 324 323 +CONECT 322 321 +CONECT 323 321 +CONECT 324 321 +CONECT 325 328 327 319 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 330 331 317 +CONECT 330 329 +CONECT 331 333 329 332 +CONECT 332 331 +CONECT 333 335 334 341 331 +CONECT 334 333 +CONECT 335 338 336 337 333 +CONECT 336 335 +CONECT 337 335 +CONECT 338 339 340 335 +CONECT 339 338 +CONECT 340 338 +CONECT 341 333 343 342 +CONECT 342 341 +CONECT 343 344 341 345 +CONECT 344 343 +CONECT 345 343 365 364 346 +CONECT 346 347 348 349 345 +CONECT 347 346 +CONECT 348 346 +CONECT 349 346 350 363 +CONECT 350 349 351 352 +CONECT 351 350 +CONECT 352 350 353 354 +CONECT 353 352 +CONECT 354 352 355 363 +CONECT 355 354 356 357 +CONECT 356 355 +CONECT 357 355 358 359 +CONECT 358 357 +CONECT 359 357 360 361 +CONECT 360 359 +CONECT 361 359 362 363 +CONECT 362 361 +CONECT 363 349 354 361 +CONECT 364 345 +CONECT 365 367 345 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 370 375 +CONECT 370 369 +CONECT 371 373 372 374 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 371 +CONECT 375 369 376 377 +CONECT 376 375 +CONECT 377 375 378 379 +CONECT 378 377 +CONECT 379 377 381 380 390 +CONECT 380 379 +CONECT 381 384 379 382 383 +CONECT 382 381 +CONECT 383 381 +CONECT 384 385 387 386 381 +CONECT 385 384 +CONECT 386 384 +CONECT 387 389 384 388 +CONECT 388 387 +CONECT 389 387 +CONECT 390 379 392 391 +CONECT 391 390 +CONECT 392 393 390 394 +CONECT 393 392 +CONECT 394 392 396 400 395 +CONECT 395 394 +CONECT 396 397 398 394 399 +CONECT 397 396 +CONECT 398 396 +CONECT 399 396 +CONECT 400 402 394 401 +CONECT 401 400 +CONECT 402 403 404 400 +CONECT 403 402 +CONECT 404 406 402 405 415 +CONECT 405 404 +CONECT 406 407 408 409 404 +CONECT 407 406 +CONECT 408 406 +CONECT 409 412 406 411 410 +CONECT 410 409 +CONECT 411 409 +CONECT 412 413 414 409 +CONECT 413 412 +CONECT 414 412 +CONECT 415 404 417 416 +CONECT 416 415 +CONECT 417 418 415 419 +CONECT 418 417 +CONECT 419 417 421 420 437 +CONECT 420 419 +CONECT 421 424 422 423 419 +CONECT 422 421 +CONECT 423 421 +CONECT 424 427 426 425 421 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 428 424 429 +CONECT 428 427 +CONECT 429 427 +CONECT 430 433 432 431 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 436 435 434 430 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 419 439 438 +CONECT 438 437 +CONECT 439 440 437 441 +CONECT 440 439 +CONECT 441 439 443 442 457 +CONECT 442 441 +CONECT 443 446 444 441 445 +CONECT 444 443 +CONECT 445 443 +CONECT 446 447 455 443 +CONECT 447 449 448 446 +CONECT 448 447 +CONECT 449 450 451 447 +CONECT 450 449 +CONECT 451 452 449 453 +CONECT 452 451 +CONECT 453 451 454 455 +CONECT 454 453 +CONECT 455 453 446 456 +CONECT 456 455 +CONECT 457 441 459 458 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 463 459 471 462 +CONECT 462 461 +CONECT 463 464 469 465 461 +CONECT 464 463 +CONECT 465 466 463 467 468 +CONECT 466 465 +CONECT 467 465 +CONECT 468 465 +CONECT 469 470 463 +CONECT 470 469 +CONECT 471 473 461 472 +CONECT 472 471 +CONECT 473 474 475 471 +CONECT 474 473 +CONECT 475 477 473 476 493 +CONECT 476 475 +CONECT 477 480 478 479 475 +CONECT 478 477 +CONECT 479 477 +CONECT 480 483 482 481 477 +CONECT 481 480 +CONECT 482 480 +CONECT 483 486 484 485 480 +CONECT 484 483 +CONECT 485 483 +CONECT 486 488 489 487 483 +CONECT 487 486 +CONECT 488 486 +CONECT 489 491 486 490 492 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 +CONECT 493 475 495 494 +CONECT 494 493 +CONECT 495 496 493 497 +CONECT 496 495 +CONECT 497 495 499 498 503 +CONECT 498 497 +CONECT 499 501 502 497 500 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 497 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 524 523 508 +CONECT 508 509 510 511 507 +CONECT 509 508 +CONECT 510 508 +CONECT 511 508 512 513 514 +CONECT 512 511 +CONECT 513 511 +CONECT 514 511 515 516 517 +CONECT 515 514 +CONECT 516 514 +CONECT 517 514 518 519 520 +CONECT 518 517 +CONECT 519 517 +CONECT 520 517 521 522 +CONECT 521 520 +CONECT 522 520 +CONECT 523 507 +CONECT 524 526 507 525 +CONECT 525 524 +CONECT 526 527 528 524 +CONECT 527 526 +CONECT 528 530 526 534 529 +CONECT 529 528 +CONECT 530 531 532 533 528 +CONECT 531 530 +CONECT 532 530 +CONECT 533 530 +CONECT 534 536 528 535 +CONECT 535 534 +CONECT 536 537 538 534 +CONECT 537 536 +CONECT 538 540 536 539 548 +CONECT 539 538 +CONECT 540 543 541 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 545 544 540 +CONECT 544 543 +CONECT 545 547 546 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 538 550 549 +CONECT 549 548 +CONECT 550 551 548 552 +CONECT 551 550 +CONECT 552 550 553 554 560 +CONECT 553 552 +CONECT 554 555 552 557 556 +CONECT 555 554 +CONECT 556 554 +CONECT 557 558 559 554 +CONECT 558 557 +CONECT 559 557 +CONECT 560 552 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 580 579 565 +CONECT 565 566 567 568 564 +CONECT 566 565 +CONECT 567 565 +CONECT 568 565 569 577 +CONECT 569 568 570 571 +CONECT 570 569 +CONECT 571 569 572 573 +CONECT 572 571 +CONECT 573 571 574 575 +CONECT 574 573 +CONECT 575 573 576 577 +CONECT 576 575 +CONECT 577 568 575 578 +CONECT 578 577 +CONECT 579 564 +CONECT 580 582 564 581 +CONECT 581 580 +CONECT 582 583 584 580 +CONECT 583 582 +CONECT 584 587 586 582 585 +CONECT 585 584 +CONECT 586 584 +CONECT 587 589 588 584 +CONECT 588 587 +CONECT 589 591 590 587 +CONECT 590 589 +CONECT 591 611 610 589 592 +CONECT 592 593 594 595 591 +CONECT 593 592 +CONECT 594 592 +CONECT 595 592 596 597 598 +CONECT 596 595 +CONECT 597 595 +CONECT 598 595 599 600 601 +CONECT 599 598 +CONECT 600 598 +CONECT 601 598 602 603 +CONECT 602 601 +CONECT 603 601 604 607 +CONECT 604 603 605 606 +CONECT 605 604 +CONECT 606 604 +CONECT 607 603 608 609 +CONECT 608 607 +CONECT 609 607 +CONECT 610 591 +CONECT 611 613 612 591 +CONECT 612 611 +CONECT 613 615 614 611 +CONECT 614 613 +CONECT 615 617 623 616 613 +CONECT 616 615 +CONECT 617 620 618 619 615 +CONECT 618 617 +CONECT 619 617 +CONECT 620 622 621 617 +CONECT 621 620 +CONECT 622 620 +CONECT 623 624 625 615 +CONECT 624 623 +CONECT 625 627 623 626 +CONECT 626 625 +CONECT 627 630 628 629 625 +CONECT 628 627 +CONECT 629 627 +CONECT 630 632 631 627 +CONECT 631 630 +CONECT 632 634 633 630 +CONECT 633 632 +CONECT 634 636 635 645 632 +CONECT 635 634 +CONECT 636 638 639 637 634 +CONECT 637 636 +CONECT 638 636 +CONECT 639 641 642 636 640 +CONECT 640 639 +CONECT 641 639 +CONECT 642 643 639 644 +CONECT 643 642 +CONECT 644 642 +CONECT 645 647 634 646 +CONECT 646 645 +CONECT 647 648 649 645 +CONECT 648 647 +CONECT 649 655 647 654 650 +CONECT 650 651 652 653 649 +CONECT 651 650 +CONECT 652 650 +CONECT 653 650 +CONECT 654 649 +CONECT 655 656 657 649 +CONECT 656 655 +CONECT 657 659 655 658 +CONECT 658 657 +CONECT 659 660 661 669 657 +CONECT 660 659 +CONECT 661 663 667 659 662 +CONECT 662 661 +CONECT 663 666 665 664 661 +CONECT 664 663 +CONECT 665 663 +CONECT 666 663 +CONECT 667 661 668 +CONECT 668 667 +CONECT 669 671 659 670 +CONECT 670 669 +CONECT 671 672 673 669 +CONECT 672 671 +CONECT 673 688 671 687 674 +CONECT 674 675 676 680 673 +CONECT 675 674 +CONECT 676 674 677 678 679 +CONECT 677 676 +CONECT 678 676 +CONECT 679 676 +CONECT 680 674 681 682 683 +CONECT 681 680 +CONECT 682 680 +CONECT 683 680 684 685 686 +CONECT 684 683 +CONECT 685 683 +CONECT 686 683 +CONECT 687 673 +CONECT 688 689 690 673 +CONECT 689 688 +CONECT 690 692 688 691 +CONECT 691 690 +CONECT 692 693 700 694 690 +CONECT 693 692 +CONECT 694 697 692 695 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 699 698 694 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 692 701 +CONECT 701 700 +CONECT 702 703 704 700 +CONECT 703 702 +CONECT 704 706 702 712 705 +CONECT 705 704 +CONECT 706 708 709 707 704 +CONECT 707 706 +CONECT 708 706 +CONECT 709 710 706 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 704 713 +CONECT 713 712 +CONECT 714 715 716 712 +CONECT 715 714 +CONECT 716 718 717 714 722 +CONECT 717 716 +CONECT 718 721 719 720 716 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 +CONECT 722 716 723 724 +CONECT 723 722 +CONECT 724 722 725 726 +CONECT 725 724 +CONECT 726 724 727 728 736 +CONECT 727 726 +CONECT 728 730 726 734 729 +CONECT 729 728 +CONECT 730 732 733 731 728 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 735 728 +CONECT 735 734 +CONECT 736 726 738 737 +CONECT 737 736 +CONECT 738 739 740 736 +CONECT 739 738 +CONECT 740 741 738 742 758 +CONECT 741 740 +CONECT 742 745 740 744 743 +CONECT 743 742 +CONECT 744 742 +CONECT 745 748 746 747 742 +CONECT 746 745 +CONECT 747 745 +CONECT 748 751 750 749 745 +CONECT 749 748 +CONECT 750 748 +CONECT 751 754 753 752 748 +CONECT 752 751 +CONECT 753 751 +CONECT 754 756 755 757 751 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 +CONECT 758 740 760 759 +CONECT 759 758 +CONECT 760 761 758 762 +CONECT 761 760 +CONECT 762 760 772 764 763 +CONECT 763 762 +CONECT 764 765 762 770 766 +CONECT 765 764 +CONECT 766 764 767 768 769 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 771 764 +CONECT 771 770 +CONECT 772 773 762 774 +CONECT 773 772 +CONECT 774 772 776 775 +CONECT 775 774 +CONECT 776 777 774 778 792 +CONECT 777 776 +CONECT 778 781 776 780 779 +CONECT 779 778 +CONECT 780 778 +CONECT 781 790 782 778 +CONECT 782 784 781 783 +CONECT 783 782 +CONECT 784 786 785 782 +CONECT 785 784 +CONECT 786 787 788 784 +CONECT 787 786 +CONECT 788 789 786 790 +CONECT 789 788 +CONECT 790 788 791 781 +CONECT 791 790 +CONECT 792 776 794 793 +CONECT 793 792 +CONECT 794 795 792 796 +CONECT 795 794 +CONECT 796 794 798 806 797 +CONECT 797 796 +CONECT 798 804 800 799 796 +CONECT 799 798 +CONECT 800 801 803 798 802 +CONECT 801 800 +CONECT 802 800 +CONECT 803 800 +CONECT 804 805 798 +CONECT 805 804 +CONECT 806 807 796 808 +CONECT 807 806 +CONECT 808 806 810 809 +CONECT 809 808 +CONECT 810 820 819 808 811 +CONECT 811 812 813 817 810 +CONECT 812 811 +CONECT 813 811 814 815 816 +CONECT 814 813 +CONECT 815 813 +CONECT 816 813 +CONECT 817 811 818 +CONECT 818 817 +CONECT 819 810 +CONECT 820 822 821 810 +CONECT 821 820 +CONECT 822 824 823 820 +CONECT 823 822 +CONECT 824 836 822 837 825 +CONECT 825 826 827 828 824 +CONECT 826 825 +CONECT 827 825 +CONECT 828 825 829 830 831 +CONECT 829 828 +CONECT 830 828 +CONECT 831 828 832 833 +CONECT 832 831 +CONECT 833 831 834 835 +CONECT 834 833 +CONECT 835 833 +CONECT 836 824 +CONECT 837 824 839 838 +CONECT 838 837 +CONECT 839 840 837 841 +CONECT 840 839 +CONECT 841 843 839 852 842 +CONECT 842 841 +CONECT 843 845 844 846 841 +CONECT 844 843 +CONECT 845 843 +CONECT 846 847 843 848 849 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 850 851 +CONECT 850 849 +CONECT 851 849 +CONECT 852 854 841 853 +CONECT 853 852 +CONECT 854 852 +CONECT 855 87 282 856 251 +CONECT 856 855 858 +CONECT 857 860 858 861 859 +CONECT 858 856 857 +CONECT 859 857 +CONECT 860 857 +CONECT 861 857 +CONECT 862 863 +CONECT 863 862 864 +CONECT 864 863 +MASTER 0 0 0 0 0 0 0 0 864 0 864 0 +END diff --git a/tests/nsga2/min_mol_iter_0.pdb b/tests/nsga2/min_mol_iter_0.pdb new file mode 100644 index 0000000..0a0d82b --- /dev/null +++ b/tests/nsga2/min_mol_iter_0.pdb @@ -0,0 +1,1753 @@ +COMPND ./work_dir/frame0/min_nosolv.pdb +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 55.366 58.077 52.044 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.215 37.914 23.523 1.00 0.00 N +ATOM 2 H1 MET 1 15.201 38.296 24.464 1.00 0.00 H +ATOM 3 H2 MET 1 14.443 38.284 22.998 1.00 0.00 H +ATOM 4 H3 MET 1 16.084 38.206 23.097 1.00 0.00 H +ATOM 5 CA MET 1 15.167 36.444 23.594 1.00 0.00 C +ATOM 6 HA MET 1 14.223 36.155 24.051 1.00 0.00 H +ATOM 7 CB MET 1 15.256 35.794 22.200 1.00 0.00 C +ATOM 8 HB2 MET 1 14.404 36.123 21.604 1.00 0.00 H +ATOM 9 HB3 MET 1 16.168 36.123 21.701 1.00 0.00 H +ATOM 10 CG MET 1 15.256 34.254 22.251 1.00 0.00 C +ATOM 11 HG2 MET 1 16.133 33.929 22.814 1.00 0.00 H +ATOM 12 HG3 MET 1 14.367 33.916 22.786 1.00 0.00 H +ATOM 13 SD MET 1 15.317 33.393 20.646 1.00 0.00 S +ATOM 14 CE MET 1 13.636 33.641 20.008 1.00 0.00 C +ATOM 15 HE1 MET 1 13.415 34.705 19.929 1.00 0.00 H +ATOM 16 HE2 MET 1 13.557 33.192 19.017 1.00 0.00 H +ATOM 17 HE3 MET 1 12.912 33.164 20.670 1.00 0.00 H +ATOM 18 C MET 1 16.285 35.966 24.511 1.00 0.00 C +ATOM 19 O MET 1 17.429 36.370 24.340 1.00 0.00 O +ATOM 20 N GLN 2 15.963 35.099 25.473 1.00 0.00 N +ATOM 21 H GLN 2 14.992 34.874 25.632 1.00 0.00 H +ATOM 22 CA GLN 2 16.928 34.438 26.358 1.00 0.00 C +ATOM 23 HA GLN 2 17.697 35.150 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 16.177 34.003 27.636 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.213 33.562 27.357 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.744 33.245 28.172 1.00 0.00 H +ATOM 27 CG GLN 2 15.930 35.169 28.587 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.504 36.019 28.045 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.177 34.846 29.297 1.00 0.00 H +ATOM 30 CD GLN 2 17.140 35.548 29.441 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.211 34.972 29.368 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.976 36.450 30.363 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.748 36.615 30.982 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.068 36.818 30.542 1.00 0.00 H +ATOM 35 C GLN 2 17.653 33.291 25.623 1.00 0.00 C +ATOM 36 O GLN 2 17.281 32.121 25.734 1.00 0.00 O +ATOM 37 N TYR 3 18.675 33.646 24.841 1.00 0.00 N +ATOM 38 H TYR 3 18.926 34.635 24.813 1.00 0.00 H +ATOM 39 CA TYR 3 19.508 32.709 24.085 1.00 0.00 C +ATOM 40 HA TYR 3 18.854 32.101 23.459 1.00 0.00 H +ATOM 41 CB TYR 3 20.458 33.508 23.197 1.00 0.00 C +ATOM 42 HB2 TYR 3 21.071 34.153 23.827 1.00 0.00 H +ATOM 43 HB3 TYR 3 21.125 32.817 22.690 1.00 0.00 H +ATOM 44 CG TYR 3 19.760 34.349 22.152 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.102 33.711 21.087 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.079 32.633 21.039 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.519 34.465 20.054 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.049 33.973 19.217 1.00 0.00 H +ATOM 49 CZ TYR 3 18.571 35.872 20.103 1.00 0.00 C +ATOM 50 OH TYR 3 18.027 36.608 19.103 1.00 0.00 O +ATOM 51 HH TYR 3 18.041 36.130 18.273 1.00 0.00 H +ATOM 52 CE2 TYR 3 19.176 36.515 21.200 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.196 37.592 21.223 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.774 35.755 22.224 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.247 36.252 23.059 1.00 0.00 H +ATOM 56 C TYR 3 20.295 31.786 25.023 1.00 0.00 C +ATOM 57 O TYR 3 20.806 32.243 26.044 1.00 0.00 O +ATOM 58 N LYS 4 20.410 30.492 24.696 1.00 0.00 N +ATOM 59 H LYS 4 20.118 30.201 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 21.014 29.461 25.566 1.00 0.00 C +ATOM 61 HA LYS 4 20.744 29.654 26.602 1.00 0.00 H +ATOM 62 CB LYS 4 20.480 28.067 25.177 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.496 27.976 24.094 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.160 27.307 25.570 1.00 0.00 H +ATOM 65 CG LYS 4 19.070 27.701 25.676 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.897 26.669 25.374 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.060 27.742 26.766 1.00 0.00 H +ATOM 68 CD LYS 4 17.920 28.560 25.120 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.927 29.535 25.607 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.090 28.713 24.052 1.00 0.00 H +ATOM 71 CE LYS 4 16.533 27.909 25.279 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.777 28.600 24.894 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.509 27.012 24.654 1.00 0.00 H +ATOM 74 NZ LYS 4 16.205 27.518 26.673 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.269 28.291 27.318 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.276 27.107 26.716 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.829 26.763 26.958 1.00 0.00 H +ATOM 78 C LYS 4 22.547 29.475 25.513 1.00 0.00 C +ATOM 79 O LYS 4 23.144 29.819 24.501 1.00 0.00 O +HETATM 80 N HX1 5 23.203 29.039 26.584 1.00 0.00 N +HETATM 81 CA HX1 5 24.662 28.868 26.669 1.00 0.00 C +HETATM 82 C HX1 5 24.985 27.668 27.567 1.00 0.00 C +HETATM 83 O HX1 5 24.522 27.612 28.710 1.00 0.00 O +HETATM 84 CB HX1 5 25.294 30.185 27.169 1.00 0.00 C +HETATM 85 CG HX1 5 26.807 30.275 27.239 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.721 29.336 26.838 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.483 31.361 27.814 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.782 31.031 27.730 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.957 29.808 27.202 1.00 0.00 N +HETATM 90 H HX1 5 22.658 28.869 27.426 1.00 0.00 H +HETATM 91 HA HX1 5 25.052 28.661 25.672 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.899 30.401 28.163 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.958 30.992 26.516 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.539 28.374 26.378 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.578 31.603 28.187 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.812 29.251 27.293 1.00 0.00 H +ATOM 97 N ILE 6 25.726 26.695 27.028 1.00 0.00 N +ATOM 98 H ILE 6 26.046 26.815 26.070 1.00 0.00 H +ATOM 99 CA ILE 6 26.199 25.479 27.709 1.00 0.00 C +ATOM 100 HA ILE 6 25.697 25.404 28.676 1.00 0.00 H +ATOM 101 CB ILE 6 25.811 24.216 26.902 1.00 0.00 C +ATOM 102 HB ILE 6 26.234 24.306 25.901 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.373 22.929 27.541 1.00 0.00 C +ATOM 104 HG21 ILE 6 26.002 22.820 28.562 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.078 22.054 26.963 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.464 22.944 27.545 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.270 24.130 26.784 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.842 24.047 27.783 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.891 25.046 26.331 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.745 22.969 25.931 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.890 22.021 26.449 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.678 23.107 25.758 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.263 22.948 24.971 1.00 0.00 H +ATOM 114 C ILE 6 27.708 25.597 28.003 1.00 0.00 C +ATOM 115 O ILE 6 28.447 26.273 27.288 1.00 0.00 O +ATOM 116 N VAL 7 28.126 24.994 29.115 1.00 0.00 N +ATOM 117 H VAL 7 27.488 24.344 29.551 1.00 0.00 H +ATOM 118 CA VAL 7 29.238 25.447 29.963 1.00 0.00 C +ATOM 119 HA VAL 7 29.296 26.533 29.871 1.00 0.00 H +ATOM 120 CB VAL 7 28.813 25.143 31.416 1.00 0.00 C +ATOM 121 HB VAL 7 27.762 25.424 31.517 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.895 23.654 31.773 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.924 23.309 31.694 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.538 23.499 32.790 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.276 23.071 31.090 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.567 25.988 32.435 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.358 27.041 32.248 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.232 25.736 33.441 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.636 25.813 32.353 1.00 0.00 H +ATOM 130 C VAL 7 30.639 24.901 29.585 1.00 0.00 C +ATOM 131 O VAL 7 30.785 23.764 29.143 1.00 0.00 O +ATOM 132 N GLU 8 31.685 25.707 29.802 1.00 0.00 N +ATOM 133 H GLU 8 31.473 26.676 30.027 1.00 0.00 H +ATOM 134 CA GLU 8 33.119 25.383 29.624 1.00 0.00 C +ATOM 135 HA GLU 8 33.310 25.152 28.575 1.00 0.00 H +ATOM 136 CB GLU 8 33.917 26.667 29.977 1.00 0.00 C +ATOM 137 HB2 GLU 8 33.712 27.426 29.223 1.00 0.00 H +ATOM 138 HB3 GLU 8 33.497 27.048 30.911 1.00 0.00 H +ATOM 139 CG GLU 8 35.447 26.584 30.222 1.00 0.00 C +ATOM 140 HG2 GLU 8 35.729 27.498 30.753 1.00 0.00 H +ATOM 141 HG3 GLU 8 35.683 25.765 30.900 1.00 0.00 H +ATOM 142 CD GLU 8 36.359 26.500 28.992 1.00 0.00 C +ATOM 143 OE1 GLU 8 36.012 27.041 27.916 1.00 0.00 O +ATOM 144 OE2 GLU 8 37.521 26.054 29.135 1.00 0.00 O +ATOM 145 C GLU 8 33.570 24.164 30.464 1.00 0.00 C +ATOM 146 O GLU 8 33.840 24.286 31.658 1.00 0.00 O +ATOM 147 N GLY 9 33.696 22.982 29.849 1.00 0.00 N +ATOM 148 H GLY 9 33.287 22.892 28.929 1.00 0.00 H +ATOM 149 CA GLY 9 34.345 21.797 30.438 1.00 0.00 C +ATOM 150 HA2 GLY 9 35.247 21.575 29.868 1.00 0.00 H +ATOM 151 HA3 GLY 9 34.650 22.011 31.462 1.00 0.00 H +ATOM 152 C GLY 9 33.492 20.522 30.448 1.00 0.00 C +ATOM 153 O GLY 9 32.620 20.332 29.602 1.00 0.00 O +ATOM 154 N LYS 10 33.792 19.600 31.384 1.00 0.00 N +ATOM 155 H LYS 10 34.546 19.810 32.024 1.00 0.00 H +ATOM 156 CA LYS 10 33.231 18.228 31.369 1.00 0.00 C +ATOM 157 HA LYS 10 32.207 18.313 30.994 1.00 0.00 H +ATOM 158 CB LYS 10 34.029 17.371 30.353 1.00 0.00 C +ATOM 159 HB2 LYS 10 34.519 18.019 29.622 1.00 0.00 H +ATOM 160 HB3 LYS 10 34.809 16.806 30.866 1.00 0.00 H +ATOM 161 CG LYS 10 33.125 16.407 29.565 1.00 0.00 C +ATOM 162 HG2 LYS 10 32.575 15.759 30.248 1.00 0.00 H +ATOM 163 HG3 LYS 10 32.406 16.996 28.991 1.00 0.00 H +ATOM 164 CD LYS 10 33.941 15.541 28.595 1.00 0.00 C +ATOM 165 HD2 LYS 10 34.578 16.183 27.985 1.00 0.00 H +ATOM 166 HD3 LYS 10 34.568 14.847 29.158 1.00 0.00 H +ATOM 167 CE LYS 10 32.994 14.759 27.678 1.00 0.00 C +ATOM 168 HE2 LYS 10 32.438 14.025 28.267 1.00 0.00 H +ATOM 169 HE3 LYS 10 32.275 15.460 27.247 1.00 0.00 H +ATOM 170 NZ LYS 10 33.721 14.092 26.575 1.00 0.00 N +ATOM 171 HZ1 LYS 10 34.417 13.448 26.913 1.00 0.00 H +ATOM 172 HZ2 LYS 10 33.061 13.594 25.979 1.00 0.00 H +ATOM 173 HZ3 LYS 10 34.203 14.795 26.004 1.00 0.00 H +ATOM 174 C LYS 10 33.089 17.528 32.737 1.00 0.00 C +ATOM 175 O LYS 10 33.156 16.303 32.800 1.00 0.00 O +ATOM 176 N ARG 11 32.949 18.273 33.841 1.00 0.00 N +ATOM 177 H ARG 11 32.915 19.267 33.709 1.00 0.00 H +ATOM 178 CA ARG 11 32.662 17.722 35.194 1.00 0.00 C +ATOM 179 HA ARG 11 32.758 16.632 35.161 1.00 0.00 H +ATOM 180 CB ARG 11 33.685 18.237 36.231 1.00 0.00 C +ATOM 181 HB2 ARG 11 33.709 19.326 36.208 1.00 0.00 H +ATOM 182 HB3 ARG 11 33.355 17.924 37.222 1.00 0.00 H +ATOM 183 CG ARG 11 35.099 17.680 35.989 1.00 0.00 C +ATOM 184 HG2 ARG 11 35.055 16.589 35.999 1.00 0.00 H +ATOM 185 HG3 ARG 11 35.449 18.007 35.010 1.00 0.00 H +ATOM 186 CD ARG 11 36.103 18.142 37.058 1.00 0.00 C +ATOM 187 HD2 ARG 11 36.071 19.228 37.118 1.00 0.00 H +ATOM 188 HD3 ARG 11 35.803 17.740 38.029 1.00 0.00 H +ATOM 189 NE ARG 11 37.479 17.692 36.740 1.00 0.00 N +ATOM 190 HE ARG 11 37.569 16.946 36.073 1.00 0.00 H +ATOM 191 CZ ARG 11 38.615 18.198 37.201 1.00 0.00 C +ATOM 192 NH1 ARG 11 38.667 19.233 37.987 1.00 0.00 N +ATOM 193 HH11 ARG 11 37.829 19.772 38.112 1.00 0.00 H +ATOM 194 HH12 ARG 11 39.560 19.686 38.132 1.00 0.00 H +ATOM 195 NH2 ARG 11 39.749 17.650 36.875 1.00 0.00 N +ATOM 196 HH21 ARG 11 39.795 16.894 36.219 1.00 0.00 H +ATOM 197 HH22 ARG 11 40.609 18.031 37.266 1.00 0.00 H +ATOM 198 C ARG 11 31.206 17.954 35.609 1.00 0.00 C +ATOM 199 O ARG 11 30.490 17.005 35.900 1.00 0.00 O +ATOM 200 N TYR 12 30.762 19.208 35.566 1.00 0.00 N +ATOM 201 H TYR 12 31.434 19.929 35.379 1.00 0.00 H +ATOM 202 CA TYR 12 29.346 19.607 35.531 1.00 0.00 C +ATOM 203 HA TYR 12 28.789 18.986 36.247 1.00 0.00 H +ATOM 204 CB TYR 12 29.234 21.066 36.001 1.00 0.00 C +ATOM 205 HB2 TYR 12 28.187 21.379 35.945 1.00 0.00 H +ATOM 206 HB3 TYR 12 29.493 21.077 37.062 1.00 0.00 H +ATOM 207 CG TYR 12 30.105 22.126 35.333 1.00 0.00 C +ATOM 208 CD1 TYR 12 30.870 21.891 34.171 1.00 0.00 C +ATOM 209 HD1 TYR 12 30.824 20.950 33.636 1.00 0.00 H +ATOM 210 CE1 TYR 12 31.738 22.879 33.670 1.00 0.00 C +ATOM 211 HE1 TYR 12 32.313 22.692 32.776 1.00 0.00 H +ATOM 212 CZ TYR 12 31.833 24.123 34.322 1.00 0.00 C +ATOM 213 OH TYR 12 32.699 25.074 33.898 1.00 0.00 O +ATOM 214 HH TYR 12 33.108 24.847 33.030 1.00 0.00 H +ATOM 215 CE2 TYR 12 30.999 24.398 35.419 1.00 0.00 C +ATOM 216 HE2 TYR 12 31.006 25.385 35.861 1.00 0.00 H +ATOM 217 CD2 TYR 12 30.158 23.394 35.933 1.00 0.00 C +ATOM 218 HD2 TYR 12 29.558 23.604 36.815 1.00 0.00 H +ATOM 219 C TYR 12 28.690 19.397 34.145 1.00 0.00 C +ATOM 220 O TYR 12 29.368 19.005 33.196 1.00 0.00 O +ATOM 221 N LYS 13 27.382 19.683 34.028 1.00 0.00 N +ATOM 222 H LYS 13 26.894 19.964 34.865 1.00 0.00 H +ATOM 223 CA LYS 13 26.590 19.509 32.789 1.00 0.00 C +ATOM 224 HA LYS 13 27.257 19.685 31.944 1.00 0.00 H +ATOM 225 CB LYS 13 26.113 18.042 32.728 1.00 0.00 C +ATOM 226 HB2 LYS 13 26.870 17.413 33.196 1.00 0.00 H +ATOM 227 HB3 LYS 13 25.191 17.936 33.302 1.00 0.00 H +ATOM 228 CG LYS 13 25.912 17.515 31.295 1.00 0.00 C +ATOM 229 HG2 LYS 13 25.056 18.000 30.825 1.00 0.00 H +ATOM 230 HG3 LYS 13 26.803 17.746 30.711 1.00 0.00 H +ATOM 231 CD LYS 13 25.715 15.990 31.282 1.00 0.00 C +ATOM 232 HD2 LYS 13 25.753 15.643 30.248 1.00 0.00 H +ATOM 233 HD3 LYS 13 26.543 15.525 31.821 1.00 0.00 H +ATOM 234 CE LYS 13 24.376 15.549 31.892 1.00 0.00 C +ATOM 235 HE2 LYS 13 24.136 16.182 32.751 1.00 0.00 H +ATOM 236 HE3 LYS 13 23.603 15.708 31.133 1.00 0.00 H +ATOM 237 NZ LYS 13 24.406 14.121 32.306 1.00 0.00 N +ATOM 238 HZ1 LYS 13 24.934 13.975 33.159 1.00 0.00 H +ATOM 239 HZ2 LYS 13 23.466 13.759 32.451 1.00 0.00 H +ATOM 240 HZ3 LYS 13 24.860 13.553 31.592 1.00 0.00 H +ATOM 241 C LYS 13 25.440 20.533 32.632 1.00 0.00 C +ATOM 242 O LYS 13 24.397 20.233 32.051 1.00 0.00 O +ATOM 243 N GLY 14 25.597 21.720 33.227 1.00 0.00 N +ATOM 244 H GLY 14 26.491 21.921 33.646 1.00 0.00 H +ATOM 245 CA GLY 14 24.547 22.749 33.314 1.00 0.00 C +ATOM 246 HA2 GLY 14 23.595 22.255 33.508 1.00 0.00 H +ATOM 247 HA3 GLY 14 24.753 23.393 34.169 1.00 0.00 H +ATOM 248 C GLY 14 24.384 23.636 32.065 1.00 0.00 C +ATOM 249 O GLY 14 25.241 23.673 31.182 1.00 0.00 O +ATOM 250 N VAL 15 23.283 24.395 32.031 1.00 0.00 N +ATOM 251 H VAL 15 22.640 24.337 32.808 1.00 0.00 H +ATOM 252 CA VAL 15 22.902 25.355 30.981 1.00 0.00 C +ATOM 253 HA VAL 15 23.781 25.595 30.382 1.00 0.00 H +ATOM 254 CB VAL 15 21.857 24.717 30.034 1.00 0.00 C +ATOM 255 HB VAL 15 22.299 23.817 29.609 1.00 0.00 H +ATOM 256 CG1 VAL 15 20.551 24.300 30.731 1.00 0.00 C +ATOM 257 HG11 VAL 15 20.049 25.165 31.169 1.00 0.00 H +ATOM 258 HG12 VAL 15 19.882 23.832 30.007 1.00 0.00 H +ATOM 259 HG13 VAL 15 20.757 23.573 31.519 1.00 0.00 H +ATOM 260 CG2 VAL 15 21.481 25.640 28.867 1.00 0.00 C +ATOM 261 HG21 VAL 15 22.382 25.990 28.366 1.00 0.00 H +ATOM 262 HG22 VAL 15 20.879 25.084 28.146 1.00 0.00 H +ATOM 263 HG23 VAL 15 20.901 26.492 29.221 1.00 0.00 H +ATOM 264 C VAL 15 22.399 26.651 31.633 1.00 0.00 C +ATOM 265 O VAL 15 21.845 26.618 32.728 1.00 0.00 O +HETATM 266 N HY1 16 22.593 27.795 30.980 1.00 0.00 N +HETATM 267 CA HY1 16 22.005 29.092 31.344 1.00 0.00 C +HETATM 268 C HY1 16 21.694 29.890 30.062 1.00 0.00 C +HETATM 269 O HY1 16 21.860 29.375 28.949 1.00 0.00 O +HETATM 270 CB HY1 16 22.928 29.838 32.334 1.00 0.00 C +HETATM 271 CG HY1 16 24.278 30.202 31.763 1.00 0.00 C +HETATM 272 CD2 HY1 16 24.599 31.380 31.142 1.00 0.00 C +HETATM 273 ND1 HY1 16 25.407 29.412 31.750 1.00 0.00 N +HETATM 274 CE1 HY1 16 26.387 30.121 31.164 1.00 0.00 C +HETATM 275 NE2 HY1 16 25.942 31.324 30.761 1.00 0.00 N +HETATM 276 H HY1 16 23.089 27.760 30.095 1.00 0.00 H +HETATM 277 HA HY1 16 21.042 28.937 31.836 1.00 0.00 H +HETATM 278 HB2 HY1 16 22.448 30.747 32.701 1.00 0.00 H +HETATM 279 HB3 HY1 16 23.076 29.209 33.217 1.00 0.00 H +HETATM 280 HD1 HY1 16 25.502 28.501 32.177 1.00 0.00 H +HETATM 281 HD2 HY1 16 23.933 32.219 30.992 1.00 0.00 H +HETATM 282 HE1 HY1 16 27.419 29.794 31.067 1.00 0.00 H +ATOM 283 N THR 17 21.213 31.125 30.221 1.00 0.00 N +ATOM 284 H THR 17 21.084 31.439 31.169 1.00 0.00 H +ATOM 285 CA THR 17 20.771 32.009 29.122 1.00 0.00 C +ATOM 286 HA THR 17 21.190 31.603 28.215 1.00 0.00 H +ATOM 287 CB THR 17 19.244 32.008 28.942 1.00 0.00 C +ATOM 288 HB THR 17 19.023 32.578 28.042 1.00 0.00 H +ATOM 289 CG2 THR 17 18.642 30.640 28.642 1.00 0.00 C +ATOM 290 HG21 THR 17 18.864 29.923 29.430 1.00 0.00 H +ATOM 291 HG22 THR 17 17.562 30.744 28.553 1.00 0.00 H +ATOM 292 HG23 THR 17 19.034 30.311 27.693 1.00 0.00 H +ATOM 293 OG1 THR 17 18.523 32.465 30.065 1.00 0.00 O +ATOM 294 HG1 THR 17 18.606 33.430 30.107 1.00 0.00 H +ATOM 295 C THR 17 21.279 33.458 29.181 1.00 0.00 C +ATOM 296 O THR 17 21.726 33.926 30.226 1.00 0.00 O +HETATM 297 N HY2 18 21.213 34.175 28.055 1.00 0.00 N +HETATM 298 CA HY2 18 21.495 35.612 27.957 1.00 0.00 C +HETATM 299 C HY2 18 20.395 36.305 27.153 1.00 0.00 C +HETATM 300 O HY2 18 20.079 35.863 26.049 1.00 0.00 O +HETATM 301 CB HY2 18 22.848 35.842 27.247 1.00 0.00 C +HETATM 302 CG HY2 18 24.050 35.344 28.020 1.00 0.00 C +HETATM 303 CD2 HY2 18 24.548 34.066 28.017 1.00 0.00 C +HETATM 304 ND1 HY2 18 24.828 36.083 28.888 1.00 0.00 N +HETATM 305 CE1 HY2 18 25.770 35.264 29.383 1.00 0.00 C +HETATM 306 NE2 HY2 18 25.640 34.024 28.889 1.00 0.00 N +HETATM 307 H HY2 18 20.908 33.715 27.202 1.00 0.00 H +HETATM 308 HA HY2 18 21.529 36.051 28.954 1.00 0.00 H +HETATM 309 HB2 HY2 18 22.822 35.342 26.280 1.00 0.00 H +HETATM 310 HB3 HY2 18 22.973 36.910 27.064 1.00 0.00 H +HETATM 311 HD1 HY2 18 24.725 37.067 29.105 1.00 0.00 H +HETATM 312 HD2 HY2 18 24.156 33.232 27.450 1.00 0.00 H +HETATM 313 HE1 HY2 18 26.531 35.559 30.091 1.00 0.00 H +ATOM 314 N GLU 19 19.822 37.382 27.687 1.00 0.00 N +ATOM 315 H GLU 19 20.120 37.688 28.599 1.00 0.00 H +ATOM 316 CA GLU 19 18.828 38.211 26.992 1.00 0.00 C +ATOM 317 HA GLU 19 18.106 37.555 26.510 1.00 0.00 H +ATOM 318 CB GLU 19 18.086 39.074 28.032 1.00 0.00 C +ATOM 319 HB2 GLU 19 17.783 38.444 28.864 1.00 0.00 H +ATOM 320 HB3 GLU 19 18.779 39.814 28.429 1.00 0.00 H +ATOM 321 CG GLU 19 16.839 39.798 27.502 1.00 0.00 C +ATOM 322 HG2 GLU 19 16.549 40.555 28.233 1.00 0.00 H +ATOM 323 HG3 GLU 19 17.073 40.313 26.569 1.00 0.00 H +ATOM 324 CD GLU 19 15.667 38.828 27.300 1.00 0.00 C +ATOM 325 OE1 GLU 19 15.544 38.285 26.172 1.00 0.00 O +ATOM 326 OE2 GLU 19 14.908 38.603 28.271 1.00 0.00 O +ATOM 327 C GLU 19 19.483 39.095 25.913 1.00 0.00 C +ATOM 328 O GLU 19 20.430 39.823 26.208 1.00 0.00 O +ATOM 329 N ALA 20 18.977 39.059 24.676 1.00 0.00 N +ATOM 330 H ALA 20 18.268 38.367 24.467 1.00 0.00 H +ATOM 331 CA ALA 20 19.340 40.004 23.612 1.00 0.00 C +ATOM 332 HA ALA 20 19.410 41.004 24.042 1.00 0.00 H +ATOM 333 CB ALA 20 20.714 39.620 23.042 1.00 0.00 C +ATOM 334 HB1 ALA 20 20.657 38.642 22.573 1.00 0.00 H +ATOM 335 HB2 ALA 20 21.036 40.351 22.302 1.00 0.00 H +ATOM 336 HB3 ALA 20 21.459 39.585 23.834 1.00 0.00 H +ATOM 337 C ALA 20 18.286 40.039 22.486 1.00 0.00 C +ATOM 338 O ALA 20 17.384 39.200 22.439 1.00 0.00 O +ATOM 339 N VAL 21 18.416 40.981 21.545 1.00 0.00 N +ATOM 340 H VAL 21 19.145 41.670 21.653 1.00 0.00 H +ATOM 341 CA VAL 21 17.672 40.975 20.262 1.00 0.00 C +ATOM 342 HA VAL 21 16.689 40.537 20.427 1.00 0.00 H +ATOM 343 CB VAL 21 17.448 42.410 19.731 1.00 0.00 C +ATOM 344 HB VAL 21 16.804 42.345 18.853 1.00 0.00 H +ATOM 345 CG1 VAL 21 16.721 43.284 20.761 1.00 0.00 C +ATOM 346 HG11 VAL 21 17.357 43.476 21.625 1.00 0.00 H +ATOM 347 HG12 VAL 21 16.455 44.237 20.303 1.00 0.00 H +ATOM 348 HG13 VAL 21 15.806 42.790 21.088 1.00 0.00 H +ATOM 349 CG2 VAL 21 18.744 43.117 19.309 1.00 0.00 C +ATOM 350 HG21 VAL 21 19.218 42.578 18.489 1.00 0.00 H +ATOM 351 HG22 VAL 21 18.510 44.121 18.954 1.00 0.00 H +ATOM 352 HG23 VAL 21 19.441 43.191 20.143 1.00 0.00 H +ATOM 353 C VAL 21 18.344 40.117 19.176 1.00 0.00 C +ATOM 354 O VAL 21 17.744 39.875 18.133 1.00 0.00 O +ATOM 355 N ASP 22 19.590 39.693 19.410 1.00 0.00 N +ATOM 356 H ASP 22 20.003 39.905 20.303 1.00 0.00 H +ATOM 357 CA ASP 22 20.496 39.093 18.428 1.00 0.00 C +ATOM 358 HA ASP 22 19.939 38.443 17.752 1.00 0.00 H +ATOM 359 CB ASP 22 21.118 40.245 17.617 1.00 0.00 C +ATOM 360 HB2 ASP 22 20.331 40.741 17.046 1.00 0.00 H +ATOM 361 HB3 ASP 22 21.537 40.973 18.314 1.00 0.00 H +ATOM 362 CG ASP 22 22.212 39.808 16.646 1.00 0.00 C +ATOM 363 OD1 ASP 22 23.135 40.614 16.431 1.00 0.00 O +ATOM 364 OD2 ASP 22 22.150 38.658 16.158 1.00 0.00 O +ATOM 365 C ASP 22 21.589 38.257 19.129 1.00 0.00 C +ATOM 366 O ASP 22 22.026 38.601 20.232 1.00 0.00 O +ATOM 367 N PHE 23 22.075 37.194 18.482 1.00 0.00 N +ATOM 368 H PHE 23 21.801 37.088 17.511 1.00 0.00 H +ATOM 369 CA PHE 23 23.223 36.413 18.957 1.00 0.00 C +ATOM 370 HA PHE 23 23.033 36.100 19.983 1.00 0.00 H +ATOM 371 CB PHE 23 23.435 35.163 18.098 1.00 0.00 C +ATOM 372 HB2 PHE 23 23.449 35.439 17.042 1.00 0.00 H +ATOM 373 HB3 PHE 23 24.415 34.748 18.336 1.00 0.00 H +ATOM 374 CG PHE 23 22.418 34.075 18.332 1.00 0.00 C +ATOM 375 CD1 PHE 23 21.326 33.930 17.460 1.00 0.00 C +ATOM 376 HD1 PHE 23 21.215 34.591 16.613 1.00 0.00 H +ATOM 377 CE1 PHE 23 20.387 32.912 17.686 1.00 0.00 C +ATOM 378 HE1 PHE 23 19.553 32.789 17.010 1.00 0.00 H +ATOM 379 CZ PHE 23 20.545 32.053 18.784 1.00 0.00 C +ATOM 380 HZ PHE 23 19.804 31.307 18.977 1.00 0.00 H +ATOM 381 CE2 PHE 23 21.642 32.183 19.650 1.00 0.00 C +ATOM 382 HE2 PHE 23 21.763 31.512 20.488 1.00 0.00 H +ATOM 383 CD2 PHE 23 22.581 33.199 19.421 1.00 0.00 C +ATOM 384 HD2 PHE 23 23.433 33.303 20.076 1.00 0.00 H +ATOM 385 C PHE 23 24.522 37.216 18.948 1.00 0.00 C +ATOM 386 O PHE 23 25.288 37.123 19.906 1.00 0.00 O +ATOM 387 N ALA 24 24.777 38.032 17.920 1.00 0.00 N +ATOM 388 H ALA 24 24.098 38.127 17.167 1.00 0.00 H +ATOM 389 CA ALA 24 26.004 38.826 17.863 1.00 0.00 C +ATOM 390 HA ALA 24 26.836 38.166 18.118 1.00 0.00 H +ATOM 391 CB ALA 24 26.244 39.297 16.423 1.00 0.00 C +ATOM 392 HB1 ALA 24 25.486 40.016 16.122 1.00 0.00 H +ATOM 393 HB2 ALA 24 27.226 39.763 16.347 1.00 0.00 H +ATOM 394 HB3 ALA 24 26.209 38.442 15.744 1.00 0.00 H +ATOM 395 C ALA 24 26.024 39.969 18.904 1.00 0.00 C +ATOM 396 O ALA 24 27.084 40.536 19.172 1.00 0.00 O +ATOM 397 N GLU 25 24.892 40.281 19.545 1.00 0.00 N +ATOM 398 H GLU 25 24.041 39.856 19.205 1.00 0.00 H +ATOM 399 CA GLU 25 24.819 41.085 20.776 1.00 0.00 C +ATOM 400 HA GLU 25 25.636 41.806 20.796 1.00 0.00 H +ATOM 401 CB GLU 25 23.498 41.871 20.814 1.00 0.00 C +ATOM 402 HB2 GLU 25 22.673 41.163 20.774 1.00 0.00 H +ATOM 403 HB3 GLU 25 23.429 42.408 21.760 1.00 0.00 H +ATOM 404 CG GLU 25 23.310 42.881 19.671 1.00 0.00 C +ATOM 405 HG2 GLU 25 23.577 42.429 18.714 1.00 0.00 H +ATOM 406 HG3 GLU 25 22.247 43.135 19.624 1.00 0.00 H +ATOM 407 CD GLU 25 24.114 44.170 19.880 1.00 0.00 C +ATOM 408 OE1 GLU 25 23.462 45.220 20.101 1.00 0.00 O +ATOM 409 OE2 GLU 25 25.371 44.098 19.811 1.00 0.00 O +ATOM 410 C GLU 25 24.959 40.215 22.041 1.00 0.00 C +ATOM 411 O GLU 25 25.732 40.553 22.938 1.00 0.00 O +ATOM 412 N ALA 26 24.299 39.050 22.103 1.00 0.00 N +ATOM 413 H ALA 26 23.662 38.814 21.352 1.00 0.00 H +ATOM 414 CA ALA 26 24.423 38.100 23.218 1.00 0.00 C +ATOM 415 HA ALA 26 24.130 38.609 24.131 1.00 0.00 H +ATOM 416 CB ALA 26 23.471 36.923 22.993 1.00 0.00 C +ATOM 417 HB1 ALA 26 23.770 36.368 22.108 1.00 0.00 H +ATOM 418 HB2 ALA 26 23.499 36.260 23.854 1.00 0.00 H +ATOM 419 HB3 ALA 26 22.460 37.285 22.860 1.00 0.00 H +ATOM 420 C ALA 26 25.868 37.595 23.424 1.00 0.00 C +ATOM 421 O ALA 26 26.292 37.316 24.550 1.00 0.00 O +ATOM 422 N GLU 27 26.659 37.515 22.348 1.00 0.00 N +ATOM 423 H GLU 27 26.221 37.663 21.441 1.00 0.00 H +ATOM 424 CA GLU 27 28.109 37.261 22.347 1.00 0.00 C +ATOM 425 HA GLU 27 28.316 36.315 22.855 1.00 0.00 H +ATOM 426 CB GLU 27 28.586 37.117 20.887 1.00 0.00 C +ATOM 427 HB2 GLU 27 28.014 36.303 20.438 1.00 0.00 H +ATOM 428 HB3 GLU 27 28.354 38.028 20.337 1.00 0.00 H +ATOM 429 CG GLU 27 30.079 36.836 20.757 1.00 0.00 C +ATOM 430 HG2 GLU 27 30.614 37.779 20.882 1.00 0.00 H +ATOM 431 HG3 GLU 27 30.401 36.162 21.554 1.00 0.00 H +ATOM 432 CD GLU 27 30.366 36.227 19.390 1.00 0.00 C +ATOM 433 OE1 GLU 27 30.986 36.917 18.564 1.00 0.00 O +ATOM 434 OE2 GLU 27 29.944 35.073 19.158 1.00 0.00 O +ATOM 435 C GLU 27 28.855 38.375 23.112 1.00 0.00 C +ATOM 436 O GLU 27 29.633 38.083 24.023 1.00 0.00 O +ATOM 437 N LYS 28 28.553 39.656 22.836 1.00 0.00 N +ATOM 438 H LYS 28 27.822 39.830 22.156 1.00 0.00 H +ATOM 439 CA LYS 28 29.116 40.802 23.576 1.00 0.00 C +ATOM 440 HA LYS 28 30.202 40.719 23.569 1.00 0.00 H +ATOM 441 CB LYS 28 28.725 42.140 22.919 1.00 0.00 C +ATOM 442 HB2 LYS 28 27.648 42.281 22.995 1.00 0.00 H +ATOM 443 HB3 LYS 28 29.205 42.945 23.473 1.00 0.00 H +ATOM 444 CG LYS 28 29.135 42.250 21.442 1.00 0.00 C +ATOM 445 HG2 LYS 28 30.206 42.069 21.341 1.00 0.00 H +ATOM 446 HG3 LYS 28 28.602 41.496 20.871 1.00 0.00 H +ATOM 447 CD LYS 28 28.806 43.646 20.888 1.00 0.00 C +ATOM 448 HD2 LYS 28 27.796 43.939 21.184 1.00 0.00 H +ATOM 449 HD3 LYS 28 29.505 44.362 21.322 1.00 0.00 H +ATOM 450 CE LYS 28 28.917 43.732 19.359 1.00 0.00 C +ATOM 451 HE2 LYS 28 29.049 44.784 19.086 1.00 0.00 H +ATOM 452 HE3 LYS 28 29.802 43.181 19.025 1.00 0.00 H +ATOM 453 NZ LYS 28 27.696 43.214 18.694 1.00 0.00 N +ATOM 454 HZ1 LYS 28 26.858 43.680 19.063 1.00 0.00 H +ATOM 455 HZ2 LYS 28 27.718 43.355 17.696 1.00 0.00 H +ATOM 456 HZ3 LYS 28 27.563 42.223 18.882 1.00 0.00 H +ATOM 457 C LYS 28 28.694 40.774 25.048 1.00 0.00 C +ATOM 458 O LYS 28 29.531 40.971 25.922 1.00 0.00 O +ATOM 459 N PHE 29 27.433 40.461 25.351 1.00 0.00 N +ATOM 460 H PHE 29 26.770 40.367 24.587 1.00 0.00 H +ATOM 461 CA PHE 29 26.956 40.324 26.737 1.00 0.00 C +ATOM 462 HA PHE 29 27.288 41.196 27.301 1.00 0.00 H +ATOM 463 CB PHE 29 25.418 40.308 26.753 1.00 0.00 C +ATOM 464 HB2 PHE 29 25.082 39.379 26.290 1.00 0.00 H +ATOM 465 HB3 PHE 29 25.083 40.298 27.791 1.00 0.00 H +ATOM 466 CG PHE 29 24.734 41.474 26.050 1.00 0.00 C +ATOM 467 CD1 PHE 29 23.512 41.261 25.382 1.00 0.00 C +ATOM 468 HD1 PHE 29 23.048 40.287 25.399 1.00 0.00 H +ATOM 469 CE1 PHE 29 22.881 42.313 24.694 1.00 0.00 C +ATOM 470 HE1 PHE 29 21.946 42.138 24.183 1.00 0.00 H +ATOM 471 CZ PHE 29 23.462 43.592 24.675 1.00 0.00 C +ATOM 472 HZ PHE 29 22.980 44.397 24.138 1.00 0.00 H +ATOM 473 CE2 PHE 29 24.664 43.823 25.367 1.00 0.00 C +ATOM 474 HE2 PHE 29 25.105 44.809 25.369 1.00 0.00 H +ATOM 475 CD2 PHE 29 25.293 42.771 26.056 1.00 0.00 C +ATOM 476 HD2 PHE 29 26.211 42.971 26.586 1.00 0.00 H +ATOM 477 C PHE 29 27.555 39.107 27.465 1.00 0.00 C +ATOM 478 O PHE 29 27.773 39.150 28.677 1.00 0.00 O +ATOM 479 N THR 30 27.896 38.038 26.741 1.00 0.00 N +ATOM 480 H THR 30 27.619 38.016 25.764 1.00 0.00 H +ATOM 481 CA THR 30 28.673 36.905 27.271 1.00 0.00 C +ATOM 482 HA THR 30 28.197 36.550 28.185 1.00 0.00 H +ATOM 483 CB THR 30 28.682 35.736 26.276 1.00 0.00 C +ATOM 484 HB THR 30 29.041 36.062 25.302 1.00 0.00 H +ATOM 485 CG2 THR 30 29.498 34.534 26.746 1.00 0.00 C +ATOM 486 HG21 THR 30 29.142 34.220 27.721 1.00 0.00 H +ATOM 487 HG22 THR 30 29.367 33.720 26.036 1.00 0.00 H +ATOM 488 HG23 THR 30 30.560 34.772 26.807 1.00 0.00 H +ATOM 489 OG1 THR 30 27.360 35.286 26.150 1.00 0.00 O +ATOM 490 HG1 THR 30 26.921 35.901 25.540 1.00 0.00 H +ATOM 491 C THR 30 30.096 37.329 27.627 1.00 0.00 C +ATOM 492 O THR 30 30.588 36.990 28.705 1.00 0.00 O +ATOM 493 N LYS 31 30.738 38.118 26.757 1.00 0.00 N +ATOM 494 H LYS 31 30.278 38.309 25.872 1.00 0.00 H +ATOM 495 CA LYS 31 32.079 38.688 26.976 1.00 0.00 C +ATOM 496 HA LYS 31 32.743 37.884 27.300 1.00 0.00 H +ATOM 497 CB LYS 31 32.621 39.274 25.671 1.00 0.00 C +ATOM 498 HB2 LYS 31 31.903 39.978 25.246 1.00 0.00 H +ATOM 499 HB3 LYS 31 33.541 39.820 25.894 1.00 0.00 H +ATOM 500 CG LYS 31 32.944 38.173 24.651 1.00 0.00 C +ATOM 501 HG2 LYS 31 33.671 37.499 25.091 1.00 0.00 H +ATOM 502 HG3 LYS 31 32.056 37.589 24.426 1.00 0.00 H +ATOM 503 CD LYS 31 33.506 38.765 23.356 1.00 0.00 C +ATOM 504 HD2 LYS 31 32.713 39.327 22.866 1.00 0.00 H +ATOM 505 HD3 LYS 31 34.316 39.458 23.597 1.00 0.00 H +ATOM 506 CE LYS 31 34.009 37.678 22.410 1.00 0.00 C +ATOM 507 HE2 LYS 31 33.210 36.951 22.212 1.00 0.00 H +ATOM 508 HE3 LYS 31 34.294 38.148 21.459 1.00 0.00 H +ATOM 509 NZ LYS 31 35.192 36.994 22.980 1.00 0.00 N +ATOM 510 HZ1 LYS 31 34.970 36.242 23.631 1.00 0.00 H +ATOM 511 HZ2 LYS 31 35.696 36.535 22.223 1.00 0.00 H +ATOM 512 HZ3 LYS 31 35.853 37.636 23.423 1.00 0.00 H +ATOM 513 C LYS 31 32.124 39.737 28.088 1.00 0.00 C +ATOM 514 O LYS 31 33.110 39.767 28.820 1.00 0.00 O +ATOM 515 N ALA 32 31.066 40.529 28.271 1.00 0.00 N +ATOM 516 H ALA 32 30.350 40.537 27.557 1.00 0.00 H +ATOM 517 CA ALA 32 30.916 41.417 29.424 1.00 0.00 C +ATOM 518 HA ALA 32 31.761 42.109 29.453 1.00 0.00 H +ATOM 519 CB ALA 32 29.630 42.243 29.272 1.00 0.00 C +ATOM 520 HB1 ALA 32 28.757 41.591 29.251 1.00 0.00 H +ATOM 521 HB2 ALA 32 29.539 42.927 30.118 1.00 0.00 H +ATOM 522 HB3 ALA 32 29.672 42.826 28.351 1.00 0.00 H +ATOM 523 C ALA 32 30.942 40.605 30.729 1.00 0.00 C +ATOM 524 O ALA 32 31.851 40.784 31.532 1.00 0.00 O +ATOM 525 N GLH 33 30.050 39.611 30.870 1.00 0.00 N +ATOM 526 H GLH 33 29.333 39.496 30.165 1.00 0.00 H +ATOM 527 CA GLH 33 30.047 38.725 32.041 1.00 0.00 C +ATOM 528 HA GLH 33 29.911 39.335 32.935 1.00 0.00 H +ATOM 529 CB GLH 33 28.891 37.715 31.963 1.00 0.00 C +ATOM 530 HB2 GLH 33 28.942 37.165 31.022 1.00 0.00 H +ATOM 531 HB3 GLH 33 29.025 37.002 32.778 1.00 0.00 H +ATOM 532 CG GLH 33 27.500 38.357 32.108 1.00 0.00 C +ATOM 533 HG2 GLH 33 27.504 39.042 32.957 1.00 0.00 H +ATOM 534 HG3 GLH 33 27.261 38.931 31.214 1.00 0.00 H +ATOM 535 CD GLH 33 26.406 37.318 32.358 1.00 0.00 C +ATOM 536 OE1 GLH 33 26.558 36.242 32.918 1.00 0.00 O +ATOM 537 OE2 GLH 33 25.174 37.633 31.910 1.00 0.00 O +ATOM 538 HE2 GLH 33 24.616 36.913 32.215 1.00 0.00 H +ATOM 539 C GLH 33 31.373 37.970 32.231 1.00 0.00 C +ATOM 540 O GLH 33 31.760 37.707 33.362 1.00 0.00 O +ATOM 541 N ALA 34 32.084 37.609 31.158 1.00 0.00 N +ATOM 542 H ALA 34 31.708 37.793 30.237 1.00 0.00 H +ATOM 543 CA ALA 34 33.402 36.984 31.269 1.00 0.00 C +ATOM 544 HA ALA 34 33.329 36.147 31.965 1.00 0.00 H +ATOM 545 CB ALA 34 33.799 36.424 29.900 1.00 0.00 C +ATOM 546 HB1 ALA 34 34.021 37.239 29.214 1.00 0.00 H +ATOM 547 HB2 ALA 34 34.684 35.801 30.018 1.00 0.00 H +ATOM 548 HB3 ALA 34 32.997 35.812 29.491 1.00 0.00 H +ATOM 549 C ALA 34 34.464 37.950 31.840 1.00 0.00 C +ATOM 550 O ALA 34 35.200 37.571 32.750 1.00 0.00 O +ATOM 551 N ASN 35 34.500 39.207 31.376 1.00 0.00 N +ATOM 552 H ASN 35 33.842 39.482 30.658 1.00 0.00 H +ATOM 553 CA ASN 35 35.384 40.242 31.928 1.00 0.00 C +ATOM 554 HA ASN 35 36.374 39.806 32.012 1.00 0.00 H +ATOM 555 CB ASN 35 35.506 41.432 30.957 1.00 0.00 C +ATOM 556 HB2 ASN 35 34.515 41.759 30.649 1.00 0.00 H +ATOM 557 HB3 ASN 35 35.980 42.260 31.484 1.00 0.00 H +ATOM 558 CG ASN 35 36.370 41.137 29.738 1.00 0.00 C +ATOM 559 OD1 ASN 35 37.587 41.194 29.762 1.00 0.00 O +ATOM 560 ND2 ASN 35 35.776 40.836 28.613 1.00 0.00 N +ATOM 561 HD21 ASN 35 36.375 40.628 27.819 1.00 0.00 H +ATOM 562 HD22 ASN 35 34.782 40.669 28.608 1.00 0.00 H +ATOM 563 C ASN 35 34.989 40.686 33.358 1.00 0.00 C +ATOM 564 O ASN 35 35.858 41.125 34.108 1.00 0.00 O +ATOM 565 N ASP 36 33.730 40.502 33.781 1.00 0.00 N +ATOM 566 H ASP 36 33.014 40.300 33.091 1.00 0.00 H +ATOM 567 CA ASP 36 33.323 40.680 35.189 1.00 0.00 C +ATOM 568 HA ASP 36 33.626 41.677 35.506 1.00 0.00 H +ATOM 569 CB ASP 36 31.790 40.605 35.367 1.00 0.00 C +ATOM 570 HB2 ASP 36 31.453 39.608 35.113 1.00 0.00 H +ATOM 571 HB3 ASP 36 31.583 40.721 36.432 1.00 0.00 H +ATOM 572 CG ASP 36 30.936 41.606 34.560 1.00 0.00 C +ATOM 573 OD1 ASP 36 31.454 42.673 34.150 1.00 0.00 O +ATOM 574 OD2 ASP 36 29.729 41.321 34.369 1.00 0.00 O +ATOM 575 C ASP 36 34.022 39.677 36.139 1.00 0.00 C +ATOM 576 O ASP 36 34.366 40.036 37.265 1.00 0.00 O +ATOM 577 N TYR 37 34.279 38.436 35.693 1.00 0.00 N +ATOM 578 H TYR 37 33.929 38.187 34.778 1.00 0.00 H +ATOM 579 CA TYR 37 35.150 37.478 36.405 1.00 0.00 C +ATOM 580 HA TYR 37 35.031 37.637 37.477 1.00 0.00 H +ATOM 581 CB TYR 37 34.728 36.029 36.102 1.00 0.00 C +ATOM 582 HB2 TYR 37 34.894 35.833 35.042 1.00 0.00 H +ATOM 583 HB3 TYR 37 35.387 35.360 36.657 1.00 0.00 H +ATOM 584 CG TYR 37 33.295 35.659 36.456 1.00 0.00 C +ATOM 585 CD1 TYR 37 32.330 35.550 35.437 1.00 0.00 C +ATOM 586 HD1 TYR 37 32.623 35.735 34.416 1.00 0.00 H +ATOM 587 CE1 TYR 37 30.995 35.227 35.746 1.00 0.00 C +ATOM 588 HE1 TYR 37 30.257 35.181 34.963 1.00 0.00 H +ATOM 589 CZ TYR 37 30.630 34.968 37.084 1.00 0.00 C +ATOM 590 OH TYR 37 29.350 34.633 37.395 1.00 0.00 O +ATOM 591 HH TYR 37 28.718 35.000 36.775 1.00 0.00 H +ATOM 592 CE2 TYR 37 31.601 35.043 38.103 1.00 0.00 C +ATOM 593 HE2 TYR 37 31.310 34.844 39.122 1.00 0.00 H +ATOM 594 CD2 TYR 37 32.930 35.393 37.791 1.00 0.00 C +ATOM 595 HD2 TYR 37 33.670 35.453 38.575 1.00 0.00 H +ATOM 596 C TYR 37 36.653 37.661 36.084 1.00 0.00 C +ATOM 597 O TYR 37 37.509 37.230 36.866 1.00 0.00 O +ATOM 598 N GLY 38 36.981 38.278 34.941 1.00 0.00 N +ATOM 599 H GLY 38 36.217 38.563 34.340 1.00 0.00 H +ATOM 600 CA GLY 38 38.332 38.695 34.549 1.00 0.00 C +ATOM 601 HA2 GLY 38 38.510 39.692 34.952 1.00 0.00 H +ATOM 602 HA3 GLY 38 39.067 38.019 34.987 1.00 0.00 H +ATOM 603 C GLY 38 38.572 38.753 33.033 1.00 0.00 C +ATOM 604 O GLY 38 38.680 39.832 32.466 1.00 0.00 O +ATOM 605 N VAL 39 38.769 37.587 32.407 1.00 0.00 N +ATOM 606 H VAL 39 38.528 36.772 32.947 1.00 0.00 H +ATOM 607 CA VAL 39 39.120 37.334 30.982 1.00 0.00 C +ATOM 608 HA VAL 39 39.589 36.353 31.045 1.00 0.00 H +ATOM 609 CB VAL 39 40.278 38.199 30.408 1.00 0.00 C +ATOM 610 HB VAL 39 39.887 39.155 30.060 1.00 0.00 H +ATOM 611 CG1 VAL 39 41.410 38.442 31.429 1.00 0.00 C +ATOM 612 HG11 VAL 39 41.633 37.519 31.969 1.00 0.00 H +ATOM 613 HG12 VAL 39 42.308 38.801 30.921 1.00 0.00 H +ATOM 614 HG13 VAL 39 41.103 39.214 32.136 1.00 0.00 H +ATOM 615 CG2 VAL 39 40.949 37.487 29.219 1.00 0.00 C +ATOM 616 HG21 VAL 39 41.725 38.123 28.799 1.00 0.00 H +ATOM 617 HG22 VAL 39 41.401 36.553 29.543 1.00 0.00 H +ATOM 618 HG23 VAL 39 40.242 37.276 28.424 1.00 0.00 H +ATOM 619 C VAL 39 37.923 37.009 30.055 1.00 0.00 C +ATOM 620 O VAL 39 37.209 36.068 30.396 1.00 0.00 O +ATOM 621 N ASP 40 37.721 37.611 28.865 1.00 0.00 N +ATOM 622 H ASP 40 38.260 38.435 28.629 1.00 0.00 H +ATOM 623 CA ASP 40 36.920 36.948 27.802 1.00 0.00 C +ATOM 624 HA ASP 40 36.182 36.330 28.311 1.00 0.00 H +ATOM 625 CB ASP 40 36.053 37.904 26.947 1.00 0.00 C +ATOM 626 HB2 ASP 40 35.316 37.280 26.435 1.00 0.00 H +ATOM 627 HB3 ASP 40 35.494 38.546 27.614 1.00 0.00 H +ATOM 628 CG ASP 40 36.769 38.774 25.899 1.00 0.00 C +ATOM 629 OD1 ASP 40 37.171 39.908 26.230 1.00 0.00 O +ATOM 630 OD2 ASP 40 36.863 38.346 24.717 1.00 0.00 O +ATOM 631 C ASP 40 37.719 35.999 26.893 1.00 0.00 C +ATOM 632 O ASP 40 38.616 36.413 26.153 1.00 0.00 O +ATOM 633 N GLY 41 37.291 34.734 26.866 1.00 0.00 N +ATOM 634 H GLY 41 36.626 34.447 27.571 1.00 0.00 H +ATOM 635 CA GLY 41 37.610 33.768 25.816 1.00 0.00 C +ATOM 636 HA2 GLY 41 38.623 33.946 25.456 1.00 0.00 H +ATOM 637 HA3 GLY 41 37.580 32.771 26.242 1.00 0.00 H +ATOM 638 C GLY 41 36.655 33.826 24.612 1.00 0.00 C +ATOM 639 O GLY 41 35.774 34.683 24.510 1.00 0.00 O +ATOM 640 N GLU 42 36.792 32.855 23.705 1.00 0.00 N +ATOM 641 H GLU 42 37.487 32.129 23.865 1.00 0.00 H +ATOM 642 CA GLU 42 36.009 32.689 22.461 1.00 0.00 C +ATOM 643 HA GLU 42 35.334 33.540 22.334 1.00 0.00 H +ATOM 644 CB GLU 42 36.923 32.654 21.234 1.00 0.00 C +ATOM 645 HB2 GLU 42 37.390 31.662 21.199 1.00 0.00 H +ATOM 646 HB3 GLU 42 36.257 32.698 20.374 1.00 0.00 H +ATOM 647 CG GLU 42 37.926 33.780 21.144 1.00 0.00 C +ATOM 648 HG2 GLU 42 38.767 33.538 21.797 1.00 0.00 H +ATOM 649 HG3 GLU 42 38.362 33.796 20.165 1.00 0.00 H +ATOM 650 CD GLU 42 37.448 35.144 21.511 1.00 0.00 C +ATOM 651 OE1 GLU 42 36.392 35.531 21.013 1.00 0.00 O +ATOM 652 OE2 GLU 42 38.019 35.817 22.405 1.00 0.00 O +ATOM 653 C GLU 42 35.098 31.428 22.559 1.00 0.00 C +ATOM 654 O GLU 42 35.470 30.440 23.214 1.00 0.00 O +ATOM 655 N ILE 43 33.966 31.444 21.825 1.00 0.00 N +ATOM 656 H ILE 43 33.809 32.250 21.208 1.00 0.00 H +ATOM 657 CA ILE 43 32.887 30.421 21.861 1.00 0.00 C +ATOM 658 HA ILE 43 33.331 29.490 22.218 1.00 0.00 H +ATOM 659 CB ILE 43 31.749 30.833 22.843 1.00 0.00 C +ATOM 660 HB ILE 43 30.876 30.251 22.570 1.00 0.00 H +ATOM 661 CG2 ILE 43 32.120 30.445 24.279 1.00 0.00 C +ATOM 662 HG21 ILE 43 32.995 30.995 24.605 1.00 0.00 H +ATOM 663 HG22 ILE 43 31.282 30.667 24.932 1.00 0.00 H +ATOM 664 HG23 ILE 43 32.325 29.379 24.324 1.00 0.00 H +ATOM 665 CG1 ILE 43 31.340 32.325 22.832 1.00 0.00 C +ATOM 666 HG12 ILE 43 30.451 32.421 23.459 1.00 0.00 H +ATOM 667 HG13 ILE 43 32.122 32.931 23.275 1.00 0.00 H +ATOM 668 CD1 ILE 43 30.995 32.906 21.457 1.00 0.00 C +ATOM 669 HD11 ILE 43 30.366 32.224 20.891 1.00 0.00 H +ATOM 670 HD12 ILE 43 30.466 33.847 21.588 1.00 0.00 H +ATOM 671 HD13 ILE 43 31.907 33.103 20.890 1.00 0.00 H +ATOM 672 C ILE 43 32.351 30.121 20.452 1.00 0.00 C +ATOM 673 O ILE 43 32.559 30.895 19.514 1.00 0.00 O +ATOM 674 N THR 44 31.619 29.018 20.340 1.00 0.00 N +ATOM 675 H THR 44 31.486 28.447 21.169 1.00 0.00 H +ATOM 676 CA THR 44 30.903 28.600 19.128 1.00 0.00 C +ATOM 677 HA THR 44 31.230 29.213 18.290 1.00 0.00 H +ATOM 678 CB THR 44 31.269 27.144 18.781 1.00 0.00 C +ATOM 679 HB THR 44 31.001 26.477 19.600 1.00 0.00 H +ATOM 680 CG2 THR 44 30.624 26.613 17.495 1.00 0.00 C +ATOM 681 HG21 THR 44 30.802 27.305 16.665 1.00 0.00 H +ATOM 682 HG22 THR 44 31.041 25.628 17.235 1.00 0.00 H +ATOM 683 HG23 THR 44 29.544 26.485 17.639 1.00 0.00 H +ATOM 684 OG1 THR 44 32.661 27.056 18.558 1.00 0.00 O +ATOM 685 HG1 THR 44 32.846 26.251 18.066 1.00 0.00 H +ATOM 686 C THR 44 29.392 28.779 19.281 1.00 0.00 C +ATOM 687 O THR 44 28.876 28.725 20.395 1.00 0.00 O +ATOM 688 N GLN 45 28.679 29.026 18.178 1.00 0.00 N +ATOM 689 H GLN 45 29.149 29.020 17.288 1.00 0.00 H +ATOM 690 CA GLN 45 27.222 29.231 18.139 1.00 0.00 C +ATOM 691 HA GLN 45 26.819 29.205 19.153 1.00 0.00 H +ATOM 692 CB GLN 45 26.897 30.607 17.518 1.00 0.00 C +ATOM 693 HB2 GLN 45 27.284 30.625 16.500 1.00 0.00 H +ATOM 694 HB3 GLN 45 25.809 30.696 17.459 1.00 0.00 H +ATOM 695 CG GLN 45 27.454 31.826 18.281 1.00 0.00 C +ATOM 696 HG2 GLN 45 27.104 31.768 19.310 1.00 0.00 H +ATOM 697 HG3 GLN 45 28.542 31.780 18.287 1.00 0.00 H +ATOM 698 CD GLN 45 27.016 33.162 17.659 1.00 0.00 C +ATOM 699 OE1 GLN 45 26.064 33.244 16.898 1.00 0.00 O +ATOM 700 NE2 GLN 45 27.679 34.270 17.903 1.00 0.00 N +ATOM 701 HE21 GLN 45 27.355 35.101 17.453 1.00 0.00 H +ATOM 702 HE22 GLN 45 28.552 34.317 18.441 1.00 0.00 H +ATOM 703 C GLN 45 26.480 28.159 17.312 1.00 0.00 C +ATOM 704 O GLN 45 27.046 27.601 16.370 1.00 0.00 O +ATOM 705 N ASP 46 25.191 27.966 17.604 1.00 0.00 N +ATOM 706 H ASP 46 24.838 28.365 18.468 1.00 0.00 H +ATOM 707 CA ASP 46 24.203 27.294 16.751 1.00 0.00 C +ATOM 708 HA ASP 46 24.528 27.356 15.711 1.00 0.00 H +ATOM 709 CB ASP 46 24.079 25.812 17.147 1.00 0.00 C +ATOM 710 HB2 ASP 46 24.979 25.272 16.851 1.00 0.00 H +ATOM 711 HB3 ASP 46 23.981 25.747 18.230 1.00 0.00 H +ATOM 712 CG ASP 46 22.852 25.158 16.507 1.00 0.00 C +ATOM 713 OD1 ASP 46 22.104 24.474 17.241 1.00 0.00 O +ATOM 714 OD2 ASP 46 22.584 25.407 15.313 1.00 0.00 O +ATOM 715 C ASP 46 22.831 27.991 16.868 1.00 0.00 C +ATOM 716 O ASP 46 22.288 28.138 17.964 1.00 0.00 O +ATOM 717 N ASP 47 22.230 28.373 15.739 1.00 0.00 N +ATOM 718 H ASP 47 22.690 28.167 14.865 1.00 0.00 H +ATOM 719 CA ASP 47 20.867 28.919 15.690 1.00 0.00 C +ATOM 720 HA ASP 47 20.729 29.593 16.537 1.00 0.00 H +ATOM 721 CB ASP 47 20.693 29.766 14.416 1.00 0.00 C +ATOM 722 HB2 ASP 47 21.415 30.585 14.422 1.00 0.00 H +ATOM 723 HB3 ASP 47 20.882 29.148 13.536 1.00 0.00 H +ATOM 724 CG ASP 47 19.278 30.347 14.340 1.00 0.00 C +ATOM 725 OD1 ASP 47 18.430 29.775 13.625 1.00 0.00 O +ATOM 726 OD2 ASP 47 18.941 31.266 15.120 1.00 0.00 O +ATOM 727 C ASP 47 19.773 27.830 15.792 1.00 0.00 C +ATOM 728 O ASP 47 18.707 28.086 16.356 1.00 0.00 O +ATOM 729 N ALA 48 20.006 26.600 15.319 1.00 0.00 N +ATOM 730 H ALA 48 20.951 26.350 15.024 1.00 0.00 H +ATOM 731 CA ALA 48 18.970 25.560 15.236 1.00 0.00 C +ATOM 732 HA ALA 48 18.105 25.984 14.723 1.00 0.00 H +ATOM 733 CB ALA 48 19.510 24.405 14.386 1.00 0.00 C +ATOM 734 HB1 ALA 48 20.362 23.940 14.885 1.00 0.00 H +ATOM 735 HB2 ALA 48 18.729 23.659 14.239 1.00 0.00 H +ATOM 736 HB3 ALA 48 19.832 24.783 13.415 1.00 0.00 H +ATOM 737 C ALA 48 18.489 25.071 16.618 1.00 0.00 C +ATOM 738 O ALA 48 17.304 24.774 16.796 1.00 0.00 O +ATOM 739 N THR 49 19.392 25.037 17.602 1.00 0.00 N +ATOM 740 H THR 49 20.372 25.112 17.325 1.00 0.00 H +ATOM 741 CA THR 49 19.113 24.869 19.043 1.00 0.00 C +ATOM 742 HA THR 49 18.084 24.531 19.159 1.00 0.00 H +ATOM 743 CB THR 49 20.020 23.800 19.672 1.00 0.00 C +ATOM 744 HB THR 49 19.698 23.651 20.702 1.00 0.00 H +ATOM 745 CG2 THR 49 19.958 22.443 18.975 1.00 0.00 C +ATOM 746 HG21 THR 49 20.321 22.522 17.950 1.00 0.00 H +ATOM 747 HG22 THR 49 20.590 21.745 19.521 1.00 0.00 H +ATOM 748 HG23 THR 49 18.931 22.081 18.973 1.00 0.00 H +ATOM 749 OG1 THR 49 21.361 24.217 19.698 1.00 0.00 O +ATOM 750 HG1 THR 49 21.679 24.247 18.761 1.00 0.00 H +ATOM 751 C THR 49 19.231 26.177 19.841 1.00 0.00 C +ATOM 752 O THR 49 19.101 26.167 21.068 1.00 0.00 O +ATOM 753 N LYS 50 19.468 27.312 19.167 1.00 0.00 N +ATOM 754 H LYS 50 19.560 27.226 18.161 1.00 0.00 H +ATOM 755 CA LYS 50 19.589 28.671 19.731 1.00 0.00 C +ATOM 756 HA LYS 50 20.008 29.273 18.928 1.00 0.00 H +ATOM 757 CB LYS 50 18.185 29.226 20.094 1.00 0.00 C +ATOM 758 HB2 LYS 50 17.768 28.587 20.874 1.00 0.00 H +ATOM 759 HB3 LYS 50 18.294 30.221 20.527 1.00 0.00 H +ATOM 760 CG LYS 50 17.144 29.315 18.956 1.00 0.00 C +ATOM 761 HG2 LYS 50 17.135 28.389 18.385 1.00 0.00 H +ATOM 762 HG3 LYS 50 16.161 29.418 19.417 1.00 0.00 H +ATOM 763 CD LYS 50 17.338 30.517 18.014 1.00 0.00 C +ATOM 764 HD2 LYS 50 17.289 31.432 18.604 1.00 0.00 H +ATOM 765 HD3 LYS 50 18.319 30.466 17.544 1.00 0.00 H +ATOM 766 CE LYS 50 16.255 30.586 16.925 1.00 0.00 C +ATOM 767 HE2 LYS 50 15.311 30.225 17.334 1.00 0.00 H +ATOM 768 HE3 LYS 50 16.117 31.628 16.628 1.00 0.00 H +ATOM 769 NZ LYS 50 16.628 29.801 15.728 1.00 0.00 N +ATOM 770 HZ1 LYS 50 17.134 28.955 15.975 1.00 0.00 H +ATOM 771 HZ2 LYS 50 15.839 29.559 15.145 1.00 0.00 H +ATOM 772 HZ3 LYS 50 17.313 30.309 15.154 1.00 0.00 H +ATOM 773 C LYS 50 20.608 28.778 20.892 1.00 0.00 C +ATOM 774 O LYS 50 20.304 29.382 21.927 1.00 0.00 O +ATOM 775 N THR 51 21.791 28.170 20.745 1.00 0.00 N +ATOM 776 H THR 51 22.017 27.827 19.813 1.00 0.00 H +ATOM 777 CA THR 51 22.737 27.843 21.835 1.00 0.00 C +ATOM 778 HA THR 51 22.433 28.389 22.721 1.00 0.00 H +ATOM 779 CB THR 51 22.629 26.341 22.176 1.00 0.00 C +ATOM 780 HB THR 51 22.792 25.755 21.272 1.00 0.00 H +ATOM 781 CG2 THR 51 23.614 25.869 23.247 1.00 0.00 C +ATOM 782 HG21 THR 51 23.549 26.508 24.126 1.00 0.00 H +ATOM 783 HG22 THR 51 23.377 24.843 23.525 1.00 0.00 H +ATOM 784 HG23 THR 51 24.627 25.883 22.852 1.00 0.00 H +ATOM 785 OG1 THR 51 21.358 26.039 22.712 1.00 0.00 O +ATOM 786 HG1 THR 51 20.709 26.084 21.991 1.00 0.00 H +ATOM 787 C THR 51 24.207 28.217 21.545 1.00 0.00 C +ATOM 788 O THR 51 24.716 27.973 20.456 1.00 0.00 O +ATOM 789 N PHE 52 24.918 28.749 22.550 1.00 0.00 N +ATOM 790 H PHE 52 24.402 29.020 23.376 1.00 0.00 H +ATOM 791 CA PHE 52 26.389 28.875 22.610 1.00 0.00 C +ATOM 792 HA PHE 52 26.783 28.971 21.598 1.00 0.00 H +ATOM 793 CB PHE 52 26.774 30.130 23.412 1.00 0.00 C +ATOM 794 HB2 PHE 52 26.267 30.101 24.374 1.00 0.00 H +ATOM 795 HB3 PHE 52 27.845 30.085 23.622 1.00 0.00 H +ATOM 796 CG PHE 52 26.494 31.471 22.766 1.00 0.00 C +ATOM 797 CD1 PHE 52 25.266 32.130 22.966 1.00 0.00 C +ATOM 798 HD1 PHE 52 24.487 31.661 23.545 1.00 0.00 H +ATOM 799 CE1 PHE 52 25.047 33.404 22.412 1.00 0.00 C +ATOM 800 HE1 PHE 52 24.099 33.900 22.556 1.00 0.00 H +ATOM 801 CZ PHE 52 26.060 34.026 21.662 1.00 0.00 C +ATOM 802 HZ PHE 52 25.893 34.995 21.218 1.00 0.00 H +ATOM 803 CE2 PHE 52 27.293 33.379 21.473 1.00 0.00 C +ATOM 804 HE2 PHE 52 28.070 33.856 20.889 1.00 0.00 H +ATOM 805 CD2 PHE 52 27.503 32.100 22.017 1.00 0.00 C +ATOM 806 HD2 PHE 52 28.441 31.592 21.854 1.00 0.00 H +ATOM 807 C PHE 52 27.066 27.661 23.288 1.00 0.00 C +ATOM 808 O PHE 52 26.544 27.156 24.288 1.00 0.00 O +ATOM 809 N THR 53 28.266 27.263 22.839 1.00 0.00 N +ATOM 810 H THR 53 28.641 27.723 22.012 1.00 0.00 H +ATOM 811 CA THR 53 29.074 26.151 23.403 1.00 0.00 C +ATOM 812 HA THR 53 28.798 26.016 24.449 1.00 0.00 H +ATOM 813 CB THR 53 28.800 24.819 22.672 1.00 0.00 C +ATOM 814 HB THR 53 29.387 24.035 23.153 1.00 0.00 H +ATOM 815 CG2 THR 53 27.341 24.373 22.695 1.00 0.00 C +ATOM 816 HG21 THR 53 26.734 25.036 22.079 1.00 0.00 H +ATOM 817 HG22 THR 53 27.264 23.356 22.311 1.00 0.00 H +ATOM 818 HG23 THR 53 26.972 24.389 23.719 1.00 0.00 H +ATOM 819 OG1 THR 53 29.192 24.898 21.323 1.00 0.00 O +ATOM 820 HG1 THR 53 28.756 24.184 20.851 1.00 0.00 H +ATOM 821 C THR 53 30.594 26.406 23.377 1.00 0.00 C +ATOM 822 O THR 53 31.083 27.326 22.718 1.00 0.00 O +ATOM 823 N ALA 54 31.348 25.564 24.100 1.00 0.00 N +ATOM 824 H ALA 54 30.876 24.846 24.626 1.00 0.00 H +ATOM 825 CA ALA 54 32.812 25.456 24.054 1.00 0.00 C +ATOM 826 HA ALA 54 33.210 26.268 23.442 1.00 0.00 H +ATOM 827 CB ALA 54 33.366 25.629 25.475 1.00 0.00 C +ATOM 828 HB1 ALA 54 33.015 24.817 26.113 1.00 0.00 H +ATOM 829 HB2 ALA 54 34.457 25.616 25.456 1.00 0.00 H +ATOM 830 HB3 ALA 54 33.038 26.583 25.891 1.00 0.00 H +ATOM 831 C ALA 54 33.278 24.123 23.415 1.00 0.00 C +ATOM 832 O ALA 54 32.505 23.167 23.298 1.00 0.00 O +ATOM 833 N GLH 55 34.548 24.067 22.999 1.00 0.00 N +ATOM 834 H GLH 55 35.146 24.849 23.215 1.00 0.00 H +ATOM 835 CA GLH 55 35.168 22.922 22.308 1.00 0.00 C +ATOM 836 HA GLH 55 34.398 22.426 21.716 1.00 0.00 H +ATOM 837 CB GLH 55 36.234 23.451 21.327 1.00 0.00 C +ATOM 838 HB2 GLH 55 36.972 24.031 21.884 1.00 0.00 H +ATOM 839 HB3 GLH 55 36.743 22.608 20.858 1.00 0.00 H +ATOM 840 CG GLH 55 35.617 24.327 20.216 1.00 0.00 C +ATOM 841 HG2 GLH 55 34.958 23.714 19.601 1.00 0.00 H +ATOM 842 HG3 GLH 55 35.020 25.129 20.650 1.00 0.00 H +ATOM 843 CD GLH 55 36.655 24.987 19.312 1.00 0.00 C +ATOM 844 OE1 GLH 55 37.842 25.121 19.573 1.00 0.00 O +ATOM 845 OE2 GLH 55 36.155 25.451 18.149 1.00 0.00 O +ATOM 846 HE2 GLH 55 36.883 25.858 17.675 1.00 0.00 H +ATOM 847 C GLH 55 35.736 21.856 23.279 1.00 0.00 C +ATOM 848 O GLH 55 36.043 22.164 24.428 1.00 0.00 O +ATOM 849 N GLU 56 35.854 20.603 22.810 1.00 0.00 N +ATOM 850 H GLU 56 35.627 20.451 21.842 1.00 0.00 H +ATOM 851 CA GLU 56 36.225 19.391 23.580 1.00 0.00 C +ATOM 852 HA GLU 56 35.760 19.455 24.564 1.00 0.00 H +ATOM 853 CB GLU 56 35.617 18.165 22.855 1.00 0.00 C +ATOM 854 HB2 GLU 56 34.541 18.196 23.027 1.00 0.00 H +ATOM 855 HB3 GLU 56 35.768 18.297 21.782 1.00 0.00 H +ATOM 856 CG GLU 56 36.111 16.739 23.193 1.00 0.00 C +ATOM 857 HG2 GLU 56 35.454 16.031 22.680 1.00 0.00 H +ATOM 858 HG3 GLU 56 37.100 16.595 22.754 1.00 0.00 H +ATOM 859 CD GLU 56 36.165 16.375 24.688 1.00 0.00 C +ATOM 860 OE1 GLU 56 37.290 16.354 25.251 1.00 0.00 O +ATOM 861 OE2 GLU 56 35.109 16.022 25.266 1.00 0.00 O +ATOM 862 C GLU 56 37.723 19.244 23.888 1.00 0.00 C +ATOM 863 O GLU 56 38.090 19.361 25.078 1.00 0.00 O +ATOM 864 OXT GLU 56 38.506 18.730 23.060 1.00 0.00 O +HETATM 865 ZN ZN1 57 26.762 32.444 29.336 1.00 0.00 Zn +HETATM 866 N AN1 58 28.364 33.308 30.222 1.00 0.00 N +HETATM 867 C AN1 58 30.678 34.028 31.184 1.00 0.00 C +HETATM 868 C1 AN1 58 29.379 33.629 30.674 1.00 0.00 C +HETATM 869 H AN1 58 30.582 34.423 32.200 1.00 0.00 H +HETATM 870 H1 AN1 58 31.113 34.795 30.535 1.00 0.00 H +HETATM 871 H2 AN1 58 31.336 33.149 31.202 1.00 0.00 H +HETATM 872 N1 AZI 59 30.830 28.620 29.341 1.00 0.00 N +HETATM 873 N2 AZI 59 30.309 29.481 30.054 1.00 0.00 N +HETATM 874 N3 AZI 59 29.759 30.371 30.755 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 68 62 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 73 72 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 77 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 865 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 121 122 126 +CONECT 121 120 +CONECT 122 125 120 123 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 127 129 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 145 +CONECT 135 134 +CONECT 136 137 134 139 138 +CONECT 137 136 +CONECT 138 136 +CONECT 139 142 136 140 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 144 139 +CONECT 143 142 +CONECT 144 142 +CONECT 145 134 147 146 +CONECT 146 145 +CONECT 147 148 149 145 +CONECT 148 147 +CONECT 149 147 150 152 151 +CONECT 150 149 +CONECT 151 149 +CONECT 152 153 149 154 +CONECT 153 152 +CONECT 154 152 156 155 +CONECT 155 154 +CONECT 156 158 157 154 174 +CONECT 157 156 +CONECT 158 161 159 160 156 +CONECT 159 158 +CONECT 160 158 +CONECT 161 164 163 162 158 +CONECT 162 161 +CONECT 163 161 +CONECT 164 167 165 166 161 +CONECT 165 164 +CONECT 166 164 +CONECT 167 170 169 168 164 +CONECT 168 167 +CONECT 169 167 +CONECT 170 172 173 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 170 +CONECT 174 156 175 176 +CONECT 175 174 +CONECT 176 174 177 178 +CONECT 177 176 +CONECT 178 176 179 198 180 +CONECT 179 178 +CONECT 180 178 183 181 182 +CONECT 181 180 +CONECT 182 180 +CONECT 183 185 184 180 186 +CONECT 184 183 +CONECT 185 183 +CONECT 186 183 189 187 188 +CONECT 187 186 +CONECT 188 186 +CONECT 189 190 186 191 +CONECT 190 189 +CONECT 191 189 195 192 +CONECT 192 191 193 194 +CONECT 193 192 +CONECT 194 192 +CONECT 195 196 191 197 +CONECT 196 195 +CONECT 197 195 +CONECT 198 178 200 199 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 219 200 204 203 +CONECT 203 202 +CONECT 204 207 202 205 206 +CONECT 205 204 +CONECT 206 204 +CONECT 207 208 217 204 +CONECT 208 209 210 207 +CONECT 209 208 +CONECT 210 211 208 212 +CONECT 211 210 +CONECT 212 210 213 215 +CONECT 213 214 212 +CONECT 214 213 +CONECT 215 212 216 217 +CONECT 216 215 +CONECT 217 207 215 218 +CONECT 218 217 +CONECT 219 220 221 202 +CONECT 220 219 +CONECT 221 223 219 222 +CONECT 222 221 +CONECT 223 224 241 225 221 +CONECT 224 223 +CONECT 225 228 223 226 227 +CONECT 226 225 +CONECT 227 225 +CONECT 228 230 229 231 225 +CONECT 229 228 +CONECT 230 228 +CONECT 231 232 228 233 234 +CONECT 232 231 +CONECT 233 231 +CONECT 234 236 231 237 235 +CONECT 235 234 +CONECT 236 234 +CONECT 237 240 234 239 238 +CONECT 238 237 +CONECT 239 237 +CONECT 240 237 +CONECT 241 242 223 243 +CONECT 242 241 +CONECT 243 241 245 244 +CONECT 244 243 +CONECT 245 248 243 246 247 +CONECT 246 245 +CONECT 247 245 +CONECT 248 249 250 245 +CONECT 249 248 +CONECT 250 252 248 251 +CONECT 251 250 +CONECT 252 254 253 264 250 +CONECT 253 252 +CONECT 254 260 255 256 252 +CONECT 255 254 +CONECT 256 258 254 257 259 +CONECT 257 256 +CONECT 258 256 +CONECT 259 256 +CONECT 260 262 261 263 254 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 252 265 +CONECT 265 264 +CONECT 266 276 267 264 +CONECT 267 268 266 277 270 +CONECT 268 269 283 267 +CONECT 269 268 +CONECT 270 267 271 278 279 +CONECT 271 272 273 270 +CONECT 272 275 281 271 +CONECT 273 274 271 280 +CONECT 274 275 282 273 +CONECT 275 865 272 274 +CONECT 276 266 +CONECT 277 267 +CONECT 278 270 +CONECT 279 270 +CONECT 280 273 +CONECT 281 272 +CONECT 282 274 +CONECT 283 285 268 284 +CONECT 284 283 +CONECT 285 286 287 295 283 +CONECT 286 285 +CONECT 287 288 289 285 293 +CONECT 288 287 +CONECT 289 292 291 287 290 +CONECT 290 289 +CONECT 291 289 +CONECT 292 289 +CONECT 293 287 294 +CONECT 294 293 +CONECT 295 297 285 296 +CONECT 296 295 +CONECT 297 307 298 295 +CONECT 298 299 301 297 308 +CONECT 299 300 314 298 +CONECT 300 299 +CONECT 301 309 310 298 302 +CONECT 302 301 303 304 +CONECT 303 312 302 306 +CONECT 304 302 311 305 +CONECT 305 304 306 313 +CONECT 306 303 865 305 +CONECT 307 297 +CONECT 308 298 +CONECT 309 301 +CONECT 310 301 +CONECT 311 304 +CONECT 312 303 +CONECT 313 305 +CONECT 314 316 299 315 +CONECT 315 314 +CONECT 316 327 317 314 318 +CONECT 317 316 +CONECT 318 316 321 320 319 +CONECT 319 318 +CONECT 320 318 +CONECT 321 323 324 318 322 +CONECT 322 321 +CONECT 323 321 +CONECT 324 325 321 326 +CONECT 325 324 +CONECT 326 324 +CONECT 327 329 328 316 +CONECT 328 327 +CONECT 329 331 330 327 +CONECT 330 329 +CONECT 331 337 333 332 329 +CONECT 332 331 +CONECT 333 335 334 331 336 +CONECT 334 333 +CONECT 335 333 +CONECT 336 333 +CONECT 337 339 338 331 +CONECT 338 337 +CONECT 339 341 340 337 +CONECT 340 339 +CONECT 341 353 343 342 339 +CONECT 342 341 +CONECT 343 344 349 341 345 +CONECT 344 343 +CONECT 345 343 347 348 346 +CONECT 346 345 +CONECT 347 345 +CONECT 348 345 +CONECT 349 350 351 343 352 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 341 +CONECT 354 353 +CONECT 355 357 353 356 +CONECT 356 355 +CONECT 357 359 358 365 355 +CONECT 358 357 +CONECT 359 362 360 361 357 +CONECT 360 359 +CONECT 361 359 +CONECT 362 364 363 359 +CONECT 363 362 +CONECT 364 362 +CONECT 365 357 367 366 +CONECT 366 365 +CONECT 367 368 369 365 +CONECT 368 367 +CONECT 369 371 367 385 370 +CONECT 370 369 +CONECT 371 372 374 373 369 +CONECT 372 371 +CONECT 373 371 +CONECT 374 375 371 383 +CONECT 375 376 377 374 +CONECT 376 375 +CONECT 377 378 375 379 +CONECT 378 377 +CONECT 379 377 380 381 +CONECT 380 379 +CONECT 381 379 383 382 +CONECT 382 381 +CONECT 383 374 381 384 +CONECT 384 383 +CONECT 385 387 369 386 +CONECT 386 385 +CONECT 387 388 389 385 +CONECT 388 387 +CONECT 389 391 387 390 395 +CONECT 390 389 +CONECT 391 394 392 393 389 +CONECT 392 391 +CONECT 393 391 +CONECT 394 391 +CONECT 395 389 396 397 +CONECT 396 395 +CONECT 397 395 398 399 +CONECT 398 397 +CONECT 399 397 400 401 410 +CONECT 400 399 +CONECT 401 404 402 399 403 +CONECT 402 401 +CONECT 403 401 +CONECT 404 405 406 407 401 +CONECT 405 404 +CONECT 406 404 +CONECT 407 404 409 408 +CONECT 408 407 +CONECT 409 407 +CONECT 410 399 412 411 +CONECT 411 410 +CONECT 412 413 410 414 +CONECT 413 412 +CONECT 414 412 416 420 415 +CONECT 415 414 +CONECT 416 417 419 414 418 +CONECT 417 416 +CONECT 418 416 +CONECT 419 416 +CONECT 420 422 414 421 +CONECT 421 420 +CONECT 422 423 424 420 +CONECT 423 422 +CONECT 424 426 422 425 435 +CONECT 425 424 +CONECT 426 428 427 429 424 +CONECT 427 426 +CONECT 428 426 +CONECT 429 432 430 426 431 +CONECT 430 429 +CONECT 431 429 +CONECT 432 433 434 429 +CONECT 433 432 +CONECT 434 432 +CONECT 435 424 437 436 +CONECT 436 435 +CONECT 437 438 435 439 +CONECT 438 437 +CONECT 439 437 441 440 457 +CONECT 440 439 +CONECT 441 444 442 443 439 +CONECT 442 441 +CONECT 443 441 +CONECT 444 446 447 445 441 +CONECT 445 444 +CONECT 446 444 +CONECT 447 450 448 449 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 452 451 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 455 456 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 453 +CONECT 457 439 459 458 +CONECT 458 457 +CONECT 459 460 457 461 +CONECT 460 459 +CONECT 461 459 463 462 477 +CONECT 462 461 +CONECT 463 466 464 461 465 +CONECT 464 463 +CONECT 465 463 +CONECT 466 467 475 463 +CONECT 467 469 468 466 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 472 469 473 +CONECT 472 471 +CONECT 473 471 474 475 +CONECT 474 473 +CONECT 475 473 466 476 +CONECT 476 475 +CONECT 477 461 479 478 +CONECT 478 477 +CONECT 479 480 481 477 +CONECT 480 479 +CONECT 481 483 479 491 482 +CONECT 482 481 +CONECT 483 484 489 485 481 +CONECT 484 483 +CONECT 485 487 483 488 486 +CONECT 486 485 +CONECT 487 485 +CONECT 488 485 +CONECT 489 490 483 +CONECT 490 489 +CONECT 491 493 481 492 +CONECT 492 491 +CONECT 493 494 495 491 +CONECT 494 493 +CONECT 495 497 493 496 513 +CONECT 496 495 +CONECT 497 500 498 499 495 +CONECT 498 497 +CONECT 499 497 +CONECT 500 503 502 501 497 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 504 505 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 508 507 509 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 506 512 510 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 495 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 518 523 +CONECT 518 517 +CONECT 519 522 520 517 521 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 +CONECT 523 517 525 524 +CONECT 524 523 +CONECT 525 526 523 527 +CONECT 526 525 +CONECT 527 525 529 539 528 +CONECT 528 527 +CONECT 529 530 527 532 531 +CONECT 530 529 +CONECT 531 529 +CONECT 532 534 529 535 533 +CONECT 533 532 +CONECT 534 532 +CONECT 535 537 532 536 +CONECT 536 535 +CONECT 537 538 535 +CONECT 538 537 +CONECT 539 541 527 540 +CONECT 540 539 +CONECT 541 542 543 539 +CONECT 542 541 +CONECT 543 545 541 549 544 +CONECT 544 543 +CONECT 545 546 548 547 543 +CONECT 546 545 +CONECT 547 545 +CONECT 548 545 +CONECT 549 543 551 550 +CONECT 550 549 +CONECT 551 552 549 553 +CONECT 552 551 +CONECT 553 555 551 554 563 +CONECT 554 553 +CONECT 555 558 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 560 559 555 +CONECT 559 558 +CONECT 560 561 562 558 +CONECT 561 560 +CONECT 562 560 +CONECT 563 553 565 564 +CONECT 564 563 +CONECT 565 566 563 567 +CONECT 566 565 +CONECT 567 565 569 568 575 +CONECT 568 567 +CONECT 569 572 570 567 571 +CONECT 570 569 +CONECT 571 569 +CONECT 572 573 574 569 +CONECT 573 572 +CONECT 574 572 +CONECT 575 567 577 576 +CONECT 576 575 +CONECT 577 578 575 579 +CONECT 578 577 +CONECT 579 577 596 581 580 +CONECT 580 579 +CONECT 581 582 579 584 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 585 581 594 +CONECT 585 586 587 584 +CONECT 586 585 +CONECT 587 588 585 589 +CONECT 588 587 +CONECT 589 587 590 592 +CONECT 590 591 589 +CONECT 591 590 +CONECT 592 589 594 593 +CONECT 593 592 +CONECT 594 584 592 595 +CONECT 595 594 +CONECT 596 598 579 597 +CONECT 597 596 +CONECT 598 599 600 596 +CONECT 599 598 +CONECT 600 603 598 601 602 +CONECT 601 600 +CONECT 602 600 +CONECT 603 605 604 600 +CONECT 604 603 +CONECT 605 607 606 603 +CONECT 606 605 +CONECT 607 619 609 608 605 +CONECT 608 607 +CONECT 609 615 610 607 611 +CONECT 610 609 +CONECT 611 609 613 612 614 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 +CONECT 615 618 616 617 609 +CONECT 616 615 +CONECT 617 615 +CONECT 618 615 +CONECT 619 621 620 607 +CONECT 620 619 +CONECT 621 623 622 619 +CONECT 622 621 +CONECT 623 631 625 624 621 +CONECT 624 623 +CONECT 625 628 626 627 623 +CONECT 626 625 +CONECT 627 625 +CONECT 628 630 629 625 +CONECT 629 628 +CONECT 630 628 +CONECT 631 632 633 623 +CONECT 632 631 +CONECT 633 635 631 634 +CONECT 634 633 +CONECT 635 638 636 637 633 +CONECT 636 635 +CONECT 637 635 +CONECT 638 640 639 635 +CONECT 639 638 +CONECT 640 642 641 638 +CONECT 641 640 +CONECT 642 644 643 653 640 +CONECT 643 642 +CONECT 644 646 647 645 642 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 644 650 648 +CONECT 648 647 +CONECT 649 647 +CONECT 650 651 647 652 +CONECT 651 650 +CONECT 652 650 +CONECT 653 655 642 654 +CONECT 654 653 +CONECT 655 656 657 653 +CONECT 656 655 +CONECT 657 672 655 658 659 +CONECT 658 657 +CONECT 659 657 660 665 661 +CONECT 660 659 +CONECT 661 659 664 662 663 +CONECT 662 661 +CONECT 663 661 +CONECT 664 661 +CONECT 665 668 659 667 666 +CONECT 666 665 +CONECT 667 665 +CONECT 668 671 669 670 665 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 +CONECT 672 673 674 657 +CONECT 673 672 +CONECT 674 676 672 675 +CONECT 675 674 +CONECT 676 677 678 686 674 +CONECT 677 676 +CONECT 678 680 684 676 679 +CONECT 679 678 +CONECT 680 681 682 683 678 +CONECT 681 680 +CONECT 682 680 +CONECT 683 680 +CONECT 684 685 678 +CONECT 685 684 +CONECT 686 688 676 687 +CONECT 687 686 +CONECT 688 689 690 686 +CONECT 689 688 +CONECT 690 703 692 688 691 +CONECT 691 690 +CONECT 692 693 694 690 695 +CONECT 693 692 +CONECT 694 692 +CONECT 695 692 698 697 696 +CONECT 696 695 +CONECT 697 695 +CONECT 698 699 700 695 +CONECT 699 698 +CONECT 700 701 698 702 +CONECT 701 700 +CONECT 702 700 +CONECT 703 704 705 690 +CONECT 704 703 +CONECT 705 707 703 706 +CONECT 706 705 +CONECT 707 708 715 709 705 +CONECT 708 707 +CONECT 709 712 707 710 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 714 709 713 +CONECT 713 712 +CONECT 714 712 +CONECT 715 717 707 716 +CONECT 716 715 +CONECT 717 718 719 715 +CONECT 718 717 +CONECT 719 721 717 727 720 +CONECT 720 719 +CONECT 721 723 724 722 719 +CONECT 722 721 +CONECT 723 721 +CONECT 724 725 721 726 +CONECT 725 724 +CONECT 726 724 +CONECT 727 729 719 728 +CONECT 728 727 +CONECT 729 730 731 727 +CONECT 730 729 +CONECT 731 733 732 729 737 +CONECT 732 731 +CONECT 733 736 735 734 731 +CONECT 734 733 +CONECT 735 733 +CONECT 736 733 +CONECT 737 731 738 739 +CONECT 738 737 +CONECT 739 737 740 741 +CONECT 740 739 +CONECT 741 739 742 743 751 +CONECT 742 741 +CONECT 743 745 741 749 744 +CONECT 744 743 +CONECT 745 746 748 747 743 +CONECT 746 745 +CONECT 747 745 +CONECT 748 745 +CONECT 749 750 743 +CONECT 750 749 +CONECT 751 741 753 752 +CONECT 752 751 +CONECT 753 754 755 751 +CONECT 754 753 +CONECT 755 756 753 757 773 +CONECT 756 755 +CONECT 757 760 755 759 758 +CONECT 758 757 +CONECT 759 757 +CONECT 760 763 761 762 757 +CONECT 761 760 +CONECT 762 760 +CONECT 763 766 765 764 760 +CONECT 764 763 +CONECT 765 763 +CONECT 766 769 768 767 763 +CONECT 767 766 +CONECT 768 766 +CONECT 769 771 772 770 766 +CONECT 770 769 +CONECT 771 769 +CONECT 772 769 +CONECT 773 755 775 774 +CONECT 774 773 +CONECT 775 776 773 777 +CONECT 776 775 +CONECT 777 775 787 779 778 +CONECT 778 777 +CONECT 779 780 777 785 781 +CONECT 780 779 +CONECT 781 779 784 783 782 +CONECT 782 781 +CONECT 783 781 +CONECT 784 781 +CONECT 785 786 779 +CONECT 786 785 +CONECT 787 788 777 789 +CONECT 788 787 +CONECT 789 787 791 790 +CONECT 790 789 +CONECT 791 792 789 807 793 +CONECT 792 791 +CONECT 793 791 796 795 794 +CONECT 794 793 +CONECT 795 793 +CONECT 796 805 797 793 +CONECT 797 799 796 798 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 804 801 805 +CONECT 804 803 +CONECT 805 803 806 796 +CONECT 806 805 +CONECT 807 791 809 808 +CONECT 808 807 +CONECT 809 810 807 811 +CONECT 810 809 +CONECT 811 813 809 821 812 +CONECT 812 811 +CONECT 813 819 815 814 811 +CONECT 814 813 +CONECT 815 816 817 813 818 +CONECT 816 815 +CONECT 817 815 +CONECT 818 815 +CONECT 819 820 813 +CONECT 820 819 +CONECT 821 822 811 823 +CONECT 822 821 +CONECT 823 821 825 824 +CONECT 824 823 +CONECT 825 831 826 823 827 +CONECT 826 825 +CONECT 827 825 829 830 828 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 833 832 825 +CONECT 832 831 +CONECT 833 835 834 831 +CONECT 834 833 +CONECT 835 837 836 833 847 +CONECT 836 835 +CONECT 837 840 839 838 835 +CONECT 838 837 +CONECT 839 837 +CONECT 840 843 841 842 837 +CONECT 841 840 +CONECT 842 840 +CONECT 843 845 844 840 +CONECT 844 843 +CONECT 845 846 843 +CONECT 846 845 +CONECT 847 835 849 848 +CONECT 848 847 +CONECT 849 850 847 851 +CONECT 850 849 +CONECT 851 849 853 862 852 +CONECT 852 851 +CONECT 853 855 854 856 851 +CONECT 854 853 +CONECT 855 853 +CONECT 856 857 858 853 859 +CONECT 857 856 +CONECT 858 856 +CONECT 859 856 860 861 +CONECT 860 859 +CONECT 861 859 +CONECT 862 864 851 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 87 306 866 275 +CONECT 866 865 868 +CONECT 867 870 868 871 869 +CONECT 868 866 867 +CONECT 869 867 +CONECT 870 867 +CONECT 871 867 +CONECT 872 873 +CONECT 873 872 874 +CONECT 874 873 +MASTER 0 0 0 0 0 0 0 0 874 0 874 0 +END diff --git a/tests/nsga2/min_mol_iter_1.pdb b/tests/nsga2/min_mol_iter_1.pdb new file mode 100644 index 0000000..6fcd112 --- /dev/null +++ b/tests/nsga2/min_mol_iter_1.pdb @@ -0,0 +1,1745 @@ +COMPND fitness: -2.8894 84.35416666666652 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 56.210 58.077 51.862 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.610 37.835 23.460 1.00 0.00 N +ATOM 2 H1 MET 1 14.587 38.236 24.394 1.00 0.00 H +ATOM 3 H2 MET 1 13.812 38.148 22.935 1.00 0.00 H +ATOM 4 H3 MET 1 15.464 38.178 23.039 1.00 0.00 H +ATOM 5 CA MET 1 14.662 36.367 23.555 1.00 0.00 C +ATOM 6 HA MET 1 13.728 36.021 23.999 1.00 0.00 H +ATOM 7 CB MET 1 14.806 35.736 22.157 1.00 0.00 C +ATOM 8 HB2 MET 1 13.928 35.994 21.567 1.00 0.00 H +ATOM 9 HB3 MET 1 15.682 36.159 21.666 1.00 0.00 H +ATOM 10 CG MET 1 14.957 34.205 22.185 1.00 0.00 C +ATOM 11 HG2 MET 1 15.847 33.953 22.764 1.00 0.00 H +ATOM 12 HG3 MET 1 14.092 33.769 22.688 1.00 0.00 H +ATOM 13 SD MET 1 15.133 33.423 20.557 1.00 0.00 S +ATOM 14 CE MET 1 13.430 33.524 19.932 1.00 0.00 C +ATOM 15 HE1 MET 1 13.103 34.563 19.883 1.00 0.00 H +ATOM 16 HE2 MET 1 13.381 33.092 18.933 1.00 0.00 H +ATOM 17 HE3 MET 1 12.763 32.967 20.591 1.00 0.00 H +ATOM 18 C MET 1 15.802 35.945 24.478 1.00 0.00 C +ATOM 19 O MET 1 16.945 36.312 24.240 1.00 0.00 O +ATOM 20 N GLN 2 15.501 35.116 25.481 1.00 0.00 N +ATOM 21 H GLN 2 14.536 34.897 25.661 1.00 0.00 H +ATOM 22 CA GLN 2 16.493 34.445 26.330 1.00 0.00 C +ATOM 23 HA GLN 2 17.239 35.169 26.657 1.00 0.00 H +ATOM 24 CB GLN 2 15.772 33.892 27.577 1.00 0.00 C +ATOM 25 HB2 GLN 2 14.850 33.401 27.264 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.383 33.136 28.064 1.00 0.00 H +ATOM 27 CG GLN 2 15.424 34.965 28.621 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.944 35.807 28.133 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.697 34.542 29.314 1.00 0.00 H +ATOM 30 CD GLN 2 16.606 35.446 29.461 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.750 35.034 29.311 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.365 36.275 30.448 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.141 36.537 31.027 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.429 36.623 30.586 1.00 0.00 H +ATOM 35 C GLN 2 17.242 33.339 25.554 1.00 0.00 C +ATOM 36 O GLN 2 16.895 32.159 25.641 1.00 0.00 O +ATOM 37 N TYR 3 18.267 33.710 24.779 1.00 0.00 N +ATOM 38 H TYR 3 18.507 34.698 24.761 1.00 0.00 H +ATOM 39 CA TYR 3 19.130 32.772 24.050 1.00 0.00 C +ATOM 40 HA TYR 3 18.508 32.164 23.394 1.00 0.00 H +ATOM 41 CB TYR 3 20.138 33.545 23.190 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.628 34.306 23.802 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.913 32.853 22.855 1.00 0.00 H +ATOM 44 CG TYR 3 19.537 34.200 21.959 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.394 33.447 20.777 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.704 32.411 20.758 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.869 34.045 19.616 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.784 33.476 18.703 1.00 0.00 H +ATOM 49 CZ TYR 3 18.472 35.400 19.642 1.00 0.00 C +ATOM 50 OH TYR 3 17.979 35.981 18.519 1.00 0.00 O +ATOM 51 HH TYR 3 17.916 35.355 17.795 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.600 36.150 20.830 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.290 37.185 20.841 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.136 35.550 21.987 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.235 36.130 22.896 1.00 0.00 H +ATOM 56 C TYR 3 19.865 31.833 25.021 1.00 0.00 C +ATOM 57 O TYR 3 20.356 32.276 26.061 1.00 0.00 O +ATOM 58 N LYS 4 19.933 30.534 24.705 1.00 0.00 N +ATOM 59 H LYS 4 19.658 30.251 23.767 1.00 0.00 H +ATOM 60 CA LYS 4 20.470 29.488 25.599 1.00 0.00 C +ATOM 61 HA LYS 4 20.193 29.725 26.622 1.00 0.00 H +ATOM 62 CB LYS 4 19.857 28.117 25.237 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.784 28.034 24.153 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.538 27.331 25.568 1.00 0.00 H +ATOM 65 CG LYS 4 18.476 27.805 25.856 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.226 26.778 25.589 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.551 27.859 26.942 1.00 0.00 H +ATOM 68 CD LYS 4 17.329 28.710 25.376 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.488 29.726 25.728 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.350 28.733 24.285 1.00 0.00 H +ATOM 71 CE LYS 4 15.930 28.229 25.815 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.191 28.785 25.230 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.824 27.174 25.545 1.00 0.00 H +ATOM 74 NZ LYS 4 15.640 28.425 27.266 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.696 29.397 27.534 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.693 28.146 27.503 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.250 27.898 27.886 1.00 0.00 H +ATOM 78 C LYS 4 22.000 29.450 25.582 1.00 0.00 C +ATOM 79 O LYS 4 22.635 29.697 24.563 1.00 0.00 O +HETATM 80 N HX1 5 22.614 29.087 26.706 1.00 0.00 N +HETATM 81 CA HX1 5 24.068 28.924 26.868 1.00 0.00 C +HETATM 82 C HX1 5 24.352 27.735 27.797 1.00 0.00 C +HETATM 83 O HX1 5 23.963 27.749 28.965 1.00 0.00 O +HETATM 84 CB HX1 5 24.686 30.249 27.361 1.00 0.00 C +HETATM 85 CG HX1 5 26.205 30.328 27.453 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.096 29.341 27.126 1.00 0.00 C +HETATM 87 ND1 HX1 5 26.899 31.425 27.989 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.188 31.059 27.927 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.345 29.815 27.484 1.00 0.00 N +HETATM 90 H HX1 5 22.036 28.964 27.535 1.00 0.00 H +HETATM 91 HA HX1 5 24.511 28.691 25.903 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.270 30.493 28.340 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.367 31.041 26.681 1.00 0.00 H +HETATM 94 HD2 HX1 5 26.901 28.351 26.753 1.00 0.00 H +HETATM 95 HE1 HX1 5 28.999 31.640 28.362 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.166 29.232 27.691 1.00 0.00 H +ATOM 97 N ILE 6 24.976 26.694 27.247 1.00 0.00 N +ATOM 98 H ILE 6 25.273 26.764 26.279 1.00 0.00 H +ATOM 99 CA ILE 6 25.416 25.484 27.957 1.00 0.00 C +ATOM 100 HA ILE 6 24.791 25.350 28.841 1.00 0.00 H +ATOM 101 CB ILE 6 25.219 24.234 27.066 1.00 0.00 C +ATOM 102 HB ILE 6 25.717 24.411 26.111 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.833 22.967 27.697 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.377 22.767 28.667 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.684 22.105 27.049 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.912 23.079 27.816 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.703 24.039 26.816 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.199 23.911 27.773 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.300 24.935 26.343 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.331 22.853 25.919 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.511 21.913 26.441 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.269 22.909 25.674 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.912 22.881 24.996 1.00 0.00 H +ATOM 114 C ILE 6 26.855 25.666 28.457 1.00 0.00 C +ATOM 115 O ILE 6 27.669 26.350 27.833 1.00 0.00 O +ATOM 116 N VAL 7 27.116 25.088 29.628 1.00 0.00 N +ATOM 117 H VAL 7 26.386 24.493 30.005 1.00 0.00 H +ATOM 118 CA VAL 7 28.247 25.361 30.522 1.00 0.00 C +ATOM 119 HA VAL 7 28.279 26.437 30.666 1.00 0.00 H +ATOM 120 CB VAL 7 27.910 24.707 31.877 1.00 0.00 C +ATOM 121 HB VAL 7 26.872 24.951 32.111 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.029 23.177 31.837 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.076 22.879 31.779 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.576 22.749 32.720 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.511 22.784 30.962 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.732 25.253 33.046 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.660 26.340 33.068 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.348 24.861 33.986 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.770 24.958 32.940 1.00 0.00 H +ATOM 130 C VAL 7 29.638 24.925 30.014 1.00 0.00 C +ATOM 131 O VAL 7 29.787 23.876 29.396 1.00 0.00 O +ATOM 132 N ARG 8 30.669 25.690 30.392 1.00 0.00 N +ATOM 133 H ARG 8 30.448 26.631 30.693 1.00 0.00 H +ATOM 134 CA ARG 8 32.095 25.295 30.376 1.00 0.00 C +ATOM 135 HA ARG 8 32.337 25.066 29.335 1.00 0.00 H +ATOM 136 CB ARG 8 33.001 26.478 30.815 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.031 26.191 30.597 1.00 0.00 H +ATOM 138 HB3 ARG 8 32.778 27.341 30.186 1.00 0.00 H +ATOM 139 CG ARG 8 32.964 26.926 32.298 1.00 0.00 C +ATOM 140 HG2 ARG 8 33.166 26.074 32.950 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.772 27.646 32.453 1.00 0.00 H +ATOM 142 CD ARG 8 31.641 27.598 32.706 1.00 0.00 C +ATOM 143 HD2 ARG 8 31.523 28.498 32.102 1.00 0.00 H +ATOM 144 HD3 ARG 8 30.811 26.937 32.492 1.00 0.00 H +ATOM 145 NE ARG 8 31.554 27.975 34.136 1.00 0.00 N +ATOM 146 HE ARG 8 31.477 28.963 34.328 1.00 0.00 H +ATOM 147 CZ ARG 8 31.360 27.181 35.177 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.436 25.880 35.096 1.00 0.00 N +ATOM 149 HH11 ARG 8 31.653 25.451 34.206 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.280 25.329 35.915 1.00 0.00 H +ATOM 151 NH2 ARG 8 31.059 27.706 36.329 1.00 0.00 N +ATOM 152 HH21 ARG 8 30.883 28.704 36.414 1.00 0.00 H +ATOM 153 HH22 ARG 8 30.972 27.170 37.183 1.00 0.00 H +ATOM 154 C ARG 8 32.399 24.032 31.197 1.00 0.00 C +ATOM 155 O ARG 8 31.989 23.928 32.359 1.00 0.00 O +ATOM 156 N GLY 9 33.235 23.149 30.643 1.00 0.00 N +ATOM 157 H GLY 9 33.483 23.302 29.677 1.00 0.00 H +ATOM 158 CA GLY 9 33.803 21.970 31.313 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.769 21.741 30.856 1.00 0.00 H +ATOM 160 HA3 GLY 9 33.977 22.203 32.366 1.00 0.00 H +ATOM 161 C GLY 9 32.930 20.700 31.255 1.00 0.00 C +ATOM 162 O GLY 9 31.748 20.758 30.940 1.00 0.00 O +ATOM 163 N LYS 10 33.531 19.549 31.601 1.00 0.00 N +ATOM 164 H LYS 10 34.504 19.593 31.865 1.00 0.00 H +ATOM 165 CA LYS 10 32.919 18.202 31.470 1.00 0.00 C +ATOM 166 HA LYS 10 31.934 18.338 31.024 1.00 0.00 H +ATOM 167 CB LYS 10 33.740 17.354 30.479 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.240 18.008 29.765 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.509 16.801 31.019 1.00 0.00 H +ATOM 170 CG LYS 10 32.870 16.377 29.670 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.314 15.722 30.339 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.155 16.955 29.085 1.00 0.00 H +ATOM 173 CD LYS 10 33.734 15.532 28.729 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.372 16.192 28.137 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.363 14.862 29.315 1.00 0.00 H +ATOM 176 CE LYS 10 32.861 14.716 27.778 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.249 14.019 28.356 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.207 15.410 27.249 1.00 0.00 H +ATOM 179 NZ LYS 10 33.702 14.007 26.788 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.337 13.350 27.224 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.169 13.532 26.081 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.296 14.687 26.297 1.00 0.00 H +ATOM 183 C LYS 10 32.637 17.486 32.799 1.00 0.00 C +ATOM 184 O LYS 10 32.284 16.311 32.824 1.00 0.00 O +ATOM 185 N TRP 11 32.824 18.177 33.926 1.00 0.00 N +ATOM 186 H TRP 11 33.243 19.090 33.848 1.00 0.00 H +ATOM 187 CA TRP 11 32.126 17.892 35.182 1.00 0.00 C +ATOM 188 HA TRP 11 31.901 16.824 35.268 1.00 0.00 H +ATOM 189 CB TRP 11 33.036 18.283 36.357 1.00 0.00 C +ATOM 190 HB2 TRP 11 32.535 18.015 37.294 1.00 0.00 H +ATOM 191 HB3 TRP 11 33.950 17.689 36.296 1.00 0.00 H +ATOM 192 CG TRP 11 33.419 19.737 36.406 1.00 0.00 C +ATOM 193 CD1 TRP 11 32.861 20.665 37.216 1.00 0.00 C +ATOM 194 HD1 TRP 11 32.089 20.465 37.950 1.00 0.00 H +ATOM 195 NE1 TRP 11 33.403 21.907 36.943 1.00 0.00 N +ATOM 196 HE1 TRP 11 33.141 22.745 37.445 1.00 0.00 H +ATOM 197 CE2 TRP 11 34.318 21.848 35.912 1.00 0.00 C +ATOM 198 CZ2 TRP 11 35.085 22.819 35.250 1.00 0.00 C +ATOM 199 HZ2 TRP 11 35.003 23.862 35.519 1.00 0.00 H +ATOM 200 CH2 TRP 11 35.984 22.415 34.248 1.00 0.00 C +ATOM 201 HH2 TRP 11 36.605 23.145 33.744 1.00 0.00 H +ATOM 202 CZ3 TRP 11 36.107 21.052 33.924 1.00 0.00 C +ATOM 203 HZ3 TRP 11 36.838 20.745 33.183 1.00 0.00 H +ATOM 204 CE3 TRP 11 35.320 20.087 34.584 1.00 0.00 C +ATOM 205 HE3 TRP 11 35.461 19.041 34.352 1.00 0.00 H +ATOM 206 CD2 TRP 11 34.391 20.460 35.583 1.00 0.00 C +ATOM 207 C TRP 11 30.804 18.683 35.243 1.00 0.00 C +ATOM 208 O TRP 11 29.944 18.363 36.056 1.00 0.00 O +ATOM 209 N VAL 12 30.660 19.740 34.430 1.00 0.00 N +ATOM 210 H VAL 12 31.413 19.900 33.802 1.00 0.00 H +ATOM 211 CA VAL 12 29.415 20.530 34.220 1.00 0.00 C +ATOM 212 HA VAL 12 29.656 21.259 33.447 1.00 0.00 H +ATOM 213 CB VAL 12 29.101 21.349 35.518 1.00 0.00 C +ATOM 214 HB VAL 12 29.296 20.712 36.378 1.00 0.00 H +ATOM 215 CG1 VAL 12 27.725 21.975 35.716 1.00 0.00 C +ATOM 216 HG11 VAL 12 26.970 21.208 35.955 1.00 0.00 H +ATOM 217 HG12 VAL 12 27.751 22.645 36.588 1.00 0.00 H +ATOM 218 HG13 VAL 12 27.441 22.553 34.835 1.00 0.00 H +ATOM 219 CG2 VAL 12 30.126 22.530 35.519 1.00 0.00 C +ATOM 220 HG21 VAL 12 29.940 23.175 34.670 1.00 0.00 H +ATOM 221 HG22 VAL 12 30.055 23.143 36.414 1.00 0.00 H +ATOM 222 HG23 VAL 12 31.147 22.192 35.430 1.00 0.00 H +ATOM 223 C VAL 12 28.340 19.651 33.542 1.00 0.00 C +ATOM 224 O VAL 12 28.703 18.718 32.836 1.00 0.00 O +ATOM 225 N LYS 13 27.051 19.990 33.615 1.00 0.00 N +ATOM 226 H LYS 13 26.818 20.626 34.355 1.00 0.00 H +ATOM 227 CA LYS 13 26.031 19.654 32.590 1.00 0.00 C +ATOM 228 HA LYS 13 26.538 19.769 31.626 1.00 0.00 H +ATOM 229 CB LYS 13 25.592 18.175 32.709 1.00 0.00 C +ATOM 230 HB2 LYS 13 26.368 17.610 33.220 1.00 0.00 H +ATOM 231 HB3 LYS 13 24.698 18.118 33.320 1.00 0.00 H +ATOM 232 CG LYS 13 25.353 17.514 31.333 1.00 0.00 C +ATOM 233 HG2 LYS 13 24.456 17.931 30.874 1.00 0.00 H +ATOM 234 HG3 LYS 13 26.197 17.751 30.683 1.00 0.00 H +ATOM 235 CD LYS 13 25.238 15.981 31.410 1.00 0.00 C +ATOM 236 HD2 LYS 13 25.170 15.578 30.397 1.00 0.00 H +ATOM 237 HD3 LYS 13 26.145 15.589 31.878 1.00 0.00 H +ATOM 238 CE LYS 13 24.004 15.541 32.208 1.00 0.00 C +ATOM 239 HE2 LYS 13 23.955 16.153 33.114 1.00 0.00 H +ATOM 240 HE3 LYS 13 23.108 15.743 31.609 1.00 0.00 H +ATOM 241 NZ LYS 13 24.068 14.106 32.592 1.00 0.00 N +ATOM 242 HZ1 LYS 13 24.999 13.834 32.897 1.00 0.00 H +ATOM 243 HZ2 LYS 13 23.472 13.932 33.399 1.00 0.00 H +ATOM 244 HZ3 LYS 13 23.792 13.478 31.849 1.00 0.00 H +ATOM 245 C LYS 13 24.841 20.629 32.531 1.00 0.00 C +ATOM 246 O LYS 13 23.849 20.366 31.856 1.00 0.00 O +ATOM 247 N GLY 14 24.939 21.740 33.268 1.00 0.00 N +ATOM 248 H GLY 14 25.799 21.915 33.754 1.00 0.00 H +ATOM 249 CA GLY 14 23.872 22.731 33.398 1.00 0.00 C +ATOM 250 HA2 GLY 14 22.917 22.216 33.519 1.00 0.00 H +ATOM 251 HA3 GLY 14 24.041 23.329 34.294 1.00 0.00 H +ATOM 252 C GLY 14 23.740 23.693 32.199 1.00 0.00 C +ATOM 253 O GLY 14 24.623 23.800 31.347 1.00 0.00 O +ATOM 254 N VAL 15 22.630 24.433 32.175 1.00 0.00 N +ATOM 255 H VAL 15 21.967 24.310 32.924 1.00 0.00 H +ATOM 256 CA VAL 15 22.258 25.391 31.125 1.00 0.00 C +ATOM 257 HA VAL 15 23.156 25.664 30.577 1.00 0.00 H +ATOM 258 CB VAL 15 21.291 24.727 30.116 1.00 0.00 C +ATOM 259 HB VAL 15 21.791 23.839 29.715 1.00 0.00 H +ATOM 260 CG1 VAL 15 19.966 24.264 30.749 1.00 0.00 C +ATOM 261 HG11 VAL 15 19.406 25.113 31.134 1.00 0.00 H +ATOM 262 HG12 VAL 15 19.365 23.754 29.993 1.00 0.00 H +ATOM 263 HG13 VAL 15 20.160 23.557 31.554 1.00 0.00 H +ATOM 264 CG2 VAL 15 20.963 25.647 28.933 1.00 0.00 C +ATOM 265 HG21 VAL 15 21.883 26.004 28.474 1.00 0.00 H +ATOM 266 HG22 VAL 15 20.402 25.080 28.186 1.00 0.00 H +ATOM 267 HG23 VAL 15 20.358 26.490 29.258 1.00 0.00 H +ATOM 268 C VAL 15 21.686 26.658 31.751 1.00 0.00 C +ATOM 269 O VAL 15 20.993 26.607 32.770 1.00 0.00 O +HETATM 270 N HY1 16 21.983 27.814 31.152 1.00 0.00 N +HETATM 271 CA HY1 16 21.415 29.132 31.476 1.00 0.00 C +HETATM 272 C HY1 16 21.134 29.908 30.177 1.00 0.00 C +HETATM 273 O HY1 16 21.275 29.361 29.086 1.00 0.00 O +HETATM 274 CB HY1 16 22.356 29.875 32.450 1.00 0.00 C +HETATM 275 CG HY1 16 23.709 30.229 31.878 1.00 0.00 C +HETATM 276 CD2 HY1 16 24.068 31.431 31.324 1.00 0.00 C +HETATM 277 ND1 HY1 16 24.813 29.410 31.817 1.00 0.00 N +HETATM 278 CE1 HY1 16 25.816 30.121 31.269 1.00 0.00 C +HETATM 279 NE2 HY1 16 25.412 31.360 30.935 1.00 0.00 N +HETATM 280 H HY1 16 22.553 27.772 30.305 1.00 0.00 H +HETATM 281 HA HY1 16 20.458 28.981 31.988 1.00 0.00 H +HETATM 282 HB2 HY1 16 21.869 30.793 32.788 1.00 0.00 H +HETATM 283 HB3 HY1 16 22.504 29.262 33.342 1.00 0.00 H +HETATM 284 HD1 HY1 16 24.881 28.463 32.165 1.00 0.00 H +HETATM 285 HD2 HY1 16 23.428 32.300 31.222 1.00 0.00 H +HETATM 286 HE1 HY1 16 26.831 29.752 31.127 1.00 0.00 H +ATOM 287 N THR 17 20.733 31.171 30.282 1.00 0.00 N +ATOM 288 H THR 17 20.606 31.590 31.189 1.00 0.00 H +ATOM 289 CA THR 17 20.339 32.027 29.148 1.00 0.00 C +ATOM 290 HA THR 17 20.769 31.599 28.239 1.00 0.00 H +ATOM 291 CB THR 17 18.804 32.054 28.997 1.00 0.00 C +ATOM 292 HB THR 17 18.548 32.701 28.154 1.00 0.00 H +ATOM 293 CG2 THR 17 18.153 30.699 28.714 1.00 0.00 C +ATOM 294 HG21 THR 17 18.358 29.982 29.502 1.00 0.00 H +ATOM 295 HG22 THR 17 17.081 30.790 28.628 1.00 0.00 H +ATOM 296 HG23 THR 17 18.516 30.287 27.783 1.00 0.00 H +ATOM 297 OG1 THR 17 18.212 32.553 30.159 1.00 0.00 O +ATOM 298 HG1 THR 17 18.144 33.518 30.025 1.00 0.00 H +ATOM 299 C THR 17 20.886 33.446 29.236 1.00 0.00 C +ATOM 300 O THR 17 21.350 33.861 30.295 1.00 0.00 O +HETATM 301 N HY2 18 20.813 34.187 28.127 1.00 0.00 N +HETATM 302 CA HY2 18 21.081 35.625 28.066 1.00 0.00 C +HETATM 303 C HY2 18 19.976 36.319 27.265 1.00 0.00 C +HETATM 304 O HY2 18 19.648 35.866 26.170 1.00 0.00 O +HETATM 305 CB HY2 18 22.427 35.918 27.401 1.00 0.00 C +HETATM 306 CG HY2 18 23.623 35.439 28.194 1.00 0.00 C +HETATM 307 CD2 HY2 18 24.155 34.177 28.162 1.00 0.00 C +HETATM 308 ND1 HY2 18 24.312 36.145 29.158 1.00 0.00 N +HETATM 309 CE1 HY2 18 25.247 35.326 29.676 1.00 0.00 C +HETATM 310 NE2 HY2 18 25.185 34.110 29.103 1.00 0.00 N +HETATM 311 H HY2 18 20.458 33.740 27.282 1.00 0.00 H +HETATM 312 HA HY2 18 21.088 36.044 29.084 1.00 0.00 H +HETATM 313 HB2 HY2 18 22.454 35.451 26.408 1.00 0.00 H +HETATM 314 HB3 HY2 18 22.525 37.001 27.258 1.00 0.00 H +HETATM 315 HD1 HY2 18 24.160 37.108 29.430 1.00 0.00 H +HETATM 316 HD2 HY2 18 23.816 33.363 27.535 1.00 0.00 H +HETATM 317 HE1 HY2 18 25.945 35.606 30.456 1.00 0.00 H +ATOM 318 N GLU 19 19.430 37.417 27.787 1.00 0.00 N +ATOM 319 H GLU 19 19.758 37.740 28.682 1.00 0.00 H +ATOM 320 CA GLU 19 18.419 38.226 27.104 1.00 0.00 C +ATOM 321 HA GLU 19 17.699 37.546 26.656 1.00 0.00 H +ATOM 322 CB GLU 19 17.705 39.102 28.147 1.00 0.00 C +ATOM 323 HB2 GLU 19 17.377 38.469 28.971 1.00 0.00 H +ATOM 324 HB3 GLU 19 18.414 39.828 28.557 1.00 0.00 H +ATOM 325 CG GLU 19 16.477 39.854 27.616 1.00 0.00 C +ATOM 326 HG2 GLU 19 15.971 40.349 28.452 1.00 0.00 H +ATOM 327 HG3 GLU 19 16.810 40.632 26.924 1.00 0.00 H +ATOM 328 CD GLU 19 15.524 38.897 26.903 1.00 0.00 C +ATOM 329 OE1 GLU 19 15.614 38.801 25.661 1.00 0.00 O +ATOM 330 OE2 GLU 19 14.785 38.158 27.578 1.00 0.00 O +ATOM 331 C GLU 19 19.040 39.069 25.978 1.00 0.00 C +ATOM 332 O GLU 19 20.090 39.684 26.183 1.00 0.00 O +ATOM 333 N ALA 20 18.406 39.106 24.798 1.00 0.00 N +ATOM 334 H ALA 20 17.526 38.600 24.725 1.00 0.00 H +ATOM 335 CA ALA 20 18.770 39.982 23.679 1.00 0.00 C +ATOM 336 HA ALA 20 18.902 40.994 24.063 1.00 0.00 H +ATOM 337 CB ALA 20 20.096 39.515 23.062 1.00 0.00 C +ATOM 338 HB1 ALA 20 19.972 38.533 22.606 1.00 0.00 H +ATOM 339 HB2 ALA 20 20.416 40.226 22.305 1.00 0.00 H +ATOM 340 HB3 ALA 20 20.879 39.462 23.817 1.00 0.00 H +ATOM 341 C ALA 20 17.694 40.018 22.571 1.00 0.00 C +ATOM 342 O ALA 20 16.874 39.108 22.434 1.00 0.00 O +ATOM 343 N VAL 21 17.756 41.039 21.709 1.00 0.00 N +ATOM 344 H VAL 21 18.418 41.780 21.884 1.00 0.00 H +ATOM 345 CA VAL 21 17.017 41.071 20.423 1.00 0.00 C +ATOM 346 HA VAL 21 16.020 40.661 20.587 1.00 0.00 H +ATOM 347 CB VAL 21 16.842 42.514 19.898 1.00 0.00 C +ATOM 348 HB VAL 21 16.188 42.472 19.027 1.00 0.00 H +ATOM 349 CG1 VAL 21 16.159 43.411 20.937 1.00 0.00 C +ATOM 350 HG11 VAL 21 16.810 43.579 21.795 1.00 0.00 H +ATOM 351 HG12 VAL 21 15.918 44.373 20.486 1.00 0.00 H +ATOM 352 HG13 VAL 21 15.232 42.951 21.279 1.00 0.00 H +ATOM 353 CG2 VAL 21 18.158 43.176 19.464 1.00 0.00 C +ATOM 354 HG21 VAL 21 18.596 42.634 18.626 1.00 0.00 H +ATOM 355 HG22 VAL 21 17.964 44.195 19.129 1.00 0.00 H +ATOM 356 HG23 VAL 21 18.872 43.205 20.287 1.00 0.00 H +ATOM 357 C VAL 21 17.666 40.197 19.339 1.00 0.00 C +ATOM 358 O VAL 21 16.989 39.788 18.400 1.00 0.00 O +ATOM 359 N ASP 22 18.962 39.912 19.481 1.00 0.00 N +ATOM 360 H ASP 22 19.441 40.273 20.289 1.00 0.00 H +ATOM 361 CA ASP 22 19.803 39.155 18.549 1.00 0.00 C +ATOM 362 HA ASP 22 19.204 38.379 18.068 1.00 0.00 H +ATOM 363 CB ASP 22 20.347 40.115 17.467 1.00 0.00 C +ATOM 364 HB2 ASP 22 19.507 40.640 17.014 1.00 0.00 H +ATOM 365 HB3 ASP 22 20.969 40.862 17.961 1.00 0.00 H +ATOM 366 CG ASP 22 21.171 39.445 16.351 1.00 0.00 C +ATOM 367 OD1 ASP 22 21.358 40.133 15.304 1.00 0.00 O +ATOM 368 OD2 ASP 22 21.600 38.297 16.500 1.00 0.00 O +ATOM 369 C ASP 22 20.940 38.484 19.342 1.00 0.00 C +ATOM 370 O ASP 22 21.503 39.076 20.270 1.00 0.00 O +ATOM 371 N LEU 23 21.311 37.261 18.968 1.00 0.00 N +ATOM 372 H LEU 23 20.939 36.925 18.089 1.00 0.00 H +ATOM 373 CA LEU 23 22.452 36.571 19.560 1.00 0.00 C +ATOM 374 HA LEU 23 22.285 36.550 20.632 1.00 0.00 H +ATOM 375 CB LEU 23 22.485 35.111 19.082 1.00 0.00 C +ATOM 376 HB2 LEU 23 21.546 34.665 19.394 1.00 0.00 H +ATOM 377 HB3 LEU 23 22.522 35.056 17.994 1.00 0.00 H +ATOM 378 CG LEU 23 23.640 34.288 19.690 1.00 0.00 C +ATOM 379 HG LEU 23 23.819 34.622 20.711 1.00 0.00 H +ATOM 380 CD1 LEU 23 23.243 32.811 19.763 1.00 0.00 C +ATOM 381 HD11 LEU 23 22.968 32.445 18.779 1.00 0.00 H +ATOM 382 HD12 LEU 23 24.071 32.222 20.159 1.00 0.00 H +ATOM 383 HD13 LEU 23 22.398 32.707 20.441 1.00 0.00 H +ATOM 384 CD2 LEU 23 24.930 34.430 18.880 1.00 0.00 C +ATOM 385 HD21 LEU 23 25.532 35.241 19.277 1.00 0.00 H +ATOM 386 HD22 LEU 23 25.534 33.529 18.950 1.00 0.00 H +ATOM 387 HD23 LEU 23 24.718 34.659 17.839 1.00 0.00 H +ATOM 388 C LEU 23 23.771 37.324 19.343 1.00 0.00 C +ATOM 389 O LEU 23 24.614 37.294 20.233 1.00 0.00 O +ATOM 390 N ALA 24 23.950 38.060 18.242 1.00 0.00 N +ATOM 391 H ALA 24 23.204 38.085 17.546 1.00 0.00 H +ATOM 392 CA ALA 24 25.158 38.865 18.025 1.00 0.00 C +ATOM 393 HA ALA 24 26.018 38.218 18.197 1.00 0.00 H +ATOM 394 CB ALA 24 25.202 39.299 16.558 1.00 0.00 C +ATOM 395 HB1 ALA 24 24.369 39.964 16.325 1.00 0.00 H +ATOM 396 HB2 ALA 24 26.142 39.815 16.363 1.00 0.00 H +ATOM 397 HB3 ALA 24 25.148 38.425 15.906 1.00 0.00 H +ATOM 398 C ALA 24 25.306 40.056 19.005 1.00 0.00 C +ATOM 399 O ALA 24 26.389 40.642 19.118 1.00 0.00 O +ATOM 400 N GLU 25 24.251 40.394 19.761 1.00 0.00 N +ATOM 401 H GLU 25 23.380 39.906 19.598 1.00 0.00 H +ATOM 402 CA GLU 25 24.335 41.202 20.988 1.00 0.00 C +ATOM 403 HA GLU 25 25.200 41.864 20.931 1.00 0.00 H +ATOM 404 CB GLU 25 23.081 42.091 21.112 1.00 0.00 C +ATOM 405 HB2 GLU 25 22.197 41.461 21.036 1.00 0.00 H +ATOM 406 HB3 GLU 25 23.072 42.547 22.099 1.00 0.00 H +ATOM 407 CG GLU 25 22.993 43.209 20.067 1.00 0.00 C +ATOM 408 HG2 GLU 25 23.178 42.799 19.072 1.00 0.00 H +ATOM 409 HG3 GLU 25 21.977 43.613 20.061 1.00 0.00 H +ATOM 410 CD GLU 25 23.989 44.335 20.372 1.00 0.00 C +ATOM 411 OE1 GLU 25 23.587 45.318 21.037 1.00 0.00 O +ATOM 412 OE2 GLU 25 25.166 44.185 19.957 1.00 0.00 O +ATOM 413 C GLU 25 24.520 40.324 22.230 1.00 0.00 C +ATOM 414 O GLU 25 25.355 40.629 23.079 1.00 0.00 O +ATOM 415 N ALA 26 23.838 39.165 22.340 1.00 0.00 N +ATOM 416 H ALA 26 23.144 38.939 21.634 1.00 0.00 H +ATOM 417 CA ALA 26 24.041 38.207 23.435 1.00 0.00 C +ATOM 418 HA ALA 26 23.857 38.735 24.370 1.00 0.00 H +ATOM 419 CB ALA 26 23.053 37.055 23.307 1.00 0.00 C +ATOM 420 HB1 ALA 26 23.352 36.400 22.493 1.00 0.00 H +ATOM 421 HB2 ALA 26 23.041 36.471 24.227 1.00 0.00 H +ATOM 422 HB3 ALA 26 22.059 37.460 23.119 1.00 0.00 H +ATOM 423 C ALA 26 25.475 37.640 23.529 1.00 0.00 C +ATOM 424 O ALA 26 25.878 37.199 24.606 1.00 0.00 O +ATOM 425 N GLU 27 26.225 37.656 22.426 1.00 0.00 N +ATOM 426 H GLU 27 25.728 37.822 21.561 1.00 0.00 H +ATOM 427 CA GLU 27 27.657 37.363 22.351 1.00 0.00 C +ATOM 428 HA GLU 27 27.828 36.387 22.786 1.00 0.00 H +ATOM 429 CB GLU 27 28.049 37.295 20.810 1.00 0.00 C +ATOM 430 HB2 GLU 27 27.320 36.650 20.339 1.00 0.00 H +ATOM 431 HB3 GLU 27 27.974 38.279 20.364 1.00 0.00 H +ATOM 432 CG GLU 27 29.432 36.733 20.511 1.00 0.00 C +ATOM 433 HG2 GLU 27 30.208 37.425 20.927 1.00 0.00 H +ATOM 434 HG3 GLU 27 29.562 35.764 21.055 1.00 0.00 H +ATOM 435 CD GLU 27 29.655 36.541 18.998 1.00 0.00 C +ATOM 436 OE1 GLU 27 30.446 37.312 18.444 1.00 0.00 O +ATOM 437 OE2 GLU 27 29.027 35.659 18.399 1.00 0.00 O +ATOM 438 C GLU 27 28.483 38.382 23.126 1.00 0.00 C +ATOM 439 O GLU 27 29.294 38.026 23.980 1.00 0.00 O +ATOM 440 N LYS 28 28.171 39.676 22.949 1.00 0.00 N +ATOM 441 H LYS 28 27.412 39.874 22.302 1.00 0.00 H +ATOM 442 CA LYS 28 28.730 40.786 23.720 1.00 0.00 C +ATOM 443 HA LYS 28 29.826 40.697 23.712 1.00 0.00 H +ATOM 444 CB LYS 28 28.359 42.145 23.096 1.00 0.00 C +ATOM 445 HB2 LYS 28 27.290 42.317 23.207 1.00 0.00 H +ATOM 446 HB3 LYS 28 28.886 42.916 23.652 1.00 0.00 H +ATOM 447 CG LYS 28 28.732 42.265 21.607 1.00 0.00 C +ATOM 448 HG2 LYS 28 29.789 42.022 21.483 1.00 0.00 H +ATOM 449 HG3 LYS 28 28.138 41.561 21.024 1.00 0.00 H +ATOM 450 CD LYS 28 28.480 43.692 21.087 1.00 0.00 C +ATOM 451 HD2 LYS 28 27.472 44.012 21.359 1.00 0.00 H +ATOM 452 HD3 LYS 28 29.187 44.367 21.577 1.00 0.00 H +ATOM 453 CE LYS 28 28.656 43.806 19.568 1.00 0.00 C +ATOM 454 HE2 LYS 28 28.808 44.863 19.321 1.00 0.00 H +ATOM 455 HE3 LYS 28 29.558 43.270 19.263 1.00 0.00 H +ATOM 456 NZ LYS 28 27.462 43.300 18.844 1.00 0.00 N +ATOM 457 HZ1 LYS 28 26.620 43.776 19.187 1.00 0.00 H +ATOM 458 HZ2 LYS 28 27.524 43.469 17.852 1.00 0.00 H +ATOM 459 HZ3 LYS 28 27.296 42.311 19.010 1.00 0.00 H +ATOM 460 C LYS 28 28.293 40.734 25.190 1.00 0.00 C +ATOM 461 O LYS 28 29.136 40.838 26.076 1.00 0.00 O +ATOM 462 N PHE 29 27.019 40.477 25.467 1.00 0.00 N +ATOM 463 H PHE 29 26.355 40.453 24.698 1.00 0.00 H +ATOM 464 CA PHE 29 26.517 40.332 26.846 1.00 0.00 C +ATOM 465 HA PHE 29 26.806 41.218 27.411 1.00 0.00 H +ATOM 466 CB PHE 29 24.977 40.304 26.842 1.00 0.00 C +ATOM 467 HB2 PHE 29 24.659 39.367 26.390 1.00 0.00 H +ATOM 468 HB3 PHE 29 24.625 40.303 27.880 1.00 0.00 H +ATOM 469 CG PHE 29 24.287 41.460 26.136 1.00 0.00 C +ATOM 470 CD1 PHE 29 23.049 41.246 25.495 1.00 0.00 C +ATOM 471 HD1 PHE 29 22.579 40.275 25.527 1.00 0.00 H +ATOM 472 CE1 PHE 29 22.410 42.297 24.807 1.00 0.00 C +ATOM 473 HE1 PHE 29 21.469 42.116 24.311 1.00 0.00 H +ATOM 474 CZ PHE 29 23.003 43.573 24.765 1.00 0.00 C +ATOM 475 HZ PHE 29 22.524 44.372 24.222 1.00 0.00 H +ATOM 476 CE2 PHE 29 24.219 43.806 25.428 1.00 0.00 C +ATOM 477 HE2 PHE 29 24.669 44.778 25.408 1.00 0.00 H +ATOM 478 CD2 PHE 29 24.853 42.757 26.115 1.00 0.00 C +ATOM 479 HD2 PHE 29 25.782 42.959 26.619 1.00 0.00 H +ATOM 480 C PHE 29 27.097 39.092 27.576 1.00 0.00 C +ATOM 481 O PHE 29 27.242 39.121 28.804 1.00 0.00 O +ATOM 482 N THR 30 27.471 38.019 26.855 1.00 0.00 N +ATOM 483 H THR 30 27.262 38.018 25.867 1.00 0.00 H +ATOM 484 CA THR 30 28.208 36.874 27.383 1.00 0.00 C +ATOM 485 HA THR 30 27.806 36.552 28.340 1.00 0.00 H +ATOM 486 CB THR 30 28.165 35.642 26.355 1.00 0.00 C +ATOM 487 HB THR 30 28.671 35.982 25.465 1.00 0.00 H +ATOM 488 CG2 THR 30 29.010 34.482 26.856 1.00 0.00 C +ATOM 489 HG21 THR 30 28.763 34.155 27.853 1.00 0.00 H +ATOM 490 HG22 THR 30 28.991 33.595 26.210 1.00 0.00 H +ATOM 491 HG23 THR 30 30.047 34.791 26.859 1.00 0.00 H +ATOM 492 OG1 THR 30 26.844 35.210 26.048 1.00 0.00 O +ATOM 493 HG1 THR 30 26.349 35.962 25.650 1.00 0.00 H +ATOM 494 C THR 30 29.681 37.276 27.719 1.00 0.00 C +ATOM 495 O THR 30 30.155 36.942 28.795 1.00 0.00 O +ATOM 496 N LYS 31 30.332 38.079 26.889 1.00 0.00 N +ATOM 497 H LYS 31 29.871 38.384 26.044 1.00 0.00 H +ATOM 498 CA LYS 31 31.674 38.634 27.157 1.00 0.00 C +ATOM 499 HA LYS 31 32.350 37.837 27.474 1.00 0.00 H +ATOM 500 CB LYS 31 32.241 39.245 25.864 1.00 0.00 C +ATOM 501 HB2 LYS 31 31.523 39.940 25.448 1.00 0.00 H +ATOM 502 HB3 LYS 31 33.157 39.786 26.103 1.00 0.00 H +ATOM 503 CG LYS 31 32.581 38.157 24.832 1.00 0.00 C +ATOM 504 HG2 LYS 31 33.317 37.480 25.261 1.00 0.00 H +ATOM 505 HG3 LYS 31 31.704 37.566 24.575 1.00 0.00 H +ATOM 506 CD LYS 31 33.154 38.798 23.560 1.00 0.00 C +ATOM 507 HD2 LYS 31 32.363 39.356 23.055 1.00 0.00 H +ATOM 508 HD3 LYS 31 33.951 39.488 23.827 1.00 0.00 H +ATOM 509 CE LYS 31 33.714 37.746 22.591 1.00 0.00 C +ATOM 510 HE2 LYS 31 32.948 37.001 22.373 1.00 0.00 H +ATOM 511 HE3 LYS 31 33.955 38.245 21.648 1.00 0.00 H +ATOM 512 NZ LYS 31 34.933 37.089 23.115 1.00 0.00 N +ATOM 513 HZ1 LYS 31 34.746 36.340 23.769 1.00 0.00 H +ATOM 514 HZ2 LYS 31 35.437 36.639 22.348 1.00 0.00 H +ATOM 515 HZ3 LYS 31 35.592 37.732 23.552 1.00 0.00 H +ATOM 516 C LYS 31 31.693 39.656 28.305 1.00 0.00 C +ATOM 517 O LYS 31 32.674 39.678 29.044 1.00 0.00 O +ATOM 518 N ALA 32 30.615 40.417 28.505 1.00 0.00 N +ATOM 519 H ALA 32 29.893 40.433 27.798 1.00 0.00 H +ATOM 520 CA ALA 32 30.452 41.245 29.699 1.00 0.00 C +ATOM 521 HA ALA 32 31.287 41.943 29.769 1.00 0.00 H +ATOM 522 CB ALA 32 29.160 42.059 29.583 1.00 0.00 C +ATOM 523 HB1 ALA 32 28.295 41.401 29.522 1.00 0.00 H +ATOM 524 HB2 ALA 32 29.045 42.699 30.464 1.00 0.00 H +ATOM 525 HB3 ALA 32 29.194 42.691 28.695 1.00 0.00 H +ATOM 526 C ALA 32 30.481 40.374 30.974 1.00 0.00 C +ATOM 527 O ALA 32 31.390 40.511 31.786 1.00 0.00 O +ATOM 528 N ALA 33 29.599 39.373 31.058 1.00 0.00 N +ATOM 529 H ALA 33 28.886 39.292 30.345 1.00 0.00 H +ATOM 530 CA ALA 33 29.555 38.428 32.181 1.00 0.00 C +ATOM 531 HA ALA 33 29.465 39.008 33.099 1.00 0.00 H +ATOM 532 CB ALA 33 28.289 37.575 32.028 1.00 0.00 C +ATOM 533 HB1 ALA 33 28.346 36.978 31.119 1.00 0.00 H +ATOM 534 HB2 ALA 33 28.181 36.909 32.886 1.00 0.00 H +ATOM 535 HB3 ALA 33 27.410 38.219 31.981 1.00 0.00 H +ATOM 536 C ALA 33 30.821 37.541 32.333 1.00 0.00 C +ATOM 537 O ALA 33 30.921 36.798 33.305 1.00 0.00 O +ATOM 538 N ALA 34 31.757 37.568 31.379 1.00 0.00 N +ATOM 539 H ALA 34 31.589 38.159 30.584 1.00 0.00 H +ATOM 540 CA ALA 34 33.091 36.966 31.505 1.00 0.00 C +ATOM 541 HA ALA 34 33.037 36.139 32.213 1.00 0.00 H +ATOM 542 CB ALA 34 33.508 36.399 30.143 1.00 0.00 C +ATOM 543 HB1 ALA 34 33.649 37.207 29.426 1.00 0.00 H +ATOM 544 HB2 ALA 34 34.450 35.861 30.259 1.00 0.00 H +ATOM 545 HB3 ALA 34 32.750 35.708 29.774 1.00 0.00 H +ATOM 546 C ALA 34 34.123 37.961 32.063 1.00 0.00 C +ATOM 547 O ALA 34 34.832 37.631 33.008 1.00 0.00 O +ATOM 548 N ASN 35 34.171 39.202 31.560 1.00 0.00 N +ATOM 549 H ASN 35 33.544 39.440 30.800 1.00 0.00 H +ATOM 550 CA ASN 35 35.041 40.256 32.096 1.00 0.00 C +ATOM 551 HA ASN 35 36.050 39.850 32.215 1.00 0.00 H +ATOM 552 CB ASN 35 35.128 41.408 31.082 1.00 0.00 C +ATOM 553 HB2 ASN 35 34.128 41.702 30.765 1.00 0.00 H +ATOM 554 HB3 ASN 35 35.595 42.264 31.566 1.00 0.00 H +ATOM 555 CG ASN 35 35.989 41.053 29.876 1.00 0.00 C +ATOM 556 OD1 ASN 35 37.202 40.998 29.943 1.00 0.00 O +ATOM 557 ND2 ASN 35 35.397 40.799 28.737 1.00 0.00 N +ATOM 558 HD21 ASN 35 36.007 40.585 27.947 1.00 0.00 H +ATOM 559 HD22 ASN 35 34.398 40.684 28.702 1.00 0.00 H +ATOM 560 C ASN 35 34.614 40.741 33.504 1.00 0.00 C +ATOM 561 O ASN 35 35.469 41.137 34.290 1.00 0.00 O +ATOM 562 N ASP 36 33.333 40.617 33.865 1.00 0.00 N +ATOM 563 H ASP 36 32.647 40.420 33.146 1.00 0.00 H +ATOM 564 CA ASP 36 32.837 40.768 35.249 1.00 0.00 C +ATOM 565 HA ASP 36 33.163 41.738 35.630 1.00 0.00 H +ATOM 566 CB ASP 36 31.291 40.753 35.253 1.00 0.00 C +ATOM 567 HB2 ASP 36 30.950 39.847 34.749 1.00 0.00 H +ATOM 568 HB3 ASP 36 30.954 40.684 36.289 1.00 0.00 H +ATOM 569 CG ASP 36 30.604 41.992 34.634 1.00 0.00 C +ATOM 570 OD1 ASP 36 31.204 43.091 34.688 1.00 0.00 O +ATOM 571 OD2 ASP 36 29.439 41.870 34.172 1.00 0.00 O +ATOM 572 C ASP 36 33.415 39.697 36.211 1.00 0.00 C +ATOM 573 O ASP 36 33.441 39.908 37.424 1.00 0.00 O +ATOM 574 N LEU 37 33.904 38.557 35.688 1.00 0.00 N +ATOM 575 H LEU 37 33.842 38.450 34.686 1.00 0.00 H +ATOM 576 CA LEU 37 34.657 37.527 36.423 1.00 0.00 C +ATOM 577 HA LEU 37 34.464 37.650 37.491 1.00 0.00 H +ATOM 578 CB LEU 37 34.109 36.145 35.994 1.00 0.00 C +ATOM 579 HB2 LEU 37 33.040 36.119 36.207 1.00 0.00 H +ATOM 580 HB3 LEU 37 34.231 36.052 34.917 1.00 0.00 H +ATOM 581 CG LEU 37 34.771 34.914 36.645 1.00 0.00 C +ATOM 582 HG LEU 37 35.840 34.913 36.439 1.00 0.00 H +ATOM 583 CD1 LEU 37 34.551 34.857 38.159 1.00 0.00 C +ATOM 584 HD11 LEU 37 33.486 34.879 38.385 1.00 0.00 H +ATOM 585 HD12 LEU 37 34.992 33.944 38.560 1.00 0.00 H +ATOM 586 HD13 LEU 37 35.040 35.710 38.628 1.00 0.00 H +ATOM 587 CD2 LEU 37 34.177 33.637 36.042 1.00 0.00 C +ATOM 588 HD21 LEU 37 34.355 33.629 34.966 1.00 0.00 H +ATOM 589 HD22 LEU 37 34.662 32.764 36.478 1.00 0.00 H +ATOM 590 HD23 LEU 37 33.105 33.596 36.231 1.00 0.00 H +ATOM 591 C LEU 37 36.190 37.649 36.238 1.00 0.00 C +ATOM 592 O LEU 37 36.941 37.271 37.137 1.00 0.00 O +ATOM 593 N GLY 38 36.655 38.181 35.100 1.00 0.00 N +ATOM 594 H GLY 38 35.977 38.417 34.388 1.00 0.00 H +ATOM 595 CA GLY 38 38.057 38.532 34.848 1.00 0.00 C +ATOM 596 HA2 GLY 38 38.314 39.395 35.466 1.00 0.00 H +ATOM 597 HA3 GLY 38 38.690 37.700 35.160 1.00 0.00 H +ATOM 598 C GLY 38 38.413 38.871 33.391 1.00 0.00 C +ATOM 599 O GLY 38 38.929 39.957 33.136 1.00 0.00 O +ATOM 600 N GLU 39 38.171 37.961 32.437 1.00 0.00 N +ATOM 601 H GLU 39 37.657 37.131 32.691 1.00 0.00 H +ATOM 602 CA GLU 39 38.661 38.018 31.042 1.00 0.00 C +ATOM 603 HA GLU 39 38.763 39.061 30.726 1.00 0.00 H +ATOM 604 CB GLU 39 40.065 37.322 30.944 1.00 0.00 C +ATOM 605 HB2 GLU 39 39.944 36.313 31.317 1.00 0.00 H +ATOM 606 HB3 GLU 39 40.335 37.260 29.892 1.00 0.00 H +ATOM 607 CG GLU 39 41.245 37.986 31.688 1.00 0.00 C +ATOM 608 HG2 GLU 39 41.553 38.894 31.136 1.00 0.00 H +ATOM 609 HG3 GLU 39 40.915 38.320 32.684 1.00 0.00 H +ATOM 610 CD GLU 39 42.450 37.039 31.915 1.00 0.00 C +ATOM 611 OE1 GLU 39 42.260 36.003 32.575 1.00 0.00 O +ATOM 612 OE2 GLU 39 43.569 37.372 31.481 1.00 0.00 O +ATOM 613 C GLU 39 37.685 37.298 30.075 1.00 0.00 C +ATOM 614 O GLU 39 37.024 36.351 30.492 1.00 0.00 O +ATOM 615 N ASP 40 37.585 37.685 28.788 1.00 0.00 N +ATOM 616 H ASP 40 38.100 38.498 28.476 1.00 0.00 H +ATOM 617 CA ASP 40 36.738 36.968 27.799 1.00 0.00 C +ATOM 618 HA ASP 40 36.030 36.362 28.365 1.00 0.00 H +ATOM 619 CB ASP 40 35.858 37.913 26.964 1.00 0.00 C +ATOM 620 HB2 ASP 40 35.160 37.288 26.414 1.00 0.00 H +ATOM 621 HB3 ASP 40 35.261 38.533 27.625 1.00 0.00 H +ATOM 622 CG ASP 40 36.587 38.798 25.952 1.00 0.00 C +ATOM 623 OD1 ASP 40 36.893 39.965 26.276 1.00 0.00 O +ATOM 624 OD2 ASP 40 36.761 38.351 24.790 1.00 0.00 O +ATOM 625 C ASP 40 37.475 35.994 26.856 1.00 0.00 C +ATOM 626 O ASP 40 38.374 36.376 26.101 1.00 0.00 O +ATOM 627 N GLY 41 36.973 34.756 26.794 1.00 0.00 N +ATOM 628 H GLY 41 36.288 34.510 27.490 1.00 0.00 H +ATOM 629 CA GLY 41 37.271 33.768 25.747 1.00 0.00 C +ATOM 630 HA2 GLY 41 38.295 33.916 25.381 1.00 0.00 H +ATOM 631 HA3 GLY 41 37.211 32.770 26.191 1.00 0.00 H +ATOM 632 C GLY 41 36.313 33.811 24.533 1.00 0.00 C +ATOM 633 O GLY 41 35.386 34.624 24.460 1.00 0.00 O +ATOM 634 N GLU 42 36.534 32.906 23.574 1.00 0.00 N +ATOM 635 H GLU 42 37.265 32.233 23.726 1.00 0.00 H +ATOM 636 CA GLU 42 35.795 32.783 22.304 1.00 0.00 C +ATOM 637 HA GLU 42 35.112 33.628 22.215 1.00 0.00 H +ATOM 638 CB GLU 42 36.768 32.852 21.111 1.00 0.00 C +ATOM 639 HB2 GLU 42 37.359 31.939 21.083 1.00 0.00 H +ATOM 640 HB3 GLU 42 36.185 32.904 20.190 1.00 0.00 H +ATOM 641 CG GLU 42 37.742 34.046 21.132 1.00 0.00 C +ATOM 642 HG2 GLU 42 38.542 33.823 21.835 1.00 0.00 H +ATOM 643 HG3 GLU 42 38.198 34.176 20.150 1.00 0.00 H +ATOM 644 CD GLU 42 37.078 35.358 21.545 1.00 0.00 C +ATOM 645 OE1 GLU 42 35.962 35.662 21.073 1.00 0.00 O +ATOM 646 OE2 GLU 42 37.603 36.077 22.430 1.00 0.00 O +ATOM 647 C GLU 42 34.925 31.518 22.249 1.00 0.00 C +ATOM 648 O GLU 42 35.177 30.549 22.970 1.00 0.00 O +ATOM 649 N HIP 43 33.822 31.561 21.482 1.00 0.00 N +ATOM 650 H HIP 43 33.691 32.332 20.837 1.00 0.00 H +ATOM 651 CA HIP 43 32.635 30.779 21.863 1.00 0.00 C +ATOM 652 HA HIP 43 32.953 29.805 22.240 1.00 0.00 H +ATOM 653 CB HIP 43 32.036 31.564 23.060 1.00 0.00 C +ATOM 654 HB2 HIP 43 32.780 31.722 23.836 1.00 0.00 H +ATOM 655 HB3 HIP 43 31.707 32.547 22.731 1.00 0.00 H +ATOM 656 CG HIP 43 30.884 30.844 23.669 1.00 0.00 C +ATOM 657 ND1 HIP 43 29.715 30.591 23.008 1.00 0.00 N +ATOM 658 HD1 HIP 43 29.496 30.960 22.088 1.00 0.00 H +ATOM 659 CE1 HIP 43 29.197 29.496 23.532 1.00 0.00 C +ATOM 660 HE1 HIP 43 28.471 28.891 23.007 1.00 0.00 H +ATOM 661 NE2 HIP 43 29.859 29.132 24.623 1.00 0.00 N +ATOM 662 HE2 HIP 43 29.751 28.262 25.124 1.00 0.00 H +ATOM 663 CD2 HIP 43 30.964 29.967 24.715 1.00 0.00 C +ATOM 664 HD2 HIP 43 31.813 29.800 25.339 1.00 0.00 H +ATOM 665 C HIP 43 31.587 30.500 20.744 1.00 0.00 C +ATOM 666 O HIP 43 30.815 31.391 20.404 1.00 0.00 O +ATOM 667 N THR 44 31.412 29.241 20.315 1.00 0.00 N +ATOM 668 H THR 44 32.062 28.545 20.651 1.00 0.00 H +ATOM 669 CA THR 44 30.539 28.792 19.194 1.00 0.00 C +ATOM 670 HA THR 44 30.768 29.416 18.330 1.00 0.00 H +ATOM 671 CB THR 44 30.915 27.341 18.825 1.00 0.00 C +ATOM 672 HB THR 44 30.653 26.672 19.649 1.00 0.00 H +ATOM 673 CG2 THR 44 30.280 26.804 17.538 1.00 0.00 C +ATOM 674 HG21 THR 44 30.421 27.512 16.723 1.00 0.00 H +ATOM 675 HG22 THR 44 30.737 25.852 17.265 1.00 0.00 H +ATOM 676 HG23 THR 44 29.217 26.625 17.692 1.00 0.00 H +ATOM 677 OG1 THR 44 32.307 27.274 18.626 1.00 0.00 O +ATOM 678 HG1 THR 44 32.492 26.533 18.040 1.00 0.00 H +ATOM 679 C THR 44 29.005 28.885 19.426 1.00 0.00 C +ATOM 680 O THR 44 28.541 28.793 20.567 1.00 0.00 O +ATOM 681 N LYS 45 28.231 29.030 18.329 1.00 0.00 N +ATOM 682 H LYS 45 28.718 29.046 17.443 1.00 0.00 H +ATOM 683 CA LYS 45 26.747 29.105 18.236 1.00 0.00 C +ATOM 684 HA LYS 45 26.318 29.062 19.233 1.00 0.00 H +ATOM 685 CB LYS 45 26.374 30.459 17.574 1.00 0.00 C +ATOM 686 HB2 LYS 45 26.571 31.266 18.282 1.00 0.00 H +ATOM 687 HB3 LYS 45 27.024 30.615 16.712 1.00 0.00 H +ATOM 688 CG LYS 45 24.919 30.571 17.071 1.00 0.00 C +ATOM 689 HG2 LYS 45 24.730 29.762 16.369 1.00 0.00 H +ATOM 690 HG3 LYS 45 24.253 30.451 17.926 1.00 0.00 H +ATOM 691 CD LYS 45 24.581 31.864 16.313 1.00 0.00 C +ATOM 692 HD2 LYS 45 24.789 32.715 16.943 1.00 0.00 H +ATOM 693 HD3 LYS 45 25.176 31.930 15.400 1.00 0.00 H +ATOM 694 CE LYS 45 23.091 31.825 15.971 1.00 0.00 C +ATOM 695 HE2 LYS 45 22.923 30.987 15.292 1.00 0.00 H +ATOM 696 HE3 LYS 45 22.532 31.602 16.886 1.00 0.00 H +ATOM 697 NZ LYS 45 22.573 33.072 15.345 1.00 0.00 N +ATOM 698 HZ1 LYS 45 22.962 33.227 14.424 1.00 0.00 H +ATOM 699 HZ2 LYS 45 21.559 32.954 15.239 1.00 0.00 H +ATOM 700 HZ3 LYS 45 22.712 33.892 15.912 1.00 0.00 H +ATOM 701 C LYS 45 26.138 27.945 17.423 1.00 0.00 C +ATOM 702 O LYS 45 26.705 27.569 16.405 1.00 0.00 O +ATOM 703 N ASP 46 24.922 27.524 17.775 1.00 0.00 N +ATOM 704 H ASP 46 24.578 27.808 18.689 1.00 0.00 H +ATOM 705 CA ASP 46 23.873 27.044 16.843 1.00 0.00 C +ATOM 706 HA ASP 46 24.249 27.121 15.818 1.00 0.00 H +ATOM 707 CB ASP 46 23.528 25.569 17.148 1.00 0.00 C +ATOM 708 HB2 ASP 46 24.366 24.916 16.878 1.00 0.00 H +ATOM 709 HB3 ASP 46 23.378 25.489 18.232 1.00 0.00 H +ATOM 710 CG ASP 46 22.266 25.098 16.426 1.00 0.00 C +ATOM 711 OD1 ASP 46 21.392 24.557 17.117 1.00 0.00 O +ATOM 712 OD2 ASP 46 22.087 25.409 15.235 1.00 0.00 O +ATOM 713 C ASP 46 22.613 27.944 16.957 1.00 0.00 C +ATOM 714 O ASP 46 22.294 28.456 18.027 1.00 0.00 O +ATOM 715 N ASP 47 21.897 28.140 15.849 1.00 0.00 N +ATOM 716 H ASP 47 22.146 27.562 15.057 1.00 0.00 H +ATOM 717 CA ASP 47 20.588 28.850 15.794 1.00 0.00 C +ATOM 718 HA ASP 47 20.554 29.519 16.646 1.00 0.00 H +ATOM 719 CB ASP 47 20.475 29.756 14.572 1.00 0.00 C +ATOM 720 HB2 ASP 47 21.461 30.108 14.286 1.00 0.00 H +ATOM 721 HB3 ASP 47 20.085 29.213 13.702 1.00 0.00 H +ATOM 722 CG ASP 47 19.637 30.995 14.888 1.00 0.00 C +ATOM 723 OD1 ASP 47 18.471 31.071 14.473 1.00 0.00 O +ATOM 724 OD2 ASP 47 20.169 31.881 15.573 1.00 0.00 O +ATOM 725 C ASP 47 19.357 27.933 15.861 1.00 0.00 C +ATOM 726 O ASP 47 18.316 28.355 16.366 1.00 0.00 O +ATOM 727 N ALA 48 19.457 26.676 15.411 1.00 0.00 N +ATOM 728 H ALA 48 20.368 26.307 15.139 1.00 0.00 H +ATOM 729 CA ALA 48 18.317 25.752 15.378 1.00 0.00 C +ATOM 730 HA ALA 48 17.480 26.224 14.859 1.00 0.00 H +ATOM 731 CB ALA 48 18.730 24.511 14.577 1.00 0.00 C +ATOM 732 HB1 ALA 48 19.555 24.007 15.072 1.00 0.00 H +ATOM 733 HB2 ALA 48 17.894 23.821 14.498 1.00 0.00 H +ATOM 734 HB3 ALA 48 19.047 24.788 13.575 1.00 0.00 H +ATOM 735 C ALA 48 17.839 25.388 16.792 1.00 0.00 C +ATOM 736 O ALA 48 16.640 25.354 17.075 1.00 0.00 O +ATOM 737 N THR 49 18.778 25.160 17.711 1.00 0.00 N +ATOM 738 H THR 49 19.736 25.037 17.377 1.00 0.00 H +ATOM 739 CA THR 49 18.557 25.051 19.154 1.00 0.00 C +ATOM 740 HA THR 49 17.530 24.709 19.314 1.00 0.00 H +ATOM 741 CB THR 49 19.524 24.022 19.753 1.00 0.00 C +ATOM 742 HB THR 49 19.326 23.946 20.820 1.00 0.00 H +ATOM 743 CG2 THR 49 19.398 22.626 19.153 1.00 0.00 C +ATOM 744 HG21 THR 49 19.665 22.630 18.098 1.00 0.00 H +ATOM 745 HG22 THR 49 20.090 21.979 19.684 1.00 0.00 H +ATOM 746 HG23 THR 49 18.383 22.250 19.269 1.00 0.00 H +ATOM 747 OG1 THR 49 20.861 24.413 19.589 1.00 0.00 O +ATOM 748 HG1 THR 49 21.066 24.338 18.620 1.00 0.00 H +ATOM 749 C THR 49 18.714 26.378 19.910 1.00 0.00 C +ATOM 750 O THR 49 18.618 26.395 21.136 1.00 0.00 O +ATOM 751 N LYS 50 18.968 27.490 19.206 1.00 0.00 N +ATOM 752 H LYS 50 18.980 27.378 18.203 1.00 0.00 H +ATOM 753 CA LYS 50 19.202 28.853 19.749 1.00 0.00 C +ATOM 754 HA LYS 50 19.637 29.449 18.943 1.00 0.00 H +ATOM 755 CB LYS 50 17.845 29.491 20.149 1.00 0.00 C +ATOM 756 HB2 LYS 50 17.408 28.860 20.925 1.00 0.00 H +ATOM 757 HB3 LYS 50 18.038 30.471 20.598 1.00 0.00 H +ATOM 758 CG LYS 50 16.812 29.667 19.017 1.00 0.00 C +ATOM 759 HG2 LYS 50 16.742 28.752 18.424 1.00 0.00 H +ATOM 760 HG3 LYS 50 15.841 29.837 19.491 1.00 0.00 H +ATOM 761 CD LYS 50 17.113 30.878 18.105 1.00 0.00 C +ATOM 762 HD2 LYS 50 17.122 31.775 18.732 1.00 0.00 H +ATOM 763 HD3 LYS 50 18.108 30.766 17.643 1.00 0.00 H +ATOM 764 CE LYS 50 16.028 31.055 17.026 1.00 0.00 C +ATOM 765 HE2 LYS 50 15.056 30.783 17.436 1.00 0.00 H +ATOM 766 HE3 LYS 50 15.985 32.104 16.719 1.00 0.00 H +ATOM 767 NZ LYS 50 16.278 30.207 15.837 1.00 0.00 N +ATOM 768 HZ1 LYS 50 16.593 29.271 16.077 1.00 0.00 H +ATOM 769 HZ2 LYS 50 15.486 30.195 15.189 1.00 0.00 H +ATOM 770 HZ3 LYS 50 17.047 30.589 15.285 1.00 0.00 H +ATOM 771 C LYS 50 20.238 28.865 20.885 1.00 0.00 C +ATOM 772 O LYS 50 20.046 29.552 21.897 1.00 0.00 O +ATOM 773 N THR 51 21.297 28.053 20.758 1.00 0.00 N +ATOM 774 H THR 51 21.447 27.626 19.852 1.00 0.00 H +ATOM 775 CA THR 51 22.186 27.666 21.861 1.00 0.00 C +ATOM 776 HA THR 51 21.925 28.266 22.727 1.00 0.00 H +ATOM 777 CB THR 51 21.978 26.182 22.276 1.00 0.00 C +ATOM 778 HB THR 51 22.103 25.558 21.392 1.00 0.00 H +ATOM 779 CG2 THR 51 22.971 25.680 23.326 1.00 0.00 C +ATOM 780 HG21 THR 51 22.987 26.306 24.214 1.00 0.00 H +ATOM 781 HG22 THR 51 22.722 24.667 23.637 1.00 0.00 H +ATOM 782 HG23 THR 51 23.978 25.634 22.923 1.00 0.00 H +ATOM 783 OG1 THR 51 20.695 26.001 22.835 1.00 0.00 O +ATOM 784 HG1 THR 51 20.033 26.112 22.126 1.00 0.00 H +ATOM 785 C THR 51 23.691 27.954 21.606 1.00 0.00 C +ATOM 786 O THR 51 24.250 27.693 20.552 1.00 0.00 O +ATOM 787 N PHE 52 24.339 28.470 22.636 1.00 0.00 N +ATOM 788 H PHE 52 23.782 28.767 23.426 1.00 0.00 H +ATOM 789 CA PHE 52 25.782 28.625 22.774 1.00 0.00 C +ATOM 790 HA PHE 52 26.236 28.756 21.800 1.00 0.00 H +ATOM 791 CB PHE 52 25.970 29.903 23.630 1.00 0.00 C +ATOM 792 HB2 PHE 52 25.178 29.934 24.366 1.00 0.00 H +ATOM 793 HB3 PHE 52 26.858 29.811 24.241 1.00 0.00 H +ATOM 794 CG PHE 52 25.990 31.261 22.933 1.00 0.00 C +ATOM 795 CD1 PHE 52 25.313 32.345 23.501 1.00 0.00 C +ATOM 796 HD1 PHE 52 24.705 32.206 24.369 1.00 0.00 H +ATOM 797 CE1 PHE 52 25.445 33.639 22.970 1.00 0.00 C +ATOM 798 HE1 PHE 52 24.940 34.476 23.432 1.00 0.00 H +ATOM 799 CZ PHE 52 26.270 33.846 21.867 1.00 0.00 C +ATOM 800 HZ PHE 52 26.395 34.832 21.472 1.00 0.00 H +ATOM 801 CE2 PHE 52 26.935 32.771 21.258 1.00 0.00 C +ATOM 802 HE2 PHE 52 27.570 32.946 20.399 1.00 0.00 H +ATOM 803 CD2 PHE 52 26.777 31.489 21.786 1.00 0.00 C +ATOM 804 HD2 PHE 52 27.285 30.683 21.316 1.00 0.00 H +ATOM 805 C PHE 52 26.423 27.398 23.470 1.00 0.00 C +ATOM 806 O PHE 52 26.087 27.106 24.623 1.00 0.00 O +ATOM 807 N THR 53 27.436 26.751 22.856 1.00 0.00 N +ATOM 808 H THR 53 27.650 26.995 21.888 1.00 0.00 H +ATOM 809 CA THR 53 28.305 25.685 23.436 1.00 0.00 C +ATOM 810 HA THR 53 28.048 25.541 24.487 1.00 0.00 H +ATOM 811 CB THR 53 28.082 24.339 22.718 1.00 0.00 C +ATOM 812 HB THR 53 28.786 23.607 23.118 1.00 0.00 H +ATOM 813 CG2 THR 53 26.676 23.788 22.896 1.00 0.00 C +ATOM 814 HG21 THR 53 25.950 24.428 22.394 1.00 0.00 H +ATOM 815 HG22 THR 53 26.625 22.786 22.468 1.00 0.00 H +ATOM 816 HG23 THR 53 26.442 23.727 23.958 1.00 0.00 H +ATOM 817 OG1 THR 53 28.319 24.486 21.337 1.00 0.00 O +ATOM 818 HG1 THR 53 28.141 23.636 20.917 1.00 0.00 H +ATOM 819 C THR 53 29.812 26.007 23.366 1.00 0.00 C +ATOM 820 O THR 53 30.224 26.906 22.642 1.00 0.00 O +ATOM 821 N THR 54 30.650 25.304 24.140 1.00 0.00 N +ATOM 822 H THR 54 30.284 24.592 24.758 1.00 0.00 H +ATOM 823 CA THR 54 32.131 25.256 23.974 1.00 0.00 C +ATOM 824 HA THR 54 32.450 26.113 23.366 1.00 0.00 H +ATOM 825 CB THR 54 32.874 25.346 25.323 1.00 0.00 C +ATOM 826 HB THR 54 33.948 25.303 25.140 1.00 0.00 H +ATOM 827 CG2 THR 54 32.594 26.656 26.070 1.00 0.00 C +ATOM 828 HG21 THR 54 31.547 26.724 26.352 1.00 0.00 H +ATOM 829 HG22 THR 54 33.190 26.709 26.976 1.00 0.00 H +ATOM 830 HG23 THR 54 32.855 27.511 25.448 1.00 0.00 H +ATOM 831 OG1 THR 54 32.529 24.279 26.170 1.00 0.00 O +ATOM 832 HG1 THR 54 32.961 23.475 25.847 1.00 0.00 H +ATOM 833 C THR 54 32.580 23.997 23.228 1.00 0.00 C +ATOM 834 O THR 54 31.810 23.044 23.101 1.00 0.00 O +ATOM 835 N ALA 55 33.833 23.981 22.756 1.00 0.00 N +ATOM 836 H ALA 55 34.417 24.785 22.911 1.00 0.00 H +ATOM 837 CA ALA 55 34.476 22.803 22.162 1.00 0.00 C +ATOM 838 HA ALA 55 33.773 22.349 21.450 1.00 0.00 H +ATOM 839 CB ALA 55 35.709 23.293 21.391 1.00 0.00 C +ATOM 840 HB1 ALA 55 36.439 23.718 22.088 1.00 0.00 H +ATOM 841 HB2 ALA 55 36.172 22.454 20.859 1.00 0.00 H +ATOM 842 HB3 ALA 55 35.413 24.049 20.657 1.00 0.00 H +ATOM 843 C ALA 55 34.820 21.700 23.201 1.00 0.00 C +ATOM 844 O ALA 55 34.564 21.870 24.395 1.00 0.00 O +ATOM 845 N GLU 56 35.391 20.590 22.719 1.00 0.00 N +ATOM 846 H GLU 56 35.619 20.592 21.742 1.00 0.00 H +ATOM 847 CA GLU 56 35.949 19.442 23.462 1.00 0.00 C +ATOM 848 HA GLU 56 35.837 19.619 24.529 1.00 0.00 H +ATOM 849 CB GLU 56 35.174 18.158 23.066 1.00 0.00 C +ATOM 850 HB2 GLU 56 34.120 18.283 23.304 1.00 0.00 H +ATOM 851 HB3 GLU 56 35.231 18.083 21.976 1.00 0.00 H +ATOM 852 CG GLU 56 35.683 16.816 23.642 1.00 0.00 C +ATOM 853 HG2 GLU 56 35.524 16.058 22.873 1.00 0.00 H +ATOM 854 HG3 GLU 56 36.759 16.858 23.777 1.00 0.00 H +ATOM 855 CD GLU 56 35.019 16.305 24.943 1.00 0.00 C +ATOM 856 OE1 GLU 56 35.650 15.485 25.657 1.00 0.00 O +ATOM 857 OE2 GLU 56 33.830 16.592 25.213 1.00 0.00 O +ATOM 858 C GLU 56 37.466 19.312 23.206 1.00 0.00 C +ATOM 859 O GLU 56 38.207 19.293 24.214 1.00 0.00 O +ATOM 860 OXT GLU 56 37.851 19.278 22.005 1.00 0.00 O +HETATM 861 ZN ZN1 57 26.252 32.500 29.543 1.00 0.00 Zn +HETATM 862 N AN1 58 27.946 33.231 30.455 1.00 0.00 N +HETATM 863 C AN1 58 30.237 34.165 31.270 1.00 0.00 C +HETATM 864 C1 AN1 58 28.941 33.637 30.825 1.00 0.00 C +HETATM 865 H AN1 58 30.152 34.562 32.288 1.00 0.00 H +HETATM 866 H1 AN1 58 30.560 34.975 30.607 1.00 0.00 H +HETATM 867 H2 AN1 58 30.993 33.374 31.265 1.00 0.00 H +HETATM 868 N1 AZI 59 30.423 28.665 29.019 1.00 0.00 N +HETATM 869 N2 AZI 59 29.754 28.732 30.028 1.00 0.00 N +HETATM 870 N3 AZI 59 29.036 28.794 31.085 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 69 71 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 68 73 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 861 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 105 101 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 142 140 +CONECT 140 139 +CONECT 141 139 +CONECT 142 143 139 144 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 207 188 189 +CONECT 188 187 +CONECT 189 187 191 192 190 +CONECT 190 189 +CONECT 191 189 +CONECT 192 206 189 193 +CONECT 193 192 195 194 +CONECT 194 193 +CONECT 195 197 193 196 +CONECT 196 195 +CONECT 197 198 206 195 +CONECT 198 200 199 197 +CONECT 199 198 +CONECT 200 201 202 198 +CONECT 201 200 +CONECT 202 203 200 204 +CONECT 203 202 +CONECT 204 202 205 206 +CONECT 205 204 +CONECT 206 204 197 192 +CONECT 207 209 187 208 +CONECT 208 207 +CONECT 209 210 211 207 +CONECT 210 209 +CONECT 211 212 223 209 213 +CONECT 212 211 +CONECT 213 211 219 215 214 +CONECT 214 213 +CONECT 215 218 213 216 217 +CONECT 216 215 +CONECT 217 215 +CONECT 218 215 +CONECT 219 220 222 213 221 +CONECT 220 219 +CONECT 221 219 +CONECT 222 219 +CONECT 223 224 225 211 +CONECT 224 223 +CONECT 225 227 223 226 +CONECT 226 225 +CONECT 227 228 245 229 225 +CONECT 228 227 +CONECT 229 232 227 230 231 +CONECT 230 229 +CONECT 231 229 +CONECT 232 234 233 235 229 +CONECT 233 232 +CONECT 234 232 +CONECT 235 236 232 237 238 +CONECT 236 235 +CONECT 237 235 +CONECT 238 235 240 241 239 +CONECT 239 238 +CONECT 240 238 +CONECT 241 244 238 242 243 +CONECT 242 241 +CONECT 243 241 +CONECT 244 241 +CONECT 245 246 227 247 +CONECT 246 245 +CONECT 247 245 249 248 +CONECT 248 247 +CONECT 249 252 247 250 251 +CONECT 250 249 +CONECT 251 249 +CONECT 252 253 254 249 +CONECT 253 252 +CONECT 254 256 252 255 +CONECT 255 254 +CONECT 256 258 257 268 254 +CONECT 257 256 +CONECT 258 264 259 260 256 +CONECT 259 258 +CONECT 260 262 258 261 263 +CONECT 261 260 +CONECT 262 260 +CONECT 263 260 +CONECT 264 266 265 267 258 +CONECT 265 264 +CONECT 266 264 +CONECT 267 264 +CONECT 268 256 270 269 +CONECT 269 268 +CONECT 270 280 271 268 +CONECT 271 272 270 281 274 +CONECT 272 273 287 271 +CONECT 273 272 +CONECT 274 271 275 282 283 +CONECT 275 276 277 274 +CONECT 276 279 285 275 +CONECT 277 278 275 284 +CONECT 278 279 286 277 +CONECT 279 861 278 276 +CONECT 280 270 +CONECT 281 271 +CONECT 282 274 +CONECT 283 274 +CONECT 284 277 +CONECT 285 276 +CONECT 286 278 +CONECT 287 289 272 288 +CONECT 288 287 +CONECT 289 290 291 299 287 +CONECT 290 289 +CONECT 291 292 293 289 297 +CONECT 292 291 +CONECT 293 296 295 291 294 +CONECT 294 293 +CONECT 295 293 +CONECT 296 293 +CONECT 297 291 298 +CONECT 298 297 +CONECT 299 301 289 300 +CONECT 300 299 +CONECT 301 311 302 299 +CONECT 302 303 305 301 312 +CONECT 303 304 318 302 +CONECT 304 303 +CONECT 305 313 314 302 306 +CONECT 306 305 307 308 +CONECT 307 316 306 310 +CONECT 308 306 315 309 +CONECT 309 310 308 317 +CONECT 310 307 861 309 +CONECT 311 301 +CONECT 312 302 +CONECT 313 305 +CONECT 314 305 +CONECT 315 308 +CONECT 316 307 +CONECT 317 309 +CONECT 318 320 303 319 +CONECT 319 318 +CONECT 320 331 321 318 322 +CONECT 321 320 +CONECT 322 320 325 324 323 +CONECT 323 322 +CONECT 324 322 +CONECT 325 328 327 322 326 +CONECT 326 325 +CONECT 327 325 +CONECT 328 329 330 325 +CONECT 329 328 +CONECT 330 328 +CONECT 331 333 332 320 +CONECT 332 331 +CONECT 333 335 334 331 +CONECT 334 333 +CONECT 335 341 337 336 333 +CONECT 336 335 +CONECT 337 339 338 335 340 +CONECT 338 337 +CONECT 339 337 +CONECT 340 337 +CONECT 341 343 342 335 +CONECT 342 341 +CONECT 343 345 344 341 +CONECT 344 343 +CONECT 345 357 347 346 343 +CONECT 346 345 +CONECT 347 348 353 345 349 +CONECT 348 347 +CONECT 349 347 351 352 350 +CONECT 350 349 +CONECT 351 349 +CONECT 352 349 +CONECT 353 354 355 347 356 +CONECT 354 353 +CONECT 355 353 +CONECT 356 353 +CONECT 357 358 359 345 +CONECT 358 357 +CONECT 359 361 357 360 +CONECT 360 359 +CONECT 361 363 362 369 359 +CONECT 362 361 +CONECT 363 366 364 365 361 +CONECT 364 363 +CONECT 365 363 +CONECT 366 367 368 363 +CONECT 367 366 +CONECT 368 366 +CONECT 369 361 371 370 +CONECT 370 369 +CONECT 371 372 369 373 +CONECT 372 371 +CONECT 373 371 375 388 374 +CONECT 374 373 +CONECT 375 377 376 373 378 +CONECT 376 375 +CONECT 377 375 +CONECT 378 384 375 380 379 +CONECT 379 378 +CONECT 380 381 378 382 383 +CONECT 381 380 +CONECT 382 380 +CONECT 383 380 +CONECT 384 387 386 385 378 +CONECT 385 384 +CONECT 386 384 +CONECT 387 384 +CONECT 388 390 373 389 +CONECT 389 388 +CONECT 390 391 392 388 +CONECT 391 390 +CONECT 392 394 393 390 398 +CONECT 393 392 +CONECT 394 397 395 396 392 +CONECT 395 394 +CONECT 396 394 +CONECT 397 394 +CONECT 398 392 399 400 +CONECT 399 398 +CONECT 400 398 401 402 +CONECT 401 400 +CONECT 402 400 403 404 413 +CONECT 403 402 +CONECT 404 407 402 405 406 +CONECT 405 404 +CONECT 406 404 +CONECT 407 408 409 410 404 +CONECT 408 407 +CONECT 409 407 +CONECT 410 412 407 411 +CONECT 411 410 +CONECT 412 410 +CONECT 413 402 415 414 +CONECT 414 413 +CONECT 415 416 413 417 +CONECT 416 415 +CONECT 417 415 419 423 418 +CONECT 418 417 +CONECT 419 420 422 417 421 +CONECT 420 419 +CONECT 421 419 +CONECT 422 419 +CONECT 423 425 417 424 +CONECT 424 423 +CONECT 425 426 427 423 +CONECT 426 425 +CONECT 427 429 425 428 438 +CONECT 428 427 +CONECT 429 430 431 432 427 +CONECT 430 429 +CONECT 431 429 +CONECT 432 435 429 433 434 +CONECT 433 432 +CONECT 434 432 +CONECT 435 437 436 432 +CONECT 436 435 +CONECT 437 435 +CONECT 438 427 440 439 +CONECT 439 438 +CONECT 440 441 438 442 +CONECT 441 440 +CONECT 442 440 444 443 460 +CONECT 443 442 +CONECT 444 447 445 446 442 +CONECT 445 444 +CONECT 446 444 +CONECT 447 449 450 448 444 +CONECT 448 447 +CONECT 449 447 +CONECT 450 453 451 452 447 +CONECT 451 450 +CONECT 452 450 +CONECT 453 456 455 454 450 +CONECT 454 453 +CONECT 455 453 +CONECT 456 458 459 457 453 +CONECT 457 456 +CONECT 458 456 +CONECT 459 456 +CONECT 460 442 462 461 +CONECT 461 460 +CONECT 462 463 460 464 +CONECT 463 462 +CONECT 464 462 466 465 480 +CONECT 465 464 +CONECT 466 469 467 464 468 +CONECT 467 466 +CONECT 468 466 +CONECT 469 470 478 466 +CONECT 470 472 471 469 +CONECT 471 470 +CONECT 472 473 474 470 +CONECT 473 472 +CONECT 474 475 472 476 +CONECT 475 474 +CONECT 476 474 477 478 +CONECT 477 476 +CONECT 478 476 469 479 +CONECT 479 478 +CONECT 480 464 482 481 +CONECT 481 480 +CONECT 482 483 484 480 +CONECT 483 482 +CONECT 484 486 482 494 485 +CONECT 485 484 +CONECT 486 487 492 488 484 +CONECT 487 486 +CONECT 488 490 486 491 489 +CONECT 489 488 +CONECT 490 488 +CONECT 491 488 +CONECT 492 493 486 +CONECT 493 492 +CONECT 494 496 484 495 +CONECT 495 494 +CONECT 496 497 498 494 +CONECT 497 496 +CONECT 498 500 496 499 516 +CONECT 499 498 +CONECT 500 503 501 502 498 +CONECT 501 500 +CONECT 502 500 +CONECT 503 506 505 504 500 +CONECT 504 503 +CONECT 505 503 +CONECT 506 509 507 508 503 +CONECT 507 506 +CONECT 508 506 +CONECT 509 511 510 512 506 +CONECT 510 509 +CONECT 511 509 +CONECT 512 514 509 515 513 +CONECT 513 512 +CONECT 514 512 +CONECT 515 512 +CONECT 516 498 518 517 +CONECT 517 516 +CONECT 518 519 516 520 +CONECT 519 518 +CONECT 520 518 522 521 526 +CONECT 521 520 +CONECT 522 525 523 520 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 522 +CONECT 526 520 528 527 +CONECT 527 526 +CONECT 528 529 526 530 +CONECT 529 528 +CONECT 530 528 532 536 531 +CONECT 531 530 +CONECT 532 533 535 530 534 +CONECT 533 532 +CONECT 534 532 +CONECT 535 532 +CONECT 536 538 530 537 +CONECT 537 536 +CONECT 538 539 540 536 +CONECT 539 538 +CONECT 540 542 538 546 541 +CONECT 541 540 +CONECT 542 543 545 544 540 +CONECT 543 542 +CONECT 544 542 +CONECT 545 542 +CONECT 546 540 548 547 +CONECT 547 546 +CONECT 548 549 546 550 +CONECT 549 548 +CONECT 550 552 548 551 560 +CONECT 551 550 +CONECT 552 555 553 554 550 +CONECT 553 552 +CONECT 554 552 +CONECT 555 557 556 552 +CONECT 556 555 +CONECT 557 558 559 555 +CONECT 558 557 +CONECT 559 557 +CONECT 560 550 562 561 +CONECT 561 560 +CONECT 562 563 560 564 +CONECT 563 562 +CONECT 564 562 566 565 572 +CONECT 565 564 +CONECT 566 569 567 564 568 +CONECT 567 566 +CONECT 568 566 +CONECT 569 571 570 566 +CONECT 570 569 +CONECT 571 569 +CONECT 572 564 574 573 +CONECT 573 572 +CONECT 574 575 572 576 +CONECT 575 574 +CONECT 576 574 578 591 577 +CONECT 577 576 +CONECT 578 580 579 576 581 +CONECT 579 578 +CONECT 580 578 +CONECT 581 578 587 582 583 +CONECT 582 581 +CONECT 583 581 584 585 586 +CONECT 584 583 +CONECT 585 583 +CONECT 586 583 +CONECT 587 588 590 589 581 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 +CONECT 591 593 576 592 +CONECT 592 591 +CONECT 593 594 595 591 +CONECT 594 593 +CONECT 595 598 593 597 596 +CONECT 596 595 +CONECT 597 595 +CONECT 598 600 599 595 +CONECT 599 598 +CONECT 600 602 601 598 +CONECT 601 600 +CONECT 602 613 603 604 600 +CONECT 603 602 +CONECT 604 606 602 605 607 +CONECT 605 604 +CONECT 606 604 +CONECT 607 604 608 610 609 +CONECT 608 607 +CONECT 609 607 +CONECT 610 612 607 611 +CONECT 611 610 +CONECT 612 610 +CONECT 613 615 614 602 +CONECT 614 613 +CONECT 615 617 616 613 +CONECT 616 615 +CONECT 617 625 619 618 615 +CONECT 618 617 +CONECT 619 622 620 621 617 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 619 +CONECT 623 622 +CONECT 624 622 +CONECT 625 626 627 617 +CONECT 626 625 +CONECT 627 629 625 628 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 636 635 632 +CONECT 635 634 +CONECT 636 638 637 647 634 +CONECT 637 636 +CONECT 638 640 639 641 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 638 644 642 +CONECT 642 641 +CONECT 643 641 +CONECT 644 645 641 646 +CONECT 645 644 +CONECT 646 644 +CONECT 647 649 636 648 +CONECT 648 647 +CONECT 649 650 651 647 +CONECT 650 649 +CONECT 651 665 649 652 653 +CONECT 652 651 +CONECT 653 651 655 656 654 +CONECT 654 653 +CONECT 655 653 +CONECT 656 657 653 663 +CONECT 657 658 659 656 +CONECT 658 657 +CONECT 659 660 657 661 +CONECT 660 659 +CONECT 661 659 663 662 +CONECT 662 661 +CONECT 663 656 661 664 +CONECT 664 663 +CONECT 665 667 666 651 +CONECT 666 665 +CONECT 667 669 668 665 +CONECT 668 667 +CONECT 669 670 671 679 667 +CONECT 670 669 +CONECT 671 673 677 669 672 +CONECT 672 671 +CONECT 673 674 675 676 671 +CONECT 674 673 +CONECT 675 673 +CONECT 676 673 +CONECT 677 678 671 +CONECT 678 677 +CONECT 679 681 669 680 +CONECT 680 679 +CONECT 681 682 683 679 +CONECT 682 681 +CONECT 683 701 685 681 684 +CONECT 684 683 +CONECT 685 687 688 683 686 +CONECT 686 685 +CONECT 687 685 +CONECT 688 691 689 685 690 +CONECT 689 688 +CONECT 690 688 +CONECT 691 693 694 692 688 +CONECT 692 691 +CONECT 693 691 +CONECT 694 695 697 691 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 698 699 700 694 +CONECT 698 697 +CONECT 699 697 +CONECT 700 697 +CONECT 701 702 703 683 +CONECT 702 701 +CONECT 703 705 701 704 +CONECT 704 703 +CONECT 705 706 713 707 703 +CONECT 706 705 +CONECT 707 710 705 708 709 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 711 707 +CONECT 711 710 +CONECT 712 710 +CONECT 713 715 705 714 +CONECT 714 713 +CONECT 715 716 717 713 +CONECT 716 715 +CONECT 717 719 715 725 718 +CONECT 718 717 +CONECT 719 721 720 722 717 +CONECT 720 719 +CONECT 721 719 +CONECT 722 723 719 724 +CONECT 723 722 +CONECT 724 722 +CONECT 725 727 717 726 +CONECT 726 725 +CONECT 727 728 729 725 +CONECT 728 727 +CONECT 729 731 730 727 735 +CONECT 730 729 +CONECT 731 734 733 732 729 +CONECT 732 731 +CONECT 733 731 +CONECT 734 731 +CONECT 735 729 736 737 +CONECT 736 735 +CONECT 737 735 738 739 +CONECT 738 737 +CONECT 739 737 740 741 749 +CONECT 740 739 +CONECT 741 743 739 747 742 +CONECT 742 741 +CONECT 743 744 746 745 741 +CONECT 744 743 +CONECT 745 743 +CONECT 746 743 +CONECT 747 748 741 +CONECT 748 747 +CONECT 749 739 751 750 +CONECT 750 749 +CONECT 751 752 753 749 +CONECT 752 751 +CONECT 753 754 751 755 771 +CONECT 754 753 +CONECT 755 758 753 757 756 +CONECT 756 755 +CONECT 757 755 +CONECT 758 761 759 760 755 +CONECT 759 758 +CONECT 760 758 +CONECT 761 764 763 762 758 +CONECT 762 761 +CONECT 763 761 +CONECT 764 767 766 765 761 +CONECT 765 764 +CONECT 766 764 +CONECT 767 769 770 768 764 +CONECT 768 767 +CONECT 769 767 +CONECT 770 767 +CONECT 771 753 773 772 +CONECT 772 771 +CONECT 773 774 771 775 +CONECT 774 773 +CONECT 775 773 785 777 776 +CONECT 776 775 +CONECT 777 778 775 783 779 +CONECT 778 777 +CONECT 779 777 782 781 780 +CONECT 780 779 +CONECT 781 779 +CONECT 782 779 +CONECT 783 784 777 +CONECT 784 783 +CONECT 785 786 775 787 +CONECT 786 785 +CONECT 787 785 789 788 +CONECT 788 787 +CONECT 789 790 787 805 791 +CONECT 790 789 +CONECT 791 789 794 793 792 +CONECT 792 791 +CONECT 793 791 +CONECT 794 803 795 791 +CONECT 795 794 797 796 +CONECT 796 795 +CONECT 797 799 798 795 +CONECT 798 797 +CONECT 799 801 800 797 +CONECT 800 799 +CONECT 801 802 803 799 +CONECT 802 801 +CONECT 803 801 804 794 +CONECT 804 803 +CONECT 805 789 807 806 +CONECT 806 805 +CONECT 807 808 809 805 +CONECT 808 807 +CONECT 809 811 807 819 810 +CONECT 810 809 +CONECT 811 817 813 812 809 +CONECT 812 811 +CONECT 813 814 815 811 816 +CONECT 814 813 +CONECT 815 813 +CONECT 816 813 +CONECT 817 818 811 +CONECT 818 817 +CONECT 819 820 809 821 +CONECT 820 819 +CONECT 821 819 823 822 +CONECT 822 821 +CONECT 823 833 824 821 825 +CONECT 824 823 +CONECT 825 823 826 827 831 +CONECT 826 825 +CONECT 827 825 830 828 829 +CONECT 828 827 +CONECT 829 827 +CONECT 830 827 +CONECT 831 825 832 +CONECT 832 831 +CONECT 833 835 834 823 +CONECT 834 833 +CONECT 835 837 836 833 +CONECT 836 835 +CONECT 837 839 838 835 843 +CONECT 838 837 +CONECT 839 842 841 840 837 +CONECT 840 839 +CONECT 841 839 +CONECT 842 839 +CONECT 843 837 845 844 +CONECT 844 843 +CONECT 845 846 843 847 +CONECT 846 845 +CONECT 847 845 849 858 848 +CONECT 848 847 +CONECT 849 851 850 847 852 +CONECT 850 849 +CONECT 851 849 +CONECT 852 853 849 854 855 +CONECT 853 852 +CONECT 854 852 +CONECT 855 852 857 856 +CONECT 856 855 +CONECT 857 855 +CONECT 858 860 847 859 +CONECT 859 858 +CONECT 860 858 +CONECT 861 87 310 862 279 +CONECT 862 861 864 +CONECT 863 866 864 867 865 +CONECT 864 862 863 +CONECT 865 863 +CONECT 866 863 +CONECT 867 863 +CONECT 868 869 +CONECT 869 868 870 +CONECT 870 869 +MASTER 0 0 0 0 0 0 0 0 870 0 870 0 +END diff --git a/tests/nsga2/min_mol_iter_2.pdb b/tests/nsga2/min_mol_iter_2.pdb new file mode 100644 index 0000000..48f1266 --- /dev/null +++ b/tests/nsga2/min_mol_iter_2.pdb @@ -0,0 +1,1759 @@ +COMPND fitness: -3.7512 86.6599999999994 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 56.210 58.077 52.044 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 14.606 37.843 23.332 1.00 0.00 N +ATOM 2 H1 MET 1 14.561 38.256 24.258 1.00 0.00 H +ATOM 3 H2 MET 1 13.827 38.164 22.783 1.00 0.00 H +ATOM 4 H3 MET 1 15.475 38.170 22.930 1.00 0.00 H +ATOM 5 CA MET 1 14.630 36.376 23.447 1.00 0.00 C +ATOM 6 HA MET 1 13.686 36.053 23.885 1.00 0.00 H +ATOM 7 CB MET 1 14.779 35.725 22.058 1.00 0.00 C +ATOM 8 HB2 MET 1 13.905 35.984 21.460 1.00 0.00 H +ATOM 9 HB3 MET 1 15.663 36.132 21.565 1.00 0.00 H +ATOM 10 CG MET 1 14.914 34.195 22.110 1.00 0.00 C +ATOM 11 HG2 MET 1 15.809 33.940 22.680 1.00 0.00 H +ATOM 12 HG3 MET 1 14.049 33.777 22.629 1.00 0.00 H +ATOM 13 SD MET 1 15.062 33.382 20.493 1.00 0.00 S +ATOM 14 CE MET 1 13.359 33.515 19.876 1.00 0.00 C +ATOM 15 HE1 MET 1 13.058 34.560 19.812 1.00 0.00 H +ATOM 16 HE2 MET 1 13.297 33.070 18.883 1.00 0.00 H +ATOM 17 HE3 MET 1 12.684 32.982 20.546 1.00 0.00 H +ATOM 18 C MET 1 15.751 35.940 24.383 1.00 0.00 C +ATOM 19 O MET 1 16.896 36.328 24.187 1.00 0.00 O +ATOM 20 N GLN 2 15.440 35.074 25.351 1.00 0.00 N +ATOM 21 H GLN 2 14.472 34.834 25.495 1.00 0.00 H +ATOM 22 CA GLN 2 16.413 34.386 26.209 1.00 0.00 C +ATOM 23 HA GLN 2 17.163 35.101 26.548 1.00 0.00 H +ATOM 24 CB GLN 2 15.660 33.839 27.442 1.00 0.00 C +ATOM 25 HB2 GLN 2 14.728 33.382 27.108 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.234 33.053 27.924 1.00 0.00 H +ATOM 27 CG GLN 2 15.332 34.909 28.498 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.887 35.771 28.013 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.582 34.501 29.177 1.00 0.00 H +ATOM 30 CD GLN 2 16.524 35.361 29.339 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.655 34.909 29.191 1.00 0.00 O +ATOM 32 NE2 GLN 2 16.312 36.233 30.300 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.089 36.502 30.869 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.408 36.678 30.366 1.00 0.00 H +ATOM 35 C GLN 2 17.162 33.270 25.440 1.00 0.00 C +ATOM 36 O GLN 2 16.821 32.092 25.554 1.00 0.00 O +ATOM 37 N TYR 3 18.180 33.629 24.652 1.00 0.00 N +ATOM 38 H TYR 3 18.418 34.618 24.614 1.00 0.00 H +ATOM 39 CA TYR 3 19.046 32.686 23.920 1.00 0.00 C +ATOM 40 HA TYR 3 18.430 32.099 23.237 1.00 0.00 H +ATOM 41 CB TYR 3 20.075 33.468 23.090 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.560 34.213 23.724 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.851 32.777 22.757 1.00 0.00 H +ATOM 44 CG TYR 3 19.504 34.151 21.860 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.421 33.432 20.651 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.751 32.402 20.611 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.934 34.054 19.487 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.898 33.509 18.555 1.00 0.00 H +ATOM 49 CZ TYR 3 18.516 35.401 19.533 1.00 0.00 C +ATOM 50 OH TYR 3 18.068 36.006 18.402 1.00 0.00 O +ATOM 51 HH TYR 3 18.265 35.478 17.625 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.582 36.118 20.747 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.264 37.151 20.769 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.081 35.495 21.908 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.142 36.054 22.834 1.00 0.00 H +ATOM 56 C TYR 3 19.758 31.718 24.880 1.00 0.00 C +ATOM 57 O TYR 3 20.253 32.137 25.927 1.00 0.00 O +ATOM 58 N LYS 4 19.814 30.420 24.558 1.00 0.00 N +ATOM 59 H LYS 4 19.564 30.159 23.606 1.00 0.00 H +ATOM 60 CA LYS 4 20.327 29.351 25.441 1.00 0.00 C +ATOM 61 HA LYS 4 20.068 29.589 26.469 1.00 0.00 H +ATOM 62 CB LYS 4 19.670 28.002 25.066 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.603 27.928 23.981 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.325 27.194 25.394 1.00 0.00 H +ATOM 65 CG LYS 4 18.278 27.723 25.675 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.001 26.705 25.397 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.346 27.765 26.762 1.00 0.00 H +ATOM 68 CD LYS 4 17.162 28.667 25.194 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.336 29.665 25.587 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.218 28.723 24.104 1.00 0.00 H +ATOM 71 CE LYS 4 15.739 28.200 25.570 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.031 28.787 24.974 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.626 27.156 25.262 1.00 0.00 H +ATOM 74 NZ LYS 4 15.398 28.355 27.015 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.453 29.321 27.308 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.441 28.062 27.197 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.999 27.808 27.619 1.00 0.00 H +ATOM 78 C LYS 4 21.859 29.250 25.406 1.00 0.00 C +ATOM 79 O LYS 4 22.510 29.627 24.436 1.00 0.00 O +HETATM 80 N HX1 5 22.468 28.722 26.466 1.00 0.00 N +HETATM 81 CA HX1 5 23.925 28.531 26.561 1.00 0.00 C +HETATM 82 C HX1 5 24.291 27.414 27.546 1.00 0.00 C +HETATM 83 O HX1 5 23.816 27.403 28.683 1.00 0.00 O +HETATM 84 CB HX1 5 24.559 29.858 26.974 1.00 0.00 C +HETATM 85 CG HX1 5 26.066 29.960 27.018 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.022 29.042 26.675 1.00 0.00 C +HETATM 87 ND1 HX1 5 26.676 31.061 27.599 1.00 0.00 N +HETATM 88 CE1 HX1 5 27.991 30.818 27.497 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.228 29.585 27.032 1.00 0.00 N +HETATM 90 H HX1 5 21.913 28.579 27.306 1.00 0.00 H +HETATM 91 HA HX1 5 24.318 28.260 25.581 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.179 30.134 27.959 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.214 30.629 26.287 1.00 0.00 H +HETATM 94 HD2 HX1 5 26.886 28.045 26.285 1.00 0.00 H +HETATM 95 HE1 HX1 5 28.763 31.447 27.914 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.102 29.078 27.222 1.00 0.00 H +ATOM 97 N ILE 6 25.132 26.489 27.085 1.00 0.00 N +ATOM 98 H ILE 6 25.458 26.571 26.126 1.00 0.00 H +ATOM 99 CA ILE 6 25.644 25.322 27.819 1.00 0.00 C +ATOM 100 HA ILE 6 25.110 25.241 28.770 1.00 0.00 H +ATOM 101 CB ILE 6 25.327 24.038 27.013 1.00 0.00 C +ATOM 102 HB ILE 6 25.787 24.132 26.028 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.904 22.774 27.676 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.503 22.652 28.681 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.658 21.888 27.095 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.991 22.817 27.722 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.792 23.903 26.833 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.330 23.794 27.813 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.398 24.811 26.380 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.329 22.747 25.939 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.496 21.792 26.437 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.260 22.854 25.747 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.867 22.770 24.990 1.00 0.00 H +ATOM 114 C ILE 6 27.131 25.511 28.167 1.00 0.00 C +ATOM 115 O ILE 6 27.874 26.246 27.505 1.00 0.00 O +ATOM 116 N VAL 7 27.523 24.924 29.300 1.00 0.00 N +ATOM 117 H VAL 7 26.889 24.232 29.696 1.00 0.00 H +ATOM 118 CA VAL 7 28.566 25.434 30.206 1.00 0.00 C +ATOM 119 HA VAL 7 28.518 26.524 30.150 1.00 0.00 H +ATOM 120 CB VAL 7 28.126 25.043 31.634 1.00 0.00 C +ATOM 121 HB VAL 7 27.059 25.240 31.715 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.312 23.552 31.929 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.350 23.255 31.825 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.977 23.323 32.941 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.718 22.960 31.234 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.754 25.899 32.738 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.446 26.934 32.614 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.393 25.561 33.711 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.836 25.844 32.729 1.00 0.00 H +ATOM 130 C VAL 7 30.027 25.023 29.878 1.00 0.00 C +ATOM 131 O VAL 7 30.259 23.980 29.272 1.00 0.00 O +ATOM 132 N ARG 8 31.025 25.803 30.343 1.00 0.00 N +ATOM 133 H ARG 8 30.730 26.642 30.829 1.00 0.00 H +ATOM 134 CA ARG 8 32.494 25.697 30.079 1.00 0.00 C +ATOM 135 HA ARG 8 32.641 25.654 29.002 1.00 0.00 H +ATOM 136 CB ARG 8 33.190 27.021 30.529 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.243 26.980 30.258 1.00 0.00 H +ATOM 138 HB3 ARG 8 32.752 27.856 29.977 1.00 0.00 H +ATOM 139 CG ARG 8 33.078 27.338 32.034 1.00 0.00 C +ATOM 140 HG2 ARG 8 32.080 27.673 32.284 1.00 0.00 H +ATOM 141 HG3 ARG 8 33.275 26.434 32.583 1.00 0.00 H +ATOM 142 CD ARG 8 34.135 28.324 32.567 1.00 0.00 C +ATOM 143 HD2 ARG 8 35.114 28.005 32.227 1.00 0.00 H +ATOM 144 HD3 ARG 8 33.944 29.313 32.150 1.00 0.00 H +ATOM 145 NE ARG 8 34.140 28.392 34.050 1.00 0.00 N +ATOM 146 HE ARG 8 33.745 29.220 34.456 1.00 0.00 H +ATOM 147 CZ ARG 8 34.700 27.536 34.893 1.00 0.00 C +ATOM 148 NH1 ARG 8 35.207 26.395 34.516 1.00 0.00 N +ATOM 149 HH11 ARG 8 35.120 26.109 33.554 1.00 0.00 H +ATOM 150 HH12 ARG 8 35.645 25.786 35.187 1.00 0.00 H +ATOM 151 NH2 ARG 8 34.752 27.809 36.166 1.00 0.00 N +ATOM 152 HH21 ARG 8 34.458 28.703 36.519 1.00 0.00 H +ATOM 153 HH22 ARG 8 35.271 27.201 36.780 1.00 0.00 H +ATOM 154 C ARG 8 33.221 24.420 30.618 1.00 0.00 C +ATOM 155 O ARG 8 34.140 24.545 31.425 1.00 0.00 O +ATOM 156 N GLY 9 32.794 23.192 30.314 1.00 0.00 N +ATOM 157 H GLY 9 31.936 23.085 29.778 1.00 0.00 H +ATOM 158 CA GLY 9 33.551 21.973 30.680 1.00 0.00 C +ATOM 159 HA2 GLY 9 34.358 21.821 29.958 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.023 22.124 31.650 1.00 0.00 H +ATOM 161 C GLY 9 32.693 20.696 30.769 1.00 0.00 C +ATOM 162 O GLY 9 31.554 20.681 30.307 1.00 0.00 O +ATOM 163 N LYS 10 33.209 19.638 31.434 1.00 0.00 N +ATOM 164 H LYS 10 34.139 19.753 31.822 1.00 0.00 H +ATOM 165 CA LYS 10 32.675 18.250 31.389 1.00 0.00 C +ATOM 166 HA LYS 10 31.669 18.289 30.975 1.00 0.00 H +ATOM 167 CB LYS 10 33.543 17.448 30.389 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.001 18.124 29.659 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.358 16.937 30.916 1.00 0.00 H +ATOM 170 CG LYS 10 32.733 16.420 29.582 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.183 15.759 30.254 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.013 16.957 28.963 1.00 0.00 H +ATOM 173 CD LYS 10 33.643 15.574 28.686 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.296 16.229 28.107 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.260 14.923 29.303 1.00 0.00 H +ATOM 176 CE LYS 10 32.827 14.724 27.709 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.193 14.038 28.269 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.190 15.392 27.127 1.00 0.00 H +ATOM 179 NZ LYS 10 33.711 13.988 26.778 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.326 13.343 27.264 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.201 13.485 26.071 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.315 14.654 26.284 1.00 0.00 H +ATOM 183 C LYS 10 32.518 17.528 32.747 1.00 0.00 C +ATOM 184 O LYS 10 32.596 16.307 32.801 1.00 0.00 O +ATOM 185 N ASN 11 32.378 18.251 33.862 1.00 0.00 N +ATOM 186 H ASN 11 32.311 19.238 33.729 1.00 0.00 H +ATOM 187 CA ASN 11 32.101 17.706 35.213 1.00 0.00 C +ATOM 188 HA ASN 11 32.387 16.648 35.230 1.00 0.00 H +ATOM 189 CB ASN 11 33.024 18.458 36.211 1.00 0.00 C +ATOM 190 HB2 ASN 11 34.053 18.194 36.010 1.00 0.00 H +ATOM 191 HB3 ASN 11 32.920 19.530 36.035 1.00 0.00 H +ATOM 192 CG ASN 11 32.702 18.222 37.671 1.00 0.00 C +ATOM 193 OD1 ASN 11 31.653 18.588 38.170 1.00 0.00 O +ATOM 194 ND2 ASN 11 33.609 17.657 38.430 1.00 0.00 N +ATOM 195 HD21 ASN 11 33.341 17.524 39.395 1.00 0.00 H +ATOM 196 HD22 ASN 11 34.511 17.380 38.074 1.00 0.00 H +ATOM 197 C ASN 11 30.600 17.753 35.520 1.00 0.00 C +ATOM 198 O ASN 11 29.907 16.749 35.462 1.00 0.00 O +ATOM 199 N TYR 12 30.095 18.967 35.742 1.00 0.00 N +ATOM 200 H TYR 12 30.736 19.709 35.899 1.00 0.00 H +ATOM 201 CA TYR 12 28.678 19.398 35.675 1.00 0.00 C +ATOM 202 HA TYR 12 28.082 18.749 36.359 1.00 0.00 H +ATOM 203 CB TYR 12 28.666 20.825 36.150 1.00 0.00 C +ATOM 204 HB2 TYR 12 27.626 21.198 36.151 1.00 0.00 H +ATOM 205 HB3 TYR 12 28.941 20.842 37.215 1.00 0.00 H +ATOM 206 CG TYR 12 29.561 21.851 35.412 1.00 0.00 C +ATOM 207 CD1 TYR 12 30.331 21.560 34.255 1.00 0.00 C +ATOM 208 HD1 TYR 12 30.263 20.582 33.755 1.00 0.00 H +ATOM 209 CE1 TYR 12 31.155 22.501 33.648 1.00 0.00 C +ATOM 210 HE1 TYR 12 31.680 22.275 32.733 1.00 0.00 H +ATOM 211 CZ TYR 12 31.213 23.780 34.184 1.00 0.00 C +ATOM 212 OH TYR 12 31.987 24.732 33.569 1.00 0.00 O +ATOM 213 HH TYR 12 32.324 24.387 32.701 1.00 0.00 H +ATOM 214 CE2 TYR 12 30.474 24.127 35.305 1.00 0.00 C +ATOM 215 HE2 TYR 12 30.501 25.147 35.689 1.00 0.00 H +ATOM 216 CD2 TYR 12 29.651 23.171 35.908 1.00 0.00 C +ATOM 217 HD2 TYR 12 29.043 23.443 36.787 1.00 0.00 H +ATOM 218 C TYR 12 28.090 19.253 34.250 1.00 0.00 C +ATOM 219 O TYR 12 28.788 18.862 33.309 1.00 0.00 O +ATOM 220 N LYS 13 26.821 19.647 34.065 1.00 0.00 N +ATOM 221 H LYS 13 26.305 19.925 34.884 1.00 0.00 H +ATOM 222 CA LYS 13 26.094 19.541 32.776 1.00 0.00 C +ATOM 223 HA LYS 13 26.805 19.717 31.969 1.00 0.00 H +ATOM 224 CB LYS 13 25.593 18.087 32.650 1.00 0.00 C +ATOM 225 HB2 LYS 13 26.320 17.429 33.127 1.00 0.00 H +ATOM 226 HB3 LYS 13 24.654 17.988 33.195 1.00 0.00 H +ATOM 227 CG LYS 13 25.425 17.587 31.203 1.00 0.00 C +ATOM 228 HG2 LYS 13 24.549 18.045 30.741 1.00 0.00 H +ATOM 229 HG3 LYS 13 26.302 17.868 30.624 1.00 0.00 H +ATOM 230 CD LYS 13 25.291 16.049 31.158 1.00 0.00 C +ATOM 231 HD2 LYS 13 25.230 15.725 30.117 1.00 0.00 H +ATOM 232 HD3 LYS 13 26.195 15.616 31.594 1.00 0.00 H +ATOM 233 CE LYS 13 24.053 15.554 31.925 1.00 0.00 C +ATOM 234 HE2 LYS 13 23.979 16.117 32.855 1.00 0.00 H +ATOM 235 HE3 LYS 13 23.165 15.772 31.325 1.00 0.00 H +ATOM 236 NZ LYS 13 24.127 14.113 32.260 1.00 0.00 N +ATOM 237 HZ1 LYS 13 25.032 13.871 32.657 1.00 0.00 H +ATOM 238 HZ2 LYS 13 23.461 13.886 32.994 1.00 0.00 H +ATOM 239 HZ3 LYS 13 23.964 13.519 31.457 1.00 0.00 H +ATOM 240 C LYS 13 24.980 20.595 32.595 1.00 0.00 C +ATOM 241 O LYS 13 23.956 20.338 31.967 1.00 0.00 O +ATOM 242 N GLY 14 25.140 21.770 33.215 1.00 0.00 N +ATOM 243 H GLY 14 26.023 21.941 33.667 1.00 0.00 H +ATOM 244 CA GLY 14 24.092 22.793 33.319 1.00 0.00 C +ATOM 245 HA2 GLY 14 23.148 22.298 33.541 1.00 0.00 H +ATOM 246 HA3 GLY 14 24.315 23.453 34.156 1.00 0.00 H +ATOM 247 C GLY 14 23.874 23.669 32.071 1.00 0.00 C +ATOM 248 O GLY 14 24.749 23.819 31.213 1.00 0.00 O +ATOM 249 N VAL 15 22.695 24.302 32.017 1.00 0.00 N +ATOM 250 H VAL 15 22.053 24.151 32.781 1.00 0.00 H +ATOM 251 CA VAL 15 22.244 25.234 30.969 1.00 0.00 C +ATOM 252 HA VAL 15 23.112 25.536 30.386 1.00 0.00 H +ATOM 253 CB VAL 15 21.252 24.543 30.003 1.00 0.00 C +ATOM 254 HB VAL 15 21.734 23.644 29.616 1.00 0.00 H +ATOM 255 CG1 VAL 15 19.942 24.128 30.686 1.00 0.00 C +ATOM 256 HG11 VAL 15 19.401 25.000 31.051 1.00 0.00 H +ATOM 257 HG12 VAL 15 19.310 23.599 29.968 1.00 0.00 H +ATOM 258 HG13 VAL 15 20.149 23.452 31.516 1.00 0.00 H +ATOM 259 CG2 VAL 15 20.890 25.430 28.802 1.00 0.00 C +ATOM 260 HG21 VAL 15 21.796 25.776 28.306 1.00 0.00 H +ATOM 261 HG22 VAL 15 20.312 24.845 28.084 1.00 0.00 H +ATOM 262 HG23 VAL 15 20.288 26.282 29.113 1.00 0.00 H +ATOM 263 C VAL 15 21.642 26.495 31.603 1.00 0.00 C +ATOM 264 O VAL 15 21.073 26.439 32.694 1.00 0.00 O +HETATM 265 N HY1 16 21.783 27.631 30.929 1.00 0.00 N +HETATM 266 CA HY1 16 21.218 28.928 31.326 1.00 0.00 C +HETATM 267 C HY1 16 21.036 29.822 30.068 1.00 0.00 C +HETATM 268 O HY1 16 21.371 29.383 28.958 1.00 0.00 O +HETATM 269 CB HY1 16 22.137 29.545 32.394 1.00 0.00 C +HETATM 270 CG HY1 16 23.542 29.763 31.898 1.00 0.00 C +HETATM 271 CD2 HY1 16 23.897 30.825 31.132 1.00 0.00 C +HETATM 272 ND1 HY1 16 24.612 28.888 31.897 1.00 0.00 N +HETATM 273 CE1 HY1 16 25.588 29.437 31.139 1.00 0.00 C +HETATM 274 NE2 HY1 16 25.183 30.623 30.647 1.00 0.00 N +HETATM 275 H HY1 16 22.297 27.605 30.055 1.00 0.00 H +HETATM 276 HA HY1 16 20.231 28.774 31.762 1.00 0.00 H +HETATM 277 HB2 HY1 16 21.721 30.492 32.738 1.00 0.00 H +HETATM 278 HB3 HY1 16 22.169 28.880 33.267 1.00 0.00 H +HETATM 279 HD1 HY1 16 24.657 28.001 32.388 1.00 0.00 H +HETATM 280 HD2 HY1 16 23.233 31.636 30.872 1.00 0.00 H +HETATM 281 HE1 HY1 16 26.569 28.993 30.965 1.00 0.00 H +ATOM 282 N THR 17 20.509 31.046 30.201 1.00 0.00 N +ATOM 283 H THR 17 20.226 31.383 31.101 1.00 0.00 H +ATOM 284 CA THR 17 20.080 31.865 29.044 1.00 0.00 C +ATOM 285 HA THR 17 20.517 31.448 28.143 1.00 0.00 H +ATOM 286 CB THR 17 18.549 31.829 28.895 1.00 0.00 C +ATOM 287 HB THR 17 18.274 32.454 28.059 1.00 0.00 H +ATOM 288 CG2 THR 17 17.977 30.425 28.652 1.00 0.00 C +ATOM 289 HG21 THR 17 18.205 29.759 29.472 1.00 0.00 H +ATOM 290 HG22 THR 17 16.890 30.494 28.552 1.00 0.00 H +ATOM 291 HG23 THR 17 18.376 30.025 27.734 1.00 0.00 H +ATOM 292 OG1 THR 17 17.946 32.336 30.061 1.00 0.00 O +ATOM 293 HG1 THR 17 17.908 33.302 29.951 1.00 0.00 H +ATOM 294 C THR 17 20.520 33.329 29.097 1.00 0.00 C +ATOM 295 O THR 17 20.892 33.824 30.166 1.00 0.00 O +HETATM 296 N HY2 18 20.484 34.015 27.941 1.00 0.00 N +HETATM 297 CA HY2 18 20.882 35.411 27.722 1.00 0.00 C +HETATM 298 C HY2 18 19.851 36.210 26.928 1.00 0.00 C +HETATM 299 O HY2 18 19.572 35.885 25.778 1.00 0.00 O +HETATM 300 CB HY2 18 22.273 35.475 27.050 1.00 0.00 C +HETATM 301 CG HY2 18 23.272 34.804 27.979 1.00 0.00 C +HETATM 302 CD2 HY2 18 23.969 33.646 27.739 1.00 0.00 C +HETATM 303 ND1 HY2 18 23.279 34.994 29.343 1.00 0.00 N +HETATM 304 CE1 HY2 18 23.808 33.906 29.896 1.00 0.00 C +HETATM 305 NE2 HY2 18 24.364 33.102 28.972 1.00 0.00 N +HETATM 306 H HY2 18 20.201 33.487 27.121 1.00 0.00 H +HETATM 307 HA HY2 18 20.970 35.912 28.681 1.00 0.00 H +HETATM 308 HB2 HY2 18 22.237 34.978 26.082 1.00 0.00 H +HETATM 309 HB3 HY2 18 22.557 36.514 26.883 1.00 0.00 H +HETATM 310 HD1 HY2 18 22.704 35.669 29.851 1.00 0.00 H +HETATM 311 HD2 HY2 18 24.054 33.162 26.778 1.00 0.00 H +HETATM 312 HE1 HY2 18 23.733 33.703 30.955 1.00 0.00 H +ATOM 313 N GLU 19 19.305 37.253 27.550 1.00 0.00 N +ATOM 314 H GLU 19 19.560 37.468 28.502 1.00 0.00 H +ATOM 315 CA GLU 19 18.335 38.139 26.909 1.00 0.00 C +ATOM 316 HA GLU 19 17.580 37.512 26.437 1.00 0.00 H +ATOM 317 CB GLU 19 17.681 39.005 27.999 1.00 0.00 C +ATOM 318 HB2 GLU 19 17.352 38.353 28.807 1.00 0.00 H +ATOM 319 HB3 GLU 19 18.428 39.691 28.402 1.00 0.00 H +ATOM 320 CG GLU 19 16.471 39.813 27.518 1.00 0.00 C +ATOM 321 HG2 GLU 19 16.008 40.295 28.382 1.00 0.00 H +ATOM 322 HG3 GLU 19 16.809 40.595 26.832 1.00 0.00 H +ATOM 323 CD GLU 19 15.468 38.898 26.817 1.00 0.00 C +ATOM 324 OE1 GLU 19 15.493 38.853 25.568 1.00 0.00 O +ATOM 325 OE2 GLU 19 14.771 38.123 27.500 1.00 0.00 O +ATOM 326 C GLU 19 18.993 39.011 25.829 1.00 0.00 C +ATOM 327 O GLU 19 20.034 39.622 26.077 1.00 0.00 O +ATOM 328 N ALA 20 18.393 39.062 24.639 1.00 0.00 N +ATOM 329 H ALA 20 17.534 38.535 24.527 1.00 0.00 H +ATOM 330 CA ALA 20 18.794 39.928 23.528 1.00 0.00 C +ATOM 331 HA ALA 20 18.938 40.939 23.911 1.00 0.00 H +ATOM 332 CB ALA 20 20.120 39.430 22.936 1.00 0.00 C +ATOM 333 HB1 ALA 20 19.981 38.442 22.498 1.00 0.00 H +ATOM 334 HB2 ALA 20 20.463 40.118 22.165 1.00 0.00 H +ATOM 335 HB3 ALA 20 20.891 39.377 23.704 1.00 0.00 H +ATOM 336 C ALA 20 17.730 39.970 22.414 1.00 0.00 C +ATOM 337 O ALA 20 16.877 39.085 22.300 1.00 0.00 O +ATOM 338 N VAL 21 17.828 40.967 21.527 1.00 0.00 N +ATOM 339 H VAL 21 18.517 41.687 21.688 1.00 0.00 H +ATOM 340 CA VAL 21 17.108 40.983 20.235 1.00 0.00 C +ATOM 341 HA VAL 21 16.112 40.569 20.390 1.00 0.00 H +ATOM 342 CB VAL 21 16.922 42.424 19.708 1.00 0.00 C +ATOM 343 HB VAL 21 16.284 42.377 18.825 1.00 0.00 H +ATOM 344 CG1 VAL 21 16.207 43.312 20.736 1.00 0.00 C +ATOM 345 HG11 VAL 21 16.841 43.487 21.604 1.00 0.00 H +ATOM 346 HG12 VAL 21 15.962 44.273 20.283 1.00 0.00 H +ATOM 347 HG13 VAL 21 15.281 42.837 21.061 1.00 0.00 H +ATOM 348 CG2 VAL 21 18.238 43.102 19.302 1.00 0.00 C +ATOM 349 HG21 VAL 21 18.700 42.562 18.476 1.00 0.00 H +ATOM 350 HG22 VAL 21 18.040 44.118 18.959 1.00 0.00 H +ATOM 351 HG23 VAL 21 18.934 43.140 20.139 1.00 0.00 H +ATOM 352 C VAL 21 17.781 40.114 19.160 1.00 0.00 C +ATOM 353 O VAL 21 17.147 39.785 18.160 1.00 0.00 O +ATOM 354 N ASP 22 19.050 39.749 19.368 1.00 0.00 N +ATOM 355 H ASP 22 19.476 40.007 20.243 1.00 0.00 H +ATOM 356 CA ASP 22 19.944 39.093 18.406 1.00 0.00 C +ATOM 357 HA ASP 22 19.370 38.425 17.764 1.00 0.00 H +ATOM 358 CB ASP 22 20.556 40.186 17.509 1.00 0.00 C +ATOM 359 HB2 ASP 22 19.748 40.807 17.120 1.00 0.00 H +ATOM 360 HB3 ASP 22 21.211 40.830 18.090 1.00 0.00 H +ATOM 361 CG ASP 22 21.364 39.655 16.331 1.00 0.00 C +ATOM 362 OD1 ASP 22 21.470 40.449 15.361 1.00 0.00 O +ATOM 363 OD2 ASP 22 21.882 38.534 16.368 1.00 0.00 O +ATOM 364 C ASP 22 21.010 38.262 19.152 1.00 0.00 C +ATOM 365 O ASP 22 21.519 38.679 20.197 1.00 0.00 O +ATOM 366 N LEU 23 21.373 37.097 18.612 1.00 0.00 N +ATOM 367 H LEU 23 21.060 36.924 17.665 1.00 0.00 H +ATOM 368 CA LEU 23 22.451 36.256 19.128 1.00 0.00 C +ATOM 369 HA LEU 23 22.232 36.042 20.172 1.00 0.00 H +ATOM 370 CB LEU 23 22.427 34.919 18.362 1.00 0.00 C +ATOM 371 HB2 LEU 23 21.429 34.495 18.470 1.00 0.00 H +ATOM 372 HB3 LEU 23 22.588 35.105 17.300 1.00 0.00 H +ATOM 373 CG LEU 23 23.460 33.898 18.881 1.00 0.00 C +ATOM 374 HG LEU 23 23.719 34.148 19.908 1.00 0.00 H +ATOM 375 CD1 LEU 23 22.889 32.478 18.888 1.00 0.00 C +ATOM 376 HD11 LEU 23 22.614 32.176 17.877 1.00 0.00 H +ATOM 377 HD12 LEU 23 23.634 31.788 19.283 1.00 0.00 H +ATOM 378 HD13 LEU 23 22.009 32.440 19.528 1.00 0.00 H +ATOM 379 CD2 LEU 23 24.722 33.893 18.016 1.00 0.00 C +ATOM 380 HD21 LEU 23 25.158 34.890 17.970 1.00 0.00 H +ATOM 381 HD22 LEU 23 25.459 33.219 18.446 1.00 0.00 H +ATOM 382 HD23 LEU 23 24.480 33.567 17.004 1.00 0.00 H +ATOM 383 C LEU 23 23.818 36.971 19.075 1.00 0.00 C +ATOM 384 O LEU 23 24.632 36.796 19.983 1.00 0.00 O +ATOM 385 N ALA 24 24.054 37.834 18.081 1.00 0.00 N +ATOM 386 H ALA 24 23.334 37.955 17.366 1.00 0.00 H +ATOM 387 CA ALA 24 25.275 38.639 17.954 1.00 0.00 C +ATOM 388 HA ALA 24 26.125 37.990 18.164 1.00 0.00 H +ATOM 389 CB ALA 24 25.385 39.106 16.501 1.00 0.00 C +ATOM 390 HB1 ALA 24 24.557 39.771 16.254 1.00 0.00 H +ATOM 391 HB2 ALA 24 26.329 39.629 16.356 1.00 0.00 H +ATOM 392 HB3 ALA 24 25.359 38.244 15.834 1.00 0.00 H +ATOM 393 C ALA 24 25.361 39.827 18.944 1.00 0.00 C +ATOM 394 O ALA 24 26.433 40.412 19.133 1.00 0.00 O +ATOM 395 N GLU 25 24.256 40.178 19.611 1.00 0.00 N +ATOM 396 H GLU 25 23.395 39.702 19.373 1.00 0.00 H +ATOM 397 CA GLU 25 24.264 41.004 20.827 1.00 0.00 C +ATOM 398 HA GLU 25 25.120 41.680 20.813 1.00 0.00 H +ATOM 399 CB GLU 25 22.987 41.862 20.899 1.00 0.00 C +ATOM 400 HB2 GLU 25 22.123 41.221 20.735 1.00 0.00 H +ATOM 401 HB3 GLU 25 22.902 42.280 21.899 1.00 0.00 H +ATOM 402 CG GLU 25 22.951 43.019 19.891 1.00 0.00 C +ATOM 403 HG2 GLU 25 23.195 42.648 18.896 1.00 0.00 H +ATOM 404 HG3 GLU 25 21.933 43.412 19.851 1.00 0.00 H +ATOM 405 CD GLU 25 23.913 44.144 20.293 1.00 0.00 C +ATOM 406 OE1 GLU 25 23.478 45.087 20.985 1.00 0.00 O +ATOM 407 OE2 GLU 25 25.113 44.027 19.919 1.00 0.00 O +ATOM 408 C GLU 25 24.432 40.126 22.081 1.00 0.00 C +ATOM 409 O GLU 25 25.224 40.456 22.965 1.00 0.00 O +ATOM 410 N ALA 26 23.788 38.950 22.138 1.00 0.00 N +ATOM 411 H ALA 26 23.138 38.715 21.394 1.00 0.00 H +ATOM 412 CA ALA 26 23.981 37.984 23.225 1.00 0.00 C +ATOM 413 HA ALA 26 23.762 38.494 24.162 1.00 0.00 H +ATOM 414 CB ALA 26 22.974 36.842 23.061 1.00 0.00 C +ATOM 415 HB1 ALA 26 23.199 36.283 22.157 1.00 0.00 H +ATOM 416 HB2 ALA 26 23.034 36.172 23.915 1.00 0.00 H +ATOM 417 HB3 ALA 26 21.964 37.238 22.992 1.00 0.00 H +ATOM 418 C ALA 26 25.427 37.446 23.335 1.00 0.00 C +ATOM 419 O ALA 26 25.824 37.003 24.418 1.00 0.00 O +ATOM 420 N GLU 27 26.226 37.506 22.263 1.00 0.00 N +ATOM 421 H GLU 27 25.786 37.697 21.366 1.00 0.00 H +ATOM 422 CA GLU 27 27.682 37.297 22.299 1.00 0.00 C +ATOM 423 HA GLU 27 27.873 36.349 22.802 1.00 0.00 H +ATOM 424 CB GLU 27 28.250 37.195 20.869 1.00 0.00 C +ATOM 425 HB2 GLU 27 27.652 36.495 20.285 1.00 0.00 H +ATOM 426 HB3 GLU 27 28.190 38.174 20.391 1.00 0.00 H +ATOM 427 CG GLU 27 29.709 36.707 20.879 1.00 0.00 C +ATOM 428 HG2 GLU 27 30.246 37.147 21.723 1.00 0.00 H +ATOM 429 HG3 GLU 27 29.712 35.623 21.031 1.00 0.00 H +ATOM 430 CD GLU 27 30.466 37.088 19.601 1.00 0.00 C +ATOM 431 OE1 GLU 27 30.854 38.276 19.503 1.00 0.00 O +ATOM 432 OE2 GLU 27 30.694 36.185 18.769 1.00 0.00 O +ATOM 433 C GLU 27 28.399 38.403 23.095 1.00 0.00 C +ATOM 434 O GLU 27 29.144 38.111 24.035 1.00 0.00 O +ATOM 435 N LYS 28 28.111 39.679 22.804 1.00 0.00 N +ATOM 436 H LYS 28 27.456 39.856 22.053 1.00 0.00 H +ATOM 437 CA LYS 28 28.669 40.829 23.542 1.00 0.00 C +ATOM 438 HA LYS 28 29.757 40.759 23.523 1.00 0.00 H +ATOM 439 CB LYS 28 28.255 42.157 22.883 1.00 0.00 C +ATOM 440 HB2 LYS 28 27.172 42.278 22.942 1.00 0.00 H +ATOM 441 HB3 LYS 28 28.719 42.971 23.444 1.00 0.00 H +ATOM 442 CG LYS 28 28.686 42.263 21.411 1.00 0.00 C +ATOM 443 HG2 LYS 28 29.750 42.034 21.326 1.00 0.00 H +ATOM 444 HG3 LYS 28 28.124 41.540 20.822 1.00 0.00 H +ATOM 445 CD LYS 28 28.432 43.680 20.873 1.00 0.00 C +ATOM 446 HD2 LYS 28 27.437 44.018 21.168 1.00 0.00 H +ATOM 447 HD3 LYS 28 29.160 44.358 21.322 1.00 0.00 H +ATOM 448 CE LYS 28 28.554 43.752 19.344 1.00 0.00 C +ATOM 449 HE2 LYS 28 28.652 44.804 19.060 1.00 0.00 H +ATOM 450 HE3 LYS 28 29.462 43.233 19.027 1.00 0.00 H +ATOM 451 NZ LYS 28 27.361 43.170 18.683 1.00 0.00 N +ATOM 452 HZ1 LYS 28 26.512 43.612 19.055 1.00 0.00 H +ATOM 453 HZ2 LYS 28 27.376 43.317 17.686 1.00 0.00 H +ATOM 454 HZ3 LYS 28 27.262 42.177 18.881 1.00 0.00 H +ATOM 455 C LYS 28 28.248 40.810 25.012 1.00 0.00 C +ATOM 456 O LYS 28 29.093 40.897 25.903 1.00 0.00 O +ATOM 457 N PHE 29 26.965 40.568 25.284 1.00 0.00 N +ATOM 458 H PHE 29 26.308 40.561 24.505 1.00 0.00 H +ATOM 459 CA PHE 29 26.454 40.372 26.647 1.00 0.00 C +ATOM 460 HA PHE 29 26.755 41.229 27.250 1.00 0.00 H +ATOM 461 CB PHE 29 24.918 40.333 26.629 1.00 0.00 C +ATOM 462 HB2 PHE 29 24.608 39.412 26.136 1.00 0.00 H +ATOM 463 HB3 PHE 29 24.565 40.293 27.662 1.00 0.00 H +ATOM 464 CG PHE 29 24.218 41.505 25.955 1.00 0.00 C +ATOM 465 CD1 PHE 29 22.999 41.289 25.282 1.00 0.00 C +ATOM 466 HD1 PHE 29 22.551 40.307 25.269 1.00 0.00 H +ATOM 467 CE1 PHE 29 22.362 42.347 24.611 1.00 0.00 C +ATOM 468 HE1 PHE 29 21.440 42.167 24.079 1.00 0.00 H +ATOM 469 CZ PHE 29 22.937 43.630 24.611 1.00 0.00 C +ATOM 470 HZ PHE 29 22.467 44.436 24.065 1.00 0.00 H +ATOM 471 CE2 PHE 29 24.132 43.861 25.313 1.00 0.00 C +ATOM 472 HE2 PHE 29 24.573 44.845 25.321 1.00 0.00 H +ATOM 473 CD2 PHE 29 24.766 42.805 25.989 1.00 0.00 C +ATOM 474 HD2 PHE 29 25.684 43.004 26.519 1.00 0.00 H +ATOM 475 C PHE 29 27.025 39.110 27.331 1.00 0.00 C +ATOM 476 O PHE 29 27.057 39.034 28.559 1.00 0.00 O +ATOM 477 N THR 30 27.519 38.123 26.569 1.00 0.00 N +ATOM 478 H THR 30 27.472 38.226 25.559 1.00 0.00 H +ATOM 479 CA THR 30 28.282 36.990 27.101 1.00 0.00 C +ATOM 480 HA THR 30 27.799 36.696 28.022 1.00 0.00 H +ATOM 481 CB THR 30 28.255 35.769 26.144 1.00 0.00 C +ATOM 482 HB THR 30 28.535 36.074 25.144 1.00 0.00 H +ATOM 483 CG2 THR 30 29.213 34.641 26.549 1.00 0.00 C +ATOM 484 HG21 THR 30 29.091 34.356 27.586 1.00 0.00 H +ATOM 485 HG22 THR 30 29.060 33.765 25.915 1.00 0.00 H +ATOM 486 HG23 THR 30 30.235 34.981 26.383 1.00 0.00 H +ATOM 487 OG1 THR 30 26.949 35.222 26.159 1.00 0.00 O +ATOM 488 HG1 THR 30 26.411 35.804 25.580 1.00 0.00 H +ATOM 489 C THR 30 29.697 37.395 27.517 1.00 0.00 C +ATOM 490 O THR 30 30.116 36.977 28.596 1.00 0.00 O +ATOM 491 N LYS 31 30.396 38.237 26.743 1.00 0.00 N +ATOM 492 H LYS 31 29.969 38.548 25.875 1.00 0.00 H +ATOM 493 CA LYS 31 31.759 38.733 27.030 1.00 0.00 C +ATOM 494 HA LYS 31 32.393 37.903 27.349 1.00 0.00 H +ATOM 495 CB LYS 31 32.356 39.316 25.742 1.00 0.00 C +ATOM 496 HB2 LYS 31 31.677 40.067 25.331 1.00 0.00 H +ATOM 497 HB3 LYS 31 33.304 39.811 25.970 1.00 0.00 H +ATOM 498 CG LYS 31 32.616 38.226 24.689 1.00 0.00 C +ATOM 499 HG2 LYS 31 33.308 37.492 25.095 1.00 0.00 H +ATOM 500 HG3 LYS 31 31.691 37.710 24.439 1.00 0.00 H +ATOM 501 CD LYS 31 33.202 38.836 23.409 1.00 0.00 C +ATOM 502 HD2 LYS 31 32.420 39.421 22.919 1.00 0.00 H +ATOM 503 HD3 LYS 31 34.019 39.511 23.668 1.00 0.00 H +ATOM 504 CE LYS 31 33.717 37.773 22.435 1.00 0.00 C +ATOM 505 HE2 LYS 31 32.924 37.052 22.218 1.00 0.00 H +ATOM 506 HE3 LYS 31 33.962 38.263 21.487 1.00 0.00 H +ATOM 507 NZ LYS 31 34.922 37.074 22.949 1.00 0.00 N +ATOM 508 HZ1 LYS 31 34.715 36.322 23.594 1.00 0.00 H +ATOM 509 HZ2 LYS 31 35.427 36.621 22.180 1.00 0.00 H +ATOM 510 HZ3 LYS 31 35.585 37.695 23.408 1.00 0.00 H +ATOM 511 C LYS 31 31.821 39.756 28.169 1.00 0.00 C +ATOM 512 O LYS 31 32.781 39.726 28.936 1.00 0.00 O +ATOM 513 N ALA 32 30.796 40.598 28.331 1.00 0.00 N +ATOM 514 H ALA 32 30.099 40.631 27.594 1.00 0.00 H +ATOM 515 CA ALA 32 30.739 41.633 29.373 1.00 0.00 C +ATOM 516 HA ALA 32 31.499 42.384 29.163 1.00 0.00 H +ATOM 517 CB ALA 32 29.356 42.306 29.300 1.00 0.00 C +ATOM 518 HB1 ALA 32 28.554 41.574 29.415 1.00 0.00 H +ATOM 519 HB2 ALA 32 29.262 43.050 30.092 1.00 0.00 H +ATOM 520 HB3 ALA 32 29.243 42.801 28.337 1.00 0.00 H +ATOM 521 C ALA 32 31.031 41.072 30.780 1.00 0.00 C +ATOM 522 O ALA 32 32.064 41.340 31.385 1.00 0.00 O +ATOM 523 N ARG 33 30.166 40.171 31.235 1.00 0.00 N +ATOM 524 H ARG 33 29.351 39.998 30.664 1.00 0.00 H +ATOM 525 CA ARG 33 30.294 39.444 32.510 1.00 0.00 C +ATOM 526 HA ARG 33 30.422 40.178 33.297 1.00 0.00 H +ATOM 527 CB ARG 33 28.995 38.699 32.794 1.00 0.00 C +ATOM 528 HB2 ARG 33 29.130 38.075 33.679 1.00 0.00 H +ATOM 529 HB3 ARG 33 28.177 39.395 32.979 1.00 0.00 H +ATOM 530 CG ARG 33 28.687 37.855 31.561 1.00 0.00 C +ATOM 531 HG2 ARG 33 28.076 38.434 30.871 1.00 0.00 H +ATOM 532 HG3 ARG 33 29.601 37.582 31.040 1.00 0.00 H +ATOM 533 CD ARG 33 27.984 36.569 31.880 1.00 0.00 C +ATOM 534 HD2 ARG 33 28.538 36.004 32.635 1.00 0.00 H +ATOM 535 HD3 ARG 33 26.985 36.812 32.252 1.00 0.00 H +ATOM 536 NE ARG 33 27.901 35.843 30.611 1.00 0.00 N +ATOM 537 HE ARG 33 28.490 36.185 29.860 1.00 0.00 H +ATOM 538 CZ ARG 33 26.904 35.066 30.309 1.00 0.00 C +ATOM 539 NH1 ARG 33 26.635 34.799 29.061 1.00 0.00 N +ATOM 540 HH11 ARG 33 27.186 35.168 28.300 1.00 0.00 H +ATOM 541 HH12 ARG 33 25.727 34.451 28.800 1.00 0.00 H +ATOM 542 NH2 ARG 33 26.203 34.541 31.276 1.00 0.00 N +ATOM 543 HH21 ARG 33 26.473 34.757 32.221 1.00 0.00 H +ATOM 544 HH22 ARG 33 25.586 33.777 31.106 1.00 0.00 H +ATOM 545 C ARG 33 31.465 38.449 32.604 1.00 0.00 C +ATOM 546 O ARG 33 31.778 37.990 33.697 1.00 0.00 O +ATOM 547 N ALA 34 32.072 38.042 31.482 1.00 0.00 N +ATOM 548 H ALA 34 31.783 38.439 30.604 1.00 0.00 H +ATOM 549 CA ALA 34 33.302 37.246 31.503 1.00 0.00 C +ATOM 550 HA ALA 34 33.202 36.446 32.236 1.00 0.00 H +ATOM 551 CB ALA 34 33.538 36.601 30.123 1.00 0.00 C +ATOM 552 HB1 ALA 34 33.762 37.355 29.372 1.00 0.00 H +ATOM 553 HB2 ALA 34 34.384 35.912 30.170 1.00 0.00 H +ATOM 554 HB3 ALA 34 32.660 36.035 29.815 1.00 0.00 H +ATOM 555 C ALA 34 34.457 38.136 31.984 1.00 0.00 C +ATOM 556 O ALA 34 35.219 37.724 32.850 1.00 0.00 O +ATOM 557 N ASN 35 34.474 39.401 31.551 1.00 0.00 N +ATOM 558 H ASN 35 33.784 39.677 30.864 1.00 0.00 H +ATOM 559 CA ASN 35 35.325 40.453 32.107 1.00 0.00 C +ATOM 560 HA ASN 35 36.327 40.046 32.242 1.00 0.00 H +ATOM 561 CB ASN 35 35.440 41.586 31.075 1.00 0.00 C +ATOM 562 HB2 ASN 35 34.453 41.945 30.796 1.00 0.00 H +ATOM 563 HB3 ASN 35 35.979 42.414 31.532 1.00 0.00 H +ATOM 564 CG ASN 35 36.209 41.162 29.832 1.00 0.00 C +ATOM 565 OD1 ASN 35 37.424 41.107 29.816 1.00 0.00 O +ATOM 566 ND2 ASN 35 35.544 40.847 28.746 1.00 0.00 N +ATOM 567 HD21 ASN 35 36.101 40.597 27.934 1.00 0.00 H +ATOM 568 HD22 ASN 35 34.541 40.769 28.766 1.00 0.00 H +ATOM 569 C ASN 35 34.886 40.937 33.515 1.00 0.00 C +ATOM 570 O ASN 35 35.755 41.332 34.288 1.00 0.00 O +ATOM 571 N ASP 36 33.604 40.835 33.915 1.00 0.00 N +ATOM 572 H ASP 36 32.883 40.704 33.220 1.00 0.00 H +ATOM 573 CA ASP 36 33.222 40.978 35.343 1.00 0.00 C +ATOM 574 HA ASP 36 33.609 41.930 35.704 1.00 0.00 H +ATOM 575 CB ASP 36 31.690 41.001 35.561 1.00 0.00 C +ATOM 576 HB2 ASP 36 31.275 40.064 35.211 1.00 0.00 H +ATOM 577 HB3 ASP 36 31.510 41.010 36.635 1.00 0.00 H +ATOM 578 CG ASP 36 30.917 42.200 34.975 1.00 0.00 C +ATOM 579 OD1 ASP 36 31.468 43.323 35.011 1.00 0.00 O +ATOM 580 OD2 ASP 36 29.741 42.011 34.563 1.00 0.00 O +ATOM 581 C ASP 36 33.862 39.877 36.225 1.00 0.00 C +ATOM 582 O ASP 36 34.232 40.144 37.368 1.00 0.00 O +ATOM 583 N LEU 37 34.028 38.649 35.706 1.00 0.00 N +ATOM 584 H LEU 37 33.645 38.474 34.786 1.00 0.00 H +ATOM 585 CA LEU 37 34.769 37.561 36.371 1.00 0.00 C +ATOM 586 HA LEU 37 34.582 37.645 37.443 1.00 0.00 H +ATOM 587 CB LEU 37 34.192 36.213 35.882 1.00 0.00 C +ATOM 588 HB2 LEU 37 33.118 36.210 36.069 1.00 0.00 H +ATOM 589 HB3 LEU 37 34.342 36.154 34.805 1.00 0.00 H +ATOM 590 CG LEU 37 34.805 34.945 36.516 1.00 0.00 C +ATOM 591 HG LEU 37 35.876 34.913 36.321 1.00 0.00 H +ATOM 592 CD1 LEU 37 34.566 34.864 38.026 1.00 0.00 C +ATOM 593 HD11 LEU 37 33.499 34.915 38.242 1.00 0.00 H +ATOM 594 HD12 LEU 37 34.975 33.932 38.415 1.00 0.00 H +ATOM 595 HD13 LEU 37 35.076 35.691 38.518 1.00 0.00 H +ATOM 596 CD2 LEU 37 34.181 33.694 35.888 1.00 0.00 C +ATOM 597 HD21 LEU 37 34.363 33.701 34.813 1.00 0.00 H +ATOM 598 HD22 LEU 37 34.644 32.804 36.314 1.00 0.00 H +ATOM 599 HD23 LEU 37 33.108 33.675 36.077 1.00 0.00 H +ATOM 600 C LEU 37 36.304 37.655 36.183 1.00 0.00 C +ATOM 601 O LEU 37 37.049 37.195 37.049 1.00 0.00 O +ATOM 602 N GLY 38 36.774 38.237 35.074 1.00 0.00 N +ATOM 603 H GLY 38 36.097 38.511 34.376 1.00 0.00 H +ATOM 604 CA GLY 38 38.182 38.550 34.809 1.00 0.00 C +ATOM 605 HA2 GLY 38 38.459 39.417 35.411 1.00 0.00 H +ATOM 606 HA3 GLY 38 38.795 37.709 35.131 1.00 0.00 H +ATOM 607 C GLY 38 38.540 38.860 33.342 1.00 0.00 C +ATOM 608 O GLY 38 39.143 39.896 33.084 1.00 0.00 O +ATOM 609 N GLU 39 38.201 37.985 32.384 1.00 0.00 N +ATOM 610 H GLU 39 37.589 37.219 32.631 1.00 0.00 H +ATOM 611 CA GLU 39 38.667 38.020 30.972 1.00 0.00 C +ATOM 612 HA GLU 39 38.785 39.059 30.656 1.00 0.00 H +ATOM 613 CB GLU 39 40.040 37.296 30.846 1.00 0.00 C +ATOM 614 HB2 GLU 39 39.905 36.277 31.208 1.00 0.00 H +ATOM 615 HB3 GLU 39 40.298 37.242 29.788 1.00 0.00 H +ATOM 616 CG GLU 39 41.235 37.941 31.588 1.00 0.00 C +ATOM 617 HG2 GLU 39 41.429 38.925 31.147 1.00 0.00 H +ATOM 618 HG3 GLU 39 40.970 38.086 32.638 1.00 0.00 H +ATOM 619 CD GLU 39 42.521 37.093 31.582 1.00 0.00 C +ATOM 620 OE1 GLU 39 42.422 35.846 31.671 1.00 0.00 O +ATOM 621 OE2 GLU 39 43.632 37.676 31.560 1.00 0.00 O +ATOM 622 C GLU 39 37.648 37.338 30.014 1.00 0.00 C +ATOM 623 O GLU 39 36.929 36.433 30.444 1.00 0.00 O +ATOM 624 N ASP 40 37.580 37.703 28.713 1.00 0.00 N +ATOM 625 H ASP 40 38.152 38.477 28.401 1.00 0.00 H +ATOM 626 CA ASP 40 36.731 37.006 27.712 1.00 0.00 C +ATOM 627 HA ASP 40 36.019 36.400 28.273 1.00 0.00 H +ATOM 628 CB ASP 40 35.856 37.950 26.869 1.00 0.00 C +ATOM 629 HB2 ASP 40 35.149 37.321 26.332 1.00 0.00 H +ATOM 630 HB3 ASP 40 35.268 38.580 27.529 1.00 0.00 H +ATOM 631 CG ASP 40 36.582 38.819 25.835 1.00 0.00 C +ATOM 632 OD1 ASP 40 36.945 39.969 26.162 1.00 0.00 O +ATOM 633 OD2 ASP 40 36.695 38.391 24.657 1.00 0.00 O +ATOM 634 C ASP 40 37.463 36.031 26.766 1.00 0.00 C +ATOM 635 O ASP 40 38.376 36.411 26.026 1.00 0.00 O +ATOM 636 N GLY 41 36.937 34.801 26.687 1.00 0.00 N +ATOM 637 H GLY 41 36.209 34.568 27.343 1.00 0.00 H +ATOM 638 CA GLY 41 37.260 33.807 25.655 1.00 0.00 C +ATOM 639 HA2 GLY 41 38.284 33.968 25.307 1.00 0.00 H +ATOM 640 HA3 GLY 41 37.212 32.809 26.099 1.00 0.00 H +ATOM 641 C GLY 41 36.319 33.835 24.428 1.00 0.00 C +ATOM 642 O GLY 41 35.379 34.632 24.345 1.00 0.00 O +ATOM 643 N GLU 42 36.572 32.930 23.480 1.00 0.00 N +ATOM 644 H GLU 42 37.303 32.262 23.657 1.00 0.00 H +ATOM 645 CA GLU 42 35.849 32.773 22.198 1.00 0.00 C +ATOM 646 HA GLU 42 35.155 33.605 22.083 1.00 0.00 H +ATOM 647 CB GLU 42 36.832 32.823 21.014 1.00 0.00 C +ATOM 648 HB2 GLU 42 37.410 31.899 20.996 1.00 0.00 H +ATOM 649 HB3 GLU 42 36.250 32.852 20.091 1.00 0.00 H +ATOM 650 CG GLU 42 37.808 34.026 21.041 1.00 0.00 C +ATOM 651 HG2 GLU 42 38.582 33.822 21.785 1.00 0.00 H +ATOM 652 HG3 GLU 42 38.302 34.092 20.068 1.00 0.00 H +ATOM 653 CD GLU 42 37.130 35.373 21.376 1.00 0.00 C +ATOM 654 OE1 GLU 42 35.967 35.572 20.965 1.00 0.00 O +ATOM 655 OE2 GLU 42 37.694 36.214 22.124 1.00 0.00 O +ATOM 656 C GLU 42 34.999 31.500 22.160 1.00 0.00 C +ATOM 657 O GLU 42 35.269 30.539 22.888 1.00 0.00 O +ATOM 658 N HIP 43 33.891 31.517 21.396 1.00 0.00 N +ATOM 659 H HIP 43 33.753 32.283 20.746 1.00 0.00 H +ATOM 660 CA HIP 43 32.711 30.745 21.803 1.00 0.00 C +ATOM 661 HA HIP 43 33.033 29.779 22.194 1.00 0.00 H +ATOM 662 CB HIP 43 32.123 31.562 22.981 1.00 0.00 C +ATOM 663 HB2 HIP 43 32.868 31.705 23.765 1.00 0.00 H +ATOM 664 HB3 HIP 43 31.824 32.549 22.633 1.00 0.00 H +ATOM 665 CG HIP 43 30.942 30.884 23.586 1.00 0.00 C +ATOM 666 ND1 HIP 43 29.754 30.730 22.930 1.00 0.00 N +ATOM 667 HD1 HIP 43 29.562 31.132 22.014 1.00 0.00 H +ATOM 668 CE1 HIP 43 29.202 29.607 23.386 1.00 0.00 C +ATOM 669 HE1 HIP 43 28.474 29.044 22.833 1.00 0.00 H +ATOM 670 NE2 HIP 43 29.897 29.146 24.436 1.00 0.00 N +ATOM 671 HE2 HIP 43 29.817 28.199 24.785 1.00 0.00 H +ATOM 672 CD2 HIP 43 31.021 29.930 24.558 1.00 0.00 C +ATOM 673 HD2 HIP 43 31.900 29.678 25.124 1.00 0.00 H +ATOM 674 C HIP 43 31.650 30.454 20.697 1.00 0.00 C +ATOM 675 O HIP 43 30.841 31.328 20.397 1.00 0.00 O +ATOM 676 N THR 44 31.523 29.200 20.247 1.00 0.00 N +ATOM 677 H THR 44 32.201 28.523 20.559 1.00 0.00 H +ATOM 678 CA THR 44 30.635 28.728 19.143 1.00 0.00 C +ATOM 679 HA THR 44 30.827 29.355 18.270 1.00 0.00 H +ATOM 680 CB THR 44 31.019 27.279 18.766 1.00 0.00 C +ATOM 681 HB THR 44 30.729 26.605 19.575 1.00 0.00 H +ATOM 682 CG2 THR 44 30.403 26.764 17.461 1.00 0.00 C +ATOM 683 HG21 THR 44 30.532 27.498 16.665 1.00 0.00 H +ATOM 684 HG22 THR 44 30.870 25.825 17.164 1.00 0.00 H +ATOM 685 HG23 THR 44 29.340 26.566 17.601 1.00 0.00 H +ATOM 686 OG1 THR 44 32.417 27.197 18.606 1.00 0.00 O +ATOM 687 HG1 THR 44 32.604 26.452 18.027 1.00 0.00 H +ATOM 688 C THR 44 29.114 28.795 19.411 1.00 0.00 C +ATOM 689 O THR 44 28.661 28.721 20.558 1.00 0.00 O +ATOM 690 N GLN 45 28.319 28.898 18.337 1.00 0.00 N +ATOM 691 H GLN 45 28.789 29.017 17.446 1.00 0.00 H +ATOM 692 CA GLN 45 26.865 29.110 18.294 1.00 0.00 C +ATOM 693 HA GLN 45 26.462 28.962 19.295 1.00 0.00 H +ATOM 694 CB GLN 45 26.599 30.578 17.884 1.00 0.00 C +ATOM 695 HB2 GLN 45 25.572 30.804 18.169 1.00 0.00 H +ATOM 696 HB3 GLN 45 27.242 31.234 18.473 1.00 0.00 H +ATOM 697 CG GLN 45 26.741 30.947 16.382 1.00 0.00 C +ATOM 698 HG2 GLN 45 26.052 30.342 15.794 1.00 0.00 H +ATOM 699 HG3 GLN 45 26.425 31.983 16.257 1.00 0.00 H +ATOM 700 CD GLN 45 28.143 30.823 15.768 1.00 0.00 C +ATOM 701 OE1 GLN 45 29.158 30.708 16.436 1.00 0.00 O +ATOM 702 NE2 GLN 45 28.276 30.835 14.462 1.00 0.00 N +ATOM 703 HE21 GLN 45 29.214 30.785 14.109 1.00 0.00 H +ATOM 704 HE22 GLN 45 27.485 30.864 13.826 1.00 0.00 H +ATOM 705 C GLN 45 26.106 28.148 17.353 1.00 0.00 C +ATOM 706 O GLN 45 26.651 27.691 16.350 1.00 0.00 O +ATOM 707 N ASP 46 24.816 27.938 17.631 1.00 0.00 N +ATOM 708 H ASP 46 24.469 28.232 18.538 1.00 0.00 H +ATOM 709 CA ASP 46 23.806 27.349 16.739 1.00 0.00 C +ATOM 710 HA ASP 46 24.147 27.428 15.708 1.00 0.00 H +ATOM 711 CB ASP 46 23.590 25.860 17.075 1.00 0.00 C +ATOM 712 HB2 ASP 46 24.463 25.284 16.756 1.00 0.00 H +ATOM 713 HB3 ASP 46 23.496 25.765 18.157 1.00 0.00 H +ATOM 714 CG ASP 46 22.341 25.292 16.395 1.00 0.00 C +ATOM 715 OD1 ASP 46 21.515 24.680 17.113 1.00 0.00 O +ATOM 716 OD2 ASP 46 22.135 25.545 15.195 1.00 0.00 O +ATOM 717 C ASP 46 22.471 28.108 16.864 1.00 0.00 C +ATOM 718 O ASP 46 22.025 28.431 17.966 1.00 0.00 O +ATOM 719 N ASP 47 21.809 28.361 15.735 1.00 0.00 N +ATOM 720 H ASP 47 22.178 27.953 14.884 1.00 0.00 H +ATOM 721 CA ASP 47 20.481 28.990 15.695 1.00 0.00 C +ATOM 722 HA ASP 47 20.396 29.652 16.550 1.00 0.00 H +ATOM 723 CB ASP 47 20.358 29.872 14.438 1.00 0.00 C +ATOM 724 HB2 ASP 47 21.220 30.541 14.390 1.00 0.00 H +ATOM 725 HB3 ASP 47 20.363 29.240 13.547 1.00 0.00 H +ATOM 726 CG ASP 47 19.084 30.708 14.499 1.00 0.00 C +ATOM 727 OD1 ASP 47 18.127 30.409 13.761 1.00 0.00 O +ATOM 728 OD2 ASP 47 18.939 31.541 15.419 1.00 0.00 O +ATOM 729 C ASP 47 19.313 27.985 15.776 1.00 0.00 C +ATOM 730 O ASP 47 18.260 28.318 16.326 1.00 0.00 O +ATOM 731 N ALA 48 19.476 26.741 15.304 1.00 0.00 N +ATOM 732 H ALA 48 20.408 26.439 15.014 1.00 0.00 H +ATOM 733 CA ALA 48 18.394 25.746 15.250 1.00 0.00 C +ATOM 734 HA ALA 48 17.536 26.176 14.732 1.00 0.00 H +ATOM 735 CB ALA 48 18.895 24.541 14.445 1.00 0.00 C +ATOM 736 HB1 ALA 48 19.748 24.085 14.950 1.00 0.00 H +ATOM 737 HB2 ALA 48 18.099 23.805 14.350 1.00 0.00 H +ATOM 738 HB3 ALA 48 19.206 24.861 13.450 1.00 0.00 H +ATOM 739 C ALA 48 17.916 25.322 16.650 1.00 0.00 C +ATOM 740 O ALA 48 16.721 25.152 16.897 1.00 0.00 O +ATOM 741 N THR 49 18.847 25.199 17.595 1.00 0.00 N +ATOM 742 H THR 49 19.823 25.180 17.290 1.00 0.00 H +ATOM 743 CA THR 49 18.582 25.048 19.034 1.00 0.00 C +ATOM 744 HA THR 49 17.557 24.704 19.161 1.00 0.00 H +ATOM 745 CB THR 49 19.520 23.996 19.644 1.00 0.00 C +ATOM 746 HB THR 49 19.269 23.888 20.697 1.00 0.00 H +ATOM 747 CG2 THR 49 19.421 22.621 18.993 1.00 0.00 C +ATOM 748 HG21 THR 49 19.747 22.665 17.954 1.00 0.00 H +ATOM 749 HG22 THR 49 20.077 21.947 19.538 1.00 0.00 H +ATOM 750 HG23 THR 49 18.398 22.254 19.040 1.00 0.00 H +ATOM 751 OG1 THR 49 20.859 24.396 19.551 1.00 0.00 O +ATOM 752 HG1 THR 49 21.108 24.393 18.591 1.00 0.00 H +ATOM 753 C THR 49 18.705 26.359 19.819 1.00 0.00 C +ATOM 754 O THR 49 18.601 26.347 21.047 1.00 0.00 O +ATOM 755 N LYS 50 18.935 27.492 19.139 1.00 0.00 N +ATOM 756 H LYS 50 18.973 27.403 18.132 1.00 0.00 H +ATOM 757 CA LYS 50 19.167 28.835 19.712 1.00 0.00 C +ATOM 758 HA LYS 50 19.597 29.451 18.919 1.00 0.00 H +ATOM 759 CB LYS 50 17.826 29.468 20.157 1.00 0.00 C +ATOM 760 HB2 LYS 50 17.370 28.808 20.900 1.00 0.00 H +ATOM 761 HB3 LYS 50 18.015 30.425 20.646 1.00 0.00 H +ATOM 762 CG LYS 50 16.794 29.705 19.037 1.00 0.00 C +ATOM 763 HG2 LYS 50 16.716 28.820 18.405 1.00 0.00 H +ATOM 764 HG3 LYS 50 15.824 29.873 19.507 1.00 0.00 H +ATOM 765 CD LYS 50 17.127 30.944 18.184 1.00 0.00 C +ATOM 766 HD2 LYS 50 17.102 31.820 18.837 1.00 0.00 H +ATOM 767 HD3 LYS 50 18.129 30.854 17.760 1.00 0.00 H +ATOM 768 CE LYS 50 16.090 31.145 17.073 1.00 0.00 C +ATOM 769 HE2 LYS 50 15.096 30.898 17.457 1.00 0.00 H +ATOM 770 HE3 LYS 50 16.103 32.201 16.787 1.00 0.00 H +ATOM 771 NZ LYS 50 16.421 30.345 15.873 1.00 0.00 N +ATOM 772 HZ1 LYS 50 16.767 29.414 16.087 1.00 0.00 H +ATOM 773 HZ2 LYS 50 15.699 30.310 15.174 1.00 0.00 H +ATOM 774 HZ3 LYS 50 17.223 30.766 15.390 1.00 0.00 H +ATOM 775 C LYS 50 20.222 28.825 20.831 1.00 0.00 C +ATOM 776 O LYS 50 20.055 29.510 21.843 1.00 0.00 O +ATOM 777 N THR 51 21.259 27.993 20.691 1.00 0.00 N +ATOM 778 H THR 51 21.409 27.592 19.762 1.00 0.00 H +ATOM 779 CA THR 51 22.172 27.599 21.771 1.00 0.00 C +ATOM 780 HA THR 51 21.917 28.210 22.629 1.00 0.00 H +ATOM 781 CB THR 51 21.970 26.124 22.200 1.00 0.00 C +ATOM 782 HB THR 51 22.136 25.481 21.351 1.00 0.00 H +ATOM 783 CG2 THR 51 22.951 25.655 23.296 1.00 0.00 C +ATOM 784 HG21 THR 51 22.956 26.297 24.162 1.00 0.00 H +ATOM 785 HG22 THR 51 22.722 24.643 23.608 1.00 0.00 H +ATOM 786 HG23 THR 51 23.956 25.620 22.870 1.00 0.00 H +ATOM 787 OG1 THR 51 20.670 25.917 22.733 1.00 0.00 O +ATOM 788 HG1 THR 51 20.030 26.045 22.006 1.00 0.00 H +ATOM 789 C THR 51 23.652 27.888 21.483 1.00 0.00 C +ATOM 790 O THR 51 24.206 27.618 20.424 1.00 0.00 O +ATOM 791 N PHE 52 24.319 28.422 22.500 1.00 0.00 N +ATOM 792 H PHE 52 23.768 28.734 23.281 1.00 0.00 H +ATOM 793 CA PHE 52 25.768 28.588 22.617 1.00 0.00 C +ATOM 794 HA PHE 52 26.209 28.718 21.624 1.00 0.00 H +ATOM 795 CB PHE 52 25.934 29.876 23.433 1.00 0.00 C +ATOM 796 HB2 PHE 52 25.158 29.901 24.199 1.00 0.00 H +ATOM 797 HB3 PHE 52 26.852 29.852 24.017 1.00 0.00 H +ATOM 798 CG PHE 52 25.885 31.198 22.680 1.00 0.00 C +ATOM 799 CD1 PHE 52 25.012 32.221 23.103 1.00 0.00 C +ATOM 800 HD1 PHE 52 24.320 32.041 23.903 1.00 0.00 H +ATOM 801 CE1 PHE 52 25.045 33.487 22.491 1.00 0.00 C +ATOM 802 HE1 PHE 52 24.379 34.268 22.818 1.00 0.00 H +ATOM 803 CZ PHE 52 25.956 33.741 21.454 1.00 0.00 C +ATOM 804 HZ PHE 52 25.988 34.712 20.988 1.00 0.00 H +ATOM 805 CE2 PHE 52 26.810 32.725 21.004 1.00 0.00 C +ATOM 806 HE2 PHE 52 27.499 32.922 20.194 1.00 0.00 H +ATOM 807 CD2 PHE 52 26.762 31.458 21.608 1.00 0.00 C +ATOM 808 HD2 PHE 52 27.415 30.692 21.242 1.00 0.00 H +ATOM 809 C PHE 52 26.431 27.347 23.282 1.00 0.00 C +ATOM 810 O PHE 52 26.004 26.944 24.366 1.00 0.00 O +ATOM 811 N THR 53 27.533 26.805 22.728 1.00 0.00 N +ATOM 812 H THR 53 27.815 27.125 21.802 1.00 0.00 H +ATOM 813 CA THR 53 28.350 25.688 23.289 1.00 0.00 C +ATOM 814 HA THR 53 28.083 25.538 24.333 1.00 0.00 H +ATOM 815 CB THR 53 28.074 24.368 22.548 1.00 0.00 C +ATOM 816 HB THR 53 28.722 23.593 22.958 1.00 0.00 H +ATOM 817 CG2 THR 53 26.632 23.889 22.679 1.00 0.00 C +ATOM 818 HG21 THR 53 25.960 24.557 22.139 1.00 0.00 H +ATOM 819 HG22 THR 53 26.550 22.885 22.263 1.00 0.00 H +ATOM 820 HG23 THR 53 26.352 23.855 23.730 1.00 0.00 H +ATOM 821 OG1 THR 53 28.366 24.524 21.181 1.00 0.00 O +ATOM 822 HG1 THR 53 28.124 23.708 20.725 1.00 0.00 H +ATOM 823 C THR 53 29.872 25.956 23.241 1.00 0.00 C +ATOM 824 O THR 53 30.300 26.968 22.690 1.00 0.00 O +ATOM 825 N MET 54 30.713 25.105 23.856 1.00 0.00 N +ATOM 826 H MET 54 30.334 24.273 24.286 1.00 0.00 H +ATOM 827 CA MET 54 32.182 25.105 23.663 1.00 0.00 C +ATOM 828 HA MET 54 32.446 25.938 23.009 1.00 0.00 H +ATOM 829 CB MET 54 32.941 25.336 24.987 1.00 0.00 C +ATOM 830 HB2 MET 54 33.969 25.599 24.737 1.00 0.00 H +ATOM 831 HB3 MET 54 32.509 26.192 25.507 1.00 0.00 H +ATOM 832 CG MET 54 32.985 24.135 25.949 1.00 0.00 C +ATOM 833 HG2 MET 54 31.992 23.991 26.371 1.00 0.00 H +ATOM 834 HG3 MET 54 33.253 23.231 25.406 1.00 0.00 H +ATOM 835 SD MET 54 34.168 24.322 27.314 1.00 0.00 S +ATOM 836 CE MET 54 35.724 23.824 26.523 1.00 0.00 C +ATOM 837 HE1 MET 54 35.888 24.409 25.619 1.00 0.00 H +ATOM 838 HE2 MET 54 36.551 23.987 27.212 1.00 0.00 H +ATOM 839 HE3 MET 54 35.680 22.766 26.267 1.00 0.00 H +ATOM 840 C MET 54 32.662 23.829 22.946 1.00 0.00 C +ATOM 841 O MET 54 31.929 22.843 22.877 1.00 0.00 O +ATOM 842 N ALA 55 33.892 23.859 22.423 1.00 0.00 N +ATOM 843 H ALA 55 34.450 24.686 22.561 1.00 0.00 H +ATOM 844 CA ALA 55 34.554 22.718 21.782 1.00 0.00 C +ATOM 845 HA ALA 55 33.844 22.246 21.100 1.00 0.00 H +ATOM 846 CB ALA 55 35.732 23.266 20.959 1.00 0.00 C +ATOM 847 HB1 ALA 55 36.461 23.734 21.623 1.00 0.00 H +ATOM 848 HB2 ALA 55 36.219 22.451 20.421 1.00 0.00 H +ATOM 849 HB3 ALA 55 35.371 24.000 20.235 1.00 0.00 H +ATOM 850 C ALA 55 35.017 21.628 22.779 1.00 0.00 C +ATOM 851 O ALA 55 35.021 21.847 23.989 1.00 0.00 O +ATOM 852 N GLU 56 35.431 20.479 22.234 1.00 0.00 N +ATOM 853 H GLU 56 35.452 20.421 21.231 1.00 0.00 H +ATOM 854 CA GLU 56 36.104 19.352 22.911 1.00 0.00 C +ATOM 855 HA GLU 56 36.199 19.575 23.974 1.00 0.00 H +ATOM 856 CB GLU 56 35.238 18.076 22.755 1.00 0.00 C +ATOM 857 HB2 GLU 56 34.213 18.295 23.051 1.00 0.00 H +ATOM 858 HB3 GLU 56 35.204 17.849 21.688 1.00 0.00 H +ATOM 859 CG GLU 56 35.736 16.811 23.492 1.00 0.00 C +ATOM 860 HG2 GLU 56 35.664 15.981 22.790 1.00 0.00 H +ATOM 861 HG3 GLU 56 36.794 16.912 23.710 1.00 0.00 H +ATOM 862 CD GLU 56 34.988 16.399 24.782 1.00 0.00 C +ATOM 863 OE1 GLU 56 35.523 15.530 25.516 1.00 0.00 O +ATOM 864 OE2 GLU 56 33.843 16.839 25.048 1.00 0.00 O +ATOM 865 C GLU 56 37.541 19.172 22.368 1.00 0.00 C +ATOM 866 O GLU 56 38.465 19.135 23.205 1.00 0.00 O +ATOM 867 OXT GLU 56 37.715 19.114 21.119 1.00 0.00 O +HETATM 868 ZN ZN1 57 25.930 31.773 29.258 1.00 0.00 Zn +HETATM 869 N AN1 58 27.732 32.212 30.227 1.00 0.00 N +HETATM 870 C AN1 58 30.202 32.363 31.070 1.00 0.00 C +HETATM 871 C1 AN1 58 28.815 32.265 30.631 1.00 0.00 C +HETATM 872 H AN1 58 30.258 32.653 32.123 1.00 0.00 H +HETATM 873 H1 AN1 58 30.745 33.103 30.462 1.00 0.00 H +HETATM 874 H2 AN1 58 30.695 31.392 30.947 1.00 0.00 H +HETATM 875 N1 AZI 59 30.363 29.082 28.864 1.00 0.00 N +HETATM 876 N2 AZI 59 29.718 29.024 29.896 1.00 0.00 N +HETATM 877 N3 AZI 59 29.034 28.987 30.964 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 64 60 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 68 73 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 85 89 +CONECT 87 85 88 868 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 115 99 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 121 122 126 +CONECT 121 120 +CONECT 122 125 120 123 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 127 129 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 118 132 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 134 137 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 140 142 141 +CONECT 140 139 +CONECT 141 139 +CONECT 142 139 144 143 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 159 156 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 197 189 +CONECT 188 187 +CONECT 189 187 190 191 192 +CONECT 190 189 +CONECT 191 189 +CONECT 192 189 193 194 +CONECT 193 192 +CONECT 194 192 196 195 +CONECT 195 194 +CONECT 196 194 +CONECT 197 187 198 199 +CONECT 198 197 +CONECT 199 197 201 200 +CONECT 200 199 +CONECT 201 218 199 203 202 +CONECT 202 201 +CONECT 203 206 201 204 205 +CONECT 204 203 +CONECT 205 203 +CONECT 206 207 216 203 +CONECT 207 209 208 206 +CONECT 208 207 +CONECT 209 210 211 207 +CONECT 210 209 +CONECT 211 212 209 214 +CONECT 212 213 211 +CONECT 213 212 +CONECT 214 211 215 216 +CONECT 215 214 +CONECT 216 214 206 217 +CONECT 217 216 +CONECT 218 219 220 201 +CONECT 219 218 +CONECT 220 222 218 221 +CONECT 221 220 +CONECT 222 223 240 224 220 +CONECT 223 222 +CONECT 224 227 222 225 226 +CONECT 225 224 +CONECT 226 224 +CONECT 227 229 228 230 224 +CONECT 228 227 +CONECT 229 227 +CONECT 230 231 227 232 233 +CONECT 231 230 +CONECT 232 230 +CONECT 233 230 235 236 234 +CONECT 234 233 +CONECT 235 233 +CONECT 236 239 233 237 238 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 241 222 242 +CONECT 241 240 +CONECT 242 240 244 243 +CONECT 243 242 +CONECT 244 247 242 245 246 +CONECT 245 244 +CONECT 246 244 +CONECT 247 248 249 244 +CONECT 248 247 +CONECT 249 251 247 250 +CONECT 250 249 +CONECT 251 253 252 263 249 +CONECT 252 251 +CONECT 253 259 254 255 251 +CONECT 254 253 +CONECT 255 257 253 256 258 +CONECT 256 255 +CONECT 257 255 +CONECT 258 255 +CONECT 259 261 260 262 253 +CONECT 260 259 +CONECT 261 259 +CONECT 262 259 +CONECT 263 265 251 264 +CONECT 264 263 +CONECT 265 275 266 263 +CONECT 266 267 265 276 269 +CONECT 267 268 282 266 +CONECT 268 267 +CONECT 269 266 270 277 278 +CONECT 270 271 272 269 +CONECT 271 274 280 270 +CONECT 272 273 270 279 +CONECT 273 274 281 272 +CONECT 274 868 271 273 +CONECT 275 265 +CONECT 276 266 +CONECT 277 269 +CONECT 278 269 +CONECT 279 272 +CONECT 280 271 +CONECT 281 273 +CONECT 282 284 267 283 +CONECT 283 282 +CONECT 284 285 286 294 282 +CONECT 285 284 +CONECT 286 287 288 284 292 +CONECT 287 286 +CONECT 288 291 290 286 289 +CONECT 289 288 +CONECT 290 288 +CONECT 291 288 +CONECT 292 286 293 +CONECT 293 292 +CONECT 294 296 284 295 +CONECT 295 294 +CONECT 296 306 297 294 +CONECT 297 298 300 296 307 +CONECT 298 299 313 297 +CONECT 299 298 +CONECT 300 308 309 297 301 +CONECT 301 300 302 303 +CONECT 302 311 301 305 +CONECT 303 301 310 304 +CONECT 304 305 303 312 +CONECT 305 302 868 304 +CONECT 306 296 +CONECT 307 297 +CONECT 308 300 +CONECT 309 300 +CONECT 310 303 +CONECT 311 302 +CONECT 312 304 +CONECT 313 315 298 314 +CONECT 314 313 +CONECT 315 326 316 313 317 +CONECT 316 315 +CONECT 317 315 320 319 318 +CONECT 318 317 +CONECT 319 317 +CONECT 320 323 322 317 321 +CONECT 321 320 +CONECT 322 320 +CONECT 323 324 325 320 +CONECT 324 323 +CONECT 325 323 +CONECT 326 328 327 315 +CONECT 327 326 +CONECT 328 330 329 326 +CONECT 329 328 +CONECT 330 336 332 331 328 +CONECT 331 330 +CONECT 332 334 333 330 335 +CONECT 333 332 +CONECT 334 332 +CONECT 335 332 +CONECT 336 338 337 330 +CONECT 337 336 +CONECT 338 340 339 336 +CONECT 339 338 +CONECT 340 352 342 341 338 +CONECT 341 340 +CONECT 342 343 348 340 344 +CONECT 343 342 +CONECT 344 342 346 347 345 +CONECT 345 344 +CONECT 346 344 +CONECT 347 344 +CONECT 348 349 350 342 351 +CONECT 349 348 +CONECT 350 348 +CONECT 351 348 +CONECT 352 353 354 340 +CONECT 353 352 +CONECT 354 356 352 355 +CONECT 355 354 +CONECT 356 358 357 364 354 +CONECT 357 356 +CONECT 358 361 359 360 356 +CONECT 359 358 +CONECT 360 358 +CONECT 361 362 363 358 +CONECT 362 361 +CONECT 363 361 +CONECT 364 356 366 365 +CONECT 365 364 +CONECT 366 367 368 364 +CONECT 367 366 +CONECT 368 370 366 383 369 +CONECT 369 368 +CONECT 370 372 371 373 368 +CONECT 371 370 +CONECT 372 370 +CONECT 373 379 370 375 374 +CONECT 374 373 +CONECT 375 376 373 377 378 +CONECT 376 375 +CONECT 377 375 +CONECT 378 375 +CONECT 379 382 380 381 373 +CONECT 380 379 +CONECT 381 379 +CONECT 382 379 +CONECT 383 385 368 384 +CONECT 384 383 +CONECT 385 386 387 383 +CONECT 386 385 +CONECT 387 389 385 388 393 +CONECT 388 387 +CONECT 389 392 390 391 387 +CONECT 390 389 +CONECT 391 389 +CONECT 392 389 +CONECT 393 387 394 395 +CONECT 394 393 +CONECT 395 393 396 397 +CONECT 396 395 +CONECT 397 395 398 399 408 +CONECT 398 397 +CONECT 399 402 400 397 401 +CONECT 400 399 +CONECT 401 399 +CONECT 402 403 404 405 399 +CONECT 403 402 +CONECT 404 402 +CONECT 405 402 407 406 +CONECT 406 405 +CONECT 407 405 +CONECT 408 397 410 409 +CONECT 409 408 +CONECT 410 411 408 412 +CONECT 411 410 +CONECT 412 410 414 418 413 +CONECT 413 412 +CONECT 414 415 417 412 416 +CONECT 415 414 +CONECT 416 414 +CONECT 417 414 +CONECT 418 420 412 419 +CONECT 419 418 +CONECT 420 421 422 418 +CONECT 421 420 +CONECT 422 424 420 423 433 +CONECT 423 422 +CONECT 424 425 426 427 422 +CONECT 425 424 +CONECT 426 424 +CONECT 427 430 424 429 428 +CONECT 428 427 +CONECT 429 427 +CONECT 430 432 431 427 +CONECT 431 430 +CONECT 432 430 +CONECT 433 422 435 434 +CONECT 434 433 +CONECT 435 436 433 437 +CONECT 436 435 +CONECT 437 435 439 438 455 +CONECT 438 437 +CONECT 439 442 440 441 437 +CONECT 440 439 +CONECT 441 439 +CONECT 442 444 445 443 439 +CONECT 443 442 +CONECT 444 442 +CONECT 445 448 446 447 442 +CONECT 446 445 +CONECT 447 445 +CONECT 448 451 450 449 445 +CONECT 449 448 +CONECT 450 448 +CONECT 451 453 454 452 448 +CONECT 452 451 +CONECT 453 451 +CONECT 454 451 +CONECT 455 437 457 456 +CONECT 456 455 +CONECT 457 458 455 459 +CONECT 458 457 +CONECT 459 457 461 460 475 +CONECT 460 459 +CONECT 461 464 462 459 463 +CONECT 462 461 +CONECT 463 461 +CONECT 464 465 473 461 +CONECT 465 467 466 464 +CONECT 466 465 +CONECT 467 468 469 465 +CONECT 468 467 +CONECT 469 470 467 471 +CONECT 470 469 +CONECT 471 469 472 473 +CONECT 472 471 +CONECT 473 471 464 474 +CONECT 474 473 +CONECT 475 477 459 476 +CONECT 476 475 +CONECT 477 478 479 475 +CONECT 478 477 +CONECT 479 481 477 489 480 +CONECT 480 479 +CONECT 481 482 487 483 479 +CONECT 482 481 +CONECT 483 485 481 486 484 +CONECT 484 483 +CONECT 485 483 +CONECT 486 483 +CONECT 487 488 481 +CONECT 488 487 +CONECT 489 491 479 490 +CONECT 490 489 +CONECT 491 492 493 489 +CONECT 492 491 +CONECT 493 495 491 494 511 +CONECT 494 493 +CONECT 495 498 496 497 493 +CONECT 496 495 +CONECT 497 495 +CONECT 498 501 500 499 495 +CONECT 499 498 +CONECT 500 498 +CONECT 501 504 502 503 498 +CONECT 502 501 +CONECT 503 501 +CONECT 504 506 505 507 501 +CONECT 505 504 +CONECT 506 504 +CONECT 507 509 504 510 508 +CONECT 508 507 +CONECT 509 507 +CONECT 510 507 +CONECT 511 493 513 512 +CONECT 512 511 +CONECT 513 514 511 515 +CONECT 514 513 +CONECT 515 513 516 517 521 +CONECT 516 515 +CONECT 517 520 515 518 519 +CONECT 518 517 +CONECT 519 517 +CONECT 520 517 +CONECT 521 515 523 522 +CONECT 522 521 +CONECT 523 524 521 525 +CONECT 524 523 +CONECT 525 523 545 527 526 +CONECT 526 525 +CONECT 527 530 525 529 528 +CONECT 528 527 +CONECT 529 527 +CONECT 530 531 532 533 527 +CONECT 531 530 +CONECT 532 530 +CONECT 533 536 530 535 534 +CONECT 534 533 +CONECT 535 533 +CONECT 536 537 538 533 +CONECT 537 536 +CONECT 538 539 536 542 +CONECT 539 540 541 538 +CONECT 540 539 +CONECT 541 539 +CONECT 542 538 544 543 +CONECT 543 542 +CONECT 544 542 +CONECT 545 547 525 546 +CONECT 546 545 +CONECT 547 548 549 545 +CONECT 548 547 +CONECT 549 551 547 555 550 +CONECT 550 549 +CONECT 551 552 554 553 549 +CONECT 552 551 +CONECT 553 551 +CONECT 554 551 +CONECT 555 549 557 556 +CONECT 556 555 +CONECT 557 558 555 559 +CONECT 558 557 +CONECT 559 561 557 560 569 +CONECT 560 559 +CONECT 561 564 562 563 559 +CONECT 562 561 +CONECT 563 561 +CONECT 564 566 565 561 +CONECT 565 564 +CONECT 566 567 568 564 +CONECT 567 566 +CONECT 568 566 +CONECT 569 559 571 570 +CONECT 570 569 +CONECT 571 572 569 573 +CONECT 572 571 +CONECT 573 571 575 574 581 +CONECT 574 573 +CONECT 575 578 576 573 577 +CONECT 576 575 +CONECT 577 575 +CONECT 578 580 579 575 +CONECT 579 578 +CONECT 580 578 +CONECT 581 573 583 582 +CONECT 582 581 +CONECT 583 584 581 585 +CONECT 584 583 +CONECT 585 583 587 600 586 +CONECT 586 585 +CONECT 587 589 588 585 590 +CONECT 588 587 +CONECT 589 587 +CONECT 590 587 596 591 592 +CONECT 591 590 +CONECT 592 590 593 594 595 +CONECT 593 592 +CONECT 594 592 +CONECT 595 592 +CONECT 596 597 599 598 590 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 +CONECT 600 602 585 601 +CONECT 601 600 +CONECT 602 603 604 600 +CONECT 603 602 +CONECT 604 607 602 606 605 +CONECT 605 604 +CONECT 606 604 +CONECT 607 609 608 604 +CONECT 608 607 +CONECT 609 611 610 607 +CONECT 610 609 +CONECT 611 622 612 613 609 +CONECT 612 611 +CONECT 613 615 611 614 616 +CONECT 614 613 +CONECT 615 613 +CONECT 616 613 617 619 618 +CONECT 617 616 +CONECT 618 616 +CONECT 619 621 616 620 +CONECT 620 619 +CONECT 621 619 +CONECT 622 624 623 611 +CONECT 623 622 +CONECT 624 626 625 622 +CONECT 625 624 +CONECT 626 634 628 627 624 +CONECT 627 626 +CONECT 628 631 629 630 626 +CONECT 629 628 +CONECT 630 628 +CONECT 631 633 632 628 +CONECT 632 631 +CONECT 633 631 +CONECT 634 635 636 626 +CONECT 635 634 +CONECT 636 638 634 637 +CONECT 637 636 +CONECT 638 641 639 640 636 +CONECT 639 638 +CONECT 640 638 +CONECT 641 643 642 638 +CONECT 642 641 +CONECT 643 645 644 641 +CONECT 644 643 +CONECT 645 647 646 656 643 +CONECT 646 645 +CONECT 647 649 648 650 645 +CONECT 648 647 +CONECT 649 647 +CONECT 650 652 647 653 651 +CONECT 651 650 +CONECT 652 650 +CONECT 653 654 650 655 +CONECT 654 653 +CONECT 655 653 +CONECT 656 658 645 657 +CONECT 657 656 +CONECT 658 659 660 656 +CONECT 659 658 +CONECT 660 674 658 661 662 +CONECT 661 660 +CONECT 662 660 664 665 663 +CONECT 663 662 +CONECT 664 662 +CONECT 665 666 662 672 +CONECT 666 667 668 665 +CONECT 667 666 +CONECT 668 669 666 670 +CONECT 669 668 +CONECT 670 668 672 671 +CONECT 671 670 +CONECT 672 665 670 673 +CONECT 673 672 +CONECT 674 676 675 660 +CONECT 675 674 +CONECT 676 678 677 674 +CONECT 677 676 +CONECT 678 679 680 688 676 +CONECT 679 678 +CONECT 680 682 686 678 681 +CONECT 681 680 +CONECT 682 683 684 685 680 +CONECT 683 682 +CONECT 684 682 +CONECT 685 682 +CONECT 686 687 680 +CONECT 687 686 +CONECT 688 690 678 689 +CONECT 689 688 +CONECT 690 691 692 688 +CONECT 691 690 +CONECT 692 705 694 690 693 +CONECT 693 692 +CONECT 694 697 695 692 696 +CONECT 695 694 +CONECT 696 694 +CONECT 697 700 698 699 694 +CONECT 698 697 +CONECT 699 697 +CONECT 700 702 697 701 +CONECT 701 700 +CONECT 702 704 703 700 +CONECT 703 702 +CONECT 704 702 +CONECT 705 706 707 692 +CONECT 706 705 +CONECT 707 709 705 708 +CONECT 708 707 +CONECT 709 710 717 711 707 +CONECT 710 709 +CONECT 711 714 709 712 713 +CONECT 712 711 +CONECT 713 711 +CONECT 714 716 711 715 +CONECT 715 714 +CONECT 716 714 +CONECT 717 719 709 718 +CONECT 718 717 +CONECT 719 720 721 717 +CONECT 720 719 +CONECT 721 723 719 729 722 +CONECT 722 721 +CONECT 723 725 724 726 721 +CONECT 724 723 +CONECT 725 723 +CONECT 726 727 723 728 +CONECT 727 726 +CONECT 728 726 +CONECT 729 731 721 730 +CONECT 730 729 +CONECT 731 732 733 729 +CONECT 732 731 +CONECT 733 735 734 731 739 +CONECT 734 733 +CONECT 735 738 737 736 733 +CONECT 736 735 +CONECT 737 735 +CONECT 738 735 +CONECT 739 733 740 741 +CONECT 740 739 +CONECT 741 739 742 743 +CONECT 742 741 +CONECT 743 741 744 745 753 +CONECT 744 743 +CONECT 745 747 743 751 746 +CONECT 746 745 +CONECT 747 748 750 749 745 +CONECT 748 747 +CONECT 749 747 +CONECT 750 747 +CONECT 751 752 745 +CONECT 752 751 +CONECT 753 743 755 754 +CONECT 754 753 +CONECT 755 756 757 753 +CONECT 756 755 +CONECT 757 758 755 759 775 +CONECT 758 757 +CONECT 759 762 757 761 760 +CONECT 760 759 +CONECT 761 759 +CONECT 762 765 763 764 759 +CONECT 763 762 +CONECT 764 762 +CONECT 765 768 767 766 762 +CONECT 766 765 +CONECT 767 765 +CONECT 768 771 770 769 765 +CONECT 769 768 +CONECT 770 768 +CONECT 771 773 774 772 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 771 +CONECT 775 757 777 776 +CONECT 776 775 +CONECT 777 778 775 779 +CONECT 778 777 +CONECT 779 777 789 781 780 +CONECT 780 779 +CONECT 781 782 779 787 783 +CONECT 782 781 +CONECT 783 781 786 785 784 +CONECT 784 783 +CONECT 785 783 +CONECT 786 783 +CONECT 787 788 781 +CONECT 788 787 +CONECT 789 790 779 791 +CONECT 790 789 +CONECT 791 789 793 792 +CONECT 792 791 +CONECT 793 794 791 809 795 +CONECT 794 793 +CONECT 795 793 798 797 796 +CONECT 796 795 +CONECT 797 795 +CONECT 798 807 799 795 +CONECT 799 801 798 800 +CONECT 800 799 +CONECT 801 803 802 799 +CONECT 802 801 +CONECT 803 804 805 801 +CONECT 804 803 +CONECT 805 806 803 807 +CONECT 806 805 +CONECT 807 805 808 798 +CONECT 808 807 +CONECT 809 793 811 810 +CONECT 810 809 +CONECT 811 812 809 813 +CONECT 812 811 +CONECT 813 815 811 823 814 +CONECT 814 813 +CONECT 815 821 817 816 813 +CONECT 816 815 +CONECT 817 818 819 815 820 +CONECT 818 817 +CONECT 819 817 +CONECT 820 817 +CONECT 821 822 815 +CONECT 822 821 +CONECT 823 824 813 825 +CONECT 824 823 +CONECT 825 823 827 826 +CONECT 826 825 +CONECT 827 840 828 825 829 +CONECT 828 827 +CONECT 829 827 830 831 832 +CONECT 830 829 +CONECT 831 829 +CONECT 832 829 834 833 835 +CONECT 833 832 +CONECT 834 832 +CONECT 835 832 836 +CONECT 836 837 839 838 835 +CONECT 837 836 +CONECT 838 836 +CONECT 839 836 +CONECT 840 842 841 827 +CONECT 841 840 +CONECT 842 844 843 840 +CONECT 843 842 +CONECT 844 846 845 842 850 +CONECT 845 844 +CONECT 846 849 848 847 844 +CONECT 847 846 +CONECT 848 846 +CONECT 849 846 +CONECT 850 844 852 851 +CONECT 851 850 +CONECT 852 853 850 854 +CONECT 853 852 +CONECT 854 852 865 856 855 +CONECT 855 854 +CONECT 856 858 854 857 859 +CONECT 857 856 +CONECT 858 856 +CONECT 859 856 860 861 862 +CONECT 860 859 +CONECT 861 859 +CONECT 862 859 864 863 +CONECT 863 862 +CONECT 864 862 +CONECT 865 867 854 866 +CONECT 866 865 +CONECT 867 865 +CONECT 868 87 305 869 274 +CONECT 869 868 871 +CONECT 870 873 871 874 872 +CONECT 871 869 870 +CONECT 872 870 +CONECT 873 870 +CONECT 874 870 +CONECT 875 876 +CONECT 876 875 877 +CONECT 877 876 +MASTER 0 0 0 0 0 0 0 0 877 0 877 0 +END diff --git a/tests/nsga2/min_mol_iter_3.pdb b/tests/nsga2/min_mol_iter_3.pdb new file mode 100644 index 0000000..93ef165 --- /dev/null +++ b/tests/nsga2/min_mol_iter_3.pdb @@ -0,0 +1,1785 @@ +COMPND fitness: -6.2239 90.03083333333325 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 50.124 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.128 37.937 23.379 1.00 0.00 N +ATOM 2 H1 MET 1 15.115 38.352 24.304 1.00 0.00 H +ATOM 3 H2 MET 1 14.353 38.281 22.845 1.00 0.00 H +ATOM 4 H3 MET 1 15.989 38.231 22.950 1.00 0.00 H +ATOM 5 CA MET 1 15.114 36.469 23.492 1.00 0.00 C +ATOM 6 HA MET 1 14.154 36.172 23.930 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.810 22.104 1.00 0.00 C +ATOM 8 HB2 MET 1 14.395 36.081 21.502 1.00 0.00 H +ATOM 9 HB3 MET 1 16.151 36.200 21.624 1.00 0.00 H +ATOM 10 CG MET 1 15.368 34.269 22.154 1.00 0.00 C +ATOM 11 HG2 MET 1 16.256 34.008 22.740 1.00 0.00 H +ATOM 12 HG3 MET 1 14.490 33.864 22.670 1.00 0.00 H +ATOM 13 SD MET 1 15.523 33.454 20.540 1.00 0.00 S +ATOM 14 CE MET 1 13.825 33.570 19.902 1.00 0.00 C +ATOM 15 HE1 MET 1 13.514 34.612 19.846 1.00 0.00 H +ATOM 16 HE2 MET 1 13.786 33.136 18.902 1.00 0.00 H +ATOM 17 HE3 MET 1 13.144 33.019 20.553 1.00 0.00 H +ATOM 18 C MET 1 16.215 36.013 24.449 1.00 0.00 C +ATOM 19 O MET 1 17.372 36.346 24.223 1.00 0.00 O +ATOM 20 N GLN 2 15.871 35.224 25.474 1.00 0.00 N +ATOM 21 H GLN 2 14.897 35.087 25.675 1.00 0.00 H +ATOM 22 CA GLN 2 16.831 34.496 26.306 1.00 0.00 C +ATOM 23 HA GLN 2 17.643 35.162 26.593 1.00 0.00 H +ATOM 24 CB GLN 2 16.127 34.008 27.587 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.159 33.579 27.318 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.708 33.210 28.060 1.00 0.00 H +ATOM 27 CG GLN 2 15.903 35.114 28.632 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.477 35.983 28.143 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.171 34.756 29.353 1.00 0.00 H +ATOM 30 CD GLN 2 17.153 35.508 29.416 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.264 35.044 29.192 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.019 36.331 30.429 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.839 36.559 30.955 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.114 36.721 30.646 1.00 0.00 H +ATOM 35 C GLN 2 17.469 33.325 25.522 1.00 0.00 C +ATOM 36 O GLN 2 17.052 32.167 25.651 1.00 0.00 O +ATOM 37 N TYR 3 18.463 33.623 24.678 1.00 0.00 N +ATOM 38 H TYR 3 18.765 34.592 24.628 1.00 0.00 H +ATOM 39 CA TYR 3 19.234 32.609 23.954 1.00 0.00 C +ATOM 40 HA TYR 3 18.545 31.959 23.422 1.00 0.00 H +ATOM 41 CB TYR 3 20.170 33.262 22.941 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.877 33.900 23.476 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.723 32.438 22.497 1.00 0.00 H +ATOM 44 CG TYR 3 19.600 34.062 21.781 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.519 33.459 20.512 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.802 32.423 20.390 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.149 34.213 19.385 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.118 33.754 18.409 1.00 0.00 H +ATOM 49 CZ TYR 3 18.855 35.585 19.528 1.00 0.00 C +ATOM 50 OH TYR 3 18.517 36.324 18.441 1.00 0.00 O +ATOM 51 HH TYR 3 18.718 35.875 17.614 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.941 36.195 20.795 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.739 37.253 20.885 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.327 35.436 21.918 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.448 35.924 22.876 1.00 0.00 H +ATOM 56 C TYR 3 20.072 31.754 24.926 1.00 0.00 C +ATOM 57 O TYR 3 20.489 32.242 25.980 1.00 0.00 O +ATOM 58 N LYS 4 20.339 30.479 24.600 1.00 0.00 N +ATOM 59 H LYS 4 20.151 30.180 23.644 1.00 0.00 H +ATOM 60 CA LYS 4 20.960 29.479 25.496 1.00 0.00 C +ATOM 61 HA LYS 4 20.692 29.716 26.523 1.00 0.00 H +ATOM 62 CB LYS 4 20.389 28.078 25.169 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.359 27.961 24.086 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.082 27.325 25.544 1.00 0.00 H +ATOM 65 CG LYS 4 18.993 27.726 25.738 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.817 26.675 25.502 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.009 27.823 26.824 1.00 0.00 H +ATOM 68 CD LYS 4 17.809 28.534 25.173 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.798 29.537 25.609 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.962 28.643 24.097 1.00 0.00 H +ATOM 71 CE LYS 4 16.441 27.842 25.378 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.715 28.351 24.738 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.517 26.807 25.026 1.00 0.00 H +ATOM 74 NZ LYS 4 15.935 27.871 26.782 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.755 28.812 27.098 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.064 27.350 26.889 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.572 27.463 27.463 1.00 0.00 H +ATOM 78 C LYS 4 22.499 29.490 25.466 1.00 0.00 C +ATOM 79 O LYS 4 23.140 29.867 24.490 1.00 0.00 O +HETATM 80 N HX1 5 23.130 29.035 26.548 1.00 0.00 N +HETATM 81 CA HX1 5 24.591 28.856 26.679 1.00 0.00 C +HETATM 82 C HX1 5 24.878 27.688 27.631 1.00 0.00 C +HETATM 83 O HX1 5 24.428 27.708 28.777 1.00 0.00 O +HETATM 84 CB HX1 5 25.222 30.175 27.180 1.00 0.00 C +HETATM 85 CG HX1 5 26.737 30.247 27.288 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.646 29.286 26.930 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.420 31.336 27.850 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.719 30.994 27.776 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.886 29.754 27.285 1.00 0.00 N +HETATM 90 H HX1 5 22.559 28.844 27.370 1.00 0.00 H +HETATM 91 HA HX1 5 25.018 28.612 25.702 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.806 30.413 28.160 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.913 30.973 26.501 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.458 28.305 26.513 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.519 31.581 28.203 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.738 29.194 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.579 26.661 27.147 1.00 0.00 N +ATOM 98 H ILE 6 25.921 26.711 26.193 1.00 0.00 H +ATOM 99 CA ILE 6 25.970 25.469 27.917 1.00 0.00 C +ATOM 100 HA ILE 6 25.283 25.357 28.755 1.00 0.00 H +ATOM 101 CB ILE 6 25.813 24.203 27.035 1.00 0.00 C +ATOM 102 HB ILE 6 26.347 24.367 26.099 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.392 22.937 27.698 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.889 22.736 28.645 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.267 22.079 27.038 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.465 23.049 27.864 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.304 24.011 26.726 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.764 23.868 27.661 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.914 24.914 26.252 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.964 22.843 25.793 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.140 21.891 26.293 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.908 22.895 25.523 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.564 22.899 24.885 1.00 0.00 H +ATOM 114 C ILE 6 27.370 25.661 28.537 1.00 0.00 C +ATOM 115 O ILE 6 28.186 26.422 28.017 1.00 0.00 O +ATOM 116 N VAL 7 27.605 25.035 29.694 1.00 0.00 N +ATOM 117 H VAL 7 26.884 24.405 30.032 1.00 0.00 H +ATOM 118 CA VAL 7 28.769 25.251 30.572 1.00 0.00 C +ATOM 119 HA VAL 7 28.849 26.325 30.732 1.00 0.00 H +ATOM 120 CB VAL 7 28.470 24.592 31.936 1.00 0.00 C +ATOM 121 HB VAL 7 27.460 24.891 32.229 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.498 23.060 31.893 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.507 22.695 31.701 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.158 22.662 32.842 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.845 22.689 31.104 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.397 25.060 33.063 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.408 26.149 33.096 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.024 24.680 34.015 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.403 24.676 32.902 1.00 0.00 H +ATOM 130 C VAL 7 30.119 24.780 29.995 1.00 0.00 C +ATOM 131 O VAL 7 30.207 23.763 29.310 1.00 0.00 O +ATOM 132 N ARG 8 31.201 25.497 30.343 1.00 0.00 N +ATOM 133 H ARG 8 31.031 26.423 30.713 1.00 0.00 H +ATOM 134 CA ARG 8 32.608 25.082 30.154 1.00 0.00 C +ATOM 135 HA ARG 8 32.717 24.857 29.094 1.00 0.00 H +ATOM 136 CB ARG 8 33.575 26.241 30.501 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.546 25.995 30.072 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.247 27.151 30.004 1.00 0.00 H +ATOM 139 CG ARG 8 33.814 26.544 32.001 1.00 0.00 C +ATOM 140 HG2 ARG 8 34.126 25.632 32.506 1.00 0.00 H +ATOM 141 HG3 ARG 8 34.652 27.235 32.093 1.00 0.00 H +ATOM 142 CD ARG 8 32.636 27.142 32.778 1.00 0.00 C +ATOM 143 HD2 ARG 8 31.766 26.524 32.631 1.00 0.00 H +ATOM 144 HD3 ARG 8 32.851 27.100 33.836 1.00 0.00 H +ATOM 145 NE ARG 8 32.321 28.531 32.389 1.00 0.00 N +ATOM 146 HE ARG 8 31.868 28.645 31.483 1.00 0.00 H +ATOM 147 CZ ARG 8 32.417 29.619 33.139 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.818 30.717 32.782 1.00 0.00 N +ATOM 149 HH11 ARG 8 31.188 30.675 31.981 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.731 31.448 33.453 1.00 0.00 H +ATOM 151 NH2 ARG 8 33.086 29.637 34.256 1.00 0.00 N +ATOM 152 HH21 ARG 8 33.619 28.829 34.514 1.00 0.00 H +ATOM 153 HH22 ARG 8 33.065 30.431 34.886 1.00 0.00 H +ATOM 154 C ARG 8 32.993 23.796 30.906 1.00 0.00 C +ATOM 155 O ARG 8 32.490 23.532 31.997 1.00 0.00 O +ATOM 156 N GLY 9 33.997 23.086 30.385 1.00 0.00 N +ATOM 157 H GLY 9 34.336 23.350 29.474 1.00 0.00 H +ATOM 158 CA GLY 9 34.544 21.859 30.982 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.546 21.680 30.585 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.627 21.989 32.066 1.00 0.00 H +ATOM 161 C GLY 9 33.690 20.615 30.703 1.00 0.00 C +ATOM 162 O GLY 9 32.893 20.602 29.772 1.00 0.00 O +ATOM 163 N LYS 10 33.877 19.558 31.507 1.00 0.00 N +ATOM 164 H LYS 10 34.624 19.619 32.176 1.00 0.00 H +ATOM 165 CA LYS 10 33.145 18.277 31.372 1.00 0.00 C +ATOM 166 HA LYS 10 32.234 18.481 30.799 1.00 0.00 H +ATOM 167 CB LYS 10 34.004 17.293 30.544 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.660 17.868 29.891 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.633 16.707 31.215 1.00 0.00 H +ATOM 170 CG LYS 10 33.182 16.351 29.644 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.576 15.685 30.259 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.517 16.953 29.025 1.00 0.00 H +ATOM 173 CD LYS 10 34.095 15.518 28.728 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.765 16.189 28.186 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.693 14.843 29.337 1.00 0.00 H +ATOM 176 CE LYS 10 33.287 14.702 27.711 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.727 13.931 28.247 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.567 15.368 27.228 1.00 0.00 H +ATOM 179 NZ LYS 10 34.153 14.097 26.667 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.950 13.593 27.047 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.637 13.513 26.029 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.558 14.828 26.065 1.00 0.00 H +ATOM 183 C LYS 10 32.647 17.678 32.701 1.00 0.00 C +ATOM 184 O LYS 10 31.863 16.738 32.687 1.00 0.00 O +ATOM 185 N SER 11 33.082 18.223 33.848 1.00 0.00 N +ATOM 186 H SER 11 33.752 18.967 33.790 1.00 0.00 H +ATOM 187 CA SER 11 32.570 17.839 35.182 1.00 0.00 C +ATOM 188 HA SER 11 32.446 16.755 35.225 1.00 0.00 H +ATOM 189 CB SER 11 33.539 18.260 36.295 1.00 0.00 C +ATOM 190 HB2 SER 11 33.665 19.345 36.284 1.00 0.00 H +ATOM 191 HB3 SER 11 33.107 17.977 37.259 1.00 0.00 H +ATOM 192 OG SER 11 34.809 17.642 36.180 1.00 0.00 O +ATOM 193 HG SER 11 35.427 18.251 35.756 1.00 0.00 H +ATOM 194 C SER 11 31.199 18.462 35.496 1.00 0.00 C +ATOM 195 O SER 11 30.406 17.878 36.230 1.00 0.00 O +ATOM 196 N CYS 12 30.923 19.656 34.964 1.00 0.00 N +ATOM 197 H CYS 12 31.599 20.053 34.332 1.00 0.00 H +ATOM 198 CA CYS 12 29.611 20.301 35.006 1.00 0.00 C +ATOM 199 HA CYS 12 29.036 19.906 35.847 1.00 0.00 H +ATOM 200 CB CYS 12 29.796 21.821 35.196 1.00 0.00 C +ATOM 201 HB2 CYS 12 30.330 22.228 34.334 1.00 0.00 H +ATOM 202 HB3 CYS 12 28.812 22.284 35.254 1.00 0.00 H +ATOM 203 SG CYS 12 30.722 22.206 36.721 1.00 0.00 S +ATOM 204 HG CYS 12 29.845 23.085 37.226 1.00 0.00 H +ATOM 205 C CYS 12 28.846 19.994 33.710 1.00 0.00 C +ATOM 206 O CYS 12 29.461 19.846 32.657 1.00 0.00 O +ATOM 207 N LYS 13 27.505 19.956 33.760 1.00 0.00 N +ATOM 208 H LYS 13 27.067 20.025 34.666 1.00 0.00 H +ATOM 209 CA LYS 13 26.638 19.689 32.587 1.00 0.00 C +ATOM 210 HA LYS 13 27.243 19.869 31.686 1.00 0.00 H +ATOM 211 CB LYS 13 26.243 18.193 32.591 1.00 0.00 C +ATOM 212 HB2 LYS 13 27.073 17.620 33.007 1.00 0.00 H +ATOM 213 HB3 LYS 13 25.379 18.062 33.237 1.00 0.00 H +ATOM 214 CG LYS 13 25.952 17.630 31.186 1.00 0.00 C +ATOM 215 HG2 LYS 13 25.065 18.101 30.761 1.00 0.00 H +ATOM 216 HG3 LYS 13 26.801 17.853 30.536 1.00 0.00 H +ATOM 217 CD LYS 13 25.755 16.105 31.210 1.00 0.00 C +ATOM 218 HD2 LYS 13 25.746 15.739 30.181 1.00 0.00 H +ATOM 219 HD3 LYS 13 26.602 15.645 31.726 1.00 0.00 H +ATOM 220 CE LYS 13 24.441 15.690 31.887 1.00 0.00 C +ATOM 221 HE2 LYS 13 24.310 16.264 32.808 1.00 0.00 H +ATOM 222 HE3 LYS 13 23.614 15.945 31.214 1.00 0.00 H +ATOM 223 NZ LYS 13 24.411 14.238 32.200 1.00 0.00 N +ATOM 224 HZ1 LYS 13 25.113 13.979 32.890 1.00 0.00 H +ATOM 225 HZ2 LYS 13 23.525 13.972 32.618 1.00 0.00 H +ATOM 226 HZ3 LYS 13 24.608 13.675 31.375 1.00 0.00 H +ATOM 227 C LYS 13 25.442 20.651 32.462 1.00 0.00 C +ATOM 228 O LYS 13 24.474 20.361 31.772 1.00 0.00 O +ATOM 229 N GLY 14 25.489 21.778 33.176 1.00 0.00 N +ATOM 230 H GLY 14 26.334 21.976 33.674 1.00 0.00 H +ATOM 231 CA GLY 14 24.400 22.746 33.252 1.00 0.00 C +ATOM 232 HA2 GLY 14 23.453 22.214 33.347 1.00 0.00 H +ATOM 233 HA3 GLY 14 24.522 23.365 34.139 1.00 0.00 H +ATOM 234 C GLY 14 24.283 23.694 32.040 1.00 0.00 C +ATOM 235 O GLY 14 25.205 23.839 31.229 1.00 0.00 O +ATOM 236 N VAL 15 23.147 24.397 31.969 1.00 0.00 N +ATOM 237 H VAL 15 22.465 24.249 32.702 1.00 0.00 H +ATOM 238 CA VAL 15 22.785 25.364 30.936 1.00 0.00 C +ATOM 239 HA VAL 15 23.676 25.622 30.371 1.00 0.00 H +ATOM 240 CB VAL 15 21.782 24.726 29.948 1.00 0.00 C +ATOM 241 HB VAL 15 22.261 23.828 29.523 1.00 0.00 H +ATOM 242 CG1 VAL 15 20.463 24.268 30.608 1.00 0.00 C +ATOM 243 HG11 VAL 15 19.940 25.116 31.035 1.00 0.00 H +ATOM 244 HG12 VAL 15 19.832 23.789 29.857 1.00 0.00 H +ATOM 245 HG13 VAL 15 20.672 23.536 31.384 1.00 0.00 H +ATOM 246 CG2 VAL 15 21.431 25.652 28.775 1.00 0.00 C +ATOM 247 HG21 VAL 15 22.344 26.000 28.296 1.00 0.00 H +ATOM 248 HG22 VAL 15 20.849 25.095 28.039 1.00 0.00 H +ATOM 249 HG23 VAL 15 20.845 26.497 29.121 1.00 0.00 H +ATOM 250 C VAL 15 22.255 26.634 31.587 1.00 0.00 C +ATOM 251 O VAL 15 21.634 26.597 32.639 1.00 0.00 O +HETATM 252 N HY1 16 22.503 27.793 30.973 1.00 0.00 N +HETATM 253 CA HY1 16 21.907 29.109 31.309 1.00 0.00 C +HETATM 254 C HY1 16 21.626 29.889 30.030 1.00 0.00 C +HETATM 255 O HY1 16 21.803 29.384 28.934 1.00 0.00 O +HETATM 256 CB HY1 16 22.834 29.825 32.330 1.00 0.00 C +HETATM 257 CG HY1 16 24.188 30.197 31.783 1.00 0.00 C +HETATM 258 CD2 HY1 16 24.521 31.376 31.162 1.00 0.00 C +HETATM 259 ND1 HY1 16 25.320 29.420 31.809 1.00 0.00 N +HETATM 260 CE1 HY1 16 26.313 30.124 31.227 1.00 0.00 C +HETATM 261 NE2 HY1 16 25.875 31.326 30.803 1.00 0.00 N +HETATM 262 H HY1 16 23.045 27.766 30.100 1.00 0.00 H +HETATM 263 HA HY1 16 20.949 28.916 31.823 1.00 0.00 H +HETATM 264 HB2 HY1 16 22.325 30.741 32.671 1.00 0.00 H +HETATM 265 HB3 HY1 16 22.960 29.204 33.207 1.00 0.00 H +HETATM 266 HD1 HY1 16 25.420 28.523 32.269 1.00 0.00 H +HETATM 267 HD2 HY1 16 23.853 32.210 30.983 1.00 0.00 H +HETATM 268 HE1 HY1 16 27.347 29.785 31.131 1.00 0.00 H +ATOM 269 N THR 17 21.180 31.133 30.157 1.00 0.00 N +ATOM 270 H THR 17 21.010 31.533 31.074 1.00 0.00 H +ATOM 271 CA THR 17 20.738 32.013 29.045 1.00 0.00 C +ATOM 272 HA THR 17 21.170 31.561 28.112 1.00 0.00 H +ATOM 273 CB THR 17 19.231 32.020 28.904 1.00 0.00 C +ATOM 274 HB THR 17 18.946 32.674 28.050 1.00 0.00 H +ATOM 275 CG2 THR 17 18.569 30.688 28.614 1.00 0.00 C +ATOM 276 HG21 THR 17 18.780 29.952 29.396 1.00 0.00 H +ATOM 277 HG22 THR 17 17.520 30.750 28.519 1.00 0.00 H +ATOM 278 HG23 THR 17 18.943 30.252 27.683 1.00 0.00 H +ATOM 279 OG1 THR 17 18.633 32.525 30.065 1.00 0.00 O +ATOM 280 HG1 THR 17 18.590 33.499 29.935 1.00 0.00 H +ATOM 281 C THR 17 21.325 33.419 29.080 1.00 0.00 C +ATOM 282 O THR 17 21.830 33.841 30.105 1.00 0.00 O +HETATM 283 N HY2 18 21.199 34.131 27.962 1.00 0.00 N +HETATM 284 CA HY2 18 21.498 35.567 27.862 1.00 0.00 C +HETATM 285 C HY2 18 20.379 36.266 27.075 1.00 0.00 C +HETATM 286 O HY2 18 20.033 35.823 25.984 1.00 0.00 O +HETATM 287 CB HY2 18 22.831 35.804 27.169 1.00 0.00 C +HETATM 288 CG HY2 18 24.029 35.337 27.962 1.00 0.00 C +HETATM 289 CD2 HY2 18 24.563 34.072 27.954 1.00 0.00 C +HETATM 290 ND1 HY2 18 24.707 36.053 28.927 1.00 0.00 N +HETATM 291 CE1 HY2 18 25.640 35.241 29.456 1.00 0.00 C +HETATM 292 NE2 HY2 18 25.591 34.016 28.902 1.00 0.00 N +HETATM 293 H HY2 18 20.786 33.675 27.148 1.00 0.00 H +HETATM 294 HA HY2 18 21.526 36.010 28.879 1.00 0.00 H +HETATM 295 HB2 HY2 18 22.841 35.309 26.183 1.00 0.00 H +HETATM 296 HB3 HY2 18 22.951 36.890 26.989 1.00 0.00 H +HETATM 297 HD1 HY2 18 24.548 37.015 29.189 1.00 0.00 H +HETATM 298 HD2 HY2 18 24.231 33.250 27.332 1.00 0.00 H +HETATM 299 HE1 HY2 18 26.337 35.534 30.234 1.00 0.00 H +ATOM 300 N GLU 19 19.854 37.365 27.613 1.00 0.00 N +ATOM 301 H GLU 19 20.181 37.657 28.514 1.00 0.00 H +ATOM 302 CA GLU 19 18.861 38.214 26.953 1.00 0.00 C +ATOM 303 HA GLU 19 18.118 37.567 26.510 1.00 0.00 H +ATOM 304 CB GLU 19 18.201 39.105 28.007 1.00 0.00 C +ATOM 305 HB2 GLU 19 17.888 38.497 28.852 1.00 0.00 H +ATOM 306 HB3 GLU 19 18.937 39.829 28.382 1.00 0.00 H +ATOM 307 CG GLU 19 16.971 39.870 27.494 1.00 0.00 C +ATOM 308 HG2 GLU 19 16.593 40.510 28.305 1.00 0.00 H +ATOM 309 HG3 GLU 19 17.267 40.530 26.668 1.00 0.00 H +ATOM 310 CD GLU 19 15.891 38.899 27.051 1.00 0.00 C +ATOM 311 OE1 GLU 19 15.841 38.587 25.838 1.00 0.00 O +ATOM 312 OE2 GLU 19 15.168 38.381 27.921 1.00 0.00 O +ATOM 313 C GLU 19 19.511 39.051 25.841 1.00 0.00 C +ATOM 314 O GLU 19 20.557 39.666 26.070 1.00 0.00 O +ATOM 315 N ALA 20 18.896 39.088 24.651 1.00 0.00 N +ATOM 316 H ALA 20 18.064 38.515 24.532 1.00 0.00 H +ATOM 317 CA ALA 20 19.271 39.983 23.548 1.00 0.00 C +ATOM 318 HA ALA 20 19.436 40.983 23.947 1.00 0.00 H +ATOM 319 CB ALA 20 20.578 39.484 22.920 1.00 0.00 C +ATOM 320 HB1 ALA 20 20.424 38.505 22.460 1.00 0.00 H +ATOM 321 HB2 ALA 20 20.915 40.186 22.161 1.00 0.00 H +ATOM 322 HB3 ALA 20 21.364 39.400 23.667 1.00 0.00 H +ATOM 323 C ALA 20 18.183 40.055 22.465 1.00 0.00 C +ATOM 324 O ALA 20 17.362 39.144 22.322 1.00 0.00 O +ATOM 325 N VAL 21 18.199 41.109 21.636 1.00 0.00 N +ATOM 326 H VAL 21 18.866 41.851 21.810 1.00 0.00 H +ATOM 327 CA VAL 21 17.428 41.159 20.367 1.00 0.00 C +ATOM 328 HA VAL 21 16.429 40.760 20.548 1.00 0.00 H +ATOM 329 CB VAL 21 17.259 42.610 19.852 1.00 0.00 C +ATOM 330 HB VAL 21 16.584 42.573 18.993 1.00 0.00 H +ATOM 331 CG1 VAL 21 16.606 43.510 20.912 1.00 0.00 C +ATOM 332 HG11 VAL 21 17.283 43.665 21.747 1.00 0.00 H +ATOM 333 HG12 VAL 21 16.368 44.469 20.461 1.00 0.00 H +ATOM 334 HG13 VAL 21 15.686 43.051 21.264 1.00 0.00 H +ATOM 335 CG2 VAL 21 18.574 43.260 19.386 1.00 0.00 C +ATOM 336 HG21 VAL 21 18.969 42.728 18.522 1.00 0.00 H +ATOM 337 HG22 VAL 21 18.382 44.286 19.080 1.00 0.00 H +ATOM 338 HG23 VAL 21 19.313 43.256 20.184 1.00 0.00 H +ATOM 339 C VAL 21 18.056 40.311 19.265 1.00 0.00 C +ATOM 340 O VAL 21 17.372 39.908 18.335 1.00 0.00 O +ATOM 341 N ASP 22 19.356 40.045 19.380 1.00 0.00 N +ATOM 342 H ASP 22 19.840 40.370 20.200 1.00 0.00 H +ATOM 343 CA ASP 22 20.203 39.414 18.367 1.00 0.00 C +ATOM 344 HA ASP 22 19.591 38.740 17.749 1.00 0.00 H +ATOM 345 CB ASP 22 20.808 40.497 17.447 1.00 0.00 C +ATOM 346 HB2 ASP 22 20.011 40.913 16.813 1.00 0.00 H +ATOM 347 HB3 ASP 22 21.216 41.310 18.079 1.00 0.00 H +ATOM 348 CG ASP 22 21.904 39.924 16.576 1.00 0.00 C +ATOM 349 OD1 ASP 22 23.061 40.332 16.776 1.00 0.00 O +ATOM 350 OD2 ASP 22 21.645 38.936 15.850 1.00 0.00 O +ATOM 351 C ASP 22 21.312 38.577 19.024 1.00 0.00 C +ATOM 352 O ASP 22 21.786 38.862 20.125 1.00 0.00 O +ATOM 353 N TRP 23 21.758 37.546 18.320 1.00 0.00 N +ATOM 354 H TRP 23 21.457 37.488 17.356 1.00 0.00 H +ATOM 355 CA TRP 23 22.777 36.618 18.774 1.00 0.00 C +ATOM 356 HA TRP 23 22.545 36.338 19.799 1.00 0.00 H +ATOM 357 CB TRP 23 22.654 35.377 17.900 1.00 0.00 C +ATOM 358 HB2 TRP 23 21.626 35.019 17.952 1.00 0.00 H +ATOM 359 HB3 TRP 23 22.841 35.665 16.862 1.00 0.00 H +ATOM 360 CG TRP 23 23.539 34.241 18.269 1.00 0.00 C +ATOM 361 CD1 TRP 23 24.465 33.691 17.461 1.00 0.00 C +ATOM 362 HD1 TRP 23 24.709 34.023 16.459 1.00 0.00 H +ATOM 363 NE1 TRP 23 25.028 32.616 18.105 1.00 0.00 N +ATOM 364 HE1 TRP 23 25.775 32.071 17.710 1.00 0.00 H +ATOM 365 CE2 TRP 23 24.471 32.396 19.344 1.00 0.00 C +ATOM 366 CZ2 TRP 23 24.645 31.401 20.312 1.00 0.00 C +ATOM 367 HZ2 TRP 23 25.308 30.566 20.135 1.00 0.00 H +ATOM 368 CH2 TRP 23 23.967 31.535 21.529 1.00 0.00 C +ATOM 369 HH2 TRP 23 24.088 30.820 22.312 1.00 0.00 H +ATOM 370 CZ3 TRP 23 23.194 32.666 21.795 1.00 0.00 C +ATOM 371 HZ3 TRP 23 22.789 32.798 22.788 1.00 0.00 H +ATOM 372 CE3 TRP 23 22.960 33.611 20.781 1.00 0.00 C +ATOM 373 HE3 TRP 23 22.305 34.442 20.972 1.00 0.00 H +ATOM 374 CD2 TRP 23 23.577 33.487 19.517 1.00 0.00 C +ATOM 375 C TRP 23 24.201 37.200 18.775 1.00 0.00 C +ATOM 376 O TRP 23 24.979 36.883 19.677 1.00 0.00 O +ATOM 377 N ALA 24 24.536 38.109 17.850 1.00 0.00 N +ATOM 378 H ALA 24 23.837 38.430 17.182 1.00 0.00 H +ATOM 379 CA ALA 24 25.826 38.805 17.840 1.00 0.00 C +ATOM 380 HA ALA 24 26.592 38.098 18.148 1.00 0.00 H +ATOM 381 CB ALA 24 26.163 39.206 16.400 1.00 0.00 C +ATOM 382 HB1 ALA 24 25.465 39.956 16.034 1.00 0.00 H +ATOM 383 HB2 ALA 24 27.173 39.612 16.353 1.00 0.00 H +ATOM 384 HB3 ALA 24 26.113 38.333 15.751 1.00 0.00 H +ATOM 385 C ALA 24 25.896 39.988 18.834 1.00 0.00 C +ATOM 386 O ALA 24 26.984 40.488 19.139 1.00 0.00 O +ATOM 387 N GLU 25 24.765 40.408 19.414 1.00 0.00 N +ATOM 388 H GLU 25 23.891 40.105 18.996 1.00 0.00 H +ATOM 389 CA GLU 25 24.725 41.188 20.666 1.00 0.00 C +ATOM 390 HA GLU 25 25.581 41.863 20.687 1.00 0.00 H +ATOM 391 CB GLU 25 23.451 42.045 20.730 1.00 0.00 C +ATOM 392 HB2 GLU 25 22.582 41.422 20.516 1.00 0.00 H +ATOM 393 HB3 GLU 25 23.342 42.425 21.740 1.00 0.00 H +ATOM 394 CG GLU 25 23.468 43.249 19.777 1.00 0.00 C +ATOM 395 HG2 GLU 25 23.540 42.881 18.748 1.00 0.00 H +ATOM 396 HG3 GLU 25 22.512 43.776 19.855 1.00 0.00 H +ATOM 397 CD GLU 25 24.619 44.199 20.081 1.00 0.00 C +ATOM 398 OE1 GLU 25 24.524 44.975 21.065 1.00 0.00 O +ATOM 399 OE2 GLU 25 25.648 44.107 19.362 1.00 0.00 O +ATOM 400 C GLU 25 24.874 40.287 21.906 1.00 0.00 C +ATOM 401 O GLU 25 25.688 40.579 22.784 1.00 0.00 O +ATOM 402 N ALA 26 24.201 39.125 21.956 1.00 0.00 N +ATOM 403 H ALA 26 23.518 38.919 21.232 1.00 0.00 H +ATOM 404 CA ALA 26 24.463 38.107 22.990 1.00 0.00 C +ATOM 405 HA ALA 26 24.293 38.571 23.963 1.00 0.00 H +ATOM 406 CB ALA 26 23.482 36.944 22.834 1.00 0.00 C +ATOM 407 HB1 ALA 26 23.667 36.421 21.901 1.00 0.00 H +ATOM 408 HB2 ALA 26 23.605 36.247 23.660 1.00 0.00 H +ATOM 409 HB3 ALA 26 22.458 37.314 22.841 1.00 0.00 H +ATOM 410 C ALA 26 25.930 37.609 22.973 1.00 0.00 C +ATOM 411 O ALA 26 26.453 37.180 24.015 1.00 0.00 O +ATOM 412 N GLU 27 26.614 37.710 21.825 1.00 0.00 N +ATOM 413 H GLU 27 26.089 37.904 20.980 1.00 0.00 H +ATOM 414 CA GLU 27 28.052 37.490 21.713 1.00 0.00 C +ATOM 415 HA GLU 27 28.210 36.457 21.940 1.00 0.00 H +ATOM 416 CB GLU 27 28.583 37.614 20.270 1.00 0.00 C +ATOM 417 HB2 GLU 27 27.924 37.058 19.610 1.00 0.00 H +ATOM 418 HB3 GLU 27 28.620 38.658 19.970 1.00 0.00 H +ATOM 419 CG GLU 27 29.988 36.996 20.197 1.00 0.00 C +ATOM 420 HG2 GLU 27 30.676 37.588 20.819 1.00 0.00 H +ATOM 421 HG3 GLU 27 29.956 35.983 20.634 1.00 0.00 H +ATOM 422 CD GLU 27 30.513 36.934 18.769 1.00 0.00 C +ATOM 423 OE1 GLU 27 30.943 38.000 18.278 1.00 0.00 O +ATOM 424 OE2 GLU 27 30.501 35.827 18.191 1.00 0.00 O +ATOM 425 C GLU 27 28.828 38.374 22.706 1.00 0.00 C +ATOM 426 O GLU 27 29.568 37.849 23.548 1.00 0.00 O +ATOM 427 N LYS 28 28.541 39.682 22.661 1.00 0.00 N +ATOM 428 H LYS 28 27.831 39.957 21.987 1.00 0.00 H +ATOM 429 CA LYS 28 29.121 40.758 23.481 1.00 0.00 C +ATOM 430 HA LYS 28 30.206 40.658 23.479 1.00 0.00 H +ATOM 431 CB LYS 28 28.761 42.131 22.873 1.00 0.00 C +ATOM 432 HB2 LYS 28 27.685 42.299 22.951 1.00 0.00 H +ATOM 433 HB3 LYS 28 29.264 42.909 23.451 1.00 0.00 H +ATOM 434 CG LYS 28 29.172 42.274 21.396 1.00 0.00 C +ATOM 435 HG2 LYS 28 30.244 42.100 21.301 1.00 0.00 H +ATOM 436 HG3 LYS 28 28.646 41.528 20.802 1.00 0.00 H +ATOM 437 CD LYS 28 28.833 43.668 20.845 1.00 0.00 C +ATOM 438 HD2 LYS 28 27.793 43.910 21.048 1.00 0.00 H +ATOM 439 HD3 LYS 28 29.453 44.406 21.356 1.00 0.00 H +ATOM 440 CE LYS 28 29.082 43.754 19.331 1.00 0.00 C +ATOM 441 HE2 LYS 28 29.159 44.812 19.054 1.00 0.00 H +ATOM 442 HE3 LYS 28 30.045 43.295 19.106 1.00 0.00 H +ATOM 443 NZ LYS 28 27.999 43.108 18.548 1.00 0.00 N +ATOM 444 HZ1 LYS 28 27.111 43.575 18.756 1.00 0.00 H +ATOM 445 HZ2 LYS 28 28.147 43.172 17.552 1.00 0.00 H +ATOM 446 HZ3 LYS 28 27.858 42.139 18.817 1.00 0.00 H +ATOM 447 C LYS 28 28.671 40.699 24.942 1.00 0.00 C +ATOM 448 O LYS 28 29.516 40.726 25.833 1.00 0.00 O +ATOM 449 N PHE 29 27.376 40.527 25.225 1.00 0.00 N +ATOM 450 H PHE 29 26.709 40.552 24.455 1.00 0.00 H +ATOM 451 CA PHE 29 26.873 40.474 26.615 1.00 0.00 C +ATOM 452 HA PHE 29 27.188 41.382 27.129 1.00 0.00 H +ATOM 453 CB PHE 29 25.335 40.437 26.615 1.00 0.00 C +ATOM 454 HB2 PHE 29 25.018 39.493 26.171 1.00 0.00 H +ATOM 455 HB3 PHE 29 24.990 40.451 27.649 1.00 0.00 H +ATOM 456 CG PHE 29 24.643 41.578 25.884 1.00 0.00 C +ATOM 457 CD1 PHE 29 23.461 41.323 25.164 1.00 0.00 C +ATOM 458 HD1 PHE 29 23.037 40.333 25.146 1.00 0.00 H +ATOM 459 CE1 PHE 29 22.822 42.359 24.462 1.00 0.00 C +ATOM 460 HE1 PHE 29 21.922 42.155 23.902 1.00 0.00 H +ATOM 461 CZ PHE 29 23.361 43.658 24.478 1.00 0.00 C +ATOM 462 HZ PHE 29 22.885 44.450 23.917 1.00 0.00 H +ATOM 463 CE2 PHE 29 24.520 43.928 25.225 1.00 0.00 C +ATOM 464 HE2 PHE 29 24.924 44.927 25.252 1.00 0.00 H +ATOM 465 CD2 PHE 29 25.155 42.893 25.932 1.00 0.00 C +ATOM 466 HD2 PHE 29 26.038 43.124 26.504 1.00 0.00 H +ATOM 467 C PHE 29 27.437 39.300 27.430 1.00 0.00 C +ATOM 468 O PHE 29 27.531 39.370 28.654 1.00 0.00 O +ATOM 469 N THR 30 27.865 38.222 26.770 1.00 0.00 N +ATOM 470 H THR 30 27.724 38.182 25.766 1.00 0.00 H +ATOM 471 CA THR 30 28.618 37.144 27.427 1.00 0.00 C +ATOM 472 HA THR 30 28.163 36.900 28.387 1.00 0.00 H +ATOM 473 CB THR 30 28.621 35.900 26.536 1.00 0.00 C +ATOM 474 HB THR 30 29.132 36.191 25.639 1.00 0.00 H +ATOM 475 CG2 THR 30 29.346 34.706 27.138 1.00 0.00 C +ATOM 476 HG21 THR 30 28.984 34.522 28.133 1.00 0.00 H +ATOM 477 HG22 THR 30 29.193 33.814 26.546 1.00 0.00 H +ATOM 478 HG23 THR 30 30.428 34.887 27.191 1.00 0.00 H +ATOM 479 OG1 THR 30 27.298 35.471 26.245 1.00 0.00 O +ATOM 480 HG1 THR 30 26.888 36.131 25.657 1.00 0.00 H +ATOM 481 C THR 30 30.081 37.537 27.695 1.00 0.00 C +ATOM 482 O THR 30 30.624 37.146 28.731 1.00 0.00 O +ATOM 483 N LYS 31 30.720 38.306 26.804 1.00 0.00 N +ATOM 484 H LYS 31 30.198 38.651 26.014 1.00 0.00 H +ATOM 485 CA LYS 31 32.070 38.835 27.005 1.00 0.00 C +ATOM 486 HA LYS 31 32.733 38.032 27.315 1.00 0.00 H +ATOM 487 CB LYS 31 32.647 39.415 25.683 1.00 0.00 C +ATOM 488 HB2 LYS 31 31.948 40.110 25.246 1.00 0.00 H +ATOM 489 HB3 LYS 31 33.566 39.953 25.914 1.00 0.00 H +ATOM 490 CG LYS 31 32.996 38.312 24.666 1.00 0.00 C +ATOM 491 HG2 LYS 31 33.730 37.640 25.106 1.00 0.00 H +ATOM 492 HG3 LYS 31 32.107 37.731 24.423 1.00 0.00 H +ATOM 493 CD LYS 31 33.567 38.923 23.384 1.00 0.00 C +ATOM 494 HD2 LYS 31 32.778 39.479 22.879 1.00 0.00 H +ATOM 495 HD3 LYS 31 34.355 39.629 23.638 1.00 0.00 H +ATOM 496 CE LYS 31 34.151 37.892 22.391 1.00 0.00 C +ATOM 497 HE2 LYS 31 33.409 37.129 22.159 1.00 0.00 H +ATOM 498 HE3 LYS 31 34.379 38.403 21.457 1.00 0.00 H +ATOM 499 NZ LYS 31 35.390 37.255 22.898 1.00 0.00 N +ATOM 500 HZ1 LYS 31 35.201 36.470 23.500 1.00 0.00 H +ATOM 501 HZ2 LYS 31 35.932 36.859 22.126 1.00 0.00 H +ATOM 502 HZ3 LYS 31 35.985 37.896 23.428 1.00 0.00 H +ATOM 503 C LYS 31 32.129 39.879 28.130 1.00 0.00 C +ATOM 504 O LYS 31 33.139 39.914 28.834 1.00 0.00 O +ATOM 505 N ALA 32 31.036 40.609 28.382 1.00 0.00 N +ATOM 506 H ALA 32 30.297 40.611 27.689 1.00 0.00 H +ATOM 507 CA ALA 32 30.856 41.387 29.608 1.00 0.00 C +ATOM 508 HA ALA 32 31.679 42.095 29.692 1.00 0.00 H +ATOM 509 CB ALA 32 29.558 42.200 29.527 1.00 0.00 C +ATOM 510 HB1 ALA 32 28.691 41.544 29.473 1.00 0.00 H +ATOM 511 HB2 ALA 32 29.463 42.823 30.421 1.00 0.00 H +ATOM 512 HB3 ALA 32 29.578 42.846 28.650 1.00 0.00 H +ATOM 513 C ALA 32 30.927 40.489 30.858 1.00 0.00 C +ATOM 514 O ALA 32 31.924 40.546 31.574 1.00 0.00 O +ATOM 515 N LYN 33 29.996 39.531 31.025 1.00 0.00 N +ATOM 516 H LYN 33 29.190 39.542 30.415 1.00 0.00 H +ATOM 517 CA LYN 33 30.009 38.573 32.151 1.00 0.00 C +ATOM 518 HA LYN 33 29.910 39.148 33.071 1.00 0.00 H +ATOM 519 CB LYN 33 28.774 37.649 32.038 1.00 0.00 C +ATOM 520 HB2 LYN 33 27.879 38.255 31.901 1.00 0.00 H +ATOM 521 HB3 LYN 33 28.890 37.020 31.159 1.00 0.00 H +ATOM 522 CG LYN 33 28.554 36.757 33.275 1.00 0.00 C +ATOM 523 HG2 LYN 33 29.439 36.152 33.441 1.00 0.00 H +ATOM 524 HG3 LYN 33 28.421 37.387 34.152 1.00 0.00 H +ATOM 525 CD LYN 33 27.373 35.776 33.182 1.00 0.00 C +ATOM 526 HD2 LYN 33 27.409 35.248 32.236 1.00 0.00 H +ATOM 527 HD3 LYN 33 27.480 35.041 33.977 1.00 0.00 H +ATOM 528 CE LYN 33 26.005 36.448 33.325 1.00 0.00 C +ATOM 529 HE2 LYN 33 26.005 37.059 34.229 1.00 0.00 H +ATOM 530 HE3 LYN 33 25.827 37.088 32.462 1.00 0.00 H +ATOM 531 NZ LYN 33 24.926 35.449 33.420 1.00 0.00 N +ATOM 532 HZ2 LYN 33 24.037 35.924 33.515 1.00 0.00 H +ATOM 533 HZ3 LYN 33 24.894 34.884 32.590 1.00 0.00 H +ATOM 534 C LYN 33 31.326 37.768 32.264 1.00 0.00 C +ATOM 535 O LYN 33 31.650 37.212 33.313 1.00 0.00 O +ATOM 536 N ALA 34 32.102 37.650 31.186 1.00 0.00 N +ATOM 537 H ALA 34 31.786 38.093 30.336 1.00 0.00 H +ATOM 538 CA ALA 34 33.415 37.025 31.197 1.00 0.00 C +ATOM 539 HA ALA 34 33.379 36.199 31.902 1.00 0.00 H +ATOM 540 CB ALA 34 33.660 36.419 29.822 1.00 0.00 C +ATOM 541 HB1 ALA 34 33.759 37.224 29.100 1.00 0.00 H +ATOM 542 HB2 ALA 34 34.569 35.830 29.857 1.00 0.00 H +ATOM 543 HB3 ALA 34 32.833 35.773 29.533 1.00 0.00 H +ATOM 544 C ALA 34 34.561 37.964 31.644 1.00 0.00 C +ATOM 545 O ALA 34 35.485 37.474 32.295 1.00 0.00 O +ATOM 546 N ASN 35 34.515 39.269 31.348 1.00 0.00 N +ATOM 547 H ASN 35 33.732 39.616 30.804 1.00 0.00 H +ATOM 548 CA ASN 35 35.446 40.284 31.873 1.00 0.00 C +ATOM 549 HA ASN 35 36.435 39.832 31.976 1.00 0.00 H +ATOM 550 CB ASN 35 35.582 41.433 30.859 1.00 0.00 C +ATOM 551 HB2 ASN 35 34.603 41.733 30.493 1.00 0.00 H +ATOM 552 HB3 ASN 35 36.033 42.295 31.352 1.00 0.00 H +ATOM 553 CG ASN 35 36.493 41.030 29.719 1.00 0.00 C +ATOM 554 OD1 ASN 35 37.698 40.971 29.868 1.00 0.00 O +ATOM 555 ND2 ASN 35 35.956 40.693 28.578 1.00 0.00 N +ATOM 556 HD21 ASN 35 36.601 40.354 27.860 1.00 0.00 H +ATOM 557 HD22 ASN 35 34.954 40.631 28.488 1.00 0.00 H +ATOM 558 C ASN 35 35.078 40.777 33.276 1.00 0.00 C +ATOM 559 O ASN 35 35.967 41.126 34.052 1.00 0.00 O +ATOM 560 N ASP 36 33.802 40.685 33.673 1.00 0.00 N +ATOM 561 H ASP 36 33.078 40.563 32.970 1.00 0.00 H +ATOM 562 CA ASP 36 33.357 40.843 35.067 1.00 0.00 C +ATOM 563 HA ASP 36 33.630 41.847 35.410 1.00 0.00 H +ATOM 564 CB ASP 36 31.839 40.739 35.150 1.00 0.00 C +ATOM 565 HB2 ASP 36 31.563 39.728 34.867 1.00 0.00 H +ATOM 566 HB3 ASP 36 31.542 40.818 36.195 1.00 0.00 H +ATOM 567 CG ASP 36 30.985 41.711 34.324 1.00 0.00 C +ATOM 568 OD1 ASP 36 31.462 42.836 34.035 1.00 0.00 O +ATOM 569 OD2 ASP 36 29.825 41.345 33.996 1.00 0.00 O +ATOM 570 C ASP 36 34.066 39.828 35.995 1.00 0.00 C +ATOM 571 O ASP 36 34.498 40.176 37.098 1.00 0.00 O +ATOM 572 N LYS 37 34.277 38.580 35.528 1.00 0.00 N +ATOM 573 H LYS 37 33.863 38.350 34.636 1.00 0.00 H +ATOM 574 CA LYS 37 35.150 37.580 36.183 1.00 0.00 C +ATOM 575 HA LYS 37 35.130 37.789 37.253 1.00 0.00 H +ATOM 576 CB LYS 37 34.565 36.152 36.027 1.00 0.00 C +ATOM 577 HB2 LYS 37 35.078 35.490 36.724 1.00 0.00 H +ATOM 578 HB3 LYS 37 33.508 36.149 36.288 1.00 0.00 H +ATOM 579 CG LYS 37 34.759 35.601 34.608 1.00 0.00 C +ATOM 580 HG2 LYS 37 34.139 36.177 33.928 1.00 0.00 H +ATOM 581 HG3 LYS 37 35.798 35.735 34.318 1.00 0.00 H +ATOM 582 CD LYS 37 34.436 34.122 34.422 1.00 0.00 C +ATOM 583 HD2 LYS 37 34.578 33.610 35.373 1.00 0.00 H +ATOM 584 HD3 LYS 37 33.395 34.014 34.154 1.00 0.00 H +ATOM 585 CE LYS 37 35.328 33.472 33.330 1.00 0.00 C +ATOM 586 HE2 LYS 37 36.315 33.292 33.762 1.00 0.00 H +ATOM 587 HE3 LYS 37 34.983 32.454 33.128 1.00 0.00 H +ATOM 588 NZ LYS 37 35.470 34.267 32.074 1.00 0.00 N +ATOM 589 HZ1 LYS 37 35.901 35.166 32.277 1.00 0.00 H +ATOM 590 HZ2 LYS 37 36.069 33.816 31.389 1.00 0.00 H +ATOM 591 HZ3 LYS 37 34.567 34.433 31.674 1.00 0.00 H +ATOM 592 C LYS 37 36.641 37.666 35.797 1.00 0.00 C +ATOM 593 O LYS 37 37.388 36.717 36.024 1.00 0.00 O +ATOM 594 N GLY 38 37.093 38.753 35.163 1.00 0.00 N +ATOM 595 H GLY 38 36.427 39.500 35.014 1.00 0.00 H +ATOM 596 CA GLY 38 38.497 39.081 34.900 1.00 0.00 C +ATOM 597 HA2 GLY 38 38.673 40.099 35.250 1.00 0.00 H +ATOM 598 HA3 GLY 38 39.136 38.422 35.493 1.00 0.00 H +ATOM 599 C GLY 38 38.992 39.003 33.451 1.00 0.00 C +ATOM 600 O GLY 38 39.908 39.749 33.113 1.00 0.00 O +ATOM 601 N ARG 39 38.439 38.123 32.592 1.00 0.00 N +ATOM 602 H ARG 39 37.620 37.630 32.924 1.00 0.00 H +ATOM 603 CA ARG 39 38.850 37.918 31.183 1.00 0.00 C +ATOM 604 HA ARG 39 38.819 38.900 30.702 1.00 0.00 H +ATOM 605 CB ARG 39 40.315 37.408 31.055 1.00 0.00 C +ATOM 606 HB2 ARG 39 40.570 37.429 29.993 1.00 0.00 H +ATOM 607 HB3 ARG 39 40.992 38.115 31.533 1.00 0.00 H +ATOM 608 CG ARG 39 40.642 35.990 31.575 1.00 0.00 C +ATOM 609 HG2 ARG 39 40.011 35.274 31.049 1.00 0.00 H +ATOM 610 HG3 ARG 39 41.676 35.759 31.313 1.00 0.00 H +ATOM 611 CD ARG 39 40.486 35.825 33.102 1.00 0.00 C +ATOM 612 HD2 ARG 39 41.184 36.504 33.600 1.00 0.00 H +ATOM 613 HD3 ARG 39 39.476 36.100 33.403 1.00 0.00 H +ATOM 614 NE ARG 39 40.739 34.451 33.582 1.00 0.00 N +ATOM 615 HE ARG 39 41.505 34.326 34.228 1.00 0.00 H +ATOM 616 CZ ARG 39 39.961 33.401 33.419 1.00 0.00 C +ATOM 617 NH1 ARG 39 38.912 33.425 32.650 1.00 0.00 N +ATOM 618 HH11 ARG 39 38.753 34.219 32.059 1.00 0.00 H +ATOM 619 HH12 ARG 39 38.395 32.553 32.564 1.00 0.00 H +ATOM 620 NH2 ARG 39 40.208 32.279 34.029 1.00 0.00 N +ATOM 621 HH21 ARG 39 41.021 32.194 34.618 1.00 0.00 H +ATOM 622 HH22 ARG 39 39.586 31.492 33.869 1.00 0.00 H +ATOM 623 C ARG 39 37.906 37.010 30.382 1.00 0.00 C +ATOM 624 O ARG 39 37.450 35.970 30.889 1.00 0.00 O +ATOM 625 N ASP 40 37.643 37.373 29.123 1.00 0.00 N +ATOM 626 H ASP 40 38.049 38.236 28.768 1.00 0.00 H +ATOM 627 CA ASP 40 36.914 36.559 28.147 1.00 0.00 C +ATOM 628 HA ASP 40 36.250 35.909 28.701 1.00 0.00 H +ATOM 629 CB ASP 40 36.024 37.438 27.250 1.00 0.00 C +ATOM 630 HB2 ASP 40 35.359 36.797 26.672 1.00 0.00 H +ATOM 631 HB3 ASP 40 35.373 38.034 27.885 1.00 0.00 H +ATOM 632 CG ASP 40 36.757 38.385 26.309 1.00 0.00 C +ATOM 633 OD1 ASP 40 37.565 39.185 26.826 1.00 0.00 O +ATOM 634 OD2 ASP 40 36.426 38.367 25.105 1.00 0.00 O +ATOM 635 C ASP 40 37.774 35.579 27.330 1.00 0.00 C +ATOM 636 O ASP 40 38.983 35.480 27.496 1.00 0.00 O +ATOM 637 N GLY 41 37.089 34.803 26.488 1.00 0.00 N +ATOM 638 H GLY 41 36.101 34.991 26.421 1.00 0.00 H +ATOM 639 CA GLY 41 37.618 33.880 25.478 1.00 0.00 C +ATOM 640 HA2 GLY 41 38.494 34.335 24.987 1.00 0.00 H +ATOM 641 HA3 GLY 41 37.896 32.927 25.956 1.00 0.00 H +ATOM 642 C GLY 41 36.528 33.613 24.424 1.00 0.00 C +ATOM 643 O GLY 41 35.445 34.207 24.475 1.00 0.00 O +ATOM 644 N GLU 42 36.788 32.709 23.482 1.00 0.00 N +ATOM 645 H GLU 42 37.670 32.237 23.523 1.00 0.00 H +ATOM 646 CA GLU 42 35.905 32.412 22.347 1.00 0.00 C +ATOM 647 HA GLU 42 35.125 33.167 22.344 1.00 0.00 H +ATOM 648 CB GLU 42 36.664 32.525 21.011 1.00 0.00 C +ATOM 649 HB2 GLU 42 37.366 31.695 20.944 1.00 0.00 H +ATOM 650 HB3 GLU 42 35.944 32.414 20.201 1.00 0.00 H +ATOM 651 CG GLU 42 37.443 33.834 20.782 1.00 0.00 C +ATOM 652 HG2 GLU 42 38.311 33.827 21.446 1.00 0.00 H +ATOM 653 HG3 GLU 42 37.826 33.837 19.759 1.00 0.00 H +ATOM 654 CD GLU 42 36.645 35.123 21.033 1.00 0.00 C +ATOM 655 OE1 GLU 42 35.399 35.099 21.148 1.00 0.00 O +ATOM 656 OE2 GLU 42 37.273 36.191 21.218 1.00 0.00 O +ATOM 657 C GLU 42 35.155 31.079 22.449 1.00 0.00 C +ATOM 658 O GLU 42 35.545 30.177 23.201 1.00 0.00 O +ATOM 659 N ARG 43 34.045 30.983 21.696 1.00 0.00 N +ATOM 660 H ARG 43 33.859 31.729 21.028 1.00 0.00 H +ATOM 661 CA ARG 43 33.015 29.940 21.796 1.00 0.00 C +ATOM 662 HA ARG 43 33.495 28.981 22.001 1.00 0.00 H +ATOM 663 CB ARG 43 32.087 30.275 22.974 1.00 0.00 C +ATOM 664 HB2 ARG 43 31.317 29.508 23.057 1.00 0.00 H +ATOM 665 HB3 ARG 43 32.669 30.262 23.897 1.00 0.00 H +ATOM 666 CG ARG 43 31.391 31.637 22.844 1.00 0.00 C +ATOM 667 HG2 ARG 43 32.110 32.434 22.660 1.00 0.00 H +ATOM 668 HG3 ARG 43 30.694 31.612 22.010 1.00 0.00 H +ATOM 669 CD ARG 43 30.634 31.967 24.121 1.00 0.00 C +ATOM 670 HD2 ARG 43 30.147 31.059 24.480 1.00 0.00 H +ATOM 671 HD3 ARG 43 31.339 32.284 24.887 1.00 0.00 H +ATOM 672 NE ARG 43 29.619 32.996 23.893 1.00 0.00 N +ATOM 673 HE ARG 43 28.685 32.661 23.712 1.00 0.00 H +ATOM 674 CZ ARG 43 29.781 34.291 23.756 1.00 0.00 C +ATOM 675 NH1 ARG 43 30.924 34.915 23.764 1.00 0.00 N +ATOM 676 HH11 ARG 43 31.776 34.380 23.737 1.00 0.00 H +ATOM 677 HH12 ARG 43 30.928 35.903 23.564 1.00 0.00 H +ATOM 678 NH2 ARG 43 28.724 35.010 23.622 1.00 0.00 N +ATOM 679 HH21 ARG 43 27.818 34.575 23.525 1.00 0.00 H +ATOM 680 HH22 ARG 43 28.806 36.015 23.611 1.00 0.00 H +ATOM 681 C ARG 43 32.226 29.788 20.491 1.00 0.00 C +ATOM 682 O ARG 43 32.016 30.775 19.792 1.00 0.00 O +ATOM 683 N THR 44 31.769 28.574 20.199 1.00 0.00 N +ATOM 684 H THR 44 31.893 27.856 20.903 1.00 0.00 H +ATOM 685 CA THR 44 31.059 28.197 18.965 1.00 0.00 C +ATOM 686 HA THR 44 31.367 28.878 18.171 1.00 0.00 H +ATOM 687 CB THR 44 31.491 26.779 18.541 1.00 0.00 C +ATOM 688 HB THR 44 31.284 26.073 19.347 1.00 0.00 H +ATOM 689 CG2 THR 44 30.877 26.255 17.242 1.00 0.00 C +ATOM 690 HG21 THR 44 30.980 26.998 16.449 1.00 0.00 H +ATOM 691 HG22 THR 44 31.383 25.337 16.935 1.00 0.00 H +ATOM 692 HG23 THR 44 29.824 26.016 17.397 1.00 0.00 H +ATOM 693 OG1 THR 44 32.880 26.818 18.313 1.00 0.00 O +ATOM 694 HG1 THR 44 33.143 26.013 17.857 1.00 0.00 H +ATOM 695 C THR 44 29.537 28.364 19.112 1.00 0.00 C +ATOM 696 O THR 44 29.024 28.513 20.225 1.00 0.00 O +ATOM 697 N ILE 45 28.813 28.404 17.984 1.00 0.00 N +ATOM 698 H ILE 45 29.281 28.200 17.114 1.00 0.00 H +ATOM 699 CA ILE 45 27.405 28.808 17.888 1.00 0.00 C +ATOM 700 HA ILE 45 26.992 28.796 18.898 1.00 0.00 H +ATOM 701 CB ILE 45 27.300 30.258 17.349 1.00 0.00 C +ATOM 702 HB ILE 45 26.234 30.493 17.386 1.00 0.00 H +ATOM 703 CG2 ILE 45 28.017 31.233 18.293 1.00 0.00 C +ATOM 704 HG21 ILE 45 29.094 31.074 18.238 1.00 0.00 H +ATOM 705 HG22 ILE 45 27.806 32.268 18.025 1.00 0.00 H +ATOM 706 HG23 ILE 45 27.671 31.042 19.300 1.00 0.00 H +ATOM 707 CG1 ILE 45 27.759 30.525 15.895 1.00 0.00 C +ATOM 708 HG12 ILE 45 28.047 31.568 15.812 1.00 0.00 H +ATOM 709 HG13 ILE 45 28.654 29.949 15.680 1.00 0.00 H +ATOM 710 CD1 ILE 45 26.691 30.279 14.822 1.00 0.00 C +ATOM 711 HD11 ILE 45 25.759 30.773 15.114 1.00 0.00 H +ATOM 712 HD12 ILE 45 27.018 30.695 13.866 1.00 0.00 H +ATOM 713 HD13 ILE 45 26.512 29.212 14.695 1.00 0.00 H +ATOM 714 C ILE 45 26.527 27.858 17.072 1.00 0.00 C +ATOM 715 O ILE 45 27.017 27.114 16.226 1.00 0.00 O +ATOM 716 N ASP 46 25.216 27.950 17.304 1.00 0.00 N +ATOM 717 H ASP 46 24.910 28.475 18.111 1.00 0.00 H +ATOM 718 CA ASP 46 24.153 27.357 16.483 1.00 0.00 C +ATOM 719 HA ASP 46 24.474 27.365 15.437 1.00 0.00 H +ATOM 720 CB ASP 46 23.935 25.904 16.910 1.00 0.00 C +ATOM 721 HB2 ASP 46 24.821 25.306 16.686 1.00 0.00 H +ATOM 722 HB3 ASP 46 23.790 25.882 17.995 1.00 0.00 H +ATOM 723 CG ASP 46 22.728 25.281 16.224 1.00 0.00 C +ATOM 724 OD1 ASP 46 21.961 24.603 16.947 1.00 0.00 O +ATOM 725 OD2 ASP 46 22.511 25.554 15.040 1.00 0.00 O +ATOM 726 C ASP 46 22.834 28.159 16.594 1.00 0.00 C +ATOM 727 O ASP 46 22.399 28.488 17.698 1.00 0.00 O +ATOM 728 N ASP 47 22.184 28.437 15.458 1.00 0.00 N +ATOM 729 H ASP 47 22.559 28.038 14.608 1.00 0.00 H +ATOM 730 CA ASP 47 20.840 29.039 15.391 1.00 0.00 C +ATOM 731 HA ASP 47 20.745 29.781 16.186 1.00 0.00 H +ATOM 732 CB ASP 47 20.651 29.780 14.049 1.00 0.00 C +ATOM 733 HB2 ASP 47 21.371 30.599 13.994 1.00 0.00 H +ATOM 734 HB3 ASP 47 20.869 29.092 13.229 1.00 0.00 H +ATOM 735 CG ASP 47 19.236 30.338 13.866 1.00 0.00 C +ATOM 736 OD1 ASP 47 18.366 29.642 13.294 1.00 0.00 O +ATOM 737 OD2 ASP 47 18.910 31.439 14.376 1.00 0.00 O +ATOM 738 C ASP 47 19.712 28.006 15.601 1.00 0.00 C +ATOM 739 O ASP 47 18.680 28.354 16.177 1.00 0.00 O +ATOM 740 N ALA 48 19.891 26.748 15.189 1.00 0.00 N +ATOM 741 H ALA 48 20.815 26.444 14.883 1.00 0.00 H +ATOM 742 CA ALA 48 18.830 25.738 15.223 1.00 0.00 C +ATOM 743 HA ALA 48 17.947 26.136 14.721 1.00 0.00 H +ATOM 744 CB ALA 48 19.314 24.506 14.451 1.00 0.00 C +ATOM 745 HB1 ALA 48 20.173 24.065 14.961 1.00 0.00 H +ATOM 746 HB2 ALA 48 18.518 23.764 14.391 1.00 0.00 H +ATOM 747 HB3 ALA 48 19.617 24.791 13.444 1.00 0.00 H +ATOM 748 C ALA 48 18.413 25.386 16.665 1.00 0.00 C +ATOM 749 O ALA 48 17.226 25.293 16.965 1.00 0.00 O +ATOM 750 N THR 49 19.383 25.251 17.569 1.00 0.00 N +ATOM 751 H THR 49 20.338 25.173 17.219 1.00 0.00 H +ATOM 752 CA THR 49 19.192 25.102 19.021 1.00 0.00 C +ATOM 753 HA THR 49 18.164 24.774 19.188 1.00 0.00 H +ATOM 754 CB THR 49 20.126 24.025 19.584 1.00 0.00 C +ATOM 755 HB THR 49 19.898 23.910 20.645 1.00 0.00 H +ATOM 756 CG2 THR 49 19.960 22.658 18.926 1.00 0.00 C +ATOM 757 HG21 THR 49 20.258 22.695 17.880 1.00 0.00 H +ATOM 758 HG22 THR 49 20.593 21.942 19.444 1.00 0.00 H +ATOM 759 HG23 THR 49 18.922 22.334 18.992 1.00 0.00 H +ATOM 760 OG1 THR 49 21.483 24.396 19.468 1.00 0.00 O +ATOM 761 HG1 THR 49 21.694 24.365 18.500 1.00 0.00 H +ATOM 762 C THR 49 19.397 26.401 19.808 1.00 0.00 C +ATOM 763 O THR 49 19.269 26.396 21.031 1.00 0.00 O +ATOM 764 N LYS 50 19.705 27.522 19.134 1.00 0.00 N +ATOM 765 H LYS 50 19.806 27.421 18.131 1.00 0.00 H +ATOM 766 CA LYS 50 19.900 28.882 19.702 1.00 0.00 C +ATOM 767 HA LYS 50 20.324 29.504 18.914 1.00 0.00 H +ATOM 768 CB LYS 50 18.514 29.466 20.090 1.00 0.00 C +ATOM 769 HB2 LYS 50 18.082 28.812 20.847 1.00 0.00 H +ATOM 770 HB3 LYS 50 18.662 30.440 20.569 1.00 0.00 H +ATOM 771 CG LYS 50 17.483 29.640 18.962 1.00 0.00 C +ATOM 772 HG2 LYS 50 17.406 28.724 18.377 1.00 0.00 H +ATOM 773 HG3 LYS 50 16.511 29.807 19.436 1.00 0.00 H +ATOM 774 CD LYS 50 17.771 30.842 18.048 1.00 0.00 C +ATOM 775 HD2 LYS 50 17.847 31.729 18.684 1.00 0.00 H +ATOM 776 HD3 LYS 50 18.722 30.709 17.525 1.00 0.00 H +ATOM 777 CE LYS 50 16.636 31.087 17.042 1.00 0.00 C +ATOM 778 HE2 LYS 50 15.680 30.851 17.523 1.00 0.00 H +ATOM 779 HE3 LYS 50 16.620 32.152 16.793 1.00 0.00 H +ATOM 780 NZ LYS 50 16.785 30.318 15.786 1.00 0.00 N +ATOM 781 HZ1 LYS 50 17.027 29.345 15.942 1.00 0.00 H +ATOM 782 HZ2 LYS 50 15.966 30.404 15.186 1.00 0.00 H +ATOM 783 HZ3 LYS 50 17.558 30.688 15.237 1.00 0.00 H +ATOM 784 C LYS 50 20.929 28.907 20.853 1.00 0.00 C +ATOM 785 O LYS 50 20.644 29.476 21.914 1.00 0.00 O +ATOM 786 N THR 51 22.073 28.246 20.666 1.00 0.00 N +ATOM 787 H THR 51 22.280 27.904 19.746 1.00 0.00 H +ATOM 788 CA THR 51 22.978 27.855 21.776 1.00 0.00 C +ATOM 789 HA THR 51 22.713 28.424 22.656 1.00 0.00 H +ATOM 790 CB THR 51 22.769 26.349 22.149 1.00 0.00 C +ATOM 791 HB THR 51 22.913 25.751 21.244 1.00 0.00 H +ATOM 792 CG2 THR 51 23.726 25.829 23.195 1.00 0.00 C +ATOM 793 HG21 THR 51 23.724 26.423 24.104 1.00 0.00 H +ATOM 794 HG22 THR 51 23.491 24.809 23.488 1.00 0.00 H +ATOM 795 HG23 THR 51 24.752 25.794 22.838 1.00 0.00 H +ATOM 796 OG1 THR 51 21.477 26.147 22.676 1.00 0.00 O +ATOM 797 HG1 THR 51 20.828 26.213 21.948 1.00 0.00 H +ATOM 798 C THR 51 24.498 28.160 21.552 1.00 0.00 C +ATOM 799 O THR 51 25.031 27.978 20.458 1.00 0.00 O +ATOM 800 N PHE 52 25.195 28.618 22.604 1.00 0.00 N +ATOM 801 H PHE 52 24.659 28.844 23.435 1.00 0.00 H +ATOM 802 CA PHE 52 26.648 28.754 22.682 1.00 0.00 C +ATOM 803 HA PHE 52 27.066 28.878 21.704 1.00 0.00 H +ATOM 804 CB PHE 52 27.049 29.989 23.564 1.00 0.00 C +ATOM 805 HB2 PHE 52 26.439 29.970 24.449 1.00 0.00 H +ATOM 806 HB3 PHE 52 28.080 29.863 23.877 1.00 0.00 H +ATOM 807 CG PHE 52 26.956 31.369 22.935 1.00 0.00 C +ATOM 808 CD1 PHE 52 26.137 32.360 23.496 1.00 0.00 C +ATOM 809 HD1 PHE 52 25.515 32.134 24.347 1.00 0.00 H +ATOM 810 CE1 PHE 52 26.022 33.613 22.875 1.00 0.00 C +ATOM 811 HE1 PHE 52 25.306 34.345 23.243 1.00 0.00 H +ATOM 812 CZ PHE 52 26.749 33.887 21.707 1.00 0.00 C +ATOM 813 HZ PHE 52 26.610 34.820 21.179 1.00 0.00 H +ATOM 814 CE2 PHE 52 27.660 32.942 21.218 1.00 0.00 C +ATOM 815 HE2 PHE 52 28.252 33.169 20.337 1.00 0.00 H +ATOM 816 CD2 PHE 52 27.757 31.680 21.826 1.00 0.00 C +ATOM 817 HD2 PHE 52 28.421 30.934 21.415 1.00 0.00 H +ATOM 818 C PHE 52 27.299 27.528 23.345 1.00 0.00 C +ATOM 819 O PHE 52 26.801 27.060 24.382 1.00 0.00 O +ATOM 820 N THR 53 28.455 27.080 22.828 1.00 0.00 N +ATOM 821 H THR 53 28.794 27.502 21.960 1.00 0.00 H +ATOM 822 CA THR 53 29.257 25.944 23.360 1.00 0.00 C +ATOM 823 HA THR 53 29.018 25.811 24.412 1.00 0.00 H +ATOM 824 CB THR 53 28.922 24.628 22.631 1.00 0.00 C +ATOM 825 HB THR 53 29.523 23.828 23.066 1.00 0.00 H +ATOM 826 CG2 THR 53 27.455 24.219 22.728 1.00 0.00 C +ATOM 827 HG21 THR 53 26.839 24.900 22.141 1.00 0.00 H +ATOM 828 HG22 THR 53 27.330 23.206 22.345 1.00 0.00 H +ATOM 829 HG23 THR 53 27.136 24.241 23.767 1.00 0.00 H +ATOM 830 OG1 THR 53 29.241 24.729 21.261 1.00 0.00 O +ATOM 831 HG1 THR 53 28.872 23.960 20.816 1.00 0.00 H +ATOM 832 C THR 53 30.775 26.169 23.265 1.00 0.00 C +ATOM 833 O THR 53 31.247 27.039 22.536 1.00 0.00 O +ATOM 834 N THR 54 31.550 25.363 23.995 1.00 0.00 N +ATOM 835 H THR 54 31.108 24.674 24.581 1.00 0.00 H +ATOM 836 CA THR 54 33.026 25.280 23.900 1.00 0.00 C +ATOM 837 HA THR 54 33.389 26.087 23.264 1.00 0.00 H +ATOM 838 CB THR 54 33.679 25.465 25.287 1.00 0.00 C +ATOM 839 HB THR 54 33.366 24.653 25.943 1.00 0.00 H +ATOM 840 CG2 THR 54 35.209 25.527 25.270 1.00 0.00 C +ATOM 841 HG21 THR 54 35.551 26.282 24.560 1.00 0.00 H +ATOM 842 HG22 THR 54 35.586 25.776 26.261 1.00 0.00 H +ATOM 843 HG23 THR 54 35.625 24.558 24.996 1.00 0.00 H +ATOM 844 OG1 THR 54 33.257 26.688 25.848 1.00 0.00 O +ATOM 845 HG1 THR 54 33.703 26.791 26.690 1.00 0.00 H +ATOM 846 C THR 54 33.453 23.948 23.240 1.00 0.00 C +ATOM 847 O THR 54 32.725 22.957 23.330 1.00 0.00 O +ATOM 848 N GLN 55 34.608 23.941 22.569 1.00 0.00 N +ATOM 849 H GLN 55 35.143 24.792 22.563 1.00 0.00 H +ATOM 850 CA GLN 55 35.230 22.769 21.928 1.00 0.00 C +ATOM 851 HA GLN 55 34.472 22.294 21.307 1.00 0.00 H +ATOM 852 CB GLN 55 36.356 23.273 20.997 1.00 0.00 C +ATOM 853 HB2 GLN 55 36.747 22.431 20.418 1.00 0.00 H +ATOM 854 HB3 GLN 55 35.915 23.976 20.284 1.00 0.00 H +ATOM 855 CG GLN 55 37.529 23.975 21.718 1.00 0.00 C +ATOM 856 HG2 GLN 55 37.135 24.635 22.490 1.00 0.00 H +ATOM 857 HG3 GLN 55 38.153 23.228 22.202 1.00 0.00 H +ATOM 858 CD GLN 55 38.400 24.813 20.772 1.00 0.00 C +ATOM 859 OE1 GLN 55 38.699 24.456 19.644 1.00 0.00 O +ATOM 860 NE2 GLN 55 38.838 25.984 21.186 1.00 0.00 N +ATOM 861 HE21 GLN 55 39.398 26.495 20.531 1.00 0.00 H +ATOM 862 HE22 GLN 55 38.530 26.390 22.059 1.00 0.00 H +ATOM 863 C GLN 55 35.729 21.702 22.920 1.00 0.00 C +ATOM 864 O GLN 55 35.936 21.998 24.098 1.00 0.00 O +ATOM 865 N GLU 56 35.911 20.461 22.436 1.00 0.00 N +ATOM 866 H GLU 56 35.764 20.328 21.453 1.00 0.00 H +ATOM 867 CA GLU 56 36.591 19.326 23.126 1.00 0.00 C +ATOM 868 HA GLU 56 36.581 19.527 24.209 1.00 0.00 H +ATOM 869 CB GLU 56 35.802 18.011 22.873 1.00 0.00 C +ATOM 870 HB2 GLU 56 34.794 18.115 23.271 1.00 0.00 H +ATOM 871 HB3 GLU 56 35.670 17.896 21.805 1.00 0.00 H +ATOM 872 CG GLU 56 36.406 16.708 23.419 1.00 0.00 C +ATOM 873 HG2 GLU 56 36.588 16.049 22.597 1.00 0.00 H +ATOM 874 HG3 GLU 56 37.378 16.911 23.804 1.00 0.00 H +ATOM 875 CD GLU 56 35.639 15.935 24.519 1.00 0.00 C +ATOM 876 OE1 GLU 56 36.261 15.255 25.395 1.00 0.00 O +ATOM 877 OE2 GLU 56 34.388 15.901 24.484 1.00 0.00 O +ATOM 878 C GLU 56 38.064 19.234 22.739 1.00 0.00 C +ATOM 879 O GLU 56 38.897 19.678 23.554 1.00 0.00 O +ATOM 880 OXT GLU 56 38.365 18.739 21.612 1.00 0.00 O +HETATM 881 ZN ZN1 57 26.696 32.427 29.378 1.00 0.00 Zn +HETATM 882 N AN1 58 28.269 33.325 30.318 1.00 0.00 N +HETATM 883 C AN1 58 30.569 34.237 31.119 1.00 0.00 C +HETATM 884 C1 AN1 58 29.262 33.721 30.709 1.00 0.00 C +HETATM 885 H AN1 58 30.559 34.480 32.185 1.00 0.00 H +HETATM 886 H1 AN1 58 30.794 35.142 30.544 1.00 0.00 H +HETATM 887 H2 AN1 58 31.328 33.474 30.919 1.00 0.00 H +HETATM 888 N1 AZI 59 30.711 28.496 29.887 1.00 0.00 N +HETATM 889 N2 AZI 59 30.239 29.556 30.281 1.00 0.00 N +HETATM 890 N3 AZI 59 29.793 30.642 30.720 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 881 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 137 134 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 140 142 +CONECT 140 139 +CONECT 141 139 +CONECT 142 139 145 143 144 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 142 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 194 189 +CONECT 188 187 +CONECT 189 187 192 190 191 +CONECT 190 189 +CONECT 191 189 +CONECT 192 193 189 +CONECT 193 192 +CONECT 194 196 187 195 +CONECT 195 194 +CONECT 196 197 198 194 +CONECT 197 196 +CONECT 198 205 196 200 199 +CONECT 199 198 +CONECT 200 201 198 202 203 +CONECT 201 200 +CONECT 202 200 +CONECT 203 200 204 +CONECT 204 203 +CONECT 205 206 207 198 +CONECT 206 205 +CONECT 207 209 205 208 +CONECT 208 207 +CONECT 209 210 227 211 207 +CONECT 210 209 +CONECT 211 214 209 212 213 +CONECT 212 211 +CONECT 213 211 +CONECT 214 216 215 217 211 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 214 219 220 +CONECT 218 217 +CONECT 219 217 +CONECT 220 217 222 223 221 +CONECT 221 220 +CONECT 222 220 +CONECT 223 226 220 225 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 223 +CONECT 227 228 209 229 +CONECT 228 227 +CONECT 229 227 231 230 +CONECT 230 229 +CONECT 231 234 229 232 233 +CONECT 232 231 +CONECT 233 231 +CONECT 234 235 236 231 +CONECT 235 234 +CONECT 236 238 234 237 +CONECT 237 236 +CONECT 238 240 239 250 236 +CONECT 239 238 +CONECT 240 246 241 242 238 +CONECT 241 240 +CONECT 242 244 240 243 245 +CONECT 243 242 +CONECT 244 242 +CONECT 245 242 +CONECT 246 248 247 249 240 +CONECT 247 246 +CONECT 248 246 +CONECT 249 246 +CONECT 250 238 252 251 +CONECT 251 250 +CONECT 252 262 253 250 +CONECT 253 254 252 263 256 +CONECT 254 255 269 253 +CONECT 255 254 +CONECT 256 253 257 264 265 +CONECT 257 258 259 256 +CONECT 258 261 267 257 +CONECT 259 260 257 266 +CONECT 260 261 268 259 +CONECT 261 881 258 260 +CONECT 262 252 +CONECT 263 253 +CONECT 264 256 +CONECT 265 256 +CONECT 266 259 +CONECT 267 258 +CONECT 268 260 +CONECT 269 271 254 270 +CONECT 270 269 +CONECT 271 272 273 281 269 +CONECT 272 271 +CONECT 273 274 275 271 279 +CONECT 274 273 +CONECT 275 278 277 273 276 +CONECT 276 275 +CONECT 277 275 +CONECT 278 275 +CONECT 279 273 280 +CONECT 280 279 +CONECT 281 283 271 282 +CONECT 282 281 +CONECT 283 293 284 281 +CONECT 284 285 287 283 294 +CONECT 285 286 300 284 +CONECT 286 285 +CONECT 287 295 296 284 288 +CONECT 288 287 289 290 +CONECT 289 298 288 292 +CONECT 290 288 297 291 +CONECT 291 292 290 299 +CONECT 292 289 881 291 +CONECT 293 283 +CONECT 294 284 +CONECT 295 287 +CONECT 296 287 +CONECT 297 290 +CONECT 298 289 +CONECT 299 291 +CONECT 300 302 285 301 +CONECT 301 300 +CONECT 302 313 303 300 304 +CONECT 303 302 +CONECT 304 302 307 306 305 +CONECT 305 304 +CONECT 306 304 +CONECT 307 309 310 304 308 +CONECT 308 307 +CONECT 309 307 +CONECT 310 311 307 312 +CONECT 311 310 +CONECT 312 310 +CONECT 313 315 314 302 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 323 319 318 315 +CONECT 318 317 +CONECT 319 321 320 317 322 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 325 324 317 +CONECT 324 323 +CONECT 325 327 326 323 +CONECT 326 325 +CONECT 327 339 329 328 325 +CONECT 328 327 +CONECT 329 330 335 327 331 +CONECT 330 329 +CONECT 331 329 333 334 332 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 336 337 329 338 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 340 341 327 +CONECT 340 339 +CONECT 341 343 339 342 +CONECT 342 341 +CONECT 343 345 344 351 341 +CONECT 344 343 +CONECT 345 348 346 347 343 +CONECT 346 345 +CONECT 347 345 +CONECT 348 350 349 345 +CONECT 349 348 +CONECT 350 348 +CONECT 351 353 343 352 +CONECT 352 351 +CONECT 353 354 355 351 +CONECT 354 353 +CONECT 355 357 353 375 356 +CONECT 356 355 +CONECT 357 359 358 360 355 +CONECT 358 357 +CONECT 359 357 +CONECT 360 361 357 374 +CONECT 361 362 363 360 +CONECT 362 361 +CONECT 363 361 364 365 +CONECT 364 363 +CONECT 365 363 374 366 +CONECT 366 365 367 368 +CONECT 367 366 +CONECT 368 366 370 369 +CONECT 369 368 +CONECT 370 372 368 371 +CONECT 371 370 +CONECT 372 374 373 370 +CONECT 373 372 +CONECT 374 360 365 372 +CONECT 375 377 355 376 +CONECT 376 375 +CONECT 377 378 379 375 +CONECT 378 377 +CONECT 379 381 377 380 385 +CONECT 380 379 +CONECT 381 384 382 383 379 +CONECT 382 381 +CONECT 383 381 +CONECT 384 381 +CONECT 385 379 386 387 +CONECT 386 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 390 391 400 +CONECT 390 389 +CONECT 391 394 392 389 393 +CONECT 392 391 +CONECT 393 391 +CONECT 394 395 396 397 391 +CONECT 395 394 +CONECT 396 394 +CONECT 397 399 394 398 +CONECT 398 397 +CONECT 399 397 +CONECT 400 389 402 401 +CONECT 401 400 +CONECT 402 403 400 404 +CONECT 403 402 +CONECT 404 402 406 410 405 +CONECT 405 404 +CONECT 406 407 409 404 408 +CONECT 407 406 +CONECT 408 406 +CONECT 409 406 +CONECT 410 412 404 411 +CONECT 411 410 +CONECT 412 413 414 410 +CONECT 413 412 +CONECT 414 416 412 415 425 +CONECT 415 414 +CONECT 416 417 418 419 414 +CONECT 417 416 +CONECT 418 416 +CONECT 419 422 416 421 420 +CONECT 420 419 +CONECT 421 419 +CONECT 422 424 423 419 +CONECT 423 422 +CONECT 424 422 +CONECT 425 414 427 426 +CONECT 426 425 +CONECT 427 428 425 429 +CONECT 428 427 +CONECT 429 427 431 430 447 +CONECT 430 429 +CONECT 431 434 432 433 429 +CONECT 432 431 +CONECT 433 431 +CONECT 434 436 437 435 431 +CONECT 435 434 +CONECT 436 434 +CONECT 437 440 438 439 434 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 441 442 437 +CONECT 441 440 +CONECT 442 440 +CONECT 443 445 444 446 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 +CONECT 447 429 449 448 +CONECT 448 447 +CONECT 449 450 447 451 +CONECT 450 449 +CONECT 451 449 453 452 467 +CONECT 452 451 +CONECT 453 456 454 451 455 +CONECT 454 453 +CONECT 455 453 +CONECT 456 457 465 453 +CONECT 457 459 458 456 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 462 459 463 +CONECT 462 461 +CONECT 463 461 464 465 +CONECT 464 463 +CONECT 465 463 456 466 +CONECT 466 465 +CONECT 467 451 469 468 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 473 469 481 472 +CONECT 472 471 +CONECT 473 474 479 475 471 +CONECT 474 473 +CONECT 475 473 477 478 476 +CONECT 476 475 +CONECT 477 475 +CONECT 478 475 +CONECT 479 480 473 +CONECT 480 479 +CONECT 481 483 471 482 +CONECT 482 481 +CONECT 483 484 485 481 +CONECT 484 483 +CONECT 485 487 483 486 503 +CONECT 486 485 +CONECT 487 490 488 489 485 +CONECT 488 487 +CONECT 489 487 +CONECT 490 493 492 491 487 +CONECT 491 490 +CONECT 492 490 +CONECT 493 496 494 495 490 +CONECT 494 493 +CONECT 495 493 +CONECT 496 498 497 499 493 +CONECT 497 496 +CONECT 498 496 +CONECT 499 501 496 502 500 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 485 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 508 513 +CONECT 508 507 +CONECT 509 512 510 507 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 507 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 534 518 +CONECT 518 517 +CONECT 519 521 520 517 522 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 525 523 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 526 522 528 527 +CONECT 526 525 +CONECT 527 525 +CONECT 528 530 525 531 529 +CONECT 529 528 +CONECT 530 528 +CONECT 531 533 528 532 +CONECT 532 531 +CONECT 533 531 +CONECT 534 536 517 535 +CONECT 535 534 +CONECT 536 537 538 534 +CONECT 537 536 +CONECT 538 540 536 544 539 +CONECT 539 538 +CONECT 540 541 543 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 +CONECT 544 538 546 545 +CONECT 545 544 +CONECT 546 547 544 548 +CONECT 547 546 +CONECT 548 550 546 549 558 +CONECT 549 548 +CONECT 550 553 551 552 548 +CONECT 551 550 +CONECT 552 550 +CONECT 553 555 554 550 +CONECT 554 553 +CONECT 555 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 548 560 559 +CONECT 559 558 +CONECT 560 561 558 562 +CONECT 561 560 +CONECT 562 560 564 563 570 +CONECT 563 562 +CONECT 564 567 565 562 566 +CONECT 565 564 +CONECT 566 564 +CONECT 567 569 568 564 +CONECT 568 567 +CONECT 569 567 +CONECT 570 562 572 571 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 592 576 575 +CONECT 575 574 +CONECT 576 579 574 578 577 +CONECT 577 576 +CONECT 578 576 +CONECT 579 580 581 582 576 +CONECT 580 579 +CONECT 581 579 +CONECT 582 585 584 579 583 +CONECT 583 582 +CONECT 584 582 +CONECT 585 588 587 586 582 +CONECT 586 585 +CONECT 587 585 +CONECT 588 590 591 589 585 +CONECT 589 588 +CONECT 590 588 +CONECT 591 588 +CONECT 592 594 593 574 +CONECT 593 592 +CONECT 594 596 595 592 +CONECT 595 594 +CONECT 596 599 594 597 598 +CONECT 597 596 +CONECT 598 596 +CONECT 599 601 600 596 +CONECT 600 599 +CONECT 601 603 602 599 +CONECT 602 601 +CONECT 603 623 604 605 601 +CONECT 604 603 +CONECT 605 606 603 607 608 +CONECT 606 605 +CONECT 607 605 +CONECT 608 609 605 610 611 +CONECT 609 608 +CONECT 610 608 +CONECT 611 608 613 614 612 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 616 615 +CONECT 615 614 +CONECT 616 617 614 620 +CONECT 617 618 619 616 +CONECT 618 617 +CONECT 619 617 +CONECT 620 616 622 621 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 603 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 629 635 628 625 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 632 +CONECT 635 637 636 627 +CONECT 636 635 +CONECT 637 639 638 635 +CONECT 638 637 +CONECT 639 642 640 641 637 +CONECT 640 639 +CONECT 641 639 +CONECT 642 644 643 639 +CONECT 643 642 +CONECT 644 646 645 642 +CONECT 645 644 +CONECT 646 648 647 657 644 +CONECT 647 646 +CONECT 648 650 651 649 646 +CONECT 649 648 +CONECT 650 648 +CONECT 651 653 648 654 652 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 655 656 +CONECT 655 654 +CONECT 656 654 +CONECT 657 659 646 658 +CONECT 658 657 +CONECT 659 660 661 657 +CONECT 660 659 +CONECT 661 681 659 662 663 +CONECT 662 661 +CONECT 663 661 666 664 665 +CONECT 664 663 +CONECT 665 663 +CONECT 666 668 667 663 669 +CONECT 667 666 +CONECT 668 666 +CONECT 669 666 672 670 671 +CONECT 670 669 +CONECT 671 669 +CONECT 672 673 674 669 +CONECT 673 672 +CONECT 674 678 675 672 +CONECT 675 677 676 674 +CONECT 676 675 +CONECT 677 675 +CONECT 678 679 680 674 +CONECT 679 678 +CONECT 680 678 +CONECT 681 682 683 661 +CONECT 682 681 +CONECT 683 685 681 684 +CONECT 684 683 +CONECT 685 686 687 695 683 +CONECT 686 685 +CONECT 687 689 693 685 688 +CONECT 688 687 +CONECT 689 690 691 692 687 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 +CONECT 693 694 687 +CONECT 694 693 +CONECT 695 697 685 696 +CONECT 696 695 +CONECT 697 698 699 695 +CONECT 698 697 +CONECT 699 714 701 697 700 +CONECT 700 699 +CONECT 701 707 702 699 703 +CONECT 702 701 +CONECT 703 701 705 704 706 +CONECT 704 703 +CONECT 705 703 +CONECT 706 703 +CONECT 707 710 709 708 701 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 713 711 707 +CONECT 711 710 +CONECT 712 710 +CONECT 713 710 +CONECT 714 715 716 699 +CONECT 715 714 +CONECT 716 718 714 717 +CONECT 717 716 +CONECT 718 719 726 720 716 +CONECT 719 718 +CONECT 720 723 718 721 722 +CONECT 721 720 +CONECT 722 720 +CONECT 723 725 720 724 +CONECT 724 723 +CONECT 725 723 +CONECT 726 728 718 727 +CONECT 727 726 +CONECT 728 729 730 726 +CONECT 729 728 +CONECT 730 732 728 738 731 +CONECT 731 730 +CONECT 732 734 735 733 730 +CONECT 733 732 +CONECT 734 732 +CONECT 735 736 732 737 +CONECT 736 735 +CONECT 737 735 +CONECT 738 740 730 739 +CONECT 739 738 +CONECT 740 741 742 738 +CONECT 741 740 +CONECT 742 744 743 740 748 +CONECT 743 742 +CONECT 744 747 746 745 742 +CONECT 745 744 +CONECT 746 744 +CONECT 747 744 +CONECT 748 742 749 750 +CONECT 749 748 +CONECT 750 748 751 752 +CONECT 751 750 +CONECT 752 750 753 754 762 +CONECT 753 752 +CONECT 754 756 752 760 755 +CONECT 755 754 +CONECT 756 757 759 758 754 +CONECT 757 756 +CONECT 758 756 +CONECT 759 756 +CONECT 760 761 754 +CONECT 761 760 +CONECT 762 752 764 763 +CONECT 763 762 +CONECT 764 765 766 762 +CONECT 765 764 +CONECT 766 767 764 768 784 +CONECT 767 766 +CONECT 768 771 766 770 769 +CONECT 769 768 +CONECT 770 768 +CONECT 771 774 772 773 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 777 776 775 771 +CONECT 775 774 +CONECT 776 774 +CONECT 777 780 779 778 774 +CONECT 778 777 +CONECT 779 777 +CONECT 780 782 783 781 777 +CONECT 781 780 +CONECT 782 780 +CONECT 783 780 +CONECT 784 766 786 785 +CONECT 785 784 +CONECT 786 787 784 788 +CONECT 787 786 +CONECT 788 786 798 790 789 +CONECT 789 788 +CONECT 790 791 788 796 792 +CONECT 791 790 +CONECT 792 790 795 794 793 +CONECT 793 792 +CONECT 794 792 +CONECT 795 792 +CONECT 796 797 790 +CONECT 797 796 +CONECT 798 799 788 800 +CONECT 799 798 +CONECT 800 798 802 801 +CONECT 801 800 +CONECT 802 803 800 818 804 +CONECT 803 802 +CONECT 804 802 807 806 805 +CONECT 805 804 +CONECT 806 804 +CONECT 807 816 808 804 +CONECT 808 810 807 809 +CONECT 809 808 +CONECT 810 812 811 808 +CONECT 811 810 +CONECT 812 813 814 810 +CONECT 813 812 +CONECT 814 815 812 816 +CONECT 815 814 +CONECT 816 814 817 807 +CONECT 817 816 +CONECT 818 802 820 819 +CONECT 819 818 +CONECT 820 821 818 822 +CONECT 821 820 +CONECT 822 824 820 832 823 +CONECT 823 822 +CONECT 824 830 826 825 822 +CONECT 825 824 +CONECT 826 827 828 824 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 +CONECT 830 831 824 +CONECT 831 830 +CONECT 832 833 822 834 +CONECT 833 832 +CONECT 834 832 836 835 +CONECT 835 834 +CONECT 836 846 837 834 838 +CONECT 837 836 +CONECT 838 836 840 844 839 +CONECT 839 838 +CONECT 840 841 843 838 842 +CONECT 841 840 +CONECT 842 840 +CONECT 843 840 +CONECT 844 838 845 +CONECT 845 844 +CONECT 846 848 847 836 +CONECT 847 846 +CONECT 848 850 849 846 +CONECT 849 848 +CONECT 850 852 851 848 863 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 858 852 857 856 +CONECT 856 855 +CONECT 857 855 +CONECT 858 859 860 855 +CONECT 859 858 +CONECT 860 861 858 862 +CONECT 861 860 +CONECT 862 860 +CONECT 863 850 865 864 +CONECT 864 863 +CONECT 865 866 863 867 +CONECT 866 865 +CONECT 867 865 878 869 868 +CONECT 868 867 +CONECT 869 871 867 870 872 +CONECT 870 869 +CONECT 871 869 +CONECT 872 873 869 874 875 +CONECT 873 872 +CONECT 874 872 +CONECT 875 872 877 876 +CONECT 876 875 +CONECT 877 875 +CONECT 878 880 867 879 +CONECT 879 878 +CONECT 880 878 +CONECT 881 87 292 882 261 +CONECT 882 881 884 +CONECT 883 886 884 887 885 +CONECT 884 882 883 +CONECT 885 883 +CONECT 886 883 +CONECT 887 883 +CONECT 888 889 +CONECT 889 888 890 +CONECT 890 889 +MASTER 0 0 0 0 0 0 0 0 890 0 890 0 +END diff --git a/tests/nsga2/min_mol_iter_4.pdb b/tests/nsga2/min_mol_iter_4.pdb new file mode 100644 index 0000000..93ef165 --- /dev/null +++ b/tests/nsga2/min_mol_iter_4.pdb @@ -0,0 +1,1785 @@ +COMPND fitness: -6.2239 90.03083333333325 +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +CRYST1 54.779 58.077 50.124 90.00 90.00 90.00 P 1 1 +ATOM 1 N MET 1 15.128 37.937 23.379 1.00 0.00 N +ATOM 2 H1 MET 1 15.115 38.352 24.304 1.00 0.00 H +ATOM 3 H2 MET 1 14.353 38.281 22.845 1.00 0.00 H +ATOM 4 H3 MET 1 15.989 38.231 22.950 1.00 0.00 H +ATOM 5 CA MET 1 15.114 36.469 23.492 1.00 0.00 C +ATOM 6 HA MET 1 14.154 36.172 23.930 1.00 0.00 H +ATOM 7 CB MET 1 15.258 35.810 22.104 1.00 0.00 C +ATOM 8 HB2 MET 1 14.395 36.081 21.502 1.00 0.00 H +ATOM 9 HB3 MET 1 16.151 36.200 21.624 1.00 0.00 H +ATOM 10 CG MET 1 15.368 34.269 22.154 1.00 0.00 C +ATOM 11 HG2 MET 1 16.256 34.008 22.740 1.00 0.00 H +ATOM 12 HG3 MET 1 14.490 33.864 22.670 1.00 0.00 H +ATOM 13 SD MET 1 15.523 33.454 20.540 1.00 0.00 S +ATOM 14 CE MET 1 13.825 33.570 19.902 1.00 0.00 C +ATOM 15 HE1 MET 1 13.514 34.612 19.846 1.00 0.00 H +ATOM 16 HE2 MET 1 13.786 33.136 18.902 1.00 0.00 H +ATOM 17 HE3 MET 1 13.144 33.019 20.553 1.00 0.00 H +ATOM 18 C MET 1 16.215 36.013 24.449 1.00 0.00 C +ATOM 19 O MET 1 17.372 36.346 24.223 1.00 0.00 O +ATOM 20 N GLN 2 15.871 35.224 25.474 1.00 0.00 N +ATOM 21 H GLN 2 14.897 35.087 25.675 1.00 0.00 H +ATOM 22 CA GLN 2 16.831 34.496 26.306 1.00 0.00 C +ATOM 23 HA GLN 2 17.643 35.162 26.593 1.00 0.00 H +ATOM 24 CB GLN 2 16.127 34.008 27.587 1.00 0.00 C +ATOM 25 HB2 GLN 2 15.159 33.579 27.318 1.00 0.00 H +ATOM 26 HB3 GLN 2 16.708 33.210 28.060 1.00 0.00 H +ATOM 27 CG GLN 2 15.903 35.114 28.632 1.00 0.00 C +ATOM 28 HG2 GLN 2 15.477 35.983 28.143 1.00 0.00 H +ATOM 29 HG3 GLN 2 15.171 34.756 29.353 1.00 0.00 H +ATOM 30 CD GLN 2 17.153 35.508 29.416 1.00 0.00 C +ATOM 31 OE1 GLN 2 18.264 35.044 29.192 1.00 0.00 O +ATOM 32 NE2 GLN 2 17.019 36.331 30.429 1.00 0.00 N +ATOM 33 HE21 GLN 2 17.839 36.559 30.955 1.00 0.00 H +ATOM 34 HE22 GLN 2 16.114 36.721 30.646 1.00 0.00 H +ATOM 35 C GLN 2 17.469 33.325 25.522 1.00 0.00 C +ATOM 36 O GLN 2 17.052 32.167 25.651 1.00 0.00 O +ATOM 37 N TYR 3 18.463 33.623 24.678 1.00 0.00 N +ATOM 38 H TYR 3 18.765 34.592 24.628 1.00 0.00 H +ATOM 39 CA TYR 3 19.234 32.609 23.954 1.00 0.00 C +ATOM 40 HA TYR 3 18.545 31.959 23.422 1.00 0.00 H +ATOM 41 CB TYR 3 20.170 33.262 22.941 1.00 0.00 C +ATOM 42 HB2 TYR 3 20.877 33.900 23.476 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.723 32.438 22.497 1.00 0.00 H +ATOM 44 CG TYR 3 19.600 34.062 21.781 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.519 33.459 20.512 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.802 32.423 20.390 1.00 0.00 H +ATOM 47 CE1 TYR 3 19.149 34.213 19.385 1.00 0.00 C +ATOM 48 HE1 TYR 3 19.118 33.754 18.409 1.00 0.00 H +ATOM 49 CZ TYR 3 18.855 35.585 19.528 1.00 0.00 C +ATOM 50 OH TYR 3 18.517 36.324 18.441 1.00 0.00 O +ATOM 51 HH TYR 3 18.718 35.875 17.614 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.941 36.195 20.795 1.00 0.00 C +ATOM 53 HE2 TYR 3 18.739 37.253 20.885 1.00 0.00 H +ATOM 54 CD2 TYR 3 19.327 35.436 21.918 1.00 0.00 C +ATOM 55 HD2 TYR 3 19.448 35.924 22.876 1.00 0.00 H +ATOM 56 C TYR 3 20.072 31.754 24.926 1.00 0.00 C +ATOM 57 O TYR 3 20.489 32.242 25.980 1.00 0.00 O +ATOM 58 N LYS 4 20.339 30.479 24.600 1.00 0.00 N +ATOM 59 H LYS 4 20.151 30.180 23.644 1.00 0.00 H +ATOM 60 CA LYS 4 20.960 29.479 25.496 1.00 0.00 C +ATOM 61 HA LYS 4 20.692 29.716 26.523 1.00 0.00 H +ATOM 62 CB LYS 4 20.389 28.078 25.169 1.00 0.00 C +ATOM 63 HB2 LYS 4 20.359 27.961 24.086 1.00 0.00 H +ATOM 64 HB3 LYS 4 21.082 27.325 25.544 1.00 0.00 H +ATOM 65 CG LYS 4 18.993 27.726 25.738 1.00 0.00 C +ATOM 66 HG2 LYS 4 18.817 26.675 25.502 1.00 0.00 H +ATOM 67 HG3 LYS 4 19.009 27.823 26.824 1.00 0.00 H +ATOM 68 CD LYS 4 17.809 28.534 25.173 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.798 29.537 25.609 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.962 28.643 24.097 1.00 0.00 H +ATOM 71 CE LYS 4 16.441 27.842 25.378 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.715 28.351 24.738 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.517 26.807 25.026 1.00 0.00 H +ATOM 74 NZ LYS 4 15.935 27.871 26.782 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.755 28.812 27.098 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.064 27.350 26.889 1.00 0.00 H +ATOM 77 HZ3 LYS 4 16.572 27.463 27.463 1.00 0.00 H +ATOM 78 C LYS 4 22.499 29.490 25.466 1.00 0.00 C +ATOM 79 O LYS 4 23.140 29.867 24.490 1.00 0.00 O +HETATM 80 N HX1 5 23.130 29.035 26.548 1.00 0.00 N +HETATM 81 CA HX1 5 24.591 28.856 26.679 1.00 0.00 C +HETATM 82 C HX1 5 24.878 27.688 27.631 1.00 0.00 C +HETATM 83 O HX1 5 24.428 27.708 28.777 1.00 0.00 O +HETATM 84 CB HX1 5 25.222 30.175 27.180 1.00 0.00 C +HETATM 85 CG HX1 5 26.737 30.247 27.288 1.00 0.00 C +HETATM 86 CD2 HX1 5 27.646 29.286 26.930 1.00 0.00 C +HETATM 87 ND1 HX1 5 27.420 31.336 27.850 1.00 0.00 N +HETATM 88 CE1 HX1 5 28.719 30.994 27.776 1.00 0.00 C +HETATM 89 NE2 HX1 5 28.886 29.754 27.285 1.00 0.00 N +HETATM 90 H HX1 5 22.559 28.844 27.370 1.00 0.00 H +HETATM 91 HA HX1 5 25.018 28.612 25.702 1.00 0.00 H +HETATM 92 HB2 HX1 5 24.806 30.413 28.160 1.00 0.00 H +HETATM 93 HB3 HX1 5 24.913 30.973 26.501 1.00 0.00 H +HETATM 94 HD2 HX1 5 27.458 28.305 26.513 1.00 0.00 H +HETATM 95 HE1 HX1 5 29.519 31.581 28.203 1.00 0.00 H +HETATM 96 HE2 HX1 5 29.738 29.194 27.351 1.00 0.00 H +ATOM 97 N ILE 6 25.579 26.661 27.147 1.00 0.00 N +ATOM 98 H ILE 6 25.921 26.711 26.193 1.00 0.00 H +ATOM 99 CA ILE 6 25.970 25.469 27.917 1.00 0.00 C +ATOM 100 HA ILE 6 25.283 25.357 28.755 1.00 0.00 H +ATOM 101 CB ILE 6 25.813 24.203 27.035 1.00 0.00 C +ATOM 102 HB ILE 6 26.347 24.367 26.099 1.00 0.00 H +ATOM 103 CG2 ILE 6 26.392 22.937 27.698 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.889 22.736 28.645 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.267 22.079 27.038 1.00 0.00 H +ATOM 106 HG23 ILE 6 27.465 23.049 27.864 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.304 24.011 26.726 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.764 23.868 27.661 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.914 24.914 26.252 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.964 22.843 25.793 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.140 21.891 26.293 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.908 22.895 25.523 1.00 0.00 H +ATOM 113 HD13 ILE 6 24.564 22.899 24.885 1.00 0.00 H +ATOM 114 C ILE 6 27.370 25.661 28.537 1.00 0.00 C +ATOM 115 O ILE 6 28.186 26.422 28.017 1.00 0.00 O +ATOM 116 N VAL 7 27.605 25.035 29.694 1.00 0.00 N +ATOM 117 H VAL 7 26.884 24.405 30.032 1.00 0.00 H +ATOM 118 CA VAL 7 28.769 25.251 30.572 1.00 0.00 C +ATOM 119 HA VAL 7 28.849 26.325 30.732 1.00 0.00 H +ATOM 120 CB VAL 7 28.470 24.592 31.936 1.00 0.00 C +ATOM 121 HB VAL 7 27.460 24.891 32.229 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.498 23.060 31.893 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.507 22.695 31.701 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.158 22.662 32.842 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.845 22.689 31.104 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.397 25.060 33.063 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.408 26.149 33.096 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.024 24.680 34.015 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.403 24.676 32.902 1.00 0.00 H +ATOM 130 C VAL 7 30.119 24.780 29.995 1.00 0.00 C +ATOM 131 O VAL 7 30.207 23.763 29.310 1.00 0.00 O +ATOM 132 N ARG 8 31.201 25.497 30.343 1.00 0.00 N +ATOM 133 H ARG 8 31.031 26.423 30.713 1.00 0.00 H +ATOM 134 CA ARG 8 32.608 25.082 30.154 1.00 0.00 C +ATOM 135 HA ARG 8 32.717 24.857 29.094 1.00 0.00 H +ATOM 136 CB ARG 8 33.575 26.241 30.501 1.00 0.00 C +ATOM 137 HB2 ARG 8 34.546 25.995 30.072 1.00 0.00 H +ATOM 138 HB3 ARG 8 33.247 27.151 30.004 1.00 0.00 H +ATOM 139 CG ARG 8 33.814 26.544 32.001 1.00 0.00 C +ATOM 140 HG2 ARG 8 34.126 25.632 32.506 1.00 0.00 H +ATOM 141 HG3 ARG 8 34.652 27.235 32.093 1.00 0.00 H +ATOM 142 CD ARG 8 32.636 27.142 32.778 1.00 0.00 C +ATOM 143 HD2 ARG 8 31.766 26.524 32.631 1.00 0.00 H +ATOM 144 HD3 ARG 8 32.851 27.100 33.836 1.00 0.00 H +ATOM 145 NE ARG 8 32.321 28.531 32.389 1.00 0.00 N +ATOM 146 HE ARG 8 31.868 28.645 31.483 1.00 0.00 H +ATOM 147 CZ ARG 8 32.417 29.619 33.139 1.00 0.00 C +ATOM 148 NH1 ARG 8 31.818 30.717 32.782 1.00 0.00 N +ATOM 149 HH11 ARG 8 31.188 30.675 31.981 1.00 0.00 H +ATOM 150 HH12 ARG 8 31.731 31.448 33.453 1.00 0.00 H +ATOM 151 NH2 ARG 8 33.086 29.637 34.256 1.00 0.00 N +ATOM 152 HH21 ARG 8 33.619 28.829 34.514 1.00 0.00 H +ATOM 153 HH22 ARG 8 33.065 30.431 34.886 1.00 0.00 H +ATOM 154 C ARG 8 32.993 23.796 30.906 1.00 0.00 C +ATOM 155 O ARG 8 32.490 23.532 31.997 1.00 0.00 O +ATOM 156 N GLY 9 33.997 23.086 30.385 1.00 0.00 N +ATOM 157 H GLY 9 34.336 23.350 29.474 1.00 0.00 H +ATOM 158 CA GLY 9 34.544 21.859 30.982 1.00 0.00 C +ATOM 159 HA2 GLY 9 35.546 21.680 30.585 1.00 0.00 H +ATOM 160 HA3 GLY 9 34.627 21.989 32.066 1.00 0.00 H +ATOM 161 C GLY 9 33.690 20.615 30.703 1.00 0.00 C +ATOM 162 O GLY 9 32.893 20.602 29.772 1.00 0.00 O +ATOM 163 N LYS 10 33.877 19.558 31.507 1.00 0.00 N +ATOM 164 H LYS 10 34.624 19.619 32.176 1.00 0.00 H +ATOM 165 CA LYS 10 33.145 18.277 31.372 1.00 0.00 C +ATOM 166 HA LYS 10 32.234 18.481 30.799 1.00 0.00 H +ATOM 167 CB LYS 10 34.004 17.293 30.544 1.00 0.00 C +ATOM 168 HB2 LYS 10 34.660 17.868 29.891 1.00 0.00 H +ATOM 169 HB3 LYS 10 34.633 16.707 31.215 1.00 0.00 H +ATOM 170 CG LYS 10 33.182 16.351 29.644 1.00 0.00 C +ATOM 171 HG2 LYS 10 32.576 15.685 30.259 1.00 0.00 H +ATOM 172 HG3 LYS 10 32.517 16.953 29.025 1.00 0.00 H +ATOM 173 CD LYS 10 34.095 15.518 28.728 1.00 0.00 C +ATOM 174 HD2 LYS 10 34.765 16.189 28.186 1.00 0.00 H +ATOM 175 HD3 LYS 10 34.693 14.843 29.337 1.00 0.00 H +ATOM 176 CE LYS 10 33.287 14.702 27.711 1.00 0.00 C +ATOM 177 HE2 LYS 10 32.727 13.931 28.247 1.00 0.00 H +ATOM 178 HE3 LYS 10 32.567 15.368 27.228 1.00 0.00 H +ATOM 179 NZ LYS 10 34.153 14.097 26.667 1.00 0.00 N +ATOM 180 HZ1 LYS 10 34.950 13.593 27.047 1.00 0.00 H +ATOM 181 HZ2 LYS 10 33.637 13.513 26.029 1.00 0.00 H +ATOM 182 HZ3 LYS 10 34.558 14.828 26.065 1.00 0.00 H +ATOM 183 C LYS 10 32.647 17.678 32.701 1.00 0.00 C +ATOM 184 O LYS 10 31.863 16.738 32.687 1.00 0.00 O +ATOM 185 N SER 11 33.082 18.223 33.848 1.00 0.00 N +ATOM 186 H SER 11 33.752 18.967 33.790 1.00 0.00 H +ATOM 187 CA SER 11 32.570 17.839 35.182 1.00 0.00 C +ATOM 188 HA SER 11 32.446 16.755 35.225 1.00 0.00 H +ATOM 189 CB SER 11 33.539 18.260 36.295 1.00 0.00 C +ATOM 190 HB2 SER 11 33.665 19.345 36.284 1.00 0.00 H +ATOM 191 HB3 SER 11 33.107 17.977 37.259 1.00 0.00 H +ATOM 192 OG SER 11 34.809 17.642 36.180 1.00 0.00 O +ATOM 193 HG SER 11 35.427 18.251 35.756 1.00 0.00 H +ATOM 194 C SER 11 31.199 18.462 35.496 1.00 0.00 C +ATOM 195 O SER 11 30.406 17.878 36.230 1.00 0.00 O +ATOM 196 N CYS 12 30.923 19.656 34.964 1.00 0.00 N +ATOM 197 H CYS 12 31.599 20.053 34.332 1.00 0.00 H +ATOM 198 CA CYS 12 29.611 20.301 35.006 1.00 0.00 C +ATOM 199 HA CYS 12 29.036 19.906 35.847 1.00 0.00 H +ATOM 200 CB CYS 12 29.796 21.821 35.196 1.00 0.00 C +ATOM 201 HB2 CYS 12 30.330 22.228 34.334 1.00 0.00 H +ATOM 202 HB3 CYS 12 28.812 22.284 35.254 1.00 0.00 H +ATOM 203 SG CYS 12 30.722 22.206 36.721 1.00 0.00 S +ATOM 204 HG CYS 12 29.845 23.085 37.226 1.00 0.00 H +ATOM 205 C CYS 12 28.846 19.994 33.710 1.00 0.00 C +ATOM 206 O CYS 12 29.461 19.846 32.657 1.00 0.00 O +ATOM 207 N LYS 13 27.505 19.956 33.760 1.00 0.00 N +ATOM 208 H LYS 13 27.067 20.025 34.666 1.00 0.00 H +ATOM 209 CA LYS 13 26.638 19.689 32.587 1.00 0.00 C +ATOM 210 HA LYS 13 27.243 19.869 31.686 1.00 0.00 H +ATOM 211 CB LYS 13 26.243 18.193 32.591 1.00 0.00 C +ATOM 212 HB2 LYS 13 27.073 17.620 33.007 1.00 0.00 H +ATOM 213 HB3 LYS 13 25.379 18.062 33.237 1.00 0.00 H +ATOM 214 CG LYS 13 25.952 17.630 31.186 1.00 0.00 C +ATOM 215 HG2 LYS 13 25.065 18.101 30.761 1.00 0.00 H +ATOM 216 HG3 LYS 13 26.801 17.853 30.536 1.00 0.00 H +ATOM 217 CD LYS 13 25.755 16.105 31.210 1.00 0.00 C +ATOM 218 HD2 LYS 13 25.746 15.739 30.181 1.00 0.00 H +ATOM 219 HD3 LYS 13 26.602 15.645 31.726 1.00 0.00 H +ATOM 220 CE LYS 13 24.441 15.690 31.887 1.00 0.00 C +ATOM 221 HE2 LYS 13 24.310 16.264 32.808 1.00 0.00 H +ATOM 222 HE3 LYS 13 23.614 15.945 31.214 1.00 0.00 H +ATOM 223 NZ LYS 13 24.411 14.238 32.200 1.00 0.00 N +ATOM 224 HZ1 LYS 13 25.113 13.979 32.890 1.00 0.00 H +ATOM 225 HZ2 LYS 13 23.525 13.972 32.618 1.00 0.00 H +ATOM 226 HZ3 LYS 13 24.608 13.675 31.375 1.00 0.00 H +ATOM 227 C LYS 13 25.442 20.651 32.462 1.00 0.00 C +ATOM 228 O LYS 13 24.474 20.361 31.772 1.00 0.00 O +ATOM 229 N GLY 14 25.489 21.778 33.176 1.00 0.00 N +ATOM 230 H GLY 14 26.334 21.976 33.674 1.00 0.00 H +ATOM 231 CA GLY 14 24.400 22.746 33.252 1.00 0.00 C +ATOM 232 HA2 GLY 14 23.453 22.214 33.347 1.00 0.00 H +ATOM 233 HA3 GLY 14 24.522 23.365 34.139 1.00 0.00 H +ATOM 234 C GLY 14 24.283 23.694 32.040 1.00 0.00 C +ATOM 235 O GLY 14 25.205 23.839 31.229 1.00 0.00 O +ATOM 236 N VAL 15 23.147 24.397 31.969 1.00 0.00 N +ATOM 237 H VAL 15 22.465 24.249 32.702 1.00 0.00 H +ATOM 238 CA VAL 15 22.785 25.364 30.936 1.00 0.00 C +ATOM 239 HA VAL 15 23.676 25.622 30.371 1.00 0.00 H +ATOM 240 CB VAL 15 21.782 24.726 29.948 1.00 0.00 C +ATOM 241 HB VAL 15 22.261 23.828 29.523 1.00 0.00 H +ATOM 242 CG1 VAL 15 20.463 24.268 30.608 1.00 0.00 C +ATOM 243 HG11 VAL 15 19.940 25.116 31.035 1.00 0.00 H +ATOM 244 HG12 VAL 15 19.832 23.789 29.857 1.00 0.00 H +ATOM 245 HG13 VAL 15 20.672 23.536 31.384 1.00 0.00 H +ATOM 246 CG2 VAL 15 21.431 25.652 28.775 1.00 0.00 C +ATOM 247 HG21 VAL 15 22.344 26.000 28.296 1.00 0.00 H +ATOM 248 HG22 VAL 15 20.849 25.095 28.039 1.00 0.00 H +ATOM 249 HG23 VAL 15 20.845 26.497 29.121 1.00 0.00 H +ATOM 250 C VAL 15 22.255 26.634 31.587 1.00 0.00 C +ATOM 251 O VAL 15 21.634 26.597 32.639 1.00 0.00 O +HETATM 252 N HY1 16 22.503 27.793 30.973 1.00 0.00 N +HETATM 253 CA HY1 16 21.907 29.109 31.309 1.00 0.00 C +HETATM 254 C HY1 16 21.626 29.889 30.030 1.00 0.00 C +HETATM 255 O HY1 16 21.803 29.384 28.934 1.00 0.00 O +HETATM 256 CB HY1 16 22.834 29.825 32.330 1.00 0.00 C +HETATM 257 CG HY1 16 24.188 30.197 31.783 1.00 0.00 C +HETATM 258 CD2 HY1 16 24.521 31.376 31.162 1.00 0.00 C +HETATM 259 ND1 HY1 16 25.320 29.420 31.809 1.00 0.00 N +HETATM 260 CE1 HY1 16 26.313 30.124 31.227 1.00 0.00 C +HETATM 261 NE2 HY1 16 25.875 31.326 30.803 1.00 0.00 N +HETATM 262 H HY1 16 23.045 27.766 30.100 1.00 0.00 H +HETATM 263 HA HY1 16 20.949 28.916 31.823 1.00 0.00 H +HETATM 264 HB2 HY1 16 22.325 30.741 32.671 1.00 0.00 H +HETATM 265 HB3 HY1 16 22.960 29.204 33.207 1.00 0.00 H +HETATM 266 HD1 HY1 16 25.420 28.523 32.269 1.00 0.00 H +HETATM 267 HD2 HY1 16 23.853 32.210 30.983 1.00 0.00 H +HETATM 268 HE1 HY1 16 27.347 29.785 31.131 1.00 0.00 H +ATOM 269 N THR 17 21.180 31.133 30.157 1.00 0.00 N +ATOM 270 H THR 17 21.010 31.533 31.074 1.00 0.00 H +ATOM 271 CA THR 17 20.738 32.013 29.045 1.00 0.00 C +ATOM 272 HA THR 17 21.170 31.561 28.112 1.00 0.00 H +ATOM 273 CB THR 17 19.231 32.020 28.904 1.00 0.00 C +ATOM 274 HB THR 17 18.946 32.674 28.050 1.00 0.00 H +ATOM 275 CG2 THR 17 18.569 30.688 28.614 1.00 0.00 C +ATOM 276 HG21 THR 17 18.780 29.952 29.396 1.00 0.00 H +ATOM 277 HG22 THR 17 17.520 30.750 28.519 1.00 0.00 H +ATOM 278 HG23 THR 17 18.943 30.252 27.683 1.00 0.00 H +ATOM 279 OG1 THR 17 18.633 32.525 30.065 1.00 0.00 O +ATOM 280 HG1 THR 17 18.590 33.499 29.935 1.00 0.00 H +ATOM 281 C THR 17 21.325 33.419 29.080 1.00 0.00 C +ATOM 282 O THR 17 21.830 33.841 30.105 1.00 0.00 O +HETATM 283 N HY2 18 21.199 34.131 27.962 1.00 0.00 N +HETATM 284 CA HY2 18 21.498 35.567 27.862 1.00 0.00 C +HETATM 285 C HY2 18 20.379 36.266 27.075 1.00 0.00 C +HETATM 286 O HY2 18 20.033 35.823 25.984 1.00 0.00 O +HETATM 287 CB HY2 18 22.831 35.804 27.169 1.00 0.00 C +HETATM 288 CG HY2 18 24.029 35.337 27.962 1.00 0.00 C +HETATM 289 CD2 HY2 18 24.563 34.072 27.954 1.00 0.00 C +HETATM 290 ND1 HY2 18 24.707 36.053 28.927 1.00 0.00 N +HETATM 291 CE1 HY2 18 25.640 35.241 29.456 1.00 0.00 C +HETATM 292 NE2 HY2 18 25.591 34.016 28.902 1.00 0.00 N +HETATM 293 H HY2 18 20.786 33.675 27.148 1.00 0.00 H +HETATM 294 HA HY2 18 21.526 36.010 28.879 1.00 0.00 H +HETATM 295 HB2 HY2 18 22.841 35.309 26.183 1.00 0.00 H +HETATM 296 HB3 HY2 18 22.951 36.890 26.989 1.00 0.00 H +HETATM 297 HD1 HY2 18 24.548 37.015 29.189 1.00 0.00 H +HETATM 298 HD2 HY2 18 24.231 33.250 27.332 1.00 0.00 H +HETATM 299 HE1 HY2 18 26.337 35.534 30.234 1.00 0.00 H +ATOM 300 N GLU 19 19.854 37.365 27.613 1.00 0.00 N +ATOM 301 H GLU 19 20.181 37.657 28.514 1.00 0.00 H +ATOM 302 CA GLU 19 18.861 38.214 26.953 1.00 0.00 C +ATOM 303 HA GLU 19 18.118 37.567 26.510 1.00 0.00 H +ATOM 304 CB GLU 19 18.201 39.105 28.007 1.00 0.00 C +ATOM 305 HB2 GLU 19 17.888 38.497 28.852 1.00 0.00 H +ATOM 306 HB3 GLU 19 18.937 39.829 28.382 1.00 0.00 H +ATOM 307 CG GLU 19 16.971 39.870 27.494 1.00 0.00 C +ATOM 308 HG2 GLU 19 16.593 40.510 28.305 1.00 0.00 H +ATOM 309 HG3 GLU 19 17.267 40.530 26.668 1.00 0.00 H +ATOM 310 CD GLU 19 15.891 38.899 27.051 1.00 0.00 C +ATOM 311 OE1 GLU 19 15.841 38.587 25.838 1.00 0.00 O +ATOM 312 OE2 GLU 19 15.168 38.381 27.921 1.00 0.00 O +ATOM 313 C GLU 19 19.511 39.051 25.841 1.00 0.00 C +ATOM 314 O GLU 19 20.557 39.666 26.070 1.00 0.00 O +ATOM 315 N ALA 20 18.896 39.088 24.651 1.00 0.00 N +ATOM 316 H ALA 20 18.064 38.515 24.532 1.00 0.00 H +ATOM 317 CA ALA 20 19.271 39.983 23.548 1.00 0.00 C +ATOM 318 HA ALA 20 19.436 40.983 23.947 1.00 0.00 H +ATOM 319 CB ALA 20 20.578 39.484 22.920 1.00 0.00 C +ATOM 320 HB1 ALA 20 20.424 38.505 22.460 1.00 0.00 H +ATOM 321 HB2 ALA 20 20.915 40.186 22.161 1.00 0.00 H +ATOM 322 HB3 ALA 20 21.364 39.400 23.667 1.00 0.00 H +ATOM 323 C ALA 20 18.183 40.055 22.465 1.00 0.00 C +ATOM 324 O ALA 20 17.362 39.144 22.322 1.00 0.00 O +ATOM 325 N VAL 21 18.199 41.109 21.636 1.00 0.00 N +ATOM 326 H VAL 21 18.866 41.851 21.810 1.00 0.00 H +ATOM 327 CA VAL 21 17.428 41.159 20.367 1.00 0.00 C +ATOM 328 HA VAL 21 16.429 40.760 20.548 1.00 0.00 H +ATOM 329 CB VAL 21 17.259 42.610 19.852 1.00 0.00 C +ATOM 330 HB VAL 21 16.584 42.573 18.993 1.00 0.00 H +ATOM 331 CG1 VAL 21 16.606 43.510 20.912 1.00 0.00 C +ATOM 332 HG11 VAL 21 17.283 43.665 21.747 1.00 0.00 H +ATOM 333 HG12 VAL 21 16.368 44.469 20.461 1.00 0.00 H +ATOM 334 HG13 VAL 21 15.686 43.051 21.264 1.00 0.00 H +ATOM 335 CG2 VAL 21 18.574 43.260 19.386 1.00 0.00 C +ATOM 336 HG21 VAL 21 18.969 42.728 18.522 1.00 0.00 H +ATOM 337 HG22 VAL 21 18.382 44.286 19.080 1.00 0.00 H +ATOM 338 HG23 VAL 21 19.313 43.256 20.184 1.00 0.00 H +ATOM 339 C VAL 21 18.056 40.311 19.265 1.00 0.00 C +ATOM 340 O VAL 21 17.372 39.908 18.335 1.00 0.00 O +ATOM 341 N ASP 22 19.356 40.045 19.380 1.00 0.00 N +ATOM 342 H ASP 22 19.840 40.370 20.200 1.00 0.00 H +ATOM 343 CA ASP 22 20.203 39.414 18.367 1.00 0.00 C +ATOM 344 HA ASP 22 19.591 38.740 17.749 1.00 0.00 H +ATOM 345 CB ASP 22 20.808 40.497 17.447 1.00 0.00 C +ATOM 346 HB2 ASP 22 20.011 40.913 16.813 1.00 0.00 H +ATOM 347 HB3 ASP 22 21.216 41.310 18.079 1.00 0.00 H +ATOM 348 CG ASP 22 21.904 39.924 16.576 1.00 0.00 C +ATOM 349 OD1 ASP 22 23.061 40.332 16.776 1.00 0.00 O +ATOM 350 OD2 ASP 22 21.645 38.936 15.850 1.00 0.00 O +ATOM 351 C ASP 22 21.312 38.577 19.024 1.00 0.00 C +ATOM 352 O ASP 22 21.786 38.862 20.125 1.00 0.00 O +ATOM 353 N TRP 23 21.758 37.546 18.320 1.00 0.00 N +ATOM 354 H TRP 23 21.457 37.488 17.356 1.00 0.00 H +ATOM 355 CA TRP 23 22.777 36.618 18.774 1.00 0.00 C +ATOM 356 HA TRP 23 22.545 36.338 19.799 1.00 0.00 H +ATOM 357 CB TRP 23 22.654 35.377 17.900 1.00 0.00 C +ATOM 358 HB2 TRP 23 21.626 35.019 17.952 1.00 0.00 H +ATOM 359 HB3 TRP 23 22.841 35.665 16.862 1.00 0.00 H +ATOM 360 CG TRP 23 23.539 34.241 18.269 1.00 0.00 C +ATOM 361 CD1 TRP 23 24.465 33.691 17.461 1.00 0.00 C +ATOM 362 HD1 TRP 23 24.709 34.023 16.459 1.00 0.00 H +ATOM 363 NE1 TRP 23 25.028 32.616 18.105 1.00 0.00 N +ATOM 364 HE1 TRP 23 25.775 32.071 17.710 1.00 0.00 H +ATOM 365 CE2 TRP 23 24.471 32.396 19.344 1.00 0.00 C +ATOM 366 CZ2 TRP 23 24.645 31.401 20.312 1.00 0.00 C +ATOM 367 HZ2 TRP 23 25.308 30.566 20.135 1.00 0.00 H +ATOM 368 CH2 TRP 23 23.967 31.535 21.529 1.00 0.00 C +ATOM 369 HH2 TRP 23 24.088 30.820 22.312 1.00 0.00 H +ATOM 370 CZ3 TRP 23 23.194 32.666 21.795 1.00 0.00 C +ATOM 371 HZ3 TRP 23 22.789 32.798 22.788 1.00 0.00 H +ATOM 372 CE3 TRP 23 22.960 33.611 20.781 1.00 0.00 C +ATOM 373 HE3 TRP 23 22.305 34.442 20.972 1.00 0.00 H +ATOM 374 CD2 TRP 23 23.577 33.487 19.517 1.00 0.00 C +ATOM 375 C TRP 23 24.201 37.200 18.775 1.00 0.00 C +ATOM 376 O TRP 23 24.979 36.883 19.677 1.00 0.00 O +ATOM 377 N ALA 24 24.536 38.109 17.850 1.00 0.00 N +ATOM 378 H ALA 24 23.837 38.430 17.182 1.00 0.00 H +ATOM 379 CA ALA 24 25.826 38.805 17.840 1.00 0.00 C +ATOM 380 HA ALA 24 26.592 38.098 18.148 1.00 0.00 H +ATOM 381 CB ALA 24 26.163 39.206 16.400 1.00 0.00 C +ATOM 382 HB1 ALA 24 25.465 39.956 16.034 1.00 0.00 H +ATOM 383 HB2 ALA 24 27.173 39.612 16.353 1.00 0.00 H +ATOM 384 HB3 ALA 24 26.113 38.333 15.751 1.00 0.00 H +ATOM 385 C ALA 24 25.896 39.988 18.834 1.00 0.00 C +ATOM 386 O ALA 24 26.984 40.488 19.139 1.00 0.00 O +ATOM 387 N GLU 25 24.765 40.408 19.414 1.00 0.00 N +ATOM 388 H GLU 25 23.891 40.105 18.996 1.00 0.00 H +ATOM 389 CA GLU 25 24.725 41.188 20.666 1.00 0.00 C +ATOM 390 HA GLU 25 25.581 41.863 20.687 1.00 0.00 H +ATOM 391 CB GLU 25 23.451 42.045 20.730 1.00 0.00 C +ATOM 392 HB2 GLU 25 22.582 41.422 20.516 1.00 0.00 H +ATOM 393 HB3 GLU 25 23.342 42.425 21.740 1.00 0.00 H +ATOM 394 CG GLU 25 23.468 43.249 19.777 1.00 0.00 C +ATOM 395 HG2 GLU 25 23.540 42.881 18.748 1.00 0.00 H +ATOM 396 HG3 GLU 25 22.512 43.776 19.855 1.00 0.00 H +ATOM 397 CD GLU 25 24.619 44.199 20.081 1.00 0.00 C +ATOM 398 OE1 GLU 25 24.524 44.975 21.065 1.00 0.00 O +ATOM 399 OE2 GLU 25 25.648 44.107 19.362 1.00 0.00 O +ATOM 400 C GLU 25 24.874 40.287 21.906 1.00 0.00 C +ATOM 401 O GLU 25 25.688 40.579 22.784 1.00 0.00 O +ATOM 402 N ALA 26 24.201 39.125 21.956 1.00 0.00 N +ATOM 403 H ALA 26 23.518 38.919 21.232 1.00 0.00 H +ATOM 404 CA ALA 26 24.463 38.107 22.990 1.00 0.00 C +ATOM 405 HA ALA 26 24.293 38.571 23.963 1.00 0.00 H +ATOM 406 CB ALA 26 23.482 36.944 22.834 1.00 0.00 C +ATOM 407 HB1 ALA 26 23.667 36.421 21.901 1.00 0.00 H +ATOM 408 HB2 ALA 26 23.605 36.247 23.660 1.00 0.00 H +ATOM 409 HB3 ALA 26 22.458 37.314 22.841 1.00 0.00 H +ATOM 410 C ALA 26 25.930 37.609 22.973 1.00 0.00 C +ATOM 411 O ALA 26 26.453 37.180 24.015 1.00 0.00 O +ATOM 412 N GLU 27 26.614 37.710 21.825 1.00 0.00 N +ATOM 413 H GLU 27 26.089 37.904 20.980 1.00 0.00 H +ATOM 414 CA GLU 27 28.052 37.490 21.713 1.00 0.00 C +ATOM 415 HA GLU 27 28.210 36.457 21.940 1.00 0.00 H +ATOM 416 CB GLU 27 28.583 37.614 20.270 1.00 0.00 C +ATOM 417 HB2 GLU 27 27.924 37.058 19.610 1.00 0.00 H +ATOM 418 HB3 GLU 27 28.620 38.658 19.970 1.00 0.00 H +ATOM 419 CG GLU 27 29.988 36.996 20.197 1.00 0.00 C +ATOM 420 HG2 GLU 27 30.676 37.588 20.819 1.00 0.00 H +ATOM 421 HG3 GLU 27 29.956 35.983 20.634 1.00 0.00 H +ATOM 422 CD GLU 27 30.513 36.934 18.769 1.00 0.00 C +ATOM 423 OE1 GLU 27 30.943 38.000 18.278 1.00 0.00 O +ATOM 424 OE2 GLU 27 30.501 35.827 18.191 1.00 0.00 O +ATOM 425 C GLU 27 28.828 38.374 22.706 1.00 0.00 C +ATOM 426 O GLU 27 29.568 37.849 23.548 1.00 0.00 O +ATOM 427 N LYS 28 28.541 39.682 22.661 1.00 0.00 N +ATOM 428 H LYS 28 27.831 39.957 21.987 1.00 0.00 H +ATOM 429 CA LYS 28 29.121 40.758 23.481 1.00 0.00 C +ATOM 430 HA LYS 28 30.206 40.658 23.479 1.00 0.00 H +ATOM 431 CB LYS 28 28.761 42.131 22.873 1.00 0.00 C +ATOM 432 HB2 LYS 28 27.685 42.299 22.951 1.00 0.00 H +ATOM 433 HB3 LYS 28 29.264 42.909 23.451 1.00 0.00 H +ATOM 434 CG LYS 28 29.172 42.274 21.396 1.00 0.00 C +ATOM 435 HG2 LYS 28 30.244 42.100 21.301 1.00 0.00 H +ATOM 436 HG3 LYS 28 28.646 41.528 20.802 1.00 0.00 H +ATOM 437 CD LYS 28 28.833 43.668 20.845 1.00 0.00 C +ATOM 438 HD2 LYS 28 27.793 43.910 21.048 1.00 0.00 H +ATOM 439 HD3 LYS 28 29.453 44.406 21.356 1.00 0.00 H +ATOM 440 CE LYS 28 29.082 43.754 19.331 1.00 0.00 C +ATOM 441 HE2 LYS 28 29.159 44.812 19.054 1.00 0.00 H +ATOM 442 HE3 LYS 28 30.045 43.295 19.106 1.00 0.00 H +ATOM 443 NZ LYS 28 27.999 43.108 18.548 1.00 0.00 N +ATOM 444 HZ1 LYS 28 27.111 43.575 18.756 1.00 0.00 H +ATOM 445 HZ2 LYS 28 28.147 43.172 17.552 1.00 0.00 H +ATOM 446 HZ3 LYS 28 27.858 42.139 18.817 1.00 0.00 H +ATOM 447 C LYS 28 28.671 40.699 24.942 1.00 0.00 C +ATOM 448 O LYS 28 29.516 40.726 25.833 1.00 0.00 O +ATOM 449 N PHE 29 27.376 40.527 25.225 1.00 0.00 N +ATOM 450 H PHE 29 26.709 40.552 24.455 1.00 0.00 H +ATOM 451 CA PHE 29 26.873 40.474 26.615 1.00 0.00 C +ATOM 452 HA PHE 29 27.188 41.382 27.129 1.00 0.00 H +ATOM 453 CB PHE 29 25.335 40.437 26.615 1.00 0.00 C +ATOM 454 HB2 PHE 29 25.018 39.493 26.171 1.00 0.00 H +ATOM 455 HB3 PHE 29 24.990 40.451 27.649 1.00 0.00 H +ATOM 456 CG PHE 29 24.643 41.578 25.884 1.00 0.00 C +ATOM 457 CD1 PHE 29 23.461 41.323 25.164 1.00 0.00 C +ATOM 458 HD1 PHE 29 23.037 40.333 25.146 1.00 0.00 H +ATOM 459 CE1 PHE 29 22.822 42.359 24.462 1.00 0.00 C +ATOM 460 HE1 PHE 29 21.922 42.155 23.902 1.00 0.00 H +ATOM 461 CZ PHE 29 23.361 43.658 24.478 1.00 0.00 C +ATOM 462 HZ PHE 29 22.885 44.450 23.917 1.00 0.00 H +ATOM 463 CE2 PHE 29 24.520 43.928 25.225 1.00 0.00 C +ATOM 464 HE2 PHE 29 24.924 44.927 25.252 1.00 0.00 H +ATOM 465 CD2 PHE 29 25.155 42.893 25.932 1.00 0.00 C +ATOM 466 HD2 PHE 29 26.038 43.124 26.504 1.00 0.00 H +ATOM 467 C PHE 29 27.437 39.300 27.430 1.00 0.00 C +ATOM 468 O PHE 29 27.531 39.370 28.654 1.00 0.00 O +ATOM 469 N THR 30 27.865 38.222 26.770 1.00 0.00 N +ATOM 470 H THR 30 27.724 38.182 25.766 1.00 0.00 H +ATOM 471 CA THR 30 28.618 37.144 27.427 1.00 0.00 C +ATOM 472 HA THR 30 28.163 36.900 28.387 1.00 0.00 H +ATOM 473 CB THR 30 28.621 35.900 26.536 1.00 0.00 C +ATOM 474 HB THR 30 29.132 36.191 25.639 1.00 0.00 H +ATOM 475 CG2 THR 30 29.346 34.706 27.138 1.00 0.00 C +ATOM 476 HG21 THR 30 28.984 34.522 28.133 1.00 0.00 H +ATOM 477 HG22 THR 30 29.193 33.814 26.546 1.00 0.00 H +ATOM 478 HG23 THR 30 30.428 34.887 27.191 1.00 0.00 H +ATOM 479 OG1 THR 30 27.298 35.471 26.245 1.00 0.00 O +ATOM 480 HG1 THR 30 26.888 36.131 25.657 1.00 0.00 H +ATOM 481 C THR 30 30.081 37.537 27.695 1.00 0.00 C +ATOM 482 O THR 30 30.624 37.146 28.731 1.00 0.00 O +ATOM 483 N LYS 31 30.720 38.306 26.804 1.00 0.00 N +ATOM 484 H LYS 31 30.198 38.651 26.014 1.00 0.00 H +ATOM 485 CA LYS 31 32.070 38.835 27.005 1.00 0.00 C +ATOM 486 HA LYS 31 32.733 38.032 27.315 1.00 0.00 H +ATOM 487 CB LYS 31 32.647 39.415 25.683 1.00 0.00 C +ATOM 488 HB2 LYS 31 31.948 40.110 25.246 1.00 0.00 H +ATOM 489 HB3 LYS 31 33.566 39.953 25.914 1.00 0.00 H +ATOM 490 CG LYS 31 32.996 38.312 24.666 1.00 0.00 C +ATOM 491 HG2 LYS 31 33.730 37.640 25.106 1.00 0.00 H +ATOM 492 HG3 LYS 31 32.107 37.731 24.423 1.00 0.00 H +ATOM 493 CD LYS 31 33.567 38.923 23.384 1.00 0.00 C +ATOM 494 HD2 LYS 31 32.778 39.479 22.879 1.00 0.00 H +ATOM 495 HD3 LYS 31 34.355 39.629 23.638 1.00 0.00 H +ATOM 496 CE LYS 31 34.151 37.892 22.391 1.00 0.00 C +ATOM 497 HE2 LYS 31 33.409 37.129 22.159 1.00 0.00 H +ATOM 498 HE3 LYS 31 34.379 38.403 21.457 1.00 0.00 H +ATOM 499 NZ LYS 31 35.390 37.255 22.898 1.00 0.00 N +ATOM 500 HZ1 LYS 31 35.201 36.470 23.500 1.00 0.00 H +ATOM 501 HZ2 LYS 31 35.932 36.859 22.126 1.00 0.00 H +ATOM 502 HZ3 LYS 31 35.985 37.896 23.428 1.00 0.00 H +ATOM 503 C LYS 31 32.129 39.879 28.130 1.00 0.00 C +ATOM 504 O LYS 31 33.139 39.914 28.834 1.00 0.00 O +ATOM 505 N ALA 32 31.036 40.609 28.382 1.00 0.00 N +ATOM 506 H ALA 32 30.297 40.611 27.689 1.00 0.00 H +ATOM 507 CA ALA 32 30.856 41.387 29.608 1.00 0.00 C +ATOM 508 HA ALA 32 31.679 42.095 29.692 1.00 0.00 H +ATOM 509 CB ALA 32 29.558 42.200 29.527 1.00 0.00 C +ATOM 510 HB1 ALA 32 28.691 41.544 29.473 1.00 0.00 H +ATOM 511 HB2 ALA 32 29.463 42.823 30.421 1.00 0.00 H +ATOM 512 HB3 ALA 32 29.578 42.846 28.650 1.00 0.00 H +ATOM 513 C ALA 32 30.927 40.489 30.858 1.00 0.00 C +ATOM 514 O ALA 32 31.924 40.546 31.574 1.00 0.00 O +ATOM 515 N LYN 33 29.996 39.531 31.025 1.00 0.00 N +ATOM 516 H LYN 33 29.190 39.542 30.415 1.00 0.00 H +ATOM 517 CA LYN 33 30.009 38.573 32.151 1.00 0.00 C +ATOM 518 HA LYN 33 29.910 39.148 33.071 1.00 0.00 H +ATOM 519 CB LYN 33 28.774 37.649 32.038 1.00 0.00 C +ATOM 520 HB2 LYN 33 27.879 38.255 31.901 1.00 0.00 H +ATOM 521 HB3 LYN 33 28.890 37.020 31.159 1.00 0.00 H +ATOM 522 CG LYN 33 28.554 36.757 33.275 1.00 0.00 C +ATOM 523 HG2 LYN 33 29.439 36.152 33.441 1.00 0.00 H +ATOM 524 HG3 LYN 33 28.421 37.387 34.152 1.00 0.00 H +ATOM 525 CD LYN 33 27.373 35.776 33.182 1.00 0.00 C +ATOM 526 HD2 LYN 33 27.409 35.248 32.236 1.00 0.00 H +ATOM 527 HD3 LYN 33 27.480 35.041 33.977 1.00 0.00 H +ATOM 528 CE LYN 33 26.005 36.448 33.325 1.00 0.00 C +ATOM 529 HE2 LYN 33 26.005 37.059 34.229 1.00 0.00 H +ATOM 530 HE3 LYN 33 25.827 37.088 32.462 1.00 0.00 H +ATOM 531 NZ LYN 33 24.926 35.449 33.420 1.00 0.00 N +ATOM 532 HZ2 LYN 33 24.037 35.924 33.515 1.00 0.00 H +ATOM 533 HZ3 LYN 33 24.894 34.884 32.590 1.00 0.00 H +ATOM 534 C LYN 33 31.326 37.768 32.264 1.00 0.00 C +ATOM 535 O LYN 33 31.650 37.212 33.313 1.00 0.00 O +ATOM 536 N ALA 34 32.102 37.650 31.186 1.00 0.00 N +ATOM 537 H ALA 34 31.786 38.093 30.336 1.00 0.00 H +ATOM 538 CA ALA 34 33.415 37.025 31.197 1.00 0.00 C +ATOM 539 HA ALA 34 33.379 36.199 31.902 1.00 0.00 H +ATOM 540 CB ALA 34 33.660 36.419 29.822 1.00 0.00 C +ATOM 541 HB1 ALA 34 33.759 37.224 29.100 1.00 0.00 H +ATOM 542 HB2 ALA 34 34.569 35.830 29.857 1.00 0.00 H +ATOM 543 HB3 ALA 34 32.833 35.773 29.533 1.00 0.00 H +ATOM 544 C ALA 34 34.561 37.964 31.644 1.00 0.00 C +ATOM 545 O ALA 34 35.485 37.474 32.295 1.00 0.00 O +ATOM 546 N ASN 35 34.515 39.269 31.348 1.00 0.00 N +ATOM 547 H ASN 35 33.732 39.616 30.804 1.00 0.00 H +ATOM 548 CA ASN 35 35.446 40.284 31.873 1.00 0.00 C +ATOM 549 HA ASN 35 36.435 39.832 31.976 1.00 0.00 H +ATOM 550 CB ASN 35 35.582 41.433 30.859 1.00 0.00 C +ATOM 551 HB2 ASN 35 34.603 41.733 30.493 1.00 0.00 H +ATOM 552 HB3 ASN 35 36.033 42.295 31.352 1.00 0.00 H +ATOM 553 CG ASN 35 36.493 41.030 29.719 1.00 0.00 C +ATOM 554 OD1 ASN 35 37.698 40.971 29.868 1.00 0.00 O +ATOM 555 ND2 ASN 35 35.956 40.693 28.578 1.00 0.00 N +ATOM 556 HD21 ASN 35 36.601 40.354 27.860 1.00 0.00 H +ATOM 557 HD22 ASN 35 34.954 40.631 28.488 1.00 0.00 H +ATOM 558 C ASN 35 35.078 40.777 33.276 1.00 0.00 C +ATOM 559 O ASN 35 35.967 41.126 34.052 1.00 0.00 O +ATOM 560 N ASP 36 33.802 40.685 33.673 1.00 0.00 N +ATOM 561 H ASP 36 33.078 40.563 32.970 1.00 0.00 H +ATOM 562 CA ASP 36 33.357 40.843 35.067 1.00 0.00 C +ATOM 563 HA ASP 36 33.630 41.847 35.410 1.00 0.00 H +ATOM 564 CB ASP 36 31.839 40.739 35.150 1.00 0.00 C +ATOM 565 HB2 ASP 36 31.563 39.728 34.867 1.00 0.00 H +ATOM 566 HB3 ASP 36 31.542 40.818 36.195 1.00 0.00 H +ATOM 567 CG ASP 36 30.985 41.711 34.324 1.00 0.00 C +ATOM 568 OD1 ASP 36 31.462 42.836 34.035 1.00 0.00 O +ATOM 569 OD2 ASP 36 29.825 41.345 33.996 1.00 0.00 O +ATOM 570 C ASP 36 34.066 39.828 35.995 1.00 0.00 C +ATOM 571 O ASP 36 34.498 40.176 37.098 1.00 0.00 O +ATOM 572 N LYS 37 34.277 38.580 35.528 1.00 0.00 N +ATOM 573 H LYS 37 33.863 38.350 34.636 1.00 0.00 H +ATOM 574 CA LYS 37 35.150 37.580 36.183 1.00 0.00 C +ATOM 575 HA LYS 37 35.130 37.789 37.253 1.00 0.00 H +ATOM 576 CB LYS 37 34.565 36.152 36.027 1.00 0.00 C +ATOM 577 HB2 LYS 37 35.078 35.490 36.724 1.00 0.00 H +ATOM 578 HB3 LYS 37 33.508 36.149 36.288 1.00 0.00 H +ATOM 579 CG LYS 37 34.759 35.601 34.608 1.00 0.00 C +ATOM 580 HG2 LYS 37 34.139 36.177 33.928 1.00 0.00 H +ATOM 581 HG3 LYS 37 35.798 35.735 34.318 1.00 0.00 H +ATOM 582 CD LYS 37 34.436 34.122 34.422 1.00 0.00 C +ATOM 583 HD2 LYS 37 34.578 33.610 35.373 1.00 0.00 H +ATOM 584 HD3 LYS 37 33.395 34.014 34.154 1.00 0.00 H +ATOM 585 CE LYS 37 35.328 33.472 33.330 1.00 0.00 C +ATOM 586 HE2 LYS 37 36.315 33.292 33.762 1.00 0.00 H +ATOM 587 HE3 LYS 37 34.983 32.454 33.128 1.00 0.00 H +ATOM 588 NZ LYS 37 35.470 34.267 32.074 1.00 0.00 N +ATOM 589 HZ1 LYS 37 35.901 35.166 32.277 1.00 0.00 H +ATOM 590 HZ2 LYS 37 36.069 33.816 31.389 1.00 0.00 H +ATOM 591 HZ3 LYS 37 34.567 34.433 31.674 1.00 0.00 H +ATOM 592 C LYS 37 36.641 37.666 35.797 1.00 0.00 C +ATOM 593 O LYS 37 37.388 36.717 36.024 1.00 0.00 O +ATOM 594 N GLY 38 37.093 38.753 35.163 1.00 0.00 N +ATOM 595 H GLY 38 36.427 39.500 35.014 1.00 0.00 H +ATOM 596 CA GLY 38 38.497 39.081 34.900 1.00 0.00 C +ATOM 597 HA2 GLY 38 38.673 40.099 35.250 1.00 0.00 H +ATOM 598 HA3 GLY 38 39.136 38.422 35.493 1.00 0.00 H +ATOM 599 C GLY 38 38.992 39.003 33.451 1.00 0.00 C +ATOM 600 O GLY 38 39.908 39.749 33.113 1.00 0.00 O +ATOM 601 N ARG 39 38.439 38.123 32.592 1.00 0.00 N +ATOM 602 H ARG 39 37.620 37.630 32.924 1.00 0.00 H +ATOM 603 CA ARG 39 38.850 37.918 31.183 1.00 0.00 C +ATOM 604 HA ARG 39 38.819 38.900 30.702 1.00 0.00 H +ATOM 605 CB ARG 39 40.315 37.408 31.055 1.00 0.00 C +ATOM 606 HB2 ARG 39 40.570 37.429 29.993 1.00 0.00 H +ATOM 607 HB3 ARG 39 40.992 38.115 31.533 1.00 0.00 H +ATOM 608 CG ARG 39 40.642 35.990 31.575 1.00 0.00 C +ATOM 609 HG2 ARG 39 40.011 35.274 31.049 1.00 0.00 H +ATOM 610 HG3 ARG 39 41.676 35.759 31.313 1.00 0.00 H +ATOM 611 CD ARG 39 40.486 35.825 33.102 1.00 0.00 C +ATOM 612 HD2 ARG 39 41.184 36.504 33.600 1.00 0.00 H +ATOM 613 HD3 ARG 39 39.476 36.100 33.403 1.00 0.00 H +ATOM 614 NE ARG 39 40.739 34.451 33.582 1.00 0.00 N +ATOM 615 HE ARG 39 41.505 34.326 34.228 1.00 0.00 H +ATOM 616 CZ ARG 39 39.961 33.401 33.419 1.00 0.00 C +ATOM 617 NH1 ARG 39 38.912 33.425 32.650 1.00 0.00 N +ATOM 618 HH11 ARG 39 38.753 34.219 32.059 1.00 0.00 H +ATOM 619 HH12 ARG 39 38.395 32.553 32.564 1.00 0.00 H +ATOM 620 NH2 ARG 39 40.208 32.279 34.029 1.00 0.00 N +ATOM 621 HH21 ARG 39 41.021 32.194 34.618 1.00 0.00 H +ATOM 622 HH22 ARG 39 39.586 31.492 33.869 1.00 0.00 H +ATOM 623 C ARG 39 37.906 37.010 30.382 1.00 0.00 C +ATOM 624 O ARG 39 37.450 35.970 30.889 1.00 0.00 O +ATOM 625 N ASP 40 37.643 37.373 29.123 1.00 0.00 N +ATOM 626 H ASP 40 38.049 38.236 28.768 1.00 0.00 H +ATOM 627 CA ASP 40 36.914 36.559 28.147 1.00 0.00 C +ATOM 628 HA ASP 40 36.250 35.909 28.701 1.00 0.00 H +ATOM 629 CB ASP 40 36.024 37.438 27.250 1.00 0.00 C +ATOM 630 HB2 ASP 40 35.359 36.797 26.672 1.00 0.00 H +ATOM 631 HB3 ASP 40 35.373 38.034 27.885 1.00 0.00 H +ATOM 632 CG ASP 40 36.757 38.385 26.309 1.00 0.00 C +ATOM 633 OD1 ASP 40 37.565 39.185 26.826 1.00 0.00 O +ATOM 634 OD2 ASP 40 36.426 38.367 25.105 1.00 0.00 O +ATOM 635 C ASP 40 37.774 35.579 27.330 1.00 0.00 C +ATOM 636 O ASP 40 38.983 35.480 27.496 1.00 0.00 O +ATOM 637 N GLY 41 37.089 34.803 26.488 1.00 0.00 N +ATOM 638 H GLY 41 36.101 34.991 26.421 1.00 0.00 H +ATOM 639 CA GLY 41 37.618 33.880 25.478 1.00 0.00 C +ATOM 640 HA2 GLY 41 38.494 34.335 24.987 1.00 0.00 H +ATOM 641 HA3 GLY 41 37.896 32.927 25.956 1.00 0.00 H +ATOM 642 C GLY 41 36.528 33.613 24.424 1.00 0.00 C +ATOM 643 O GLY 41 35.445 34.207 24.475 1.00 0.00 O +ATOM 644 N GLU 42 36.788 32.709 23.482 1.00 0.00 N +ATOM 645 H GLU 42 37.670 32.237 23.523 1.00 0.00 H +ATOM 646 CA GLU 42 35.905 32.412 22.347 1.00 0.00 C +ATOM 647 HA GLU 42 35.125 33.167 22.344 1.00 0.00 H +ATOM 648 CB GLU 42 36.664 32.525 21.011 1.00 0.00 C +ATOM 649 HB2 GLU 42 37.366 31.695 20.944 1.00 0.00 H +ATOM 650 HB3 GLU 42 35.944 32.414 20.201 1.00 0.00 H +ATOM 651 CG GLU 42 37.443 33.834 20.782 1.00 0.00 C +ATOM 652 HG2 GLU 42 38.311 33.827 21.446 1.00 0.00 H +ATOM 653 HG3 GLU 42 37.826 33.837 19.759 1.00 0.00 H +ATOM 654 CD GLU 42 36.645 35.123 21.033 1.00 0.00 C +ATOM 655 OE1 GLU 42 35.399 35.099 21.148 1.00 0.00 O +ATOM 656 OE2 GLU 42 37.273 36.191 21.218 1.00 0.00 O +ATOM 657 C GLU 42 35.155 31.079 22.449 1.00 0.00 C +ATOM 658 O GLU 42 35.545 30.177 23.201 1.00 0.00 O +ATOM 659 N ARG 43 34.045 30.983 21.696 1.00 0.00 N +ATOM 660 H ARG 43 33.859 31.729 21.028 1.00 0.00 H +ATOM 661 CA ARG 43 33.015 29.940 21.796 1.00 0.00 C +ATOM 662 HA ARG 43 33.495 28.981 22.001 1.00 0.00 H +ATOM 663 CB ARG 43 32.087 30.275 22.974 1.00 0.00 C +ATOM 664 HB2 ARG 43 31.317 29.508 23.057 1.00 0.00 H +ATOM 665 HB3 ARG 43 32.669 30.262 23.897 1.00 0.00 H +ATOM 666 CG ARG 43 31.391 31.637 22.844 1.00 0.00 C +ATOM 667 HG2 ARG 43 32.110 32.434 22.660 1.00 0.00 H +ATOM 668 HG3 ARG 43 30.694 31.612 22.010 1.00 0.00 H +ATOM 669 CD ARG 43 30.634 31.967 24.121 1.00 0.00 C +ATOM 670 HD2 ARG 43 30.147 31.059 24.480 1.00 0.00 H +ATOM 671 HD3 ARG 43 31.339 32.284 24.887 1.00 0.00 H +ATOM 672 NE ARG 43 29.619 32.996 23.893 1.00 0.00 N +ATOM 673 HE ARG 43 28.685 32.661 23.712 1.00 0.00 H +ATOM 674 CZ ARG 43 29.781 34.291 23.756 1.00 0.00 C +ATOM 675 NH1 ARG 43 30.924 34.915 23.764 1.00 0.00 N +ATOM 676 HH11 ARG 43 31.776 34.380 23.737 1.00 0.00 H +ATOM 677 HH12 ARG 43 30.928 35.903 23.564 1.00 0.00 H +ATOM 678 NH2 ARG 43 28.724 35.010 23.622 1.00 0.00 N +ATOM 679 HH21 ARG 43 27.818 34.575 23.525 1.00 0.00 H +ATOM 680 HH22 ARG 43 28.806 36.015 23.611 1.00 0.00 H +ATOM 681 C ARG 43 32.226 29.788 20.491 1.00 0.00 C +ATOM 682 O ARG 43 32.016 30.775 19.792 1.00 0.00 O +ATOM 683 N THR 44 31.769 28.574 20.199 1.00 0.00 N +ATOM 684 H THR 44 31.893 27.856 20.903 1.00 0.00 H +ATOM 685 CA THR 44 31.059 28.197 18.965 1.00 0.00 C +ATOM 686 HA THR 44 31.367 28.878 18.171 1.00 0.00 H +ATOM 687 CB THR 44 31.491 26.779 18.541 1.00 0.00 C +ATOM 688 HB THR 44 31.284 26.073 19.347 1.00 0.00 H +ATOM 689 CG2 THR 44 30.877 26.255 17.242 1.00 0.00 C +ATOM 690 HG21 THR 44 30.980 26.998 16.449 1.00 0.00 H +ATOM 691 HG22 THR 44 31.383 25.337 16.935 1.00 0.00 H +ATOM 692 HG23 THR 44 29.824 26.016 17.397 1.00 0.00 H +ATOM 693 OG1 THR 44 32.880 26.818 18.313 1.00 0.00 O +ATOM 694 HG1 THR 44 33.143 26.013 17.857 1.00 0.00 H +ATOM 695 C THR 44 29.537 28.364 19.112 1.00 0.00 C +ATOM 696 O THR 44 29.024 28.513 20.225 1.00 0.00 O +ATOM 697 N ILE 45 28.813 28.404 17.984 1.00 0.00 N +ATOM 698 H ILE 45 29.281 28.200 17.114 1.00 0.00 H +ATOM 699 CA ILE 45 27.405 28.808 17.888 1.00 0.00 C +ATOM 700 HA ILE 45 26.992 28.796 18.898 1.00 0.00 H +ATOM 701 CB ILE 45 27.300 30.258 17.349 1.00 0.00 C +ATOM 702 HB ILE 45 26.234 30.493 17.386 1.00 0.00 H +ATOM 703 CG2 ILE 45 28.017 31.233 18.293 1.00 0.00 C +ATOM 704 HG21 ILE 45 29.094 31.074 18.238 1.00 0.00 H +ATOM 705 HG22 ILE 45 27.806 32.268 18.025 1.00 0.00 H +ATOM 706 HG23 ILE 45 27.671 31.042 19.300 1.00 0.00 H +ATOM 707 CG1 ILE 45 27.759 30.525 15.895 1.00 0.00 C +ATOM 708 HG12 ILE 45 28.047 31.568 15.812 1.00 0.00 H +ATOM 709 HG13 ILE 45 28.654 29.949 15.680 1.00 0.00 H +ATOM 710 CD1 ILE 45 26.691 30.279 14.822 1.00 0.00 C +ATOM 711 HD11 ILE 45 25.759 30.773 15.114 1.00 0.00 H +ATOM 712 HD12 ILE 45 27.018 30.695 13.866 1.00 0.00 H +ATOM 713 HD13 ILE 45 26.512 29.212 14.695 1.00 0.00 H +ATOM 714 C ILE 45 26.527 27.858 17.072 1.00 0.00 C +ATOM 715 O ILE 45 27.017 27.114 16.226 1.00 0.00 O +ATOM 716 N ASP 46 25.216 27.950 17.304 1.00 0.00 N +ATOM 717 H ASP 46 24.910 28.475 18.111 1.00 0.00 H +ATOM 718 CA ASP 46 24.153 27.357 16.483 1.00 0.00 C +ATOM 719 HA ASP 46 24.474 27.365 15.437 1.00 0.00 H +ATOM 720 CB ASP 46 23.935 25.904 16.910 1.00 0.00 C +ATOM 721 HB2 ASP 46 24.821 25.306 16.686 1.00 0.00 H +ATOM 722 HB3 ASP 46 23.790 25.882 17.995 1.00 0.00 H +ATOM 723 CG ASP 46 22.728 25.281 16.224 1.00 0.00 C +ATOM 724 OD1 ASP 46 21.961 24.603 16.947 1.00 0.00 O +ATOM 725 OD2 ASP 46 22.511 25.554 15.040 1.00 0.00 O +ATOM 726 C ASP 46 22.834 28.159 16.594 1.00 0.00 C +ATOM 727 O ASP 46 22.399 28.488 17.698 1.00 0.00 O +ATOM 728 N ASP 47 22.184 28.437 15.458 1.00 0.00 N +ATOM 729 H ASP 47 22.559 28.038 14.608 1.00 0.00 H +ATOM 730 CA ASP 47 20.840 29.039 15.391 1.00 0.00 C +ATOM 731 HA ASP 47 20.745 29.781 16.186 1.00 0.00 H +ATOM 732 CB ASP 47 20.651 29.780 14.049 1.00 0.00 C +ATOM 733 HB2 ASP 47 21.371 30.599 13.994 1.00 0.00 H +ATOM 734 HB3 ASP 47 20.869 29.092 13.229 1.00 0.00 H +ATOM 735 CG ASP 47 19.236 30.338 13.866 1.00 0.00 C +ATOM 736 OD1 ASP 47 18.366 29.642 13.294 1.00 0.00 O +ATOM 737 OD2 ASP 47 18.910 31.439 14.376 1.00 0.00 O +ATOM 738 C ASP 47 19.712 28.006 15.601 1.00 0.00 C +ATOM 739 O ASP 47 18.680 28.354 16.177 1.00 0.00 O +ATOM 740 N ALA 48 19.891 26.748 15.189 1.00 0.00 N +ATOM 741 H ALA 48 20.815 26.444 14.883 1.00 0.00 H +ATOM 742 CA ALA 48 18.830 25.738 15.223 1.00 0.00 C +ATOM 743 HA ALA 48 17.947 26.136 14.721 1.00 0.00 H +ATOM 744 CB ALA 48 19.314 24.506 14.451 1.00 0.00 C +ATOM 745 HB1 ALA 48 20.173 24.065 14.961 1.00 0.00 H +ATOM 746 HB2 ALA 48 18.518 23.764 14.391 1.00 0.00 H +ATOM 747 HB3 ALA 48 19.617 24.791 13.444 1.00 0.00 H +ATOM 748 C ALA 48 18.413 25.386 16.665 1.00 0.00 C +ATOM 749 O ALA 48 17.226 25.293 16.965 1.00 0.00 O +ATOM 750 N THR 49 19.383 25.251 17.569 1.00 0.00 N +ATOM 751 H THR 49 20.338 25.173 17.219 1.00 0.00 H +ATOM 752 CA THR 49 19.192 25.102 19.021 1.00 0.00 C +ATOM 753 HA THR 49 18.164 24.774 19.188 1.00 0.00 H +ATOM 754 CB THR 49 20.126 24.025 19.584 1.00 0.00 C +ATOM 755 HB THR 49 19.898 23.910 20.645 1.00 0.00 H +ATOM 756 CG2 THR 49 19.960 22.658 18.926 1.00 0.00 C +ATOM 757 HG21 THR 49 20.258 22.695 17.880 1.00 0.00 H +ATOM 758 HG22 THR 49 20.593 21.942 19.444 1.00 0.00 H +ATOM 759 HG23 THR 49 18.922 22.334 18.992 1.00 0.00 H +ATOM 760 OG1 THR 49 21.483 24.396 19.468 1.00 0.00 O +ATOM 761 HG1 THR 49 21.694 24.365 18.500 1.00 0.00 H +ATOM 762 C THR 49 19.397 26.401 19.808 1.00 0.00 C +ATOM 763 O THR 49 19.269 26.396 21.031 1.00 0.00 O +ATOM 764 N LYS 50 19.705 27.522 19.134 1.00 0.00 N +ATOM 765 H LYS 50 19.806 27.421 18.131 1.00 0.00 H +ATOM 766 CA LYS 50 19.900 28.882 19.702 1.00 0.00 C +ATOM 767 HA LYS 50 20.324 29.504 18.914 1.00 0.00 H +ATOM 768 CB LYS 50 18.514 29.466 20.090 1.00 0.00 C +ATOM 769 HB2 LYS 50 18.082 28.812 20.847 1.00 0.00 H +ATOM 770 HB3 LYS 50 18.662 30.440 20.569 1.00 0.00 H +ATOM 771 CG LYS 50 17.483 29.640 18.962 1.00 0.00 C +ATOM 772 HG2 LYS 50 17.406 28.724 18.377 1.00 0.00 H +ATOM 773 HG3 LYS 50 16.511 29.807 19.436 1.00 0.00 H +ATOM 774 CD LYS 50 17.771 30.842 18.048 1.00 0.00 C +ATOM 775 HD2 LYS 50 17.847 31.729 18.684 1.00 0.00 H +ATOM 776 HD3 LYS 50 18.722 30.709 17.525 1.00 0.00 H +ATOM 777 CE LYS 50 16.636 31.087 17.042 1.00 0.00 C +ATOM 778 HE2 LYS 50 15.680 30.851 17.523 1.00 0.00 H +ATOM 779 HE3 LYS 50 16.620 32.152 16.793 1.00 0.00 H +ATOM 780 NZ LYS 50 16.785 30.318 15.786 1.00 0.00 N +ATOM 781 HZ1 LYS 50 17.027 29.345 15.942 1.00 0.00 H +ATOM 782 HZ2 LYS 50 15.966 30.404 15.186 1.00 0.00 H +ATOM 783 HZ3 LYS 50 17.558 30.688 15.237 1.00 0.00 H +ATOM 784 C LYS 50 20.929 28.907 20.853 1.00 0.00 C +ATOM 785 O LYS 50 20.644 29.476 21.914 1.00 0.00 O +ATOM 786 N THR 51 22.073 28.246 20.666 1.00 0.00 N +ATOM 787 H THR 51 22.280 27.904 19.746 1.00 0.00 H +ATOM 788 CA THR 51 22.978 27.855 21.776 1.00 0.00 C +ATOM 789 HA THR 51 22.713 28.424 22.656 1.00 0.00 H +ATOM 790 CB THR 51 22.769 26.349 22.149 1.00 0.00 C +ATOM 791 HB THR 51 22.913 25.751 21.244 1.00 0.00 H +ATOM 792 CG2 THR 51 23.726 25.829 23.195 1.00 0.00 C +ATOM 793 HG21 THR 51 23.724 26.423 24.104 1.00 0.00 H +ATOM 794 HG22 THR 51 23.491 24.809 23.488 1.00 0.00 H +ATOM 795 HG23 THR 51 24.752 25.794 22.838 1.00 0.00 H +ATOM 796 OG1 THR 51 21.477 26.147 22.676 1.00 0.00 O +ATOM 797 HG1 THR 51 20.828 26.213 21.948 1.00 0.00 H +ATOM 798 C THR 51 24.498 28.160 21.552 1.00 0.00 C +ATOM 799 O THR 51 25.031 27.978 20.458 1.00 0.00 O +ATOM 800 N PHE 52 25.195 28.618 22.604 1.00 0.00 N +ATOM 801 H PHE 52 24.659 28.844 23.435 1.00 0.00 H +ATOM 802 CA PHE 52 26.648 28.754 22.682 1.00 0.00 C +ATOM 803 HA PHE 52 27.066 28.878 21.704 1.00 0.00 H +ATOM 804 CB PHE 52 27.049 29.989 23.564 1.00 0.00 C +ATOM 805 HB2 PHE 52 26.439 29.970 24.449 1.00 0.00 H +ATOM 806 HB3 PHE 52 28.080 29.863 23.877 1.00 0.00 H +ATOM 807 CG PHE 52 26.956 31.369 22.935 1.00 0.00 C +ATOM 808 CD1 PHE 52 26.137 32.360 23.496 1.00 0.00 C +ATOM 809 HD1 PHE 52 25.515 32.134 24.347 1.00 0.00 H +ATOM 810 CE1 PHE 52 26.022 33.613 22.875 1.00 0.00 C +ATOM 811 HE1 PHE 52 25.306 34.345 23.243 1.00 0.00 H +ATOM 812 CZ PHE 52 26.749 33.887 21.707 1.00 0.00 C +ATOM 813 HZ PHE 52 26.610 34.820 21.179 1.00 0.00 H +ATOM 814 CE2 PHE 52 27.660 32.942 21.218 1.00 0.00 C +ATOM 815 HE2 PHE 52 28.252 33.169 20.337 1.00 0.00 H +ATOM 816 CD2 PHE 52 27.757 31.680 21.826 1.00 0.00 C +ATOM 817 HD2 PHE 52 28.421 30.934 21.415 1.00 0.00 H +ATOM 818 C PHE 52 27.299 27.528 23.345 1.00 0.00 C +ATOM 819 O PHE 52 26.801 27.060 24.382 1.00 0.00 O +ATOM 820 N THR 53 28.455 27.080 22.828 1.00 0.00 N +ATOM 821 H THR 53 28.794 27.502 21.960 1.00 0.00 H +ATOM 822 CA THR 53 29.257 25.944 23.360 1.00 0.00 C +ATOM 823 HA THR 53 29.018 25.811 24.412 1.00 0.00 H +ATOM 824 CB THR 53 28.922 24.628 22.631 1.00 0.00 C +ATOM 825 HB THR 53 29.523 23.828 23.066 1.00 0.00 H +ATOM 826 CG2 THR 53 27.455 24.219 22.728 1.00 0.00 C +ATOM 827 HG21 THR 53 26.839 24.900 22.141 1.00 0.00 H +ATOM 828 HG22 THR 53 27.330 23.206 22.345 1.00 0.00 H +ATOM 829 HG23 THR 53 27.136 24.241 23.767 1.00 0.00 H +ATOM 830 OG1 THR 53 29.241 24.729 21.261 1.00 0.00 O +ATOM 831 HG1 THR 53 28.872 23.960 20.816 1.00 0.00 H +ATOM 832 C THR 53 30.775 26.169 23.265 1.00 0.00 C +ATOM 833 O THR 53 31.247 27.039 22.536 1.00 0.00 O +ATOM 834 N THR 54 31.550 25.363 23.995 1.00 0.00 N +ATOM 835 H THR 54 31.108 24.674 24.581 1.00 0.00 H +ATOM 836 CA THR 54 33.026 25.280 23.900 1.00 0.00 C +ATOM 837 HA THR 54 33.389 26.087 23.264 1.00 0.00 H +ATOM 838 CB THR 54 33.679 25.465 25.287 1.00 0.00 C +ATOM 839 HB THR 54 33.366 24.653 25.943 1.00 0.00 H +ATOM 840 CG2 THR 54 35.209 25.527 25.270 1.00 0.00 C +ATOM 841 HG21 THR 54 35.551 26.282 24.560 1.00 0.00 H +ATOM 842 HG22 THR 54 35.586 25.776 26.261 1.00 0.00 H +ATOM 843 HG23 THR 54 35.625 24.558 24.996 1.00 0.00 H +ATOM 844 OG1 THR 54 33.257 26.688 25.848 1.00 0.00 O +ATOM 845 HG1 THR 54 33.703 26.791 26.690 1.00 0.00 H +ATOM 846 C THR 54 33.453 23.948 23.240 1.00 0.00 C +ATOM 847 O THR 54 32.725 22.957 23.330 1.00 0.00 O +ATOM 848 N GLN 55 34.608 23.941 22.569 1.00 0.00 N +ATOM 849 H GLN 55 35.143 24.792 22.563 1.00 0.00 H +ATOM 850 CA GLN 55 35.230 22.769 21.928 1.00 0.00 C +ATOM 851 HA GLN 55 34.472 22.294 21.307 1.00 0.00 H +ATOM 852 CB GLN 55 36.356 23.273 20.997 1.00 0.00 C +ATOM 853 HB2 GLN 55 36.747 22.431 20.418 1.00 0.00 H +ATOM 854 HB3 GLN 55 35.915 23.976 20.284 1.00 0.00 H +ATOM 855 CG GLN 55 37.529 23.975 21.718 1.00 0.00 C +ATOM 856 HG2 GLN 55 37.135 24.635 22.490 1.00 0.00 H +ATOM 857 HG3 GLN 55 38.153 23.228 22.202 1.00 0.00 H +ATOM 858 CD GLN 55 38.400 24.813 20.772 1.00 0.00 C +ATOM 859 OE1 GLN 55 38.699 24.456 19.644 1.00 0.00 O +ATOM 860 NE2 GLN 55 38.838 25.984 21.186 1.00 0.00 N +ATOM 861 HE21 GLN 55 39.398 26.495 20.531 1.00 0.00 H +ATOM 862 HE22 GLN 55 38.530 26.390 22.059 1.00 0.00 H +ATOM 863 C GLN 55 35.729 21.702 22.920 1.00 0.00 C +ATOM 864 O GLN 55 35.936 21.998 24.098 1.00 0.00 O +ATOM 865 N GLU 56 35.911 20.461 22.436 1.00 0.00 N +ATOM 866 H GLU 56 35.764 20.328 21.453 1.00 0.00 H +ATOM 867 CA GLU 56 36.591 19.326 23.126 1.00 0.00 C +ATOM 868 HA GLU 56 36.581 19.527 24.209 1.00 0.00 H +ATOM 869 CB GLU 56 35.802 18.011 22.873 1.00 0.00 C +ATOM 870 HB2 GLU 56 34.794 18.115 23.271 1.00 0.00 H +ATOM 871 HB3 GLU 56 35.670 17.896 21.805 1.00 0.00 H +ATOM 872 CG GLU 56 36.406 16.708 23.419 1.00 0.00 C +ATOM 873 HG2 GLU 56 36.588 16.049 22.597 1.00 0.00 H +ATOM 874 HG3 GLU 56 37.378 16.911 23.804 1.00 0.00 H +ATOM 875 CD GLU 56 35.639 15.935 24.519 1.00 0.00 C +ATOM 876 OE1 GLU 56 36.261 15.255 25.395 1.00 0.00 O +ATOM 877 OE2 GLU 56 34.388 15.901 24.484 1.00 0.00 O +ATOM 878 C GLU 56 38.064 19.234 22.739 1.00 0.00 C +ATOM 879 O GLU 56 38.897 19.678 23.554 1.00 0.00 O +ATOM 880 OXT GLU 56 38.365 18.739 21.612 1.00 0.00 O +HETATM 881 ZN ZN1 57 26.696 32.427 29.378 1.00 0.00 Zn +HETATM 882 N AN1 58 28.269 33.325 30.318 1.00 0.00 N +HETATM 883 C AN1 58 30.569 34.237 31.119 1.00 0.00 C +HETATM 884 C1 AN1 58 29.262 33.721 30.709 1.00 0.00 C +HETATM 885 H AN1 58 30.559 34.480 32.185 1.00 0.00 H +HETATM 886 H1 AN1 58 30.794 35.142 30.544 1.00 0.00 H +HETATM 887 H2 AN1 58 31.328 33.474 30.919 1.00 0.00 H +HETATM 888 N1 AZI 59 30.711 28.496 29.887 1.00 0.00 N +HETATM 889 N2 AZI 59 30.239 29.556 30.281 1.00 0.00 N +HETATM 890 N3 AZI 59 29.793 30.642 30.720 1.00 0.00 N +CONECT 1 3 4 5 2 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 7 1 6 18 +CONECT 6 5 +CONECT 7 8 9 10 5 +CONECT 8 7 +CONECT 9 7 +CONECT 10 13 7 12 11 +CONECT 11 10 +CONECT 12 10 +CONECT 13 14 10 +CONECT 14 16 15 13 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 23 24 +CONECT 23 22 +CONECT 24 22 25 26 27 +CONECT 25 24 +CONECT 26 24 +CONECT 27 24 28 29 30 +CONECT 28 27 +CONECT 29 27 +CONECT 30 27 31 32 +CONECT 31 30 +CONECT 32 30 34 33 +CONECT 33 32 +CONECT 34 32 +CONECT 35 37 36 22 +CONECT 36 35 +CONECT 37 39 38 35 +CONECT 38 37 +CONECT 39 41 40 37 56 +CONECT 40 39 +CONECT 41 44 43 42 39 +CONECT 42 41 +CONECT 43 41 +CONECT 44 45 54 41 +CONECT 45 47 46 44 +CONECT 46 45 +CONECT 47 48 49 45 +CONECT 48 47 +CONECT 49 50 47 52 +CONECT 50 51 49 +CONECT 51 50 +CONECT 52 49 53 54 +CONECT 53 52 +CONECT 54 52 44 55 +CONECT 55 54 +CONECT 56 39 58 57 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 62 78 61 +CONECT 61 60 +CONECT 62 63 60 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 68 66 67 +CONECT 66 65 +CONECT 67 65 +CONECT 68 70 71 69 65 +CONECT 69 68 +CONECT 70 68 +CONECT 71 72 73 68 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 76 75 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 +CONECT 78 79 60 80 +CONECT 79 78 +CONECT 80 78 81 90 +CONECT 81 91 80 84 82 +CONECT 82 81 97 83 +CONECT 83 82 +CONECT 84 93 81 85 92 +CONECT 85 86 84 87 +CONECT 86 94 89 85 +CONECT 87 85 88 881 +CONECT 88 89 87 95 +CONECT 89 86 96 88 +CONECT 90 80 +CONECT 91 81 +CONECT 92 84 +CONECT 93 84 +CONECT 94 86 +CONECT 95 88 +CONECT 96 89 +CONECT 97 98 82 99 +CONECT 98 97 +CONECT 99 101 97 114 100 +CONECT 100 99 +CONECT 101 102 107 103 99 +CONECT 102 101 +CONECT 103 101 105 106 104 +CONECT 104 103 +CONECT 105 103 +CONECT 106 103 +CONECT 107 110 109 101 108 +CONECT 108 107 +CONECT 109 107 +CONECT 110 113 112 111 107 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 +CONECT 114 99 115 116 +CONECT 115 114 +CONECT 116 114 117 118 +CONECT 117 116 +CONECT 118 116 130 119 120 +CONECT 119 118 +CONECT 120 118 122 121 126 +CONECT 121 120 +CONECT 122 125 123 120 124 +CONECT 123 122 +CONECT 124 122 +CONECT 125 122 +CONECT 126 120 129 127 128 +CONECT 127 126 +CONECT 128 126 +CONECT 129 126 +CONECT 130 131 132 118 +CONECT 131 130 +CONECT 132 130 134 133 +CONECT 133 132 +CONECT 134 135 132 136 154 +CONECT 135 134 +CONECT 136 138 137 134 139 +CONECT 137 136 +CONECT 138 136 +CONECT 139 136 141 140 142 +CONECT 140 139 +CONECT 141 139 +CONECT 142 139 145 143 144 +CONECT 143 142 +CONECT 144 142 +CONECT 145 146 142 147 +CONECT 146 145 +CONECT 147 145 148 151 +CONECT 148 149 147 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 147 152 153 +CONECT 152 151 +CONECT 153 151 +CONECT 154 134 156 155 +CONECT 155 154 +CONECT 156 157 154 158 +CONECT 157 156 +CONECT 158 156 159 161 160 +CONECT 159 158 +CONECT 160 158 +CONECT 161 162 158 163 +CONECT 162 161 +CONECT 163 161 165 164 +CONECT 164 163 +CONECT 165 167 166 163 183 +CONECT 166 165 +CONECT 167 170 168 169 165 +CONECT 168 167 +CONECT 169 167 +CONECT 170 173 172 171 167 +CONECT 171 170 +CONECT 172 170 +CONECT 173 176 174 175 170 +CONECT 174 173 +CONECT 175 173 +CONECT 176 179 178 177 173 +CONECT 177 176 +CONECT 178 176 +CONECT 179 181 182 180 176 +CONECT 180 179 +CONECT 181 179 +CONECT 182 179 +CONECT 183 165 184 185 +CONECT 184 183 +CONECT 185 183 186 187 +CONECT 186 185 +CONECT 187 185 188 194 189 +CONECT 188 187 +CONECT 189 187 192 190 191 +CONECT 190 189 +CONECT 191 189 +CONECT 192 193 189 +CONECT 193 192 +CONECT 194 196 187 195 +CONECT 195 194 +CONECT 196 197 198 194 +CONECT 197 196 +CONECT 198 205 196 200 199 +CONECT 199 198 +CONECT 200 201 198 202 203 +CONECT 201 200 +CONECT 202 200 +CONECT 203 200 204 +CONECT 204 203 +CONECT 205 206 207 198 +CONECT 206 205 +CONECT 207 209 205 208 +CONECT 208 207 +CONECT 209 210 227 211 207 +CONECT 210 209 +CONECT 211 214 209 212 213 +CONECT 212 211 +CONECT 213 211 +CONECT 214 216 215 217 211 +CONECT 215 214 +CONECT 216 214 +CONECT 217 218 214 219 220 +CONECT 218 217 +CONECT 219 217 +CONECT 220 217 222 223 221 +CONECT 221 220 +CONECT 222 220 +CONECT 223 226 220 225 224 +CONECT 224 223 +CONECT 225 223 +CONECT 226 223 +CONECT 227 228 209 229 +CONECT 228 227 +CONECT 229 227 231 230 +CONECT 230 229 +CONECT 231 234 229 232 233 +CONECT 232 231 +CONECT 233 231 +CONECT 234 235 236 231 +CONECT 235 234 +CONECT 236 238 234 237 +CONECT 237 236 +CONECT 238 240 239 250 236 +CONECT 239 238 +CONECT 240 246 241 242 238 +CONECT 241 240 +CONECT 242 244 240 243 245 +CONECT 243 242 +CONECT 244 242 +CONECT 245 242 +CONECT 246 248 247 249 240 +CONECT 247 246 +CONECT 248 246 +CONECT 249 246 +CONECT 250 238 252 251 +CONECT 251 250 +CONECT 252 262 253 250 +CONECT 253 254 252 263 256 +CONECT 254 255 269 253 +CONECT 255 254 +CONECT 256 253 257 264 265 +CONECT 257 258 259 256 +CONECT 258 261 267 257 +CONECT 259 260 257 266 +CONECT 260 261 268 259 +CONECT 261 881 258 260 +CONECT 262 252 +CONECT 263 253 +CONECT 264 256 +CONECT 265 256 +CONECT 266 259 +CONECT 267 258 +CONECT 268 260 +CONECT 269 271 254 270 +CONECT 270 269 +CONECT 271 272 273 281 269 +CONECT 272 271 +CONECT 273 274 275 271 279 +CONECT 274 273 +CONECT 275 278 277 273 276 +CONECT 276 275 +CONECT 277 275 +CONECT 278 275 +CONECT 279 273 280 +CONECT 280 279 +CONECT 281 283 271 282 +CONECT 282 281 +CONECT 283 293 284 281 +CONECT 284 285 287 283 294 +CONECT 285 286 300 284 +CONECT 286 285 +CONECT 287 295 296 284 288 +CONECT 288 287 289 290 +CONECT 289 298 288 292 +CONECT 290 288 297 291 +CONECT 291 292 290 299 +CONECT 292 289 881 291 +CONECT 293 283 +CONECT 294 284 +CONECT 295 287 +CONECT 296 287 +CONECT 297 290 +CONECT 298 289 +CONECT 299 291 +CONECT 300 302 285 301 +CONECT 301 300 +CONECT 302 313 303 300 304 +CONECT 303 302 +CONECT 304 302 307 306 305 +CONECT 305 304 +CONECT 306 304 +CONECT 307 309 310 304 308 +CONECT 308 307 +CONECT 309 307 +CONECT 310 311 307 312 +CONECT 311 310 +CONECT 312 310 +CONECT 313 315 314 302 +CONECT 314 313 +CONECT 315 317 316 313 +CONECT 316 315 +CONECT 317 323 319 318 315 +CONECT 318 317 +CONECT 319 321 320 317 322 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 325 324 317 +CONECT 324 323 +CONECT 325 327 326 323 +CONECT 326 325 +CONECT 327 339 329 328 325 +CONECT 328 327 +CONECT 329 330 335 327 331 +CONECT 330 329 +CONECT 331 329 333 334 332 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 336 337 329 338 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 340 341 327 +CONECT 340 339 +CONECT 341 343 339 342 +CONECT 342 341 +CONECT 343 345 344 351 341 +CONECT 344 343 +CONECT 345 348 346 347 343 +CONECT 346 345 +CONECT 347 345 +CONECT 348 350 349 345 +CONECT 349 348 +CONECT 350 348 +CONECT 351 353 343 352 +CONECT 352 351 +CONECT 353 354 355 351 +CONECT 354 353 +CONECT 355 357 353 375 356 +CONECT 356 355 +CONECT 357 359 358 360 355 +CONECT 358 357 +CONECT 359 357 +CONECT 360 361 357 374 +CONECT 361 362 363 360 +CONECT 362 361 +CONECT 363 361 364 365 +CONECT 364 363 +CONECT 365 363 374 366 +CONECT 366 365 367 368 +CONECT 367 366 +CONECT 368 366 370 369 +CONECT 369 368 +CONECT 370 372 368 371 +CONECT 371 370 +CONECT 372 374 373 370 +CONECT 373 372 +CONECT 374 360 365 372 +CONECT 375 377 355 376 +CONECT 376 375 +CONECT 377 378 379 375 +CONECT 378 377 +CONECT 379 381 377 380 385 +CONECT 380 379 +CONECT 381 384 382 383 379 +CONECT 382 381 +CONECT 383 381 +CONECT 384 381 +CONECT 385 379 386 387 +CONECT 386 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 390 391 400 +CONECT 390 389 +CONECT 391 394 392 389 393 +CONECT 392 391 +CONECT 393 391 +CONECT 394 395 396 397 391 +CONECT 395 394 +CONECT 396 394 +CONECT 397 399 394 398 +CONECT 398 397 +CONECT 399 397 +CONECT 400 389 402 401 +CONECT 401 400 +CONECT 402 403 400 404 +CONECT 403 402 +CONECT 404 402 406 410 405 +CONECT 405 404 +CONECT 406 407 409 404 408 +CONECT 407 406 +CONECT 408 406 +CONECT 409 406 +CONECT 410 412 404 411 +CONECT 411 410 +CONECT 412 413 414 410 +CONECT 413 412 +CONECT 414 416 412 415 425 +CONECT 415 414 +CONECT 416 417 418 419 414 +CONECT 417 416 +CONECT 418 416 +CONECT 419 422 416 421 420 +CONECT 420 419 +CONECT 421 419 +CONECT 422 424 423 419 +CONECT 423 422 +CONECT 424 422 +CONECT 425 414 427 426 +CONECT 426 425 +CONECT 427 428 425 429 +CONECT 428 427 +CONECT 429 427 431 430 447 +CONECT 430 429 +CONECT 431 434 432 433 429 +CONECT 432 431 +CONECT 433 431 +CONECT 434 436 437 435 431 +CONECT 435 434 +CONECT 436 434 +CONECT 437 440 438 439 434 +CONECT 438 437 +CONECT 439 437 +CONECT 440 443 441 442 437 +CONECT 441 440 +CONECT 442 440 +CONECT 443 445 444 446 440 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 +CONECT 447 429 449 448 +CONECT 448 447 +CONECT 449 450 447 451 +CONECT 450 449 +CONECT 451 449 453 452 467 +CONECT 452 451 +CONECT 453 456 454 451 455 +CONECT 454 453 +CONECT 455 453 +CONECT 456 457 465 453 +CONECT 457 459 458 456 +CONECT 458 457 +CONECT 459 460 461 457 +CONECT 460 459 +CONECT 461 462 459 463 +CONECT 462 461 +CONECT 463 461 464 465 +CONECT 464 463 +CONECT 465 463 456 466 +CONECT 466 465 +CONECT 467 451 469 468 +CONECT 468 467 +CONECT 469 470 471 467 +CONECT 470 469 +CONECT 471 473 469 481 472 +CONECT 472 471 +CONECT 473 474 479 475 471 +CONECT 474 473 +CONECT 475 473 477 478 476 +CONECT 476 475 +CONECT 477 475 +CONECT 478 475 +CONECT 479 480 473 +CONECT 480 479 +CONECT 481 483 471 482 +CONECT 482 481 +CONECT 483 484 485 481 +CONECT 484 483 +CONECT 485 487 483 486 503 +CONECT 486 485 +CONECT 487 490 488 489 485 +CONECT 488 487 +CONECT 489 487 +CONECT 490 493 492 491 487 +CONECT 491 490 +CONECT 492 490 +CONECT 493 496 494 495 490 +CONECT 494 493 +CONECT 495 493 +CONECT 496 498 497 499 493 +CONECT 497 496 +CONECT 498 496 +CONECT 499 501 496 502 500 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 +CONECT 503 485 505 504 +CONECT 504 503 +CONECT 505 506 503 507 +CONECT 506 505 +CONECT 507 505 509 508 513 +CONECT 508 507 +CONECT 509 512 510 507 511 +CONECT 510 509 +CONECT 511 509 +CONECT 512 509 +CONECT 513 507 515 514 +CONECT 514 513 +CONECT 515 516 513 517 +CONECT 516 515 +CONECT 517 515 519 534 518 +CONECT 518 517 +CONECT 519 521 520 517 522 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 525 523 524 +CONECT 523 522 +CONECT 524 522 +CONECT 525 526 522 528 527 +CONECT 526 525 +CONECT 527 525 +CONECT 528 530 525 531 529 +CONECT 529 528 +CONECT 530 528 +CONECT 531 533 528 532 +CONECT 532 531 +CONECT 533 531 +CONECT 534 536 517 535 +CONECT 535 534 +CONECT 536 537 538 534 +CONECT 537 536 +CONECT 538 540 536 544 539 +CONECT 539 538 +CONECT 540 541 543 542 538 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 +CONECT 544 538 546 545 +CONECT 545 544 +CONECT 546 547 544 548 +CONECT 547 546 +CONECT 548 550 546 549 558 +CONECT 549 548 +CONECT 550 553 551 552 548 +CONECT 551 550 +CONECT 552 550 +CONECT 553 555 554 550 +CONECT 554 553 +CONECT 555 556 557 553 +CONECT 556 555 +CONECT 557 555 +CONECT 558 548 560 559 +CONECT 559 558 +CONECT 560 561 558 562 +CONECT 561 560 +CONECT 562 560 564 563 570 +CONECT 563 562 +CONECT 564 567 565 562 566 +CONECT 565 564 +CONECT 566 564 +CONECT 567 569 568 564 +CONECT 568 567 +CONECT 569 567 +CONECT 570 562 572 571 +CONECT 571 570 +CONECT 572 573 570 574 +CONECT 573 572 +CONECT 574 572 592 576 575 +CONECT 575 574 +CONECT 576 579 574 578 577 +CONECT 577 576 +CONECT 578 576 +CONECT 579 580 581 582 576 +CONECT 580 579 +CONECT 581 579 +CONECT 582 585 584 579 583 +CONECT 583 582 +CONECT 584 582 +CONECT 585 588 587 586 582 +CONECT 586 585 +CONECT 587 585 +CONECT 588 590 591 589 585 +CONECT 589 588 +CONECT 590 588 +CONECT 591 588 +CONECT 592 594 593 574 +CONECT 593 592 +CONECT 594 596 595 592 +CONECT 595 594 +CONECT 596 599 594 597 598 +CONECT 597 596 +CONECT 598 596 +CONECT 599 601 600 596 +CONECT 600 599 +CONECT 601 603 602 599 +CONECT 602 601 +CONECT 603 623 604 605 601 +CONECT 604 603 +CONECT 605 606 603 607 608 +CONECT 606 605 +CONECT 607 605 +CONECT 608 609 605 610 611 +CONECT 609 608 +CONECT 610 608 +CONECT 611 608 613 614 612 +CONECT 612 611 +CONECT 613 611 +CONECT 614 611 616 615 +CONECT 615 614 +CONECT 616 617 614 620 +CONECT 617 618 619 616 +CONECT 618 617 +CONECT 619 617 +CONECT 620 616 622 621 +CONECT 621 620 +CONECT 622 620 +CONECT 623 625 624 603 +CONECT 624 623 +CONECT 625 627 626 623 +CONECT 626 625 +CONECT 627 629 635 628 625 +CONECT 628 627 +CONECT 629 632 630 631 627 +CONECT 630 629 +CONECT 631 629 +CONECT 632 634 633 629 +CONECT 633 632 +CONECT 634 632 +CONECT 635 637 636 627 +CONECT 636 635 +CONECT 637 639 638 635 +CONECT 638 637 +CONECT 639 642 640 641 637 +CONECT 640 639 +CONECT 641 639 +CONECT 642 644 643 639 +CONECT 643 642 +CONECT 644 646 645 642 +CONECT 645 644 +CONECT 646 648 647 657 644 +CONECT 647 646 +CONECT 648 650 651 649 646 +CONECT 649 648 +CONECT 650 648 +CONECT 651 653 648 654 652 +CONECT 652 651 +CONECT 653 651 +CONECT 654 651 655 656 +CONECT 655 654 +CONECT 656 654 +CONECT 657 659 646 658 +CONECT 658 657 +CONECT 659 660 661 657 +CONECT 660 659 +CONECT 661 681 659 662 663 +CONECT 662 661 +CONECT 663 661 666 664 665 +CONECT 664 663 +CONECT 665 663 +CONECT 666 668 667 663 669 +CONECT 667 666 +CONECT 668 666 +CONECT 669 666 672 670 671 +CONECT 670 669 +CONECT 671 669 +CONECT 672 673 674 669 +CONECT 673 672 +CONECT 674 678 675 672 +CONECT 675 677 676 674 +CONECT 676 675 +CONECT 677 675 +CONECT 678 679 680 674 +CONECT 679 678 +CONECT 680 678 +CONECT 681 682 683 661 +CONECT 682 681 +CONECT 683 685 681 684 +CONECT 684 683 +CONECT 685 686 687 695 683 +CONECT 686 685 +CONECT 687 689 693 685 688 +CONECT 688 687 +CONECT 689 690 691 692 687 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 +CONECT 693 694 687 +CONECT 694 693 +CONECT 695 697 685 696 +CONECT 696 695 +CONECT 697 698 699 695 +CONECT 698 697 +CONECT 699 714 701 697 700 +CONECT 700 699 +CONECT 701 707 702 699 703 +CONECT 702 701 +CONECT 703 701 705 704 706 +CONECT 704 703 +CONECT 705 703 +CONECT 706 703 +CONECT 707 710 709 708 701 +CONECT 708 707 +CONECT 709 707 +CONECT 710 712 713 711 707 +CONECT 711 710 +CONECT 712 710 +CONECT 713 710 +CONECT 714 715 716 699 +CONECT 715 714 +CONECT 716 718 714 717 +CONECT 717 716 +CONECT 718 719 726 720 716 +CONECT 719 718 +CONECT 720 723 718 721 722 +CONECT 721 720 +CONECT 722 720 +CONECT 723 725 720 724 +CONECT 724 723 +CONECT 725 723 +CONECT 726 728 718 727 +CONECT 727 726 +CONECT 728 729 730 726 +CONECT 729 728 +CONECT 730 732 728 738 731 +CONECT 731 730 +CONECT 732 734 735 733 730 +CONECT 733 732 +CONECT 734 732 +CONECT 735 736 732 737 +CONECT 736 735 +CONECT 737 735 +CONECT 738 740 730 739 +CONECT 739 738 +CONECT 740 741 742 738 +CONECT 741 740 +CONECT 742 744 743 740 748 +CONECT 743 742 +CONECT 744 747 746 745 742 +CONECT 745 744 +CONECT 746 744 +CONECT 747 744 +CONECT 748 742 749 750 +CONECT 749 748 +CONECT 750 748 751 752 +CONECT 751 750 +CONECT 752 750 753 754 762 +CONECT 753 752 +CONECT 754 756 752 760 755 +CONECT 755 754 +CONECT 756 757 759 758 754 +CONECT 757 756 +CONECT 758 756 +CONECT 759 756 +CONECT 760 761 754 +CONECT 761 760 +CONECT 762 752 764 763 +CONECT 763 762 +CONECT 764 765 766 762 +CONECT 765 764 +CONECT 766 767 764 768 784 +CONECT 767 766 +CONECT 768 771 766 770 769 +CONECT 769 768 +CONECT 770 768 +CONECT 771 774 772 773 768 +CONECT 772 771 +CONECT 773 771 +CONECT 774 777 776 775 771 +CONECT 775 774 +CONECT 776 774 +CONECT 777 780 779 778 774 +CONECT 778 777 +CONECT 779 777 +CONECT 780 782 783 781 777 +CONECT 781 780 +CONECT 782 780 +CONECT 783 780 +CONECT 784 766 786 785 +CONECT 785 784 +CONECT 786 787 784 788 +CONECT 787 786 +CONECT 788 786 798 790 789 +CONECT 789 788 +CONECT 790 791 788 796 792 +CONECT 791 790 +CONECT 792 790 795 794 793 +CONECT 793 792 +CONECT 794 792 +CONECT 795 792 +CONECT 796 797 790 +CONECT 797 796 +CONECT 798 799 788 800 +CONECT 799 798 +CONECT 800 798 802 801 +CONECT 801 800 +CONECT 802 803 800 818 804 +CONECT 803 802 +CONECT 804 802 807 806 805 +CONECT 805 804 +CONECT 806 804 +CONECT 807 816 808 804 +CONECT 808 810 807 809 +CONECT 809 808 +CONECT 810 812 811 808 +CONECT 811 810 +CONECT 812 813 814 810 +CONECT 813 812 +CONECT 814 815 812 816 +CONECT 815 814 +CONECT 816 814 817 807 +CONECT 817 816 +CONECT 818 802 820 819 +CONECT 819 818 +CONECT 820 821 818 822 +CONECT 821 820 +CONECT 822 824 820 832 823 +CONECT 823 822 +CONECT 824 830 826 825 822 +CONECT 825 824 +CONECT 826 827 828 824 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 +CONECT 830 831 824 +CONECT 831 830 +CONECT 832 833 822 834 +CONECT 833 832 +CONECT 834 832 836 835 +CONECT 835 834 +CONECT 836 846 837 834 838 +CONECT 837 836 +CONECT 838 836 840 844 839 +CONECT 839 838 +CONECT 840 841 843 838 842 +CONECT 841 840 +CONECT 842 840 +CONECT 843 840 +CONECT 844 838 845 +CONECT 845 844 +CONECT 846 848 847 836 +CONECT 847 846 +CONECT 848 850 849 846 +CONECT 849 848 +CONECT 850 852 851 848 863 +CONECT 851 850 +CONECT 852 854 853 855 850 +CONECT 853 852 +CONECT 854 852 +CONECT 855 858 852 857 856 +CONECT 856 855 +CONECT 857 855 +CONECT 858 859 860 855 +CONECT 859 858 +CONECT 860 861 858 862 +CONECT 861 860 +CONECT 862 860 +CONECT 863 850 865 864 +CONECT 864 863 +CONECT 865 866 863 867 +CONECT 866 865 +CONECT 867 865 878 869 868 +CONECT 868 867 +CONECT 869 871 867 870 872 +CONECT 870 869 +CONECT 871 869 +CONECT 872 873 869 874 875 +CONECT 873 872 +CONECT 874 872 +CONECT 875 872 877 876 +CONECT 876 875 +CONECT 877 875 +CONECT 878 880 867 879 +CONECT 879 878 +CONECT 880 878 +CONECT 881 87 292 882 261 +CONECT 882 881 884 +CONECT 883 886 884 887 885 +CONECT 884 882 883 +CONECT 885 883 +CONECT 886 883 +CONECT 887 883 +CONECT 888 889 +CONECT 889 888 890 +CONECT 890 889 +MASTER 0 0 0 0 0 0 0 0 890 0 890 0 +END diff --git a/tests/nsga2/pdbs_rename/cluster0.pdb b/tests/nsga2/pdbs_rename/cluster0.pdb new file mode 100644 index 0000000..b666530 --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster0.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.003 -82.385 -13.374 1.00 0.00 N +ATOM 2 H1 MET 1 14.002 -82.237 -13.397 1.00 0.00 H +ATOM 3 H2 MET 1 12.617 -82.051 -12.503 1.00 0.00 H +ATOM 4 H3 MET 1 12.504 -81.958 -14.141 1.00 0.00 H +ATOM 5 CA MET 1 12.817 -83.815 -13.490 1.00 0.00 C +ATOM 6 HA MET 1 11.778 -84.048 -13.256 1.00 0.00 H +ATOM 7 CB MET 1 13.115 -84.298 -14.885 1.00 0.00 C +ATOM 8 HB2 MET 1 12.606 -83.694 -15.637 1.00 0.00 H +ATOM 9 HB3 MET 1 14.200 -84.279 -14.995 1.00 0.00 H +ATOM 10 CG MET 1 12.731 -85.746 -15.065 1.00 0.00 C +ATOM 11 HG2 MET 1 13.407 -86.338 -14.449 1.00 0.00 H +ATOM 12 HG3 MET 1 11.721 -85.895 -14.683 1.00 0.00 H +ATOM 13 SD MET 1 12.823 -86.418 -16.750 1.00 0.00 S +ATOM 14 CE MET 1 14.431 -85.904 -17.273 1.00 0.00 C +ATOM 15 HE1 MET 1 14.505 -84.817 -17.243 1.00 0.00 H +ATOM 16 HE2 MET 1 14.645 -86.267 -18.278 1.00 0.00 H +ATOM 17 HE3 MET 1 15.153 -86.228 -16.522 1.00 0.00 H +ATOM 18 C MET 1 13.793 -84.410 -12.415 1.00 0.00 C +ATOM 19 O MET 1 14.945 -84.014 -12.426 1.00 0.00 O +ATOM 20 N GLN 2 13.498 -85.513 -11.769 1.00 0.00 N +ATOM 21 H GLN 2 12.549 -85.852 -11.842 1.00 0.00 H +ATOM 22 CA GLN 2 14.392 -86.212 -10.788 1.00 0.00 C +ATOM 23 HA GLN 2 15.109 -85.500 -10.379 1.00 0.00 H +ATOM 24 CB GLN 2 13.532 -86.703 -9.584 1.00 0.00 C +ATOM 25 HB2 GLN 2 12.804 -87.367 -10.050 1.00 0.00 H +ATOM 26 HB3 GLN 2 14.174 -87.312 -8.948 1.00 0.00 H +ATOM 27 CG GLN 2 12.872 -85.678 -8.664 1.00 0.00 C +ATOM 28 HG2 GLN 2 12.717 -84.745 -9.207 1.00 0.00 H +ATOM 29 HG3 GLN 2 11.843 -86.032 -8.594 1.00 0.00 H +ATOM 30 CD GLN 2 13.455 -85.553 -7.230 1.00 0.00 C +ATOM 31 OE1 GLN 2 14.595 -85.887 -6.905 1.00 0.00 O +ATOM 32 NE2 GLN 2 12.745 -84.855 -6.361 1.00 0.00 N +ATOM 33 HE21 GLN 2 13.149 -84.584 -5.476 1.00 0.00 H +ATOM 34 HE22 GLN 2 11.825 -84.541 -6.635 1.00 0.00 H +ATOM 35 C GLN 2 15.364 -87.269 -11.360 1.00 0.00 C +ATOM 36 O GLN 2 15.084 -88.492 -11.421 1.00 0.00 O +ATOM 37 N TYR 3 16.524 -86.790 -11.746 1.00 0.00 N +ATOM 38 H TYR 3 16.697 -85.805 -11.600 1.00 0.00 H +ATOM 39 CA TYR 3 17.652 -87.622 -12.295 1.00 0.00 C +ATOM 40 HA TYR 3 17.346 -88.300 -13.092 1.00 0.00 H +ATOM 41 CB TYR 3 18.732 -86.723 -12.825 1.00 0.00 C +ATOM 42 HB2 TYR 3 18.930 -85.993 -12.040 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.577 -87.393 -12.988 1.00 0.00 H +ATOM 44 CG TYR 3 18.239 -85.944 -14.076 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.512 -86.427 -15.374 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.989 -87.392 -15.466 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.208 -85.626 -16.456 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.401 -85.981 -17.457 1.00 0.00 H +ATOM 49 CZ TYR 3 17.537 -84.430 -16.197 1.00 0.00 C +ATOM 50 OH TYR 3 17.251 -83.606 -17.273 1.00 0.00 O +ATOM 51 HH TYR 3 17.750 -83.947 -18.018 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.080 -83.989 -14.937 1.00 0.00 C +ATOM 53 HE2 TYR 3 16.489 -83.091 -14.826 1.00 0.00 H +ATOM 54 CD2 TYR 3 17.557 -84.744 -13.876 1.00 0.00 C +ATOM 55 HD2 TYR 3 17.250 -84.430 -12.890 1.00 0.00 H +ATOM 56 C TYR 3 18.233 -88.485 -11.236 1.00 0.00 C +ATOM 57 O TYR 3 18.255 -88.097 -10.086 1.00 0.00 O +ATOM 58 N LYS 4 18.815 -89.665 -11.571 1.00 0.00 N +ATOM 59 H LYS 4 18.746 -89.897 -12.552 1.00 0.00 H +ATOM 60 CA LYS 4 19.306 -90.687 -10.646 1.00 0.00 C +ATOM 61 HA LYS 4 18.862 -90.648 -9.652 1.00 0.00 H +ATOM 62 CB LYS 4 18.907 -92.011 -11.231 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.018 -92.083 -12.313 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.503 -92.764 -10.715 1.00 0.00 H +ATOM 65 CG LYS 4 17.494 -92.443 -10.928 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.555 -93.455 -11.326 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.327 -92.579 -9.859 1.00 0.00 H +ATOM 68 CD LYS 4 16.367 -91.656 -11.615 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.479 -90.608 -11.336 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.460 -91.723 -12.699 1.00 0.00 H +ATOM 71 CE LYS 4 15.044 -92.119 -11.098 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.905 -93.136 -11.464 1.00 0.00 H +ATOM 73 HE3 LYS 4 14.909 -92.215 -10.021 1.00 0.00 H +ATOM 74 NZ LYS 4 13.859 -91.347 -11.574 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.011 -91.799 -11.263 1.00 0.00 H +ATOM 76 HZ2 LYS 4 13.927 -91.300 -12.580 1.00 0.00 H +ATOM 77 HZ3 LYS 4 13.863 -90.405 -11.208 1.00 0.00 H +ATOM 78 C LYS 4 20.764 -90.556 -10.378 1.00 0.00 C +ATOM 79 O LYS 4 21.451 -89.991 -11.198 1.00 0.00 O +ATOM 80 N HX1 5 21.236 -90.868 -9.176 1.00 0.00 N +ATOM 81 CA HX1 5 22.633 -90.844 -8.790 1.00 0.00 C +ATOM 82 C HX1 5 22.860 -91.880 -7.748 1.00 0.00 C +ATOM 83 O HX1 5 22.130 -91.930 -6.740 1.00 0.00 O +ATOM 84 CB HX1 5 23.000 -89.454 -8.200 1.00 0.00 C +ATOM 85 CG HX1 5 24.375 -89.185 -7.655 1.00 0.00 C +ATOM 86 CD2 HX1 5 25.595 -89.645 -8.102 1.00 0.00 C +ATOM 87 ND1 HX1 5 24.610 -88.515 -6.436 1.00 0.00 N +ATOM 88 CE1 HX1 5 25.927 -88.544 -6.216 1.00 0.00 C +ATOM 89 NE2 HX1 5 26.563 -89.214 -7.195 1.00 0.00 N +ATOM 90 H HX1 5 20.551 -91.052 -8.456 1.00 0.00 H +ATOM 91 HA HX1 5 23.202 -90.939 -9.715 1.00 0.00 H +ATOM 92 HB2 HX1 5 22.281 -89.349 -7.387 1.00 0.00 H +ATOM 93 HB3 HX1 5 22.813 -88.724 -8.987 1.00 0.00 H +ATOM 94 HD2 HX1 5 25.748 -90.244 -8.988 1.00 0.00 H +ATOM 95 HE1 HX1 5 26.353 -88.113 -5.321 1.00 0.00 H +ATOM 96 HE2 HX1 5 27.558 -89.358 -7.283 1.00 0.00 H +ATOM 97 N ILE 6 23.793 -92.766 -8.096 1.00 0.00 N +ATOM 98 H ILE 6 24.340 -92.519 -8.908 1.00 0.00 H +ATOM 99 CA ILE 6 24.284 -93.842 -7.256 1.00 0.00 C +ATOM 100 HA ILE 6 23.487 -94.109 -6.561 1.00 0.00 H +ATOM 101 CB ILE 6 24.784 -95.053 -8.041 1.00 0.00 C +ATOM 102 HB ILE 6 25.551 -94.655 -8.705 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.653 -96.002 -7.134 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.787 -97.003 -7.544 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.091 -96.213 -6.224 1.00 0.00 H +ATOM 106 HG23 ILE 6 26.668 -95.658 -6.934 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.708 -95.750 -8.838 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.000 -96.203 -8.144 1.00 0.00 H +ATOM 109 HG13 ILE 6 23.233 -94.940 -9.390 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.159 -96.794 -9.808 1.00 0.00 C +ATOM 111 HD11 ILE 6 23.643 -97.733 -9.607 1.00 0.00 H +ATOM 112 HD12 ILE 6 25.244 -96.801 -9.916 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.832 -96.454 -10.790 1.00 0.00 H +ATOM 114 C ILE 6 25.375 -93.259 -6.384 1.00 0.00 C +ATOM 115 O ILE 6 26.051 -92.352 -6.818 1.00 0.00 O +ATOM 116 N VAL 7 25.483 -93.673 -5.108 1.00 0.00 N +ATOM 117 H VAL 7 24.735 -94.223 -4.710 1.00 0.00 H +ATOM 118 CA VAL 7 26.464 -93.171 -4.144 1.00 0.00 C +ATOM 119 HA VAL 7 26.160 -92.151 -3.909 1.00 0.00 H +ATOM 120 CB VAL 7 26.371 -94.134 -2.892 1.00 0.00 C +ATOM 121 HB VAL 7 25.315 -94.325 -2.706 1.00 0.00 H +ATOM 122 CG1 VAL 7 26.987 -95.528 -3.080 1.00 0.00 C +ATOM 123 HG11 VAL 7 26.815 -96.170 -2.216 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.551 -96.054 -3.929 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.075 -95.496 -3.137 1.00 0.00 H +ATOM 126 CG2 VAL 7 26.863 -93.468 -1.556 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.944 -93.325 -1.522 1.00 0.00 H +ATOM 128 HG22 VAL 7 26.444 -92.465 -1.623 1.00 0.00 H +ATOM 129 HG23 VAL 7 26.450 -93.911 -0.650 1.00 0.00 H +ATOM 130 C VAL 7 27.920 -93.106 -4.626 1.00 0.00 C +ATOM 131 O VAL 7 28.384 -94.132 -5.137 1.00 0.00 O +ATOM 132 N ASN 8 28.705 -91.990 -4.436 1.00 0.00 N +ATOM 133 H ASN 8 28.205 -91.186 -4.084 1.00 0.00 H +ATOM 134 CA ASN 8 30.076 -91.774 -4.932 1.00 0.00 C +ATOM 135 HA ASN 8 30.106 -92.084 -5.977 1.00 0.00 H +ATOM 136 CB ASN 8 30.499 -90.318 -4.922 1.00 0.00 C +ATOM 137 HB2 ASN 8 30.667 -89.870 -3.943 1.00 0.00 H +ATOM 138 HB3 ASN 8 31.421 -90.273 -5.501 1.00 0.00 H +ATOM 139 CG ASN 8 29.611 -89.516 -5.873 1.00 0.00 C +ATOM 140 OD1 ASN 8 29.312 -89.960 -6.946 1.00 0.00 O +ATOM 141 ND2 ASN 8 29.325 -88.294 -5.555 1.00 0.00 N +ATOM 142 HD21 ASN 8 29.622 -87.946 -4.655 1.00 0.00 H +ATOM 143 HD22 ASN 8 28.724 -87.755 -6.162 1.00 0.00 H +ATOM 144 C ASN 8 31.162 -92.680 -4.209 1.00 0.00 C +ATOM 145 O ASN 8 32.221 -93.053 -4.794 1.00 0.00 O +ATOM 146 N GLY 9 31.065 -92.866 -2.886 1.00 0.00 N +ATOM 147 H GLY 9 30.240 -92.520 -2.416 1.00 0.00 H +ATOM 148 CA GLY 9 32.126 -93.588 -2.175 1.00 0.00 C +ATOM 149 HA2 GLY 9 33.081 -93.109 -2.393 1.00 0.00 H +ATOM 150 HA3 GLY 9 31.883 -93.412 -1.127 1.00 0.00 H +ATOM 151 C GLY 9 32.181 -95.107 -2.483 1.00 0.00 C +ATOM 152 O GLY 9 31.118 -95.718 -2.522 1.00 0.00 O +ATOM 153 N LYS 10 33.396 -95.646 -2.719 1.00 0.00 N +ATOM 154 H LYS 10 34.226 -95.072 -2.755 1.00 0.00 H +ATOM 155 CA LYS 10 33.694 -97.050 -3.089 1.00 0.00 C +ATOM 156 HA LYS 10 33.113 -97.278 -3.982 1.00 0.00 H +ATOM 157 CB LYS 10 35.170 -97.299 -3.292 1.00 0.00 C +ATOM 158 HB2 LYS 10 35.542 -96.397 -3.778 1.00 0.00 H +ATOM 159 HB3 LYS 10 35.747 -97.466 -2.382 1.00 0.00 H +ATOM 160 CG LYS 10 35.547 -98.488 -4.193 1.00 0.00 C +ATOM 161 HG2 LYS 10 36.578 -98.814 -4.058 1.00 0.00 H +ATOM 162 HG3 LYS 10 34.990 -99.341 -3.806 1.00 0.00 H +ATOM 163 CD LYS 10 35.244 -98.240 -5.663 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.165 -98.319 -5.796 1.00 0.00 H +ATOM 165 HD3 LYS 10 35.592 -97.241 -5.925 1.00 0.00 H +ATOM 166 CE LYS 10 36.083 -99.280 -6.461 1.00 0.00 C +ATOM 167 HE2 LYS 10 36.916 -98.665 -6.803 1.00 0.00 H +ATOM 168 HE3 LYS 10 36.334-100.150 -5.854 1.00 0.00 H +ATOM 169 NZ LYS 10 35.389 -99.738 -7.669 1.00 0.00 N +ATOM 170 HZ1 LYS 10 36.005-100.420 -8.089 1.00 0.00 H +ATOM 171 HZ2 LYS 10 35.281 -99.070 -8.420 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.510-100.213 -7.521 1.00 0.00 H +ATOM 173 C LYS 10 33.207 -97.944 -2.011 1.00 0.00 C +ATOM 174 O LYS 10 32.723 -99.071 -2.275 1.00 0.00 O +ATOM 175 N THR 11 33.314 -97.513 -0.694 1.00 0.00 N +ATOM 176 H THR 11 33.703 -96.599 -0.508 1.00 0.00 H +ATOM 177 CA THR 11 32.898 -98.349 0.466 1.00 0.00 C +ATOM 178 HA THR 11 33.208 -99.375 0.272 1.00 0.00 H +ATOM 179 CB THR 11 33.655 -97.924 1.744 1.00 0.00 C +ATOM 180 HB THR 11 33.382 -96.901 2.001 1.00 0.00 H +ATOM 181 CG2 THR 11 33.385 -98.912 2.893 1.00 0.00 C +ATOM 182 HG21 THR 11 33.667 -99.910 2.556 1.00 0.00 H +ATOM 183 HG22 THR 11 32.352 -98.822 3.228 1.00 0.00 H +ATOM 184 HG23 THR 11 33.848 -98.545 3.809 1.00 0.00 H +ATOM 185 OG1 THR 11 34.980 -97.861 1.431 1.00 0.00 O +ATOM 186 HG1 THR 11 35.242 -97.154 2.024 1.00 0.00 H +ATOM 187 C THR 11 31.353 -98.380 0.721 1.00 0.00 C +ATOM 188 O THR 11 30.780 -99.420 1.019 1.00 0.00 O +ATOM 189 N LEU 12 30.675 -97.257 0.441 1.00 0.00 N +ATOM 190 H LEU 12 31.225 -96.475 0.115 1.00 0.00 H +ATOM 191 CA LEU 12 29.285 -97.049 0.680 1.00 0.00 C +ATOM 192 HA LEU 12 29.101 -97.412 1.691 1.00 0.00 H +ATOM 193 CB LEU 12 28.963 -95.525 0.513 1.00 0.00 C +ATOM 194 HB2 LEU 12 29.250 -95.173 -0.478 1.00 0.00 H +ATOM 195 HB3 LEU 12 27.893 -95.317 0.507 1.00 0.00 H +ATOM 196 CG LEU 12 29.583 -94.518 1.481 1.00 0.00 C +ATOM 197 HG LEU 12 30.652 -94.444 1.284 1.00 0.00 H +ATOM 198 CD1 LEU 12 29.129 -93.101 1.110 1.00 0.00 C +ATOM 199 HD11 LEU 12 29.552 -92.878 0.130 1.00 0.00 H +ATOM 200 HD12 LEU 12 29.562 -92.324 1.740 1.00 0.00 H +ATOM 201 HD13 LEU 12 28.040 -93.111 1.066 1.00 0.00 H +ATOM 202 CD2 LEU 12 29.367 -94.965 2.920 1.00 0.00 C +ATOM 203 HD21 LEU 12 28.315 -94.824 3.168 1.00 0.00 H +ATOM 204 HD22 LEU 12 29.944 -94.271 3.532 1.00 0.00 H +ATOM 205 HD23 LEU 12 29.799 -95.902 3.270 1.00 0.00 H +ATOM 206 C LEU 12 28.295 -97.900 -0.191 1.00 0.00 C +ATOM 207 O LEU 12 28.691 -98.433 -1.246 1.00 0.00 O +ATOM 208 N LYS 13 27.025 -97.994 0.162 1.00 0.00 N +ATOM 209 H LYS 13 26.862 -97.638 1.094 1.00 0.00 H +ATOM 210 CA LYS 13 25.924 -98.405 -0.769 1.00 0.00 C +ATOM 211 HA LYS 13 26.326 -98.434 -1.781 1.00 0.00 H +ATOM 212 CB LYS 13 25.310 -99.722 -0.435 1.00 0.00 C +ATOM 213 HB2 LYS 13 26.035-100.303 0.135 1.00 0.00 H +ATOM 214 HB3 LYS 13 24.446 -99.623 0.222 1.00 0.00 H +ATOM 215 CG LYS 13 24.919-100.548 -1.680 1.00 0.00 C +ATOM 216 HG2 LYS 13 24.240-100.011 -2.343 1.00 0.00 H +ATOM 217 HG3 LYS 13 25.826-100.676 -2.271 1.00 0.00 H +ATOM 218 CD LYS 13 24.390-102.004 -1.364 1.00 0.00 C +ATOM 219 HD2 LYS 13 25.125-102.576 -0.797 1.00 0.00 H +ATOM 220 HD3 LYS 13 23.508-101.938 -0.728 1.00 0.00 H +ATOM 221 CE LYS 13 24.059-102.705 -2.632 1.00 0.00 C +ATOM 222 HE2 LYS 13 23.166-102.224 -3.031 1.00 0.00 H +ATOM 223 HE3 LYS 13 24.895-102.557 -3.316 1.00 0.00 H +ATOM 224 NZ LYS 13 23.906-104.154 -2.391 1.00 0.00 N +ATOM 225 HZ1 LYS 13 23.756-104.732 -3.206 1.00 0.00 H +ATOM 226 HZ2 LYS 13 23.095-104.467 -1.877 1.00 0.00 H +ATOM 227 HZ3 LYS 13 24.791-104.463 -2.013 1.00 0.00 H +ATOM 228 C LYS 13 24.865 -97.255 -0.794 1.00 0.00 C +ATOM 229 O LYS 13 24.654 -96.482 0.149 1.00 0.00 O +ATOM 230 N GLY 14 24.127 -97.175 -1.987 1.00 0.00 N +ATOM 231 H GLY 14 24.487 -97.719 -2.759 1.00 0.00 H +ATOM 232 CA GLY 14 22.835 -96.591 -2.119 1.00 0.00 C +ATOM 233 HA2 GLY 14 22.083 -97.380 -2.118 1.00 0.00 H +ATOM 234 HA3 GLY 14 22.598 -95.895 -1.314 1.00 0.00 H +ATOM 235 C GLY 14 22.633 -95.846 -3.437 1.00 0.00 C +ATOM 236 O GLY 14 23.468 -95.809 -4.331 1.00 0.00 O +ATOM 237 N VAL 15 21.367 -95.348 -3.615 1.00 0.00 N +ATOM 238 H VAL 15 20.730 -95.486 -2.843 1.00 0.00 H +ATOM 239 CA VAL 15 20.878 -94.707 -4.872 1.00 0.00 C +ATOM 240 HA VAL 15 21.671 -94.016 -5.156 1.00 0.00 H +ATOM 241 CB VAL 15 20.427 -95.687 -6.008 1.00 0.00 C +ATOM 242 HB VAL 15 21.280 -96.162 -6.493 1.00 0.00 H +ATOM 243 CG1 VAL 15 19.523 -96.806 -5.380 1.00 0.00 C +ATOM 244 HG11 VAL 15 20.028 -97.324 -4.565 1.00 0.00 H +ATOM 245 HG12 VAL 15 18.753 -96.250 -4.846 1.00 0.00 H +ATOM 246 HG13 VAL 15 19.151 -97.440 -6.185 1.00 0.00 H +ATOM 247 CG2 VAL 15 19.564 -95.065 -7.114 1.00 0.00 C +ATOM 248 HG21 VAL 15 18.561 -94.833 -6.757 1.00 0.00 H +ATOM 249 HG22 VAL 15 19.947 -94.090 -7.415 1.00 0.00 H +ATOM 250 HG23 VAL 15 19.540 -95.683 -8.012 1.00 0.00 H +ATOM 251 C VAL 15 19.774 -93.788 -4.383 1.00 0.00 C +ATOM 252 O VAL 15 18.964 -94.140 -3.529 1.00 0.00 O +ATOM 253 N HY1 16 19.776 -92.607 -4.950 1.00 0.00 N +ATOM 254 CA HY1 16 18.705 -91.571 -4.726 1.00 0.00 C +ATOM 255 C HY1 16 18.539 -90.671 -5.984 1.00 0.00 C +ATOM 256 O HY1 16 19.152 -90.970 -6.975 1.00 0.00 O +ATOM 257 CB HY1 16 18.923 -90.757 -3.425 1.00 0.00 C +ATOM 258 CG HY1 16 20.327 -90.259 -3.395 1.00 0.00 C +ATOM 259 CD2 HY1 16 20.818 -89.181 -4.103 1.00 0.00 C +ATOM 260 ND1 HY1 16 21.461 -90.840 -2.819 1.00 0.00 N +ATOM 261 CE1 HY1 16 22.547 -90.140 -3.210 1.00 0.00 C +ATOM 262 NE2 HY1 16 22.189 -89.185 -4.079 1.00 0.00 N +ATOM 263 H HY1 16 20.277 -92.551 -5.825 1.00 0.00 H +ATOM 264 HA HY1 16 17.775 -92.127 -4.611 1.00 0.00 H +ATOM 265 HB2 HY1 16 18.177 -89.985 -3.233 1.00 0.00 H +ATOM 266 HB3 HY1 16 18.929 -91.458 -2.591 1.00 0.00 H +ATOM 267 HD1 HY1 16 21.402 -91.458 -2.023 1.00 0.00 H +ATOM 268 HD2 HY1 16 20.307 -88.536 -4.803 1.00 0.00 H +ATOM 269 HE1 HY1 16 23.556 -90.472 -3.017 1.00 0.00 H +ATOM 270 N THR 17 17.803 -89.554 -5.942 1.00 0.00 N +ATOM 271 H THR 17 17.407 -89.228 -5.072 1.00 0.00 H +ATOM 272 CA THR 17 17.554 -88.605 -7.052 1.00 0.00 C +ATOM 273 HA THR 17 18.405 -88.789 -7.708 1.00 0.00 H +ATOM 274 CB THR 17 16.200 -88.825 -7.683 1.00 0.00 C +ATOM 275 HB THR 17 16.109 -88.094 -8.486 1.00 0.00 H +ATOM 276 CG2 THR 17 15.863 -90.180 -8.250 1.00 0.00 C +ATOM 277 HG21 THR 17 14.884 -90.078 -8.718 1.00 0.00 H +ATOM 278 HG22 THR 17 15.887 -90.930 -7.459 1.00 0.00 H +ATOM 279 HG23 THR 17 16.699 -90.433 -8.901 1.00 0.00 H +ATOM 280 OG1 THR 17 15.228 -88.538 -6.755 1.00 0.00 O +ATOM 281 HG1 THR 17 15.314 -87.586 -6.667 1.00 0.00 H +ATOM 282 C THR 17 17.702 -87.154 -6.642 1.00 0.00 C +ATOM 283 O THR 17 17.601 -86.727 -5.469 1.00 0.00 O +ATOM 284 N HY2 18 18.069 -86.402 -7.655 1.00 0.00 N +ATOM 285 CA HY2 18 18.252 -84.946 -7.689 1.00 0.00 C +ATOM 286 C HY2 18 17.313 -84.220 -8.672 1.00 0.00 C +ATOM 287 O HY2 18 17.365 -84.402 -9.885 1.00 0.00 O +ATOM 288 CB HY2 18 19.705 -84.616 -8.062 1.00 0.00 C +ATOM 289 CG HY2 18 20.667 -85.115 -6.967 1.00 0.00 C +ATOM 290 CD2 HY2 18 21.429 -86.246 -7.020 1.00 0.00 C +ATOM 291 ND1 HY2 18 20.822 -84.630 -5.709 1.00 0.00 N +ATOM 292 CE1 HY2 18 21.768 -85.352 -5.134 1.00 0.00 C +ATOM 293 NE2 HY2 18 22.197 -86.357 -5.891 1.00 0.00 N +ATOM 294 H HY2 18 18.099 -86.919 -8.522 1.00 0.00 H +ATOM 295 HA HY2 18 18.136 -84.590 -6.665 1.00 0.00 H +ATOM 296 HB2 HY2 18 19.966 -84.994 -9.050 1.00 0.00 H +ATOM 297 HB3 HY2 18 19.844 -83.535 -8.091 1.00 0.00 H +ATOM 298 HD1 HY2 18 20.305 -83.884 -5.265 1.00 0.00 H +ATOM 299 HD2 HY2 18 21.492 -86.986 -7.804 1.00 0.00 H +ATOM 300 HE1 HY2 18 22.098 -85.277 -4.108 1.00 0.00 H +ATOM 301 N GLU 19 16.425 -83.470 -8.041 1.00 0.00 N +ATOM 302 H GLU 19 16.326 -83.468 -7.036 1.00 0.00 H +ATOM 303 CA GLU 19 15.612 -82.532 -8.833 1.00 0.00 C +ATOM 304 HA GLU 19 15.308 -83.097 -9.714 1.00 0.00 H +ATOM 305 CB GLU 19 14.413 -82.083 -7.946 1.00 0.00 C +ATOM 306 HB2 GLU 19 13.737 -82.892 -7.669 1.00 0.00 H +ATOM 307 HB3 GLU 19 14.683 -81.729 -6.951 1.00 0.00 H +ATOM 308 CG GLU 19 13.594 -80.995 -8.686 1.00 0.00 C +ATOM 309 HG2 GLU 19 12.624 -81.040 -8.192 1.00 0.00 H +ATOM 310 HG3 GLU 19 14.051 -80.030 -8.470 1.00 0.00 H +ATOM 311 CD GLU 19 13.315 -81.269 -10.163 1.00 0.00 C +ATOM 312 OE1 GLU 19 13.381 -80.373 -11.030 1.00 0.00 O +ATOM 313 OE2 GLU 19 13.083 -82.420 -10.513 1.00 0.00 O +ATOM 314 C GLU 19 16.449 -81.390 -9.456 1.00 0.00 C +ATOM 315 O GLU 19 17.164 -80.695 -8.743 1.00 0.00 O +ATOM 316 N ALA 20 16.420 -81.418 -10.836 1.00 0.00 N +ATOM 317 H ALA 20 15.655 -81.905 -11.281 1.00 0.00 H +ATOM 318 CA ALA 20 17.282 -80.691 -11.785 1.00 0.00 C +ATOM 319 HA ALA 20 17.631 -79.732 -11.401 1.00 0.00 H +ATOM 320 CB ALA 20 18.579 -81.539 -11.940 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.182 -81.429 -11.038 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.115 -81.118 -12.790 1.00 0.00 H +ATOM 323 HB3 ALA 20 18.303 -82.574 -12.140 1.00 0.00 H +ATOM 324 C ALA 20 16.456 -80.252 -13.046 1.00 0.00 C +ATOM 325 O ALA 20 15.700 -81.034 -13.624 1.00 0.00 O +ATOM 326 N VAL 21 16.724 -79.046 -13.503 1.00 0.00 N +ATOM 327 H VAL 21 17.183 -78.470 -12.812 1.00 0.00 H +ATOM 328 CA VAL 21 16.105 -78.400 -14.665 1.00 0.00 C +ATOM 329 HA VAL 21 15.042 -78.628 -14.747 1.00 0.00 H +ATOM 330 CB VAL 21 16.256 -76.900 -14.405 1.00 0.00 C +ATOM 331 HB VAL 21 15.945 -76.700 -13.380 1.00 0.00 H +ATOM 332 CG1 VAL 21 17.738 -76.329 -14.474 1.00 0.00 C +ATOM 333 HG11 VAL 21 18.385 -76.866 -13.781 1.00 0.00 H +ATOM 334 HG12 VAL 21 17.594 -75.302 -14.138 1.00 0.00 H +ATOM 335 HG13 VAL 21 18.235 -76.274 -15.443 1.00 0.00 H +ATOM 336 CG2 VAL 21 15.316 -76.103 -15.267 1.00 0.00 C +ATOM 337 HG21 VAL 21 14.297 -76.277 -14.922 1.00 0.00 H +ATOM 338 HG22 VAL 21 15.450 -76.334 -16.324 1.00 0.00 H +ATOM 339 HG23 VAL 21 15.624 -75.066 -15.135 1.00 0.00 H +ATOM 340 C VAL 21 16.767 -78.909 -15.951 1.00 0.00 C +ATOM 341 O VAL 21 16.074 -78.833 -16.983 1.00 0.00 O +ATOM 342 N ASP 22 17.887 -79.606 -15.953 1.00 0.00 N +ATOM 343 H ASP 22 18.542 -79.463 -15.198 1.00 0.00 H +ATOM 344 CA ASP 22 18.521 -80.345 -17.055 1.00 0.00 C +ATOM 345 HA ASP 22 17.806 -81.057 -17.467 1.00 0.00 H +ATOM 346 CB ASP 22 18.888 -79.364 -18.181 1.00 0.00 C +ATOM 347 HB2 ASP 22 17.970 -78.837 -18.443 1.00 0.00 H +ATOM 348 HB3 ASP 22 19.726 -78.735 -17.882 1.00 0.00 H +ATOM 349 CG ASP 22 19.322 -80.039 -19.504 1.00 0.00 C +ATOM 350 OD1 ASP 22 19.088 -81.229 -19.805 1.00 0.00 O +ATOM 351 OD2 ASP 22 19.862 -79.356 -20.406 1.00 0.00 O +ATOM 352 C ASP 22 19.768 -81.124 -16.601 1.00 0.00 C +ATOM 353 O ASP 22 20.262 -80.957 -15.494 1.00 0.00 O +ATOM 354 N ALA 23 20.315 -82.021 -17.433 1.00 0.00 N +ATOM 355 H ALA 23 20.053 -82.073 -18.407 1.00 0.00 H +ATOM 356 CA ALA 23 21.369 -82.966 -17.042 1.00 0.00 C +ATOM 357 HA ALA 23 21.146 -83.639 -16.214 1.00 0.00 H +ATOM 358 CB ALA 23 21.749 -83.931 -18.250 1.00 0.00 C +ATOM 359 HB1 ALA 23 21.277 -84.913 -18.230 1.00 0.00 H +ATOM 360 HB2 ALA 23 22.812 -84.172 -18.275 1.00 0.00 H +ATOM 361 HB3 ALA 23 21.400 -83.469 -19.174 1.00 0.00 H +ATOM 362 C ALA 23 22.657 -82.173 -16.647 1.00 0.00 C +ATOM 363 O ALA 23 23.513 -82.680 -15.914 1.00 0.00 O +ATOM 364 N ALA 24 22.923 -81.031 -17.224 1.00 0.00 N +ATOM 365 H ALA 24 22.510 -80.847 -18.127 1.00 0.00 H +ATOM 366 CA ALA 24 24.006 -80.199 -16.705 1.00 0.00 C +ATOM 367 HA ALA 24 24.983 -80.631 -16.918 1.00 0.00 H +ATOM 368 CB ALA 24 23.858 -78.891 -17.419 1.00 0.00 C +ATOM 369 HB1 ALA 24 24.709 -78.243 -17.207 1.00 0.00 H +ATOM 370 HB2 ALA 24 22.978 -78.368 -17.046 1.00 0.00 H +ATOM 371 HB3 ALA 24 23.710 -79.094 -18.479 1.00 0.00 H +ATOM 372 C ALA 24 23.897 -80.018 -15.236 1.00 0.00 C +ATOM 373 O ALA 24 24.856 -80.180 -14.468 1.00 0.00 O +ATOM 374 N GLU 25 22.679 -79.672 -14.732 1.00 0.00 N +ATOM 375 H GLU 25 21.900 -79.746 -15.371 1.00 0.00 H +ATOM 376 CA GLU 25 22.427 -79.307 -13.339 1.00 0.00 C +ATOM 377 HA GLU 25 23.289 -78.739 -12.990 1.00 0.00 H +ATOM 378 CB GLU 25 21.163 -78.514 -13.289 1.00 0.00 C +ATOM 379 HB2 GLU 25 21.171 -77.708 -14.022 1.00 0.00 H +ATOM 380 HB3 GLU 25 20.298 -79.120 -13.557 1.00 0.00 H +ATOM 381 CG GLU 25 20.850 -77.842 -11.942 1.00 0.00 C +ATOM 382 HG2 GLU 25 19.841 -77.431 -11.912 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.827 -78.581 -11.141 1.00 0.00 H +ATOM 384 CD GLU 25 21.895 -76.813 -11.415 1.00 0.00 C +ATOM 385 OE1 GLU 25 22.995 -76.660 -12.007 1.00 0.00 O +ATOM 386 OE2 GLU 25 21.546 -76.123 -10.467 1.00 0.00 O +ATOM 387 C GLU 25 22.456 -80.563 -12.368 1.00 0.00 C +ATOM 388 O GLU 25 22.920 -80.544 -11.204 1.00 0.00 O +ATOM 389 N ALA 26 22.038 -81.730 -12.815 1.00 0.00 N +ATOM 390 H ALA 26 21.868 -81.727 -13.810 1.00 0.00 H +ATOM 391 CA ALA 26 22.154 -83.037 -12.252 1.00 0.00 C +ATOM 392 HA ALA 26 21.780 -82.944 -11.232 1.00 0.00 H +ATOM 393 CB ALA 26 21.242 -84.009 -13.103 1.00 0.00 C +ATOM 394 HB1 ALA 26 20.272 -83.545 -13.283 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.043 -84.922 -12.542 1.00 0.00 H +ATOM 396 HB3 ALA 26 21.625 -84.101 -14.119 1.00 0.00 H +ATOM 397 C ALA 26 23.616 -83.574 -12.104 1.00 0.00 C +ATOM 398 O ALA 26 24.058 -84.137 -11.121 1.00 0.00 O +ATOM 399 N GLU 27 24.428 -83.275 -13.081 1.00 0.00 N +ATOM 400 H GLU 27 24.082 -82.964 -13.977 1.00 0.00 H +ATOM 401 CA GLU 27 25.873 -83.634 -13.013 1.00 0.00 C +ATOM 402 HA GLU 27 25.991 -84.679 -12.728 1.00 0.00 H +ATOM 403 CB GLU 27 26.535 -83.623 -14.373 1.00 0.00 C +ATOM 404 HB2 GLU 27 25.873 -84.118 -15.083 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.644 -82.611 -14.762 1.00 0.00 H +ATOM 406 CG GLU 27 27.879 -84.361 -14.545 1.00 0.00 C +ATOM 407 HG2 GLU 27 28.554 -83.741 -13.954 1.00 0.00 H +ATOM 408 HG3 GLU 27 27.867 -85.323 -14.033 1.00 0.00 H +ATOM 409 CD GLU 27 28.477 -84.565 -15.977 1.00 0.00 C +ATOM 410 OE1 GLU 27 28.276 -83.726 -16.873 1.00 0.00 O +ATOM 411 OE2 GLU 27 29.291 -85.484 -16.225 1.00 0.00 O +ATOM 412 C GLU 27 26.675 -82.855 -12.004 1.00 0.00 C +ATOM 413 O GLU 27 27.556 -83.410 -11.359 1.00 0.00 O +ATOM 414 N LYS 28 26.219 -81.598 -11.784 1.00 0.00 N +ATOM 415 H LYS 28 25.359 -81.401 -12.276 1.00 0.00 H +ATOM 416 CA LYS 28 26.609 -80.705 -10.709 1.00 0.00 C +ATOM 417 HA LYS 28 27.695 -80.743 -10.621 1.00 0.00 H +ATOM 418 CB LYS 28 26.048 -79.324 -10.868 1.00 0.00 C +ATOM 419 HB2 LYS 28 26.059 -79.063 -11.926 1.00 0.00 H +ATOM 420 HB3 LYS 28 25.026 -79.221 -10.504 1.00 0.00 H +ATOM 421 CG LYS 28 26.803 -78.262 -10.161 1.00 0.00 C +ATOM 422 HG2 LYS 28 26.999 -78.589 -9.140 1.00 0.00 H +ATOM 423 HG3 LYS 28 27.745 -78.196 -10.705 1.00 0.00 H +ATOM 424 CD LYS 28 26.015 -76.937 -10.142 1.00 0.00 C +ATOM 425 HD2 LYS 28 26.713 -76.148 -9.863 1.00 0.00 H +ATOM 426 HD3 LYS 28 25.617 -76.634 -11.111 1.00 0.00 H +ATOM 427 CE LYS 28 24.938 -76.779 -9.092 1.00 0.00 C +ATOM 428 HE2 LYS 28 24.247 -77.623 -9.094 1.00 0.00 H +ATOM 429 HE3 LYS 28 25.423 -76.791 -8.116 1.00 0.00 H +ATOM 430 NZ LYS 28 24.217 -75.465 -9.203 1.00 0.00 N +ATOM 431 HZ1 LYS 28 23.775 -75.543 -10.108 1.00 0.00 H +ATOM 432 HZ2 LYS 28 24.853 -74.683 -9.253 1.00 0.00 H +ATOM 433 HZ3 LYS 28 23.419 -75.295 -8.607 1.00 0.00 H +ATOM 434 C LYS 28 26.151 -81.335 -9.350 1.00 0.00 C +ATOM 435 O LYS 28 27.015 -81.743 -8.567 1.00 0.00 O +ATOM 436 N PHE 29 24.865 -81.528 -9.052 1.00 0.00 N +ATOM 437 H PHE 29 24.172 -81.229 -9.724 1.00 0.00 H +ATOM 438 CA PHE 29 24.394 -82.219 -7.841 1.00 0.00 C +ATOM 439 HA PHE 29 24.837 -81.639 -7.031 1.00 0.00 H +ATOM 440 CB PHE 29 22.863 -82.138 -7.771 1.00 0.00 C +ATOM 441 HB2 PHE 29 22.511 -82.718 -8.624 1.00 0.00 H +ATOM 442 HB3 PHE 29 22.567 -82.429 -6.763 1.00 0.00 H +ATOM 443 CG PHE 29 22.136 -80.856 -8.074 1.00 0.00 C +ATOM 444 CD1 PHE 29 20.965 -80.784 -8.796 1.00 0.00 C +ATOM 445 HD1 PHE 29 20.436 -81.637 -9.197 1.00 0.00 H +ATOM 446 CE1 PHE 29 20.202 -79.595 -8.777 1.00 0.00 C +ATOM 447 HE1 PHE 29 19.240 -79.727 -9.248 1.00 0.00 H +ATOM 448 CZ PHE 29 20.640 -78.463 -8.121 1.00 0.00 C +ATOM 449 HZ PHE 29 20.036 -77.570 -8.196 1.00 0.00 H +ATOM 450 CE2 PHE 29 21.842 -78.499 -7.464 1.00 0.00 C +ATOM 451 HE2 PHE 29 22.213 -77.633 -6.936 1.00 0.00 H +ATOM 452 CD2 PHE 29 22.629 -79.719 -7.460 1.00 0.00 C +ATOM 453 HD2 PHE 29 23.546 -79.666 -6.893 1.00 0.00 H +ATOM 454 C PHE 29 24.873 -83.687 -7.674 1.00 0.00 C +ATOM 455 O PHE 29 24.630 -84.308 -6.684 1.00 0.00 O +ATOM 456 N THR 30 25.432 -84.263 -8.734 1.00 0.00 N +ATOM 457 H THR 30 25.332 -83.795 -9.624 1.00 0.00 H +ATOM 458 CA THR 30 26.236 -85.502 -8.605 1.00 0.00 C +ATOM 459 HA THR 30 25.623 -86.189 -8.020 1.00 0.00 H +ATOM 460 CB THR 30 26.361 -86.163 -9.978 1.00 0.00 C +ATOM 461 HB THR 30 26.457 -85.494 -10.834 1.00 0.00 H +ATOM 462 CG2 THR 30 27.407 -87.240 -10.150 1.00 0.00 C +ATOM 463 HG21 THR 30 28.338 -86.672 -10.176 1.00 0.00 H +ATOM 464 HG22 THR 30 27.446 -87.999 -9.368 1.00 0.00 H +ATOM 465 HG23 THR 30 27.222 -87.776 -11.080 1.00 0.00 H +ATOM 466 OG1 THR 30 25.104 -86.750 -10.174 1.00 0.00 O +ATOM 467 HG1 THR 30 24.513 -85.995 -10.223 1.00 0.00 H +ATOM 468 C THR 30 27.581 -85.401 -7.877 1.00 0.00 C +ATOM 469 O THR 30 27.843 -86.348 -7.161 1.00 0.00 O +ATOM 470 N LYS 31 28.327 -84.376 -8.073 1.00 0.00 N +ATOM 471 H LYS 31 27.861 -83.647 -8.594 1.00 0.00 H +ATOM 472 CA LYS 31 29.754 -84.265 -7.656 1.00 0.00 C +ATOM 473 HA LYS 31 30.064 -85.101 -7.030 1.00 0.00 H +ATOM 474 CB LYS 31 30.635 -84.242 -8.939 1.00 0.00 C +ATOM 475 HB2 LYS 31 31.634 -84.493 -8.580 1.00 0.00 H +ATOM 476 HB3 LYS 31 30.252 -84.971 -9.653 1.00 0.00 H +ATOM 477 CG LYS 31 30.724 -82.881 -9.608 1.00 0.00 C +ATOM 478 HG2 LYS 31 29.700 -82.549 -9.783 1.00 0.00 H +ATOM 479 HG3 LYS 31 31.178 -82.106 -8.991 1.00 0.00 H +ATOM 480 CD LYS 31 31.531 -83.075 -10.901 1.00 0.00 C +ATOM 481 HD2 LYS 31 32.588 -82.904 -10.694 1.00 0.00 H +ATOM 482 HD3 LYS 31 31.500 -84.047 -11.393 1.00 0.00 H +ATOM 483 CE LYS 31 31.132 -81.948 -11.907 1.00 0.00 C +ATOM 484 HE2 LYS 31 30.043 -81.976 -11.950 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.238 -80.940 -11.506 1.00 0.00 H +ATOM 486 NZ LYS 31 31.945 -82.152 -13.105 1.00 0.00 N +ATOM 487 HZ1 LYS 31 32.905 -82.148 -12.792 1.00 0.00 H +ATOM 488 HZ2 LYS 31 31.750 -81.454 -13.809 1.00 0.00 H +ATOM 489 HZ3 LYS 31 31.845 -83.057 -13.542 1.00 0.00 H +ATOM 490 C LYS 31 30.051 -83.074 -6.793 1.00 0.00 C +ATOM 491 O LYS 31 31.191 -82.892 -6.386 1.00 0.00 O +ATOM 492 N ALA 32 29.097 -82.244 -6.391 1.00 0.00 N +ATOM 493 H ALA 32 28.125 -82.371 -6.633 1.00 0.00 H +ATOM 494 CA ALA 32 29.379 -81.000 -5.661 1.00 0.00 C +ATOM 495 HA ALA 32 30.133 -80.404 -6.176 1.00 0.00 H +ATOM 496 CB ALA 32 28.237 -80.054 -5.840 1.00 0.00 C +ATOM 497 HB1 ALA 32 28.276 -79.645 -6.850 1.00 0.00 H +ATOM 498 HB2 ALA 32 27.284 -80.540 -5.631 1.00 0.00 H +ATOM 499 HB3 ALA 32 28.407 -79.138 -5.275 1.00 0.00 H +ATOM 500 C ALA 32 29.818 -81.217 -4.150 1.00 0.00 C +ATOM 501 O ALA 32 30.452 -80.343 -3.589 1.00 0.00 O +ATOM 502 N ASP 33 29.490 -82.287 -3.511 1.00 0.00 N +ATOM 503 H ASP 33 29.135 -83.042 -4.080 1.00 0.00 H +ATOM 504 CA ASP 33 30.077 -82.624 -2.211 1.00 0.00 C +ATOM 505 HA ASP 33 30.322 -81.705 -1.679 1.00 0.00 H +ATOM 506 CB ASP 33 28.995 -83.209 -1.253 1.00 0.00 C +ATOM 507 HB2 ASP 33 29.416 -83.447 -0.276 1.00 0.00 H +ATOM 508 HB3 ASP 33 28.120 -82.560 -1.208 1.00 0.00 H +ATOM 509 CG ASP 33 28.479 -84.568 -1.759 1.00 0.00 C +ATOM 510 OD1 ASP 33 28.863 -85.631 -1.283 1.00 0.00 O +ATOM 511 OD2 ASP 33 27.665 -84.598 -2.711 1.00 0.00 O +ATOM 512 C ASP 33 31.307 -83.534 -2.268 1.00 0.00 C +ATOM 513 O ASP 33 32.078 -83.638 -1.313 1.00 0.00 O +ATOM 514 N ALA 34 31.496 -84.201 -3.424 1.00 0.00 N +ATOM 515 H ALA 34 30.779 -84.243 -4.134 1.00 0.00 H +ATOM 516 CA ALA 34 32.733 -84.860 -3.774 1.00 0.00 C +ATOM 517 HA ALA 34 32.951 -85.596 -3.000 1.00 0.00 H +ATOM 518 CB ALA 34 32.310 -85.804 -4.929 1.00 0.00 C +ATOM 519 HB1 ALA 34 33.114 -86.440 -5.299 1.00 0.00 H +ATOM 520 HB2 ALA 34 31.950 -85.307 -5.830 1.00 0.00 H +ATOM 521 HB3 ALA 34 31.480 -86.385 -4.526 1.00 0.00 H +ATOM 522 C ALA 34 33.831 -83.836 -4.032 1.00 0.00 C +ATOM 523 O ALA 34 34.984 -84.065 -3.594 1.00 0.00 O +ATOM 524 N ASN 35 33.603 -82.701 -4.642 1.00 0.00 N +ATOM 525 H ASN 35 32.709 -82.536 -5.082 1.00 0.00 H +ATOM 526 CA ASN 35 34.538 -81.623 -4.774 1.00 0.00 C +ATOM 527 HA ASN 35 35.429 -82.022 -5.259 1.00 0.00 H +ATOM 528 CB ASN 35 33.786 -80.524 -5.542 1.00 0.00 C +ATOM 529 HB2 ASN 35 33.242 -80.826 -6.437 1.00 0.00 H +ATOM 530 HB3 ASN 35 33.030 -80.056 -4.911 1.00 0.00 H +ATOM 531 CG ASN 35 34.593 -79.341 -5.873 1.00 0.00 C +ATOM 532 OD1 ASN 35 35.286 -78.723 -5.085 1.00 0.00 O +ATOM 533 ND2 ASN 35 34.514 -78.885 -7.060 1.00 0.00 N +ATOM 534 HD21 ASN 35 33.911 -79.383 -7.699 1.00 0.00 H +ATOM 535 HD22 ASN 35 35.186 -78.189 -7.349 1.00 0.00 H +ATOM 536 C ASN 35 35.101 -81.198 -3.375 1.00 0.00 C +ATOM 537 O ASN 35 36.273 -80.925 -3.302 1.00 0.00 O +ATOM 538 N ASP 36 34.215 -81.026 -2.349 1.00 0.00 N +ATOM 539 H ASP 36 33.242 -81.266 -2.467 1.00 0.00 H +ATOM 540 CA ASP 36 34.549 -80.676 -0.967 1.00 0.00 C +ATOM 541 HA ASP 36 35.275 -79.874 -1.096 1.00 0.00 H +ATOM 542 CB ASP 36 33.265 -80.255 -0.251 1.00 0.00 C +ATOM 543 HB2 ASP 36 32.621 -81.094 0.014 1.00 0.00 H +ATOM 544 HB3 ASP 36 33.587 -79.987 0.755 1.00 0.00 H +ATOM 545 CG ASP 36 32.370 -79.110 -0.745 1.00 0.00 C +ATOM 546 OD1 ASP 36 31.173 -79.106 -0.339 1.00 0.00 O +ATOM 547 OD2 ASP 36 32.744 -78.041 -1.298 1.00 0.00 O +ATOM 548 C ASP 36 35.327 -81.810 -0.260 1.00 0.00 C +ATOM 549 O ASP 36 36.251 -81.454 0.485 1.00 0.00 O +ATOM 550 N LYS 37 34.986 -83.081 -0.445 1.00 0.00 N +ATOM 551 H LYS 37 34.105 -83.272 -0.901 1.00 0.00 H +ATOM 552 CA LYS 37 35.806 -84.166 0.129 1.00 0.00 C +ATOM 553 HA LYS 37 35.848 -84.121 1.217 1.00 0.00 H +ATOM 554 CB LYS 37 34.988 -85.458 -0.215 1.00 0.00 C +ATOM 555 HB2 LYS 37 35.531 -86.397 -0.110 1.00 0.00 H +ATOM 556 HB3 LYS 37 34.731 -85.421 -1.274 1.00 0.00 H +ATOM 557 CG LYS 37 33.690 -85.554 0.636 1.00 0.00 C +ATOM 558 HG2 LYS 37 33.068 -84.667 0.517 1.00 0.00 H +ATOM 559 HG3 LYS 37 33.958 -85.623 1.690 1.00 0.00 H +ATOM 560 CD LYS 37 32.932 -86.857 0.214 1.00 0.00 C +ATOM 561 HD2 LYS 37 32.683 -86.751 -0.842 1.00 0.00 H +ATOM 562 HD3 LYS 37 33.392 -87.797 0.521 1.00 0.00 H +ATOM 563 CE LYS 37 31.625 -87.061 0.863 1.00 0.00 C +ATOM 564 HE2 LYS 37 31.172 -88.005 0.561 1.00 0.00 H +ATOM 565 HE3 LYS 37 31.761 -87.114 1.943 1.00 0.00 H +ATOM 566 NZ LYS 37 30.636 -85.996 0.646 1.00 0.00 N +ATOM 567 HZ1 LYS 37 30.326 -85.814 -0.298 1.00 0.00 H +ATOM 568 HZ2 LYS 37 29.928 -85.893 1.360 1.00 0.00 H +ATOM 569 HZ3 LYS 37 31.143 -85.142 0.828 1.00 0.00 H +ATOM 570 C LYS 37 37.250 -84.222 -0.304 1.00 0.00 C +ATOM 571 O LYS 37 38.032 -84.825 0.368 1.00 0.00 O +ATOM 572 N GLY 38 37.482 -83.648 -1.463 1.00 0.00 N +ATOM 573 H GLY 38 36.686 -83.455 -2.055 1.00 0.00 H +ATOM 574 CA GLY 38 38.757 -83.610 -2.168 1.00 0.00 C +ATOM 575 HA2 GLY 38 38.890 -82.650 -2.668 1.00 0.00 H +ATOM 576 HA3 GLY 38 39.533 -83.657 -1.405 1.00 0.00 H +ATOM 577 C GLY 38 38.999 -84.774 -3.167 1.00 0.00 C +ATOM 578 O GLY 38 40.067 -85.317 -3.239 1.00 0.00 O +ATOM 579 N VAL 39 37.958 -85.187 -3.923 1.00 0.00 N +ATOM 580 H VAL 39 37.062 -84.728 -3.843 1.00 0.00 H +ATOM 581 CA VAL 39 37.854 -86.391 -4.709 1.00 0.00 C +ATOM 582 HA VAL 39 38.222 -87.200 -4.078 1.00 0.00 H +ATOM 583 CB VAL 39 36.369 -86.696 -4.990 1.00 0.00 C +ATOM 584 HB VAL 39 35.786 -85.835 -5.319 1.00 0.00 H +ATOM 585 CG1 VAL 39 36.025 -87.642 -6.120 1.00 0.00 C +ATOM 586 HG11 VAL 39 35.008 -88.027 -6.199 1.00 0.00 H +ATOM 587 HG12 VAL 39 36.457 -88.591 -5.803 1.00 0.00 H +ATOM 588 HG13 VAL 39 36.427 -87.348 -7.089 1.00 0.00 H +ATOM 589 CG2 VAL 39 35.680 -87.237 -3.699 1.00 0.00 C +ATOM 590 HG21 VAL 39 35.878 -86.487 -2.932 1.00 0.00 H +ATOM 591 HG22 VAL 39 36.176 -88.171 -3.438 1.00 0.00 H +ATOM 592 HG23 VAL 39 34.660 -87.575 -3.879 1.00 0.00 H +ATOM 593 C VAL 39 38.570 -86.375 -6.056 1.00 0.00 C +ATOM 594 O VAL 39 38.425 -85.421 -6.883 1.00 0.00 O +ATOM 595 N ASP 40 39.301 -87.453 -6.333 1.00 0.00 N +ATOM 596 H ASP 40 39.311 -88.161 -5.612 1.00 0.00 H +ATOM 597 CA ASP 40 40.034 -87.651 -7.597 1.00 0.00 C +ATOM 598 HA ASP 40 40.339 -86.707 -8.048 1.00 0.00 H +ATOM 599 CB ASP 40 41.261 -88.624 -7.423 1.00 0.00 C +ATOM 600 HB2 ASP 40 40.792 -89.496 -6.968 1.00 0.00 H +ATOM 601 HB3 ASP 40 41.783 -88.890 -8.342 1.00 0.00 H +ATOM 602 CG ASP 40 42.342 -88.174 -6.419 1.00 0.00 C +ATOM 603 OD1 ASP 40 43.030 -87.181 -6.650 1.00 0.00 O +ATOM 604 OD2 ASP 40 42.498 -88.814 -5.360 1.00 0.00 O +ATOM 605 C ASP 40 39.157 -88.306 -8.722 1.00 0.00 C +ATOM 606 O ASP 40 39.552 -88.251 -9.906 1.00 0.00 O +ATOM 607 N GLY 41 37.899 -88.745 -8.480 1.00 0.00 N +ATOM 608 H GLY 41 37.464 -88.448 -7.618 1.00 0.00 H +ATOM 609 CA GLY 41 37.042 -89.393 -9.497 1.00 0.00 C +ATOM 610 HA2 GLY 41 37.684 -90.199 -9.853 1.00 0.00 H +ATOM 611 HA3 GLY 41 36.127 -89.730 -9.009 1.00 0.00 H +ATOM 612 C GLY 41 36.520 -88.496 -10.645 1.00 0.00 C +ATOM 613 O GLY 41 36.667 -87.320 -10.633 1.00 0.00 O +ATOM 614 N GLU 42 35.863 -89.181 -11.596 1.00 0.00 N +ATOM 615 H GLU 42 35.775 -90.185 -11.661 1.00 0.00 H +ATOM 616 CA GLU 42 35.126 -88.499 -12.729 1.00 0.00 C +ATOM 617 HA GLU 42 34.832 -87.535 -12.314 1.00 0.00 H +ATOM 618 CB GLU 42 36.042 -88.184 -13.965 1.00 0.00 C +ATOM 619 HB2 GLU 42 36.883 -87.600 -13.591 1.00 0.00 H +ATOM 620 HB3 GLU 42 36.450 -89.155 -14.245 1.00 0.00 H +ATOM 621 CG GLU 42 35.404 -87.462 -15.172 1.00 0.00 C +ATOM 622 HG2 GLU 42 36.198 -87.317 -15.906 1.00 0.00 H +ATOM 623 HG3 GLU 42 34.653 -88.015 -15.737 1.00 0.00 H +ATOM 624 CD GLU 42 34.676 -86.147 -14.809 1.00 0.00 C +ATOM 625 OE1 GLU 42 35.224 -85.424 -13.906 1.00 0.00 O +ATOM 626 OE2 GLU 42 33.549 -85.907 -15.236 1.00 0.00 O +ATOM 627 C GLU 42 33.885 -89.317 -13.141 1.00 0.00 C +ATOM 628 O GLU 42 33.835 -90.577 -13.093 1.00 0.00 O +ATOM 629 N TRP 43 32.845 -88.586 -13.568 1.00 0.00 N +ATOM 630 H TRP 43 32.952 -87.643 -13.915 1.00 0.00 H +ATOM 631 CA TRP 43 31.447 -89.085 -13.794 1.00 0.00 C +ATOM 632 HA TRP 43 31.244 -89.982 -13.208 1.00 0.00 H +ATOM 633 CB TRP 43 30.463 -88.012 -13.160 1.00 0.00 C +ATOM 634 HB2 TRP 43 30.633 -87.037 -13.617 1.00 0.00 H +ATOM 635 HB3 TRP 43 29.414 -88.219 -13.371 1.00 0.00 H +ATOM 636 CG TRP 43 30.598 -88.075 -11.685 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.833 -88.833 -10.840 1.00 0.00 C +ATOM 638 HD1 TRP 43 29.017 -89.506 -11.059 1.00 0.00 H +ATOM 639 NE1 TRP 43 30.301 -88.753 -9.543 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.965 -89.332 -8.788 1.00 0.00 H +ATOM 641 CE2 TRP 43 31.346 -87.881 -9.472 1.00 0.00 C +ATOM 642 CZ2 TRP 43 32.159 -87.436 -8.393 1.00 0.00 C +ATOM 643 HZ2 TRP 43 31.895 -87.734 -7.389 1.00 0.00 H +ATOM 644 CH2 TRP 43 33.237 -86.576 -8.663 1.00 0.00 C +ATOM 645 HH2 TRP 43 33.781 -86.166 -7.824 1.00 0.00 H +ATOM 646 CZ3 TRP 43 33.507 -86.168 -9.972 1.00 0.00 C +ATOM 647 HZ3 TRP 43 34.249 -85.408 -10.170 1.00 0.00 H +ATOM 648 CE3 TRP 43 32.671 -86.599 -11.051 1.00 0.00 C +ATOM 649 HE3 TRP 43 32.888 -86.229 -12.042 1.00 0.00 H +ATOM 650 CD2 TRP 43 31.652 -87.536 -10.834 1.00 0.00 C +ATOM 651 C TRP 43 30.984 -89.476 -15.202 1.00 0.00 C +ATOM 652 O TRP 43 31.747 -89.252 -16.157 1.00 0.00 O +ATOM 653 N THR 44 29.855 -90.233 -15.354 1.00 0.00 N +ATOM 654 H THR 44 29.460 -90.605 -14.502 1.00 0.00 H +ATOM 655 CA THR 44 29.200 -90.637 -16.640 1.00 0.00 C +ATOM 656 HA THR 44 29.474 -90.012 -17.489 1.00 0.00 H +ATOM 657 CB THR 44 29.687 -92.079 -17.003 1.00 0.00 C +ATOM 658 HB THR 44 30.776 -92.032 -17.016 1.00 0.00 H +ATOM 659 CG2 THR 44 29.196 -93.158 -16.047 1.00 0.00 C +ATOM 660 HG21 THR 44 29.864 -94.000 -16.232 1.00 0.00 H +ATOM 661 HG22 THR 44 28.160 -93.428 -16.248 1.00 0.00 H +ATOM 662 HG23 THR 44 29.319 -92.873 -15.002 1.00 0.00 H +ATOM 663 OG1 THR 44 29.410 -92.542 -18.304 1.00 0.00 O +ATOM 664 HG1 THR 44 30.140 -92.182 -18.813 1.00 0.00 H +ATOM 665 C THR 44 27.685 -90.558 -16.584 1.00 0.00 C +ATOM 666 O THR 44 27.135 -90.735 -15.466 1.00 0.00 O +ATOM 667 N TYR 45 27.014 -90.422 -17.682 1.00 0.00 N +ATOM 668 H TYR 45 27.499 -90.330 -18.563 1.00 0.00 H +ATOM 669 CA TYR 45 25.599 -90.288 -17.748 1.00 0.00 C +ATOM 670 HA TYR 45 25.193 -90.409 -16.744 1.00 0.00 H +ATOM 671 CB TYR 45 25.219 -88.871 -18.135 1.00 0.00 C +ATOM 672 HB2 TYR 45 25.501 -88.214 -17.313 1.00 0.00 H +ATOM 673 HB3 TYR 45 25.703 -88.608 -19.076 1.00 0.00 H +ATOM 674 CG TYR 45 23.741 -88.648 -18.345 1.00 0.00 C +ATOM 675 CD1 TYR 45 22.812 -88.913 -17.276 1.00 0.00 C +ATOM 676 HD1 TYR 45 23.153 -89.162 -16.282 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.440 -88.568 -17.468 1.00 0.00 C +ATOM 678 HE1 TYR 45 20.762 -88.662 -16.634 1.00 0.00 H +ATOM 679 CZ TYR 45 20.993 -88.058 -18.675 1.00 0.00 C +ATOM 680 OH TYR 45 19.690 -87.783 -18.858 1.00 0.00 O +ATOM 681 HH TYR 45 19.596 -87.383 -19.725 1.00 0.00 H +ATOM 682 CE2 TYR 45 21.871 -87.924 -19.790 1.00 0.00 C +ATOM 683 HE2 TYR 45 21.528 -87.638 -20.773 1.00 0.00 H +ATOM 684 CD2 TYR 45 23.283 -88.190 -19.560 1.00 0.00 C +ATOM 685 HD2 TYR 45 23.968 -88.058 -20.384 1.00 0.00 H +ATOM 686 C TYR 45 25.056 -91.453 -18.571 1.00 0.00 C +ATOM 687 O TYR 45 25.503 -91.719 -19.687 1.00 0.00 O +ATOM 688 N ASP 46 23.955 -92.072 -18.193 1.00 0.00 N +ATOM 689 H ASP 46 23.602 -91.794 -17.289 1.00 0.00 H +ATOM 690 CA ASP 46 23.118 -92.872 -19.108 1.00 0.00 C +ATOM 691 HA ASP 46 23.589 -92.879 -20.091 1.00 0.00 H +ATOM 692 CB ASP 46 22.876 -94.314 -18.595 1.00 0.00 C +ATOM 693 HB2 ASP 46 23.895 -94.642 -18.392 1.00 0.00 H +ATOM 694 HB3 ASP 46 22.338 -94.307 -17.647 1.00 0.00 H +ATOM 695 CG ASP 46 22.177 -95.214 -19.623 1.00 0.00 C +ATOM 696 OD1 ASP 46 21.265 -95.928 -19.224 1.00 0.00 O +ATOM 697 OD2 ASP 46 22.486 -95.098 -20.850 1.00 0.00 O +ATOM 698 C ASP 46 21.771 -92.131 -19.370 1.00 0.00 C +ATOM 699 O ASP 46 20.816 -92.037 -18.539 1.00 0.00 O +ATOM 700 N ASP 47 21.603 -91.517 -20.509 1.00 0.00 N +ATOM 701 H ASP 47 22.253 -91.634 -21.274 1.00 0.00 H +ATOM 702 CA ASP 47 20.325 -90.875 -20.896 1.00 0.00 C +ATOM 703 HA ASP 47 20.150 -90.144 -20.107 1.00 0.00 H +ATOM 704 CB ASP 47 20.583 -90.030 -22.187 1.00 0.00 C +ATOM 705 HB2 ASP 47 21.477 -89.447 -21.967 1.00 0.00 H +ATOM 706 HB3 ASP 47 20.893 -90.578 -23.077 1.00 0.00 H +ATOM 707 CG ASP 47 19.410 -89.180 -22.489 1.00 0.00 C +ATOM 708 OD1 ASP 47 19.177 -88.398 -21.550 1.00 0.00 O +ATOM 709 OD2 ASP 47 18.837 -89.223 -23.605 1.00 0.00 O +ATOM 710 C ASP 47 19.128 -91.784 -21.032 1.00 0.00 C +ATOM 711 O ASP 47 17.952 -91.393 -20.821 1.00 0.00 O +ATOM 712 N ALA 48 19.382 -93.059 -21.356 1.00 0.00 N +ATOM 713 H ALA 48 20.329 -93.204 -21.674 1.00 0.00 H +ATOM 714 CA ALA 48 18.312 -94.149 -21.383 1.00 0.00 C +ATOM 715 HA ALA 48 17.506 -93.766 -22.010 1.00 0.00 H +ATOM 716 CB ALA 48 18.907 -95.437 -21.922 1.00 0.00 C +ATOM 717 HB1 ALA 48 18.084 -96.059 -22.273 1.00 0.00 H +ATOM 718 HB2 ALA 48 19.340 -95.984 -21.084 1.00 0.00 H +ATOM 719 HB3 ALA 48 19.484 -95.299 -22.836 1.00 0.00 H +ATOM 720 C ALA 48 17.673 -94.398 -19.978 1.00 0.00 C +ATOM 721 O ALA 48 16.549 -94.828 -19.875 1.00 0.00 O +ATOM 722 N THR 49 18.364 -94.098 -18.894 1.00 0.00 N +ATOM 723 H THR 49 19.232 -93.634 -19.120 1.00 0.00 H +ATOM 724 CA THR 49 17.893 -94.471 -17.507 1.00 0.00 C +ATOM 725 HA THR 49 16.824 -94.674 -17.557 1.00 0.00 H +ATOM 726 CB THR 49 18.686 -95.654 -16.840 1.00 0.00 C +ATOM 727 HB THR 49 18.397 -95.584 -15.791 1.00 0.00 H +ATOM 728 CG2 THR 49 18.424 -97.120 -17.344 1.00 0.00 C +ATOM 729 HG21 THR 49 17.356 -97.320 -17.254 1.00 0.00 H +ATOM 730 HG22 THR 49 19.025 -97.802 -16.743 1.00 0.00 H +ATOM 731 HG23 THR 49 18.693 -97.144 -18.400 1.00 0.00 H +ATOM 732 OG1 THR 49 20.039 -95.427 -16.944 1.00 0.00 O +ATOM 733 HG1 THR 49 20.311 -95.518 -17.860 1.00 0.00 H +ATOM 734 C THR 49 18.027 -93.258 -16.601 1.00 0.00 C +ATOM 735 O THR 49 17.858 -93.336 -15.385 1.00 0.00 O +ATOM 736 N LYS 50 18.394 -92.109 -17.113 1.00 0.00 N +ATOM 737 H LYS 50 18.607 -92.060 -18.099 1.00 0.00 H +ATOM 738 CA LYS 50 18.641 -90.839 -16.493 1.00 0.00 C +ATOM 739 HA LYS 50 19.172 -90.262 -17.250 1.00 0.00 H +ATOM 740 CB LYS 50 17.275 -90.257 -16.156 1.00 0.00 C +ATOM 741 HB2 LYS 50 16.783 -90.842 -15.379 1.00 0.00 H +ATOM 742 HB3 LYS 50 17.373 -89.297 -15.649 1.00 0.00 H +ATOM 743 CG LYS 50 16.260 -90.142 -17.325 1.00 0.00 C +ATOM 744 HG2 LYS 50 16.045 -91.138 -17.711 1.00 0.00 H +ATOM 745 HG3 LYS 50 15.348 -89.732 -16.892 1.00 0.00 H +ATOM 746 CD LYS 50 16.666 -89.169 -18.397 1.00 0.00 C +ATOM 747 HD2 LYS 50 16.516 -88.190 -17.942 1.00 0.00 H +ATOM 748 HD3 LYS 50 17.734 -89.198 -18.610 1.00 0.00 H +ATOM 749 CE LYS 50 15.787 -89.250 -19.626 1.00 0.00 C +ATOM 750 HE2 LYS 50 15.380 -90.235 -19.852 1.00 0.00 H +ATOM 751 HE3 LYS 50 14.855 -88.690 -19.543 1.00 0.00 H +ATOM 752 NZ LYS 50 16.454 -88.757 -20.820 1.00 0.00 N +ATOM 753 HZ1 LYS 50 16.322 -87.761 -20.916 1.00 0.00 H +ATOM 754 HZ2 LYS 50 16.006 -88.999 -21.692 1.00 0.00 H +ATOM 755 HZ3 LYS 50 17.437 -88.978 -20.893 1.00 0.00 H +ATOM 756 C LYS 50 19.563 -90.789 -15.316 1.00 0.00 C +ATOM 757 O LYS 50 19.460 -89.987 -14.409 1.00 0.00 O +ATOM 758 N THR 51 20.589 -91.709 -15.350 1.00 0.00 N +ATOM 759 H THR 51 20.749 -92.297 -16.156 1.00 0.00 H +ATOM 760 CA THR 51 21.429 -91.967 -14.222 1.00 0.00 C +ATOM 761 HA THR 51 20.984 -91.579 -13.305 1.00 0.00 H +ATOM 762 CB THR 51 21.480 -93.477 -13.900 1.00 0.00 C +ATOM 763 HB THR 51 21.853 -94.030 -14.762 1.00 0.00 H +ATOM 764 CG2 THR 51 22.289 -93.792 -12.642 1.00 0.00 C +ATOM 765 HG21 THR 51 22.050 -94.813 -12.344 1.00 0.00 H +ATOM 766 HG22 THR 51 22.063 -93.060 -11.866 1.00 0.00 H +ATOM 767 HG23 THR 51 23.355 -93.687 -12.844 1.00 0.00 H +ATOM 768 OG1 THR 51 20.206 -93.986 -13.526 1.00 0.00 O +ATOM 769 HG1 THR 51 19.630 -93.641 -14.212 1.00 0.00 H +ATOM 770 C THR 51 22.800 -91.398 -14.407 1.00 0.00 C +ATOM 771 O THR 51 23.462 -91.734 -15.365 1.00 0.00 O +ATOM 772 N PHE 52 23.282 -90.751 -13.357 1.00 0.00 N +ATOM 773 H PHE 52 22.695 -90.583 -12.552 1.00 0.00 H +ATOM 774 CA PHE 52 24.653 -90.434 -13.150 1.00 0.00 C +ATOM 775 HA PHE 52 25.175 -90.499 -14.105 1.00 0.00 H +ATOM 776 CB PHE 52 24.779 -89.010 -12.592 1.00 0.00 C +ATOM 777 HB2 PHE 52 24.272 -88.864 -11.638 1.00 0.00 H +ATOM 778 HB3 PHE 52 25.842 -88.851 -12.408 1.00 0.00 H +ATOM 779 CG PHE 52 24.291 -87.940 -13.639 1.00 0.00 C +ATOM 780 CD1 PHE 52 22.920 -87.601 -13.642 1.00 0.00 C +ATOM 781 HD1 PHE 52 22.347 -87.916 -12.782 1.00 0.00 H +ATOM 782 CE1 PHE 52 22.366 -86.778 -14.618 1.00 0.00 C +ATOM 783 HE1 PHE 52 21.298 -86.619 -14.635 1.00 0.00 H +ATOM 784 CZ PHE 52 23.251 -86.274 -15.639 1.00 0.00 C +ATOM 785 HZ PHE 52 22.790 -85.720 -16.444 1.00 0.00 H +ATOM 786 CE2 PHE 52 24.617 -86.554 -15.603 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.211 -86.099 -16.381 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.175 -87.332 -14.560 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.238 -87.521 -14.548 1.00 0.00 H +ATOM 790 C PHE 52 25.333 -91.434 -12.262 1.00 0.00 C +ATOM 791 O PHE 52 24.888 -91.679 -11.080 1.00 0.00 O +ATOM 792 N THR 53 26.500 -91.876 -12.634 1.00 0.00 N +ATOM 793 H THR 53 26.839 -91.611 -13.548 1.00 0.00 H +ATOM 794 CA THR 53 27.460 -92.652 -11.790 1.00 0.00 C +ATOM 795 HA THR 53 27.198 -92.509 -10.742 1.00 0.00 H +ATOM 796 CB THR 53 27.461 -94.153 -12.356 1.00 0.00 C +ATOM 797 HB THR 53 28.140 -94.831 -11.838 1.00 0.00 H +ATOM 798 CG2 THR 53 26.066 -94.762 -12.190 1.00 0.00 C +ATOM 799 HG21 THR 53 26.147 -95.816 -12.457 1.00 0.00 H +ATOM 800 HG22 THR 53 25.367 -94.257 -12.856 1.00 0.00 H +ATOM 801 HG23 THR 53 25.660 -94.632 -11.186 1.00 0.00 H +ATOM 802 OG1 THR 53 27.763 -94.344 -13.714 1.00 0.00 O +ATOM 803 HG1 THR 53 28.317 -95.111 -13.876 1.00 0.00 H +ATOM 804 C THR 53 28.861 -92.044 -11.808 1.00 0.00 C +ATOM 805 O THR 53 29.178 -91.322 -12.747 1.00 0.00 O +ATOM 806 N VAL 54 29.662 -92.315 -10.726 1.00 0.00 N +ATOM 807 H VAL 54 29.360 -92.813 -9.901 1.00 0.00 H +ATOM 808 CA VAL 54 31.118 -92.047 -10.754 1.00 0.00 C +ATOM 809 HA VAL 54 31.227 -91.087 -11.258 1.00 0.00 H +ATOM 810 CB VAL 54 31.756 -91.933 -9.347 1.00 0.00 C +ATOM 811 HB VAL 54 31.186 -91.265 -8.701 1.00 0.00 H +ATOM 812 CG1 VAL 54 31.875 -93.166 -8.570 1.00 0.00 C +ATOM 813 HG11 VAL 54 32.467 -93.877 -9.146 1.00 0.00 H +ATOM 814 HG12 VAL 54 30.910 -93.563 -8.254 1.00 0.00 H +ATOM 815 HG13 VAL 54 32.445 -92.965 -7.663 1.00 0.00 H +ATOM 816 CG2 VAL 54 33.141 -91.318 -9.447 1.00 0.00 C +ATOM 817 HG21 VAL 54 33.027 -90.549 -10.212 1.00 0.00 H +ATOM 818 HG22 VAL 54 33.855 -92.047 -9.831 1.00 0.00 H +ATOM 819 HG23 VAL 54 33.570 -91.017 -8.491 1.00 0.00 H +ATOM 820 C VAL 54 31.747 -93.236 -11.489 1.00 0.00 C +ATOM 821 O VAL 54 31.154 -94.302 -11.502 1.00 0.00 O +ATOM 822 N THR 55 32.825 -93.071 -12.225 1.00 0.00 N +ATOM 823 H THR 55 33.222 -92.143 -12.267 1.00 0.00 H +ATOM 824 CA THR 55 33.448 -94.137 -12.971 1.00 0.00 C +ATOM 825 HA THR 55 32.819 -94.901 -13.427 1.00 0.00 H +ATOM 826 CB THR 55 34.250 -93.589 -14.144 1.00 0.00 C +ATOM 827 HB THR 55 34.813 -94.469 -14.453 1.00 0.00 H +ATOM 828 CG2 THR 55 33.274 -93.104 -15.236 1.00 0.00 C +ATOM 829 HG21 THR 55 33.841 -93.067 -16.167 1.00 0.00 H +ATOM 830 HG22 THR 55 32.881 -92.184 -14.806 1.00 0.00 H +ATOM 831 HG23 THR 55 32.420 -93.781 -15.227 1.00 0.00 H +ATOM 832 OG1 THR 55 35.179 -92.569 -13.759 1.00 0.00 O +ATOM 833 HG1 THR 55 34.698 -91.752 -13.610 1.00 0.00 H +ATOM 834 C THR 55 34.333 -95.037 -12.158 1.00 0.00 C +ATOM 835 O THR 55 34.939 -95.972 -12.713 1.00 0.00 O +ATOM 836 N GLU 56 34.624 -94.752 -10.883 1.00 0.00 N +ATOM 837 H GLU 56 34.153 -93.950 -10.487 1.00 0.00 H +ATOM 838 CA GLU 56 35.479 -95.643 -10.031 1.00 0.00 C +ATOM 839 HA GLU 56 36.244 -96.128 -10.637 1.00 0.00 H +ATOM 840 CB GLU 56 36.171 -94.743 -8.949 1.00 0.00 C +ATOM 841 HB2 GLU 56 36.595 -93.841 -9.390 1.00 0.00 H +ATOM 842 HB3 GLU 56 35.423 -94.372 -8.248 1.00 0.00 H +ATOM 843 CG GLU 56 37.240 -95.427 -8.121 1.00 0.00 C +ATOM 844 HG2 GLU 56 36.764 -96.258 -7.601 1.00 0.00 H +ATOM 845 HG3 GLU 56 38.020 -95.859 -8.748 1.00 0.00 H +ATOM 846 CD GLU 56 37.882 -94.614 -6.927 1.00 0.00 C +ATOM 847 OE1 GLU 56 37.631 -93.416 -6.824 1.00 0.00 O +ATOM 848 OE2 GLU 56 38.755 -95.207 -6.239 1.00 0.00 O +ATOM 849 C GLU 56 34.611 -96.753 -9.416 1.00 0.00 C +ATOM 850 O GLU 56 33.525 -96.464 -8.904 1.00 0.00 O +ATOM 851 OXT GLU 56 34.987 -97.898 -9.681 1.00 0.00 O +ATOM 852 ZN ZN1 57 23.286 -87.843 -5.235 1.00 0.00 ZN +ATOM 853 N AN1 58 24.247 -86.891 -3.605 1.00 0.00 N +ATOM 854 C AN1 58 25.528 -86.334 -1.430 1.00 0.00 C +ATOM 855 C1 AN1 58 24.831 -86.692 -2.639 1.00 0.00 C +ATOM 856 H AN1 58 24.954 -86.539 -0.519 1.00 0.00 H +ATOM 857 H1 AN1 58 25.675 -85.271 -1.204 1.00 0.00 H +ATOM 858 H2 AN1 58 26.505 -86.827 -1.353 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 25.354 -89.992 -1.364 1.00 0.00 N +ATOM 860 N2 AZI 59 26.182 -89.857 -2.203 1.00 0.00 N +ATOM 861 N3 AZI 59 27.156 -89.740 -3.029 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/pdbs_rename/cluster101.pdb b/tests/nsga2/pdbs_rename/cluster101.pdb new file mode 100644 index 0000000..e07eafb --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster101.pdb @@ -0,0 +1,864 @@ +CRYST1 51.602 53.229 47.329 90.00 90.00 90.00 1 +ATOM 1 N MET 1 17.837 19.331 33.717 1.00 0.00 N +ATOM 2 H1 MET 1 17.289 18.609 34.163 1.00 0.00 H +ATOM 3 H2 MET 1 18.134 19.022 32.803 1.00 0.00 H +ATOM 4 H3 MET 1 17.242 20.146 33.734 1.00 0.00 H +ATOM 5 CA MET 1 19.083 19.722 34.406 1.00 0.00 C +ATOM 6 HA MET 1 18.957 20.225 35.365 1.00 0.00 H +ATOM 7 CB MET 1 20.022 18.462 34.524 1.00 0.00 C +ATOM 8 HB2 MET 1 20.894 18.888 35.020 1.00 0.00 H +ATOM 9 HB3 MET 1 19.639 17.681 35.181 1.00 0.00 H +ATOM 10 CG MET 1 20.354 17.803 33.215 1.00 0.00 C +ATOM 11 HG2 MET 1 19.537 17.105 33.036 1.00 0.00 H +ATOM 12 HG3 MET 1 20.327 18.454 32.341 1.00 0.00 H +ATOM 13 SD MET 1 21.968 17.051 33.094 1.00 0.00 S +ATOM 14 CE MET 1 21.687 15.586 34.066 1.00 0.00 C +ATOM 15 HE1 MET 1 21.301 15.900 35.036 1.00 0.00 H +ATOM 16 HE2 MET 1 22.643 15.076 34.185 1.00 0.00 H +ATOM 17 HE3 MET 1 20.989 15.001 33.466 1.00 0.00 H +ATOM 18 C MET 1 19.662 20.874 33.597 1.00 0.00 C +ATOM 19 O MET 1 19.304 21.112 32.471 1.00 0.00 O +ATOM 20 N GLN 2 20.657 21.565 34.150 1.00 0.00 N +ATOM 21 H GLN 2 20.853 21.280 35.098 1.00 0.00 H +ATOM 22 CA GLN 2 21.224 22.718 33.626 1.00 0.00 C +ATOM 23 HA GLN 2 20.513 23.261 33.003 1.00 0.00 H +ATOM 24 CB GLN 2 21.638 23.665 34.873 1.00 0.00 C +ATOM 25 HB2 GLN 2 22.203 23.106 35.619 1.00 0.00 H +ATOM 26 HB3 GLN 2 22.288 24.455 34.496 1.00 0.00 H +ATOM 27 CG GLN 2 20.329 24.244 35.537 1.00 0.00 C +ATOM 28 HG2 GLN 2 19.534 24.281 34.792 1.00 0.00 H +ATOM 29 HG3 GLN 2 20.007 23.479 36.243 1.00 0.00 H +ATOM 30 CD GLN 2 20.475 25.630 36.159 1.00 0.00 C +ATOM 31 OE1 GLN 2 19.598 26.429 36.007 1.00 0.00 O +ATOM 32 NE2 GLN 2 21.436 26.003 37.053 1.00 0.00 N +ATOM 33 HE21 GLN 2 21.542 26.964 37.345 1.00 0.00 H +ATOM 34 HE22 GLN 2 22.209 25.410 37.319 1.00 0.00 H +ATOM 35 C GLN 2 22.458 22.433 32.660 1.00 0.00 C +ATOM 36 O GLN 2 23.508 21.967 33.145 1.00 0.00 O +ATOM 37 N TYR 3 22.436 22.846 31.366 1.00 0.00 N +ATOM 38 H TYR 3 21.528 23.142 31.039 1.00 0.00 H +ATOM 39 CA TYR 3 23.581 22.968 30.527 1.00 0.00 C +ATOM 40 HA TYR 3 24.467 22.436 30.873 1.00 0.00 H +ATOM 41 CB TYR 3 23.278 22.199 29.221 1.00 0.00 C +ATOM 42 HB2 TYR 3 22.592 22.774 28.599 1.00 0.00 H +ATOM 43 HB3 TYR 3 24.253 22.042 28.760 1.00 0.00 H +ATOM 44 CG TYR 3 22.631 20.789 29.364 1.00 0.00 C +ATOM 45 CD1 TYR 3 23.383 19.670 29.041 1.00 0.00 C +ATOM 46 HD1 TYR 3 24.440 19.817 28.874 1.00 0.00 H +ATOM 47 CE1 TYR 3 22.748 18.427 28.919 1.00 0.00 C +ATOM 48 HE1 TYR 3 23.353 17.548 28.751 1.00 0.00 H +ATOM 49 CZ TYR 3 21.380 18.211 29.241 1.00 0.00 C +ATOM 50 OH TYR 3 20.755 17.004 29.328 1.00 0.00 O +ATOM 51 HH TYR 3 21.282 16.262 29.023 1.00 0.00 H +ATOM 52 CE2 TYR 3 20.634 19.398 29.620 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.607 19.261 29.924 1.00 0.00 H +ATOM 54 CD2 TYR 3 21.242 20.612 29.608 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.708 21.471 29.986 1.00 0.00 H +ATOM 56 C TYR 3 24.006 24.375 30.307 1.00 0.00 C +ATOM 57 O TYR 3 23.281 25.270 29.877 1.00 0.00 O +ATOM 58 N LYS 4 25.362 24.561 30.559 1.00 0.00 N +ATOM 59 H LYS 4 25.933 23.766 30.810 1.00 0.00 H +ATOM 60 CA LYS 4 26.000 25.873 30.263 1.00 0.00 C +ATOM 61 HA LYS 4 25.331 26.606 30.714 1.00 0.00 H +ATOM 62 CB LYS 4 27.307 26.012 30.999 1.00 0.00 C +ATOM 63 HB2 LYS 4 27.844 25.064 30.990 1.00 0.00 H +ATOM 64 HB3 LYS 4 28.010 26.720 30.562 1.00 0.00 H +ATOM 65 CG LYS 4 27.154 26.456 32.425 1.00 0.00 C +ATOM 66 HG2 LYS 4 26.854 27.499 32.518 1.00 0.00 H +ATOM 67 HG3 LYS 4 26.464 25.743 32.876 1.00 0.00 H +ATOM 68 CD LYS 4 28.456 26.455 33.169 1.00 0.00 C +ATOM 69 HD2 LYS 4 28.957 25.489 33.102 1.00 0.00 H +ATOM 70 HD3 LYS 4 29.059 27.325 32.909 1.00 0.00 H +ATOM 71 CE LYS 4 27.964 26.576 34.643 1.00 0.00 C +ATOM 72 HE2 LYS 4 27.304 27.438 34.733 1.00 0.00 H +ATOM 73 HE3 LYS 4 27.362 25.722 34.952 1.00 0.00 H +ATOM 74 NZ LYS 4 29.187 26.687 35.555 1.00 0.00 N +ATOM 75 HZ1 LYS 4 28.916 26.239 36.418 1.00 0.00 H +ATOM 76 HZ2 LYS 4 29.628 27.593 35.623 1.00 0.00 H +ATOM 77 HZ3 LYS 4 29.917 26.117 35.152 1.00 0.00 H +ATOM 78 C LYS 4 26.059 26.370 28.816 1.00 0.00 C +ATOM 79 O LYS 4 25.888 25.590 27.895 1.00 0.00 O +ATOM 80 N HX1 5 26.340 27.659 28.679 1.00 0.00 N +ATOM 81 CA HX1 5 26.331 28.444 27.452 1.00 0.00 C +ATOM 82 C HX1 5 27.438 29.558 27.540 1.00 0.00 C +ATOM 83 O HX1 5 27.259 30.497 28.312 1.00 0.00 O +ATOM 84 CB HX1 5 24.951 29.091 27.196 1.00 0.00 C +ATOM 85 CG HX1 5 24.721 29.939 25.922 1.00 0.00 C +ATOM 86 CD2 HX1 5 25.571 30.000 24.784 1.00 0.00 C +ATOM 87 ND1 HX1 5 23.586 30.738 25.680 1.00 0.00 N +ATOM 88 CE1 HX1 5 23.699 31.236 24.410 1.00 0.00 C +ATOM 89 NE2 HX1 5 24.923 30.821 23.881 1.00 0.00 N +ATOM 90 H HX1 5 26.394 28.135 29.568 1.00 0.00 H +ATOM 91 HA HX1 5 26.693 27.815 26.639 1.00 0.00 H +ATOM 92 HB2 HX1 5 24.527 29.621 28.049 1.00 0.00 H +ATOM 93 HB3 HX1 5 24.375 28.190 26.985 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.469 29.441 24.568 1.00 0.00 H +ATOM 95 HE1 HX1 5 22.991 31.778 23.801 1.00 0.00 H +ATOM 96 HE2 HX1 5 25.079 30.943 22.890 1.00 0.00 H +ATOM 97 N ILE 6 28.589 29.399 26.891 1.00 0.00 N +ATOM 98 H ILE 6 28.612 28.577 26.305 1.00 0.00 H +ATOM 99 CA ILE 6 29.519 30.589 26.677 1.00 0.00 C +ATOM 100 HA ILE 6 29.489 31.269 27.529 1.00 0.00 H +ATOM 101 CB ILE 6 31.000 30.133 26.262 1.00 0.00 C +ATOM 102 HB ILE 6 30.832 29.560 25.351 1.00 0.00 H +ATOM 103 CG2 ILE 6 31.913 31.404 26.015 1.00 0.00 C +ATOM 104 HG21 ILE 6 32.210 31.783 26.993 1.00 0.00 H +ATOM 105 HG22 ILE 6 31.354 32.186 25.500 1.00 0.00 H +ATOM 106 HG23 ILE 6 32.767 31.148 25.387 1.00 0.00 H +ATOM 107 CG1 ILE 6 31.654 29.099 27.137 1.00 0.00 C +ATOM 108 HG12 ILE 6 31.810 29.609 28.088 1.00 0.00 H +ATOM 109 HG13 ILE 6 30.981 28.250 27.253 1.00 0.00 H +ATOM 110 CD1 ILE 6 32.890 28.510 26.584 1.00 0.00 C +ATOM 111 HD11 ILE 6 33.701 29.237 26.522 1.00 0.00 H +ATOM 112 HD12 ILE 6 32.467 28.063 25.685 1.00 0.00 H +ATOM 113 HD13 ILE 6 33.261 27.718 27.235 1.00 0.00 H +ATOM 114 C ILE 6 28.944 31.380 25.515 1.00 0.00 C +ATOM 115 O ILE 6 28.781 30.799 24.427 1.00 0.00 O +ATOM 116 N VAL 7 28.784 32.712 25.682 1.00 0.00 N +ATOM 117 H VAL 7 29.060 33.122 26.563 1.00 0.00 H +ATOM 118 CA VAL 7 28.305 33.575 24.603 1.00 0.00 C +ATOM 119 HA VAL 7 27.631 33.085 23.901 1.00 0.00 H +ATOM 120 CB VAL 7 27.544 34.847 25.170 1.00 0.00 C +ATOM 121 HB VAL 7 27.132 35.392 24.322 1.00 0.00 H +ATOM 122 CG1 VAL 7 26.408 34.379 26.093 1.00 0.00 C +ATOM 123 HG11 VAL 7 25.705 33.732 25.567 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.759 33.916 27.014 1.00 0.00 H +ATOM 125 HG13 VAL 7 25.854 35.293 26.309 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.425 35.855 25.957 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.128 36.221 25.209 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.776 36.671 26.274 1.00 0.00 H +ATOM 129 HG23 VAL 7 28.853 35.389 26.846 1.00 0.00 H +ATOM 130 C VAL 7 29.414 34.047 23.730 1.00 0.00 C +ATOM 131 O VAL 7 30.549 34.170 24.131 1.00 0.00 O +ATOM 132 N ASN 8 29.160 34.416 22.520 1.00 0.00 N +ATOM 133 H ASN 8 28.180 34.351 22.285 1.00 0.00 H +ATOM 134 CA ASN 8 30.090 34.671 21.453 1.00 0.00 C +ATOM 135 HA ASN 8 30.741 33.797 21.485 1.00 0.00 H +ATOM 136 CB ASN 8 29.315 34.726 20.146 1.00 0.00 C +ATOM 137 HB2 ASN 8 30.004 34.738 19.301 1.00 0.00 H +ATOM 138 HB3 ASN 8 28.768 33.793 20.015 1.00 0.00 H +ATOM 139 CG ASN 8 28.356 35.887 19.935 1.00 0.00 C +ATOM 140 OD1 ASN 8 28.421 36.919 20.593 1.00 0.00 O +ATOM 141 ND2 ASN 8 27.384 35.682 19.085 1.00 0.00 N +ATOM 142 HD21 ASN 8 27.323 34.898 18.452 1.00 0.00 H +ATOM 143 HD22 ASN 8 26.618 36.339 19.133 1.00 0.00 H +ATOM 144 C ASN 8 31.031 35.951 21.696 1.00 0.00 C +ATOM 145 O ASN 8 30.842 36.730 22.643 1.00 0.00 O +ATOM 146 N GLY 9 31.964 36.157 20.758 1.00 0.00 N +ATOM 147 H GLY 9 31.930 35.430 20.058 1.00 0.00 H +ATOM 148 CA GLY 9 33.051 37.177 20.834 1.00 0.00 C +ATOM 149 HA2 GLY 9 33.603 36.869 21.722 1.00 0.00 H +ATOM 150 HA3 GLY 9 33.731 37.094 19.987 1.00 0.00 H +ATOM 151 C GLY 9 32.510 38.625 20.828 1.00 0.00 C +ATOM 152 O GLY 9 33.005 39.502 21.526 1.00 0.00 O +ATOM 153 N LYS 10 31.491 38.828 20.053 1.00 0.00 N +ATOM 154 H LYS 10 31.193 37.995 19.566 1.00 0.00 H +ATOM 155 CA LYS 10 30.890 40.184 19.908 1.00 0.00 C +ATOM 156 HA LYS 10 31.582 41.013 20.056 1.00 0.00 H +ATOM 157 CB LYS 10 30.238 40.323 18.527 1.00 0.00 C +ATOM 158 HB2 LYS 10 29.801 41.320 18.457 1.00 0.00 H +ATOM 159 HB3 LYS 10 31.024 40.236 17.777 1.00 0.00 H +ATOM 160 CG LYS 10 29.041 39.309 18.436 1.00 0.00 C +ATOM 161 HG2 LYS 10 29.291 38.284 18.711 1.00 0.00 H +ATOM 162 HG3 LYS 10 28.315 39.769 19.105 1.00 0.00 H +ATOM 163 CD LYS 10 28.495 39.200 17.021 1.00 0.00 C +ATOM 164 HD2 LYS 10 28.313 40.243 16.758 1.00 0.00 H +ATOM 165 HD3 LYS 10 29.217 38.837 16.289 1.00 0.00 H +ATOM 166 CE LYS 10 27.224 38.393 17.042 1.00 0.00 C +ATOM 167 HE2 LYS 10 27.288 37.344 17.332 1.00 0.00 H +ATOM 168 HE3 LYS 10 26.562 38.728 17.840 1.00 0.00 H +ATOM 169 NZ LYS 10 26.566 38.529 15.704 1.00 0.00 N +ATOM 170 HZ1 LYS 10 25.593 38.260 15.719 1.00 0.00 H +ATOM 171 HZ2 LYS 10 27.064 37.983 15.016 1.00 0.00 H +ATOM 172 HZ3 LYS 10 26.518 39.493 15.405 1.00 0.00 H +ATOM 173 C LYS 10 29.907 40.448 21.051 1.00 0.00 C +ATOM 174 O LYS 10 29.539 41.597 21.250 1.00 0.00 O +ATOM 175 N THR 11 29.575 39.393 21.901 1.00 0.00 N +ATOM 176 H THR 11 29.808 38.470 21.562 1.00 0.00 H +ATOM 177 CA THR 11 28.965 39.621 23.224 1.00 0.00 C +ATOM 178 HA THR 11 28.668 40.649 23.428 1.00 0.00 H +ATOM 179 CB THR 11 27.814 38.633 23.365 1.00 0.00 C +ATOM 180 HB THR 11 28.252 37.645 23.503 1.00 0.00 H +ATOM 181 CG2 THR 11 26.806 38.978 24.418 1.00 0.00 C +ATOM 182 HG21 THR 11 27.317 38.811 25.367 1.00 0.00 H +ATOM 183 HG22 THR 11 25.940 38.318 24.372 1.00 0.00 H +ATOM 184 HG23 THR 11 26.482 40.004 24.242 1.00 0.00 H +ATOM 185 OG1 THR 11 27.010 38.531 22.169 1.00 0.00 O +ATOM 186 HG1 THR 11 27.553 38.065 21.529 1.00 0.00 H +ATOM 187 C THR 11 30.041 39.437 24.321 1.00 0.00 C +ATOM 188 O THR 11 29.638 39.210 25.464 1.00 0.00 O +ATOM 189 N LEU 12 31.301 39.630 24.052 1.00 0.00 N +ATOM 190 H LEU 12 31.580 39.871 23.112 1.00 0.00 H +ATOM 191 CA LEU 12 32.412 39.649 25.011 1.00 0.00 C +ATOM 192 HA LEU 12 33.277 39.821 24.371 1.00 0.00 H +ATOM 193 CB LEU 12 32.370 40.861 26.001 1.00 0.00 C +ATOM 194 HB2 LEU 12 31.809 40.565 26.888 1.00 0.00 H +ATOM 195 HB3 LEU 12 33.394 41.067 26.315 1.00 0.00 H +ATOM 196 CG LEU 12 31.953 42.262 25.377 1.00 0.00 C +ATOM 197 HG LEU 12 31.067 42.149 24.751 1.00 0.00 H +ATOM 198 CD1 LEU 12 31.634 43.253 26.532 1.00 0.00 C +ATOM 199 HD11 LEU 12 31.205 44.194 26.187 1.00 0.00 H +ATOM 200 HD12 LEU 12 32.522 43.494 27.115 1.00 0.00 H +ATOM 201 HD13 LEU 12 30.882 42.746 27.138 1.00 0.00 H +ATOM 202 CD2 LEU 12 33.034 42.871 24.534 1.00 0.00 C +ATOM 203 HD21 LEU 12 32.598 43.740 24.041 1.00 0.00 H +ATOM 204 HD22 LEU 12 33.266 42.286 23.644 1.00 0.00 H +ATOM 205 HD23 LEU 12 33.961 43.096 25.061 1.00 0.00 H +ATOM 206 C LEU 12 32.828 38.312 25.795 1.00 0.00 C +ATOM 207 O LEU 12 33.499 38.393 26.797 1.00 0.00 O +ATOM 208 N LYS 13 32.398 37.136 25.328 1.00 0.00 N +ATOM 209 H LYS 13 31.855 37.176 24.477 1.00 0.00 H +ATOM 210 CA LYS 13 32.787 35.838 25.952 1.00 0.00 C +ATOM 211 HA LYS 13 32.175 35.093 25.443 1.00 0.00 H +ATOM 212 CB LYS 13 34.337 35.531 25.623 1.00 0.00 C +ATOM 213 HB2 LYS 13 35.083 36.086 26.192 1.00 0.00 H +ATOM 214 HB3 LYS 13 34.591 34.544 26.010 1.00 0.00 H +ATOM 215 CG LYS 13 34.767 35.575 24.136 1.00 0.00 C +ATOM 216 HG2 LYS 13 34.382 36.488 23.682 1.00 0.00 H +ATOM 217 HG3 LYS 13 35.850 35.657 24.038 1.00 0.00 H +ATOM 218 CD LYS 13 34.193 34.455 23.224 1.00 0.00 C +ATOM 219 HD2 LYS 13 33.133 34.337 23.447 1.00 0.00 H +ATOM 220 HD3 LYS 13 34.306 34.772 22.187 1.00 0.00 H +ATOM 221 CE LYS 13 34.990 33.179 23.372 1.00 0.00 C +ATOM 222 HE2 LYS 13 35.918 33.267 22.807 1.00 0.00 H +ATOM 223 HE3 LYS 13 35.214 32.861 24.390 1.00 0.00 H +ATOM 224 NZ LYS 13 34.216 32.107 22.723 1.00 0.00 N +ATOM 225 HZ1 LYS 13 34.335 32.079 21.721 1.00 0.00 H +ATOM 226 HZ2 LYS 13 33.232 32.296 22.848 1.00 0.00 H +ATOM 227 HZ3 LYS 13 34.530 31.191 23.010 1.00 0.00 H +ATOM 228 C LYS 13 32.470 35.507 27.415 1.00 0.00 C +ATOM 229 O LYS 13 33.176 34.770 28.112 1.00 0.00 O +ATOM 230 N GLY 14 31.411 36.061 27.969 1.00 0.00 N +ATOM 231 H GLY 14 30.890 36.707 27.393 1.00 0.00 H +ATOM 232 CA GLY 14 30.916 35.614 29.224 1.00 0.00 C +ATOM 233 HA2 GLY 14 31.709 35.491 29.961 1.00 0.00 H +ATOM 234 HA3 GLY 14 30.139 36.228 29.680 1.00 0.00 H +ATOM 235 C GLY 14 30.194 34.239 29.200 1.00 0.00 C +ATOM 236 O GLY 14 30.211 33.517 28.186 1.00 0.00 O +ATOM 237 N VAL 15 29.621 33.775 30.280 1.00 0.00 N +ATOM 238 H VAL 15 29.668 34.200 31.195 1.00 0.00 H +ATOM 239 CA VAL 15 29.058 32.405 30.355 1.00 0.00 C +ATOM 240 HA VAL 15 28.669 32.057 29.398 1.00 0.00 H +ATOM 241 CB VAL 15 30.160 31.373 30.798 1.00 0.00 C +ATOM 242 HB VAL 15 30.959 31.327 30.057 1.00 0.00 H +ATOM 243 CG1 VAL 15 30.840 31.618 32.160 1.00 0.00 C +ATOM 244 HG11 VAL 15 31.648 30.895 32.274 1.00 0.00 H +ATOM 245 HG12 VAL 15 31.228 32.633 32.243 1.00 0.00 H +ATOM 246 HG13 VAL 15 30.148 31.295 32.938 1.00 0.00 H +ATOM 247 CG2 VAL 15 29.623 30.002 30.879 1.00 0.00 C +ATOM 248 HG21 VAL 15 29.256 29.668 29.908 1.00 0.00 H +ATOM 249 HG22 VAL 15 30.418 29.272 31.032 1.00 0.00 H +ATOM 250 HG23 VAL 15 28.935 29.916 31.720 1.00 0.00 H +ATOM 251 C VAL 15 27.920 32.376 31.304 1.00 0.00 C +ATOM 252 O VAL 15 27.955 33.151 32.261 1.00 0.00 O +ATOM 253 N HY1 16 26.862 31.565 31.058 1.00 0.00 N +ATOM 254 CA HY1 16 25.676 31.361 31.974 1.00 0.00 C +ATOM 255 C HY1 16 25.000 30.021 31.601 1.00 0.00 C +ATOM 256 O HY1 16 25.591 29.232 30.810 1.00 0.00 O +ATOM 257 CB HY1 16 24.763 32.607 31.896 1.00 0.00 C +ATOM 258 CG HY1 16 24.250 32.779 30.487 1.00 0.00 C +ATOM 259 CD2 HY1 16 23.224 32.015 29.859 1.00 0.00 C +ATOM 260 ND1 HY1 16 24.726 33.699 29.569 1.00 0.00 N +ATOM 261 CE1 HY1 16 23.984 33.582 28.454 1.00 0.00 C +ATOM 262 NE2 HY1 16 23.150 32.545 28.552 1.00 0.00 N +ATOM 263 H HY1 16 26.950 30.964 30.251 1.00 0.00 H +ATOM 264 HA HY1 16 26.091 31.286 32.978 1.00 0.00 H +ATOM 265 HB2 HY1 16 23.955 32.624 32.627 1.00 0.00 H +ATOM 266 HB3 HY1 16 25.481 33.375 32.183 1.00 0.00 H +ATOM 267 HD1 HY1 16 25.391 34.445 29.719 1.00 0.00 H +ATOM 268 HD2 HY1 16 22.714 31.151 30.260 1.00 0.00 H +ATOM 269 HE1 HY1 16 23.986 34.294 27.642 1.00 0.00 H +ATOM 270 N THR 17 23.942 29.627 32.230 1.00 0.00 N +ATOM 271 H THR 17 23.609 30.247 32.954 1.00 0.00 H +ATOM 272 CA THR 17 23.327 28.235 32.131 1.00 0.00 C +ATOM 273 HA THR 17 23.809 27.753 31.280 1.00 0.00 H +ATOM 274 CB THR 17 23.747 27.448 33.352 1.00 0.00 C +ATOM 275 HB THR 17 24.766 27.775 33.557 1.00 0.00 H +ATOM 276 CG2 THR 17 22.842 27.649 34.552 1.00 0.00 C +ATOM 277 HG21 THR 17 21.817 27.332 34.357 1.00 0.00 H +ATOM 278 HG22 THR 17 22.881 28.664 34.947 1.00 0.00 H +ATOM 279 HG23 THR 17 23.314 26.953 35.246 1.00 0.00 H +ATOM 280 OG1 THR 17 23.759 26.117 32.970 1.00 0.00 O +ATOM 281 HG1 THR 17 24.318 25.733 33.649 1.00 0.00 H +ATOM 282 C THR 17 21.796 28.104 31.785 1.00 0.00 C +ATOM 283 O THR 17 21.009 29.038 32.058 1.00 0.00 O +ATOM 284 N HY2 18 21.407 27.047 31.156 1.00 0.00 N +ATOM 285 CA HY2 18 20.091 26.751 30.701 1.00 0.00 C +ATOM 286 C HY2 18 19.589 25.299 30.877 1.00 0.00 C +ATOM 287 O HY2 18 20.223 24.312 30.537 1.00 0.00 O +ATOM 288 CB HY2 18 20.036 27.059 29.155 1.00 0.00 C +ATOM 289 CG HY2 18 20.273 28.510 28.716 1.00 0.00 C +ATOM 290 CD2 HY2 18 21.292 29.036 27.959 1.00 0.00 C +ATOM 291 ND1 HY2 18 19.403 29.600 28.972 1.00 0.00 N +ATOM 292 CE1 HY2 18 19.955 30.690 28.361 1.00 0.00 C +ATOM 293 NE2 HY2 18 21.045 30.343 27.698 1.00 0.00 N +ATOM 294 H HY2 18 22.127 26.343 31.074 1.00 0.00 H +ATOM 295 HA HY2 18 19.410 27.428 31.217 1.00 0.00 H +ATOM 296 HB2 HY2 18 20.661 26.380 28.575 1.00 0.00 H +ATOM 297 HB3 HY2 18 19.043 26.722 28.854 1.00 0.00 H +ATOM 298 HD1 HY2 18 18.608 29.514 29.589 1.00 0.00 H +ATOM 299 HD2 HY2 18 22.073 28.447 27.500 1.00 0.00 H +ATOM 300 HE1 HY2 18 19.381 31.600 28.269 1.00 0.00 H +ATOM 301 N GLU 19 18.411 25.329 31.401 1.00 0.00 N +ATOM 302 H GLU 19 18.093 26.220 31.753 1.00 0.00 H +ATOM 303 CA GLU 19 17.689 24.070 31.697 1.00 0.00 C +ATOM 304 HA GLU 19 18.370 23.395 32.216 1.00 0.00 H +ATOM 305 CB GLU 19 16.676 24.450 32.771 1.00 0.00 C +ATOM 306 HB2 GLU 19 17.111 24.562 33.764 1.00 0.00 H +ATOM 307 HB3 GLU 19 16.246 25.435 32.589 1.00 0.00 H +ATOM 308 CG GLU 19 15.544 23.412 32.995 1.00 0.00 C +ATOM 309 HG2 GLU 19 14.817 23.793 33.712 1.00 0.00 H +ATOM 310 HG3 GLU 19 14.994 23.206 32.077 1.00 0.00 H +ATOM 311 CD GLU 19 16.127 22.065 33.502 1.00 0.00 C +ATOM 312 OE1 GLU 19 15.682 21.011 33.068 1.00 0.00 O +ATOM 313 OE2 GLU 19 16.969 22.014 34.393 1.00 0.00 O +ATOM 314 C GLU 19 17.167 23.443 30.415 1.00 0.00 C +ATOM 315 O GLU 19 16.691 24.096 29.452 1.00 0.00 O +ATOM 316 N ALA 20 17.108 22.062 30.382 1.00 0.00 N +ATOM 317 H ALA 20 17.579 21.671 31.185 1.00 0.00 H +ATOM 318 CA ALA 20 16.412 21.201 29.454 1.00 0.00 C +ATOM 319 HA ALA 20 15.424 21.648 29.351 1.00 0.00 H +ATOM 320 CB ALA 20 17.237 21.164 28.172 1.00 0.00 C +ATOM 321 HB1 ALA 20 17.602 22.136 27.840 1.00 0.00 H +ATOM 322 HB2 ALA 20 16.740 20.563 27.410 1.00 0.00 H +ATOM 323 HB3 ALA 20 18.128 20.592 28.431 1.00 0.00 H +ATOM 324 C ALA 20 16.256 19.692 29.956 1.00 0.00 C +ATOM 325 O ALA 20 16.824 19.248 30.936 1.00 0.00 O +ATOM 326 N VAL 21 15.442 18.847 29.258 1.00 0.00 N +ATOM 327 H VAL 21 14.927 19.280 28.504 1.00 0.00 H +ATOM 328 CA VAL 21 15.315 17.366 29.481 1.00 0.00 C +ATOM 329 HA VAL 21 15.574 17.157 30.519 1.00 0.00 H +ATOM 330 CB VAL 21 13.861 16.909 29.164 1.00 0.00 C +ATOM 331 HB VAL 21 13.150 17.624 29.577 1.00 0.00 H +ATOM 332 CG1 VAL 21 13.564 16.892 27.673 1.00 0.00 C +ATOM 333 HG11 VAL 21 12.494 16.792 27.489 1.00 0.00 H +ATOM 334 HG12 VAL 21 14.192 16.090 27.285 1.00 0.00 H +ATOM 335 HG13 VAL 21 13.822 17.798 27.124 1.00 0.00 H +ATOM 336 CG2 VAL 21 13.650 15.561 29.790 1.00 0.00 C +ATOM 337 HG21 VAL 21 12.701 15.214 29.381 1.00 0.00 H +ATOM 338 HG22 VAL 21 13.702 15.656 30.875 1.00 0.00 H +ATOM 339 HG23 VAL 21 14.472 14.945 29.426 1.00 0.00 H +ATOM 340 C VAL 21 16.441 16.535 28.804 1.00 0.00 C +ATOM 341 O VAL 21 16.819 15.467 29.260 1.00 0.00 O +ATOM 342 N ASP 22 17.018 17.062 27.664 1.00 0.00 N +ATOM 343 H ASP 22 16.777 18.002 27.382 1.00 0.00 H +ATOM 344 CA ASP 22 17.969 16.349 26.766 1.00 0.00 C +ATOM 345 HA ASP 22 18.459 15.585 27.369 1.00 0.00 H +ATOM 346 CB ASP 22 17.091 15.659 25.708 1.00 0.00 C +ATOM 347 HB2 ASP 22 16.409 14.985 26.226 1.00 0.00 H +ATOM 348 HB3 ASP 22 16.452 16.383 25.204 1.00 0.00 H +ATOM 349 CG ASP 22 17.915 14.855 24.680 1.00 0.00 C +ATOM 350 OD1 ASP 22 17.303 14.175 23.793 1.00 0.00 O +ATOM 351 OD2 ASP 22 19.142 14.922 24.771 1.00 0.00 O +ATOM 352 C ASP 22 19.023 17.399 26.221 1.00 0.00 C +ATOM 353 O ASP 22 18.644 18.547 25.939 1.00 0.00 O +ATOM 354 N ALA 23 20.249 16.981 26.052 1.00 0.00 N +ATOM 355 H ALA 23 20.363 15.994 26.236 1.00 0.00 H +ATOM 356 CA ALA 23 21.339 17.593 25.224 1.00 0.00 C +ATOM 357 HA ALA 23 21.704 18.459 25.776 1.00 0.00 H +ATOM 358 CB ALA 23 22.323 16.498 25.043 1.00 0.00 C +ATOM 359 HB1 ALA 23 21.946 15.582 24.587 1.00 0.00 H +ATOM 360 HB2 ALA 23 22.789 16.168 25.971 1.00 0.00 H +ATOM 361 HB3 ALA 23 23.181 16.830 24.459 1.00 0.00 H +ATOM 362 C ALA 23 20.799 18.053 23.875 1.00 0.00 C +ATOM 363 O ALA 23 21.270 19.097 23.336 1.00 0.00 O +ATOM 364 N ALA 24 19.857 17.229 23.297 1.00 0.00 N +ATOM 365 H ALA 24 19.472 16.461 23.829 1.00 0.00 H +ATOM 366 CA ALA 24 19.209 17.579 22.038 1.00 0.00 C +ATOM 367 HA ALA 24 19.944 18.043 21.380 1.00 0.00 H +ATOM 368 CB ALA 24 18.806 16.334 21.234 1.00 0.00 C +ATOM 369 HB1 ALA 24 19.676 15.913 20.732 1.00 0.00 H +ATOM 370 HB2 ALA 24 18.089 16.510 20.433 1.00 0.00 H +ATOM 371 HB3 ALA 24 18.401 15.587 21.917 1.00 0.00 H +ATOM 372 C ALA 24 18.031 18.582 22.155 1.00 0.00 C +ATOM 373 O ALA 24 17.656 19.149 21.138 1.00 0.00 O +ATOM 374 N GLU 25 17.553 18.933 23.377 1.00 0.00 N +ATOM 375 H GLU 25 17.921 18.391 24.146 1.00 0.00 H +ATOM 376 CA GLU 25 16.896 20.218 23.591 1.00 0.00 C +ATOM 377 HA GLU 25 16.409 20.551 22.674 1.00 0.00 H +ATOM 378 CB GLU 25 15.752 20.053 24.609 1.00 0.00 C +ATOM 379 HB2 GLU 25 16.148 19.563 25.498 1.00 0.00 H +ATOM 380 HB3 GLU 25 15.312 20.988 24.954 1.00 0.00 H +ATOM 381 CG GLU 25 14.613 19.205 24.063 1.00 0.00 C +ATOM 382 HG2 GLU 25 15.027 18.267 23.693 1.00 0.00 H +ATOM 383 HG3 GLU 25 13.956 19.020 24.913 1.00 0.00 H +ATOM 384 CD GLU 25 13.873 19.744 22.831 1.00 0.00 C +ATOM 385 OE1 GLU 25 13.212 18.902 22.176 1.00 0.00 O +ATOM 386 OE2 GLU 25 14.050 20.908 22.357 1.00 0.00 O +ATOM 387 C GLU 25 17.762 21.422 24.080 1.00 0.00 C +ATOM 388 O GLU 25 17.500 22.595 23.671 1.00 0.00 O +ATOM 389 N ALA 26 18.841 21.139 24.852 1.00 0.00 N +ATOM 390 H ALA 26 18.836 20.170 25.137 1.00 0.00 H +ATOM 391 CA ALA 26 19.752 22.128 25.410 1.00 0.00 C +ATOM 392 HA ALA 26 19.222 22.885 25.987 1.00 0.00 H +ATOM 393 CB ALA 26 20.656 21.332 26.397 1.00 0.00 C +ATOM 394 HB1 ALA 26 21.094 21.991 27.146 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.501 20.892 25.867 1.00 0.00 H +ATOM 396 HB3 ALA 26 20.115 20.610 27.008 1.00 0.00 H +ATOM 397 C ALA 26 20.557 22.922 24.312 1.00 0.00 C +ATOM 398 O ALA 26 20.673 24.146 24.309 1.00 0.00 O +ATOM 399 N GLU 27 20.968 22.222 23.283 1.00 0.00 N +ATOM 400 H GLU 27 20.863 21.217 23.314 1.00 0.00 H +ATOM 401 CA GLU 27 21.663 22.691 22.041 1.00 0.00 C +ATOM 402 HA GLU 27 22.612 22.948 22.511 1.00 0.00 H +ATOM 403 CB GLU 27 21.845 21.515 21.030 1.00 0.00 C +ATOM 404 HB2 GLU 27 22.413 21.974 20.221 1.00 0.00 H +ATOM 405 HB3 GLU 27 22.301 20.614 21.439 1.00 0.00 H +ATOM 406 CG GLU 27 20.493 21.072 20.388 1.00 0.00 C +ATOM 407 HG2 GLU 27 19.723 20.769 21.098 1.00 0.00 H +ATOM 408 HG3 GLU 27 20.194 21.921 19.774 1.00 0.00 H +ATOM 409 CD GLU 27 20.767 19.999 19.343 1.00 0.00 C +ATOM 410 OE1 GLU 27 21.364 18.898 19.564 1.00 0.00 O +ATOM 411 OE2 GLU 27 20.407 20.180 18.159 1.00 0.00 O +ATOM 412 C GLU 27 21.072 24.011 21.504 1.00 0.00 C +ATOM 413 O GLU 27 21.793 24.852 20.980 1.00 0.00 O +ATOM 414 N LYS 28 19.747 24.204 21.584 1.00 0.00 N +ATOM 415 H LYS 28 19.176 23.520 22.060 1.00 0.00 H +ATOM 416 CA LYS 28 19.049 25.280 20.800 1.00 0.00 C +ATOM 417 HA LYS 28 19.313 25.143 19.752 1.00 0.00 H +ATOM 418 CB LYS 28 17.509 25.236 20.977 1.00 0.00 C +ATOM 419 HB2 LYS 28 17.245 25.364 22.026 1.00 0.00 H +ATOM 420 HB3 LYS 28 17.090 26.047 20.382 1.00 0.00 H +ATOM 421 CG LYS 28 16.905 23.895 20.411 1.00 0.00 C +ATOM 422 HG2 LYS 28 17.250 23.789 19.382 1.00 0.00 H +ATOM 423 HG3 LYS 28 17.283 23.078 21.025 1.00 0.00 H +ATOM 424 CD LYS 28 15.344 23.875 20.471 1.00 0.00 C +ATOM 425 HD2 LYS 28 14.994 24.563 19.701 1.00 0.00 H +ATOM 426 HD3 LYS 28 14.977 22.910 20.121 1.00 0.00 H +ATOM 427 CE LYS 28 14.519 24.389 21.743 1.00 0.00 C +ATOM 428 HE2 LYS 28 14.798 25.399 22.045 1.00 0.00 H +ATOM 429 HE3 LYS 28 13.491 24.511 21.403 1.00 0.00 H +ATOM 430 NZ LYS 28 14.563 23.527 22.937 1.00 0.00 N +ATOM 431 HZ1 LYS 28 13.711 23.592 23.475 1.00 0.00 H +ATOM 432 HZ2 LYS 28 15.375 23.729 23.502 1.00 0.00 H +ATOM 433 HZ3 LYS 28 14.593 22.547 22.696 1.00 0.00 H +ATOM 434 C LYS 28 19.554 26.705 21.221 1.00 0.00 C +ATOM 435 O LYS 28 19.709 27.600 20.297 1.00 0.00 O +ATOM 436 N PHE 29 19.704 26.939 22.482 1.00 0.00 N +ATOM 437 H PHE 29 19.530 26.189 23.136 1.00 0.00 H +ATOM 438 CA PHE 29 20.132 28.202 23.032 1.00 0.00 C +ATOM 439 HA PHE 29 19.498 29.047 22.763 1.00 0.00 H +ATOM 440 CB PHE 29 20.279 28.134 24.615 1.00 0.00 C +ATOM 441 HB2 PHE 29 20.824 27.223 24.861 1.00 0.00 H +ATOM 442 HB3 PHE 29 20.823 29.025 24.929 1.00 0.00 H +ATOM 443 CG PHE 29 18.972 28.068 25.408 1.00 0.00 C +ATOM 444 CD1 PHE 29 18.218 29.228 25.529 1.00 0.00 C +ATOM 445 HD1 PHE 29 18.529 30.128 25.018 1.00 0.00 H +ATOM 446 CE1 PHE 29 16.985 29.126 26.179 1.00 0.00 C +ATOM 447 HE1 PHE 29 16.335 29.987 26.237 1.00 0.00 H +ATOM 448 CZ PHE 29 16.613 27.943 26.863 1.00 0.00 C +ATOM 449 HZ PHE 29 15.724 27.934 27.477 1.00 0.00 H +ATOM 450 CE2 PHE 29 17.374 26.746 26.782 1.00 0.00 C +ATOM 451 HE2 PHE 29 17.076 25.841 27.291 1.00 0.00 H +ATOM 452 CD2 PHE 29 18.550 26.841 25.983 1.00 0.00 C +ATOM 453 HD2 PHE 29 19.138 25.944 25.854 1.00 0.00 H +ATOM 454 C PHE 29 21.473 28.640 22.414 1.00 0.00 C +ATOM 455 O PHE 29 21.813 29.835 22.537 1.00 0.00 O +ATOM 456 N THR 30 22.313 27.667 22.019 1.00 0.00 N +ATOM 457 H THR 30 22.060 26.714 22.237 1.00 0.00 H +ATOM 458 CA THR 30 23.548 27.803 21.345 1.00 0.00 C +ATOM 459 HA THR 30 23.934 28.735 21.758 1.00 0.00 H +ATOM 460 CB THR 30 24.575 26.833 21.833 1.00 0.00 C +ATOM 461 HB THR 30 24.263 25.790 21.777 1.00 0.00 H +ATOM 462 CG2 THR 30 25.925 26.919 21.088 1.00 0.00 C +ATOM 463 HG21 THR 30 26.282 27.949 21.075 1.00 0.00 H +ATOM 464 HG22 THR 30 26.664 26.400 21.698 1.00 0.00 H +ATOM 465 HG23 THR 30 25.928 26.531 20.069 1.00 0.00 H +ATOM 466 OG1 THR 30 24.829 27.130 23.219 1.00 0.00 O +ATOM 467 HG1 THR 30 24.212 26.586 23.713 1.00 0.00 H +ATOM 468 C THR 30 23.529 27.915 19.858 1.00 0.00 C +ATOM 469 O THR 30 24.354 28.625 19.225 1.00 0.00 O +ATOM 470 N LYS 31 22.587 27.274 19.209 1.00 0.00 N +ATOM 471 H LYS 31 21.935 26.737 19.763 1.00 0.00 H +ATOM 472 CA LYS 31 22.513 27.101 17.709 1.00 0.00 C +ATOM 473 HA LYS 31 23.471 26.764 17.314 1.00 0.00 H +ATOM 474 CB LYS 31 21.427 26.032 17.444 1.00 0.00 C +ATOM 475 HB2 LYS 31 20.617 26.034 18.173 1.00 0.00 H +ATOM 476 HB3 LYS 31 20.920 26.191 16.492 1.00 0.00 H +ATOM 477 CG LYS 31 22.058 24.634 17.416 1.00 0.00 C +ATOM 478 HG2 LYS 31 23.014 24.603 16.892 1.00 0.00 H +ATOM 479 HG3 LYS 31 22.208 24.263 18.430 1.00 0.00 H +ATOM 480 CD LYS 31 21.114 23.651 16.737 1.00 0.00 C +ATOM 481 HD2 LYS 31 20.938 23.980 15.713 1.00 0.00 H +ATOM 482 HD3 LYS 31 21.595 22.673 16.719 1.00 0.00 H +ATOM 483 CE LYS 31 19.662 23.423 17.223 1.00 0.00 C +ATOM 484 HE2 LYS 31 19.837 22.873 18.148 1.00 0.00 H +ATOM 485 HE3 LYS 31 19.164 24.367 17.447 1.00 0.00 H +ATOM 486 NZ LYS 31 18.836 22.708 16.234 1.00 0.00 N +ATOM 487 HZ1 LYS 31 18.712 23.226 15.376 1.00 0.00 H +ATOM 488 HZ2 LYS 31 17.926 22.604 16.661 1.00 0.00 H +ATOM 489 HZ3 LYS 31 19.130 21.781 15.965 1.00 0.00 H +ATOM 490 C LYS 31 22.234 28.405 16.972 1.00 0.00 C +ATOM 491 O LYS 31 22.508 28.565 15.755 1.00 0.00 O +ATOM 492 N ALA 32 21.655 29.419 17.633 1.00 0.00 N +ATOM 493 H ALA 32 21.472 29.243 18.610 1.00 0.00 H +ATOM 494 CA ALA 32 21.274 30.715 17.115 1.00 0.00 C +ATOM 495 HA ALA 32 20.866 30.667 16.105 1.00 0.00 H +ATOM 496 CB ALA 32 20.324 31.434 18.093 1.00 0.00 C +ATOM 497 HB1 ALA 32 19.294 31.112 17.944 1.00 0.00 H +ATOM 498 HB2 ALA 32 20.687 31.271 19.108 1.00 0.00 H +ATOM 499 HB3 ALA 32 20.304 32.493 17.835 1.00 0.00 H +ATOM 500 C ALA 32 22.545 31.547 16.989 1.00 0.00 C +ATOM 501 O ALA 32 22.670 32.369 16.051 1.00 0.00 O +ATOM 502 N ASP 33 23.585 31.289 17.821 1.00 0.00 N +ATOM 503 H ASP 33 23.430 30.688 18.618 1.00 0.00 H +ATOM 504 CA ASP 33 24.945 31.853 17.720 1.00 0.00 C +ATOM 505 HA ASP 33 24.985 32.903 17.429 1.00 0.00 H +ATOM 506 CB ASP 33 25.802 31.582 18.958 1.00 0.00 C +ATOM 507 HB2 ASP 33 25.965 30.505 18.933 1.00 0.00 H +ATOM 508 HB3 ASP 33 26.812 31.971 18.824 1.00 0.00 H +ATOM 509 CG ASP 33 25.199 32.106 20.261 1.00 0.00 C +ATOM 510 OD1 ASP 33 24.426 33.077 20.152 1.00 0.00 O +ATOM 511 OD2 ASP 33 25.586 31.716 21.394 1.00 0.00 O +ATOM 512 C ASP 33 25.717 31.153 16.591 1.00 0.00 C +ATOM 513 O ASP 33 26.478 31.804 15.840 1.00 0.00 O +ATOM 514 N ALA 34 25.553 29.857 16.427 1.00 0.00 N +ATOM 515 H ALA 34 24.996 29.394 17.131 1.00 0.00 H +ATOM 516 CA ALA 34 26.117 29.120 15.301 1.00 0.00 C +ATOM 517 HA ALA 34 27.195 29.276 15.324 1.00 0.00 H +ATOM 518 CB ALA 34 25.869 27.569 15.533 1.00 0.00 C +ATOM 519 HB1 ALA 34 26.065 26.981 14.636 1.00 0.00 H +ATOM 520 HB2 ALA 34 24.877 27.218 15.819 1.00 0.00 H +ATOM 521 HB3 ALA 34 26.479 27.136 16.325 1.00 0.00 H +ATOM 522 C ALA 34 25.541 29.512 13.984 1.00 0.00 C +ATOM 523 O ALA 34 26.266 29.833 13.033 1.00 0.00 O +ATOM 524 N ASN 35 24.262 29.715 13.920 1.00 0.00 N +ATOM 525 H ASN 35 23.672 29.417 14.683 1.00 0.00 H +ATOM 526 CA ASN 35 23.590 30.448 12.829 1.00 0.00 C +ATOM 527 HA ASN 35 23.736 30.032 11.833 1.00 0.00 H +ATOM 528 CB ASN 35 22.080 30.489 13.090 1.00 0.00 C +ATOM 529 HB2 ASN 35 21.666 29.510 13.328 1.00 0.00 H +ATOM 530 HB3 ASN 35 21.870 31.214 13.877 1.00 0.00 H +ATOM 531 CG ASN 35 21.388 30.984 11.851 1.00 0.00 C +ATOM 532 OD1 ASN 35 21.339 30.180 10.903 1.00 0.00 O +ATOM 533 ND2 ASN 35 20.866 32.202 11.838 1.00 0.00 N +ATOM 534 HD21 ASN 35 20.829 32.788 12.660 1.00 0.00 H +ATOM 535 HD22 ASN 35 20.494 32.518 10.954 1.00 0.00 H +ATOM 536 C ASN 35 24.020 31.879 12.636 1.00 0.00 C +ATOM 537 O ASN 35 24.302 32.297 11.501 1.00 0.00 O +ATOM 538 N ASP 36 24.261 32.688 13.681 1.00 0.00 N +ATOM 539 H ASP 36 24.059 32.376 14.620 1.00 0.00 H +ATOM 540 CA ASP 36 24.789 34.023 13.534 1.00 0.00 C +ATOM 541 HA ASP 36 24.105 34.517 12.844 1.00 0.00 H +ATOM 542 CB ASP 36 24.467 34.696 14.791 1.00 0.00 C +ATOM 543 HB2 ASP 36 23.537 34.362 15.251 1.00 0.00 H +ATOM 544 HB3 ASP 36 25.231 34.446 15.527 1.00 0.00 H +ATOM 545 CG ASP 36 24.487 36.267 14.809 1.00 0.00 C +ATOM 546 OD1 ASP 36 24.788 36.952 13.807 1.00 0.00 O +ATOM 547 OD2 ASP 36 24.274 36.798 15.911 1.00 0.00 O +ATOM 548 C ASP 36 26.270 34.195 13.127 1.00 0.00 C +ATOM 549 O ASP 36 26.706 35.224 12.581 1.00 0.00 O +ATOM 550 N LYS 37 27.040 33.117 13.275 1.00 0.00 N +ATOM 551 H LYS 37 26.669 32.351 13.819 1.00 0.00 H +ATOM 552 CA LYS 37 28.294 32.895 12.653 1.00 0.00 C +ATOM 553 HA LYS 37 28.711 33.902 12.634 1.00 0.00 H +ATOM 554 CB LYS 37 29.130 31.886 13.434 1.00 0.00 C +ATOM 555 HB2 LYS 37 28.745 30.883 13.254 1.00 0.00 H +ATOM 556 HB3 LYS 37 29.042 31.992 14.515 1.00 0.00 H +ATOM 557 CG LYS 37 30.663 31.895 13.074 1.00 0.00 C +ATOM 558 HG2 LYS 37 31.045 32.789 13.566 1.00 0.00 H +ATOM 559 HG3 LYS 37 30.622 32.050 11.996 1.00 0.00 H +ATOM 560 CD LYS 37 31.355 30.614 13.506 1.00 0.00 C +ATOM 561 HD2 LYS 37 31.012 30.519 14.536 1.00 0.00 H +ATOM 562 HD3 LYS 37 30.988 29.758 12.941 1.00 0.00 H +ATOM 563 CE LYS 37 32.858 30.792 13.353 1.00 0.00 C +ATOM 564 HE2 LYS 37 33.146 30.911 12.309 1.00 0.00 H +ATOM 565 HE3 LYS 37 33.140 31.712 13.864 1.00 0.00 H +ATOM 566 NZ LYS 37 33.571 29.709 13.937 1.00 0.00 N +ATOM 567 HZ1 LYS 37 33.504 29.660 14.943 1.00 0.00 H +ATOM 568 HZ2 LYS 37 33.300 28.874 13.438 1.00 0.00 H +ATOM 569 HZ3 LYS 37 34.553 29.843 13.743 1.00 0.00 H +ATOM 570 C LYS 37 28.098 32.489 11.201 1.00 0.00 C +ATOM 571 O LYS 37 28.801 33.116 10.327 1.00 0.00 O +ATOM 572 N GLY 38 27.169 31.559 10.925 1.00 0.00 N +ATOM 573 H GLY 38 26.545 31.312 11.679 1.00 0.00 H +ATOM 574 CA GLY 38 26.937 31.081 9.468 1.00 0.00 C +ATOM 575 HA2 GLY 38 26.701 31.955 8.861 1.00 0.00 H +ATOM 576 HA3 GLY 38 27.836 30.699 8.986 1.00 0.00 H +ATOM 577 C GLY 38 25.837 30.028 9.244 1.00 0.00 C +ATOM 578 O GLY 38 24.982 30.182 8.367 1.00 0.00 O +ATOM 579 N VAL 39 25.891 28.944 10.025 1.00 0.00 N +ATOM 580 H VAL 39 26.422 28.958 10.885 1.00 0.00 H +ATOM 581 CA VAL 39 24.972 27.860 9.998 1.00 0.00 C +ATOM 582 HA VAL 39 23.981 28.261 9.788 1.00 0.00 H +ATOM 583 CB VAL 39 25.355 26.761 8.875 1.00 0.00 C +ATOM 584 HB VAL 39 25.472 27.274 7.920 1.00 0.00 H +ATOM 585 CG1 VAL 39 26.722 26.078 9.101 1.00 0.00 C +ATOM 586 HG11 VAL 39 27.423 26.907 9.004 1.00 0.00 H +ATOM 587 HG12 VAL 39 26.995 25.443 8.259 1.00 0.00 H +ATOM 588 HG13 VAL 39 26.676 25.588 10.074 1.00 0.00 H +ATOM 589 CG2 VAL 39 24.427 25.517 8.721 1.00 0.00 C +ATOM 590 HG21 VAL 39 24.469 24.836 9.571 1.00 0.00 H +ATOM 591 HG22 VAL 39 24.630 24.988 7.790 1.00 0.00 H +ATOM 592 HG23 VAL 39 23.396 25.867 8.770 1.00 0.00 H +ATOM 593 C VAL 39 24.781 27.235 11.371 1.00 0.00 C +ATOM 594 O VAL 39 25.762 27.087 12.122 1.00 0.00 O +ATOM 595 N ASP 40 23.642 26.724 11.722 1.00 0.00 N +ATOM 596 H ASP 40 22.799 26.777 11.168 1.00 0.00 H +ATOM 597 CA ASP 40 23.366 26.156 13.053 1.00 0.00 C +ATOM 598 HA ASP 40 23.606 26.976 13.729 1.00 0.00 H +ATOM 599 CB ASP 40 21.853 25.869 13.054 1.00 0.00 C +ATOM 600 HB2 ASP 40 21.514 25.663 14.069 1.00 0.00 H +ATOM 601 HB3 ASP 40 21.323 26.734 12.657 1.00 0.00 H +ATOM 602 CG ASP 40 21.386 24.579 12.321 1.00 0.00 C +ATOM 603 OD1 ASP 40 20.153 24.536 12.104 1.00 0.00 O +ATOM 604 OD2 ASP 40 22.161 23.680 11.893 1.00 0.00 O +ATOM 605 C ASP 40 24.192 24.877 13.479 1.00 0.00 C +ATOM 606 O ASP 40 23.870 24.441 14.585 1.00 0.00 O +ATOM 607 N GLY 41 25.174 24.417 12.667 1.00 0.00 N +ATOM 608 H GLY 41 25.198 24.910 11.785 1.00 0.00 H +ATOM 609 CA GLY 41 26.038 23.314 12.928 1.00 0.00 C +ATOM 610 HA2 GLY 41 25.453 22.724 13.633 1.00 0.00 H +ATOM 611 HA3 GLY 41 26.014 22.777 11.980 1.00 0.00 H +ATOM 612 C GLY 41 27.403 23.740 13.412 1.00 0.00 C +ATOM 613 O GLY 41 28.121 22.902 14.008 1.00 0.00 O +ATOM 614 N GLU 42 27.810 25.003 13.358 1.00 0.00 N +ATOM 615 H GLU 42 27.188 25.641 12.882 1.00 0.00 H +ATOM 616 CA GLU 42 29.132 25.461 13.864 1.00 0.00 C +ATOM 617 HA GLU 42 29.915 24.754 13.587 1.00 0.00 H +ATOM 618 CB GLU 42 29.516 26.760 13.139 1.00 0.00 C +ATOM 619 HB2 GLU 42 28.798 27.482 13.528 1.00 0.00 H +ATOM 620 HB3 GLU 42 30.551 26.943 13.426 1.00 0.00 H +ATOM 621 CG GLU 42 29.591 26.689 11.549 1.00 0.00 C +ATOM 622 HG2 GLU 42 28.583 26.723 11.136 1.00 0.00 H +ATOM 623 HG3 GLU 42 30.153 27.573 11.246 1.00 0.00 H +ATOM 624 CD GLU 42 30.293 25.478 10.985 1.00 0.00 C +ATOM 625 OE1 GLU 42 31.555 25.591 11.047 1.00 0.00 O +ATOM 626 OE2 GLU 42 29.701 24.522 10.459 1.00 0.00 O +ATOM 627 C GLU 42 29.162 25.678 15.372 1.00 0.00 C +ATOM 628 O GLU 42 29.277 26.765 15.950 1.00 0.00 O +ATOM 629 N TRP 43 29.057 24.564 16.030 1.00 0.00 N +ATOM 630 H TRP 43 28.849 23.717 15.521 1.00 0.00 H +ATOM 631 CA TRP 43 29.134 24.483 17.533 1.00 0.00 C +ATOM 632 HA TRP 43 29.684 25.346 17.910 1.00 0.00 H +ATOM 633 CB TRP 43 27.778 24.694 18.155 1.00 0.00 C +ATOM 634 HB2 TRP 43 27.828 24.777 19.241 1.00 0.00 H +ATOM 635 HB3 TRP 43 27.481 25.681 17.801 1.00 0.00 H +ATOM 636 CG TRP 43 26.761 23.685 17.803 1.00 0.00 C +ATOM 637 CD1 TRP 43 25.817 23.907 16.844 1.00 0.00 C +ATOM 638 HD1 TRP 43 25.874 24.799 16.239 1.00 0.00 H +ATOM 639 NE1 TRP 43 25.000 22.828 16.752 1.00 0.00 N +ATOM 640 HE1 TRP 43 24.180 22.817 16.161 1.00 0.00 H +ATOM 641 CE2 TRP 43 25.318 21.892 17.690 1.00 0.00 C +ATOM 642 CZ2 TRP 43 24.680 20.680 18.094 1.00 0.00 C +ATOM 643 HZ2 TRP 43 23.754 20.395 17.616 1.00 0.00 H +ATOM 644 CH2 TRP 43 25.153 19.975 19.202 1.00 0.00 C +ATOM 645 HH2 TRP 43 24.568 19.149 19.578 1.00 0.00 H +ATOM 646 CZ3 TRP 43 26.259 20.476 19.924 1.00 0.00 C +ATOM 647 HZ3 TRP 43 26.472 19.940 20.837 1.00 0.00 H +ATOM 648 CE3 TRP 43 26.889 21.673 19.581 1.00 0.00 C +ATOM 649 HE3 TRP 43 27.581 22.160 20.253 1.00 0.00 H +ATOM 650 CD2 TRP 43 26.379 22.411 18.443 1.00 0.00 C +ATOM 651 C TRP 43 29.856 23.269 18.109 1.00 0.00 C +ATOM 652 O TRP 43 30.067 22.339 17.412 1.00 0.00 O +ATOM 653 N THR 44 30.293 23.380 19.363 1.00 0.00 N +ATOM 654 H THR 44 30.122 24.225 19.890 1.00 0.00 H +ATOM 655 CA THR 44 31.196 22.417 20.094 1.00 0.00 C +ATOM 656 HA THR 44 31.301 21.471 19.563 1.00 0.00 H +ATOM 657 CB THR 44 32.574 22.945 20.256 1.00 0.00 C +ATOM 658 HB THR 44 32.522 23.876 20.820 1.00 0.00 H +ATOM 659 CG2 THR 44 33.592 21.975 20.903 1.00 0.00 C +ATOM 660 HG21 THR 44 33.653 21.109 20.244 1.00 0.00 H +ATOM 661 HG22 THR 44 33.240 21.592 21.861 1.00 0.00 H +ATOM 662 HG23 THR 44 34.605 22.373 20.960 1.00 0.00 H +ATOM 663 OG1 THR 44 33.073 23.170 18.964 1.00 0.00 O +ATOM 664 HG1 THR 44 32.796 24.026 18.628 1.00 0.00 H +ATOM 665 C THR 44 30.670 22.099 21.493 1.00 0.00 C +ATOM 666 O THR 44 30.573 22.973 22.348 1.00 0.00 O +ATOM 667 N TYR 45 30.185 20.867 21.776 1.00 0.00 N +ATOM 668 H TYR 45 30.236 20.162 21.055 1.00 0.00 H +ATOM 669 CA TYR 45 29.654 20.464 23.123 1.00 0.00 C +ATOM 670 HA TYR 45 29.413 21.371 23.677 1.00 0.00 H +ATOM 671 CB TYR 45 28.295 19.754 22.944 1.00 0.00 C +ATOM 672 HB2 TYR 45 27.631 20.511 22.528 1.00 0.00 H +ATOM 673 HB3 TYR 45 28.499 18.965 22.221 1.00 0.00 H +ATOM 674 CG TYR 45 27.648 19.146 24.180 1.00 0.00 C +ATOM 675 CD1 TYR 45 27.297 19.878 25.364 1.00 0.00 C +ATOM 676 HD1 TYR 45 27.546 20.924 25.466 1.00 0.00 H +ATOM 677 CE1 TYR 45 26.678 19.155 26.400 1.00 0.00 C +ATOM 678 HE1 TYR 45 26.314 19.780 27.202 1.00 0.00 H +ATOM 679 CZ TYR 45 26.532 17.752 26.346 1.00 0.00 C +ATOM 680 OH TYR 45 25.965 17.162 27.406 1.00 0.00 O +ATOM 681 HH TYR 45 26.419 16.368 27.699 1.00 0.00 H +ATOM 682 CE2 TYR 45 26.860 17.066 25.221 1.00 0.00 C +ATOM 683 HE2 TYR 45 26.638 16.010 25.181 1.00 0.00 H +ATOM 684 CD2 TYR 45 27.434 17.728 24.101 1.00 0.00 C +ATOM 685 HD2 TYR 45 27.635 17.068 23.271 1.00 0.00 H +ATOM 686 C TYR 45 30.636 19.748 24.052 1.00 0.00 C +ATOM 687 O TYR 45 31.263 18.756 23.724 1.00 0.00 O +ATOM 688 N ASP 46 30.702 20.118 25.257 1.00 0.00 N +ATOM 689 H ASP 46 30.053 20.860 25.477 1.00 0.00 H +ATOM 690 CA ASP 46 31.466 19.480 26.365 1.00 0.00 C +ATOM 691 HA ASP 46 32.172 18.775 25.926 1.00 0.00 H +ATOM 692 CB ASP 46 32.260 20.517 27.069 1.00 0.00 C +ATOM 693 HB2 ASP 46 32.975 20.918 26.351 1.00 0.00 H +ATOM 694 HB3 ASP 46 31.748 21.387 27.481 1.00 0.00 H +ATOM 695 CG ASP 46 33.008 19.911 28.244 1.00 0.00 C +ATOM 696 OD1 ASP 46 33.142 18.655 28.291 1.00 0.00 O +ATOM 697 OD2 ASP 46 33.314 20.671 29.183 1.00 0.00 O +ATOM 698 C ASP 46 30.646 18.649 27.294 1.00 0.00 C +ATOM 699 O ASP 46 30.120 19.206 28.287 1.00 0.00 O +ATOM 700 N ASP 47 30.493 17.301 27.075 1.00 0.00 N +ATOM 701 H ASP 47 31.016 16.972 26.276 1.00 0.00 H +ATOM 702 CA ASP 47 29.680 16.471 27.869 1.00 0.00 C +ATOM 703 HA ASP 47 28.751 17.031 27.978 1.00 0.00 H +ATOM 704 CB ASP 47 29.399 15.147 27.137 1.00 0.00 C +ATOM 705 HB2 ASP 47 29.257 15.495 26.114 1.00 0.00 H +ATOM 706 HB3 ASP 47 30.303 14.539 27.134 1.00 0.00 H +ATOM 707 CG ASP 47 28.215 14.395 27.650 1.00 0.00 C +ATOM 708 OD1 ASP 47 27.094 14.921 27.901 1.00 0.00 O +ATOM 709 OD2 ASP 47 28.332 13.167 27.901 1.00 0.00 O +ATOM 710 C ASP 47 30.085 16.183 29.345 1.00 0.00 C +ATOM 711 O ASP 47 29.336 15.608 30.129 1.00 0.00 O +ATOM 712 N ALA 48 31.320 16.636 29.802 1.00 0.00 N +ATOM 713 H ALA 48 31.891 16.976 29.042 1.00 0.00 H +ATOM 714 CA ALA 48 31.882 16.518 31.185 1.00 0.00 C +ATOM 715 HA ALA 48 31.403 15.634 31.605 1.00 0.00 H +ATOM 716 CB ALA 48 33.387 16.354 31.063 1.00 0.00 C +ATOM 717 HB1 ALA 48 33.516 15.540 30.350 1.00 0.00 H +ATOM 718 HB2 ALA 48 33.867 16.056 31.995 1.00 0.00 H +ATOM 719 HB3 ALA 48 33.814 17.256 30.624 1.00 0.00 H +ATOM 720 C ALA 48 31.556 17.726 32.056 1.00 0.00 C +ATOM 721 O ALA 48 31.241 17.501 33.190 1.00 0.00 O +ATOM 722 N THR 49 31.580 18.934 31.494 1.00 0.00 N +ATOM 723 H THR 49 31.998 19.021 30.579 1.00 0.00 H +ATOM 724 CA THR 49 31.019 20.118 32.240 1.00 0.00 C +ATOM 725 HA THR 49 31.029 19.944 33.316 1.00 0.00 H +ATOM 726 CB THR 49 31.724 21.401 32.058 1.00 0.00 C +ATOM 727 HB THR 49 31.257 22.141 32.707 1.00 0.00 H +ATOM 728 CG2 THR 49 33.219 21.240 32.401 1.00 0.00 C +ATOM 729 HG21 THR 49 33.354 20.606 33.278 1.00 0.00 H +ATOM 730 HG22 THR 49 33.627 22.238 32.556 1.00 0.00 H +ATOM 731 HG23 THR 49 33.826 20.863 31.578 1.00 0.00 H +ATOM 732 OG1 THR 49 31.666 21.805 30.685 1.00 0.00 O +ATOM 733 HG1 THR 49 32.450 21.440 30.268 1.00 0.00 H +ATOM 734 C THR 49 29.556 20.304 31.958 1.00 0.00 C +ATOM 735 O THR 49 28.976 21.174 32.618 1.00 0.00 O +ATOM 736 N LYS 50 29.057 19.721 30.844 1.00 0.00 N +ATOM 737 H LYS 50 29.726 19.097 30.416 1.00 0.00 H +ATOM 738 CA LYS 50 27.842 20.166 30.212 1.00 0.00 C +ATOM 739 HA LYS 50 27.763 19.470 29.378 1.00 0.00 H +ATOM 740 CB LYS 50 26.591 19.875 31.114 1.00 0.00 C +ATOM 741 HB2 LYS 50 26.380 20.722 31.767 1.00 0.00 H +ATOM 742 HB3 LYS 50 25.817 19.904 30.346 1.00 0.00 H +ATOM 743 CG LYS 50 26.481 18.478 31.783 1.00 0.00 C +ATOM 744 HG2 LYS 50 27.315 18.273 32.454 1.00 0.00 H +ATOM 745 HG3 LYS 50 25.595 18.510 32.417 1.00 0.00 H +ATOM 746 CD LYS 50 26.399 17.307 30.782 1.00 0.00 C +ATOM 747 HD2 LYS 50 25.480 17.464 30.218 1.00 0.00 H +ATOM 748 HD3 LYS 50 27.253 17.341 30.106 1.00 0.00 H +ATOM 749 CE LYS 50 26.375 15.903 31.309 1.00 0.00 C +ATOM 750 HE2 LYS 50 27.381 15.606 31.606 1.00 0.00 H +ATOM 751 HE3 LYS 50 25.771 15.887 32.216 1.00 0.00 H +ATOM 752 NZ LYS 50 25.759 14.893 30.384 1.00 0.00 N +ATOM 753 HZ1 LYS 50 24.855 15.020 29.953 1.00 0.00 H +ATOM 754 HZ2 LYS 50 25.758 14.110 31.021 1.00 0.00 H +ATOM 755 HZ3 LYS 50 26.384 14.665 29.624 1.00 0.00 H +ATOM 756 C LYS 50 27.950 21.536 29.581 1.00 0.00 C +ATOM 757 O LYS 50 26.914 22.204 29.684 1.00 0.00 O +ATOM 758 N THR 51 29.080 21.965 29.019 1.00 0.00 N +ATOM 759 H THR 51 29.907 21.391 29.098 1.00 0.00 H +ATOM 760 CA THR 51 29.031 23.345 28.324 1.00 0.00 C +ATOM 761 HA THR 51 28.225 23.989 28.677 1.00 0.00 H +ATOM 762 CB THR 51 30.406 24.054 28.620 1.00 0.00 C +ATOM 763 HB THR 51 31.334 23.493 28.513 1.00 0.00 H +ATOM 764 CG2 THR 51 30.468 25.322 27.808 1.00 0.00 C +ATOM 765 HG21 THR 51 31.233 25.901 28.326 1.00 0.00 H +ATOM 766 HG22 THR 51 29.648 26.012 28.009 1.00 0.00 H +ATOM 767 HG23 THR 51 30.769 25.233 26.764 1.00 0.00 H +ATOM 768 OG1 THR 51 30.283 24.377 29.983 1.00 0.00 O +ATOM 769 HG1 THR 51 30.355 23.609 30.553 1.00 0.00 H +ATOM 770 C THR 51 28.802 23.298 26.773 1.00 0.00 C +ATOM 771 O THR 51 29.401 22.543 26.055 1.00 0.00 O +ATOM 772 N PHE 52 27.825 24.126 26.255 1.00 0.00 N +ATOM 773 H PHE 52 27.173 24.581 26.877 1.00 0.00 H +ATOM 774 CA PHE 52 27.638 24.491 24.868 1.00 0.00 C +ATOM 775 HA PHE 52 28.130 23.729 24.264 1.00 0.00 H +ATOM 776 CB PHE 52 26.217 24.412 24.385 1.00 0.00 C +ATOM 777 HB2 PHE 52 25.648 25.152 24.948 1.00 0.00 H +ATOM 778 HB3 PHE 52 26.227 24.709 23.336 1.00 0.00 H +ATOM 779 CG PHE 52 25.514 23.048 24.397 1.00 0.00 C +ATOM 780 CD1 PHE 52 24.844 22.569 25.560 1.00 0.00 C +ATOM 781 HD1 PHE 52 24.947 23.140 26.471 1.00 0.00 H +ATOM 782 CE1 PHE 52 24.121 21.368 25.445 1.00 0.00 C +ATOM 783 HE1 PHE 52 23.579 21.047 26.323 1.00 0.00 H +ATOM 784 CZ PHE 52 24.013 20.685 24.282 1.00 0.00 C +ATOM 785 HZ PHE 52 23.599 19.689 24.228 1.00 0.00 H +ATOM 786 CE2 PHE 52 24.645 21.181 23.137 1.00 0.00 C +ATOM 787 HE2 PHE 52 24.572 20.572 22.248 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.453 22.324 23.181 1.00 0.00 C +ATOM 789 HD2 PHE 52 25.865 22.749 22.277 1.00 0.00 H +ATOM 790 C PHE 52 28.310 25.861 24.577 1.00 0.00 C +ATOM 791 O PHE 52 28.217 26.927 25.311 1.00 0.00 O +ATOM 792 N THR 53 28.871 25.912 23.409 1.00 0.00 N +ATOM 793 H THR 53 28.923 25.021 22.935 1.00 0.00 H +ATOM 794 CA THR 53 29.459 27.070 22.729 1.00 0.00 C +ATOM 795 HA THR 53 28.849 27.904 23.076 1.00 0.00 H +ATOM 796 CB THR 53 30.846 27.377 23.303 1.00 0.00 C +ATOM 797 HB THR 53 30.760 27.508 24.382 1.00 0.00 H +ATOM 798 CG2 THR 53 31.876 26.289 22.990 1.00 0.00 C +ATOM 799 HG21 THR 53 31.422 25.367 23.353 1.00 0.00 H +ATOM 800 HG22 THR 53 32.810 26.367 23.547 1.00 0.00 H +ATOM 801 HG23 THR 53 32.016 26.131 21.921 1.00 0.00 H +ATOM 802 OG1 THR 53 31.328 28.642 22.733 1.00 0.00 O +ATOM 803 HG1 THR 53 32.248 28.428 22.562 1.00 0.00 H +ATOM 804 C THR 53 29.524 26.992 21.185 1.00 0.00 C +ATOM 805 O THR 53 29.688 25.894 20.643 1.00 0.00 O +ATOM 806 N VAL 54 29.447 28.125 20.512 1.00 0.00 N +ATOM 807 H VAL 54 29.257 28.924 21.099 1.00 0.00 H +ATOM 808 CA VAL 54 29.764 28.304 19.069 1.00 0.00 C +ATOM 809 HA VAL 54 29.181 27.526 18.576 1.00 0.00 H +ATOM 810 CB VAL 54 29.376 29.765 18.579 1.00 0.00 C +ATOM 811 HB VAL 54 28.286 29.779 18.593 1.00 0.00 H +ATOM 812 CG1 VAL 54 29.810 30.976 19.413 1.00 0.00 C +ATOM 813 HG11 VAL 54 29.131 31.798 19.187 1.00 0.00 H +ATOM 814 HG12 VAL 54 30.813 31.330 19.172 1.00 0.00 H +ATOM 815 HG13 VAL 54 29.768 30.871 20.497 1.00 0.00 H +ATOM 816 CG2 VAL 54 29.794 30.020 17.165 1.00 0.00 C +ATOM 817 HG21 VAL 54 29.499 29.247 16.456 1.00 0.00 H +ATOM 818 HG22 VAL 54 30.860 30.213 17.045 1.00 0.00 H +ATOM 819 HG23 VAL 54 29.260 30.921 16.863 1.00 0.00 H +ATOM 820 C VAL 54 31.191 27.991 18.836 1.00 0.00 C +ATOM 821 O VAL 54 32.089 28.285 19.670 1.00 0.00 O +ATOM 822 N THR 55 31.437 27.239 17.782 1.00 0.00 N +ATOM 823 H THR 55 30.663 26.939 17.207 1.00 0.00 H +ATOM 824 CA THR 55 32.824 26.897 17.428 1.00 0.00 C +ATOM 825 HA THR 55 33.395 26.440 18.236 1.00 0.00 H +ATOM 826 CB THR 55 32.898 25.937 16.275 1.00 0.00 C +ATOM 827 HB THR 55 32.282 26.205 15.416 1.00 0.00 H +ATOM 828 CG2 THR 55 34.338 25.423 15.775 1.00 0.00 C +ATOM 829 HG21 THR 55 34.370 24.342 15.641 1.00 0.00 H +ATOM 830 HG22 THR 55 35.173 25.638 16.442 1.00 0.00 H +ATOM 831 HG23 THR 55 34.598 25.970 14.868 1.00 0.00 H +ATOM 832 OG1 THR 55 32.155 24.816 16.707 1.00 0.00 O +ATOM 833 HG1 THR 55 32.228 24.131 16.038 1.00 0.00 H +ATOM 834 C THR 55 33.678 28.109 17.119 1.00 0.00 C +ATOM 835 O THR 55 33.154 29.076 16.470 1.00 0.00 O +ATOM 836 N GLU 56 34.995 28.164 17.379 1.00 0.00 N +ATOM 837 H GLU 56 35.408 27.387 17.874 1.00 0.00 H +ATOM 838 CA GLU 56 35.890 29.279 17.033 1.00 0.00 C +ATOM 839 HA GLU 56 35.254 30.162 16.971 1.00 0.00 H +ATOM 840 CB GLU 56 37.090 29.315 18.055 1.00 0.00 C +ATOM 841 HB2 GLU 56 37.628 28.368 18.023 1.00 0.00 H +ATOM 842 HB3 GLU 56 37.816 30.063 17.737 1.00 0.00 H +ATOM 843 CG GLU 56 36.723 29.576 19.531 1.00 0.00 C +ATOM 844 HG2 GLU 56 36.050 28.760 19.795 1.00 0.00 H +ATOM 845 HG3 GLU 56 37.675 29.542 20.061 1.00 0.00 H +ATOM 846 CD GLU 56 36.042 30.936 19.684 1.00 0.00 C +ATOM 847 OE1 GLU 56 34.910 31.096 20.169 1.00 0.00 O +ATOM 848 OE2 GLU 56 36.678 31.881 19.156 1.00 0.00 O +ATOM 849 C GLU 56 36.320 29.197 15.568 1.00 0.00 C +ATOM 850 O GLU 56 35.978 30.112 14.827 1.00 0.00 O +ATOM 851 OXT GLU 56 36.896 28.179 15.147 1.00 0.00 O +ATOM 852 ZN ZN1 57 22.438 31.593 26.978 1.00 0.00 ZN +ATOM 853 N AN1 58 21.407 33.028 25.982 1.00 0.00 N +ATOM 854 C AN1 58 20.587 35.181 24.711 1.00 0.00 C +ATOM 855 C1 AN1 58 21.058 34.024 25.469 1.00 0.00 C +ATOM 856 H AN1 58 19.821 34.731 24.067 1.00 0.00 H +ATOM 857 H1 AN1 58 21.430 35.521 24.097 1.00 0.00 H +ATOM 858 H2 AN1 58 20.073 35.933 25.322 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 23.253 36.369 26.590 1.00 0.00 N +ATOM 860 N2 AZI 59 22.284 36.298 27.376 1.00 0.00 N +ATOM 861 N3 AZI 59 21.360 36.380 28.225 1.00 0.00 N +TER 862 AZI 59 diff --git a/tests/nsga2/pdbs_rename/cluster14.pdb b/tests/nsga2/pdbs_rename/cluster14.pdb new file mode 100644 index 0000000..8606965 --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster14.pdb @@ -0,0 +1,864 @@ +CRYST1 51.642 53.271 47.366 90.00 90.00 90.00 1 +ATOM 1 N MET 1 17.848 20.878 33.887 1.00 0.00 N +ATOM 2 H1 MET 1 17.338 21.749 33.841 1.00 0.00 H +ATOM 3 H2 MET 1 17.313 20.196 34.405 1.00 0.00 H +ATOM 4 H3 MET 1 17.817 20.401 32.998 1.00 0.00 H +ATOM 5 CA MET 1 19.164 21.097 34.398 1.00 0.00 C +ATOM 6 HA MET 1 19.122 21.288 35.470 1.00 0.00 H +ATOM 7 CB MET 1 19.944 19.804 34.330 1.00 0.00 C +ATOM 8 HB2 MET 1 19.550 19.096 35.059 1.00 0.00 H +ATOM 9 HB3 MET 1 19.851 19.291 33.372 1.00 0.00 H +ATOM 10 CG MET 1 21.436 20.026 34.540 1.00 0.00 C +ATOM 11 HG2 MET 1 21.950 20.622 33.786 1.00 0.00 H +ATOM 12 HG3 MET 1 21.556 20.470 35.528 1.00 0.00 H +ATOM 13 SD MET 1 22.382 18.493 34.745 1.00 0.00 S +ATOM 14 CE MET 1 21.750 17.877 36.362 1.00 0.00 C +ATOM 15 HE1 MET 1 20.666 17.979 36.408 1.00 0.00 H +ATOM 16 HE2 MET 1 22.004 18.570 37.164 1.00 0.00 H +ATOM 17 HE3 MET 1 22.175 16.888 36.534 1.00 0.00 H +ATOM 18 C MET 1 19.781 22.250 33.574 1.00 0.00 C +ATOM 19 O MET 1 19.477 22.328 32.367 1.00 0.00 O +ATOM 20 N GLN 2 20.569 23.113 34.226 1.00 0.00 N +ATOM 21 H GLN 2 20.731 23.102 35.222 1.00 0.00 H +ATOM 22 CA GLN 2 21.259 24.172 33.576 1.00 0.00 C +ATOM 23 HA GLN 2 20.608 24.499 32.766 1.00 0.00 H +ATOM 24 CB GLN 2 21.649 25.252 34.612 1.00 0.00 C +ATOM 25 HB2 GLN 2 22.130 24.781 35.470 1.00 0.00 H +ATOM 26 HB3 GLN 2 22.459 25.821 34.157 1.00 0.00 H +ATOM 27 CG GLN 2 20.451 26.082 35.202 1.00 0.00 C +ATOM 28 HG2 GLN 2 19.645 25.364 35.352 1.00 0.00 H +ATOM 29 HG3 GLN 2 20.685 26.596 36.134 1.00 0.00 H +ATOM 30 CD GLN 2 19.945 27.222 34.189 1.00 0.00 C +ATOM 31 OE1 GLN 2 20.558 27.360 33.113 1.00 0.00 O +ATOM 32 NE2 GLN 2 19.013 28.012 34.481 1.00 0.00 N +ATOM 33 HE21 GLN 2 18.724 28.785 33.900 1.00 0.00 H +ATOM 34 HE22 GLN 2 18.489 27.739 35.300 1.00 0.00 H +ATOM 35 C GLN 2 22.540 23.757 32.868 1.00 0.00 C +ATOM 36 O GLN 2 23.444 23.130 33.520 1.00 0.00 O +ATOM 37 N TYR 3 22.636 23.851 31.515 1.00 0.00 N +ATOM 38 H TYR 3 21.857 24.222 30.990 1.00 0.00 H +ATOM 39 CA TYR 3 23.843 23.469 30.767 1.00 0.00 C +ATOM 40 HA TYR 3 24.504 22.866 31.389 1.00 0.00 H +ATOM 41 CB TYR 3 23.387 22.662 29.524 1.00 0.00 C +ATOM 42 HB2 TYR 3 22.791 23.238 28.817 1.00 0.00 H +ATOM 43 HB3 TYR 3 24.308 22.506 28.961 1.00 0.00 H +ATOM 44 CG TYR 3 22.666 21.409 29.808 1.00 0.00 C +ATOM 45 CD1 TYR 3 23.366 20.229 29.986 1.00 0.00 C +ATOM 46 HD1 TYR 3 24.436 20.269 29.842 1.00 0.00 H +ATOM 47 CE1 TYR 3 22.706 19.068 30.246 1.00 0.00 C +ATOM 48 HE1 TYR 3 23.194 18.110 30.346 1.00 0.00 H +ATOM 49 CZ TYR 3 21.321 19.008 30.444 1.00 0.00 C +ATOM 50 OH TYR 3 20.691 17.887 30.914 1.00 0.00 O +ATOM 51 HH TYR 3 21.322 17.178 31.059 1.00 0.00 H +ATOM 52 CE2 TYR 3 20.570 20.136 30.345 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.498 20.146 30.477 1.00 0.00 H +ATOM 54 CD2 TYR 3 21.216 21.353 29.976 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.640 22.266 29.995 1.00 0.00 H +ATOM 56 C TYR 3 24.620 24.745 30.392 1.00 0.00 C +ATOM 57 O TYR 3 24.093 25.719 29.884 1.00 0.00 O +ATOM 58 N LYS 4 25.934 24.641 30.616 1.00 0.00 N +ATOM 59 H LYS 4 26.362 23.771 30.899 1.00 0.00 H +ATOM 60 CA LYS 4 26.830 25.766 30.219 1.00 0.00 C +ATOM 61 HA LYS 4 26.335 26.721 30.395 1.00 0.00 H +ATOM 62 CB LYS 4 28.138 25.693 31.008 1.00 0.00 C +ATOM 63 HB2 LYS 4 27.966 25.697 32.084 1.00 0.00 H +ATOM 64 HB3 LYS 4 28.643 24.740 30.851 1.00 0.00 H +ATOM 65 CG LYS 4 29.124 26.855 30.718 1.00 0.00 C +ATOM 66 HG2 LYS 4 29.539 26.711 29.721 1.00 0.00 H +ATOM 67 HG3 LYS 4 28.619 27.819 30.652 1.00 0.00 H +ATOM 68 CD LYS 4 30.230 27.017 31.684 1.00 0.00 C +ATOM 69 HD2 LYS 4 30.825 27.874 31.367 1.00 0.00 H +ATOM 70 HD3 LYS 4 29.785 27.248 32.652 1.00 0.00 H +ATOM 71 CE LYS 4 31.242 25.906 31.766 1.00 0.00 C +ATOM 72 HE2 LYS 4 30.751 25.032 32.194 1.00 0.00 H +ATOM 73 HE3 LYS 4 31.562 25.511 30.802 1.00 0.00 H +ATOM 74 NZ LYS 4 32.390 26.363 32.510 1.00 0.00 N +ATOM 75 HZ1 LYS 4 32.926 27.137 32.143 1.00 0.00 H +ATOM 76 HZ2 LYS 4 33.087 25.647 32.655 1.00 0.00 H +ATOM 77 HZ3 LYS 4 32.021 26.619 33.414 1.00 0.00 H +ATOM 78 C LYS 4 27.055 25.724 28.693 1.00 0.00 C +ATOM 79 O LYS 4 27.271 24.689 28.058 1.00 0.00 O +ATOM 80 N HX1 5 27.128 26.940 28.195 1.00 0.00 N +ATOM 81 CA HX1 5 27.523 27.414 26.851 1.00 0.00 C +ATOM 82 C HX1 5 28.718 28.374 26.842 1.00 0.00 C +ATOM 83 O HX1 5 28.496 29.602 26.894 1.00 0.00 O +ATOM 84 CB HX1 5 26.356 28.048 26.064 1.00 0.00 C +ATOM 85 CG HX1 5 26.626 28.198 24.569 1.00 0.00 C +ATOM 86 CD2 HX1 5 27.726 27.738 23.829 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.744 28.879 23.761 1.00 0.00 N +ATOM 88 CE1 HX1 5 26.224 28.746 22.528 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.428 28.091 22.517 1.00 0.00 N +ATOM 90 H HX1 5 27.001 27.677 28.874 1.00 0.00 H +ATOM 91 HA HX1 5 27.859 26.531 26.308 1.00 0.00 H +ATOM 92 HB2 HX1 5 26.098 29.067 26.354 1.00 0.00 H +ATOM 93 HB3 HX1 5 25.457 27.433 26.102 1.00 0.00 H +ATOM 94 HD2 HX1 5 28.640 27.257 24.144 1.00 0.00 H +ATOM 95 HE1 HX1 5 25.782 29.102 21.609 1.00 0.00 H +ATOM 96 HE2 HX1 5 27.976 27.902 21.690 1.00 0.00 H +ATOM 97 N ILE 6 29.913 27.813 26.633 1.00 0.00 N +ATOM 98 H ILE 6 29.998 26.808 26.666 1.00 0.00 H +ATOM 99 CA ILE 6 31.127 28.626 26.271 1.00 0.00 C +ATOM 100 HA ILE 6 31.195 29.552 26.842 1.00 0.00 H +ATOM 101 CB ILE 6 32.472 27.954 26.722 1.00 0.00 C +ATOM 102 HB ILE 6 32.710 27.169 26.004 1.00 0.00 H +ATOM 103 CG2 ILE 6 33.573 29.120 26.740 1.00 0.00 C +ATOM 104 HG21 ILE 6 34.550 28.648 26.848 1.00 0.00 H +ATOM 105 HG22 ILE 6 33.436 29.828 27.558 1.00 0.00 H +ATOM 106 HG23 ILE 6 33.554 29.747 25.849 1.00 0.00 H +ATOM 107 CG1 ILE 6 32.366 27.296 28.124 1.00 0.00 C +ATOM 108 HG12 ILE 6 32.212 28.082 28.863 1.00 0.00 H +ATOM 109 HG13 ILE 6 31.597 26.544 28.298 1.00 0.00 H +ATOM 110 CD1 ILE 6 33.675 26.624 28.553 1.00 0.00 C +ATOM 111 HD11 ILE 6 34.367 27.350 28.979 1.00 0.00 H +ATOM 112 HD12 ILE 6 34.205 26.133 27.737 1.00 0.00 H +ATOM 113 HD13 ILE 6 33.582 25.816 29.280 1.00 0.00 H +ATOM 114 C ILE 6 31.118 29.059 24.797 1.00 0.00 C +ATOM 115 O ILE 6 30.775 28.237 23.948 1.00 0.00 O +ATOM 116 N VAL 7 31.551 30.245 24.458 1.00 0.00 N +ATOM 117 H VAL 7 31.954 30.760 25.228 1.00 0.00 H +ATOM 118 CA VAL 7 31.203 31.009 23.213 1.00 0.00 C +ATOM 119 HA VAL 7 30.961 30.318 22.406 1.00 0.00 H +ATOM 120 CB VAL 7 30.042 31.987 23.544 1.00 0.00 C +ATOM 121 HB VAL 7 29.858 32.665 22.711 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.713 31.194 23.889 1.00 0.00 C +ATOM 123 HG11 VAL 7 27.859 31.869 23.949 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.440 30.412 23.181 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.697 30.756 24.887 1.00 0.00 H +ATOM 126 CG2 VAL 7 30.453 32.941 24.637 1.00 0.00 C +ATOM 127 HG21 VAL 7 29.530 33.430 24.949 1.00 0.00 H +ATOM 128 HG22 VAL 7 30.990 32.401 25.417 1.00 0.00 H +ATOM 129 HG23 VAL 7 31.138 33.755 24.399 1.00 0.00 H +ATOM 130 C VAL 7 32.376 31.850 22.664 1.00 0.00 C +ATOM 131 O VAL 7 33.263 32.285 23.417 1.00 0.00 O +ATOM 132 N ASN 8 32.294 32.365 21.383 1.00 0.00 N +ATOM 133 H ASN 8 31.477 32.185 20.817 1.00 0.00 H +ATOM 134 CA ASN 8 33.320 33.228 20.800 1.00 0.00 C +ATOM 135 HA ASN 8 34.307 32.770 20.874 1.00 0.00 H +ATOM 136 CB ASN 8 33.001 33.310 19.290 1.00 0.00 C +ATOM 137 HB2 ASN 8 33.043 32.299 18.884 1.00 0.00 H +ATOM 138 HB3 ASN 8 32.022 33.779 19.191 1.00 0.00 H +ATOM 139 CG ASN 8 33.975 34.164 18.463 1.00 0.00 C +ATOM 140 OD1 ASN 8 34.174 35.325 18.756 1.00 0.00 O +ATOM 141 ND2 ASN 8 34.752 33.676 17.534 1.00 0.00 N +ATOM 142 HD21 ASN 8 34.716 32.739 17.158 1.00 0.00 H +ATOM 143 HD22 ASN 8 35.625 34.153 17.360 1.00 0.00 H +ATOM 144 C ASN 8 33.400 34.563 21.595 1.00 0.00 C +ATOM 145 O ASN 8 32.309 35.162 21.860 1.00 0.00 O +ATOM 146 N GLY 9 34.580 35.191 21.734 1.00 0.00 N +ATOM 147 H GLY 9 35.399 34.830 21.266 1.00 0.00 H +ATOM 148 CA GLY 9 34.740 36.458 22.509 1.00 0.00 C +ATOM 149 HA2 GLY 9 34.342 36.418 23.523 1.00 0.00 H +ATOM 150 HA3 GLY 9 35.813 36.525 22.687 1.00 0.00 H +ATOM 151 C GLY 9 34.275 37.705 21.869 1.00 0.00 C +ATOM 152 O GLY 9 34.102 38.729 22.509 1.00 0.00 O +ATOM 153 N LYS 10 33.939 37.679 20.579 1.00 0.00 N +ATOM 154 H LYS 10 34.105 36.804 20.103 1.00 0.00 H +ATOM 155 CA LYS 10 33.099 38.659 19.922 1.00 0.00 C +ATOM 156 HA LYS 10 33.606 39.607 20.106 1.00 0.00 H +ATOM 157 CB LYS 10 33.211 38.439 18.412 1.00 0.00 C +ATOM 158 HB2 LYS 10 32.815 37.444 18.206 1.00 0.00 H +ATOM 159 HB3 LYS 10 32.581 39.198 17.947 1.00 0.00 H +ATOM 160 CG LYS 10 34.638 38.475 17.847 1.00 0.00 C +ATOM 161 HG2 LYS 10 35.071 39.442 18.106 1.00 0.00 H +ATOM 162 HG3 LYS 10 35.272 37.700 18.275 1.00 0.00 H +ATOM 163 CD LYS 10 34.651 38.442 16.331 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.066 39.227 15.853 1.00 0.00 H +ATOM 165 HD3 LYS 10 35.660 38.563 15.935 1.00 0.00 H +ATOM 166 CE LYS 10 34.195 37.099 15.891 1.00 0.00 C +ATOM 167 HE2 LYS 10 34.720 36.252 16.334 1.00 0.00 H +ATOM 168 HE3 LYS 10 33.186 36.933 16.267 1.00 0.00 H +ATOM 169 NZ LYS 10 34.314 36.848 14.470 1.00 0.00 N +ATOM 170 HZ1 LYS 10 33.851 35.990 14.205 1.00 0.00 H +ATOM 171 HZ2 LYS 10 35.296 36.663 14.323 1.00 0.00 H +ATOM 172 HZ3 LYS 10 34.000 37.626 13.908 1.00 0.00 H +ATOM 173 C LYS 10 31.692 38.822 20.444 1.00 0.00 C +ATOM 174 O LYS 10 31.027 39.818 20.082 1.00 0.00 O +ATOM 175 N THR 11 31.113 37.691 20.886 1.00 0.00 N +ATOM 176 H THR 11 31.776 36.935 20.976 1.00 0.00 H +ATOM 177 CA THR 11 29.726 37.593 21.261 1.00 0.00 C +ATOM 178 HA THR 11 29.228 38.034 20.398 1.00 0.00 H +ATOM 179 CB THR 11 29.136 36.224 21.581 1.00 0.00 C +ATOM 180 HB THR 11 28.065 36.170 21.773 1.00 0.00 H +ATOM 181 CG2 THR 11 29.276 35.422 20.404 1.00 0.00 C +ATOM 182 HG21 THR 11 28.711 35.844 19.572 1.00 0.00 H +ATOM 183 HG22 THR 11 28.931 34.403 20.581 1.00 0.00 H +ATOM 184 HG23 THR 11 30.297 35.370 20.028 1.00 0.00 H +ATOM 185 OG1 THR 11 29.786 35.556 22.613 1.00 0.00 O +ATOM 186 HG1 THR 11 30.738 35.519 22.497 1.00 0.00 H +ATOM 187 C THR 11 29.450 38.500 22.463 1.00 0.00 C +ATOM 188 O THR 11 30.242 38.594 23.391 1.00 0.00 O +ATOM 189 N LEU 12 28.254 39.162 22.383 1.00 0.00 N +ATOM 190 H LEU 12 27.655 38.945 21.599 1.00 0.00 H +ATOM 191 CA LEU 12 27.947 40.086 23.439 1.00 0.00 C +ATOM 192 HA LEU 12 28.861 40.665 23.570 1.00 0.00 H +ATOM 193 CB LEU 12 26.837 41.046 22.998 1.00 0.00 C +ATOM 194 HB2 LEU 12 26.062 40.400 22.585 1.00 0.00 H +ATOM 195 HB3 LEU 12 26.388 41.604 23.819 1.00 0.00 H +ATOM 196 CG LEU 12 27.200 42.156 21.987 1.00 0.00 C +ATOM 197 HG LEU 12 27.406 41.676 21.030 1.00 0.00 H +ATOM 198 CD1 LEU 12 25.943 42.931 21.662 1.00 0.00 C +ATOM 199 HD11 LEU 12 25.167 42.206 21.415 1.00 0.00 H +ATOM 200 HD12 LEU 12 26.012 43.636 20.834 1.00 0.00 H +ATOM 201 HD13 LEU 12 25.552 43.499 22.506 1.00 0.00 H +ATOM 202 CD2 LEU 12 28.341 43.090 22.282 1.00 0.00 C +ATOM 203 HD21 LEU 12 28.152 43.545 23.254 1.00 0.00 H +ATOM 204 HD22 LEU 12 28.346 43.952 21.615 1.00 0.00 H +ATOM 205 HD23 LEU 12 29.370 42.766 22.127 1.00 0.00 H +ATOM 206 C LEU 12 27.554 39.316 24.703 1.00 0.00 C +ATOM 207 O LEU 12 26.702 38.439 24.634 1.00 0.00 O +ATOM 208 N LYS 13 27.948 39.778 25.850 1.00 0.00 N +ATOM 209 H LYS 13 28.593 40.553 25.785 1.00 0.00 H +ATOM 210 CA LYS 13 27.661 39.180 27.189 1.00 0.00 C +ATOM 211 HA LYS 13 28.032 39.904 27.914 1.00 0.00 H +ATOM 212 CB LYS 13 26.145 38.966 27.452 1.00 0.00 C +ATOM 213 HB2 LYS 13 25.533 39.741 26.989 1.00 0.00 H +ATOM 214 HB3 LYS 13 25.786 38.089 26.913 1.00 0.00 H +ATOM 215 CG LYS 13 25.617 38.871 28.809 1.00 0.00 C +ATOM 216 HG2 LYS 13 24.616 38.450 28.711 1.00 0.00 H +ATOM 217 HG3 LYS 13 26.174 38.123 29.373 1.00 0.00 H +ATOM 218 CD LYS 13 25.635 40.308 29.488 1.00 0.00 C +ATOM 219 HD2 LYS 13 26.555 40.861 29.302 1.00 0.00 H +ATOM 220 HD3 LYS 13 24.892 41.049 29.192 1.00 0.00 H +ATOM 221 CE LYS 13 25.561 40.210 30.965 1.00 0.00 C +ATOM 222 HE2 LYS 13 24.682 39.624 31.232 1.00 0.00 H +ATOM 223 HE3 LYS 13 26.451 39.669 31.286 1.00 0.00 H +ATOM 224 NZ LYS 13 25.568 41.465 31.666 1.00 0.00 N +ATOM 225 HZ1 LYS 13 24.904 42.154 31.343 1.00 0.00 H +ATOM 226 HZ2 LYS 13 26.474 41.908 31.615 1.00 0.00 H +ATOM 227 HZ3 LYS 13 25.365 41.261 32.635 1.00 0.00 H +ATOM 228 C LYS 13 28.492 37.950 27.578 1.00 0.00 C +ATOM 229 O LYS 13 28.781 37.748 28.736 1.00 0.00 O +ATOM 230 N GLY 14 28.901 37.173 26.520 1.00 0.00 N +ATOM 231 H GLY 14 28.544 37.369 25.596 1.00 0.00 H +ATOM 232 CA GLY 14 29.907 36.118 26.526 1.00 0.00 C +ATOM 233 HA2 GLY 14 30.380 35.931 25.562 1.00 0.00 H +ATOM 234 HA3 GLY 14 30.803 36.251 27.132 1.00 0.00 H +ATOM 235 C GLY 14 29.250 34.841 27.077 1.00 0.00 C +ATOM 236 O GLY 14 28.065 34.541 26.832 1.00 0.00 O +ATOM 237 N VAL 15 30.063 34.065 27.744 1.00 0.00 N +ATOM 238 H VAL 15 31.007 34.356 27.954 1.00 0.00 H +ATOM 239 CA VAL 15 29.754 32.652 28.368 1.00 0.00 C +ATOM 240 HA VAL 15 29.634 31.951 27.542 1.00 0.00 H +ATOM 241 CB VAL 15 31.002 32.175 29.064 1.00 0.00 C +ATOM 242 HB VAL 15 31.809 32.110 28.334 1.00 0.00 H +ATOM 243 CG1 VAL 15 31.467 32.936 30.270 1.00 0.00 C +ATOM 244 HG11 VAL 15 31.599 33.988 30.018 1.00 0.00 H +ATOM 245 HG12 VAL 15 30.730 32.873 31.070 1.00 0.00 H +ATOM 246 HG13 VAL 15 32.390 32.478 30.625 1.00 0.00 H +ATOM 247 CG2 VAL 15 30.752 30.685 29.514 1.00 0.00 C +ATOM 248 HG21 VAL 15 30.150 30.174 28.762 1.00 0.00 H +ATOM 249 HG22 VAL 15 31.689 30.208 29.800 1.00 0.00 H +ATOM 250 HG23 VAL 15 30.165 30.694 30.432 1.00 0.00 H +ATOM 251 C VAL 15 28.498 32.613 29.199 1.00 0.00 C +ATOM 252 O VAL 15 28.418 33.425 30.106 1.00 0.00 O +ATOM 253 N HY1 16 27.531 31.742 28.949 1.00 0.00 N +ATOM 254 CA HY1 16 26.171 31.753 29.568 1.00 0.00 C +ATOM 255 C HY1 16 25.679 30.330 29.596 1.00 0.00 C +ATOM 256 O HY1 16 26.298 29.336 29.224 1.00 0.00 O +ATOM 257 CB HY1 16 25.288 32.673 28.779 1.00 0.00 C +ATOM 258 CG HY1 16 25.204 32.360 27.280 1.00 0.00 C +ATOM 259 CD2 HY1 16 24.317 31.431 26.758 1.00 0.00 C +ATOM 260 ND1 HY1 16 25.875 32.875 26.268 1.00 0.00 N +ATOM 261 CE1 HY1 16 25.475 32.373 25.089 1.00 0.00 C +ATOM 262 NE2 HY1 16 24.549 31.387 25.374 1.00 0.00 N +ATOM 263 H HY1 16 27.706 31.019 28.266 1.00 0.00 H +ATOM 264 HA HY1 16 26.222 32.103 30.599 1.00 0.00 H +ATOM 265 HB2 HY1 16 24.296 32.758 29.224 1.00 0.00 H +ATOM 266 HB3 HY1 16 25.749 33.645 28.955 1.00 0.00 H +ATOM 267 HD1 HY1 16 26.661 33.509 26.294 1.00 0.00 H +ATOM 268 HD2 HY1 16 23.546 30.856 27.248 1.00 0.00 H +ATOM 269 HE1 HY1 16 25.797 32.625 24.089 1.00 0.00 H +ATOM 270 N THR 17 24.447 30.164 30.147 1.00 0.00 N +ATOM 271 H THR 17 23.895 30.997 30.296 1.00 0.00 H +ATOM 272 CA THR 17 23.797 28.861 30.346 1.00 0.00 C +ATOM 273 HA THR 17 24.460 28.099 29.937 1.00 0.00 H +ATOM 274 CB THR 17 23.602 28.594 31.883 1.00 0.00 C +ATOM 275 HB THR 17 23.347 27.534 31.863 1.00 0.00 H +ATOM 276 CG2 THR 17 24.837 28.940 32.688 1.00 0.00 C +ATOM 277 HG21 THR 17 25.856 28.880 32.303 1.00 0.00 H +ATOM 278 HG22 THR 17 24.854 28.185 33.473 1.00 0.00 H +ATOM 279 HG23 THR 17 24.658 29.928 33.112 1.00 0.00 H +ATOM 280 OG1 THR 17 22.421 29.271 32.330 1.00 0.00 O +ATOM 281 HG1 THR 17 21.812 28.582 32.603 1.00 0.00 H +ATOM 282 C THR 17 22.480 28.711 29.610 1.00 0.00 C +ATOM 283 O THR 17 21.928 29.678 29.083 1.00 0.00 O +ATOM 284 N HY2 18 22.029 27.466 29.501 1.00 0.00 N +ATOM 285 CA HY2 18 20.708 27.124 28.957 1.00 0.00 C +ATOM 286 C HY2 18 20.084 25.945 29.841 1.00 0.00 C +ATOM 287 O HY2 18 20.680 24.926 29.964 1.00 0.00 O +ATOM 288 CB HY2 18 20.807 26.719 27.474 1.00 0.00 C +ATOM 289 CG HY2 18 21.368 27.741 26.533 1.00 0.00 C +ATOM 290 CD2 HY2 18 22.520 27.796 25.834 1.00 0.00 C +ATOM 291 ND1 HY2 18 20.726 28.897 26.207 1.00 0.00 N +ATOM 292 CE1 HY2 18 21.319 29.485 25.242 1.00 0.00 C +ATOM 293 NE2 HY2 18 22.517 28.856 24.952 1.00 0.00 N +ATOM 294 H HY2 18 22.602 26.723 29.875 1.00 0.00 H +ATOM 295 HA HY2 18 20.056 27.995 29.023 1.00 0.00 H +ATOM 296 HB2 HY2 18 21.484 25.865 27.503 1.00 0.00 H +ATOM 297 HB3 HY2 18 19.905 26.290 27.037 1.00 0.00 H +ATOM 298 HD1 HY2 18 19.760 29.077 26.438 1.00 0.00 H +ATOM 299 HD2 HY2 18 23.214 26.971 25.771 1.00 0.00 H +ATOM 300 HE1 HY2 18 21.099 30.442 24.793 1.00 0.00 H +ATOM 301 N GLU 19 18.887 26.199 30.452 1.00 0.00 N +ATOM 302 H GLU 19 18.463 27.098 30.272 1.00 0.00 H +ATOM 303 CA GLU 19 18.121 25.145 31.134 1.00 0.00 C +ATOM 304 HA GLU 19 18.770 24.560 31.785 1.00 0.00 H +ATOM 305 CB GLU 19 17.030 25.703 32.075 1.00 0.00 C +ATOM 306 HB2 GLU 19 17.546 25.914 33.011 1.00 0.00 H +ATOM 307 HB3 GLU 19 16.576 26.632 31.731 1.00 0.00 H +ATOM 308 CG GLU 19 15.826 24.766 32.404 1.00 0.00 C +ATOM 309 HG2 GLU 19 14.952 25.294 32.786 1.00 0.00 H +ATOM 310 HG3 GLU 19 15.548 24.304 31.457 1.00 0.00 H +ATOM 311 CD GLU 19 16.266 23.633 33.270 1.00 0.00 C +ATOM 312 OE1 GLU 19 15.583 22.535 33.107 1.00 0.00 O +ATOM 313 OE2 GLU 19 17.302 23.664 33.967 1.00 0.00 O +ATOM 314 C GLU 19 17.536 24.133 30.130 1.00 0.00 C +ATOM 315 O GLU 19 16.788 24.641 29.290 1.00 0.00 O +ATOM 316 N ALA 20 17.698 22.822 30.304 1.00 0.00 N +ATOM 317 H ALA 20 18.223 22.460 31.087 1.00 0.00 H +ATOM 318 CA ALA 20 17.016 21.840 29.396 1.00 0.00 C +ATOM 319 HA ALA 20 16.027 22.206 29.122 1.00 0.00 H +ATOM 320 CB ALA 20 17.792 21.638 28.049 1.00 0.00 C +ATOM 321 HB1 ALA 20 17.217 20.925 27.457 1.00 0.00 H +ATOM 322 HB2 ALA 20 18.813 21.266 28.141 1.00 0.00 H +ATOM 323 HB3 ALA 20 17.778 22.566 27.477 1.00 0.00 H +ATOM 324 C ALA 20 16.807 20.512 30.111 1.00 0.00 C +ATOM 325 O ALA 20 17.300 20.260 31.139 1.00 0.00 O +ATOM 326 N VAL 21 15.923 19.666 29.500 1.00 0.00 N +ATOM 327 H VAL 21 15.657 19.968 28.573 1.00 0.00 H +ATOM 328 CA VAL 21 15.883 18.231 29.828 1.00 0.00 C +ATOM 329 HA VAL 21 15.892 18.115 30.912 1.00 0.00 H +ATOM 330 CB VAL 21 14.545 17.632 29.434 1.00 0.00 C +ATOM 331 HB VAL 21 13.740 18.085 30.011 1.00 0.00 H +ATOM 332 CG1 VAL 21 14.194 17.716 27.983 1.00 0.00 C +ATOM 333 HG11 VAL 21 13.594 16.883 27.616 1.00 0.00 H +ATOM 334 HG12 VAL 21 15.044 17.914 27.330 1.00 0.00 H +ATOM 335 HG13 VAL 21 13.558 18.597 27.898 1.00 0.00 H +ATOM 336 CG2 VAL 21 14.464 16.170 29.850 1.00 0.00 C +ATOM 337 HG21 VAL 21 14.839 16.071 30.869 1.00 0.00 H +ATOM 338 HG22 VAL 21 14.982 15.503 29.160 1.00 0.00 H +ATOM 339 HG23 VAL 21 13.413 15.907 29.970 1.00 0.00 H +ATOM 340 C VAL 21 17.069 17.462 29.325 1.00 0.00 C +ATOM 341 O VAL 21 17.477 16.536 30.076 1.00 0.00 O +ATOM 342 N ASP 22 17.650 17.858 28.211 1.00 0.00 N +ATOM 343 H ASP 22 17.272 18.609 27.652 1.00 0.00 H +ATOM 344 CA ASP 22 18.754 17.160 27.550 1.00 0.00 C +ATOM 345 HA ASP 22 19.258 16.636 28.362 1.00 0.00 H +ATOM 346 CB ASP 22 18.337 16.020 26.622 1.00 0.00 C +ATOM 347 HB2 ASP 22 17.805 15.298 27.243 1.00 0.00 H +ATOM 348 HB3 ASP 22 17.570 16.377 25.934 1.00 0.00 H +ATOM 349 CG ASP 22 19.504 15.181 25.976 1.00 0.00 C +ATOM 350 OD1 ASP 22 20.697 15.405 26.228 1.00 0.00 O +ATOM 351 OD2 ASP 22 19.203 14.331 25.139 1.00 0.00 O +ATOM 352 C ASP 22 19.661 18.208 26.967 1.00 0.00 C +ATOM 353 O ASP 22 19.150 19.094 26.296 1.00 0.00 O +ATOM 354 N ALA 23 20.974 18.077 27.138 1.00 0.00 N +ATOM 355 H ALA 23 21.309 17.337 27.739 1.00 0.00 H +ATOM 356 CA ALA 23 21.980 19.010 26.456 1.00 0.00 C +ATOM 357 HA ALA 23 22.033 19.951 27.002 1.00 0.00 H +ATOM 358 CB ALA 23 23.379 18.286 26.579 1.00 0.00 C +ATOM 359 HB1 ALA 23 23.359 17.329 26.057 1.00 0.00 H +ATOM 360 HB2 ALA 23 23.583 18.143 27.640 1.00 0.00 H +ATOM 361 HB3 ALA 23 24.128 18.983 26.202 1.00 0.00 H +ATOM 362 C ALA 23 21.707 19.188 24.929 1.00 0.00 C +ATOM 363 O ALA 23 21.693 20.335 24.507 1.00 0.00 O +ATOM 364 N ALA 24 21.312 18.124 24.263 1.00 0.00 N +ATOM 365 H ALA 24 21.066 17.332 24.838 1.00 0.00 H +ATOM 366 CA ALA 24 20.940 18.200 22.795 1.00 0.00 C +ATOM 367 HA ALA 24 21.756 18.445 22.115 1.00 0.00 H +ATOM 368 CB ALA 24 20.498 16.798 22.370 1.00 0.00 C +ATOM 369 HB1 ALA 24 20.007 16.841 21.398 1.00 0.00 H +ATOM 370 HB2 ALA 24 19.779 16.409 23.091 1.00 0.00 H +ATOM 371 HB3 ALA 24 21.256 16.025 22.247 1.00 0.00 H +ATOM 372 C ALA 24 19.733 19.101 22.462 1.00 0.00 C +ATOM 373 O ALA 24 19.556 19.642 21.376 1.00 0.00 O +ATOM 374 N GLU 25 18.843 19.253 23.452 1.00 0.00 N +ATOM 375 H GLU 25 18.990 18.730 24.303 1.00 0.00 H +ATOM 376 CA GLU 25 17.670 20.245 23.384 1.00 0.00 C +ATOM 377 HA GLU 25 17.182 20.203 22.411 1.00 0.00 H +ATOM 378 CB GLU 25 16.613 19.835 24.387 1.00 0.00 C +ATOM 379 HB2 GLU 25 16.859 19.921 25.445 1.00 0.00 H +ATOM 380 HB3 GLU 25 15.805 20.559 24.285 1.00 0.00 H +ATOM 381 CG GLU 25 16.090 18.452 24.182 1.00 0.00 C +ATOM 382 HG2 GLU 25 16.864 17.747 24.485 1.00 0.00 H +ATOM 383 HG3 GLU 25 15.236 18.291 24.840 1.00 0.00 H +ATOM 384 CD GLU 25 15.727 18.101 22.754 1.00 0.00 C +ATOM 385 OE1 GLU 25 16.393 17.293 22.099 1.00 0.00 O +ATOM 386 OE2 GLU 25 14.730 18.676 22.195 1.00 0.00 O +ATOM 387 C GLU 25 18.033 21.726 23.727 1.00 0.00 C +ATOM 388 O GLU 25 17.271 22.594 23.314 1.00 0.00 O +ATOM 389 N ALA 26 19.152 21.978 24.346 1.00 0.00 N +ATOM 390 H ALA 26 19.644 21.211 24.782 1.00 0.00 H +ATOM 391 CA ALA 26 19.761 23.324 24.354 1.00 0.00 C +ATOM 392 HA ALA 26 19.034 24.136 24.375 1.00 0.00 H +ATOM 393 CB ALA 26 20.557 23.475 25.692 1.00 0.00 C +ATOM 394 HB1 ALA 26 21.123 22.559 25.861 1.00 0.00 H +ATOM 395 HB2 ALA 26 19.859 23.473 26.529 1.00 0.00 H +ATOM 396 HB3 ALA 26 21.289 24.283 25.704 1.00 0.00 H +ATOM 397 C ALA 26 20.710 23.594 23.154 1.00 0.00 C +ATOM 398 O ALA 26 20.752 24.757 22.698 1.00 0.00 O +ATOM 399 N GLU 27 21.381 22.547 22.612 1.00 0.00 N +ATOM 400 H GLU 27 21.518 21.680 23.112 1.00 0.00 H +ATOM 401 CA GLU 27 22.020 22.637 21.284 1.00 0.00 C +ATOM 402 HA GLU 27 22.868 23.321 21.282 1.00 0.00 H +ATOM 403 CB GLU 27 22.541 21.281 20.886 1.00 0.00 C +ATOM 404 HB2 GLU 27 23.142 21.008 21.754 1.00 0.00 H +ATOM 405 HB3 GLU 27 21.740 20.547 20.798 1.00 0.00 H +ATOM 406 CG GLU 27 23.469 21.254 19.611 1.00 0.00 C +ATOM 407 HG2 GLU 27 22.764 21.260 18.779 1.00 0.00 H +ATOM 408 HG3 GLU 27 24.030 22.187 19.647 1.00 0.00 H +ATOM 409 CD GLU 27 24.362 19.993 19.574 1.00 0.00 C +ATOM 410 OE1 GLU 27 25.452 20.099 18.934 1.00 0.00 O +ATOM 411 OE2 GLU 27 23.932 18.944 20.015 1.00 0.00 O +ATOM 412 C GLU 27 21.128 23.157 20.131 1.00 0.00 C +ATOM 413 O GLU 27 21.482 24.085 19.423 1.00 0.00 O +ATOM 414 N LYS 28 19.909 22.657 20.053 1.00 0.00 N +ATOM 415 H LYS 28 19.582 21.887 20.619 1.00 0.00 H +ATOM 416 CA LYS 28 19.018 23.071 18.968 1.00 0.00 C +ATOM 417 HA LYS 28 19.631 23.044 18.067 1.00 0.00 H +ATOM 418 CB LYS 28 17.933 21.939 18.663 1.00 0.00 C +ATOM 419 HB2 LYS 28 17.368 22.142 17.753 1.00 0.00 H +ATOM 420 HB3 LYS 28 18.503 21.035 18.446 1.00 0.00 H +ATOM 421 CG LYS 28 17.106 21.743 19.936 1.00 0.00 C +ATOM 422 HG2 LYS 28 17.754 21.485 20.773 1.00 0.00 H +ATOM 423 HG3 LYS 28 16.633 22.680 20.230 1.00 0.00 H +ATOM 424 CD LYS 28 16.026 20.609 19.720 1.00 0.00 C +ATOM 425 HD2 LYS 28 15.481 20.510 20.658 1.00 0.00 H +ATOM 426 HD3 LYS 28 15.279 20.952 19.003 1.00 0.00 H +ATOM 427 CE LYS 28 16.657 19.350 19.355 1.00 0.00 C +ATOM 428 HE2 LYS 28 16.817 19.354 18.276 1.00 0.00 H +ATOM 429 HE3 LYS 28 17.557 19.293 19.966 1.00 0.00 H +ATOM 430 NZ LYS 28 15.896 18.142 19.627 1.00 0.00 N +ATOM 431 HZ1 LYS 28 16.147 17.373 19.022 1.00 0.00 H +ATOM 432 HZ2 LYS 28 14.915 18.371 19.567 1.00 0.00 H +ATOM 433 HZ3 LYS 28 16.137 17.795 20.544 1.00 0.00 H +ATOM 434 C LYS 28 18.493 24.483 19.252 1.00 0.00 C +ATOM 435 O LYS 28 18.394 25.192 18.230 1.00 0.00 O +ATOM 436 N PHE 29 18.320 24.961 20.472 1.00 0.00 N +ATOM 437 H PHE 29 18.347 24.291 21.228 1.00 0.00 H +ATOM 438 CA PHE 29 18.159 26.342 20.826 1.00 0.00 C +ATOM 439 HA PHE 29 17.205 26.594 20.362 1.00 0.00 H +ATOM 440 CB PHE 29 17.875 26.420 22.351 1.00 0.00 C +ATOM 441 HB2 PHE 29 16.975 25.814 22.455 1.00 0.00 H +ATOM 442 HB3 PHE 29 18.643 25.953 22.968 1.00 0.00 H +ATOM 443 CG PHE 29 17.444 27.755 22.926 1.00 0.00 C +ATOM 444 CD1 PHE 29 18.421 28.725 23.249 1.00 0.00 C +ATOM 445 HD1 PHE 29 19.468 28.465 23.207 1.00 0.00 H +ATOM 446 CE1 PHE 29 17.994 29.995 23.674 1.00 0.00 C +ATOM 447 HE1 PHE 29 18.734 30.733 23.944 1.00 0.00 H +ATOM 448 CZ PHE 29 16.660 30.281 23.874 1.00 0.00 C +ATOM 449 HZ PHE 29 16.332 31.269 24.161 1.00 0.00 H +ATOM 450 CE2 PHE 29 15.718 29.298 23.708 1.00 0.00 C +ATOM 451 HE2 PHE 29 14.673 29.390 23.964 1.00 0.00 H +ATOM 452 CD2 PHE 29 16.108 28.054 23.109 1.00 0.00 C +ATOM 453 HD2 PHE 29 15.363 27.282 22.986 1.00 0.00 H +ATOM 454 C PHE 29 19.361 27.284 20.431 1.00 0.00 C +ATOM 455 O PHE 29 19.194 28.303 19.788 1.00 0.00 O +ATOM 456 N THR 30 20.538 26.814 20.722 1.00 0.00 N +ATOM 457 H THR 30 20.580 26.006 21.326 1.00 0.00 H +ATOM 458 CA THR 30 21.814 27.417 20.303 1.00 0.00 C +ATOM 459 HA THR 30 21.869 28.437 20.684 1.00 0.00 H +ATOM 460 CB THR 30 22.981 26.622 20.906 1.00 0.00 C +ATOM 461 HB THR 30 22.681 25.575 20.915 1.00 0.00 H +ATOM 462 CG2 THR 30 24.367 26.815 20.291 1.00 0.00 C +ATOM 463 HG21 THR 30 25.140 26.356 20.908 1.00 0.00 H +ATOM 464 HG22 THR 30 24.365 26.155 19.424 1.00 0.00 H +ATOM 465 HG23 THR 30 24.575 27.868 20.099 1.00 0.00 H +ATOM 466 OG1 THR 30 23.011 26.657 22.248 1.00 0.00 O +ATOM 467 HG1 THR 30 22.372 25.992 22.515 1.00 0.00 H +ATOM 468 C THR 30 21.945 27.553 18.806 1.00 0.00 C +ATOM 469 O THR 30 22.298 28.659 18.319 1.00 0.00 O +ATOM 470 N LYS 31 21.607 26.525 17.989 1.00 0.00 N +ATOM 471 H LYS 31 21.374 25.663 18.461 1.00 0.00 H +ATOM 472 CA LYS 31 21.621 26.588 16.506 1.00 0.00 C +ATOM 473 HA LYS 31 22.559 27.055 16.205 1.00 0.00 H +ATOM 474 CB LYS 31 21.371 25.168 15.929 1.00 0.00 C +ATOM 475 HB2 LYS 31 20.651 24.723 16.616 1.00 0.00 H +ATOM 476 HB3 LYS 31 20.981 25.149 14.911 1.00 0.00 H +ATOM 477 CG LYS 31 22.650 24.365 16.135 1.00 0.00 C +ATOM 478 HG2 LYS 31 23.477 24.797 15.572 1.00 0.00 H +ATOM 479 HG3 LYS 31 23.011 24.344 17.163 1.00 0.00 H +ATOM 480 CD LYS 31 22.660 22.907 15.612 1.00 0.00 C +ATOM 481 HD2 LYS 31 22.311 22.195 16.360 1.00 0.00 H +ATOM 482 HD3 LYS 31 22.172 22.842 14.640 1.00 0.00 H +ATOM 483 CE LYS 31 24.156 22.495 15.514 1.00 0.00 C +ATOM 484 HE2 LYS 31 24.527 22.879 16.465 1.00 0.00 H +ATOM 485 HE3 LYS 31 24.180 21.411 15.404 1.00 0.00 H +ATOM 486 NZ LYS 31 24.755 23.050 14.314 1.00 0.00 N +ATOM 487 HZ1 LYS 31 24.792 24.057 14.381 1.00 0.00 H +ATOM 488 HZ2 LYS 31 24.340 22.745 13.445 1.00 0.00 H +ATOM 489 HZ3 LYS 31 25.744 22.862 14.225 1.00 0.00 H +ATOM 490 C LYS 31 20.482 27.482 15.991 1.00 0.00 C +ATOM 491 O LYS 31 20.769 28.187 15.021 1.00 0.00 O +ATOM 492 N ALA 32 19.396 27.611 16.692 1.00 0.00 N +ATOM 493 H ALA 32 19.303 27.081 17.547 1.00 0.00 H +ATOM 494 CA ALA 32 18.309 28.384 16.191 1.00 0.00 C +ATOM 495 HA ALA 32 18.011 28.148 15.169 1.00 0.00 H +ATOM 496 CB ALA 32 17.068 28.040 17.046 1.00 0.00 C +ATOM 497 HB1 ALA 32 16.503 27.142 16.796 1.00 0.00 H +ATOM 498 HB2 ALA 32 17.281 28.110 18.112 1.00 0.00 H +ATOM 499 HB3 ALA 32 16.327 28.825 16.896 1.00 0.00 H +ATOM 500 C ALA 32 18.687 29.906 16.401 1.00 0.00 C +ATOM 501 O ALA 32 18.703 30.680 15.427 1.00 0.00 O +ATOM 502 N ASP 33 19.035 30.251 17.649 1.00 0.00 N +ATOM 503 H ASP 33 19.083 29.541 18.365 1.00 0.00 H +ATOM 504 CA ASP 33 19.541 31.552 18.081 1.00 0.00 C +ATOM 505 HA ASP 33 18.719 32.244 17.896 1.00 0.00 H +ATOM 506 CB ASP 33 19.831 31.559 19.636 1.00 0.00 C +ATOM 507 HB2 ASP 33 19.019 31.148 20.236 1.00 0.00 H +ATOM 508 HB3 ASP 33 20.725 30.956 19.796 1.00 0.00 H +ATOM 509 CG ASP 33 19.895 32.958 20.183 1.00 0.00 C +ATOM 510 OD1 ASP 33 18.877 33.727 20.094 1.00 0.00 O +ATOM 511 OD2 ASP 33 20.953 33.271 20.776 1.00 0.00 O +ATOM 512 C ASP 33 20.749 32.073 17.279 1.00 0.00 C +ATOM 513 O ASP 33 20.768 33.220 16.799 1.00 0.00 O +ATOM 514 N ALA 34 21.591 31.100 16.970 1.00 0.00 N +ATOM 515 H ALA 34 21.606 30.173 17.372 1.00 0.00 H +ATOM 516 CA ALA 34 22.713 31.452 16.055 1.00 0.00 C +ATOM 517 HA ALA 34 23.241 32.276 16.535 1.00 0.00 H +ATOM 518 CB ALA 34 23.783 30.382 15.918 1.00 0.00 C +ATOM 519 HB1 ALA 34 24.707 30.960 15.895 1.00 0.00 H +ATOM 520 HB2 ALA 34 23.614 29.735 15.058 1.00 0.00 H +ATOM 521 HB3 ALA 34 23.914 29.879 16.876 1.00 0.00 H +ATOM 522 C ALA 34 22.241 31.754 14.622 1.00 0.00 C +ATOM 523 O ALA 34 22.964 32.494 13.955 1.00 0.00 O +ATOM 524 N ASN 35 21.301 31.061 14.082 1.00 0.00 N +ATOM 525 H ASN 35 20.740 30.435 14.642 1.00 0.00 H +ATOM 526 CA ASN 35 20.728 31.579 12.836 1.00 0.00 C +ATOM 527 HA ASN 35 21.562 31.734 12.151 1.00 0.00 H +ATOM 528 CB ASN 35 19.782 30.439 12.358 1.00 0.00 C +ATOM 529 HB2 ASN 35 19.134 30.074 13.155 1.00 0.00 H +ATOM 530 HB3 ASN 35 19.187 30.841 11.538 1.00 0.00 H +ATOM 531 CG ASN 35 20.499 29.198 11.849 1.00 0.00 C +ATOM 532 OD1 ASN 35 21.702 29.163 11.710 1.00 0.00 O +ATOM 533 ND2 ASN 35 19.728 28.194 11.524 1.00 0.00 N +ATOM 534 HD21 ASN 35 18.737 28.176 11.717 1.00 0.00 H +ATOM 535 HD22 ASN 35 20.223 27.394 11.157 1.00 0.00 H +ATOM 536 C ASN 35 20.014 32.931 12.967 1.00 0.00 C +ATOM 537 O ASN 35 20.092 33.739 12.022 1.00 0.00 O +ATOM 538 N ASP 36 19.310 33.225 14.110 1.00 0.00 N +ATOM 539 H ASP 36 19.174 32.515 14.815 1.00 0.00 H +ATOM 540 CA ASP 36 18.684 34.581 14.244 1.00 0.00 C +ATOM 541 HA ASP 36 18.030 34.707 13.381 1.00 0.00 H +ATOM 542 CB ASP 36 17.728 34.447 15.414 1.00 0.00 C +ATOM 543 HB2 ASP 36 16.953 33.703 15.230 1.00 0.00 H +ATOM 544 HB3 ASP 36 18.299 34.282 16.328 1.00 0.00 H +ATOM 545 CG ASP 36 16.928 35.797 15.625 1.00 0.00 C +ATOM 546 OD1 ASP 36 16.706 36.135 16.801 1.00 0.00 O +ATOM 547 OD2 ASP 36 16.596 36.460 14.665 1.00 0.00 O +ATOM 548 C ASP 36 19.597 35.717 14.452 1.00 0.00 C +ATOM 549 O ASP 36 19.478 36.787 13.766 1.00 0.00 O +ATOM 550 N LYS 37 20.690 35.515 15.194 1.00 0.00 N +ATOM 551 H LYS 37 20.665 34.714 15.809 1.00 0.00 H +ATOM 552 CA LYS 37 21.841 36.479 15.249 1.00 0.00 C +ATOM 553 HA LYS 37 21.503 37.466 15.564 1.00 0.00 H +ATOM 554 CB LYS 37 22.809 35.979 16.302 1.00 0.00 C +ATOM 555 HB2 LYS 37 23.729 36.550 16.173 1.00 0.00 H +ATOM 556 HB3 LYS 37 22.963 34.923 16.083 1.00 0.00 H +ATOM 557 CG LYS 37 22.147 36.153 17.674 1.00 0.00 C +ATOM 558 HG2 LYS 37 21.246 35.540 17.685 1.00 0.00 H +ATOM 559 HG3 LYS 37 21.885 37.210 17.700 1.00 0.00 H +ATOM 560 CD LYS 37 22.860 35.875 18.956 1.00 0.00 C +ATOM 561 HD2 LYS 37 22.982 34.818 19.191 1.00 0.00 H +ATOM 562 HD3 LYS 37 23.905 36.172 18.876 1.00 0.00 H +ATOM 563 CE LYS 37 22.202 36.632 20.144 1.00 0.00 C +ATOM 564 HE2 LYS 37 22.821 36.641 21.041 1.00 0.00 H +ATOM 565 HE3 LYS 37 22.114 37.688 19.888 1.00 0.00 H +ATOM 566 NZ LYS 37 20.822 36.057 20.417 1.00 0.00 N +ATOM 567 HZ1 LYS 37 20.280 35.915 19.576 1.00 0.00 H +ATOM 568 HZ2 LYS 37 21.024 35.135 20.778 1.00 0.00 H +ATOM 569 HZ3 LYS 37 20.238 36.564 21.066 1.00 0.00 H +ATOM 570 C LYS 37 22.581 36.592 13.861 1.00 0.00 C +ATOM 571 O LYS 37 23.087 37.650 13.516 1.00 0.00 O +ATOM 572 N GLY 38 22.691 35.511 13.091 1.00 0.00 N +ATOM 573 H GLY 38 22.285 34.666 13.469 1.00 0.00 H +ATOM 574 CA GLY 38 23.238 35.423 11.729 1.00 0.00 C +ATOM 575 HA2 GLY 38 22.981 34.460 11.288 1.00 0.00 H +ATOM 576 HA3 GLY 38 22.884 36.239 11.098 1.00 0.00 H +ATOM 577 C GLY 38 24.746 35.255 11.712 1.00 0.00 C +ATOM 578 O GLY 38 25.331 36.181 11.113 1.00 0.00 O +ATOM 579 N VAL 39 25.271 34.160 12.295 1.00 0.00 N +ATOM 580 H VAL 39 24.705 33.372 12.575 1.00 0.00 H +ATOM 581 CA VAL 39 26.702 33.873 12.346 1.00 0.00 C +ATOM 582 HA VAL 39 27.226 34.418 11.561 1.00 0.00 H +ATOM 583 CB VAL 39 27.283 34.366 13.717 1.00 0.00 C +ATOM 584 HB VAL 39 26.903 33.806 14.571 1.00 0.00 H +ATOM 585 CG1 VAL 39 28.794 34.206 13.562 1.00 0.00 C +ATOM 586 HG11 VAL 39 29.233 34.532 14.505 1.00 0.00 H +ATOM 587 HG12 VAL 39 29.116 34.814 12.717 1.00 0.00 H +ATOM 588 HG13 VAL 39 29.180 33.187 13.529 1.00 0.00 H +ATOM 589 CG2 VAL 39 26.985 35.805 13.964 1.00 0.00 C +ATOM 590 HG21 VAL 39 25.992 36.007 14.365 1.00 0.00 H +ATOM 591 HG22 VAL 39 27.137 36.340 13.027 1.00 0.00 H +ATOM 592 HG23 VAL 39 27.694 36.234 14.673 1.00 0.00 H +ATOM 593 C VAL 39 26.847 32.341 12.111 1.00 0.00 C +ATOM 594 O VAL 39 26.257 31.590 12.945 1.00 0.00 O +ATOM 595 N ASP 40 27.642 31.818 11.133 1.00 0.00 N +ATOM 596 H ASP 40 28.085 32.547 10.591 1.00 0.00 H +ATOM 597 CA ASP 40 28.067 30.440 11.009 1.00 0.00 C +ATOM 598 HA ASP 40 27.193 29.841 10.752 1.00 0.00 H +ATOM 599 CB ASP 40 29.047 30.332 9.844 1.00 0.00 C +ATOM 600 HB2 ASP 40 30.022 30.681 10.183 1.00 0.00 H +ATOM 601 HB3 ASP 40 29.178 29.259 9.705 1.00 0.00 H +ATOM 602 CG ASP 40 28.576 30.796 8.450 1.00 0.00 C +ATOM 603 OD1 ASP 40 29.392 30.725 7.542 1.00 0.00 O +ATOM 604 OD2 ASP 40 27.371 31.111 8.178 1.00 0.00 O +ATOM 605 C ASP 40 28.746 29.989 12.286 1.00 0.00 C +ATOM 606 O ASP 40 29.389 30.743 13.029 1.00 0.00 O +ATOM 607 N GLY 41 28.685 28.690 12.655 1.00 0.00 N +ATOM 608 H GLY 41 27.999 28.077 12.238 1.00 0.00 H +ATOM 609 CA GLY 41 29.287 28.189 13.855 1.00 0.00 C +ATOM 610 HA2 GLY 41 30.360 28.355 13.755 1.00 0.00 H +ATOM 611 HA3 GLY 41 29.104 28.896 14.664 1.00 0.00 H +ATOM 612 C GLY 41 28.991 26.749 14.179 1.00 0.00 C +ATOM 613 O GLY 41 27.930 26.234 13.780 1.00 0.00 O +ATOM 614 N GLU 42 29.772 26.130 15.028 1.00 0.00 N +ATOM 615 H GLU 42 30.555 26.627 15.427 1.00 0.00 H +ATOM 616 CA GLU 42 29.475 24.868 15.657 1.00 0.00 C +ATOM 617 HA GLU 42 28.400 24.714 15.742 1.00 0.00 H +ATOM 618 CB GLU 42 30.095 23.697 14.858 1.00 0.00 C +ATOM 619 HB2 GLU 42 30.032 23.874 13.785 1.00 0.00 H +ATOM 620 HB3 GLU 42 31.137 23.575 15.154 1.00 0.00 H +ATOM 621 CG GLU 42 29.421 22.410 15.208 1.00 0.00 C +ATOM 622 HG2 GLU 42 29.903 21.571 14.706 1.00 0.00 H +ATOM 623 HG3 GLU 42 29.629 22.185 16.254 1.00 0.00 H +ATOM 624 CD GLU 42 27.845 22.296 14.955 1.00 0.00 C +ATOM 625 OE1 GLU 42 27.162 21.871 15.949 1.00 0.00 O +ATOM 626 OE2 GLU 42 27.371 22.366 13.808 1.00 0.00 O +ATOM 627 C GLU 42 30.129 24.822 17.049 1.00 0.00 C +ATOM 628 O GLU 42 31.190 25.457 17.311 1.00 0.00 O +ATOM 629 N TRP 43 29.552 24.138 17.996 1.00 0.00 N +ATOM 630 H TRP 43 28.712 23.616 17.793 1.00 0.00 H +ATOM 631 CA TRP 43 30.090 23.881 19.309 1.00 0.00 C +ATOM 632 HA TRP 43 31.129 24.208 19.263 1.00 0.00 H +ATOM 633 CB TRP 43 29.264 24.614 20.380 1.00 0.00 C +ATOM 634 HB2 TRP 43 28.333 24.076 20.559 1.00 0.00 H +ATOM 635 HB3 TRP 43 29.693 24.332 21.341 1.00 0.00 H +ATOM 636 CG TRP 43 29.135 26.087 20.172 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.796 27.108 20.869 1.00 0.00 C +ATOM 638 HD1 TRP 43 30.415 26.966 21.743 1.00 0.00 H +ATOM 639 NE1 TRP 43 29.464 28.316 20.298 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.722 29.253 20.571 1.00 0.00 H +ATOM 641 CE2 TRP 43 28.645 28.117 19.178 1.00 0.00 C +ATOM 642 CZ2 TRP 43 28.084 29.070 18.284 1.00 0.00 C +ATOM 643 HZ2 TRP 43 28.330 30.114 18.405 1.00 0.00 H +ATOM 644 CH2 TRP 43 27.132 28.610 17.328 1.00 0.00 C +ATOM 645 HH2 TRP 43 26.791 29.306 16.576 1.00 0.00 H +ATOM 646 CZ3 TRP 43 26.787 27.227 17.287 1.00 0.00 C +ATOM 647 HZ3 TRP 43 26.181 26.850 16.477 1.00 0.00 H +ATOM 648 CE3 TRP 43 27.408 26.349 18.144 1.00 0.00 C +ATOM 649 HE3 TRP 43 27.254 25.280 18.118 1.00 0.00 H +ATOM 650 CD2 TRP 43 28.314 26.741 19.185 1.00 0.00 C +ATOM 651 C TRP 43 30.170 22.360 19.690 1.00 0.00 C +ATOM 652 O TRP 43 29.270 21.576 19.285 1.00 0.00 O +ATOM 653 N THR 44 31.133 21.855 20.509 1.00 0.00 N +ATOM 654 H THR 44 31.765 22.541 20.896 1.00 0.00 H +ATOM 655 CA THR 44 31.203 20.482 20.970 1.00 0.00 C +ATOM 656 HA THR 44 30.587 19.895 20.289 1.00 0.00 H +ATOM 657 CB THR 44 32.643 20.025 20.724 1.00 0.00 C +ATOM 658 HB THR 44 32.841 20.171 19.662 1.00 0.00 H +ATOM 659 CG2 THR 44 33.858 20.538 21.451 1.00 0.00 C +ATOM 660 HG21 THR 44 33.764 20.117 22.452 1.00 0.00 H +ATOM 661 HG22 THR 44 33.881 21.626 21.509 1.00 0.00 H +ATOM 662 HG23 THR 44 34.744 20.208 20.910 1.00 0.00 H +ATOM 663 OG1 THR 44 32.589 18.621 20.908 1.00 0.00 O +ATOM 664 HG1 THR 44 32.026 18.385 20.167 1.00 0.00 H +ATOM 665 C THR 44 30.758 20.267 22.447 1.00 0.00 C +ATOM 666 O THR 44 30.899 21.228 23.203 1.00 0.00 O +ATOM 667 N TYR 45 30.296 19.075 22.852 1.00 0.00 N +ATOM 668 H TYR 45 30.312 18.259 22.257 1.00 0.00 H +ATOM 669 CA TYR 45 29.786 18.897 24.196 1.00 0.00 C +ATOM 670 HA TYR 45 29.601 19.865 24.661 1.00 0.00 H +ATOM 671 CB TYR 45 28.342 18.291 24.152 1.00 0.00 C +ATOM 672 HB2 TYR 45 27.682 18.915 23.549 1.00 0.00 H +ATOM 673 HB3 TYR 45 28.299 17.380 23.555 1.00 0.00 H +ATOM 674 CG TYR 45 27.622 17.991 25.434 1.00 0.00 C +ATOM 675 CD1 TYR 45 27.160 19.042 26.244 1.00 0.00 C +ATOM 676 HD1 TYR 45 27.373 20.073 26.003 1.00 0.00 H +ATOM 677 CE1 TYR 45 26.410 18.761 27.410 1.00 0.00 C +ATOM 678 HE1 TYR 45 26.164 19.567 28.085 1.00 0.00 H +ATOM 679 CZ TYR 45 26.098 17.406 27.727 1.00 0.00 C +ATOM 680 OH TYR 45 25.473 17.253 28.951 1.00 0.00 O +ATOM 681 HH TYR 45 25.393 16.320 29.165 1.00 0.00 H +ATOM 682 CE2 TYR 45 26.525 16.323 26.904 1.00 0.00 C +ATOM 683 HE2 TYR 45 26.263 15.287 27.058 1.00 0.00 H +ATOM 684 CD2 TYR 45 27.248 16.636 25.720 1.00 0.00 C +ATOM 685 HD2 TYR 45 27.410 15.863 24.983 1.00 0.00 H +ATOM 686 C TYR 45 30.780 18.118 25.147 1.00 0.00 C +ATOM 687 O TYR 45 31.771 17.532 24.684 1.00 0.00 O +ATOM 688 N ASP 46 30.503 18.155 26.455 1.00 0.00 N +ATOM 689 H ASP 46 29.633 18.617 26.677 1.00 0.00 H +ATOM 690 CA ASP 46 31.129 17.353 27.577 1.00 0.00 C +ATOM 691 HA ASP 46 31.488 16.441 27.100 1.00 0.00 H +ATOM 692 CB ASP 46 32.340 18.074 28.173 1.00 0.00 C +ATOM 693 HB2 ASP 46 33.100 18.278 27.419 1.00 0.00 H +ATOM 694 HB3 ASP 46 31.952 18.964 28.667 1.00 0.00 H +ATOM 695 CG ASP 46 32.998 17.244 29.273 1.00 0.00 C +ATOM 696 OD1 ASP 46 33.195 17.860 30.344 1.00 0.00 O +ATOM 697 OD2 ASP 46 33.228 16.013 29.096 1.00 0.00 O +ATOM 698 C ASP 46 30.035 17.092 28.580 1.00 0.00 C +ATOM 699 O ASP 46 29.716 17.983 29.308 1.00 0.00 O +ATOM 700 N ASP 47 29.526 15.835 28.641 1.00 0.00 N +ATOM 701 H ASP 47 29.873 15.152 27.983 1.00 0.00 H +ATOM 702 CA ASP 47 28.520 15.546 29.670 1.00 0.00 C +ATOM 703 HA ASP 47 27.661 16.193 29.493 1.00 0.00 H +ATOM 704 CB ASP 47 28.034 14.067 29.565 1.00 0.00 C +ATOM 705 HB2 ASP 47 27.852 13.801 28.524 1.00 0.00 H +ATOM 706 HB3 ASP 47 28.846 13.395 29.843 1.00 0.00 H +ATOM 707 CG ASP 47 26.736 13.842 30.288 1.00 0.00 C +ATOM 708 OD1 ASP 47 25.838 14.739 30.404 1.00 0.00 O +ATOM 709 OD2 ASP 47 26.564 12.695 30.807 1.00 0.00 O +ATOM 710 C ASP 47 29.119 15.617 31.084 1.00 0.00 C +ATOM 711 O ASP 47 28.488 16.176 31.953 1.00 0.00 O +ATOM 712 N ALA 48 30.399 15.223 31.219 1.00 0.00 N +ATOM 713 H ALA 48 30.888 14.674 30.527 1.00 0.00 H +ATOM 714 CA ALA 48 31.211 15.411 32.497 1.00 0.00 C +ATOM 715 HA ALA 48 30.739 14.774 33.244 1.00 0.00 H +ATOM 716 CB ALA 48 32.675 14.976 32.321 1.00 0.00 C +ATOM 717 HB1 ALA 48 33.116 14.786 33.300 1.00 0.00 H +ATOM 718 HB2 ALA 48 33.134 15.795 31.767 1.00 0.00 H +ATOM 719 HB3 ALA 48 32.673 14.043 31.758 1.00 0.00 H +ATOM 720 C ALA 48 31.132 16.726 33.245 1.00 0.00 C +ATOM 721 O ALA 48 30.958 16.720 34.491 1.00 0.00 O +ATOM 722 N THR 49 31.159 17.818 32.465 1.00 0.00 N +ATOM 723 H THR 49 31.335 17.756 31.473 1.00 0.00 H +ATOM 724 CA THR 49 30.953 19.261 32.915 1.00 0.00 C +ATOM 725 HA THR 49 30.677 19.300 33.969 1.00 0.00 H +ATOM 726 CB THR 49 32.160 20.208 32.583 1.00 0.00 C +ATOM 727 HB THR 49 32.023 21.254 32.857 1.00 0.00 H +ATOM 728 CG2 THR 49 33.456 19.977 33.353 1.00 0.00 C +ATOM 729 HG21 THR 49 33.325 20.215 34.409 1.00 0.00 H +ATOM 730 HG22 THR 49 34.292 20.522 32.915 1.00 0.00 H +ATOM 731 HG23 THR 49 33.675 18.909 33.331 1.00 0.00 H +ATOM 732 OG1 THR 49 32.385 20.305 31.160 1.00 0.00 O +ATOM 733 HG1 THR 49 32.837 19.477 30.979 1.00 0.00 H +ATOM 734 C THR 49 29.752 19.942 32.307 1.00 0.00 C +ATOM 735 O THR 49 29.643 21.171 32.481 1.00 0.00 O +ATOM 736 N LYS 50 28.797 19.159 31.772 1.00 0.00 N +ATOM 737 H LYS 50 29.035 18.194 31.592 1.00 0.00 H +ATOM 738 CA LYS 50 27.580 19.679 31.238 1.00 0.00 C +ATOM 739 HA LYS 50 27.249 18.896 30.556 1.00 0.00 H +ATOM 740 CB LYS 50 26.531 19.895 32.316 1.00 0.00 C +ATOM 741 HB2 LYS 50 26.867 20.704 32.965 1.00 0.00 H +ATOM 742 HB3 LYS 50 25.602 20.144 31.804 1.00 0.00 H +ATOM 743 CG LYS 50 26.156 18.747 33.331 1.00 0.00 C +ATOM 744 HG2 LYS 50 27.049 18.296 33.764 1.00 0.00 H +ATOM 745 HG3 LYS 50 25.574 19.243 34.109 1.00 0.00 H +ATOM 746 CD LYS 50 25.243 17.699 32.656 1.00 0.00 C +ATOM 747 HD2 LYS 50 24.284 18.188 32.483 1.00 0.00 H +ATOM 748 HD3 LYS 50 25.723 17.513 31.695 1.00 0.00 H +ATOM 749 CE LYS 50 24.967 16.357 33.413 1.00 0.00 C +ATOM 750 HE2 LYS 50 24.979 16.581 34.480 1.00 0.00 H +ATOM 751 HE3 LYS 50 23.995 15.980 33.095 1.00 0.00 H +ATOM 752 NZ LYS 50 25.927 15.353 32.975 1.00 0.00 N +ATOM 753 HZ1 LYS 50 26.903 15.610 32.982 1.00 0.00 H +ATOM 754 HZ2 LYS 50 25.697 15.171 32.009 1.00 0.00 H +ATOM 755 HZ3 LYS 50 25.689 14.459 33.381 1.00 0.00 H +ATOM 756 C LYS 50 27.723 20.822 30.276 1.00 0.00 C +ATOM 757 O LYS 50 26.993 21.837 30.339 1.00 0.00 O +ATOM 758 N THR 51 28.790 20.789 29.407 1.00 0.00 N +ATOM 759 H THR 51 29.339 19.943 29.453 1.00 0.00 H +ATOM 760 CA THR 51 29.301 22.028 28.777 1.00 0.00 C +ATOM 761 HA THR 51 28.623 22.838 29.049 1.00 0.00 H +ATOM 762 CB THR 51 30.745 22.393 29.298 1.00 0.00 C +ATOM 763 HB THR 51 31.421 21.549 29.159 1.00 0.00 H +ATOM 764 CG2 THR 51 31.306 23.600 28.598 1.00 0.00 C +ATOM 765 HG21 THR 51 30.661 24.436 28.867 1.00 0.00 H +ATOM 766 HG22 THR 51 31.341 23.427 27.522 1.00 0.00 H +ATOM 767 HG23 THR 51 32.336 23.720 28.934 1.00 0.00 H +ATOM 768 OG1 THR 51 30.717 22.748 30.617 1.00 0.00 O +ATOM 769 HG1 THR 51 30.215 22.175 31.201 1.00 0.00 H +ATOM 770 C THR 51 29.356 21.856 27.267 1.00 0.00 C +ATOM 771 O THR 51 30.030 21.024 26.716 1.00 0.00 O +ATOM 772 N PHE 52 28.662 22.734 26.521 1.00 0.00 N +ATOM 773 H PHE 52 28.067 23.398 26.995 1.00 0.00 H +ATOM 774 CA PHE 52 29.099 23.089 25.125 1.00 0.00 C +ATOM 775 HA PHE 52 29.591 22.203 24.724 1.00 0.00 H +ATOM 776 CB PHE 52 27.966 23.484 24.190 1.00 0.00 C +ATOM 777 HB2 PHE 52 27.478 24.370 24.595 1.00 0.00 H +ATOM 778 HB3 PHE 52 28.347 23.832 23.231 1.00 0.00 H +ATOM 779 CG PHE 52 26.996 22.378 23.915 1.00 0.00 C +ATOM 780 CD1 PHE 52 25.941 22.278 24.777 1.00 0.00 C +ATOM 781 HD1 PHE 52 25.785 23.012 25.554 1.00 0.00 H +ATOM 782 CE1 PHE 52 25.034 21.233 24.651 1.00 0.00 C +ATOM 783 HE1 PHE 52 24.261 21.067 25.387 1.00 0.00 H +ATOM 784 CZ PHE 52 25.206 20.282 23.591 1.00 0.00 C +ATOM 785 HZ PHE 52 24.511 19.469 23.439 1.00 0.00 H +ATOM 786 CE2 PHE 52 26.240 20.433 22.652 1.00 0.00 C +ATOM 787 HE2 PHE 52 26.378 19.772 21.809 1.00 0.00 H +ATOM 788 CD2 PHE 52 27.183 21.525 22.832 1.00 0.00 C +ATOM 789 HD2 PHE 52 28.084 21.588 22.240 1.00 0.00 H +ATOM 790 C PHE 52 30.230 24.161 25.093 1.00 0.00 C +ATOM 791 O PHE 52 30.147 25.220 25.677 1.00 0.00 O +ATOM 792 N THR 53 31.178 23.943 24.170 1.00 0.00 N +ATOM 793 H THR 53 31.193 23.058 23.684 1.00 0.00 H +ATOM 794 CA THR 53 32.214 24.954 23.844 1.00 0.00 C +ATOM 795 HA THR 53 31.955 25.938 24.236 1.00 0.00 H +ATOM 796 CB THR 53 33.481 24.501 24.607 1.00 0.00 C +ATOM 797 HB THR 53 33.226 24.330 25.653 1.00 0.00 H +ATOM 798 CG2 THR 53 34.251 23.403 23.896 1.00 0.00 C +ATOM 799 HG21 THR 53 33.559 22.571 23.762 1.00 0.00 H +ATOM 800 HG22 THR 53 35.091 23.162 24.548 1.00 0.00 H +ATOM 801 HG23 THR 53 34.687 23.711 22.946 1.00 0.00 H +ATOM 802 OG1 THR 53 34.395 25.528 24.716 1.00 0.00 O +ATOM 803 HG1 THR 53 34.990 25.211 25.400 1.00 0.00 H +ATOM 804 C THR 53 32.593 25.142 22.371 1.00 0.00 C +ATOM 805 O THR 53 32.219 24.203 21.634 1.00 0.00 O +ATOM 806 N VAL 54 33.151 26.270 22.002 1.00 0.00 N +ATOM 807 H VAL 54 33.377 26.985 22.679 1.00 0.00 H +ATOM 808 CA VAL 54 33.614 26.642 20.607 1.00 0.00 C +ATOM 809 HA VAL 54 32.763 26.722 19.930 1.00 0.00 H +ATOM 810 CB VAL 54 34.296 28.010 20.598 1.00 0.00 C +ATOM 811 HB VAL 54 35.209 27.966 21.191 1.00 0.00 H +ATOM 812 CG1 VAL 54 34.695 28.360 19.185 1.00 0.00 C +ATOM 813 HG11 VAL 54 35.545 27.802 18.792 1.00 0.00 H +ATOM 814 HG12 VAL 54 35.041 29.392 19.236 1.00 0.00 H +ATOM 815 HG13 VAL 54 33.835 28.328 18.516 1.00 0.00 H +ATOM 816 CG2 VAL 54 33.395 29.168 21.127 1.00 0.00 C +ATOM 817 HG21 VAL 54 33.955 30.101 21.187 1.00 0.00 H +ATOM 818 HG22 VAL 54 32.973 28.990 22.116 1.00 0.00 H +ATOM 819 HG23 VAL 54 32.541 29.297 20.462 1.00 0.00 H +ATOM 820 C VAL 54 34.490 25.489 20.015 1.00 0.00 C +ATOM 821 O VAL 54 35.522 25.024 20.535 1.00 0.00 O +ATOM 822 N THR 55 34.059 24.992 18.867 1.00 0.00 N +ATOM 823 H THR 55 33.199 25.293 18.431 1.00 0.00 H +ATOM 824 CA THR 55 34.784 23.942 18.063 1.00 0.00 C +ATOM 825 HA THR 55 34.995 23.141 18.771 1.00 0.00 H +ATOM 826 CB THR 55 33.897 23.493 16.862 1.00 0.00 C +ATOM 827 HB THR 55 33.606 24.347 16.251 1.00 0.00 H +ATOM 828 CG2 THR 55 34.492 22.438 15.929 1.00 0.00 C +ATOM 829 HG21 THR 55 33.806 22.144 15.134 1.00 0.00 H +ATOM 830 HG22 THR 55 34.824 21.585 16.521 1.00 0.00 H +ATOM 831 HG23 THR 55 35.403 22.773 15.432 1.00 0.00 H +ATOM 832 OG1 THR 55 32.616 23.011 17.277 1.00 0.00 O +ATOM 833 HG1 THR 55 32.018 23.748 17.132 1.00 0.00 H +ATOM 834 C THR 55 36.126 24.355 17.518 1.00 0.00 C +ATOM 835 O THR 55 36.285 25.546 17.158 1.00 0.00 O +ATOM 836 N GLU 56 37.139 23.432 17.686 1.00 0.00 N +ATOM 837 H GLU 56 36.874 22.462 17.782 1.00 0.00 H +ATOM 838 CA GLU 56 38.562 23.828 17.521 1.00 0.00 C +ATOM 839 HA GLU 56 38.636 24.746 16.937 1.00 0.00 H +ATOM 840 CB GLU 56 39.121 24.203 18.910 1.00 0.00 C +ATOM 841 HB2 GLU 56 38.411 24.952 19.260 1.00 0.00 H +ATOM 842 HB3 GLU 56 39.063 23.337 19.570 1.00 0.00 H +ATOM 843 CG GLU 56 40.499 24.815 18.833 1.00 0.00 C +ATOM 844 HG2 GLU 56 41.083 24.057 18.311 1.00 0.00 H +ATOM 845 HG3 GLU 56 40.396 25.775 18.328 1.00 0.00 H +ATOM 846 CD GLU 56 40.901 25.112 20.310 1.00 0.00 C +ATOM 847 OE1 GLU 56 40.215 25.990 20.864 1.00 0.00 O +ATOM 848 OE2 GLU 56 41.925 24.529 20.799 1.00 0.00 O +ATOM 849 C GLU 56 39.384 22.772 16.778 1.00 0.00 C +ATOM 850 O GLU 56 39.691 23.046 15.579 1.00 0.00 O +ATOM 851 OXT GLU 56 39.652 21.668 17.344 1.00 0.00 O +ATOM 852 ZN ZN1 57 24.086 29.918 24.242 1.00 0.00 ZN +ATOM 853 N AN1 58 23.545 30.697 22.350 1.00 0.00 N +ATOM 854 C AN1 58 23.314 31.662 19.913 1.00 0.00 C +ATOM 855 C1 AN1 58 23.361 31.043 21.261 1.00 0.00 C +ATOM 856 H AN1 58 22.572 31.066 19.367 1.00 0.00 H +ATOM 857 H1 AN1 58 24.356 31.487 19.617 1.00 0.00 H +ATOM 858 H2 AN1 58 23.053 32.725 19.986 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 26.146 32.983 21.542 1.00 0.00 N +ATOM 860 N2 AZI 59 26.756 32.068 21.038 1.00 0.00 N +ATOM 861 N3 AZI 59 27.449 31.232 20.390 1.00 0.00 N +TER 862 AZI 59 \ No newline at end of file diff --git a/tests/nsga2/pdbs_rename/cluster17.pdb b/tests/nsga2/pdbs_rename/cluster17.pdb new file mode 100644 index 0000000..d97bf4b --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster17.pdb @@ -0,0 +1,864 @@ +CRYST1 51.573 53.199 47.303 90.00 90.00 90.00 1 +ATOM 1 N MET 1 17.868 20.925 34.097 1.00 0.00 N +ATOM 2 H1 MET 1 17.633 20.665 33.149 1.00 0.00 H +ATOM 3 H2 MET 1 17.418 21.776 34.402 1.00 0.00 H +ATOM 4 H3 MET 1 17.502 20.212 34.711 1.00 0.00 H +ATOM 5 CA MET 1 19.369 20.948 34.258 1.00 0.00 C +ATOM 6 HA MET 1 19.531 20.858 35.332 1.00 0.00 H +ATOM 7 CB MET 1 20.002 19.709 33.600 1.00 0.00 C +ATOM 8 HB2 MET 1 19.578 18.806 34.040 1.00 0.00 H +ATOM 9 HB3 MET 1 19.738 19.681 32.543 1.00 0.00 H +ATOM 10 CG MET 1 21.504 19.634 33.585 1.00 0.00 C +ATOM 11 HG2 MET 1 21.970 20.373 32.933 1.00 0.00 H +ATOM 12 HG3 MET 1 21.898 19.859 34.576 1.00 0.00 H +ATOM 13 SD MET 1 22.271 18.034 33.099 1.00 0.00 S +ATOM 14 CE MET 1 21.885 16.890 34.518 1.00 0.00 C +ATOM 15 HE1 MET 1 22.208 17.272 35.486 1.00 0.00 H +ATOM 16 HE2 MET 1 22.548 16.030 34.429 1.00 0.00 H +ATOM 17 HE3 MET 1 20.858 16.526 34.480 1.00 0.00 H +ATOM 18 C MET 1 19.898 22.256 33.666 1.00 0.00 C +ATOM 19 O MET 1 19.428 22.650 32.604 1.00 0.00 O +ATOM 20 N GLN 2 20.902 22.881 34.369 1.00 0.00 N +ATOM 21 H GLN 2 21.229 22.502 35.246 1.00 0.00 H +ATOM 22 CA GLN 2 21.651 24.027 33.751 1.00 0.00 C +ATOM 23 HA GLN 2 20.966 24.487 33.039 1.00 0.00 H +ATOM 24 CB GLN 2 21.988 25.109 34.805 1.00 0.00 C +ATOM 25 HB2 GLN 2 22.627 24.651 35.561 1.00 0.00 H +ATOM 26 HB3 GLN 2 22.570 25.915 34.358 1.00 0.00 H +ATOM 27 CG GLN 2 20.617 25.658 35.147 1.00 0.00 C +ATOM 28 HG2 GLN 2 20.124 26.001 34.237 1.00 0.00 H +ATOM 29 HG3 GLN 2 20.080 24.896 35.711 1.00 0.00 H +ATOM 30 CD GLN 2 20.719 26.865 36.081 1.00 0.00 C +ATOM 31 OE1 GLN 2 21.840 27.239 36.562 1.00 0.00 O +ATOM 32 NE2 GLN 2 19.665 27.626 36.097 1.00 0.00 N +ATOM 33 HE21 GLN 2 19.642 28.267 36.878 1.00 0.00 H +ATOM 34 HE22 GLN 2 18.808 27.401 35.613 1.00 0.00 H +ATOM 35 C GLN 2 22.847 23.503 32.865 1.00 0.00 C +ATOM 36 O GLN 2 23.714 22.789 33.373 1.00 0.00 O +ATOM 37 N TYR 3 22.835 23.971 31.613 1.00 0.00 N +ATOM 38 H TYR 3 22.101 24.642 31.434 1.00 0.00 H +ATOM 39 CA TYR 3 23.891 23.793 30.634 1.00 0.00 C +ATOM 40 HA TYR 3 24.617 23.140 31.120 1.00 0.00 H +ATOM 41 CB TYR 3 23.369 23.153 29.303 1.00 0.00 C +ATOM 42 HB2 TYR 3 22.693 23.916 28.917 1.00 0.00 H +ATOM 43 HB3 TYR 3 24.145 22.896 28.581 1.00 0.00 H +ATOM 44 CG TYR 3 22.620 21.819 29.436 1.00 0.00 C +ATOM 45 CD1 TYR 3 23.213 20.612 29.075 1.00 0.00 C +ATOM 46 HD1 TYR 3 24.269 20.692 28.868 1.00 0.00 H +ATOM 47 CE1 TYR 3 22.606 19.390 29.434 1.00 0.00 C +ATOM 48 HE1 TYR 3 23.172 18.483 29.281 1.00 0.00 H +ATOM 49 CZ TYR 3 21.257 19.331 29.884 1.00 0.00 C +ATOM 50 OH TYR 3 20.642 18.168 30.222 1.00 0.00 O +ATOM 51 HH TYR 3 21.330 17.516 30.368 1.00 0.00 H +ATOM 52 CE2 TYR 3 20.691 20.584 30.209 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.680 20.579 30.587 1.00 0.00 H +ATOM 54 CD2 TYR 3 21.385 21.816 30.056 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.860 22.745 30.229 1.00 0.00 H +ATOM 56 C TYR 3 24.619 25.055 30.224 1.00 0.00 C +ATOM 57 O TYR 3 24.020 26.029 29.867 1.00 0.00 O +ATOM 58 N LYS 4 25.938 25.036 30.365 1.00 0.00 N +ATOM 59 H LYS 4 26.392 24.157 30.570 1.00 0.00 H +ATOM 60 CA LYS 4 26.845 26.183 30.137 1.00 0.00 C +ATOM 61 HA LYS 4 26.332 27.062 30.525 1.00 0.00 H +ATOM 62 CB LYS 4 28.100 26.081 31.001 1.00 0.00 C +ATOM 63 HB2 LYS 4 27.796 26.221 32.038 1.00 0.00 H +ATOM 64 HB3 LYS 4 28.614 25.120 30.984 1.00 0.00 H +ATOM 65 CG LYS 4 29.076 27.186 30.610 1.00 0.00 C +ATOM 66 HG2 LYS 4 29.530 27.081 29.625 1.00 0.00 H +ATOM 67 HG3 LYS 4 28.484 28.098 30.538 1.00 0.00 H +ATOM 68 CD LYS 4 30.284 27.275 31.626 1.00 0.00 C +ATOM 69 HD2 LYS 4 30.837 28.202 31.470 1.00 0.00 H +ATOM 70 HD3 LYS 4 29.953 27.276 32.665 1.00 0.00 H +ATOM 71 CE LYS 4 31.291 26.087 31.604 1.00 0.00 C +ATOM 72 HE2 LYS 4 30.834 25.187 32.016 1.00 0.00 H +ATOM 73 HE3 LYS 4 31.753 25.938 30.627 1.00 0.00 H +ATOM 74 NZ LYS 4 32.551 26.330 32.397 1.00 0.00 N +ATOM 75 HZ1 LYS 4 32.489 25.967 33.337 1.00 0.00 H +ATOM 76 HZ2 LYS 4 32.859 27.291 32.346 1.00 0.00 H +ATOM 77 HZ3 LYS 4 33.315 25.851 31.942 1.00 0.00 H +ATOM 78 C LYS 4 27.048 26.368 28.627 1.00 0.00 C +ATOM 79 O LYS 4 27.035 25.380 27.871 1.00 0.00 O +ATOM 80 N HX1 5 27.090 27.600 28.122 1.00 0.00 N +ATOM 81 CA HX1 5 27.123 27.946 26.675 1.00 0.00 C +ATOM 82 C HX1 5 28.157 29.072 26.384 1.00 0.00 C +ATOM 83 O HX1 5 27.907 30.258 26.508 1.00 0.00 O +ATOM 84 CB HX1 5 25.798 28.327 26.127 1.00 0.00 C +ATOM 85 CG HX1 5 25.682 28.344 24.663 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.589 27.724 23.743 1.00 0.00 C +ATOM 87 ND1 HX1 5 24.647 29.027 23.982 1.00 0.00 N +ATOM 88 CE1 HX1 5 24.906 28.925 22.671 1.00 0.00 C +ATOM 89 NE2 HX1 5 26.121 28.205 22.483 1.00 0.00 N +ATOM 90 H HX1 5 27.094 28.355 28.793 1.00 0.00 H +ATOM 91 HA HX1 5 27.417 27.024 26.174 1.00 0.00 H +ATOM 92 HB2 HX1 5 25.321 29.239 26.485 1.00 0.00 H +ATOM 93 HB3 HX1 5 25.148 27.519 26.461 1.00 0.00 H +ATOM 94 HD2 HX1 5 27.471 27.162 24.012 1.00 0.00 H +ATOM 95 HE1 HX1 5 24.379 29.519 21.939 1.00 0.00 H +ATOM 96 HE2 HX1 5 26.614 28.190 21.602 1.00 0.00 H +ATOM 97 N ILE 6 29.307 28.577 25.772 1.00 0.00 N +ATOM 98 H ILE 6 29.485 27.585 25.717 1.00 0.00 H +ATOM 99 CA ILE 6 30.463 29.421 25.354 1.00 0.00 C +ATOM 100 HA ILE 6 30.608 30.311 25.967 1.00 0.00 H +ATOM 101 CB ILE 6 31.795 28.676 25.505 1.00 0.00 C +ATOM 102 HB ILE 6 31.767 27.755 24.921 1.00 0.00 H +ATOM 103 CG2 ILE 6 32.960 29.608 25.027 1.00 0.00 C +ATOM 104 HG21 ILE 6 32.981 29.635 23.937 1.00 0.00 H +ATOM 105 HG22 ILE 6 33.880 29.083 25.284 1.00 0.00 H +ATOM 106 HG23 ILE 6 32.910 30.545 25.581 1.00 0.00 H +ATOM 107 CG1 ILE 6 32.138 28.190 26.926 1.00 0.00 C +ATOM 108 HG12 ILE 6 32.605 28.990 27.499 1.00 0.00 H +ATOM 109 HG13 ILE 6 31.217 27.837 27.391 1.00 0.00 H +ATOM 110 CD1 ILE 6 33.068 27.024 26.968 1.00 0.00 C +ATOM 111 HD11 ILE 6 32.703 26.225 26.322 1.00 0.00 H +ATOM 112 HD12 ILE 6 32.916 26.688 27.993 1.00 0.00 H +ATOM 113 HD13 ILE 6 34.143 27.206 26.974 1.00 0.00 H +ATOM 114 C ILE 6 30.250 29.875 23.908 1.00 0.00 C +ATOM 115 O ILE 6 29.875 29.113 23.060 1.00 0.00 O +ATOM 116 N VAL 7 30.502 31.185 23.697 1.00 0.00 N +ATOM 117 H VAL 7 30.882 31.665 24.501 1.00 0.00 H +ATOM 118 CA VAL 7 29.858 31.982 22.697 1.00 0.00 C +ATOM 119 HA VAL 7 29.722 31.346 21.823 1.00 0.00 H +ATOM 120 CB VAL 7 28.428 32.465 23.153 1.00 0.00 C +ATOM 121 HB VAL 7 28.063 33.359 22.646 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.421 31.318 22.996 1.00 0.00 C +ATOM 123 HG11 VAL 7 27.630 30.726 22.105 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.368 30.763 23.933 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.482 31.869 22.940 1.00 0.00 H +ATOM 126 CG2 VAL 7 28.519 33.044 24.591 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.604 33.473 25.001 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.781 32.196 25.223 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.367 33.727 24.564 1.00 0.00 H +ATOM 130 C VAL 7 30.848 33.120 22.374 1.00 0.00 C +ATOM 131 O VAL 7 31.970 33.216 22.961 1.00 0.00 O +ATOM 132 N ASN 8 30.484 33.973 21.462 1.00 0.00 N +ATOM 133 H ASN 8 29.629 33.805 20.952 1.00 0.00 H +ATOM 134 CA ASN 8 31.317 35.075 21.031 1.00 0.00 C +ATOM 135 HA ASN 8 32.262 34.635 20.710 1.00 0.00 H +ATOM 136 CB ASN 8 30.684 35.809 19.831 1.00 0.00 C +ATOM 137 HB2 ASN 8 30.654 35.251 18.895 1.00 0.00 H +ATOM 138 HB3 ASN 8 29.636 35.929 20.105 1.00 0.00 H +ATOM 139 CG ASN 8 31.293 37.148 19.543 1.00 0.00 C +ATOM 140 OD1 ASN 8 30.676 38.223 19.606 1.00 0.00 O +ATOM 141 ND2 ASN 8 32.590 37.122 19.229 1.00 0.00 N +ATOM 142 HD21 ASN 8 32.945 36.183 19.115 1.00 0.00 H +ATOM 143 HD22 ASN 8 33.058 38.005 19.085 1.00 0.00 H +ATOM 144 C ASN 8 31.609 36.078 22.179 1.00 0.00 C +ATOM 145 O ASN 8 30.770 36.555 22.912 1.00 0.00 O +ATOM 146 N GLY 9 32.923 36.470 22.188 1.00 0.00 N +ATOM 147 H GLY 9 33.656 36.096 21.602 1.00 0.00 H +ATOM 148 CA GLY 9 33.537 37.360 23.203 1.00 0.00 C +ATOM 149 HA2 GLY 9 33.779 36.923 24.172 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.439 37.715 22.705 1.00 0.00 H +ATOM 151 C GLY 9 32.794 38.682 23.331 1.00 0.00 C +ATOM 152 O GLY 9 32.702 39.172 24.477 1.00 0.00 O +ATOM 153 N LYS 10 32.199 39.239 22.299 1.00 0.00 N +ATOM 154 H LYS 10 32.298 38.874 21.362 1.00 0.00 H +ATOM 155 CA LYS 10 31.428 40.493 22.426 1.00 0.00 C +ATOM 156 HA LYS 10 31.987 41.293 22.911 1.00 0.00 H +ATOM 157 CB LYS 10 31.094 41.079 21.032 1.00 0.00 C +ATOM 158 HB2 LYS 10 30.234 40.501 20.697 1.00 0.00 H +ATOM 159 HB3 LYS 10 30.714 42.071 21.279 1.00 0.00 H +ATOM 160 CG LYS 10 32.159 41.175 20.062 1.00 0.00 C +ATOM 161 HG2 LYS 10 32.848 41.907 20.482 1.00 0.00 H +ATOM 162 HG3 LYS 10 32.662 40.221 19.905 1.00 0.00 H +ATOM 163 CD LYS 10 31.725 41.632 18.669 1.00 0.00 C +ATOM 164 HD2 LYS 10 32.465 41.431 17.894 1.00 0.00 H +ATOM 165 HD3 LYS 10 30.909 40.952 18.424 1.00 0.00 H +ATOM 166 CE LYS 10 31.532 43.155 18.820 1.00 0.00 C +ATOM 167 HE2 LYS 10 30.813 43.302 19.626 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.474 43.678 18.985 1.00 0.00 H +ATOM 169 NZ LYS 10 30.982 43.752 17.594 1.00 0.00 N +ATOM 170 HZ1 LYS 10 30.963 43.073 16.847 1.00 0.00 H +ATOM 171 HZ2 LYS 10 31.567 44.544 17.367 1.00 0.00 H +ATOM 172 HZ3 LYS 10 30.021 44.047 17.692 1.00 0.00 H +ATOM 173 C LYS 10 30.192 40.504 23.315 1.00 0.00 C +ATOM 174 O LYS 10 29.729 41.570 23.688 1.00 0.00 O +ATOM 175 N THR 11 29.683 39.254 23.610 1.00 0.00 N +ATOM 176 H THR 11 30.170 38.497 23.152 1.00 0.00 H +ATOM 177 CA THR 11 28.563 39.092 24.661 1.00 0.00 C +ATOM 178 HA THR 11 27.908 39.878 24.286 1.00 0.00 H +ATOM 179 CB THR 11 27.804 37.718 24.432 1.00 0.00 C +ATOM 180 HB THR 11 27.065 37.623 25.228 1.00 0.00 H +ATOM 181 CG2 THR 11 27.195 37.464 23.044 1.00 0.00 C +ATOM 182 HG21 THR 11 26.517 36.627 23.215 1.00 0.00 H +ATOM 183 HG22 THR 11 27.914 37.486 22.225 1.00 0.00 H +ATOM 184 HG23 THR 11 26.506 38.293 22.880 1.00 0.00 H +ATOM 185 OG1 THR 11 28.583 36.582 24.640 1.00 0.00 O +ATOM 186 HG1 THR 11 29.318 36.467 24.033 1.00 0.00 H +ATOM 187 C THR 11 29.083 39.294 26.075 1.00 0.00 C +ATOM 188 O THR 11 30.214 39.244 26.461 1.00 0.00 O +ATOM 189 N LEU 12 28.145 39.510 26.986 1.00 0.00 N +ATOM 190 H LEU 12 27.169 39.591 26.738 1.00 0.00 H +ATOM 191 CA LEU 12 28.365 39.382 28.457 1.00 0.00 C +ATOM 192 HA LEU 12 28.899 40.312 28.646 1.00 0.00 H +ATOM 193 CB LEU 12 26.934 39.446 29.088 1.00 0.00 C +ATOM 194 HB2 LEU 12 26.416 40.377 28.859 1.00 0.00 H +ATOM 195 HB3 LEU 12 26.272 38.683 28.678 1.00 0.00 H +ATOM 196 CG LEU 12 26.988 39.383 30.659 1.00 0.00 C +ATOM 197 HG LEU 12 27.333 38.412 31.013 1.00 0.00 H +ATOM 198 CD1 LEU 12 27.972 40.545 30.967 1.00 0.00 C +ATOM 199 HD11 LEU 12 29.013 40.230 30.903 1.00 0.00 H +ATOM 200 HD12 LEU 12 27.755 40.983 31.941 1.00 0.00 H +ATOM 201 HD13 LEU 12 27.917 41.359 30.244 1.00 0.00 H +ATOM 202 CD2 LEU 12 25.635 39.720 31.317 1.00 0.00 C +ATOM 203 HD21 LEU 12 25.336 40.733 31.049 1.00 0.00 H +ATOM 204 HD22 LEU 12 25.702 39.813 32.401 1.00 0.00 H +ATOM 205 HD23 LEU 12 24.898 38.965 31.046 1.00 0.00 H +ATOM 206 C LEU 12 29.194 38.172 28.872 1.00 0.00 C +ATOM 207 O LEU 12 28.789 36.997 28.788 1.00 0.00 O +ATOM 208 N LYS 13 30.483 38.447 29.209 1.00 0.00 N +ATOM 209 H LYS 13 30.811 39.386 29.389 1.00 0.00 H +ATOM 210 CA LYS 13 31.624 37.458 29.481 1.00 0.00 C +ATOM 211 HA LYS 13 32.439 38.179 29.534 1.00 0.00 H +ATOM 212 CB LYS 13 31.401 36.865 30.954 1.00 0.00 C +ATOM 213 HB2 LYS 13 30.581 36.167 30.788 1.00 0.00 H +ATOM 214 HB3 LYS 13 32.277 36.283 31.242 1.00 0.00 H +ATOM 215 CG LYS 13 31.077 37.838 32.112 1.00 0.00 C +ATOM 216 HG2 LYS 13 31.805 38.647 32.054 1.00 0.00 H +ATOM 217 HG3 LYS 13 30.196 38.384 31.774 1.00 0.00 H +ATOM 218 CD LYS 13 30.763 37.253 33.440 1.00 0.00 C +ATOM 219 HD2 LYS 13 30.141 36.375 33.266 1.00 0.00 H +ATOM 220 HD3 LYS 13 31.689 36.773 33.757 1.00 0.00 H +ATOM 221 CE LYS 13 30.336 38.244 34.470 1.00 0.00 C +ATOM 222 HE2 LYS 13 31.229 38.846 34.643 1.00 0.00 H +ATOM 223 HE3 LYS 13 29.603 38.921 34.031 1.00 0.00 H +ATOM 224 NZ LYS 13 29.808 37.688 35.745 1.00 0.00 N +ATOM 225 HZ1 LYS 13 29.001 37.100 35.594 1.00 0.00 H +ATOM 226 HZ2 LYS 13 29.572 38.397 36.424 1.00 0.00 H +ATOM 227 HZ3 LYS 13 30.507 37.092 36.164 1.00 0.00 H +ATOM 228 C LYS 13 32.060 36.476 28.365 1.00 0.00 C +ATOM 229 O LYS 13 32.971 35.730 28.675 1.00 0.00 O +ATOM 230 N GLY 14 31.390 36.529 27.223 1.00 0.00 N +ATOM 231 H GLY 14 30.612 37.161 27.102 1.00 0.00 H +ATOM 232 CA GLY 14 31.597 35.493 26.260 1.00 0.00 C +ATOM 233 HA2 GLY 14 31.055 35.690 25.336 1.00 0.00 H +ATOM 234 HA3 GLY 14 32.667 35.541 26.057 1.00 0.00 H +ATOM 235 C GLY 14 31.203 34.106 26.746 1.00 0.00 C +ATOM 236 O GLY 14 31.538 33.168 26.056 1.00 0.00 O +ATOM 237 N VAL 15 30.291 33.975 27.742 1.00 0.00 N +ATOM 238 H VAL 15 30.094 34.877 28.152 1.00 0.00 H +ATOM 239 CA VAL 15 29.666 32.740 28.273 1.00 0.00 C +ATOM 240 HA VAL 15 29.346 32.055 27.489 1.00 0.00 H +ATOM 241 CB VAL 15 30.756 31.930 29.052 1.00 0.00 C +ATOM 242 HB VAL 15 31.613 31.744 28.405 1.00 0.00 H +ATOM 243 CG1 VAL 15 31.384 32.839 30.204 1.00 0.00 C +ATOM 244 HG11 VAL 15 31.603 33.855 29.875 1.00 0.00 H +ATOM 245 HG12 VAL 15 30.626 32.969 30.977 1.00 0.00 H +ATOM 246 HG13 VAL 15 32.298 32.413 30.618 1.00 0.00 H +ATOM 247 CG2 VAL 15 30.283 30.483 29.474 1.00 0.00 C +ATOM 248 HG21 VAL 15 29.563 30.476 30.293 1.00 0.00 H +ATOM 249 HG22 VAL 15 29.846 29.929 28.644 1.00 0.00 H +ATOM 250 HG23 VAL 15 31.217 29.988 29.741 1.00 0.00 H +ATOM 251 C VAL 15 28.468 33.111 29.186 1.00 0.00 C +ATOM 252 O VAL 15 28.368 34.049 29.988 1.00 0.00 O +ATOM 253 N HY1 16 27.381 32.294 29.085 1.00 0.00 N +ATOM 254 CA HY1 16 26.182 32.315 29.954 1.00 0.00 C +ATOM 255 C HY1 16 25.721 30.822 30.115 1.00 0.00 C +ATOM 256 O HY1 16 26.247 29.981 29.429 1.00 0.00 O +ATOM 257 CB HY1 16 25.246 33.225 29.204 1.00 0.00 C +ATOM 258 CG HY1 16 24.885 32.794 27.814 1.00 0.00 C +ATOM 259 CD2 HY1 16 23.832 32.074 27.411 1.00 0.00 C +ATOM 260 ND1 HY1 16 25.499 33.205 26.680 1.00 0.00 N +ATOM 261 CE1 HY1 16 24.911 32.655 25.615 1.00 0.00 C +ATOM 262 NE2 HY1 16 23.917 31.882 25.981 1.00 0.00 N +ATOM 263 H HY1 16 27.407 31.492 28.472 1.00 0.00 H +ATOM 264 HA HY1 16 26.390 32.798 30.908 1.00 0.00 H +ATOM 265 HB2 HY1 16 24.367 33.351 29.836 1.00 0.00 H +ATOM 266 HB3 HY1 16 25.705 34.205 29.079 1.00 0.00 H +ATOM 267 HD1 HY1 16 26.147 33.976 26.595 1.00 0.00 H +ATOM 268 HD2 HY1 16 23.123 31.480 27.970 1.00 0.00 H +ATOM 269 HE1 HY1 16 25.129 32.918 24.590 1.00 0.00 H +ATOM 270 N THR 17 24.707 30.602 30.987 1.00 0.00 N +ATOM 271 H THR 17 24.293 31.412 31.425 1.00 0.00 H +ATOM 272 CA THR 17 24.003 29.279 31.075 1.00 0.00 C +ATOM 273 HA THR 17 24.577 28.558 30.493 1.00 0.00 H +ATOM 274 CB THR 17 23.953 28.747 32.564 1.00 0.00 C +ATOM 275 HB THR 17 24.941 28.823 33.018 1.00 0.00 H +ATOM 276 CG2 THR 17 23.003 29.518 33.501 1.00 0.00 C +ATOM 277 HG21 THR 17 22.216 30.049 32.965 1.00 0.00 H +ATOM 278 HG22 THR 17 23.562 30.278 34.046 1.00 0.00 H +ATOM 279 HG23 THR 17 22.583 28.834 34.240 1.00 0.00 H +ATOM 280 OG1 THR 17 23.648 27.362 32.679 1.00 0.00 O +ATOM 281 HG1 THR 17 24.262 26.860 33.220 1.00 0.00 H +ATOM 282 C THR 17 22.563 29.265 30.578 1.00 0.00 C +ATOM 283 O THR 17 21.927 30.292 30.479 1.00 0.00 O +ATOM 284 N HY2 18 22.105 28.057 30.254 1.00 0.00 N +ATOM 285 CA HY2 18 20.714 27.746 29.934 1.00 0.00 C +ATOM 286 C HY2 18 20.074 26.609 30.785 1.00 0.00 C +ATOM 287 O HY2 18 20.684 25.563 30.870 1.00 0.00 O +ATOM 288 CB HY2 18 20.676 27.266 28.470 1.00 0.00 C +ATOM 289 CG HY2 18 20.986 28.396 27.481 1.00 0.00 C +ATOM 290 CD2 HY2 18 22.033 28.427 26.602 1.00 0.00 C +ATOM 291 ND1 HY2 18 20.153 29.421 27.117 1.00 0.00 N +ATOM 292 CE1 HY2 18 20.684 30.102 26.107 1.00 0.00 C +ATOM 293 NE2 HY2 18 21.884 29.484 25.742 1.00 0.00 N +ATOM 294 H HY2 18 22.716 27.275 30.442 1.00 0.00 H +ATOM 295 HA HY2 18 20.133 28.662 30.046 1.00 0.00 H +ATOM 296 HB2 HY2 18 21.346 26.411 28.387 1.00 0.00 H +ATOM 297 HB3 HY2 18 19.626 27.029 28.296 1.00 0.00 H +ATOM 298 HD1 HY2 18 19.276 29.587 27.590 1.00 0.00 H +ATOM 299 HD2 HY2 18 22.786 27.675 26.416 1.00 0.00 H +ATOM 300 HE1 HY2 18 20.239 30.891 25.518 1.00 0.00 H +ATOM 301 N GLU 19 18.823 26.728 31.297 1.00 0.00 N +ATOM 302 H GLU 19 18.428 27.656 31.258 1.00 0.00 H +ATOM 303 CA GLU 19 18.035 25.593 31.828 1.00 0.00 C +ATOM 304 HA GLU 19 18.684 24.857 32.302 1.00 0.00 H +ATOM 305 CB GLU 19 17.062 25.939 33.003 1.00 0.00 C +ATOM 306 HB2 GLU 19 17.677 26.174 33.872 1.00 0.00 H +ATOM 307 HB3 GLU 19 16.438 26.784 32.712 1.00 0.00 H +ATOM 308 CG GLU 19 15.962 24.874 33.438 1.00 0.00 C +ATOM 309 HG2 GLU 19 15.074 25.310 33.896 1.00 0.00 H +ATOM 310 HG3 GLU 19 15.577 24.314 32.585 1.00 0.00 H +ATOM 311 CD GLU 19 16.439 23.743 34.328 1.00 0.00 C +ATOM 312 OE1 GLU 19 15.709 22.720 34.373 1.00 0.00 O +ATOM 313 OE2 GLU 19 17.390 23.739 35.097 1.00 0.00 O +ATOM 314 C GLU 19 17.283 24.881 30.696 1.00 0.00 C +ATOM 315 O GLU 19 16.757 25.597 29.811 1.00 0.00 O +ATOM 316 N ALA 20 17.308 23.555 30.695 1.00 0.00 N +ATOM 317 H ALA 20 17.978 23.142 31.329 1.00 0.00 H +ATOM 318 CA ALA 20 16.506 22.620 29.788 1.00 0.00 C +ATOM 319 HA ALA 20 15.553 23.100 29.565 1.00 0.00 H +ATOM 320 CB ALA 20 17.274 22.412 28.460 1.00 0.00 C +ATOM 321 HB1 ALA 20 18.041 21.658 28.635 1.00 0.00 H +ATOM 322 HB2 ALA 20 17.664 23.372 28.121 1.00 0.00 H +ATOM 323 HB3 ALA 20 16.640 21.973 27.690 1.00 0.00 H +ATOM 324 C ALA 20 16.153 21.334 30.532 1.00 0.00 C +ATOM 325 O ALA 20 16.804 20.930 31.509 1.00 0.00 O +ATOM 326 N VAL 21 15.180 20.608 29.952 1.00 0.00 N +ATOM 327 H VAL 21 14.978 20.904 29.008 1.00 0.00 H +ATOM 328 CA VAL 21 14.823 19.190 30.262 1.00 0.00 C +ATOM 329 HA VAL 21 14.654 19.134 31.338 1.00 0.00 H +ATOM 330 CB VAL 21 13.523 18.794 29.486 1.00 0.00 C +ATOM 331 HB VAL 21 13.710 18.751 28.413 1.00 0.00 H +ATOM 332 CG1 VAL 21 13.199 17.274 29.864 1.00 0.00 C +ATOM 333 HG11 VAL 21 13.880 16.587 29.360 1.00 0.00 H +ATOM 334 HG12 VAL 21 12.203 17.002 29.515 1.00 0.00 H +ATOM 335 HG13 VAL 21 13.221 17.125 30.943 1.00 0.00 H +ATOM 336 CG2 VAL 21 12.298 19.637 29.809 1.00 0.00 C +ATOM 337 HG21 VAL 21 11.925 19.526 30.828 1.00 0.00 H +ATOM 338 HG22 VAL 21 11.495 19.299 29.154 1.00 0.00 H +ATOM 339 HG23 VAL 21 12.567 20.680 29.640 1.00 0.00 H +ATOM 340 C VAL 21 15.885 18.180 29.774 1.00 0.00 C +ATOM 341 O VAL 21 16.058 17.148 30.453 1.00 0.00 O +ATOM 342 N ASP 22 16.640 18.471 28.696 1.00 0.00 N +ATOM 343 H ASP 22 16.544 19.312 28.145 1.00 0.00 H +ATOM 344 CA ASP 22 17.747 17.617 28.275 1.00 0.00 C +ATOM 345 HA ASP 22 18.206 17.309 29.214 1.00 0.00 H +ATOM 346 CB ASP 22 17.245 16.441 27.443 1.00 0.00 C +ATOM 347 HB2 ASP 22 16.303 16.069 27.846 1.00 0.00 H +ATOM 348 HB3 ASP 22 17.073 16.739 26.409 1.00 0.00 H +ATOM 349 CG ASP 22 18.099 15.122 27.436 1.00 0.00 C +ATOM 350 OD1 ASP 22 17.578 14.161 27.981 1.00 0.00 O +ATOM 351 OD2 ASP 22 19.262 15.159 26.931 1.00 0.00 O +ATOM 352 C ASP 22 18.814 18.339 27.444 1.00 0.00 C +ATOM 353 O ASP 22 18.641 19.467 27.063 1.00 0.00 O +ATOM 354 N ALA 23 19.961 17.769 27.329 1.00 0.00 N +ATOM 355 H ALA 23 20.198 16.937 27.849 1.00 0.00 H +ATOM 356 CA ALA 23 21.159 18.099 26.431 1.00 0.00 C +ATOM 357 HA ALA 23 21.544 19.053 26.792 1.00 0.00 H +ATOM 358 CB ALA 23 22.221 16.976 26.407 1.00 0.00 C +ATOM 359 HB1 ALA 23 21.844 15.997 26.702 1.00 0.00 H +ATOM 360 HB2 ALA 23 23.107 17.227 26.991 1.00 0.00 H +ATOM 361 HB3 ALA 23 22.628 16.840 25.405 1.00 0.00 H +ATOM 362 C ALA 23 20.671 18.360 24.997 1.00 0.00 C +ATOM 363 O ALA 23 21.171 19.233 24.313 1.00 0.00 O +ATOM 364 N ALA 24 19.652 17.607 24.669 1.00 0.00 N +ATOM 365 H ALA 24 19.411 16.923 25.373 1.00 0.00 H +ATOM 366 CA ALA 24 18.942 17.613 23.439 1.00 0.00 C +ATOM 367 HA ALA 24 19.663 17.573 22.623 1.00 0.00 H +ATOM 368 CB ALA 24 18.108 16.334 23.303 1.00 0.00 C +ATOM 369 HB1 ALA 24 18.809 15.501 23.353 1.00 0.00 H +ATOM 370 HB2 ALA 24 17.597 16.314 22.340 1.00 0.00 H +ATOM 371 HB3 ALA 24 17.311 16.306 24.047 1.00 0.00 H +ATOM 372 C ALA 24 18.052 18.784 23.224 1.00 0.00 C +ATOM 373 O ALA 24 17.906 19.320 22.131 1.00 0.00 O +ATOM 374 N GLU 25 17.462 19.374 24.295 1.00 0.00 N +ATOM 375 H GLU 25 17.664 19.009 25.214 1.00 0.00 H +ATOM 376 CA GLU 25 16.716 20.628 24.262 1.00 0.00 C +ATOM 377 HA GLU 25 16.161 20.613 23.324 1.00 0.00 H +ATOM 378 CB GLU 25 15.719 20.660 25.366 1.00 0.00 C +ATOM 379 HB2 GLU 25 16.245 20.573 26.317 1.00 0.00 H +ATOM 380 HB3 GLU 25 15.302 21.665 25.432 1.00 0.00 H +ATOM 381 CG GLU 25 14.561 19.623 25.211 1.00 0.00 C +ATOM 382 HG2 GLU 25 15.071 18.660 25.229 1.00 0.00 H +ATOM 383 HG3 GLU 25 13.831 19.672 26.019 1.00 0.00 H +ATOM 384 CD GLU 25 13.785 19.837 23.893 1.00 0.00 C +ATOM 385 OE1 GLU 25 13.011 20.771 23.819 1.00 0.00 O +ATOM 386 OE2 GLU 25 14.034 19.213 22.869 1.00 0.00 O +ATOM 387 C GLU 25 17.588 21.917 24.444 1.00 0.00 C +ATOM 388 O GLU 25 17.307 22.884 23.766 1.00 0.00 O +ATOM 389 N ALA 26 18.697 21.861 25.205 1.00 0.00 N +ATOM 390 H ALA 26 18.687 21.129 25.901 1.00 0.00 H +ATOM 391 CA ALA 26 19.744 22.858 25.225 1.00 0.00 C +ATOM 392 HA ALA 26 19.228 23.776 25.509 1.00 0.00 H +ATOM 393 CB ALA 26 20.793 22.489 26.276 1.00 0.00 C +ATOM 394 HB1 ALA 26 20.242 22.281 27.194 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.569 23.251 26.348 1.00 0.00 H +ATOM 396 HB3 ALA 26 21.271 21.562 25.960 1.00 0.00 H +ATOM 397 C ALA 26 20.445 23.147 23.906 1.00 0.00 C +ATOM 398 O ALA 26 20.767 24.315 23.539 1.00 0.00 O +ATOM 399 N GLU 27 20.714 22.052 23.126 1.00 0.00 N +ATOM 400 H GLU 27 20.554 21.088 23.384 1.00 0.00 H +ATOM 401 CA GLU 27 21.349 22.107 21.803 1.00 0.00 C +ATOM 402 HA GLU 27 22.354 22.456 22.040 1.00 0.00 H +ATOM 403 CB GLU 27 21.400 20.657 21.232 1.00 0.00 C +ATOM 404 HB2 GLU 27 21.908 20.051 21.982 1.00 0.00 H +ATOM 405 HB3 GLU 27 20.346 20.411 21.108 1.00 0.00 H +ATOM 406 CG GLU 27 22.118 20.443 19.884 1.00 0.00 C +ATOM 407 HG2 GLU 27 21.745 21.042 19.053 1.00 0.00 H +ATOM 408 HG3 GLU 27 23.173 20.716 19.855 1.00 0.00 H +ATOM 409 CD GLU 27 22.067 18.983 19.527 1.00 0.00 C +ATOM 410 OE1 GLU 27 21.175 18.652 18.699 1.00 0.00 O +ATOM 411 OE2 GLU 27 22.926 18.193 20.044 1.00 0.00 O +ATOM 412 C GLU 27 20.725 23.101 20.796 1.00 0.00 C +ATOM 413 O GLU 27 21.391 23.707 19.954 1.00 0.00 O +ATOM 414 N LYS 28 19.458 23.340 21.011 1.00 0.00 N +ATOM 415 H LYS 28 18.953 22.823 21.717 1.00 0.00 H +ATOM 416 CA LYS 28 18.615 24.268 20.189 1.00 0.00 C +ATOM 417 HA LYS 28 18.490 23.916 19.164 1.00 0.00 H +ATOM 418 CB LYS 28 17.189 24.254 20.770 1.00 0.00 C +ATOM 419 HB2 LYS 28 17.204 24.441 21.844 1.00 0.00 H +ATOM 420 HB3 LYS 28 16.603 25.058 20.326 1.00 0.00 H +ATOM 421 CG LYS 28 16.358 22.968 20.658 1.00 0.00 C +ATOM 422 HG2 LYS 28 16.315 22.706 19.601 1.00 0.00 H +ATOM 423 HG3 LYS 28 16.776 22.112 21.187 1.00 0.00 H +ATOM 424 CD LYS 28 14.906 23.251 21.097 1.00 0.00 C +ATOM 425 HD2 LYS 28 14.746 23.049 22.156 1.00 0.00 H +ATOM 426 HD3 LYS 28 14.688 24.281 20.815 1.00 0.00 H +ATOM 427 CE LYS 28 13.993 22.227 20.339 1.00 0.00 C +ATOM 428 HE2 LYS 28 12.948 22.492 20.495 1.00 0.00 H +ATOM 429 HE3 LYS 28 14.138 22.302 19.261 1.00 0.00 H +ATOM 430 NZ LYS 28 14.181 20.750 20.623 1.00 0.00 N +ATOM 431 HZ1 LYS 28 15.155 20.562 20.434 1.00 0.00 H +ATOM 432 HZ2 LYS 28 13.675 20.190 19.952 1.00 0.00 H +ATOM 433 HZ3 LYS 28 13.905 20.513 21.566 1.00 0.00 H +ATOM 434 C LYS 28 19.028 25.765 20.275 1.00 0.00 C +ATOM 435 O LYS 28 19.152 26.388 19.226 1.00 0.00 O +ATOM 436 N PHE 29 19.298 26.307 21.512 1.00 0.00 N +ATOM 437 H PHE 29 19.287 25.643 22.272 1.00 0.00 H +ATOM 438 CA PHE 29 19.929 27.624 21.659 1.00 0.00 C +ATOM 439 HA PHE 29 19.295 28.394 21.220 1.00 0.00 H +ATOM 440 CB PHE 29 20.055 27.939 23.146 1.00 0.00 C +ATOM 441 HB2 PHE 29 20.823 27.256 23.507 1.00 0.00 H +ATOM 442 HB3 PHE 29 20.319 28.991 23.250 1.00 0.00 H +ATOM 443 CG PHE 29 18.800 27.902 23.970 1.00 0.00 C +ATOM 444 CD1 PHE 29 17.717 28.698 23.621 1.00 0.00 C +ATOM 445 HD1 PHE 29 17.733 29.341 22.754 1.00 0.00 H +ATOM 446 CE1 PHE 29 16.490 28.589 24.196 1.00 0.00 C +ATOM 447 HE1 PHE 29 15.607 29.135 23.897 1.00 0.00 H +ATOM 448 CZ PHE 29 16.322 27.636 25.214 1.00 0.00 C +ATOM 449 HZ PHE 29 15.402 27.762 25.765 1.00 0.00 H +ATOM 450 CE2 PHE 29 17.366 26.822 25.565 1.00 0.00 C +ATOM 451 HE2 PHE 29 17.204 26.177 26.416 1.00 0.00 H +ATOM 452 CD2 PHE 29 18.611 26.914 24.992 1.00 0.00 C +ATOM 453 HD2 PHE 29 19.427 26.206 25.019 1.00 0.00 H +ATOM 454 C PHE 29 21.451 27.694 21.096 1.00 0.00 C +ATOM 455 O PHE 29 21.848 28.811 20.721 1.00 0.00 O +ATOM 456 N THR 30 22.114 26.584 20.866 1.00 0.00 N +ATOM 457 H THR 30 21.612 25.718 21.001 1.00 0.00 H +ATOM 458 CA THR 30 23.490 26.503 20.302 1.00 0.00 C +ATOM 459 HA THR 30 24.079 27.387 20.545 1.00 0.00 H +ATOM 460 CB THR 30 24.334 25.294 20.811 1.00 0.00 C +ATOM 461 HB THR 30 23.741 24.380 20.816 1.00 0.00 H +ATOM 462 CG2 THR 30 25.569 24.928 20.095 1.00 0.00 C +ATOM 463 HG21 THR 30 25.237 24.326 19.250 1.00 0.00 H +ATOM 464 HG22 THR 30 26.180 25.722 19.664 1.00 0.00 H +ATOM 465 HG23 THR 30 26.260 24.331 20.690 1.00 0.00 H +ATOM 466 OG1 THR 30 24.733 25.648 22.135 1.00 0.00 O +ATOM 467 HG1 THR 30 23.999 25.866 22.714 1.00 0.00 H +ATOM 468 C THR 30 23.436 26.494 18.772 1.00 0.00 C +ATOM 469 O THR 30 24.089 27.295 18.127 1.00 0.00 O +ATOM 470 N LYS 31 22.546 25.660 18.250 1.00 0.00 N +ATOM 471 H LYS 31 22.182 25.003 18.925 1.00 0.00 H +ATOM 472 CA LYS 31 22.022 25.582 16.871 1.00 0.00 C +ATOM 473 HA LYS 31 22.752 25.304 16.111 1.00 0.00 H +ATOM 474 CB LYS 31 20.939 24.448 16.818 1.00 0.00 C +ATOM 475 HB2 LYS 31 21.382 23.557 17.263 1.00 0.00 H +ATOM 476 HB3 LYS 31 20.097 24.625 17.487 1.00 0.00 H +ATOM 477 CG LYS 31 20.364 24.039 15.468 1.00 0.00 C +ATOM 478 HG2 LYS 31 19.644 23.221 15.486 1.00 0.00 H +ATOM 479 HG3 LYS 31 19.844 24.912 15.074 1.00 0.00 H +ATOM 480 CD LYS 31 21.401 23.575 14.490 1.00 0.00 C +ATOM 481 HD2 LYS 31 21.950 24.419 14.073 1.00 0.00 H +ATOM 482 HD3 LYS 31 22.049 22.793 14.886 1.00 0.00 H +ATOM 483 CE LYS 31 20.660 22.977 13.341 1.00 0.00 C +ATOM 484 HE2 LYS 31 20.076 22.168 13.779 1.00 0.00 H +ATOM 485 HE3 LYS 31 20.013 23.755 12.938 1.00 0.00 H +ATOM 486 NZ LYS 31 21.644 22.496 12.418 1.00 0.00 N +ATOM 487 HZ1 LYS 31 21.250 21.791 11.812 1.00 0.00 H +ATOM 488 HZ2 LYS 31 22.462 22.105 12.864 1.00 0.00 H +ATOM 489 HZ3 LYS 31 21.974 23.225 11.802 1.00 0.00 H +ATOM 490 C LYS 31 21.458 26.935 16.309 1.00 0.00 C +ATOM 491 O LYS 31 21.742 27.362 15.185 1.00 0.00 O +ATOM 492 N ALA 32 20.677 27.588 17.089 1.00 0.00 N +ATOM 493 H ALA 32 20.534 27.265 18.035 1.00 0.00 H +ATOM 494 CA ALA 32 20.045 28.866 16.863 1.00 0.00 C +ATOM 495 HA ALA 32 19.742 28.897 15.816 1.00 0.00 H +ATOM 496 CB ALA 32 18.852 29.180 17.831 1.00 0.00 C +ATOM 497 HB1 ALA 32 19.231 29.247 18.851 1.00 0.00 H +ATOM 498 HB2 ALA 32 18.424 30.131 17.516 1.00 0.00 H +ATOM 499 HB3 ALA 32 18.120 28.373 17.806 1.00 0.00 H +ATOM 500 C ALA 32 21.097 29.966 16.838 1.00 0.00 C +ATOM 501 O ALA 32 21.049 30.740 15.829 1.00 0.00 O +ATOM 502 N ASP 33 22.110 29.966 17.772 1.00 0.00 N +ATOM 503 H ASP 33 22.039 29.378 18.590 1.00 0.00 H +ATOM 504 CA ASP 33 23.200 30.995 17.820 1.00 0.00 C +ATOM 505 HA ASP 33 22.788 31.955 17.509 1.00 0.00 H +ATOM 506 CB ASP 33 23.739 30.925 19.217 1.00 0.00 C +ATOM 507 HB2 ASP 33 22.973 31.330 19.878 1.00 0.00 H +ATOM 508 HB3 ASP 33 23.982 29.897 19.488 1.00 0.00 H +ATOM 509 CG ASP 33 24.951 31.739 19.430 1.00 0.00 C +ATOM 510 OD1 ASP 33 25.982 31.160 19.862 1.00 0.00 O +ATOM 511 OD2 ASP 33 24.961 32.990 19.229 1.00 0.00 O +ATOM 512 C ASP 33 24.207 30.900 16.735 1.00 0.00 C +ATOM 513 O ASP 33 24.661 31.889 16.159 1.00 0.00 O +ATOM 514 N ALA 34 24.552 29.673 16.349 1.00 0.00 N +ATOM 515 H ALA 34 24.328 28.897 16.955 1.00 0.00 H +ATOM 516 CA ALA 34 25.319 29.306 15.082 1.00 0.00 C +ATOM 517 HA ALA 34 26.244 29.878 15.002 1.00 0.00 H +ATOM 518 CB ALA 34 25.571 27.797 15.124 1.00 0.00 C +ATOM 519 HB1 ALA 34 26.050 27.539 14.180 1.00 0.00 H +ATOM 520 HB2 ALA 34 24.591 27.358 15.310 1.00 0.00 H +ATOM 521 HB3 ALA 34 26.310 27.628 15.907 1.00 0.00 H +ATOM 522 C ALA 34 24.550 29.665 13.780 1.00 0.00 C +ATOM 523 O ALA 34 25.235 29.941 12.755 1.00 0.00 O +ATOM 524 N ASN 35 23.179 29.748 13.838 1.00 0.00 N +ATOM 525 H ASN 35 22.744 29.413 14.686 1.00 0.00 H +ATOM 526 CA ASN 35 22.468 30.371 12.693 1.00 0.00 C +ATOM 527 HA ASN 35 22.997 30.162 11.764 1.00 0.00 H +ATOM 528 CB ASN 35 21.099 29.659 12.554 1.00 0.00 C +ATOM 529 HB2 ASN 35 20.600 29.479 13.506 1.00 0.00 H +ATOM 530 HB3 ASN 35 20.510 30.323 11.922 1.00 0.00 H +ATOM 531 CG ASN 35 21.191 28.344 11.840 1.00 0.00 C +ATOM 532 OD1 ASN 35 21.210 28.200 10.626 1.00 0.00 O +ATOM 533 ND2 ASN 35 21.448 27.270 12.538 1.00 0.00 N +ATOM 534 HD21 ASN 35 21.256 27.339 13.527 1.00 0.00 H +ATOM 535 HD22 ASN 35 21.442 26.362 12.094 1.00 0.00 H +ATOM 536 C ASN 35 22.456 31.965 12.661 1.00 0.00 C +ATOM 537 O ASN 35 22.483 32.562 11.574 1.00 0.00 O +ATOM 538 N ASP 36 22.497 32.601 13.828 1.00 0.00 N +ATOM 539 H ASP 36 22.426 32.144 14.726 1.00 0.00 H +ATOM 540 CA ASP 36 22.856 34.029 13.949 1.00 0.00 C +ATOM 541 HA ASP 36 22.157 34.612 13.350 1.00 0.00 H +ATOM 542 CB ASP 36 22.604 34.590 15.368 1.00 0.00 C +ATOM 543 HB2 ASP 36 23.455 34.371 16.013 1.00 0.00 H +ATOM 544 HB3 ASP 36 22.566 35.679 15.384 1.00 0.00 H +ATOM 545 CG ASP 36 21.274 34.171 15.989 1.00 0.00 C +ATOM 546 OD1 ASP 36 20.241 34.194 15.324 1.00 0.00 O +ATOM 547 OD2 ASP 36 21.194 33.710 17.098 1.00 0.00 O +ATOM 548 C ASP 36 24.293 34.451 13.552 1.00 0.00 C +ATOM 549 O ASP 36 24.520 35.603 13.136 1.00 0.00 O +ATOM 550 N LYS 37 25.156 33.466 13.742 1.00 0.00 N +ATOM 551 H LYS 37 24.853 32.766 14.403 1.00 0.00 H +ATOM 552 CA LYS 37 26.514 33.377 13.294 1.00 0.00 C +ATOM 553 HA LYS 37 27.034 34.315 13.490 1.00 0.00 H +ATOM 554 CB LYS 37 27.267 32.393 14.166 1.00 0.00 C +ATOM 555 HB2 LYS 37 27.053 31.396 13.780 1.00 0.00 H +ATOM 556 HB3 LYS 37 26.906 32.425 15.194 1.00 0.00 H +ATOM 557 CG LYS 37 28.776 32.634 14.220 1.00 0.00 C +ATOM 558 HG2 LYS 37 28.987 33.638 14.586 1.00 0.00 H +ATOM 559 HG3 LYS 37 29.200 32.515 13.223 1.00 0.00 H +ATOM 560 CD LYS 37 29.425 31.615 15.169 1.00 0.00 C +ATOM 561 HD2 LYS 37 29.325 30.587 14.821 1.00 0.00 H +ATOM 562 HD3 LYS 37 30.492 31.834 15.140 1.00 0.00 H +ATOM 563 CE LYS 37 29.106 31.637 16.684 1.00 0.00 C +ATOM 564 HE2 LYS 37 28.019 31.571 16.729 1.00 0.00 H +ATOM 565 HE3 LYS 37 29.472 30.732 17.169 1.00 0.00 H +ATOM 566 NZ LYS 37 29.836 32.735 17.344 1.00 0.00 N +ATOM 567 HZ1 LYS 37 29.557 32.853 18.308 1.00 0.00 H +ATOM 568 HZ2 LYS 37 30.817 32.511 17.432 1.00 0.00 H +ATOM 569 HZ3 LYS 37 29.669 33.586 16.825 1.00 0.00 H +ATOM 570 C LYS 37 26.611 33.113 11.766 1.00 0.00 C +ATOM 571 O LYS 37 27.663 33.414 11.259 1.00 0.00 O +ATOM 572 N GLY 38 25.583 32.483 11.101 1.00 0.00 N +ATOM 573 H GLY 38 24.772 32.276 11.666 1.00 0.00 H +ATOM 574 CA GLY 38 25.629 32.043 9.710 1.00 0.00 C +ATOM 575 HA2 GLY 38 24.688 32.071 9.160 1.00 0.00 H +ATOM 576 HA3 GLY 38 26.319 32.801 9.339 1.00 0.00 H +ATOM 577 C GLY 38 26.330 30.701 9.389 1.00 0.00 C +ATOM 578 O GLY 38 26.827 30.659 8.264 1.00 0.00 O +ATOM 579 N VAL 39 26.538 29.815 10.345 1.00 0.00 N +ATOM 580 H VAL 39 26.263 30.079 11.280 1.00 0.00 H +ATOM 581 CA VAL 39 27.458 28.688 10.209 1.00 0.00 C +ATOM 582 HA VAL 39 27.605 28.476 9.150 1.00 0.00 H +ATOM 583 CB VAL 39 28.811 29.064 10.877 1.00 0.00 C +ATOM 584 HB VAL 39 29.008 30.077 10.525 1.00 0.00 H +ATOM 585 CG1 VAL 39 28.756 29.037 12.389 1.00 0.00 C +ATOM 586 HG11 VAL 39 27.893 29.590 12.760 1.00 0.00 H +ATOM 587 HG12 VAL 39 29.663 29.370 12.894 1.00 0.00 H +ATOM 588 HG13 VAL 39 28.665 28.013 12.750 1.00 0.00 H +ATOM 589 CG2 VAL 39 30.017 28.199 10.459 1.00 0.00 C +ATOM 590 HG21 VAL 39 29.827 27.151 10.691 1.00 0.00 H +ATOM 591 HG22 VAL 39 30.839 28.521 11.099 1.00 0.00 H +ATOM 592 HG23 VAL 39 30.277 28.293 9.405 1.00 0.00 H +ATOM 593 C VAL 39 26.884 27.372 10.742 1.00 0.00 C +ATOM 594 O VAL 39 27.435 26.310 10.611 1.00 0.00 O +ATOM 595 N ASP 40 25.662 27.366 11.275 1.00 0.00 N +ATOM 596 H ASP 40 25.283 28.302 11.304 1.00 0.00 H +ATOM 597 CA ASP 40 24.693 26.304 11.535 1.00 0.00 C +ATOM 598 HA ASP 40 23.863 26.698 12.121 1.00 0.00 H +ATOM 599 CB ASP 40 24.065 25.929 10.200 1.00 0.00 C +ATOM 600 HB2 ASP 40 23.521 26.807 9.853 1.00 0.00 H +ATOM 601 HB3 ASP 40 24.842 25.607 9.507 1.00 0.00 H +ATOM 602 CG ASP 40 22.952 24.914 10.259 1.00 0.00 C +ATOM 603 OD1 ASP 40 22.100 24.903 11.165 1.00 0.00 O +ATOM 604 OD2 ASP 40 22.938 24.075 9.344 1.00 0.00 O +ATOM 605 C ASP 40 25.099 25.158 12.519 1.00 0.00 C +ATOM 606 O ASP 40 24.481 25.152 13.592 1.00 0.00 O +ATOM 607 N GLY 41 26.059 24.350 12.142 1.00 0.00 N +ATOM 608 H GLY 41 26.523 24.670 11.304 1.00 0.00 H +ATOM 609 CA GLY 41 26.452 23.087 12.690 1.00 0.00 C +ATOM 610 HA2 GLY 41 25.785 22.725 13.472 1.00 0.00 H +ATOM 611 HA3 GLY 41 26.545 22.305 11.937 1.00 0.00 H +ATOM 612 C GLY 41 27.859 23.120 13.329 1.00 0.00 C +ATOM 613 O GLY 41 28.215 22.094 13.898 1.00 0.00 O +ATOM 614 N GLU 42 28.711 24.149 13.243 1.00 0.00 N +ATOM 615 H GLU 42 28.334 24.953 12.762 1.00 0.00 H +ATOM 616 CA GLU 42 30.075 24.185 13.721 1.00 0.00 C +ATOM 617 HA GLU 42 30.439 23.184 13.488 1.00 0.00 H +ATOM 618 CB GLU 42 30.881 25.239 12.878 1.00 0.00 C +ATOM 619 HB2 GLU 42 30.462 25.306 11.875 1.00 0.00 H +ATOM 620 HB3 GLU 42 30.612 26.260 13.148 1.00 0.00 H +ATOM 621 CG GLU 42 32.386 25.027 12.817 1.00 0.00 C +ATOM 622 HG2 GLU 42 32.780 25.999 12.519 1.00 0.00 H +ATOM 623 HG3 GLU 42 32.623 24.636 13.807 1.00 0.00 H +ATOM 624 CD GLU 42 32.779 24.002 11.751 1.00 0.00 C +ATOM 625 OE1 GLU 42 32.187 22.893 11.789 1.00 0.00 O +ATOM 626 OE2 GLU 42 33.488 24.330 10.788 1.00 0.00 O +ATOM 627 C GLU 42 30.384 24.316 15.191 1.00 0.00 C +ATOM 628 O GLU 42 30.841 25.324 15.764 1.00 0.00 O +ATOM 629 N TRP 43 29.923 23.313 15.943 1.00 0.00 N +ATOM 630 H TRP 43 29.309 22.705 15.420 1.00 0.00 H +ATOM 631 CA TRP 43 29.831 23.438 17.418 1.00 0.00 C +ATOM 632 HA TRP 43 30.615 24.130 17.727 1.00 0.00 H +ATOM 633 CB TRP 43 28.442 24.018 17.813 1.00 0.00 C +ATOM 634 HB2 TRP 43 28.252 24.175 18.875 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.430 25.061 17.500 1.00 0.00 H +ATOM 636 CG TRP 43 27.193 23.409 17.045 1.00 0.00 C +ATOM 637 CD1 TRP 43 26.483 24.175 16.215 1.00 0.00 C +ATOM 638 HD1 TRP 43 26.806 25.155 15.894 1.00 0.00 H +ATOM 639 NE1 TRP 43 25.317 23.532 15.977 1.00 0.00 N +ATOM 640 HE1 TRP 43 24.627 23.930 15.355 1.00 0.00 H +ATOM 641 CE2 TRP 43 25.278 22.285 16.481 1.00 0.00 C +ATOM 642 CZ2 TRP 43 24.314 21.152 16.431 1.00 0.00 C +ATOM 643 HZ2 TRP 43 23.382 21.303 15.908 1.00 0.00 H +ATOM 644 CH2 TRP 43 24.673 19.959 17.119 1.00 0.00 C +ATOM 645 HH2 TRP 43 24.037 19.087 17.092 1.00 0.00 H +ATOM 646 CZ3 TRP 43 25.766 19.956 17.973 1.00 0.00 C +ATOM 647 HZ3 TRP 43 25.977 19.060 18.537 1.00 0.00 H +ATOM 648 CE3 TRP 43 26.657 21.052 18.012 1.00 0.00 C +ATOM 649 HE3 TRP 43 27.463 20.955 18.725 1.00 0.00 H +ATOM 650 CD2 TRP 43 26.429 22.215 17.278 1.00 0.00 C +ATOM 651 C TRP 43 30.188 22.139 18.059 1.00 0.00 C +ATOM 652 O TRP 43 30.290 21.071 17.417 1.00 0.00 O +ATOM 653 N THR 44 30.404 22.036 19.376 1.00 0.00 N +ATOM 654 H THR 44 30.352 22.915 19.871 1.00 0.00 H +ATOM 655 CA THR 44 30.545 20.782 20.070 1.00 0.00 C +ATOM 656 HA THR 44 29.948 20.053 19.521 1.00 0.00 H +ATOM 657 CB THR 44 31.990 20.370 20.088 1.00 0.00 C +ATOM 658 HB THR 44 32.324 20.407 19.051 1.00 0.00 H +ATOM 659 CG2 THR 44 32.746 21.338 20.951 1.00 0.00 C +ATOM 660 HG21 THR 44 32.590 22.363 20.615 1.00 0.00 H +ATOM 661 HG22 THR 44 33.811 21.106 20.972 1.00 0.00 H +ATOM 662 HG23 THR 44 32.349 21.139 21.946 1.00 0.00 H +ATOM 663 OG1 THR 44 32.033 19.115 20.609 1.00 0.00 O +ATOM 664 HG1 THR 44 31.985 18.515 19.860 1.00 0.00 H +ATOM 665 C THR 44 29.866 20.762 21.423 1.00 0.00 C +ATOM 666 O THR 44 29.268 21.820 21.806 1.00 0.00 O +ATOM 667 N TYR 45 29.869 19.636 22.156 1.00 0.00 N +ATOM 668 H TYR 45 30.611 18.984 21.946 1.00 0.00 H +ATOM 669 CA TYR 45 29.133 19.450 23.384 1.00 0.00 C +ATOM 670 HA TYR 45 29.065 20.417 23.881 1.00 0.00 H +ATOM 671 CB TYR 45 27.711 18.916 23.213 1.00 0.00 C +ATOM 672 HB2 TYR 45 27.118 19.665 22.688 1.00 0.00 H +ATOM 673 HB3 TYR 45 27.712 18.009 22.608 1.00 0.00 H +ATOM 674 CG TYR 45 26.945 18.667 24.555 1.00 0.00 C +ATOM 675 CD1 TYR 45 26.841 19.709 25.511 1.00 0.00 C +ATOM 676 HD1 TYR 45 27.022 20.757 25.323 1.00 0.00 H +ATOM 677 CE1 TYR 45 26.222 19.348 26.726 1.00 0.00 C +ATOM 678 HE1 TYR 45 25.997 20.113 27.456 1.00 0.00 H +ATOM 679 CZ TYR 45 25.735 18.047 27.046 1.00 0.00 C +ATOM 680 OH TYR 45 25.133 17.821 28.215 1.00 0.00 O +ATOM 681 HH TYR 45 24.851 16.910 28.321 1.00 0.00 H +ATOM 682 CE2 TYR 45 26.020 17.013 26.098 1.00 0.00 C +ATOM 683 HE2 TYR 45 25.783 16.005 26.408 1.00 0.00 H +ATOM 684 CD2 TYR 45 26.523 17.310 24.799 1.00 0.00 C +ATOM 685 HD2 TYR 45 26.564 16.460 24.135 1.00 0.00 H +ATOM 686 C TYR 45 29.912 18.500 24.247 1.00 0.00 C +ATOM 687 O TYR 45 30.618 17.613 23.795 1.00 0.00 O +ATOM 688 N ASP 46 29.835 18.641 25.550 1.00 0.00 N +ATOM 689 H ASP 46 29.454 19.531 25.835 1.00 0.00 H +ATOM 690 CA ASP 46 30.524 17.837 26.492 1.00 0.00 C +ATOM 691 HA ASP 46 30.880 16.963 25.948 1.00 0.00 H +ATOM 692 CB ASP 46 31.738 18.614 26.903 1.00 0.00 C +ATOM 693 HB2 ASP 46 32.294 18.827 25.990 1.00 0.00 H +ATOM 694 HB3 ASP 46 31.316 19.509 27.359 1.00 0.00 H +ATOM 695 CG ASP 46 32.557 17.800 27.930 1.00 0.00 C +ATOM 696 OD1 ASP 46 33.349 18.475 28.690 1.00 0.00 O +ATOM 697 OD2 ASP 46 32.531 16.592 27.979 1.00 0.00 O +ATOM 698 C ASP 46 29.667 17.365 27.764 1.00 0.00 C +ATOM 699 O ASP 46 29.257 18.213 28.611 1.00 0.00 O +ATOM 700 N ASP 47 29.604 16.078 28.027 1.00 0.00 N +ATOM 701 H ASP 47 29.861 15.381 27.342 1.00 0.00 H +ATOM 702 CA ASP 47 28.744 15.636 29.162 1.00 0.00 C +ATOM 703 HA ASP 47 27.839 16.244 29.166 1.00 0.00 H +ATOM 704 CB ASP 47 28.356 14.264 28.859 1.00 0.00 C +ATOM 705 HB2 ASP 47 27.706 14.234 27.984 1.00 0.00 H +ATOM 706 HB3 ASP 47 29.244 13.678 28.621 1.00 0.00 H +ATOM 707 CG ASP 47 27.489 13.712 29.891 1.00 0.00 C +ATOM 708 OD1 ASP 47 27.903 12.734 30.437 1.00 0.00 O +ATOM 709 OD2 ASP 47 26.394 14.308 30.128 1.00 0.00 O +ATOM 710 C ASP 47 29.458 15.844 30.510 1.00 0.00 C +ATOM 711 O ASP 47 28.806 16.225 31.510 1.00 0.00 O +ATOM 712 N ALA 48 30.737 15.553 30.486 1.00 0.00 N +ATOM 713 H ALA 48 31.167 15.340 29.598 1.00 0.00 H +ATOM 714 CA ALA 48 31.571 15.574 31.707 1.00 0.00 C +ATOM 715 HA ALA 48 31.130 14.894 32.436 1.00 0.00 H +ATOM 716 CB ALA 48 33.063 15.483 31.450 1.00 0.00 C +ATOM 717 HB1 ALA 48 33.206 14.524 30.952 1.00 0.00 H +ATOM 718 HB2 ALA 48 33.597 15.486 32.401 1.00 0.00 H +ATOM 719 HB3 ALA 48 33.222 16.317 30.768 1.00 0.00 H +ATOM 720 C ALA 48 31.519 16.953 32.425 1.00 0.00 C +ATOM 721 O ALA 48 31.868 17.176 33.579 1.00 0.00 O +ATOM 722 N THR 49 31.147 18.006 31.613 1.00 0.00 N +ATOM 723 H THR 49 30.877 17.766 30.670 1.00 0.00 H +ATOM 724 CA THR 49 31.059 19.429 32.043 1.00 0.00 C +ATOM 725 HA THR 49 31.019 19.452 33.132 1.00 0.00 H +ATOM 726 CB THR 49 32.108 20.339 31.495 1.00 0.00 C +ATOM 727 HB THR 49 31.934 21.374 31.788 1.00 0.00 H +ATOM 728 CG2 THR 49 33.539 19.891 31.809 1.00 0.00 C +ATOM 729 HG21 THR 49 34.304 20.420 31.243 1.00 0.00 H +ATOM 730 HG22 THR 49 33.730 18.821 31.728 1.00 0.00 H +ATOM 731 HG23 THR 49 33.735 20.175 32.843 1.00 0.00 H +ATOM 732 OG1 THR 49 31.982 20.206 30.087 1.00 0.00 O +ATOM 733 HG1 THR 49 32.724 19.725 29.711 1.00 0.00 H +ATOM 734 C THR 49 29.662 19.990 31.764 1.00 0.00 C +ATOM 735 O THR 49 29.420 21.102 32.336 1.00 0.00 O +ATOM 736 N LYS 50 28.679 19.369 31.036 1.00 0.00 N +ATOM 737 H LYS 50 28.894 18.511 30.547 1.00 0.00 H +ATOM 738 CA LYS 50 27.381 19.982 30.611 1.00 0.00 C +ATOM 739 HA LYS 50 26.914 19.294 29.906 1.00 0.00 H +ATOM 740 CB LYS 50 26.423 20.086 31.777 1.00 0.00 C +ATOM 741 HB2 LYS 50 26.755 20.819 32.513 1.00 0.00 H +ATOM 742 HB3 LYS 50 25.456 20.462 31.445 1.00 0.00 H +ATOM 743 CG LYS 50 26.230 18.697 32.400 1.00 0.00 C +ATOM 744 HG2 LYS 50 27.174 18.437 32.878 1.00 0.00 H +ATOM 745 HG3 LYS 50 25.566 18.827 33.255 1.00 0.00 H +ATOM 746 CD LYS 50 25.746 17.449 31.622 1.00 0.00 C +ATOM 747 HD2 LYS 50 24.827 17.740 31.113 1.00 0.00 H +ATOM 748 HD3 LYS 50 26.488 17.229 30.854 1.00 0.00 H +ATOM 749 CE LYS 50 25.485 16.423 32.736 1.00 0.00 C +ATOM 750 HE2 LYS 50 26.380 16.125 33.283 1.00 0.00 H +ATOM 751 HE3 LYS 50 24.802 16.926 33.420 1.00 0.00 H +ATOM 752 NZ LYS 50 24.823 15.237 32.107 1.00 0.00 N +ATOM 753 HZ1 LYS 50 25.490 14.809 31.482 1.00 0.00 H +ATOM 754 HZ2 LYS 50 24.031 15.557 31.568 1.00 0.00 H +ATOM 755 HZ3 LYS 50 24.596 14.502 32.761 1.00 0.00 H +ATOM 756 C LYS 50 27.447 21.244 29.836 1.00 0.00 C +ATOM 757 O LYS 50 26.624 22.166 29.919 1.00 0.00 O +ATOM 758 N THR 51 28.486 21.333 29.031 1.00 0.00 N +ATOM 759 H THR 51 29.103 20.540 29.137 1.00 0.00 H +ATOM 760 CA THR 51 28.986 22.605 28.412 1.00 0.00 C +ATOM 761 HA THR 51 28.315 23.424 28.672 1.00 0.00 H +ATOM 762 CB THR 51 30.345 23.087 28.864 1.00 0.00 C +ATOM 763 HB THR 51 31.039 22.368 28.429 1.00 0.00 H +ATOM 764 CG2 THR 51 30.713 24.494 28.423 1.00 0.00 C +ATOM 765 HG21 THR 51 31.740 24.747 28.689 1.00 0.00 H +ATOM 766 HG22 THR 51 30.014 25.119 28.978 1.00 0.00 H +ATOM 767 HG23 THR 51 30.674 24.547 27.335 1.00 0.00 H +ATOM 768 OG1 THR 51 30.635 22.963 30.280 1.00 0.00 O +ATOM 769 HG1 THR 51 31.368 22.345 30.318 1.00 0.00 H +ATOM 770 C THR 51 29.025 22.584 26.871 1.00 0.00 C +ATOM 771 O THR 51 29.653 21.700 26.237 1.00 0.00 O +ATOM 772 N PHE 52 28.269 23.460 26.238 1.00 0.00 N +ATOM 773 H PHE 52 27.769 24.191 26.723 1.00 0.00 H +ATOM 774 CA PHE 52 28.286 23.650 24.785 1.00 0.00 C +ATOM 775 HA PHE 52 28.582 22.742 24.261 1.00 0.00 H +ATOM 776 CB PHE 52 26.953 24.072 24.274 1.00 0.00 C +ATOM 777 HB2 PHE 52 26.621 24.985 24.767 1.00 0.00 H +ATOM 778 HB3 PHE 52 27.062 24.410 23.243 1.00 0.00 H +ATOM 779 CG PHE 52 25.894 23.024 24.418 1.00 0.00 C +ATOM 780 CD1 PHE 52 25.097 22.898 25.566 1.00 0.00 C +ATOM 781 HD1 PHE 52 25.259 23.607 26.364 1.00 0.00 H +ATOM 782 CE1 PHE 52 24.209 21.791 25.658 1.00 0.00 C +ATOM 783 HE1 PHE 52 23.616 21.542 26.525 1.00 0.00 H +ATOM 784 CZ PHE 52 24.020 20.903 24.564 1.00 0.00 C +ATOM 785 HZ PHE 52 23.310 20.098 24.679 1.00 0.00 H +ATOM 786 CE2 PHE 52 24.755 21.162 23.359 1.00 0.00 C +ATOM 787 HE2 PHE 52 24.493 20.627 22.458 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.668 22.205 23.300 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.090 22.464 22.340 1.00 0.00 H +ATOM 790 C PHE 52 29.331 24.698 24.393 1.00 0.00 C +ATOM 791 O PHE 52 29.434 25.766 25.064 1.00 0.00 O +ATOM 792 N THR 53 29.940 24.512 23.248 1.00 0.00 N +ATOM 793 H THR 53 29.982 23.554 22.931 1.00 0.00 H +ATOM 794 CA THR 53 30.884 25.494 22.596 1.00 0.00 C +ATOM 795 HA THR 53 30.731 26.447 23.103 1.00 0.00 H +ATOM 796 CB THR 53 32.292 25.123 22.831 1.00 0.00 C +ATOM 797 HB THR 53 32.547 24.156 22.398 1.00 0.00 H +ATOM 798 CG2 THR 53 33.348 26.106 22.204 1.00 0.00 C +ATOM 799 HG21 THR 53 34.328 25.946 22.653 1.00 0.00 H +ATOM 800 HG22 THR 53 33.057 27.149 22.335 1.00 0.00 H +ATOM 801 HG23 THR 53 33.394 25.952 21.126 1.00 0.00 H +ATOM 802 OG1 THR 53 32.620 25.042 24.220 1.00 0.00 O +ATOM 803 HG1 THR 53 32.107 24.312 24.574 1.00 0.00 H +ATOM 804 C THR 53 30.644 25.637 21.095 1.00 0.00 C +ATOM 805 O THR 53 30.170 24.691 20.504 1.00 0.00 O +ATOM 806 N VAL 54 30.979 26.781 20.467 1.00 0.00 N +ATOM 807 H VAL 54 31.490 27.492 20.970 1.00 0.00 H +ATOM 808 CA VAL 54 30.825 27.080 19.032 1.00 0.00 C +ATOM 809 HA VAL 54 30.840 26.124 18.508 1.00 0.00 H +ATOM 810 CB VAL 54 29.462 27.749 18.748 1.00 0.00 C +ATOM 811 HB VAL 54 28.651 27.047 18.941 1.00 0.00 H +ATOM 812 CG1 VAL 54 29.410 29.155 19.503 1.00 0.00 C +ATOM 813 HG11 VAL 54 28.527 29.679 19.137 1.00 0.00 H +ATOM 814 HG12 VAL 54 30.190 29.851 19.193 1.00 0.00 H +ATOM 815 HG13 VAL 54 29.354 29.117 20.591 1.00 0.00 H +ATOM 816 CG2 VAL 54 29.275 28.099 17.265 1.00 0.00 C +ATOM 817 HG21 VAL 54 29.334 27.171 16.697 1.00 0.00 H +ATOM 818 HG22 VAL 54 30.025 28.755 16.823 1.00 0.00 H +ATOM 819 HG23 VAL 54 28.271 28.494 17.105 1.00 0.00 H +ATOM 820 C VAL 54 32.079 27.914 18.512 1.00 0.00 C +ATOM 821 O VAL 54 32.707 28.683 19.324 1.00 0.00 O +ATOM 822 N THR 55 32.334 27.707 17.202 1.00 0.00 N +ATOM 823 H THR 55 31.766 27.041 16.698 1.00 0.00 H +ATOM 824 CA THR 55 33.340 28.457 16.443 1.00 0.00 C +ATOM 825 HA THR 55 34.309 28.016 16.680 1.00 0.00 H +ATOM 826 CB THR 55 33.274 28.170 14.911 1.00 0.00 C +ATOM 827 HB THR 55 33.136 27.113 14.686 1.00 0.00 H +ATOM 828 CG2 THR 55 32.038 28.814 14.276 1.00 0.00 C +ATOM 829 HG21 THR 55 32.013 29.895 14.415 1.00 0.00 H +ATOM 830 HG22 THR 55 31.121 28.343 14.631 1.00 0.00 H +ATOM 831 HG23 THR 55 32.082 28.646 13.200 1.00 0.00 H +ATOM 832 OG1 THR 55 34.510 28.636 14.367 1.00 0.00 O +ATOM 833 HG1 THR 55 35.032 27.831 14.345 1.00 0.00 H +ATOM 834 C THR 55 33.284 29.957 16.682 1.00 0.00 C +ATOM 835 O THR 55 32.252 30.575 17.044 1.00 0.00 O +ATOM 836 N GLU 56 34.459 30.576 16.607 1.00 0.00 N +ATOM 837 H GLU 56 35.196 30.104 16.104 1.00 0.00 H +ATOM 838 CA GLU 56 34.658 32.000 17.018 1.00 0.00 C +ATOM 839 HA GLU 56 33.691 32.462 17.218 1.00 0.00 H +ATOM 840 CB GLU 56 35.528 32.047 18.300 1.00 0.00 C +ATOM 841 HB2 GLU 56 35.080 31.504 19.132 1.00 0.00 H +ATOM 842 HB3 GLU 56 36.416 31.437 18.132 1.00 0.00 H +ATOM 843 CG GLU 56 35.884 33.449 18.887 1.00 0.00 C +ATOM 844 HG2 GLU 56 36.636 33.379 19.672 1.00 0.00 H +ATOM 845 HG3 GLU 56 36.344 34.046 18.100 1.00 0.00 H +ATOM 846 CD GLU 56 34.666 34.199 19.421 1.00 0.00 C +ATOM 847 OE1 GLU 56 34.891 34.837 20.494 1.00 0.00 O +ATOM 848 OE2 GLU 56 33.536 34.244 18.835 1.00 0.00 O +ATOM 849 C GLU 56 35.293 32.700 15.775 1.00 0.00 C +ATOM 850 O GLU 56 34.881 33.809 15.334 1.00 0.00 O +ATOM 851 OXT GLU 56 36.276 32.048 15.301 1.00 0.00 O +ATOM 852 ZN ZN1 57 23.302 30.379 24.804 1.00 0.00 ZN +ATOM 853 N AN1 58 22.188 31.163 23.450 1.00 0.00 N +ATOM 854 C AN1 58 20.645 32.490 21.898 1.00 0.00 C +ATOM 855 C1 AN1 58 21.639 31.867 22.725 1.00 0.00 C +ATOM 856 H AN1 58 20.510 33.529 22.222 1.00 0.00 H +ATOM 857 H1 AN1 58 19.676 31.979 21.851 1.00 0.00 H +ATOM 858 H2 AN1 58 21.013 32.608 20.872 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 23.562 34.277 23.183 1.00 0.00 N +ATOM 860 N2 AZI 59 23.747 35.207 23.950 1.00 0.00 N +ATOM 861 N3 AZI 59 23.920 36.149 24.705 1.00 0.00 N +TER 862 AZI 59 \ No newline at end of file diff --git a/tests/nsga2/pdbs_rename/cluster22.pdb b/tests/nsga2/pdbs_rename/cluster22.pdb new file mode 100644 index 0000000..2c5a19e --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster22.pdb @@ -0,0 +1,864 @@ +CRYST1 51.657 53.286 47.380 90.00 90.00 90.00 1 +ATOM 1 N MET 1 17.623 21.953 33.668 1.00 0.00 N +ATOM 2 H1 MET 1 17.361 21.710 32.723 1.00 0.00 H +ATOM 3 H2 MET 1 17.073 22.758 33.929 1.00 0.00 H +ATOM 4 H3 MET 1 17.345 21.158 34.227 1.00 0.00 H +ATOM 5 CA MET 1 19.109 22.165 33.724 1.00 0.00 C +ATOM 6 HA MET 1 19.425 22.301 34.758 1.00 0.00 H +ATOM 7 CB MET 1 19.681 20.821 33.296 1.00 0.00 C +ATOM 8 HB2 MET 1 19.505 20.173 34.154 1.00 0.00 H +ATOM 9 HB3 MET 1 19.117 20.370 32.479 1.00 0.00 H +ATOM 10 CG MET 1 21.196 20.796 33.125 1.00 0.00 C +ATOM 11 HG2 MET 1 21.371 19.739 32.925 1.00 0.00 H +ATOM 12 HG3 MET 1 21.475 21.338 32.222 1.00 0.00 H +ATOM 13 SD MET 1 22.440 21.357 34.353 1.00 0.00 S +ATOM 14 CE MET 1 21.956 20.221 35.711 1.00 0.00 C +ATOM 15 HE1 MET 1 20.896 20.288 35.955 1.00 0.00 H +ATOM 16 HE2 MET 1 22.598 20.411 36.570 1.00 0.00 H +ATOM 17 HE3 MET 1 22.197 19.236 35.310 1.00 0.00 H +ATOM 18 C MET 1 19.562 23.317 32.927 1.00 0.00 C +ATOM 19 O MET 1 19.256 23.429 31.784 1.00 0.00 O +ATOM 20 N GLN 2 20.196 24.257 33.699 1.00 0.00 N +ATOM 21 H GLN 2 20.253 24.213 34.707 1.00 0.00 H +ATOM 22 CA GLN 2 20.855 25.440 33.057 1.00 0.00 C +ATOM 23 HA GLN 2 20.350 25.921 32.220 1.00 0.00 H +ATOM 24 CB GLN 2 21.019 26.620 34.009 1.00 0.00 C +ATOM 25 HB2 GLN 2 21.478 26.149 34.878 1.00 0.00 H +ATOM 26 HB3 GLN 2 21.713 27.326 33.554 1.00 0.00 H +ATOM 27 CG GLN 2 19.663 27.334 34.352 1.00 0.00 C +ATOM 28 HG2 GLN 2 18.821 26.655 34.220 1.00 0.00 H +ATOM 29 HG3 GLN 2 19.731 27.575 35.413 1.00 0.00 H +ATOM 30 CD GLN 2 19.520 28.689 33.619 1.00 0.00 C +ATOM 31 OE1 GLN 2 20.009 28.953 32.590 1.00 0.00 O +ATOM 32 NE2 GLN 2 18.537 29.529 34.012 1.00 0.00 N +ATOM 33 HE21 GLN 2 18.250 30.211 33.324 1.00 0.00 H +ATOM 34 HE22 GLN 2 17.992 29.262 34.819 1.00 0.00 H +ATOM 35 C GLN 2 22.251 24.924 32.533 1.00 0.00 C +ATOM 36 O GLN 2 23.231 25.028 33.220 1.00 0.00 O +ATOM 37 N TYR 3 22.375 24.451 31.303 1.00 0.00 N +ATOM 38 H TYR 3 21.557 24.469 30.711 1.00 0.00 H +ATOM 39 CA TYR 3 23.602 24.125 30.596 1.00 0.00 C +ATOM 40 HA TYR 3 24.167 23.369 31.140 1.00 0.00 H +ATOM 41 CB TYR 3 23.102 23.476 29.312 1.00 0.00 C +ATOM 42 HB2 TYR 3 22.517 24.265 28.839 1.00 0.00 H +ATOM 43 HB3 TYR 3 24.014 23.396 28.720 1.00 0.00 H +ATOM 44 CG TYR 3 22.505 22.130 29.531 1.00 0.00 C +ATOM 45 CD1 TYR 3 23.403 21.085 29.694 1.00 0.00 C +ATOM 46 HD1 TYR 3 24.459 21.309 29.690 1.00 0.00 H +ATOM 47 CE1 TYR 3 22.909 19.789 29.930 1.00 0.00 C +ATOM 48 HE1 TYR 3 23.507 18.891 29.982 1.00 0.00 H +ATOM 49 CZ TYR 3 21.545 19.487 30.028 1.00 0.00 C +ATOM 50 OH TYR 3 21.021 18.311 30.260 1.00 0.00 O +ATOM 51 HH TYR 3 20.314 18.261 30.907 1.00 0.00 H +ATOM 52 CE2 TYR 3 20.615 20.561 29.981 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.570 20.306 30.084 1.00 0.00 H +ATOM 54 CD2 TYR 3 21.123 21.880 29.693 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.544 22.791 29.712 1.00 0.00 H +ATOM 56 C TYR 3 24.358 25.463 30.389 1.00 0.00 C +ATOM 57 O TYR 3 23.750 26.389 29.852 1.00 0.00 O +ATOM 58 N LYS 4 25.593 25.481 30.848 1.00 0.00 N +ATOM 59 H LYS 4 25.831 24.603 31.286 1.00 0.00 H +ATOM 60 CA LYS 4 26.589 26.503 30.412 1.00 0.00 C +ATOM 61 HA LYS 4 26.169 27.475 30.669 1.00 0.00 H +ATOM 62 CB LYS 4 27.897 26.243 31.143 1.00 0.00 C +ATOM 63 HB2 LYS 4 27.610 26.237 32.195 1.00 0.00 H +ATOM 64 HB3 LYS 4 28.216 25.230 30.896 1.00 0.00 H +ATOM 65 CG LYS 4 29.073 27.305 30.911 1.00 0.00 C +ATOM 66 HG2 LYS 4 29.302 27.402 29.850 1.00 0.00 H +ATOM 67 HG3 LYS 4 28.670 28.279 31.188 1.00 0.00 H +ATOM 68 CD LYS 4 30.399 27.134 31.721 1.00 0.00 C +ATOM 69 HD2 LYS 4 30.683 26.082 31.693 1.00 0.00 H +ATOM 70 HD3 LYS 4 31.089 27.816 31.225 1.00 0.00 H +ATOM 71 CE LYS 4 30.419 27.556 33.173 1.00 0.00 C +ATOM 72 HE2 LYS 4 30.200 28.616 33.305 1.00 0.00 H +ATOM 73 HE3 LYS 4 29.566 27.138 33.709 1.00 0.00 H +ATOM 74 NZ LYS 4 31.565 26.998 33.844 1.00 0.00 N +ATOM 75 HZ1 LYS 4 32.458 27.387 33.578 1.00 0.00 H +ATOM 76 HZ2 LYS 4 31.663 26.000 33.719 1.00 0.00 H +ATOM 77 HZ3 LYS 4 31.546 27.037 34.853 1.00 0.00 H +ATOM 78 C LYS 4 26.752 26.564 28.911 1.00 0.00 C +ATOM 79 O LYS 4 26.612 25.560 28.207 1.00 0.00 O +ATOM 80 N HX1 5 26.981 27.761 28.340 1.00 0.00 N +ATOM 81 CA HX1 5 27.210 28.040 26.948 1.00 0.00 C +ATOM 82 C HX1 5 28.217 29.129 26.819 1.00 0.00 C +ATOM 83 O HX1 5 27.921 30.138 27.304 1.00 0.00 O +ATOM 84 CB HX1 5 25.928 28.400 26.258 1.00 0.00 C +ATOM 85 CG HX1 5 26.011 28.853 24.775 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.941 28.516 23.911 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.046 29.678 24.167 1.00 0.00 N +ATOM 88 CE1 HX1 5 25.499 29.686 22.909 1.00 0.00 C +ATOM 89 NE2 HX1 5 26.680 29.124 22.771 1.00 0.00 N +ATOM 90 H HX1 5 26.941 28.546 28.974 1.00 0.00 H +ATOM 91 HA HX1 5 27.624 27.127 26.520 1.00 0.00 H +ATOM 92 HB2 HX1 5 25.574 29.273 26.807 1.00 0.00 H +ATOM 93 HB3 HX1 5 25.253 27.545 26.299 1.00 0.00 H +ATOM 94 HD2 HX1 5 27.778 27.859 24.093 1.00 0.00 H +ATOM 95 HE1 HX1 5 24.989 30.116 22.060 1.00 0.00 H +ATOM 96 HE2 HX1 5 27.280 29.049 21.963 1.00 0.00 H +ATOM 97 N ILE 6 29.400 28.844 26.230 1.00 0.00 N +ATOM 98 H ILE 6 29.425 27.947 25.766 1.00 0.00 H +ATOM 99 CA ILE 6 30.511 29.795 26.062 1.00 0.00 C +ATOM 100 HA ILE 6 30.371 30.667 26.700 1.00 0.00 H +ATOM 101 CB ILE 6 31.863 29.041 26.382 1.00 0.00 C +ATOM 102 HB ILE 6 31.701 28.024 26.025 1.00 0.00 H +ATOM 103 CG2 ILE 6 33.163 29.621 25.770 1.00 0.00 C +ATOM 104 HG21 ILE 6 33.936 28.852 25.764 1.00 0.00 H +ATOM 105 HG22 ILE 6 33.455 30.586 26.184 1.00 0.00 H +ATOM 106 HG23 ILE 6 33.016 30.016 24.765 1.00 0.00 H +ATOM 107 CG1 ILE 6 31.924 28.943 27.945 1.00 0.00 C +ATOM 108 HG12 ILE 6 31.943 29.921 28.424 1.00 0.00 H +ATOM 109 HG13 ILE 6 31.047 28.360 28.227 1.00 0.00 H +ATOM 110 CD1 ILE 6 33.186 28.160 28.436 1.00 0.00 C +ATOM 111 HD11 ILE 6 33.331 28.293 29.508 1.00 0.00 H +ATOM 112 HD12 ILE 6 34.069 28.608 27.982 1.00 0.00 H +ATOM 113 HD13 ILE 6 33.183 27.130 28.080 1.00 0.00 H +ATOM 114 C ILE 6 30.421 30.305 24.616 1.00 0.00 C +ATOM 115 O ILE 6 30.216 29.597 23.629 1.00 0.00 O +ATOM 116 N VAL 7 30.615 31.592 24.511 1.00 0.00 N +ATOM 117 H VAL 7 30.688 32.092 25.385 1.00 0.00 H +ATOM 118 CA VAL 7 30.457 32.296 23.201 1.00 0.00 C +ATOM 119 HA VAL 7 30.418 31.602 22.361 1.00 0.00 H +ATOM 120 CB VAL 7 29.190 33.233 23.256 1.00 0.00 C +ATOM 121 HB VAL 7 29.259 33.815 22.337 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.979 32.259 23.219 1.00 0.00 C +ATOM 123 HG11 VAL 7 27.968 31.630 22.329 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.931 31.720 24.165 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.025 32.785 23.238 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.135 34.244 24.429 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.281 34.907 24.290 1.00 0.00 H +ATOM 128 HG22 VAL 7 29.011 33.692 25.360 1.00 0.00 H +ATOM 129 HG23 VAL 7 30.021 34.861 24.576 1.00 0.00 H +ATOM 130 C VAL 7 31.748 33.085 22.952 1.00 0.00 C +ATOM 131 O VAL 7 32.722 33.023 23.666 1.00 0.00 O +ATOM 132 N ASN 8 31.761 33.831 21.827 1.00 0.00 N +ATOM 133 H ASN 8 31.080 33.563 21.131 1.00 0.00 H +ATOM 134 CA ASN 8 32.944 34.550 21.346 1.00 0.00 C +ATOM 135 HA ASN 8 33.821 34.074 21.785 1.00 0.00 H +ATOM 136 CB ASN 8 33.087 34.354 19.848 1.00 0.00 C +ATOM 137 HB2 ASN 8 32.609 33.446 19.484 1.00 0.00 H +ATOM 138 HB3 ASN 8 32.478 35.096 19.331 1.00 0.00 H +ATOM 139 CG ASN 8 34.536 34.454 19.381 1.00 0.00 C +ATOM 140 OD1 ASN 8 35.482 34.654 20.180 1.00 0.00 O +ATOM 141 ND2 ASN 8 34.721 34.160 18.099 1.00 0.00 N +ATOM 142 HD21 ASN 8 33.905 33.834 17.601 1.00 0.00 H +ATOM 143 HD22 ASN 8 35.676 34.178 17.771 1.00 0.00 H +ATOM 144 C ASN 8 32.915 36.070 21.756 1.00 0.00 C +ATOM 145 O ASN 8 33.998 36.644 21.980 1.00 0.00 O +ATOM 146 N GLY 9 31.764 36.703 21.870 1.00 0.00 N +ATOM 147 H GLY 9 31.013 36.108 21.551 1.00 0.00 H +ATOM 148 CA GLY 9 31.583 38.069 22.452 1.00 0.00 C +ATOM 149 HA2 GLY 9 32.041 38.821 21.809 1.00 0.00 H +ATOM 150 HA3 GLY 9 30.523 38.298 22.570 1.00 0.00 H +ATOM 151 C GLY 9 32.286 38.289 23.783 1.00 0.00 C +ATOM 152 O GLY 9 32.436 37.430 24.661 1.00 0.00 O +ATOM 153 N LYS 10 32.792 39.500 23.931 1.00 0.00 N +ATOM 154 H LYS 10 32.694 40.139 23.155 1.00 0.00 H +ATOM 155 CA LYS 10 33.416 40.033 25.188 1.00 0.00 C +ATOM 156 HA LYS 10 34.190 39.359 25.555 1.00 0.00 H +ATOM 157 CB LYS 10 33.971 41.475 24.964 1.00 0.00 C +ATOM 158 HB2 LYS 10 33.123 42.159 24.992 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.577 41.659 25.851 1.00 0.00 H +ATOM 160 CG LYS 10 34.815 41.728 23.682 1.00 0.00 C +ATOM 161 HG2 LYS 10 35.546 40.920 23.722 1.00 0.00 H +ATOM 162 HG3 LYS 10 34.207 41.527 22.800 1.00 0.00 H +ATOM 163 CD LYS 10 35.423 43.170 23.563 1.00 0.00 C +ATOM 164 HD2 LYS 10 34.511 43.765 23.608 1.00 0.00 H +ATOM 165 HD3 LYS 10 36.071 43.373 24.416 1.00 0.00 H +ATOM 166 CE LYS 10 36.229 43.283 22.208 1.00 0.00 C +ATOM 167 HE2 LYS 10 36.940 42.462 22.301 1.00 0.00 H +ATOM 168 HE3 LYS 10 35.557 43.239 21.351 1.00 0.00 H +ATOM 169 NZ LYS 10 36.946 44.530 22.121 1.00 0.00 N +ATOM 170 HZ1 LYS 10 37.694 44.562 21.443 1.00 0.00 H +ATOM 171 HZ2 LYS 10 37.283 44.830 23.024 1.00 0.00 H +ATOM 172 HZ3 LYS 10 36.340 45.327 21.992 1.00 0.00 H +ATOM 173 C LYS 10 32.431 40.052 26.387 1.00 0.00 C +ATOM 174 O LYS 10 32.776 39.921 27.571 1.00 0.00 O +ATOM 175 N THR 11 31.166 40.219 26.061 1.00 0.00 N +ATOM 176 H THR 11 31.008 40.472 25.096 1.00 0.00 H +ATOM 177 CA THR 11 30.011 40.254 27.034 1.00 0.00 C +ATOM 178 HA THR 11 30.164 41.124 27.673 1.00 0.00 H +ATOM 179 CB THR 11 28.761 40.344 26.261 1.00 0.00 C +ATOM 180 HB THR 11 28.714 39.626 25.442 1.00 0.00 H +ATOM 181 CG2 THR 11 27.509 40.387 27.103 1.00 0.00 C +ATOM 182 HG21 THR 11 27.370 39.459 27.656 1.00 0.00 H +ATOM 183 HG22 THR 11 26.659 40.410 26.421 1.00 0.00 H +ATOM 184 HG23 THR 11 27.496 41.283 27.724 1.00 0.00 H +ATOM 185 OG1 THR 11 28.593 41.597 25.572 1.00 0.00 O +ATOM 186 HG1 THR 11 27.658 41.579 25.355 1.00 0.00 H +ATOM 187 C THR 11 30.039 39.151 28.068 1.00 0.00 C +ATOM 188 O THR 11 30.228 38.006 27.632 1.00 0.00 O +ATOM 189 N LEU 12 29.905 39.469 29.380 1.00 0.00 N +ATOM 190 H LEU 12 29.683 40.408 29.679 1.00 0.00 H +ATOM 191 CA LEU 12 29.909 38.416 30.420 1.00 0.00 C +ATOM 192 HA LEU 12 29.936 39.039 31.314 1.00 0.00 H +ATOM 193 CB LEU 12 28.534 37.701 30.538 1.00 0.00 C +ATOM 194 HB2 LEU 12 28.332 37.282 29.552 1.00 0.00 H +ATOM 195 HB3 LEU 12 28.695 36.893 31.251 1.00 0.00 H +ATOM 196 CG LEU 12 27.293 38.655 30.979 1.00 0.00 C +ATOM 197 HG LEU 12 27.284 39.581 30.404 1.00 0.00 H +ATOM 198 CD1 LEU 12 26.025 37.934 30.542 1.00 0.00 C +ATOM 199 HD11 LEU 12 25.105 38.278 31.015 1.00 0.00 H +ATOM 200 HD12 LEU 12 26.116 36.870 30.760 1.00 0.00 H +ATOM 201 HD13 LEU 12 26.084 38.035 29.459 1.00 0.00 H +ATOM 202 CD2 LEU 12 27.345 39.042 32.445 1.00 0.00 C +ATOM 203 HD21 LEU 12 26.354 39.138 32.889 1.00 0.00 H +ATOM 204 HD22 LEU 12 27.730 40.061 32.491 1.00 0.00 H +ATOM 205 HD23 LEU 12 28.098 38.494 33.011 1.00 0.00 H +ATOM 206 C LEU 12 31.129 37.496 30.519 1.00 0.00 C +ATOM 207 O LEU 12 31.129 36.335 31.037 1.00 0.00 O +ATOM 208 N LYS 13 32.274 37.992 30.043 1.00 0.00 N +ATOM 209 H LYS 13 32.209 38.890 29.586 1.00 0.00 H +ATOM 210 CA LYS 13 33.550 37.221 29.975 1.00 0.00 C +ATOM 211 HA LYS 13 34.269 37.897 29.513 1.00 0.00 H +ATOM 212 CB LYS 13 34.176 36.914 31.392 1.00 0.00 C +ATOM 213 HB2 LYS 13 33.607 36.208 31.996 1.00 0.00 H +ATOM 214 HB3 LYS 13 35.142 36.416 31.313 1.00 0.00 H +ATOM 215 CG LYS 13 34.362 38.089 32.442 1.00 0.00 C +ATOM 216 HG2 LYS 13 33.465 38.706 32.503 1.00 0.00 H +ATOM 217 HG3 LYS 13 34.620 37.729 33.438 1.00 0.00 H +ATOM 218 CD LYS 13 35.535 38.971 31.976 1.00 0.00 C +ATOM 219 HD2 LYS 13 36.407 38.317 31.955 1.00 0.00 H +ATOM 220 HD3 LYS 13 35.467 39.344 30.954 1.00 0.00 H +ATOM 221 CE LYS 13 35.708 40.110 32.981 1.00 0.00 C +ATOM 222 HE2 LYS 13 34.714 40.496 33.204 1.00 0.00 H +ATOM 223 HE3 LYS 13 36.095 39.683 33.906 1.00 0.00 H +ATOM 224 NZ LYS 13 36.644 41.192 32.537 1.00 0.00 N +ATOM 225 HZ1 LYS 13 36.417 41.477 31.594 1.00 0.00 H +ATOM 226 HZ2 LYS 13 37.577 40.806 32.503 1.00 0.00 H +ATOM 227 HZ3 LYS 13 36.638 41.991 33.155 1.00 0.00 H +ATOM 228 C LYS 13 33.424 35.975 29.062 1.00 0.00 C +ATOM 229 O LYS 13 34.011 34.977 29.401 1.00 0.00 O +ATOM 230 N GLY 14 32.567 36.047 28.061 1.00 0.00 N +ATOM 231 H GLY 14 31.945 36.842 28.066 1.00 0.00 H +ATOM 232 CA GLY 14 32.224 34.965 27.124 1.00 0.00 C +ATOM 233 HA2 GLY 14 31.732 35.331 26.222 1.00 0.00 H +ATOM 234 HA3 GLY 14 33.145 34.562 26.702 1.00 0.00 H +ATOM 235 C GLY 14 31.434 33.744 27.674 1.00 0.00 C +ATOM 236 O GLY 14 31.067 32.892 26.905 1.00 0.00 O +ATOM 237 N VAL 15 31.079 33.753 28.953 1.00 0.00 N +ATOM 238 H VAL 15 31.296 34.582 29.487 1.00 0.00 H +ATOM 239 CA VAL 15 30.429 32.734 29.720 1.00 0.00 C +ATOM 240 HA VAL 15 30.115 31.880 29.119 1.00 0.00 H +ATOM 241 CB VAL 15 31.473 32.108 30.703 1.00 0.00 C +ATOM 242 HB VAL 15 32.258 31.605 30.139 1.00 0.00 H +ATOM 243 CG1 VAL 15 32.087 33.106 31.728 1.00 0.00 C +ATOM 244 HG11 VAL 15 31.371 33.813 32.148 1.00 0.00 H +ATOM 245 HG12 VAL 15 32.588 32.589 32.546 1.00 0.00 H +ATOM 246 HG13 VAL 15 32.822 33.670 31.154 1.00 0.00 H +ATOM 247 CG2 VAL 15 30.687 31.045 31.480 1.00 0.00 C +ATOM 248 HG21 VAL 15 31.329 30.386 32.066 1.00 0.00 H +ATOM 249 HG22 VAL 15 30.083 31.587 32.208 1.00 0.00 H +ATOM 250 HG23 VAL 15 30.196 30.383 30.766 1.00 0.00 H +ATOM 251 C VAL 15 29.074 33.142 30.371 1.00 0.00 C +ATOM 252 O VAL 15 28.878 34.166 31.028 1.00 0.00 O +ATOM 253 N HY1 16 28.142 32.260 30.085 1.00 0.00 N +ATOM 254 CA HY1 16 26.728 32.248 30.552 1.00 0.00 C +ATOM 255 C HY1 16 25.960 30.892 30.399 1.00 0.00 C +ATOM 256 O HY1 16 26.493 29.807 30.036 1.00 0.00 O +ATOM 257 CB HY1 16 25.938 33.321 29.792 1.00 0.00 C +ATOM 258 CG HY1 16 25.790 33.137 28.271 1.00 0.00 C +ATOM 259 CD2 HY1 16 24.873 32.320 27.689 1.00 0.00 C +ATOM 260 ND1 HY1 16 26.326 33.924 27.242 1.00 0.00 N +ATOM 261 CE1 HY1 16 25.775 33.577 26.108 1.00 0.00 C +ATOM 262 NE2 HY1 16 24.922 32.560 26.319 1.00 0.00 N +ATOM 263 H HY1 16 28.396 31.503 29.467 1.00 0.00 H +ATOM 264 HA HY1 16 26.598 32.590 31.578 1.00 0.00 H +ATOM 265 HB2 HY1 16 24.945 33.487 30.209 1.00 0.00 H +ATOM 266 HB3 HY1 16 26.435 34.291 29.763 1.00 0.00 H +ATOM 267 HD1 HY1 16 26.885 34.752 27.390 1.00 0.00 H +ATOM 268 HD2 HY1 16 24.179 31.668 28.197 1.00 0.00 H +ATOM 269 HE1 HY1 16 25.969 33.992 25.130 1.00 0.00 H +ATOM 270 N THR 17 24.704 30.790 30.840 1.00 0.00 N +ATOM 271 H THR 17 24.341 31.670 31.180 1.00 0.00 H +ATOM 272 CA THR 17 23.808 29.593 30.798 1.00 0.00 C +ATOM 273 HA THR 17 24.339 28.808 30.259 1.00 0.00 H +ATOM 274 CB THR 17 23.532 29.098 32.219 1.00 0.00 C +ATOM 275 HB THR 17 22.763 28.340 32.067 1.00 0.00 H +ATOM 276 CG2 THR 17 24.620 28.400 32.911 1.00 0.00 C +ATOM 277 HG21 THR 17 24.868 27.474 32.393 1.00 0.00 H +ATOM 278 HG22 THR 17 24.547 28.233 33.986 1.00 0.00 H +ATOM 279 HG23 THR 17 25.492 29.045 32.809 1.00 0.00 H +ATOM 280 OG1 THR 17 22.979 30.180 33.056 1.00 0.00 O +ATOM 281 HG1 THR 17 23.222 29.925 33.950 1.00 0.00 H +ATOM 282 C THR 17 22.454 29.814 30.069 1.00 0.00 C +ATOM 283 O THR 17 21.947 30.894 29.857 1.00 0.00 O +ATOM 284 N HY2 18 21.886 28.675 29.703 1.00 0.00 N +ATOM 285 CA HY2 18 20.457 28.563 29.342 1.00 0.00 C +ATOM 286 C HY2 18 19.797 27.229 29.809 1.00 0.00 C +ATOM 287 O HY2 18 20.464 26.171 29.871 1.00 0.00 O +ATOM 288 CB HY2 18 20.285 28.582 27.824 1.00 0.00 C +ATOM 289 CG HY2 18 20.896 29.789 27.077 1.00 0.00 C +ATOM 290 CD2 HY2 18 22.160 29.794 26.554 1.00 0.00 C +ATOM 291 ND1 HY2 18 20.251 30.957 26.624 1.00 0.00 N +ATOM 292 CE1 HY2 18 21.146 31.531 25.770 1.00 0.00 C +ATOM 293 NE2 HY2 18 22.388 30.899 25.808 1.00 0.00 N +ATOM 294 H HY2 18 22.299 27.791 29.963 1.00 0.00 H +ATOM 295 HA HY2 18 19.884 29.337 29.852 1.00 0.00 H +ATOM 296 HB2 HY2 18 20.842 27.700 27.507 1.00 0.00 H +ATOM 297 HB3 HY2 18 19.245 28.401 27.551 1.00 0.00 H +ATOM 298 HD1 HY2 18 19.262 31.155 26.659 1.00 0.00 H +ATOM 299 HD2 HY2 18 22.843 28.985 26.766 1.00 0.00 H +ATOM 300 HE1 HY2 18 20.917 32.347 25.100 1.00 0.00 H +ATOM 301 N GLU 19 18.517 27.315 30.250 1.00 0.00 N +ATOM 302 H GLU 19 17.985 28.167 30.148 1.00 0.00 H +ATOM 303 CA GLU 19 17.787 26.196 30.808 1.00 0.00 C +ATOM 304 HA GLU 19 18.509 25.579 31.343 1.00 0.00 H +ATOM 305 CB GLU 19 16.680 26.781 31.799 1.00 0.00 C +ATOM 306 HB2 GLU 19 17.107 27.256 32.682 1.00 0.00 H +ATOM 307 HB3 GLU 19 16.201 27.591 31.250 1.00 0.00 H +ATOM 308 CG GLU 19 15.570 25.805 32.214 1.00 0.00 C +ATOM 309 HG2 GLU 19 15.034 26.315 33.014 1.00 0.00 H +ATOM 310 HG3 GLU 19 14.868 25.691 31.388 1.00 0.00 H +ATOM 311 CD GLU 19 16.045 24.536 32.834 1.00 0.00 C +ATOM 312 OE1 GLU 19 17.046 24.521 33.624 1.00 0.00 O +ATOM 313 OE2 GLU 19 15.343 23.539 32.555 1.00 0.00 O +ATOM 314 C GLU 19 17.068 25.338 29.655 1.00 0.00 C +ATOM 315 O GLU 19 16.241 25.890 28.858 1.00 0.00 O +ATOM 316 N ALA 20 17.338 24.047 29.766 1.00 0.00 N +ATOM 317 H ALA 20 18.027 23.821 30.470 1.00 0.00 H +ATOM 318 CA ALA 20 16.469 23.009 29.173 1.00 0.00 C +ATOM 319 HA ALA 20 15.507 23.430 28.881 1.00 0.00 H +ATOM 320 CB ALA 20 16.979 22.616 27.773 1.00 0.00 C +ATOM 321 HB1 ALA 20 16.956 23.455 27.077 1.00 0.00 H +ATOM 322 HB2 ALA 20 16.496 21.704 27.423 1.00 0.00 H +ATOM 323 HB3 ALA 20 18.054 22.453 27.850 1.00 0.00 H +ATOM 324 C ALA 20 16.371 21.622 29.928 1.00 0.00 C +ATOM 325 O ALA 20 17.084 21.422 30.884 1.00 0.00 O +ATOM 326 N VAL 21 15.495 20.627 29.538 1.00 0.00 N +ATOM 327 H VAL 21 14.852 20.822 28.784 1.00 0.00 H +ATOM 328 CA VAL 21 15.258 19.383 30.241 1.00 0.00 C +ATOM 329 HA VAL 21 15.240 19.529 31.321 1.00 0.00 H +ATOM 330 CB VAL 21 13.821 18.798 29.816 1.00 0.00 C +ATOM 331 HB VAL 21 13.062 19.541 30.062 1.00 0.00 H +ATOM 332 CG1 VAL 21 13.767 18.552 28.324 1.00 0.00 C +ATOM 333 HG11 VAL 21 13.972 19.452 27.744 1.00 0.00 H +ATOM 334 HG12 VAL 21 12.731 18.272 28.134 1.00 0.00 H +ATOM 335 HG13 VAL 21 14.395 17.712 28.027 1.00 0.00 H +ATOM 336 CG2 VAL 21 13.333 17.634 30.615 1.00 0.00 C +ATOM 337 HG21 VAL 21 12.280 17.451 30.402 1.00 0.00 H +ATOM 338 HG22 VAL 21 13.407 17.963 31.652 1.00 0.00 H +ATOM 339 HG23 VAL 21 13.899 16.711 30.493 1.00 0.00 H +ATOM 340 C VAL 21 16.404 18.387 30.010 1.00 0.00 C +ATOM 341 O VAL 21 16.596 17.379 30.776 1.00 0.00 O +ATOM 342 N ASP 22 17.121 18.536 28.882 1.00 0.00 N +ATOM 343 H ASP 22 16.926 19.304 28.256 1.00 0.00 H +ATOM 344 CA ASP 22 18.163 17.574 28.399 1.00 0.00 C +ATOM 345 HA ASP 22 18.849 17.240 29.177 1.00 0.00 H +ATOM 346 CB ASP 22 17.458 16.362 27.774 1.00 0.00 C +ATOM 347 HB2 ASP 22 16.549 16.049 28.288 1.00 0.00 H +ATOM 348 HB3 ASP 22 17.204 16.676 26.762 1.00 0.00 H +ATOM 349 CG ASP 22 18.411 15.185 27.458 1.00 0.00 C +ATOM 350 OD1 ASP 22 18.821 15.007 26.284 1.00 0.00 O +ATOM 351 OD2 ASP 22 18.899 14.560 28.404 1.00 0.00 O +ATOM 352 C ASP 22 19.026 18.323 27.367 1.00 0.00 C +ATOM 353 O ASP 22 18.481 19.146 26.631 1.00 0.00 O +ATOM 354 N ALA 23 20.309 17.968 27.233 1.00 0.00 N +ATOM 355 H ALA 23 20.723 17.312 27.880 1.00 0.00 H +ATOM 356 CA ALA 23 21.125 18.577 26.231 1.00 0.00 C +ATOM 357 HA ALA 23 21.220 19.659 26.318 1.00 0.00 H +ATOM 358 CB ALA 23 22.551 18.006 26.266 1.00 0.00 C +ATOM 359 HB1 ALA 23 22.861 17.991 27.311 1.00 0.00 H +ATOM 360 HB2 ALA 23 23.244 18.567 25.639 1.00 0.00 H +ATOM 361 HB3 ALA 23 22.388 16.968 25.975 1.00 0.00 H +ATOM 362 C ALA 23 20.594 18.321 24.756 1.00 0.00 C +ATOM 363 O ALA 23 20.868 19.175 23.942 1.00 0.00 O +ATOM 364 N ALA 24 19.757 17.254 24.494 1.00 0.00 N +ATOM 365 H ALA 24 19.726 16.541 25.209 1.00 0.00 H +ATOM 366 CA ALA 24 19.115 16.959 23.206 1.00 0.00 C +ATOM 367 HA ALA 24 19.895 16.942 22.444 1.00 0.00 H +ATOM 368 CB ALA 24 18.424 15.612 23.365 1.00 0.00 C +ATOM 369 HB1 ALA 24 17.570 15.916 23.970 1.00 0.00 H +ATOM 370 HB2 ALA 24 19.091 14.795 23.643 1.00 0.00 H +ATOM 371 HB3 ALA 24 18.015 15.333 22.394 1.00 0.00 H +ATOM 372 C ALA 24 18.169 18.102 22.716 1.00 0.00 C +ATOM 373 O ALA 24 18.218 18.455 21.548 1.00 0.00 O +ATOM 374 N GLU 25 17.435 18.837 23.613 1.00 0.00 N +ATOM 375 H GLU 25 17.478 18.575 24.588 1.00 0.00 H +ATOM 376 CA GLU 25 16.707 20.008 23.239 1.00 0.00 C +ATOM 377 HA GLU 25 16.303 19.864 22.237 1.00 0.00 H +ATOM 378 CB GLU 25 15.490 20.144 24.206 1.00 0.00 C +ATOM 379 HB2 GLU 25 15.985 20.389 25.146 1.00 0.00 H +ATOM 380 HB3 GLU 25 14.852 20.993 23.959 1.00 0.00 H +ATOM 381 CG GLU 25 14.681 18.754 24.456 1.00 0.00 C +ATOM 382 HG2 GLU 25 15.326 18.077 25.016 1.00 0.00 H +ATOM 383 HG3 GLU 25 13.768 19.033 24.981 1.00 0.00 H +ATOM 384 CD GLU 25 14.177 17.993 23.242 1.00 0.00 C +ATOM 385 OE1 GLU 25 14.938 17.523 22.391 1.00 0.00 O +ATOM 386 OE2 GLU 25 12.944 18.031 23.058 1.00 0.00 O +ATOM 387 C GLU 25 17.511 21.310 23.199 1.00 0.00 C +ATOM 388 O GLU 25 17.410 22.048 22.261 1.00 0.00 O +ATOM 389 N ALA 26 18.427 21.526 24.230 1.00 0.00 N +ATOM 390 H ALA 26 18.514 20.826 24.953 1.00 0.00 H +ATOM 391 CA ALA 26 19.448 22.554 24.283 1.00 0.00 C +ATOM 392 HA ALA 26 18.968 23.531 24.345 1.00 0.00 H +ATOM 393 CB ALA 26 20.210 22.361 25.533 1.00 0.00 C +ATOM 394 HB1 ALA 26 20.951 21.561 25.526 1.00 0.00 H +ATOM 395 HB2 ALA 26 19.596 22.217 26.422 1.00 0.00 H +ATOM 396 HB3 ALA 26 20.870 23.215 25.683 1.00 0.00 H +ATOM 397 C ALA 26 20.253 22.694 22.939 1.00 0.00 C +ATOM 398 O ALA 26 20.444 23.774 22.450 1.00 0.00 O +ATOM 399 N GLU 27 20.720 21.568 22.460 1.00 0.00 N +ATOM 400 H GLU 27 20.603 20.741 23.029 1.00 0.00 H +ATOM 401 CA GLU 27 21.442 21.486 21.188 1.00 0.00 C +ATOM 402 HA GLU 27 22.370 22.056 21.229 1.00 0.00 H +ATOM 403 CB GLU 27 21.865 19.990 20.967 1.00 0.00 C +ATOM 404 HB2 GLU 27 22.672 19.786 21.671 1.00 0.00 H +ATOM 405 HB3 GLU 27 21.003 19.345 21.135 1.00 0.00 H +ATOM 406 CG GLU 27 22.478 19.767 19.601 1.00 0.00 C +ATOM 407 HG2 GLU 27 21.683 19.726 18.857 1.00 0.00 H +ATOM 408 HG3 GLU 27 23.168 20.545 19.276 1.00 0.00 H +ATOM 409 CD GLU 27 23.355 18.535 19.425 1.00 0.00 C +ATOM 410 OE1 GLU 27 23.021 17.453 19.935 1.00 0.00 O +ATOM 411 OE2 GLU 27 24.425 18.651 18.741 1.00 0.00 O +ATOM 412 C GLU 27 20.623 21.998 20.004 1.00 0.00 C +ATOM 413 O GLU 27 21.132 22.823 19.247 1.00 0.00 O +ATOM 414 N LYS 28 19.327 21.751 19.888 1.00 0.00 N +ATOM 415 H LYS 28 18.893 21.384 20.723 1.00 0.00 H +ATOM 416 CA LYS 28 18.448 22.301 18.849 1.00 0.00 C +ATOM 417 HA LYS 28 18.951 22.249 17.884 1.00 0.00 H +ATOM 418 CB LYS 28 17.172 21.431 18.672 1.00 0.00 C +ATOM 419 HB2 LYS 28 16.687 21.362 19.646 1.00 0.00 H +ATOM 420 HB3 LYS 28 16.489 21.922 17.979 1.00 0.00 H +ATOM 421 CG LYS 28 17.298 20.053 18.113 1.00 0.00 C +ATOM 422 HG2 LYS 28 17.888 20.250 17.218 1.00 0.00 H +ATOM 423 HG3 LYS 28 17.839 19.462 18.851 1.00 0.00 H +ATOM 424 CD LYS 28 15.919 19.363 17.830 1.00 0.00 C +ATOM 425 HD2 LYS 28 15.288 20.144 17.404 1.00 0.00 H +ATOM 426 HD3 LYS 28 16.122 18.594 17.084 1.00 0.00 H +ATOM 427 CE LYS 28 15.159 18.864 19.055 1.00 0.00 C +ATOM 428 HE2 LYS 28 15.094 19.735 19.708 1.00 0.00 H +ATOM 429 HE3 LYS 28 14.194 18.483 18.720 1.00 0.00 H +ATOM 430 NZ LYS 28 15.825 17.861 19.830 1.00 0.00 N +ATOM 431 HZ1 LYS 28 15.889 16.938 19.425 1.00 0.00 H +ATOM 432 HZ2 LYS 28 15.276 17.710 20.664 1.00 0.00 H +ATOM 433 HZ3 LYS 28 16.762 18.162 20.058 1.00 0.00 H +ATOM 434 C LYS 28 18.058 23.786 19.111 1.00 0.00 C +ATOM 435 O LYS 28 17.991 24.564 18.142 1.00 0.00 O +ATOM 436 N PHE 29 18.046 24.220 20.353 1.00 0.00 N +ATOM 437 H PHE 29 17.810 23.576 21.095 1.00 0.00 H +ATOM 438 CA PHE 29 17.948 25.649 20.598 1.00 0.00 C +ATOM 439 HA PHE 29 17.186 26.090 19.954 1.00 0.00 H +ATOM 440 CB PHE 29 17.498 25.867 22.058 1.00 0.00 C +ATOM 441 HB2 PHE 29 18.283 25.757 22.806 1.00 0.00 H +ATOM 442 HB3 PHE 29 17.229 26.923 22.065 1.00 0.00 H +ATOM 443 CG PHE 29 16.272 25.057 22.482 1.00 0.00 C +ATOM 444 CD1 PHE 29 15.113 25.008 21.662 1.00 0.00 C +ATOM 445 HD1 PHE 29 15.137 25.489 20.696 1.00 0.00 H +ATOM 446 CE1 PHE 29 13.962 24.458 22.177 1.00 0.00 C +ATOM 447 HE1 PHE 29 13.068 24.455 21.572 1.00 0.00 H +ATOM 448 CZ PHE 29 13.998 23.694 23.380 1.00 0.00 C +ATOM 449 HZ PHE 29 13.093 23.190 23.687 1.00 0.00 H +ATOM 450 CE2 PHE 29 15.144 23.690 24.168 1.00 0.00 C +ATOM 451 HE2 PHE 29 15.078 23.250 25.152 1.00 0.00 H +ATOM 452 CD2 PHE 29 16.305 24.416 23.698 1.00 0.00 C +ATOM 453 HD2 PHE 29 17.118 24.563 24.394 1.00 0.00 H +ATOM 454 C PHE 29 19.286 26.343 20.261 1.00 0.00 C +ATOM 455 O PHE 29 19.226 27.324 19.491 1.00 0.00 O +ATOM 456 N THR 30 20.444 25.797 20.585 1.00 0.00 N +ATOM 457 H THR 30 20.441 24.930 21.103 1.00 0.00 H +ATOM 458 CA THR 30 21.717 26.303 20.255 1.00 0.00 C +ATOM 459 HA THR 30 21.811 27.373 20.443 1.00 0.00 H +ATOM 460 CB THR 30 22.832 25.558 20.932 1.00 0.00 C +ATOM 461 HB THR 30 22.808 24.535 20.557 1.00 0.00 H +ATOM 462 CG2 THR 30 24.279 26.066 20.714 1.00 0.00 C +ATOM 463 HG21 THR 30 24.347 27.116 20.998 1.00 0.00 H +ATOM 464 HG22 THR 30 25.017 25.577 21.349 1.00 0.00 H +ATOM 465 HG23 THR 30 24.557 25.906 19.672 1.00 0.00 H +ATOM 466 OG1 THR 30 22.628 25.569 22.316 1.00 0.00 O +ATOM 467 HG1 THR 30 21.793 25.105 22.417 1.00 0.00 H +ATOM 468 C THR 30 21.982 26.188 18.740 1.00 0.00 C +ATOM 469 O THR 30 22.837 26.958 18.259 1.00 0.00 O +ATOM 470 N LYS 31 21.420 25.265 17.981 1.00 0.00 N +ATOM 471 H LYS 31 21.041 24.467 18.471 1.00 0.00 H +ATOM 472 CA LYS 31 21.499 25.117 16.509 1.00 0.00 C +ATOM 473 HA LYS 31 22.522 25.431 16.306 1.00 0.00 H +ATOM 474 CB LYS 31 21.135 23.687 15.883 1.00 0.00 C +ATOM 475 HB2 LYS 31 20.155 23.248 16.067 1.00 0.00 H +ATOM 476 HB3 LYS 31 21.195 23.809 14.802 1.00 0.00 H +ATOM 477 CG LYS 31 22.200 22.615 16.238 1.00 0.00 C +ATOM 478 HG2 LYS 31 23.156 22.692 15.721 1.00 0.00 H +ATOM 479 HG3 LYS 31 22.398 22.575 17.309 1.00 0.00 H +ATOM 480 CD LYS 31 21.790 21.233 15.675 1.00 0.00 C +ATOM 481 HD2 LYS 31 20.840 20.870 16.069 1.00 0.00 H +ATOM 482 HD3 LYS 31 21.662 21.227 14.592 1.00 0.00 H +ATOM 483 CE LYS 31 22.832 20.205 16.047 1.00 0.00 C +ATOM 484 HE2 LYS 31 23.815 20.562 15.739 1.00 0.00 H +ATOM 485 HE3 LYS 31 22.826 20.166 17.136 1.00 0.00 H +ATOM 486 NZ LYS 31 22.574 18.905 15.412 1.00 0.00 N +ATOM 487 HZ1 LYS 31 22.461 19.052 14.419 1.00 0.00 H +ATOM 488 HZ2 LYS 31 21.693 18.534 15.738 1.00 0.00 H +ATOM 489 HZ3 LYS 31 23.243 18.152 15.492 1.00 0.00 H +ATOM 490 C LYS 31 20.582 26.151 15.917 1.00 0.00 C +ATOM 491 O LYS 31 20.956 26.922 15.043 1.00 0.00 O +ATOM 492 N ALA 32 19.382 26.375 16.406 1.00 0.00 N +ATOM 493 H ALA 32 19.079 25.726 17.117 1.00 0.00 H +ATOM 494 CA ALA 32 18.494 27.440 15.934 1.00 0.00 C +ATOM 495 HA ALA 32 18.320 27.176 14.891 1.00 0.00 H +ATOM 496 CB ALA 32 17.163 27.299 16.655 1.00 0.00 C +ATOM 497 HB1 ALA 32 16.813 26.267 16.635 1.00 0.00 H +ATOM 498 HB2 ALA 32 17.326 27.630 17.681 1.00 0.00 H +ATOM 499 HB3 ALA 32 16.388 27.871 16.145 1.00 0.00 H +ATOM 500 C ALA 32 18.946 28.921 16.070 1.00 0.00 C +ATOM 501 O ALA 32 18.891 29.641 15.083 1.00 0.00 O +ATOM 502 N ASP 33 19.590 29.301 17.172 1.00 0.00 N +ATOM 503 H ASP 33 19.593 28.696 17.981 1.00 0.00 H +ATOM 504 CA ASP 33 20.490 30.437 17.284 1.00 0.00 C +ATOM 505 HA ASP 33 19.908 31.333 17.065 1.00 0.00 H +ATOM 506 CB ASP 33 21.001 30.475 18.714 1.00 0.00 C +ATOM 507 HB2 ASP 33 21.571 29.559 18.872 1.00 0.00 H +ATOM 508 HB3 ASP 33 21.570 31.399 18.821 1.00 0.00 H +ATOM 509 CG ASP 33 19.836 30.585 19.715 1.00 0.00 C +ATOM 510 OD1 ASP 33 18.912 31.466 19.574 1.00 0.00 O +ATOM 511 OD2 ASP 33 19.966 29.888 20.756 1.00 0.00 O +ATOM 512 C ASP 33 21.688 30.518 16.333 1.00 0.00 C +ATOM 513 O ASP 33 21.939 31.590 15.801 1.00 0.00 O +ATOM 514 N ALA 34 22.425 29.384 16.049 1.00 0.00 N +ATOM 515 H ALA 34 22.208 28.526 16.536 1.00 0.00 H +ATOM 516 CA ALA 34 23.499 29.356 15.055 1.00 0.00 C +ATOM 517 HA ALA 34 24.209 30.163 15.236 1.00 0.00 H +ATOM 518 CB ALA 34 24.197 28.002 15.279 1.00 0.00 C +ATOM 519 HB1 ALA 34 23.444 27.245 15.062 1.00 0.00 H +ATOM 520 HB2 ALA 34 24.558 27.888 16.302 1.00 0.00 H +ATOM 521 HB3 ALA 34 24.922 27.995 14.465 1.00 0.00 H +ATOM 522 C ALA 34 23.014 29.507 13.640 1.00 0.00 C +ATOM 523 O ALA 34 23.736 30.158 12.867 1.00 0.00 O +ATOM 524 N ASN 35 21.946 28.861 13.273 1.00 0.00 N +ATOM 525 H ASN 35 21.370 28.445 13.992 1.00 0.00 H +ATOM 526 CA ASN 35 21.280 29.157 11.983 1.00 0.00 C +ATOM 527 HA ASN 35 22.043 29.209 11.206 1.00 0.00 H +ATOM 528 CB ASN 35 20.172 28.124 11.626 1.00 0.00 C +ATOM 529 HB2 ASN 35 19.449 28.174 12.439 1.00 0.00 H +ATOM 530 HB3 ASN 35 19.651 28.441 10.723 1.00 0.00 H +ATOM 531 CG ASN 35 20.753 26.718 11.255 1.00 0.00 C +ATOM 532 OD1 ASN 35 21.627 26.578 10.442 1.00 0.00 O +ATOM 533 ND2 ASN 35 20.297 25.665 11.908 1.00 0.00 N +ATOM 534 HD21 ASN 35 19.538 25.948 12.511 1.00 0.00 H +ATOM 535 HD22 ASN 35 20.634 24.752 11.639 1.00 0.00 H +ATOM 536 C ASN 35 20.795 30.562 11.802 1.00 0.00 C +ATOM 537 O ASN 35 20.804 31.193 10.744 1.00 0.00 O +ATOM 538 N ASP 36 20.527 31.250 12.962 1.00 0.00 N +ATOM 539 H ASP 36 20.617 30.851 13.885 1.00 0.00 H +ATOM 540 CA ASP 36 20.224 32.725 12.952 1.00 0.00 C +ATOM 541 HA ASP 36 19.475 32.894 12.178 1.00 0.00 H +ATOM 542 CB ASP 36 19.632 33.258 14.304 1.00 0.00 C +ATOM 543 HB2 ASP 36 18.771 32.634 14.542 1.00 0.00 H +ATOM 544 HB3 ASP 36 20.394 33.129 15.073 1.00 0.00 H +ATOM 545 CG ASP 36 19.096 34.660 14.116 1.00 0.00 C +ATOM 546 OD1 ASP 36 18.471 34.989 13.068 1.00 0.00 O +ATOM 547 OD2 ASP 36 19.292 35.511 15.043 1.00 0.00 O +ATOM 548 C ASP 36 21.531 33.522 12.577 1.00 0.00 C +ATOM 549 O ASP 36 21.508 34.254 11.611 1.00 0.00 O +ATOM 550 N LYS 37 22.706 33.249 13.276 1.00 0.00 N +ATOM 551 H LYS 37 22.563 32.584 14.022 1.00 0.00 H +ATOM 552 CA LYS 37 24.020 33.869 13.040 1.00 0.00 C +ATOM 553 HA LYS 37 23.860 34.938 13.181 1.00 0.00 H +ATOM 554 CB LYS 37 24.887 33.332 14.125 1.00 0.00 C +ATOM 555 HB2 LYS 37 25.144 32.304 13.869 1.00 0.00 H +ATOM 556 HB3 LYS 37 24.268 33.200 15.013 1.00 0.00 H +ATOM 557 CG LYS 37 26.228 34.140 14.272 1.00 0.00 C +ATOM 558 HG2 LYS 37 25.958 35.168 14.512 1.00 0.00 H +ATOM 559 HG3 LYS 37 26.729 34.173 13.305 1.00 0.00 H +ATOM 560 CD LYS 37 27.191 33.518 15.215 1.00 0.00 C +ATOM 561 HD2 LYS 37 26.749 33.322 16.192 1.00 0.00 H +ATOM 562 HD3 LYS 37 27.341 32.488 14.892 1.00 0.00 H +ATOM 563 CE LYS 37 28.555 34.303 15.378 1.00 0.00 C +ATOM 564 HE2 LYS 37 28.366 35.340 15.654 1.00 0.00 H +ATOM 565 HE3 LYS 37 29.017 33.767 16.208 1.00 0.00 H +ATOM 566 NZ LYS 37 29.301 34.138 14.041 1.00 0.00 N +ATOM 567 HZ1 LYS 37 28.863 34.597 13.255 1.00 0.00 H +ATOM 568 HZ2 LYS 37 30.169 34.628 14.206 1.00 0.00 H +ATOM 569 HZ3 LYS 37 29.614 33.199 13.839 1.00 0.00 H +ATOM 570 C LYS 37 24.498 33.598 11.596 1.00 0.00 C +ATOM 571 O LYS 37 25.066 34.505 10.926 1.00 0.00 O +ATOM 572 N GLY 38 24.305 32.360 11.113 1.00 0.00 N +ATOM 573 H GLY 38 24.035 31.655 11.785 1.00 0.00 H +ATOM 574 CA GLY 38 24.219 32.128 9.610 1.00 0.00 C +ATOM 575 HA2 GLY 38 23.414 32.715 9.169 1.00 0.00 H +ATOM 576 HA3 GLY 38 25.075 32.621 9.150 1.00 0.00 H +ATOM 577 C GLY 38 24.027 30.687 9.115 1.00 0.00 C +ATOM 578 O GLY 38 23.407 30.350 8.111 1.00 0.00 O +ATOM 579 N VAL 39 24.469 29.753 10.007 1.00 0.00 N +ATOM 580 H VAL 39 24.605 30.032 10.968 1.00 0.00 H +ATOM 581 CA VAL 39 24.585 28.309 9.793 1.00 0.00 C +ATOM 582 HA VAL 39 23.651 27.946 9.365 1.00 0.00 H +ATOM 583 CB VAL 39 25.786 28.058 8.821 1.00 0.00 C +ATOM 584 HB VAL 39 25.622 28.694 7.951 1.00 0.00 H +ATOM 585 CG1 VAL 39 27.190 28.617 9.240 1.00 0.00 C +ATOM 586 HG11 VAL 39 27.142 29.697 9.104 1.00 0.00 H +ATOM 587 HG12 VAL 39 28.004 28.159 8.677 1.00 0.00 H +ATOM 588 HG13 VAL 39 27.556 28.306 10.219 1.00 0.00 H +ATOM 589 CG2 VAL 39 26.077 26.620 8.406 1.00 0.00 C +ATOM 590 HG21 VAL 39 25.239 26.350 7.763 1.00 0.00 H +ATOM 591 HG22 VAL 39 26.019 25.901 9.223 1.00 0.00 H +ATOM 592 HG23 VAL 39 26.910 26.630 7.704 1.00 0.00 H +ATOM 593 C VAL 39 24.951 27.532 11.082 1.00 0.00 C +ATOM 594 O VAL 39 25.637 28.072 11.894 1.00 0.00 O +ATOM 595 N ASP 40 24.466 26.274 11.254 1.00 0.00 N +ATOM 596 H ASP 40 23.722 26.105 10.591 1.00 0.00 H +ATOM 597 CA ASP 40 24.680 25.358 12.396 1.00 0.00 C +ATOM 598 HA ASP 40 24.594 26.005 13.269 1.00 0.00 H +ATOM 599 CB ASP 40 23.617 24.310 12.603 1.00 0.00 C +ATOM 600 HB2 ASP 40 23.941 23.778 13.498 1.00 0.00 H +ATOM 601 HB3 ASP 40 22.735 24.889 12.877 1.00 0.00 H +ATOM 602 CG ASP 40 23.410 23.273 11.514 1.00 0.00 C +ATOM 603 OD1 ASP 40 24.471 22.791 10.994 1.00 0.00 O +ATOM 604 OD2 ASP 40 22.220 22.871 11.342 1.00 0.00 O +ATOM 605 C ASP 40 26.126 24.835 12.500 1.00 0.00 C +ATOM 606 O ASP 40 26.849 24.778 11.531 1.00 0.00 O +ATOM 607 N GLY 41 26.529 24.308 13.707 1.00 0.00 N +ATOM 608 H GLY 41 25.927 24.304 14.518 1.00 0.00 H +ATOM 609 CA GLY 41 27.854 23.846 14.029 1.00 0.00 C +ATOM 610 HA2 GLY 41 27.849 23.118 14.841 1.00 0.00 H +ATOM 611 HA3 GLY 41 28.326 23.413 13.147 1.00 0.00 H +ATOM 612 C GLY 41 28.710 24.992 14.566 1.00 0.00 C +ATOM 613 O GLY 41 29.934 24.765 14.619 1.00 0.00 O +ATOM 614 N GLU 42 28.155 26.142 15.091 1.00 0.00 N +ATOM 615 H GLU 42 27.155 26.282 15.065 1.00 0.00 H +ATOM 616 CA GLU 42 28.856 27.228 15.714 1.00 0.00 C +ATOM 617 HA GLU 42 29.701 27.624 15.151 1.00 0.00 H +ATOM 618 CB GLU 42 27.905 28.437 15.868 1.00 0.00 C +ATOM 619 HB2 GLU 42 27.568 28.722 14.871 1.00 0.00 H +ATOM 620 HB3 GLU 42 27.090 28.208 16.554 1.00 0.00 H +ATOM 621 CG GLU 42 28.670 29.753 16.382 1.00 0.00 C +ATOM 622 HG2 GLU 42 27.877 30.502 16.386 1.00 0.00 H +ATOM 623 HG3 GLU 42 29.115 29.640 17.371 1.00 0.00 H +ATOM 624 CD GLU 42 29.623 30.437 15.398 1.00 0.00 C +ATOM 625 OE1 GLU 42 29.430 30.714 14.239 1.00 0.00 O +ATOM 626 OE2 GLU 42 30.719 30.698 15.950 1.00 0.00 O +ATOM 627 C GLU 42 29.313 26.827 17.119 1.00 0.00 C +ATOM 628 O GLU 42 30.472 27.197 17.419 1.00 0.00 O +ATOM 629 N TRP 43 28.591 25.985 17.875 1.00 0.00 N +ATOM 630 H TRP 43 27.720 25.683 17.462 1.00 0.00 H +ATOM 631 CA TRP 43 28.990 25.553 19.211 1.00 0.00 C +ATOM 632 HA TRP 43 29.962 26.023 19.357 1.00 0.00 H +ATOM 633 CB TRP 43 28.035 26.259 20.229 1.00 0.00 C +ATOM 634 HB2 TRP 43 27.001 25.949 20.078 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.258 25.924 21.243 1.00 0.00 H +ATOM 636 CG TRP 43 28.058 27.765 20.169 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.015 28.576 20.661 1.00 0.00 C +ATOM 638 HD1 TRP 43 29.942 28.219 21.085 1.00 0.00 H +ATOM 639 NE1 TRP 43 28.691 29.908 20.434 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.324 30.694 20.475 1.00 0.00 H +ATOM 641 CE2 TRP 43 27.490 29.962 19.754 1.00 0.00 C +ATOM 642 CZ2 TRP 43 26.711 31.100 19.449 1.00 0.00 C +ATOM 643 HZ2 TRP 43 27.081 32.106 19.578 1.00 0.00 H +ATOM 644 CH2 TRP 43 25.421 30.877 18.924 1.00 0.00 C +ATOM 645 HH2 TRP 43 24.717 31.690 18.828 1.00 0.00 H +ATOM 646 CZ3 TRP 43 25.084 29.569 18.502 1.00 0.00 C +ATOM 647 HZ3 TRP 43 24.165 29.333 17.986 1.00 0.00 H +ATOM 648 CE3 TRP 43 25.825 28.481 18.944 1.00 0.00 C +ATOM 649 HE3 TRP 43 25.509 27.498 18.628 1.00 0.00 H +ATOM 650 CD2 TRP 43 27.056 28.625 19.604 1.00 0.00 C +ATOM 651 C TRP 43 29.021 24.028 19.303 1.00 0.00 C +ATOM 652 O TRP 43 27.965 23.466 19.176 1.00 0.00 O +ATOM 653 N THR 44 30.165 23.435 19.554 1.00 0.00 N +ATOM 654 H THR 44 31.023 23.958 19.451 1.00 0.00 H +ATOM 655 CA THR 44 30.207 22.051 19.928 1.00 0.00 C +ATOM 656 HA THR 44 29.419 21.568 19.350 1.00 0.00 H +ATOM 657 CB THR 44 31.524 21.501 19.415 1.00 0.00 C +ATOM 658 HB THR 44 31.569 21.594 18.329 1.00 0.00 H +ATOM 659 CG2 THR 44 32.751 22.050 20.097 1.00 0.00 C +ATOM 660 HG21 THR 44 33.667 21.702 19.619 1.00 0.00 H +ATOM 661 HG22 THR 44 32.645 21.770 21.145 1.00 0.00 H +ATOM 662 HG23 THR 44 32.810 23.138 20.067 1.00 0.00 H +ATOM 663 OG1 THR 44 31.514 20.158 19.696 1.00 0.00 O +ATOM 664 HG1 THR 44 31.469 19.683 18.863 1.00 0.00 H +ATOM 665 C THR 44 29.854 21.670 21.362 1.00 0.00 C +ATOM 666 O THR 44 30.137 22.449 22.293 1.00 0.00 O +ATOM 667 N TYR 45 29.143 20.530 21.613 1.00 0.00 N +ATOM 668 H TYR 45 28.825 19.951 20.849 1.00 0.00 H +ATOM 669 CA TYR 45 28.738 20.192 22.978 1.00 0.00 C +ATOM 670 HA TYR 45 28.579 21.177 23.417 1.00 0.00 H +ATOM 671 CB TYR 45 27.481 19.424 23.012 1.00 0.00 C +ATOM 672 HB2 TYR 45 26.783 19.897 22.322 1.00 0.00 H +ATOM 673 HB3 TYR 45 27.737 18.472 22.548 1.00 0.00 H +ATOM 674 CG TYR 45 26.906 19.179 24.358 1.00 0.00 C +ATOM 675 CD1 TYR 45 26.733 20.202 25.276 1.00 0.00 C +ATOM 676 HD1 TYR 45 26.852 21.234 24.980 1.00 0.00 H +ATOM 677 CE1 TYR 45 26.282 19.962 26.586 1.00 0.00 C +ATOM 678 HE1 TYR 45 26.156 20.783 27.276 1.00 0.00 H +ATOM 679 CZ TYR 45 25.990 18.624 26.941 1.00 0.00 C +ATOM 680 OH TYR 45 25.439 18.381 28.184 1.00 0.00 O +ATOM 681 HH TYR 45 25.354 17.438 28.341 1.00 0.00 H +ATOM 682 CE2 TYR 45 26.116 17.551 26.013 1.00 0.00 C +ATOM 683 HE2 TYR 45 26.052 16.523 26.339 1.00 0.00 H +ATOM 684 CD2 TYR 45 26.634 17.841 24.730 1.00 0.00 C +ATOM 685 HD2 TYR 45 26.675 16.987 24.069 1.00 0.00 H +ATOM 686 C TYR 45 29.849 19.426 23.777 1.00 0.00 C +ATOM 687 O TYR 45 30.532 18.606 23.134 1.00 0.00 O +ATOM 688 N ASP 46 29.809 19.508 25.081 1.00 0.00 N +ATOM 689 H ASP 46 29.162 20.182 25.466 1.00 0.00 H +ATOM 690 CA ASP 46 30.815 18.926 25.976 1.00 0.00 C +ATOM 691 HA ASP 46 31.338 18.166 25.395 1.00 0.00 H +ATOM 692 CB ASP 46 31.912 19.977 26.157 1.00 0.00 C +ATOM 693 HB2 ASP 46 32.453 20.237 25.246 1.00 0.00 H +ATOM 694 HB3 ASP 46 31.559 20.891 26.633 1.00 0.00 H +ATOM 695 CG ASP 46 32.902 19.305 27.021 1.00 0.00 C +ATOM 696 OD1 ASP 46 33.641 19.967 27.716 1.00 0.00 O +ATOM 697 OD2 ASP 46 33.036 18.048 27.043 1.00 0.00 O +ATOM 698 C ASP 46 30.167 18.290 27.246 1.00 0.00 C +ATOM 699 O ASP 46 29.933 18.999 28.250 1.00 0.00 O +ATOM 700 N ASP 47 29.898 16.975 27.154 1.00 0.00 N +ATOM 701 H ASP 47 30.062 16.548 26.253 1.00 0.00 H +ATOM 702 CA ASP 47 29.259 16.234 28.239 1.00 0.00 C +ATOM 703 HA ASP 47 28.362 16.803 28.484 1.00 0.00 H +ATOM 704 CB ASP 47 28.850 14.873 27.798 1.00 0.00 C +ATOM 705 HB2 ASP 47 28.141 14.865 26.970 1.00 0.00 H +ATOM 706 HB3 ASP 47 29.685 14.271 27.439 1.00 0.00 H +ATOM 707 CG ASP 47 28.192 14.069 28.933 1.00 0.00 C +ATOM 708 OD1 ASP 47 28.850 13.096 29.330 1.00 0.00 O +ATOM 709 OD2 ASP 47 27.134 14.447 29.384 1.00 0.00 O +ATOM 710 C ASP 47 30.178 16.060 29.479 1.00 0.00 C +ATOM 711 O ASP 47 29.727 15.853 30.578 1.00 0.00 O +ATOM 712 N ALA 48 31.446 16.242 29.287 1.00 0.00 N +ATOM 713 H ALA 48 31.713 16.441 28.334 1.00 0.00 H +ATOM 714 CA ALA 48 32.376 16.178 30.390 1.00 0.00 C +ATOM 715 HA ALA 48 32.004 15.390 31.044 1.00 0.00 H +ATOM 716 CB ALA 48 33.772 15.749 29.935 1.00 0.00 C +ATOM 717 HB1 ALA 48 33.704 14.825 29.361 1.00 0.00 H +ATOM 718 HB2 ALA 48 34.559 15.638 30.681 1.00 0.00 H +ATOM 719 HB3 ALA 48 34.092 16.456 29.170 1.00 0.00 H +ATOM 720 C ALA 48 32.371 17.474 31.222 1.00 0.00 C +ATOM 721 O ALA 48 33.166 17.575 32.126 1.00 0.00 O +ATOM 722 N THR 49 31.499 18.499 30.908 1.00 0.00 N +ATOM 723 H THR 49 30.906 18.305 30.114 1.00 0.00 H +ATOM 724 CA THR 49 31.319 19.737 31.665 1.00 0.00 C +ATOM 725 HA THR 49 31.408 19.507 32.727 1.00 0.00 H +ATOM 726 CB THR 49 32.268 20.830 31.179 1.00 0.00 C +ATOM 727 HB THR 49 32.053 21.756 31.711 1.00 0.00 H +ATOM 728 CG2 THR 49 33.749 20.533 31.464 1.00 0.00 C +ATOM 729 HG21 THR 49 33.800 20.164 32.488 1.00 0.00 H +ATOM 730 HG22 THR 49 34.284 21.467 31.289 1.00 0.00 H +ATOM 731 HG23 THR 49 34.150 19.788 30.776 1.00 0.00 H +ATOM 732 OG1 THR 49 32.211 21.058 29.839 1.00 0.00 O +ATOM 733 HG1 THR 49 32.665 20.408 29.297 1.00 0.00 H +ATOM 734 C THR 49 29.888 20.286 31.596 1.00 0.00 C +ATOM 735 O THR 49 29.739 21.318 32.156 1.00 0.00 O +ATOM 736 N LYS 50 28.951 19.675 30.877 1.00 0.00 N +ATOM 737 H LYS 50 29.269 18.904 30.308 1.00 0.00 H +ATOM 738 CA LYS 50 27.579 20.175 30.547 1.00 0.00 C +ATOM 739 HA LYS 50 27.077 19.504 29.851 1.00 0.00 H +ATOM 740 CB LYS 50 26.600 20.049 31.741 1.00 0.00 C +ATOM 741 HB2 LYS 50 26.536 21.004 32.262 1.00 0.00 H +ATOM 742 HB3 LYS 50 25.645 19.888 31.241 1.00 0.00 H +ATOM 743 CG LYS 50 26.837 18.894 32.729 1.00 0.00 C +ATOM 744 HG2 LYS 50 27.699 18.999 33.388 1.00 0.00 H +ATOM 745 HG3 LYS 50 25.940 18.803 33.343 1.00 0.00 H +ATOM 746 CD LYS 50 26.872 17.574 31.969 1.00 0.00 C +ATOM 747 HD2 LYS 50 25.939 17.468 31.417 1.00 0.00 H +ATOM 748 HD3 LYS 50 27.752 17.569 31.325 1.00 0.00 H +ATOM 749 CE LYS 50 26.989 16.300 32.816 1.00 0.00 C +ATOM 750 HE2 LYS 50 27.609 16.618 33.654 1.00 0.00 H +ATOM 751 HE3 LYS 50 25.959 16.093 33.107 1.00 0.00 H +ATOM 752 NZ LYS 50 27.570 15.161 32.088 1.00 0.00 N +ATOM 753 HZ1 LYS 50 28.498 15.388 31.761 1.00 0.00 H +ATOM 754 HZ2 LYS 50 27.051 14.947 31.248 1.00 0.00 H +ATOM 755 HZ3 LYS 50 27.617 14.401 32.752 1.00 0.00 H +ATOM 756 C LYS 50 27.636 21.548 29.909 1.00 0.00 C +ATOM 757 O LYS 50 27.015 22.501 30.341 1.00 0.00 O +ATOM 758 N THR 51 28.459 21.682 28.774 1.00 0.00 N +ATOM 759 H THR 51 28.886 20.911 28.280 1.00 0.00 H +ATOM 760 CA THR 51 28.806 22.962 28.182 1.00 0.00 C +ATOM 761 HA THR 51 28.225 23.752 28.657 1.00 0.00 H +ATOM 762 CB THR 51 30.286 23.328 28.444 1.00 0.00 C +ATOM 763 HB THR 51 30.920 22.592 27.949 1.00 0.00 H +ATOM 764 CG2 THR 51 30.740 24.641 27.847 1.00 0.00 C +ATOM 765 HG21 THR 51 31.670 24.845 28.379 1.00 0.00 H +ATOM 766 HG22 THR 51 30.009 25.433 28.007 1.00 0.00 H +ATOM 767 HG23 THR 51 30.971 24.379 26.814 1.00 0.00 H +ATOM 768 OG1 THR 51 30.487 23.291 29.809 1.00 0.00 O +ATOM 769 HG1 THR 51 30.610 22.378 30.078 1.00 0.00 H +ATOM 770 C THR 51 28.712 22.911 26.674 1.00 0.00 C +ATOM 771 O THR 51 29.127 21.900 26.099 1.00 0.00 O +ATOM 772 N PHE 52 28.235 23.944 25.990 1.00 0.00 N +ATOM 773 H PHE 52 27.717 24.671 26.462 1.00 0.00 H +ATOM 774 CA PHE 52 28.495 24.192 24.555 1.00 0.00 C +ATOM 775 HA PHE 52 28.806 23.216 24.183 1.00 0.00 H +ATOM 776 CB PHE 52 27.230 24.681 23.843 1.00 0.00 C +ATOM 777 HB2 PHE 52 27.030 25.605 24.386 1.00 0.00 H +ATOM 778 HB3 PHE 52 27.589 24.846 22.827 1.00 0.00 H +ATOM 779 CG PHE 52 26.149 23.643 23.847 1.00 0.00 C +ATOM 780 CD1 PHE 52 25.340 23.458 24.961 1.00 0.00 C +ATOM 781 HD1 PHE 52 25.382 24.044 25.868 1.00 0.00 H +ATOM 782 CE1 PHE 52 24.271 22.494 24.966 1.00 0.00 C +ATOM 783 HE1 PHE 52 23.773 22.262 25.896 1.00 0.00 H +ATOM 784 CZ PHE 52 24.054 21.793 23.822 1.00 0.00 C +ATOM 785 HZ PHE 52 23.289 21.031 23.817 1.00 0.00 H +ATOM 786 CE2 PHE 52 24.866 21.967 22.668 1.00 0.00 C +ATOM 787 HE2 PHE 52 24.711 21.318 21.820 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.950 22.895 22.730 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.599 22.899 21.866 1.00 0.00 H +ATOM 790 C PHE 52 29.675 25.230 24.398 1.00 0.00 C +ATOM 791 O PHE 52 29.794 26.036 25.343 1.00 0.00 O +ATOM 792 N THR 53 30.478 25.246 23.391 1.00 0.00 N +ATOM 793 H THR 53 30.414 24.573 22.641 1.00 0.00 H +ATOM 794 CA THR 53 31.576 26.106 23.296 1.00 0.00 C +ATOM 795 HA THR 53 31.311 27.028 23.814 1.00 0.00 H +ATOM 796 CB THR 53 32.892 25.464 23.941 1.00 0.00 C +ATOM 797 HB THR 53 32.495 25.205 24.923 1.00 0.00 H +ATOM 798 CG2 THR 53 33.407 24.153 23.351 1.00 0.00 C +ATOM 799 HG21 THR 53 33.925 24.333 22.409 1.00 0.00 H +ATOM 800 HG22 THR 53 32.629 23.421 23.131 1.00 0.00 H +ATOM 801 HG23 THR 53 34.079 23.679 24.067 1.00 0.00 H +ATOM 802 OG1 THR 53 33.950 26.275 24.159 1.00 0.00 O +ATOM 803 HG1 THR 53 34.534 25.897 24.820 1.00 0.00 H +ATOM 804 C THR 53 31.955 26.421 21.852 1.00 0.00 C +ATOM 805 O THR 53 31.748 25.627 20.971 1.00 0.00 O +ATOM 806 N VAL 54 32.674 27.548 21.672 1.00 0.00 N +ATOM 807 H VAL 54 32.935 27.964 22.554 1.00 0.00 H +ATOM 808 CA VAL 54 33.135 28.114 20.454 1.00 0.00 C +ATOM 809 HA VAL 54 32.298 28.034 19.761 1.00 0.00 H +ATOM 810 CB VAL 54 33.734 29.591 20.600 1.00 0.00 C +ATOM 811 HB VAL 54 34.136 29.950 19.652 1.00 0.00 H +ATOM 812 CG1 VAL 54 32.562 30.558 20.961 1.00 0.00 C +ATOM 813 HG11 VAL 54 32.020 30.243 21.853 1.00 0.00 H +ATOM 814 HG12 VAL 54 31.893 30.586 20.101 1.00 0.00 H +ATOM 815 HG13 VAL 54 32.937 31.544 21.235 1.00 0.00 H +ATOM 816 CG2 VAL 54 34.839 29.602 21.657 1.00 0.00 C +ATOM 817 HG21 VAL 54 35.648 28.943 21.343 1.00 0.00 H +ATOM 818 HG22 VAL 54 34.581 29.456 22.706 1.00 0.00 H +ATOM 819 HG23 VAL 54 35.223 30.616 21.539 1.00 0.00 H +ATOM 820 C VAL 54 34.084 27.144 19.708 1.00 0.00 C +ATOM 821 O VAL 54 35.048 26.610 20.261 1.00 0.00 O +ATOM 822 N THR 55 33.972 26.994 18.432 1.00 0.00 N +ATOM 823 H THR 55 33.261 27.595 18.040 1.00 0.00 H +ATOM 824 CA THR 55 34.779 26.189 17.519 1.00 0.00 C +ATOM 825 HA THR 55 35.816 26.233 17.851 1.00 0.00 H +ATOM 826 CB THR 55 34.170 24.760 17.464 1.00 0.00 C +ATOM 827 HB THR 55 33.956 24.474 18.494 1.00 0.00 H +ATOM 828 CG2 THR 55 32.913 24.663 16.575 1.00 0.00 C +ATOM 829 HG21 THR 55 32.525 23.647 16.499 1.00 0.00 H +ATOM 830 HG22 THR 55 33.166 24.966 15.559 1.00 0.00 H +ATOM 831 HG23 THR 55 32.079 25.298 16.872 1.00 0.00 H +ATOM 832 OG1 THR 55 35.239 23.952 16.986 1.00 0.00 O +ATOM 833 HG1 THR 55 35.287 23.974 16.028 1.00 0.00 H +ATOM 834 C THR 55 35.061 26.798 16.087 1.00 0.00 C +ATOM 835 O THR 55 35.823 26.101 15.389 1.00 0.00 O +ATOM 836 N GLU 56 34.549 27.937 15.592 1.00 0.00 N +ATOM 837 H GLU 56 33.916 28.416 16.217 1.00 0.00 H +ATOM 838 CA GLU 56 34.776 28.391 14.200 1.00 0.00 C +ATOM 839 HA GLU 56 35.044 27.559 13.549 1.00 0.00 H +ATOM 840 CB GLU 56 33.408 28.993 13.788 1.00 0.00 C +ATOM 841 HB2 GLU 56 33.039 29.731 14.500 1.00 0.00 H +ATOM 842 HB3 GLU 56 33.689 29.552 12.895 1.00 0.00 H +ATOM 843 CG GLU 56 32.398 27.809 13.608 1.00 0.00 C +ATOM 844 HG2 GLU 56 32.461 26.956 14.284 1.00 0.00 H +ATOM 845 HG3 GLU 56 31.391 28.190 13.781 1.00 0.00 H +ATOM 846 CD GLU 56 32.405 27.320 12.131 1.00 0.00 C +ATOM 847 OE1 GLU 56 31.746 28.069 11.327 1.00 0.00 O +ATOM 848 OE2 GLU 56 32.712 26.147 11.872 1.00 0.00 O +ATOM 849 C GLU 56 35.944 29.378 14.039 1.00 0.00 C +ATOM 850 O GLU 56 37.007 28.966 13.577 1.00 0.00 O +ATOM 851 OXT GLU 56 35.835 30.497 14.595 1.00 0.00 O +ATOM 852 ZN ZN1 57 24.101 31.306 24.915 1.00 0.00 ZN +ATOM 853 N AN1 58 23.604 32.447 23.417 1.00 0.00 N +ATOM 854 C AN1 58 23.177 33.557 21.156 1.00 0.00 C +ATOM 855 C1 AN1 58 23.311 32.893 22.435 1.00 0.00 C +ATOM 856 H AN1 58 22.133 33.888 21.087 1.00 0.00 H +ATOM 857 H1 AN1 58 23.563 32.978 20.309 1.00 0.00 H +ATOM 858 H2 AN1 58 23.792 34.461 21.240 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 25.606 35.634 23.412 1.00 0.00 N +ATOM 860 N2 AZI 59 24.409 35.840 23.693 1.00 0.00 N +ATOM 861 N3 AZI 59 23.173 36.083 24.013 1.00 0.00 N +TER 862 AZI 59 \ No newline at end of file diff --git a/tests/nsga2/pdbs_rename/cluster4.pdb b/tests/nsga2/pdbs_rename/cluster4.pdb new file mode 100644 index 0000000..21f509e --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster4.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.742 -82.001 -13.195 1.00 0.00 N +ATOM 2 H1 MET 1 14.660 -81.584 -13.256 1.00 0.00 H +ATOM 3 H2 MET 1 13.346 -81.921 -12.270 1.00 0.00 H +ATOM 4 H3 MET 1 13.166 -81.464 -13.828 1.00 0.00 H +ATOM 5 CA MET 1 13.695 -83.453 -13.524 1.00 0.00 C +ATOM 6 HA MET 1 12.662 -83.726 -13.307 1.00 0.00 H +ATOM 7 CB MET 1 14.014 -83.690 -14.987 1.00 0.00 C +ATOM 8 HB2 MET 1 13.118 -83.478 -15.570 1.00 0.00 H +ATOM 9 HB3 MET 1 14.799 -83.000 -15.296 1.00 0.00 H +ATOM 10 CG MET 1 14.468 -85.152 -15.240 1.00 0.00 C +ATOM 11 HG2 MET 1 15.527 -85.171 -14.983 1.00 0.00 H +ATOM 12 HG3 MET 1 13.937 -85.890 -14.638 1.00 0.00 H +ATOM 13 SD MET 1 14.500 -85.601 -17.012 1.00 0.00 S +ATOM 14 CE MET 1 12.831 -86.320 -17.251 1.00 0.00 C +ATOM 15 HE1 MET 1 12.127 -85.605 -16.825 1.00 0.00 H +ATOM 16 HE2 MET 1 12.743 -87.163 -16.565 1.00 0.00 H +ATOM 17 HE3 MET 1 12.742 -86.570 -18.308 1.00 0.00 H +ATOM 18 C MET 1 14.563 -84.116 -12.464 1.00 0.00 C +ATOM 19 O MET 1 15.647 -83.580 -12.064 1.00 0.00 O +ATOM 20 N GLN 2 14.131 -85.285 -11.892 1.00 0.00 N +ATOM 21 H GLN 2 13.228 -85.659 -12.144 1.00 0.00 H +ATOM 22 CA GLN 2 14.816 -86.157 -10.835 1.00 0.00 C +ATOM 23 HA GLN 2 15.168 -85.566 -9.990 1.00 0.00 H +ATOM 24 CB GLN 2 13.794 -87.177 -10.135 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.219 -87.751 -10.861 1.00 0.00 H +ATOM 26 HB3 GLN 2 14.411 -87.822 -9.508 1.00 0.00 H +ATOM 27 CG GLN 2 12.863 -86.628 -9.037 1.00 0.00 C +ATOM 28 HG2 GLN 2 12.372 -87.465 -8.541 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.457 -86.064 -8.318 1.00 0.00 H +ATOM 30 CD GLN 2 11.784 -85.668 -9.486 1.00 0.00 C +ATOM 31 OE1 GLN 2 11.368 -85.631 -10.637 1.00 0.00 O +ATOM 32 NE2 GLN 2 11.201 -84.845 -8.633 1.00 0.00 N +ATOM 33 HE21 GLN 2 10.492 -84.248 -9.036 1.00 0.00 H +ATOM 34 HE22 GLN 2 11.466 -84.899 -7.660 1.00 0.00 H +ATOM 35 C GLN 2 16.072 -86.794 -11.472 1.00 0.00 C +ATOM 36 O GLN 2 15.915 -87.264 -12.585 1.00 0.00 O +ATOM 37 N TYR 3 17.136 -87.099 -10.748 1.00 0.00 N +ATOM 38 H TYR 3 17.085 -86.687 -9.828 1.00 0.00 H +ATOM 39 CA TYR 3 18.311 -87.773 -11.218 1.00 0.00 C +ATOM 40 HA TYR 3 18.021 -88.415 -12.049 1.00 0.00 H +ATOM 41 CB TYR 3 19.328 -86.679 -11.689 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.468 -86.079 -10.790 1.00 0.00 H +ATOM 43 HB3 TYR 3 20.306 -87.093 -11.932 1.00 0.00 H +ATOM 44 CG TYR 3 18.992 -85.864 -12.904 1.00 0.00 C +ATOM 45 CD1 TYR 3 19.033 -86.517 -14.161 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.485 -87.497 -14.197 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.569 -85.804 -15.280 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.609 -86.256 -16.260 1.00 0.00 H +ATOM 49 CZ TYR 3 18.009 -84.521 -15.132 1.00 0.00 C +ATOM 50 OH TYR 3 17.745 -83.828 -16.286 1.00 0.00 O +ATOM 51 HH TYR 3 17.637 -84.335 -17.094 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.836 -83.937 -13.881 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.336 -82.980 -13.880 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.360 -84.615 -12.779 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.204 -84.203 -11.793 1.00 0.00 H +ATOM 56 C TYR 3 18.893 -88.680 -10.144 1.00 0.00 C +ATOM 57 O TYR 3 19.111 -88.180 -8.985 1.00 0.00 O +ATOM 58 N LYS 4 19.086 -89.936 -10.371 1.00 0.00 N +ATOM 59 H LYS 4 18.893 -90.251 -11.311 1.00 0.00 H +ATOM 60 CA LYS 4 19.763 -90.830 -9.402 1.00 0.00 C +ATOM 61 HA LYS 4 19.378 -90.752 -8.385 1.00 0.00 H +ATOM 62 CB LYS 4 19.295 -92.266 -9.777 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.210 -92.396 -10.856 1.00 0.00 H +ATOM 64 HB3 LYS 4 20.030 -92.979 -9.404 1.00 0.00 H +ATOM 65 CG LYS 4 17.907 -92.713 -9.185 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.963 -92.741 -8.097 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.128 -91.986 -9.417 1.00 0.00 H +ATOM 68 CD LYS 4 17.517 -94.086 -9.732 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.544 -94.068 -10.822 1.00 0.00 H +ATOM 70 HD3 LYS 4 18.218 -94.812 -9.321 1.00 0.00 H +ATOM 71 CE LYS 4 16.067 -94.410 -9.298 1.00 0.00 C +ATOM 72 HE2 LYS 4 16.040 -94.204 -8.228 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.341 -93.735 -9.751 1.00 0.00 H +ATOM 74 NZ LYS 4 15.751 -95.839 -9.542 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.521 -96.423 -9.249 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.416 -96.087 -10.462 1.00 0.00 H +ATOM 77 HZ3 LYS 4 14.946 -96.157 -9.022 1.00 0.00 H +ATOM 78 C LYS 4 21.231 -90.770 -9.415 1.00 0.00 C +ATOM 79 O LYS 4 21.788 -90.265 -10.396 1.00 0.00 O +ATOM 80 N HX1 5 21.892 -91.064 -8.290 1.00 0.00 N +ATOM 81 CA HX1 5 23.319 -90.865 -8.075 1.00 0.00 C +ATOM 82 C HX1 5 23.721 -91.955 -7.054 1.00 0.00 C +ATOM 83 O HX1 5 23.072 -92.224 -6.040 1.00 0.00 O +ATOM 84 CB HX1 5 23.563 -89.478 -7.425 1.00 0.00 C +ATOM 85 CG HX1 5 25.073 -89.214 -7.110 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.197 -89.643 -7.785 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.391 -88.177 -6.228 1.00 0.00 N +ATOM 88 CE1 HX1 5 26.719 -88.065 -6.337 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.203 -88.919 -7.256 1.00 0.00 N +ATOM 90 H HX1 5 21.298 -91.289 -7.505 1.00 0.00 H +ATOM 91 HA HX1 5 23.925 -90.922 -8.980 1.00 0.00 H +ATOM 92 HB2 HX1 5 22.879 -89.370 -6.583 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.283 -88.622 -8.040 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.243 -90.348 -8.602 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.336 -87.573 -5.600 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.168 -88.972 -7.550 1.00 0.00 H +ATOM 97 N ILE 6 24.801 -92.645 -7.359 1.00 0.00 N +ATOM 98 H ILE 6 25.257 -92.573 -8.258 1.00 0.00 H +ATOM 99 CA ILE 6 25.255 -93.700 -6.469 1.00 0.00 C +ATOM 100 HA ILE 6 24.438 -94.314 -6.091 1.00 0.00 H +ATOM 101 CB ILE 6 26.171 -94.739 -7.178 1.00 0.00 C +ATOM 102 HB ILE 6 26.431 -95.510 -6.452 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.455 -95.481 -8.281 1.00 0.00 C +ATOM 104 HG21 ILE 6 26.095 -96.301 -8.606 1.00 0.00 H +ATOM 105 HG22 ILE 6 25.274 -94.846 -9.149 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.485 -95.780 -7.886 1.00 0.00 H +ATOM 107 CG1 ILE 6 27.397 -94.028 -7.797 1.00 0.00 C +ATOM 108 HG12 ILE 6 27.184 -93.252 -8.532 1.00 0.00 H +ATOM 109 HG13 ILE 6 27.935 -93.515 -6.999 1.00 0.00 H +ATOM 110 CD1 ILE 6 28.400 -95.011 -8.486 1.00 0.00 C +ATOM 111 HD11 ILE 6 28.127 -94.955 -9.540 1.00 0.00 H +ATOM 112 HD12 ILE 6 28.315 -96.032 -8.114 1.00 0.00 H +ATOM 113 HD13 ILE 6 29.419 -94.633 -8.407 1.00 0.00 H +ATOM 114 C ILE 6 25.835 -93.186 -5.149 1.00 0.00 C +ATOM 115 O ILE 6 26.258 -92.057 -5.123 1.00 0.00 O +ATOM 116 N VAL 7 25.777 -93.934 -4.084 1.00 0.00 N +ATOM 117 H VAL 7 25.343 -94.842 -4.001 1.00 0.00 H +ATOM 118 CA VAL 7 26.569 -93.682 -2.865 1.00 0.00 C +ATOM 119 HA VAL 7 26.357 -92.658 -2.558 1.00 0.00 H +ATOM 120 CB VAL 7 26.167 -94.775 -1.836 1.00 0.00 C +ATOM 121 HB VAL 7 25.082 -94.862 -1.783 1.00 0.00 H +ATOM 122 CG1 VAL 7 26.828 -96.070 -2.330 1.00 0.00 C +ATOM 123 HG11 VAL 7 26.423 -96.820 -1.651 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.577 -96.232 -3.379 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.909 -96.038 -2.200 1.00 0.00 H +ATOM 126 CG2 VAL 7 26.738 -94.543 -0.394 1.00 0.00 C +ATOM 127 HG21 VAL 7 26.223 -93.715 0.093 1.00 0.00 H +ATOM 128 HG22 VAL 7 26.607 -95.363 0.312 1.00 0.00 H +ATOM 129 HG23 VAL 7 27.808 -94.378 -0.521 1.00 0.00 H +ATOM 130 C VAL 7 28.097 -93.659 -3.164 1.00 0.00 C +ATOM 131 O VAL 7 28.471 -94.184 -4.223 1.00 0.00 O +ATOM 132 N ASN 8 28.913 -92.962 -2.355 1.00 0.00 N +ATOM 133 H ASN 8 28.503 -92.549 -1.529 1.00 0.00 H +ATOM 134 CA ASN 8 30.299 -92.908 -2.810 1.00 0.00 C +ATOM 135 HA ASN 8 30.317 -92.731 -3.885 1.00 0.00 H +ATOM 136 CB ASN 8 30.983 -91.676 -2.189 1.00 0.00 C +ATOM 137 HB2 ASN 8 30.285 -90.839 -2.146 1.00 0.00 H +ATOM 138 HB3 ASN 8 31.190 -91.820 -1.129 1.00 0.00 H +ATOM 139 CG ASN 8 32.266 -91.262 -2.831 1.00 0.00 C +ATOM 140 OD1 ASN 8 33.317 -91.616 -2.417 1.00 0.00 O +ATOM 141 ND2 ASN 8 32.208 -90.346 -3.823 1.00 0.00 N +ATOM 142 HD21 ASN 8 31.269 -90.021 -4.002 1.00 0.00 H +ATOM 143 HD22 ASN 8 33.045 -89.866 -4.121 1.00 0.00 H +ATOM 144 C ASN 8 31.131 -94.221 -2.587 1.00 0.00 C +ATOM 145 O ASN 8 31.942 -94.568 -3.467 1.00 0.00 O +ATOM 146 N GLY 9 30.928 -95.098 -1.597 1.00 0.00 N +ATOM 147 H GLY 9 30.142 -94.866 -1.007 1.00 0.00 H +ATOM 148 CA GLY 9 31.767 -96.306 -1.329 1.00 0.00 C +ATOM 149 HA2 GLY 9 32.836 -96.096 -1.334 1.00 0.00 H +ATOM 150 HA3 GLY 9 31.530 -96.685 -0.335 1.00 0.00 H +ATOM 151 C GLY 9 31.508 -97.421 -2.362 1.00 0.00 C +ATOM 152 O GLY 9 30.364 -97.687 -2.711 1.00 0.00 O +ATOM 153 N LYS 10 32.536 -97.943 -3.016 1.00 0.00 N +ATOM 154 H LYS 10 33.443 -97.542 -2.822 1.00 0.00 H +ATOM 155 CA LYS 10 32.372 -98.827 -4.213 1.00 0.00 C +ATOM 156 HA LYS 10 31.504 -98.467 -4.766 1.00 0.00 H +ATOM 157 CB LYS 10 33.584 -98.722 -5.069 1.00 0.00 C +ATOM 158 HB2 LYS 10 34.406 -99.161 -4.505 1.00 0.00 H +ATOM 159 HB3 LYS 10 33.476 -99.309 -5.980 1.00 0.00 H +ATOM 160 CG LYS 10 34.050 -97.302 -5.538 1.00 0.00 C +ATOM 161 HG2 LYS 10 34.411 -96.683 -4.717 1.00 0.00 H +ATOM 162 HG3 LYS 10 34.990 -97.422 -6.077 1.00 0.00 H +ATOM 163 CD LYS 10 33.057 -96.484 -6.378 1.00 0.00 C +ATOM 164 HD2 LYS 10 32.772 -97.176 -7.170 1.00 0.00 H +ATOM 165 HD3 LYS 10 32.097 -96.342 -5.881 1.00 0.00 H +ATOM 166 CE LYS 10 33.486 -95.098 -6.779 1.00 0.00 C +ATOM 167 HE2 LYS 10 34.424 -95.265 -7.308 1.00 0.00 H +ATOM 168 HE3 LYS 10 32.836 -94.676 -7.545 1.00 0.00 H +ATOM 169 NZ LYS 10 33.717 -94.146 -5.658 1.00 0.00 N +ATOM 170 HZ1 LYS 10 34.019 -93.265 -6.051 1.00 0.00 H +ATOM 171 HZ2 LYS 10 34.446 -94.545 -5.085 1.00 0.00 H +ATOM 172 HZ3 LYS 10 32.940 -93.947 -5.045 1.00 0.00 H +ATOM 173 C LYS 10 31.994-100.261 -3.878 1.00 0.00 C +ATOM 174 O LYS 10 31.485-101.031 -4.675 1.00 0.00 O +ATOM 175 N THR 11 32.122-100.685 -2.602 1.00 0.00 N +ATOM 176 H THR 11 32.544 -99.963 -2.037 1.00 0.00 H +ATOM 177 CA THR 11 31.408-101.825 -1.972 1.00 0.00 C +ATOM 178 HA THR 11 31.347-102.602 -2.735 1.00 0.00 H +ATOM 179 CB THR 11 32.268-102.429 -0.847 1.00 0.00 C +ATOM 180 HB THR 11 32.226-101.779 0.027 1.00 0.00 H +ATOM 181 CG2 THR 11 31.711-103.770 -0.331 1.00 0.00 C +ATOM 182 HG21 THR 11 32.416-104.189 0.387 1.00 0.00 H +ATOM 183 HG22 THR 11 31.501-104.526 -1.088 1.00 0.00 H +ATOM 184 HG23 THR 11 30.764-103.681 0.201 1.00 0.00 H +ATOM 185 OG1 THR 11 33.481-102.789 -1.332 1.00 0.00 O +ATOM 186 HG1 THR 11 33.962-101.958 -1.333 1.00 0.00 H +ATOM 187 C THR 11 29.920-101.519 -1.603 1.00 0.00 C +ATOM 188 O THR 11 29.125-102.425 -1.678 1.00 0.00 O +ATOM 189 N LEU 12 29.600-100.298 -1.142 1.00 0.00 N +ATOM 190 H LEU 12 30.315 -99.584 -1.145 1.00 0.00 H +ATOM 191 CA LEU 12 28.324-100.009 -0.485 1.00 0.00 C +ATOM 192 HA LEU 12 28.116-100.724 0.311 1.00 0.00 H +ATOM 193 CB LEU 12 28.313 -98.628 0.150 1.00 0.00 C +ATOM 194 HB2 LEU 12 28.802 -98.005 -0.599 1.00 0.00 H +ATOM 195 HB3 LEU 12 27.315 -98.200 0.248 1.00 0.00 H +ATOM 196 CG LEU 12 29.162 -98.539 1.397 1.00 0.00 C +ATOM 197 HG LEU 12 30.199 -98.827 1.228 1.00 0.00 H +ATOM 198 CD1 LEU 12 29.111 -97.086 1.900 1.00 0.00 C +ATOM 199 HD11 LEU 12 29.699 -96.427 1.262 1.00 0.00 H +ATOM 200 HD12 LEU 12 29.685 -97.039 2.825 1.00 0.00 H +ATOM 201 HD13 LEU 12 28.052 -96.834 1.958 1.00 0.00 H +ATOM 202 CD2 LEU 12 28.546 -99.424 2.518 1.00 0.00 C +ATOM 203 HD21 LEU 12 28.935 -99.146 3.498 1.00 0.00 H +ATOM 204 HD22 LEU 12 28.712-100.497 2.421 1.00 0.00 H +ATOM 205 HD23 LEU 12 27.470 -99.336 2.669 1.00 0.00 H +ATOM 206 C LEU 12 27.112-100.093 -1.506 1.00 0.00 C +ATOM 207 O LEU 12 26.055-100.674 -1.211 1.00 0.00 O +ATOM 208 N LYS 13 27.289 -99.702 -2.743 1.00 0.00 N +ATOM 209 H LYS 13 28.239 -99.425 -2.945 1.00 0.00 H +ATOM 210 CA LYS 13 26.341 -99.834 -3.955 1.00 0.00 C +ATOM 211 HA LYS 13 26.836 -99.343 -4.792 1.00 0.00 H +ATOM 212 CB LYS 13 26.306-101.332 -4.279 1.00 0.00 C +ATOM 213 HB2 LYS 13 26.029-101.894 -3.386 1.00 0.00 H +ATOM 214 HB3 LYS 13 25.534-101.491 -5.032 1.00 0.00 H +ATOM 215 CG LYS 13 27.642-101.923 -4.771 1.00 0.00 C +ATOM 216 HG2 LYS 13 28.095-101.301 -5.542 1.00 0.00 H +ATOM 217 HG3 LYS 13 28.453-101.944 -4.043 1.00 0.00 H +ATOM 218 CD LYS 13 27.341-103.304 -5.332 1.00 0.00 C +ATOM 219 HD2 LYS 13 26.575-103.228 -6.103 1.00 0.00 H +ATOM 220 HD3 LYS 13 28.285-103.605 -5.788 1.00 0.00 H +ATOM 221 CE LYS 13 26.970-104.363 -4.267 1.00 0.00 C +ATOM 222 HE2 LYS 13 25.962-104.211 -3.881 1.00 0.00 H +ATOM 223 HE3 LYS 13 26.925-105.261 -4.884 1.00 0.00 H +ATOM 224 NZ LYS 13 27.950-104.519 -3.205 1.00 0.00 N +ATOM 225 HZ1 LYS 13 28.839-104.834 -3.565 1.00 0.00 H +ATOM 226 HZ2 LYS 13 27.672-105.193 -2.506 1.00 0.00 H +ATOM 227 HZ3 LYS 13 28.180-103.670 -2.708 1.00 0.00 H +ATOM 228 C LYS 13 24.936 -99.184 -3.798 1.00 0.00 C +ATOM 229 O LYS 13 24.202 -99.164 -4.740 1.00 0.00 O +ATOM 230 N GLY 14 24.586 -98.668 -2.652 1.00 0.00 N +ATOM 231 H GLY 14 25.267 -98.781 -1.915 1.00 0.00 H +ATOM 232 CA GLY 14 23.301 -97.988 -2.482 1.00 0.00 C +ATOM 233 HA2 GLY 14 22.550 -98.746 -2.704 1.00 0.00 H +ATOM 234 HA3 GLY 14 23.052 -97.814 -1.435 1.00 0.00 H +ATOM 235 C GLY 14 23.056 -96.736 -3.405 1.00 0.00 C +ATOM 236 O GLY 14 24.023 -96.090 -3.888 1.00 0.00 O +ATOM 237 N VAL 15 21.770 -96.334 -3.572 1.00 0.00 N +ATOM 238 H VAL 15 21.014 -96.794 -3.085 1.00 0.00 H +ATOM 239 CA VAL 15 21.434 -95.170 -4.425 1.00 0.00 C +ATOM 240 HA VAL 15 22.293 -94.527 -4.616 1.00 0.00 H +ATOM 241 CB VAL 15 20.641 -95.679 -5.780 1.00 0.00 C +ATOM 242 HB VAL 15 19.817 -96.354 -5.547 1.00 0.00 H +ATOM 243 CG1 VAL 15 20.293 -94.603 -6.769 1.00 0.00 C +ATOM 244 HG11 VAL 15 21.145 -93.958 -6.985 1.00 0.00 H +ATOM 245 HG12 VAL 15 19.889 -95.003 -7.698 1.00 0.00 H +ATOM 246 HG13 VAL 15 19.463 -94.041 -6.341 1.00 0.00 H +ATOM 247 CG2 VAL 15 21.662 -96.600 -6.523 1.00 0.00 C +ATOM 248 HG21 VAL 15 21.681 -97.553 -5.994 1.00 0.00 H +ATOM 249 HG22 VAL 15 21.350 -96.743 -7.558 1.00 0.00 H +ATOM 250 HG23 VAL 15 22.705 -96.299 -6.428 1.00 0.00 H +ATOM 251 C VAL 15 20.483 -94.208 -3.693 1.00 0.00 C +ATOM 252 O VAL 15 19.622 -94.538 -2.872 1.00 0.00 O +ATOM 253 N HY1 16 20.563 -92.988 -4.195 1.00 0.00 N +ATOM 254 CA HY1 16 19.755 -91.836 -3.717 1.00 0.00 C +ATOM 255 C HY1 16 19.546 -90.904 -5.011 1.00 0.00 C +ATOM 256 O HY1 16 20.203 -91.106 -6.041 1.00 0.00 O +ATOM 257 CB HY1 16 20.449 -90.956 -2.572 1.00 0.00 C +ATOM 258 CG HY1 16 21.810 -90.503 -2.958 1.00 0.00 C +ATOM 259 CD2 HY1 16 22.277 -89.202 -3.152 1.00 0.00 C +ATOM 260 ND1 HY1 16 22.927 -91.297 -3.056 1.00 0.00 N +ATOM 261 CE1 HY1 16 23.957 -90.518 -3.401 1.00 0.00 C +ATOM 262 NE2 HY1 16 23.642 -89.198 -3.526 1.00 0.00 N +ATOM 263 H HY1 16 21.265 -92.733 -4.874 1.00 0.00 H +ATOM 264 HA HY1 16 18.847 -92.360 -3.420 1.00 0.00 H +ATOM 265 HB2 HY1 16 19.807 -90.106 -2.340 1.00 0.00 H +ATOM 266 HB3 HY1 16 20.502 -91.541 -1.654 1.00 0.00 H +ATOM 267 HD1 HY1 16 22.905 -92.260 -2.754 1.00 0.00 H +ATOM 268 HD2 HY1 16 21.702 -88.288 -3.182 1.00 0.00 H +ATOM 269 HE1 HY1 16 24.975 -90.881 -3.412 1.00 0.00 H +ATOM 270 N THR 17 18.624 -89.926 -4.910 1.00 0.00 N +ATOM 271 H THR 17 18.265 -89.873 -3.968 1.00 0.00 H +ATOM 272 CA THR 17 18.106 -88.927 -5.887 1.00 0.00 C +ATOM 273 HA THR 17 18.662 -89.089 -6.810 1.00 0.00 H +ATOM 274 CB THR 17 16.679 -89.423 -6.244 1.00 0.00 C +ATOM 275 HB THR 17 16.169 -89.567 -5.292 1.00 0.00 H +ATOM 276 CG2 THR 17 15.809 -88.605 -7.113 1.00 0.00 C +ATOM 277 HG21 THR 17 14.763 -88.879 -6.971 1.00 0.00 H +ATOM 278 HG22 THR 17 16.162 -88.596 -8.144 1.00 0.00 H +ATOM 279 HG23 THR 17 15.898 -87.545 -6.875 1.00 0.00 H +ATOM 280 OG1 THR 17 16.616 -90.622 -6.811 1.00 0.00 O +ATOM 281 HG1 THR 17 16.850 -91.292 -6.164 1.00 0.00 H +ATOM 282 C THR 17 18.174 -87.450 -5.640 1.00 0.00 C +ATOM 283 O THR 17 17.535 -86.924 -4.717 1.00 0.00 O +ATOM 284 N HY2 18 18.759 -86.697 -6.598 1.00 0.00 N +ATOM 285 CA HY2 18 18.803 -85.191 -6.773 1.00 0.00 C +ATOM 286 C HY2 18 17.761 -84.715 -7.873 1.00 0.00 C +ATOM 287 O HY2 18 16.980 -85.461 -8.438 1.00 0.00 O +ATOM 288 CB HY2 18 20.236 -84.798 -7.164 1.00 0.00 C +ATOM 289 CG HY2 18 21.266 -85.243 -6.241 1.00 0.00 C +ATOM 290 CD2 HY2 18 22.048 -86.344 -6.304 1.00 0.00 C +ATOM 291 ND1 HY2 18 21.564 -84.690 -4.987 1.00 0.00 N +ATOM 292 CE1 HY2 18 22.443 -85.437 -4.323 1.00 0.00 C +ATOM 293 NE2 HY2 18 22.705 -86.474 -5.098 1.00 0.00 N +ATOM 294 H HY2 18 19.086 -87.189 -7.417 1.00 0.00 H +ATOM 295 HA HY2 18 18.572 -84.773 -5.793 1.00 0.00 H +ATOM 296 HB2 HY2 18 20.398 -85.331 -8.101 1.00 0.00 H +ATOM 297 HB3 HY2 18 20.265 -83.755 -7.480 1.00 0.00 H +ATOM 298 HD1 HY2 18 21.111 -83.882 -4.585 1.00 0.00 H +ATOM 299 HD2 HY2 18 22.097 -86.971 -7.181 1.00 0.00 H +ATOM 300 HE1 HY2 18 22.755 -85.273 -3.302 1.00 0.00 H +ATOM 301 N GLU 19 17.620 -83.412 -8.072 1.00 0.00 N +ATOM 302 H GLU 19 17.909 -82.838 -7.293 1.00 0.00 H +ATOM 303 CA GLU 19 16.617 -82.815 -9.051 1.00 0.00 C +ATOM 304 HA GLU 19 16.452 -83.509 -9.876 1.00 0.00 H +ATOM 305 CB GLU 19 15.291 -82.627 -8.277 1.00 0.00 C +ATOM 306 HB2 GLU 19 15.233 -83.569 -7.731 1.00 0.00 H +ATOM 307 HB3 GLU 19 15.356 -81.749 -7.634 1.00 0.00 H +ATOM 308 CG GLU 19 14.001 -82.410 -9.133 1.00 0.00 C +ATOM 309 HG2 GLU 19 14.032 -83.056 -10.011 1.00 0.00 H +ATOM 310 HG3 GLU 19 13.058 -82.660 -8.646 1.00 0.00 H +ATOM 311 CD GLU 19 13.982 -80.932 -9.619 1.00 0.00 C +ATOM 312 OE1 GLU 19 13.836 -80.678 -10.827 1.00 0.00 O +ATOM 313 OE2 GLU 19 14.122 -79.979 -8.804 1.00 0.00 O +ATOM 314 C GLU 19 17.332 -81.605 -9.695 1.00 0.00 C +ATOM 315 O GLU 19 17.887 -80.742 -8.944 1.00 0.00 O +ATOM 316 N ALA 20 17.270 -81.314 -11.015 1.00 0.00 N +ATOM 317 H ALA 20 16.686 -81.887 -11.607 1.00 0.00 H +ATOM 318 CA ALA 20 17.722 -80.133 -11.780 1.00 0.00 C +ATOM 319 HA ALA 20 17.617 -79.235 -11.171 1.00 0.00 H +ATOM 320 CB ALA 20 19.244 -80.152 -12.150 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.711 -80.193 -11.167 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.553 -79.270 -12.711 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.517 -81.070 -12.672 1.00 0.00 H +ATOM 324 C ALA 20 16.793 -79.923 -13.019 1.00 0.00 C +ATOM 325 O ALA 20 16.205 -80.873 -13.482 1.00 0.00 O +ATOM 326 N VAL 21 16.780 -78.802 -13.622 1.00 0.00 N +ATOM 327 H VAL 21 17.330 -78.066 -13.204 1.00 0.00 H +ATOM 328 CA VAL 21 16.167 -78.638 -14.960 1.00 0.00 C +ATOM 329 HA VAL 21 15.153 -79.020 -14.843 1.00 0.00 H +ATOM 330 CB VAL 21 16.189 -77.213 -15.402 1.00 0.00 C +ATOM 331 HB VAL 21 15.661 -76.531 -14.736 1.00 0.00 H +ATOM 332 CG1 VAL 21 17.686 -76.670 -15.361 1.00 0.00 C +ATOM 333 HG11 VAL 21 18.417 -77.210 -14.760 1.00 0.00 H +ATOM 334 HG12 VAL 21 17.676 -75.641 -15.003 1.00 0.00 H +ATOM 335 HG13 VAL 21 18.150 -76.702 -16.347 1.00 0.00 H +ATOM 336 CG2 VAL 21 15.525 -77.006 -16.731 1.00 0.00 C +ATOM 337 HG21 VAL 21 14.486 -77.337 -16.711 1.00 0.00 H +ATOM 338 HG22 VAL 21 16.141 -77.451 -17.513 1.00 0.00 H +ATOM 339 HG23 VAL 21 15.550 -75.929 -16.891 1.00 0.00 H +ATOM 340 C VAL 21 16.844 -79.554 -16.010 1.00 0.00 C +ATOM 341 O VAL 21 16.171 -79.894 -16.982 1.00 0.00 O +ATOM 342 N ASP 22 18.133 -79.936 -15.925 1.00 0.00 N +ATOM 343 H ASP 22 18.678 -79.621 -15.136 1.00 0.00 H +ATOM 344 CA ASP 22 18.932 -80.377 -17.057 1.00 0.00 C +ATOM 345 HA ASP 22 18.311 -80.935 -17.758 1.00 0.00 H +ATOM 346 CB ASP 22 19.491 -79.060 -17.707 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.655 -78.364 -17.786 1.00 0.00 H +ATOM 348 HB3 ASP 22 20.245 -78.649 -17.037 1.00 0.00 H +ATOM 349 CG ASP 22 20.190 -79.219 -19.079 1.00 0.00 C +ATOM 350 OD1 ASP 22 20.835 -80.258 -19.333 1.00 0.00 O +ATOM 351 OD2 ASP 22 20.167 -78.287 -19.875 1.00 0.00 O +ATOM 352 C ASP 22 20.068 -81.342 -16.546 1.00 0.00 C +ATOM 353 O ASP 22 20.686 -80.974 -15.529 1.00 0.00 O +ATOM 354 N ALA 23 20.418 -82.450 -17.253 1.00 0.00 N +ATOM 355 H ALA 23 19.805 -82.600 -18.041 1.00 0.00 H +ATOM 356 CA ALA 23 21.569 -83.267 -17.004 1.00 0.00 C +ATOM 357 HA ALA 23 21.438 -83.669 -15.999 1.00 0.00 H +ATOM 358 CB ALA 23 21.633 -84.343 -18.118 1.00 0.00 C +ATOM 359 HB1 ALA 23 20.838 -85.083 -18.026 1.00 0.00 H +ATOM 360 HB2 ALA 23 22.588 -84.864 -18.050 1.00 0.00 H +ATOM 361 HB3 ALA 23 21.541 -83.910 -19.114 1.00 0.00 H +ATOM 362 C ALA 23 22.923 -82.321 -16.998 1.00 0.00 C +ATOM 363 O ALA 23 23.927 -82.653 -16.384 1.00 0.00 O +ATOM 364 N ALA 24 22.925 -81.181 -17.657 1.00 0.00 N +ATOM 365 H ALA 24 22.173 -80.961 -18.295 1.00 0.00 H +ATOM 366 CA ALA 24 24.095 -80.307 -17.800 1.00 0.00 C +ATOM 367 HA ALA 24 24.952 -80.979 -17.764 1.00 0.00 H +ATOM 368 CB ALA 24 23.920 -79.460 -19.054 1.00 0.00 C +ATOM 369 HB1 ALA 24 24.781 -78.817 -19.235 1.00 0.00 H +ATOM 370 HB2 ALA 24 22.995 -78.885 -19.009 1.00 0.00 H +ATOM 371 HB3 ALA 24 23.707 -80.030 -19.958 1.00 0.00 H +ATOM 372 C ALA 24 24.228 -79.358 -16.511 1.00 0.00 C +ATOM 373 O ALA 24 25.308 -79.004 -16.070 1.00 0.00 O +ATOM 374 N GLU 25 23.101 -79.141 -15.883 1.00 0.00 N +ATOM 375 H GLU 25 22.264 -79.529 -16.294 1.00 0.00 H +ATOM 376 CA GLU 25 23.138 -78.485 -14.564 1.00 0.00 C +ATOM 377 HA GLU 25 23.921 -77.735 -14.678 1.00 0.00 H +ATOM 378 CB GLU 25 21.773 -77.926 -14.231 1.00 0.00 C +ATOM 379 HB2 GLU 25 20.973 -78.644 -14.411 1.00 0.00 H +ATOM 380 HB3 GLU 25 21.760 -77.733 -13.158 1.00 0.00 H +ATOM 381 CG GLU 25 21.459 -76.578 -14.949 1.00 0.00 C +ATOM 382 HG2 GLU 25 21.322 -76.730 -16.020 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.596 -76.097 -14.489 1.00 0.00 H +ATOM 384 CD GLU 25 22.567 -75.544 -14.820 1.00 0.00 C +ATOM 385 OE1 GLU 25 23.326 -75.512 -13.800 1.00 0.00 O +ATOM 386 OE2 GLU 25 22.908 -74.913 -15.824 1.00 0.00 O +ATOM 387 C GLU 25 23.572 -79.485 -13.501 1.00 0.00 C +ATOM 388 O GLU 25 24.475 -79.255 -12.660 1.00 0.00 O +ATOM 389 N ALA 26 23.047 -80.709 -13.557 1.00 0.00 N +ATOM 390 H ALA 26 22.397 -80.907 -14.304 1.00 0.00 H +ATOM 391 CA ALA 26 23.261 -81.814 -12.679 1.00 0.00 C +ATOM 392 HA ALA 26 23.121 -81.591 -11.622 1.00 0.00 H +ATOM 393 CB ALA 26 22.203 -82.819 -13.179 1.00 0.00 C +ATOM 394 HB1 ALA 26 22.451 -83.186 -14.175 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.263 -82.268 -13.219 1.00 0.00 H +ATOM 396 HB3 ALA 26 22.118 -83.590 -12.413 1.00 0.00 H +ATOM 397 C ALA 26 24.681 -82.371 -12.822 1.00 0.00 C +ATOM 398 O ALA 26 25.192 -82.998 -11.887 1.00 0.00 O +ATOM 399 N GLU 27 25.438 -82.098 -13.914 1.00 0.00 N +ATOM 400 H GLU 27 24.963 -81.828 -14.764 1.00 0.00 H +ATOM 401 CA GLU 27 26.839 -82.385 -14.000 1.00 0.00 C +ATOM 402 HA GLU 27 27.068 -83.361 -13.572 1.00 0.00 H +ATOM 403 CB GLU 27 27.124 -82.428 -15.491 1.00 0.00 C +ATOM 404 HB2 GLU 27 26.577 -83.300 -15.850 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.682 -81.513 -15.886 1.00 0.00 H +ATOM 406 CG GLU 27 28.623 -82.540 -15.868 1.00 0.00 C +ATOM 407 HG2 GLU 27 29.186 -81.784 -15.321 1.00 0.00 H +ATOM 408 HG3 GLU 27 29.128 -83.379 -15.390 1.00 0.00 H +ATOM 409 CD GLU 27 28.974 -82.413 -17.386 1.00 0.00 C +ATOM 410 OE1 GLU 27 28.663 -83.350 -18.204 1.00 0.00 O +ATOM 411 OE2 GLU 27 29.475 -81.343 -17.812 1.00 0.00 O +ATOM 412 C GLU 27 27.719 -81.366 -13.222 1.00 0.00 C +ATOM 413 O GLU 27 28.583 -81.709 -12.430 1.00 0.00 O +ATOM 414 N LYS 28 27.352 -80.136 -13.403 1.00 0.00 N +ATOM 415 H LYS 28 26.676 -79.933 -14.125 1.00 0.00 H +ATOM 416 CA LYS 28 28.037 -78.942 -12.746 1.00 0.00 C +ATOM 417 HA LYS 28 29.107 -79.073 -12.909 1.00 0.00 H +ATOM 418 CB LYS 28 27.543 -77.626 -13.441 1.00 0.00 C +ATOM 419 HB2 LYS 28 26.454 -77.572 -13.421 1.00 0.00 H +ATOM 420 HB3 LYS 28 27.704 -76.719 -12.858 1.00 0.00 H +ATOM 421 CG LYS 28 28.194 -77.303 -14.799 1.00 0.00 C +ATOM 422 HG2 LYS 28 29.270 -77.133 -14.754 1.00 0.00 H +ATOM 423 HG3 LYS 28 28.051 -78.089 -15.541 1.00 0.00 H +ATOM 424 CD LYS 28 27.652 -76.060 -15.405 1.00 0.00 C +ATOM 425 HD2 LYS 28 27.989 -75.238 -14.773 1.00 0.00 H +ATOM 426 HD3 LYS 28 28.142 -75.989 -16.376 1.00 0.00 H +ATOM 427 CE LYS 28 26.127 -76.053 -15.800 1.00 0.00 C +ATOM 428 HE2 LYS 28 25.930 -76.784 -16.584 1.00 0.00 H +ATOM 429 HE3 LYS 28 25.567 -76.445 -14.951 1.00 0.00 H +ATOM 430 NZ LYS 28 25.683 -74.739 -16.287 1.00 0.00 N +ATOM 431 HZ1 LYS 28 26.057 -74.531 -17.202 1.00 0.00 H +ATOM 432 HZ2 LYS 28 25.994 -74.014 -15.656 1.00 0.00 H +ATOM 433 HZ3 LYS 28 24.684 -74.615 -16.210 1.00 0.00 H +ATOM 434 C LYS 28 27.814 -79.048 -11.191 1.00 0.00 C +ATOM 435 O LYS 28 28.737 -78.802 -10.422 1.00 0.00 O +ATOM 436 N PHE 29 26.655 -79.461 -10.761 1.00 0.00 N +ATOM 437 H PHE 29 25.903 -79.580 -11.425 1.00 0.00 H +ATOM 438 CA PHE 29 26.347 -79.554 -9.316 1.00 0.00 C +ATOM 439 HA PHE 29 26.818 -78.719 -8.797 1.00 0.00 H +ATOM 440 CB PHE 29 24.820 -79.546 -9.123 1.00 0.00 C +ATOM 441 HB2 PHE 29 24.295 -80.387 -9.576 1.00 0.00 H +ATOM 442 HB3 PHE 29 24.584 -79.678 -8.067 1.00 0.00 H +ATOM 443 CG PHE 29 24.027 -78.297 -9.438 1.00 0.00 C +ATOM 444 CD1 PHE 29 24.575 -77.089 -9.013 1.00 0.00 C +ATOM 445 HD1 PHE 29 25.313 -77.097 -8.224 1.00 0.00 H +ATOM 446 CE1 PHE 29 23.943 -75.869 -9.324 1.00 0.00 C +ATOM 447 HE1 PHE 29 24.297 -74.891 -9.034 1.00 0.00 H +ATOM 448 CZ PHE 29 22.720 -75.863 -10.020 1.00 0.00 C +ATOM 449 HZ PHE 29 22.135 -74.976 -10.212 1.00 0.00 H +ATOM 450 CE2 PHE 29 22.151 -77.096 -10.396 1.00 0.00 C +ATOM 451 HE2 PHE 29 21.151 -77.104 -10.804 1.00 0.00 H +ATOM 452 CD2 PHE 29 22.801 -78.323 -10.114 1.00 0.00 C +ATOM 453 HD2 PHE 29 22.417 -79.274 -10.454 1.00 0.00 H +ATOM 454 C PHE 29 26.924 -80.834 -8.678 1.00 0.00 C +ATOM 455 O PHE 29 27.403 -80.777 -7.586 1.00 0.00 O +ATOM 456 N THR 30 26.921 -81.901 -9.421 1.00 0.00 N +ATOM 457 H THR 30 26.589 -81.849 -10.374 1.00 0.00 H +ATOM 458 CA THR 30 27.516 -83.208 -8.955 1.00 0.00 C +ATOM 459 HA THR 30 27.046 -83.516 -8.021 1.00 0.00 H +ATOM 460 CB THR 30 27.284 -84.230 -10.031 1.00 0.00 C +ATOM 461 HB THR 30 27.678 -83.824 -10.962 1.00 0.00 H +ATOM 462 CG2 THR 30 28.046 -85.638 -9.719 1.00 0.00 C +ATOM 463 HG21 THR 30 28.143 -85.872 -8.659 1.00 0.00 H +ATOM 464 HG22 THR 30 27.690 -86.417 -10.393 1.00 0.00 H +ATOM 465 HG23 THR 30 29.070 -85.597 -10.090 1.00 0.00 H +ATOM 466 OG1 THR 30 25.905 -84.509 -10.173 1.00 0.00 O +ATOM 467 HG1 THR 30 25.456 -84.055 -10.890 1.00 0.00 H +ATOM 468 C THR 30 29.030 -83.045 -8.703 1.00 0.00 C +ATOM 469 O THR 30 29.579 -83.387 -7.646 1.00 0.00 O +ATOM 470 N LYS 31 29.738 -82.356 -9.547 1.00 0.00 N +ATOM 471 H LYS 31 29.317 -82.227 -10.456 1.00 0.00 H +ATOM 472 CA LYS 31 31.180 -81.947 -9.307 1.00 0.00 C +ATOM 473 HA LYS 31 31.801 -82.816 -9.090 1.00 0.00 H +ATOM 474 CB LYS 31 31.721 -81.356 -10.638 1.00 0.00 C +ATOM 475 HB2 LYS 31 30.931 -80.720 -11.036 1.00 0.00 H +ATOM 476 HB3 LYS 31 32.724 -80.948 -10.515 1.00 0.00 H +ATOM 477 CG LYS 31 31.813 -82.530 -11.653 1.00 0.00 C +ATOM 478 HG2 LYS 31 32.647 -83.219 -11.517 1.00 0.00 H +ATOM 479 HG3 LYS 31 30.929 -83.164 -11.593 1.00 0.00 H +ATOM 480 CD LYS 31 32.112 -82.036 -13.148 1.00 0.00 C +ATOM 481 HD2 LYS 31 31.525 -81.119 -13.204 1.00 0.00 H +ATOM 482 HD3 LYS 31 33.200 -82.013 -13.204 1.00 0.00 H +ATOM 483 CE LYS 31 31.616 -83.017 -14.212 1.00 0.00 C +ATOM 484 HE2 LYS 31 30.555 -83.223 -14.071 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.605 -82.644 -15.236 1.00 0.00 H +ATOM 486 NZ LYS 31 32.390 -84.321 -14.251 1.00 0.00 N +ATOM 487 HZ1 LYS 31 33.389 -84.208 -14.348 1.00 0.00 H +ATOM 488 HZ2 LYS 31 32.108 -84.897 -15.031 1.00 0.00 H +ATOM 489 HZ3 LYS 31 32.256 -84.800 -13.373 1.00 0.00 H +ATOM 490 C LYS 31 31.396 -80.848 -8.206 1.00 0.00 C +ATOM 491 O LYS 31 32.371 -80.940 -7.495 1.00 0.00 O +ATOM 492 N ALA 32 30.384 -80.065 -7.962 1.00 0.00 N +ATOM 493 H ALA 32 29.657 -80.058 -8.662 1.00 0.00 H +ATOM 494 CA ALA 32 30.432 -78.974 -7.003 1.00 0.00 C +ATOM 495 HA ALA 32 31.459 -78.611 -6.970 1.00 0.00 H +ATOM 496 CB ALA 32 29.390 -77.889 -7.301 1.00 0.00 C +ATOM 497 HB1 ALA 32 29.341 -77.626 -8.357 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.430 -78.233 -6.915 1.00 0.00 H +ATOM 499 HB3 ALA 32 29.596 -77.024 -6.670 1.00 0.00 H +ATOM 500 C ALA 32 30.301 -79.588 -5.585 1.00 0.00 C +ATOM 501 O ALA 32 30.914 -79.110 -4.636 1.00 0.00 O +ATOM 502 N ASP 33 29.480 -80.590 -5.385 1.00 0.00 N +ATOM 503 H ASP 33 28.933 -81.013 -6.121 1.00 0.00 H +ATOM 504 CA ASP 33 29.354 -81.209 -4.042 1.00 0.00 C +ATOM 505 HA ASP 33 29.290 -80.371 -3.348 1.00 0.00 H +ATOM 506 CB ASP 33 28.085 -82.035 -3.903 1.00 0.00 C +ATOM 507 HB2 ASP 33 28.001 -82.713 -4.752 1.00 0.00 H +ATOM 508 HB3 ASP 33 28.272 -82.659 -3.029 1.00 0.00 H +ATOM 509 CG ASP 33 26.805 -81.212 -3.806 1.00 0.00 C +ATOM 510 OD1 ASP 33 26.832 -79.971 -3.607 1.00 0.00 O +ATOM 511 OD2 ASP 33 25.698 -81.796 -3.801 1.00 0.00 O +ATOM 512 C ASP 33 30.593 -81.992 -3.683 1.00 0.00 C +ATOM 513 O ASP 33 31.024 -81.932 -2.510 1.00 0.00 O +ATOM 514 N ALA 34 31.174 -82.728 -4.664 1.00 0.00 N +ATOM 515 H ALA 34 30.691 -82.802 -5.548 1.00 0.00 H +ATOM 516 CA ALA 34 32.464 -83.379 -4.446 1.00 0.00 C +ATOM 517 HA ALA 34 32.430 -84.077 -3.609 1.00 0.00 H +ATOM 518 CB ALA 34 32.933 -84.108 -5.688 1.00 0.00 C +ATOM 519 HB1 ALA 34 32.505 -85.110 -5.667 1.00 0.00 H +ATOM 520 HB2 ALA 34 33.998 -84.331 -5.626 1.00 0.00 H +ATOM 521 HB3 ALA 34 32.613 -83.671 -6.634 1.00 0.00 H +ATOM 522 C ALA 34 33.442 -82.363 -3.965 1.00 0.00 C +ATOM 523 O ALA 34 34.204 -82.594 -2.970 1.00 0.00 O +ATOM 524 N ASN 35 33.472 -81.171 -4.570 1.00 0.00 N +ATOM 525 H ASN 35 32.668 -80.895 -5.115 1.00 0.00 H +ATOM 526 CA ASN 35 34.434 -80.124 -4.211 1.00 0.00 C +ATOM 527 HA ASN 35 35.457 -80.496 -4.155 1.00 0.00 H +ATOM 528 CB ASN 35 34.437 -79.041 -5.301 1.00 0.00 C +ATOM 529 HB2 ASN 35 34.769 -79.393 -6.278 1.00 0.00 H +ATOM 530 HB3 ASN 35 33.505 -78.479 -5.248 1.00 0.00 H +ATOM 531 CG ASN 35 35.554 -78.147 -4.865 1.00 0.00 C +ATOM 532 OD1 ASN 35 36.708 -78.466 -4.769 1.00 0.00 O +ATOM 533 ND2 ASN 35 35.274 -76.837 -4.638 1.00 0.00 N +ATOM 534 HD21 ASN 35 34.364 -76.437 -4.815 1.00 0.00 H +ATOM 535 HD22 ASN 35 35.970 -76.226 -4.236 1.00 0.00 H +ATOM 536 C ASN 35 34.098 -79.475 -2.887 1.00 0.00 C +ATOM 537 O ASN 35 35.068 -79.199 -2.198 1.00 0.00 O +ATOM 538 N ASP 36 32.793 -79.365 -2.410 1.00 0.00 N +ATOM 539 H ASP 36 32.145 -79.625 -3.140 1.00 0.00 H +ATOM 540 CA ASP 36 32.380 -79.060 -1.026 1.00 0.00 C +ATOM 541 HA ASP 36 32.931 -78.130 -0.883 1.00 0.00 H +ATOM 542 CB ASP 36 30.912 -78.764 -0.955 1.00 0.00 C +ATOM 543 HB2 ASP 36 30.374 -79.640 -1.317 1.00 0.00 H +ATOM 544 HB3 ASP 36 30.701 -78.542 0.091 1.00 0.00 H +ATOM 545 CG ASP 36 30.367 -77.502 -1.713 1.00 0.00 C +ATOM 546 OD1 ASP 36 31.149 -76.538 -2.030 1.00 0.00 O +ATOM 547 OD2 ASP 36 29.126 -77.390 -1.707 1.00 0.00 O +ATOM 548 C ASP 36 32.745 -80.087 0.014 1.00 0.00 C +ATOM 549 O ASP 36 32.970 -79.681 1.147 1.00 0.00 O +ATOM 550 N LYS 37 33.013 -81.315 -0.431 1.00 0.00 N +ATOM 551 H LYS 37 32.716 -81.562 -1.364 1.00 0.00 H +ATOM 552 CA LYS 37 33.636 -82.348 0.414 1.00 0.00 C +ATOM 553 HA LYS 37 33.413 -82.198 1.471 1.00 0.00 H +ATOM 554 CB LYS 37 32.951 -83.658 0.080 1.00 0.00 C +ATOM 555 HB2 LYS 37 33.074 -83.872 -0.982 1.00 0.00 H +ATOM 556 HB3 LYS 37 31.893 -83.654 0.341 1.00 0.00 H +ATOM 557 CG LYS 37 33.432 -84.988 0.712 1.00 0.00 C +ATOM 558 HG2 LYS 37 34.402 -85.228 0.277 1.00 0.00 H +ATOM 559 HG3 LYS 37 32.639 -85.678 0.423 1.00 0.00 H +ATOM 560 CD LYS 37 33.367 -85.139 2.227 1.00 0.00 C +ATOM 561 HD2 LYS 37 34.014 -84.429 2.743 1.00 0.00 H +ATOM 562 HD3 LYS 37 32.342 -84.995 2.567 1.00 0.00 H +ATOM 563 CE LYS 37 33.815 -86.561 2.578 1.00 0.00 C +ATOM 564 HE2 LYS 37 32.918 -87.135 2.344 1.00 0.00 H +ATOM 565 HE3 LYS 37 34.642 -86.919 1.967 1.00 0.00 H +ATOM 566 NZ LYS 37 34.100 -86.642 4.016 1.00 0.00 N +ATOM 567 HZ1 LYS 37 34.719 -85.869 4.214 1.00 0.00 H +ATOM 568 HZ2 LYS 37 33.307 -86.487 4.621 1.00 0.00 H +ATOM 569 HZ3 LYS 37 34.526 -87.522 4.268 1.00 0.00 H +ATOM 570 C LYS 37 35.160 -82.343 0.320 1.00 0.00 C +ATOM 571 O LYS 37 35.771 -82.832 1.269 1.00 0.00 O +ATOM 572 N GLY 38 35.674 -81.629 -0.662 1.00 0.00 N +ATOM 573 H GLY 38 35.087 -81.182 -1.351 1.00 0.00 H +ATOM 574 CA GLY 38 37.113 -81.501 -0.748 1.00 0.00 C +ATOM 575 HA2 GLY 38 37.379 -80.701 -1.439 1.00 0.00 H +ATOM 576 HA3 GLY 38 37.628 -81.308 0.193 1.00 0.00 H +ATOM 577 C GLY 38 37.665 -82.842 -1.267 1.00 0.00 C +ATOM 578 O GLY 38 38.794 -83.245 -0.990 1.00 0.00 O +ATOM 579 N VAL 39 36.835 -83.667 -1.948 1.00 0.00 N +ATOM 580 H VAL 39 35.914 -83.312 -2.162 1.00 0.00 H +ATOM 581 CA VAL 39 37.266 -84.992 -2.463 1.00 0.00 C +ATOM 582 HA VAL 39 38.353 -85.076 -2.472 1.00 0.00 H +ATOM 583 CB VAL 39 36.854 -86.198 -1.547 1.00 0.00 C +ATOM 584 HB VAL 39 35.765 -86.143 -1.545 1.00 0.00 H +ATOM 585 CG1 VAL 39 37.208 -87.635 -2.051 1.00 0.00 C +ATOM 586 HG11 VAL 39 37.024 -88.395 -1.292 1.00 0.00 H +ATOM 587 HG12 VAL 39 38.247 -87.550 -2.370 1.00 0.00 H +ATOM 588 HG13 VAL 39 36.569 -87.913 -2.889 1.00 0.00 H +ATOM 589 CG2 VAL 39 37.485 -86.049 -0.153 1.00 0.00 C +ATOM 590 HG21 VAL 39 37.291 -86.889 0.516 1.00 0.00 H +ATOM 591 HG22 VAL 39 36.905 -85.267 0.336 1.00 0.00 H +ATOM 592 HG23 VAL 39 38.548 -85.831 -0.248 1.00 0.00 H +ATOM 593 C VAL 39 36.779 -85.337 -3.926 1.00 0.00 C +ATOM 594 O VAL 39 35.598 -85.638 -4.138 1.00 0.00 O +ATOM 595 N ASP 40 37.673 -85.271 -4.894 1.00 0.00 N +ATOM 596 H ASP 40 38.591 -84.924 -4.653 1.00 0.00 H +ATOM 597 CA ASP 40 37.337 -85.499 -6.251 1.00 0.00 C +ATOM 598 HA ASP 40 36.570 -84.756 -6.472 1.00 0.00 H +ATOM 599 CB ASP 40 38.561 -85.175 -7.159 1.00 0.00 C +ATOM 600 HB2 ASP 40 38.994 -84.204 -6.920 1.00 0.00 H +ATOM 601 HB3 ASP 40 39.365 -85.830 -6.822 1.00 0.00 H +ATOM 602 CG ASP 40 38.317 -85.086 -8.650 1.00 0.00 C +ATOM 603 OD1 ASP 40 37.114 -85.063 -9.080 1.00 0.00 O +ATOM 604 OD2 ASP 40 39.324 -85.048 -9.413 1.00 0.00 O +ATOM 605 C ASP 40 36.796 -86.875 -6.626 1.00 0.00 C +ATOM 606 O ASP 40 37.214 -87.903 -6.100 1.00 0.00 O +ATOM 607 N GLY 41 35.855 -86.878 -7.560 1.00 0.00 N +ATOM 608 H GLY 41 35.937 -86.077 -8.170 1.00 0.00 H +ATOM 609 CA GLY 41 35.094 -87.999 -8.141 1.00 0.00 C +ATOM 610 HA2 GLY 41 35.731 -88.839 -8.420 1.00 0.00 H +ATOM 611 HA3 GLY 41 34.272 -88.377 -7.533 1.00 0.00 H +ATOM 612 C GLY 41 34.381 -87.525 -9.408 1.00 0.00 C +ATOM 613 O GLY 41 34.362 -86.404 -9.824 1.00 0.00 O +ATOM 614 N GLU 42 33.788 -88.603 -10.007 1.00 0.00 N +ATOM 615 H GLU 42 33.596 -89.414 -9.436 1.00 0.00 H +ATOM 616 CA GLU 42 33.365 -88.715 -11.465 1.00 0.00 C +ATOM 617 HA GLU 42 32.810 -87.821 -11.751 1.00 0.00 H +ATOM 618 CB GLU 42 34.449 -88.929 -12.532 1.00 0.00 C +ATOM 619 HB2 GLU 42 33.912 -88.915 -13.480 1.00 0.00 H +ATOM 620 HB3 GLU 42 35.156 -88.106 -12.424 1.00 0.00 H +ATOM 621 CG GLU 42 35.290 -90.205 -12.356 1.00 0.00 C +ATOM 622 HG2 GLU 42 34.631 -91.069 -12.269 1.00 0.00 H +ATOM 623 HG3 GLU 42 35.773 -90.386 -13.316 1.00 0.00 H +ATOM 624 CD GLU 42 36.275 -90.282 -11.236 1.00 0.00 C +ATOM 625 OE1 GLU 42 36.232 -91.255 -10.473 1.00 0.00 O +ATOM 626 OE2 GLU 42 37.059 -89.291 -11.092 1.00 0.00 O +ATOM 627 C GLU 42 32.328 -89.925 -11.589 1.00 0.00 C +ATOM 628 O GLU 42 32.322 -90.781 -10.667 1.00 0.00 O +ATOM 629 N TRP 43 31.494 -89.889 -12.661 1.00 0.00 N +ATOM 630 H TRP 43 31.684 -89.055 -13.198 1.00 0.00 H +ATOM 631 CA TRP 43 30.263 -90.591 -12.828 1.00 0.00 C +ATOM 632 HA TRP 43 30.294 -91.606 -12.431 1.00 0.00 H +ATOM 633 CB TRP 43 29.061 -89.988 -12.128 1.00 0.00 C +ATOM 634 HB2 TRP 43 29.013 -88.955 -12.473 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.084 -90.387 -12.400 1.00 0.00 H +ATOM 636 CG TRP 43 29.228 -90.038 -10.630 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.011 -91.169 -9.938 1.00 0.00 C +ATOM 638 HD1 TRP 43 28.689 -92.120 -10.336 1.00 0.00 H +ATOM 639 NE1 TRP 43 29.370 -90.960 -8.622 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.200 -91.660 -7.915 1.00 0.00 H +ATOM 641 CE2 TRP 43 29.906 -89.706 -8.453 1.00 0.00 C +ATOM 642 CZ2 TRP 43 30.379 -89.110 -7.292 1.00 0.00 C +ATOM 643 HZ2 TRP 43 30.133 -89.541 -6.333 1.00 0.00 H +ATOM 644 CH2 TRP 43 30.959 -87.853 -7.435 1.00 0.00 C +ATOM 645 HH2 TRP 43 31.348 -87.404 -6.532 1.00 0.00 H +ATOM 646 CZ3 TRP 43 30.958 -87.154 -8.600 1.00 0.00 C +ATOM 647 HZ3 TRP 43 31.304 -86.131 -8.624 1.00 0.00 H +ATOM 648 CE3 TRP 43 30.454 -87.794 -9.778 1.00 0.00 C +ATOM 649 HE3 TRP 43 30.495 -87.211 -10.686 1.00 0.00 H +ATOM 650 CD2 TRP 43 29.862 -89.110 -9.715 1.00 0.00 C +ATOM 651 C TRP 43 30.043 -90.680 -14.341 1.00 0.00 C +ATOM 652 O TRP 43 30.186 -89.681 -15.115 1.00 0.00 O +ATOM 653 N THR 44 29.711 -91.860 -14.795 1.00 0.00 N +ATOM 654 H THR 44 29.473 -92.576 -14.124 1.00 0.00 H +ATOM 655 CA THR 44 29.059 -92.060 -16.020 1.00 0.00 C +ATOM 656 HA THR 44 29.593 -91.695 -16.897 1.00 0.00 H +ATOM 657 CB THR 44 28.991 -93.575 -16.240 1.00 0.00 C +ATOM 658 HB THR 44 28.438 -94.137 -15.487 1.00 0.00 H +ATOM 659 CG2 THR 44 28.340 -93.904 -17.570 1.00 0.00 C +ATOM 660 HG21 THR 44 27.398 -93.356 -17.544 1.00 0.00 H +ATOM 661 HG22 THR 44 28.183 -94.980 -17.645 1.00 0.00 H +ATOM 662 HG23 THR 44 28.856 -93.608 -18.484 1.00 0.00 H +ATOM 663 OG1 THR 44 30.225 -94.180 -16.279 1.00 0.00 O +ATOM 664 HG1 THR 44 30.246 -94.831 -15.574 1.00 0.00 H +ATOM 665 C THR 44 27.680 -91.437 -15.944 1.00 0.00 C +ATOM 666 O THR 44 27.121 -91.386 -14.813 1.00 0.00 O +ATOM 667 N TYR 45 27.179 -90.839 -17.003 1.00 0.00 N +ATOM 668 H TYR 45 27.673 -90.716 -17.876 1.00 0.00 H +ATOM 669 CA TYR 45 25.709 -90.507 -17.155 1.00 0.00 C +ATOM 670 HA TYR 45 25.280 -90.574 -16.155 1.00 0.00 H +ATOM 671 CB TYR 45 25.538 -89.088 -17.672 1.00 0.00 C +ATOM 672 HB2 TYR 45 26.120 -88.381 -17.080 1.00 0.00 H +ATOM 673 HB3 TYR 45 25.979 -89.153 -18.667 1.00 0.00 H +ATOM 674 CG TYR 45 24.026 -88.715 -17.750 1.00 0.00 C +ATOM 675 CD1 TYR 45 23.160 -88.474 -16.613 1.00 0.00 C +ATOM 676 HD1 TYR 45 23.544 -88.432 -15.605 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.846 -88.256 -16.927 1.00 0.00 C +ATOM 678 HE1 TYR 45 21.165 -88.235 -16.088 1.00 0.00 H +ATOM 679 CZ TYR 45 21.278 -88.131 -18.222 1.00 0.00 C +ATOM 680 OH TYR 45 19.938 -87.846 -18.352 1.00 0.00 O +ATOM 681 HH TYR 45 19.562 -87.976 -19.226 1.00 0.00 H +ATOM 682 CE2 TYR 45 22.133 -88.380 -19.311 1.00 0.00 C +ATOM 683 HE2 TYR 45 21.730 -88.417 -20.312 1.00 0.00 H +ATOM 684 CD2 TYR 45 23.514 -88.717 -19.106 1.00 0.00 C +ATOM 685 HD2 TYR 45 24.205 -88.919 -19.911 1.00 0.00 H +ATOM 686 C TYR 45 24.975 -91.572 -17.968 1.00 0.00 C +ATOM 687 O TYR 45 25.273 -91.791 -19.146 1.00 0.00 O +ATOM 688 N ASP 46 23.921 -92.180 -17.374 1.00 0.00 N +ATOM 689 H ASP 46 23.677 -91.884 -16.440 1.00 0.00 H +ATOM 690 CA ASP 46 23.041 -93.149 -17.940 1.00 0.00 C +ATOM 691 HA ASP 46 23.513 -93.575 -18.826 1.00 0.00 H +ATOM 692 CB ASP 46 22.922 -94.353 -17.065 1.00 0.00 C +ATOM 693 HB2 ASP 46 23.924 -94.741 -16.881 1.00 0.00 H +ATOM 694 HB3 ASP 46 22.454 -94.075 -16.120 1.00 0.00 H +ATOM 695 CG ASP 46 22.035 -95.459 -17.645 1.00 0.00 C +ATOM 696 OD1 ASP 46 22.224 -95.853 -18.809 1.00 0.00 O +ATOM 697 OD2 ASP 46 21.113 -95.995 -16.967 1.00 0.00 O +ATOM 698 C ASP 46 21.650 -92.653 -18.312 1.00 0.00 C +ATOM 699 O ASP 46 20.692 -92.658 -17.500 1.00 0.00 O +ATOM 700 N ASP 47 21.420 -92.211 -19.550 1.00 0.00 N +ATOM 701 H ASP 47 22.040 -92.334 -20.338 1.00 0.00 H +ATOM 702 CA ASP 47 20.166 -91.504 -19.928 1.00 0.00 C +ATOM 703 HA ASP 47 20.096 -90.741 -19.152 1.00 0.00 H +ATOM 704 CB ASP 47 20.279 -90.710 -21.195 1.00 0.00 C +ATOM 705 HB2 ASP 47 21.244 -90.205 -21.221 1.00 0.00 H +ATOM 706 HB3 ASP 47 20.335 -91.301 -22.110 1.00 0.00 H +ATOM 707 CG ASP 47 19.152 -89.717 -21.405 1.00 0.00 C +ATOM 708 OD1 ASP 47 18.161 -90.018 -22.131 1.00 0.00 O +ATOM 709 OD2 ASP 47 19.101 -88.751 -20.621 1.00 0.00 O +ATOM 710 C ASP 47 18.973 -92.463 -19.912 1.00 0.00 C +ATOM 711 O ASP 47 17.855 -91.957 -19.869 1.00 0.00 O +ATOM 712 N ALA 48 19.233 -93.770 -20.015 1.00 0.00 N +ATOM 713 H ALA 48 20.179 -94.124 -20.036 1.00 0.00 H +ATOM 714 CA ALA 48 18.179 -94.779 -19.994 1.00 0.00 C +ATOM 715 HA ALA 48 17.395 -94.450 -20.676 1.00 0.00 H +ATOM 716 CB ALA 48 18.823 -96.100 -20.402 1.00 0.00 C +ATOM 717 HB1 ALA 48 18.043 -96.836 -20.596 1.00 0.00 H +ATOM 718 HB2 ALA 48 19.482 -96.538 -19.652 1.00 0.00 H +ATOM 719 HB3 ALA 48 19.399 -95.927 -21.312 1.00 0.00 H +ATOM 720 C ALA 48 17.535 -94.930 -18.593 1.00 0.00 C +ATOM 721 O ALA 48 16.617 -95.711 -18.427 1.00 0.00 O +ATOM 722 N THR 49 18.049 -94.226 -17.545 1.00 0.00 N +ATOM 723 H THR 49 18.971 -93.829 -17.658 1.00 0.00 H +ATOM 724 CA THR 49 17.521 -94.114 -16.203 1.00 0.00 C +ATOM 725 HA THR 49 16.451 -94.290 -16.313 1.00 0.00 H +ATOM 726 CB THR 49 18.134 -95.227 -15.229 1.00 0.00 C +ATOM 727 HB THR 49 17.592 -95.055 -14.300 1.00 0.00 H +ATOM 728 CG2 THR 49 17.946 -96.697 -15.694 1.00 0.00 C +ATOM 729 HG21 THR 49 18.666 -97.248 -15.089 1.00 0.00 H +ATOM 730 HG22 THR 49 18.116 -96.906 -16.750 1.00 0.00 H +ATOM 731 HG23 THR 49 16.946 -97.051 -15.446 1.00 0.00 H +ATOM 732 OG1 THR 49 19.566 -94.976 -15.157 1.00 0.00 O +ATOM 733 HG1 THR 49 19.846 -95.298 -16.016 1.00 0.00 H +ATOM 734 C THR 49 17.754 -92.747 -15.553 1.00 0.00 C +ATOM 735 O THR 49 17.460 -92.657 -14.332 1.00 0.00 O +ATOM 736 N LYS 50 18.327 -91.678 -16.184 1.00 0.00 N +ATOM 737 H LYS 50 18.549 -91.847 -17.154 1.00 0.00 H +ATOM 738 CA LYS 50 18.583 -90.384 -15.623 1.00 0.00 C +ATOM 739 HA LYS 50 19.260 -89.881 -16.314 1.00 0.00 H +ATOM 740 CB LYS 50 17.279 -89.704 -15.491 1.00 0.00 C +ATOM 741 HB2 LYS 50 16.671 -90.134 -14.695 1.00 0.00 H +ATOM 742 HB3 LYS 50 17.475 -88.727 -15.050 1.00 0.00 H +ATOM 743 CG LYS 50 16.318 -89.510 -16.735 1.00 0.00 C +ATOM 744 HG2 LYS 50 15.854 -90.449 -17.037 1.00 0.00 H +ATOM 745 HG3 LYS 50 15.465 -88.934 -16.376 1.00 0.00 H +ATOM 746 CD LYS 50 16.952 -88.926 -18.020 1.00 0.00 C +ATOM 747 HD2 LYS 50 17.243 -87.900 -17.795 1.00 0.00 H +ATOM 748 HD3 LYS 50 17.753 -89.597 -18.328 1.00 0.00 H +ATOM 749 CE LYS 50 15.978 -88.915 -19.250 1.00 0.00 C +ATOM 750 HE2 LYS 50 15.848 -89.966 -19.510 1.00 0.00 H +ATOM 751 HE3 LYS 50 15.047 -88.400 -19.016 1.00 0.00 H +ATOM 752 NZ LYS 50 16.523 -88.240 -20.405 1.00 0.00 N +ATOM 753 HZ1 LYS 50 17.483 -88.514 -20.558 1.00 0.00 H +ATOM 754 HZ2 LYS 50 16.524 -87.236 -20.303 1.00 0.00 H +ATOM 755 HZ3 LYS 50 16.015 -88.377 -21.268 1.00 0.00 H +ATOM 756 C LYS 50 19.504 -90.479 -14.377 1.00 0.00 C +ATOM 757 O LYS 50 19.151 -90.057 -13.299 1.00 0.00 O +ATOM 758 N THR 51 20.618 -91.263 -14.509 1.00 0.00 N +ATOM 759 H THR 51 20.740 -91.704 -15.409 1.00 0.00 H +ATOM 760 CA THR 51 21.520 -91.696 -13.384 1.00 0.00 C +ATOM 761 HA THR 51 21.218 -91.175 -12.476 1.00 0.00 H +ATOM 762 CB THR 51 21.388 -93.254 -13.098 1.00 0.00 C +ATOM 763 HB THR 51 21.838 -93.893 -13.858 1.00 0.00 H +ATOM 764 CG2 THR 51 22.157 -93.724 -11.804 1.00 0.00 C +ATOM 765 HG21 THR 51 21.567 -93.672 -10.889 1.00 0.00 H +ATOM 766 HG22 THR 51 23.145 -93.289 -11.657 1.00 0.00 H +ATOM 767 HG23 THR 51 22.374 -94.781 -11.959 1.00 0.00 H +ATOM 768 OG1 THR 51 20.085 -93.726 -12.775 1.00 0.00 O +ATOM 769 HG1 THR 51 19.560 -93.816 -13.573 1.00 0.00 H +ATOM 770 C THR 51 22.956 -91.301 -13.584 1.00 0.00 C +ATOM 771 O THR 51 23.551 -91.549 -14.698 1.00 0.00 O +ATOM 772 N PHE 52 23.576 -90.694 -12.576 1.00 0.00 N +ATOM 773 H PHE 52 22.986 -90.307 -11.853 1.00 0.00 H +ATOM 774 CA PHE 52 25.013 -90.566 -12.354 1.00 0.00 C +ATOM 775 HA PHE 52 25.510 -90.453 -13.317 1.00 0.00 H +ATOM 776 CB PHE 52 25.155 -89.223 -11.541 1.00 0.00 C +ATOM 777 HB2 PHE 52 24.597 -89.203 -10.605 1.00 0.00 H +ATOM 778 HB3 PHE 52 26.205 -89.077 -11.290 1.00 0.00 H +ATOM 779 CG PHE 52 24.761 -88.029 -12.410 1.00 0.00 C +ATOM 780 CD1 PHE 52 23.515 -87.448 -12.335 1.00 0.00 C +ATOM 781 HD1 PHE 52 22.977 -87.760 -11.452 1.00 0.00 H +ATOM 782 CE1 PHE 52 23.148 -86.369 -13.118 1.00 0.00 C +ATOM 783 HE1 PHE 52 22.157 -85.940 -13.089 1.00 0.00 H +ATOM 784 CZ PHE 52 23.994 -85.955 -14.139 1.00 0.00 C +ATOM 785 HZ PHE 52 23.702 -85.130 -14.772 1.00 0.00 H +ATOM 786 CE2 PHE 52 25.278 -86.585 -14.341 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.927 -86.455 -15.195 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.656 -87.587 -13.416 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.525 -88.226 -13.485 1.00 0.00 H +ATOM 790 C PHE 52 25.600 -91.781 -11.594 1.00 0.00 C +ATOM 791 O PHE 52 25.349 -91.980 -10.374 1.00 0.00 O +ATOM 792 N THR 53 26.281 -92.585 -12.373 1.00 0.00 N +ATOM 793 H THR 53 26.430 -92.282 -13.325 1.00 0.00 H +ATOM 794 CA THR 53 26.632 -94.021 -12.076 1.00 0.00 C +ATOM 795 HA THR 53 26.473 -94.151 -11.005 1.00 0.00 H +ATOM 796 CB THR 53 25.661 -94.950 -12.790 1.00 0.00 C +ATOM 797 HB THR 53 24.626 -94.799 -12.484 1.00 0.00 H +ATOM 798 CG2 THR 53 25.785 -95.196 -14.345 1.00 0.00 C +ATOM 799 HG21 THR 53 24.951 -95.830 -14.647 1.00 0.00 H +ATOM 800 HG22 THR 53 26.721 -95.690 -14.610 1.00 0.00 H +ATOM 801 HG23 THR 53 25.559 -94.302 -14.926 1.00 0.00 H +ATOM 802 OG1 THR 53 25.883 -96.177 -12.138 1.00 0.00 O +ATOM 803 HG1 THR 53 25.068 -96.683 -12.166 1.00 0.00 H +ATOM 804 C THR 53 28.049 -94.430 -12.344 1.00 0.00 C +ATOM 805 O THR 53 28.883 -93.497 -12.552 1.00 0.00 O +ATOM 806 N VAL 54 28.387 -95.692 -12.146 1.00 0.00 N +ATOM 807 H VAL 54 27.708 -96.438 -12.094 1.00 0.00 H +ATOM 808 CA VAL 54 29.809 -96.129 -11.985 1.00 0.00 C +ATOM 809 HA VAL 54 30.282 -95.580 -11.170 1.00 0.00 H +ATOM 810 CB VAL 54 29.835 -97.652 -11.706 1.00 0.00 C +ATOM 811 HB VAL 54 30.838 -98.068 -11.801 1.00 0.00 H +ATOM 812 CG1 VAL 54 29.289 -98.055 -10.305 1.00 0.00 C +ATOM 813 HG11 VAL 54 29.365 -99.137 -10.196 1.00 0.00 H +ATOM 814 HG12 VAL 54 28.226 -97.827 -10.225 1.00 0.00 H +ATOM 815 HG13 VAL 54 29.882 -97.635 -9.492 1.00 0.00 H +ATOM 816 CG2 VAL 54 29.058 -98.412 -12.706 1.00 0.00 C +ATOM 817 HG21 VAL 54 28.019 -98.107 -12.838 1.00 0.00 H +ATOM 818 HG22 VAL 54 29.032 -99.467 -12.431 1.00 0.00 H +ATOM 819 HG23 VAL 54 29.464 -98.371 -13.717 1.00 0.00 H +ATOM 820 C VAL 54 30.662 -95.830 -13.249 1.00 0.00 C +ATOM 821 O VAL 54 30.105 -95.946 -14.354 1.00 0.00 O +ATOM 822 N THR 55 31.988 -95.572 -12.966 1.00 0.00 N +ATOM 823 H THR 55 32.271 -95.408 -12.011 1.00 0.00 H +ATOM 824 CA THR 55 33.055 -95.396 -13.974 1.00 0.00 C +ATOM 825 HA THR 55 32.527 -95.075 -14.872 1.00 0.00 H +ATOM 826 CB THR 55 34.036 -94.276 -13.664 1.00 0.00 C +ATOM 827 HB THR 55 34.842 -94.538 -12.979 1.00 0.00 H +ATOM 828 CG2 THR 55 34.681 -93.748 -14.963 1.00 0.00 C +ATOM 829 HG21 THR 55 35.128 -92.763 -14.823 1.00 0.00 H +ATOM 830 HG22 THR 55 33.961 -93.678 -15.778 1.00 0.00 H +ATOM 831 HG23 THR 55 35.238 -94.559 -15.431 1.00 0.00 H +ATOM 832 OG1 THR 55 33.328 -93.015 -13.204 1.00 0.00 O +ATOM 833 HG1 THR 55 33.385 -92.970 -12.246 1.00 0.00 H +ATOM 834 C THR 55 33.905 -96.698 -14.166 1.00 0.00 C +ATOM 835 O THR 55 34.494 -97.170 -13.205 1.00 0.00 O +ATOM 836 N GLU 56 33.979 -97.251 -15.366 1.00 0.00 N +ATOM 837 H GLU 56 33.397 -96.793 -16.052 1.00 0.00 H +ATOM 838 CA GLU 56 34.666 -98.532 -15.761 1.00 0.00 C +ATOM 839 HA GLU 56 35.495 -98.715 -15.077 1.00 0.00 H +ATOM 840 CB GLU 56 33.668 -99.641 -15.638 1.00 0.00 C +ATOM 841 HB2 GLU 56 33.244 -99.711 -14.637 1.00 0.00 H +ATOM 842 HB3 GLU 56 32.773 -99.356 -16.191 1.00 0.00 H +ATOM 843 CG GLU 56 34.130-101.051 -16.059 1.00 0.00 C +ATOM 844 HG2 GLU 56 33.347-101.808 -16.007 1.00 0.00 H +ATOM 845 HG3 GLU 56 34.375-101.110 -17.119 1.00 0.00 H +ATOM 846 CD GLU 56 35.319-101.546 -15.251 1.00 0.00 C +ATOM 847 OE1 GLU 56 36.026-102.428 -15.760 1.00 0.00 O +ATOM 848 OE2 GLU 56 35.559-101.093 -14.114 1.00 0.00 O +ATOM 849 C GLU 56 35.318 -98.483 -17.157 1.00 0.00 C +ATOM 850 O GLU 56 34.579 -98.206 -18.083 1.00 0.00 O +ATOM 851 OXT GLU 56 36.550 -98.638 -17.194 1.00 0.00 O +ATOM 852 ZN ZN1 57 24.315 -87.683 -4.676 1.00 0.00 ZN +ATOM 853 N AN1 58 25.477 -86.586 -3.491 1.00 0.00 N +ATOM 854 C AN1 58 26.619 -85.064 -1.671 1.00 0.00 C +ATOM 855 C1 AN1 58 26.057 -85.997 -2.692 1.00 0.00 C +ATOM 856 H AN1 58 26.186 -84.057 -1.706 1.00 0.00 H +ATOM 857 H1 AN1 58 27.710 -85.052 -1.552 1.00 0.00 H +ATOM 858 H2 AN1 58 26.410 -85.529 -0.700 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 27.178 -90.340 -1.361 1.00 0.00 N +ATOM 860 N2 AZI 59 26.182 -89.679 -1.087 1.00 0.00 N +ATOM 861 N3 AZI 59 25.129 -89.015 -0.745 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/pdbs_rename/cluster5.pdb b/tests/nsga2/pdbs_rename/cluster5.pdb new file mode 100644 index 0000000..fb7d3a1 --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster5.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.496 -81.728 -12.696 1.00 0.00 N +ATOM 2 H1 MET 1 13.556 -81.576 -11.699 1.00 0.00 H +ATOM 3 H2 MET 1 12.638 -81.373 -13.092 1.00 0.00 H +ATOM 4 H3 MET 1 14.282 -81.277 -13.143 1.00 0.00 H +ATOM 5 CA MET 1 13.482 -83.157 -12.927 1.00 0.00 C +ATOM 6 HA MET 1 12.450 -83.445 -12.729 1.00 0.00 H +ATOM 7 CB MET 1 13.834 -83.502 -14.365 1.00 0.00 C +ATOM 8 HB2 MET 1 13.142 -83.178 -15.143 1.00 0.00 H +ATOM 9 HB3 MET 1 14.846 -83.170 -14.598 1.00 0.00 H +ATOM 10 CG MET 1 13.848 -85.010 -14.759 1.00 0.00 C +ATOM 11 HG2 MET 1 13.928 -85.235 -15.823 1.00 0.00 H +ATOM 12 HG3 MET 1 14.673 -85.452 -14.199 1.00 0.00 H +ATOM 13 SD MET 1 12.244 -85.835 -14.186 1.00 0.00 S +ATOM 14 CE MET 1 11.389 -86.092 -15.741 1.00 0.00 C +ATOM 15 HE1 MET 1 10.530 -86.700 -15.457 1.00 0.00 H +ATOM 16 HE2 MET 1 11.947 -86.651 -16.493 1.00 0.00 H +ATOM 17 HE3 MET 1 11.027 -85.155 -16.163 1.00 0.00 H +ATOM 18 C MET 1 14.448 -83.743 -11.931 1.00 0.00 C +ATOM 19 O MET 1 15.580 -83.304 -11.808 1.00 0.00 O +ATOM 20 N GLN 2 14.102 -84.883 -11.292 1.00 0.00 N +ATOM 21 H GLN 2 13.242 -85.379 -11.480 1.00 0.00 H +ATOM 22 CA GLN 2 14.980 -85.564 -10.283 1.00 0.00 C +ATOM 23 HA GLN 2 15.645 -84.890 -9.743 1.00 0.00 H +ATOM 24 CB GLN 2 14.106 -86.197 -9.177 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.416 -86.878 -9.674 1.00 0.00 H +ATOM 26 HB3 GLN 2 14.782 -86.744 -8.519 1.00 0.00 H +ATOM 27 CG GLN 2 13.388 -85.156 -8.321 1.00 0.00 C +ATOM 28 HG2 GLN 2 13.941 -84.219 -8.384 1.00 0.00 H +ATOM 29 HG3 GLN 2 12.415 -84.978 -8.778 1.00 0.00 H +ATOM 30 CD GLN 2 13.154 -85.564 -6.877 1.00 0.00 C +ATOM 31 OE1 GLN 2 13.238 -84.800 -5.998 1.00 0.00 O +ATOM 32 NE2 GLN 2 12.974 -86.850 -6.553 1.00 0.00 N +ATOM 33 HE21 GLN 2 12.712 -87.099 -5.609 1.00 0.00 H +ATOM 34 HE22 GLN 2 12.843 -87.545 -7.274 1.00 0.00 H +ATOM 35 C GLN 2 15.802 -86.534 -11.048 1.00 0.00 C +ATOM 36 O GLN 2 15.178 -87.435 -11.566 1.00 0.00 O +ATOM 37 N TYR 3 17.175 -86.285 -11.113 1.00 0.00 N +ATOM 38 H TYR 3 17.528 -85.437 -10.694 1.00 0.00 H +ATOM 39 CA TYR 3 18.151 -87.144 -11.678 1.00 0.00 C +ATOM 40 HA TYR 3 17.666 -87.810 -12.393 1.00 0.00 H +ATOM 41 CB TYR 3 19.108 -86.320 -12.493 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.809 -85.661 -11.979 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.824 -86.993 -12.965 1.00 0.00 H +ATOM 44 CG TYR 3 18.418 -85.580 -13.622 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.292 -86.212 -14.861 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.565 -87.247 -15.006 1.00 0.00 H +ATOM 47 CE1 TYR 3 17.517 -85.644 -15.933 1.00 0.00 C +ATOM 48 HE1 TYR 3 17.357 -86.155 -16.871 1.00 0.00 H +ATOM 49 CZ TYR 3 17.108 -84.295 -15.917 1.00 0.00 C +ATOM 50 OH TYR 3 16.498 -83.774 -16.977 1.00 0.00 O +ATOM 51 HH TYR 3 16.630 -84.315 -17.759 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.417 -83.638 -14.719 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.132 -82.622 -14.493 1.00 0.00 H +ATOM 54 CD2 TYR 3 17.984 -84.269 -13.625 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.074 -83.780 -12.666 1.00 0.00 H +ATOM 56 C TYR 3 18.897 -87.913 -10.590 1.00 0.00 C +ATOM 57 O TYR 3 19.688 -87.289 -9.857 1.00 0.00 O +ATOM 58 N LYS 4 18.590 -89.212 -10.539 1.00 0.00 N +ATOM 59 H LYS 4 18.001 -89.567 -11.279 1.00 0.00 H +ATOM 60 CA LYS 4 19.174 -90.200 -9.595 1.00 0.00 C +ATOM 61 HA LYS 4 18.905 -89.884 -8.587 1.00 0.00 H +ATOM 62 CB LYS 4 18.501 -91.551 -9.898 1.00 0.00 C +ATOM 63 HB2 LYS 4 17.428 -91.372 -9.965 1.00 0.00 H +ATOM 64 HB3 LYS 4 18.853 -91.987 -10.833 1.00 0.00 H +ATOM 65 CG LYS 4 18.730 -92.615 -8.785 1.00 0.00 C +ATOM 66 HG2 LYS 4 19.729 -93.026 -8.929 1.00 0.00 H +ATOM 67 HG3 LYS 4 18.736 -92.147 -7.800 1.00 0.00 H +ATOM 68 CD LYS 4 17.684 -93.717 -8.921 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.640 -94.238 -7.964 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.675 -93.306 -8.948 1.00 0.00 H +ATOM 71 CE LYS 4 17.867 -94.846 -10.017 1.00 0.00 C +ATOM 72 HE2 LYS 4 18.895 -95.204 -10.078 1.00 0.00 H +ATOM 73 HE3 LYS 4 17.105 -95.591 -9.787 1.00 0.00 H +ATOM 74 NZ LYS 4 17.539 -94.478 -11.368 1.00 0.00 N +ATOM 75 HZ1 LYS 4 16.617 -94.068 -11.406 1.00 0.00 H +ATOM 76 HZ2 LYS 4 17.594 -95.225 -12.045 1.00 0.00 H +ATOM 77 HZ3 LYS 4 18.214 -93.844 -11.770 1.00 0.00 H +ATOM 78 C LYS 4 20.655 -90.227 -9.687 1.00 0.00 C +ATOM 79 O LYS 4 21.247 -90.000 -10.756 1.00 0.00 O +ATOM 80 N HX1 5 21.407 -90.504 -8.598 1.00 0.00 N +ATOM 81 CA HX1 5 22.875 -90.774 -8.664 1.00 0.00 C +ATOM 82 C HX1 5 23.193 -91.849 -7.672 1.00 0.00 C +ATOM 83 O HX1 5 22.731 -91.777 -6.536 1.00 0.00 O +ATOM 84 CB HX1 5 23.666 -89.504 -8.446 1.00 0.00 C +ATOM 85 CG HX1 5 25.153 -89.475 -8.445 1.00 0.00 C +ATOM 86 CD2 HX1 5 25.950 -90.520 -8.740 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.849 -88.360 -8.003 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.103 -88.846 -7.953 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.196 -90.164 -8.356 1.00 0.00 N +ATOM 90 H HX1 5 20.862 -90.604 -7.754 1.00 0.00 H +ATOM 91 HA HX1 5 23.126 -91.209 -9.631 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.410 -89.259 -7.415 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.193 -88.740 -9.063 1.00 0.00 H +ATOM 94 HD2 HX1 5 25.686 -91.493 -9.129 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.996 -88.347 -7.605 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.012 -90.756 -8.310 1.00 0.00 H +ATOM 97 N ILE 6 23.559 -93.009 -8.215 1.00 0.00 N +ATOM 98 H ILE 6 23.771 -93.078 -9.200 1.00 0.00 H +ATOM 99 CA ILE 6 23.856 -94.192 -7.518 1.00 0.00 C +ATOM 100 HA ILE 6 23.198 -94.208 -6.649 1.00 0.00 H +ATOM 101 CB ILE 6 23.494 -95.464 -8.398 1.00 0.00 C +ATOM 102 HB ILE 6 23.463 -96.279 -7.675 1.00 0.00 H +ATOM 103 CG2 ILE 6 22.012 -95.437 -8.831 1.00 0.00 C +ATOM 104 HG21 ILE 6 21.315 -95.038 -8.094 1.00 0.00 H +ATOM 105 HG22 ILE 6 21.701 -96.446 -9.100 1.00 0.00 H +ATOM 106 HG23 ILE 6 21.974 -94.785 -9.704 1.00 0.00 H +ATOM 107 CG1 ILE 6 24.493 -95.641 -9.517 1.00 0.00 C +ATOM 108 HG12 ILE 6 24.396 -94.861 -10.273 1.00 0.00 H +ATOM 109 HG13 ILE 6 25.518 -95.701 -9.151 1.00 0.00 H +ATOM 110 CD1 ILE 6 24.272 -96.967 -10.314 1.00 0.00 C +ATOM 111 HD11 ILE 6 24.348 -97.778 -9.590 1.00 0.00 H +ATOM 112 HD12 ILE 6 25.134 -96.987 -10.980 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.313 -96.997 -10.833 1.00 0.00 H +ATOM 114 C ILE 6 25.295 -94.090 -7.054 1.00 0.00 C +ATOM 115 O ILE 6 26.057 -93.397 -7.704 1.00 0.00 O +ATOM 116 N VAL 7 25.540 -94.665 -5.897 1.00 0.00 N +ATOM 117 H VAL 7 24.818 -95.241 -5.488 1.00 0.00 H +ATOM 118 CA VAL 7 26.853 -94.510 -5.182 1.00 0.00 C +ATOM 119 HA VAL 7 27.533 -93.893 -5.771 1.00 0.00 H +ATOM 120 CB VAL 7 26.589 -93.792 -3.840 1.00 0.00 C +ATOM 121 HB VAL 7 25.924 -94.453 -3.285 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.837 -93.387 -3.099 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.524 -92.860 -3.761 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.511 -92.732 -2.292 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.384 -94.228 -2.672 1.00 0.00 H +ATOM 126 CG2 VAL 7 25.777 -92.507 -4.081 1.00 0.00 C +ATOM 127 HG21 VAL 7 25.813 -91.912 -3.169 1.00 0.00 H +ATOM 128 HG22 VAL 7 26.122 -91.986 -4.974 1.00 0.00 H +ATOM 129 HG23 VAL 7 24.749 -92.728 -4.368 1.00 0.00 H +ATOM 130 C VAL 7 27.468 -95.866 -5.088 1.00 0.00 C +ATOM 131 O VAL 7 26.833 -96.930 -5.164 1.00 0.00 O +ATOM 132 N ASN 8 28.828 -95.756 -4.910 1.00 0.00 N +ATOM 133 H ASN 8 29.269 -94.856 -4.786 1.00 0.00 H +ATOM 134 CA ASN 8 29.845 -96.798 -4.856 1.00 0.00 C +ATOM 135 HA ASN 8 29.422 -97.787 -5.028 1.00 0.00 H +ATOM 136 CB ASN 8 30.714 -96.561 -6.052 1.00 0.00 C +ATOM 137 HB2 ASN 8 29.989 -96.662 -6.860 1.00 0.00 H +ATOM 138 HB3 ASN 8 31.115 -95.560 -5.891 1.00 0.00 H +ATOM 139 CG ASN 8 31.870 -97.542 -6.260 1.00 0.00 C +ATOM 140 OD1 ASN 8 32.993 -97.449 -5.775 1.00 0.00 O +ATOM 141 ND2 ASN 8 31.619 -98.508 -7.112 1.00 0.00 N +ATOM 142 HD21 ASN 8 30.701 -98.489 -7.531 1.00 0.00 H +ATOM 143 HD22 ASN 8 32.354 -99.170 -7.320 1.00 0.00 H +ATOM 144 C ASN 8 30.464 -96.897 -3.413 1.00 0.00 C +ATOM 145 O ASN 8 30.860 -95.889 -2.773 1.00 0.00 O +ATOM 146 N GLY 9 30.693 -98.117 -2.974 1.00 0.00 N +ATOM 147 H GLY 9 30.316 -98.880 -3.518 1.00 0.00 H +ATOM 148 CA GLY 9 31.159 -98.375 -1.614 1.00 0.00 C +ATOM 149 HA2 GLY 9 31.848 -97.547 -1.448 1.00 0.00 H +ATOM 150 HA3 GLY 9 30.317 -98.421 -0.924 1.00 0.00 H +ATOM 151 C GLY 9 31.897 -99.697 -1.502 1.00 0.00 C +ATOM 152 O GLY 9 31.832-100.563 -2.330 1.00 0.00 O +ATOM 153 N LYS 10 32.696 -99.914 -0.459 1.00 0.00 N +ATOM 154 H LYS 10 32.711 -99.148 0.200 1.00 0.00 H +ATOM 155 CA LYS 10 33.611-101.070 -0.193 1.00 0.00 C +ATOM 156 HA LYS 10 34.260-101.177 -1.062 1.00 0.00 H +ATOM 157 CB LYS 10 34.479-100.809 1.069 1.00 0.00 C +ATOM 158 HB2 LYS 10 33.824-100.381 1.828 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.788-101.825 1.318 1.00 0.00 H +ATOM 160 CG LYS 10 35.676 -99.869 0.750 1.00 0.00 C +ATOM 161 HG2 LYS 10 36.200-100.395 -0.048 1.00 0.00 H +ATOM 162 HG3 LYS 10 35.329 -98.888 0.424 1.00 0.00 H +ATOM 163 CD LYS 10 36.691 -99.652 1.917 1.00 0.00 C +ATOM 164 HD2 LYS 10 37.273 -98.746 1.749 1.00 0.00 H +ATOM 165 HD3 LYS 10 36.048 -99.415 2.764 1.00 0.00 H +ATOM 166 CE LYS 10 37.621-100.790 2.356 1.00 0.00 C +ATOM 167 HE2 LYS 10 38.124-100.424 3.251 1.00 0.00 H +ATOM 168 HE3 LYS 10 37.020-101.665 2.605 1.00 0.00 H +ATOM 169 NZ LYS 10 38.592-101.087 1.244 1.00 0.00 N +ATOM 170 HZ1 LYS 10 38.919-100.220 0.843 1.00 0.00 H +ATOM 171 HZ2 LYS 10 38.154-101.569 0.471 1.00 0.00 H +ATOM 172 HZ3 LYS 10 39.430-101.488 1.641 1.00 0.00 H +ATOM 173 C LYS 10 32.831-102.328 -0.104 1.00 0.00 C +ATOM 174 O LYS 10 33.182-103.323 -0.773 1.00 0.00 O +ATOM 175 N THR 11 31.585-102.251 0.460 1.00 0.00 N +ATOM 176 H THR 11 31.343-101.448 1.022 1.00 0.00 H +ATOM 177 CA THR 11 30.586-103.321 0.661 1.00 0.00 C +ATOM 178 HA THR 11 30.854-104.065 -0.090 1.00 0.00 H +ATOM 179 CB THR 11 30.642-103.858 2.066 1.00 0.00 C +ATOM 180 HB THR 11 29.823-104.577 2.052 1.00 0.00 H +ATOM 181 CG2 THR 11 31.906-104.658 2.306 1.00 0.00 C +ATOM 182 HG21 THR 11 32.045-105.549 1.694 1.00 0.00 H +ATOM 183 HG22 THR 11 31.894-105.111 3.297 1.00 0.00 H +ATOM 184 HG23 THR 11 32.841-104.131 2.120 1.00 0.00 H +ATOM 185 OG1 THR 11 30.402-102.936 3.145 1.00 0.00 O +ATOM 186 HG1 THR 11 29.496-103.157 3.371 1.00 0.00 H +ATOM 187 C THR 11 29.108-102.885 0.459 1.00 0.00 C +ATOM 188 O THR 11 28.272-103.787 0.443 1.00 0.00 O +ATOM 189 N LEU 12 28.843-101.597 0.246 1.00 0.00 N +ATOM 190 H LEU 12 29.602-100.943 0.116 1.00 0.00 H +ATOM 191 CA LEU 12 27.573-100.899 0.158 1.00 0.00 C +ATOM 192 HA LEU 12 26.745-101.607 0.202 1.00 0.00 H +ATOM 193 CB LEU 12 27.402 -99.851 1.265 1.00 0.00 C +ATOM 194 HB2 LEU 12 28.184 -99.098 1.169 1.00 0.00 H +ATOM 195 HB3 LEU 12 26.493 -99.280 1.071 1.00 0.00 H +ATOM 196 CG LEU 12 27.435-100.459 2.701 1.00 0.00 C +ATOM 197 HG LEU 12 28.218-101.210 2.813 1.00 0.00 H +ATOM 198 CD1 LEU 12 27.680 -99.317 3.736 1.00 0.00 C +ATOM 199 HD11 LEU 12 28.721 -99.052 3.549 1.00 0.00 H +ATOM 200 HD12 LEU 12 27.549 -99.733 4.735 1.00 0.00 H +ATOM 201 HD13 LEU 12 27.041 -98.443 3.610 1.00 0.00 H +ATOM 202 CD2 LEU 12 26.095-101.055 3.201 1.00 0.00 C +ATOM 203 HD21 LEU 12 25.729-101.810 2.506 1.00 0.00 H +ATOM 204 HD22 LEU 12 25.328-100.295 3.345 1.00 0.00 H +ATOM 205 HD23 LEU 12 26.396-101.612 4.089 1.00 0.00 H +ATOM 206 C LEU 12 27.442-100.233 -1.244 1.00 0.00 C +ATOM 207 O LEU 12 28.476 -99.823 -1.833 1.00 0.00 O +ATOM 208 N LYS 13 26.209-100.166 -1.794 1.00 0.00 N +ATOM 209 H LYS 13 25.424-100.564 -1.299 1.00 0.00 H +ATOM 210 CA LYS 13 25.936 -99.329 -2.980 1.00 0.00 C +ATOM 211 HA LYS 13 26.800 -98.701 -3.200 1.00 0.00 H +ATOM 212 CB LYS 13 25.688-100.285 -4.158 1.00 0.00 C +ATOM 213 HB2 LYS 13 24.957-101.023 -3.829 1.00 0.00 H +ATOM 214 HB3 LYS 13 25.237 -99.618 -4.893 1.00 0.00 H +ATOM 215 CG LYS 13 26.920-101.016 -4.720 1.00 0.00 C +ATOM 216 HG2 LYS 13 27.748-100.312 -4.792 1.00 0.00 H +ATOM 217 HG3 LYS 13 27.317-101.717 -3.987 1.00 0.00 H +ATOM 218 CD LYS 13 26.639-101.804 -6.018 1.00 0.00 C +ATOM 219 HD2 LYS 13 26.191-101.146 -6.763 1.00 0.00 H +ATOM 220 HD3 LYS 13 27.543-102.228 -6.455 1.00 0.00 H +ATOM 221 CE LYS 13 25.684-102.980 -5.646 1.00 0.00 C +ATOM 222 HE2 LYS 13 26.336-103.723 -5.187 1.00 0.00 H +ATOM 223 HE3 LYS 13 24.932-102.754 -4.890 1.00 0.00 H +ATOM 224 NZ LYS 13 25.118-103.480 -6.926 1.00 0.00 N +ATOM 225 HZ1 LYS 13 24.563-102.731 -7.317 1.00 0.00 H +ATOM 226 HZ2 LYS 13 24.512-104.270 -6.758 1.00 0.00 H +ATOM 227 HZ3 LYS 13 25.863-103.717 -7.565 1.00 0.00 H +ATOM 228 C LYS 13 24.749 -98.447 -2.760 1.00 0.00 C +ATOM 229 O LYS 13 23.618 -98.742 -3.084 1.00 0.00 O +ATOM 230 N GLY 14 25.011 -97.328 -2.064 1.00 0.00 N +ATOM 231 H GLY 14 25.838 -97.357 -1.486 1.00 0.00 H +ATOM 232 CA GLY 14 24.016 -96.337 -1.718 1.00 0.00 C +ATOM 233 HA2 GLY 14 23.232 -96.881 -1.192 1.00 0.00 H +ATOM 234 HA3 GLY 14 24.437 -95.588 -1.048 1.00 0.00 H +ATOM 235 C GLY 14 23.449 -95.609 -2.945 1.00 0.00 C +ATOM 236 O GLY 14 23.906 -95.840 -4.089 1.00 0.00 O +ATOM 237 N VAL 15 22.401 -94.801 -2.776 1.00 0.00 N +ATOM 238 H VAL 15 22.186 -94.669 -1.798 1.00 0.00 H +ATOM 239 CA VAL 15 21.716 -93.947 -3.847 1.00 0.00 C +ATOM 240 HA VAL 15 22.528 -93.680 -4.523 1.00 0.00 H +ATOM 241 CB VAL 15 20.813 -94.806 -4.675 1.00 0.00 C +ATOM 242 HB VAL 15 21.377 -95.655 -5.061 1.00 0.00 H +ATOM 243 CG1 VAL 15 19.706 -95.422 -3.883 1.00 0.00 C +ATOM 244 HG11 VAL 15 19.235 -96.129 -4.566 1.00 0.00 H +ATOM 245 HG12 VAL 15 20.100 -95.919 -2.997 1.00 0.00 H +ATOM 246 HG13 VAL 15 19.041 -94.651 -3.492 1.00 0.00 H +ATOM 247 CG2 VAL 15 20.208 -94.056 -5.884 1.00 0.00 C +ATOM 248 HG21 VAL 15 19.698 -94.710 -6.591 1.00 0.00 H +ATOM 249 HG22 VAL 15 19.484 -93.319 -5.538 1.00 0.00 H +ATOM 250 HG23 VAL 15 20.965 -93.518 -6.454 1.00 0.00 H +ATOM 251 C VAL 15 21.150 -92.634 -3.263 1.00 0.00 C +ATOM 252 O VAL 15 20.576 -92.554 -2.177 1.00 0.00 O +ATOM 253 N HY1 16 21.181 -91.594 -4.087 1.00 0.00 N +ATOM 254 CA HY1 16 20.470 -90.352 -3.858 1.00 0.00 C +ATOM 255 C HY1 16 20.036 -89.734 -5.241 1.00 0.00 C +ATOM 256 O HY1 16 19.864 -90.400 -6.259 1.00 0.00 O +ATOM 257 CB HY1 16 21.334 -89.332 -3.032 1.00 0.00 C +ATOM 258 CG HY1 16 22.639 -88.999 -3.709 1.00 0.00 C +ATOM 259 CD2 HY1 16 22.857 -88.044 -4.670 1.00 0.00 C +ATOM 260 ND1 HY1 16 23.833 -89.615 -3.476 1.00 0.00 N +ATOM 261 CE1 HY1 16 24.716 -89.037 -4.305 1.00 0.00 C +ATOM 262 NE2 HY1 16 24.211 -88.008 -4.995 1.00 0.00 N +ATOM 263 H HY1 16 21.689 -91.693 -4.954 1.00 0.00 H +ATOM 264 HA HY1 16 19.518 -90.634 -3.409 1.00 0.00 H +ATOM 265 HB2 HY1 16 20.848 -88.415 -2.697 1.00 0.00 H +ATOM 266 HB3 HY1 16 21.596 -89.764 -2.066 1.00 0.00 H +ATOM 267 HD1 HY1 16 23.965 -90.470 -2.956 1.00 0.00 H +ATOM 268 HD2 HY1 16 22.075 -87.472 -5.145 1.00 0.00 H +ATOM 269 HE1 HY1 16 25.752 -89.334 -4.240 1.00 0.00 H +ATOM 270 N THR 17 19.739 -88.454 -5.222 1.00 0.00 N +ATOM 271 H THR 17 19.691 -87.926 -4.363 1.00 0.00 H +ATOM 272 CA THR 17 19.223 -87.730 -6.408 1.00 0.00 C +ATOM 273 HA THR 17 19.623 -88.215 -7.298 1.00 0.00 H +ATOM 274 CB THR 17 17.684 -87.801 -6.403 1.00 0.00 C +ATOM 275 HB THR 17 17.323 -88.820 -6.267 1.00 0.00 H +ATOM 276 CG2 THR 17 16.969 -86.795 -5.465 1.00 0.00 C +ATOM 277 HG21 THR 17 16.850 -85.787 -5.864 1.00 0.00 H +ATOM 278 HG22 THR 17 17.501 -86.713 -4.517 1.00 0.00 H +ATOM 279 HG23 THR 17 15.941 -87.130 -5.331 1.00 0.00 H +ATOM 280 OG1 THR 17 17.250 -87.539 -7.705 1.00 0.00 O +ATOM 281 HG1 THR 17 16.565 -88.123 -8.039 1.00 0.00 H +ATOM 282 C THR 17 19.581 -86.260 -6.472 1.00 0.00 C +ATOM 283 O THR 17 20.256 -85.743 -5.627 1.00 0.00 O +ATOM 284 N HY2 18 19.253 -85.633 -7.542 1.00 0.00 N +ATOM 285 CA HY2 18 19.599 -84.225 -7.918 1.00 0.00 C +ATOM 286 C HY2 18 18.494 -83.616 -8.790 1.00 0.00 C +ATOM 287 O HY2 18 18.308 -83.942 -9.978 1.00 0.00 O +ATOM 288 CB HY2 18 20.928 -84.131 -8.622 1.00 0.00 C +ATOM 289 CG HY2 18 22.152 -84.443 -7.768 1.00 0.00 C +ATOM 290 CD2 HY2 18 23.030 -85.439 -8.016 1.00 0.00 C +ATOM 291 ND1 HY2 18 22.497 -83.902 -6.522 1.00 0.00 N +ATOM 292 CE1 HY2 18 23.728 -84.419 -6.226 1.00 0.00 C +ATOM 293 NE2 HY2 18 24.021 -85.473 -7.031 1.00 0.00 N +ATOM 294 H HY2 18 18.784 -86.288 -8.152 1.00 0.00 H +ATOM 295 HA HY2 18 19.604 -83.604 -7.022 1.00 0.00 H +ATOM 296 HB2 HY2 18 20.879 -84.853 -9.437 1.00 0.00 H +ATOM 297 HB3 HY2 18 21.043 -83.100 -8.958 1.00 0.00 H +ATOM 298 HD1 HY2 18 22.140 -83.079 -6.059 1.00 0.00 H +ATOM 299 HD2 HY2 18 23.009 -86.090 -8.878 1.00 0.00 H +ATOM 300 HE1 HY2 18 24.302 -84.255 -5.326 1.00 0.00 H +ATOM 301 N GLU 19 17.821 -82.566 -8.312 1.00 0.00 N +ATOM 302 H GLU 19 17.981 -82.379 -7.332 1.00 0.00 H +ATOM 303 CA GLU 19 16.706 -81.915 -8.975 1.00 0.00 C +ATOM 304 HA GLU 19 16.181 -82.674 -9.555 1.00 0.00 H +ATOM 305 CB GLU 19 15.859 -81.325 -7.850 1.00 0.00 C +ATOM 306 HB2 GLU 19 15.274 -82.089 -7.338 1.00 0.00 H +ATOM 307 HB3 GLU 19 16.475 -80.898 -7.059 1.00 0.00 H +ATOM 308 CG GLU 19 14.756 -80.287 -8.300 1.00 0.00 C +ATOM 309 HG2 GLU 19 14.086 -80.009 -7.486 1.00 0.00 H +ATOM 310 HG3 GLU 19 15.414 -79.456 -8.550 1.00 0.00 H +ATOM 311 CD GLU 19 13.967 -80.701 -9.549 1.00 0.00 C +ATOM 312 OE1 GLU 19 13.764 -79.872 -10.472 1.00 0.00 O +ATOM 313 OE2 GLU 19 13.489 -81.831 -9.722 1.00 0.00 O +ATOM 314 C GLU 19 17.341 -80.872 -9.837 1.00 0.00 C +ATOM 315 O GLU 19 17.910 -79.933 -9.343 1.00 0.00 O +ATOM 316 N ALA 20 17.177 -80.955 -11.171 1.00 0.00 N +ATOM 317 H ALA 20 16.921 -81.880 -11.485 1.00 0.00 H +ATOM 318 CA ALA 20 17.572 -79.889 -12.061 1.00 0.00 C +ATOM 319 HA ALA 20 17.557 -79.009 -11.418 1.00 0.00 H +ATOM 320 CB ALA 20 19.050 -80.056 -12.524 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.309 -79.222 -13.175 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.164 -81.071 -12.904 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.561 -79.949 -11.567 1.00 0.00 H +ATOM 324 C ALA 20 16.728 -79.637 -13.278 1.00 0.00 C +ATOM 325 O ALA 20 15.906 -80.452 -13.569 1.00 0.00 O +ATOM 326 N VAL 21 16.942 -78.471 -14.018 1.00 0.00 N +ATOM 327 H VAL 21 17.427 -77.727 -13.538 1.00 0.00 H +ATOM 328 CA VAL 21 16.254 -78.217 -15.245 1.00 0.00 C +ATOM 329 HA VAL 21 15.230 -78.549 -15.072 1.00 0.00 H +ATOM 330 CB VAL 21 16.213 -76.648 -15.533 1.00 0.00 C +ATOM 331 HB VAL 21 15.838 -76.548 -16.552 1.00 0.00 H +ATOM 332 CG1 VAL 21 15.388 -75.930 -14.471 1.00 0.00 C +ATOM 333 HG11 VAL 21 15.829 -75.832 -13.479 1.00 0.00 H +ATOM 334 HG12 VAL 21 14.474 -76.516 -14.370 1.00 0.00 H +ATOM 335 HG13 VAL 21 15.092 -74.945 -14.834 1.00 0.00 H +ATOM 336 CG2 VAL 21 17.625 -76.035 -15.568 1.00 0.00 C +ATOM 337 HG21 VAL 21 18.227 -76.418 -16.392 1.00 0.00 H +ATOM 338 HG22 VAL 21 18.001 -76.169 -14.554 1.00 0.00 H +ATOM 339 HG23 VAL 21 17.634 -74.969 -15.795 1.00 0.00 H +ATOM 340 C VAL 21 16.845 -79.023 -16.417 1.00 0.00 C +ATOM 341 O VAL 21 16.236 -79.191 -17.475 1.00 0.00 O +ATOM 342 N ASP 22 18.068 -79.561 -16.299 1.00 0.00 N +ATOM 343 H ASP 22 18.530 -79.493 -15.403 1.00 0.00 H +ATOM 344 CA ASP 22 18.668 -80.469 -17.297 1.00 0.00 C +ATOM 345 HA ASP 22 17.880 -81.008 -17.822 1.00 0.00 H +ATOM 346 CB ASP 22 19.248 -79.554 -18.504 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.518 -78.818 -18.842 1.00 0.00 H +ATOM 348 HB3 ASP 22 19.944 -78.824 -18.090 1.00 0.00 H +ATOM 349 CG ASP 22 19.804 -80.314 -19.648 1.00 0.00 C +ATOM 350 OD1 ASP 22 20.716 -79.751 -20.389 1.00 0.00 O +ATOM 351 OD2 ASP 22 19.308 -81.459 -19.881 1.00 0.00 O +ATOM 352 C ASP 22 19.749 -81.343 -16.703 1.00 0.00 C +ATOM 353 O ASP 22 20.332 -80.965 -15.621 1.00 0.00 O +ATOM 354 N ALA 23 20.109 -82.459 -17.321 1.00 0.00 N +ATOM 355 H ALA 23 19.537 -82.802 -18.079 1.00 0.00 H +ATOM 356 CA ALA 23 21.034 -83.372 -16.600 1.00 0.00 C +ATOM 357 HA ALA 23 20.687 -83.474 -15.572 1.00 0.00 H +ATOM 358 CB ALA 23 20.861 -84.826 -17.253 1.00 0.00 C +ATOM 359 HB1 ALA 23 19.813 -85.125 -17.280 1.00 0.00 H +ATOM 360 HB2 ALA 23 21.406 -85.576 -16.679 1.00 0.00 H +ATOM 361 HB3 ALA 23 21.234 -84.897 -18.275 1.00 0.00 H +ATOM 362 C ALA 23 22.482 -82.792 -16.501 1.00 0.00 C +ATOM 363 O ALA 23 23.161 -83.031 -15.514 1.00 0.00 O +ATOM 364 N ALA 24 22.945 -81.990 -17.499 1.00 0.00 N +ATOM 365 H ALA 24 22.450 -81.867 -18.371 1.00 0.00 H +ATOM 366 CA ALA 24 24.213 -81.288 -17.323 1.00 0.00 C +ATOM 367 HA ALA 24 25.012 -82.002 -17.123 1.00 0.00 H +ATOM 368 CB ALA 24 24.586 -80.547 -18.665 1.00 0.00 C +ATOM 369 HB1 ALA 24 23.764 -79.883 -18.933 1.00 0.00 H +ATOM 370 HB2 ALA 24 24.633 -81.240 -19.505 1.00 0.00 H +ATOM 371 HB3 ALA 24 25.520 -79.988 -18.613 1.00 0.00 H +ATOM 372 C ALA 24 24.288 -80.304 -16.207 1.00 0.00 C +ATOM 373 O ALA 24 25.385 -79.967 -15.808 1.00 0.00 O +ATOM 374 N GLU 25 23.221 -79.844 -15.649 1.00 0.00 N +ATOM 375 H GLU 25 22.366 -80.152 -16.090 1.00 0.00 H +ATOM 376 CA GLU 25 23.107 -79.040 -14.421 1.00 0.00 C +ATOM 377 HA GLU 25 24.023 -78.456 -14.330 1.00 0.00 H +ATOM 378 CB GLU 25 21.870 -78.152 -14.483 1.00 0.00 C +ATOM 379 HB2 GLU 25 20.925 -78.693 -14.423 1.00 0.00 H +ATOM 380 HB3 GLU 25 21.876 -77.499 -13.610 1.00 0.00 H +ATOM 381 CG GLU 25 21.929 -77.100 -15.662 1.00 0.00 C +ATOM 382 HG2 GLU 25 22.111 -77.599 -16.613 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.947 -76.639 -15.550 1.00 0.00 H +ATOM 384 CD GLU 25 22.967 -75.926 -15.575 1.00 0.00 C +ATOM 385 OE1 GLU 25 23.817 -75.854 -16.479 1.00 0.00 O +ATOM 386 OE2 GLU 25 22.922 -75.185 -14.567 1.00 0.00 O +ATOM 387 C GLU 25 22.880 -79.952 -13.128 1.00 0.00 C +ATOM 388 O GLU 25 23.545 -79.611 -12.122 1.00 0.00 O +ATOM 389 N ALA 26 22.248 -81.127 -13.212 1.00 0.00 N +ATOM 390 H ALA 26 21.838 -81.445 -14.079 1.00 0.00 H +ATOM 391 CA ALA 26 22.394 -82.095 -12.107 1.00 0.00 C +ATOM 392 HA ALA 26 22.021 -81.630 -11.194 1.00 0.00 H +ATOM 393 CB ALA 26 21.390 -83.290 -12.252 1.00 0.00 C +ATOM 394 HB1 ALA 26 21.817 -84.159 -11.752 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.298 -83.504 -13.317 1.00 0.00 H +ATOM 396 HB3 ALA 26 20.462 -82.921 -11.814 1.00 0.00 H +ATOM 397 C ALA 26 23.805 -82.591 -11.887 1.00 0.00 C +ATOM 398 O ALA 26 24.120 -82.926 -10.743 1.00 0.00 O +ATOM 399 N GLU 27 24.522 -82.693 -13.007 1.00 0.00 N +ATOM 400 H GLU 27 24.082 -82.517 -13.899 1.00 0.00 H +ATOM 401 CA GLU 27 25.933 -83.107 -13.055 1.00 0.00 C +ATOM 402 HA GLU 27 26.151 -84.105 -12.674 1.00 0.00 H +ATOM 403 CB GLU 27 26.341 -83.131 -14.490 1.00 0.00 C +ATOM 404 HB2 GLU 27 25.722 -83.898 -14.955 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.201 -82.147 -14.938 1.00 0.00 H +ATOM 406 CG GLU 27 27.852 -83.532 -14.601 1.00 0.00 C +ATOM 407 HG2 GLU 27 28.468 -83.237 -13.751 1.00 0.00 H +ATOM 408 HG3 GLU 27 27.878 -84.619 -14.683 1.00 0.00 H +ATOM 409 CD GLU 27 28.486 -82.940 -15.830 1.00 0.00 C +ATOM 410 OE1 GLU 27 27.826 -82.335 -16.720 1.00 0.00 O +ATOM 411 OE2 GLU 27 29.682 -83.191 -16.031 1.00 0.00 O +ATOM 412 C GLU 27 26.735 -82.073 -12.257 1.00 0.00 C +ATOM 413 O GLU 27 27.583 -82.465 -11.425 1.00 0.00 O +ATOM 414 N LYS 28 26.560 -80.714 -12.454 1.00 0.00 N +ATOM 415 H LYS 28 25.776 -80.562 -13.072 1.00 0.00 H +ATOM 416 CA LYS 28 27.187 -79.640 -11.682 1.00 0.00 C +ATOM 417 HA LYS 28 28.267 -79.704 -11.818 1.00 0.00 H +ATOM 418 CB LYS 28 26.884 -78.253 -12.235 1.00 0.00 C +ATOM 419 HB2 LYS 28 25.806 -78.090 -12.207 1.00 0.00 H +ATOM 420 HB3 LYS 28 27.331 -77.510 -11.575 1.00 0.00 H +ATOM 421 CG LYS 28 27.338 -78.021 -13.724 1.00 0.00 C +ATOM 422 HG2 LYS 28 28.426 -78.076 -13.767 1.00 0.00 H +ATOM 423 HG3 LYS 28 26.929 -78.850 -14.302 1.00 0.00 H +ATOM 424 CD LYS 28 26.968 -76.720 -14.340 1.00 0.00 C +ATOM 425 HD2 LYS 28 25.887 -76.680 -14.212 1.00 0.00 H +ATOM 426 HD3 LYS 28 27.542 -75.873 -13.963 1.00 0.00 H +ATOM 427 CE LYS 28 27.260 -76.778 -15.826 1.00 0.00 C +ATOM 428 HE2 LYS 28 28.334 -76.947 -15.914 1.00 0.00 H +ATOM 429 HE3 LYS 28 26.750 -77.647 -16.239 1.00 0.00 H +ATOM 430 NZ LYS 28 26.761 -75.474 -16.439 1.00 0.00 N +ATOM 431 HZ1 LYS 28 27.189 -74.637 -16.070 1.00 0.00 H +ATOM 432 HZ2 LYS 28 25.756 -75.419 -16.347 1.00 0.00 H +ATOM 433 HZ3 LYS 28 26.965 -75.658 -17.411 1.00 0.00 H +ATOM 434 C LYS 28 26.876 -79.718 -10.220 1.00 0.00 C +ATOM 435 O LYS 28 27.782 -79.740 -9.373 1.00 0.00 O +ATOM 436 N PHE 29 25.622 -79.980 -9.846 1.00 0.00 N +ATOM 437 H PHE 29 25.002 -80.146 -10.626 1.00 0.00 H +ATOM 438 CA PHE 29 25.245 -80.297 -8.470 1.00 0.00 C +ATOM 439 HA PHE 29 25.648 -79.501 -7.843 1.00 0.00 H +ATOM 440 CB PHE 29 23.687 -80.381 -8.283 1.00 0.00 C +ATOM 441 HB2 PHE 29 23.307 -81.072 -9.035 1.00 0.00 H +ATOM 442 HB3 PHE 29 23.392 -80.720 -7.290 1.00 0.00 H +ATOM 443 CG PHE 29 22.948 -79.118 -8.484 1.00 0.00 C +ATOM 444 CD1 PHE 29 21.808 -79.072 -9.276 1.00 0.00 C +ATOM 445 HD1 PHE 29 21.467 -79.981 -9.749 1.00 0.00 H +ATOM 446 CE1 PHE 29 21.001 -77.890 -9.305 1.00 0.00 C +ATOM 447 HE1 PHE 29 20.176 -77.857 -10.001 1.00 0.00 H +ATOM 448 CZ PHE 29 21.433 -76.732 -8.687 1.00 0.00 C +ATOM 449 HZ PHE 29 20.889 -75.799 -8.721 1.00 0.00 H +ATOM 450 CE2 PHE 29 22.578 -76.704 -7.896 1.00 0.00 C +ATOM 451 HE2 PHE 29 22.822 -75.769 -7.414 1.00 0.00 H +ATOM 452 CD2 PHE 29 23.358 -77.925 -7.815 1.00 0.00 C +ATOM 453 HD2 PHE 29 24.271 -77.910 -7.238 1.00 0.00 H +ATOM 454 C PHE 29 25.972 -81.600 -7.896 1.00 0.00 C +ATOM 455 O PHE 29 26.456 -81.595 -6.742 1.00 0.00 O +ATOM 456 N THR 30 26.142 -82.591 -8.718 1.00 0.00 N +ATOM 457 H THR 30 25.568 -82.582 -9.549 1.00 0.00 H +ATOM 458 CA THR 30 26.857 -83.834 -8.415 1.00 0.00 C +ATOM 459 HA THR 30 26.483 -84.328 -7.518 1.00 0.00 H +ATOM 460 CB THR 30 26.893 -84.886 -9.525 1.00 0.00 C +ATOM 461 HB THR 30 26.855 -84.570 -10.568 1.00 0.00 H +ATOM 462 CG2 THR 30 28.139 -85.872 -9.503 1.00 0.00 C +ATOM 463 HG21 THR 30 28.530 -86.018 -8.496 1.00 0.00 H +ATOM 464 HG22 THR 30 27.768 -86.813 -9.911 1.00 0.00 H +ATOM 465 HG23 THR 30 28.930 -85.505 -10.157 1.00 0.00 H +ATOM 466 OG1 THR 30 25.723 -85.602 -9.308 1.00 0.00 O +ATOM 467 HG1 THR 30 24.935 -85.054 -9.285 1.00 0.00 H +ATOM 468 C THR 30 28.342 -83.488 -8.072 1.00 0.00 C +ATOM 469 O THR 30 28.838 -83.864 -7.018 1.00 0.00 O +ATOM 470 N LYS 31 29.058 -82.692 -8.924 1.00 0.00 N +ATOM 471 H LYS 31 28.525 -82.366 -9.718 1.00 0.00 H +ATOM 472 CA LYS 31 30.458 -82.190 -8.755 1.00 0.00 C +ATOM 473 HA LYS 31 31.129 -83.024 -8.547 1.00 0.00 H +ATOM 474 CB LYS 31 30.941 -81.586 -10.123 1.00 0.00 C +ATOM 475 HB2 LYS 31 30.087 -81.032 -10.513 1.00 0.00 H +ATOM 476 HB3 LYS 31 31.803 -80.932 -9.991 1.00 0.00 H +ATOM 477 CG LYS 31 31.253 -82.699 -11.156 1.00 0.00 C +ATOM 478 HG2 LYS 31 32.178 -83.209 -10.885 1.00 0.00 H +ATOM 479 HG3 LYS 31 30.416 -83.378 -11.320 1.00 0.00 H +ATOM 480 CD LYS 31 31.445 -82.169 -12.569 1.00 0.00 C +ATOM 481 HD2 LYS 31 30.515 -81.698 -12.889 1.00 0.00 H +ATOM 482 HD3 LYS 31 32.212 -81.398 -12.647 1.00 0.00 H +ATOM 483 CE LYS 31 31.802 -83.408 -13.371 1.00 0.00 C +ATOM 484 HE2 LYS 31 32.576 -83.897 -12.779 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.033 -84.171 -13.251 1.00 0.00 H +ATOM 486 NZ LYS 31 32.199 -83.177 -14.747 1.00 0.00 N +ATOM 487 HZ1 LYS 31 32.945 -82.496 -14.751 1.00 0.00 H +ATOM 488 HZ2 LYS 31 31.424 -82.829 -15.293 1.00 0.00 H +ATOM 489 HZ3 LYS 31 32.443 -84.057 -15.179 1.00 0.00 H +ATOM 490 C LYS 31 30.562 -81.202 -7.557 1.00 0.00 C +ATOM 491 O LYS 31 31.665 -80.941 -6.960 1.00 0.00 O +ATOM 492 N ALA 32 29.473 -80.496 -7.147 1.00 0.00 N +ATOM 493 H ALA 32 28.584 -80.627 -7.608 1.00 0.00 H +ATOM 494 CA ALA 32 29.512 -79.488 -6.130 1.00 0.00 C +ATOM 495 HA ALA 32 30.427 -78.897 -6.178 1.00 0.00 H +ATOM 496 CB ALA 32 28.384 -78.506 -6.431 1.00 0.00 C +ATOM 497 HB1 ALA 32 27.470 -79.101 -6.449 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.367 -77.712 -5.684 1.00 0.00 H +ATOM 499 HB3 ALA 32 28.452 -77.914 -7.344 1.00 0.00 H +ATOM 500 C ALA 32 29.614 -80.096 -4.704 1.00 0.00 C +ATOM 501 O ALA 32 30.437 -79.745 -3.936 1.00 0.00 O +ATOM 502 N ASP 33 28.779 -81.100 -4.452 1.00 0.00 N +ATOM 503 H ASP 33 28.017 -81.220 -5.104 1.00 0.00 H +ATOM 504 CA ASP 33 28.804 -81.948 -3.239 1.00 0.00 C +ATOM 505 HA ASP 33 28.730 -81.228 -2.424 1.00 0.00 H +ATOM 506 CB ASP 33 27.624 -82.915 -3.175 1.00 0.00 C +ATOM 507 HB2 ASP 33 27.611 -83.534 -4.072 1.00 0.00 H +ATOM 508 HB3 ASP 33 27.812 -83.565 -2.321 1.00 0.00 H +ATOM 509 CG ASP 33 26.255 -82.245 -3.046 1.00 0.00 C +ATOM 510 OD1 ASP 33 25.282 -83.010 -3.137 1.00 0.00 O +ATOM 511 OD2 ASP 33 26.136 -81.060 -2.905 1.00 0.00 O +ATOM 512 C ASP 33 30.071 -82.818 -3.068 1.00 0.00 C +ATOM 513 O ASP 33 30.568 -83.002 -1.930 1.00 0.00 O +ATOM 514 N ALA 34 30.690 -83.107 -4.169 1.00 0.00 N +ATOM 515 H ALA 34 30.160 -82.993 -5.021 1.00 0.00 H +ATOM 516 CA ALA 34 32.075 -83.675 -4.340 1.00 0.00 C +ATOM 517 HA ALA 34 32.227 -84.435 -3.573 1.00 0.00 H +ATOM 518 CB ALA 34 32.051 -84.354 -5.774 1.00 0.00 C +ATOM 519 HB1 ALA 34 33.067 -84.729 -5.895 1.00 0.00 H +ATOM 520 HB2 ALA 34 31.840 -83.647 -6.576 1.00 0.00 H +ATOM 521 HB3 ALA 34 31.485 -85.279 -5.886 1.00 0.00 H +ATOM 522 C ALA 34 33.166 -82.697 -4.118 1.00 0.00 C +ATOM 523 O ALA 34 34.180 -83.040 -3.436 1.00 0.00 O +ATOM 524 N ASN 35 33.022 -81.436 -4.608 1.00 0.00 N +ATOM 525 H ASN 35 32.207 -81.169 -5.142 1.00 0.00 H +ATOM 526 CA ASN 35 34.016 -80.421 -4.337 1.00 0.00 C +ATOM 527 HA ASN 35 34.999 -80.794 -4.626 1.00 0.00 H +ATOM 528 CB ASN 35 33.792 -79.128 -5.187 1.00 0.00 C +ATOM 529 HB2 ASN 35 33.602 -79.293 -6.247 1.00 0.00 H +ATOM 530 HB3 ASN 35 32.826 -78.797 -4.806 1.00 0.00 H +ATOM 531 CG ASN 35 34.751 -78.052 -5.039 1.00 0.00 C +ATOM 532 OD1 ASN 35 35.959 -78.247 -4.969 1.00 0.00 O +ATOM 533 ND2 ASN 35 34.256 -76.869 -4.938 1.00 0.00 N +ATOM 534 HD21 ASN 35 33.259 -76.783 -4.798 1.00 0.00 H +ATOM 535 HD22 ASN 35 34.956 -76.150 -4.826 1.00 0.00 H +ATOM 536 C ASN 35 34.090 -80.187 -2.777 1.00 0.00 C +ATOM 537 O ASN 35 35.232 -80.163 -2.262 1.00 0.00 O +ATOM 538 N ASP 36 32.913 -80.091 -2.124 1.00 0.00 N +ATOM 539 H ASP 36 32.062 -79.999 -2.659 1.00 0.00 H +ATOM 540 CA ASP 36 32.903 -80.039 -0.672 1.00 0.00 C +ATOM 541 HA ASP 36 33.285 -79.088 -0.299 1.00 0.00 H +ATOM 542 CB ASP 36 31.424 -80.109 -0.256 1.00 0.00 C +ATOM 543 HB2 ASP 36 30.862 -80.974 -0.607 1.00 0.00 H +ATOM 544 HB3 ASP 36 31.478 -80.108 0.833 1.00 0.00 H +ATOM 545 CG ASP 36 30.585 -78.928 -0.786 1.00 0.00 C +ATOM 546 OD1 ASP 36 29.346 -79.042 -1.011 1.00 0.00 O +ATOM 547 OD2 ASP 36 31.090 -77.787 -1.059 1.00 0.00 O +ATOM 548 C ASP 36 33.613 -81.176 0.078 1.00 0.00 C +ATOM 549 O ASP 36 33.971 -81.039 1.250 1.00 0.00 O +ATOM 550 N LYS 37 33.576 -82.386 -0.425 1.00 0.00 N +ATOM 551 H LYS 37 33.143 -82.490 -1.331 1.00 0.00 H +ATOM 552 CA LYS 37 34.163 -83.569 0.235 1.00 0.00 C +ATOM 553 HA LYS 37 34.176 -83.470 1.320 1.00 0.00 H +ATOM 554 CB LYS 37 33.309 -84.788 -0.120 1.00 0.00 C +ATOM 555 HB2 LYS 37 33.743 -85.750 0.155 1.00 0.00 H +ATOM 556 HB3 LYS 37 33.098 -84.775 -1.189 1.00 0.00 H +ATOM 557 CG LYS 37 31.961 -84.898 0.670 1.00 0.00 C +ATOM 558 HG2 LYS 37 31.411 -83.958 0.716 1.00 0.00 H +ATOM 559 HG3 LYS 37 32.094 -85.309 1.671 1.00 0.00 H +ATOM 560 CD LYS 37 31.040 -85.850 -0.065 1.00 0.00 C +ATOM 561 HD2 LYS 37 30.665 -85.485 -1.021 1.00 0.00 H +ATOM 562 HD3 LYS 37 31.539 -86.807 -0.216 1.00 0.00 H +ATOM 563 CE LYS 37 29.762 -86.143 0.685 1.00 0.00 C +ATOM 564 HE2 LYS 37 29.999 -86.532 1.675 1.00 0.00 H +ATOM 565 HE3 LYS 37 29.245 -85.188 0.771 1.00 0.00 H +ATOM 566 NZ LYS 37 28.844 -87.037 -0.139 1.00 0.00 N +ATOM 567 HZ1 LYS 37 28.448 -86.547 -0.928 1.00 0.00 H +ATOM 568 HZ2 LYS 37 29.378 -87.782 -0.563 1.00 0.00 H +ATOM 569 HZ3 LYS 37 28.203 -87.641 0.356 1.00 0.00 H +ATOM 570 C LYS 37 35.566 -83.821 -0.267 1.00 0.00 C +ATOM 571 O LYS 37 36.233 -84.609 0.398 1.00 0.00 O +ATOM 572 N GLY 38 35.980 -83.165 -1.348 1.00 0.00 N +ATOM 573 H GLY 38 35.370 -82.446 -1.710 1.00 0.00 H +ATOM 574 CA GLY 38 37.338 -83.427 -1.939 1.00 0.00 C +ATOM 575 HA2 GLY 38 37.740 -82.582 -2.497 1.00 0.00 H +ATOM 576 HA3 GLY 38 38.050 -83.561 -1.124 1.00 0.00 H +ATOM 577 C GLY 38 37.472 -84.638 -2.824 1.00 0.00 C +ATOM 578 O GLY 38 38.592 -85.106 -2.991 1.00 0.00 O +ATOM 579 N VAL 39 36.387 -85.059 -3.515 1.00 0.00 N +ATOM 580 H VAL 39 35.528 -84.538 -3.406 1.00 0.00 H +ATOM 581 CA VAL 39 36.374 -86.144 -4.544 1.00 0.00 C +ATOM 582 HA VAL 39 37.206 -86.799 -4.284 1.00 0.00 H +ATOM 583 CB VAL 39 35.023 -86.770 -4.491 1.00 0.00 C +ATOM 584 HB VAL 39 34.390 -85.972 -4.878 1.00 0.00 H +ATOM 585 CG1 VAL 39 34.953 -88.058 -5.460 1.00 0.00 C +ATOM 586 HG11 VAL 39 33.938 -88.442 -5.563 1.00 0.00 H +ATOM 587 HG12 VAL 39 35.685 -88.787 -5.112 1.00 0.00 H +ATOM 588 HG13 VAL 39 35.279 -87.767 -6.458 1.00 0.00 H +ATOM 589 CG2 VAL 39 34.662 -87.223 -3.041 1.00 0.00 C +ATOM 590 HG21 VAL 39 34.416 -86.395 -2.376 1.00 0.00 H +ATOM 591 HG22 VAL 39 35.426 -87.744 -2.464 1.00 0.00 H +ATOM 592 HG23 VAL 39 33.761 -87.836 -3.027 1.00 0.00 H +ATOM 593 C VAL 39 36.699 -85.670 -5.965 1.00 0.00 C +ATOM 594 O VAL 39 35.867 -84.944 -6.562 1.00 0.00 O +ATOM 595 N ASP 40 37.822 -86.089 -6.581 1.00 0.00 N +ATOM 596 H ASP 40 38.331 -86.755 -6.018 1.00 0.00 H +ATOM 597 CA ASP 40 38.367 -85.753 -7.913 1.00 0.00 C +ATOM 598 HA ASP 40 37.885 -84.816 -8.190 1.00 0.00 H +ATOM 599 CB ASP 40 39.876 -85.597 -7.897 1.00 0.00 C +ATOM 600 HB2 ASP 40 40.263 -85.200 -8.836 1.00 0.00 H +ATOM 601 HB3 ASP 40 40.110 -84.790 -7.203 1.00 0.00 H +ATOM 602 CG ASP 40 40.739 -86.788 -7.433 1.00 0.00 C +ATOM 603 OD1 ASP 40 41.981 -86.815 -7.557 1.00 0.00 O +ATOM 604 OD2 ASP 40 40.178 -87.637 -6.708 1.00 0.00 O +ATOM 605 C ASP 40 37.929 -86.724 -9.078 1.00 0.00 C +ATOM 606 O ASP 40 38.610 -86.810 -10.053 1.00 0.00 O +ATOM 607 N GLY 41 36.961 -87.573 -8.845 1.00 0.00 N +ATOM 608 H GLY 41 36.719 -87.739 -7.878 1.00 0.00 H +ATOM 609 CA GLY 41 36.333 -88.573 -9.785 1.00 0.00 C +ATOM 610 HA2 GLY 41 37.003 -89.361 -10.130 1.00 0.00 H +ATOM 611 HA3 GLY 41 35.439 -88.946 -9.286 1.00 0.00 H +ATOM 612 C GLY 41 35.779 -87.786 -11.057 1.00 0.00 C +ATOM 613 O GLY 41 35.797 -86.560 -11.146 1.00 0.00 O +ATOM 614 N GLU 42 35.168 -88.527 -11.976 1.00 0.00 N +ATOM 615 H GLU 42 35.388 -89.512 -12.019 1.00 0.00 H +ATOM 616 CA GLU 42 34.254 -88.015 -13.053 1.00 0.00 C +ATOM 617 HA GLU 42 34.091 -86.947 -12.908 1.00 0.00 H +ATOM 618 CB GLU 42 34.997 -87.972 -14.404 1.00 0.00 C +ATOM 619 HB2 GLU 42 35.946 -87.468 -14.220 1.00 0.00 H +ATOM 620 HB3 GLU 42 35.368 -88.979 -14.599 1.00 0.00 H +ATOM 621 CG GLU 42 34.365 -87.413 -15.715 1.00 0.00 C +ATOM 622 HG2 GLU 42 35.153 -87.328 -16.462 1.00 0.00 H +ATOM 623 HG3 GLU 42 33.608 -88.113 -16.070 1.00 0.00 H +ATOM 624 CD GLU 42 33.727 -86.054 -15.502 1.00 0.00 C +ATOM 625 OE1 GLU 42 34.416 -85.047 -15.764 1.00 0.00 O +ATOM 626 OE2 GLU 42 32.543 -85.969 -15.170 1.00 0.00 O +ATOM 627 C GLU 42 32.910 -88.730 -12.994 1.00 0.00 C +ATOM 628 O GLU 42 32.817 -89.826 -12.438 1.00 0.00 O +ATOM 629 N TRP 43 31.841 -88.173 -13.602 1.00 0.00 N +ATOM 630 H TRP 43 31.980 -87.296 -14.084 1.00 0.00 H +ATOM 631 CA TRP 43 30.439 -88.639 -13.453 1.00 0.00 C +ATOM 632 HA TRP 43 30.534 -89.617 -12.982 1.00 0.00 H +ATOM 633 CB TRP 43 29.707 -87.763 -12.495 1.00 0.00 C +ATOM 634 HB2 TRP 43 29.945 -86.747 -12.807 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.639 -87.944 -12.614 1.00 0.00 H +ATOM 636 CG TRP 43 30.071 -87.943 -11.045 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.746 -89.024 -10.335 1.00 0.00 C +ATOM 638 HD1 TRP 43 29.201 -89.901 -10.649 1.00 0.00 H +ATOM 639 NE1 TRP 43 30.329 -88.881 -9.092 1.00 0.00 N +ATOM 640 HE1 TRP 43 30.242 -89.550 -8.340 1.00 0.00 H +ATOM 641 CE2 TRP 43 31.225 -87.863 -9.035 1.00 0.00 C +ATOM 642 CZ2 TRP 43 32.161 -87.481 -8.071 1.00 0.00 C +ATOM 643 HZ2 TRP 43 32.236 -87.997 -7.126 1.00 0.00 H +ATOM 644 CH2 TRP 43 32.938 -86.419 -8.392 1.00 0.00 C +ATOM 645 HH2 TRP 43 33.617 -86.102 -7.615 1.00 0.00 H +ATOM 646 CZ3 TRP 43 32.931 -85.783 -9.643 1.00 0.00 C +ATOM 647 HZ3 TRP 43 33.694 -85.038 -9.816 1.00 0.00 H +ATOM 648 CE3 TRP 43 32.033 -86.207 -10.630 1.00 0.00 C +ATOM 649 HE3 TRP 43 32.044 -85.730 -11.599 1.00 0.00 H +ATOM 650 CD2 TRP 43 31.130 -87.228 -10.316 1.00 0.00 C +ATOM 651 C TRP 43 29.791 -88.846 -14.841 1.00 0.00 C +ATOM 652 O TRP 43 29.446 -87.858 -15.495 1.00 0.00 O +ATOM 653 N THR 44 29.650 -90.123 -15.157 1.00 0.00 N +ATOM 654 H THR 44 29.754 -90.799 -14.414 1.00 0.00 H +ATOM 655 CA THR 44 28.887 -90.553 -16.344 1.00 0.00 C +ATOM 656 HA THR 44 29.088 -89.850 -17.152 1.00 0.00 H +ATOM 657 CB THR 44 29.276 -91.946 -16.752 1.00 0.00 C +ATOM 658 HB THR 44 30.342 -91.919 -16.976 1.00 0.00 H +ATOM 659 CG2 THR 44 29.281 -93.006 -15.636 1.00 0.00 C +ATOM 660 HG21 THR 44 30.111 -92.844 -14.948 1.00 0.00 H +ATOM 661 HG22 THR 44 29.348 -93.964 -16.149 1.00 0.00 H +ATOM 662 HG23 THR 44 28.328 -92.975 -15.106 1.00 0.00 H +ATOM 663 OG1 THR 44 28.457 -92.517 -17.770 1.00 0.00 O +ATOM 664 HG1 THR 44 28.668 -92.057 -18.586 1.00 0.00 H +ATOM 665 C THR 44 27.355 -90.550 -16.066 1.00 0.00 C +ATOM 666 O THR 44 26.888 -90.639 -14.957 1.00 0.00 O +ATOM 667 N TYR 45 26.642 -90.403 -17.162 1.00 0.00 N +ATOM 668 H TYR 45 27.169 -90.436 -18.023 1.00 0.00 H +ATOM 669 CA TYR 45 25.204 -90.270 -17.251 1.00 0.00 C +ATOM 670 HA TYR 45 24.753 -90.423 -16.270 1.00 0.00 H +ATOM 671 CB TYR 45 24.801 -88.850 -17.600 1.00 0.00 C +ATOM 672 HB2 TYR 45 25.235 -88.176 -16.861 1.00 0.00 H +ATOM 673 HB3 TYR 45 25.322 -88.593 -18.523 1.00 0.00 H +ATOM 674 CG TYR 45 23.303 -88.530 -17.635 1.00 0.00 C +ATOM 675 CD1 TYR 45 22.503 -88.741 -16.501 1.00 0.00 C +ATOM 676 HD1 TYR 45 22.982 -89.030 -15.577 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.072 -88.681 -16.562 1.00 0.00 C +ATOM 678 HE1 TYR 45 20.508 -88.877 -15.662 1.00 0.00 H +ATOM 679 CZ TYR 45 20.451 -88.219 -17.748 1.00 0.00 C +ATOM 680 OH TYR 45 19.066 -88.077 -17.738 1.00 0.00 O +ATOM 681 HH TYR 45 18.789 -87.577 -18.510 1.00 0.00 H +ATOM 682 CE2 TYR 45 21.237 -87.951 -18.898 1.00 0.00 C +ATOM 683 HE2 TYR 45 20.813 -87.750 -19.871 1.00 0.00 H +ATOM 684 CD2 TYR 45 22.652 -88.108 -18.773 1.00 0.00 C +ATOM 685 HD2 TYR 45 23.325 -87.990 -19.609 1.00 0.00 H +ATOM 686 C TYR 45 24.527 -91.391 -18.105 1.00 0.00 C +ATOM 687 O TYR 45 24.962 -91.667 -19.253 1.00 0.00 O +ATOM 688 N ASP 46 23.422 -91.931 -17.658 1.00 0.00 N +ATOM 689 H ASP 46 22.985 -91.617 -16.803 1.00 0.00 H +ATOM 690 CA ASP 46 22.600 -92.924 -18.380 1.00 0.00 C +ATOM 691 HA ASP 46 22.919 -92.979 -19.421 1.00 0.00 H +ATOM 692 CB ASP 46 22.596 -94.331 -17.804 1.00 0.00 C +ATOM 693 HB2 ASP 46 23.638 -94.649 -17.847 1.00 0.00 H +ATOM 694 HB3 ASP 46 22.288 -94.306 -16.759 1.00 0.00 H +ATOM 695 CG ASP 46 21.683 -95.290 -18.566 1.00 0.00 C +ATOM 696 OD1 ASP 46 21.097 -96.220 -17.917 1.00 0.00 O +ATOM 697 OD2 ASP 46 21.400 -95.011 -19.805 1.00 0.00 O +ATOM 698 C ASP 46 21.126 -92.334 -18.442 1.00 0.00 C +ATOM 699 O ASP 46 20.309 -92.481 -17.555 1.00 0.00 O +ATOM 700 N ASP 47 20.786 -91.808 -19.634 1.00 0.00 N +ATOM 701 H ASP 47 21.408 -91.987 -20.410 1.00 0.00 H +ATOM 702 CA ASP 47 19.528 -91.210 -19.974 1.00 0.00 C +ATOM 703 HA ASP 47 19.270 -90.405 -19.287 1.00 0.00 H +ATOM 704 CB ASP 47 19.787 -90.507 -21.374 1.00 0.00 C +ATOM 705 HB2 ASP 47 20.622 -89.816 -21.265 1.00 0.00 H +ATOM 706 HB3 ASP 47 20.040 -91.279 -22.101 1.00 0.00 H +ATOM 707 CG ASP 47 18.615 -89.643 -21.876 1.00 0.00 C +ATOM 708 OD1 ASP 47 17.620 -89.446 -21.158 1.00 0.00 O +ATOM 709 OD2 ASP 47 18.794 -89.093 -23.003 1.00 0.00 O +ATOM 710 C ASP 47 18.390 -92.228 -19.926 1.00 0.00 C +ATOM 711 O ASP 47 17.228 -92.011 -19.469 1.00 0.00 O +ATOM 712 N ALA 48 18.646 -93.476 -20.387 1.00 0.00 N +ATOM 713 H ALA 48 19.548 -93.543 -20.836 1.00 0.00 H +ATOM 714 CA ALA 48 17.613 -94.569 -20.428 1.00 0.00 C +ATOM 715 HA ALA 48 16.780 -94.154 -20.995 1.00 0.00 H +ATOM 716 CB ALA 48 18.243 -95.791 -21.114 1.00 0.00 C +ATOM 717 HB1 ALA 48 19.150 -96.080 -20.584 1.00 0.00 H +ATOM 718 HB2 ALA 48 18.516 -95.451 -22.113 1.00 0.00 H +ATOM 719 HB3 ALA 48 17.541 -96.623 -21.064 1.00 0.00 H +ATOM 720 C ALA 48 17.132 -94.818 -18.993 1.00 0.00 C +ATOM 721 O ALA 48 15.907 -95.015 -18.819 1.00 0.00 O +ATOM 722 N THR 49 17.922 -94.755 -17.922 1.00 0.00 N +ATOM 723 H THR 49 18.893 -94.693 -18.193 1.00 0.00 H +ATOM 724 CA THR 49 17.426 -94.861 -16.502 1.00 0.00 C +ATOM 725 HA THR 49 16.431 -95.305 -16.536 1.00 0.00 H +ATOM 726 CB THR 49 18.217 -95.924 -15.679 1.00 0.00 C +ATOM 727 HB THR 49 17.994 -95.904 -14.613 1.00 0.00 H +ATOM 728 CG2 THR 49 18.418 -97.345 -16.170 1.00 0.00 C +ATOM 729 HG21 THR 49 18.841 -97.440 -17.170 1.00 0.00 H +ATOM 730 HG22 THR 49 17.405 -97.715 -16.331 1.00 0.00 H +ATOM 731 HG23 THR 49 19.021 -98.014 -15.557 1.00 0.00 H +ATOM 732 OG1 THR 49 19.552 -95.468 -15.810 1.00 0.00 O +ATOM 733 HG1 THR 49 19.923 -95.812 -16.626 1.00 0.00 H +ATOM 734 C THR 49 17.421 -93.573 -15.671 1.00 0.00 C +ATOM 735 O THR 49 17.174 -93.600 -14.452 1.00 0.00 O +ATOM 736 N LYS 50 17.782 -92.422 -16.316 1.00 0.00 N +ATOM 737 H LYS 50 18.132 -92.635 -17.239 1.00 0.00 H +ATOM 738 CA LYS 50 17.876 -91.084 -15.709 1.00 0.00 C +ATOM 739 HA LYS 50 18.433 -90.477 -16.423 1.00 0.00 H +ATOM 740 CB LYS 50 16.542 -90.484 -15.317 1.00 0.00 C +ATOM 741 HB2 LYS 50 16.115 -91.046 -14.486 1.00 0.00 H +ATOM 742 HB3 LYS 50 16.644 -89.457 -14.966 1.00 0.00 H +ATOM 743 CG LYS 50 15.587 -90.483 -16.482 1.00 0.00 C +ATOM 744 HG2 LYS 50 15.415 -91.502 -16.829 1.00 0.00 H +ATOM 745 HG3 LYS 50 14.645 -90.031 -16.173 1.00 0.00 H +ATOM 746 CD LYS 50 16.058 -89.536 -17.616 1.00 0.00 C +ATOM 747 HD2 LYS 50 16.273 -88.554 -17.196 1.00 0.00 H +ATOM 748 HD3 LYS 50 16.958 -89.948 -18.073 1.00 0.00 H +ATOM 749 CE LYS 50 14.977 -89.328 -18.637 1.00 0.00 C +ATOM 750 HE2 LYS 50 14.718 -90.244 -19.168 1.00 0.00 H +ATOM 751 HE3 LYS 50 14.095 -88.969 -18.107 1.00 0.00 H +ATOM 752 NZ LYS 50 15.515 -88.431 -19.696 1.00 0.00 N +ATOM 753 HZ1 LYS 50 16.033 -87.612 -19.411 1.00 0.00 H +ATOM 754 HZ2 LYS 50 14.765 -88.073 -20.269 1.00 0.00 H +ATOM 755 HZ3 LYS 50 16.199 -88.930 -20.248 1.00 0.00 H +ATOM 756 C LYS 50 18.888 -90.991 -14.559 1.00 0.00 C +ATOM 757 O LYS 50 18.547 -90.562 -13.462 1.00 0.00 O +ATOM 758 N THR 51 20.022 -91.601 -14.770 1.00 0.00 N +ATOM 759 H THR 51 20.095 -91.955 -15.713 1.00 0.00 H +ATOM 760 CA THR 51 20.996 -91.998 -13.672 1.00 0.00 C +ATOM 761 HA THR 51 20.639 -91.552 -12.743 1.00 0.00 H +ATOM 762 CB THR 51 20.958 -93.521 -13.437 1.00 0.00 C +ATOM 763 HB THR 51 21.435 -94.080 -14.242 1.00 0.00 H +ATOM 764 CG2 THR 51 21.669 -93.919 -12.122 1.00 0.00 C +ATOM 765 HG21 THR 51 21.319 -93.311 -11.287 1.00 0.00 H +ATOM 766 HG22 THR 51 22.706 -93.636 -12.305 1.00 0.00 H +ATOM 767 HG23 THR 51 21.564 -94.989 -11.943 1.00 0.00 H +ATOM 768 OG1 THR 51 19.675 -94.077 -13.258 1.00 0.00 O +ATOM 769 HG1 THR 51 19.357 -94.048 -14.164 1.00 0.00 H +ATOM 770 C THR 51 22.464 -91.653 -13.897 1.00 0.00 C +ATOM 771 O THR 51 23.052 -91.885 -14.942 1.00 0.00 O +ATOM 772 N PHE 52 23.010 -90.969 -12.900 1.00 0.00 N +ATOM 773 H PHE 52 22.385 -90.847 -12.116 1.00 0.00 H +ATOM 774 CA PHE 52 24.443 -90.694 -12.851 1.00 0.00 C +ATOM 775 HA PHE 52 24.870 -90.599 -13.849 1.00 0.00 H +ATOM 776 CB PHE 52 24.650 -89.364 -12.073 1.00 0.00 C +ATOM 777 HB2 PHE 52 23.967 -89.291 -11.227 1.00 0.00 H +ATOM 778 HB3 PHE 52 25.651 -89.206 -11.673 1.00 0.00 H +ATOM 779 CG PHE 52 24.362 -88.248 -13.050 1.00 0.00 C +ATOM 780 CD1 PHE 52 23.031 -87.758 -13.200 1.00 0.00 C +ATOM 781 HD1 PHE 52 22.227 -88.112 -12.572 1.00 0.00 H +ATOM 782 CE1 PHE 52 22.776 -86.696 -14.080 1.00 0.00 C +ATOM 783 HE1 PHE 52 21.802 -86.242 -14.185 1.00 0.00 H +ATOM 784 CZ PHE 52 23.794 -86.192 -14.870 1.00 0.00 C +ATOM 785 HZ PHE 52 23.596 -85.505 -15.679 1.00 0.00 H +ATOM 786 CE2 PHE 52 25.082 -86.608 -14.670 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.831 -86.099 -15.259 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.423 -87.631 -13.732 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.432 -88.011 -13.675 1.00 0.00 H +ATOM 790 C PHE 52 25.239 -91.768 -12.039 1.00 0.00 C +ATOM 791 O PHE 52 24.699 -92.411 -11.113 1.00 0.00 O +ATOM 792 N THR 53 26.512 -91.952 -12.414 1.00 0.00 N +ATOM 793 H THR 53 26.798 -91.257 -13.088 1.00 0.00 H +ATOM 794 CA THR 53 27.486 -92.947 -11.870 1.00 0.00 C +ATOM 795 HA THR 53 27.202 -93.228 -10.856 1.00 0.00 H +ATOM 796 CB THR 53 27.348 -94.303 -12.631 1.00 0.00 C +ATOM 797 HB THR 53 27.978 -94.251 -13.519 1.00 0.00 H +ATOM 798 CG2 THR 53 27.875 -95.508 -11.840 1.00 0.00 C +ATOM 799 HG21 THR 53 27.505 -96.437 -12.273 1.00 0.00 H +ATOM 800 HG22 THR 53 27.590 -95.398 -10.794 1.00 0.00 H +ATOM 801 HG23 THR 53 28.964 -95.478 -11.826 1.00 0.00 H +ATOM 802 OG1 THR 53 25.999 -94.654 -12.964 1.00 0.00 O +ATOM 803 HG1 THR 53 25.829 -94.330 -13.852 1.00 0.00 H +ATOM 804 C THR 53 28.969 -92.484 -11.831 1.00 0.00 C +ATOM 805 O THR 53 29.362 -91.697 -12.697 1.00 0.00 O +ATOM 806 N VAL 54 29.726 -92.738 -10.762 1.00 0.00 N +ATOM 807 H VAL 54 29.409 -93.303 -9.988 1.00 0.00 H +ATOM 808 CA VAL 54 31.163 -92.409 -10.710 1.00 0.00 C +ATOM 809 HA VAL 54 31.230 -91.414 -11.148 1.00 0.00 H +ATOM 810 CB VAL 54 31.657 -92.418 -9.199 1.00 0.00 C +ATOM 811 HB VAL 54 31.019 -91.742 -8.630 1.00 0.00 H +ATOM 812 CG1 VAL 54 31.640 -93.855 -8.735 1.00 0.00 C +ATOM 813 HG11 VAL 54 32.516 -94.328 -9.178 1.00 0.00 H +ATOM 814 HG12 VAL 54 30.709 -94.344 -9.021 1.00 0.00 H +ATOM 815 HG13 VAL 54 31.687 -93.885 -7.646 1.00 0.00 H +ATOM 816 CG2 VAL 54 33.070 -91.832 -9.069 1.00 0.00 C +ATOM 817 HG21 VAL 54 33.239 -91.745 -7.996 1.00 0.00 H +ATOM 818 HG22 VAL 54 33.172 -90.865 -9.561 1.00 0.00 H +ATOM 819 HG23 VAL 54 33.829 -92.477 -9.511 1.00 0.00 H +ATOM 820 C VAL 54 31.980 -93.258 -11.627 1.00 0.00 C +ATOM 821 O VAL 54 31.733 -94.412 -11.869 1.00 0.00 O +ATOM 822 N THR 55 32.994 -92.622 -12.226 1.00 0.00 N +ATOM 823 H THR 55 33.091 -91.620 -12.307 1.00 0.00 H +ATOM 824 CA THR 55 34.078 -93.319 -12.841 1.00 0.00 C +ATOM 825 HA THR 55 34.062 -94.365 -12.533 1.00 0.00 H +ATOM 826 CB THR 55 33.877 -93.370 -14.348 1.00 0.00 C +ATOM 827 HB THR 55 32.924 -93.884 -14.475 1.00 0.00 H +ATOM 828 CG2 THR 55 33.894 -92.120 -15.172 1.00 0.00 C +ATOM 829 HG21 THR 55 34.894 -91.740 -15.377 1.00 0.00 H +ATOM 830 HG22 THR 55 33.327 -91.391 -14.593 1.00 0.00 H +ATOM 831 HG23 THR 55 33.416 -92.254 -16.143 1.00 0.00 H +ATOM 832 OG1 THR 55 34.949 -94.141 -14.881 1.00 0.00 O +ATOM 833 HG1 THR 55 34.589 -94.612 -15.636 1.00 0.00 H +ATOM 834 C THR 55 35.385 -92.656 -12.519 1.00 0.00 C +ATOM 835 O THR 55 35.544 -91.459 -12.379 1.00 0.00 O +ATOM 836 N GLU 56 36.379 -93.530 -12.262 1.00 0.00 N +ATOM 837 H GLU 56 36.062 -94.470 -12.448 1.00 0.00 H +ATOM 838 CA GLU 56 37.616 -93.250 -11.595 1.00 0.00 C +ATOM 839 HA GLU 56 37.604 -92.240 -11.184 1.00 0.00 H +ATOM 840 CB GLU 56 37.866 -94.143 -10.385 1.00 0.00 C +ATOM 841 HB2 GLU 56 37.899 -95.206 -10.622 1.00 0.00 H +ATOM 842 HB3 GLU 56 38.762 -93.842 -9.843 1.00 0.00 H +ATOM 843 CG GLU 56 36.670 -93.986 -9.445 1.00 0.00 C +ATOM 844 HG2 GLU 56 36.396 -92.932 -9.391 1.00 0.00 H +ATOM 845 HG3 GLU 56 35.834 -94.624 -9.732 1.00 0.00 H +ATOM 846 CD GLU 56 37.068 -94.292 -7.961 1.00 0.00 C +ATOM 847 OE1 GLU 56 37.875 -93.586 -7.298 1.00 0.00 O +ATOM 848 OE2 GLU 56 36.524 -95.253 -7.436 1.00 0.00 O +ATOM 849 C GLU 56 38.740 -93.284 -12.623 1.00 0.00 C +ATOM 850 O GLU 56 39.000 -92.299 -13.292 1.00 0.00 O +ATOM 851 OXT GLU 56 39.381 -94.364 -12.719 1.00 0.00 O +ATOM 852 ZN ZN1 57 25.100 -87.152 -6.560 1.00 0.00 ZN +ATOM 853 N AN1 58 26.967 -86.664 -5.694 1.00 0.00 N +ATOM 854 C AN1 58 29.314 -86.682 -4.687 1.00 0.00 C +ATOM 855 C1 AN1 58 27.986 -86.551 -5.171 1.00 0.00 C +ATOM 856 H AN1 58 29.917 -86.607 -5.600 1.00 0.00 H +ATOM 857 H1 AN1 58 29.495 -87.631 -4.167 1.00 0.00 H +ATOM 858 H2 AN1 58 29.640 -85.822 -4.090 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 29.727 -90.743 -6.412 1.00 0.00 N +ATOM 860 N2 AZI 59 29.040 -90.347 -5.478 1.00 0.00 N +ATOM 861 N3 AZI 59 28.347 -89.841 -4.556 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/pdbs_rename/cluster6.pdb b/tests/nsga2/pdbs_rename/cluster6.pdb new file mode 100644 index 0000000..c59b8ee --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster6.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.667 -82.176 -12.164 1.00 0.00 N +ATOM 2 H1 MET 1 13.345 -81.872 -11.257 1.00 0.00 H +ATOM 3 H2 MET 1 13.089 -81.931 -12.955 1.00 0.00 H +ATOM 4 H3 MET 1 14.636 -81.918 -12.289 1.00 0.00 H +ATOM 5 CA MET 1 13.747 -83.651 -12.043 1.00 0.00 C +ATOM 6 HA MET 1 12.886 -84.113 -11.559 1.00 0.00 H +ATOM 7 CB MET 1 13.926 -84.174 -13.437 1.00 0.00 C +ATOM 8 HB2 MET 1 13.255 -83.660 -14.126 1.00 0.00 H +ATOM 9 HB3 MET 1 14.935 -84.037 -13.828 1.00 0.00 H +ATOM 10 CG MET 1 13.762 -85.696 -13.636 1.00 0.00 C +ATOM 11 HG2 MET 1 14.476 -86.251 -13.026 1.00 0.00 H +ATOM 12 HG3 MET 1 12.758 -85.874 -13.252 1.00 0.00 H +ATOM 13 SD MET 1 13.949 -86.291 -15.359 1.00 0.00 S +ATOM 14 CE MET 1 12.198 -86.649 -15.785 1.00 0.00 C +ATOM 15 HE1 MET 1 11.658 -85.734 -16.028 1.00 0.00 H +ATOM 16 HE2 MET 1 11.702 -87.201 -14.987 1.00 0.00 H +ATOM 17 HE3 MET 1 12.225 -87.181 -16.737 1.00 0.00 H +ATOM 18 C MET 1 14.875 -83.961 -11.106 1.00 0.00 C +ATOM 19 O MET 1 15.974 -83.430 -11.324 1.00 0.00 O +ATOM 20 N GLN 2 14.545 -84.841 -10.100 1.00 0.00 N +ATOM 21 H GLN 2 13.558 -85.048 -10.055 1.00 0.00 H +ATOM 22 CA GLN 2 15.493 -85.432 -9.104 1.00 0.00 C +ATOM 23 HA GLN 2 16.198 -84.699 -8.711 1.00 0.00 H +ATOM 24 CB GLN 2 14.681 -85.886 -7.808 1.00 0.00 C +ATOM 25 HB2 GLN 2 13.662 -86.068 -8.147 1.00 0.00 H +ATOM 26 HB3 GLN 2 15.074 -86.833 -7.437 1.00 0.00 H +ATOM 27 CG GLN 2 14.637 -84.856 -6.657 1.00 0.00 C +ATOM 28 HG2 GLN 2 14.366 -83.916 -7.138 1.00 0.00 H +ATOM 29 HG3 GLN 2 13.786 -85.013 -5.993 1.00 0.00 H +ATOM 30 CD GLN 2 15.896 -84.647 -5.773 1.00 0.00 C +ATOM 31 OE1 GLN 2 17.005 -85.003 -6.063 1.00 0.00 O +ATOM 32 NE2 GLN 2 15.841 -83.918 -4.661 1.00 0.00 N +ATOM 33 HE21 GLN 2 16.786 -83.730 -4.360 1.00 0.00 H +ATOM 34 HE22 GLN 2 15.007 -83.429 -4.369 1.00 0.00 H +ATOM 35 C GLN 2 16.261 -86.517 -9.873 1.00 0.00 C +ATOM 36 O GLN 2 15.834 -87.664 -9.829 1.00 0.00 O +ATOM 37 N TYR 3 17.269 -86.107 -10.647 1.00 0.00 N +ATOM 38 H TYR 3 17.660 -85.178 -10.584 1.00 0.00 H +ATOM 39 CA TYR 3 18.103 -87.083 -11.400 1.00 0.00 C +ATOM 40 HA TYR 3 17.375 -87.614 -12.013 1.00 0.00 H +ATOM 41 CB TYR 3 19.081 -86.342 -12.286 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.652 -85.588 -11.745 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.878 -87.044 -12.535 1.00 0.00 H +ATOM 44 CG TYR 3 18.592 -85.713 -13.593 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.407 -86.519 -14.793 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.655 -87.569 -14.830 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.058 -85.841 -15.953 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.017 -86.390 -16.882 1.00 0.00 H +ATOM 49 CZ TYR 3 17.660 -84.486 -15.943 1.00 0.00 C +ATOM 50 OH TYR 3 17.191 -83.845 -17.042 1.00 0.00 O +ATOM 51 HH TYR 3 16.915 -84.440 -17.743 1.00 0.00 H +ATOM 52 CE2 TYR 3 17.664 -83.740 -14.738 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.438 -82.685 -14.789 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.219 -84.325 -13.565 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.314 -83.710 -12.682 1.00 0.00 H +ATOM 56 C TYR 3 18.816 -88.038 -10.506 1.00 0.00 C +ATOM 57 O TYR 3 19.433 -87.532 -9.527 1.00 0.00 O +ATOM 58 N LYS 4 19.125 -89.290 -10.854 1.00 0.00 N +ATOM 59 H LYS 4 18.883 -89.476 -11.817 1.00 0.00 H +ATOM 60 CA LYS 4 19.659 -90.434 -10.051 1.00 0.00 C +ATOM 61 HA LYS 4 19.382 -90.313 -9.004 1.00 0.00 H +ATOM 62 CB LYS 4 19.018 -91.748 -10.594 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.896 -91.660 -11.674 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.709 -92.560 -10.367 1.00 0.00 H +ATOM 65 CG LYS 4 17.668 -92.066 -10.056 1.00 0.00 C +ATOM 66 HG2 LYS 4 17.405 -93.049 -10.446 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.705 -92.185 -8.974 1.00 0.00 H +ATOM 68 CD LYS 4 16.541 -91.124 -10.387 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.586 -90.210 -9.794 1.00 0.00 H +ATOM 70 HD3 LYS 4 16.586 -90.913 -11.456 1.00 0.00 H +ATOM 71 CE LYS 4 15.139 -91.799 -10.099 1.00 0.00 C +ATOM 72 HE2 LYS 4 14.295 -91.304 -10.579 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.214 -92.786 -10.555 1.00 0.00 H +ATOM 74 NZ LYS 4 14.745 -91.872 -8.686 1.00 0.00 N +ATOM 75 HZ1 LYS 4 13.849 -92.308 -8.516 1.00 0.00 H +ATOM 76 HZ2 LYS 4 14.635 -90.940 -8.313 1.00 0.00 H +ATOM 77 HZ3 LYS 4 15.455 -92.339 -8.140 1.00 0.00 H +ATOM 78 C LYS 4 21.160 -90.434 -10.131 1.00 0.00 C +ATOM 79 O LYS 4 21.768 -90.126 -11.151 1.00 0.00 O +ATOM 80 N HX1 5 21.743 -90.838 -9.009 1.00 0.00 N +ATOM 81 CA HX1 5 23.157 -91.103 -8.854 1.00 0.00 C +ATOM 82 C HX1 5 23.300 -92.305 -7.854 1.00 0.00 C +ATOM 83 O HX1 5 22.707 -92.294 -6.788 1.00 0.00 O +ATOM 84 CB HX1 5 23.707 -89.740 -8.343 1.00 0.00 C +ATOM 85 CG HX1 5 25.186 -89.730 -8.194 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.196 -90.461 -8.792 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.765 -88.622 -7.573 1.00 0.00 N +ATOM 88 CE1 HX1 5 27.032 -88.750 -7.789 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.384 -89.832 -8.470 1.00 0.00 N +ATOM 90 H HX1 5 21.228 -90.820 -8.141 1.00 0.00 H +ATOM 91 HA HX1 5 23.648 -91.397 -9.781 1.00 0.00 H +ATOM 92 HB2 HX1 5 23.338 -89.554 -7.334 1.00 0.00 H +ATOM 93 HB3 HX1 5 23.333 -88.951 -8.995 1.00 0.00 H +ATOM 94 HD2 HX1 5 26.091 -91.163 -9.606 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.810 -88.162 -7.324 1.00 0.00 H +ATOM 96 HE2 HX1 5 28.307 -90.204 -8.642 1.00 0.00 H +ATOM 97 N ILE 6 24.131 -93.282 -8.297 1.00 0.00 N +ATOM 98 H ILE 6 24.752 -93.123 -9.078 1.00 0.00 H +ATOM 99 CA ILE 6 24.461 -94.449 -7.464 1.00 0.00 C +ATOM 100 HA ILE 6 23.713 -94.533 -6.676 1.00 0.00 H +ATOM 101 CB ILE 6 24.252 -95.758 -8.382 1.00 0.00 C +ATOM 102 HB ILE 6 24.797 -95.720 -9.326 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.722 -97.042 -7.772 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.804 -97.023 -7.638 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.375 -97.920 -8.316 1.00 0.00 H +ATOM 106 HG23 ILE 6 24.291 -97.189 -6.782 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.778 -95.880 -8.650 1.00 0.00 C +ATOM 108 HG12 ILE 6 22.345 -95.846 -7.650 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.380 -94.981 -9.121 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.195 -97.097 -9.472 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.449 -97.069 -10.532 1.00 0.00 H +ATOM 112 HD12 ILE 6 21.120 -97.079 -9.290 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.496 -98.069 -9.081 1.00 0.00 H +ATOM 114 C ILE 6 25.907 -94.311 -6.946 1.00 0.00 C +ATOM 115 O ILE 6 26.751 -93.686 -7.559 1.00 0.00 O +ATOM 116 N VAL 7 26.151 -94.902 -5.742 1.00 0.00 N +ATOM 117 H VAL 7 25.516 -95.526 -5.264 1.00 0.00 H +ATOM 118 CA VAL 7 27.372 -94.653 -4.940 1.00 0.00 C +ATOM 119 HA VAL 7 27.497 -93.596 -4.705 1.00 0.00 H +ATOM 120 CB VAL 7 27.122 -95.410 -3.526 1.00 0.00 C +ATOM 121 HB VAL 7 26.089 -95.262 -3.211 1.00 0.00 H +ATOM 122 CG1 VAL 7 27.221 -96.936 -3.654 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.272 -97.169 -3.822 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.890 -97.387 -2.719 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.560 -97.324 -4.429 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.999 -94.909 -2.393 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.824 -93.843 -2.253 1.00 0.00 H +ATOM 128 HG22 VAL 7 27.522 -95.360 -1.522 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.007 -95.264 -2.608 1.00 0.00 H +ATOM 130 C VAL 7 28.726 -95.057 -5.556 1.00 0.00 C +ATOM 131 O VAL 7 28.780 -95.823 -6.475 1.00 0.00 O +ATOM 132 N ASN 8 29.899 -94.565 -4.960 1.00 0.00 N +ATOM 133 H ASN 8 29.714 -93.930 -4.197 1.00 0.00 H +ATOM 134 CA ASN 8 31.309 -95.009 -5.046 1.00 0.00 C +ATOM 135 HA ASN 8 31.482 -95.165 -6.111 1.00 0.00 H +ATOM 136 CB ASN 8 32.146 -93.816 -4.501 1.00 0.00 C +ATOM 137 HB2 ASN 8 31.899 -92.888 -5.015 1.00 0.00 H +ATOM 138 HB3 ASN 8 31.764 -93.743 -3.483 1.00 0.00 H +ATOM 139 CG ASN 8 33.605 -94.026 -4.560 1.00 0.00 C +ATOM 140 OD1 ASN 8 34.120 -94.429 -5.587 1.00 0.00 O +ATOM 141 ND2 ASN 8 34.230 -93.804 -3.459 1.00 0.00 N +ATOM 142 HD21 ASN 8 33.763 -93.677 -2.573 1.00 0.00 H +ATOM 143 HD22 ASN 8 35.231 -93.787 -3.589 1.00 0.00 H +ATOM 144 C ASN 8 31.623 -96.322 -4.359 1.00 0.00 C +ATOM 145 O ASN 8 30.968 -96.715 -3.402 1.00 0.00 O +ATOM 146 N GLY 9 32.768 -96.919 -4.808 1.00 0.00 N +ATOM 147 H GLY 9 33.363 -96.521 -5.521 1.00 0.00 H +ATOM 148 CA GLY 9 33.156 -98.183 -4.299 1.00 0.00 C +ATOM 149 HA2 GLY 9 34.204 -98.393 -4.516 1.00 0.00 H +ATOM 150 HA3 GLY 9 33.094 -98.139 -3.211 1.00 0.00 H +ATOM 151 C GLY 9 32.385 -99.421 -4.775 1.00 0.00 C +ATOM 152 O GLY 9 31.857 -99.435 -5.933 1.00 0.00 O +ATOM 153 N LYS 10 32.266-100.412 -3.893 1.00 0.00 N +ATOM 154 H LYS 10 32.751-100.263 -3.019 1.00 0.00 H +ATOM 155 CA LYS 10 31.491-101.593 -4.134 1.00 0.00 C +ATOM 156 HA LYS 10 30.664-101.283 -4.772 1.00 0.00 H +ATOM 157 CB LYS 10 32.409-102.668 -4.824 1.00 0.00 C +ATOM 158 HB2 LYS 10 33.136-102.140 -5.442 1.00 0.00 H +ATOM 159 HB3 LYS 10 32.861-103.318 -4.075 1.00 0.00 H +ATOM 160 CG LYS 10 31.455-103.454 -5.798 1.00 0.00 C +ATOM 161 HG2 LYS 10 30.660-103.882 -5.187 1.00 0.00 H +ATOM 162 HG3 LYS 10 30.972-102.803 -6.526 1.00 0.00 H +ATOM 163 CD LYS 10 32.290-104.566 -6.497 1.00 0.00 C +ATOM 164 HD2 LYS 10 32.935-104.020 -7.184 1.00 0.00 H +ATOM 165 HD3 LYS 10 32.885-105.037 -5.715 1.00 0.00 H +ATOM 166 CE LYS 10 31.316-105.532 -7.234 1.00 0.00 C +ATOM 167 HE2 LYS 10 30.498-105.730 -6.543 1.00 0.00 H +ATOM 168 HE3 LYS 10 30.944-104.921 -8.057 1.00 0.00 H +ATOM 169 NZ LYS 10 32.046-106.725 -7.738 1.00 0.00 N +ATOM 170 HZ1 LYS 10 32.381-107.284 -6.967 1.00 0.00 H +ATOM 171 HZ2 LYS 10 32.878-106.436 -8.232 1.00 0.00 H +ATOM 172 HZ3 LYS 10 31.423-107.235 -8.348 1.00 0.00 H +ATOM 173 C LYS 10 30.905-102.168 -2.803 1.00 0.00 C +ATOM 174 O LYS 10 30.273-103.222 -2.816 1.00 0.00 O +ATOM 175 N THR 11 31.460-101.708 -1.640 1.00 0.00 N +ATOM 176 H THR 11 32.091-100.920 -1.692 1.00 0.00 H +ATOM 177 CA THR 11 31.097-101.976 -0.262 1.00 0.00 C +ATOM 178 HA THR 11 31.036-103.064 -0.268 1.00 0.00 H +ATOM 179 CB THR 11 32.204-101.575 0.708 1.00 0.00 C +ATOM 180 HB THR 11 32.357-100.511 0.524 1.00 0.00 H +ATOM 181 CG2 THR 11 31.844-101.737 2.186 1.00 0.00 C +ATOM 182 HG21 THR 11 31.939-102.768 2.527 1.00 0.00 H +ATOM 183 HG22 THR 11 30.866-101.287 2.359 1.00 0.00 H +ATOM 184 HG23 THR 11 32.641-101.220 2.720 1.00 0.00 H +ATOM 185 OG1 THR 11 33.395-102.365 0.540 1.00 0.00 O +ATOM 186 HG1 THR 11 33.889-101.797 -0.056 1.00 0.00 H +ATOM 187 C THR 11 29.693-101.456 0.085 1.00 0.00 C +ATOM 188 O THR 11 28.931-102.158 0.709 1.00 0.00 O +ATOM 189 N LEU 12 29.334-100.250 -0.348 1.00 0.00 N +ATOM 190 H LEU 12 30.049 -99.688 -0.789 1.00 0.00 H +ATOM 191 CA LEU 12 27.972 -99.742 -0.384 1.00 0.00 C +ATOM 192 HA LEU 12 27.387-100.206 0.411 1.00 0.00 H +ATOM 193 CB LEU 12 28.128 -98.251 -0.163 1.00 0.00 C +ATOM 194 HB2 LEU 12 28.747 -97.809 -0.944 1.00 0.00 H +ATOM 195 HB3 LEU 12 27.159 -97.765 -0.285 1.00 0.00 H +ATOM 196 CG LEU 12 28.691 -97.864 1.224 1.00 0.00 C +ATOM 197 HG LEU 12 29.731 -98.167 1.352 1.00 0.00 H +ATOM 198 CD1 LEU 12 28.636 -96.332 1.379 1.00 0.00 C +ATOM 199 HD11 LEU 12 27.594 -96.036 1.503 1.00 0.00 H +ATOM 200 HD12 LEU 12 28.995 -95.783 0.508 1.00 0.00 H +ATOM 201 HD13 LEU 12 29.219 -95.938 2.212 1.00 0.00 H +ATOM 202 CD2 LEU 12 27.939 -98.536 2.321 1.00 0.00 C +ATOM 203 HD21 LEU 12 26.858 -98.614 2.209 1.00 0.00 H +ATOM 204 HD22 LEU 12 28.012 -97.961 3.244 1.00 0.00 H +ATOM 205 HD23 LEU 12 28.324 -99.549 2.439 1.00 0.00 H +ATOM 206 C LEU 12 27.297-100.039 -1.733 1.00 0.00 C +ATOM 207 O LEU 12 27.999-100.466 -2.659 1.00 0.00 O +ATOM 208 N LYS 13 25.944 -99.848 -1.880 1.00 0.00 N +ATOM 209 H LYS 13 25.635 -99.454 -1.003 1.00 0.00 H +ATOM 210 CA LYS 13 25.102-100.117 -3.010 1.00 0.00 C +ATOM 211 HA LYS 13 25.635 -99.817 -3.912 1.00 0.00 H +ATOM 212 CB LYS 13 24.795-101.570 -3.121 1.00 0.00 C +ATOM 213 HB2 LYS 13 25.679-102.060 -2.714 1.00 0.00 H +ATOM 214 HB3 LYS 13 23.957-101.847 -2.481 1.00 0.00 H +ATOM 215 CG LYS 13 24.564-102.129 -4.461 1.00 0.00 C +ATOM 216 HG2 LYS 13 23.690-101.657 -4.909 1.00 0.00 H +ATOM 217 HG3 LYS 13 25.417-102.009 -5.129 1.00 0.00 H +ATOM 218 CD LYS 13 24.350-103.649 -4.396 1.00 0.00 C +ATOM 219 HD2 LYS 13 24.457-103.984 -5.428 1.00 0.00 H +ATOM 220 HD3 LYS 13 25.145-104.071 -3.782 1.00 0.00 H +ATOM 221 CE LYS 13 22.965-104.052 -3.813 1.00 0.00 C +ATOM 222 HE2 LYS 13 22.834-103.504 -2.879 1.00 0.00 H +ATOM 223 HE3 LYS 13 22.161-103.846 -4.520 1.00 0.00 H +ATOM 224 NZ LYS 13 23.017-105.478 -3.459 1.00 0.00 N +ATOM 225 HZ1 LYS 13 22.206-105.765 -2.931 1.00 0.00 H +ATOM 226 HZ2 LYS 13 23.829-105.715 -2.906 1.00 0.00 H +ATOM 227 HZ3 LYS 13 23.113-106.070 -4.272 1.00 0.00 H +ATOM 228 C LYS 13 23.842 -99.251 -3.093 1.00 0.00 C +ATOM 229 O LYS 13 23.023 -99.515 -3.981 1.00 0.00 O +ATOM 230 N GLY 14 23.763 -98.191 -2.282 1.00 0.00 N +ATOM 231 H GLY 14 24.503 -98.245 -1.596 1.00 0.00 H +ATOM 232 CA GLY 14 22.652 -97.215 -2.132 1.00 0.00 C +ATOM 233 HA2 GLY 14 21.774 -97.855 -2.220 1.00 0.00 H +ATOM 234 HA3 GLY 14 22.643 -96.693 -1.176 1.00 0.00 H +ATOM 235 C GLY 14 22.615 -96.170 -3.256 1.00 0.00 C +ATOM 236 O GLY 14 23.558 -95.997 -4.049 1.00 0.00 O +ATOM 237 N VAL 15 21.543 -95.390 -3.302 1.00 0.00 N +ATOM 238 H VAL 15 20.819 -95.534 -2.613 1.00 0.00 H +ATOM 239 CA VAL 15 21.101 -94.576 -4.404 1.00 0.00 C +ATOM 240 HA VAL 15 22.036 -94.331 -4.909 1.00 0.00 H +ATOM 241 CB VAL 15 20.204 -95.353 -5.387 1.00 0.00 C +ATOM 242 HB VAL 15 20.781 -96.180 -5.798 1.00 0.00 H +ATOM 243 CG1 VAL 15 18.907 -95.850 -4.661 1.00 0.00 C +ATOM 244 HG11 VAL 15 19.150 -96.368 -3.733 1.00 0.00 H +ATOM 245 HG12 VAL 15 18.317 -94.978 -4.379 1.00 0.00 H +ATOM 246 HG13 VAL 15 18.297 -96.522 -5.264 1.00 0.00 H +ATOM 247 CG2 VAL 15 19.836 -94.489 -6.605 1.00 0.00 C +ATOM 248 HG21 VAL 15 19.200 -93.659 -6.296 1.00 0.00 H +ATOM 249 HG22 VAL 15 20.618 -94.052 -7.226 1.00 0.00 H +ATOM 250 HG23 VAL 15 19.115 -95.037 -7.211 1.00 0.00 H +ATOM 251 C VAL 15 20.481 -93.228 -4.012 1.00 0.00 C +ATOM 252 O VAL 15 19.513 -93.178 -3.248 1.00 0.00 O +ATOM 253 N HY1 16 20.951 -92.123 -4.563 1.00 0.00 N +ATOM 254 CA HY1 16 20.357 -90.837 -4.242 1.00 0.00 C +ATOM 255 C HY1 16 20.019 -90.061 -5.468 1.00 0.00 C +ATOM 256 O HY1 16 20.269 -90.519 -6.588 1.00 0.00 O +ATOM 257 CB HY1 16 21.257 -90.105 -3.173 1.00 0.00 C +ATOM 258 CG HY1 16 22.604 -89.680 -3.690 1.00 0.00 C +ATOM 259 CD2 HY1 16 22.938 -88.499 -4.281 1.00 0.00 C +ATOM 260 ND1 HY1 16 23.756 -90.525 -3.843 1.00 0.00 N +ATOM 261 CE1 HY1 16 24.711 -89.791 -4.337 1.00 0.00 C +ATOM 262 NE2 HY1 16 24.224 -88.609 -4.737 1.00 0.00 N +ATOM 263 H HY1 16 21.513 -92.215 -5.398 1.00 0.00 H +ATOM 264 HA HY1 16 19.431 -90.940 -3.676 1.00 0.00 H +ATOM 265 HB2 HY1 16 20.822 -89.193 -2.766 1.00 0.00 H +ATOM 266 HB3 HY1 16 21.470 -90.750 -2.321 1.00 0.00 H +ATOM 267 HD1 HY1 16 23.903 -91.485 -3.567 1.00 0.00 H +ATOM 268 HD2 HY1 16 22.312 -87.653 -4.525 1.00 0.00 H +ATOM 269 HE1 HY1 16 25.704 -90.179 -4.510 1.00 0.00 H +ATOM 270 N THR 17 19.687 -88.783 -5.357 1.00 0.00 N +ATOM 271 H THR 17 19.604 -88.381 -4.434 1.00 0.00 H +ATOM 272 CA THR 17 19.293 -87.910 -6.485 1.00 0.00 C +ATOM 273 HA THR 17 19.744 -88.252 -7.416 1.00 0.00 H +ATOM 274 CB THR 17 17.750 -88.011 -6.717 1.00 0.00 C +ATOM 275 HB THR 17 17.626 -87.440 -7.637 1.00 0.00 H +ATOM 276 CG2 THR 17 17.129 -89.401 -6.924 1.00 0.00 C +ATOM 277 HG21 THR 17 17.405 -89.852 -7.877 1.00 0.00 H +ATOM 278 HG22 THR 17 16.046 -89.303 -7.002 1.00 0.00 H +ATOM 279 HG23 THR 17 17.378 -90.157 -6.179 1.00 0.00 H +ATOM 280 OG1 THR 17 17.128 -87.503 -5.511 1.00 0.00 O +ATOM 281 HG1 THR 17 17.086 -86.544 -5.500 1.00 0.00 H +ATOM 282 C THR 17 19.817 -86.471 -6.303 1.00 0.00 C +ATOM 283 O THR 17 20.098 -86.023 -5.210 1.00 0.00 O +ATOM 284 N HY2 18 19.810 -85.736 -7.428 1.00 0.00 N +ATOM 285 CA HY2 18 20.113 -84.275 -7.478 1.00 0.00 C +ATOM 286 C HY2 18 18.960 -83.619 -8.315 1.00 0.00 C +ATOM 287 O HY2 18 18.743 -83.967 -9.476 1.00 0.00 O +ATOM 288 CB HY2 18 21.403 -83.791 -8.200 1.00 0.00 C +ATOM 289 CG HY2 18 22.595 -84.384 -7.472 1.00 0.00 C +ATOM 290 CD2 HY2 18 23.160 -85.632 -7.631 1.00 0.00 C +ATOM 291 ND1 HY2 18 23.424 -83.728 -6.549 1.00 0.00 N +ATOM 292 CE1 HY2 18 24.384 -84.578 -6.115 1.00 0.00 C +ATOM 293 NE2 HY2 18 24.234 -85.775 -6.753 1.00 0.00 N +ATOM 294 H HY2 18 19.570 -86.155 -8.315 1.00 0.00 H +ATOM 295 HA HY2 18 20.066 -83.847 -6.476 1.00 0.00 H +ATOM 296 HB2 HY2 18 21.352 -84.158 -9.225 1.00 0.00 H +ATOM 297 HB3 HY2 18 21.586 -82.723 -8.319 1.00 0.00 H +ATOM 298 HD1 HY2 18 23.251 -82.784 -6.232 1.00 0.00 H +ATOM 299 HD2 HY2 18 22.825 -86.315 -8.398 1.00 0.00 H +ATOM 300 HE1 HY2 18 24.971 -84.319 -5.246 1.00 0.00 H +ATOM 301 N GLU 19 18.427 -82.512 -7.718 1.00 0.00 N +ATOM 302 H GLU 19 18.769 -82.137 -6.845 1.00 0.00 H +ATOM 303 CA GLU 19 17.319 -81.694 -8.437 1.00 0.00 C +ATOM 304 HA GLU 19 16.671 -82.425 -8.920 1.00 0.00 H +ATOM 305 CB GLU 19 16.676 -80.754 -7.422 1.00 0.00 C +ATOM 306 HB2 GLU 19 16.366 -81.410 -6.609 1.00 0.00 H +ATOM 307 HB3 GLU 19 17.343 -80.053 -6.922 1.00 0.00 H +ATOM 308 CG GLU 19 15.513 -79.963 -8.022 1.00 0.00 C +ATOM 309 HG2 GLU 19 15.280 -79.332 -7.164 1.00 0.00 H +ATOM 310 HG3 GLU 19 15.856 -79.435 -8.912 1.00 0.00 H +ATOM 311 CD GLU 19 14.330 -80.872 -8.360 1.00 0.00 C +ATOM 312 OE1 GLU 19 14.122 -81.089 -9.540 1.00 0.00 O +ATOM 313 OE2 GLU 19 13.505 -81.256 -7.496 1.00 0.00 O +ATOM 314 C GLU 19 17.977 -80.831 -9.472 1.00 0.00 C +ATOM 315 O GLU 19 18.854 -80.037 -9.220 1.00 0.00 O +ATOM 316 N ALA 20 17.451 -81.010 -10.687 1.00 0.00 N +ATOM 317 H ALA 20 16.703 -81.657 -10.896 1.00 0.00 H +ATOM 318 CA ALA 20 17.824 -80.137 -11.795 1.00 0.00 C +ATOM 319 HA ALA 20 17.860 -79.113 -11.424 1.00 0.00 H +ATOM 320 CB ALA 20 19.139 -80.611 -12.327 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.851 -80.751 -11.513 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.528 -79.796 -12.938 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.111 -81.429 -13.046 1.00 0.00 H +ATOM 324 C ALA 20 16.730 -80.115 -12.926 1.00 0.00 C +ATOM 325 O ALA 20 15.945 -81.080 -13.072 1.00 0.00 O +ATOM 326 N VAL 21 16.751 -79.121 -13.810 1.00 0.00 N +ATOM 327 H VAL 21 17.549 -78.505 -13.742 1.00 0.00 H +ATOM 328 CA VAL 21 16.076 -79.145 -15.113 1.00 0.00 C +ATOM 329 HA VAL 21 15.085 -79.561 -14.932 1.00 0.00 H +ATOM 330 CB VAL 21 15.875 -77.683 -15.662 1.00 0.00 C +ATOM 331 HB VAL 21 15.154 -77.812 -16.469 1.00 0.00 H +ATOM 332 CG1 VAL 21 15.365 -76.737 -14.571 1.00 0.00 C +ATOM 333 HG11 VAL 21 14.940 -75.857 -15.055 1.00 0.00 H +ATOM 334 HG12 VAL 21 16.006 -76.444 -13.740 1.00 0.00 H +ATOM 335 HG13 VAL 21 14.485 -77.202 -14.126 1.00 0.00 H +ATOM 336 CG2 VAL 21 17.162 -77.094 -16.279 1.00 0.00 C +ATOM 337 HG21 VAL 21 17.955 -77.287 -15.557 1.00 0.00 H +ATOM 338 HG22 VAL 21 16.946 -76.032 -16.393 1.00 0.00 H +ATOM 339 HG23 VAL 21 17.453 -77.563 -17.219 1.00 0.00 H +ATOM 340 C VAL 21 16.741 -80.098 -16.104 1.00 0.00 C +ATOM 341 O VAL 21 15.989 -80.601 -16.996 1.00 0.00 O +ATOM 342 N ASP 22 18.050 -80.354 -16.051 1.00 0.00 N +ATOM 343 H ASP 22 18.533 -80.069 -15.211 1.00 0.00 H +ATOM 344 CA ASP 22 18.928 -80.953 -17.033 1.00 0.00 C +ATOM 345 HA ASP 22 18.270 -81.538 -17.676 1.00 0.00 H +ATOM 346 CB ASP 22 19.648 -79.746 -17.740 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.981 -79.081 -18.288 1.00 0.00 H +ATOM 348 HB3 ASP 22 20.276 -79.146 -17.082 1.00 0.00 H +ATOM 349 CG ASP 22 20.724 -80.202 -18.725 1.00 0.00 C +ATOM 350 OD1 ASP 22 21.459 -79.296 -19.181 1.00 0.00 O +ATOM 351 OD2 ASP 22 20.869 -81.376 -19.090 1.00 0.00 O +ATOM 352 C ASP 22 20.012 -81.789 -16.335 1.00 0.00 C +ATOM 353 O ASP 22 20.624 -81.204 -15.491 1.00 0.00 O +ATOM 354 N ALA 23 20.338 -83.050 -16.743 1.00 0.00 N +ATOM 355 H ALA 23 19.733 -83.376 -17.483 1.00 0.00 H +ATOM 356 CA ALA 23 21.419 -83.874 -16.165 1.00 0.00 C +ATOM 357 HA ALA 23 21.177 -83.968 -15.107 1.00 0.00 H +ATOM 358 CB ALA 23 21.411 -85.209 -16.800 1.00 0.00 C +ATOM 359 HB1 ALA 23 20.431 -85.678 -16.716 1.00 0.00 H +ATOM 360 HB2 ALA 23 22.276 -85.746 -16.411 1.00 0.00 H +ATOM 361 HB3 ALA 23 21.537 -85.216 -17.883 1.00 0.00 H +ATOM 362 C ALA 23 22.840 -83.159 -16.243 1.00 0.00 C +ATOM 363 O ALA 23 23.672 -83.452 -15.427 1.00 0.00 O +ATOM 364 N ALA 24 23.109 -82.381 -17.277 1.00 0.00 N +ATOM 365 H ALA 24 22.401 -82.154 -17.961 1.00 0.00 H +ATOM 366 CA ALA 24 24.357 -81.600 -17.423 1.00 0.00 C +ATOM 367 HA ALA 24 25.232 -82.166 -17.106 1.00 0.00 H +ATOM 368 CB ALA 24 24.452 -81.255 -18.925 1.00 0.00 C +ATOM 369 HB1 ALA 24 23.790 -80.406 -19.094 1.00 0.00 H +ATOM 370 HB2 ALA 24 24.175 -82.062 -19.603 1.00 0.00 H +ATOM 371 HB3 ALA 24 25.490 -80.945 -19.050 1.00 0.00 H +ATOM 372 C ALA 24 24.372 -80.300 -16.519 1.00 0.00 C +ATOM 373 O ALA 24 25.416 -79.761 -16.210 1.00 0.00 O +ATOM 374 N GLU 25 23.201 -79.856 -16.002 1.00 0.00 N +ATOM 375 H GLU 25 22.321 -80.298 -16.225 1.00 0.00 H +ATOM 376 CA GLU 25 23.251 -78.986 -14.776 1.00 0.00 C +ATOM 377 HA GLU 25 24.130 -78.345 -14.700 1.00 0.00 H +ATOM 378 CB GLU 25 22.001 -78.096 -14.704 1.00 0.00 C +ATOM 379 HB2 GLU 25 21.098 -78.704 -14.757 1.00 0.00 H +ATOM 380 HB3 GLU 25 22.031 -77.616 -13.726 1.00 0.00 H +ATOM 381 CG GLU 25 21.895 -76.928 -15.732 1.00 0.00 C +ATOM 382 HG2 GLU 25 21.660 -77.290 -16.733 1.00 0.00 H +ATOM 383 HG3 GLU 25 21.067 -76.270 -15.466 1.00 0.00 H +ATOM 384 CD GLU 25 23.216 -76.051 -15.780 1.00 0.00 C +ATOM 385 OE1 GLU 25 23.433 -75.240 -14.840 1.00 0.00 O +ATOM 386 OE2 GLU 25 24.133 -76.356 -16.583 1.00 0.00 O +ATOM 387 C GLU 25 23.424 -79.823 -13.499 1.00 0.00 C +ATOM 388 O GLU 25 24.203 -79.466 -12.643 1.00 0.00 O +ATOM 389 N ALA 26 22.713 -81.018 -13.428 1.00 0.00 N +ATOM 390 H ALA 26 22.171 -81.322 -14.224 1.00 0.00 H +ATOM 391 CA ALA 26 22.871 -81.907 -12.311 1.00 0.00 C +ATOM 392 HA ALA 26 22.536 -81.322 -11.455 1.00 0.00 H +ATOM 393 CB ALA 26 21.936 -83.126 -12.329 1.00 0.00 C +ATOM 394 HB1 ALA 26 22.132 -83.723 -13.220 1.00 0.00 H +ATOM 395 HB2 ALA 26 20.921 -82.744 -12.441 1.00 0.00 H +ATOM 396 HB3 ALA 26 22.119 -83.660 -11.397 1.00 0.00 H +ATOM 397 C ALA 26 24.340 -82.356 -12.104 1.00 0.00 C +ATOM 398 O ALA 26 24.706 -82.655 -10.977 1.00 0.00 O +ATOM 399 N GLU 27 25.122 -82.484 -13.202 1.00 0.00 N +ATOM 400 H GLU 27 24.631 -82.486 -14.085 1.00 0.00 H +ATOM 401 CA GLU 27 26.561 -82.720 -13.245 1.00 0.00 C +ATOM 402 HA GLU 27 26.868 -83.636 -12.740 1.00 0.00 H +ATOM 403 CB GLU 27 27.065 -82.779 -14.691 1.00 0.00 C +ATOM 404 HB2 GLU 27 26.417 -83.345 -15.359 1.00 0.00 H +ATOM 405 HB3 GLU 27 27.009 -81.812 -15.192 1.00 0.00 H +ATOM 406 CG GLU 27 28.508 -83.425 -14.785 1.00 0.00 C +ATOM 407 HG2 GLU 27 29.269 -82.819 -14.293 1.00 0.00 H +ATOM 408 HG3 GLU 27 28.551 -84.423 -14.348 1.00 0.00 H +ATOM 409 CD GLU 27 28.834 -83.409 -16.308 1.00 0.00 C +ATOM 410 OE1 GLU 27 28.654 -82.376 -17.012 1.00 0.00 O +ATOM 411 OE2 GLU 27 29.481 -84.414 -16.705 1.00 0.00 O +ATOM 412 C GLU 27 27.266 -81.633 -12.426 1.00 0.00 C +ATOM 413 O GLU 27 27.947 -81.966 -11.431 1.00 0.00 O +ATOM 414 N LYS 28 27.125 -80.351 -12.713 1.00 0.00 N +ATOM 415 H LYS 28 26.584 -80.197 -13.552 1.00 0.00 H +ATOM 416 CA LYS 28 27.671 -79.224 -11.955 1.00 0.00 C +ATOM 417 HA LYS 28 28.733 -79.452 -11.870 1.00 0.00 H +ATOM 418 CB LYS 28 27.356 -77.831 -12.608 1.00 0.00 C +ATOM 419 HB2 LYS 28 26.383 -77.425 -12.330 1.00 0.00 H +ATOM 420 HB3 LYS 28 27.995 -77.098 -12.116 1.00 0.00 H +ATOM 421 CG LYS 28 27.734 -77.795 -14.105 1.00 0.00 C +ATOM 422 HG2 LYS 28 28.770 -78.070 -14.299 1.00 0.00 H +ATOM 423 HG3 LYS 28 27.157 -78.619 -14.525 1.00 0.00 H +ATOM 424 CD LYS 28 27.347 -76.422 -14.653 1.00 0.00 C +ATOM 425 HD2 LYS 28 26.272 -76.263 -14.566 1.00 0.00 H +ATOM 426 HD3 LYS 28 27.757 -75.689 -13.958 1.00 0.00 H +ATOM 427 CE LYS 28 28.016 -76.288 -16.078 1.00 0.00 C +ATOM 428 HE2 LYS 28 28.716 -75.455 -16.141 1.00 0.00 H +ATOM 429 HE3 LYS 28 28.635 -77.171 -16.239 1.00 0.00 H +ATOM 430 NZ LYS 28 26.991 -76.234 -17.183 1.00 0.00 N +ATOM 431 HZ1 LYS 28 26.158 -75.718 -16.936 1.00 0.00 H +ATOM 432 HZ2 LYS 28 26.679 -77.163 -17.426 1.00 0.00 H +ATOM 433 HZ3 LYS 28 27.447 -75.851 -17.999 1.00 0.00 H +ATOM 434 C LYS 28 27.213 -79.210 -10.452 1.00 0.00 C +ATOM 435 O LYS 28 28.094 -79.023 -9.622 1.00 0.00 O +ATOM 436 N PHE 29 25.985 -79.486 -10.149 1.00 0.00 N +ATOM 437 H PHE 29 25.360 -79.562 -10.939 1.00 0.00 H +ATOM 438 CA PHE 29 25.551 -79.477 -8.719 1.00 0.00 C +ATOM 439 HA PHE 29 25.742 -78.560 -8.162 1.00 0.00 H +ATOM 440 CB PHE 29 23.996 -79.474 -8.732 1.00 0.00 C +ATOM 441 HB2 PHE 29 23.785 -80.452 -9.163 1.00 0.00 H +ATOM 442 HB3 PHE 29 23.669 -79.442 -7.693 1.00 0.00 H +ATOM 443 CG PHE 29 23.193 -78.354 -9.423 1.00 0.00 C +ATOM 444 CD1 PHE 29 22.062 -78.579 -10.198 1.00 0.00 C +ATOM 445 HD1 PHE 29 21.606 -79.558 -10.206 1.00 0.00 H +ATOM 446 CE1 PHE 29 21.434 -77.627 -10.986 1.00 0.00 C +ATOM 447 HE1 PHE 29 20.531 -77.911 -11.506 1.00 0.00 H +ATOM 448 CZ PHE 29 21.868 -76.303 -10.941 1.00 0.00 C +ATOM 449 HZ PHE 29 21.333 -75.515 -11.450 1.00 0.00 H +ATOM 450 CE2 PHE 29 22.926 -76.054 -10.031 1.00 0.00 C +ATOM 451 HE2 PHE 29 23.257 -75.028 -9.968 1.00 0.00 H +ATOM 452 CD2 PHE 29 23.696 -77.071 -9.458 1.00 0.00 C +ATOM 453 HD2 PHE 29 24.644 -76.855 -8.987 1.00 0.00 H +ATOM 454 C PHE 29 26.096 -80.744 -7.970 1.00 0.00 C +ATOM 455 O PHE 29 26.207 -80.704 -6.736 1.00 0.00 O +ATOM 456 N THR 30 26.474 -81.871 -8.565 1.00 0.00 N +ATOM 457 H THR 30 26.426 -81.899 -9.573 1.00 0.00 H +ATOM 458 CA THR 30 27.168 -83.046 -8.036 1.00 0.00 C +ATOM 459 HA THR 30 26.615 -83.356 -7.149 1.00 0.00 H +ATOM 460 CB THR 30 27.342 -84.203 -9.080 1.00 0.00 C +ATOM 461 HB THR 30 27.953 -83.888 -9.926 1.00 0.00 H +ATOM 462 CG2 THR 30 28.017 -85.412 -8.566 1.00 0.00 C +ATOM 463 HG21 THR 30 28.140 -86.135 -9.372 1.00 0.00 H +ATOM 464 HG22 THR 30 29.011 -85.203 -8.172 1.00 0.00 H +ATOM 465 HG23 THR 30 27.464 -85.851 -7.735 1.00 0.00 H +ATOM 466 OG1 THR 30 26.028 -84.567 -9.550 1.00 0.00 O +ATOM 467 HG1 THR 30 25.526 -83.783 -9.787 1.00 0.00 H +ATOM 468 C THR 30 28.556 -82.594 -7.681 1.00 0.00 C +ATOM 469 O THR 30 29.076 -83.028 -6.629 1.00 0.00 O +ATOM 470 N LYS 31 29.212 -81.787 -8.547 1.00 0.00 N +ATOM 471 H LYS 31 28.821 -81.508 -9.436 1.00 0.00 H +ATOM 472 CA LYS 31 30.531 -81.286 -8.331 1.00 0.00 C +ATOM 473 HA LYS 31 31.196 -82.067 -7.962 1.00 0.00 H +ATOM 474 CB LYS 31 31.156 -80.605 -9.496 1.00 0.00 C +ATOM 475 HB2 LYS 31 30.424 -79.879 -9.850 1.00 0.00 H +ATOM 476 HB3 LYS 31 32.062 -80.067 -9.214 1.00 0.00 H +ATOM 477 CG LYS 31 31.534 -81.600 -10.550 1.00 0.00 C +ATOM 478 HG2 LYS 31 32.301 -82.287 -10.193 1.00 0.00 H +ATOM 479 HG3 LYS 31 30.700 -82.238 -10.843 1.00 0.00 H +ATOM 480 CD LYS 31 31.952 -80.940 -11.969 1.00 0.00 C +ATOM 481 HD2 LYS 31 31.166 -80.246 -12.267 1.00 0.00 H +ATOM 482 HD3 LYS 31 32.769 -80.271 -11.702 1.00 0.00 H +ATOM 483 CE LYS 31 32.303 -81.983 -13.036 1.00 0.00 C +ATOM 484 HE2 LYS 31 31.521 -82.734 -12.926 1.00 0.00 H +ATOM 485 HE3 LYS 31 32.189 -81.470 -13.990 1.00 0.00 H +ATOM 486 NZ LYS 31 33.590 -82.671 -12.953 1.00 0.00 N +ATOM 487 HZ1 LYS 31 34.302 -81.976 -12.779 1.00 0.00 H +ATOM 488 HZ2 LYS 31 33.873 -83.156 -13.793 1.00 0.00 H +ATOM 489 HZ3 LYS 31 33.680 -83.305 -12.172 1.00 0.00 H +ATOM 490 C LYS 31 30.544 -80.305 -7.179 1.00 0.00 C +ATOM 491 O LYS 31 31.599 -80.141 -6.644 1.00 0.00 O +ATOM 492 N ALA 32 29.404 -79.674 -6.917 1.00 0.00 N +ATOM 493 H ALA 32 28.605 -80.010 -7.435 1.00 0.00 H +ATOM 494 CA ALA 32 29.316 -78.793 -5.803 1.00 0.00 C +ATOM 495 HA ALA 32 30.174 -78.121 -5.772 1.00 0.00 H +ATOM 496 CB ALA 32 28.090 -77.927 -5.915 1.00 0.00 C +ATOM 497 HB1 ALA 32 28.082 -77.114 -5.189 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.197 -77.351 -6.834 1.00 0.00 H +ATOM 499 HB3 ALA 32 27.238 -78.606 -5.951 1.00 0.00 H +ATOM 500 C ALA 32 29.293 -79.586 -4.541 1.00 0.00 C +ATOM 501 O ALA 32 30.169 -79.441 -3.687 1.00 0.00 O +ATOM 502 N ASP 33 28.393 -80.593 -4.320 1.00 0.00 N +ATOM 503 H ASP 33 27.536 -80.578 -4.855 1.00 0.00 H +ATOM 504 CA ASP 33 28.484 -81.545 -3.147 1.00 0.00 C +ATOM 505 HA ASP 33 28.440 -81.092 -2.157 1.00 0.00 H +ATOM 506 CB ASP 33 27.285 -82.550 -3.275 1.00 0.00 C +ATOM 507 HB2 ASP 33 27.070 -82.631 -4.341 1.00 0.00 H +ATOM 508 HB3 ASP 33 27.480 -83.490 -2.758 1.00 0.00 H +ATOM 509 CG ASP 33 26.062 -81.973 -2.556 1.00 0.00 C +ATOM 510 OD1 ASP 33 26.059 -81.149 -1.590 1.00 0.00 O +ATOM 511 OD2 ASP 33 24.981 -82.468 -2.893 1.00 0.00 O +ATOM 512 C ASP 33 29.846 -82.222 -3.072 1.00 0.00 C +ATOM 513 O ASP 33 30.275 -82.470 -1.981 1.00 0.00 O +ATOM 514 N ALA 34 30.574 -82.659 -4.125 1.00 0.00 N +ATOM 515 H ALA 34 30.164 -82.442 -5.022 1.00 0.00 H +ATOM 516 CA ALA 34 31.924 -83.106 -3.948 1.00 0.00 C +ATOM 517 HA ALA 34 31.899 -83.810 -3.117 1.00 0.00 H +ATOM 518 CB ALA 34 32.546 -83.872 -5.227 1.00 0.00 C +ATOM 519 HB1 ALA 34 32.970 -83.246 -6.013 1.00 0.00 H +ATOM 520 HB2 ALA 34 31.724 -84.354 -5.756 1.00 0.00 H +ATOM 521 HB3 ALA 34 33.192 -84.697 -4.929 1.00 0.00 H +ATOM 522 C ALA 34 32.861 -81.970 -3.502 1.00 0.00 C +ATOM 523 O ALA 34 33.513 -82.108 -2.494 1.00 0.00 O +ATOM 524 N ASN 35 32.933 -80.729 -4.030 1.00 0.00 N +ATOM 525 H ASN 35 32.401 -80.508 -4.859 1.00 0.00 H +ATOM 526 CA ASN 35 33.903 -79.733 -3.538 1.00 0.00 C +ATOM 527 HA ASN 35 34.870 -80.210 -3.380 1.00 0.00 H +ATOM 528 CB ASN 35 34.132 -78.617 -4.701 1.00 0.00 C +ATOM 529 HB2 ASN 35 33.165 -78.317 -5.106 1.00 0.00 H +ATOM 530 HB3 ASN 35 34.693 -77.867 -4.143 1.00 0.00 H +ATOM 531 CG ASN 35 34.987 -79.043 -5.894 1.00 0.00 C +ATOM 532 OD1 ASN 35 36.161 -79.033 -5.808 1.00 0.00 O +ATOM 533 ND2 ASN 35 34.433 -79.485 -6.995 1.00 0.00 N +ATOM 534 HD21 ASN 35 33.434 -79.495 -7.144 1.00 0.00 H +ATOM 535 HD22 ASN 35 35.073 -79.854 -7.684 1.00 0.00 H +ATOM 536 C ASN 35 33.491 -79.240 -2.128 1.00 0.00 C +ATOM 537 O ASN 35 34.342 -78.763 -1.428 1.00 0.00 O +ATOM 538 N ASP 36 32.281 -79.480 -1.683 1.00 0.00 N +ATOM 539 H ASP 36 31.591 -79.879 -2.303 1.00 0.00 H +ATOM 540 CA ASP 36 31.889 -79.293 -0.232 1.00 0.00 C +ATOM 541 HA ASP 36 32.161 -78.262 -0.007 1.00 0.00 H +ATOM 542 CB ASP 36 30.409 -79.452 -0.003 1.00 0.00 C +ATOM 543 HB2 ASP 36 30.062 -80.264 -0.644 1.00 0.00 H +ATOM 544 HB3 ASP 36 30.337 -79.730 1.049 1.00 0.00 H +ATOM 545 CG ASP 36 29.486 -78.278 -0.212 1.00 0.00 C +ATOM 546 OD1 ASP 36 29.933 -77.147 -0.313 1.00 0.00 O +ATOM 547 OD2 ASP 36 28.270 -78.534 -0.134 1.00 0.00 O +ATOM 548 C ASP 36 32.677 -80.202 0.670 1.00 0.00 C +ATOM 549 O ASP 36 33.080 -79.773 1.736 1.00 0.00 O +ATOM 550 N LYS 37 32.867 -81.456 0.267 1.00 0.00 N +ATOM 551 H LYS 37 32.410 -81.767 -0.579 1.00 0.00 H +ATOM 552 CA LYS 37 33.581 -82.534 0.994 1.00 0.00 C +ATOM 553 HA LYS 37 33.284 -82.364 2.029 1.00 0.00 H +ATOM 554 CB LYS 37 33.044 -83.890 0.492 1.00 0.00 C +ATOM 555 HB2 LYS 37 33.704 -84.182 -0.324 1.00 0.00 H +ATOM 556 HB3 LYS 37 32.044 -83.685 0.109 1.00 0.00 H +ATOM 557 CG LYS 37 33.023 -85.092 1.498 1.00 0.00 C +ATOM 558 HG2 LYS 37 34.055 -85.316 1.771 1.00 0.00 H +ATOM 559 HG3 LYS 37 32.588 -86.026 1.143 1.00 0.00 H +ATOM 560 CD LYS 37 32.368 -84.647 2.798 1.00 0.00 C +ATOM 561 HD2 LYS 37 33.041 -83.989 3.348 1.00 0.00 H +ATOM 562 HD3 LYS 37 31.481 -84.078 2.521 1.00 0.00 H +ATOM 563 CE LYS 37 31.843 -85.740 3.758 1.00 0.00 C +ATOM 564 HE2 LYS 37 31.269 -86.486 3.209 1.00 0.00 H +ATOM 565 HE3 LYS 37 32.782 -86.119 4.162 1.00 0.00 H +ATOM 566 NZ LYS 37 30.964 -85.188 4.782 1.00 0.00 N +ATOM 567 HZ1 LYS 37 30.663 -85.862 5.471 1.00 0.00 H +ATOM 568 HZ2 LYS 37 31.341 -84.446 5.354 1.00 0.00 H +ATOM 569 HZ3 LYS 37 30.082 -84.950 4.352 1.00 0.00 H +ATOM 570 C LYS 37 35.061 -82.464 0.702 1.00 0.00 C +ATOM 571 O LYS 37 35.878 -82.971 1.483 1.00 0.00 O +ATOM 572 N GLY 38 35.504 -81.812 -0.403 1.00 0.00 N +ATOM 573 H GLY 38 34.790 -81.464 -1.027 1.00 0.00 H +ATOM 574 CA GLY 38 36.913 -81.469 -0.791 1.00 0.00 C +ATOM 575 HA2 GLY 38 37.298 -80.729 -0.089 1.00 0.00 H +ATOM 576 HA3 GLY 38 37.497 -82.369 -0.598 1.00 0.00 H +ATOM 577 C GLY 38 37.151 -81.044 -2.187 1.00 0.00 C +ATOM 578 O GLY 38 37.717 -79.978 -2.445 1.00 0.00 O +ATOM 579 N VAL 39 36.894 -82.065 -3.040 1.00 0.00 N +ATOM 580 H VAL 39 36.550 -82.959 -2.719 1.00 0.00 H +ATOM 581 CA VAL 39 37.400 -82.088 -4.432 1.00 0.00 C +ATOM 582 HA VAL 39 37.267 -81.082 -4.830 1.00 0.00 H +ATOM 583 CB VAL 39 38.891 -82.524 -4.462 1.00 0.00 C +ATOM 584 HB VAL 39 39.317 -81.884 -3.689 1.00 0.00 H +ATOM 585 CG1 VAL 39 39.045 -84.024 -4.046 1.00 0.00 C +ATOM 586 HG11 VAL 39 38.540 -84.751 -4.683 1.00 0.00 H +ATOM 587 HG12 VAL 39 38.662 -84.168 -3.035 1.00 0.00 H +ATOM 588 HG13 VAL 39 40.112 -84.247 -4.020 1.00 0.00 H +ATOM 589 CG2 VAL 39 39.643 -82.296 -5.727 1.00 0.00 C +ATOM 590 HG21 VAL 39 39.691 -81.242 -5.998 1.00 0.00 H +ATOM 591 HG22 VAL 39 39.506 -83.026 -6.525 1.00 0.00 H +ATOM 592 HG23 VAL 39 40.685 -82.416 -5.433 1.00 0.00 H +ATOM 593 C VAL 39 36.475 -82.957 -5.311 1.00 0.00 C +ATOM 594 O VAL 39 35.960 -83.965 -4.923 1.00 0.00 O +ATOM 595 N ASP 40 36.273 -82.643 -6.611 1.00 0.00 N +ATOM 596 H ASP 40 36.933 -82.001 -7.027 1.00 0.00 H +ATOM 597 CA ASP 40 35.411 -83.426 -7.504 1.00 0.00 C +ATOM 598 HA ASP 40 34.822 -84.123 -6.907 1.00 0.00 H +ATOM 599 CB ASP 40 34.464 -82.524 -8.351 1.00 0.00 C +ATOM 600 HB2 ASP 40 33.701 -83.112 -8.862 1.00 0.00 H +ATOM 601 HB3 ASP 40 34.024 -81.852 -7.614 1.00 0.00 H +ATOM 602 CG ASP 40 35.175 -81.701 -9.435 1.00 0.00 C +ATOM 603 OD1 ASP 40 35.933 -80.745 -9.110 1.00 0.00 O +ATOM 604 OD2 ASP 40 34.972 -81.913 -10.661 1.00 0.00 O +ATOM 605 C ASP 40 36.223 -84.326 -8.347 1.00 0.00 C +ATOM 606 O ASP 40 37.344 -84.055 -8.767 1.00 0.00 O +ATOM 607 N GLY 41 35.602 -85.444 -8.704 1.00 0.00 N +ATOM 608 H GLY 41 34.769 -85.722 -8.204 1.00 0.00 H +ATOM 609 CA GLY 41 36.157 -86.277 -9.773 1.00 0.00 C +ATOM 610 HA2 GLY 41 37.127 -85.859 -10.041 1.00 0.00 H +ATOM 611 HA3 GLY 41 36.312 -87.290 -9.401 1.00 0.00 H +ATOM 612 C GLY 41 35.192 -86.132 -10.981 1.00 0.00 C +ATOM 613 O GLY 41 34.784 -85.061 -11.348 1.00 0.00 O +ATOM 614 N GLU 42 34.902 -87.264 -11.542 1.00 0.00 N +ATOM 615 H GLU 42 35.073 -88.112 -11.021 1.00 0.00 H +ATOM 616 CA GLU 42 34.101 -87.353 -12.732 1.00 0.00 C +ATOM 617 HA GLU 42 33.521 -86.440 -12.871 1.00 0.00 H +ATOM 618 CB GLU 42 35.039 -87.450 -13.991 1.00 0.00 C +ATOM 619 HB2 GLU 42 35.583 -88.362 -13.743 1.00 0.00 H +ATOM 620 HB3 GLU 42 34.322 -87.560 -14.805 1.00 0.00 H +ATOM 621 CG GLU 42 36.029 -86.265 -14.269 1.00 0.00 C +ATOM 622 HG2 GLU 42 36.810 -86.224 -13.510 1.00 0.00 H +ATOM 623 HG3 GLU 42 36.524 -86.501 -15.211 1.00 0.00 H +ATOM 624 CD GLU 42 35.428 -84.865 -14.380 1.00 0.00 C +ATOM 625 OE1 GLU 42 34.229 -84.749 -14.789 1.00 0.00 O +ATOM 626 OE2 GLU 42 36.156 -83.875 -13.984 1.00 0.00 O +ATOM 627 C GLU 42 33.098 -88.580 -12.767 1.00 0.00 C +ATOM 628 O GLU 42 33.328 -89.518 -11.986 1.00 0.00 O +ATOM 629 N TRP 43 31.965 -88.444 -13.500 1.00 0.00 N +ATOM 630 H TRP 43 31.812 -87.700 -14.165 1.00 0.00 H +ATOM 631 CA TRP 43 30.936 -89.483 -13.468 1.00 0.00 C +ATOM 632 HA TRP 43 31.308 -90.459 -13.159 1.00 0.00 H +ATOM 633 CB TRP 43 29.876 -89.029 -12.444 1.00 0.00 C +ATOM 634 HB2 TRP 43 29.503 -88.069 -12.801 1.00 0.00 H +ATOM 635 HB3 TRP 43 29.062 -89.753 -12.459 1.00 0.00 H +ATOM 636 CG TRP 43 30.277 -88.851 -10.984 1.00 0.00 C +ATOM 637 CD1 TRP 43 30.211 -89.826 -10.086 1.00 0.00 C +ATOM 638 HD1 TRP 43 29.901 -90.849 -10.237 1.00 0.00 H +ATOM 639 NE1 TRP 43 30.313 -89.311 -8.803 1.00 0.00 N +ATOM 640 HE1 TRP 43 30.143 -89.896 -7.998 1.00 0.00 H +ATOM 641 CE2 TRP 43 30.850 -88.041 -8.852 1.00 0.00 C +ATOM 642 CZ2 TRP 43 31.574 -87.297 -7.879 1.00 0.00 C +ATOM 643 HZ2 TRP 43 31.872 -87.675 -6.913 1.00 0.00 H +ATOM 644 CH2 TRP 43 32.072 -86.069 -8.368 1.00 0.00 C +ATOM 645 HH2 TRP 43 32.606 -85.462 -7.652 1.00 0.00 H +ATOM 646 CZ3 TRP 43 31.842 -85.605 -9.645 1.00 0.00 C +ATOM 647 HZ3 TRP 43 32.178 -84.591 -9.804 1.00 0.00 H +ATOM 648 CE3 TRP 43 31.196 -86.439 -10.563 1.00 0.00 C +ATOM 649 HE3 TRP 43 31.112 -86.096 -11.583 1.00 0.00 H +ATOM 650 CD2 TRP 43 30.704 -87.685 -10.223 1.00 0.00 C +ATOM 651 C TRP 43 30.201 -89.731 -14.791 1.00 0.00 C +ATOM 652 O TRP 43 29.993 -88.746 -15.495 1.00 0.00 O +ATOM 653 N THR 44 29.974 -90.981 -15.170 1.00 0.00 N +ATOM 654 H THR 44 30.328 -91.729 -14.592 1.00 0.00 H +ATOM 655 CA THR 44 29.299 -91.384 -16.482 1.00 0.00 C +ATOM 656 HA THR 44 29.603 -90.663 -17.240 1.00 0.00 H +ATOM 657 CB THR 44 29.890 -92.698 -16.933 1.00 0.00 C +ATOM 658 HB THR 44 29.892 -93.277 -16.010 1.00 0.00 H +ATOM 659 CG2 THR 44 29.130 -93.365 -18.038 1.00 0.00 C +ATOM 660 HG21 THR 44 28.165 -93.751 -17.711 1.00 0.00 H +ATOM 661 HG22 THR 44 29.615 -94.305 -18.301 1.00 0.00 H +ATOM 662 HG23 THR 44 29.122 -92.769 -18.951 1.00 0.00 H +ATOM 663 OG1 THR 44 31.213 -92.512 -17.397 1.00 0.00 O +ATOM 664 HG1 THR 44 31.909 -92.550 -16.737 1.00 0.00 H +ATOM 665 C THR 44 27.778 -91.351 -16.355 1.00 0.00 C +ATOM 666 O THR 44 27.242 -91.724 -15.285 1.00 0.00 O +ATOM 667 N TYR 45 27.101 -90.933 -17.447 1.00 0.00 N +ATOM 668 H TYR 45 27.683 -90.369 -18.050 1.00 0.00 H +ATOM 669 CA TYR 45 25.637 -90.734 -17.368 1.00 0.00 C +ATOM 670 HA TYR 45 25.316 -91.086 -16.387 1.00 0.00 H +ATOM 671 CB TYR 45 25.262 -89.237 -17.471 1.00 0.00 C +ATOM 672 HB2 TYR 45 25.896 -88.648 -16.809 1.00 0.00 H +ATOM 673 HB3 TYR 45 25.626 -88.921 -18.449 1.00 0.00 H +ATOM 674 CG TYR 45 23.793 -88.837 -17.410 1.00 0.00 C +ATOM 675 CD1 TYR 45 23.124 -88.997 -16.190 1.00 0.00 C +ATOM 676 HD1 TYR 45 23.701 -89.314 -15.334 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.732 -88.954 -16.201 1.00 0.00 C +ATOM 678 HE1 TYR 45 21.212 -89.071 -15.262 1.00 0.00 H +ATOM 679 CZ TYR 45 21.040 -88.543 -17.373 1.00 0.00 C +ATOM 680 OH TYR 45 19.674 -88.445 -17.471 1.00 0.00 O +ATOM 681 HH TYR 45 19.332 -87.944 -18.215 1.00 0.00 H +ATOM 682 CE2 TYR 45 21.775 -88.308 -18.512 1.00 0.00 C +ATOM 683 HE2 TYR 45 21.234 -88.095 -19.423 1.00 0.00 H +ATOM 684 CD2 TYR 45 23.183 -88.420 -18.594 1.00 0.00 C +ATOM 685 HD2 TYR 45 23.697 -88.354 -19.542 1.00 0.00 H +ATOM 686 C TYR 45 24.807 -91.507 -18.374 1.00 0.00 C +ATOM 687 O TYR 45 25.262 -91.852 -19.428 1.00 0.00 O +ATOM 688 N ASP 46 23.594 -91.831 -17.887 1.00 0.00 N +ATOM 689 H ASP 46 23.228 -91.476 -17.015 1.00 0.00 H +ATOM 690 CA ASP 46 22.684 -92.644 -18.723 1.00 0.00 C +ATOM 691 HA ASP 46 23.065 -92.630 -19.744 1.00 0.00 H +ATOM 692 CB ASP 46 22.603 -94.094 -18.213 1.00 0.00 C +ATOM 693 HB2 ASP 46 23.534 -94.651 -18.327 1.00 0.00 H +ATOM 694 HB3 ASP 46 22.252 -94.083 -17.182 1.00 0.00 H +ATOM 695 CG ASP 46 21.632 -94.823 -19.028 1.00 0.00 C +ATOM 696 OD1 ASP 46 20.970 -95.753 -18.519 1.00 0.00 O +ATOM 697 OD2 ASP 46 21.433 -94.613 -20.286 1.00 0.00 O +ATOM 698 C ASP 46 21.311 -92.016 -18.655 1.00 0.00 C +ATOM 699 O ASP 46 20.727 -92.023 -17.578 1.00 0.00 O +ATOM 700 N ASP 47 20.755 -91.646 -19.831 1.00 0.00 N +ATOM 701 H ASP 47 21.367 -91.739 -20.629 1.00 0.00 H +ATOM 702 CA ASP 47 19.481 -91.008 -19.949 1.00 0.00 C +ATOM 703 HA ASP 47 19.485 -90.253 -19.163 1.00 0.00 H +ATOM 704 CB ASP 47 19.350 -90.132 -21.238 1.00 0.00 C +ATOM 705 HB2 ASP 47 19.979 -89.258 -21.069 1.00 0.00 H +ATOM 706 HB3 ASP 47 19.695 -90.807 -22.020 1.00 0.00 H +ATOM 707 CG ASP 47 17.897 -89.707 -21.546 1.00 0.00 C +ATOM 708 OD1 ASP 47 17.371 -90.181 -22.593 1.00 0.00 O +ATOM 709 OD2 ASP 47 17.315 -88.923 -20.736 1.00 0.00 O +ATOM 710 C ASP 47 18.339 -91.977 -19.792 1.00 0.00 C +ATOM 711 O ASP 47 17.344 -91.639 -19.213 1.00 0.00 O +ATOM 712 N ALA 48 18.588 -93.213 -20.219 1.00 0.00 N +ATOM 713 H ALA 48 19.507 -93.431 -20.576 1.00 0.00 H +ATOM 714 CA ALA 48 17.517 -94.226 -20.269 1.00 0.00 C +ATOM 715 HA ALA 48 16.740 -93.640 -20.759 1.00 0.00 H +ATOM 716 CB ALA 48 17.961 -95.413 -21.152 1.00 0.00 C +ATOM 717 HB1 ALA 48 17.167 -96.159 -21.136 1.00 0.00 H +ATOM 718 HB2 ALA 48 18.828 -95.989 -20.828 1.00 0.00 H +ATOM 719 HB3 ALA 48 18.098 -95.033 -22.164 1.00 0.00 H +ATOM 720 C ALA 48 17.020 -94.675 -18.895 1.00 0.00 C +ATOM 721 O ALA 48 15.855 -94.952 -18.660 1.00 0.00 O +ATOM 722 N THR 49 17.917 -94.524 -17.912 1.00 0.00 N +ATOM 723 H THR 49 18.883 -94.616 -18.194 1.00 0.00 H +ATOM 724 CA THR 49 17.640 -94.711 -16.487 1.00 0.00 C +ATOM 725 HA THR 49 16.634 -95.096 -16.325 1.00 0.00 H +ATOM 726 CB THR 49 18.640 -95.766 -15.937 1.00 0.00 C +ATOM 727 HB THR 49 18.484 -95.943 -14.873 1.00 0.00 H +ATOM 728 CG2 THR 49 18.586 -97.155 -16.552 1.00 0.00 C +ATOM 729 HG21 THR 49 19.167 -97.883 -15.986 1.00 0.00 H +ATOM 730 HG22 THR 49 19.013 -97.092 -17.553 1.00 0.00 H +ATOM 731 HG23 THR 49 17.623 -97.658 -16.650 1.00 0.00 H +ATOM 732 OG1 THR 49 19.988 -95.440 -16.001 1.00 0.00 O +ATOM 733 HG1 THR 49 20.329 -95.586 -16.886 1.00 0.00 H +ATOM 734 C THR 49 17.770 -93.462 -15.682 1.00 0.00 C +ATOM 735 O THR 49 17.756 -93.445 -14.456 1.00 0.00 O +ATOM 736 N LYS 50 18.122 -92.327 -16.344 1.00 0.00 N +ATOM 737 H LYS 50 18.243 -92.335 -17.347 1.00 0.00 H +ATOM 738 CA LYS 50 18.241 -90.940 -15.712 1.00 0.00 C +ATOM 739 HA LYS 50 18.510 -90.312 -16.562 1.00 0.00 H +ATOM 740 CB LYS 50 16.867 -90.531 -15.170 1.00 0.00 C +ATOM 741 HB2 LYS 50 16.483 -91.167 -14.372 1.00 0.00 H +ATOM 742 HB3 LYS 50 16.946 -89.566 -14.670 1.00 0.00 H +ATOM 743 CG LYS 50 15.793 -90.267 -16.217 1.00 0.00 C +ATOM 744 HG2 LYS 50 15.691 -91.154 -16.842 1.00 0.00 H +ATOM 745 HG3 LYS 50 14.849 -90.029 -15.726 1.00 0.00 H +ATOM 746 CD LYS 50 16.133 -89.045 -17.052 1.00 0.00 C +ATOM 747 HD2 LYS 50 16.074 -88.223 -16.339 1.00 0.00 H +ATOM 748 HD3 LYS 50 17.111 -89.192 -17.511 1.00 0.00 H +ATOM 749 CE LYS 50 15.065 -88.666 -18.118 1.00 0.00 C +ATOM 750 HE2 LYS 50 14.055 -88.777 -17.722 1.00 0.00 H +ATOM 751 HE3 LYS 50 15.171 -87.593 -18.282 1.00 0.00 H +ATOM 752 NZ LYS 50 15.099 -89.610 -19.284 1.00 0.00 N +ATOM 753 HZ1 LYS 50 16.012 -89.735 -19.696 1.00 0.00 H +ATOM 754 HZ2 LYS 50 14.437 -89.330 -19.993 1.00 0.00 H +ATOM 755 HZ3 LYS 50 14.788 -90.522 -18.982 1.00 0.00 H +ATOM 756 C LYS 50 19.290 -90.952 -14.647 1.00 0.00 C +ATOM 757 O LYS 50 19.098 -90.268 -13.625 1.00 0.00 O +ATOM 758 N THR 51 20.453 -91.655 -14.818 1.00 0.00 N +ATOM 759 H THR 51 20.613 -92.023 -15.745 1.00 0.00 H +ATOM 760 CA THR 51 21.341 -92.061 -13.805 1.00 0.00 C +ATOM 761 HA THR 51 21.021 -91.573 -12.884 1.00 0.00 H +ATOM 762 CB THR 51 21.299 -93.574 -13.464 1.00 0.00 C +ATOM 763 HB THR 51 21.568 -94.173 -14.334 1.00 0.00 H +ATOM 764 CG2 THR 51 22.249 -93.938 -12.344 1.00 0.00 C +ATOM 765 HG21 THR 51 23.263 -94.196 -12.649 1.00 0.00 H +ATOM 766 HG22 THR 51 21.757 -94.757 -11.818 1.00 0.00 H +ATOM 767 HG23 THR 51 22.337 -93.128 -11.619 1.00 0.00 H +ATOM 768 OG1 THR 51 19.987 -93.846 -13.084 1.00 0.00 O +ATOM 769 HG1 THR 51 19.297 -93.639 -13.718 1.00 0.00 H +ATOM 770 C THR 51 22.817 -91.786 -14.026 1.00 0.00 C +ATOM 771 O THR 51 23.404 -92.125 -15.050 1.00 0.00 O +ATOM 772 N PHE 52 23.546 -91.202 -13.042 1.00 0.00 N +ATOM 773 H PHE 52 23.063 -90.682 -12.323 1.00 0.00 H +ATOM 774 CA PHE 52 24.978 -91.216 -12.951 1.00 0.00 C +ATOM 775 HA PHE 52 25.466 -91.264 -13.924 1.00 0.00 H +ATOM 776 CB PHE 52 25.564 -89.995 -12.373 1.00 0.00 C +ATOM 777 HB2 PHE 52 25.076 -89.812 -11.415 1.00 0.00 H +ATOM 778 HB3 PHE 52 26.644 -90.045 -12.238 1.00 0.00 H +ATOM 779 CG PHE 52 25.275 -88.751 -13.146 1.00 0.00 C +ATOM 780 CD1 PHE 52 24.079 -87.965 -12.993 1.00 0.00 C +ATOM 781 HD1 PHE 52 23.325 -88.365 -12.331 1.00 0.00 H +ATOM 782 CE1 PHE 52 24.002 -86.746 -13.669 1.00 0.00 C +ATOM 783 HE1 PHE 52 23.099 -86.162 -13.573 1.00 0.00 H +ATOM 784 CZ PHE 52 25.008 -86.245 -14.489 1.00 0.00 C +ATOM 785 HZ PHE 52 25.007 -85.232 -14.863 1.00 0.00 H +ATOM 786 CE2 PHE 52 26.210 -86.927 -14.643 1.00 0.00 C +ATOM 787 HE2 PHE 52 27.083 -86.535 -15.145 1.00 0.00 H +ATOM 788 CD2 PHE 52 26.305 -88.201 -13.985 1.00 0.00 C +ATOM 789 HD2 PHE 52 27.227 -88.758 -14.059 1.00 0.00 H +ATOM 790 C PHE 52 25.633 -92.405 -12.250 1.00 0.00 C +ATOM 791 O PHE 52 25.090 -92.803 -11.248 1.00 0.00 O +ATOM 792 N THR 53 26.852 -92.857 -12.671 1.00 0.00 N +ATOM 793 H THR 53 27.204 -92.315 -13.448 1.00 0.00 H +ATOM 794 CA THR 53 27.718 -93.906 -12.043 1.00 0.00 C +ATOM 795 HA THR 53 27.555 -94.044 -10.974 1.00 0.00 H +ATOM 796 CB THR 53 27.515 -95.265 -12.664 1.00 0.00 C +ATOM 797 HB THR 53 28.137 -95.980 -12.125 1.00 0.00 H +ATOM 798 CG2 THR 53 26.072 -95.710 -12.540 1.00 0.00 C +ATOM 799 HG21 THR 53 25.572 -95.208 -13.367 1.00 0.00 H +ATOM 800 HG22 THR 53 25.579 -95.601 -11.574 1.00 0.00 H +ATOM 801 HG23 THR 53 25.969 -96.777 -12.738 1.00 0.00 H +ATOM 802 OG1 THR 53 27.908 -95.227 -14.029 1.00 0.00 O +ATOM 803 HG1 THR 53 27.185 -94.999 -14.619 1.00 0.00 H +ATOM 804 C THR 53 29.203 -93.510 -12.096 1.00 0.00 C +ATOM 805 O THR 53 29.653 -92.608 -12.794 1.00 0.00 O +ATOM 806 N VAL 54 30.009 -94.278 -11.313 1.00 0.00 N +ATOM 807 H VAL 54 29.541 -94.985 -10.764 1.00 0.00 H +ATOM 808 CA VAL 54 31.507 -94.409 -11.504 1.00 0.00 C +ATOM 809 HA VAL 54 31.919 -93.594 -12.099 1.00 0.00 H +ATOM 810 CB VAL 54 32.330 -94.494 -10.152 1.00 0.00 C +ATOM 811 HB VAL 54 33.344 -94.863 -10.307 1.00 0.00 H +ATOM 812 CG1 VAL 54 32.412 -93.108 -9.426 1.00 0.00 C +ATOM 813 HG11 VAL 54 31.413 -92.672 -9.392 1.00 0.00 H +ATOM 814 HG12 VAL 54 32.793 -92.426 -10.185 1.00 0.00 H +ATOM 815 HG13 VAL 54 32.996 -93.249 -8.517 1.00 0.00 H +ATOM 816 CG2 VAL 54 31.697 -95.463 -9.131 1.00 0.00 C +ATOM 817 HG21 VAL 54 31.735 -96.514 -9.416 1.00 0.00 H +ATOM 818 HG22 VAL 54 30.696 -95.192 -8.795 1.00 0.00 H +ATOM 819 HG23 VAL 54 32.270 -95.399 -8.206 1.00 0.00 H +ATOM 820 C VAL 54 31.855 -95.733 -12.216 1.00 0.00 C +ATOM 821 O VAL 54 31.006 -96.557 -12.411 1.00 0.00 O +ATOM 822 N THR 55 33.066 -95.878 -12.676 1.00 0.00 N +ATOM 823 H THR 55 33.726 -95.121 -12.568 1.00 0.00 H +ATOM 824 CA THR 55 33.652 -97.021 -13.454 1.00 0.00 C +ATOM 825 HA THR 55 32.766 -97.401 -13.962 1.00 0.00 H +ATOM 826 CB THR 55 34.669 -96.370 -14.416 1.00 0.00 C +ATOM 827 HB THR 55 35.283 -97.152 -14.861 1.00 0.00 H +ATOM 828 CG2 THR 55 34.047 -95.619 -15.548 1.00 0.00 C +ATOM 829 HG21 THR 55 33.407 -96.285 -16.127 1.00 0.00 H +ATOM 830 HG22 THR 55 34.741 -95.280 -16.318 1.00 0.00 H +ATOM 831 HG23 THR 55 33.461 -94.791 -15.149 1.00 0.00 H +ATOM 832 OG1 THR 55 35.654 -95.595 -13.719 1.00 0.00 O +ATOM 833 HG1 THR 55 36.236 -96.212 -13.269 1.00 0.00 H +ATOM 834 C THR 55 34.372 -98.017 -12.571 1.00 0.00 C +ATOM 835 O THR 55 34.832 -97.642 -11.468 1.00 0.00 O +ATOM 836 N GLU 56 34.345 -99.306 -12.901 1.00 0.00 N +ATOM 837 H GLU 56 33.833 -99.574 -13.730 1.00 0.00 H +ATOM 838 CA GLU 56 34.938-100.499 -12.232 1.00 0.00 C +ATOM 839 HA GLU 56 34.452-100.584 -11.260 1.00 0.00 H +ATOM 840 CB GLU 56 34.452-101.695 -13.095 1.00 0.00 C +ATOM 841 HB2 GLU 56 33.378-101.859 -13.010 1.00 0.00 H +ATOM 842 HB3 GLU 56 34.875-101.494 -14.080 1.00 0.00 H +ATOM 843 CG GLU 56 35.036-103.111 -12.764 1.00 0.00 C +ATOM 844 HG2 GLU 56 34.473-103.717 -13.474 1.00 0.00 H +ATOM 845 HG3 GLU 56 36.067-102.976 -13.092 1.00 0.00 H +ATOM 846 CD GLU 56 34.821-103.684 -11.375 1.00 0.00 C +ATOM 847 OE1 GLU 56 35.696-104.508 -10.966 1.00 0.00 O +ATOM 848 OE2 GLU 56 33.676-103.522 -10.883 1.00 0.00 O +ATOM 849 C GLU 56 36.464-100.433 -12.078 1.00 0.00 C +ATOM 850 O GLU 56 36.969-100.743 -10.981 1.00 0.00 O +ATOM 851 OXT GLU 56 37.096-100.019 -13.072 1.00 0.00 O +ATOM 852 ZN ZN1 57 25.031 -87.529 -6.096 1.00 0.00 ZN +ATOM 853 N AN1 58 26.689 -86.671 -5.273 1.00 0.00 N +ATOM 854 C AN1 58 29.038 -85.773 -4.684 1.00 0.00 C +ATOM 855 C1 AN1 58 27.749 -86.275 -4.953 1.00 0.00 C +ATOM 856 H AN1 58 28.844 -84.947 -3.989 1.00 0.00 H +ATOM 857 H1 AN1 58 29.514 -85.392 -5.596 1.00 0.00 H +ATOM 858 H2 AN1 58 29.673 -86.450 -4.100 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 29.646 -90.939 -6.459 1.00 0.00 N +ATOM 860 N2 AZI 59 28.976 -90.355 -5.601 1.00 0.00 N +ATOM 861 N3 AZI 59 28.363 -89.733 -4.666 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/pdbs_rename/cluster61.pdb b/tests/nsga2/pdbs_rename/cluster61.pdb new file mode 100644 index 0000000..2509bbc --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster61.pdb @@ -0,0 +1,864 @@ +CRYST1 51.604 53.231 47.331 90.00 90.00 90.00 1 +ATOM 1 N MET 1 17.774 21.962 33.535 1.00 0.00 N +ATOM 2 H1 MET 1 17.481 21.255 34.194 1.00 0.00 H +ATOM 3 H2 MET 1 17.555 21.733 32.575 1.00 0.00 H +ATOM 4 H3 MET 1 17.343 22.832 33.811 1.00 0.00 H +ATOM 5 CA MET 1 19.274 22.097 33.633 1.00 0.00 C +ATOM 6 HA MET 1 19.516 22.321 34.672 1.00 0.00 H +ATOM 7 CB MET 1 20.107 20.898 33.190 1.00 0.00 C +ATOM 8 HB2 MET 1 19.774 20.144 33.903 1.00 0.00 H +ATOM 9 HB3 MET 1 19.854 20.614 32.169 1.00 0.00 H +ATOM 10 CG MET 1 21.620 21.233 33.280 1.00 0.00 C +ATOM 11 HG2 MET 1 22.237 20.452 32.834 1.00 0.00 H +ATOM 12 HG3 MET 1 21.845 22.201 32.833 1.00 0.00 H +ATOM 13 SD MET 1 22.245 21.550 34.999 1.00 0.00 S +ATOM 14 CE MET 1 23.949 22.272 34.690 1.00 0.00 C +ATOM 15 HE1 MET 1 24.488 21.704 33.932 1.00 0.00 H +ATOM 16 HE2 MET 1 24.520 22.222 35.617 1.00 0.00 H +ATOM 17 HE3 MET 1 23.933 23.313 34.369 1.00 0.00 H +ATOM 18 C MET 1 19.628 23.357 32.850 1.00 0.00 C +ATOM 19 O MET 1 19.559 23.478 31.618 1.00 0.00 O +ATOM 20 N GLN 2 20.243 24.288 33.623 1.00 0.00 N +ATOM 21 H GLN 2 20.517 24.124 34.581 1.00 0.00 H +ATOM 22 CA GLN 2 20.938 25.509 33.231 1.00 0.00 C +ATOM 23 HA GLN 2 20.367 26.017 32.453 1.00 0.00 H +ATOM 24 CB GLN 2 20.935 26.539 34.338 1.00 0.00 C +ATOM 25 HB2 GLN 2 21.141 26.033 35.282 1.00 0.00 H +ATOM 26 HB3 GLN 2 21.750 27.258 34.258 1.00 0.00 H +ATOM 27 CG GLN 2 19.614 27.305 34.418 1.00 0.00 C +ATOM 28 HG2 GLN 2 18.751 26.640 34.418 1.00 0.00 H +ATOM 29 HG3 GLN 2 19.600 27.962 35.288 1.00 0.00 H +ATOM 30 CD GLN 2 19.393 28.357 33.309 1.00 0.00 C +ATOM 31 OE1 GLN 2 20.366 28.575 32.537 1.00 0.00 O +ATOM 32 NE2 GLN 2 18.219 29.014 33.246 1.00 0.00 N +ATOM 33 HE21 GLN 2 18.034 29.329 32.304 1.00 0.00 H +ATOM 34 HE22 GLN 2 17.569 28.873 34.006 1.00 0.00 H +ATOM 35 C GLN 2 22.246 25.208 32.548 1.00 0.00 C +ATOM 36 O GLN 2 23.339 25.561 33.004 1.00 0.00 O +ATOM 37 N TYR 3 22.241 24.503 31.473 1.00 0.00 N +ATOM 38 H TYR 3 21.356 24.114 31.182 1.00 0.00 H +ATOM 39 CA TYR 3 23.449 24.122 30.722 1.00 0.00 C +ATOM 40 HA TYR 3 23.950 23.440 31.409 1.00 0.00 H +ATOM 41 CB TYR 3 23.103 23.490 29.341 1.00 0.00 C +ATOM 42 HB2 TYR 3 22.418 24.116 28.769 1.00 0.00 H +ATOM 43 HB3 TYR 3 24.018 23.515 28.749 1.00 0.00 H +ATOM 44 CG TYR 3 22.562 22.099 29.427 1.00 0.00 C +ATOM 45 CD1 TYR 3 23.403 21.006 29.786 1.00 0.00 C +ATOM 46 HD1 TYR 3 24.468 21.180 29.758 1.00 0.00 H +ATOM 47 CE1 TYR 3 22.967 19.676 29.952 1.00 0.00 C +ATOM 48 HE1 TYR 3 23.661 18.890 30.209 1.00 0.00 H +ATOM 49 CZ TYR 3 21.605 19.453 29.866 1.00 0.00 C +ATOM 50 OH TYR 3 21.171 18.189 30.096 1.00 0.00 O +ATOM 51 HH TYR 3 21.898 17.649 30.418 1.00 0.00 H +ATOM 52 CE2 TYR 3 20.651 20.536 29.600 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.575 20.452 29.650 1.00 0.00 H +ATOM 54 CD2 TYR 3 21.172 21.852 29.430 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.447 22.653 29.433 1.00 0.00 H +ATOM 56 C TYR 3 24.389 25.278 30.381 1.00 0.00 C +ATOM 57 O TYR 3 23.941 26.300 29.878 1.00 0.00 O +ATOM 58 N LYS 4 25.690 25.164 30.673 1.00 0.00 N +ATOM 59 H LYS 4 26.042 24.288 31.034 1.00 0.00 H +ATOM 60 CA LYS 4 26.638 26.287 30.343 1.00 0.00 C +ATOM 61 HA LYS 4 26.299 27.278 30.646 1.00 0.00 H +ATOM 62 CB LYS 4 27.990 26.092 30.935 1.00 0.00 C +ATOM 63 HB2 LYS 4 27.953 25.527 31.867 1.00 0.00 H +ATOM 64 HB3 LYS 4 28.571 25.411 30.313 1.00 0.00 H +ATOM 65 CG LYS 4 28.745 27.395 31.195 1.00 0.00 C +ATOM 66 HG2 LYS 4 29.055 27.794 30.229 1.00 0.00 H +ATOM 67 HG3 LYS 4 28.032 28.136 31.555 1.00 0.00 H +ATOM 68 CD LYS 4 29.900 27.214 32.241 1.00 0.00 C +ATOM 69 HD2 LYS 4 30.159 28.223 32.563 1.00 0.00 H +ATOM 70 HD3 LYS 4 29.701 26.590 33.112 1.00 0.00 H +ATOM 71 CE LYS 4 31.137 26.613 31.599 1.00 0.00 C +ATOM 72 HE2 LYS 4 30.802 25.674 31.159 1.00 0.00 H +ATOM 73 HE3 LYS 4 31.414 27.254 30.762 1.00 0.00 H +ATOM 74 NZ LYS 4 32.267 26.375 32.494 1.00 0.00 N +ATOM 75 HZ1 LYS 4 32.805 27.216 32.651 1.00 0.00 H +ATOM 76 HZ2 LYS 4 32.919 25.707 32.108 1.00 0.00 H +ATOM 77 HZ3 LYS 4 31.926 25.991 33.363 1.00 0.00 H +ATOM 78 C LYS 4 26.837 26.457 28.833 1.00 0.00 C +ATOM 79 O LYS 4 26.788 25.547 27.973 1.00 0.00 O +ATOM 80 N HX1 5 27.004 27.717 28.432 1.00 0.00 N +ATOM 81 CA HX1 5 27.416 27.984 26.997 1.00 0.00 C +ATOM 82 C HX1 5 28.533 29.111 27.068 1.00 0.00 C +ATOM 83 O HX1 5 28.321 30.051 27.796 1.00 0.00 O +ATOM 84 CB HX1 5 26.160 28.559 26.336 1.00 0.00 C +ATOM 85 CG HX1 5 26.368 29.039 24.926 1.00 0.00 C +ATOM 86 CD2 HX1 5 27.427 28.773 24.113 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.455 29.777 24.178 1.00 0.00 N +ATOM 88 CE1 HX1 5 25.985 29.911 22.953 1.00 0.00 C +ATOM 89 NE2 HX1 5 27.267 29.440 22.958 1.00 0.00 N +ATOM 90 H HX1 5 26.859 28.527 29.017 1.00 0.00 H +ATOM 91 HA HX1 5 27.626 27.050 26.475 1.00 0.00 H +ATOM 92 HB2 HX1 5 25.639 29.328 26.906 1.00 0.00 H +ATOM 93 HB3 HX1 5 25.448 27.736 26.273 1.00 0.00 H +ATOM 94 HD2 HX1 5 28.327 28.195 24.264 1.00 0.00 H +ATOM 95 HE1 HX1 5 25.427 30.435 22.192 1.00 0.00 H +ATOM 96 HE2 HX1 5 27.950 29.543 22.221 1.00 0.00 H +ATOM 97 N ILE 6 29.653 28.843 26.417 1.00 0.00 N +ATOM 98 H ILE 6 29.673 27.936 25.972 1.00 0.00 H +ATOM 99 CA ILE 6 30.772 29.819 26.193 1.00 0.00 C +ATOM 100 HA ILE 6 30.669 30.580 26.966 1.00 0.00 H +ATOM 101 CB ILE 6 32.136 29.161 26.266 1.00 0.00 C +ATOM 102 HB ILE 6 31.991 28.257 25.675 1.00 0.00 H +ATOM 103 CG2 ILE 6 33.205 29.908 25.580 1.00 0.00 C +ATOM 104 HG21 ILE 6 32.950 30.162 24.551 1.00 0.00 H +ATOM 105 HG22 ILE 6 34.114 29.308 25.550 1.00 0.00 H +ATOM 106 HG23 ILE 6 33.421 30.798 26.170 1.00 0.00 H +ATOM 107 CG1 ILE 6 32.432 28.753 27.736 1.00 0.00 C +ATOM 108 HG12 ILE 6 32.669 29.613 28.362 1.00 0.00 H +ATOM 109 HG13 ILE 6 31.473 28.450 28.155 1.00 0.00 H +ATOM 110 CD1 ILE 6 33.593 27.816 27.880 1.00 0.00 C +ATOM 111 HD11 ILE 6 33.375 26.912 27.312 1.00 0.00 H +ATOM 112 HD12 ILE 6 33.772 27.563 28.925 1.00 0.00 H +ATOM 113 HD13 ILE 6 34.552 28.300 27.691 1.00 0.00 H +ATOM 114 C ILE 6 30.565 30.432 24.799 1.00 0.00 C +ATOM 115 O ILE 6 30.285 29.690 23.874 1.00 0.00 O +ATOM 116 N VAL 7 30.741 31.740 24.654 1.00 0.00 N +ATOM 117 H VAL 7 31.050 32.161 25.519 1.00 0.00 H +ATOM 118 CA VAL 7 30.707 32.479 23.348 1.00 0.00 C +ATOM 119 HA VAL 7 30.572 31.767 22.534 1.00 0.00 H +ATOM 120 CB VAL 7 29.446 33.398 23.253 1.00 0.00 C +ATOM 121 HB VAL 7 29.386 33.793 22.239 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.237 32.558 23.541 1.00 0.00 C +ATOM 123 HG11 VAL 7 28.248 31.771 22.787 1.00 0.00 H +ATOM 124 HG12 VAL 7 28.262 32.246 24.585 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.304 33.111 23.428 1.00 0.00 H +ATOM 126 CG2 VAL 7 29.365 34.572 24.233 1.00 0.00 C +ATOM 127 HG21 VAL 7 30.212 35.235 24.055 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.455 35.118 23.987 1.00 0.00 H +ATOM 129 HG23 VAL 7 29.358 34.250 25.274 1.00 0.00 H +ATOM 130 C VAL 7 31.984 33.315 23.030 1.00 0.00 C +ATOM 131 O VAL 7 32.773 33.515 23.948 1.00 0.00 O +ATOM 132 N ASN 8 32.215 33.739 21.823 1.00 0.00 N +ATOM 133 H ASN 8 31.540 33.450 21.129 1.00 0.00 H +ATOM 134 CA ASN 8 33.473 34.477 21.459 1.00 0.00 C +ATOM 135 HA ASN 8 34.234 34.105 22.144 1.00 0.00 H +ATOM 136 CB ASN 8 33.768 33.973 20.038 1.00 0.00 C +ATOM 137 HB2 ASN 8 33.619 32.895 19.992 1.00 0.00 H +ATOM 138 HB3 ASN 8 33.025 34.420 19.378 1.00 0.00 H +ATOM 139 CG ASN 8 35.155 34.183 19.592 1.00 0.00 C +ATOM 140 OD1 ASN 8 36.169 33.760 20.146 1.00 0.00 O +ATOM 141 ND2 ASN 8 35.291 34.607 18.374 1.00 0.00 N +ATOM 142 HD21 ASN 8 34.497 34.794 17.778 1.00 0.00 H +ATOM 143 HD22 ASN 8 36.140 34.476 17.842 1.00 0.00 H +ATOM 144 C ASN 8 33.404 35.919 21.597 1.00 0.00 C +ATOM 145 O ASN 8 34.388 36.628 21.365 1.00 0.00 O +ATOM 146 N GLY 9 32.265 36.522 21.881 1.00 0.00 N +ATOM 147 H GLY 9 31.440 35.954 21.749 1.00 0.00 H +ATOM 148 CA GLY 9 32.042 37.889 22.358 1.00 0.00 C +ATOM 149 HA2 GLY 9 32.288 38.654 21.621 1.00 0.00 H +ATOM 150 HA3 GLY 9 30.966 37.989 22.504 1.00 0.00 H +ATOM 151 C GLY 9 32.766 38.227 23.690 1.00 0.00 C +ATOM 152 O GLY 9 32.929 37.396 24.632 1.00 0.00 O +ATOM 153 N LYS 10 33.062 39.518 23.788 1.00 0.00 N +ATOM 154 H LYS 10 32.851 40.203 23.077 1.00 0.00 H +ATOM 155 CA LYS 10 33.628 40.053 25.054 1.00 0.00 C +ATOM 156 HA LYS 10 34.034 39.250 25.668 1.00 0.00 H +ATOM 157 CB LYS 10 34.856 40.982 24.768 1.00 0.00 C +ATOM 158 HB2 LYS 10 35.500 40.393 24.116 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.529 41.791 24.114 1.00 0.00 H +ATOM 160 CG LYS 10 35.698 41.545 25.935 1.00 0.00 C +ATOM 161 HG2 LYS 10 35.017 42.188 26.491 1.00 0.00 H +ATOM 162 HG3 LYS 10 36.242 40.837 26.560 1.00 0.00 H +ATOM 163 CD LYS 10 36.732 42.512 25.273 1.00 0.00 C +ATOM 164 HD2 LYS 10 36.240 43.423 24.931 1.00 0.00 H +ATOM 165 HD3 LYS 10 37.458 42.893 25.991 1.00 0.00 H +ATOM 166 CE LYS 10 37.568 41.993 24.112 1.00 0.00 C +ATOM 167 HE2 LYS 10 36.970 41.484 23.356 1.00 0.00 H +ATOM 168 HE3 LYS 10 38.054 42.850 23.646 1.00 0.00 H +ATOM 169 NZ LYS 10 38.638 41.127 24.636 1.00 0.00 N +ATOM 170 HZ1 LYS 10 38.293 40.246 24.991 1.00 0.00 H +ATOM 171 HZ2 LYS 10 39.154 41.648 25.331 1.00 0.00 H +ATOM 172 HZ3 LYS 10 39.267 40.798 23.919 1.00 0.00 H +ATOM 173 C LYS 10 32.482 40.590 25.978 1.00 0.00 C +ATOM 174 O LYS 10 32.578 40.401 27.218 1.00 0.00 O +ATOM 175 N THR 11 31.387 41.175 25.431 1.00 0.00 N +ATOM 176 H THR 11 31.584 41.566 24.521 1.00 0.00 H +ATOM 177 CA THR 11 30.384 41.805 26.212 1.00 0.00 C +ATOM 178 HA THR 11 30.913 42.225 27.067 1.00 0.00 H +ATOM 179 CB THR 11 29.701 42.881 25.317 1.00 0.00 C +ATOM 180 HB THR 11 30.456 43.568 24.936 1.00 0.00 H +ATOM 181 CG2 THR 11 29.094 42.318 24.077 1.00 0.00 C +ATOM 182 HG21 THR 11 28.909 43.162 23.413 1.00 0.00 H +ATOM 183 HG22 THR 11 28.128 41.944 24.417 1.00 0.00 H +ATOM 184 HG23 THR 11 29.602 41.560 23.480 1.00 0.00 H +ATOM 185 OG1 THR 11 28.855 43.681 26.049 1.00 0.00 O +ATOM 186 HG1 THR 11 28.914 44.508 25.564 1.00 0.00 H +ATOM 187 C THR 11 29.468 40.768 26.827 1.00 0.00 C +ATOM 188 O THR 11 29.454 39.659 26.282 1.00 0.00 O +ATOM 189 N LEU 12 28.985 41.002 28.059 1.00 0.00 N +ATOM 190 H LEU 12 29.068 41.984 28.279 1.00 0.00 H +ATOM 191 CA LEU 12 28.394 40.004 28.937 1.00 0.00 C +ATOM 192 HA LEU 12 28.388 40.554 29.878 1.00 0.00 H +ATOM 193 CB LEU 12 26.975 39.574 28.502 1.00 0.00 C +ATOM 194 HB2 LEU 12 27.071 39.099 27.526 1.00 0.00 H +ATOM 195 HB3 LEU 12 26.543 38.844 29.187 1.00 0.00 H +ATOM 196 CG LEU 12 25.939 40.701 28.266 1.00 0.00 C +ATOM 197 HG LEU 12 26.284 41.434 27.536 1.00 0.00 H +ATOM 198 CD1 LEU 12 24.750 40.020 27.538 1.00 0.00 C +ATOM 199 HD11 LEU 12 25.024 39.351 26.723 1.00 0.00 H +ATOM 200 HD12 LEU 12 24.131 40.792 27.079 1.00 0.00 H +ATOM 201 HD13 LEU 12 24.157 39.592 28.347 1.00 0.00 H +ATOM 202 CD2 LEU 12 25.359 41.321 29.539 1.00 0.00 C +ATOM 203 HD21 LEU 12 24.729 42.158 29.241 1.00 0.00 H +ATOM 204 HD22 LEU 12 26.140 41.769 30.153 1.00 0.00 H +ATOM 205 HD23 LEU 12 24.806 40.596 30.137 1.00 0.00 H +ATOM 206 C LEU 12 29.412 38.854 29.255 1.00 0.00 C +ATOM 207 O LEU 12 28.968 37.709 29.221 1.00 0.00 O +ATOM 208 N LYS 13 30.729 39.178 29.427 1.00 0.00 N +ATOM 209 H LYS 13 30.961 40.160 29.375 1.00 0.00 H +ATOM 210 CA LYS 13 31.873 38.256 29.773 1.00 0.00 C +ATOM 211 HA LYS 13 32.795 38.836 29.723 1.00 0.00 H +ATOM 212 CB LYS 13 31.750 37.865 31.240 1.00 0.00 C +ATOM 213 HB2 LYS 13 30.753 37.476 31.446 1.00 0.00 H +ATOM 214 HB3 LYS 13 32.437 37.040 31.432 1.00 0.00 H +ATOM 215 CG LYS 13 32.061 39.045 32.220 1.00 0.00 C +ATOM 216 HG2 LYS 13 32.985 39.423 31.783 1.00 0.00 H +ATOM 217 HG3 LYS 13 31.398 39.911 32.222 1.00 0.00 H +ATOM 218 CD LYS 13 32.229 38.618 33.659 1.00 0.00 C +ATOM 219 HD2 LYS 13 31.276 38.256 34.044 1.00 0.00 H +ATOM 220 HD3 LYS 13 32.968 37.818 33.717 1.00 0.00 H +ATOM 221 CE LYS 13 32.710 39.792 34.489 1.00 0.00 C +ATOM 222 HE2 LYS 13 32.060 40.636 34.261 1.00 0.00 H +ATOM 223 HE3 LYS 13 32.452 39.562 35.522 1.00 0.00 H +ATOM 224 NZ LYS 13 34.101 40.205 34.197 1.00 0.00 N +ATOM 225 HZ1 LYS 13 34.666 39.368 34.187 1.00 0.00 H +ATOM 226 HZ2 LYS 13 34.389 40.836 34.931 1.00 0.00 H +ATOM 227 HZ3 LYS 13 34.228 40.725 33.341 1.00 0.00 H +ATOM 228 C LYS 13 32.150 37.018 28.903 1.00 0.00 C +ATOM 229 O LYS 13 33.037 36.166 29.187 1.00 0.00 O +ATOM 230 N GLY 14 31.414 36.859 27.811 1.00 0.00 N +ATOM 231 H GLY 14 30.745 37.596 27.640 1.00 0.00 H +ATOM 232 CA GLY 14 31.301 35.636 26.947 1.00 0.00 C +ATOM 233 HA2 GLY 14 30.550 35.794 26.174 1.00 0.00 H +ATOM 234 HA3 GLY 14 32.237 35.641 26.389 1.00 0.00 H +ATOM 235 C GLY 14 31.168 34.263 27.698 1.00 0.00 C +ATOM 236 O GLY 14 31.548 33.244 27.096 1.00 0.00 O +ATOM 237 N VAL 15 30.531 34.196 28.905 1.00 0.00 N +ATOM 238 H VAL 15 30.327 35.056 29.394 1.00 0.00 H +ATOM 239 CA VAL 15 30.093 32.938 29.480 1.00 0.00 C +ATOM 240 HA VAL 15 30.099 32.257 28.629 1.00 0.00 H +ATOM 241 CB VAL 15 31.115 32.355 30.411 1.00 0.00 C +ATOM 242 HB VAL 15 31.163 32.996 31.292 1.00 0.00 H +ATOM 243 CG1 VAL 15 30.753 30.904 30.824 1.00 0.00 C +ATOM 244 HG11 VAL 15 31.556 30.574 31.484 1.00 0.00 H +ATOM 245 HG12 VAL 15 29.781 30.771 31.300 1.00 0.00 H +ATOM 246 HG13 VAL 15 30.820 30.398 29.861 1.00 0.00 H +ATOM 247 CG2 VAL 15 32.523 32.370 29.848 1.00 0.00 C +ATOM 248 HG21 VAL 15 33.200 31.863 30.535 1.00 0.00 H +ATOM 249 HG22 VAL 15 32.573 31.866 28.883 1.00 0.00 H +ATOM 250 HG23 VAL 15 32.824 33.415 29.777 1.00 0.00 H +ATOM 251 C VAL 15 28.644 33.005 30.075 1.00 0.00 C +ATOM 252 O VAL 15 28.449 33.891 30.995 1.00 0.00 O +ATOM 253 N HY1 16 27.726 32.092 29.852 1.00 0.00 N +ATOM 254 CA HY1 16 26.364 32.140 30.452 1.00 0.00 C +ATOM 255 C HY1 16 25.694 30.766 30.325 1.00 0.00 C +ATOM 256 O HY1 16 26.379 29.761 30.096 1.00 0.00 O +ATOM 257 CB HY1 16 25.565 33.258 29.744 1.00 0.00 C +ATOM 258 CG HY1 16 25.523 33.048 28.273 1.00 0.00 C +ATOM 259 CD2 HY1 16 24.648 32.255 27.609 1.00 0.00 C +ATOM 260 ND1 HY1 16 26.249 33.747 27.318 1.00 0.00 N +ATOM 261 CE1 HY1 16 25.820 33.341 26.135 1.00 0.00 C +ATOM 262 NE2 HY1 16 24.805 32.439 26.234 1.00 0.00 N +ATOM 263 H HY1 16 27.899 31.347 29.193 1.00 0.00 H +ATOM 264 HA HY1 16 26.375 32.395 31.511 1.00 0.00 H +ATOM 265 HB2 HY1 16 24.515 33.228 30.033 1.00 0.00 H +ATOM 266 HB3 HY1 16 25.936 34.224 30.084 1.00 0.00 H +ATOM 267 HD1 HY1 16 27.000 34.372 27.574 1.00 0.00 H +ATOM 268 HD2 HY1 16 23.790 31.745 28.021 1.00 0.00 H +ATOM 269 HE1 HY1 16 26.160 33.789 25.213 1.00 0.00 H +ATOM 270 N THR 17 24.402 30.703 30.649 1.00 0.00 N +ATOM 271 H THR 17 23.881 31.506 30.970 1.00 0.00 H +ATOM 272 CA THR 17 23.669 29.327 30.690 1.00 0.00 C +ATOM 273 HA THR 17 24.379 28.680 30.175 1.00 0.00 H +ATOM 274 CB THR 17 23.497 28.874 32.128 1.00 0.00 C +ATOM 275 HB THR 17 22.909 27.983 31.909 1.00 0.00 H +ATOM 276 CG2 THR 17 24.728 28.440 32.861 1.00 0.00 C +ATOM 277 HG21 THR 17 24.412 28.147 33.862 1.00 0.00 H +ATOM 278 HG22 THR 17 25.468 29.224 33.024 1.00 0.00 H +ATOM 279 HG23 THR 17 25.186 27.572 32.388 1.00 0.00 H +ATOM 280 OG1 THR 17 22.827 29.759 32.890 1.00 0.00 O +ATOM 281 HG1 THR 17 21.964 29.570 32.514 1.00 0.00 H +ATOM 282 C THR 17 22.252 29.382 30.003 1.00 0.00 C +ATOM 283 O THR 17 21.673 30.407 29.862 1.00 0.00 O +ATOM 284 N HY2 18 21.691 28.202 29.545 1.00 0.00 N +ATOM 285 CA HY2 18 20.340 28.082 29.020 1.00 0.00 C +ATOM 286 C HY2 18 19.627 26.862 29.569 1.00 0.00 C +ATOM 287 O HY2 18 20.249 25.785 29.669 1.00 0.00 O +ATOM 288 CB HY2 18 20.323 28.015 27.494 1.00 0.00 C +ATOM 289 CG HY2 18 20.998 29.150 26.849 1.00 0.00 C +ATOM 290 CD2 HY2 18 22.258 29.177 26.281 1.00 0.00 C +ATOM 291 ND1 HY2 18 20.508 30.469 26.808 1.00 0.00 N +ATOM 292 CE1 HY2 18 21.375 31.277 26.158 1.00 0.00 C +ATOM 293 NE2 HY2 18 22.470 30.532 25.905 1.00 0.00 N +ATOM 294 H HY2 18 22.060 27.303 29.819 1.00 0.00 H +ATOM 295 HA HY2 18 19.786 28.950 29.379 1.00 0.00 H +ATOM 296 HB2 HY2 18 20.958 27.145 27.331 1.00 0.00 H +ATOM 297 HB3 HY2 18 19.299 27.839 27.165 1.00 0.00 H +ATOM 298 HD1 HY2 18 19.593 30.784 27.096 1.00 0.00 H +ATOM 299 HD2 HY2 18 23.063 28.457 26.291 1.00 0.00 H +ATOM 300 HE1 HY2 18 21.327 32.332 25.933 1.00 0.00 H +ATOM 301 N GLU 19 18.311 27.013 29.853 1.00 0.00 N +ATOM 302 H GLU 19 17.887 27.920 29.717 1.00 0.00 H +ATOM 303 CA GLU 19 17.406 26.054 30.555 1.00 0.00 C +ATOM 304 HA GLU 19 17.954 25.438 31.268 1.00 0.00 H +ATOM 305 CB GLU 19 16.403 26.804 31.342 1.00 0.00 C +ATOM 306 HB2 GLU 19 17.062 27.159 32.134 1.00 0.00 H +ATOM 307 HB3 GLU 19 16.019 27.645 30.765 1.00 0.00 H +ATOM 308 CG GLU 19 15.170 25.947 31.920 1.00 0.00 C +ATOM 309 HG2 GLU 19 14.666 26.600 32.633 1.00 0.00 H +ATOM 310 HG3 GLU 19 14.523 25.726 31.071 1.00 0.00 H +ATOM 311 CD GLU 19 15.558 24.647 32.633 1.00 0.00 C +ATOM 312 OE1 GLU 19 16.635 24.523 33.261 1.00 0.00 O +ATOM 313 OE2 GLU 19 14.702 23.743 32.631 1.00 0.00 O +ATOM 314 C GLU 19 16.710 25.114 29.518 1.00 0.00 C +ATOM 315 O GLU 19 15.867 25.565 28.770 1.00 0.00 O +ATOM 316 N ALA 20 17.074 23.769 29.611 1.00 0.00 N +ATOM 317 H ALA 20 17.807 23.446 30.227 1.00 0.00 H +ATOM 318 CA ALA 20 16.396 22.713 28.868 1.00 0.00 C +ATOM 319 HA ALA 20 15.415 23.099 28.593 1.00 0.00 H +ATOM 320 CB ALA 20 17.057 22.350 27.547 1.00 0.00 C +ATOM 321 HB1 ALA 20 17.028 23.213 26.881 1.00 0.00 H +ATOM 322 HB2 ALA 20 16.616 21.567 26.930 1.00 0.00 H +ATOM 323 HB3 ALA 20 18.099 22.096 27.742 1.00 0.00 H +ATOM 324 C ALA 20 16.211 21.475 29.843 1.00 0.00 C +ATOM 325 O ALA 20 16.936 21.235 30.830 1.00 0.00 O +ATOM 326 N VAL 21 15.257 20.713 29.441 1.00 0.00 N +ATOM 327 H VAL 21 14.520 21.101 28.870 1.00 0.00 H +ATOM 328 CA VAL 21 15.038 19.390 30.035 1.00 0.00 C +ATOM 329 HA VAL 21 15.003 19.532 31.115 1.00 0.00 H +ATOM 330 CB VAL 21 13.635 18.769 29.608 1.00 0.00 C +ATOM 331 HB VAL 21 12.887 19.542 29.788 1.00 0.00 H +ATOM 332 CG1 VAL 21 13.615 18.478 28.038 1.00 0.00 C +ATOM 333 HG11 VAL 21 12.560 18.506 27.764 1.00 0.00 H +ATOM 334 HG12 VAL 21 14.017 17.480 27.860 1.00 0.00 H +ATOM 335 HG13 VAL 21 14.170 19.281 27.553 1.00 0.00 H +ATOM 336 CG2 VAL 21 13.168 17.515 30.384 1.00 0.00 C +ATOM 337 HG21 VAL 21 13.438 17.732 31.417 1.00 0.00 H +ATOM 338 HG22 VAL 21 13.820 16.675 30.146 1.00 0.00 H +ATOM 339 HG23 VAL 21 12.107 17.285 30.282 1.00 0.00 H +ATOM 340 C VAL 21 16.240 18.446 29.726 1.00 0.00 C +ATOM 341 O VAL 21 16.419 17.542 30.564 1.00 0.00 O +ATOM 342 N ASP 22 16.978 18.581 28.657 1.00 0.00 N +ATOM 343 H ASP 22 16.805 19.447 28.168 1.00 0.00 H +ATOM 344 CA ASP 22 18.066 17.712 28.166 1.00 0.00 C +ATOM 345 HA ASP 22 18.585 17.455 29.089 1.00 0.00 H +ATOM 346 CB ASP 22 17.408 16.463 27.484 1.00 0.00 C +ATOM 347 HB2 ASP 22 16.464 16.268 27.992 1.00 0.00 H +ATOM 348 HB3 ASP 22 17.228 16.536 26.412 1.00 0.00 H +ATOM 349 CG ASP 22 18.188 15.216 27.821 1.00 0.00 C +ATOM 350 OD1 ASP 22 19.275 15.256 28.373 1.00 0.00 O +ATOM 351 OD2 ASP 22 17.778 14.084 27.490 1.00 0.00 O +ATOM 352 C ASP 22 19.022 18.477 27.304 1.00 0.00 C +ATOM 353 O ASP 22 18.626 19.398 26.617 1.00 0.00 O +ATOM 354 N ALA 23 20.255 17.948 27.119 1.00 0.00 N +ATOM 355 H ALA 23 20.483 17.088 27.596 1.00 0.00 H +ATOM 356 CA ALA 23 21.230 18.410 26.156 1.00 0.00 C +ATOM 357 HA ALA 23 21.391 19.476 26.313 1.00 0.00 H +ATOM 358 CB ALA 23 22.554 17.686 26.370 1.00 0.00 C +ATOM 359 HB1 ALA 23 23.090 18.001 27.266 1.00 0.00 H +ATOM 360 HB2 ALA 23 23.207 18.051 25.577 1.00 0.00 H +ATOM 361 HB3 ALA 23 22.539 16.607 26.217 1.00 0.00 H +ATOM 362 C ALA 23 20.688 18.113 24.758 1.00 0.00 C +ATOM 363 O ALA 23 20.745 18.996 23.860 1.00 0.00 O +ATOM 364 N ALA 24 20.176 16.916 24.547 1.00 0.00 N +ATOM 365 H ALA 24 20.185 16.183 25.242 1.00 0.00 H +ATOM 366 CA ALA 24 19.393 16.601 23.342 1.00 0.00 C +ATOM 367 HA ALA 24 20.019 16.411 22.470 1.00 0.00 H +ATOM 368 CB ALA 24 18.744 15.295 23.703 1.00 0.00 C +ATOM 369 HB1 ALA 24 18.010 15.413 24.499 1.00 0.00 H +ATOM 370 HB2 ALA 24 19.441 14.566 24.117 1.00 0.00 H +ATOM 371 HB3 ALA 24 18.244 14.839 22.849 1.00 0.00 H +ATOM 372 C ALA 24 18.335 17.661 22.870 1.00 0.00 C +ATOM 373 O ALA 24 18.139 17.852 21.673 1.00 0.00 O +ATOM 374 N GLU 25 17.763 18.433 23.784 1.00 0.00 N +ATOM 375 H GLU 25 17.766 18.237 24.775 1.00 0.00 H +ATOM 376 CA GLU 25 16.946 19.655 23.451 1.00 0.00 C +ATOM 377 HA GLU 25 16.450 19.505 22.492 1.00 0.00 H +ATOM 378 CB GLU 25 15.849 19.791 24.520 1.00 0.00 C +ATOM 379 HB2 GLU 25 16.394 19.696 25.458 1.00 0.00 H +ATOM 380 HB3 GLU 25 15.395 20.782 24.498 1.00 0.00 H +ATOM 381 CG GLU 25 14.878 18.635 24.475 1.00 0.00 C +ATOM 382 HG2 GLU 25 15.414 17.688 24.548 1.00 0.00 H +ATOM 383 HG3 GLU 25 14.359 18.746 25.427 1.00 0.00 H +ATOM 384 CD GLU 25 13.947 18.682 23.226 1.00 0.00 C +ATOM 385 OE1 GLU 25 13.226 19.653 22.989 1.00 0.00 O +ATOM 386 OE2 GLU 25 14.019 17.801 22.358 1.00 0.00 O +ATOM 387 C GLU 25 17.857 20.985 23.381 1.00 0.00 C +ATOM 388 O GLU 25 17.770 21.759 22.421 1.00 0.00 O +ATOM 389 N ALA 26 18.757 21.230 24.302 1.00 0.00 N +ATOM 390 H ALA 26 18.798 20.598 25.089 1.00 0.00 H +ATOM 391 CA ALA 26 19.624 22.465 24.308 1.00 0.00 C +ATOM 392 HA ALA 26 18.961 23.331 24.296 1.00 0.00 H +ATOM 393 CB ALA 26 20.548 22.348 25.536 1.00 0.00 C +ATOM 394 HB1 ALA 26 20.908 23.362 25.712 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.360 21.647 25.344 1.00 0.00 H +ATOM 396 HB3 ALA 26 19.924 21.988 26.354 1.00 0.00 H +ATOM 397 C ALA 26 20.418 22.533 23.014 1.00 0.00 C +ATOM 398 O ALA 26 20.907 23.586 22.620 1.00 0.00 O +ATOM 399 N GLU 27 20.737 21.419 22.337 1.00 0.00 N +ATOM 400 H GLU 27 20.685 20.536 22.823 1.00 0.00 H +ATOM 401 CA GLU 27 21.493 21.314 21.104 1.00 0.00 C +ATOM 402 HA GLU 27 22.314 22.027 21.182 1.00 0.00 H +ATOM 403 CB GLU 27 21.910 19.791 20.980 1.00 0.00 C +ATOM 404 HB2 GLU 27 22.639 19.639 21.776 1.00 0.00 H +ATOM 405 HB3 GLU 27 21.006 19.223 21.200 1.00 0.00 H +ATOM 406 CG GLU 27 22.527 19.367 19.668 1.00 0.00 C +ATOM 407 HG2 GLU 27 22.206 20.006 18.845 1.00 0.00 H +ATOM 408 HG3 GLU 27 23.597 19.548 19.772 1.00 0.00 H +ATOM 409 CD GLU 27 22.205 17.906 19.348 1.00 0.00 C +ATOM 410 OE1 GLU 27 21.448 17.510 18.450 1.00 0.00 O +ATOM 411 OE2 GLU 27 22.651 17.083 20.126 1.00 0.00 O +ATOM 412 C GLU 27 20.719 21.780 19.927 1.00 0.00 C +ATOM 413 O GLU 27 21.305 22.413 19.037 1.00 0.00 O +ATOM 414 N LYS 28 19.300 21.713 19.930 1.00 0.00 N +ATOM 415 H LYS 28 18.935 21.338 20.793 1.00 0.00 H +ATOM 416 CA LYS 28 18.298 22.362 19.051 1.00 0.00 C +ATOM 417 HA LYS 28 18.614 22.266 18.012 1.00 0.00 H +ATOM 418 CB LYS 28 16.885 21.694 19.261 1.00 0.00 C +ATOM 419 HB2 LYS 28 16.619 21.907 20.297 1.00 0.00 H +ATOM 420 HB3 LYS 28 16.190 22.248 18.630 1.00 0.00 H +ATOM 421 CG LYS 28 16.781 20.227 19.052 1.00 0.00 C +ATOM 422 HG2 LYS 28 16.999 20.040 18.000 1.00 0.00 H +ATOM 423 HG3 LYS 28 17.508 19.681 19.653 1.00 0.00 H +ATOM 424 CD LYS 28 15.318 19.878 19.223 1.00 0.00 C +ATOM 425 HD2 LYS 28 15.126 20.131 20.266 1.00 0.00 H +ATOM 426 HD3 LYS 28 14.643 20.453 18.590 1.00 0.00 H +ATOM 427 CE LYS 28 15.156 18.402 19.034 1.00 0.00 C +ATOM 428 HE2 LYS 28 15.184 18.217 17.960 1.00 0.00 H +ATOM 429 HE3 LYS 28 15.949 17.837 19.522 1.00 0.00 H +ATOM 430 NZ LYS 28 13.848 17.867 19.529 1.00 0.00 N +ATOM 431 HZ1 LYS 28 13.875 18.065 20.519 1.00 0.00 H +ATOM 432 HZ2 LYS 28 13.818 16.869 19.380 1.00 0.00 H +ATOM 433 HZ3 LYS 28 13.023 18.339 19.186 1.00 0.00 H +ATOM 434 C LYS 28 18.274 23.834 19.367 1.00 0.00 C +ATOM 435 O LYS 28 18.419 24.655 18.458 1.00 0.00 O +ATOM 436 N PHE 29 18.164 24.211 20.680 1.00 0.00 N +ATOM 437 H PHE 29 17.940 23.467 21.326 1.00 0.00 H +ATOM 438 CA PHE 29 18.214 25.684 21.073 1.00 0.00 C +ATOM 439 HA PHE 29 17.406 26.180 20.534 1.00 0.00 H +ATOM 440 CB PHE 29 17.804 26.002 22.525 1.00 0.00 C +ATOM 441 HB2 PHE 29 18.651 25.714 23.148 1.00 0.00 H +ATOM 442 HB3 PHE 29 17.683 27.080 22.625 1.00 0.00 H +ATOM 443 CG PHE 29 16.536 25.385 23.044 1.00 0.00 C +ATOM 444 CD1 PHE 29 15.500 24.853 22.236 1.00 0.00 C +ATOM 445 HD1 PHE 29 15.520 24.953 21.161 1.00 0.00 H +ATOM 446 CE1 PHE 29 14.319 24.401 22.891 1.00 0.00 C +ATOM 447 HE1 PHE 29 13.430 24.137 22.337 1.00 0.00 H +ATOM 448 CZ PHE 29 14.193 24.267 24.300 1.00 0.00 C +ATOM 449 HZ PHE 29 13.315 23.927 24.830 1.00 0.00 H +ATOM 450 CE2 PHE 29 15.307 24.720 25.076 1.00 0.00 C +ATOM 451 HE2 PHE 29 15.300 24.529 26.139 1.00 0.00 H +ATOM 452 CD2 PHE 29 16.394 25.366 24.497 1.00 0.00 C +ATOM 453 HD2 PHE 29 17.210 25.789 25.064 1.00 0.00 H +ATOM 454 C PHE 29 19.477 26.409 20.696 1.00 0.00 C +ATOM 455 O PHE 29 19.331 27.427 20.057 1.00 0.00 O +ATOM 456 N THR 30 20.634 25.793 20.855 1.00 0.00 N +ATOM 457 H THR 30 20.786 24.901 21.304 1.00 0.00 H +ATOM 458 CA THR 30 21.927 26.253 20.325 1.00 0.00 C +ATOM 459 HA THR 30 22.014 27.264 20.723 1.00 0.00 H +ATOM 460 CB THR 30 23.024 25.322 20.756 1.00 0.00 C +ATOM 461 HB THR 30 22.744 24.289 20.547 1.00 0.00 H +ATOM 462 CG2 THR 30 24.497 25.490 20.258 1.00 0.00 C +ATOM 463 HG21 THR 30 24.992 26.288 20.810 1.00 0.00 H +ATOM 464 HG22 THR 30 25.040 24.545 20.251 1.00 0.00 H +ATOM 465 HG23 THR 30 24.497 25.762 19.202 1.00 0.00 H +ATOM 466 OG1 THR 30 23.036 25.506 22.157 1.00 0.00 O +ATOM 467 HG1 THR 30 22.393 24.973 22.631 1.00 0.00 H +ATOM 468 C THR 30 21.909 26.306 18.792 1.00 0.00 C +ATOM 469 O THR 30 22.391 27.273 18.211 1.00 0.00 O +ATOM 470 N LYS 31 21.501 25.213 18.135 1.00 0.00 N +ATOM 471 H LYS 31 21.138 24.455 18.694 1.00 0.00 H +ATOM 472 CA LYS 31 21.393 25.190 16.659 1.00 0.00 C +ATOM 473 HA LYS 31 22.409 25.361 16.304 1.00 0.00 H +ATOM 474 CB LYS 31 20.807 23.806 16.255 1.00 0.00 C +ATOM 475 HB2 LYS 31 21.291 23.009 16.819 1.00 0.00 H +ATOM 476 HB3 LYS 31 19.760 23.685 16.536 1.00 0.00 H +ATOM 477 CG LYS 31 21.073 23.540 14.798 1.00 0.00 C +ATOM 478 HG2 LYS 31 20.719 24.330 14.136 1.00 0.00 H +ATOM 479 HG3 LYS 31 22.159 23.519 14.706 1.00 0.00 H +ATOM 480 CD LYS 31 20.398 22.187 14.355 1.00 0.00 C +ATOM 481 HD2 LYS 31 20.684 21.308 14.933 1.00 0.00 H +ATOM 482 HD3 LYS 31 19.352 22.396 14.579 1.00 0.00 H +ATOM 483 CE LYS 31 20.522 21.856 12.867 1.00 0.00 C +ATOM 484 HE2 LYS 31 19.939 20.973 12.604 1.00 0.00 H +ATOM 485 HE3 LYS 31 20.091 22.650 12.256 1.00 0.00 H +ATOM 486 NZ LYS 31 21.948 21.594 12.404 1.00 0.00 N +ATOM 487 HZ1 LYS 31 22.023 21.568 11.397 1.00 0.00 H +ATOM 488 HZ2 LYS 31 22.291 20.720 12.776 1.00 0.00 H +ATOM 489 HZ3 LYS 31 22.662 22.198 12.785 1.00 0.00 H +ATOM 490 C LYS 31 20.451 26.337 16.230 1.00 0.00 C +ATOM 491 O LYS 31 20.726 26.917 15.168 1.00 0.00 O +ATOM 492 N ALA 32 19.474 26.782 16.983 1.00 0.00 N +ATOM 493 H ALA 32 19.157 26.257 17.786 1.00 0.00 H +ATOM 494 CA ALA 32 18.766 28.070 16.719 1.00 0.00 C +ATOM 495 HA ALA 32 18.508 28.061 15.660 1.00 0.00 H +ATOM 496 CB ALA 32 17.410 28.068 17.336 1.00 0.00 C +ATOM 497 HB1 ALA 32 17.411 28.051 18.426 1.00 0.00 H +ATOM 498 HB2 ALA 32 16.898 28.996 17.079 1.00 0.00 H +ATOM 499 HB3 ALA 32 16.727 27.300 16.977 1.00 0.00 H +ATOM 500 C ALA 32 19.563 29.383 17.011 1.00 0.00 C +ATOM 501 O ALA 32 19.277 30.344 16.275 1.00 0.00 O +ATOM 502 N ASP 33 20.613 29.388 17.836 1.00 0.00 N +ATOM 503 H ASP 33 20.744 28.527 18.348 1.00 0.00 H +ATOM 504 CA ASP 33 21.740 30.401 17.981 1.00 0.00 C +ATOM 505 HA ASP 33 21.298 31.394 17.898 1.00 0.00 H +ATOM 506 CB ASP 33 22.527 30.283 19.272 1.00 0.00 C +ATOM 507 HB2 ASP 33 23.074 29.341 19.266 1.00 0.00 H +ATOM 508 HB3 ASP 33 23.276 31.076 19.288 1.00 0.00 H +ATOM 509 CG ASP 33 21.716 30.402 20.542 1.00 0.00 C +ATOM 510 OD1 ASP 33 22.072 29.822 21.600 1.00 0.00 O +ATOM 511 OD2 ASP 33 20.666 31.080 20.566 1.00 0.00 O +ATOM 512 C ASP 33 22.718 30.356 16.888 1.00 0.00 C +ATOM 513 O ASP 33 23.309 31.377 16.581 1.00 0.00 O +ATOM 514 N ALA 34 22.999 29.179 16.324 1.00 0.00 N +ATOM 515 H ALA 34 22.322 28.440 16.447 1.00 0.00 H +ATOM 516 CA ALA 34 23.824 29.106 15.110 1.00 0.00 C +ATOM 517 HA ALA 34 24.725 29.702 15.257 1.00 0.00 H +ATOM 518 CB ALA 34 24.236 27.605 14.944 1.00 0.00 C +ATOM 519 HB1 ALA 34 25.261 27.498 14.590 1.00 0.00 H +ATOM 520 HB2 ALA 34 23.468 27.093 14.364 1.00 0.00 H +ATOM 521 HB3 ALA 34 24.194 27.192 15.952 1.00 0.00 H +ATOM 522 C ALA 34 23.184 29.616 13.843 1.00 0.00 C +ATOM 523 O ALA 34 23.779 30.333 13.048 1.00 0.00 O +ATOM 524 N ASN 35 21.935 29.193 13.642 1.00 0.00 N +ATOM 525 H ASN 35 21.494 28.646 14.368 1.00 0.00 H +ATOM 526 CA ASN 35 21.104 29.642 12.517 1.00 0.00 C +ATOM 527 HA ASN 35 21.550 29.342 11.569 1.00 0.00 H +ATOM 528 CB ASN 35 19.705 28.980 12.636 1.00 0.00 C +ATOM 529 HB2 ASN 35 19.367 28.996 13.672 1.00 0.00 H +ATOM 530 HB3 ASN 35 18.990 29.584 12.078 1.00 0.00 H +ATOM 531 CG ASN 35 19.572 27.512 12.109 1.00 0.00 C +ATOM 532 OD1 ASN 35 18.543 26.836 12.271 1.00 0.00 O +ATOM 533 ND2 ASN 35 20.671 27.011 11.508 1.00 0.00 N +ATOM 534 HD21 ASN 35 21.520 27.545 11.625 1.00 0.00 H +ATOM 535 HD22 ASN 35 20.591 26.061 11.174 1.00 0.00 H +ATOM 536 C ASN 35 20.945 31.188 12.622 1.00 0.00 C +ATOM 537 O ASN 35 20.938 31.896 11.595 1.00 0.00 O +ATOM 538 N ASP 36 20.821 31.788 13.804 1.00 0.00 N +ATOM 539 H ASP 36 20.650 31.205 14.611 1.00 0.00 H +ATOM 540 CA ASP 36 20.898 33.227 14.082 1.00 0.00 C +ATOM 541 HA ASP 36 20.120 33.761 13.536 1.00 0.00 H +ATOM 542 CB ASP 36 20.376 33.574 15.527 1.00 0.00 C +ATOM 543 HB2 ASP 36 19.301 33.394 15.554 1.00 0.00 H +ATOM 544 HB3 ASP 36 20.891 32.884 16.196 1.00 0.00 H +ATOM 545 CG ASP 36 20.577 34.984 15.983 1.00 0.00 C +ATOM 546 OD1 ASP 36 21.173 35.261 17.039 1.00 0.00 O +ATOM 547 OD2 ASP 36 20.121 35.875 15.248 1.00 0.00 O +ATOM 548 C ASP 36 22.287 33.894 13.744 1.00 0.00 C +ATOM 549 O ASP 36 22.324 34.935 13.141 1.00 0.00 O +ATOM 550 N LYS 37 23.399 33.109 13.994 1.00 0.00 N +ATOM 551 H LYS 37 23.318 32.283 14.570 1.00 0.00 H +ATOM 552 CA LYS 37 24.702 33.384 13.333 1.00 0.00 C +ATOM 553 HA LYS 37 24.821 34.464 13.238 1.00 0.00 H +ATOM 554 CB LYS 37 25.838 32.972 14.189 1.00 0.00 C +ATOM 555 HB2 LYS 37 26.764 32.811 13.636 1.00 0.00 H +ATOM 556 HB3 LYS 37 25.649 32.057 14.751 1.00 0.00 H +ATOM 557 CG LYS 37 26.035 34.046 15.316 1.00 0.00 C +ATOM 558 HG2 LYS 37 25.064 34.122 15.806 1.00 0.00 H +ATOM 559 HG3 LYS 37 25.994 35.059 14.914 1.00 0.00 H +ATOM 560 CD LYS 37 27.236 33.811 16.225 1.00 0.00 C +ATOM 561 HD2 LYS 37 27.017 34.205 17.218 1.00 0.00 H +ATOM 562 HD3 LYS 37 27.378 32.733 16.293 1.00 0.00 H +ATOM 563 CE LYS 37 28.532 34.586 15.753 1.00 0.00 C +ATOM 564 HE2 LYS 37 28.361 35.658 15.650 1.00 0.00 H +ATOM 565 HE3 LYS 37 29.239 34.525 16.581 1.00 0.00 H +ATOM 566 NZ LYS 37 29.122 34.032 14.488 1.00 0.00 N +ATOM 567 HZ1 LYS 37 28.818 34.587 13.702 1.00 0.00 H +ATOM 568 HZ2 LYS 37 30.129 33.982 14.553 1.00 0.00 H +ATOM 569 HZ3 LYS 37 28.988 33.041 14.346 1.00 0.00 H +ATOM 570 C LYS 37 24.791 33.033 11.837 1.00 0.00 C +ATOM 571 O LYS 37 25.856 33.254 11.274 1.00 0.00 O +ATOM 572 N GLY 38 23.659 32.561 11.318 1.00 0.00 N +ATOM 573 H GLY 38 22.875 32.584 11.955 1.00 0.00 H +ATOM 574 CA GLY 38 23.411 32.254 9.924 1.00 0.00 C +ATOM 575 HA2 GLY 38 22.335 32.210 9.754 1.00 0.00 H +ATOM 576 HA3 GLY 38 23.757 33.070 9.290 1.00 0.00 H +ATOM 577 C GLY 38 23.975 30.946 9.369 1.00 0.00 C +ATOM 578 O GLY 38 24.117 30.787 8.145 1.00 0.00 O +ATOM 579 N VAL 39 24.307 30.039 10.330 1.00 0.00 N +ATOM 580 H VAL 39 24.127 30.310 11.286 1.00 0.00 H +ATOM 581 CA VAL 39 25.097 28.866 10.134 1.00 0.00 C +ATOM 582 HA VAL 39 25.262 28.678 9.073 1.00 0.00 H +ATOM 583 CB VAL 39 26.564 28.837 10.666 1.00 0.00 C +ATOM 584 HB VAL 39 27.102 27.925 10.410 1.00 0.00 H +ATOM 585 CG1 VAL 39 27.385 29.943 10.027 1.00 0.00 C +ATOM 586 HG11 VAL 39 27.496 29.855 8.947 1.00 0.00 H +ATOM 587 HG12 VAL 39 28.349 30.011 10.531 1.00 0.00 H +ATOM 588 HG13 VAL 39 26.756 30.811 10.225 1.00 0.00 H +ATOM 589 CG2 VAL 39 26.659 29.004 12.161 1.00 0.00 C +ATOM 590 HG21 VAL 39 25.998 29.841 12.386 1.00 0.00 H +ATOM 591 HG22 VAL 39 27.688 29.121 12.502 1.00 0.00 H +ATOM 592 HG23 VAL 39 26.247 28.161 12.715 1.00 0.00 H +ATOM 593 C VAL 39 24.293 27.674 10.695 1.00 0.00 C +ATOM 594 O VAL 39 23.434 27.788 11.586 1.00 0.00 O +ATOM 595 N ASP 40 24.608 26.496 10.126 1.00 0.00 N +ATOM 596 H ASP 40 25.145 26.516 9.271 1.00 0.00 H +ATOM 597 CA ASP 40 23.992 25.261 10.525 1.00 0.00 C +ATOM 598 HA ASP 40 22.944 25.559 10.551 1.00 0.00 H +ATOM 599 CB ASP 40 24.286 24.311 9.311 1.00 0.00 C +ATOM 600 HB2 ASP 40 23.846 24.658 8.376 1.00 0.00 H +ATOM 601 HB3 ASP 40 25.368 24.294 9.174 1.00 0.00 H +ATOM 602 CG ASP 40 23.770 22.839 9.459 1.00 0.00 C +ATOM 603 OD1 ASP 40 24.556 21.877 9.168 1.00 0.00 O +ATOM 604 OD2 ASP 40 22.543 22.669 9.777 1.00 0.00 O +ATOM 605 C ASP 40 24.531 24.645 11.882 1.00 0.00 C +ATOM 606 O ASP 40 24.028 23.695 12.465 1.00 0.00 O +ATOM 607 N GLY 41 25.627 25.135 12.308 1.00 0.00 N +ATOM 608 H GLY 41 26.161 25.813 11.782 1.00 0.00 H +ATOM 609 CA GLY 41 26.281 24.586 13.497 1.00 0.00 C +ATOM 610 HA2 GLY 41 25.582 24.582 14.334 1.00 0.00 H +ATOM 611 HA3 GLY 41 26.647 23.565 13.399 1.00 0.00 H +ATOM 612 C GLY 41 27.489 25.525 13.762 1.00 0.00 C +ATOM 613 O GLY 41 28.396 25.547 12.894 1.00 0.00 O +ATOM 614 N GLU 42 27.498 26.281 14.893 1.00 0.00 N +ATOM 615 H GLU 42 26.686 26.241 15.492 1.00 0.00 H +ATOM 616 CA GLU 42 28.518 27.271 15.380 1.00 0.00 C +ATOM 617 HA GLU 42 29.271 27.275 14.592 1.00 0.00 H +ATOM 618 CB GLU 42 27.914 28.647 15.551 1.00 0.00 C +ATOM 619 HB2 GLU 42 27.289 29.019 14.739 1.00 0.00 H +ATOM 620 HB3 GLU 42 27.122 28.509 16.287 1.00 0.00 H +ATOM 621 CG GLU 42 28.845 29.732 16.095 1.00 0.00 C +ATOM 622 HG2 GLU 42 28.191 30.492 16.523 1.00 0.00 H +ATOM 623 HG3 GLU 42 29.351 29.210 16.907 1.00 0.00 H +ATOM 624 CD GLU 42 29.774 30.380 15.030 1.00 0.00 C +ATOM 625 OE1 GLU 42 29.236 31.273 14.265 1.00 0.00 O +ATOM 626 OE2 GLU 42 30.918 29.910 14.821 1.00 0.00 O +ATOM 627 C GLU 42 29.221 26.586 16.578 1.00 0.00 C +ATOM 628 O GLU 42 30.444 26.488 16.590 1.00 0.00 O +ATOM 629 N TRP 43 28.524 26.078 17.603 1.00 0.00 N +ATOM 630 H TRP 43 27.518 26.170 17.619 1.00 0.00 H +ATOM 631 CA TRP 43 29.115 25.556 18.853 1.00 0.00 C +ATOM 632 HA TRP 43 30.164 25.848 18.907 1.00 0.00 H +ATOM 633 CB TRP 43 28.411 26.102 20.082 1.00 0.00 C +ATOM 634 HB2 TRP 43 27.373 25.772 20.038 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.964 25.780 20.964 1.00 0.00 H +ATOM 636 CG TRP 43 28.543 27.602 20.206 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.476 28.263 20.859 1.00 0.00 C +ATOM 638 HD1 TRP 43 30.198 27.740 21.468 1.00 0.00 H +ATOM 639 NE1 TRP 43 29.301 29.622 20.710 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.951 30.341 20.997 1.00 0.00 H +ATOM 641 CE2 TRP 43 28.172 29.882 19.908 1.00 0.00 C +ATOM 642 CZ2 TRP 43 27.459 30.974 19.594 1.00 0.00 C +ATOM 643 HZ2 TRP 43 27.954 31.908 19.819 1.00 0.00 H +ATOM 644 CH2 TRP 43 26.282 30.911 18.791 1.00 0.00 C +ATOM 645 HH2 TRP 43 25.812 31.844 18.517 1.00 0.00 H +ATOM 646 CZ3 TRP 43 25.868 29.609 18.378 1.00 0.00 C +ATOM 647 HZ3 TRP 43 24.995 29.569 17.743 1.00 0.00 H +ATOM 648 CE3 TRP 43 26.498 28.394 18.867 1.00 0.00 C +ATOM 649 HE3 TRP 43 26.099 27.428 18.596 1.00 0.00 H +ATOM 650 CD2 TRP 43 27.668 28.548 19.633 1.00 0.00 C +ATOM 651 C TRP 43 28.996 24.026 18.940 1.00 0.00 C +ATOM 652 O TRP 43 27.971 23.443 18.741 1.00 0.00 O +ATOM 653 N THR 44 30.051 23.382 19.385 1.00 0.00 N +ATOM 654 H THR 44 30.879 23.908 19.625 1.00 0.00 H +ATOM 655 CA THR 44 30.049 21.963 19.786 1.00 0.00 C +ATOM 656 HA THR 44 29.505 21.403 19.025 1.00 0.00 H +ATOM 657 CB THR 44 31.432 21.433 19.717 1.00 0.00 C +ATOM 658 HB THR 44 31.753 21.667 18.702 1.00 0.00 H +ATOM 659 CG2 THR 44 32.376 22.137 20.683 1.00 0.00 C +ATOM 660 HG21 THR 44 32.450 23.186 20.398 1.00 0.00 H +ATOM 661 HG22 THR 44 33.297 21.570 20.542 1.00 0.00 H +ATOM 662 HG23 THR 44 32.067 21.975 21.716 1.00 0.00 H +ATOM 663 OG1 THR 44 31.474 20.063 19.952 1.00 0.00 O +ATOM 664 HG1 THR 44 31.072 19.627 19.196 1.00 0.00 H +ATOM 665 C THR 44 29.480 21.734 21.218 1.00 0.00 C +ATOM 666 O THR 44 29.235 22.773 21.864 1.00 0.00 O +ATOM 667 N TYR 45 29.145 20.509 21.652 1.00 0.00 N +ATOM 668 H TYR 45 29.276 19.751 20.998 1.00 0.00 H +ATOM 669 CA TYR 45 28.761 20.245 23.013 1.00 0.00 C +ATOM 670 HA TYR 45 28.572 21.145 23.598 1.00 0.00 H +ATOM 671 CB TYR 45 27.463 19.458 23.192 1.00 0.00 C +ATOM 672 HB2 TYR 45 26.728 20.069 22.668 1.00 0.00 H +ATOM 673 HB3 TYR 45 27.613 18.545 22.617 1.00 0.00 H +ATOM 674 CG TYR 45 27.011 19.114 24.547 1.00 0.00 C +ATOM 675 CD1 TYR 45 26.574 20.190 25.379 1.00 0.00 C +ATOM 676 HD1 TYR 45 26.524 21.210 25.029 1.00 0.00 H +ATOM 677 CE1 TYR 45 26.184 19.950 26.706 1.00 0.00 C +ATOM 678 HE1 TYR 45 25.635 20.692 27.266 1.00 0.00 H +ATOM 679 CZ TYR 45 26.200 18.631 27.186 1.00 0.00 C +ATOM 680 OH TYR 45 25.808 18.397 28.453 1.00 0.00 O +ATOM 681 HH TYR 45 25.479 17.496 28.492 1.00 0.00 H +ATOM 682 CE2 TYR 45 26.756 17.597 26.369 1.00 0.00 C +ATOM 683 HE2 TYR 45 26.910 16.587 26.719 1.00 0.00 H +ATOM 684 CD2 TYR 45 27.192 17.849 25.075 1.00 0.00 C +ATOM 685 HD2 TYR 45 27.616 17.058 24.474 1.00 0.00 H +ATOM 686 C TYR 45 29.966 19.536 23.672 1.00 0.00 C +ATOM 687 O TYR 45 30.661 18.797 23.000 1.00 0.00 O +ATOM 688 N ASP 46 30.199 19.812 24.959 1.00 0.00 N +ATOM 689 H ASP 46 29.715 20.598 25.369 1.00 0.00 H +ATOM 690 CA ASP 46 31.197 19.026 25.766 1.00 0.00 C +ATOM 691 HA ASP 46 31.500 18.106 25.268 1.00 0.00 H +ATOM 692 CB ASP 46 32.322 19.953 26.117 1.00 0.00 C +ATOM 693 HB2 ASP 46 32.971 20.241 25.290 1.00 0.00 H +ATOM 694 HB3 ASP 46 31.942 20.920 26.448 1.00 0.00 H +ATOM 695 CG ASP 46 33.127 19.433 27.365 1.00 0.00 C +ATOM 696 OD1 ASP 46 33.257 18.192 27.425 1.00 0.00 O +ATOM 697 OD2 ASP 46 33.345 20.203 28.308 1.00 0.00 O +ATOM 698 C ASP 46 30.503 18.514 27.051 1.00 0.00 C +ATOM 699 O ASP 46 30.062 19.269 27.936 1.00 0.00 O +ATOM 700 N ASP 47 30.351 17.189 27.126 1.00 0.00 N +ATOM 701 H ASP 47 30.749 16.681 26.349 1.00 0.00 H +ATOM 702 CA ASP 47 29.667 16.364 28.159 1.00 0.00 C +ATOM 703 HA ASP 47 28.703 16.743 28.498 1.00 0.00 H +ATOM 704 CB ASP 47 29.436 14.942 27.598 1.00 0.00 C +ATOM 705 HB2 ASP 47 29.010 15.102 26.607 1.00 0.00 H +ATOM 706 HB3 ASP 47 30.315 14.300 27.539 1.00 0.00 H +ATOM 707 CG ASP 47 28.420 14.178 28.453 1.00 0.00 C +ATOM 708 OD1 ASP 47 28.388 12.910 28.434 1.00 0.00 O +ATOM 709 OD2 ASP 47 27.523 14.740 29.081 1.00 0.00 O +ATOM 710 C ASP 47 30.491 16.159 29.469 1.00 0.00 C +ATOM 711 O ASP 47 29.981 15.610 30.424 1.00 0.00 O +ATOM 712 N ALA 48 31.774 16.502 29.492 1.00 0.00 N +ATOM 713 H ALA 48 32.233 16.901 28.686 1.00 0.00 H +ATOM 714 CA ALA 48 32.759 16.350 30.609 1.00 0.00 C +ATOM 715 HA ALA 48 32.527 15.356 30.993 1.00 0.00 H +ATOM 716 CB ALA 48 34.180 16.244 30.083 1.00 0.00 C +ATOM 717 HB1 ALA 48 34.122 15.280 29.577 1.00 0.00 H +ATOM 718 HB2 ALA 48 34.942 16.161 30.858 1.00 0.00 H +ATOM 719 HB3 ALA 48 34.371 17.029 29.351 1.00 0.00 H +ATOM 720 C ALA 48 32.565 17.420 31.661 1.00 0.00 C +ATOM 721 O ALA 48 32.919 17.293 32.805 1.00 0.00 O +ATOM 722 N THR 49 31.946 18.522 31.214 1.00 0.00 N +ATOM 723 H THR 49 31.993 18.729 30.227 1.00 0.00 H +ATOM 724 CA THR 49 31.556 19.655 32.042 1.00 0.00 C +ATOM 725 HA THR 49 31.438 19.290 33.063 1.00 0.00 H +ATOM 726 CB THR 49 32.614 20.804 32.038 1.00 0.00 C +ATOM 727 HB THR 49 32.343 21.625 32.703 1.00 0.00 H +ATOM 728 CG2 THR 49 34.053 20.552 32.501 1.00 0.00 C +ATOM 729 HG21 THR 49 34.542 21.495 32.255 1.00 0.00 H +ATOM 730 HG22 THR 49 34.641 19.755 32.046 1.00 0.00 H +ATOM 731 HG23 THR 49 34.021 20.247 33.547 1.00 0.00 H +ATOM 732 OG1 THR 49 32.812 21.300 30.726 1.00 0.00 O +ATOM 733 HG1 THR 49 33.166 20.618 30.151 1.00 0.00 H +ATOM 734 C THR 49 30.167 20.291 31.711 1.00 0.00 C +ATOM 735 O THR 49 29.764 21.253 32.343 1.00 0.00 O +ATOM 736 N LYS 50 29.330 19.706 30.803 1.00 0.00 N +ATOM 737 H LYS 50 29.809 18.984 30.284 1.00 0.00 H +ATOM 738 CA LYS 50 27.976 20.077 30.330 1.00 0.00 C +ATOM 739 HA LYS 50 27.654 19.563 29.424 1.00 0.00 H +ATOM 740 CB LYS 50 26.874 19.765 31.431 1.00 0.00 C +ATOM 741 HB2 LYS 50 26.920 20.620 32.106 1.00 0.00 H +ATOM 742 HB3 LYS 50 25.905 19.727 30.934 1.00 0.00 H +ATOM 743 CG LYS 50 27.184 18.507 32.290 1.00 0.00 C +ATOM 744 HG2 LYS 50 28.218 18.527 32.637 1.00 0.00 H +ATOM 745 HG3 LYS 50 26.510 18.459 33.145 1.00 0.00 H +ATOM 746 CD LYS 50 26.937 17.194 31.633 1.00 0.00 C +ATOM 747 HD2 LYS 50 25.878 17.002 31.460 1.00 0.00 H +ATOM 748 HD3 LYS 50 27.357 17.089 30.633 1.00 0.00 H +ATOM 749 CE LYS 50 27.581 16.141 32.460 1.00 0.00 C +ATOM 750 HE2 LYS 50 28.652 16.332 32.531 1.00 0.00 H +ATOM 751 HE3 LYS 50 27.177 16.306 33.459 1.00 0.00 H +ATOM 752 NZ LYS 50 27.414 14.694 31.887 1.00 0.00 N +ATOM 753 HZ1 LYS 50 27.939 14.636 31.025 1.00 0.00 H +ATOM 754 HZ2 LYS 50 26.473 14.427 31.634 1.00 0.00 H +ATOM 755 HZ3 LYS 50 27.643 14.047 32.628 1.00 0.00 H +ATOM 756 C LYS 50 27.910 21.481 29.778 1.00 0.00 C +ATOM 757 O LYS 50 27.337 22.409 30.415 1.00 0.00 O +ATOM 758 N THR 51 28.670 21.754 28.750 1.00 0.00 N +ATOM 759 H THR 51 29.301 21.031 28.436 1.00 0.00 H +ATOM 760 CA THR 51 29.051 23.118 28.158 1.00 0.00 C +ATOM 761 HA THR 51 28.415 23.850 28.656 1.00 0.00 H +ATOM 762 CB THR 51 30.575 23.433 28.542 1.00 0.00 C +ATOM 763 HB THR 51 31.144 22.643 28.052 1.00 0.00 H +ATOM 764 CG2 THR 51 31.126 24.853 28.207 1.00 0.00 C +ATOM 765 HG21 THR 51 30.805 25.588 28.946 1.00 0.00 H +ATOM 766 HG22 THR 51 30.686 25.292 27.312 1.00 0.00 H +ATOM 767 HG23 THR 51 32.213 24.788 28.265 1.00 0.00 H +ATOM 768 OG1 THR 51 30.775 23.397 29.929 1.00 0.00 O +ATOM 769 HG1 THR 51 31.099 22.542 30.222 1.00 0.00 H +ATOM 770 C THR 51 28.810 22.999 26.686 1.00 0.00 C +ATOM 771 O THR 51 29.350 22.214 25.983 1.00 0.00 O +ATOM 772 N PHE 52 28.151 24.000 26.097 1.00 0.00 N +ATOM 773 H PHE 52 27.739 24.702 26.695 1.00 0.00 H +ATOM 774 CA PHE 52 28.208 24.371 24.658 1.00 0.00 C +ATOM 775 HA PHE 52 28.449 23.546 23.988 1.00 0.00 H +ATOM 776 CB PHE 52 26.898 25.071 24.251 1.00 0.00 C +ATOM 777 HB2 PHE 52 26.686 25.810 25.023 1.00 0.00 H +ATOM 778 HB3 PHE 52 27.096 25.548 23.291 1.00 0.00 H +ATOM 779 CG PHE 52 25.829 24.050 24.099 1.00 0.00 C +ATOM 780 CD1 PHE 52 25.025 23.739 25.186 1.00 0.00 C +ATOM 781 HD1 PHE 52 25.040 24.388 26.050 1.00 0.00 H +ATOM 782 CE1 PHE 52 24.063 22.653 25.178 1.00 0.00 C +ATOM 783 HE1 PHE 52 23.440 22.467 26.041 1.00 0.00 H +ATOM 784 CZ PHE 52 23.883 21.962 23.947 1.00 0.00 C +ATOM 785 HZ PHE 52 23.159 21.161 23.950 1.00 0.00 H +ATOM 786 CE2 PHE 52 24.673 22.380 22.833 1.00 0.00 C +ATOM 787 HE2 PHE 52 24.659 21.869 21.882 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.621 23.398 22.908 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.319 23.632 22.118 1.00 0.00 H +ATOM 790 C PHE 52 29.375 25.328 24.497 1.00 0.00 C +ATOM 791 O PHE 52 29.475 26.290 25.227 1.00 0.00 O +ATOM 792 N THR 53 30.269 25.074 23.508 1.00 0.00 N +ATOM 793 H THR 53 30.168 24.282 22.889 1.00 0.00 H +ATOM 794 CA THR 53 31.505 25.854 23.507 1.00 0.00 C +ATOM 795 HA THR 53 31.421 26.865 23.906 1.00 0.00 H +ATOM 796 CB THR 53 32.647 25.271 24.425 1.00 0.00 C +ATOM 797 HB THR 53 32.253 25.197 25.438 1.00 0.00 H +ATOM 798 CG2 THR 53 33.276 23.865 23.967 1.00 0.00 C +ATOM 799 HG21 THR 53 34.079 23.627 24.664 1.00 0.00 H +ATOM 800 HG22 THR 53 33.680 24.090 22.980 1.00 0.00 H +ATOM 801 HG23 THR 53 32.499 23.101 23.975 1.00 0.00 H +ATOM 802 OG1 THR 53 33.695 26.161 24.557 1.00 0.00 O +ATOM 803 HG1 THR 53 34.169 25.843 25.330 1.00 0.00 H +ATOM 804 C THR 53 32.063 26.146 22.143 1.00 0.00 C +ATOM 805 O THR 53 31.654 25.453 21.168 1.00 0.00 O +ATOM 806 N VAL 54 32.900 27.189 21.998 1.00 0.00 N +ATOM 807 H VAL 54 33.247 27.599 22.854 1.00 0.00 H +ATOM 808 CA VAL 54 33.545 27.622 20.744 1.00 0.00 C +ATOM 809 HA VAL 54 32.761 27.764 20.000 1.00 0.00 H +ATOM 810 CB VAL 54 34.152 29.022 21.049 1.00 0.00 C +ATOM 811 HB VAL 54 34.545 28.924 22.061 1.00 0.00 H +ATOM 812 CG1 VAL 54 35.141 29.540 20.061 1.00 0.00 C +ATOM 813 HG11 VAL 54 34.678 29.658 19.081 1.00 0.00 H +ATOM 814 HG12 VAL 54 36.044 28.930 20.105 1.00 0.00 H +ATOM 815 HG13 VAL 54 35.552 30.466 20.464 1.00 0.00 H +ATOM 816 CG2 VAL 54 32.922 29.965 21.104 1.00 0.00 C +ATOM 817 HG21 VAL 54 32.178 29.770 21.877 1.00 0.00 H +ATOM 818 HG22 VAL 54 32.429 29.777 20.151 1.00 0.00 H +ATOM 819 HG23 VAL 54 33.235 30.993 21.290 1.00 0.00 H +ATOM 820 C VAL 54 34.579 26.614 20.176 1.00 0.00 C +ATOM 821 O VAL 54 35.236 25.881 20.881 1.00 0.00 O +ATOM 822 N THR 55 34.738 26.610 18.858 1.00 0.00 N +ATOM 823 H THR 55 34.100 27.209 18.355 1.00 0.00 H +ATOM 824 CA THR 55 35.494 25.571 18.091 1.00 0.00 C +ATOM 825 HA THR 55 36.340 25.191 18.663 1.00 0.00 H +ATOM 826 CB THR 55 34.592 24.392 17.866 1.00 0.00 C +ATOM 827 HB THR 55 34.520 24.022 18.889 1.00 0.00 H +ATOM 828 CG2 THR 55 33.243 24.807 17.338 1.00 0.00 C +ATOM 829 HG21 THR 55 32.694 23.933 16.986 1.00 0.00 H +ATOM 830 HG22 THR 55 33.459 25.388 16.442 1.00 0.00 H +ATOM 831 HG23 THR 55 32.599 25.310 18.060 1.00 0.00 H +ATOM 832 OG1 THR 55 35.214 23.344 17.056 1.00 0.00 O +ATOM 833 HG1 THR 55 34.741 22.528 17.235 1.00 0.00 H +ATOM 834 C THR 55 35.989 26.113 16.758 1.00 0.00 C +ATOM 835 O THR 55 35.391 27.015 16.157 1.00 0.00 O +ATOM 836 N GLU 56 37.098 25.569 16.269 1.00 0.00 N +ATOM 837 H GLU 56 37.498 24.882 16.892 1.00 0.00 H +ATOM 838 CA GLU 56 37.810 26.119 15.087 1.00 0.00 C +ATOM 839 HA GLU 56 37.661 27.186 14.919 1.00 0.00 H +ATOM 840 CB GLU 56 39.258 25.834 15.420 1.00 0.00 C +ATOM 841 HB2 GLU 56 39.466 24.803 15.709 1.00 0.00 H +ATOM 842 HB3 GLU 56 39.793 26.072 14.501 1.00 0.00 H +ATOM 843 CG GLU 56 39.872 26.553 16.572 1.00 0.00 C +ATOM 844 HG2 GLU 56 40.927 26.311 16.448 1.00 0.00 H +ATOM 845 HG3 GLU 56 39.768 27.627 16.418 1.00 0.00 H +ATOM 846 CD GLU 56 39.374 26.084 17.979 1.00 0.00 C +ATOM 847 OE1 GLU 56 39.044 26.920 18.806 1.00 0.00 O +ATOM 848 OE2 GLU 56 39.372 24.874 18.302 1.00 0.00 O +ATOM 849 C GLU 56 37.291 25.363 13.773 1.00 0.00 C +ATOM 850 O GLU 56 37.116 24.120 13.828 1.00 0.00 O +ATOM 851 OXT GLU 56 37.116 26.125 12.780 1.00 0.00 O +ATOM 852 ZN ZN1 57 24.123 31.114 24.908 1.00 0.00 ZN +ATOM 853 N AN1 58 23.621 32.248 23.271 1.00 0.00 N +ATOM 854 C AN1 58 23.152 33.773 21.218 1.00 0.00 C +ATOM 855 C1 AN1 58 23.375 32.930 22.359 1.00 0.00 C +ATOM 856 H AN1 58 22.228 34.363 21.208 1.00 0.00 H +ATOM 857 H1 AN1 58 23.323 33.210 20.292 1.00 0.00 H +ATOM 858 H2 AN1 58 24.010 34.439 21.364 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 26.154 36.387 25.203 1.00 0.00 N +ATOM 860 N2 AZI 59 25.133 35.976 24.691 1.00 0.00 N +ATOM 861 N3 AZI 59 24.025 35.637 24.161 1.00 0.00 N +TER 862 AZI 59 \ No newline at end of file diff --git a/tests/nsga2/pdbs_rename/cluster8.pdb b/tests/nsga2/pdbs_rename/cluster8.pdb new file mode 100644 index 0000000..69c07ed --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster8.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.921 -81.871 -14.343 1.00 0.00 N +ATOM 2 H1 MET 1 14.869 -81.579 -14.148 1.00 0.00 H +ATOM 3 H2 MET 1 13.368 -81.557 -13.558 1.00 0.00 H +ATOM 4 H3 MET 1 13.637 -81.522 -15.247 1.00 0.00 H +ATOM 5 CA MET 1 13.777 -83.340 -14.319 1.00 0.00 C +ATOM 6 HA MET 1 12.694 -83.452 -14.273 1.00 0.00 H +ATOM 7 CB MET 1 14.417 -84.024 -15.635 1.00 0.00 C +ATOM 8 HB2 MET 1 13.739 -83.941 -16.484 1.00 0.00 H +ATOM 9 HB3 MET 1 15.258 -83.374 -15.880 1.00 0.00 H +ATOM 10 CG MET 1 14.914 -85.464 -15.548 1.00 0.00 C +ATOM 11 HG2 MET 1 15.491 -85.619 -16.460 1.00 0.00 H +ATOM 12 HG3 MET 1 15.641 -85.592 -14.746 1.00 0.00 H +ATOM 13 SD MET 1 13.694 -86.744 -15.342 1.00 0.00 S +ATOM 14 CE MET 1 12.844 -86.818 -16.891 1.00 0.00 C +ATOM 15 HE1 MET 1 12.441 -85.860 -17.221 1.00 0.00 H +ATOM 16 HE2 MET 1 12.022 -87.532 -16.842 1.00 0.00 H +ATOM 17 HE3 MET 1 13.515 -87.136 -17.689 1.00 0.00 H +ATOM 18 C MET 1 14.458 -83.816 -12.991 1.00 0.00 C +ATOM 19 O MET 1 15.523 -83.346 -12.558 1.00 0.00 O +ATOM 20 N GLN 2 13.897 -84.833 -12.374 1.00 0.00 N +ATOM 21 H GLN 2 13.021 -85.111 -12.794 1.00 0.00 H +ATOM 22 CA GLN 2 14.474 -85.680 -11.226 1.00 0.00 C +ATOM 23 HA GLN 2 14.952 -85.062 -10.466 1.00 0.00 H +ATOM 24 CB GLN 2 13.208 -86.271 -10.447 1.00 0.00 C +ATOM 25 HB2 GLN 2 12.499 -85.469 -10.247 1.00 0.00 H +ATOM 26 HB3 GLN 2 12.744 -86.972 -11.141 1.00 0.00 H +ATOM 27 CG GLN 2 13.497 -87.166 -9.295 1.00 0.00 C +ATOM 28 HG2 GLN 2 13.957 -88.104 -9.607 1.00 0.00 H +ATOM 29 HG3 GLN 2 14.251 -86.595 -8.755 1.00 0.00 H +ATOM 30 CD GLN 2 12.285 -87.400 -8.519 1.00 0.00 C +ATOM 31 OE1 GLN 2 11.637 -88.433 -8.636 1.00 0.00 O +ATOM 32 NE2 GLN 2 11.927 -86.490 -7.713 1.00 0.00 N +ATOM 33 HE21 GLN 2 11.202 -86.742 -7.057 1.00 0.00 H +ATOM 34 HE22 GLN 2 12.491 -85.656 -7.798 1.00 0.00 H +ATOM 35 C GLN 2 15.466 -86.837 -11.631 1.00 0.00 C +ATOM 36 O GLN 2 15.053 -87.916 -11.986 1.00 0.00 O +ATOM 37 N TYR 3 16.775 -86.584 -11.551 1.00 0.00 N +ATOM 38 H TYR 3 17.123 -85.735 -11.128 1.00 0.00 H +ATOM 39 CA TYR 3 17.771 -87.564 -11.964 1.00 0.00 C +ATOM 40 HA TYR 3 17.313 -88.271 -12.655 1.00 0.00 H +ATOM 41 CB TYR 3 19.006 -86.895 -12.646 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.499 -86.219 -11.948 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.700 -87.727 -12.765 1.00 0.00 H +ATOM 44 CG TYR 3 18.698 -86.159 -13.977 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.565 -86.788 -15.198 1.00 0.00 C +ATOM 46 HD1 TYR 3 18.901 -87.810 -15.289 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.148 -86.073 -16.345 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.141 -86.534 -17.322 1.00 0.00 H +ATOM 49 CZ TYR 3 17.953 -84.718 -16.219 1.00 0.00 C +ATOM 50 OH TYR 3 17.604 -83.917 -17.277 1.00 0.00 O +ATOM 51 HH TYR 3 17.237 -84.416 -18.010 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.135 -84.079 -14.926 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.941 -83.018 -14.881 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.646 -84.781 -13.840 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.734 -84.358 -12.850 1.00 0.00 H +ATOM 56 C TYR 3 18.256 -88.359 -10.791 1.00 0.00 C +ATOM 57 O TYR 3 18.335 -87.830 -9.636 1.00 0.00 O +ATOM 58 N LYS 4 18.596 -89.686 -11.012 1.00 0.00 N +ATOM 59 H LYS 4 18.517 -90.039 -11.955 1.00 0.00 H +ATOM 60 CA LYS 4 19.183 -90.476 -9.960 1.00 0.00 C +ATOM 61 HA LYS 4 18.711 -90.181 -9.023 1.00 0.00 H +ATOM 62 CB LYS 4 18.806 -91.973 -10.205 1.00 0.00 C +ATOM 63 HB2 LYS 4 19.541 -92.429 -10.868 1.00 0.00 H +ATOM 64 HB3 LYS 4 18.979 -92.557 -9.302 1.00 0.00 H +ATOM 65 CG LYS 4 17.382 -92.249 -10.829 1.00 0.00 C +ATOM 66 HG2 LYS 4 16.591 -91.848 -10.196 1.00 0.00 H +ATOM 67 HG3 LYS 4 17.198 -91.854 -11.828 1.00 0.00 H +ATOM 68 CD LYS 4 17.218 -93.746 -10.995 1.00 0.00 C +ATOM 69 HD2 LYS 4 17.874 -94.090 -11.795 1.00 0.00 H +ATOM 70 HD3 LYS 4 17.436 -94.320 -10.095 1.00 0.00 H +ATOM 71 CE LYS 4 15.773 -94.099 -11.464 1.00 0.00 C +ATOM 72 HE2 LYS 4 15.705 -95.150 -11.747 1.00 0.00 H +ATOM 73 HE3 LYS 4 15.144 -93.913 -10.593 1.00 0.00 H +ATOM 74 NZ LYS 4 15.360 -93.359 -12.729 1.00 0.00 N +ATOM 75 HZ1 LYS 4 15.844 -93.595 -13.583 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.370 -92.362 -12.569 1.00 0.00 H +ATOM 77 HZ3 LYS 4 14.403 -93.601 -12.942 1.00 0.00 H +ATOM 78 C LYS 4 20.712 -90.246 -9.868 1.00 0.00 C +ATOM 79 O LYS 4 21.339 -89.932 -10.899 1.00 0.00 O +ATOM 80 N HX1 5 21.157 -90.323 -8.628 1.00 0.00 N +ATOM 81 CA HX1 5 22.577 -90.254 -8.143 1.00 0.00 C +ATOM 82 C HX1 5 22.780 -91.510 -7.279 1.00 0.00 C +ATOM 83 O HX1 5 22.059 -91.731 -6.321 1.00 0.00 O +ATOM 84 CB HX1 5 22.905 -88.931 -7.404 1.00 0.00 C +ATOM 85 CG HX1 5 24.252 -88.842 -6.710 1.00 0.00 C +ATOM 86 CD2 HX1 5 25.467 -89.141 -7.300 1.00 0.00 C +ATOM 87 ND1 HX1 5 24.596 -88.111 -5.538 1.00 0.00 N +ATOM 88 CE1 HX1 5 25.920 -88.240 -5.320 1.00 0.00 C +ATOM 89 NE2 HX1 5 26.478 -88.827 -6.408 1.00 0.00 N +ATOM 90 H HX1 5 20.392 -90.395 -7.973 1.00 0.00 H +ATOM 91 HA HX1 5 23.185 -90.265 -9.047 1.00 0.00 H +ATOM 92 HB2 HX1 5 22.120 -88.862 -6.651 1.00 0.00 H +ATOM 93 HB3 HX1 5 22.809 -88.113 -8.118 1.00 0.00 H +ATOM 94 HD2 HX1 5 25.623 -89.543 -8.290 1.00 0.00 H +ATOM 95 HE1 HX1 5 26.409 -87.659 -4.553 1.00 0.00 H +ATOM 96 HE2 HX1 5 27.470 -88.968 -6.531 1.00 0.00 H +ATOM 97 N ILE 6 23.686 -92.419 -7.665 1.00 0.00 N +ATOM 98 H ILE 6 24.055 -92.315 -8.599 1.00 0.00 H +ATOM 99 CA ILE 6 24.259 -93.424 -6.761 1.00 0.00 C +ATOM 100 HA ILE 6 23.527 -93.868 -6.086 1.00 0.00 H +ATOM 101 CB ILE 6 24.667 -94.566 -7.730 1.00 0.00 C +ATOM 102 HB ILE 6 25.222 -94.162 -8.577 1.00 0.00 H +ATOM 103 CG2 ILE 6 25.588 -95.590 -6.983 1.00 0.00 C +ATOM 104 HG21 ILE 6 25.118 -96.116 -6.152 1.00 0.00 H +ATOM 105 HG22 ILE 6 26.458 -95.135 -6.509 1.00 0.00 H +ATOM 106 HG23 ILE 6 25.907 -96.388 -7.653 1.00 0.00 H +ATOM 107 CG1 ILE 6 23.424 -95.232 -8.324 1.00 0.00 C +ATOM 108 HG12 ILE 6 23.313 -96.194 -7.823 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.537 -94.610 -8.203 1.00 0.00 H +ATOM 110 CD1 ILE 6 23.597 -95.481 -9.893 1.00 0.00 C +ATOM 111 HD11 ILE 6 22.651 -95.808 -10.325 1.00 0.00 H +ATOM 112 HD12 ILE 6 24.342 -96.244 -10.118 1.00 0.00 H +ATOM 113 HD13 ILE 6 23.806 -94.521 -10.364 1.00 0.00 H +ATOM 114 C ILE 6 25.408 -92.835 -5.912 1.00 0.00 C +ATOM 115 O ILE 6 26.116 -91.966 -6.403 1.00 0.00 O +ATOM 116 N VAL 7 25.544 -93.263 -4.634 1.00 0.00 N +ATOM 117 H VAL 7 24.933 -94.015 -4.349 1.00 0.00 H +ATOM 118 CA VAL 7 26.579 -92.879 -3.647 1.00 0.00 C +ATOM 119 HA VAL 7 26.341 -91.871 -3.309 1.00 0.00 H +ATOM 120 CB VAL 7 26.574 -93.814 -2.429 1.00 0.00 C +ATOM 121 HB VAL 7 25.567 -93.830 -2.012 1.00 0.00 H +ATOM 122 CG1 VAL 7 26.979 -95.288 -2.559 1.00 0.00 C +ATOM 123 HG11 VAL 7 26.730 -95.829 -1.646 1.00 0.00 H +ATOM 124 HG12 VAL 7 26.303 -95.723 -3.295 1.00 0.00 H +ATOM 125 HG13 VAL 7 27.990 -95.588 -2.832 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.414 -93.280 -1.275 1.00 0.00 C +ATOM 127 HG21 VAL 7 27.284 -93.772 -0.310 1.00 0.00 H +ATOM 128 HG22 VAL 7 28.461 -93.320 -1.574 1.00 0.00 H +ATOM 129 HG23 VAL 7 27.125 -92.244 -1.098 1.00 0.00 H +ATOM 130 C VAL 7 28.064 -92.846 -4.191 1.00 0.00 C +ATOM 131 O VAL 7 28.405 -93.773 -4.954 1.00 0.00 O +ATOM 132 N ASN 8 28.799 -91.743 -3.961 1.00 0.00 N +ATOM 133 H ASN 8 28.494 -91.123 -3.224 1.00 0.00 H +ATOM 134 CA ASN 8 30.121 -91.631 -4.588 1.00 0.00 C +ATOM 135 HA ASN 8 30.116 -91.790 -5.666 1.00 0.00 H +ATOM 136 CB ASN 8 30.647 -90.195 -4.473 1.00 0.00 C +ATOM 137 HB2 ASN 8 30.543 -89.818 -3.455 1.00 0.00 H +ATOM 138 HB3 ASN 8 31.688 -90.200 -4.795 1.00 0.00 H +ATOM 139 CG ASN 8 29.933 -89.153 -5.311 1.00 0.00 C +ATOM 140 OD1 ASN 8 29.276 -89.495 -6.263 1.00 0.00 O +ATOM 141 ND2 ASN 8 29.961 -87.921 -4.910 1.00 0.00 N +ATOM 142 HD21 ASN 8 30.463 -87.646 -4.078 1.00 0.00 H +ATOM 143 HD22 ASN 8 29.417 -87.296 -5.488 1.00 0.00 H +ATOM 144 C ASN 8 31.165 -92.621 -3.962 1.00 0.00 C +ATOM 145 O ASN 8 31.866 -93.301 -4.695 1.00 0.00 O +ATOM 146 N GLY 9 31.266 -92.786 -2.627 1.00 0.00 N +ATOM 147 H GLY 9 30.597 -92.292 -2.054 1.00 0.00 H +ATOM 148 CA GLY 9 32.249 -93.661 -1.943 1.00 0.00 C +ATOM 149 HA2 GLY 9 33.280 -93.368 -2.143 1.00 0.00 H +ATOM 150 HA3 GLY 9 31.995 -93.643 -0.883 1.00 0.00 H +ATOM 151 C GLY 9 32.090 -95.108 -2.410 1.00 0.00 C +ATOM 152 O GLY 9 31.000 -95.693 -2.186 1.00 0.00 O +ATOM 153 N LYS 10 33.168 -95.675 -3.033 1.00 0.00 N +ATOM 154 H LYS 10 33.978 -95.072 -3.069 1.00 0.00 H +ATOM 155 CA LYS 10 33.069 -96.908 -3.785 1.00 0.00 C +ATOM 156 HA LYS 10 32.144 -96.896 -4.363 1.00 0.00 H +ATOM 157 CB LYS 10 34.112 -97.117 -4.909 1.00 0.00 C +ATOM 158 HB2 LYS 10 33.720 -98.014 -5.388 1.00 0.00 H +ATOM 159 HB3 LYS 10 34.131 -96.272 -5.598 1.00 0.00 H +ATOM 160 CG LYS 10 35.580 -97.413 -4.444 1.00 0.00 C +ATOM 161 HG2 LYS 10 35.943 -96.564 -3.865 1.00 0.00 H +ATOM 162 HG3 LYS 10 35.500 -98.288 -3.798 1.00 0.00 H +ATOM 163 CD LYS 10 36.768 -97.611 -5.413 1.00 0.00 C +ATOM 164 HD2 LYS 10 37.088 -96.611 -5.706 1.00 0.00 H +ATOM 165 HD3 LYS 10 37.629 -97.979 -4.856 1.00 0.00 H +ATOM 166 CE LYS 10 36.329 -98.512 -6.559 1.00 0.00 C +ATOM 167 HE2 LYS 10 35.814 -99.424 -6.258 1.00 0.00 H +ATOM 168 HE3 LYS 10 35.439 -98.090 -7.027 1.00 0.00 H +ATOM 169 NZ LYS 10 37.445 -98.857 -7.492 1.00 0.00 N +ATOM 170 HZ1 LYS 10 38.162 -99.326 -6.958 1.00 0.00 H +ATOM 171 HZ2 LYS 10 37.801 -98.084 -8.036 1.00 0.00 H +ATOM 172 HZ3 LYS 10 37.118 -99.469 -8.226 1.00 0.00 H +ATOM 173 C LYS 10 32.801 -98.179 -2.897 1.00 0.00 C +ATOM 174 O LYS 10 32.119 -99.096 -3.387 1.00 0.00 O +ATOM 175 N THR 11 33.207 -98.208 -1.641 1.00 0.00 N +ATOM 176 H THR 11 33.675 -97.388 -1.283 1.00 0.00 H +ATOM 177 CA THR 11 32.964 -99.347 -0.712 1.00 0.00 C +ATOM 178 HA THR 11 33.320-100.265 -1.179 1.00 0.00 H +ATOM 179 CB THR 11 33.737 -99.151 0.596 1.00 0.00 C +ATOM 180 HB THR 11 33.536-100.053 1.174 1.00 0.00 H +ATOM 181 CG2 THR 11 35.257 -99.083 0.399 1.00 0.00 C +ATOM 182 HG21 THR 11 35.564 -98.047 0.257 1.00 0.00 H +ATOM 183 HG22 THR 11 35.617 -99.803 -0.336 1.00 0.00 H +ATOM 184 HG23 THR 11 35.778 -99.396 1.303 1.00 0.00 H +ATOM 185 OG1 THR 11 33.319 -97.995 1.241 1.00 0.00 O +ATOM 186 HG1 THR 11 33.495 -98.200 2.162 1.00 0.00 H +ATOM 187 C THR 11 31.462 -99.528 -0.357 1.00 0.00 C +ATOM 188 O THR 11 31.008-100.485 0.337 1.00 0.00 O +ATOM 189 N LEU 12 30.633 -98.557 -0.740 1.00 0.00 N +ATOM 190 H LEU 12 31.044 -97.800 -1.268 1.00 0.00 H +ATOM 191 CA LEU 12 29.196 -98.436 -0.445 1.00 0.00 C +ATOM 192 HA LEU 12 28.849 -99.121 0.328 1.00 0.00 H +ATOM 193 CB LEU 12 28.957 -96.994 0.112 1.00 0.00 C +ATOM 194 HB2 LEU 12 29.365 -96.233 -0.552 1.00 0.00 H +ATOM 195 HB3 LEU 12 27.908 -96.797 0.333 1.00 0.00 H +ATOM 196 CG LEU 12 29.680 -96.617 1.447 1.00 0.00 C +ATOM 197 HG LEU 12 30.761 -96.664 1.313 1.00 0.00 H +ATOM 198 CD1 LEU 12 29.426 -95.151 1.753 1.00 0.00 C +ATOM 199 HD11 LEU 12 28.413 -94.909 2.078 1.00 0.00 H +ATOM 200 HD12 LEU 12 29.531 -94.591 0.824 1.00 0.00 H +ATOM 201 HD13 LEU 12 30.150 -94.710 2.438 1.00 0.00 H +ATOM 202 CD2 LEU 12 29.257 -97.424 2.695 1.00 0.00 C +ATOM 203 HD21 LEU 12 29.403 -98.503 2.637 1.00 0.00 H +ATOM 204 HD22 LEU 12 28.170 -97.373 2.755 1.00 0.00 H +ATOM 205 HD23 LEU 12 29.683 -97.057 3.628 1.00 0.00 H +ATOM 206 C LEU 12 28.286 -98.702 -1.659 1.00 0.00 C +ATOM 207 O LEU 12 28.762 -99.045 -2.707 1.00 0.00 O +ATOM 208 N LYS 13 26.971 -98.583 -1.456 1.00 0.00 N +ATOM 209 H LYS 13 26.774 -98.325 -0.500 1.00 0.00 H +ATOM 210 CA LYS 13 25.918 -98.732 -2.454 1.00 0.00 C +ATOM 211 HA LYS 13 26.291 -98.287 -3.377 1.00 0.00 H +ATOM 212 CB LYS 13 25.618-100.260 -2.728 1.00 0.00 C +ATOM 213 HB2 LYS 13 24.868-100.451 -3.496 1.00 0.00 H +ATOM 214 HB3 LYS 13 26.550-100.673 -3.113 1.00 0.00 H +ATOM 215 CG LYS 13 25.280-101.101 -1.442 1.00 0.00 C +ATOM 216 HG2 LYS 13 26.064-100.830 -0.735 1.00 0.00 H +ATOM 217 HG3 LYS 13 24.342-100.814 -0.968 1.00 0.00 H +ATOM 218 CD LYS 13 25.301-102.684 -1.590 1.00 0.00 C +ATOM 219 HD2 LYS 13 26.121-102.974 -2.246 1.00 0.00 H +ATOM 220 HD3 LYS 13 25.590-103.065 -0.610 1.00 0.00 H +ATOM 221 CE LYS 13 24.044-103.271 -2.255 1.00 0.00 C +ATOM 222 HE2 LYS 13 23.150-103.059 -1.668 1.00 0.00 H +ATOM 223 HE3 LYS 13 23.947-102.956 -3.294 1.00 0.00 H +ATOM 224 NZ LYS 13 24.118-104.768 -2.401 1.00 0.00 N +ATOM 225 HZ1 LYS 13 24.887-105.073 -2.980 1.00 0.00 H +ATOM 226 HZ2 LYS 13 23.284-105.112 -2.854 1.00 0.00 H +ATOM 227 HZ3 LYS 13 24.143-105.035 -1.427 1.00 0.00 H +ATOM 228 C LYS 13 24.659 -97.941 -2.025 1.00 0.00 C +ATOM 229 O LYS 13 24.605 -97.583 -0.845 1.00 0.00 O +ATOM 230 N GLY 14 23.662 -97.861 -2.933 1.00 0.00 N +ATOM 231 H GLY 14 23.797 -98.259 -3.851 1.00 0.00 H +ATOM 232 CA GLY 14 22.353 -97.258 -2.744 1.00 0.00 C +ATOM 233 HA2 GLY 14 21.608 -97.996 -3.042 1.00 0.00 H +ATOM 234 HA3 GLY 14 22.145 -97.029 -1.699 1.00 0.00 H +ATOM 235 C GLY 14 22.203 -96.077 -3.688 1.00 0.00 C +ATOM 236 O GLY 14 23.147 -95.354 -4.093 1.00 0.00 O +ATOM 237 N VAL 15 20.975 -95.917 -4.184 1.00 0.00 N +ATOM 238 H VAL 15 20.270 -96.291 -3.565 1.00 0.00 H +ATOM 239 CA VAL 15 20.564 -94.974 -5.240 1.00 0.00 C +ATOM 240 HA VAL 15 21.453 -94.473 -5.622 1.00 0.00 H +ATOM 241 CB VAL 15 20.112 -95.859 -6.464 1.00 0.00 C +ATOM 242 HB VAL 15 21.003 -96.342 -6.865 1.00 0.00 H +ATOM 243 CG1 VAL 15 18.995 -96.907 -6.067 1.00 0.00 C +ATOM 244 HG11 VAL 15 19.327 -97.466 -5.192 1.00 0.00 H +ATOM 245 HG12 VAL 15 18.045 -96.408 -5.877 1.00 0.00 H +ATOM 246 HG13 VAL 15 18.940 -97.571 -6.930 1.00 0.00 H +ATOM 247 CG2 VAL 15 19.538 -94.960 -7.667 1.00 0.00 C +ATOM 248 HG21 VAL 15 19.744 -95.404 -8.641 1.00 0.00 H +ATOM 249 HG22 VAL 15 18.474 -94.759 -7.544 1.00 0.00 H +ATOM 250 HG23 VAL 15 20.022 -93.985 -7.719 1.00 0.00 H +ATOM 251 C VAL 15 19.535 -93.971 -4.667 1.00 0.00 C +ATOM 252 O VAL 15 18.567 -94.484 -4.115 1.00 0.00 O +ATOM 253 N HY1 16 19.769 -92.696 -4.718 1.00 0.00 N +ATOM 254 CA HY1 16 18.792 -91.687 -4.399 1.00 0.00 C +ATOM 255 C HY1 16 18.591 -90.676 -5.515 1.00 0.00 C +ATOM 256 O HY1 16 19.446 -90.538 -6.375 1.00 0.00 O +ATOM 257 CB HY1 16 19.207 -90.885 -3.171 1.00 0.00 C +ATOM 258 CG HY1 16 20.522 -90.141 -3.148 1.00 0.00 C +ATOM 259 CD2 HY1 16 20.748 -88.870 -3.613 1.00 0.00 C +ATOM 260 ND1 HY1 16 21.730 -90.654 -2.604 1.00 0.00 N +ATOM 261 CE1 HY1 16 22.645 -89.755 -2.832 1.00 0.00 C +ATOM 262 NE2 HY1 16 22.152 -88.677 -3.472 1.00 0.00 N +ATOM 263 H HY1 16 20.656 -92.381 -5.084 1.00 0.00 H +ATOM 264 HA HY1 16 17.822 -92.144 -4.199 1.00 0.00 H +ATOM 265 HB2 HY1 16 18.534 -90.046 -2.996 1.00 0.00 H +ATOM 266 HB3 HY1 16 19.084 -91.604 -2.361 1.00 0.00 H +ATOM 267 HD1 HY1 16 21.958 -91.542 -2.182 1.00 0.00 H +ATOM 268 HD2 HY1 16 20.033 -88.220 -4.093 1.00 0.00 H +ATOM 269 HE1 HY1 16 23.717 -89.892 -2.820 1.00 0.00 H +ATOM 270 N THR 17 17.492 -89.870 -5.494 1.00 0.00 N +ATOM 271 H THR 17 16.877 -89.984 -4.701 1.00 0.00 H +ATOM 272 CA THR 17 17.430 -88.725 -6.504 1.00 0.00 C +ATOM 273 HA THR 17 17.898 -89.164 -7.384 1.00 0.00 H +ATOM 274 CB THR 17 16.005 -88.657 -6.901 1.00 0.00 C +ATOM 275 HB THR 17 15.940 -87.958 -7.735 1.00 0.00 H +ATOM 276 CG2 THR 17 15.470 -89.991 -7.446 1.00 0.00 C +ATOM 277 HG21 THR 17 14.380 -89.982 -7.422 1.00 0.00 H +ATOM 278 HG22 THR 17 15.776 -90.843 -6.840 1.00 0.00 H +ATOM 279 HG23 THR 17 15.820 -89.982 -8.478 1.00 0.00 H +ATOM 280 OG1 THR 17 15.115 -88.381 -5.845 1.00 0.00 O +ATOM 281 HG1 THR 17 15.198 -87.429 -5.751 1.00 0.00 H +ATOM 282 C THR 17 17.998 -87.343 -6.187 1.00 0.00 C +ATOM 283 O THR 17 18.177 -86.981 -5.051 1.00 0.00 O +ATOM 284 N HY2 18 18.113 -86.460 -7.175 1.00 0.00 N +ATOM 285 CA HY2 18 18.195 -85.026 -7.115 1.00 0.00 C +ATOM 286 C HY2 18 17.526 -84.339 -8.322 1.00 0.00 C +ATOM 287 O HY2 18 17.780 -84.833 -9.450 1.00 0.00 O +ATOM 288 CB HY2 18 19.633 -84.463 -7.142 1.00 0.00 C +ATOM 289 CG HY2 18 20.472 -84.863 -5.995 1.00 0.00 C +ATOM 290 CD2 HY2 18 21.612 -85.662 -6.088 1.00 0.00 C +ATOM 291 ND1 HY2 18 20.478 -84.473 -4.702 1.00 0.00 N +ATOM 292 CE1 HY2 18 21.506 -84.974 -4.051 1.00 0.00 C +ATOM 293 NE2 HY2 18 22.258 -85.733 -4.821 1.00 0.00 N +ATOM 294 H HY2 18 18.033 -86.861 -8.098 1.00 0.00 H +ATOM 295 HA HY2 18 17.655 -84.729 -6.216 1.00 0.00 H +ATOM 296 HB2 HY2 18 20.133 -84.724 -8.074 1.00 0.00 H +ATOM 297 HB3 HY2 18 19.495 -83.382 -7.119 1.00 0.00 H +ATOM 298 HD1 HY2 18 19.686 -84.065 -4.227 1.00 0.00 H +ATOM 299 HD2 HY2 18 21.945 -86.132 -7.002 1.00 0.00 H +ATOM 300 HE1 HY2 18 21.618 -84.976 -2.977 1.00 0.00 H +ATOM 301 N GLU 19 16.791 -83.316 -8.196 1.00 0.00 N +ATOM 302 H GLU 19 16.619 -82.947 -7.271 1.00 0.00 H +ATOM 303 CA GLU 19 16.189 -82.534 -9.335 1.00 0.00 C +ATOM 304 HA GLU 19 15.717 -83.199 -10.058 1.00 0.00 H +ATOM 305 CB GLU 19 15.137 -81.529 -8.866 1.00 0.00 C +ATOM 306 HB2 GLU 19 15.489 -80.967 -8.001 1.00 0.00 H +ATOM 307 HB3 GLU 19 14.979 -80.849 -9.703 1.00 0.00 H +ATOM 308 CG GLU 19 13.832 -82.232 -8.509 1.00 0.00 C +ATOM 309 HG2 GLU 19 13.133 -81.449 -8.216 1.00 0.00 H +ATOM 310 HG3 GLU 19 13.498 -82.698 -9.436 1.00 0.00 H +ATOM 311 CD GLU 19 13.874 -83.145 -7.309 1.00 0.00 C +ATOM 312 OE1 GLU 19 13.277 -84.235 -7.458 1.00 0.00 O +ATOM 313 OE2 GLU 19 14.458 -82.709 -6.268 1.00 0.00 O +ATOM 314 C GLU 19 17.251 -81.733 -10.058 1.00 0.00 C +ATOM 315 O GLU 19 18.268 -81.319 -9.500 1.00 0.00 O +ATOM 316 N ALA 20 17.028 -81.355 -11.340 1.00 0.00 N +ATOM 317 H ALA 20 16.280 -81.854 -11.799 1.00 0.00 H +ATOM 318 CA ALA 20 17.832 -80.409 -12.050 1.00 0.00 C +ATOM 319 HA ALA 20 18.005 -79.573 -11.373 1.00 0.00 H +ATOM 320 CB ALA 20 19.230 -80.954 -12.548 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.834 -80.087 -12.815 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.052 -81.464 -13.494 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.619 -81.606 -11.766 1.00 0.00 H +ATOM 324 C ALA 20 17.056 -79.787 -13.172 1.00 0.00 C +ATOM 325 O ALA 20 16.181 -80.408 -13.715 1.00 0.00 O +ATOM 326 N VAL 21 17.289 -78.553 -13.518 1.00 0.00 N +ATOM 327 H VAL 21 17.746 -78.039 -12.778 1.00 0.00 H +ATOM 328 CA VAL 21 16.732 -77.990 -14.750 1.00 0.00 C +ATOM 329 HA VAL 21 15.652 -78.087 -14.636 1.00 0.00 H +ATOM 330 CB VAL 21 17.136 -76.481 -14.780 1.00 0.00 C +ATOM 331 HB VAL 21 16.756 -76.067 -13.846 1.00 0.00 H +ATOM 332 CG1 VAL 21 18.619 -76.064 -15.092 1.00 0.00 C +ATOM 333 HG11 VAL 21 19.278 -76.406 -14.294 1.00 0.00 H +ATOM 334 HG12 VAL 21 18.706 -74.978 -15.116 1.00 0.00 H +ATOM 335 HG13 VAL 21 19.016 -76.460 -16.026 1.00 0.00 H +ATOM 336 CG2 VAL 21 16.276 -75.791 -15.898 1.00 0.00 C +ATOM 337 HG21 VAL 21 16.118 -74.740 -15.657 1.00 0.00 H +ATOM 338 HG22 VAL 21 15.270 -76.210 -15.925 1.00 0.00 H +ATOM 339 HG23 VAL 21 16.648 -75.920 -16.914 1.00 0.00 H +ATOM 340 C VAL 21 17.256 -78.738 -15.996 1.00 0.00 C +ATOM 341 O VAL 21 16.475 -78.765 -16.944 1.00 0.00 O +ATOM 342 N ASP 22 18.437 -79.309 -15.891 1.00 0.00 N +ATOM 343 H ASP 22 18.977 -79.325 -15.037 1.00 0.00 H +ATOM 344 CA ASP 22 19.048 -79.929 -17.085 1.00 0.00 C +ATOM 345 HA ASP 22 18.319 -80.415 -17.733 1.00 0.00 H +ATOM 346 CB ASP 22 19.542 -78.764 -17.995 1.00 0.00 C +ATOM 347 HB2 ASP 22 18.678 -78.140 -18.226 1.00 0.00 H +ATOM 348 HB3 ASP 22 20.326 -78.249 -17.441 1.00 0.00 H +ATOM 349 CG ASP 22 20.203 -79.111 -19.319 1.00 0.00 C +ATOM 350 OD1 ASP 22 20.289 -80.263 -19.789 1.00 0.00 O +ATOM 351 OD2 ASP 22 20.450 -78.160 -20.067 1.00 0.00 O +ATOM 352 C ASP 22 20.148 -80.929 -16.699 1.00 0.00 C +ATOM 353 O ASP 22 20.667 -80.878 -15.622 1.00 0.00 O +ATOM 354 N ALA 23 20.544 -81.877 -17.574 1.00 0.00 N +ATOM 355 H ALA 23 20.146 -81.753 -18.494 1.00 0.00 H +ATOM 356 CA ALA 23 21.479 -82.989 -17.380 1.00 0.00 C +ATOM 357 HA ALA 23 21.100 -83.658 -16.607 1.00 0.00 H +ATOM 358 CB ALA 23 21.628 -83.905 -18.579 1.00 0.00 C +ATOM 359 HB1 ALA 23 21.706 -83.265 -19.458 1.00 0.00 H +ATOM 360 HB2 ALA 23 20.749 -84.537 -18.708 1.00 0.00 H +ATOM 361 HB3 ALA 23 22.414 -84.651 -18.460 1.00 0.00 H +ATOM 362 C ALA 23 22.935 -82.526 -17.010 1.00 0.00 C +ATOM 363 O ALA 23 23.566 -83.061 -16.124 1.00 0.00 O +ATOM 364 N ALA 24 23.292 -81.350 -17.606 1.00 0.00 N +ATOM 365 H ALA 24 22.582 -80.982 -18.222 1.00 0.00 H +ATOM 366 CA ALA 24 24.481 -80.518 -17.307 1.00 0.00 C +ATOM 367 HA ALA 24 25.415 -81.069 -17.415 1.00 0.00 H +ATOM 368 CB ALA 24 24.690 -79.490 -18.349 1.00 0.00 C +ATOM 369 HB1 ALA 24 23.905 -78.739 -18.443 1.00 0.00 H +ATOM 370 HB2 ALA 24 24.836 -79.975 -19.314 1.00 0.00 H +ATOM 371 HB3 ALA 24 25.669 -79.069 -18.120 1.00 0.00 H +ATOM 372 C ALA 24 24.539 -79.932 -15.873 1.00 0.00 C +ATOM 373 O ALA 24 25.628 -79.664 -15.344 1.00 0.00 O +ATOM 374 N GLU 25 23.340 -79.686 -15.282 1.00 0.00 N +ATOM 375 H GLU 25 22.546 -79.727 -15.904 1.00 0.00 H +ATOM 376 CA GLU 25 23.192 -79.129 -13.938 1.00 0.00 C +ATOM 377 HA GLU 25 24.072 -78.636 -13.526 1.00 0.00 H +ATOM 378 CB GLU 25 22.015 -78.222 -14.035 1.00 0.00 C +ATOM 379 HB2 GLU 25 21.125 -78.805 -14.273 1.00 0.00 H +ATOM 380 HB3 GLU 25 22.004 -77.839 -13.015 1.00 0.00 H +ATOM 381 CG GLU 25 22.298 -76.987 -14.939 1.00 0.00 C +ATOM 382 HG2 GLU 25 22.107 -77.306 -15.963 1.00 0.00 H +ATOM 383 HG3 GLU 25 21.545 -76.229 -14.724 1.00 0.00 H +ATOM 384 CD GLU 25 23.723 -76.353 -14.820 1.00 0.00 C +ATOM 385 OE1 GLU 25 24.466 -76.418 -15.814 1.00 0.00 O +ATOM 386 OE2 GLU 25 24.034 -75.970 -13.669 1.00 0.00 O +ATOM 387 C GLU 25 22.970 -80.238 -12.865 1.00 0.00 C +ATOM 388 O GLU 25 23.317 -80.099 -11.679 1.00 0.00 O +ATOM 389 N ALA 26 22.554 -81.399 -13.289 1.00 0.00 N +ATOM 390 H ALA 26 22.148 -81.395 -14.214 1.00 0.00 H +ATOM 391 CA ALA 26 22.491 -82.596 -12.463 1.00 0.00 C +ATOM 392 HA ALA 26 21.949 -82.408 -11.536 1.00 0.00 H +ATOM 393 CB ALA 26 21.698 -83.718 -13.106 1.00 0.00 C +ATOM 394 HB1 ALA 26 20.714 -83.328 -13.363 1.00 0.00 H +ATOM 395 HB2 ALA 26 21.634 -84.614 -12.488 1.00 0.00 H +ATOM 396 HB3 ALA 26 22.203 -83.878 -14.059 1.00 0.00 H +ATOM 397 C ALA 26 23.873 -83.149 -12.105 1.00 0.00 C +ATOM 398 O ALA 26 24.127 -83.578 -10.974 1.00 0.00 O +ATOM 399 N GLU 27 24.793 -83.012 -13.038 1.00 0.00 N +ATOM 400 H GLU 27 24.481 -82.831 -13.981 1.00 0.00 H +ATOM 401 CA GLU 27 26.205 -83.450 -12.914 1.00 0.00 C +ATOM 402 HA GLU 27 26.268 -84.444 -12.471 1.00 0.00 H +ATOM 403 CB GLU 27 26.839 -83.500 -14.345 1.00 0.00 C +ATOM 404 HB2 GLU 27 26.255 -84.179 -14.966 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.734 -82.499 -14.764 1.00 0.00 H +ATOM 406 CG GLU 27 28.309 -83.938 -14.422 1.00 0.00 C +ATOM 407 HG2 GLU 27 28.522 -84.622 -13.600 1.00 0.00 H +ATOM 408 HG3 GLU 27 28.399 -84.453 -15.378 1.00 0.00 H +ATOM 409 CD GLU 27 29.426 -82.861 -14.512 1.00 0.00 C +ATOM 410 OE1 GLU 27 29.105 -81.716 -14.269 1.00 0.00 O +ATOM 411 OE2 GLU 27 30.585 -83.181 -14.753 1.00 0.00 O +ATOM 412 C GLU 27 26.897 -82.570 -11.818 1.00 0.00 C +ATOM 413 O GLU 27 27.492 -83.045 -10.876 1.00 0.00 O +ATOM 414 N LYS 28 26.649 -81.261 -11.833 1.00 0.00 N +ATOM 415 H LYS 28 25.898 -80.921 -12.417 1.00 0.00 H +ATOM 416 CA LYS 28 27.274 -80.280 -10.874 1.00 0.00 C +ATOM 417 HA LYS 28 28.358 -80.348 -10.777 1.00 0.00 H +ATOM 418 CB LYS 28 26.935 -78.903 -11.308 1.00 0.00 C +ATOM 419 HB2 LYS 28 25.846 -78.891 -11.331 1.00 0.00 H +ATOM 420 HB3 LYS 28 27.195 -78.109 -10.609 1.00 0.00 H +ATOM 421 CG LYS 28 27.520 -78.527 -12.699 1.00 0.00 C +ATOM 422 HG2 LYS 28 28.603 -78.628 -12.774 1.00 0.00 H +ATOM 423 HG3 LYS 28 27.174 -79.341 -13.336 1.00 0.00 H +ATOM 424 CD LYS 28 26.985 -77.201 -13.188 1.00 0.00 C +ATOM 425 HD2 LYS 28 25.922 -77.246 -13.427 1.00 0.00 H +ATOM 426 HD3 LYS 28 27.253 -76.433 -12.463 1.00 0.00 H +ATOM 427 CE LYS 28 27.690 -77.097 -14.546 1.00 0.00 C +ATOM 428 HE2 LYS 28 28.744 -76.998 -14.287 1.00 0.00 H +ATOM 429 HE3 LYS 28 27.493 -78.004 -15.118 1.00 0.00 H +ATOM 430 NZ LYS 28 27.257 -75.915 -15.329 1.00 0.00 N +ATOM 431 HZ1 LYS 28 27.358 -75.085 -14.762 1.00 0.00 H +ATOM 432 HZ2 LYS 28 26.256 -75.987 -15.441 1.00 0.00 H +ATOM 433 HZ3 LYS 28 27.714 -75.830 -16.225 1.00 0.00 H +ATOM 434 C LYS 28 26.786 -80.567 -9.464 1.00 0.00 C +ATOM 435 O LYS 28 27.544 -80.630 -8.518 1.00 0.00 O +ATOM 436 N PHE 29 25.505 -80.925 -9.299 1.00 0.00 N +ATOM 437 H PHE 29 24.835 -81.027 -10.048 1.00 0.00 H +ATOM 438 CA PHE 29 25.024 -81.260 -7.936 1.00 0.00 C +ATOM 439 HA PHE 29 25.531 -80.616 -7.217 1.00 0.00 H +ATOM 440 CB PHE 29 23.540 -81.082 -8.057 1.00 0.00 C +ATOM 441 HB2 PHE 29 23.281 -80.301 -8.772 1.00 0.00 H +ATOM 442 HB3 PHE 29 23.063 -82.034 -8.292 1.00 0.00 H +ATOM 443 CG PHE 29 22.903 -80.812 -6.686 1.00 0.00 C +ATOM 444 CD1 PHE 29 22.689 -79.462 -6.341 1.00 0.00 C +ATOM 445 HD1 PHE 29 23.000 -78.722 -7.063 1.00 0.00 H +ATOM 446 CE1 PHE 29 22.284 -79.160 -5.046 1.00 0.00 C +ATOM 447 HE1 PHE 29 22.198 -78.104 -4.836 1.00 0.00 H +ATOM 448 CZ PHE 29 21.989 -80.123 -4.104 1.00 0.00 C +ATOM 449 HZ PHE 29 21.600 -79.922 -3.117 1.00 0.00 H +ATOM 450 CE2 PHE 29 22.179 -81.449 -4.449 1.00 0.00 C +ATOM 451 HE2 PHE 29 22.033 -82.279 -3.773 1.00 0.00 H +ATOM 452 CD2 PHE 29 22.631 -81.806 -5.742 1.00 0.00 C +ATOM 453 HD2 PHE 29 22.898 -82.828 -5.966 1.00 0.00 H +ATOM 454 C PHE 29 25.461 -82.712 -7.409 1.00 0.00 C +ATOM 455 O PHE 29 25.697 -82.856 -6.236 1.00 0.00 O +ATOM 456 N THR 30 25.707 -83.621 -8.357 1.00 0.00 N +ATOM 457 H THR 30 25.635 -83.332 -9.322 1.00 0.00 H +ATOM 458 CA THR 30 26.208 -84.965 -8.066 1.00 0.00 C +ATOM 459 HA THR 30 25.608 -85.378 -7.256 1.00 0.00 H +ATOM 460 CB THR 30 26.084 -85.875 -9.308 1.00 0.00 C +ATOM 461 HB THR 30 25.874 -85.221 -10.155 1.00 0.00 H +ATOM 462 CG2 THR 30 27.196 -86.736 -9.852 1.00 0.00 C +ATOM 463 HG21 THR 30 28.153 -86.218 -9.917 1.00 0.00 H +ATOM 464 HG22 THR 30 27.390 -87.486 -9.084 1.00 0.00 H +ATOM 465 HG23 THR 30 26.874 -87.347 -10.695 1.00 0.00 H +ATOM 466 OG1 THR 30 24.959 -86.743 -9.151 1.00 0.00 O +ATOM 467 HG1 THR 30 24.150 -86.233 -9.064 1.00 0.00 H +ATOM 468 C THR 30 27.602 -84.834 -7.458 1.00 0.00 C +ATOM 469 O THR 30 27.982 -85.567 -6.536 1.00 0.00 O +ATOM 470 N LYS 31 28.389 -83.964 -8.060 1.00 0.00 N +ATOM 471 H LYS 31 28.029 -83.476 -8.867 1.00 0.00 H +ATOM 472 CA LYS 31 29.845 -83.879 -7.769 1.00 0.00 C +ATOM 473 HA LYS 31 30.125 -84.833 -7.324 1.00 0.00 H +ATOM 474 CB LYS 31 30.553 -83.808 -9.172 1.00 0.00 C +ATOM 475 HB2 LYS 31 31.586 -84.075 -8.949 1.00 0.00 H +ATOM 476 HB3 LYS 31 30.155 -84.572 -9.839 1.00 0.00 H +ATOM 477 CG LYS 31 30.439 -82.427 -9.831 1.00 0.00 C +ATOM 478 HG2 LYS 31 29.402 -82.121 -9.692 1.00 0.00 H +ATOM 479 HG3 LYS 31 31.149 -81.853 -9.235 1.00 0.00 H +ATOM 480 CD LYS 31 30.933 -82.291 -11.280 1.00 0.00 C +ATOM 481 HD2 LYS 31 30.109 -82.589 -11.929 1.00 0.00 H +ATOM 482 HD3 LYS 31 31.131 -81.238 -11.477 1.00 0.00 H +ATOM 483 CE LYS 31 32.205 -83.101 -11.598 1.00 0.00 C +ATOM 484 HE2 LYS 31 33.016 -82.806 -10.932 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.988 -84.169 -11.568 1.00 0.00 H +ATOM 486 NZ LYS 31 32.655 -82.994 -12.990 1.00 0.00 N +ATOM 487 HZ1 LYS 31 33.350 -83.694 -13.207 1.00 0.00 H +ATOM 488 HZ2 LYS 31 33.001 -82.091 -13.280 1.00 0.00 H +ATOM 489 HZ3 LYS 31 31.986 -83.157 -13.728 1.00 0.00 H +ATOM 490 C LYS 31 30.218 -82.787 -6.714 1.00 0.00 C +ATOM 491 O LYS 31 31.284 -82.775 -6.216 1.00 0.00 O +ATOM 492 N ALA 32 29.240 -81.928 -6.355 1.00 0.00 N +ATOM 493 H ALA 32 28.307 -82.010 -6.734 1.00 0.00 H +ATOM 494 CA ALA 32 29.552 -80.929 -5.322 1.00 0.00 C +ATOM 495 HA ALA 32 30.411 -80.348 -5.658 1.00 0.00 H +ATOM 496 CB ALA 32 28.294 -80.071 -5.100 1.00 0.00 C +ATOM 497 HB1 ALA 32 28.514 -79.164 -4.538 1.00 0.00 H +ATOM 498 HB2 ALA 32 28.069 -79.802 -6.132 1.00 0.00 H +ATOM 499 HB3 ALA 32 27.427 -80.647 -4.776 1.00 0.00 H +ATOM 500 C ALA 32 29.971 -81.485 -3.943 1.00 0.00 C +ATOM 501 O ALA 32 30.808 -80.916 -3.287 1.00 0.00 O +ATOM 502 N ASP 33 29.339 -82.599 -3.492 1.00 0.00 N +ATOM 503 H ASP 33 28.670 -83.085 -4.072 1.00 0.00 H +ATOM 504 CA ASP 33 29.868 -83.300 -2.330 1.00 0.00 C +ATOM 505 HA ASP 33 29.951 -82.528 -1.565 1.00 0.00 H +ATOM 506 CB ASP 33 28.813 -84.281 -1.797 1.00 0.00 C +ATOM 507 HB2 ASP 33 27.812 -83.860 -1.901 1.00 0.00 H +ATOM 508 HB3 ASP 33 28.811 -85.254 -2.288 1.00 0.00 H +ATOM 509 CG ASP 33 29.079 -84.654 -0.308 1.00 0.00 C +ATOM 510 OD1 ASP 33 28.610 -83.976 0.635 1.00 0.00 O +ATOM 511 OD2 ASP 33 29.658 -85.775 -0.187 1.00 0.00 O +ATOM 512 C ASP 33 31.261 -83.814 -2.522 1.00 0.00 C +ATOM 513 O ASP 33 32.025 -83.626 -1.546 1.00 0.00 O +ATOM 514 N ALA 34 31.686 -84.490 -3.542 1.00 0.00 N +ATOM 515 H ALA 34 30.943 -84.854 -4.121 1.00 0.00 H +ATOM 516 CA ALA 34 33.057 -84.764 -3.839 1.00 0.00 C +ATOM 517 HA ALA 34 33.458 -85.537 -3.184 1.00 0.00 H +ATOM 518 CB ALA 34 33.054 -85.408 -5.260 1.00 0.00 C +ATOM 519 HB1 ALA 34 34.060 -85.508 -5.665 1.00 0.00 H +ATOM 520 HB2 ALA 34 32.445 -84.921 -6.022 1.00 0.00 H +ATOM 521 HB3 ALA 34 32.640 -86.416 -5.279 1.00 0.00 H +ATOM 522 C ALA 34 33.945 -83.501 -3.824 1.00 0.00 C +ATOM 523 O ALA 34 35.023 -83.475 -3.188 1.00 0.00 O +ATOM 524 N ASN 35 33.497 -82.349 -4.398 1.00 0.00 N +ATOM 525 H ASN 35 32.637 -82.408 -4.923 1.00 0.00 H +ATOM 526 CA ASN 35 34.198 -81.062 -4.400 1.00 0.00 C +ATOM 527 HA ASN 35 35.192 -81.057 -4.849 1.00 0.00 H +ATOM 528 CB ASN 35 33.383 -79.949 -5.124 1.00 0.00 C +ATOM 529 HB2 ASN 35 32.376 -79.876 -4.714 1.00 0.00 H +ATOM 530 HB3 ASN 35 33.798 -78.963 -4.912 1.00 0.00 H +ATOM 531 CG ASN 35 33.231 -80.132 -6.645 1.00 0.00 C +ATOM 532 OD1 ASN 35 33.733 -81.003 -7.339 1.00 0.00 O +ATOM 533 ND2 ASN 35 32.636 -79.160 -7.299 1.00 0.00 N +ATOM 534 HD21 ASN 35 32.218 -78.407 -6.771 1.00 0.00 H +ATOM 535 HD22 ASN 35 32.609 -79.207 -8.307 1.00 0.00 H +ATOM 536 C ASN 35 34.368 -80.609 -2.923 1.00 0.00 C +ATOM 537 O ASN 35 35.388 -80.028 -2.585 1.00 0.00 O +ATOM 538 N ASP 36 33.411 -80.804 -2.035 1.00 0.00 N +ATOM 539 H ASP 36 32.502 -81.181 -2.264 1.00 0.00 H +ATOM 540 CA ASP 36 33.585 -80.452 -0.603 1.00 0.00 C +ATOM 541 HA ASP 36 33.977 -79.443 -0.479 1.00 0.00 H +ATOM 542 CB ASP 36 32.232 -80.439 0.038 1.00 0.00 C +ATOM 543 HB2 ASP 36 31.519 -79.752 -0.417 1.00 0.00 H +ATOM 544 HB3 ASP 36 31.933 -81.485 -0.036 1.00 0.00 H +ATOM 545 CG ASP 36 32.258 -80.149 1.514 1.00 0.00 C +ATOM 546 OD1 ASP 36 32.252 -81.070 2.340 1.00 0.00 O +ATOM 547 OD2 ASP 36 32.184 -78.917 1.947 1.00 0.00 O +ATOM 548 C ASP 36 34.537 -81.384 0.175 1.00 0.00 C +ATOM 549 O ASP 36 35.181 -80.968 1.120 1.00 0.00 O +ATOM 550 N LYS 37 34.569 -82.699 -0.251 1.00 0.00 N +ATOM 551 H LYS 37 33.911 -83.034 -0.940 1.00 0.00 H +ATOM 552 CA LYS 37 35.464 -83.677 0.391 1.00 0.00 C +ATOM 553 HA LYS 37 35.607 -83.403 1.436 1.00 0.00 H +ATOM 554 CB LYS 37 34.774 -85.079 0.415 1.00 0.00 C +ATOM 555 HB2 LYS 37 35.620 -85.688 0.095 1.00 0.00 H +ATOM 556 HB3 LYS 37 34.036 -85.016 -0.384 1.00 0.00 H +ATOM 557 CG LYS 37 34.332 -85.624 1.766 1.00 0.00 C +ATOM 558 HG2 LYS 37 35.217 -85.724 2.395 1.00 0.00 H +ATOM 559 HG3 LYS 37 34.044 -86.671 1.664 1.00 0.00 H +ATOM 560 CD LYS 37 33.217 -84.913 2.555 1.00 0.00 C +ATOM 561 HD2 LYS 37 32.903 -85.596 3.345 1.00 0.00 H +ATOM 562 HD3 LYS 37 33.553 -83.992 3.030 1.00 0.00 H +ATOM 563 CE LYS 37 31.972 -84.545 1.721 1.00 0.00 C +ATOM 564 HE2 LYS 37 32.338 -84.198 0.754 1.00 0.00 H +ATOM 565 HE3 LYS 37 31.457 -85.491 1.554 1.00 0.00 H +ATOM 566 NZ LYS 37 31.002 -83.633 2.403 1.00 0.00 N +ATOM 567 HZ1 LYS 37 30.261 -83.468 1.736 1.00 0.00 H +ATOM 568 HZ2 LYS 37 30.564 -84.135 3.162 1.00 0.00 H +ATOM 569 HZ3 LYS 37 31.460 -82.752 2.587 1.00 0.00 H +ATOM 570 C LYS 37 36.949 -83.669 -0.145 1.00 0.00 C +ATOM 571 O LYS 37 37.795 -84.418 0.346 1.00 0.00 O +ATOM 572 N GLY 38 37.248 -82.834 -1.113 1.00 0.00 N +ATOM 573 H GLY 38 36.498 -82.311 -1.542 1.00 0.00 H +ATOM 574 CA GLY 38 38.544 -82.741 -1.826 1.00 0.00 C +ATOM 575 HA2 GLY 38 38.697 -81.767 -2.293 1.00 0.00 H +ATOM 576 HA3 GLY 38 39.307 -82.805 -1.050 1.00 0.00 H +ATOM 577 C GLY 38 38.778 -83.829 -2.883 1.00 0.00 C +ATOM 578 O GLY 38 39.903 -84.018 -3.344 1.00 0.00 O +ATOM 579 N VAL 39 37.767 -84.595 -3.250 1.00 0.00 N +ATOM 580 H VAL 39 36.873 -84.366 -2.839 1.00 0.00 H +ATOM 581 CA VAL 39 37.951 -85.830 -4.016 1.00 0.00 C +ATOM 582 HA VAL 39 38.972 -86.165 -3.834 1.00 0.00 H +ATOM 583 CB VAL 39 36.925 -86.856 -3.405 1.00 0.00 C +ATOM 584 HB VAL 39 35.939 -86.452 -3.174 1.00 0.00 H +ATOM 585 CG1 VAL 39 36.793 -88.060 -4.383 1.00 0.00 C +ATOM 586 HG11 VAL 39 36.589 -87.687 -5.387 1.00 0.00 H +ATOM 587 HG12 VAL 39 35.921 -88.679 -4.171 1.00 0.00 H +ATOM 588 HG13 VAL 39 37.728 -88.601 -4.532 1.00 0.00 H +ATOM 589 CG2 VAL 39 37.474 -87.474 -2.145 1.00 0.00 C +ATOM 590 HG21 VAL 39 37.629 -86.699 -1.395 1.00 0.00 H +ATOM 591 HG22 VAL 39 38.441 -87.937 -2.346 1.00 0.00 H +ATOM 592 HG23 VAL 39 36.903 -88.296 -1.713 1.00 0.00 H +ATOM 593 C VAL 39 37.793 -85.484 -5.477 1.00 0.00 C +ATOM 594 O VAL 39 36.948 -84.788 -5.914 1.00 0.00 O +ATOM 595 N ASP 40 38.660 -86.095 -6.297 1.00 0.00 N +ATOM 596 H ASP 40 39.302 -86.727 -5.842 1.00 0.00 H +ATOM 597 CA ASP 40 38.614 -86.098 -7.802 1.00 0.00 C +ATOM 598 HA ASP 40 38.055 -85.216 -8.116 1.00 0.00 H +ATOM 599 CB ASP 40 39.959 -85.723 -8.445 1.00 0.00 C +ATOM 600 HB2 ASP 40 40.688 -86.527 -8.350 1.00 0.00 H +ATOM 601 HB3 ASP 40 39.865 -85.590 -9.523 1.00 0.00 H +ATOM 602 CG ASP 40 40.738 -84.520 -7.974 1.00 0.00 C +ATOM 603 OD1 ASP 40 40.132 -83.482 -7.635 1.00 0.00 O +ATOM 604 OD2 ASP 40 42.001 -84.583 -7.978 1.00 0.00 O +ATOM 605 C ASP 40 38.051 -87.384 -8.330 1.00 0.00 C +ATOM 606 O ASP 40 37.810 -88.380 -7.599 1.00 0.00 O +ATOM 607 N GLY 41 37.746 -87.408 -9.589 1.00 0.00 N +ATOM 608 H GLY 41 37.693 -86.579 -10.165 1.00 0.00 H +ATOM 609 CA GLY 41 37.288 -88.662 -10.236 1.00 0.00 C +ATOM 610 HA2 GLY 41 38.136 -89.129 -10.738 1.00 0.00 H +ATOM 611 HA3 GLY 41 36.791 -89.302 -9.506 1.00 0.00 H +ATOM 612 C GLY 41 36.272 -88.205 -11.372 1.00 0.00 C +ATOM 613 O GLY 41 36.097 -87.040 -11.673 1.00 0.00 O +ATOM 614 N GLU 42 35.594 -89.212 -11.877 1.00 0.00 N +ATOM 615 H GLU 42 35.767 -90.173 -11.620 1.00 0.00 H +ATOM 616 CA GLU 42 34.585 -88.979 -12.986 1.00 0.00 C +ATOM 617 HA GLU 42 34.450 -87.908 -13.139 1.00 0.00 H +ATOM 618 CB GLU 42 35.192 -89.345 -14.354 1.00 0.00 C +ATOM 619 HB2 GLU 42 35.174 -90.429 -14.467 1.00 0.00 H +ATOM 620 HB3 GLU 42 34.444 -89.025 -15.078 1.00 0.00 H +ATOM 621 CG GLU 42 36.573 -88.781 -14.748 1.00 0.00 C +ATOM 622 HG2 GLU 42 37.249 -89.266 -14.044 1.00 0.00 H +ATOM 623 HG3 GLU 42 36.864 -89.095 -15.750 1.00 0.00 H +ATOM 624 CD GLU 42 36.733 -87.282 -14.599 1.00 0.00 C +ATOM 625 OE1 GLU 42 35.757 -86.554 -14.853 1.00 0.00 O +ATOM 626 OE2 GLU 42 37.842 -86.853 -14.141 1.00 0.00 O +ATOM 627 C GLU 42 33.205 -89.633 -12.764 1.00 0.00 C +ATOM 628 O GLU 42 33.040 -90.563 -11.989 1.00 0.00 O +ATOM 629 N TRP 43 32.264 -89.154 -13.569 1.00 0.00 N +ATOM 630 H TRP 43 32.530 -88.646 -14.400 1.00 0.00 H +ATOM 631 CA TRP 43 30.851 -89.664 -13.515 1.00 0.00 C +ATOM 632 HA TRP 43 30.875 -90.525 -12.847 1.00 0.00 H +ATOM 633 CB TRP 43 29.864 -88.757 -12.810 1.00 0.00 C +ATOM 634 HB2 TRP 43 29.823 -87.792 -13.316 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.888 -89.238 -12.873 1.00 0.00 H +ATOM 636 CG TRP 43 30.136 -88.638 -11.352 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.390 -89.256 -10.408 1.00 0.00 C +ATOM 638 HD1 TRP 43 28.534 -89.905 -10.525 1.00 0.00 H +ATOM 639 NE1 TRP 43 29.978 -88.943 -9.164 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.668 -89.383 -8.309 1.00 0.00 H +ATOM 641 CE2 TRP 43 31.000 -88.042 -9.255 1.00 0.00 C +ATOM 642 CZ2 TRP 43 31.822 -87.436 -8.285 1.00 0.00 C +ATOM 643 HZ2 TRP 43 31.657 -87.621 -7.234 1.00 0.00 H +ATOM 644 CH2 TRP 43 32.777 -86.516 -8.704 1.00 0.00 C +ATOM 645 HH2 TRP 43 33.208 -85.869 -7.954 1.00 0.00 H +ATOM 646 CZ3 TRP 43 32.952 -86.274 -10.052 1.00 0.00 C +ATOM 647 HZ3 TRP 43 33.627 -85.504 -10.393 1.00 0.00 H +ATOM 648 CE3 TRP 43 32.181 -87.031 -10.988 1.00 0.00 C +ATOM 649 HE3 TRP 43 32.359 -86.839 -12.036 1.00 0.00 H +ATOM 650 CD2 TRP 43 31.172 -87.904 -10.661 1.00 0.00 C +ATOM 651 C TRP 43 30.379 -90.170 -14.869 1.00 0.00 C +ATOM 652 O TRP 43 30.540 -89.486 -15.895 1.00 0.00 O +ATOM 653 N THR 44 29.748 -91.335 -14.901 1.00 0.00 N +ATOM 654 H THR 44 29.573 -91.922 -14.098 1.00 0.00 H +ATOM 655 CA THR 44 29.056 -91.745 -16.059 1.00 0.00 C +ATOM 656 HA THR 44 29.475 -91.187 -16.896 1.00 0.00 H +ATOM 657 CB THR 44 29.360 -93.227 -16.425 1.00 0.00 C +ATOM 658 HB THR 44 29.019 -93.873 -15.616 1.00 0.00 H +ATOM 659 CG2 THR 44 28.609 -93.574 -17.724 1.00 0.00 C +ATOM 660 HG21 THR 44 28.817 -92.791 -18.453 1.00 0.00 H +ATOM 661 HG22 THR 44 27.559 -93.580 -17.432 1.00 0.00 H +ATOM 662 HG23 THR 44 29.008 -94.532 -18.055 1.00 0.00 H +ATOM 663 OG1 THR 44 30.732 -93.303 -16.610 1.00 0.00 O +ATOM 664 HG1 THR 44 31.128 -92.656 -16.021 1.00 0.00 H +ATOM 665 C THR 44 27.586 -91.475 -15.914 1.00 0.00 C +ATOM 666 O THR 44 26.928 -92.049 -14.997 1.00 0.00 O +ATOM 667 N TYR 45 27.019 -90.745 -16.838 1.00 0.00 N +ATOM 668 H TYR 45 27.577 -90.435 -17.621 1.00 0.00 H +ATOM 669 CA TYR 45 25.584 -90.597 -17.069 1.00 0.00 C +ATOM 670 HA TYR 45 25.015 -90.540 -16.141 1.00 0.00 H +ATOM 671 CB TYR 45 25.353 -89.363 -17.984 1.00 0.00 C +ATOM 672 HB2 TYR 45 25.812 -88.487 -17.524 1.00 0.00 H +ATOM 673 HB3 TYR 45 25.828 -89.603 -18.935 1.00 0.00 H +ATOM 674 CG TYR 45 23.929 -88.931 -18.219 1.00 0.00 C +ATOM 675 CD1 TYR 45 22.997 -88.793 -17.110 1.00 0.00 C +ATOM 676 HD1 TYR 45 23.347 -88.941 -16.099 1.00 0.00 H +ATOM 677 CE1 TYR 45 21.675 -88.391 -17.238 1.00 0.00 C +ATOM 678 HE1 TYR 45 20.996 -88.271 -16.407 1.00 0.00 H +ATOM 679 CZ TYR 45 21.159 -88.187 -18.552 1.00 0.00 C +ATOM 680 OH TYR 45 19.883 -87.833 -18.762 1.00 0.00 O +ATOM 681 HH TYR 45 19.722 -87.560 -19.668 1.00 0.00 H +ATOM 682 CE2 TYR 45 22.022 -88.295 -19.702 1.00 0.00 C +ATOM 683 HE2 TYR 45 21.530 -88.249 -20.662 1.00 0.00 H +ATOM 684 CD2 TYR 45 23.361 -88.767 -19.499 1.00 0.00 C +ATOM 685 HD2 TYR 45 24.017 -89.028 -20.316 1.00 0.00 H +ATOM 686 C TYR 45 25.097 -91.845 -17.849 1.00 0.00 C +ATOM 687 O TYR 45 25.804 -92.409 -18.736 1.00 0.00 O +ATOM 688 N ASP 46 23.866 -92.261 -17.604 1.00 0.00 N +ATOM 689 H ASP 46 23.517 -91.761 -16.800 1.00 0.00 H +ATOM 690 CA ASP 46 23.070 -93.160 -18.445 1.00 0.00 C +ATOM 691 HA ASP 46 23.597 -93.270 -19.392 1.00 0.00 H +ATOM 692 CB ASP 46 22.904 -94.482 -17.759 1.00 0.00 C +ATOM 693 HB2 ASP 46 23.911 -94.816 -17.512 1.00 0.00 H +ATOM 694 HB3 ASP 46 22.328 -94.494 -16.834 1.00 0.00 H +ATOM 695 CG ASP 46 22.157 -95.431 -18.762 1.00 0.00 C +ATOM 696 OD1 ASP 46 22.305 -95.201 -20.007 1.00 0.00 O +ATOM 697 OD2 ASP 46 21.591 -96.457 -18.370 1.00 0.00 O +ATOM 698 C ASP 46 21.640 -92.567 -18.691 1.00 0.00 C +ATOM 699 O ASP 46 20.848 -92.558 -17.703 1.00 0.00 O +ATOM 700 N ASP 47 21.310 -92.092 -19.880 1.00 0.00 N +ATOM 701 H ASP 47 22.100 -92.132 -20.508 1.00 0.00 H +ATOM 702 CA ASP 47 20.001 -91.513 -20.211 1.00 0.00 C +ATOM 703 HA ASP 47 19.785 -90.831 -19.388 1.00 0.00 H +ATOM 704 CB ASP 47 20.015 -90.786 -21.504 1.00 0.00 C +ATOM 705 HB2 ASP 47 20.898 -90.189 -21.733 1.00 0.00 H +ATOM 706 HB3 ASP 47 19.978 -91.486 -22.339 1.00 0.00 H +ATOM 707 CG ASP 47 18.890 -89.782 -21.654 1.00 0.00 C +ATOM 708 OD1 ASP 47 19.113 -88.568 -21.359 1.00 0.00 O +ATOM 709 OD2 ASP 47 17.780 -90.019 -22.080 1.00 0.00 O +ATOM 710 C ASP 47 18.824 -92.538 -20.186 1.00 0.00 C +ATOM 711 O ASP 47 17.704 -92.178 -19.801 1.00 0.00 O +ATOM 712 N ALA 48 19.030 -93.804 -20.526 1.00 0.00 N +ATOM 713 H ALA 48 19.859 -94.129 -21.002 1.00 0.00 H +ATOM 714 CA ALA 48 17.937 -94.753 -20.384 1.00 0.00 C +ATOM 715 HA ALA 48 17.033 -94.333 -20.825 1.00 0.00 H +ATOM 716 CB ALA 48 18.356 -96.064 -21.130 1.00 0.00 C +ATOM 717 HB1 ALA 48 17.441 -96.576 -21.427 1.00 0.00 H +ATOM 718 HB2 ALA 48 19.012 -96.578 -20.428 1.00 0.00 H +ATOM 719 HB3 ALA 48 18.960 -95.759 -21.985 1.00 0.00 H +ATOM 720 C ALA 48 17.508 -95.055 -18.935 1.00 0.00 C +ATOM 721 O ALA 48 16.413 -95.569 -18.817 1.00 0.00 O +ATOM 722 N THR 49 18.370 -94.747 -17.949 1.00 0.00 N +ATOM 723 H THR 49 19.286 -94.386 -18.175 1.00 0.00 H +ATOM 724 CA THR 49 17.944 -94.868 -16.529 1.00 0.00 C +ATOM 725 HA THR 49 16.930 -95.268 -16.551 1.00 0.00 H +ATOM 726 CB THR 49 18.782 -95.814 -15.696 1.00 0.00 C +ATOM 727 HB THR 49 18.595 -95.644 -14.636 1.00 0.00 H +ATOM 728 CG2 THR 49 18.422 -97.262 -15.972 1.00 0.00 C +ATOM 729 HG21 THR 49 18.583 -97.550 -17.011 1.00 0.00 H +ATOM 730 HG22 THR 49 17.407 -97.421 -15.609 1.00 0.00 H +ATOM 731 HG23 THR 49 18.945 -97.878 -15.241 1.00 0.00 H +ATOM 732 OG1 THR 49 20.202 -95.676 -15.988 1.00 0.00 O +ATOM 733 HG1 THR 49 20.403 -96.024 -16.860 1.00 0.00 H +ATOM 734 C THR 49 17.812 -93.509 -15.858 1.00 0.00 C +ATOM 735 O THR 49 17.586 -93.484 -14.653 1.00 0.00 O +ATOM 736 N LYS 50 18.108 -92.417 -16.556 1.00 0.00 N +ATOM 737 H LYS 50 18.502 -92.505 -17.482 1.00 0.00 H +ATOM 738 CA LYS 50 18.235 -91.024 -16.096 1.00 0.00 C +ATOM 739 HA LYS 50 18.742 -90.497 -16.904 1.00 0.00 H +ATOM 740 CB LYS 50 16.821 -90.400 -15.922 1.00 0.00 C +ATOM 741 HB2 LYS 50 16.297 -91.050 -15.222 1.00 0.00 H +ATOM 742 HB3 LYS 50 16.899 -89.383 -15.537 1.00 0.00 H +ATOM 743 CG LYS 50 16.032 -90.240 -17.238 1.00 0.00 C +ATOM 744 HG2 LYS 50 16.129 -91.151 -17.828 1.00 0.00 H +ATOM 745 HG3 LYS 50 14.969 -90.181 -17.002 1.00 0.00 H +ATOM 746 CD LYS 50 16.316 -89.061 -18.183 1.00 0.00 C +ATOM 747 HD2 LYS 50 16.073 -88.089 -17.754 1.00 0.00 H +ATOM 748 HD3 LYS 50 17.369 -89.075 -18.463 1.00 0.00 H +ATOM 749 CE LYS 50 15.510 -89.075 -19.445 1.00 0.00 C +ATOM 750 HE2 LYS 50 14.443 -89.042 -19.223 1.00 0.00 H +ATOM 751 HE3 LYS 50 15.681 -88.168 -20.024 1.00 0.00 H +ATOM 752 NZ LYS 50 15.806 -90.167 -20.366 1.00 0.00 N +ATOM 753 HZ1 LYS 50 16.800 -90.191 -20.543 1.00 0.00 H +ATOM 754 HZ2 LYS 50 15.379 -90.063 -21.275 1.00 0.00 H +ATOM 755 HZ3 LYS 50 15.575 -91.101 -20.058 1.00 0.00 H +ATOM 756 C LYS 50 19.323 -90.871 -14.900 1.00 0.00 C +ATOM 757 O LYS 50 19.033 -90.121 -13.978 1.00 0.00 O +ATOM 758 N THR 51 20.459 -91.637 -14.893 1.00 0.00 N +ATOM 759 H THR 51 20.643 -92.098 -15.773 1.00 0.00 H +ATOM 760 CA THR 51 21.294 -91.877 -13.686 1.00 0.00 C +ATOM 761 HA THR 51 20.831 -91.465 -12.790 1.00 0.00 H +ATOM 762 CB THR 51 21.310 -93.349 -13.465 1.00 0.00 C +ATOM 763 HB THR 51 21.674 -93.860 -14.356 1.00 0.00 H +ATOM 764 CG2 THR 51 22.110 -93.824 -12.205 1.00 0.00 C +ATOM 765 HG21 THR 51 21.706 -93.261 -11.363 1.00 0.00 H +ATOM 766 HG22 THR 51 23.175 -93.655 -12.362 1.00 0.00 H +ATOM 767 HG23 THR 51 21.787 -94.862 -12.133 1.00 0.00 H +ATOM 768 OG1 THR 51 20.062 -93.784 -13.211 1.00 0.00 O +ATOM 769 HG1 THR 51 19.684 -93.593 -14.072 1.00 0.00 H +ATOM 770 C THR 51 22.732 -91.238 -13.783 1.00 0.00 C +ATOM 771 O THR 51 23.367 -91.328 -14.826 1.00 0.00 O +ATOM 772 N PHE 52 23.278 -90.790 -12.684 1.00 0.00 N +ATOM 773 H PHE 52 22.674 -90.536 -11.915 1.00 0.00 H +ATOM 774 CA PHE 52 24.671 -90.588 -12.494 1.00 0.00 C +ATOM 775 HA PHE 52 25.135 -90.684 -13.476 1.00 0.00 H +ATOM 776 CB PHE 52 24.952 -89.137 -12.086 1.00 0.00 C +ATOM 777 HB2 PHE 52 24.410 -88.900 -11.170 1.00 0.00 H +ATOM 778 HB3 PHE 52 26.030 -89.093 -11.924 1.00 0.00 H +ATOM 779 CG PHE 52 24.513 -88.071 -13.105 1.00 0.00 C +ATOM 780 CD1 PHE 52 23.240 -87.513 -13.024 1.00 0.00 C +ATOM 781 HD1 PHE 52 22.561 -87.809 -12.238 1.00 0.00 H +ATOM 782 CE1 PHE 52 22.972 -86.665 -14.121 1.00 0.00 C +ATOM 783 HE1 PHE 52 21.945 -86.337 -14.190 1.00 0.00 H +ATOM 784 CZ PHE 52 23.885 -86.384 -15.139 1.00 0.00 C +ATOM 785 HZ PHE 52 23.585 -85.653 -15.875 1.00 0.00 H +ATOM 786 CE2 PHE 52 25.213 -86.823 -15.093 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.913 -86.342 -15.759 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.517 -87.753 -14.074 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.515 -88.133 -13.913 1.00 0.00 H +ATOM 790 C PHE 52 25.177 -91.611 -11.414 1.00 0.00 C +ATOM 791 O PHE 52 24.600 -91.858 -10.361 1.00 0.00 O +ATOM 792 N THR 53 26.311 -92.259 -11.890 1.00 0.00 N +ATOM 793 H THR 53 26.752 -91.953 -12.745 1.00 0.00 H +ATOM 794 CA THR 53 27.250 -93.154 -11.086 1.00 0.00 C +ATOM 795 HA THR 53 27.045 -93.145 -10.015 1.00 0.00 H +ATOM 796 CB THR 53 27.065 -94.658 -11.382 1.00 0.00 C +ATOM 797 HB THR 53 26.004 -94.906 -11.409 1.00 0.00 H +ATOM 798 CG2 THR 53 27.631 -95.088 -12.739 1.00 0.00 C +ATOM 799 HG21 THR 53 28.718 -95.168 -12.701 1.00 0.00 H +ATOM 800 HG22 THR 53 27.186 -94.456 -13.507 1.00 0.00 H +ATOM 801 HG23 THR 53 27.220 -96.082 -12.918 1.00 0.00 H +ATOM 802 OG1 THR 53 27.690 -95.537 -10.496 1.00 0.00 O +ATOM 803 HG1 THR 53 27.876 -96.366 -10.943 1.00 0.00 H +ATOM 804 C THR 53 28.655 -92.694 -11.337 1.00 0.00 C +ATOM 805 O THR 53 28.916 -91.947 -12.272 1.00 0.00 O +ATOM 806 N VAL 54 29.650 -93.087 -10.500 1.00 0.00 N +ATOM 807 H VAL 54 29.428 -93.703 -9.731 1.00 0.00 H +ATOM 808 CA VAL 54 31.065 -92.912 -10.720 1.00 0.00 C +ATOM 809 HA VAL 54 31.143 -91.840 -10.903 1.00 0.00 H +ATOM 810 CB VAL 54 31.832 -93.244 -9.401 1.00 0.00 C +ATOM 811 HB VAL 54 31.583 -94.248 -9.056 1.00 0.00 H +ATOM 812 CG1 VAL 54 33.337 -93.202 -9.568 1.00 0.00 C +ATOM 813 HG11 VAL 54 33.625 -94.052 -10.187 1.00 0.00 H +ATOM 814 HG12 VAL 54 33.747 -93.175 -8.559 1.00 0.00 H +ATOM 815 HG13 VAL 54 33.663 -92.273 -10.036 1.00 0.00 H +ATOM 816 CG2 VAL 54 31.483 -92.378 -8.230 1.00 0.00 C +ATOM 817 HG21 VAL 54 30.420 -92.530 -8.044 1.00 0.00 H +ATOM 818 HG22 VAL 54 31.842 -91.361 -8.387 1.00 0.00 H +ATOM 819 HG23 VAL 54 31.924 -92.766 -7.312 1.00 0.00 H +ATOM 820 C VAL 54 31.630 -93.801 -11.880 1.00 0.00 C +ATOM 821 O VAL 54 31.344 -94.997 -11.945 1.00 0.00 O +ATOM 822 N THR 55 32.463 -93.199 -12.733 1.00 0.00 N +ATOM 823 H THR 55 32.651 -92.208 -12.672 1.00 0.00 H +ATOM 824 CA THR 55 33.209 -93.945 -13.745 1.00 0.00 C +ATOM 825 HA THR 55 32.517 -94.438 -14.429 1.00 0.00 H +ATOM 826 CB THR 55 33.920 -92.938 -14.622 1.00 0.00 C +ATOM 827 HB THR 55 34.554 -92.281 -14.027 1.00 0.00 H +ATOM 828 CG2 THR 55 34.836 -93.628 -15.624 1.00 0.00 C +ATOM 829 HG21 THR 55 34.335 -94.462 -16.116 1.00 0.00 H +ATOM 830 HG22 THR 55 35.706 -94.059 -15.129 1.00 0.00 H +ATOM 831 HG23 THR 55 35.210 -92.892 -16.336 1.00 0.00 H +ATOM 832 OG1 THR 55 32.944 -92.076 -15.191 1.00 0.00 O +ATOM 833 HG1 THR 55 33.500 -91.599 -15.812 1.00 0.00 H +ATOM 834 C THR 55 34.203 -95.018 -13.310 1.00 0.00 C +ATOM 835 O THR 55 35.162 -94.900 -12.548 1.00 0.00 O +ATOM 836 N GLU 56 33.853 -96.191 -13.831 1.00 0.00 N +ATOM 837 H GLU 56 32.973 -96.122 -14.321 1.00 0.00 H +ATOM 838 CA GLU 56 34.429 -97.504 -13.580 1.00 0.00 C +ATOM 839 HA GLU 56 35.479 -97.522 -13.288 1.00 0.00 H +ATOM 840 CB GLU 56 33.623 -98.059 -12.330 1.00 0.00 C +ATOM 841 HB2 GLU 56 32.582 -97.738 -12.349 1.00 0.00 H +ATOM 842 HB3 GLU 56 33.651 -99.149 -12.350 1.00 0.00 H +ATOM 843 CG GLU 56 34.341 -97.719 -10.990 1.00 0.00 C +ATOM 844 HG2 GLU 56 34.303 -96.636 -10.866 1.00 0.00 H +ATOM 845 HG3 GLU 56 33.704 -98.213 -10.256 1.00 0.00 H +ATOM 846 CD GLU 56 35.803 -98.221 -10.845 1.00 0.00 C +ATOM 847 OE1 GLU 56 36.177 -99.118 -11.643 1.00 0.00 O +ATOM 848 OE2 GLU 56 36.611 -97.623 -10.110 1.00 0.00 O +ATOM 849 C GLU 56 34.334 -98.394 -14.839 1.00 0.00 C +ATOM 850 O GLU 56 35.068 -98.144 -15.793 1.00 0.00 O +ATOM 851 OXT GLU 56 33.499 -99.353 -14.852 1.00 0.00 O +ATOM 852 ZN ZN1 57 23.231 -87.325 -4.270 1.00 0.00 ZN +ATOM 853 N AN1 58 24.369 -86.764 -2.736 1.00 0.00 N +ATOM 854 C AN1 58 25.300 -85.919 -0.432 1.00 0.00 C +ATOM 855 C1 AN1 58 24.825 -86.465 -1.714 1.00 0.00 C +ATOM 856 H AN1 58 25.084 -84.844 -0.408 1.00 0.00 H +ATOM 857 H1 AN1 58 26.382 -86.066 -0.325 1.00 0.00 H +ATOM 858 H2 AN1 58 24.826 -86.472 0.388 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 26.075 -89.271 -2.458 1.00 0.00 N +ATOM 860 N2 AZI 59 27.232 -89.395 -2.126 1.00 0.00 N +ATOM 861 N3 AZI 59 28.453 -89.281 -1.850 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/pdbs_rename/cluster9.pdb b/tests/nsga2/pdbs_rename/cluster9.pdb new file mode 100644 index 0000000..11fbdad --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster9.pdb @@ -0,0 +1,865 @@ +CRYST1 51.599 53.226 47.327 90.00 90.00 90.00 1 +ATOM 1 N MET 1 13.280 -82.161 -12.986 1.00 0.00 N +ATOM 2 H1 MET 1 13.609 -81.951 -12.055 1.00 0.00 H +ATOM 3 H2 MET 1 12.273 -82.082 -12.973 1.00 0.00 H +ATOM 4 H3 MET 1 13.702 -81.520 -13.643 1.00 0.00 H +ATOM 5 CA MET 1 13.613 -83.553 -13.412 1.00 0.00 C +ATOM 6 HA MET 1 12.647 -84.000 -13.646 1.00 0.00 H +ATOM 7 CB MET 1 14.287 -83.532 -14.781 1.00 0.00 C +ATOM 8 HB2 MET 1 13.707 -83.147 -15.620 1.00 0.00 H +ATOM 9 HB3 MET 1 15.224 -82.983 -14.685 1.00 0.00 H +ATOM 10 CG MET 1 14.666 -84.916 -15.344 1.00 0.00 C +ATOM 11 HG2 MET 1 14.976 -84.674 -16.361 1.00 0.00 H +ATOM 12 HG3 MET 1 15.533 -85.369 -14.863 1.00 0.00 H +ATOM 13 SD MET 1 13.339 -86.079 -15.367 1.00 0.00 S +ATOM 14 CE MET 1 12.132 -85.391 -16.645 1.00 0.00 C +ATOM 15 HE1 MET 1 11.702 -86.232 -17.190 1.00 0.00 H +ATOM 16 HE2 MET 1 12.624 -84.768 -17.392 1.00 0.00 H +ATOM 17 HE3 MET 1 11.272 -84.800 -16.330 1.00 0.00 H +ATOM 18 C MET 1 14.386 -84.382 -12.397 1.00 0.00 C +ATOM 19 O MET 1 15.427 -83.891 -12.010 1.00 0.00 O +ATOM 20 N GLN 2 13.874 -85.466 -11.878 1.00 0.00 N +ATOM 21 H GLN 2 12.939 -85.745 -12.139 1.00 0.00 H +ATOM 22 CA GLN 2 14.517 -86.329 -10.818 1.00 0.00 C +ATOM 23 HA GLN 2 15.001 -85.655 -10.110 1.00 0.00 H +ATOM 24 CB GLN 2 13.301 -86.996 -10.112 1.00 0.00 C +ATOM 25 HB2 GLN 2 12.672 -87.652 -10.714 1.00 0.00 H +ATOM 26 HB3 GLN 2 13.772 -87.695 -9.422 1.00 0.00 H +ATOM 27 CG GLN 2 12.443 -86.012 -9.259 1.00 0.00 C +ATOM 28 HG2 GLN 2 12.439 -85.019 -9.708 1.00 0.00 H +ATOM 29 HG3 GLN 2 11.468 -86.479 -9.403 1.00 0.00 H +ATOM 30 CD GLN 2 12.798 -85.981 -7.801 1.00 0.00 C +ATOM 31 OE1 GLN 2 13.900 -86.364 -7.373 1.00 0.00 O +ATOM 32 NE2 GLN 2 11.960 -85.457 -6.990 1.00 0.00 N +ATOM 33 HE21 GLN 2 12.178 -85.347 -6.010 1.00 0.00 H +ATOM 34 HE22 GLN 2 11.037 -85.203 -7.313 1.00 0.00 H +ATOM 35 C GLN 2 15.507 -87.318 -11.384 1.00 0.00 C +ATOM 36 O GLN 2 15.106 -88.486 -11.649 1.00 0.00 O +ATOM 37 N TYR 3 16.816 -86.922 -11.415 1.00 0.00 N +ATOM 38 H TYR 3 16.987 -86.018 -11.000 1.00 0.00 H +ATOM 39 CA TYR 3 17.931 -87.713 -11.945 1.00 0.00 C +ATOM 40 HA TYR 3 17.565 -88.189 -12.855 1.00 0.00 H +ATOM 41 CB TYR 3 19.018 -86.768 -12.354 1.00 0.00 C +ATOM 42 HB2 TYR 3 19.281 -86.101 -11.533 1.00 0.00 H +ATOM 43 HB3 TYR 3 19.872 -87.353 -12.696 1.00 0.00 H +ATOM 44 CG TYR 3 18.638 -85.866 -13.508 1.00 0.00 C +ATOM 45 CD1 TYR 3 18.709 -86.358 -14.789 1.00 0.00 C +ATOM 46 HD1 TYR 3 19.109 -87.347 -14.962 1.00 0.00 H +ATOM 47 CE1 TYR 3 18.400 -85.460 -15.869 1.00 0.00 C +ATOM 48 HE1 TYR 3 18.468 -85.801 -16.891 1.00 0.00 H +ATOM 49 CZ TYR 3 18.010 -84.125 -15.640 1.00 0.00 C +ATOM 50 OH TYR 3 17.704 -83.356 -16.746 1.00 0.00 O +ATOM 51 HH TYR 3 17.903 -83.815 -17.565 1.00 0.00 H +ATOM 52 CE2 TYR 3 18.009 -83.621 -14.344 1.00 0.00 C +ATOM 53 HE2 TYR 3 17.641 -82.650 -14.046 1.00 0.00 H +ATOM 54 CD2 TYR 3 18.331 -84.501 -13.314 1.00 0.00 C +ATOM 55 HD2 TYR 3 18.211 -84.196 -12.285 1.00 0.00 H +ATOM 56 C TYR 3 18.408 -88.706 -10.876 1.00 0.00 C +ATOM 57 O TYR 3 18.959 -88.281 -9.848 1.00 0.00 O +ATOM 58 N LYS 4 18.304 -90.012 -11.226 1.00 0.00 N +ATOM 59 H LYS 4 17.878 -90.302 -12.094 1.00 0.00 H +ATOM 60 CA LYS 4 18.872 -91.028 -10.312 1.00 0.00 C +ATOM 61 HA LYS 4 18.513 -90.818 -9.305 1.00 0.00 H +ATOM 62 CB LYS 4 18.346 -92.448 -10.688 1.00 0.00 C +ATOM 63 HB2 LYS 4 18.415 -92.619 -11.762 1.00 0.00 H +ATOM 64 HB3 LYS 4 19.046 -93.132 -10.208 1.00 0.00 H +ATOM 65 CG LYS 4 16.840 -92.565 -10.324 1.00 0.00 C +ATOM 66 HG2 LYS 4 16.631 -92.411 -9.265 1.00 0.00 H +ATOM 67 HG3 LYS 4 16.338 -91.775 -10.883 1.00 0.00 H +ATOM 68 CD LYS 4 16.235 -93.931 -10.724 1.00 0.00 C +ATOM 69 HD2 LYS 4 16.789 -94.741 -10.250 1.00 0.00 H +ATOM 70 HD3 LYS 4 15.213 -93.903 -10.345 1.00 0.00 H +ATOM 71 CE LYS 4 16.172 -94.172 -12.279 1.00 0.00 C +ATOM 72 HE2 LYS 4 17.100 -93.687 -12.580 1.00 0.00 H +ATOM 73 HE3 LYS 4 16.124 -95.240 -12.490 1.00 0.00 H +ATOM 74 NZ LYS 4 15.011 -93.445 -12.896 1.00 0.00 N +ATOM 75 HZ1 LYS 4 14.185 -94.026 -12.916 1.00 0.00 H +ATOM 76 HZ2 LYS 4 15.289 -93.203 -13.836 1.00 0.00 H +ATOM 77 HZ3 LYS 4 14.880 -92.590 -12.374 1.00 0.00 H +ATOM 78 C LYS 4 20.384 -91.034 -10.263 1.00 0.00 C +ATOM 79 O LYS 4 20.986 -90.909 -11.348 1.00 0.00 O +ATOM 80 N HX1 5 20.976 -91.370 -9.106 1.00 0.00 N +ATOM 81 CA HX1 5 22.495 -91.359 -9.024 1.00 0.00 C +ATOM 82 C HX1 5 22.886 -92.646 -8.370 1.00 0.00 C +ATOM 83 O HX1 5 22.744 -92.705 -7.205 1.00 0.00 O +ATOM 84 CB HX1 5 23.020 -90.042 -8.530 1.00 0.00 C +ATOM 85 CG HX1 5 24.517 -89.811 -8.453 1.00 0.00 C +ATOM 86 CD2 HX1 5 25.467 -90.486 -9.137 1.00 0.00 C +ATOM 87 ND1 HX1 5 25.067 -88.841 -7.672 1.00 0.00 N +ATOM 88 CE1 HX1 5 26.367 -88.860 -7.972 1.00 0.00 C +ATOM 89 NE2 HX1 5 26.660 -89.875 -8.843 1.00 0.00 N +ATOM 90 H HX1 5 20.383 -91.469 -8.294 1.00 0.00 H +ATOM 91 HA HX1 5 22.820 -91.463 -10.059 1.00 0.00 H +ATOM 92 HB2 HX1 5 22.516 -89.922 -7.571 1.00 0.00 H +ATOM 93 HB3 HX1 5 22.663 -89.279 -9.221 1.00 0.00 H +ATOM 94 HD2 HX1 5 25.319 -91.319 -9.808 1.00 0.00 H +ATOM 95 HE1 HX1 5 27.072 -88.252 -7.424 1.00 0.00 H +ATOM 96 HE2 HX1 5 27.456 -89.907 -9.464 1.00 0.00 H +ATOM 97 N ILE 6 23.417 -93.632 -9.027 1.00 0.00 N +ATOM 98 H ILE 6 23.598 -93.338 -9.976 1.00 0.00 H +ATOM 99 CA ILE 6 24.011 -94.880 -8.558 1.00 0.00 C +ATOM 100 HA ILE 6 23.464 -95.183 -7.665 1.00 0.00 H +ATOM 101 CB ILE 6 23.901 -96.015 -9.728 1.00 0.00 C +ATOM 102 HB ILE 6 24.488 -95.668 -10.578 1.00 0.00 H +ATOM 103 CG2 ILE 6 24.555 -97.324 -9.271 1.00 0.00 C +ATOM 104 HG21 ILE 6 24.575 -97.996 -10.129 1.00 0.00 H +ATOM 105 HG22 ILE 6 24.019 -97.810 -8.456 1.00 0.00 H +ATOM 106 HG23 ILE 6 25.584 -97.043 -9.045 1.00 0.00 H +ATOM 107 CG1 ILE 6 22.406 -96.213 -10.136 1.00 0.00 C +ATOM 108 HG12 ILE 6 21.833 -96.416 -9.231 1.00 0.00 H +ATOM 109 HG13 ILE 6 22.016 -95.296 -10.578 1.00 0.00 H +ATOM 110 CD1 ILE 6 22.167 -97.381 -11.104 1.00 0.00 C +ATOM 111 HD11 ILE 6 21.221 -97.352 -11.644 1.00 0.00 H +ATOM 112 HD12 ILE 6 22.316 -98.379 -10.691 1.00 0.00 H +ATOM 113 HD13 ILE 6 22.964 -97.281 -11.841 1.00 0.00 H +ATOM 114 C ILE 6 25.528 -94.678 -8.186 1.00 0.00 C +ATOM 115 O ILE 6 26.351 -94.413 -9.066 1.00 0.00 O +ATOM 116 N VAL 7 25.869 -94.750 -6.932 1.00 0.00 N +ATOM 117 H VAL 7 25.200 -95.198 -6.322 1.00 0.00 H +ATOM 118 CA VAL 7 27.215 -94.505 -6.320 1.00 0.00 C +ATOM 119 HA VAL 7 27.865 -94.141 -7.115 1.00 0.00 H +ATOM 120 CB VAL 7 27.074 -93.343 -5.221 1.00 0.00 C +ATOM 121 HB VAL 7 28.026 -93.097 -4.750 1.00 0.00 H +ATOM 122 CG1 VAL 7 26.504 -92.114 -6.048 1.00 0.00 C +ATOM 123 HG11 VAL 7 27.197 -91.879 -6.856 1.00 0.00 H +ATOM 124 HG12 VAL 7 25.556 -92.355 -6.530 1.00 0.00 H +ATOM 125 HG13 VAL 7 26.385 -91.250 -5.394 1.00 0.00 H +ATOM 126 CG2 VAL 7 26.138 -93.692 -4.077 1.00 0.00 C +ATOM 127 HG21 VAL 7 26.045 -92.769 -3.505 1.00 0.00 H +ATOM 128 HG22 VAL 7 25.186 -94.130 -4.377 1.00 0.00 H +ATOM 129 HG23 VAL 7 26.736 -94.352 -3.449 1.00 0.00 H +ATOM 130 C VAL 7 27.868 -95.661 -5.702 1.00 0.00 C +ATOM 131 O VAL 7 27.178 -96.548 -5.152 1.00 0.00 O +ATOM 132 N ASN 8 29.211 -95.887 -5.940 1.00 0.00 N +ATOM 133 H ASN 8 29.709 -95.225 -6.518 1.00 0.00 H +ATOM 134 CA ASN 8 29.922 -97.142 -5.443 1.00 0.00 C +ATOM 135 HA ASN 8 29.470 -97.454 -4.502 1.00 0.00 H +ATOM 136 CB ASN 8 29.723 -98.233 -6.526 1.00 0.00 C +ATOM 137 HB2 ASN 8 28.838 -98.082 -7.144 1.00 0.00 H +ATOM 138 HB3 ASN 8 30.502 -98.119 -7.280 1.00 0.00 H +ATOM 139 CG ASN 8 29.898 -99.574 -5.953 1.00 0.00 C +ATOM 140 OD1 ASN 8 30.464 -99.833 -4.899 1.00 0.00 O +ATOM 141 ND2 ASN 8 29.250-100.550 -6.631 1.00 0.00 N +ATOM 142 HD21 ASN 8 28.585-100.384 -7.372 1.00 0.00 H +ATOM 143 HD22 ASN 8 29.344-101.499 -6.298 1.00 0.00 H +ATOM 144 C ASN 8 31.368 -96.798 -5.165 1.00 0.00 C +ATOM 145 O ASN 8 32.076 -96.165 -5.902 1.00 0.00 O +ATOM 146 N GLY 9 31.859 -97.405 -4.109 1.00 0.00 N +ATOM 147 H GLY 9 31.225 -97.834 -3.449 1.00 0.00 H +ATOM 148 CA GLY 9 33.247 -97.319 -3.620 1.00 0.00 C +ATOM 149 HA2 GLY 9 33.838 -97.797 -4.402 1.00 0.00 H +ATOM 150 HA3 GLY 9 33.471 -96.252 -3.643 1.00 0.00 H +ATOM 151 C GLY 9 33.539 -98.115 -2.286 1.00 0.00 C +ATOM 152 O GLY 9 32.966 -99.139 -1.989 1.00 0.00 O +ATOM 153 N LYS 10 34.487 -97.630 -1.532 1.00 0.00 N +ATOM 154 H LYS 10 34.883 -96.748 -1.822 1.00 0.00 H +ATOM 155 CA LYS 10 35.001 -98.212 -0.236 1.00 0.00 C +ATOM 156 HA LYS 10 34.601 -99.223 -0.166 1.00 0.00 H +ATOM 157 CB LYS 10 36.526 -98.105 -0.325 1.00 0.00 C +ATOM 158 HB2 LYS 10 36.803 -97.057 -0.209 1.00 0.00 H +ATOM 159 HB3 LYS 10 36.925 -98.626 0.545 1.00 0.00 H +ATOM 160 CG LYS 10 37.012 -98.798 -1.622 1.00 0.00 C +ATOM 161 HG2 LYS 10 36.541 -99.765 -1.798 1.00 0.00 H +ATOM 162 HG3 LYS 10 36.751 -98.195 -2.491 1.00 0.00 H +ATOM 163 CD LYS 10 38.474 -99.000 -1.787 1.00 0.00 C +ATOM 164 HD2 LYS 10 38.721 -99.746 -1.031 1.00 0.00 H +ATOM 165 HD3 LYS 10 38.745 -99.356 -2.781 1.00 0.00 H +ATOM 166 CE LYS 10 39.284 -97.744 -1.380 1.00 0.00 C +ATOM 167 HE2 LYS 10 38.963 -96.900 -1.990 1.00 0.00 H +ATOM 168 HE3 LYS 10 39.095 -97.521 -0.330 1.00 0.00 H +ATOM 169 NZ LYS 10 40.728 -97.939 -1.468 1.00 0.00 N +ATOM 170 HZ1 LYS 10 41.137 -98.810 -1.163 1.00 0.00 H +ATOM 171 HZ2 LYS 10 41.247 -97.182 -1.046 1.00 0.00 H +ATOM 172 HZ3 LYS 10 41.041 -98.039 -2.423 1.00 0.00 H +ATOM 173 C LYS 10 34.364 -97.545 1.003 1.00 0.00 C +ATOM 174 O LYS 10 34.689 -98.018 2.102 1.00 0.00 O +ATOM 175 N THR 11 33.483 -96.567 0.814 1.00 0.00 N +ATOM 176 H THR 11 33.278 -96.427 -0.165 1.00 0.00 H +ATOM 177 CA THR 11 32.757 -95.950 1.952 1.00 0.00 C +ATOM 178 HA THR 11 32.788 -96.637 2.798 1.00 0.00 H +ATOM 179 CB THR 11 33.510 -94.718 2.474 1.00 0.00 C +ATOM 180 HB THR 11 33.754 -94.086 1.620 1.00 0.00 H +ATOM 181 CG2 THR 11 32.699 -93.853 3.374 1.00 0.00 C +ATOM 182 HG21 THR 11 32.495 -94.501 4.226 1.00 0.00 H +ATOM 183 HG22 THR 11 31.736 -93.569 2.951 1.00 0.00 H +ATOM 184 HG23 THR 11 33.276 -92.948 3.564 1.00 0.00 H +ATOM 185 OG1 THR 11 34.693 -95.118 3.129 1.00 0.00 O +ATOM 186 HG1 THR 11 34.364 -95.834 3.677 1.00 0.00 H +ATOM 187 C THR 11 31.302 -95.696 1.471 1.00 0.00 C +ATOM 188 O THR 11 30.365 -96.152 2.190 1.00 0.00 O +ATOM 189 N LEU 12 31.046 -95.044 0.310 1.00 0.00 N +ATOM 190 H LEU 12 31.815 -94.778 -0.289 1.00 0.00 H +ATOM 191 CA LEU 12 29.809 -94.867 -0.343 1.00 0.00 C +ATOM 192 HA LEU 12 29.023 -94.555 0.345 1.00 0.00 H +ATOM 193 CB LEU 12 29.934 -93.718 -1.389 1.00 0.00 C +ATOM 194 HB2 LEU 12 30.829 -93.916 -1.979 1.00 0.00 H +ATOM 195 HB3 LEU 12 29.095 -93.783 -2.081 1.00 0.00 H +ATOM 196 CG LEU 12 30.159 -92.204 -0.851 1.00 0.00 C +ATOM 197 HG LEU 12 31.084 -91.900 -0.360 1.00 0.00 H +ATOM 198 CD1 LEU 12 30.239 -91.267 -2.104 1.00 0.00 C +ATOM 199 HD11 LEU 12 31.101 -91.470 -2.740 1.00 0.00 H +ATOM 200 HD12 LEU 12 30.487 -90.241 -1.833 1.00 0.00 H +ATOM 201 HD13 LEU 12 29.279 -91.291 -2.619 1.00 0.00 H +ATOM 202 CD2 LEU 12 28.919 -91.800 -0.017 1.00 0.00 C +ATOM 203 HD21 LEU 12 28.092 -92.241 -0.573 1.00 0.00 H +ATOM 204 HD22 LEU 12 28.883 -90.713 -0.088 1.00 0.00 H +ATOM 205 HD23 LEU 12 28.975 -92.176 1.004 1.00 0.00 H +ATOM 206 C LEU 12 29.316 -96.081 -1.133 1.00 0.00 C +ATOM 207 O LEU 12 30.070 -96.628 -1.949 1.00 0.00 O +ATOM 208 N LYS 13 28.119 -96.581 -0.957 1.00 0.00 N +ATOM 209 H LYS 13 27.378 -96.113 -0.456 1.00 0.00 H +ATOM 210 CA LYS 13 27.651 -97.695 -1.808 1.00 0.00 C +ATOM 211 HA LYS 13 28.049 -97.513 -2.807 1.00 0.00 H +ATOM 212 CB LYS 13 28.272 -99.042 -1.379 1.00 0.00 C +ATOM 213 HB2 LYS 13 29.320 -99.070 -1.676 1.00 0.00 H +ATOM 214 HB3 LYS 13 28.141 -99.166 -0.304 1.00 0.00 H +ATOM 215 CG LYS 13 27.718-100.347 -2.084 1.00 0.00 C +ATOM 216 HG2 LYS 13 26.651-100.396 -1.871 1.00 0.00 H +ATOM 217 HG3 LYS 13 27.805-100.229 -3.164 1.00 0.00 H +ATOM 218 CD LYS 13 28.391-101.622 -1.661 1.00 0.00 C +ATOM 219 HD2 LYS 13 27.935-102.112 -0.801 1.00 0.00 H +ATOM 220 HD3 LYS 13 28.123-102.354 -2.423 1.00 0.00 H +ATOM 221 CE LYS 13 29.845-101.549 -1.662 1.00 0.00 C +ATOM 222 HE2 LYS 13 30.236-101.480 -2.677 1.00 0.00 H +ATOM 223 HE3 LYS 13 30.183-100.681 -1.096 1.00 0.00 H +ATOM 224 NZ LYS 13 30.357-102.712 -0.941 1.00 0.00 N +ATOM 225 HZ1 LYS 13 29.899-102.839 -0.049 1.00 0.00 H +ATOM 226 HZ2 LYS 13 31.307-102.614 -0.614 1.00 0.00 H +ATOM 227 HZ3 LYS 13 30.195-103.604 -1.387 1.00 0.00 H +ATOM 228 C LYS 13 26.128 -97.752 -1.904 1.00 0.00 C +ATOM 229 O LYS 13 25.519 -97.910 -0.832 1.00 0.00 O +ATOM 230 N GLY 14 25.488 -97.698 -3.083 1.00 0.00 N +ATOM 231 H GLY 14 25.998 -97.649 -3.954 1.00 0.00 H +ATOM 232 CA GLY 14 24.020 -97.691 -3.253 1.00 0.00 C +ATOM 233 HA2 GLY 14 23.786 -98.721 -3.522 1.00 0.00 H +ATOM 234 HA3 GLY 14 23.537 -97.600 -2.280 1.00 0.00 H +ATOM 235 C GLY 14 23.451 -96.682 -4.231 1.00 0.00 C +ATOM 236 O GLY 14 24.222 -96.336 -5.150 1.00 0.00 O +ATOM 237 N VAL 15 22.180 -96.208 -4.024 1.00 0.00 N +ATOM 238 H VAL 15 21.584 -96.411 -3.233 1.00 0.00 H +ATOM 239 CA VAL 15 21.604 -95.283 -4.991 1.00 0.00 C +ATOM 240 HA VAL 15 22.413 -94.920 -5.623 1.00 0.00 H +ATOM 241 CB VAL 15 20.792 -96.208 -5.936 1.00 0.00 C +ATOM 242 HB VAL 15 21.510 -96.839 -6.459 1.00 0.00 H +ATOM 243 CG1 VAL 15 19.681 -97.074 -5.438 1.00 0.00 C +ATOM 244 HG11 VAL 15 19.049 -96.601 -4.687 1.00 0.00 H +ATOM 245 HG12 VAL 15 18.991 -97.311 -6.248 1.00 0.00 H +ATOM 246 HG13 VAL 15 20.057 -97.993 -4.989 1.00 0.00 H +ATOM 247 CG2 VAL 15 20.249 -95.423 -7.131 1.00 0.00 C +ATOM 248 HG21 VAL 15 19.425 -94.810 -6.765 1.00 0.00 H +ATOM 249 HG22 VAL 15 21.020 -94.808 -7.594 1.00 0.00 H +ATOM 250 HG23 VAL 15 19.914 -96.222 -7.791 1.00 0.00 H +ATOM 251 C VAL 15 20.844 -94.134 -4.327 1.00 0.00 C +ATOM 252 O VAL 15 20.251 -94.318 -3.237 1.00 0.00 O +ATOM 253 N HY1 16 20.886 -92.953 -4.884 1.00 0.00 N +ATOM 254 CA HY1 16 20.006 -91.858 -4.473 1.00 0.00 C +ATOM 255 C HY1 16 19.569 -90.957 -5.644 1.00 0.00 C +ATOM 256 O HY1 16 19.819 -91.387 -6.740 1.00 0.00 O +ATOM 257 CB HY1 16 20.563 -90.960 -3.317 1.00 0.00 C +ATOM 258 CG HY1 16 21.874 -90.319 -3.617 1.00 0.00 C +ATOM 259 CD2 HY1 16 22.061 -89.268 -4.389 1.00 0.00 C +ATOM 260 ND1 HY1 16 23.131 -90.680 -3.120 1.00 0.00 N +ATOM 261 CE1 HY1 16 24.002 -89.851 -3.717 1.00 0.00 C +ATOM 262 NE2 HY1 16 23.438 -88.993 -4.553 1.00 0.00 N +ATOM 263 H HY1 16 21.469 -92.776 -5.689 1.00 0.00 H +ATOM 264 HA HY1 16 19.047 -92.248 -4.132 1.00 0.00 H +ATOM 265 HB2 HY1 16 19.849 -90.190 -3.025 1.00 0.00 H +ATOM 266 HB3 HY1 16 20.745 -91.570 -2.432 1.00 0.00 H +ATOM 267 HD1 HY1 16 23.372 -91.286 -2.348 1.00 0.00 H +ATOM 268 HD2 HY1 16 21.331 -88.694 -4.939 1.00 0.00 H +ATOM 269 HE1 HY1 16 25.060 -89.728 -3.536 1.00 0.00 H +ATOM 270 N THR 17 18.889 -89.801 -5.488 1.00 0.00 N +ATOM 271 H THR 17 18.701 -89.546 -4.529 1.00 0.00 H +ATOM 272 CA THR 17 18.294 -88.983 -6.625 1.00 0.00 C +ATOM 273 HA THR 17 18.823 -89.219 -7.548 1.00 0.00 H +ATOM 274 CB THR 17 16.825 -89.385 -6.837 1.00 0.00 C +ATOM 275 HB THR 17 16.243 -89.363 -5.915 1.00 0.00 H +ATOM 276 CG2 THR 17 16.108 -88.680 -7.994 1.00 0.00 C +ATOM 277 HG21 THR 17 15.070 -89.010 -8.043 1.00 0.00 H +ATOM 278 HG22 THR 17 16.656 -88.900 -8.910 1.00 0.00 H +ATOM 279 HG23 THR 17 16.002 -87.613 -7.797 1.00 0.00 H +ATOM 280 OG1 THR 17 16.932 -90.709 -7.118 1.00 0.00 O +ATOM 281 HG1 THR 17 16.141 -91.184 -6.853 1.00 0.00 H +ATOM 282 C THR 17 18.435 -87.505 -6.446 1.00 0.00 C +ATOM 283 O THR 17 18.361 -87.028 -5.321 1.00 0.00 O +ATOM 284 N HY2 18 18.704 -86.766 -7.500 1.00 0.00 N +ATOM 285 CA HY2 18 18.873 -85.326 -7.560 1.00 0.00 C +ATOM 286 C HY2 18 17.744 -84.793 -8.466 1.00 0.00 C +ATOM 287 O HY2 18 17.736 -85.086 -9.678 1.00 0.00 O +ATOM 288 CB HY2 18 20.257 -84.856 -8.107 1.00 0.00 C +ATOM 289 CG HY2 18 21.408 -85.206 -7.198 1.00 0.00 C +ATOM 290 CD2 HY2 18 22.271 -86.281 -7.407 1.00 0.00 C +ATOM 291 ND1 HY2 18 21.651 -84.741 -5.930 1.00 0.00 N +ATOM 292 CE1 HY2 18 22.567 -85.525 -5.343 1.00 0.00 C +ATOM 293 NE2 HY2 18 23.020 -86.415 -6.231 1.00 0.00 N +ATOM 294 H HY2 18 18.703 -87.307 -8.353 1.00 0.00 H +ATOM 295 HA HY2 18 18.677 -84.988 -6.542 1.00 0.00 H +ATOM 296 HB2 HY2 18 20.434 -85.313 -9.080 1.00 0.00 H +ATOM 297 HB3 HY2 18 20.307 -83.777 -8.249 1.00 0.00 H +ATOM 298 HD1 HY2 18 21.081 -84.054 -5.457 1.00 0.00 H +ATOM 299 HD2 HY2 18 22.172 -87.106 -8.096 1.00 0.00 H +ATOM 300 HE1 HY2 18 22.998 -85.359 -4.367 1.00 0.00 H +ATOM 301 N GLU 19 16.802 -84.018 -7.938 1.00 0.00 N +ATOM 302 H GLU 19 16.750 -83.908 -6.935 1.00 0.00 H +ATOM 303 CA GLU 19 15.959 -82.946 -8.677 1.00 0.00 C +ATOM 304 HA GLU 19 15.427 -83.440 -9.490 1.00 0.00 H +ATOM 305 CB GLU 19 14.805 -82.399 -7.821 1.00 0.00 C +ATOM 306 HB2 GLU 19 14.035 -83.168 -7.747 1.00 0.00 H +ATOM 307 HB3 GLU 19 15.181 -82.202 -6.817 1.00 0.00 H +ATOM 308 CG GLU 19 14.360 -80.991 -8.178 1.00 0.00 C +ATOM 309 HG2 GLU 19 13.821 -80.584 -7.323 1.00 0.00 H +ATOM 310 HG3 GLU 19 15.130 -80.221 -8.214 1.00 0.00 H +ATOM 311 CD GLU 19 13.389 -81.042 -9.346 1.00 0.00 C +ATOM 312 OE1 GLU 19 12.148 -81.250 -9.209 1.00 0.00 O +ATOM 313 OE2 GLU 19 13.926 -81.049 -10.520 1.00 0.00 O +ATOM 314 C GLU 19 16.941 -81.844 -9.307 1.00 0.00 C +ATOM 315 O GLU 19 17.639 -81.132 -8.606 1.00 0.00 O +ATOM 316 N ALA 20 16.883 -81.734 -10.640 1.00 0.00 N +ATOM 317 H ALA 20 16.443 -82.457 -11.191 1.00 0.00 H +ATOM 318 CA ALA 20 17.545 -80.700 -11.413 1.00 0.00 C +ATOM 319 HA ALA 20 17.513 -79.924 -10.648 1.00 0.00 H +ATOM 320 CB ALA 20 18.975 -81.049 -11.784 1.00 0.00 C +ATOM 321 HB1 ALA 20 19.024 -81.969 -12.366 1.00 0.00 H +ATOM 322 HB2 ALA 20 19.581 -81.187 -10.889 1.00 0.00 H +ATOM 323 HB3 ALA 20 19.396 -80.299 -12.453 1.00 0.00 H +ATOM 324 C ALA 20 16.749 -80.283 -12.607 1.00 0.00 C +ATOM 325 O ALA 20 15.927 -81.106 -13.099 1.00 0.00 O +ATOM 326 N VAL 21 16.980 -79.095 -13.144 1.00 0.00 N +ATOM 327 H VAL 21 17.528 -78.396 -12.664 1.00 0.00 H +ATOM 328 CA VAL 21 16.330 -78.653 -14.380 1.00 0.00 C +ATOM 329 HA VAL 21 15.283 -78.926 -14.244 1.00 0.00 H +ATOM 330 CB VAL 21 16.391 -77.090 -14.565 1.00 0.00 C +ATOM 331 HB VAL 21 15.900 -76.619 -13.714 1.00 0.00 H +ATOM 332 CG1 VAL 21 17.855 -76.573 -14.659 1.00 0.00 C +ATOM 333 HG11 VAL 21 18.511 -76.828 -13.827 1.00 0.00 H +ATOM 334 HG12 VAL 21 17.805 -75.485 -14.640 1.00 0.00 H +ATOM 335 HG13 VAL 21 18.387 -76.796 -15.584 1.00 0.00 H +ATOM 336 CG2 VAL 21 15.685 -76.614 -15.876 1.00 0.00 C +ATOM 337 HG21 VAL 21 15.754 -75.540 -16.047 1.00 0.00 H +ATOM 338 HG22 VAL 21 14.638 -76.919 -15.872 1.00 0.00 H +ATOM 339 HG23 VAL 21 16.147 -77.200 -16.670 1.00 0.00 H +ATOM 340 C VAL 21 16.980 -79.463 -15.556 1.00 0.00 C +ATOM 341 O VAL 21 16.261 -79.888 -16.436 1.00 0.00 O +ATOM 342 N ASP 22 18.240 -79.826 -15.445 1.00 0.00 N +ATOM 343 H ASP 22 18.772 -79.382 -14.710 1.00 0.00 H +ATOM 344 CA ASP 22 19.129 -80.351 -16.531 1.00 0.00 C +ATOM 345 HA ASP 22 18.516 -80.927 -17.225 1.00 0.00 H +ATOM 346 CB ASP 22 19.747 -79.213 -17.316 1.00 0.00 C +ATOM 347 HB2 ASP 22 19.004 -78.526 -17.721 1.00 0.00 H +ATOM 348 HB3 ASP 22 20.392 -78.653 -16.639 1.00 0.00 H +ATOM 349 CG ASP 22 20.504 -79.537 -18.635 1.00 0.00 C +ATOM 350 OD1 ASP 22 20.241 -80.640 -19.198 1.00 0.00 O +ATOM 351 OD2 ASP 22 21.423 -78.793 -19.096 1.00 0.00 O +ATOM 352 C ASP 22 20.159 -81.318 -15.891 1.00 0.00 C +ATOM 353 O ASP 22 20.608 -81.062 -14.771 1.00 0.00 O +ATOM 354 N ALA 23 20.550 -82.323 -16.664 1.00 0.00 N +ATOM 355 H ALA 23 20.098 -82.486 -17.552 1.00 0.00 H +ATOM 356 CA ALA 23 21.692 -83.131 -16.246 1.00 0.00 C +ATOM 357 HA ALA 23 21.547 -83.553 -15.252 1.00 0.00 H +ATOM 358 CB ALA 23 21.845 -84.374 -17.178 1.00 0.00 C +ATOM 359 HB1 ALA 23 20.869 -84.859 -17.165 1.00 0.00 H +ATOM 360 HB2 ALA 23 22.675 -84.961 -16.783 1.00 0.00 H +ATOM 361 HB3 ALA 23 22.254 -84.179 -18.169 1.00 0.00 H +ATOM 362 C ALA 23 22.972 -82.381 -16.150 1.00 0.00 C +ATOM 363 O ALA 23 23.769 -82.750 -15.286 1.00 0.00 O +ATOM 364 N ALA 24 23.191 -81.259 -16.772 1.00 0.00 N +ATOM 365 H ALA 24 22.437 -80.843 -17.299 1.00 0.00 H +ATOM 366 CA ALA 24 24.437 -80.511 -16.616 1.00 0.00 C +ATOM 367 HA ALA 24 25.291 -81.184 -16.538 1.00 0.00 H +ATOM 368 CB ALA 24 24.680 -79.688 -17.851 1.00 0.00 C +ATOM 369 HB1 ALA 24 24.779 -80.355 -18.707 1.00 0.00 H +ATOM 370 HB2 ALA 24 25.649 -79.201 -17.742 1.00 0.00 H +ATOM 371 HB3 ALA 24 23.833 -79.018 -17.997 1.00 0.00 H +ATOM 372 C ALA 24 24.495 -79.774 -15.281 1.00 0.00 C +ATOM 373 O ALA 24 25.551 -79.682 -14.655 1.00 0.00 O +ATOM 374 N GLU 25 23.340 -79.344 -14.766 1.00 0.00 N +ATOM 375 H GLU 25 22.505 -79.535 -15.302 1.00 0.00 H +ATOM 376 CA GLU 25 23.258 -78.703 -13.501 1.00 0.00 C +ATOM 377 HA GLU 25 24.101 -78.013 -13.472 1.00 0.00 H +ATOM 378 CB GLU 25 21.922 -77.882 -13.373 1.00 0.00 C +ATOM 379 HB2 GLU 25 21.103 -78.494 -13.751 1.00 0.00 H +ATOM 380 HB3 GLU 25 21.882 -77.511 -12.349 1.00 0.00 H +ATOM 381 CG GLU 25 21.896 -76.565 -14.228 1.00 0.00 C +ATOM 382 HG2 GLU 25 21.871 -76.764 -15.300 1.00 0.00 H +ATOM 383 HG3 GLU 25 20.976 -76.040 -13.971 1.00 0.00 H +ATOM 384 CD GLU 25 23.139 -75.688 -13.901 1.00 0.00 C +ATOM 385 OE1 GLU 25 23.566 -75.704 -12.718 1.00 0.00 O +ATOM 386 OE2 GLU 25 23.735 -75.004 -14.838 1.00 0.00 O +ATOM 387 C GLU 25 23.466 -79.680 -12.350 1.00 0.00 C +ATOM 388 O GLU 25 24.169 -79.349 -11.398 1.00 0.00 O +ATOM 389 N ALA 26 22.999 -80.945 -12.388 1.00 0.00 N +ATOM 390 H ALA 26 22.549 -81.236 -13.244 1.00 0.00 H +ATOM 391 CA ALA 26 23.369 -81.993 -11.454 1.00 0.00 C +ATOM 392 HA ALA 26 22.993 -81.611 -10.505 1.00 0.00 H +ATOM 393 CB ALA 26 22.442 -83.198 -11.750 1.00 0.00 C +ATOM 394 HB1 ALA 26 21.443 -83.009 -11.356 1.00 0.00 H +ATOM 395 HB2 ALA 26 22.856 -84.055 -11.217 1.00 0.00 H +ATOM 396 HB3 ALA 26 22.364 -83.489 -12.798 1.00 0.00 H +ATOM 397 C ALA 26 24.902 -82.220 -11.583 1.00 0.00 C +ATOM 398 O ALA 26 25.628 -82.263 -10.597 1.00 0.00 O +ATOM 399 N GLU 27 25.422 -82.506 -12.784 1.00 0.00 N +ATOM 400 H GLU 27 24.737 -82.674 -13.507 1.00 0.00 H +ATOM 401 CA GLU 27 26.794 -82.950 -12.894 1.00 0.00 C +ATOM 402 HA GLU 27 26.864 -83.799 -12.214 1.00 0.00 H +ATOM 403 CB GLU 27 27.161 -83.515 -14.294 1.00 0.00 C +ATOM 404 HB2 GLU 27 27.850 -84.358 -14.333 1.00 0.00 H +ATOM 405 HB3 GLU 27 26.265 -83.924 -14.761 1.00 0.00 H +ATOM 406 CG GLU 27 27.615 -82.481 -15.199 1.00 0.00 C +ATOM 407 HG2 GLU 27 26.866 -81.690 -15.215 1.00 0.00 H +ATOM 408 HG3 GLU 27 28.512 -82.044 -14.760 1.00 0.00 H +ATOM 409 CD GLU 27 28.088 -82.922 -16.619 1.00 0.00 C +ATOM 410 OE1 GLU 27 28.851 -82.181 -17.298 1.00 0.00 O +ATOM 411 OE2 GLU 27 27.604 -84.019 -17.102 1.00 0.00 O +ATOM 412 C GLU 27 27.773 -81.847 -12.404 1.00 0.00 C +ATOM 413 O GLU 27 28.899 -82.076 -11.851 1.00 0.00 O +ATOM 414 N LYS 28 27.377 -80.569 -12.540 1.00 0.00 N +ATOM 415 H LYS 28 26.459 -80.474 -12.948 1.00 0.00 H +ATOM 416 CA LYS 28 28.021 -79.366 -12.053 1.00 0.00 C +ATOM 417 HA LYS 28 29.087 -79.517 -12.223 1.00 0.00 H +ATOM 418 CB LYS 28 27.510 -78.082 -12.812 1.00 0.00 C +ATOM 419 HB2 LYS 28 26.422 -78.121 -12.871 1.00 0.00 H +ATOM 420 HB3 LYS 28 27.705 -77.135 -12.308 1.00 0.00 H +ATOM 421 CG LYS 28 28.050 -77.938 -14.231 1.00 0.00 C +ATOM 422 HG2 LYS 28 29.131 -77.794 -14.213 1.00 0.00 H +ATOM 423 HG3 LYS 28 27.853 -78.861 -14.775 1.00 0.00 H +ATOM 424 CD LYS 28 27.405 -76.836 -15.041 1.00 0.00 C +ATOM 425 HD2 LYS 28 26.342 -77.055 -15.137 1.00 0.00 H +ATOM 426 HD3 LYS 28 27.517 -75.878 -14.534 1.00 0.00 H +ATOM 427 CE LYS 28 27.971 -76.773 -16.474 1.00 0.00 C +ATOM 428 HE2 LYS 28 29.005 -76.429 -16.440 1.00 0.00 H +ATOM 429 HE3 LYS 28 27.690 -77.658 -17.045 1.00 0.00 H +ATOM 430 NZ LYS 28 27.215 -75.776 -17.241 1.00 0.00 N +ATOM 431 HZ1 LYS 28 27.329 -74.885 -16.780 1.00 0.00 H +ATOM 432 HZ2 LYS 28 26.222 -75.940 -17.326 1.00 0.00 H +ATOM 433 HZ3 LYS 28 27.655 -75.685 -18.146 1.00 0.00 H +ATOM 434 C LYS 28 27.876 -79.178 -10.592 1.00 0.00 C +ATOM 435 O LYS 28 28.936 -79.038 -9.884 1.00 0.00 O +ATOM 436 N PHE 29 26.728 -79.475 -9.962 1.00 0.00 N +ATOM 437 H PHE 29 25.896 -79.739 -10.471 1.00 0.00 H +ATOM 438 CA PHE 29 26.505 -79.489 -8.523 1.00 0.00 C +ATOM 439 HA PHE 29 26.786 -78.478 -8.228 1.00 0.00 H +ATOM 440 CB PHE 29 25.017 -79.610 -8.304 1.00 0.00 C +ATOM 441 HB2 PHE 29 24.474 -78.740 -8.674 1.00 0.00 H +ATOM 442 HB3 PHE 29 24.593 -80.361 -8.970 1.00 0.00 H +ATOM 443 CG PHE 29 24.626 -79.880 -6.913 1.00 0.00 C +ATOM 444 CD1 PHE 29 24.848 -78.913 -5.887 1.00 0.00 C +ATOM 445 HD1 PHE 29 25.418 -78.016 -6.079 1.00 0.00 H +ATOM 446 CE1 PHE 29 24.350 -79.136 -4.606 1.00 0.00 C +ATOM 447 HE1 PHE 29 24.655 -78.439 -3.839 1.00 0.00 H +ATOM 448 CZ PHE 29 23.662 -80.373 -4.272 1.00 0.00 C +ATOM 449 HZ PHE 29 23.362 -80.528 -3.246 1.00 0.00 H +ATOM 450 CE2 PHE 29 23.592 -81.348 -5.256 1.00 0.00 C +ATOM 451 HE2 PHE 29 23.131 -82.249 -4.879 1.00 0.00 H +ATOM 452 CD2 PHE 29 23.995 -81.122 -6.578 1.00 0.00 C +ATOM 453 HD2 PHE 29 23.802 -81.863 -7.340 1.00 0.00 H +ATOM 454 C PHE 29 27.242 -80.681 -7.726 1.00 0.00 C +ATOM 455 O PHE 29 27.886 -80.422 -6.744 1.00 0.00 O +ATOM 456 N THR 30 27.255 -81.817 -8.361 1.00 0.00 N +ATOM 457 H THR 30 26.820 -81.805 -9.273 1.00 0.00 H +ATOM 458 CA THR 30 27.894 -83.032 -7.824 1.00 0.00 C +ATOM 459 HA THR 30 27.366 -83.384 -6.938 1.00 0.00 H +ATOM 460 CB THR 30 27.670 -84.175 -8.786 1.00 0.00 C +ATOM 461 HB THR 30 28.138 -83.943 -9.743 1.00 0.00 H +ATOM 462 CG2 THR 30 28.401 -85.404 -8.336 1.00 0.00 C +ATOM 463 HG21 THR 30 29.480 -85.417 -8.488 1.00 0.00 H +ATOM 464 HG22 THR 30 28.284 -85.551 -7.262 1.00 0.00 H +ATOM 465 HG23 THR 30 27.978 -86.254 -8.872 1.00 0.00 H +ATOM 466 OG1 THR 30 26.289 -84.359 -8.931 1.00 0.00 O +ATOM 467 HG1 THR 30 25.994 -83.736 -9.600 1.00 0.00 H +ATOM 468 C THR 30 29.334 -82.835 -7.619 1.00 0.00 C +ATOM 469 O THR 30 29.825 -83.145 -6.500 1.00 0.00 O +ATOM 470 N LYS 31 30.083 -82.429 -8.564 1.00 0.00 N +ATOM 471 H LYS 31 29.681 -82.228 -9.468 1.00 0.00 H +ATOM 472 CA LYS 31 31.529 -82.102 -8.388 1.00 0.00 C +ATOM 473 HA LYS 31 31.957 -82.940 -7.838 1.00 0.00 H +ATOM 474 CB LYS 31 32.179 -82.008 -9.752 1.00 0.00 C +ATOM 475 HB2 LYS 31 31.769 -81.134 -10.258 1.00 0.00 H +ATOM 476 HB3 LYS 31 33.268 -81.963 -9.749 1.00 0.00 H +ATOM 477 CG LYS 31 31.961 -83.319 -10.485 1.00 0.00 C +ATOM 478 HG2 LYS 31 32.251 -84.196 -9.907 1.00 0.00 H +ATOM 479 HG3 LYS 31 30.895 -83.456 -10.668 1.00 0.00 H +ATOM 480 CD LYS 31 32.721 -83.390 -11.821 1.00 0.00 C +ATOM 481 HD2 LYS 31 32.289 -82.623 -12.464 1.00 0.00 H +ATOM 482 HD3 LYS 31 33.802 -83.259 -11.785 1.00 0.00 H +ATOM 483 CE LYS 31 32.488 -84.760 -12.550 1.00 0.00 C +ATOM 484 HE2 LYS 31 33.033 -85.586 -12.093 1.00 0.00 H +ATOM 485 HE3 LYS 31 31.446 -85.080 -12.517 1.00 0.00 H +ATOM 486 NZ LYS 31 32.807 -84.619 -14.015 1.00 0.00 N +ATOM 487 HZ1 LYS 31 33.664 -84.092 -14.103 1.00 0.00 H +ATOM 488 HZ2 LYS 31 32.006 -84.203 -14.468 1.00 0.00 H +ATOM 489 HZ3 LYS 31 33.057 -85.528 -14.375 1.00 0.00 H +ATOM 490 C LYS 31 31.882 -80.990 -7.447 1.00 0.00 C +ATOM 491 O LYS 31 32.906 -81.080 -6.846 1.00 0.00 O +ATOM 492 N ALA 32 31.013 -79.969 -7.410 1.00 0.00 N +ATOM 493 H ALA 32 30.121 -80.051 -7.877 1.00 0.00 H +ATOM 494 CA ALA 32 31.130 -78.841 -6.512 1.00 0.00 C +ATOM 495 HA ALA 32 32.119 -78.431 -6.717 1.00 0.00 H +ATOM 496 CB ALA 32 30.123 -77.705 -6.786 1.00 0.00 C +ATOM 497 HB1 ALA 32 30.226 -76.930 -6.026 1.00 0.00 H +ATOM 498 HB2 ALA 32 30.349 -77.281 -7.764 1.00 0.00 H +ATOM 499 HB3 ALA 32 29.150 -78.176 -6.928 1.00 0.00 H +ATOM 500 C ALA 32 30.843 -79.262 -5.059 1.00 0.00 C +ATOM 501 O ALA 32 31.645 -78.908 -4.226 1.00 0.00 O +ATOM 502 N ASP 33 29.905 -80.165 -4.788 1.00 0.00 N +ATOM 503 H ASP 33 29.336 -80.490 -5.557 1.00 0.00 H +ATOM 504 CA ASP 33 29.484 -80.583 -3.453 1.00 0.00 C +ATOM 505 HA ASP 33 29.310 -79.630 -2.952 1.00 0.00 H +ATOM 506 CB ASP 33 28.118 -81.275 -3.504 1.00 0.00 C +ATOM 507 HB2 ASP 33 27.490 -80.628 -4.116 1.00 0.00 H +ATOM 508 HB3 ASP 33 28.239 -82.208 -4.056 1.00 0.00 H +ATOM 509 CG ASP 33 27.496 -81.465 -2.095 1.00 0.00 C +ATOM 510 OD1 ASP 33 27.114 -82.637 -1.769 1.00 0.00 O +ATOM 511 OD2 ASP 33 27.502 -80.521 -1.257 1.00 0.00 O +ATOM 512 C ASP 33 30.653 -81.498 -2.896 1.00 0.00 C +ATOM 513 O ASP 33 31.077 -81.360 -1.774 1.00 0.00 O +ATOM 514 N ALA 34 31.136 -82.388 -3.774 1.00 0.00 N +ATOM 515 H ALA 34 30.710 -82.374 -4.690 1.00 0.00 H +ATOM 516 CA ALA 34 32.220 -83.316 -3.531 1.00 0.00 C +ATOM 517 HA ALA 34 32.016 -83.947 -2.666 1.00 0.00 H +ATOM 518 CB ALA 34 32.248 -84.281 -4.703 1.00 0.00 C +ATOM 519 HB1 ALA 34 31.414 -84.978 -4.622 1.00 0.00 H +ATOM 520 HB2 ALA 34 33.093 -84.969 -4.721 1.00 0.00 H +ATOM 521 HB3 ALA 34 32.312 -83.793 -5.675 1.00 0.00 H +ATOM 522 C ALA 34 33.481 -82.532 -3.312 1.00 0.00 C +ATOM 523 O ALA 34 34.071 -82.651 -2.223 1.00 0.00 O +ATOM 524 N ASN 35 33.890 -81.556 -4.112 1.00 0.00 N +ATOM 525 H ASN 35 33.434 -81.286 -4.971 1.00 0.00 H +ATOM 526 CA ASN 35 35.086 -80.786 -3.732 1.00 0.00 C +ATOM 527 HA ASN 35 35.895 -81.469 -3.471 1.00 0.00 H +ATOM 528 CB ASN 35 35.410 -79.939 -4.942 1.00 0.00 C +ATOM 529 HB2 ASN 35 35.345 -80.584 -5.818 1.00 0.00 H +ATOM 530 HB3 ASN 35 34.731 -79.086 -4.974 1.00 0.00 H +ATOM 531 CG ASN 35 36.853 -79.391 -4.872 1.00 0.00 C +ATOM 532 OD1 ASN 35 37.683 -79.612 -4.017 1.00 0.00 O +ATOM 533 ND2 ASN 35 37.058 -78.405 -5.722 1.00 0.00 N +ATOM 534 HD21 ASN 35 36.408 -78.202 -6.468 1.00 0.00 H +ATOM 535 HD22 ASN 35 37.924 -77.892 -5.643 1.00 0.00 H +ATOM 536 C ASN 35 34.851 -79.989 -2.394 1.00 0.00 C +ATOM 537 O ASN 35 35.818 -79.827 -1.600 1.00 0.00 O +ATOM 538 N ASP 36 33.653 -79.568 -1.999 1.00 0.00 N +ATOM 539 H ASP 36 32.931 -79.786 -2.671 1.00 0.00 H +ATOM 540 CA ASP 36 33.397 -78.972 -0.714 1.00 0.00 C +ATOM 541 HA ASP 36 34.195 -78.240 -0.590 1.00 0.00 H +ATOM 542 CB ASP 36 32.038 -78.343 -0.586 1.00 0.00 C +ATOM 543 HB2 ASP 36 32.006 -77.586 -1.370 1.00 0.00 H +ATOM 544 HB3 ASP 36 31.314 -79.117 -0.842 1.00 0.00 H +ATOM 545 CG ASP 36 31.623 -77.869 0.830 1.00 0.00 C +ATOM 546 OD1 ASP 36 32.422 -77.450 1.691 1.00 0.00 O +ATOM 547 OD2 ASP 36 30.421 -77.974 1.049 1.00 0.00 O +ATOM 548 C ASP 36 33.542 -80.037 0.448 1.00 0.00 C +ATOM 549 O ASP 36 34.196 -79.739 1.468 1.00 0.00 O +ATOM 550 N LYS 37 33.061 -81.289 0.249 1.00 0.00 N +ATOM 551 H LYS 37 32.646 -81.497 -0.648 1.00 0.00 H +ATOM 552 CA LYS 37 33.261 -82.468 1.091 1.00 0.00 C +ATOM 553 HA LYS 37 33.239 -82.167 2.138 1.00 0.00 H +ATOM 554 CB LYS 37 32.188 -83.515 0.813 1.00 0.00 C +ATOM 555 HB2 LYS 37 32.396 -84.383 1.438 1.00 0.00 H +ATOM 556 HB3 LYS 37 32.206 -83.854 -0.223 1.00 0.00 H +ATOM 557 CG LYS 37 30.818 -82.900 1.296 1.00 0.00 C +ATOM 558 HG2 LYS 37 30.636 -81.925 0.844 1.00 0.00 H +ATOM 559 HG3 LYS 37 30.923 -82.753 2.371 1.00 0.00 H +ATOM 560 CD LYS 37 29.516 -83.646 0.959 1.00 0.00 C +ATOM 561 HD2 LYS 37 29.478 -83.610 -0.130 1.00 0.00 H +ATOM 562 HD3 LYS 37 29.630 -84.709 1.172 1.00 0.00 H +ATOM 563 CE LYS 37 28.256 -83.089 1.636 1.00 0.00 C +ATOM 564 HE2 LYS 37 27.385 -83.616 1.247 1.00 0.00 H +ATOM 565 HE3 LYS 37 28.292 -83.184 2.722 1.00 0.00 H +ATOM 566 NZ LYS 37 27.982 -81.660 1.292 1.00 0.00 N +ATOM 567 HZ1 LYS 37 27.686 -81.530 0.335 1.00 0.00 H +ATOM 568 HZ2 LYS 37 27.277 -81.201 1.851 1.00 0.00 H +ATOM 569 HZ3 LYS 37 28.780 -81.054 1.423 1.00 0.00 H +ATOM 570 C LYS 37 34.681 -83.025 0.972 1.00 0.00 C +ATOM 571 O LYS 37 34.960 -84.026 1.622 1.00 0.00 O +ATOM 572 N GLY 38 35.609 -82.396 0.235 1.00 0.00 N +ATOM 573 H GLY 38 35.365 -81.526 -0.218 1.00 0.00 H +ATOM 574 CA GLY 38 37.010 -82.827 0.163 1.00 0.00 C +ATOM 575 HA2 GLY 38 37.613 -81.932 0.010 1.00 0.00 H +ATOM 576 HA3 GLY 38 37.298 -83.323 1.090 1.00 0.00 H +ATOM 577 C GLY 38 37.366 -83.924 -0.890 1.00 0.00 C +ATOM 578 O GLY 38 38.539 -84.224 -1.043 1.00 0.00 O +ATOM 579 N VAL 39 36.436 -84.450 -1.687 1.00 0.00 N +ATOM 580 H VAL 39 35.507 -84.064 -1.777 1.00 0.00 H +ATOM 581 CA VAL 39 36.647 -85.776 -2.369 1.00 0.00 C +ATOM 582 HA VAL 39 37.714 -85.992 -2.314 1.00 0.00 H +ATOM 583 CB VAL 39 35.922 -86.925 -1.707 1.00 0.00 C +ATOM 584 HB VAL 39 36.223 -87.876 -2.145 1.00 0.00 H +ATOM 585 CG1 VAL 39 36.288 -86.964 -0.252 1.00 0.00 C +ATOM 586 HG11 VAL 39 35.738 -87.795 0.189 1.00 0.00 H +ATOM 587 HG12 VAL 39 35.856 -86.134 0.307 1.00 0.00 H +ATOM 588 HG13 VAL 39 37.360 -87.146 -0.172 1.00 0.00 H +ATOM 589 CG2 VAL 39 34.387 -86.851 -1.724 1.00 0.00 C +ATOM 590 HG21 VAL 39 34.095 -86.785 -2.772 1.00 0.00 H +ATOM 591 HG22 VAL 39 34.114 -85.879 -1.313 1.00 0.00 H +ATOM 592 HG23 VAL 39 33.857 -87.654 -1.213 1.00 0.00 H +ATOM 593 C VAL 39 36.382 -85.670 -3.905 1.00 0.00 C +ATOM 594 O VAL 39 36.043 -84.594 -4.364 1.00 0.00 O +ATOM 595 N ASP 40 36.651 -86.709 -4.703 1.00 0.00 N +ATOM 596 H ASP 40 36.766 -87.591 -4.225 1.00 0.00 H +ATOM 597 CA ASP 40 36.673 -86.682 -6.172 1.00 0.00 C +ATOM 598 HA ASP 40 36.060 -85.940 -6.683 1.00 0.00 H +ATOM 599 CB ASP 40 38.187 -86.377 -6.533 1.00 0.00 C +ATOM 600 HB2 ASP 40 38.723 -85.687 -5.881 1.00 0.00 H +ATOM 601 HB3 ASP 40 38.813 -87.270 -6.509 1.00 0.00 H +ATOM 602 CG ASP 40 38.287 -85.701 -7.923 1.00 0.00 C +ATOM 603 OD1 ASP 40 39.331 -85.074 -8.135 1.00 0.00 O +ATOM 604 OD2 ASP 40 37.386 -85.931 -8.790 1.00 0.00 O +ATOM 605 C ASP 40 36.222 -88.108 -6.755 1.00 0.00 C +ATOM 606 O ASP 40 36.269 -89.127 -6.049 1.00 0.00 O +ATOM 607 N GLY 41 35.905 -88.165 -8.058 1.00 0.00 N +ATOM 608 H GLY 41 36.029 -87.320 -8.597 1.00 0.00 H +ATOM 609 CA GLY 41 35.637 -89.310 -8.896 1.00 0.00 C +ATOM 610 HA2 GLY 41 36.551 -89.885 -9.042 1.00 0.00 H +ATOM 611 HA3 GLY 41 34.825 -89.919 -8.500 1.00 0.00 H +ATOM 612 C GLY 41 35.124 -88.899 -10.323 1.00 0.00 C +ATOM 613 O GLY 41 35.372 -87.786 -10.795 1.00 0.00 O +ATOM 614 N GLU 42 34.342 -89.831 -10.990 1.00 0.00 N +ATOM 615 H GLU 42 34.022 -90.611 -10.433 1.00 0.00 H +ATOM 616 CA GLU 42 33.690 -89.564 -12.266 1.00 0.00 C +ATOM 617 HA GLU 42 33.420 -88.510 -12.322 1.00 0.00 H +ATOM 618 CB GLU 42 34.709 -89.754 -13.445 1.00 0.00 C +ATOM 619 HB2 GLU 42 35.604 -89.173 -13.225 1.00 0.00 H +ATOM 620 HB3 GLU 42 34.920 -90.814 -13.587 1.00 0.00 H +ATOM 621 CG GLU 42 34.144 -89.306 -14.826 1.00 0.00 C +ATOM 622 HG2 GLU 42 35.078 -89.298 -15.388 1.00 0.00 H +ATOM 623 HG3 GLU 42 33.327 -89.907 -15.226 1.00 0.00 H +ATOM 624 CD GLU 42 33.725 -87.861 -14.857 1.00 0.00 C +ATOM 625 OE1 GLU 42 32.684 -87.597 -14.358 1.00 0.00 O +ATOM 626 OE2 GLU 42 34.490 -86.929 -15.164 1.00 0.00 O +ATOM 627 C GLU 42 32.486 -90.478 -12.518 1.00 0.00 C +ATOM 628 O GLU 42 32.495 -91.665 -12.220 1.00 0.00 O +ATOM 629 N TRP 43 31.528 -89.889 -13.229 1.00 0.00 N +ATOM 630 H TRP 43 31.678 -88.919 -13.467 1.00 0.00 H +ATOM 631 CA TRP 43 30.219 -90.509 -13.500 1.00 0.00 C +ATOM 632 HA TRP 43 30.182 -91.547 -13.170 1.00 0.00 H +ATOM 633 CB TRP 43 29.093 -89.971 -12.607 1.00 0.00 C +ATOM 634 HB2 TRP 43 28.703 -88.979 -12.833 1.00 0.00 H +ATOM 635 HB3 TRP 43 28.228 -90.617 -12.758 1.00 0.00 H +ATOM 636 CG TRP 43 29.393 -90.055 -11.161 1.00 0.00 C +ATOM 637 CD1 TRP 43 29.156 -91.183 -10.373 1.00 0.00 C +ATOM 638 HD1 TRP 43 28.724 -92.093 -10.761 1.00 0.00 H +ATOM 639 NE1 TRP 43 29.479 -91.025 -9.040 1.00 0.00 N +ATOM 640 HE1 TRP 43 29.448 -91.702 -8.291 1.00 0.00 H +ATOM 641 CE2 TRP 43 30.262 -89.887 -8.965 1.00 0.00 C +ATOM 642 CZ2 TRP 43 30.928 -89.297 -7.897 1.00 0.00 C +ATOM 643 HZ2 TRP 43 30.982 -89.842 -6.966 1.00 0.00 H +ATOM 644 CH2 TRP 43 31.636 -88.091 -8.018 1.00 0.00 C +ATOM 645 HH2 TRP 43 32.210 -87.709 -7.187 1.00 0.00 H +ATOM 646 CZ3 TRP 43 31.756 -87.507 -9.250 1.00 0.00 C +ATOM 647 HZ3 TRP 43 32.411 -86.650 -9.311 1.00 0.00 H +ATOM 648 CE3 TRP 43 31.006 -88.024 -10.330 1.00 0.00 C +ATOM 649 HE3 TRP 43 30.987 -87.534 -11.292 1.00 0.00 H +ATOM 650 CD2 TRP 43 30.240 -89.249 -10.241 1.00 0.00 C +ATOM 651 C TRP 43 29.827 -90.472 -15.002 1.00 0.00 C +ATOM 652 O TRP 43 30.334 -89.551 -15.662 1.00 0.00 O +ATOM 653 N THR 44 28.979 -91.338 -15.535 1.00 0.00 N +ATOM 654 H THR 44 28.545 -91.981 -14.888 1.00 0.00 H +ATOM 655 CA THR 44 28.411 -91.245 -16.845 1.00 0.00 C +ATOM 656 HA THR 44 28.581 -90.238 -17.225 1.00 0.00 H +ATOM 657 CB THR 44 29.099 -92.286 -17.720 1.00 0.00 C +ATOM 658 HB THR 44 30.128 -91.930 -17.776 1.00 0.00 H +ATOM 659 CG2 THR 44 29.095 -93.729 -17.318 1.00 0.00 C +ATOM 660 HG21 THR 44 29.848 -94.308 -17.854 1.00 0.00 H +ATOM 661 HG22 THR 44 28.147 -94.199 -17.580 1.00 0.00 H +ATOM 662 HG23 THR 44 29.293 -93.723 -16.246 1.00 0.00 H +ATOM 663 OG1 THR 44 28.684 -92.321 -19.078 1.00 0.00 O +ATOM 664 HG1 THR 44 28.881 -91.492 -19.521 1.00 0.00 H +ATOM 665 C THR 44 26.877 -91.380 -16.794 1.00 0.00 C +ATOM 666 O THR 44 26.285 -92.166 -15.992 1.00 0.00 O +ATOM 667 N TYR 45 26.141 -90.623 -17.624 1.00 0.00 N +ATOM 668 H TYR 45 26.651 -90.057 -18.288 1.00 0.00 H +ATOM 669 CA TYR 45 24.661 -90.390 -17.675 1.00 0.00 C +ATOM 670 HA TYR 45 24.239 -90.467 -16.673 1.00 0.00 H +ATOM 671 CB TYR 45 24.453 -88.934 -17.941 1.00 0.00 C +ATOM 672 HB2 TYR 45 25.059 -88.424 -17.192 1.00 0.00 H +ATOM 673 HB3 TYR 45 24.894 -88.675 -18.904 1.00 0.00 H +ATOM 674 CG TYR 45 23.063 -88.453 -17.902 1.00 0.00 C +ATOM 675 CD1 TYR 45 22.231 -88.765 -16.752 1.00 0.00 C +ATOM 676 HD1 TYR 45 22.669 -88.978 -15.788 1.00 0.00 H +ATOM 677 CE1 TYR 45 20.827 -88.516 -16.805 1.00 0.00 C +ATOM 678 HE1 TYR 45 20.214 -88.832 -15.974 1.00 0.00 H +ATOM 679 CZ TYR 45 20.218 -88.001 -17.971 1.00 0.00 C +ATOM 680 OH TYR 45 18.899 -87.821 -18.108 1.00 0.00 O +ATOM 681 HH TYR 45 18.702 -87.629 -19.028 1.00 0.00 H +ATOM 682 CE2 TYR 45 21.027 -87.737 -19.087 1.00 0.00 C +ATOM 683 HE2 TYR 45 20.647 -87.280 -19.989 1.00 0.00 H +ATOM 684 CD2 TYR 45 22.413 -87.941 -19.032 1.00 0.00 C +ATOM 685 HD2 TYR 45 23.000 -87.624 -19.881 1.00 0.00 H +ATOM 686 C TYR 45 23.947 -91.452 -18.650 1.00 0.00 C +ATOM 687 O TYR 45 24.444 -91.850 -19.711 1.00 0.00 O +ATOM 688 N ASP 46 22.707 -91.796 -18.343 1.00 0.00 N +ATOM 689 H ASP 46 22.336 -91.401 -17.490 1.00 0.00 H +ATOM 690 CA ASP 46 21.712 -92.586 -19.152 1.00 0.00 C +ATOM 691 HA ASP 46 22.182 -92.798 -20.112 1.00 0.00 H +ATOM 692 CB ASP 46 21.514 -93.914 -18.490 1.00 0.00 C +ATOM 693 HB2 ASP 46 22.440 -94.489 -18.484 1.00 0.00 H +ATOM 694 HB3 ASP 46 21.095 -93.770 -17.494 1.00 0.00 H +ATOM 695 CG ASP 46 20.430 -94.728 -19.296 1.00 0.00 C +ATOM 696 OD1 ASP 46 19.747 -95.645 -18.741 1.00 0.00 O +ATOM 697 OD2 ASP 46 20.358 -94.604 -20.518 1.00 0.00 O +ATOM 698 C ASP 46 20.357 -91.779 -19.356 1.00 0.00 C +ATOM 699 O ASP 46 19.587 -91.778 -18.400 1.00 0.00 O +ATOM 700 N ASP 47 20.075 -91.074 -20.472 1.00 0.00 N +ATOM 701 H ASP 47 20.830 -91.031 -21.141 1.00 0.00 H +ATOM 702 CA ASP 47 18.878 -90.271 -20.775 1.00 0.00 C +ATOM 703 HA ASP 47 18.749 -89.740 -19.831 1.00 0.00 H +ATOM 704 CB ASP 47 19.250 -89.309 -21.899 1.00 0.00 C +ATOM 705 HB2 ASP 47 20.263 -89.013 -21.628 1.00 0.00 H +ATOM 706 HB3 ASP 47 19.423 -89.752 -22.880 1.00 0.00 H +ATOM 707 CG ASP 47 18.363 -88.080 -21.762 1.00 0.00 C +ATOM 708 OD1 ASP 47 18.028 -87.593 -20.647 1.00 0.00 O +ATOM 709 OD2 ASP 47 18.041 -87.575 -22.877 1.00 0.00 O +ATOM 710 C ASP 47 17.584 -91.076 -20.998 1.00 0.00 C +ATOM 711 O ASP 47 16.484 -90.560 -21.011 1.00 0.00 O +ATOM 712 N ALA 48 17.764 -92.373 -21.164 1.00 0.00 N +ATOM 713 H ALA 48 18.698 -92.718 -21.336 1.00 0.00 H +ATOM 714 CA ALA 48 16.696 -93.333 -21.310 1.00 0.00 C +ATOM 715 HA ALA 48 15.944 -92.943 -21.995 1.00 0.00 H +ATOM 716 CB ALA 48 17.298 -94.557 -22.044 1.00 0.00 C +ATOM 717 HB1 ALA 48 17.995 -95.038 -21.358 1.00 0.00 H +ATOM 718 HB2 ALA 48 17.826 -94.129 -22.897 1.00 0.00 H +ATOM 719 HB3 ALA 48 16.499 -95.248 -22.312 1.00 0.00 H +ATOM 720 C ALA 48 16.080 -93.541 -19.924 1.00 0.00 C +ATOM 721 O ALA 48 14.924 -93.143 -19.728 1.00 0.00 O +ATOM 722 N THR 49 16.863 -93.976 -18.918 1.00 0.00 N +ATOM 723 H THR 49 17.798 -94.327 -19.070 1.00 0.00 H +ATOM 724 CA THR 49 16.362 -94.202 -17.562 1.00 0.00 C +ATOM 725 HA THR 49 15.294 -94.404 -17.642 1.00 0.00 H +ATOM 726 CB THR 49 17.103 -95.252 -16.710 1.00 0.00 C +ATOM 727 HB THR 49 16.747 -95.229 -15.681 1.00 0.00 H +ATOM 728 CG2 THR 49 16.977 -96.709 -17.206 1.00 0.00 C +ATOM 729 HG21 THR 49 17.914 -97.265 -17.206 1.00 0.00 H +ATOM 730 HG22 THR 49 16.660 -96.800 -18.245 1.00 0.00 H +ATOM 731 HG23 THR 49 16.179 -97.115 -16.583 1.00 0.00 H +ATOM 732 OG1 THR 49 18.426 -95.017 -16.532 1.00 0.00 O +ATOM 733 HG1 THR 49 18.856 -95.306 -17.340 1.00 0.00 H +ATOM 734 C THR 49 16.410 -92.922 -16.659 1.00 0.00 C +ATOM 735 O THR 49 15.827 -92.962 -15.581 1.00 0.00 O +ATOM 736 N LYS 50 17.123 -91.860 -17.063 1.00 0.00 N +ATOM 737 H LYS 50 17.699 -91.951 -17.888 1.00 0.00 H +ATOM 738 CA LYS 50 17.547 -90.734 -16.307 1.00 0.00 C +ATOM 739 HA LYS 50 18.097 -90.129 -17.027 1.00 0.00 H +ATOM 740 CB LYS 50 16.282 -89.938 -15.872 1.00 0.00 C +ATOM 741 HB2 LYS 50 15.666 -90.475 -15.151 1.00 0.00 H +ATOM 742 HB3 LYS 50 16.507 -89.033 -15.306 1.00 0.00 H +ATOM 743 CG LYS 50 15.263 -89.616 -16.975 1.00 0.00 C +ATOM 744 HG2 LYS 50 14.962 -90.559 -17.431 1.00 0.00 H +ATOM 745 HG3 LYS 50 14.439 -89.051 -16.537 1.00 0.00 H +ATOM 746 CD LYS 50 15.737 -88.656 -18.078 1.00 0.00 C +ATOM 747 HD2 LYS 50 15.842 -87.655 -17.658 1.00 0.00 H +ATOM 748 HD3 LYS 50 16.714 -89.006 -18.411 1.00 0.00 H +ATOM 749 CE LYS 50 14.807 -88.585 -19.270 1.00 0.00 C +ATOM 750 HE2 LYS 50 14.863 -89.469 -19.906 1.00 0.00 H +ATOM 751 HE3 LYS 50 13.811 -88.509 -18.834 1.00 0.00 H +ATOM 752 NZ LYS 50 15.069 -87.325 -19.942 1.00 0.00 N +ATOM 753 HZ1 LYS 50 14.950 -86.477 -19.405 1.00 0.00 H +ATOM 754 HZ2 LYS 50 14.484 -87.184 -20.753 1.00 0.00 H +ATOM 755 HZ3 LYS 50 16.009 -87.316 -20.311 1.00 0.00 H +ATOM 756 C LYS 50 18.534 -91.002 -15.206 1.00 0.00 C +ATOM 757 O LYS 50 18.233 -90.612 -14.098 1.00 0.00 O +ATOM 758 N THR 51 19.676 -91.665 -15.380 1.00 0.00 N +ATOM 759 H THR 51 20.035 -91.797 -16.315 1.00 0.00 H +ATOM 760 CA THR 51 20.500 -92.209 -14.276 1.00 0.00 C +ATOM 761 HA THR 51 20.178 -91.888 -13.285 1.00 0.00 H +ATOM 762 CB THR 51 20.264 -93.739 -14.213 1.00 0.00 C +ATOM 763 HB THR 51 20.565 -94.192 -15.158 1.00 0.00 H +ATOM 764 CG2 THR 51 20.965 -94.370 -12.972 1.00 0.00 C +ATOM 765 HG21 THR 51 20.704 -93.888 -12.030 1.00 0.00 H +ATOM 766 HG22 THR 51 22.050 -94.331 -13.072 1.00 0.00 H +ATOM 767 HG23 THR 51 20.708 -95.422 -12.843 1.00 0.00 H +ATOM 768 OG1 THR 51 18.966 -94.007 -14.002 1.00 0.00 O +ATOM 769 HG1 THR 51 18.734 -94.463 -14.814 1.00 0.00 H +ATOM 770 C THR 51 22.049 -91.917 -14.464 1.00 0.00 C +ATOM 771 O THR 51 22.594 -92.119 -15.565 1.00 0.00 O +ATOM 772 N PHE 52 22.666 -91.429 -13.388 1.00 0.00 N +ATOM 773 H PHE 52 22.142 -91.400 -12.526 1.00 0.00 H +ATOM 774 CA PHE 52 24.140 -91.318 -13.353 1.00 0.00 C +ATOM 775 HA PHE 52 24.514 -91.192 -14.369 1.00 0.00 H +ATOM 776 CB PHE 52 24.442 -90.043 -12.551 1.00 0.00 C +ATOM 777 HB2 PHE 52 23.910 -89.975 -11.603 1.00 0.00 H +ATOM 778 HB3 PHE 52 25.492 -90.086 -12.261 1.00 0.00 H +ATOM 779 CG PHE 52 24.238 -88.694 -13.231 1.00 0.00 C +ATOM 780 CD1 PHE 52 22.995 -87.965 -13.129 1.00 0.00 C +ATOM 781 HD1 PHE 52 22.221 -88.445 -12.548 1.00 0.00 H +ATOM 782 CE1 PHE 52 22.803 -86.730 -13.818 1.00 0.00 C +ATOM 783 HE1 PHE 52 21.864 -86.197 -13.769 1.00 0.00 H +ATOM 784 CZ PHE 52 23.891 -86.168 -14.518 1.00 0.00 C +ATOM 785 HZ PHE 52 23.745 -85.162 -14.883 1.00 0.00 H +ATOM 786 CE2 PHE 52 25.094 -86.894 -14.670 1.00 0.00 C +ATOM 787 HE2 PHE 52 25.932 -86.532 -15.248 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.275 -88.092 -13.913 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.201 -88.635 -14.034 1.00 0.00 H +ATOM 790 C PHE 52 24.674 -92.647 -12.729 1.00 0.00 C +ATOM 791 O PHE 52 24.358 -92.883 -11.542 1.00 0.00 O +ATOM 792 N THR 53 25.689 -93.234 -13.338 1.00 0.00 N +ATOM 793 H THR 53 25.922 -92.885 -14.256 1.00 0.00 H +ATOM 794 CA THR 53 26.454 -94.409 -12.892 1.00 0.00 C +ATOM 795 HA THR 53 26.055 -94.679 -11.914 1.00 0.00 H +ATOM 796 CB THR 53 26.177 -95.740 -13.674 1.00 0.00 C +ATOM 797 HB THR 53 26.623 -95.583 -14.656 1.00 0.00 H +ATOM 798 CG2 THR 53 26.860 -96.974 -13.095 1.00 0.00 C +ATOM 799 HG21 THR 53 26.487 -97.872 -13.588 1.00 0.00 H +ATOM 800 HG22 THR 53 26.545 -97.220 -12.081 1.00 0.00 H +ATOM 801 HG23 THR 53 27.926 -96.923 -13.316 1.00 0.00 H +ATOM 802 OG1 THR 53 24.882 -96.001 -13.827 1.00 0.00 O +ATOM 803 HG1 THR 53 24.559 -95.359 -14.463 1.00 0.00 H +ATOM 804 C THR 53 27.875 -94.080 -12.719 1.00 0.00 C +ATOM 805 O THR 53 28.439 -93.470 -13.607 1.00 0.00 O +ATOM 806 N VAL 54 28.467 -94.481 -11.568 1.00 0.00 N +ATOM 807 H VAL 54 27.950 -94.786 -10.755 1.00 0.00 H +ATOM 808 CA VAL 54 29.899 -94.341 -11.486 1.00 0.00 C +ATOM 809 HA VAL 54 30.049 -93.286 -11.717 1.00 0.00 H +ATOM 810 CB VAL 54 30.381 -94.643 -10.034 1.00 0.00 C +ATOM 811 HB VAL 54 29.691 -94.179 -9.330 1.00 0.00 H +ATOM 812 CG1 VAL 54 30.430 -96.109 -9.587 1.00 0.00 C +ATOM 813 HG11 VAL 54 30.752 -96.085 -8.546 1.00 0.00 H +ATOM 814 HG12 VAL 54 31.242 -96.629 -10.096 1.00 0.00 H +ATOM 815 HG13 VAL 54 29.464 -96.613 -9.587 1.00 0.00 H +ATOM 816 CG2 VAL 54 31.651 -93.871 -9.757 1.00 0.00 C +ATOM 817 HG21 VAL 54 32.512 -94.179 -10.350 1.00 0.00 H +ATOM 818 HG22 VAL 54 31.900 -93.996 -8.704 1.00 0.00 H +ATOM 819 HG23 VAL 54 31.597 -92.794 -9.915 1.00 0.00 H +ATOM 820 C VAL 54 30.695 -95.048 -12.558 1.00 0.00 C +ATOM 821 O VAL 54 30.354 -96.187 -12.866 1.00 0.00 O +ATOM 822 N THR 55 31.698 -94.425 -13.200 1.00 0.00 N +ATOM 823 H THR 55 31.831 -93.445 -12.993 1.00 0.00 H +ATOM 824 CA THR 55 32.628 -95.087 -14.124 1.00 0.00 C +ATOM 825 HA THR 55 32.096 -95.618 -14.913 1.00 0.00 H +ATOM 826 CB THR 55 33.498 -94.104 -14.896 1.00 0.00 C +ATOM 827 HB THR 55 34.112 -94.637 -15.622 1.00 0.00 H +ATOM 828 CG2 THR 55 32.532 -93.094 -15.604 1.00 0.00 C +ATOM 829 HG21 THR 55 31.859 -93.605 -16.293 1.00 0.00 H +ATOM 830 HG22 THR 55 33.239 -92.519 -16.202 1.00 0.00 H +ATOM 831 HG23 THR 55 32.010 -92.428 -14.916 1.00 0.00 H +ATOM 832 OG1 THR 55 34.408 -93.395 -14.089 1.00 0.00 O +ATOM 833 HG1 THR 55 33.804 -92.942 -13.496 1.00 0.00 H +ATOM 834 C THR 55 33.497 -95.981 -13.302 1.00 0.00 C +ATOM 835 O THR 55 33.890 -95.598 -12.188 1.00 0.00 O +ATOM 836 N GLU 56 33.755 -97.176 -13.767 1.00 0.00 N +ATOM 837 H GLU 56 33.343 -97.456 -14.645 1.00 0.00 H +ATOM 838 CA GLU 56 34.621 -98.221 -13.079 1.00 0.00 C +ATOM 839 HA GLU 56 35.316 -97.832 -12.335 1.00 0.00 H +ATOM 840 CB GLU 56 33.719 -99.263 -12.420 1.00 0.00 C +ATOM 841 HB2 GLU 56 33.113 -98.713 -11.701 1.00 0.00 H +ATOM 842 HB3 GLU 56 33.048 -99.783 -13.103 1.00 0.00 H +ATOM 843 CG GLU 56 34.533-100.266 -11.656 1.00 0.00 C +ATOM 844 HG2 GLU 56 33.914-101.059 -11.236 1.00 0.00 H +ATOM 845 HG3 GLU 56 35.187-100.829 -12.322 1.00 0.00 H +ATOM 846 CD GLU 56 35.410 -99.685 -10.463 1.00 0.00 C +ATOM 847 OE1 GLU 56 34.806 -98.970 -9.573 1.00 0.00 O +ATOM 848 OE2 GLU 56 36.645 -99.943 -10.491 1.00 0.00 O +ATOM 849 C GLU 56 35.461 -98.765 -14.136 1.00 0.00 C +ATOM 850 O GLU 56 34.871 -99.177 -15.187 1.00 0.00 O +ATOM 851 OXT GLU 56 36.719 -98.821 -14.039 1.00 0.00 O +ATOM 852 ZN ZN1 57 24.217 -87.896 -5.966 1.00 0.00 ZN +ATOM 853 N AN1 58 25.801 -86.974 -4.960 1.00 0.00 N +ATOM 854 C AN1 58 28.059 -85.994 -4.192 1.00 0.00 C +ATOM 855 C1 AN1 58 26.802 -86.540 -4.575 1.00 0.00 C +ATOM 856 H AN1 58 28.871 -86.419 -4.794 1.00 0.00 H +ATOM 857 H1 AN1 58 28.363 -86.440 -3.237 1.00 0.00 H +ATOM 858 H2 AN1 58 28.180 -84.904 -4.221 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 20.392 -87.396 -1.895 1.00 0.00 N +ATOM 860 N2 AZI 59 21.476 -86.802 -1.843 1.00 0.00 N +ATOM 861 N3 AZI 59 22.557 -86.184 -1.654 1.00 0.00 N +TER 862 AZI 59 +END diff --git a/tests/nsga2/pdbs_rename/cluster91.pdb b/tests/nsga2/pdbs_rename/cluster91.pdb new file mode 100644 index 0000000..d7e7122 --- /dev/null +++ b/tests/nsga2/pdbs_rename/cluster91.pdb @@ -0,0 +1,864 @@ +CRYST1 51.635 53.263 47.360 90.00 90.00 90.00 1 +ATOM 1 N MET 1 17.380 19.727 33.806 1.00 0.00 N +ATOM 2 H1 MET 1 16.973 18.924 34.263 1.00 0.00 H +ATOM 3 H2 MET 1 17.322 19.601 32.806 1.00 0.00 H +ATOM 4 H3 MET 1 16.872 20.586 33.962 1.00 0.00 H +ATOM 5 CA MET 1 18.869 19.857 33.953 1.00 0.00 C +ATOM 6 HA MET 1 18.986 20.007 35.026 1.00 0.00 H +ATOM 7 CB MET 1 19.562 18.633 33.369 1.00 0.00 C +ATOM 8 HB2 MET 1 19.174 17.739 33.859 1.00 0.00 H +ATOM 9 HB3 MET 1 19.160 18.540 32.360 1.00 0.00 H +ATOM 10 CG MET 1 21.055 18.743 33.536 1.00 0.00 C +ATOM 11 HG2 MET 1 21.525 17.777 33.348 1.00 0.00 H +ATOM 12 HG3 MET 1 21.517 19.538 32.950 1.00 0.00 H +ATOM 13 SD MET 1 21.369 19.196 35.244 1.00 0.00 S +ATOM 14 CE MET 1 20.976 17.627 36.229 1.00 0.00 C +ATOM 15 HE1 MET 1 19.897 17.735 36.347 1.00 0.00 H +ATOM 16 HE2 MET 1 21.554 17.527 37.148 1.00 0.00 H +ATOM 17 HE3 MET 1 21.194 16.787 35.570 1.00 0.00 H +ATOM 18 C MET 1 19.318 21.121 33.229 1.00 0.00 C +ATOM 19 O MET 1 18.836 21.520 32.195 1.00 0.00 O +ATOM 20 N GLN 2 20.217 21.835 33.921 1.00 0.00 N +ATOM 21 H GLN 2 20.532 21.565 34.842 1.00 0.00 H +ATOM 22 CA GLN 2 20.876 23.004 33.373 1.00 0.00 C +ATOM 23 HA GLN 2 20.242 23.398 32.579 1.00 0.00 H +ATOM 24 CB GLN 2 21.086 24.060 34.444 1.00 0.00 C +ATOM 25 HB2 GLN 2 21.345 23.560 35.377 1.00 0.00 H +ATOM 26 HB3 GLN 2 21.898 24.765 34.266 1.00 0.00 H +ATOM 27 CG GLN 2 19.828 24.948 34.694 1.00 0.00 C +ATOM 28 HG2 GLN 2 19.779 25.678 33.885 1.00 0.00 H +ATOM 29 HG3 GLN 2 18.903 24.379 34.601 1.00 0.00 H +ATOM 30 CD GLN 2 19.737 25.634 36.022 1.00 0.00 C +ATOM 31 OE1 GLN 2 20.657 25.623 36.868 1.00 0.00 O +ATOM 32 NE2 GLN 2 18.630 26.191 36.334 1.00 0.00 N +ATOM 33 HE21 GLN 2 18.588 26.781 37.153 1.00 0.00 H +ATOM 34 HE22 GLN 2 17.901 26.224 35.636 1.00 0.00 H +ATOM 35 C GLN 2 22.184 22.684 32.583 1.00 0.00 C +ATOM 36 O GLN 2 23.102 22.085 33.126 1.00 0.00 O +ATOM 37 N TYR 3 22.282 23.092 31.302 1.00 0.00 N +ATOM 38 H TYR 3 21.552 23.736 31.033 1.00 0.00 H +ATOM 39 CA TYR 3 23.447 22.953 30.507 1.00 0.00 C +ATOM 40 HA TYR 3 24.225 22.456 31.086 1.00 0.00 H +ATOM 41 CB TYR 3 23.193 22.119 29.270 1.00 0.00 C +ATOM 42 HB2 TYR 3 22.453 22.645 28.666 1.00 0.00 H +ATOM 43 HB3 TYR 3 24.137 22.024 28.734 1.00 0.00 H +ATOM 44 CG TYR 3 22.578 20.756 29.534 1.00 0.00 C +ATOM 45 CD1 TYR 3 23.488 19.662 29.464 1.00 0.00 C +ATOM 46 HD1 TYR 3 24.485 19.778 29.065 1.00 0.00 H +ATOM 47 CE1 TYR 3 22.939 18.406 29.674 1.00 0.00 C +ATOM 48 HE1 TYR 3 23.585 17.547 29.569 1.00 0.00 H +ATOM 49 CZ TYR 3 21.538 18.255 29.955 1.00 0.00 C +ATOM 50 OH TYR 3 21.067 17.032 30.153 1.00 0.00 O +ATOM 51 HH TYR 3 21.748 16.362 30.246 1.00 0.00 H +ATOM 52 CE2 TYR 3 20.696 19.298 30.117 1.00 0.00 C +ATOM 53 HE2 TYR 3 19.637 19.140 30.255 1.00 0.00 H +ATOM 54 CD2 TYR 3 21.206 20.578 29.890 1.00 0.00 C +ATOM 55 HD2 TYR 3 20.529 21.419 29.917 1.00 0.00 H +ATOM 56 C TYR 3 24.039 24.405 30.167 1.00 0.00 C +ATOM 57 O TYR 3 23.297 25.348 29.768 1.00 0.00 O +ATOM 58 N LYS 4 25.372 24.554 30.210 1.00 0.00 N +ATOM 59 H LYS 4 25.973 23.885 30.670 1.00 0.00 H +ATOM 60 CA LYS 4 26.009 25.877 30.108 1.00 0.00 C +ATOM 61 HA LYS 4 25.483 26.628 30.698 1.00 0.00 H +ATOM 62 CB LYS 4 27.442 25.772 30.722 1.00 0.00 C +ATOM 63 HB2 LYS 4 28.042 24.887 30.512 1.00 0.00 H +ATOM 64 HB3 LYS 4 27.997 26.600 30.282 1.00 0.00 H +ATOM 65 CG LYS 4 27.424 26.165 32.257 1.00 0.00 C +ATOM 66 HG2 LYS 4 28.448 26.507 32.406 1.00 0.00 H +ATOM 67 HG3 LYS 4 26.827 27.062 32.422 1.00 0.00 H +ATOM 68 CD LYS 4 27.081 25.084 33.281 1.00 0.00 C +ATOM 69 HD2 LYS 4 27.049 25.675 34.196 1.00 0.00 H +ATOM 70 HD3 LYS 4 26.102 24.658 33.063 1.00 0.00 H +ATOM 71 CE LYS 4 28.142 23.936 33.177 1.00 0.00 C +ATOM 72 HE2 LYS 4 27.837 23.378 32.292 1.00 0.00 H +ATOM 73 HE3 LYS 4 29.152 24.339 33.095 1.00 0.00 H +ATOM 74 NZ LYS 4 28.141 23.088 34.355 1.00 0.00 N +ATOM 75 HZ1 LYS 4 27.251 22.620 34.456 1.00 0.00 H +ATOM 76 HZ2 LYS 4 28.426 23.661 35.135 1.00 0.00 H +ATOM 77 HZ3 LYS 4 28.761 22.298 34.247 1.00 0.00 H +ATOM 78 C LYS 4 26.052 26.257 28.608 1.00 0.00 C +ATOM 79 O LYS 4 26.156 25.360 27.710 1.00 0.00 O +ATOM 80 N HX1 5 26.178 27.584 28.396 1.00 0.00 N +ATOM 81 CA HX1 5 26.497 28.172 27.111 1.00 0.00 C +ATOM 82 C HX1 5 27.377 29.335 27.450 1.00 0.00 C +ATOM 83 O HX1 5 27.065 30.244 28.318 1.00 0.00 O +ATOM 84 CB HX1 5 25.226 28.607 26.448 1.00 0.00 C +ATOM 85 CG HX1 5 25.266 29.370 25.169 1.00 0.00 C +ATOM 86 CD2 HX1 5 26.324 29.462 24.211 1.00 0.00 C +ATOM 87 ND1 HX1 5 24.160 30.090 24.771 1.00 0.00 N +ATOM 88 CE1 HX1 5 24.529 30.633 23.568 1.00 0.00 C +ATOM 89 NE2 HX1 5 25.790 30.311 23.222 1.00 0.00 N +ATOM 90 H HX1 5 26.110 28.240 29.161 1.00 0.00 H +ATOM 91 HA HX1 5 26.930 27.449 26.420 1.00 0.00 H +ATOM 92 HB2 HX1 5 24.716 29.197 27.210 1.00 0.00 H +ATOM 93 HB3 HX1 5 24.696 27.665 26.304 1.00 0.00 H +ATOM 94 HD2 HX1 5 27.284 28.974 24.294 1.00 0.00 H +ATOM 95 HE1 HX1 5 23.833 31.188 22.956 1.00 0.00 H +ATOM 96 HE2 HX1 5 26.263 30.623 22.386 1.00 0.00 H +ATOM 97 N ILE 6 28.598 29.276 26.855 1.00 0.00 N +ATOM 98 H ILE 6 28.857 28.416 26.392 1.00 0.00 H +ATOM 99 CA ILE 6 29.626 30.307 26.802 1.00 0.00 C +ATOM 100 HA ILE 6 29.600 31.006 27.638 1.00 0.00 H +ATOM 101 CB ILE 6 31.120 29.685 26.627 1.00 0.00 C +ATOM 102 HB ILE 6 31.158 28.921 25.850 1.00 0.00 H +ATOM 103 CG2 ILE 6 32.300 30.753 26.467 1.00 0.00 C +ATOM 104 HG21 ILE 6 32.095 31.481 25.682 1.00 0.00 H +ATOM 105 HG22 ILE 6 33.175 30.190 26.142 1.00 0.00 H +ATOM 106 HG23 ILE 6 32.716 31.139 27.397 1.00 0.00 H +ATOM 107 CG1 ILE 6 31.419 28.817 27.890 1.00 0.00 C +ATOM 108 HG12 ILE 6 31.452 29.429 28.791 1.00 0.00 H +ATOM 109 HG13 ILE 6 30.594 28.113 28.000 1.00 0.00 H +ATOM 110 CD1 ILE 6 32.714 28.001 27.759 1.00 0.00 C +ATOM 111 HD11 ILE 6 32.874 27.223 28.505 1.00 0.00 H +ATOM 112 HD12 ILE 6 33.575 28.669 27.737 1.00 0.00 H +ATOM 113 HD13 ILE 6 32.904 27.576 26.773 1.00 0.00 H +ATOM 114 C ILE 6 29.341 31.281 25.638 1.00 0.00 C +ATOM 115 O ILE 6 29.001 30.826 24.562 1.00 0.00 O +ATOM 116 N VAL 7 29.472 32.561 25.913 1.00 0.00 N +ATOM 117 H VAL 7 29.962 32.798 26.764 1.00 0.00 H +ATOM 118 CA VAL 7 29.175 33.598 24.887 1.00 0.00 C +ATOM 119 HA VAL 7 28.157 33.371 24.571 1.00 0.00 H +ATOM 120 CB VAL 7 29.074 34.991 25.607 1.00 0.00 C +ATOM 121 HB VAL 7 30.004 35.243 26.117 1.00 0.00 H +ATOM 122 CG1 VAL 7 28.783 36.014 24.629 1.00 0.00 C +ATOM 123 HG11 VAL 7 29.734 36.331 24.200 1.00 0.00 H +ATOM 124 HG12 VAL 7 27.987 35.750 23.934 1.00 0.00 H +ATOM 125 HG13 VAL 7 28.497 36.931 25.143 1.00 0.00 H +ATOM 126 CG2 VAL 7 27.965 35.048 26.731 1.00 0.00 C +ATOM 127 HG21 VAL 7 28.212 35.693 27.574 1.00 0.00 H +ATOM 128 HG22 VAL 7 26.969 35.348 26.406 1.00 0.00 H +ATOM 129 HG23 VAL 7 27.760 34.035 27.078 1.00 0.00 H +ATOM 130 C VAL 7 30.240 33.509 23.800 1.00 0.00 C +ATOM 131 O VAL 7 31.380 33.316 24.021 1.00 0.00 O +ATOM 132 N ASN 8 29.853 33.916 22.563 1.00 0.00 N +ATOM 133 H ASN 8 28.879 34.164 22.464 1.00 0.00 H +ATOM 134 CA ASN 8 30.639 34.086 21.389 1.00 0.00 C +ATOM 135 HA ASN 8 31.347 33.257 21.415 1.00 0.00 H +ATOM 136 CB ASN 8 29.792 33.770 20.198 1.00 0.00 C +ATOM 137 HB2 ASN 8 30.326 33.273 19.388 1.00 0.00 H +ATOM 138 HB3 ASN 8 28.953 33.152 20.515 1.00 0.00 H +ATOM 139 CG ASN 8 29.080 35.048 19.743 1.00 0.00 C +ATOM 140 OD1 ASN 8 29.690 36.015 19.213 1.00 0.00 O +ATOM 141 ND2 ASN 8 27.754 35.169 19.876 1.00 0.00 N +ATOM 142 HD21 ASN 8 27.261 34.336 20.165 1.00 0.00 H +ATOM 143 HD22 ASN 8 27.205 35.897 19.441 1.00 0.00 H +ATOM 144 C ASN 8 31.481 35.414 21.350 1.00 0.00 C +ATOM 145 O ASN 8 31.299 36.260 22.205 1.00 0.00 O +ATOM 146 N GLY 9 32.414 35.480 20.438 1.00 0.00 N +ATOM 147 H GLY 9 32.585 34.713 19.803 1.00 0.00 H +ATOM 148 CA GLY 9 33.449 36.486 20.523 1.00 0.00 C +ATOM 149 HA2 GLY 9 33.880 36.506 21.524 1.00 0.00 H +ATOM 150 HA3 GLY 9 34.241 36.217 19.824 1.00 0.00 H +ATOM 151 C GLY 9 32.982 37.897 20.123 1.00 0.00 C +ATOM 152 O GLY 9 33.797 38.817 20.060 1.00 0.00 O +ATOM 153 N LYS 10 31.681 38.084 19.820 1.00 0.00 N +ATOM 154 H LYS 10 31.030 37.324 19.954 1.00 0.00 H +ATOM 155 CA LYS 10 31.216 39.398 19.283 1.00 0.00 C +ATOM 156 HA LYS 10 31.962 39.851 18.630 1.00 0.00 H +ATOM 157 CB LYS 10 29.913 39.153 18.439 1.00 0.00 C +ATOM 158 HB2 LYS 10 29.295 38.484 19.038 1.00 0.00 H +ATOM 159 HB3 LYS 10 29.361 40.086 18.332 1.00 0.00 H +ATOM 160 CG LYS 10 30.114 38.549 17.073 1.00 0.00 C +ATOM 161 HG2 LYS 10 30.646 39.276 16.459 1.00 0.00 H +ATOM 162 HG3 LYS 10 30.759 37.671 17.064 1.00 0.00 H +ATOM 163 CD LYS 10 28.835 38.090 16.405 1.00 0.00 C +ATOM 164 HD2 LYS 10 28.279 37.394 17.033 1.00 0.00 H +ATOM 165 HD3 LYS 10 28.195 38.929 16.131 1.00 0.00 H +ATOM 166 CE LYS 10 29.178 37.345 15.187 1.00 0.00 C +ATOM 167 HE2 LYS 10 29.944 37.895 14.642 1.00 0.00 H +ATOM 168 HE3 LYS 10 29.570 36.357 15.427 1.00 0.00 H +ATOM 169 NZ LYS 10 27.977 37.103 14.322 1.00 0.00 N +ATOM 170 HZ1 LYS 10 28.062 36.425 13.579 1.00 0.00 H +ATOM 171 HZ2 LYS 10 27.666 37.945 13.860 1.00 0.00 H +ATOM 172 HZ3 LYS 10 27.195 36.749 14.856 1.00 0.00 H +ATOM 173 C LYS 10 30.860 40.453 20.270 1.00 0.00 C +ATOM 174 O LYS 10 30.736 41.607 19.932 1.00 0.00 O +ATOM 175 N THR 11 30.803 40.102 21.506 1.00 0.00 N +ATOM 176 H THR 11 31.268 39.220 21.669 1.00 0.00 H +ATOM 177 CA THR 11 30.255 40.947 22.648 1.00 0.00 C +ATOM 178 HA THR 11 30.276 42.001 22.372 1.00 0.00 H +ATOM 179 CB THR 11 28.743 40.659 22.796 1.00 0.00 C +ATOM 180 HB THR 11 28.305 40.770 21.804 1.00 0.00 H +ATOM 181 CG2 THR 11 28.458 39.312 23.291 1.00 0.00 C +ATOM 182 HG21 THR 11 27.425 38.968 23.240 1.00 0.00 H +ATOM 183 HG22 THR 11 28.796 39.116 24.308 1.00 0.00 H +ATOM 184 HG23 THR 11 29.125 38.706 22.677 1.00 0.00 H +ATOM 185 OG1 THR 11 28.076 41.622 23.480 1.00 0.00 O +ATOM 186 HG1 THR 11 28.270 42.455 23.045 1.00 0.00 H +ATOM 187 C THR 11 31.092 40.834 23.928 1.00 0.00 C +ATOM 188 O THR 11 32.196 40.287 23.960 1.00 0.00 O +ATOM 189 N LEU 12 30.712 41.537 25.002 1.00 0.00 N +ATOM 190 H LEU 12 29.733 41.783 24.979 1.00 0.00 H +ATOM 191 CA LEU 12 31.221 41.506 26.293 1.00 0.00 C +ATOM 192 HA LEU 12 32.239 41.895 26.278 1.00 0.00 H +ATOM 193 CB LEU 12 30.444 42.503 27.187 1.00 0.00 C +ATOM 194 HB2 LEU 12 29.383 42.253 27.198 1.00 0.00 H +ATOM 195 HB3 LEU 12 30.890 42.407 28.177 1.00 0.00 H +ATOM 196 CG LEU 12 30.478 44.041 26.838 1.00 0.00 C +ATOM 197 HG LEU 12 31.488 44.448 26.882 1.00 0.00 H +ATOM 198 CD1 LEU 12 29.869 44.454 25.576 1.00 0.00 C +ATOM 199 HD11 LEU 12 30.272 43.952 24.696 1.00 0.00 H +ATOM 200 HD12 LEU 12 29.881 45.535 25.442 1.00 0.00 H +ATOM 201 HD13 LEU 12 28.779 44.429 25.587 1.00 0.00 H +ATOM 202 CD2 LEU 12 29.666 44.803 27.880 1.00 0.00 C +ATOM 203 HD21 LEU 12 30.045 44.585 28.879 1.00 0.00 H +ATOM 204 HD22 LEU 12 28.625 44.518 27.729 1.00 0.00 H +ATOM 205 HD23 LEU 12 29.773 45.841 27.566 1.00 0.00 H +ATOM 206 C LEU 12 31.254 40.018 26.771 1.00 0.00 C +ATOM 207 O LEU 12 30.423 39.136 26.538 1.00 0.00 O +ATOM 208 N LYS 13 32.319 39.676 27.543 1.00 0.00 N +ATOM 209 H LYS 13 32.945 40.415 27.831 1.00 0.00 H +ATOM 210 CA LYS 13 32.561 38.252 27.962 1.00 0.00 C +ATOM 211 HA LYS 13 32.443 37.613 27.087 1.00 0.00 H +ATOM 212 CB LYS 13 34.012 38.072 28.450 1.00 0.00 C +ATOM 213 HB2 LYS 13 34.047 36.996 28.622 1.00 0.00 H +ATOM 214 HB3 LYS 13 34.678 38.465 27.682 1.00 0.00 H +ATOM 215 CG LYS 13 34.260 38.831 29.771 1.00 0.00 C +ATOM 216 HG2 LYS 13 34.064 39.896 29.651 1.00 0.00 H +ATOM 217 HG3 LYS 13 33.509 38.467 30.472 1.00 0.00 H +ATOM 218 CD LYS 13 35.673 38.817 30.378 1.00 0.00 C +ATOM 219 HD2 LYS 13 36.084 37.809 30.442 1.00 0.00 H +ATOM 220 HD3 LYS 13 36.244 39.347 29.616 1.00 0.00 H +ATOM 221 CE LYS 13 35.736 39.521 31.761 1.00 0.00 C +ATOM 222 HE2 LYS 13 36.786 39.671 32.009 1.00 0.00 H +ATOM 223 HE3 LYS 13 35.301 40.519 31.706 1.00 0.00 H +ATOM 224 NZ LYS 13 35.049 38.598 32.768 1.00 0.00 N +ATOM 225 HZ1 LYS 13 35.149 38.976 33.700 1.00 0.00 H +ATOM 226 HZ2 LYS 13 35.603 37.756 32.824 1.00 0.00 H +ATOM 227 HZ3 LYS 13 34.104 38.296 32.583 1.00 0.00 H +ATOM 228 C LYS 13 31.490 37.799 28.992 1.00 0.00 C +ATOM 229 O LYS 13 30.921 38.707 29.666 1.00 0.00 O +ATOM 230 N GLY 14 31.263 36.527 29.009 1.00 0.00 N +ATOM 231 H GLY 14 31.812 35.931 28.406 1.00 0.00 H +ATOM 232 CA GLY 14 30.120 35.841 29.762 1.00 0.00 C +ATOM 233 HA2 GLY 14 30.230 36.260 30.762 1.00 0.00 H +ATOM 234 HA3 GLY 14 29.164 36.295 29.498 1.00 0.00 H +ATOM 235 C GLY 14 30.076 34.229 29.662 1.00 0.00 C +ATOM 236 O GLY 14 30.337 33.719 28.571 1.00 0.00 O +ATOM 237 N VAL 15 29.695 33.661 30.827 1.00 0.00 N +ATOM 238 H VAL 15 29.463 34.358 31.520 1.00 0.00 H +ATOM 239 CA VAL 15 29.198 32.291 30.946 1.00 0.00 C +ATOM 240 HA VAL 15 29.005 31.895 29.950 1.00 0.00 H +ATOM 241 CB VAL 15 30.173 31.338 31.624 1.00 0.00 C +ATOM 242 HB VAL 15 30.282 31.673 32.656 1.00 0.00 H +ATOM 243 CG1 VAL 15 29.744 29.889 31.429 1.00 0.00 C +ATOM 244 HG11 VAL 15 30.012 29.602 30.412 1.00 0.00 H +ATOM 245 HG12 VAL 15 30.262 29.253 32.147 1.00 0.00 H +ATOM 246 HG13 VAL 15 28.666 29.759 31.526 1.00 0.00 H +ATOM 247 CG2 VAL 15 31.576 31.423 30.906 1.00 0.00 C +ATOM 248 HG21 VAL 15 31.677 31.242 29.835 1.00 0.00 H +ATOM 249 HG22 VAL 15 32.001 32.397 31.148 1.00 0.00 H +ATOM 250 HG23 VAL 15 32.194 30.691 31.426 1.00 0.00 H +ATOM 251 C VAL 15 27.830 32.324 31.644 1.00 0.00 C +ATOM 252 O VAL 15 27.685 32.810 32.783 1.00 0.00 O +ATOM 253 N HY1 16 26.825 31.706 30.991 1.00 0.00 N +ATOM 254 CA HY1 16 25.497 31.527 31.569 1.00 0.00 C +ATOM 255 C HY1 16 25.043 30.121 31.341 1.00 0.00 C +ATOM 256 O HY1 16 25.694 29.318 30.692 1.00 0.00 O +ATOM 257 CB HY1 16 24.526 32.575 31.066 1.00 0.00 C +ATOM 258 CG HY1 16 24.409 32.534 29.594 1.00 0.00 C +ATOM 259 CD2 HY1 16 23.426 31.904 28.864 1.00 0.00 C +ATOM 260 ND1 HY1 16 25.285 33.039 28.694 1.00 0.00 N +ATOM 261 CE1 HY1 16 24.816 32.755 27.510 1.00 0.00 C +ATOM 262 NE2 HY1 16 23.688 31.973 27.533 1.00 0.00 N +ATOM 263 H HY1 16 26.986 31.239 30.111 1.00 0.00 H +ATOM 264 HA HY1 16 25.595 31.584 32.653 1.00 0.00 H +ATOM 265 HB2 HY1 16 23.545 32.291 31.448 1.00 0.00 H +ATOM 266 HB3 HY1 16 24.710 33.553 31.511 1.00 0.00 H +ATOM 267 HD1 HY1 16 26.121 33.557 28.926 1.00 0.00 H +ATOM 268 HD2 HY1 16 22.638 31.331 29.330 1.00 0.00 H +ATOM 269 HE1 HY1 16 25.250 33.016 26.556 1.00 0.00 H +ATOM 270 N THR 17 23.863 29.732 31.821 1.00 0.00 N +ATOM 271 H THR 17 23.383 30.385 32.423 1.00 0.00 H +ATOM 272 CA THR 17 23.410 28.363 31.679 1.00 0.00 C +ATOM 273 HA THR 17 23.905 28.022 30.770 1.00 0.00 H +ATOM 274 CB THR 17 23.733 27.559 33.044 1.00 0.00 C +ATOM 275 HB THR 17 24.661 27.833 33.545 1.00 0.00 H +ATOM 276 CG2 THR 17 22.577 27.671 34.071 1.00 0.00 C +ATOM 277 HG21 THR 17 21.669 27.145 33.776 1.00 0.00 H +ATOM 278 HG22 THR 17 22.463 28.742 34.237 1.00 0.00 H +ATOM 279 HG23 THR 17 22.761 27.302 35.081 1.00 0.00 H +ATOM 280 OG1 THR 17 23.722 26.161 32.773 1.00 0.00 O +ATOM 281 HG1 THR 17 23.959 25.688 33.574 1.00 0.00 H +ATOM 282 C THR 17 21.907 28.337 31.306 1.00 0.00 C +ATOM 283 O THR 17 21.221 29.378 31.497 1.00 0.00 O +ATOM 284 N HY2 18 21.388 27.265 30.728 1.00 0.00 N +ATOM 285 CA HY2 18 19.963 27.076 30.262 1.00 0.00 C +ATOM 286 C HY2 18 19.420 25.690 30.715 1.00 0.00 C +ATOM 287 O HY2 18 20.189 24.778 30.765 1.00 0.00 O +ATOM 288 CB HY2 18 19.962 27.090 28.645 1.00 0.00 C +ATOM 289 CG HY2 18 20.377 28.465 28.066 1.00 0.00 C +ATOM 290 CD2 HY2 18 21.402 28.687 27.254 1.00 0.00 C +ATOM 291 ND1 HY2 18 19.736 29.697 28.285 1.00 0.00 N +ATOM 292 CE1 HY2 18 20.483 30.619 27.688 1.00 0.00 C +ATOM 293 NE2 HY2 18 21.432 30.063 26.974 1.00 0.00 N +ATOM 294 H HY2 18 21.968 26.462 30.535 1.00 0.00 H +ATOM 295 HA HY2 18 19.280 27.775 30.746 1.00 0.00 H +ATOM 296 HB2 HY2 18 20.498 26.232 28.239 1.00 0.00 H +ATOM 297 HB3 HY2 18 18.930 27.139 28.298 1.00 0.00 H +ATOM 298 HD1 HY2 18 19.021 29.920 28.963 1.00 0.00 H +ATOM 299 HD2 HY2 18 22.199 28.030 26.937 1.00 0.00 H +ATOM 300 HE1 HY2 18 20.343 31.686 27.778 1.00 0.00 H +ATOM 301 N GLU 19 18.202 25.676 31.139 1.00 0.00 N +ATOM 302 H GLU 19 17.654 26.498 30.928 1.00 0.00 H +ATOM 303 CA GLU 19 17.426 24.502 31.512 1.00 0.00 C +ATOM 304 HA GLU 19 17.995 23.858 32.183 1.00 0.00 H +ATOM 305 CB GLU 19 16.168 24.972 32.169 1.00 0.00 C +ATOM 306 HB2 GLU 19 16.430 25.617 33.008 1.00 0.00 H +ATOM 307 HB3 GLU 19 15.630 25.568 31.432 1.00 0.00 H +ATOM 308 CG GLU 19 15.227 23.813 32.682 1.00 0.00 C +ATOM 309 HG2 GLU 19 14.532 24.279 33.381 1.00 0.00 H +ATOM 310 HG3 GLU 19 14.714 23.376 31.826 1.00 0.00 H +ATOM 311 CD GLU 19 15.822 22.675 33.502 1.00 0.00 C +ATOM 312 OE1 GLU 19 16.764 22.897 34.327 1.00 0.00 O +ATOM 313 OE2 GLU 19 15.276 21.515 33.407 1.00 0.00 O +ATOM 314 C GLU 19 16.987 23.695 30.273 1.00 0.00 C +ATOM 315 O GLU 19 16.642 24.283 29.264 1.00 0.00 O +ATOM 316 N ALA 20 16.977 22.400 30.247 1.00 0.00 N +ATOM 317 H ALA 20 17.472 21.939 30.997 1.00 0.00 H +ATOM 318 CA ALA 20 16.393 21.603 29.130 1.00 0.00 C +ATOM 319 HA ALA 20 15.374 21.897 28.881 1.00 0.00 H +ATOM 320 CB ALA 20 17.350 21.588 27.983 1.00 0.00 C +ATOM 321 HB1 ALA 20 18.071 20.783 28.126 1.00 0.00 H +ATOM 322 HB2 ALA 20 17.842 22.527 27.731 1.00 0.00 H +ATOM 323 HB3 ALA 20 16.766 21.439 27.074 1.00 0.00 H +ATOM 324 C ALA 20 16.129 20.120 29.735 1.00 0.00 C +ATOM 325 O ALA 20 16.831 19.769 30.702 1.00 0.00 O +ATOM 326 N VAL 21 15.217 19.371 29.105 1.00 0.00 N +ATOM 327 H VAL 21 14.583 19.841 28.475 1.00 0.00 H +ATOM 328 CA VAL 21 14.885 17.960 29.383 1.00 0.00 C +ATOM 329 HA VAL 21 14.826 17.713 30.443 1.00 0.00 H +ATOM 330 CB VAL 21 13.574 17.535 28.718 1.00 0.00 C +ATOM 331 HB VAL 21 12.926 18.251 29.223 1.00 0.00 H +ATOM 332 CG1 VAL 21 13.625 17.532 27.170 1.00 0.00 C +ATOM 333 HG11 VAL 21 12.722 17.882 26.670 1.00 0.00 H +ATOM 334 HG12 VAL 21 13.942 16.577 26.752 1.00 0.00 H +ATOM 335 HG13 VAL 21 14.327 18.242 26.732 1.00 0.00 H +ATOM 336 CG2 VAL 21 13.077 16.135 29.068 1.00 0.00 C +ATOM 337 HG21 VAL 21 12.075 16.062 28.643 1.00 0.00 H +ATOM 338 HG22 VAL 21 13.031 16.083 30.155 1.00 0.00 H +ATOM 339 HG23 VAL 21 13.703 15.316 28.713 1.00 0.00 H +ATOM 340 C VAL 21 16.029 17.017 29.043 1.00 0.00 C +ATOM 341 O VAL 21 16.159 15.913 29.649 1.00 0.00 O +ATOM 342 N ASP 22 16.889 17.357 28.069 1.00 0.00 N +ATOM 343 H ASP 22 16.813 18.234 27.574 1.00 0.00 H +ATOM 344 CA ASP 22 18.070 16.500 27.763 1.00 0.00 C +ATOM 345 HA ASP 22 18.541 16.102 28.661 1.00 0.00 H +ATOM 346 CB ASP 22 17.525 15.337 26.822 1.00 0.00 C +ATOM 347 HB2 ASP 22 16.862 14.679 27.383 1.00 0.00 H +ATOM 348 HB3 ASP 22 16.954 15.783 26.008 1.00 0.00 H +ATOM 349 CG ASP 22 18.683 14.539 26.325 1.00 0.00 C +ATOM 350 OD1 ASP 22 18.866 14.417 25.050 1.00 0.00 O +ATOM 351 OD2 ASP 22 19.537 14.161 27.164 1.00 0.00 O +ATOM 352 C ASP 22 19.125 17.255 26.991 1.00 0.00 C +ATOM 353 O ASP 22 18.873 18.356 26.483 1.00 0.00 O +ATOM 354 N ALA 23 20.426 16.801 26.897 1.00 0.00 N +ATOM 355 H ALA 23 20.718 15.906 27.265 1.00 0.00 H +ATOM 356 CA ALA 23 21.500 17.509 26.164 1.00 0.00 C +ATOM 357 HA ALA 23 21.559 18.531 26.536 1.00 0.00 H +ATOM 358 CB ALA 23 22.838 16.786 26.514 1.00 0.00 C +ATOM 359 HB1 ALA 23 22.868 15.803 26.043 1.00 0.00 H +ATOM 360 HB2 ALA 23 22.762 16.756 27.601 1.00 0.00 H +ATOM 361 HB3 ALA 23 23.719 17.342 26.194 1.00 0.00 H +ATOM 362 C ALA 23 21.251 17.580 24.556 1.00 0.00 C +ATOM 363 O ALA 23 21.707 18.488 23.892 1.00 0.00 O +ATOM 364 N ALA 24 20.439 16.643 23.952 1.00 0.00 N +ATOM 365 H ALA 24 20.008 15.945 24.540 1.00 0.00 H +ATOM 366 CA ALA 24 19.944 16.826 22.622 1.00 0.00 C +ATOM 367 HA ALA 24 20.702 17.114 21.893 1.00 0.00 H +ATOM 368 CB ALA 24 19.315 15.489 22.113 1.00 0.00 C +ATOM 369 HB1 ALA 24 20.104 14.737 22.128 1.00 0.00 H +ATOM 370 HB2 ALA 24 19.006 15.562 21.070 1.00 0.00 H +ATOM 371 HB3 ALA 24 18.471 15.225 22.750 1.00 0.00 H +ATOM 372 C ALA 24 18.864 17.986 22.550 1.00 0.00 C +ATOM 373 O ALA 24 18.743 18.547 21.444 1.00 0.00 O +ATOM 374 N GLU 25 18.097 18.339 23.616 1.00 0.00 N +ATOM 375 H GLU 25 18.372 17.893 24.479 1.00 0.00 H +ATOM 376 CA GLU 25 17.185 19.467 23.575 1.00 0.00 C +ATOM 377 HA GLU 25 16.871 19.636 22.545 1.00 0.00 H +ATOM 378 CB GLU 25 16.046 19.162 24.534 1.00 0.00 C +ATOM 379 HB2 GLU 25 15.741 18.170 24.199 1.00 0.00 H +ATOM 380 HB3 GLU 25 16.404 18.958 25.543 1.00 0.00 H +ATOM 381 CG GLU 25 14.960 20.248 24.623 1.00 0.00 C +ATOM 382 HG2 GLU 25 14.222 19.972 25.376 1.00 0.00 H +ATOM 383 HG3 GLU 25 15.450 21.172 24.933 1.00 0.00 H +ATOM 384 CD GLU 25 14.138 20.497 23.329 1.00 0.00 C +ATOM 385 OE1 GLU 25 13.846 21.682 23.056 1.00 0.00 O +ATOM 386 OE2 GLU 25 13.909 19.591 22.465 1.00 0.00 O +ATOM 387 C GLU 25 17.914 20.767 24.022 1.00 0.00 C +ATOM 388 O GLU 25 17.526 21.828 23.602 1.00 0.00 O +ATOM 389 N ALA 26 18.976 20.617 24.820 1.00 0.00 N +ATOM 390 H ALA 26 19.101 19.767 25.352 1.00 0.00 H +ATOM 391 CA ALA 26 19.865 21.693 25.389 1.00 0.00 C +ATOM 392 HA ALA 26 19.324 22.499 25.886 1.00 0.00 H +ATOM 393 CB ALA 26 20.797 21.027 26.375 1.00 0.00 C +ATOM 394 HB1 ALA 26 21.518 20.403 25.846 1.00 0.00 H +ATOM 395 HB2 ALA 26 20.254 20.494 27.154 1.00 0.00 H +ATOM 396 HB3 ALA 26 21.420 21.810 26.807 1.00 0.00 H +ATOM 397 C ALA 26 20.668 22.456 24.311 1.00 0.00 C +ATOM 398 O ALA 26 21.275 23.487 24.576 1.00 0.00 O +ATOM 399 N GLU 27 20.740 21.951 23.084 1.00 0.00 N +ATOM 400 H GLU 27 20.347 21.041 22.887 1.00 0.00 H +ATOM 401 CA GLU 27 21.691 22.414 22.078 1.00 0.00 C +ATOM 402 HA GLU 27 22.645 22.780 22.457 1.00 0.00 H +ATOM 403 CB GLU 27 21.981 21.300 21.088 1.00 0.00 C +ATOM 404 HB2 GLU 27 22.709 21.787 20.438 1.00 0.00 H +ATOM 405 HB3 GLU 27 22.272 20.420 21.662 1.00 0.00 H +ATOM 406 CG GLU 27 20.816 20.898 20.185 1.00 0.00 C +ATOM 407 HG2 GLU 27 19.967 20.658 20.825 1.00 0.00 H +ATOM 408 HG3 GLU 27 20.411 21.747 19.635 1.00 0.00 H +ATOM 409 CD GLU 27 20.978 19.710 19.215 1.00 0.00 C +ATOM 410 OE1 GLU 27 20.163 19.668 18.267 1.00 0.00 O +ATOM 411 OE2 GLU 27 21.818 18.802 19.372 1.00 0.00 O +ATOM 412 C GLU 27 21.110 23.584 21.377 1.00 0.00 C +ATOM 413 O GLU 27 21.771 24.415 20.799 1.00 0.00 O +ATOM 414 N LYS 28 19.764 23.808 21.295 1.00 0.00 N +ATOM 415 H LYS 28 19.212 23.178 21.861 1.00 0.00 H +ATOM 416 CA LYS 28 19.088 24.686 20.352 1.00 0.00 C +ATOM 417 HA LYS 28 19.277 24.422 19.312 1.00 0.00 H +ATOM 418 CB LYS 28 17.604 24.557 20.519 1.00 0.00 C +ATOM 419 HB2 LYS 28 17.368 24.874 21.535 1.00 0.00 H +ATOM 420 HB3 LYS 28 17.145 25.332 19.905 1.00 0.00 H +ATOM 421 CG LYS 28 17.094 23.167 20.149 1.00 0.00 C +ATOM 422 HG2 LYS 28 17.524 22.966 19.168 1.00 0.00 H +ATOM 423 HG3 LYS 28 17.358 22.461 20.936 1.00 0.00 H +ATOM 424 CD LYS 28 15.587 23.383 20.054 1.00 0.00 C +ATOM 425 HD2 LYS 28 15.394 23.651 21.093 1.00 0.00 H +ATOM 426 HD3 LYS 28 15.250 24.148 19.354 1.00 0.00 H +ATOM 427 CE LYS 28 15.058 21.965 19.703 1.00 0.00 C +ATOM 428 HE2 LYS 28 15.120 21.876 18.619 1.00 0.00 H +ATOM 429 HE3 LYS 28 15.630 21.137 20.121 1.00 0.00 H +ATOM 430 NZ LYS 28 13.736 21.761 20.219 1.00 0.00 N +ATOM 431 HZ1 LYS 28 13.354 20.856 19.986 1.00 0.00 H +ATOM 432 HZ2 LYS 28 13.100 22.428 19.807 1.00 0.00 H +ATOM 433 HZ3 LYS 28 13.770 21.846 21.225 1.00 0.00 H +ATOM 434 C LYS 28 19.480 26.204 20.590 1.00 0.00 C +ATOM 435 O LYS 28 19.527 26.976 19.620 1.00 0.00 O +ATOM 436 N PHE 29 19.735 26.691 21.835 1.00 0.00 N +ATOM 437 H PHE 29 19.451 26.042 22.555 1.00 0.00 H +ATOM 438 CA PHE 29 20.307 28.002 22.160 1.00 0.00 C +ATOM 439 HA PHE 29 19.612 28.805 21.912 1.00 0.00 H +ATOM 440 CB PHE 29 20.443 28.078 23.680 1.00 0.00 C +ATOM 441 HB2 PHE 29 21.363 27.529 23.881 1.00 0.00 H +ATOM 442 HB3 PHE 29 20.643 29.126 23.900 1.00 0.00 H +ATOM 443 CG PHE 29 19.255 27.546 24.446 1.00 0.00 C +ATOM 444 CD1 PHE 29 18.092 28.318 24.805 1.00 0.00 C +ATOM 445 HD1 PHE 29 18.199 29.386 24.685 1.00 0.00 H +ATOM 446 CE1 PHE 29 17.023 27.807 25.495 1.00 0.00 C +ATOM 447 HE1 PHE 29 16.367 28.550 25.923 1.00 0.00 H +ATOM 448 CZ PHE 29 16.981 26.407 25.793 1.00 0.00 C +ATOM 449 HZ PHE 29 16.064 26.058 26.243 1.00 0.00 H +ATOM 450 CE2 PHE 29 18.061 25.619 25.428 1.00 0.00 C +ATOM 451 HE2 PHE 29 18.092 24.573 25.695 1.00 0.00 H +ATOM 452 CD2 PHE 29 19.214 26.135 24.745 1.00 0.00 C +ATOM 453 HD2 PHE 29 20.004 25.494 24.382 1.00 0.00 H +ATOM 454 C PHE 29 21.680 28.326 21.565 1.00 0.00 C +ATOM 455 O PHE 29 21.956 29.473 21.265 1.00 0.00 O +ATOM 456 N THR 30 22.535 27.289 21.324 1.00 0.00 N +ATOM 457 H THR 30 22.210 26.425 21.733 1.00 0.00 H +ATOM 458 CA THR 30 23.847 27.396 20.702 1.00 0.00 C +ATOM 459 HA THR 30 24.216 28.410 20.855 1.00 0.00 H +ATOM 460 CB THR 30 24.901 26.635 21.466 1.00 0.00 C +ATOM 461 HB THR 30 24.668 25.570 21.485 1.00 0.00 H +ATOM 462 CG2 THR 30 26.350 26.713 21.035 1.00 0.00 C +ATOM 463 HG21 THR 30 26.414 26.212 20.068 1.00 0.00 H +ATOM 464 HG22 THR 30 26.625 27.767 21.037 1.00 0.00 H +ATOM 465 HG23 THR 30 26.976 26.197 21.763 1.00 0.00 H +ATOM 466 OG1 THR 30 24.812 27.136 22.805 1.00 0.00 O +ATOM 467 HG1 THR 30 24.166 26.577 23.243 1.00 0.00 H +ATOM 468 C THR 30 23.805 26.944 19.277 1.00 0.00 C +ATOM 469 O THR 30 24.633 27.378 18.436 1.00 0.00 O +ATOM 470 N LYS 31 22.689 26.359 18.776 1.00 0.00 N +ATOM 471 H LYS 31 22.185 25.818 19.465 1.00 0.00 H +ATOM 472 CA LYS 31 22.424 26.332 17.314 1.00 0.00 C +ATOM 473 HA LYS 31 23.386 26.270 16.804 1.00 0.00 H +ATOM 474 CB LYS 31 21.463 25.222 16.853 1.00 0.00 C +ATOM 475 HB2 LYS 31 20.540 25.313 17.425 1.00 0.00 H +ATOM 476 HB3 LYS 31 21.244 25.397 15.799 1.00 0.00 H +ATOM 477 CG LYS 31 22.193 23.835 17.001 1.00 0.00 C +ATOM 478 HG2 LYS 31 23.042 23.867 16.318 1.00 0.00 H +ATOM 479 HG3 LYS 31 22.382 23.759 18.072 1.00 0.00 H +ATOM 480 CD LYS 31 21.257 22.569 16.677 1.00 0.00 C +ATOM 481 HD2 LYS 31 21.865 21.670 16.772 1.00 0.00 H +ATOM 482 HD3 LYS 31 20.496 22.558 17.457 1.00 0.00 H +ATOM 483 CE LYS 31 20.576 22.601 15.316 1.00 0.00 C +ATOM 484 HE2 LYS 31 20.128 21.611 15.228 1.00 0.00 H +ATOM 485 HE3 LYS 31 19.877 23.426 15.176 1.00 0.00 H +ATOM 486 NZ LYS 31 21.696 22.755 14.232 1.00 0.00 N +ATOM 487 HZ1 LYS 31 21.192 22.812 13.359 1.00 0.00 H +ATOM 488 HZ2 LYS 31 22.303 21.948 14.260 1.00 0.00 H +ATOM 489 HZ3 LYS 31 22.181 23.617 14.437 1.00 0.00 H +ATOM 490 C LYS 31 22.014 27.696 16.816 1.00 0.00 C +ATOM 491 O LYS 31 22.558 28.250 15.880 1.00 0.00 O +ATOM 492 N ALA 32 21.191 28.345 17.587 1.00 0.00 N +ATOM 493 H ALA 32 20.761 27.852 18.357 1.00 0.00 H +ATOM 494 CA ALA 32 20.790 29.798 17.385 1.00 0.00 C +ATOM 495 HA ALA 32 20.342 29.694 16.396 1.00 0.00 H +ATOM 496 CB ALA 32 19.753 30.167 18.450 1.00 0.00 C +ATOM 497 HB1 ALA 32 20.049 29.927 19.471 1.00 0.00 H +ATOM 498 HB2 ALA 32 19.577 31.242 18.484 1.00 0.00 H +ATOM 499 HB3 ALA 32 18.835 29.646 18.179 1.00 0.00 H +ATOM 500 C ALA 32 21.978 30.767 17.387 1.00 0.00 C +ATOM 501 O ALA 32 22.027 31.692 16.605 1.00 0.00 O +ATOM 502 N ASP 33 22.890 30.573 18.362 1.00 0.00 N +ATOM 503 H ASP 33 22.708 30.018 19.187 1.00 0.00 H +ATOM 504 CA ASP 33 24.174 31.392 18.377 1.00 0.00 C +ATOM 505 HA ASP 33 23.971 32.461 18.427 1.00 0.00 H +ATOM 506 CB ASP 33 24.938 31.027 19.663 1.00 0.00 C +ATOM 507 HB2 ASP 33 24.205 31.049 20.469 1.00 0.00 H +ATOM 508 HB3 ASP 33 25.272 29.995 19.551 1.00 0.00 H +ATOM 509 CG ASP 33 26.007 32.078 20.045 1.00 0.00 C +ATOM 510 OD1 ASP 33 26.744 31.872 21.047 1.00 0.00 O +ATOM 511 OD2 ASP 33 26.082 33.129 19.361 1.00 0.00 O +ATOM 512 C ASP 33 25.033 31.089 17.164 1.00 0.00 C +ATOM 513 O ASP 33 25.586 32.047 16.580 1.00 0.00 O +ATOM 514 N ALA 34 25.222 29.842 16.763 1.00 0.00 N +ATOM 515 H ALA 34 24.809 29.156 17.379 1.00 0.00 H +ATOM 516 CA ALA 34 25.908 29.399 15.505 1.00 0.00 C +ATOM 517 HA ALA 34 26.933 29.771 15.473 1.00 0.00 H +ATOM 518 CB ALA 34 25.959 27.847 15.410 1.00 0.00 C +ATOM 519 HB1 ALA 34 26.347 27.485 16.362 1.00 0.00 H +ATOM 520 HB2 ALA 34 26.598 27.536 14.583 1.00 0.00 H +ATOM 521 HB3 ALA 34 24.949 27.507 15.182 1.00 0.00 H +ATOM 522 C ALA 34 25.247 30.016 14.250 1.00 0.00 C +ATOM 523 O ALA 34 25.898 30.627 13.435 1.00 0.00 O +ATOM 524 N ASN 35 23.910 29.980 14.018 1.00 0.00 N +ATOM 525 H ASN 35 23.409 29.495 14.748 1.00 0.00 H +ATOM 526 CA ASN 35 23.138 30.759 13.018 1.00 0.00 C +ATOM 527 HA ASN 35 23.576 30.478 12.059 1.00 0.00 H +ATOM 528 CB ASN 35 21.622 30.450 13.059 1.00 0.00 C +ATOM 529 HB2 ASN 35 21.462 29.461 13.488 1.00 0.00 H +ATOM 530 HB3 ASN 35 21.047 31.146 13.671 1.00 0.00 H +ATOM 531 CG ASN 35 21.069 30.582 11.622 1.00 0.00 C +ATOM 532 OD1 ASN 35 20.655 29.697 10.967 1.00 0.00 O +ATOM 533 ND2 ASN 35 21.024 31.778 11.113 1.00 0.00 N +ATOM 534 HD21 ASN 35 21.115 32.609 11.679 1.00 0.00 H +ATOM 535 HD22 ASN 35 20.592 31.937 10.214 1.00 0.00 H +ATOM 536 C ASN 35 23.314 32.273 13.179 1.00 0.00 C +ATOM 537 O ASN 35 23.314 32.981 12.125 1.00 0.00 O +ATOM 538 N ASP 36 23.820 32.802 14.345 1.00 0.00 N +ATOM 539 H ASP 36 23.843 32.226 15.174 1.00 0.00 H +ATOM 540 CA ASP 36 24.400 34.197 14.489 1.00 0.00 C +ATOM 541 HA ASP 36 23.655 34.750 13.916 1.00 0.00 H +ATOM 542 CB ASP 36 24.397 34.731 15.937 1.00 0.00 C +ATOM 543 HB2 ASP 36 23.441 34.426 16.361 1.00 0.00 H +ATOM 544 HB3 ASP 36 25.236 34.310 16.491 1.00 0.00 H +ATOM 545 CG ASP 36 24.477 36.257 15.919 1.00 0.00 C +ATOM 546 OD1 ASP 36 23.406 36.857 15.912 1.00 0.00 O +ATOM 547 OD2 ASP 36 25.595 36.824 15.782 1.00 0.00 O +ATOM 548 C ASP 36 25.739 34.343 13.745 1.00 0.00 C +ATOM 549 O ASP 36 25.952 35.358 13.033 1.00 0.00 O +ATOM 550 N LYS 37 26.621 33.366 13.826 1.00 0.00 N +ATOM 551 H LYS 37 26.407 32.607 14.457 1.00 0.00 H +ATOM 552 CA LYS 37 27.798 33.323 12.955 1.00 0.00 C +ATOM 553 HA LYS 37 28.326 34.272 13.047 1.00 0.00 H +ATOM 554 CB LYS 37 28.725 32.244 13.498 1.00 0.00 C +ATOM 555 HB2 LYS 37 28.236 31.304 13.239 1.00 0.00 H +ATOM 556 HB3 LYS 37 28.849 32.371 14.573 1.00 0.00 H +ATOM 557 CG LYS 37 30.101 32.150 12.850 1.00 0.00 C +ATOM 558 HG2 LYS 37 30.686 33.045 13.063 1.00 0.00 H +ATOM 559 HG3 LYS 37 30.000 32.027 11.772 1.00 0.00 H +ATOM 560 CD LYS 37 30.896 30.901 13.327 1.00 0.00 C +ATOM 561 HD2 LYS 37 30.994 30.888 14.413 1.00 0.00 H +ATOM 562 HD3 LYS 37 30.352 30.012 13.009 1.00 0.00 H +ATOM 563 CE LYS 37 32.264 30.757 12.611 1.00 0.00 C +ATOM 564 HE2 LYS 37 32.174 31.328 11.687 1.00 0.00 H +ATOM 565 HE3 LYS 37 33.007 31.222 13.259 1.00 0.00 H +ATOM 566 NZ LYS 37 32.650 29.348 12.431 1.00 0.00 N +ATOM 567 HZ1 LYS 37 33.640 29.274 12.249 1.00 0.00 H +ATOM 568 HZ2 LYS 37 32.500 28.755 13.235 1.00 0.00 H +ATOM 569 HZ3 LYS 37 32.062 28.972 11.700 1.00 0.00 H +ATOM 570 C LYS 37 27.421 33.138 11.454 1.00 0.00 C +ATOM 571 O LYS 37 28.280 33.384 10.595 1.00 0.00 O +ATOM 572 N GLY 38 26.178 32.680 11.174 1.00 0.00 N +ATOM 573 H GLY 38 25.480 32.763 11.899 1.00 0.00 H +ATOM 574 CA GLY 38 25.708 32.525 9.806 1.00 0.00 C +ATOM 575 HA2 GLY 38 24.872 33.220 9.742 1.00 0.00 H +ATOM 576 HA3 GLY 38 26.519 32.879 9.170 1.00 0.00 H +ATOM 577 C GLY 38 25.286 31.132 9.376 1.00 0.00 C +ATOM 578 O GLY 38 24.795 30.947 8.286 1.00 0.00 O +ATOM 579 N VAL 39 25.585 30.102 10.123 1.00 0.00 N +ATOM 580 H VAL 39 25.946 30.288 11.048 1.00 0.00 H +ATOM 581 CA VAL 39 25.484 28.712 9.765 1.00 0.00 C +ATOM 582 HA VAL 39 24.697 28.560 9.027 1.00 0.00 H +ATOM 583 CB VAL 39 26.734 28.140 9.061 1.00 0.00 C +ATOM 584 HB VAL 39 27.463 27.836 9.812 1.00 0.00 H +ATOM 585 CG1 VAL 39 26.389 26.936 8.162 1.00 0.00 C +ATOM 586 HG11 VAL 39 25.980 26.112 8.748 1.00 0.00 H +ATOM 587 HG12 VAL 39 27.324 26.679 7.665 1.00 0.00 H +ATOM 588 HG13 VAL 39 25.651 27.158 7.391 1.00 0.00 H +ATOM 589 CG2 VAL 39 27.495 29.160 8.122 1.00 0.00 C +ATOM 590 HG21 VAL 39 27.959 29.920 8.751 1.00 0.00 H +ATOM 591 HG22 VAL 39 27.004 29.716 7.324 1.00 0.00 H +ATOM 592 HG23 VAL 39 28.347 28.624 7.703 1.00 0.00 H +ATOM 593 C VAL 39 25.290 27.909 11.027 1.00 0.00 C +ATOM 594 O VAL 39 26.208 27.696 11.805 1.00 0.00 O +ATOM 595 N ASP 40 24.046 27.482 11.223 1.00 0.00 N +ATOM 596 H ASP 40 23.320 27.644 10.539 1.00 0.00 H +ATOM 597 CA ASP 40 23.496 26.755 12.471 1.00 0.00 C +ATOM 598 HA ASP 40 23.520 27.449 13.312 1.00 0.00 H +ATOM 599 CB ASP 40 21.935 26.520 12.328 1.00 0.00 C +ATOM 600 HB2 ASP 40 21.556 26.012 13.215 1.00 0.00 H +ATOM 601 HB3 ASP 40 21.530 27.532 12.324 1.00 0.00 H +ATOM 602 CG ASP 40 21.508 25.769 11.120 1.00 0.00 C +ATOM 603 OD1 ASP 40 20.887 26.333 10.226 1.00 0.00 O +ATOM 604 OD2 ASP 40 21.893 24.576 11.002 1.00 0.00 O +ATOM 605 C ASP 40 24.255 25.457 12.937 1.00 0.00 C +ATOM 606 O ASP 40 23.862 24.705 13.854 1.00 0.00 O +ATOM 607 N GLY 41 25.270 25.064 12.201 1.00 0.00 N +ATOM 608 H GLY 41 25.468 25.699 11.441 1.00 0.00 H +ATOM 609 CA GLY 41 26.050 23.777 12.261 1.00 0.00 C +ATOM 610 HA2 GLY 41 25.478 23.036 12.820 1.00 0.00 H +ATOM 611 HA3 GLY 41 26.221 23.350 11.273 1.00 0.00 H +ATOM 612 C GLY 41 27.366 23.929 13.045 1.00 0.00 C +ATOM 613 O GLY 41 27.996 22.996 13.369 1.00 0.00 O +ATOM 614 N GLU 42 27.790 25.173 13.362 1.00 0.00 N +ATOM 615 H GLU 42 27.171 25.908 13.052 1.00 0.00 H +ATOM 616 CA GLU 42 29.038 25.533 14.093 1.00 0.00 C +ATOM 617 HA GLU 42 29.702 24.689 13.905 1.00 0.00 H +ATOM 618 CB GLU 42 29.591 26.822 13.388 1.00 0.00 C +ATOM 619 HB2 GLU 42 28.745 27.495 13.525 1.00 0.00 H +ATOM 620 HB3 GLU 42 30.397 27.232 13.997 1.00 0.00 H +ATOM 621 CG GLU 42 30.012 26.727 11.916 1.00 0.00 C +ATOM 622 HG2 GLU 42 29.368 26.032 11.377 1.00 0.00 H +ATOM 623 HG3 GLU 42 30.027 27.756 11.557 1.00 0.00 H +ATOM 624 CD GLU 42 31.413 26.122 11.799 1.00 0.00 C +ATOM 625 OE1 GLU 42 32.384 26.766 12.329 1.00 0.00 O +ATOM 626 OE2 GLU 42 31.615 24.911 11.508 1.00 0.00 O +ATOM 627 C GLU 42 28.941 25.577 15.622 1.00 0.00 C +ATOM 628 O GLU 42 29.074 26.677 16.181 1.00 0.00 O +ATOM 629 N TRP 43 28.822 24.435 16.297 1.00 0.00 N +ATOM 630 H TRP 43 28.730 23.612 15.720 1.00 0.00 H +ATOM 631 CA TRP 43 28.718 24.247 17.742 1.00 0.00 C +ATOM 632 HA TRP 43 29.097 25.133 18.251 1.00 0.00 H +ATOM 633 CB TRP 43 27.295 24.283 18.209 1.00 0.00 C +ATOM 634 HB2 TRP 43 27.232 24.430 19.287 1.00 0.00 H +ATOM 635 HB3 TRP 43 26.926 25.195 17.741 1.00 0.00 H +ATOM 636 CG TRP 43 26.427 23.175 17.792 1.00 0.00 C +ATOM 637 CD1 TRP 43 25.746 23.145 16.611 1.00 0.00 C +ATOM 638 HD1 TRP 43 25.807 23.825 15.774 1.00 0.00 H +ATOM 639 NE1 TRP 43 25.266 21.853 16.379 1.00 0.00 N +ATOM 640 HE1 TRP 43 24.861 21.423 15.560 1.00 0.00 H +ATOM 641 CE2 TRP 43 25.384 21.129 17.535 1.00 0.00 C +ATOM 642 CZ2 TRP 43 24.950 19.816 17.921 1.00 0.00 C +ATOM 643 HZ2 TRP 43 24.561 19.059 17.257 1.00 0.00 H +ATOM 644 CH2 TRP 43 25.249 19.402 19.212 1.00 0.00 C +ATOM 645 HH2 TRP 43 24.850 18.452 19.535 1.00 0.00 H +ATOM 646 CZ3 TRP 43 25.946 20.226 20.128 1.00 0.00 C +ATOM 647 HZ3 TRP 43 26.138 19.944 21.152 1.00 0.00 H +ATOM 648 CE3 TRP 43 26.479 21.488 19.734 1.00 0.00 C +ATOM 649 HE3 TRP 43 27.051 22.079 20.433 1.00 0.00 H +ATOM 650 CD2 TRP 43 26.111 21.986 18.445 1.00 0.00 C +ATOM 651 C TRP 43 29.448 23.014 18.189 1.00 0.00 C +ATOM 652 O TRP 43 29.654 22.076 17.428 1.00 0.00 O +ATOM 653 N THR 44 29.801 22.976 19.489 1.00 0.00 N +ATOM 654 H THR 44 29.601 23.806 20.028 1.00 0.00 H +ATOM 655 CA THR 44 30.452 21.834 20.140 1.00 0.00 C +ATOM 656 HA THR 44 30.082 20.913 19.689 1.00 0.00 H +ATOM 657 CB THR 44 31.997 21.846 19.916 1.00 0.00 C +ATOM 658 HB THR 44 32.167 21.864 18.840 1.00 0.00 H +ATOM 659 CG2 THR 44 32.751 23.055 20.514 1.00 0.00 C +ATOM 660 HG21 THR 44 32.230 23.981 20.271 1.00 0.00 H +ATOM 661 HG22 THR 44 33.782 23.021 20.163 1.00 0.00 H +ATOM 662 HG23 THR 44 32.583 23.052 21.591 1.00 0.00 H +ATOM 663 OG1 THR 44 32.551 20.744 20.570 1.00 0.00 O +ATOM 664 HG1 THR 44 32.172 19.934 20.220 1.00 0.00 H +ATOM 665 C THR 44 30.058 21.688 21.596 1.00 0.00 C +ATOM 666 O THR 44 29.915 22.660 22.329 1.00 0.00 O +ATOM 667 N TYR 45 29.976 20.390 22.032 1.00 0.00 N +ATOM 668 H TYR 45 30.298 19.674 21.395 1.00 0.00 H +ATOM 669 CA TYR 45 29.551 19.974 23.354 1.00 0.00 C +ATOM 670 HA TYR 45 29.171 20.884 23.817 1.00 0.00 H +ATOM 671 CB TYR 45 28.308 19.018 23.211 1.00 0.00 C +ATOM 672 HB2 TYR 45 27.685 19.676 22.605 1.00 0.00 H +ATOM 673 HB3 TYR 45 28.669 18.143 22.670 1.00 0.00 H +ATOM 674 CG TYR 45 27.545 18.737 24.520 1.00 0.00 C +ATOM 675 CD1 TYR 45 27.076 19.672 25.480 1.00 0.00 C +ATOM 676 HD1 TYR 45 27.178 20.699 25.161 1.00 0.00 H +ATOM 677 CE1 TYR 45 26.635 19.340 26.719 1.00 0.00 C +ATOM 678 HE1 TYR 45 26.248 20.101 27.380 1.00 0.00 H +ATOM 679 CZ TYR 45 26.440 17.976 27.018 1.00 0.00 C +ATOM 680 OH TYR 45 25.770 17.630 28.169 1.00 0.00 O +ATOM 681 HH TYR 45 26.000 16.747 28.468 1.00 0.00 H +ATOM 682 CE2 TYR 45 26.792 17.030 26.043 1.00 0.00 C +ATOM 683 HE2 TYR 45 26.625 15.977 26.214 1.00 0.00 H +ATOM 684 CD2 TYR 45 27.317 17.380 24.812 1.00 0.00 C +ATOM 685 HD2 TYR 45 27.659 16.604 24.145 1.00 0.00 H +ATOM 686 C TYR 45 30.661 19.346 24.227 1.00 0.00 C +ATOM 687 O TYR 45 31.610 18.833 23.684 1.00 0.00 O +ATOM 688 N ASP 46 30.447 19.250 25.524 1.00 0.00 N +ATOM 689 H ASP 46 29.507 19.488 25.805 1.00 0.00 H +ATOM 690 CA ASP 46 31.334 18.744 26.537 1.00 0.00 C +ATOM 691 HA ASP 46 31.827 17.843 26.170 1.00 0.00 H +ATOM 692 CB ASP 46 32.473 19.674 27.013 1.00 0.00 C +ATOM 693 HB2 ASP 46 33.056 19.870 26.114 1.00 0.00 H +ATOM 694 HB3 ASP 46 32.138 20.639 27.393 1.00 0.00 H +ATOM 695 CG ASP 46 33.486 19.008 28.041 1.00 0.00 C +ATOM 696 OD1 ASP 46 33.829 19.678 29.031 1.00 0.00 O +ATOM 697 OD2 ASP 46 33.871 17.818 27.860 1.00 0.00 O +ATOM 698 C ASP 46 30.432 18.298 27.719 1.00 0.00 C +ATOM 699 O ASP 46 30.054 19.129 28.575 1.00 0.00 O +ATOM 700 N ASP 47 30.075 16.997 27.842 1.00 0.00 N +ATOM 701 H ASP 47 30.244 16.340 27.093 1.00 0.00 H +ATOM 702 CA ASP 47 29.235 16.494 28.903 1.00 0.00 C +ATOM 703 HA ASP 47 28.392 17.181 28.981 1.00 0.00 H +ATOM 704 CB ASP 47 28.669 15.074 28.573 1.00 0.00 C +ATOM 705 HB2 ASP 47 28.492 14.988 27.501 1.00 0.00 H +ATOM 706 HB3 ASP 47 29.458 14.337 28.726 1.00 0.00 H +ATOM 707 CG ASP 47 27.422 14.723 29.380 1.00 0.00 C +ATOM 708 OD1 ASP 47 26.340 15.374 29.173 1.00 0.00 O +ATOM 709 OD2 ASP 47 27.554 13.871 30.224 1.00 0.00 O +ATOM 710 C ASP 47 29.929 16.434 30.228 1.00 0.00 C +ATOM 711 O ASP 47 29.226 16.551 31.223 1.00 0.00 O +ATOM 712 N ALA 48 31.273 16.349 30.272 1.00 0.00 N +ATOM 713 H ALA 48 31.744 16.191 29.392 1.00 0.00 H +ATOM 714 CA ALA 48 32.033 16.363 31.535 1.00 0.00 C +ATOM 715 HA ALA 48 31.690 15.655 32.290 1.00 0.00 H +ATOM 716 CB ALA 48 33.482 16.027 31.160 1.00 0.00 C +ATOM 717 HB1 ALA 48 33.811 16.649 30.328 1.00 0.00 H +ATOM 718 HB2 ALA 48 33.437 15.012 30.764 1.00 0.00 H +ATOM 719 HB3 ALA 48 34.271 16.194 31.893 1.00 0.00 H +ATOM 720 C ALA 48 32.125 17.759 32.210 1.00 0.00 C +ATOM 721 O ALA 48 32.400 17.807 33.400 1.00 0.00 O +ATOM 722 N THR 49 31.768 18.898 31.560 1.00 0.00 N +ATOM 723 H THR 49 31.713 18.770 30.559 1.00 0.00 H +ATOM 724 CA THR 49 31.315 20.160 32.121 1.00 0.00 C +ATOM 725 HA THR 49 31.364 20.102 33.209 1.00 0.00 H +ATOM 726 CB THR 49 32.347 21.241 31.806 1.00 0.00 C +ATOM 727 HB THR 49 32.050 22.212 32.204 1.00 0.00 H +ATOM 728 CG2 THR 49 33.793 21.099 32.240 1.00 0.00 C +ATOM 729 HG21 THR 49 34.246 22.048 32.526 1.00 0.00 H +ATOM 730 HG22 THR 49 34.441 20.664 31.479 1.00 0.00 H +ATOM 731 HG23 THR 49 33.833 20.391 33.067 1.00 0.00 H +ATOM 732 OG1 THR 49 32.401 21.338 30.398 1.00 0.00 O +ATOM 733 HG1 THR 49 32.993 20.626 30.145 1.00 0.00 H +ATOM 734 C THR 49 29.866 20.575 31.840 1.00 0.00 C +ATOM 735 O THR 49 29.513 21.632 32.279 1.00 0.00 O +ATOM 736 N LYS 50 29.127 19.815 31.111 1.00 0.00 N +ATOM 737 H LYS 50 29.681 19.013 30.848 1.00 0.00 H +ATOM 738 CA LYS 50 27.786 20.111 30.660 1.00 0.00 C +ATOM 739 HA LYS 50 27.500 19.372 29.911 1.00 0.00 H +ATOM 740 CB LYS 50 26.840 20.094 31.826 1.00 0.00 C +ATOM 741 HB2 LYS 50 27.026 20.960 32.461 1.00 0.00 H +ATOM 742 HB3 LYS 50 25.841 20.330 31.458 1.00 0.00 H +ATOM 743 CG LYS 50 26.779 18.838 32.714 1.00 0.00 C +ATOM 744 HG2 LYS 50 27.753 18.589 33.134 1.00 0.00 H +ATOM 745 HG3 LYS 50 26.114 19.003 33.561 1.00 0.00 H +ATOM 746 CD LYS 50 26.257 17.562 31.990 1.00 0.00 C +ATOM 747 HD2 LYS 50 25.226 17.845 31.778 1.00 0.00 H +ATOM 748 HD3 LYS 50 26.792 17.501 31.042 1.00 0.00 H +ATOM 749 CE LYS 50 26.370 16.279 32.787 1.00 0.00 C +ATOM 750 HE2 LYS 50 27.411 15.957 32.800 1.00 0.00 H +ATOM 751 HE3 LYS 50 26.036 16.291 33.825 1.00 0.00 H +ATOM 752 NZ LYS 50 25.637 15.199 32.100 1.00 0.00 N +ATOM 753 HZ1 LYS 50 25.662 14.394 32.708 1.00 0.00 H +ATOM 754 HZ2 LYS 50 26.105 15.074 31.213 1.00 0.00 H +ATOM 755 HZ3 LYS 50 24.661 15.441 32.008 1.00 0.00 H +ATOM 756 C LYS 50 27.788 21.421 29.931 1.00 0.00 C +ATOM 757 O LYS 50 27.030 22.324 30.204 1.00 0.00 O +ATOM 758 N THR 51 28.627 21.590 28.917 1.00 0.00 N +ATOM 759 H THR 51 29.356 20.900 28.805 1.00 0.00 H +ATOM 760 CA THR 51 28.953 22.901 28.301 1.00 0.00 C +ATOM 761 HA THR 51 28.271 23.666 28.672 1.00 0.00 H +ATOM 762 CB THR 51 30.265 23.452 28.711 1.00 0.00 C +ATOM 763 HB THR 51 31.063 22.861 28.262 1.00 0.00 H +ATOM 764 CG2 THR 51 30.642 24.884 28.194 1.00 0.00 C +ATOM 765 HG21 THR 51 31.476 25.260 28.786 1.00 0.00 H +ATOM 766 HG22 THR 51 29.840 25.621 28.208 1.00 0.00 H +ATOM 767 HG23 THR 51 31.010 24.823 27.170 1.00 0.00 H +ATOM 768 OG1 THR 51 30.238 23.496 30.101 1.00 0.00 O +ATOM 769 HG1 THR 51 30.111 22.586 30.378 1.00 0.00 H +ATOM 770 C THR 51 28.727 22.891 26.776 1.00 0.00 C +ATOM 771 O THR 51 29.172 22.032 26.067 1.00 0.00 O +ATOM 772 N PHE 52 28.138 23.923 26.252 1.00 0.00 N +ATOM 773 H PHE 52 27.821 24.583 26.947 1.00 0.00 H +ATOM 774 CA PHE 52 27.966 24.268 24.838 1.00 0.00 C +ATOM 775 HA PHE 52 28.174 23.420 24.185 1.00 0.00 H +ATOM 776 CB PHE 52 26.531 24.442 24.547 1.00 0.00 C +ATOM 777 HB2 PHE 52 26.012 25.231 25.092 1.00 0.00 H +ATOM 778 HB3 PHE 52 26.455 24.827 23.530 1.00 0.00 H +ATOM 779 CG PHE 52 25.698 23.191 24.608 1.00 0.00 C +ATOM 780 CD1 PHE 52 25.014 22.789 25.823 1.00 0.00 C +ATOM 781 HD1 PHE 52 25.024 23.379 26.727 1.00 0.00 H +ATOM 782 CE1 PHE 52 24.106 21.741 25.804 1.00 0.00 C +ATOM 783 HE1 PHE 52 23.553 21.497 26.699 1.00 0.00 H +ATOM 784 CZ PHE 52 23.920 20.991 24.626 1.00 0.00 C +ATOM 785 HZ PHE 52 23.117 20.269 24.614 1.00 0.00 H +ATOM 786 CE2 PHE 52 24.651 21.275 23.461 1.00 0.00 C +ATOM 787 HE2 PHE 52 24.727 20.563 22.652 1.00 0.00 H +ATOM 788 CD2 PHE 52 25.671 22.328 23.535 1.00 0.00 C +ATOM 789 HD2 PHE 52 26.313 22.481 22.680 1.00 0.00 H +ATOM 790 C PHE 52 28.768 25.545 24.494 1.00 0.00 C +ATOM 791 O PHE 52 28.832 26.464 25.282 1.00 0.00 O +ATOM 792 N THR 53 29.479 25.550 23.347 1.00 0.00 N +ATOM 793 H THR 53 29.541 24.705 22.797 1.00 0.00 H +ATOM 794 CA THR 53 29.997 26.804 22.682 1.00 0.00 C +ATOM 795 HA THR 53 29.355 27.629 22.992 1.00 0.00 H +ATOM 796 CB THR 53 31.352 27.037 23.270 1.00 0.00 C +ATOM 797 HB THR 53 31.242 27.140 24.350 1.00 0.00 H +ATOM 798 CG2 THR 53 32.358 25.977 22.827 1.00 0.00 C +ATOM 799 HG21 THR 53 32.341 25.949 21.737 1.00 0.00 H +ATOM 800 HG22 THR 53 32.171 25.073 23.408 1.00 0.00 H +ATOM 801 HG23 THR 53 33.360 26.295 23.116 1.00 0.00 H +ATOM 802 OG1 THR 53 31.784 28.324 22.778 1.00 0.00 O +ATOM 803 HG1 THR 53 32.550 28.532 23.318 1.00 0.00 H +ATOM 804 C THR 53 29.933 26.738 21.129 1.00 0.00 C +ATOM 805 O THR 53 29.862 25.681 20.516 1.00 0.00 O +ATOM 806 N VAL 54 30.029 27.931 20.510 1.00 0.00 N +ATOM 807 H VAL 54 29.977 28.765 21.078 1.00 0.00 H +ATOM 808 CA VAL 54 30.068 28.076 19.070 1.00 0.00 C +ATOM 809 HA VAL 54 29.412 27.349 18.591 1.00 0.00 H +ATOM 810 CB VAL 54 29.672 29.521 18.652 1.00 0.00 C +ATOM 811 HB VAL 54 30.113 30.270 19.310 1.00 0.00 H +ATOM 812 CG1 VAL 54 30.051 30.047 17.261 1.00 0.00 C +ATOM 813 HG11 VAL 54 29.560 30.995 17.045 1.00 0.00 H +ATOM 814 HG12 VAL 54 29.848 29.362 16.437 1.00 0.00 H +ATOM 815 HG13 VAL 54 31.130 30.202 17.231 1.00 0.00 H +ATOM 816 CG2 VAL 54 28.148 29.701 18.749 1.00 0.00 C +ATOM 817 HG21 VAL 54 27.486 29.298 17.982 1.00 0.00 H +ATOM 818 HG22 VAL 54 27.949 30.772 18.725 1.00 0.00 H +ATOM 819 HG23 VAL 54 27.846 29.360 19.740 1.00 0.00 H +ATOM 820 C VAL 54 31.506 27.855 18.606 1.00 0.00 C +ATOM 821 O VAL 54 32.390 28.342 19.298 1.00 0.00 O +ATOM 822 N THR 55 31.697 27.126 17.500 1.00 0.00 N +ATOM 823 H THR 55 30.946 26.878 16.872 1.00 0.00 H +ATOM 824 CA THR 55 32.995 26.786 16.876 1.00 0.00 C +ATOM 825 HA THR 55 33.696 26.717 17.708 1.00 0.00 H +ATOM 826 CB THR 55 33.040 25.457 16.069 1.00 0.00 C +ATOM 827 HB THR 55 34.017 25.382 15.593 1.00 0.00 H +ATOM 828 CG2 THR 55 32.758 24.334 17.028 1.00 0.00 C +ATOM 829 HG21 THR 55 33.353 24.443 17.935 1.00 0.00 H +ATOM 830 HG22 THR 55 33.039 23.485 16.405 1.00 0.00 H +ATOM 831 HG23 THR 55 31.705 24.408 17.300 1.00 0.00 H +ATOM 832 OG1 THR 55 32.096 25.322 15.107 1.00 0.00 O +ATOM 833 HG1 THR 55 32.382 25.848 14.356 1.00 0.00 H +ATOM 834 C THR 55 33.463 27.943 16.026 1.00 0.00 C +ATOM 835 O THR 55 32.747 28.328 15.118 1.00 0.00 O +ATOM 836 N GLU 56 34.715 28.394 16.337 1.00 0.00 N +ATOM 837 H GLU 56 35.293 27.866 16.976 1.00 0.00 H +ATOM 838 CA GLU 56 35.552 29.436 15.658 1.00 0.00 C +ATOM 839 HA GLU 56 35.269 29.592 14.617 1.00 0.00 H +ATOM 840 CB GLU 56 35.310 30.738 16.428 1.00 0.00 C +ATOM 841 HB2 GLU 56 34.250 30.977 16.346 1.00 0.00 H +ATOM 842 HB3 GLU 56 35.592 30.510 17.456 1.00 0.00 H +ATOM 843 CG GLU 56 36.133 31.886 15.807 1.00 0.00 C +ATOM 844 HG2 GLU 56 37.192 31.637 15.888 1.00 0.00 H +ATOM 845 HG3 GLU 56 35.982 31.839 14.729 1.00 0.00 H +ATOM 846 CD GLU 56 35.813 33.236 16.461 1.00 0.00 C +ATOM 847 OE1 GLU 56 34.575 33.605 16.653 1.00 0.00 O +ATOM 848 OE2 GLU 56 36.754 34.016 16.806 1.00 0.00 O +ATOM 849 C GLU 56 37.086 29.012 15.620 1.00 0.00 C +ATOM 850 O GLU 56 37.629 28.689 14.498 1.00 0.00 O +ATOM 851 OXT GLU 56 37.752 29.046 16.703 1.00 0.00 O +ATOM 852 ZN ZN1 57 22.864 31.029 26.043 1.00 0.00 ZN +ATOM 853 N AN1 58 21.895 32.435 24.861 1.00 0.00 N +ATOM 854 C AN1 58 20.141 33.918 23.747 1.00 0.00 C +ATOM 855 C1 AN1 58 21.085 33.049 24.350 1.00 0.00 C +ATOM 856 H AN1 58 19.160 33.793 24.222 1.00 0.00 H +ATOM 857 H1 AN1 58 20.118 33.705 22.671 1.00 0.00 H +ATOM 858 H2 AN1 58 20.407 34.969 23.917 1.00 0.00 H +TER 859 AN1 58 +ATOM 859 N1 AZI 59 24.330 34.009 24.478 1.00 0.00 N +ATOM 860 N2 AZI 59 24.202 34.830 25.347 1.00 0.00 N +ATOM 861 N3 AZI 59 24.065 35.662 26.234 1.00 0.00 N +TER 862 AZI 59 \ No newline at end of file diff --git a/tests/nsga2/readme.rst b/tests/nsga2/readme.rst new file mode 100644 index 0000000..197a7f7 --- /dev/null +++ b/tests/nsga2/readme.rst @@ -0,0 +1,26 @@ +| **Creation date:** 2019-04-25 +| **Metadata type:** Calculation +| **Subject:** Biochemistry +| **Project title:** Gb1 +| **Author:** Simon Duerr +| **Email:** simon.durr@epfl.ch # configuration file for create_metadata.py + + +GENERAL DESCRIPTION +=================== + +New run using two objectives and new+old input clusters +using 20 clusters + +Production run with correct thermostability measure + +DATA & FILE OVERVIEW +==================== + +Clusters were chosen out of +/share/lcbcsrv5/lcbcdata/duerr/md/GB1_AZIACN_restrained_eq3/analysis/ligand_clustering/ZN_azi_distance/100clusters + +The clusters were made using sieve10 and clustering based on Zn-Azi distance on 100ns NPT trajectory + +I picked clusters 1 2 6 9 14 17 22 61 66 91 + diff --git a/tests/nsga2/run_example.sh b/tests/nsga2/run_example.sh new file mode 100755 index 0000000..d821643 --- /dev/null +++ b/tests/nsga2/run_example.sh @@ -0,0 +1 @@ +python -u ../../main.py -input_file ga_input.in diff --git a/unittests/__init__.py b/unittests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/unittests/example_files/3GB1WT_2clust2.mol2 b/unittests/example_files/3GB1WT_2clust2.mol2 new file mode 100644 index 0000000..41f973f --- /dev/null +++ b/unittests/example_files/3GB1WT_2clust2.mol2 @@ -0,0 +1,1727 @@ +@MOLECULE +MET + 855 861 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N 19.1570 32.5760 19.1400 N.4 1 MET 0.000000 + 2 H1 18.4350 31.8700 19.1290 H 1 MET 0.000000 + 3 H2 18.9000 33.2600 18.4410 H 1 MET 0.000000 + 4 H3 19.2290 33.0730 20.0160 H 1 MET 0.000000 + 5 CA 20.4580 31.9390 18.9310 C.3 1 MET 0.000000 + 6 HA 20.4200 31.3030 18.0460 H 1 MET 0.000000 + 7 CB 21.5040 33.0150 18.7220 C.3 1 MET 0.000000 + 8 HB2 21.3520 33.5190 17.7680 H 1 MET 0.000000 + 9 HB3 21.3900 33.7640 19.5050 H 1 MET 0.000000 + 10 CG 22.9040 32.5170 18.6560 C.3 1 MET 0.000000 + 11 HG2 23.5900 33.3620 18.6010 H 1 MET 0.000000 + 12 HG3 23.1540 32.0950 19.6300 H 1 MET 0.000000 + 13 SD 23.2050 31.2690 17.3860 S.3 1 MET 0.000000 + 14 CE 22.9900 32.1370 15.8700 C.3 1 MET 0.000000 + 15 HE1 23.3390 33.1630 15.9830 H 1 MET 0.000000 + 16 HE2 21.9680 32.1280 15.4900 H 1 MET 0.000000 + 17 HE3 23.5720 31.5860 15.1320 H 1 MET 0.000000 + 18 C 20.7960 31.0170 20.1330 C.2 1 MET 0.000000 + 19 O 20.6740 31.4400 21.2970 O.2 1 MET 0.000000 + 20 N 21.1240 29.7740 19.8190 N.am 2 THR 0.000000 + 21 H 21.2790 29.5270 18.8510 H 2 THR 0.000000 + 22 CA 21.4430 28.7040 20.8610 C.3 2 THR 0.000000 + 23 HA 20.9090 28.9980 21.7640 H 2 THR 0.000000 + 24 CB 21.1140 27.2410 20.5220 C.3 2 THR 0.000000 + 25 HB 21.9450 26.8250 19.9550 H 2 THR 0.000000 + 26 CG2 20.7150 26.5580 21.8170 C.3 2 THR 0.000000 + 27 HG21 20.2030 25.6090 21.6560 H 2 THR 0.000000 + 28 HG22 20.0010 27.1370 22.4030 H 2 THR 0.000000 + 29 HG23 21.6330 26.3440 22.3630 H 2 THR 0.000000 + 30 OG1 19.9570 27.2310 19.6580 O.3 2 THR 0.000000 + 31 HG1 19.3860 27.9760 19.8640 H 2 THR 0.000000 + 32 C 22.9370 28.8920 21.0860 C.2 2 THR 0.000000 + 33 O 23.7730 28.8670 20.1810 O.2 2 THR 0.000000 + 34 N 23.2440 29.1550 22.3440 N.am 3 TYR 0.000000 + 35 H 22.5130 29.0850 23.0380 H 3 TYR 0.000000 + 36 CA 24.6280 29.3050 22.8880 C.3 3 TYR 0.000000 + 37 HA 25.2620 29.3910 22.0040 H 3 TYR 0.000000 + 38 CB 24.7440 30.5790 23.6750 C.3 3 TYR 0.000000 + 39 HB2 24.1310 30.4950 24.5720 H 3 TYR 0.000000 + 40 HB3 25.7800 30.5050 24.0080 H 3 TYR 0.000000 + 41 CG 24.4680 31.8620 22.9280 C.ar 3 TYR 0.000000 + 42 CD1 25.5250 32.5440 22.3170 C.ar 3 TYR 0.000000 + 43 HD1 26.4770 32.0390 22.3790 H 3 TYR 0.000000 + 44 CE1 25.2890 33.7610 21.6190 C.ar 3 TYR 0.000000 + 45 HE1 26.1000 34.2750 21.1220 H 3 TYR 0.000000 + 46 CZ 23.9360 34.2600 21.5790 C.ar 3 TYR 0.000000 + 47 OH 23.7740 35.2680 20.7740 O.3 3 TYR 0.000000 + 48 HH 24.4860 35.1610 20.1400 H 3 TYR 0.000000 + 49 CE2 22.8490 33.5370 22.1760 C.ar 3 TYR 0.000000 + 50 HE2 21.8680 33.9650 22.0360 H 3 TYR 0.000000 + 51 CD2 23.1100 32.2910 22.8530 C.ar 3 TYR 0.000000 + 52 HD2 22.2350 31.7520 23.1870 H 3 TYR 0.000000 + 53 C 25.0660 28.1360 23.7740 C.2 3 TYR 0.000000 + 54 O 24.2330 27.4360 24.3380 O.2 3 TYR 0.000000 + 55 N 26.3390 27.9340 23.8110 N.am 4 LYS 0.000000 + 56 H 26.9440 28.5140 23.2480 H 4 LYS 0.000000 + 57 CA 26.9820 26.9180 24.6870 C.3 4 LYS 0.000000 + 58 HA 26.2120 26.4880 25.3280 H 4 LYS 0.000000 + 59 CB 27.6430 25.8010 23.8030 C.3 4 LYS 0.000000 + 60 HB2 26.8680 25.4650 23.1130 H 4 LYS 0.000000 + 61 HB3 28.4220 26.1960 23.1510 H 4 LYS 0.000000 + 62 CG 28.2050 24.6250 24.5060 C.3 4 LYS 0.000000 + 63 HG2 29.0540 24.9160 25.1250 H 4 LYS 0.000000 + 64 HG3 27.4520 24.2780 25.2130 H 4 LYS 0.000000 + 65 CD 28.6350 23.4070 23.6780 C.3 4 LYS 0.000000 + 66 HD2 29.0030 22.6910 24.4140 H 4 LYS 0.000000 + 67 HD3 27.7370 22.9540 23.2550 H 4 LYS 0.000000 + 68 CE 29.5540 23.5750 22.5060 C.3 4 LYS 0.000000 + 69 HE2 28.8990 24.1200 21.8270 H 4 LYS 0.000000 + 70 HE3 30.4580 24.1140 22.7940 H 4 LYS 0.000000 + 71 NZ 30.0520 22.2790 21.8880 N.4 4 LYS 0.000000 + 72 HZ1 30.8310 21.8960 22.4020 H 4 LYS 0.000000 + 73 HZ2 30.4430 22.4230 20.9680 H 4 LYS 0.000000 + 74 HZ3 29.3280 21.5790 21.8050 H 4 LYS 0.000000 + 75 C 28.0030 27.5160 25.6550 C.2 4 LYS 0.000000 + 76 O 28.5790 28.5530 25.3100 O.2 4 LYS 0.000000 + 77 N 28.2450 26.7730 26.7410 N.am 5 LEU 0.000000 + 78 H 27.5440 26.0840 26.9770 H 5 LEU 0.000000 + 79 CA 29.2440 27.1180 27.7660 C.3 5 LEU 0.000000 + 80 HA 29.9160 27.8840 27.3800 H 5 LEU 0.000000 + 81 CB 28.5790 27.5070 29.0970 C.3 5 LEU 0.000000 + 82 HB2 28.0580 28.4380 28.8720 H 5 LEU 0.000000 + 83 HB3 27.8590 26.7790 29.4690 H 5 LEU 0.000000 + 84 CG 29.5510 27.7200 30.2350 C.3 5 LEU 0.000000 + 85 HG 30.1660 26.8410 30.4290 H 5 LEU 0.000000 + 86 CD1 30.4270 28.9520 29.9860 C.3 5 LEU 0.000000 + 87 HD11 31.1140 28.6830 29.1840 H 5 LEU 0.000000 + 88 HD12 31.0080 29.1200 30.8940 H 5 LEU 0.000000 + 89 HD13 29.8480 29.8610 29.8250 H 5 LEU 0.000000 + 90 CD2 28.6780 28.1150 31.4570 C.3 5 LEU 0.000000 + 91 HD21 28.2350 29.0960 31.2840 H 5 LEU 0.000000 + 92 HD22 29.3270 28.2870 32.3150 H 5 LEU 0.000000 + 93 HD23 27.9070 27.3900 31.7200 H 5 LEU 0.000000 + 94 C 30.0650 25.8160 27.9900 C.2 5 LEU 0.000000 + 95 O 29.4890 24.7680 28.3020 O.2 5 LEU 0.000000 + 96 N 31.4150 25.9540 27.9590 N.am 6 ILE 0.000000 + 97 H 31.8340 26.8220 27.6580 H 6 ILE 0.000000 + 98 CA 32.3520 24.9440 28.4380 C.3 6 ILE 0.000000 + 99 HA 31.8510 23.9780 28.4940 H 6 ILE 0.000000 + 100 CB 33.5350 24.7360 27.4340 C.3 6 ILE 0.000000 + 101 HB 34.0020 25.7060 27.2610 H 6 ILE 0.000000 + 102 CG2 34.6580 23.7960 27.9520 C.3 6 ILE 0.000000 + 103 HG21 35.0110 24.0490 28.9530 H 6 ILE 0.000000 + 104 HG22 35.6100 23.7730 27.4230 H 6 ILE 0.000000 + 105 HG23 34.3150 22.7680 28.0650 H 6 ILE 0.000000 + 106 CG1 32.9670 24.0830 26.1350 C.3 6 ILE 0.000000 + 107 HG12 32.8150 23.0140 26.2810 H 6 ILE 0.000000 + 108 HG13 32.0160 24.5480 25.8750 H 6 ILE 0.000000 + 109 CD1 33.9640 24.2280 24.9830 C.3 6 ILE 0.000000 + 110 HD11 34.2030 25.2800 24.8310 H 6 ILE 0.000000 + 111 HD12 33.5210 23.6460 24.1740 H 6 ILE 0.000000 + 112 HD13 34.8900 23.7440 25.2930 H 6 ILE 0.000000 + 113 C 32.8780 25.3800 29.8250 C.2 6 ILE 0.000000 + 114 O 33.5170 26.4490 29.9560 O.2 6 ILE 0.000000 + 115 N 32.7560 24.5480 30.8230 N.am 7 LEU 0.000000 + 116 H 32.3370 23.6490 30.6320 H 7 LEU 0.000000 + 117 CA 33.4180 24.6780 32.1280 C.3 7 LEU 0.000000 + 118 HA 33.7720 25.7020 32.2430 H 7 LEU 0.000000 + 119 CB 32.4520 24.2870 33.2690 C.3 7 LEU 0.000000 + 120 HB2 32.2350 23.2190 33.2800 H 7 LEU 0.000000 + 121 HB3 33.0250 24.4910 34.1730 H 7 LEU 0.000000 + 122 CG 31.0680 25.0800 33.2940 C.3 7 LEU 0.000000 + 123 HG 31.2340 26.0000 32.7310 H 7 LEU 0.000000 + 124 CD1 29.9570 24.1850 32.7370 C.3 7 LEU 0.000000 + 125 HD11 29.0910 24.7910 32.4720 H 7 LEU 0.000000 + 126 HD12 29.6750 23.4580 33.4970 H 7 LEU 0.000000 + 127 HD13 30.2420 23.5980 31.8630 H 7 LEU 0.000000 + 128 CD2 30.6790 25.5000 34.6660 C.3 7 LEU 0.000000 + 129 HD21 30.6920 24.6790 35.3840 H 7 LEU 0.000000 + 130 HD22 29.6780 25.9260 34.6040 H 7 LEU 0.000000 + 131 HD23 31.2660 26.3490 35.0140 H 7 LEU 0.000000 + 132 C 34.7040 23.8320 31.9820 C.2 7 LEU 0.000000 + 133 O 34.6080 22.7120 31.4340 O.2 7 LEU 0.000000 + 134 N 35.7410 24.3550 32.5660 N.am 8 ASN 0.000000 + 135 H 35.6570 25.2890 32.9430 H 8 ASN 0.000000 + 136 CA 37.0870 23.9380 32.3400 C.3 8 ASN 0.000000 + 137 HA 37.1950 22.8750 32.1280 H 8 ASN 0.000000 + 138 CB 37.6830 24.6480 31.0790 C.3 8 ASN 0.000000 + 139 HB2 37.0520 24.5140 30.1990 H 8 ASN 0.000000 + 140 HB3 37.6970 25.7010 31.3580 H 8 ASN 0.000000 + 141 CG 39.0690 24.1720 30.7530 C.2 8 ASN 0.000000 + 142 OD1 39.2930 22.9720 30.6160 O.2 8 ASN 0.000000 + 143 ND2 40.1710 24.9660 30.8340 N.am 8 ASN 0.000000 + 144 HD21 40.0640 25.9680 30.8800 H 8 ASN 0.000000 + 145 HD22 41.0730 24.5640 30.6180 H 8 ASN 0.000000 + 146 C 37.9290 24.2620 33.6020 C.2 8 ASN 0.000000 + 147 O 37.7360 25.2990 34.2340 O.2 8 ASN 0.000000 + 148 N 38.8930 23.4110 33.9370 N.am 9 GLY 0.000000 + 149 H 38.8720 22.5590 33.3940 H 9 GLY 0.000000 + 150 CA 39.9370 23.6670 34.9460 C.3 9 GLY 0.000000 + 151 HA2 40.5630 24.4960 34.6190 H 9 GLY 0.000000 + 152 HA3 39.5250 24.0580 35.8760 H 9 GLY 0.000000 + 153 C 40.8200 22.5040 35.2100 C.2 9 GLY 0.000000 + 154 O 40.8260 21.5060 34.4460 O.2 9 GLY 0.000000 + 155 N 41.4770 22.4730 36.3560 N.am 10 LYS 0.000000 + 156 H 41.4390 23.2560 36.9920 H 10 LYS 0.000000 + 157 CA 42.3210 21.3630 36.7660 C.3 10 LYS 0.000000 + 158 HA 42.8380 21.0360 35.8640 H 10 LYS 0.000000 + 159 CB 43.4350 21.8390 37.7360 C.3 10 LYS 0.000000 + 160 HB2 42.9600 22.1300 38.6730 H 10 LYS 0.000000 + 161 HB3 44.1510 21.0180 37.7870 H 10 LYS 0.000000 + 162 CG 44.1460 23.1210 37.2280 C.3 10 LYS 0.000000 + 163 HG2 44.5810 22.9590 36.2420 H 10 LYS 0.000000 + 164 HG3 43.4240 23.9340 37.1510 H 10 LYS 0.000000 + 165 CD 45.2060 23.4740 38.2690 C.3 10 LYS 0.000000 + 166 HD2 44.8340 23.3760 39.2900 H 10 LYS 0.000000 + 167 HD3 46.0450 22.7810 38.2650 H 10 LYS 0.000000 + 168 CE 45.8330 24.8660 37.9360 C.3 10 LYS 0.000000 + 169 HE2 46.8980 24.8670 38.1720 H 10 LYS 0.000000 + 170 HE3 45.6150 25.1390 36.9040 H 10 LYS 0.000000 + 171 NZ 45.3140 25.8850 38.9150 N.4 10 LYS 0.000000 + 172 HZ1 44.3180 26.0490 38.8850 H 10 LYS 0.000000 + 173 HZ2 45.8050 26.7560 38.7650 H 10 LYS 0.000000 + 174 HZ3 45.4340 25.6940 39.8990 H 10 LYS 0.000000 + 175 C 41.6080 20.1420 37.3690 C.2 10 LYS 0.000000 + 176 O 42.1360 19.0170 37.4320 O.2 10 LYS 0.000000 + 177 N 40.3160 20.4070 37.7090 N.am 11 THR 0.000000 + 178 H 40.0180 21.3730 37.7390 H 11 THR 0.000000 + 179 CA 39.3330 19.4280 38.1900 C.3 11 THR 0.000000 + 180 HA 39.6270 18.4390 37.8410 H 11 THR 0.000000 + 181 CB 39.3190 19.4970 39.7400 C.3 11 THR 0.000000 + 182 HB 38.5380 18.8090 40.0630 H 11 THR 0.000000 + 183 CG2 40.6560 18.9940 40.1970 C.3 11 THR 0.000000 + 184 HG21 40.9540 17.9910 39.8960 H 11 THR 0.000000 + 185 HG22 40.6950 18.9840 41.2860 H 11 THR 0.000000 + 186 HG23 41.4530 19.6620 39.8690 H 11 THR 0.000000 + 187 OG1 39.1180 20.7380 40.2290 O.3 11 THR 0.000000 + 188 HG1 39.3210 20.7280 41.1680 H 11 THR 0.000000 + 189 C 37.9370 19.7040 37.7500 C.2 11 THR 0.000000 + 190 O 37.1800 18.7440 37.5920 O.2 11 THR 0.000000 + 191 N 37.5720 20.9090 37.3600 N.am 12 LEU 0.000000 + 192 H 38.1000 21.7450 37.5690 H 12 LEU 0.000000 + 193 CA 36.2620 21.2940 36.7600 C.3 12 LEU 0.000000 + 194 HA 35.4270 20.8870 37.3290 H 12 LEU 0.000000 + 195 CB 36.1690 22.8730 36.7850 C.3 12 LEU 0.000000 + 196 HB2 36.5310 23.2380 37.7460 H 12 LEU 0.000000 + 197 HB3 36.8590 23.2680 36.0410 H 12 LEU 0.000000 + 198 CG 34.8240 23.4830 36.3570 C.3 12 LEU 0.000000 + 199 HG 34.4790 23.0280 35.4280 H 12 LEU 0.000000 + 200 CD1 33.8670 23.3210 37.4770 C.3 12 LEU 0.000000 + 201 HD11 32.9970 23.8770 37.1260 H 12 LEU 0.000000 + 202 HD12 34.3040 23.6910 38.4040 H 12 LEU 0.000000 + 203 HD13 33.5940 22.2650 37.5030 H 12 LEU 0.000000 + 204 CD2 34.9260 25.0520 36.1810 C.3 12 LEU 0.000000 + 205 HD21 35.3340 25.5600 37.0540 H 12 LEU 0.000000 + 206 HD22 33.9260 25.4420 35.9970 H 12 LEU 0.000000 + 207 HD23 35.5550 25.3550 35.3440 H 12 LEU 0.000000 + 208 C 36.0920 20.8050 35.2830 C.2 12 LEU 0.000000 + 209 O 36.9410 21.1020 34.4410 O.2 12 LEU 0.000000 + 210 N 35.0160 20.0800 34.9060 N.am 13 LYS 0.000000 + 211 H 34.3910 19.6970 35.6020 H 13 LYS 0.000000 + 212 CA 34.6420 19.7040 33.5710 C.3 13 LYS 0.000000 + 213 HA 35.0630 20.4210 32.8660 H 13 LYS 0.000000 + 214 CB 35.0340 18.2260 33.2440 C.3 13 LYS 0.000000 + 215 HB2 34.4970 17.5790 33.9380 H 13 LYS 0.000000 + 216 HB3 34.8490 17.9220 32.2140 H 13 LYS 0.000000 + 217 CG 36.5150 17.9230 33.4720 C.3 13 LYS 0.000000 + 218 HG2 37.1620 18.6580 32.9940 H 13 LYS 0.000000 + 219 HG3 36.7010 17.7680 34.5350 H 13 LYS 0.000000 + 220 CD 36.8040 16.4870 32.9940 C.3 13 LYS 0.000000 + 221 HD2 36.1570 15.7470 33.4650 H 13 LYS 0.000000 + 222 HD3 36.4560 16.5060 31.9620 H 13 LYS 0.000000 + 223 CE 38.2640 16.1630 32.9970 C.3 13 LYS 0.000000 + 224 HE2 38.7410 16.7320 32.1990 H 13 LYS 0.000000 + 225 HE3 38.6860 16.4240 33.9670 H 13 LYS 0.000000 + 226 NZ 38.3970 14.6720 32.8370 N.4 13 LYS 0.000000 + 227 HZ1 37.9440 14.3240 32.0050 H 13 LYS 0.000000 + 228 HZ2 37.8880 14.2390 33.5950 H 13 LYS 0.000000 + 229 HZ3 39.3670 14.3910 32.8170 H 13 LYS 0.000000 + 230 C 33.1190 19.8750 33.4000 C.2 13 LYS 0.000000 + 231 O 32.5220 20.2180 34.4480 O.2 13 LYS 0.000000 + 232 N 32.5410 19.9290 32.1820 N.am 14 GLY 0.000000 + 233 H 33.0850 19.6110 31.3920 H 14 GLY 0.000000 + 234 CA 31.1410 20.1350 31.9510 C.3 14 GLY 0.000000 + 235 HA2 30.6960 19.1430 31.8770 H 14 GLY 0.000000 + 236 HA3 30.7070 20.5000 32.8830 H 14 GLY 0.000000 + 237 C 30.7260 21.0300 30.8030 C.2 14 GLY 0.000000 + 238 O 31.4590 21.9860 30.4780 O.2 14 GLY 0.000000 + 239 N 29.6020 20.6610 30.1750 N.am 15 GLU 0.000000 + 240 H 29.2330 19.8010 30.5570 H 15 GLU 0.000000 + 241 CA 29.0530 21.5950 29.1150 C.3 15 GLU 0.000000 + 242 HA 29.4570 22.5920 29.2920 H 15 GLU 0.000000 + 243 CB 29.4520 21.1510 27.7050 C.3 15 GLU 0.000000 + 244 HB2 28.8860 21.7700 27.0090 H 15 GLU 0.000000 + 245 HB3 30.4970 21.3960 27.5120 H 15 GLU 0.000000 + 246 CG 29.1570 19.6680 27.4100 C.3 15 GLU 0.000000 + 247 HG2 29.8650 19.1040 28.0170 H 15 GLU 0.000000 + 248 HG3 28.1090 19.4560 27.6190 H 15 GLU 0.000000 + 249 CD 29.4230 19.3850 25.9680 C.2 15 GLU 0.000000 + 250 OE1 28.4580 19.2500 25.1770 O.co2 15 GLU 0.000000 + 251 OE2 30.5960 19.2970 25.5210 O.co2 15 GLU 0.000000 + 252 C 27.5630 21.8430 29.3530 C.2 15 GLU 0.000000 + 253 O 26.8140 21.0200 29.7960 O.2 15 GLU 0.000000 + 254 N 27.0800 22.9660 28.8630 N.am 16 THR 0.000000 + 255 H 27.7180 23.6470 28.4770 H 16 THR 0.000000 + 256 CA 25.6180 23.3420 28.9870 C.3 16 THR 0.000000 + 257 HA 24.9870 22.4660 28.8320 H 16 THR 0.000000 + 258 CB 25.3000 23.7550 30.4630 C.3 16 THR 0.000000 + 259 HB 25.6640 23.0280 31.1900 H 16 THR 0.000000 + 260 CG2 26.0790 25.0290 30.8510 C.3 16 THR 0.000000 + 261 HG21 26.0020 25.2120 31.9230 H 16 THR 0.000000 + 262 HG22 25.8270 25.9990 30.4200 H 16 THR 0.000000 + 263 HG23 27.1390 24.8330 30.6860 H 16 THR 0.000000 + 264 OG1 23.9190 23.8700 30.5910 O.3 16 THR 0.000000 + 265 HG1 23.6050 22.9660 30.6540 H 16 THR 0.000000 + 266 C 25.1360 24.3870 27.9560 C.2 16 THR 0.000000 + 267 O 25.8470 25.3920 27.6860 O.2 16 THR 0.000000 + 268 N 23.9440 24.1260 27.3740 N.am 17 THR 0.000000 + 269 H 23.4140 23.3000 27.6150 H 17 THR 0.000000 + 270 CA 23.3410 25.0880 26.4180 C.3 17 THR 0.000000 + 271 HA 24.1390 25.6970 25.9920 H 17 THR 0.000000 + 272 CB 22.6340 24.3990 25.2500 C.3 17 THR 0.000000 + 273 HB 22.1940 25.1420 24.5850 H 17 THR 0.000000 + 274 CG2 23.5340 23.4660 24.4060 C.3 17 THR 0.000000 + 275 HG21 22.9810 22.8750 23.6770 H 17 THR 0.000000 + 276 HG22 24.0160 22.7890 25.1120 H 17 THR 0.000000 + 277 HG23 24.3050 24.1190 23.9980 H 17 THR 0.000000 + 278 OG1 21.6180 23.5160 25.7400 O.3 17 THR 0.000000 + 279 HG1 21.1580 23.2100 24.9550 H 17 THR 0.000000 + 280 C 22.4090 26.0840 27.0800 C.2 17 THR 0.000000 + 281 O 21.8650 25.8800 28.1710 O.2 17 THR 0.000000 + 282 N 22.2840 27.1860 26.3670 N.am 18 THR 0.000000 + 283 H 22.9180 27.2110 25.5810 H 18 THR 0.000000 + 284 CA 21.3410 28.3460 26.6650 C.3 18 THR 0.000000 + 285 HA 20.4470 28.0470 27.2130 H 18 THR 0.000000 + 286 CB 21.9680 29.4240 27.6060 C.3 18 THR 0.000000 + 287 HB 22.9260 29.8000 27.2510 H 18 THR 0.000000 + 288 CG2 20.9590 30.5650 27.7470 C.3 18 THR 0.000000 + 289 HG21 21.1770 31.2320 28.5810 H 18 THR 0.000000 + 290 HG22 19.9320 30.2140 27.8380 H 18 THR 0.000000 + 291 HG23 21.0570 31.1490 26.8310 H 18 THR 0.000000 + 292 OG1 21.9830 28.9740 29.0510 O.3 18 THR 0.000000 + 293 HG1 22.8660 29.1230 29.4000 H 18 THR 0.000000 + 294 C 20.8290 28.9560 25.3540 C.2 18 THR 0.000000 + 295 O 21.5530 29.4580 24.5280 O.2 18 THR 0.000000 + 296 N 19.5420 28.8720 25.0830 N.am 19 GLU 0.000000 + 297 H 18.9190 28.5790 25.8230 H 19 GLU 0.000000 + 298 CA 18.9320 29.5760 23.9870 C.3 19 GLU 0.000000 + 299 HA 19.6790 29.5080 23.1970 H 19 GLU 0.000000 + 300 CB 17.6860 28.7850 23.6270 C.3 19 GLU 0.000000 + 301 HB2 17.8990 27.7220 23.5140 H 19 GLU 0.000000 + 302 HB3 16.9980 28.8420 24.4710 H 19 GLU 0.000000 + 303 CG 16.8520 29.2840 22.4770 C.3 19 GLU 0.000000 + 304 HG2 16.2460 28.4470 22.1280 H 19 GLU 0.000000 + 305 HG3 16.1330 30.0570 22.7480 H 19 GLU 0.000000 + 306 CD 17.7360 29.7310 21.2810 C.2 19 GLU 0.000000 + 307 OE1 18.3630 28.8000 20.6790 O.co2 19 GLU 0.000000 + 308 OE2 17.8250 30.9440 20.9200 O.co2 19 GLU 0.000000 + 309 C 18.6310 31.0490 24.3110 C.2 19 GLU 0.000000 + 310 O 17.9510 31.3360 25.2400 O.2 19 GLU 0.000000 + 311 N 19.1090 32.0520 23.6090 N.am 20 ALA 0.000000 + 312 H 19.6590 31.7660 22.8100 H 20 ALA 0.000000 + 313 CA 18.9620 33.5050 23.8850 C.3 20 ALA 0.000000 + 314 HA 17.9800 33.7420 24.2950 H 20 ALA 0.000000 + 315 CB 19.9780 33.9790 24.9610 C.3 20 ALA 0.000000 + 316 HB1 19.8070 35.0260 25.2140 H 20 ALA 0.000000 + 317 HB2 20.9830 33.9230 24.5440 H 20 ALA 0.000000 + 318 HB3 19.8000 33.4040 25.8690 H 20 ALA 0.000000 + 319 C 19.1210 34.3520 22.5950 C.2 20 ALA 0.000000 + 320 O 19.5650 33.8670 21.5410 O.2 20 ALA 0.000000 + 321 N 18.8190 35.6980 22.6660 N.am 21 VAL 0.000000 + 322 H 18.4660 36.0070 23.5610 H 21 VAL 0.000000 + 323 CA 18.7270 36.6070 21.5050 C.3 21 VAL 0.000000 + 324 HA 18.5540 36.0390 20.5920 H 21 VAL 0.000000 + 325 CB 17.4370 37.4640 21.7800 C.3 21 VAL 0.000000 + 326 HB 17.4770 38.1300 22.6420 H 21 VAL 0.000000 + 327 CG1 17.0720 38.3790 20.6730 C.3 21 VAL 0.000000 + 328 HG11 16.9910 37.8050 19.7500 H 21 VAL 0.000000 + 329 HG12 17.6850 39.2690 20.5330 H 21 VAL 0.000000 + 330 HG13 16.0810 38.7870 20.8740 H 21 VAL 0.000000 + 331 CG2 16.2510 36.5360 21.9200 C.3 21 VAL 0.000000 + 332 HG21 15.3330 37.0330 21.6050 H 21 VAL 0.000000 + 333 HG22 16.1280 36.2190 22.9560 H 21 VAL 0.000000 + 334 HG23 16.4770 35.6810 21.2840 H 21 VAL 0.000000 + 335 C 19.9760 37.5210 21.4050 C.2 21 VAL 0.000000 + 336 O 20.2950 38.0220 20.3060 O.2 21 VAL 0.000000 + 337 N 20.7280 37.6510 22.4570 N.am 22 ASP 0.000000 + 338 H 20.4600 37.1040 23.2620 H 22 ASP 0.000000 + 339 CA 21.9200 38.5170 22.5610 C.3 22 ASP 0.000000 + 340 HA 22.2180 38.7210 21.5320 H 22 ASP 0.000000 + 341 CB 21.4830 39.7010 23.3500 C.3 22 ASP 0.000000 + 342 HB2 20.6320 40.1560 22.8430 H 22 ASP 0.000000 + 343 HB3 21.1330 39.4210 24.3440 H 22 ASP 0.000000 + 344 CG 22.5760 40.7460 23.5900 C.2 22 ASP 0.000000 + 345 OD1 23.6810 40.5880 23.0430 O.co2 22 ASP 0.000000 + 346 OD2 22.3400 41.7510 24.2640 O.co2 22 ASP 0.000000 + 347 C 23.0190 37.7030 23.2940 C.2 22 ASP 0.000000 + 348 O 22.8390 37.1840 24.4120 O.2 22 ASP 0.000000 + 349 N 24.2100 37.6490 22.6940 N.am 23 ALA 0.000000 + 350 H 24.3580 38.0650 21.7860 H 23 ALA 0.000000 + 351 CA 25.4930 37.1720 23.2150 C.3 23 ALA 0.000000 + 352 HA 25.3710 36.0890 23.2210 H 23 ALA 0.000000 + 353 CB 26.7010 37.4860 22.3260 C.3 23 ALA 0.000000 + 354 HB1 26.4460 37.3090 21.2800 H 23 ALA 0.000000 + 355 HB2 27.3790 36.7080 22.6760 H 23 ALA 0.000000 + 356 HB3 27.0910 38.4940 22.4680 H 23 ALA 0.000000 + 357 C 25.7480 37.7570 24.6420 C.2 23 ALA 0.000000 + 358 O 26.0910 36.9530 25.5180 O.2 23 ALA 0.000000 + 359 N 25.5640 39.0500 24.8460 N.am 24 ALA 0.000000 + 360 H 25.2140 39.6740 24.1330 H 24 ALA 0.000000 + 361 CA 25.7450 39.6870 26.1530 C.3 24 ALA 0.000000 + 362 HA 26.7610 39.4190 26.4450 H 24 ALA 0.000000 + 363 CB 25.4900 41.1890 25.9380 C.3 24 ALA 0.000000 + 364 HB1 26.2470 41.6760 25.3250 H 24 ALA 0.000000 + 365 HB2 25.6330 41.7290 26.8740 H 24 ALA 0.000000 + 366 HB3 24.5610 41.4670 25.4400 H 24 ALA 0.000000 + 367 C 24.7960 39.1010 27.1370 C.2 24 ALA 0.000000 + 368 O 25.1160 38.9750 28.3290 O.2 24 ALA 0.000000 + 369 N 23.5770 38.6590 26.7360 N.am 25 THR 0.000000 + 370 H 23.3980 38.6810 25.7430 H 25 THR 0.000000 + 371 CA 22.5870 38.0940 27.6800 C.3 25 THR 0.000000 + 372 HA 22.7550 38.4950 28.6810 H 25 THR 0.000000 + 373 CB 21.1960 38.5490 27.2620 C.3 25 THR 0.000000 + 374 HB 20.7970 37.8830 26.4970 H 25 THR 0.000000 + 375 CG2 20.2460 38.3690 28.4380 C.3 25 THR 0.000000 + 376 HG21 20.2030 37.3290 28.7630 H 25 THR 0.000000 + 377 HG22 19.2550 38.7400 28.1760 H 25 THR 0.000000 + 378 HG23 20.5740 38.9770 29.2800 H 25 THR 0.000000 + 379 OG1 21.1990 39.9310 27.0300 O.3 25 THR 0.000000 + 380 HG1 20.2930 40.1560 26.8070 H 25 THR 0.000000 + 381 C 22.7880 36.6180 27.9280 C.2 25 THR 0.000000 + 382 O 22.6180 36.1640 29.0500 O.2 25 THR 0.000000 + 383 N 23.2160 35.8540 26.9290 N.am 26 ALA 0.000000 + 384 H 23.3150 36.2080 25.9880 H 26 ALA 0.000000 + 385 CA 23.6520 34.5130 27.1590 C.3 26 ALA 0.000000 + 386 HA 22.7810 33.9400 27.4760 H 26 ALA 0.000000 + 387 CB 24.0620 33.9130 25.7340 C.3 26 ALA 0.000000 + 388 HB1 23.1200 33.7320 25.2150 H 26 ALA 0.000000 + 389 HB2 24.6950 33.0290 25.8040 H 26 ALA 0.000000 + 390 HB3 24.7150 34.6130 25.2110 H 26 ALA 0.000000 + 391 C 24.8560 34.5230 28.0620 C.2 26 ALA 0.000000 + 392 O 24.8890 33.7450 28.9850 O.2 26 ALA 0.000000 + 393 N 25.7490 35.5000 28.0270 N.am 27 GLU 0.000000 + 394 H 25.9400 35.9330 27.1350 H 27 GLU 0.000000 + 395 CA 26.7120 35.6710 29.0370 C.3 27 GLU 0.000000 + 396 HA 27.3060 34.7570 29.0970 H 27 GLU 0.000000 + 397 CB 27.6840 36.8330 28.6050 C.3 27 GLU 0.000000 + 398 HB2 28.2700 36.5610 27.7280 H 27 GLU 0.000000 + 399 HB3 27.1780 37.7730 28.3870 H 27 GLU 0.000000 + 400 CG 28.7420 37.1650 29.6640 C.3 27 GLU 0.000000 + 401 HG2 28.1930 37.5370 30.5290 H 27 GLU 0.000000 + 402 HG3 29.2670 36.2440 29.9140 H 27 GLU 0.000000 + 403 CD 29.8870 38.2420 29.2690 C.2 27 GLU 0.000000 + 404 OE1 31.1080 37.8270 29.1640 O.co2 27 GLU 0.000000 + 405 OE2 29.5290 39.4200 29.1100 O.co2 27 GLU 0.000000 + 406 C 26.0990 35.7420 30.4500 C.2 27 GLU 0.000000 + 407 O 26.5530 35.1620 31.4140 O.2 27 GLU 0.000000 + 408 N 25.1240 36.6090 30.6040 N.am 28 LYS 0.000000 + 409 H 24.7100 37.1060 29.8270 H 28 LYS 0.000000 + 410 CA 24.5380 36.9470 31.9500 C.3 28 LYS 0.000000 + 411 HA 25.3240 37.3000 32.6180 H 28 LYS 0.000000 + 412 CB 23.5590 38.0520 31.7280 C.3 28 LYS 0.000000 + 413 HB2 24.0960 38.9430 31.4030 H 28 LYS 0.000000 + 414 HB3 22.7610 37.8110 31.0250 H 28 LYS 0.000000 + 415 CG 22.8850 38.4010 33.1500 C.3 28 LYS 0.000000 + 416 HG2 22.3430 37.5420 33.5450 H 28 LYS 0.000000 + 417 HG3 23.6380 38.6980 33.8790 H 28 LYS 0.000000 + 418 CD 21.8260 39.5790 33.0630 C.3 28 LYS 0.000000 + 419 HD2 20.9300 39.1460 32.6160 H 28 LYS 0.000000 + 420 HD3 21.6560 39.9890 34.0580 H 28 LYS 0.000000 + 421 CE 22.3590 40.8500 32.2670 C.3 28 LYS 0.000000 + 422 HE2 23.4320 40.8990 32.4490 H 28 LYS 0.000000 + 423 HE3 22.1990 40.7560 31.1930 H 28 LYS 0.000000 + 424 NZ 21.5210 42.0130 32.7150 N.4 28 LYS 0.000000 + 425 HZ1 21.6960 42.2940 33.6700 H 28 LYS 0.000000 + 426 HZ2 20.5410 41.7770 32.6530 H 28 LYS 0.000000 + 427 HZ3 21.6510 42.8270 32.1310 H 28 LYS 0.000000 + 428 C 23.8660 35.7780 32.5350 C.2 28 LYS 0.000000 + 429 O 23.9940 35.6650 33.7420 O.2 28 LYS 0.000000 + 430 N 23.3290 34.8850 31.7120 N.am 29 VAL 0.000000 + 431 H 23.2290 35.1110 30.7330 H 29 VAL 0.000000 + 432 CA 22.7360 33.6500 32.0970 C.3 29 VAL 0.000000 + 433 HA 21.9990 33.8790 32.8660 H 29 VAL 0.000000 + 434 CB 21.7350 33.1660 30.9620 C.3 29 VAL 0.000000 + 435 HB 22.3750 32.9510 30.1060 H 29 VAL 0.000000 + 436 CG1 21.1390 31.7830 31.4450 C.3 29 VAL 0.000000 + 437 HG11 20.5920 31.4130 30.5790 H 29 VAL 0.000000 + 438 HG12 20.5750 31.9080 32.3700 H 29 VAL 0.000000 + 439 HG13 21.9930 31.1130 31.5340 H 29 VAL 0.000000 + 440 CG2 20.4820 33.9920 30.5470 C.3 29 VAL 0.000000 + 441 HG21 19.9660 33.6180 29.6620 H 29 VAL 0.000000 + 442 HG22 20.7390 35.0190 30.2860 H 29 VAL 0.000000 + 443 HG23 19.8380 34.1100 31.4190 H 29 VAL 0.000000 + 444 C 23.7810 32.6420 32.4840 C.2 29 VAL 0.000000 + 445 O 23.6040 31.8760 33.4620 O.2 29 VAL 0.000000 + 446 N 24.9620 32.6410 31.7580 N.am 30 PHE 0.000000 + 447 H 24.9970 33.2870 30.9810 H 30 PHE 0.000000 + 448 CA 26.1120 31.7010 32.0330 C.3 30 PHE 0.000000 + 449 HA 25.6920 30.7530 32.3710 H 30 PHE 0.000000 + 450 CB 26.9010 31.5820 30.7130 C.3 30 PHE 0.000000 + 451 HB2 26.9660 32.5370 30.1910 H 30 PHE 0.000000 + 452 HB3 27.9280 31.2660 30.8880 H 30 PHE 0.000000 + 453 CG 26.3480 30.6000 29.6560 C.ar 30 PHE 0.000000 + 454 CD1 25.7510 29.2960 29.8780 C.ar 30 PHE 0.000000 + 455 HD1 25.7050 28.9430 30.8970 H 30 PHE 0.000000 + 456 CE1 25.3450 28.3770 28.8170 C.ar 30 PHE 0.000000 + 457 HE1 24.8100 27.4640 29.0390 H 30 PHE 0.000000 + 458 CZ 25.5340 28.8400 27.5150 C.ar 30 PHE 0.000000 + 459 HZ 25.1960 28.2670 26.6660 H 30 PHE 0.000000 + 460 CE2 26.0960 30.0990 27.2710 C.ar 30 PHE 0.000000 + 461 HE2 26.2120 30.3190 26.2190 H 30 PHE 0.000000 + 462 CD2 26.5330 30.9240 28.2970 C.ar 30 PHE 0.000000 + 463 HD2 27.1350 31.7780 28.0290 H 30 PHE 0.000000 + 464 C 26.9880 32.1890 33.2460 C.2 30 PHE 0.000000 + 465 O 27.6090 31.3440 33.9050 O.2 30 PHE 0.000000 + 466 N 27.0380 33.4460 33.5400 N.am 31 LYS 0.000000 + 467 H 26.7100 34.1050 32.8490 H 31 LYS 0.000000 + 468 CA 27.4050 34.0220 34.8540 C.3 31 LYS 0.000000 + 469 HA 28.4370 33.7640 35.0920 H 31 LYS 0.000000 + 470 CB 27.2740 35.5990 34.8580 C.3 31 LYS 0.000000 + 471 HB2 26.2420 35.7140 34.5270 H 31 LYS 0.000000 + 472 HB3 27.2920 36.0980 35.8270 H 31 LYS 0.000000 + 473 CG 28.3780 36.2750 33.9190 C.3 31 LYS 0.000000 + 474 HG2 28.5220 35.7100 32.9970 H 31 LYS 0.000000 + 475 HG3 27.9260 37.2290 33.6490 H 31 LYS 0.000000 + 476 CD 29.8230 36.4870 34.4390 C.3 31 LYS 0.000000 + 477 HD2 29.7550 36.9770 35.4110 H 31 LYS 0.000000 + 478 HD3 30.1320 35.4720 34.6840 H 31 LYS 0.000000 + 479 CE 30.7770 37.1500 33.3940 C.3 31 LYS 0.000000 + 480 HE2 30.6330 36.6300 32.4470 H 31 LYS 0.000000 + 481 HE3 30.4360 38.1580 33.1580 H 31 LYS 0.000000 + 482 NZ 32.1380 37.1210 33.9260 N.4 31 LYS 0.000000 + 483 HZ1 32.2720 37.4580 34.8690 H 31 LYS 0.000000 + 484 HZ2 32.6760 37.7770 33.3760 H 31 LYS 0.000000 + 485 HZ3 32.5550 36.2100 33.8050 H 31 LYS 0.000000 + 486 C 26.5160 33.5620 35.9830 C.2 31 LYS 0.000000 + 487 O 27.0180 32.9930 36.9430 O.2 31 LYS 0.000000 + 488 N 25.1850 33.7450 35.9530 N.am 32 GLN 0.000000 + 489 H 24.7370 34.1940 35.1660 H 32 GLN 0.000000 + 490 CA 24.3650 33.1970 37.0270 C.3 32 GLN 0.000000 + 491 HA 24.6790 33.8220 37.8630 H 32 GLN 0.000000 + 492 CB 22.8910 33.4270 36.6880 C.3 32 GLN 0.000000 + 493 HB2 22.8450 33.3660 35.6010 H 32 GLN 0.000000 + 494 HB3 22.2850 32.6850 37.2090 H 32 GLN 0.000000 + 495 CG 22.2800 34.8400 37.0280 C.3 32 GLN 0.000000 + 496 HG2 22.0390 34.8810 38.0900 H 32 GLN 0.000000 + 497 HG3 22.8990 35.7100 36.8070 H 32 GLN 0.000000 + 498 CD 20.9580 35.1240 36.1950 C.2 32 GLN 0.000000 + 499 OE1 19.8830 34.8230 36.7380 O.2 32 GLN 0.000000 + 500 NE2 20.9880 35.5300 34.9740 N.am 32 GLN 0.000000 + 501 HE21 21.9020 35.7870 34.6280 H 32 GLN 0.000000 + 502 HE22 20.1770 35.7140 34.4000 H 32 GLN 0.000000 + 503 C 24.5980 31.7070 37.2320 C.2 32 GLN 0.000000 + 504 O 24.7940 31.2930 38.3840 O.2 32 GLN 0.000000 + 505 N 24.5300 30.8750 36.1420 N.am 33 TYR 0.000000 + 506 H 24.5870 31.2740 35.2160 H 33 TYR 0.000000 + 507 CA 24.7220 29.4590 36.2170 C.3 33 TYR 0.000000 + 508 HA 23.8810 29.0420 36.7720 H 33 TYR 0.000000 + 509 CB 24.6220 28.8480 34.8420 C.3 33 TYR 0.000000 + 510 HB2 23.6210 29.0060 34.4420 H 33 TYR 0.000000 + 511 HB3 25.3530 29.3880 34.2400 H 33 TYR 0.000000 + 512 CG 24.8770 27.3040 34.7040 C.ar 33 TYR 0.000000 + 513 CD1 23.8080 26.3830 34.9380 C.ar 33 TYR 0.000000 + 514 HD1 22.8140 26.7540 35.1400 H 33 TYR 0.000000 + 515 CE1 24.0540 24.9910 35.0750 C.ar 33 TYR 0.000000 + 516 HE1 23.3000 24.2510 35.3000 H 33 TYR 0.000000 + 517 CZ 25.3990 24.5620 34.9340 C.ar 33 TYR 0.000000 + 518 OH 25.6580 23.2120 34.9830 O.3 33 TYR 0.000000 + 519 HH 26.6080 23.0800 35.0300 H 33 TYR 0.000000 + 520 CE2 26.4100 25.4590 34.7230 C.ar 33 TYR 0.000000 + 521 HE2 27.4430 25.1570 34.6300 H 33 TYR 0.000000 + 522 CD2 26.1460 26.8180 34.6020 C.ar 33 TYR 0.000000 + 523 HD2 26.9920 27.4690 34.4350 H 33 TYR 0.000000 + 524 C 26.0780 29.1550 36.8540 C.2 33 TYR 0.000000 + 525 O 26.1790 28.1860 37.5660 O.2 33 TYR 0.000000 + 526 N 27.1590 29.7880 36.5080 N.am 34 ALA 0.000000 + 527 H 26.9970 30.5630 35.8810 H 34 ALA 0.000000 + 528 CA 28.4730 29.5350 37.1000 C.3 34 ALA 0.000000 + 529 HA 28.7170 28.4760 37.0230 H 34 ALA 0.000000 + 530 CB 29.6510 30.2650 36.4020 C.3 34 ALA 0.000000 + 531 HB1 30.5770 29.8130 36.7570 H 34 ALA 0.000000 + 532 HB2 29.6190 31.2960 36.7520 H 34 ALA 0.000000 + 533 HB3 29.6810 30.1590 35.3170 H 34 ALA 0.000000 + 534 C 28.5080 29.8350 38.6140 C.2 34 ALA 0.000000 + 535 O 29.0970 29.0770 39.3890 O.2 34 ALA 0.000000 + 536 N 27.8140 30.8640 39.0240 N.am 35 ASN 0.000000 + 537 H 27.5940 31.5350 38.3010 H 35 ASN 0.000000 + 538 CA 27.7430 31.2520 40.4450 C.3 35 ASN 0.000000 + 539 HA 28.7130 31.1680 40.9350 H 35 ASN 0.000000 + 540 CB 27.2540 32.6840 40.5410 C.3 35 ASN 0.000000 + 541 HB2 27.7980 33.3610 39.8830 H 35 ASN 0.000000 + 542 HB3 26.1920 32.7270 40.3000 H 35 ASN 0.000000 + 543 CG 27.3260 33.1690 41.9470 C.2 35 ASN 0.000000 + 544 OD1 26.4930 32.7430 42.7630 O.2 35 ASN 0.000000 + 545 ND2 28.0990 34.1830 42.2230 N.am 35 ASN 0.000000 + 546 HD21 28.8670 34.3500 41.5890 H 35 ASN 0.000000 + 547 HD22 28.2760 34.3970 43.1930 H 35 ASN 0.000000 + 548 C 26.8330 30.2000 41.1270 C.2 35 ASN 0.000000 + 549 O 27.1140 29.6860 42.2380 O.2 35 ASN 0.000000 + 550 N 25.8190 29.6160 40.3950 N.am 36 ASP 0.000000 + 551 H 25.6080 30.1440 39.5600 H 36 ASP 0.000000 + 552 CA 25.0040 28.4010 40.8670 C.3 36 ASP 0.000000 + 553 HA 24.4910 28.8190 41.7330 H 36 ASP 0.000000 + 554 CB 23.8190 28.1750 39.9480 C.3 36 ASP 0.000000 + 555 HB2 23.3790 29.1170 39.6230 H 36 ASP 0.000000 + 556 HB3 24.2790 27.5860 39.1540 H 36 ASP 0.000000 + 557 CG 22.7200 27.3500 40.4700 C.2 36 ASP 0.000000 + 558 OD1 22.2140 26.4850 39.7140 O.co2 36 ASP 0.000000 + 559 OD2 22.3610 27.4550 41.6530 O.co2 36 ASP 0.000000 + 560 C 25.7930 27.1130 41.2440 C.2 36 ASP 0.000000 + 561 O 25.3570 26.3910 42.1120 O.2 36 ASP 0.000000 + 562 N 26.9910 27.0060 40.6660 N.am 37 ASN 0.000000 + 563 H 27.3060 27.7790 40.0980 H 37 ASN 0.000000 + 564 CA 27.8290 25.8140 40.6360 C.3 37 ASN 0.000000 + 565 HA 27.3780 25.1300 41.3540 H 37 ASN 0.000000 + 566 CB 27.8730 25.2810 39.1950 C.3 37 ASN 0.000000 + 567 HB2 27.9360 26.1060 38.4870 H 37 ASN 0.000000 + 568 HB3 28.7020 24.5790 39.1010 H 37 ASN 0.000000 + 569 CG 26.6520 24.4920 38.8420 C.2 37 ASN 0.000000 + 570 OD1 26.4320 23.3570 39.2820 O.2 37 ASN 0.000000 + 571 ND2 25.7060 25.0570 38.1770 N.am 37 ASN 0.000000 + 572 HD21 25.8040 26.0500 38.0160 H 37 ASN 0.000000 + 573 HD22 24.8950 24.5020 37.9470 H 37 ASN 0.000000 + 574 C 29.1960 26.0530 41.2610 C.2 37 ASN 0.000000 + 575 O 30.0640 25.1710 41.1820 O.2 37 ASN 0.000000 + 576 N 29.3580 27.1760 42.0120 N.am 38 GLY 0.000000 + 577 H 28.5560 27.7650 42.1890 H 38 GLY 0.000000 + 578 CA 30.6370 27.4600 42.6810 C.3 38 GLY 0.000000 + 579 HA2 30.4440 28.2960 43.3540 H 38 GLY 0.000000 + 580 HA3 30.9000 26.6550 43.3680 H 38 GLY 0.000000 + 581 C 31.8940 27.7740 41.7850 C.2 38 GLY 0.000000 + 582 O 33.0270 27.4290 42.1240 O.2 38 GLY 0.000000 + 583 N 31.7310 28.2870 40.5790 N.am 39 VAL 0.000000 + 584 H 30.7940 28.6240 40.4080 H 39 VAL 0.000000 + 585 CA 32.6640 28.4490 39.4030 C.3 39 VAL 0.000000 + 586 HA 33.5980 27.9110 39.5700 H 39 VAL 0.000000 + 587 CB 32.0150 27.7780 38.1790 C.3 39 VAL 0.000000 + 588 HB 31.0050 28.1580 38.0270 H 39 VAL 0.000000 + 589 CG1 32.9890 28.1210 37.0140 C.3 39 VAL 0.000000 + 590 HG11 32.6360 27.5190 36.1760 H 39 VAL 0.000000 + 591 HG12 34.0190 27.9630 37.3340 H 39 VAL 0.000000 + 592 HG13 32.8690 29.1170 36.5880 H 39 VAL 0.000000 + 593 CG2 31.9430 26.2740 38.4370 C.3 39 VAL 0.000000 + 594 HG21 31.5400 25.7290 37.5830 H 39 VAL 0.000000 + 595 HG22 31.3560 26.0860 39.3370 H 39 VAL 0.000000 + 596 HG23 32.9070 25.8630 38.7380 H 39 VAL 0.000000 + 597 C 33.0290 29.9090 39.2350 C.2 39 VAL 0.000000 + 598 O 32.1860 30.6830 38.7570 O.2 39 VAL 0.000000 + 599 N 34.2680 30.2810 39.5580 N.am 40 ASP 0.000000 + 600 H 34.8380 29.5430 39.9470 H 40 ASP 0.000000 + 601 CA 34.8750 31.5510 39.0960 C.3 40 ASP 0.000000 + 602 HA 34.1430 32.0780 38.4870 H 40 ASP 0.000000 + 603 CB 35.1830 32.4180 40.3450 C.3 40 ASP 0.000000 + 604 HB2 34.1840 32.6570 40.7100 H 40 ASP 0.000000 + 605 HB3 35.7070 31.7880 41.0650 H 40 ASP 0.000000 + 606 CG 35.8790 33.6830 40.0090 C.2 40 ASP 0.000000 + 607 OD1 35.3930 34.4100 39.0760 O.co2 40 ASP 0.000000 + 608 OD2 37.0250 33.8970 40.4600 O.co2 40 ASP 0.000000 + 609 C 36.0620 31.1690 38.2380 C.2 40 ASP 0.000000 + 610 O 36.8500 30.2750 38.6300 O.2 40 ASP 0.000000 + 611 N 36.1720 31.7510 37.1020 N.am 41 GLY 0.000000 + 612 H 35.4430 32.4080 36.8580 H 41 GLY 0.000000 + 613 CA 37.2140 31.4840 36.1890 C.3 41 GLY 0.000000 + 614 HA2 38.0720 31.0140 36.6700 H 41 GLY 0.000000 + 615 HA3 36.7610 30.6720 35.6200 H 41 GLY 0.000000 + 616 C 37.6230 32.7090 35.3790 C.2 41 GLY 0.000000 + 617 O 37.2880 33.8620 35.6860 O.2 41 GLY 0.000000 + 618 N 38.3540 32.4220 34.3160 N.am 42 GLU 0.000000 + 619 H 38.7890 31.5120 34.3680 H 42 GLU 0.000000 + 620 CA 38.6030 33.3100 33.2280 C.3 42 GLU 0.000000 + 621 HA 38.3290 34.3180 33.5410 H 42 GLU 0.000000 + 622 CB 40.1580 33.2940 33.0400 C.3 42 GLU 0.000000 + 623 HB2 40.6560 33.3980 34.0040 H 42 GLU 0.000000 + 624 HB3 40.4170 32.3260 32.6110 H 42 GLU 0.000000 + 625 CG 40.6730 34.3280 32.0460 C.3 42 GLU 0.000000 + 626 HG2 41.6060 34.0150 31.5800 H 42 GLU 0.000000 + 627 HG3 39.9700 34.5010 31.2310 H 42 GLU 0.000000 + 628 CD 41.0140 35.6130 32.8040 C.2 42 GLU 0.000000 + 629 OE1 41.9440 35.6930 33.6440 O.co2 42 GLU 0.000000 + 630 OE2 40.2180 36.6020 32.6560 O.co2 42 GLU 0.000000 + 631 C 37.7800 33.0330 32.0330 C.2 42 GLU 0.000000 + 632 O 37.5770 31.8700 31.6900 O.2 42 GLU 0.000000 + 633 N 37.2280 34.0690 31.4120 N.am 43 TRP 0.000000 + 634 H 37.4230 35.0350 31.6340 H 43 TRP 0.000000 + 635 CA 36.2330 33.9510 30.3540 C.3 43 TRP 0.000000 + 636 HA 35.8500 32.9310 30.3480 H 43 TRP 0.000000 + 637 CB 34.9840 34.8890 30.6160 C.3 43 TRP 0.000000 + 638 HB2 35.4360 35.8680 30.7710 H 43 TRP 0.000000 + 639 HB3 34.4270 34.9180 29.6790 H 43 TRP 0.000000 + 640 CG 34.1150 34.5360 31.8380 C.2 43 TRP 0.000000 + 641 CD1 34.4280 34.7080 33.1540 C.2 43 TRP 0.000000 + 642 HD1 35.3870 35.0520 33.5110 H 43 TRP 0.000000 + 643 NE1 33.3990 34.1100 33.8770 N.pl3 43 TRP 0.000000 + 644 HE1 33.5110 34.0660 34.8800 H 43 TRP 0.000000 + 645 CE2 32.4440 33.4630 33.0730 C.ar 43 TRP 0.000000 + 646 CZ2 31.2480 32.7450 33.2960 C.ar 43 TRP 0.000000 + 647 HZ2 31.0070 32.4290 34.3010 H 43 TRP 0.000000 + 648 CH2 30.5750 32.1940 32.1990 C.ar 43 TRP 0.000000 + 649 HH2 29.7400 31.5270 32.3550 H 43 TRP 0.000000 + 650 CZ3 30.9880 32.5410 30.9090 C.ar 43 TRP 0.000000 + 651 HZ3 30.4120 32.2360 30.0470 H 43 TRP 0.000000 + 652 CE3 32.1090 33.3270 30.6820 C.ar 43 TRP 0.000000 + 653 HE3 32.3970 33.6790 29.7030 H 43 TRP 0.000000 + 654 CD2 32.8700 33.8170 31.7650 C.ar 43 TRP 0.000000 + 655 C 36.9100 34.2350 29.0340 C.2 43 TRP 0.000000 + 656 O 37.6600 35.2020 28.8230 O.2 43 TRP 0.000000 + 657 N 36.4680 33.3980 28.1130 N.am 44 THR 0.000000 + 658 H 35.9190 32.5900 28.3670 H 44 THR 0.000000 + 659 CA 36.6270 33.5260 26.6680 C.3 44 THR 0.000000 + 660 HA 36.8250 34.5800 26.4740 H 44 THR 0.000000 + 661 CB 37.8130 32.7940 26.0620 C.3 44 THR 0.000000 + 662 HB 37.6950 32.7890 24.9780 H 44 THR 0.000000 + 663 CG2 39.1420 33.4110 26.4700 C.3 44 THR 0.000000 + 664 HG21 39.9710 32.8140 26.0900 H 44 THR 0.000000 + 665 HG22 39.2770 33.3950 27.5520 H 44 THR 0.000000 + 666 HG23 39.3600 34.4080 26.0880 H 44 THR 0.000000 + 667 OG1 37.8540 31.5070 26.6040 O.3 44 THR 0.000000 + 668 HG1 37.6290 30.9070 25.8890 H 44 THR 0.000000 + 669 C 35.2670 33.2950 26.0050 C.2 44 THR 0.000000 + 670 O 34.4800 32.5770 26.4440 O.2 44 THR 0.000000 + 671 N 35.1370 33.9190 24.8480 N.am 45 TYR 0.000000 + 672 H 35.9000 34.5260 24.5850 H 45 TYR 0.000000 + 673 CA 34.0510 33.6790 23.8140 C.3 45 TYR 0.000000 + 674 HA 33.5650 32.7480 24.1090 H 45 TYR 0.000000 + 675 CB 33.0610 34.8900 23.8360 C.3 45 TYR 0.000000 + 676 HB2 32.6890 35.0850 24.8430 H 45 TYR 0.000000 + 677 HB3 33.6700 35.7620 23.5960 H 45 TYR 0.000000 + 678 CG 31.8250 34.7470 22.9620 C.ar 45 TYR 0.000000 + 679 CD1 30.9550 33.6840 23.0610 C.ar 45 TYR 0.000000 + 680 HD1 31.0400 32.9450 23.8450 H 45 TYR 0.000000 + 681 CE1 29.9080 33.5560 22.1160 C.ar 45 TYR 0.000000 + 682 HE1 29.1130 32.8490 22.2910 H 45 TYR 0.000000 + 683 CZ 29.7180 34.5060 21.0940 C.ar 45 TYR 0.000000 + 684 OH 28.6580 34.3380 20.2680 O.3 45 TYR 0.000000 + 685 HH 28.4960 35.0520 19.6480 H 45 TYR 0.000000 + 686 CE2 30.6530 35.5740 21.0280 C.ar 45 TYR 0.000000 + 687 HE2 30.4900 36.2880 20.2340 H 45 TYR 0.000000 + 688 CD2 31.7520 35.6430 21.9110 C.ar 45 TYR 0.000000 + 689 HD2 32.5370 36.3460 21.6790 H 45 TYR 0.000000 + 690 C 34.5450 33.5290 22.3360 C.2 45 TYR 0.000000 + 691 O 35.2600 34.4120 21.8090 O.2 45 TYR 0.000000 + 692 N 33.9240 32.5670 21.6400 N.am 46 ASP 0.000000 + 693 H 33.2150 32.0060 22.0880 H 46 ASP 0.000000 + 694 CA 34.1090 32.2890 20.2040 C.3 46 ASP 0.000000 + 695 HA 34.8050 32.8960 19.6250 H 46 ASP 0.000000 + 696 CB 34.8180 30.9170 20.2400 C.3 46 ASP 0.000000 + 697 HB2 35.7000 31.0320 20.8710 H 46 ASP 0.000000 + 698 HB3 34.2520 30.2000 20.8340 H 46 ASP 0.000000 + 699 CG 35.2160 30.2820 18.9120 C.2 46 ASP 0.000000 + 700 OD1 34.4050 29.5070 18.3230 O.co2 46 ASP 0.000000 + 701 OD2 36.1560 30.8570 18.3650 O.co2 46 ASP 0.000000 + 702 C 32.8770 32.2750 19.3190 C.2 46 ASP 0.000000 + 703 O 31.9310 31.5170 19.5290 O.2 46 ASP 0.000000 + 704 N 32.8330 33.2200 18.4130 N.am 47 ASP 0.000000 + 705 H 33.6220 33.8520 18.4290 H 47 ASP 0.000000 + 706 CA 31.6880 33.4560 17.5540 C.3 47 ASP 0.000000 + 707 HA 30.7730 33.5610 18.1370 H 47 ASP 0.000000 + 708 CB 31.9070 34.7380 16.7470 C.3 47 ASP 0.000000 + 709 HB2 32.1130 35.5100 17.4880 H 47 ASP 0.000000 + 710 HB3 32.8530 34.6970 16.2070 H 47 ASP 0.000000 + 711 CG 30.7290 35.1870 15.8440 C.2 47 ASP 0.000000 + 712 OD1 29.5510 35.0400 16.1740 O.co2 47 ASP 0.000000 + 713 OD2 31.1170 35.7270 14.7550 O.co2 47 ASP 0.000000 + 714 C 31.5220 32.3260 16.5570 C.2 47 ASP 0.000000 + 715 O 30.3900 32.0690 16.1340 O.2 47 ASP 0.000000 + 716 N 32.5550 31.6570 16.0920 N.am 48 ALA 0.000000 + 717 H 33.4900 31.9310 16.3570 H 48 ALA 0.000000 + 718 CA 32.4370 30.6470 15.0150 C.3 48 ALA 0.000000 + 719 HA 31.7070 31.1080 14.3490 H 48 ALA 0.000000 + 720 CB 33.8210 30.4670 14.3400 C.3 48 ALA 0.000000 + 721 HB1 34.2440 31.3990 13.9640 H 48 ALA 0.000000 + 722 HB2 33.6750 29.7060 13.5730 H 48 ALA 0.000000 + 723 HB3 34.4210 29.9860 15.1120 H 48 ALA 0.000000 + 724 C 31.8550 29.3010 15.5490 C.2 48 ALA 0.000000 + 725 O 31.5480 28.4450 14.7200 O.2 48 ALA 0.000000 + 726 N 31.6190 29.1630 16.8850 N.am 49 THR 0.000000 + 727 H 31.9750 29.9290 17.4390 H 49 THR 0.000000 + 728 CA 30.8110 28.1260 17.5760 C.3 49 THR 0.000000 + 729 HA 30.3710 27.5440 16.7670 H 49 THR 0.000000 + 730 CB 31.7130 27.1000 18.3100 C.3 49 THR 0.000000 + 731 HB 31.1340 26.4200 18.9350 H 49 THR 0.000000 + 732 CG2 32.6140 26.2800 17.4360 C.3 49 THR 0.000000 + 733 HG21 33.3290 26.8680 16.8590 H 49 THR 0.000000 + 734 HG22 32.0020 25.5930 16.8530 H 49 THR 0.000000 + 735 HG23 33.3540 25.7600 18.0440 H 49 THR 0.000000 + 736 OG1 32.5070 27.8340 19.2220 O.3 49 THR 0.000000 + 737 HG1 33.1510 28.3360 18.7150 H 49 THR 0.000000 + 738 C 29.7130 28.6440 18.4680 C.2 49 THR 0.000000 + 739 O 28.9410 27.9120 19.1030 O.2 49 THR 0.000000 + 740 N 29.6280 29.9770 18.6490 N.am 50 LYS 0.000000 + 741 H 30.4190 30.5220 18.3340 H 50 LYS 0.000000 + 742 CA 28.6630 30.6950 19.5410 C.3 50 LYS 0.000000 + 743 HA 28.8470 31.7690 19.5010 H 50 LYS 0.000000 + 744 CB 27.1890 30.6250 19.0330 C.3 50 LYS 0.000000 + 745 HB2 26.9360 29.5720 19.1630 H 50 LYS 0.000000 + 746 HB3 26.4690 31.0810 19.7120 H 50 LYS 0.000000 + 747 CG 27.1190 30.9840 17.4650 C.3 50 LYS 0.000000 + 748 HG2 27.9610 30.5900 16.8950 H 50 LYS 0.000000 + 749 HG3 26.1880 30.5510 17.1000 H 50 LYS 0.000000 + 750 CD 27.0250 32.5470 17.3220 C.3 50 LYS 0.000000 + 751 HD2 26.3370 33.0990 17.9640 H 50 LYS 0.000000 + 752 HD3 28.0050 32.9130 17.6230 H 50 LYS 0.000000 + 753 CE 26.6860 32.9330 15.9300 C.3 50 LYS 0.000000 + 754 HE2 25.8290 32.3630 15.5720 H 50 LYS 0.000000 + 755 HE3 26.3040 33.9530 15.9860 H 50 LYS 0.000000 + 756 NZ 27.8610 32.9050 14.9900 N.4 50 LYS 0.000000 + 757 HZ1 28.5620 33.5070 15.3970 H 50 LYS 0.000000 + 758 HZ2 27.5970 33.3210 14.1080 H 50 LYS 0.000000 + 759 HZ3 28.2690 32.0170 14.7360 H 50 LYS 0.000000 + 760 C 28.8840 30.2500 21.0330 C.2 50 LYS 0.000000 + 761 O 27.9580 30.2060 21.8260 O.2 50 LYS 0.000000 + 762 N 30.1480 29.8200 21.3280 N.am 51 THR 0.000000 + 763 H 30.9400 30.1000 20.7660 H 51 THR 0.000000 + 764 CA 30.5030 29.2140 22.6320 C.3 51 THR 0.000000 + 765 HA 29.6800 28.7140 23.1420 H 51 THR 0.000000 + 766 CB 31.3130 27.9440 22.3690 C.3 51 THR 0.000000 + 767 HB 32.2450 28.1020 21.8260 H 51 THR 0.000000 + 768 CG2 31.7030 27.0880 23.5900 C.3 51 THR 0.000000 + 769 HG21 32.1770 26.1600 23.2720 H 51 THR 0.000000 + 770 HG22 30.7450 26.9770 24.1000 H 51 THR 0.000000 + 771 HG23 32.4010 27.6770 24.1860 H 51 THR 0.000000 + 772 OG1 30.4040 27.1610 21.6590 O.3 51 THR 0.000000 + 773 HG1 29.7570 27.6830 21.1790 H 51 THR 0.000000 + 774 C 31.2020 30.1200 23.5490 C.2 51 THR 0.000000 + 775 O 32.2000 30.7210 23.1430 O.2 51 THR 0.000000 + 776 N 31.0090 29.9260 24.8450 N.am 52 PHE 0.000000 + 777 H 30.1250 29.4790 25.0420 H 52 PHE 0.000000 + 778 CA 31.8210 30.3910 25.9410 C.3 52 PHE 0.000000 + 779 HA 32.4900 31.1920 25.6280 H 52 PHE 0.000000 + 780 CB 30.7150 30.9790 27.0070 C.3 52 PHE 0.000000 + 781 HB2 29.9880 30.2000 27.2380 H 52 PHE 0.000000 + 782 HB3 31.2500 31.2980 27.9010 H 52 PHE 0.000000 + 783 CG 30.0490 32.2220 26.5340 C.ar 52 PHE 0.000000 + 784 CD1 28.8760 32.1420 25.7810 C.ar 52 PHE 0.000000 + 785 HD1 28.4130 31.2040 25.5150 H 52 PHE 0.000000 + 786 CE1 28.3000 33.3500 25.3040 C.ar 52 PHE 0.000000 + 787 HE1 27.3030 33.3160 24.8900 H 52 PHE 0.000000 + 788 CZ 28.8800 34.5930 25.5000 C.ar 52 PHE 0.000000 + 789 HZ 28.4170 35.4600 25.0540 H 52 PHE 0.000000 + 790 CE2 30.1220 34.6650 26.1920 C.ar 52 PHE 0.000000 + 791 HE2 30.6500 35.5970 26.3330 H 52 PHE 0.000000 + 792 CD2 30.5970 33.4950 26.7950 C.ar 52 PHE 0.000000 + 793 HD2 31.4350 33.5810 27.4710 H 52 PHE 0.000000 + 794 C 32.7210 29.3430 26.5530 C.2 52 PHE 0.000000 + 795 O 32.2800 28.2400 26.6740 O.2 52 PHE 0.000000 + 796 N 33.9080 29.8290 27.0870 N.am 53 THR 0.000000 + 797 H 34.2030 30.7840 26.9380 H 53 THR 0.000000 + 798 CA 34.5770 29.0440 28.1320 C.3 53 THR 0.000000 + 799 HA 34.0030 28.1900 28.4920 H 53 THR 0.000000 + 800 CB 35.8810 28.4430 27.6840 C.3 53 THR 0.000000 + 801 HB 36.5130 29.2340 27.2800 H 53 THR 0.000000 + 802 CG2 36.6200 27.5710 28.7520 C.3 53 THR 0.000000 + 803 HG21 36.8140 28.2360 29.5950 H 53 THR 0.000000 + 804 HG22 37.5350 27.1740 28.3130 H 53 THR 0.000000 + 805 HG23 35.9240 26.7950 29.0680 H 53 THR 0.000000 + 806 OG1 35.6050 27.6490 26.5840 O.3 53 THR 0.000000 + 807 HG1 35.4590 28.1770 25.7960 H 53 THR 0.000000 + 808 C 34.7760 29.7480 29.4430 C.2 53 THR 0.000000 + 809 O 35.1460 30.9390 29.4370 O.2 53 THR 0.000000 + 810 N 34.4990 29.1350 30.6390 N.am 54 VAL 0.000000 + 811 H 34.2090 28.1730 30.5380 H 54 VAL 0.000000 + 812 CA 34.8610 29.5360 31.9820 C.3 54 VAL 0.000000 + 813 HA 35.3820 30.4930 31.9780 H 54 VAL 0.000000 + 814 CB 33.6970 29.7160 32.8690 C.3 54 VAL 0.000000 + 815 HB 32.9130 30.3350 32.4340 H 54 VAL 0.000000 + 816 CG1 33.0020 28.3940 33.2890 C.3 54 VAL 0.000000 + 817 HG11 33.6900 27.6660 33.7180 H 54 VAL 0.000000 + 818 HG12 32.6180 28.0140 32.3420 H 54 VAL 0.000000 + 819 HG13 32.0930 28.5250 33.8770 H 54 VAL 0.000000 + 820 CG2 34.1180 30.3200 34.2240 C.3 54 VAL 0.000000 + 821 HG21 34.7110 31.2280 34.1230 H 54 VAL 0.000000 + 822 HG22 34.6910 29.6640 34.8800 H 54 VAL 0.000000 + 823 HG23 33.2020 30.5510 34.7670 H 54 VAL 0.000000 + 824 C 35.9500 28.5900 32.4680 C.2 54 VAL 0.000000 + 825 O 35.7380 27.3850 32.6600 O.2 54 VAL 0.000000 + 826 N 37.1870 29.0850 32.6510 N.am 55 THR 0.000000 + 827 H 37.3260 30.0380 32.3450 H 55 THR 0.000000 + 828 CA 38.4180 28.3630 33.0710 C.3 55 THR 0.000000 + 829 HA 38.1970 27.2990 32.9910 H 55 THR 0.000000 + 830 CB 39.5740 28.5160 32.1610 C.3 55 THR 0.000000 + 831 HB 39.7570 29.5810 32.0190 H 55 THR 0.000000 + 832 CG2 40.8700 27.8980 32.7860 C.3 55 THR 0.000000 + 833 HG21 40.5830 26.8490 32.8550 H 55 THR 0.000000 + 834 HG22 41.0230 28.1900 33.8260 H 55 THR 0.000000 + 835 HG23 41.8250 28.0440 32.2800 H 55 THR 0.000000 + 836 OG1 39.2150 27.9700 30.8180 O.3 55 THR 0.000000 + 837 HG1 38.7920 28.7250 30.4010 H 55 THR 0.000000 + 838 C 38.7790 28.7250 34.4580 C.2 55 THR 0.000000 + 839 O 39.2630 29.8410 34.7350 O.2 55 THR 0.000000 + 840 N 38.7570 27.7730 35.4160 N.am 56 GLU 0.000000 + 841 H 38.4590 26.8690 35.0790 H 56 GLU 0.000000 + 842 CA 39.0450 27.9930 36.8880 C.3 56 GLU 0.000000 + 843 HA 38.6180 28.9210 37.2670 H 56 GLU 0.000000 + 844 CB 38.4020 26.9110 37.7490 C.3 56 GLU 0.000000 + 845 HB2 37.3290 27.0190 37.5930 H 56 GLU 0.000000 + 846 HB3 38.7800 25.9050 37.5630 H 56 GLU 0.000000 + 847 CG 38.4360 27.0780 39.2670 C.3 56 GLU 0.000000 + 848 HG2 39.4550 26.9680 39.6360 H 56 GLU 0.000000 + 849 HG3 38.0940 28.0970 39.4450 H 56 GLU 0.000000 + 850 CD 37.5140 26.0140 39.9180 C.2 56 GLU 0.000000 + 851 OE1 37.9050 24.8230 39.8700 O.co2 56 GLU 0.000000 + 852 OE2 36.5290 26.3270 40.6640 O.co2 56 GLU 0.000000 + 853 C 40.4880 28.1370 37.3010 C.2 56 GLU 0.000000 + 854 O 40.8070 29.0900 38.0250 O.co2 56 GLU 0.000000 + 855 OXT 41.3770 27.2710 37.0310 O.co2 56 GLU 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 1 4 1 + 4 1 5 1 + 5 5 6 1 + 6 5 7 1 + 7 5 18 1 + 8 7 8 1 + 9 7 9 1 + 10 7 10 1 + 11 10 11 1 + 12 10 12 1 + 13 10 13 1 + 14 13 14 1 + 15 14 15 1 + 16 14 16 1 + 17 14 17 1 + 18 18 19 2 + 19 18 20 am + 20 20 21 1 + 21 20 22 1 + 22 22 23 1 + 23 22 24 1 + 24 22 32 1 + 25 24 25 1 + 26 24 26 1 + 27 24 30 1 + 28 26 27 1 + 29 26 28 1 + 30 26 29 1 + 31 30 31 1 + 32 32 33 2 + 33 32 34 am + 34 34 35 1 + 35 34 36 1 + 36 36 37 1 + 37 36 38 1 + 38 36 53 1 + 39 38 39 1 + 40 38 40 1 + 41 38 41 1 + 42 41 42 ar + 43 41 51 ar + 44 42 43 1 + 45 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+@SUBSTRUCTURE + 1 MET 1 TEMP 0 **** **** 0 ROOT diff --git a/unittests/example_files/ALA20.pdb b/unittests/example_files/ALA20.pdb new file mode 100644 index 0000000..c1afd24 --- /dev/null +++ b/unittests/example_files/ALA20.pdb @@ -0,0 +1,470 @@ +COMPND PolyALA +AUTHOR GENERATED BY OPEN BABEL 2.3.2 +ATOM 1 H1 ACE A 1 -3.054 -3.171 0.465 1.00 0.00 H +ATOM 2 CH3 ACE A 1 -2.917 -2.969 -0.597 1.00 0.00 C +ATOM 3 H2 ACE A 1 -3.815 -3.045 -1.210 1.00 0.00 H +ATOM 4 H3 ACE A 1 -2.106 -3.644 -0.872 1.00 0.00 H +ATOM 5 C ACE A 1 -2.282 -1.553 -0.711 1.00 0.00 C +ATOM 6 O ACE A 1 -2.958 -0.698 -1.252 1.00 0.00 O +ATOM 7 N ALA A 2 -1.104 -1.396 -0.185 1.00 0.00 N +ATOM 8 H ALA A 2 -0.697 -2.276 0.096 1.00 0.00 H +ATOM 9 CA ALA A 2 -0.333 -0.155 -0.121 1.00 0.00 C +ATOM 10 HA ALA A 2 -0.610 0.298 -1.073 1.00 0.00 H +ATOM 11 CB ALA A 2 -0.855 0.714 0.968 1.00 0.00 C +ATOM 12 HB1 ALA A 2 -1.908 0.950 0.817 1.00 0.00 H +ATOM 13 HB2 ALA A 2 -0.696 0.268 1.950 1.00 0.00 H +ATOM 14 HB3 ALA A 2 -0.167 1.559 0.980 1.00 0.00 H +ATOM 15 C ALA A 2 1.131 -0.273 -0.199 1.00 0.00 C +ATOM 16 O ALA A 2 1.769 0.539 -0.827 1.00 0.00 O +ATOM 17 N ALA A 3 1.795 -1.211 0.498 1.00 0.00 N +ATOM 18 H ALA A 3 1.221 -1.808 1.076 1.00 0.00 H +ATOM 19 CA ALA A 3 3.262 -1.252 0.419 1.00 0.00 C +ATOM 20 HA ALA A 3 3.652 -0.256 0.628 1.00 0.00 H +ATOM 21 CB ALA A 3 3.827 -2.271 1.436 1.00 0.00 C +ATOM 22 HB1 ALA A 3 3.510 -1.948 2.428 1.00 0.00 H +ATOM 23 HB2 ALA A 3 3.389 -3.228 1.153 1.00 0.00 H +ATOM 24 HB3 ALA A 3 4.910 -2.372 1.514 1.00 0.00 H +ATOM 25 C ALA A 3 3.783 -1.597 -0.986 1.00 0.00 C +ATOM 26 O ALA A 3 4.802 -1.070 -1.378 1.00 0.00 O +ATOM 27 N ALA A 4 3.132 -2.508 -1.712 1.00 0.00 N +ATOM 28 H ALA A 4 2.361 -3.014 -1.299 1.00 0.00 H +ATOM 29 CA ALA A 4 3.470 -2.716 -3.172 1.00 0.00 C +ATOM 30 HA ALA A 4 4.559 -2.699 -3.210 1.00 0.00 H +ATOM 31 CB ALA A 4 2.900 -4.035 -3.564 1.00 0.00 C +ATOM 32 HB1 ALA A 4 3.370 -4.803 -2.950 1.00 0.00 H +ATOM 33 HB2 ALA A 4 1.845 -4.033 -3.290 1.00 0.00 H +ATOM 34 HB3 ALA A 4 3.197 -4.068 -4.612 1.00 0.00 H +ATOM 35 C ALA A 4 3.146 -1.507 -3.992 1.00 0.00 C +ATOM 36 O ALA A 4 4.003 -1.154 -4.830 1.00 0.00 O +ATOM 37 N ALA A 5 2.102 -0.798 -3.719 1.00 0.00 N +ATOM 38 H ALA A 5 1.578 -1.096 -2.909 1.00 0.00 H +ATOM 39 CA ALA A 5 1.798 0.414 -4.360 1.00 0.00 C +ATOM 40 HA ALA A 5 2.033 0.197 -5.403 1.00 0.00 H +ATOM 41 CB ALA A 5 0.257 0.848 -4.179 1.00 0.00 C +ATOM 42 HB1 ALA A 5 -0.434 0.100 -4.566 1.00 0.00 H +ATOM 43 HB2 ALA A 5 0.029 0.931 -3.116 1.00 0.00 H +ATOM 44 HB3 ALA A 5 0.160 1.812 -4.679 1.00 0.00 H +ATOM 45 C ALA A 5 2.753 1.542 -4.006 1.00 0.00 C +ATOM 46 O ALA A 5 3.074 2.358 -4.897 1.00 0.00 O +ATOM 47 N ALA A 6 3.298 1.676 -2.803 1.00 0.00 N +ATOM 48 H ALA A 6 2.836 1.294 -1.990 1.00 0.00 H +ATOM 49 CA ALA A 6 4.273 2.694 -2.399 1.00 0.00 C +ATOM 50 HA ALA A 6 3.991 3.697 -2.721 1.00 0.00 H +ATOM 51 CB ALA A 6 4.338 2.833 -0.890 1.00 0.00 C +ATOM 52 HB1 ALA A 6 3.425 3.266 -0.481 1.00 0.00 H +ATOM 53 HB2 ALA A 6 4.564 1.863 -0.449 1.00 0.00 H +ATOM 54 HB3 ALA A 6 5.247 3.402 -0.697 1.00 0.00 H +ATOM 55 C ALA A 6 5.749 2.356 -2.826 1.00 0.00 C +ATOM 56 O ALA A 6 6.538 3.204 -3.079 1.00 0.00 O +ATOM 57 N ALA A 7 5.959 1.049 -3.048 1.00 0.00 N +ATOM 58 H ALA A 7 5.304 0.423 -2.601 1.00 0.00 H +ATOM 59 CA ALA A 7 7.183 0.475 -3.563 1.00 0.00 C +ATOM 60 HA ALA A 7 7.990 1.166 -3.316 1.00 0.00 H +ATOM 61 CB ALA A 7 7.530 -0.880 -2.926 1.00 0.00 C +ATOM 62 HB1 ALA A 7 7.386 -0.936 -1.847 1.00 0.00 H +ATOM 63 HB2 ALA A 7 6.786 -1.525 -3.395 1.00 0.00 H +ATOM 64 HB3 ALA A 7 8.523 -1.178 -3.261 1.00 0.00 H +ATOM 65 C ALA A 7 7.218 0.417 -5.118 1.00 0.00 C +ATOM 66 O ALA A 7 8.320 0.602 -5.691 1.00 0.00 O +ATOM 67 N ALA A 8 6.093 0.302 -5.750 1.00 0.00 N +ATOM 68 H ALA A 8 5.324 -0.065 -5.206 1.00 0.00 H +ATOM 69 CA ALA A 8 5.982 0.524 -7.158 1.00 0.00 C +ATOM 70 HA ALA A 8 6.812 0.018 -7.650 1.00 0.00 H +ATOM 71 CB ALA A 8 4.784 -0.264 -7.698 1.00 0.00 C +ATOM 72 HB1 ALA A 8 4.911 -1.274 -7.308 1.00 0.00 H +ATOM 73 HB2 ALA A 8 3.881 0.285 -7.430 1.00 0.00 H +ATOM 74 HB3 ALA A 8 4.855 -0.199 -8.784 1.00 0.00 H +ATOM 75 C ALA A 8 5.945 2.036 -7.500 1.00 0.00 C +ATOM 76 O ALA A 8 6.554 2.371 -8.484 1.00 0.00 O +ATOM 77 N ALA A 9 5.406 2.871 -6.588 1.00 0.00 N +ATOM 78 H ALA A 9 4.829 2.524 -5.835 1.00 0.00 H +ATOM 79 CA ALA A 9 5.472 4.303 -6.694 1.00 0.00 C +ATOM 80 HA ALA A 9 5.320 4.497 -7.756 1.00 0.00 H +ATOM 81 CB ALA A 9 4.300 5.085 -6.075 1.00 0.00 C +ATOM 82 HB1 ALA A 9 3.330 4.659 -6.333 1.00 0.00 H +ATOM 83 HB2 ALA A 9 4.436 5.008 -4.996 1.00 0.00 H +ATOM 84 HB3 ALA A 9 4.315 6.151 -6.302 1.00 0.00 H +ATOM 85 C ALA A 9 6.893 4.859 -6.381 1.00 0.00 C +ATOM 86 O ALA A 9 7.444 5.619 -7.164 1.00 0.00 O +ATOM 87 N ALA A 10 7.541 4.364 -5.327 1.00 0.00 N +ATOM 88 H ALA A 10 7.021 3.870 -4.617 1.00 0.00 H +ATOM 89 CA ALA A 10 8.960 4.713 -5.050 1.00 0.00 C +ATOM 90 HA ALA A 10 8.966 5.797 -5.163 1.00 0.00 H +ATOM 91 CB ALA A 10 9.288 4.389 -3.622 1.00 0.00 C +ATOM 92 HB1 ALA A 10 8.642 4.839 -2.869 1.00 0.00 H +ATOM 93 HB2 ALA A 10 9.230 3.307 -3.504 1.00 0.00 H +ATOM 94 HB3 ALA A 10 10.344 4.615 -3.471 1.00 0.00 H +ATOM 95 C ALA A 10 9.986 4.042 -6.032 1.00 0.00 C +ATOM 96 O ALA A 10 11.142 4.565 -6.147 1.00 0.00 O +ATOM 97 N ALA A 11 9.656 2.896 -6.701 1.00 0.00 N +ATOM 98 H ALA A 11 8.894 2.276 -6.470 1.00 0.00 H +ATOM 99 CA ALA A 11 10.445 2.411 -7.813 1.00 0.00 C +ATOM 100 HA ALA A 11 11.510 2.566 -7.640 1.00 0.00 H +ATOM 101 CB ALA A 11 10.164 0.914 -8.040 1.00 0.00 C +ATOM 102 HB1 ALA A 11 10.615 0.443 -7.166 1.00 0.00 H +ATOM 103 HB2 ALA A 11 9.107 0.669 -8.142 1.00 0.00 H +ATOM 104 HB3 ALA A 11 10.719 0.516 -8.889 1.00 0.00 H +ATOM 105 C ALA A 11 10.151 3.103 -9.155 1.00 0.00 C +ATOM 106 O ALA A 11 11.041 3.166 -9.980 1.00 0.00 O +ATOM 107 N ALA A 12 8.962 3.622 -9.346 1.00 0.00 N +ATOM 108 H ALA A 12 8.246 3.385 -8.673 1.00 0.00 H +ATOM 109 CA ALA A 12 8.644 4.359 -10.533 1.00 0.00 C +ATOM 110 HA ALA A 12 9.114 3.991 -11.446 1.00 0.00 H +ATOM 111 CB ALA A 12 7.143 4.275 -10.773 1.00 0.00 C +ATOM 112 HB1 ALA A 12 6.835 3.230 -10.811 1.00 0.00 H +ATOM 113 HB2 ALA A 12 6.547 4.719 -9.976 1.00 0.00 H +ATOM 114 HB3 ALA A 12 6.930 4.661 -11.770 1.00 0.00 H +ATOM 115 C ALA A 12 8.998 5.845 -10.408 1.00 0.00 C +ATOM 116 O ALA A 12 9.206 6.435 -11.479 1.00 0.00 O +ATOM 117 N ALA A 13 9.060 6.373 -9.150 1.00 0.00 N +ATOM 118 H ALA A 13 8.710 5.815 -8.384 1.00 0.00 H +ATOM 119 CA ALA A 13 9.644 7.589 -8.707 1.00 0.00 C +ATOM 120 HA ALA A 13 9.378 8.325 -9.466 1.00 0.00 H +ATOM 121 CB ALA A 13 8.979 8.114 -7.362 1.00 0.00 C +ATOM 122 HB1 ALA A 13 7.893 8.188 -7.300 1.00 0.00 H +ATOM 123 HB2 ALA A 13 9.391 7.514 -6.550 1.00 0.00 H +ATOM 124 HB3 ALA A 13 9.297 9.138 -7.165 1.00 0.00 H +ATOM 125 C ALA A 13 11.163 7.561 -8.544 1.00 0.00 C +ATOM 126 O ALA A 13 11.753 8.643 -8.809 1.00 0.00 O +ATOM 127 N ALA A 14 11.711 6.438 -8.195 1.00 0.00 N +ATOM 128 H ALA A 14 11.201 5.708 -7.719 1.00 0.00 H +ATOM 129 CA ALA A 14 13.187 6.178 -8.377 1.00 0.00 C +ATOM 130 HA ALA A 14 13.746 7.056 -8.055 1.00 0.00 H +ATOM 131 CB ALA A 14 13.659 4.995 -7.481 1.00 0.00 C +ATOM 132 HB1 ALA A 14 13.670 5.270 -6.427 1.00 0.00 H +ATOM 133 HB2 ALA A 14 13.140 4.041 -7.573 1.00 0.00 H +ATOM 134 HB3 ALA A 14 14.732 4.857 -7.614 1.00 0.00 H +ATOM 135 C ALA A 14 13.540 5.894 -9.914 1.00 0.00 C +ATOM 136 O ALA A 14 14.638 6.393 -10.399 1.00 0.00 O +ATOM 137 N ALA A 15 12.747 5.180 -10.675 1.00 0.00 N +ATOM 138 H ALA A 15 11.928 4.701 -10.329 1.00 0.00 H +ATOM 139 CA ALA A 15 13.062 5.067 -12.046 1.00 0.00 C +ATOM 140 HA ALA A 15 14.076 4.746 -12.284 1.00 0.00 H +ATOM 141 CB ALA A 15 12.198 3.975 -12.711 1.00 0.00 C +ATOM 142 HB1 ALA A 15 12.343 3.040 -12.170 1.00 0.00 H +ATOM 143 HB2 ALA A 15 11.153 4.203 -12.506 1.00 0.00 H +ATOM 144 HB3 ALA A 15 12.380 3.968 -13.786 1.00 0.00 H +ATOM 145 C ALA A 15 12.703 6.348 -12.778 1.00 0.00 C +ATOM 146 O ALA A 15 13.510 6.684 -13.678 1.00 0.00 O +ATOM 147 N ALA A 16 11.645 7.130 -12.475 1.00 0.00 N +ATOM 148 H ALA A 16 10.893 6.780 -11.898 1.00 0.00 H +ATOM 149 CA ALA A 16 11.461 8.455 -13.029 1.00 0.00 C +ATOM 150 HA ALA A 16 11.491 8.353 -14.114 1.00 0.00 H +ATOM 151 CB ALA A 16 10.149 9.085 -12.685 1.00 0.00 C +ATOM 152 HB1 ALA A 16 9.388 8.398 -13.054 1.00 0.00 H +ATOM 153 HB2 ALA A 16 10.052 9.148 -11.601 1.00 0.00 H +ATOM 154 HB3 ALA A 16 10.063 10.057 -13.171 1.00 0.00 H +ATOM 155 C ALA A 16 12.608 9.384 -12.612 1.00 0.00 C +ATOM 156 O ALA A 16 13.039 10.222 -13.473 1.00 0.00 O +ATOM 157 N ALA A 17 13.138 9.241 -11.388 1.00 0.00 N +ATOM 158 H ALA A 17 12.604 8.788 -10.661 1.00 0.00 H +ATOM 159 CA ALA A 17 14.326 10.028 -10.964 1.00 0.00 C +ATOM 160 HA ALA A 17 14.114 11.052 -11.270 1.00 0.00 H +ATOM 161 CB ALA A 17 14.275 10.145 -9.531 1.00 0.00 C +ATOM 162 HB1 ALA A 17 13.375 10.647 -9.177 1.00 0.00 H +ATOM 163 HB2 ALA A 17 14.478 9.222 -8.988 1.00 0.00 H +ATOM 164 HB3 ALA A 17 15.023 10.861 -9.189 1.00 0.00 H +ATOM 165 C ALA A 17 15.611 9.623 -11.594 1.00 0.00 C +ATOM 166 O ALA A 17 16.445 10.488 -11.882 1.00 0.00 O +ATOM 167 N ALA A 18 15.812 8.347 -11.791 1.00 0.00 N +ATOM 168 H ALA A 18 15.210 7.647 -11.382 1.00 0.00 H +ATOM 169 CA ALA A 18 17.039 7.928 -12.446 1.00 0.00 C +ATOM 170 HA ALA A 18 17.935 8.483 -12.170 1.00 0.00 H +ATOM 171 CB ALA A 18 17.358 6.480 -12.029 1.00 0.00 C +ATOM 172 HB1 ALA A 18 17.561 6.449 -10.958 1.00 0.00 H +ATOM 173 HB2 ALA A 18 16.536 5.820 -12.307 1.00 0.00 H +ATOM 174 HB3 ALA A 18 18.323 6.159 -12.422 1.00 0.00 H +ATOM 175 C ALA A 18 16.968 8.017 -13.999 1.00 0.00 C +ATOM 176 O ALA A 18 18.024 8.143 -14.660 1.00 0.00 O +ATOM 177 N ALA A 19 15.774 8.031 -14.539 1.00 0.00 N +ATOM 178 H ALA A 19 15.110 7.729 -13.840 1.00 0.00 H +ATOM 179 CA ALA A 19 15.508 8.397 -15.942 1.00 0.00 C +ATOM 180 HA ALA A 19 16.274 7.890 -16.528 1.00 0.00 H +ATOM 181 CB ALA A 19 14.132 7.825 -16.381 1.00 0.00 C +ATOM 182 HB1 ALA A 19 14.000 6.748 -16.279 1.00 0.00 H +ATOM 183 HB2 ALA A 19 13.326 8.274 -15.801 1.00 0.00 H +ATOM 184 HB3 ALA A 19 14.129 8.183 -17.411 1.00 0.00 H +ATOM 185 C ALA A 19 15.616 9.879 -16.218 1.00 0.00 C +ATOM 186 O ALA A 19 15.925 10.312 -17.349 1.00 0.00 O +ATOM 187 N ALA A 20 15.342 10.748 -15.240 1.00 0.00 N +ATOM 188 H ALA A 20 15.274 10.304 -14.336 1.00 0.00 H +ATOM 189 CA ALA A 20 15.539 12.186 -15.310 1.00 0.00 C +ATOM 190 HA ALA A 20 15.392 12.510 -16.340 1.00 0.00 H +ATOM 191 CB ALA A 20 14.470 12.874 -14.390 1.00 0.00 C +ATOM 192 HB1 ALA A 20 13.502 12.406 -14.574 1.00 0.00 H +ATOM 193 HB2 ALA A 20 14.667 12.751 -13.325 1.00 0.00 H +ATOM 194 HB3 ALA A 20 14.411 13.936 -14.630 1.00 0.00 H +ATOM 195 C ALA A 20 16.976 12.596 -14.911 1.00 0.00 C +ATOM 196 O ALA A 20 17.474 13.502 -15.583 1.00 0.00 O +ATOM 197 N ALA A 21 17.617 12.028 -13.914 1.00 0.00 N +ATOM 198 H ALA A 21 17.079 11.380 -13.356 1.00 0.00 H +ATOM 199 CA ALA A 21 19.140 12.093 -13.649 1.00 0.00 C +ATOM 200 HA ALA A 21 19.393 13.153 -13.607 1.00 0.00 H +ATOM 201 CB ALA A 21 19.438 11.428 -12.300 1.00 0.00 C +ATOM 202 HB1 ALA A 21 18.876 12.017 -11.575 1.00 0.00 H +ATOM 203 HB2 ALA A 21 19.196 10.366 -12.277 1.00 0.00 H +ATOM 204 HB3 ALA A 21 20.473 11.677 -12.068 1.00 0.00 H +ATOM 205 C ALA A 21 19.911 11.369 -14.740 1.00 0.00 C +ATOM 206 O ALA A 21 19.370 10.700 -15.601 1.00 0.00 O +ATOM 207 N NME A 22 21.266 11.506 -14.654 1.00 0.00 N +ATOM 208 H NME A 22 21.663 12.119 -13.956 1.00 0.00 H +ATOM 209 CH3 NME A 22 22.261 10.909 -15.537 1.00 0.00 C +ATOM 210 HH31 NME A 22 21.787 10.285 -16.294 1.00 0.00 H +ATOM 211 HH32 NME A 22 22.939 11.631 -15.993 1.00 0.00 H +ATOM 212 HH33 NME A 22 22.893 10.275 -14.916 1.00 0.00 H +CONECT 1 2 +CONECT 2 1 3 4 5 +CONECT 2 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 7 +CONECT 6 5 +CONECT 7 5 8 9 +CONECT 8 7 +CONECT 9 7 10 11 15 +CONECT 9 +CONECT 10 9 +CONECT 11 9 12 13 14 +CONECT 11 +CONECT 12 11 +CONECT 13 11 +CONECT 14 11 +CONECT 15 9 16 17 +CONECT 16 15 +CONECT 17 15 18 19 +CONECT 18 17 +CONECT 19 17 20 21 25 +CONECT 19 +CONECT 20 19 +CONECT 21 19 22 23 24 +CONECT 21 +CONECT 22 21 +CONECT 23 21 +CONECT 24 21 +CONECT 25 19 26 27 +CONECT 26 25 +CONECT 27 25 28 29 +CONECT 28 27 +CONECT 29 27 30 31 35 +CONECT 29 +CONECT 30 29 +CONECT 31 29 32 33 34 +CONECT 31 +CONECT 32 31 +CONECT 33 31 +CONECT 34 31 +CONECT 35 29 36 37 +CONECT 36 35 +CONECT 37 35 38 39 +CONECT 38 37 +CONECT 39 37 40 41 45 +CONECT 39 +CONECT 40 39 +CONECT 41 39 42 43 44 +CONECT 41 +CONECT 42 41 +CONECT 43 41 +CONECT 44 41 +CONECT 45 39 46 47 +CONECT 46 45 +CONECT 47 45 48 49 +CONECT 48 47 +CONECT 49 47 50 51 55 +CONECT 49 +CONECT 50 49 +CONECT 51 49 52 53 54 +CONECT 51 +CONECT 52 51 +CONECT 53 51 +CONECT 54 51 +CONECT 55 49 56 57 +CONECT 56 55 +CONECT 57 55 58 59 +CONECT 58 57 +CONECT 59 57 60 61 65 +CONECT 59 +CONECT 60 59 +CONECT 61 59 62 63 64 +CONECT 61 +CONECT 62 61 +CONECT 63 61 +CONECT 64 61 +CONECT 65 59 66 67 +CONECT 66 65 +CONECT 67 65 68 69 +CONECT 68 67 +CONECT 69 67 70 71 75 +CONECT 69 +CONECT 70 69 +CONECT 71 69 72 73 74 +CONECT 71 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 +CONECT 75 69 76 77 +CONECT 76 75 +CONECT 77 75 78 79 +CONECT 78 77 +CONECT 79 77 80 81 85 +CONECT 79 +CONECT 80 79 +CONECT 81 79 82 83 84 +CONECT 81 +CONECT 82 81 +CONECT 83 81 +CONECT 84 81 +CONECT 85 79 86 87 +CONECT 86 85 +CONECT 87 85 88 89 +CONECT 88 87 +CONECT 89 87 90 91 95 +CONECT 89 +CONECT 90 89 +CONECT 91 89 92 93 94 +CONECT 91 +CONECT 92 91 +CONECT 93 91 +CONECT 94 91 +CONECT 95 89 96 97 +CONECT 96 95 +CONECT 97 95 98 99 +CONECT 98 97 +CONECT 99 97 100 101 105 +CONECT 99 +CONECT 100 99 +CONECT 101 99 102 103 104 +CONECT 101 +CONECT 102 101 +CONECT 103 101 +CONECT 104 101 +CONECT 105 99 106 107 +CONECT 106 105 +CONECT 107 105 108 109 +CONECT 108 107 +CONECT 109 107 110 111 115 +CONECT 109 +CONECT 110 109 +CONECT 111 109 112 113 114 +CONECT 111 +CONECT 112 111 +CONECT 113 111 +CONECT 114 111 +CONECT 115 109 116 117 +CONECT 116 115 +CONECT 117 115 118 119 +CONECT 118 117 +CONECT 119 117 120 121 125 +CONECT 119 +CONECT 120 119 +CONECT 121 119 122 123 124 +CONECT 121 +CONECT 122 121 +CONECT 123 121 +CONECT 124 121 +CONECT 125 119 126 127 +CONECT 126 125 +CONECT 127 125 128 129 +CONECT 128 127 +CONECT 129 127 130 131 135 +CONECT 129 +CONECT 130 129 +CONECT 131 129 132 133 134 +CONECT 131 +CONECT 132 131 +CONECT 133 131 +CONECT 134 131 +CONECT 135 129 136 137 +CONECT 136 135 +CONECT 137 135 138 139 +CONECT 138 137 +CONECT 139 137 140 141 145 +CONECT 139 +CONECT 140 139 +CONECT 141 139 142 143 144 +CONECT 141 +CONECT 142 141 +CONECT 143 141 +CONECT 144 141 +CONECT 145 139 146 147 +CONECT 146 145 +CONECT 147 145 148 149 +CONECT 148 147 +CONECT 149 147 150 151 155 +CONECT 149 +CONECT 150 149 +CONECT 151 149 152 153 154 +CONECT 151 +CONECT 152 151 +CONECT 153 151 +CONECT 154 151 +CONECT 155 149 156 157 +CONECT 156 155 +CONECT 157 155 158 159 +CONECT 158 157 +CONECT 159 157 160 161 165 +CONECT 159 +CONECT 160 159 +CONECT 161 159 162 163 164 +CONECT 161 +CONECT 162 161 +CONECT 163 161 +CONECT 164 161 +CONECT 165 159 166 167 +CONECT 166 165 +CONECT 167 165 168 169 +CONECT 168 167 +CONECT 169 167 170 171 175 +CONECT 169 +CONECT 170 169 +CONECT 171 169 172 173 174 +CONECT 171 +CONECT 172 171 +CONECT 173 171 +CONECT 174 171 +CONECT 175 169 176 177 +CONECT 176 175 +CONECT 177 175 178 179 +CONECT 178 177 +CONECT 179 177 180 181 185 +CONECT 179 +CONECT 180 179 +CONECT 181 179 182 183 184 +CONECT 181 +CONECT 182 181 +CONECT 183 181 +CONECT 184 181 +CONECT 185 179 186 187 +CONECT 186 185 +CONECT 187 185 188 189 +CONECT 188 187 +CONECT 189 187 190 191 195 +CONECT 189 +CONECT 190 189 +CONECT 191 189 192 193 194 +CONECT 191 +CONECT 192 191 +CONECT 193 191 +CONECT 194 191 +CONECT 195 189 196 197 +CONECT 196 195 +CONECT 197 195 198 199 +CONECT 198 197 +CONECT 199 197 200 201 205 +CONECT 199 +CONECT 200 199 +CONECT 201 199 202 203 204 +CONECT 201 +CONECT 202 201 +CONECT 203 201 +CONECT 204 201 +CONECT 205 199 206 207 +CONECT 206 205 +CONECT 207 205 208 209 +CONECT 208 207 +CONECT 209 207 210 211 212 +CONECT 209 +CONECT 210 209 +CONECT 211 209 +CONECT 212 209 +MASTER 0 0 0 0 0 0 0 0 212 0 212 0 +END diff --git a/unittests/example_files/H1A19.pdb b/unittests/example_files/H1A19.pdb new file mode 100644 index 0000000..c9a19ba --- /dev/null +++ b/unittests/example_files/H1A19.pdb @@ -0,0 +1,442 @@ +COMPND PolyALA +AUTHOR GENERATED BY OPEN BABEL 2.3.2 +ATOM 1 H1 ACE A 1 -3.054 -3.171 0.465 1.00 0.00 H +ATOM 2 CH3 ACE A 1 -2.917 -2.969 -0.597 1.00 0.00 C +ATOM 3 H2 ACE A 1 -3.815 -3.045 -1.210 1.00 0.00 H +ATOM 4 H3 ACE A 1 -2.106 -3.644 -0.872 1.00 0.00 H +ATOM 5 C ACE A 1 -2.282 -1.553 -0.711 1.00 0.00 C +ATOM 6 O ACE A 1 -2.958 -0.698 -1.252 1.00 0.00 O +ATOM 7 N HD3 A 2 -1.104 -1.396 -0.185 1.00 0.00 N +ATOM 8 H HD3 A 2 -0.697 -2.276 0.096 1.00 0.00 H +ATOM 9 CA HD3 A 2 -0.333 -0.155 -0.121 1.00 0.00 C +ATOM 10 CB HD3 A 2 -0.870 0.739 0.999 1.00 0.00 C +ATOM 11 HB2 HD3 A 2 -0.352 1.697 0.995 1.00 0.00 H +ATOM 12 HB3 HD3 A 2 -1.939 0.904 0.864 1.00 0.00 H +ATOM 13 CG HD3 A 2 -0.695 0.162 2.369 1.00 0.00 C +ATOM 14 ND1 HD3 A 2 0.481 0.272 3.078 1.00 0.00 N +ATOM 15 HD3 HD3 A 2 1.312 0.740 2.745 1.00 0.00 H +ATOM 16 CE1 HD3 A 2 0.343 -0.328 4.248 1.00 0.00 C +ATOM 17 HE1 HD3 A 2 1.169 -0.351 4.958 1.00 0.00 H +ATOM 18 NE2 HD3 A 2 -0.877 -0.823 4.323 1.00 0.00 N +ATOM 19 CD2 HD3 A 2 -1.547 -0.531 3.160 1.00 0.00 C +ATOM 20 HD2 HD3 A 2 -2.579 -0.859 3.029 1.00 0.00 H +ATOM 21 HA HD3 A 2 -0.610 0.298 -1.073 1.00 0.00 H +ATOM 22 C HD3 A 2 1.131 -0.273 -0.199 1.00 0.00 C +ATOM 23 O HD3 A 2 1.769 0.539 -0.827 1.00 0.00 O +ATOM 24 N ALA A 3 1.795 -1.211 0.498 1.00 0.00 N +ATOM 25 H ALA A 3 1.221 -1.808 1.076 1.00 0.00 H +ATOM 26 CA ALA A 3 3.262 -1.252 0.419 1.00 0.00 C +ATOM 27 HA ALA A 3 3.652 -0.256 0.628 1.00 0.00 H +ATOM 28 CB ALA A 3 3.827 -2.271 1.436 1.00 0.00 C +ATOM 29 HB1 ALA A 3 3.510 -1.948 2.428 1.00 0.00 H +ATOM 30 HB2 ALA A 3 3.389 -3.228 1.153 1.00 0.00 H +ATOM 31 HB3 ALA A 3 4.910 -2.372 1.514 1.00 0.00 H +ATOM 32 C ALA A 3 3.783 -1.597 -0.986 1.00 0.00 C +ATOM 33 O ALA A 3 4.802 -1.070 -1.378 1.00 0.00 O +ATOM 34 N ALA A 4 3.132 -2.508 -1.712 1.00 0.00 N +ATOM 35 H ALA A 4 2.361 -3.014 -1.299 1.00 0.00 H +ATOM 36 CA ALA A 4 3.470 -2.716 -3.172 1.00 0.00 C +ATOM 37 HA ALA A 4 4.559 -2.699 -3.210 1.00 0.00 H +ATOM 38 CB ALA A 4 2.900 -4.035 -3.564 1.00 0.00 C +ATOM 39 HB1 ALA A 4 3.370 -4.803 -2.950 1.00 0.00 H +ATOM 40 HB2 ALA A 4 1.845 -4.033 -3.290 1.00 0.00 H +ATOM 41 HB3 ALA A 4 3.197 -4.068 -4.612 1.00 0.00 H +ATOM 42 C ALA A 4 3.146 -1.507 -3.992 1.00 0.00 C +ATOM 43 O ALA A 4 4.003 -1.154 -4.830 1.00 0.00 O +ATOM 44 N ALA A 5 2.102 -0.798 -3.719 1.00 0.00 N +ATOM 45 H ALA A 5 1.578 -1.096 -2.909 1.00 0.00 H +ATOM 46 CA ALA A 5 1.798 0.414 -4.360 1.00 0.00 C +ATOM 47 HA ALA A 5 2.033 0.197 -5.403 1.00 0.00 H +ATOM 48 CB ALA A 5 0.257 0.848 -4.179 1.00 0.00 C +ATOM 49 HB1 ALA A 5 -0.434 0.100 -4.566 1.00 0.00 H +ATOM 50 HB2 ALA A 5 0.029 0.931 -3.116 1.00 0.00 H +ATOM 51 HB3 ALA A 5 0.160 1.812 -4.679 1.00 0.00 H +ATOM 52 C ALA A 5 2.753 1.542 -4.006 1.00 0.00 C +ATOM 53 O ALA A 5 3.074 2.358 -4.897 1.00 0.00 O +ATOM 54 N ALA A 6 3.298 1.676 -2.803 1.00 0.00 N +ATOM 55 H ALA A 6 2.836 1.294 -1.990 1.00 0.00 H +ATOM 56 CA ALA A 6 4.273 2.694 -2.399 1.00 0.00 C +ATOM 57 HA ALA A 6 3.991 3.697 -2.721 1.00 0.00 H +ATOM 58 CB ALA A 6 4.338 2.833 -0.890 1.00 0.00 C +ATOM 59 HB1 ALA A 6 3.425 3.266 -0.481 1.00 0.00 H +ATOM 60 HB2 ALA A 6 4.564 1.863 -0.449 1.00 0.00 H +ATOM 61 HB3 ALA A 6 5.247 3.402 -0.697 1.00 0.00 H +ATOM 62 C ALA A 6 5.749 2.356 -2.826 1.00 0.00 C +ATOM 63 O ALA A 6 6.538 3.204 -3.079 1.00 0.00 O +ATOM 64 N ALA A 7 5.959 1.049 -3.048 1.00 0.00 N +ATOM 65 H ALA A 7 5.304 0.423 -2.601 1.00 0.00 H +ATOM 66 CA ALA A 7 7.183 0.475 -3.563 1.00 0.00 C +ATOM 67 HA ALA A 7 7.990 1.166 -3.316 1.00 0.00 H +ATOM 68 CB ALA A 7 7.530 -0.880 -2.926 1.00 0.00 C +ATOM 69 HB1 ALA A 7 7.386 -0.936 -1.847 1.00 0.00 H +ATOM 70 HB2 ALA A 7 6.786 -1.525 -3.395 1.00 0.00 H +ATOM 71 HB3 ALA A 7 8.523 -1.178 -3.261 1.00 0.00 H +ATOM 72 C ALA A 7 7.218 0.417 -5.118 1.00 0.00 C +ATOM 73 O ALA A 7 8.320 0.602 -5.691 1.00 0.00 O +ATOM 74 N ALA A 8 6.093 0.302 -5.750 1.00 0.00 N +ATOM 75 H ALA A 8 5.324 -0.065 -5.206 1.00 0.00 H +ATOM 76 CA ALA A 8 5.982 0.524 -7.158 1.00 0.00 C +ATOM 77 HA ALA A 8 6.812 0.018 -7.650 1.00 0.00 H +ATOM 78 CB ALA A 8 4.784 -0.264 -7.698 1.00 0.00 C +ATOM 79 HB1 ALA A 8 4.911 -1.274 -7.308 1.00 0.00 H +ATOM 80 HB2 ALA A 8 3.881 0.285 -7.430 1.00 0.00 H +ATOM 81 HB3 ALA A 8 4.855 -0.199 -8.784 1.00 0.00 H +ATOM 82 C ALA A 8 5.945 2.036 -7.500 1.00 0.00 C +ATOM 83 O ALA A 8 6.554 2.371 -8.484 1.00 0.00 O +ATOM 84 N ALA A 9 5.406 2.871 -6.588 1.00 0.00 N +ATOM 85 H ALA A 9 4.829 2.524 -5.835 1.00 0.00 H +ATOM 86 CA ALA A 9 5.472 4.303 -6.694 1.00 0.00 C +ATOM 87 HA ALA A 9 5.320 4.497 -7.756 1.00 0.00 H +ATOM 88 CB ALA A 9 4.300 5.085 -6.075 1.00 0.00 C +ATOM 89 HB1 ALA A 9 3.330 4.659 -6.333 1.00 0.00 H +ATOM 90 HB2 ALA A 9 4.436 5.008 -4.996 1.00 0.00 H +ATOM 91 HB3 ALA A 9 4.315 6.151 -6.302 1.00 0.00 H +ATOM 92 C ALA A 9 6.893 4.859 -6.381 1.00 0.00 C +ATOM 93 O ALA A 9 7.444 5.619 -7.164 1.00 0.00 O +ATOM 94 N ALA A 10 7.541 4.364 -5.327 1.00 0.00 N +ATOM 95 H ALA A 10 7.021 3.870 -4.617 1.00 0.00 H +ATOM 96 CA ALA A 10 8.960 4.713 -5.050 1.00 0.00 C +ATOM 97 HA ALA A 10 8.966 5.797 -5.163 1.00 0.00 H +ATOM 98 CB ALA A 10 9.288 4.389 -3.622 1.00 0.00 C +ATOM 99 HB1 ALA A 10 8.642 4.839 -2.869 1.00 0.00 H +ATOM 100 HB2 ALA A 10 9.230 3.307 -3.504 1.00 0.00 H +ATOM 101 HB3 ALA A 10 10.344 4.615 -3.471 1.00 0.00 H +ATOM 102 C ALA A 10 9.986 4.042 -6.032 1.00 0.00 C +ATOM 103 O ALA A 10 11.142 4.565 -6.147 1.00 0.00 O +ATOM 104 N ALA A 11 9.656 2.896 -6.701 1.00 0.00 N +ATOM 105 H ALA A 11 8.894 2.276 -6.470 1.00 0.00 H +ATOM 106 CA ALA A 11 10.445 2.411 -7.813 1.00 0.00 C +ATOM 107 HA ALA A 11 11.510 2.566 -7.640 1.00 0.00 H +ATOM 108 CB ALA A 11 10.164 0.914 -8.040 1.00 0.00 C +ATOM 109 HB1 ALA A 11 10.615 0.443 -7.166 1.00 0.00 H +ATOM 110 HB2 ALA A 11 9.107 0.669 -8.142 1.00 0.00 H +ATOM 111 HB3 ALA A 11 10.719 0.516 -8.889 1.00 0.00 H +ATOM 112 C ALA A 11 10.151 3.103 -9.155 1.00 0.00 C +ATOM 113 O ALA A 11 11.041 3.166 -9.980 1.00 0.00 O +ATOM 114 N ALA A 12 8.962 3.622 -9.346 1.00 0.00 N +ATOM 115 H ALA A 12 8.246 3.385 -8.673 1.00 0.00 H +ATOM 116 CA ALA A 12 8.644 4.359 -10.533 1.00 0.00 C +ATOM 117 HA ALA A 12 9.114 3.991 -11.446 1.00 0.00 H +ATOM 118 CB ALA A 12 7.143 4.275 -10.773 1.00 0.00 C +ATOM 119 HB1 ALA A 12 6.835 3.230 -10.811 1.00 0.00 H +ATOM 120 HB2 ALA A 12 6.547 4.719 -9.976 1.00 0.00 H +ATOM 121 HB3 ALA A 12 6.930 4.661 -11.770 1.00 0.00 H +ATOM 122 C ALA A 12 8.998 5.845 -10.408 1.00 0.00 C +ATOM 123 O ALA A 12 9.206 6.435 -11.479 1.00 0.00 O +ATOM 124 N ALA A 13 9.060 6.373 -9.150 1.00 0.00 N +ATOM 125 H ALA A 13 8.710 5.815 -8.384 1.00 0.00 H +ATOM 126 CA ALA A 13 9.644 7.589 -8.707 1.00 0.00 C +ATOM 127 HA ALA A 13 9.378 8.325 -9.466 1.00 0.00 H +ATOM 128 CB ALA A 13 8.979 8.114 -7.362 1.00 0.00 C +ATOM 129 HB1 ALA A 13 7.893 8.188 -7.300 1.00 0.00 H +ATOM 130 HB2 ALA A 13 9.391 7.514 -6.550 1.00 0.00 H +ATOM 131 HB3 ALA A 13 9.297 9.138 -7.165 1.00 0.00 H +ATOM 132 C ALA A 13 11.163 7.561 -8.544 1.00 0.00 C +ATOM 133 O ALA A 13 11.753 8.643 -8.809 1.00 0.00 O +ATOM 134 N ALA A 14 11.711 6.438 -8.195 1.00 0.00 N +ATOM 135 H ALA A 14 11.201 5.708 -7.719 1.00 0.00 H +ATOM 136 CA ALA A 14 13.187 6.178 -8.377 1.00 0.00 C +ATOM 137 HA ALA A 14 13.746 7.056 -8.055 1.00 0.00 H +ATOM 138 CB ALA A 14 13.659 4.995 -7.481 1.00 0.00 C +ATOM 139 HB1 ALA A 14 13.670 5.270 -6.427 1.00 0.00 H +ATOM 140 HB2 ALA A 14 13.140 4.041 -7.573 1.00 0.00 H +ATOM 141 HB3 ALA A 14 14.732 4.857 -7.614 1.00 0.00 H +ATOM 142 C ALA A 14 13.540 5.894 -9.914 1.00 0.00 C +ATOM 143 O ALA A 14 14.638 6.393 -10.399 1.00 0.00 O +ATOM 144 N ALA A 15 12.747 5.180 -10.675 1.00 0.00 N +ATOM 145 H ALA A 15 11.928 4.701 -10.329 1.00 0.00 H +ATOM 146 CA ALA A 15 13.062 5.067 -12.046 1.00 0.00 C +ATOM 147 HA ALA A 15 14.076 4.746 -12.284 1.00 0.00 H +ATOM 148 CB ALA A 15 12.198 3.975 -12.711 1.00 0.00 C +ATOM 149 HB1 ALA A 15 12.343 3.040 -12.170 1.00 0.00 H +ATOM 150 HB2 ALA A 15 11.153 4.203 -12.506 1.00 0.00 H +ATOM 151 HB3 ALA A 15 12.380 3.968 -13.786 1.00 0.00 H +ATOM 152 C ALA A 15 12.703 6.348 -12.778 1.00 0.00 C +ATOM 153 O ALA A 15 13.510 6.684 -13.678 1.00 0.00 O +ATOM 154 N ALA A 16 11.645 7.130 -12.475 1.00 0.00 N +ATOM 155 H ALA A 16 10.893 6.780 -11.898 1.00 0.00 H +ATOM 156 CA ALA A 16 11.461 8.455 -13.029 1.00 0.00 C +ATOM 157 HA ALA A 16 11.491 8.353 -14.114 1.00 0.00 H +ATOM 158 CB ALA A 16 10.149 9.085 -12.685 1.00 0.00 C +ATOM 159 HB1 ALA A 16 9.388 8.398 -13.054 1.00 0.00 H +ATOM 160 HB2 ALA A 16 10.052 9.148 -11.601 1.00 0.00 H +ATOM 161 HB3 ALA A 16 10.063 10.057 -13.171 1.00 0.00 H +ATOM 162 C ALA A 16 12.608 9.384 -12.612 1.00 0.00 C +ATOM 163 O ALA A 16 13.039 10.222 -13.473 1.00 0.00 O +ATOM 164 N ALA A 17 13.138 9.241 -11.388 1.00 0.00 N +ATOM 165 H ALA A 17 12.604 8.788 -10.661 1.00 0.00 H +ATOM 166 CA ALA A 17 14.326 10.028 -10.964 1.00 0.00 C +ATOM 167 HA ALA A 17 14.114 11.052 -11.270 1.00 0.00 H +ATOM 168 CB ALA A 17 14.275 10.145 -9.531 1.00 0.00 C +ATOM 169 HB1 ALA A 17 13.375 10.647 -9.177 1.00 0.00 H +ATOM 170 HB2 ALA A 17 14.478 9.222 -8.988 1.00 0.00 H +ATOM 171 HB3 ALA A 17 15.023 10.861 -9.189 1.00 0.00 H +ATOM 172 C ALA A 17 15.611 9.623 -11.594 1.00 0.00 C +ATOM 173 O ALA A 17 16.445 10.488 -11.882 1.00 0.00 O +ATOM 174 N ALA A 18 15.812 8.347 -11.791 1.00 0.00 N +ATOM 175 H ALA A 18 15.210 7.647 -11.382 1.00 0.00 H +ATOM 176 CA ALA A 18 17.039 7.928 -12.446 1.00 0.00 C +ATOM 177 HA ALA A 18 17.935 8.483 -12.170 1.00 0.00 H +ATOM 178 CB ALA A 18 17.358 6.480 -12.029 1.00 0.00 C +ATOM 179 HB1 ALA A 18 17.561 6.449 -10.958 1.00 0.00 H +ATOM 180 HB2 ALA A 18 16.536 5.820 -12.307 1.00 0.00 H +ATOM 181 HB3 ALA A 18 18.323 6.159 -12.422 1.00 0.00 H +ATOM 182 C ALA A 18 16.968 8.017 -13.999 1.00 0.00 C +ATOM 183 O ALA A 18 18.024 8.143 -14.660 1.00 0.00 O +ATOM 184 N ALA A 19 15.774 8.031 -14.539 1.00 0.00 N +ATOM 185 H ALA A 19 15.110 7.729 -13.840 1.00 0.00 H +ATOM 186 CA ALA A 19 15.508 8.397 -15.942 1.00 0.00 C +ATOM 187 HA ALA A 19 16.274 7.890 -16.528 1.00 0.00 H +ATOM 188 CB ALA A 19 14.132 7.825 -16.381 1.00 0.00 C +ATOM 189 HB1 ALA A 19 14.000 6.748 -16.279 1.00 0.00 H +ATOM 190 HB2 ALA A 19 13.326 8.274 -15.801 1.00 0.00 H +ATOM 191 HB3 ALA A 19 14.129 8.183 -17.411 1.00 0.00 H +ATOM 192 C ALA A 19 15.616 9.879 -16.218 1.00 0.00 C +ATOM 193 O ALA A 19 15.925 10.312 -17.349 1.00 0.00 O +ATOM 194 N ALA A 20 15.342 10.748 -15.240 1.00 0.00 N +ATOM 195 H ALA A 20 15.274 10.304 -14.336 1.00 0.00 H +ATOM 196 CA ALA A 20 15.539 12.186 -15.310 1.00 0.00 C +ATOM 197 HA ALA A 20 15.392 12.510 -16.340 1.00 0.00 H +ATOM 198 CB ALA A 20 14.470 12.874 -14.390 1.00 0.00 C +ATOM 199 HB1 ALA A 20 13.502 12.406 -14.574 1.00 0.00 H +ATOM 200 HB2 ALA A 20 14.667 12.751 -13.325 1.00 0.00 H +ATOM 201 HB3 ALA A 20 14.411 13.936 -14.630 1.00 0.00 H +ATOM 202 C ALA A 20 16.976 12.596 -14.911 1.00 0.00 C +ATOM 203 O ALA A 20 17.474 13.502 -15.583 1.00 0.00 O +ATOM 204 N ALA A 21 17.617 12.028 -13.914 1.00 0.00 N +ATOM 205 H ALA A 21 17.079 11.380 -13.356 1.00 0.00 H +ATOM 206 CA ALA A 21 19.140 12.093 -13.649 1.00 0.00 C +ATOM 207 HA ALA A 21 19.393 13.153 -13.607 1.00 0.00 H +ATOM 208 CB ALA A 21 19.438 11.428 -12.300 1.00 0.00 C +ATOM 209 HB1 ALA A 21 18.876 12.017 -11.575 1.00 0.00 H +ATOM 210 HB2 ALA A 21 19.196 10.366 -12.277 1.00 0.00 H +ATOM 211 HB3 ALA A 21 20.473 11.677 -12.068 1.00 0.00 H +ATOM 212 C ALA A 21 19.911 11.369 -14.740 1.00 0.00 C +ATOM 213 O ALA A 21 19.370 10.700 -15.601 1.00 0.00 O +ATOM 214 N NME A 22 21.266 11.506 -14.654 1.00 0.00 N +ATOM 215 H NME A 22 21.663 12.119 -13.956 1.00 0.00 H +ATOM 216 CH3 NME A 22 22.261 10.909 -15.537 1.00 0.00 C +ATOM 217 HH31 NME A 22 21.787 10.285 -16.294 1.00 0.00 H +ATOM 218 HH32 NME A 22 22.939 11.631 -15.993 1.00 0.00 H +ATOM 219 HH33 NME A 22 22.893 10.275 -14.916 1.00 0.00 H +CONECT 1 2 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 6 7 +CONECT 6 5 5 +CONECT 7 5 8 9 +CONECT 8 7 +CONECT 9 7 21 22 10 +CONECT 10 9 11 12 13 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 19 19 +CONECT 14 13 15 16 +CONECT 15 14 +CONECT 16 14 17 18 18 +CONECT 17 16 +CONECT 18 16 16 19 +CONECT 19 13 13 18 20 +CONECT 20 19 +CONECT 21 9 +CONECT 22 9 23 23 24 +CONECT 23 22 22 +CONECT 24 22 25 26 +CONECT 25 24 +CONECT 26 24 27 28 32 +CONECT 27 26 +CONECT 28 26 29 30 31 +CONECT 29 28 +CONECT 30 28 +CONECT 31 28 +CONECT 32 26 33 33 34 +CONECT 33 32 32 +CONECT 34 32 35 36 +CONECT 35 34 +CONECT 36 34 37 38 42 +CONECT 37 36 +CONECT 38 36 39 40 41 +CONECT 39 38 +CONECT 40 38 +CONECT 41 38 +CONECT 42 36 43 43 44 +CONECT 43 42 42 +CONECT 44 42 45 46 +CONECT 45 44 +CONECT 46 44 47 48 52 +CONECT 47 46 +CONECT 48 46 49 50 51 +CONECT 49 48 +CONECT 50 48 +CONECT 51 48 +CONECT 52 46 53 53 54 +CONECT 53 52 52 +CONECT 54 52 55 56 +CONECT 55 54 +CONECT 56 54 57 58 62 +CONECT 57 56 +CONECT 58 56 59 60 61 +CONECT 59 58 +CONECT 60 58 +CONECT 61 58 +CONECT 62 56 63 63 64 +CONECT 63 62 62 +CONECT 64 62 65 66 +CONECT 65 64 +CONECT 66 64 67 68 72 +CONECT 67 66 +CONECT 68 66 69 70 71 +CONECT 69 68 +CONECT 70 68 +CONECT 71 68 +CONECT 72 66 73 73 74 +CONECT 73 72 72 +CONECT 74 72 75 76 +CONECT 75 74 +CONECT 76 74 77 78 82 +CONECT 77 76 +CONECT 78 76 79 80 81 +CONECT 79 78 +CONECT 80 78 +CONECT 81 78 +CONECT 82 76 83 83 84 +CONECT 83 82 82 +CONECT 84 82 85 86 +CONECT 85 84 +CONECT 86 84 87 88 92 +CONECT 87 86 +CONECT 88 86 89 90 91 +CONECT 89 88 +CONECT 90 88 +CONECT 91 88 +CONECT 92 86 93 93 94 +CONECT 93 92 92 +CONECT 94 92 95 96 +CONECT 95 94 +CONECT 96 94 97 98 102 +CONECT 97 96 +CONECT 98 96 99 100 101 +CONECT 99 98 +CONECT 100 98 +CONECT 101 98 +CONECT 102 96 103 103 104 +CONECT 103 102 102 +CONECT 104 102 105 106 +CONECT 105 104 +CONECT 106 104 107 108 112 +CONECT 107 106 +CONECT 108 106 109 110 111 +CONECT 109 108 +CONECT 110 108 +CONECT 111 108 +CONECT 112 106 113 113 114 +CONECT 113 112 112 +CONECT 114 112 115 116 +CONECT 115 114 +CONECT 116 114 117 118 122 +CONECT 117 116 +CONECT 118 116 119 120 121 +CONECT 119 118 +CONECT 120 118 +CONECT 121 118 +CONECT 122 116 123 123 124 +CONECT 123 122 122 +CONECT 124 122 125 126 +CONECT 125 124 +CONECT 126 124 127 128 132 +CONECT 127 126 +CONECT 128 126 129 130 131 +CONECT 129 128 +CONECT 130 128 +CONECT 131 128 +CONECT 132 126 133 133 134 +CONECT 133 132 132 +CONECT 134 132 135 136 +CONECT 135 134 +CONECT 136 134 137 138 142 +CONECT 137 136 +CONECT 138 136 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 143 144 +CONECT 143 142 142 +CONECT 144 142 145 146 +CONECT 145 144 +CONECT 146 144 147 148 152 +CONECT 147 146 +CONECT 148 146 149 150 151 +CONECT 149 148 +CONECT 150 148 +CONECT 151 148 +CONECT 152 146 153 153 154 +CONECT 153 152 152 +CONECT 154 152 155 156 +CONECT 155 154 +CONECT 156 154 157 158 162 +CONECT 157 156 +CONECT 158 156 159 160 161 +CONECT 159 158 +CONECT 160 158 +CONECT 161 158 +CONECT 162 156 163 163 164 +CONECT 163 162 162 +CONECT 164 162 165 166 +CONECT 165 164 +CONECT 166 164 167 168 172 +CONECT 167 166 +CONECT 168 166 169 170 171 +CONECT 169 168 +CONECT 170 168 +CONECT 171 168 +CONECT 172 166 173 173 174 +CONECT 173 172 172 +CONECT 174 172 175 176 +CONECT 175 174 +CONECT 176 174 177 178 182 +CONECT 177 176 +CONECT 178 176 179 180 181 +CONECT 179 178 +CONECT 180 178 +CONECT 181 178 +CONECT 182 176 183 183 184 +CONECT 183 182 182 +CONECT 184 182 185 186 +CONECT 185 184 +CONECT 186 184 187 188 192 +CONECT 187 186 +CONECT 188 186 189 190 191 +CONECT 189 188 +CONECT 190 188 +CONECT 191 188 +CONECT 192 186 193 193 194 +CONECT 193 192 192 +CONECT 194 192 195 196 +CONECT 195 194 +CONECT 196 194 197 198 202 +CONECT 197 196 +CONECT 198 196 199 200 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 +CONECT 202 196 203 203 204 +CONECT 203 202 202 +CONECT 204 202 205 206 +CONECT 205 204 +CONECT 206 204 207 208 212 +CONECT 207 206 +CONECT 208 206 209 210 211 +CONECT 209 208 +CONECT 210 208 +CONECT 211 208 +CONECT 212 206 213 213 214 +CONECT 213 212 212 +CONECT 214 212 215 216 +CONECT 215 214 +CONECT 216 214 217 218 219 +CONECT 217 216 +CONECT 218 216 +CONECT 219 216 +MASTER 0 0 0 0 0 0 0 0 219 0 219 0 +END diff --git a/unittests/example_files/H1A19_ob2.4.2.pdb b/unittests/example_files/H1A19_ob2.4.2.pdb new file mode 100644 index 0000000..17c0c4e --- /dev/null +++ b/unittests/example_files/H1A19_ob2.4.2.pdb @@ -0,0 +1,442 @@ +COMPND PolyALA +AUTHOR GENERATED BY OPEN BABEL 2.3.2 +ATOM 1 H1 ACE A 1 -3.054 -3.171 0.465 1.00 0.00 H +ATOM 2 CH3 ACE A 1 -2.917 -2.969 -0.597 1.00 0.00 C +ATOM 3 H2 ACE A 1 -3.815 -3.045 -1.210 1.00 0.00 H +ATOM 4 H3 ACE A 1 -2.106 -3.644 -0.872 1.00 0.00 H +ATOM 5 C ACE A 1 -2.282 -1.553 -0.711 1.00 0.00 C +ATOM 6 O ACE A 1 -2.958 -0.698 -1.252 1.00 0.00 O +ATOM 7 N HD3 A 2 -1.104 -1.396 -0.185 1.00 0.00 N +ATOM 8 H HD3 A 2 -0.697 -2.276 0.096 1.00 0.00 H +ATOM 9 CA HD3 A 2 -0.333 -0.155 -0.121 1.00 0.00 C +ATOM 10 CB HD3 A 2 -0.870 0.739 0.999 1.00 0.00 C +ATOM 11 HB2 HD3 A 2 -0.351 1.697 0.995 1.00 0.00 H +ATOM 12 HB3 HD3 A 2 -1.939 0.904 0.864 1.00 0.00 H +ATOM 13 CG HD3 A 2 -0.694 0.162 2.369 1.00 0.00 C +ATOM 14 ND1 HD3 A 2 0.481 0.271 3.078 1.00 0.00 N +ATOM 15 HD3 HD3 A 2 1.312 0.739 2.745 1.00 0.00 H +ATOM 16 CE1 HD3 A 2 0.344 -0.330 4.248 1.00 0.00 C +ATOM 17 HE1 HD3 A 2 1.169 -0.352 4.958 1.00 0.00 H +ATOM 18 NE2 HD3 A 2 -0.876 -0.824 4.323 1.00 0.00 N +ATOM 19 CD2 HD3 A 2 -1.547 -0.532 3.161 1.00 0.00 C +ATOM 20 HD2 HD3 A 2 -2.578 -0.860 3.029 1.00 0.00 H +ATOM 21 HA HD3 A 2 -0.610 0.298 -1.073 1.00 0.00 H +ATOM 22 C HD3 A 2 1.131 -0.273 -0.199 1.00 0.00 C +ATOM 23 O HD3 A 2 1.769 0.539 -0.827 1.00 0.00 O +ATOM 24 N ALA A 3 1.795 -1.211 0.498 1.00 0.00 N +ATOM 25 H ALA A 3 1.221 -1.808 1.076 1.00 0.00 H +ATOM 26 CA ALA A 3 3.262 -1.252 0.419 1.00 0.00 C +ATOM 27 HA ALA A 3 3.652 -0.256 0.628 1.00 0.00 H +ATOM 28 CB ALA A 3 3.827 -2.271 1.436 1.00 0.00 C +ATOM 29 HB1 ALA A 3 3.510 -1.948 2.428 1.00 0.00 H +ATOM 30 HB2 ALA A 3 3.389 -3.228 1.153 1.00 0.00 H +ATOM 31 HB3 ALA A 3 4.910 -2.372 1.514 1.00 0.00 H +ATOM 32 C ALA A 3 3.783 -1.597 -0.986 1.00 0.00 C +ATOM 33 O ALA A 3 4.802 -1.070 -1.378 1.00 0.00 O +ATOM 34 N ALA A 4 3.132 -2.508 -1.712 1.00 0.00 N +ATOM 35 H ALA A 4 2.361 -3.014 -1.299 1.00 0.00 H +ATOM 36 CA ALA A 4 3.470 -2.716 -3.172 1.00 0.00 C +ATOM 37 HA ALA A 4 4.559 -2.699 -3.210 1.00 0.00 H +ATOM 38 CB ALA A 4 2.900 -4.035 -3.564 1.00 0.00 C +ATOM 39 HB1 ALA A 4 3.370 -4.803 -2.950 1.00 0.00 H +ATOM 40 HB2 ALA A 4 1.845 -4.033 -3.290 1.00 0.00 H +ATOM 41 HB3 ALA A 4 3.197 -4.068 -4.612 1.00 0.00 H +ATOM 42 C ALA A 4 3.146 -1.507 -3.992 1.00 0.00 C +ATOM 43 O ALA A 4 4.003 -1.154 -4.830 1.00 0.00 O +ATOM 44 N ALA A 5 2.102 -0.798 -3.719 1.00 0.00 N +ATOM 45 H ALA A 5 1.578 -1.096 -2.909 1.00 0.00 H +ATOM 46 CA ALA A 5 1.798 0.414 -4.360 1.00 0.00 C +ATOM 47 HA ALA A 5 2.033 0.197 -5.403 1.00 0.00 H +ATOM 48 CB ALA A 5 0.257 0.848 -4.179 1.00 0.00 C +ATOM 49 HB1 ALA A 5 -0.434 0.100 -4.566 1.00 0.00 H +ATOM 50 HB2 ALA A 5 0.029 0.931 -3.116 1.00 0.00 H +ATOM 51 HB3 ALA A 5 0.160 1.812 -4.679 1.00 0.00 H +ATOM 52 C ALA A 5 2.753 1.542 -4.006 1.00 0.00 C +ATOM 53 O ALA A 5 3.074 2.358 -4.897 1.00 0.00 O +ATOM 54 N ALA A 6 3.298 1.676 -2.803 1.00 0.00 N +ATOM 55 H ALA A 6 2.836 1.294 -1.990 1.00 0.00 H +ATOM 56 CA ALA A 6 4.273 2.694 -2.399 1.00 0.00 C +ATOM 57 HA ALA A 6 3.991 3.697 -2.721 1.00 0.00 H +ATOM 58 CB ALA A 6 4.338 2.833 -0.890 1.00 0.00 C +ATOM 59 HB1 ALA A 6 3.425 3.266 -0.481 1.00 0.00 H +ATOM 60 HB2 ALA A 6 4.564 1.863 -0.449 1.00 0.00 H +ATOM 61 HB3 ALA A 6 5.247 3.402 -0.697 1.00 0.00 H +ATOM 62 C ALA A 6 5.749 2.356 -2.826 1.00 0.00 C +ATOM 63 O ALA A 6 6.538 3.204 -3.079 1.00 0.00 O +ATOM 64 N ALA A 7 5.959 1.049 -3.048 1.00 0.00 N +ATOM 65 H ALA A 7 5.304 0.423 -2.601 1.00 0.00 H +ATOM 66 CA ALA A 7 7.183 0.475 -3.563 1.00 0.00 C +ATOM 67 HA ALA A 7 7.990 1.166 -3.316 1.00 0.00 H +ATOM 68 CB ALA A 7 7.530 -0.880 -2.926 1.00 0.00 C +ATOM 69 HB1 ALA A 7 7.386 -0.936 -1.847 1.00 0.00 H +ATOM 70 HB2 ALA A 7 6.786 -1.525 -3.395 1.00 0.00 H +ATOM 71 HB3 ALA A 7 8.523 -1.178 -3.261 1.00 0.00 H +ATOM 72 C ALA A 7 7.218 0.417 -5.118 1.00 0.00 C +ATOM 73 O ALA A 7 8.320 0.602 -5.691 1.00 0.00 O +ATOM 74 N ALA A 8 6.093 0.302 -5.750 1.00 0.00 N +ATOM 75 H ALA A 8 5.324 -0.065 -5.206 1.00 0.00 H +ATOM 76 CA ALA A 8 5.982 0.524 -7.158 1.00 0.00 C +ATOM 77 HA ALA A 8 6.812 0.018 -7.650 1.00 0.00 H +ATOM 78 CB ALA A 8 4.784 -0.264 -7.698 1.00 0.00 C +ATOM 79 HB1 ALA A 8 4.911 -1.274 -7.308 1.00 0.00 H +ATOM 80 HB2 ALA A 8 3.881 0.285 -7.430 1.00 0.00 H +ATOM 81 HB3 ALA A 8 4.855 -0.199 -8.784 1.00 0.00 H +ATOM 82 C ALA A 8 5.945 2.036 -7.500 1.00 0.00 C +ATOM 83 O ALA A 8 6.554 2.371 -8.484 1.00 0.00 O +ATOM 84 N ALA A 9 5.406 2.871 -6.588 1.00 0.00 N +ATOM 85 H ALA A 9 4.829 2.524 -5.835 1.00 0.00 H +ATOM 86 CA ALA A 9 5.472 4.303 -6.694 1.00 0.00 C +ATOM 87 HA ALA A 9 5.320 4.497 -7.756 1.00 0.00 H +ATOM 88 CB ALA A 9 4.300 5.085 -6.075 1.00 0.00 C +ATOM 89 HB1 ALA A 9 3.330 4.659 -6.333 1.00 0.00 H +ATOM 90 HB2 ALA A 9 4.436 5.008 -4.996 1.00 0.00 H +ATOM 91 HB3 ALA A 9 4.315 6.151 -6.302 1.00 0.00 H +ATOM 92 C ALA A 9 6.893 4.859 -6.381 1.00 0.00 C +ATOM 93 O ALA A 9 7.444 5.619 -7.164 1.00 0.00 O +ATOM 94 N ALA A 10 7.541 4.364 -5.327 1.00 0.00 N +ATOM 95 H ALA A 10 7.021 3.870 -4.617 1.00 0.00 H +ATOM 96 CA ALA A 10 8.960 4.713 -5.050 1.00 0.00 C +ATOM 97 HA ALA A 10 8.966 5.797 -5.163 1.00 0.00 H +ATOM 98 CB ALA A 10 9.288 4.389 -3.622 1.00 0.00 C +ATOM 99 HB1 ALA A 10 8.642 4.839 -2.869 1.00 0.00 H +ATOM 100 HB2 ALA A 10 9.230 3.307 -3.504 1.00 0.00 H +ATOM 101 HB3 ALA A 10 10.344 4.615 -3.471 1.00 0.00 H +ATOM 102 C ALA A 10 9.986 4.042 -6.032 1.00 0.00 C +ATOM 103 O ALA A 10 11.142 4.565 -6.147 1.00 0.00 O +ATOM 104 N ALA A 11 9.656 2.896 -6.701 1.00 0.00 N +ATOM 105 H ALA A 11 8.894 2.276 -6.470 1.00 0.00 H +ATOM 106 CA ALA A 11 10.445 2.411 -7.813 1.00 0.00 C +ATOM 107 HA ALA A 11 11.510 2.566 -7.640 1.00 0.00 H +ATOM 108 CB ALA A 11 10.164 0.914 -8.040 1.00 0.00 C +ATOM 109 HB1 ALA A 11 10.615 0.443 -7.166 1.00 0.00 H +ATOM 110 HB2 ALA A 11 9.107 0.669 -8.142 1.00 0.00 H +ATOM 111 HB3 ALA A 11 10.719 0.516 -8.889 1.00 0.00 H +ATOM 112 C ALA A 11 10.151 3.103 -9.155 1.00 0.00 C +ATOM 113 O ALA A 11 11.041 3.166 -9.980 1.00 0.00 O +ATOM 114 N ALA A 12 8.962 3.622 -9.346 1.00 0.00 N +ATOM 115 H ALA A 12 8.246 3.385 -8.673 1.00 0.00 H +ATOM 116 CA ALA A 12 8.644 4.359 -10.533 1.00 0.00 C +ATOM 117 HA ALA A 12 9.114 3.991 -11.446 1.00 0.00 H +ATOM 118 CB ALA A 12 7.143 4.275 -10.773 1.00 0.00 C +ATOM 119 HB1 ALA A 12 6.835 3.230 -10.811 1.00 0.00 H +ATOM 120 HB2 ALA A 12 6.547 4.719 -9.976 1.00 0.00 H +ATOM 121 HB3 ALA A 12 6.930 4.661 -11.770 1.00 0.00 H +ATOM 122 C ALA A 12 8.998 5.845 -10.408 1.00 0.00 C +ATOM 123 O ALA A 12 9.206 6.435 -11.479 1.00 0.00 O +ATOM 124 N ALA A 13 9.060 6.373 -9.150 1.00 0.00 N +ATOM 125 H ALA A 13 8.710 5.815 -8.384 1.00 0.00 H +ATOM 126 CA ALA A 13 9.644 7.589 -8.707 1.00 0.00 C +ATOM 127 HA ALA A 13 9.378 8.325 -9.466 1.00 0.00 H +ATOM 128 CB ALA A 13 8.979 8.114 -7.362 1.00 0.00 C +ATOM 129 HB1 ALA A 13 7.893 8.188 -7.300 1.00 0.00 H +ATOM 130 HB2 ALA A 13 9.391 7.514 -6.550 1.00 0.00 H +ATOM 131 HB3 ALA A 13 9.297 9.138 -7.165 1.00 0.00 H +ATOM 132 C ALA A 13 11.163 7.561 -8.544 1.00 0.00 C +ATOM 133 O ALA A 13 11.753 8.643 -8.809 1.00 0.00 O +ATOM 134 N ALA A 14 11.711 6.438 -8.195 1.00 0.00 N +ATOM 135 H ALA A 14 11.201 5.708 -7.719 1.00 0.00 H +ATOM 136 CA ALA A 14 13.187 6.178 -8.377 1.00 0.00 C +ATOM 137 HA ALA A 14 13.746 7.056 -8.055 1.00 0.00 H +ATOM 138 CB ALA A 14 13.659 4.995 -7.481 1.00 0.00 C +ATOM 139 HB1 ALA A 14 13.670 5.270 -6.427 1.00 0.00 H +ATOM 140 HB2 ALA A 14 13.140 4.041 -7.573 1.00 0.00 H +ATOM 141 HB3 ALA A 14 14.732 4.857 -7.614 1.00 0.00 H +ATOM 142 C ALA A 14 13.540 5.894 -9.914 1.00 0.00 C +ATOM 143 O ALA A 14 14.638 6.393 -10.399 1.00 0.00 O +ATOM 144 N ALA A 15 12.747 5.180 -10.675 1.00 0.00 N +ATOM 145 H ALA A 15 11.928 4.701 -10.329 1.00 0.00 H +ATOM 146 CA ALA A 15 13.062 5.067 -12.046 1.00 0.00 C +ATOM 147 HA ALA A 15 14.076 4.746 -12.284 1.00 0.00 H +ATOM 148 CB ALA A 15 12.198 3.975 -12.711 1.00 0.00 C +ATOM 149 HB1 ALA A 15 12.343 3.040 -12.170 1.00 0.00 H +ATOM 150 HB2 ALA A 15 11.153 4.203 -12.506 1.00 0.00 H +ATOM 151 HB3 ALA A 15 12.380 3.968 -13.786 1.00 0.00 H +ATOM 152 C ALA A 15 12.703 6.348 -12.778 1.00 0.00 C +ATOM 153 O ALA A 15 13.510 6.684 -13.678 1.00 0.00 O +ATOM 154 N ALA A 16 11.645 7.130 -12.475 1.00 0.00 N +ATOM 155 H ALA A 16 10.893 6.780 -11.898 1.00 0.00 H +ATOM 156 CA ALA A 16 11.461 8.455 -13.029 1.00 0.00 C +ATOM 157 HA ALA A 16 11.491 8.353 -14.114 1.00 0.00 H +ATOM 158 CB ALA A 16 10.149 9.085 -12.685 1.00 0.00 C +ATOM 159 HB1 ALA A 16 9.388 8.398 -13.054 1.00 0.00 H +ATOM 160 HB2 ALA A 16 10.052 9.148 -11.601 1.00 0.00 H +ATOM 161 HB3 ALA A 16 10.063 10.057 -13.171 1.00 0.00 H +ATOM 162 C ALA A 16 12.608 9.384 -12.612 1.00 0.00 C +ATOM 163 O ALA A 16 13.039 10.222 -13.473 1.00 0.00 O +ATOM 164 N ALA A 17 13.138 9.241 -11.388 1.00 0.00 N +ATOM 165 H ALA A 17 12.604 8.788 -10.661 1.00 0.00 H +ATOM 166 CA ALA A 17 14.326 10.028 -10.964 1.00 0.00 C +ATOM 167 HA ALA A 17 14.114 11.052 -11.270 1.00 0.00 H +ATOM 168 CB ALA A 17 14.275 10.145 -9.531 1.00 0.00 C +ATOM 169 HB1 ALA A 17 13.375 10.647 -9.177 1.00 0.00 H +ATOM 170 HB2 ALA A 17 14.478 9.222 -8.988 1.00 0.00 H +ATOM 171 HB3 ALA A 17 15.023 10.861 -9.189 1.00 0.00 H +ATOM 172 C ALA A 17 15.611 9.623 -11.594 1.00 0.00 C +ATOM 173 O ALA A 17 16.445 10.488 -11.882 1.00 0.00 O +ATOM 174 N ALA A 18 15.812 8.347 -11.791 1.00 0.00 N +ATOM 175 H ALA A 18 15.210 7.647 -11.382 1.00 0.00 H +ATOM 176 CA ALA A 18 17.039 7.928 -12.446 1.00 0.00 C +ATOM 177 HA ALA A 18 17.935 8.483 -12.170 1.00 0.00 H +ATOM 178 CB ALA A 18 17.358 6.480 -12.029 1.00 0.00 C +ATOM 179 HB1 ALA A 18 17.561 6.449 -10.958 1.00 0.00 H +ATOM 180 HB2 ALA A 18 16.536 5.820 -12.307 1.00 0.00 H +ATOM 181 HB3 ALA A 18 18.323 6.159 -12.422 1.00 0.00 H +ATOM 182 C ALA A 18 16.968 8.017 -13.999 1.00 0.00 C +ATOM 183 O ALA A 18 18.024 8.143 -14.660 1.00 0.00 O +ATOM 184 N ALA A 19 15.774 8.031 -14.539 1.00 0.00 N +ATOM 185 H ALA A 19 15.110 7.729 -13.840 1.00 0.00 H +ATOM 186 CA ALA A 19 15.508 8.397 -15.942 1.00 0.00 C +ATOM 187 HA ALA A 19 16.274 7.890 -16.528 1.00 0.00 H +ATOM 188 CB ALA A 19 14.132 7.825 -16.381 1.00 0.00 C +ATOM 189 HB1 ALA A 19 14.000 6.748 -16.279 1.00 0.00 H +ATOM 190 HB2 ALA A 19 13.326 8.274 -15.801 1.00 0.00 H +ATOM 191 HB3 ALA A 19 14.129 8.183 -17.411 1.00 0.00 H +ATOM 192 C ALA A 19 15.616 9.879 -16.218 1.00 0.00 C +ATOM 193 O ALA A 19 15.925 10.312 -17.349 1.00 0.00 O +ATOM 194 N ALA A 20 15.342 10.748 -15.240 1.00 0.00 N +ATOM 195 H ALA A 20 15.274 10.304 -14.336 1.00 0.00 H +ATOM 196 CA ALA A 20 15.539 12.186 -15.310 1.00 0.00 C +ATOM 197 HA ALA A 20 15.392 12.510 -16.340 1.00 0.00 H +ATOM 198 CB ALA A 20 14.470 12.874 -14.390 1.00 0.00 C +ATOM 199 HB1 ALA A 20 13.502 12.406 -14.574 1.00 0.00 H +ATOM 200 HB2 ALA A 20 14.667 12.751 -13.325 1.00 0.00 H +ATOM 201 HB3 ALA A 20 14.411 13.936 -14.630 1.00 0.00 H +ATOM 202 C ALA A 20 16.976 12.596 -14.911 1.00 0.00 C +ATOM 203 O ALA A 20 17.474 13.502 -15.583 1.00 0.00 O +ATOM 204 N ALA A 21 17.617 12.028 -13.914 1.00 0.00 N +ATOM 205 H ALA A 21 17.079 11.380 -13.356 1.00 0.00 H +ATOM 206 CA ALA A 21 19.140 12.093 -13.649 1.00 0.00 C +ATOM 207 HA ALA A 21 19.393 13.153 -13.607 1.00 0.00 H +ATOM 208 CB ALA A 21 19.438 11.428 -12.300 1.00 0.00 C +ATOM 209 HB1 ALA A 21 18.876 12.017 -11.575 1.00 0.00 H +ATOM 210 HB2 ALA A 21 19.196 10.366 -12.277 1.00 0.00 H +ATOM 211 HB3 ALA A 21 20.473 11.677 -12.068 1.00 0.00 H +ATOM 212 C ALA A 21 19.911 11.369 -14.740 1.00 0.00 C +ATOM 213 O ALA A 21 19.370 10.700 -15.601 1.00 0.00 O +ATOM 214 N NME A 22 21.266 11.506 -14.654 1.00 0.00 N +ATOM 215 H NME A 22 21.663 12.119 -13.956 1.00 0.00 H +ATOM 216 CH3 NME A 22 22.261 10.909 -15.537 1.00 0.00 C +ATOM 217 HH31 NME A 22 21.787 10.285 -16.294 1.00 0.00 H +ATOM 218 HH32 NME A 22 22.939 11.631 -15.993 1.00 0.00 H +ATOM 219 HH33 NME A 22 22.893 10.275 -14.916 1.00 0.00 H +CONECT 1 2 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 7 +CONECT 6 5 +CONECT 7 5 8 9 +CONECT 8 7 +CONECT 9 7 21 22 10 +CONECT 10 11 12 13 9 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 19 +CONECT 14 13 15 16 +CONECT 15 14 +CONECT 16 14 17 18 +CONECT 17 16 +CONECT 18 16 19 +CONECT 19 13 18 20 +CONECT 20 19 +CONECT 21 9 +CONECT 22 9 23 24 +CONECT 23 22 +CONECT 24 22 25 26 +CONECT 25 24 +CONECT 26 24 27 28 32 +CONECT 27 26 +CONECT 28 26 29 30 31 +CONECT 29 28 +CONECT 30 28 +CONECT 31 28 +CONECT 32 26 33 34 +CONECT 33 32 +CONECT 34 32 35 36 +CONECT 35 34 +CONECT 36 34 37 38 42 +CONECT 37 36 +CONECT 38 36 39 40 41 +CONECT 39 38 +CONECT 40 38 +CONECT 41 38 +CONECT 42 36 43 44 +CONECT 43 42 +CONECT 44 42 45 46 +CONECT 45 44 +CONECT 46 44 47 48 52 +CONECT 47 46 +CONECT 48 46 49 50 51 +CONECT 49 48 +CONECT 50 48 +CONECT 51 48 +CONECT 52 46 53 54 +CONECT 53 52 +CONECT 54 52 55 56 +CONECT 55 54 +CONECT 56 54 57 58 62 +CONECT 57 56 +CONECT 58 56 59 60 61 +CONECT 59 58 +CONECT 60 58 +CONECT 61 58 +CONECT 62 56 63 64 +CONECT 63 62 +CONECT 64 62 65 66 +CONECT 65 64 +CONECT 66 64 67 68 72 +CONECT 67 66 +CONECT 68 66 69 70 71 +CONECT 69 68 +CONECT 70 68 +CONECT 71 68 +CONECT 72 66 73 74 +CONECT 73 72 +CONECT 74 72 75 76 +CONECT 75 74 +CONECT 76 74 77 78 82 +CONECT 77 76 +CONECT 78 76 79 80 81 +CONECT 79 78 +CONECT 80 78 +CONECT 81 78 +CONECT 82 76 83 84 +CONECT 83 82 +CONECT 84 82 85 86 +CONECT 85 84 +CONECT 86 84 87 88 92 +CONECT 87 86 +CONECT 88 86 89 90 91 +CONECT 89 88 +CONECT 90 88 +CONECT 91 88 +CONECT 92 86 93 94 +CONECT 93 92 +CONECT 94 92 95 96 +CONECT 95 94 +CONECT 96 94 97 98 102 +CONECT 97 96 +CONECT 98 96 99 100 101 +CONECT 99 98 +CONECT 100 98 +CONECT 101 98 +CONECT 102 96 103 104 +CONECT 103 102 +CONECT 104 102 105 106 +CONECT 105 104 +CONECT 106 104 107 108 112 +CONECT 107 106 +CONECT 108 106 109 110 111 +CONECT 109 108 +CONECT 110 108 +CONECT 111 108 +CONECT 112 106 113 114 +CONECT 113 112 +CONECT 114 112 115 116 +CONECT 115 114 +CONECT 116 114 117 118 122 +CONECT 117 116 +CONECT 118 116 119 120 121 +CONECT 119 118 +CONECT 120 118 +CONECT 121 118 +CONECT 122 116 123 124 +CONECT 123 122 +CONECT 124 122 125 126 +CONECT 125 124 +CONECT 126 124 127 128 132 +CONECT 127 126 +CONECT 128 126 129 130 131 +CONECT 129 128 +CONECT 130 128 +CONECT 131 128 +CONECT 132 126 133 134 +CONECT 133 132 +CONECT 134 132 135 136 +CONECT 135 134 +CONECT 136 134 137 138 142 +CONECT 137 136 +CONECT 138 136 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 144 +CONECT 143 142 +CONECT 144 142 145 146 +CONECT 145 144 +CONECT 146 144 147 148 152 +CONECT 147 146 +CONECT 148 146 149 150 151 +CONECT 149 148 +CONECT 150 148 +CONECT 151 148 +CONECT 152 146 153 154 +CONECT 153 152 +CONECT 154 152 155 156 +CONECT 155 154 +CONECT 156 154 157 158 162 +CONECT 157 156 +CONECT 158 156 159 160 161 +CONECT 159 158 +CONECT 160 158 +CONECT 161 158 +CONECT 162 156 163 164 +CONECT 163 162 +CONECT 164 162 165 166 +CONECT 165 164 +CONECT 166 164 167 168 172 +CONECT 167 166 +CONECT 168 166 169 170 171 +CONECT 169 168 +CONECT 170 168 +CONECT 171 168 +CONECT 172 166 173 174 +CONECT 173 172 +CONECT 174 172 175 176 +CONECT 175 174 +CONECT 176 174 177 178 182 +CONECT 177 176 +CONECT 178 176 179 180 181 +CONECT 179 178 +CONECT 180 178 +CONECT 181 178 +CONECT 182 176 183 184 +CONECT 183 182 +CONECT 184 182 185 186 +CONECT 185 184 +CONECT 186 184 187 188 192 +CONECT 187 186 +CONECT 188 186 189 190 191 +CONECT 189 188 +CONECT 190 188 +CONECT 191 188 +CONECT 192 186 193 194 +CONECT 193 192 +CONECT 194 192 195 196 +CONECT 195 194 +CONECT 196 194 197 198 202 +CONECT 197 196 +CONECT 198 196 199 200 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 +CONECT 202 196 203 204 +CONECT 203 202 +CONECT 204 202 205 206 +CONECT 205 204 +CONECT 206 204 207 208 212 +CONECT 207 206 +CONECT 208 206 209 210 211 +CONECT 209 208 +CONECT 210 208 +CONECT 211 208 +CONECT 212 206 213 214 +CONECT 213 212 +CONECT 214 212 215 216 +CONECT 215 214 +CONECT 216 214 217 218 219 +CONECT 217 216 +CONECT 218 216 +CONECT 219 216 +MASTER 0 0 0 0 0 0 0 0 219 0 219 0 +END diff --git a/unittests/example_files/H1A19_ob2.4.2_resname.pdb b/unittests/example_files/H1A19_ob2.4.2_resname.pdb new file mode 100644 index 0000000..3375614 --- /dev/null +++ b/unittests/example_files/H1A19_ob2.4.2_resname.pdb @@ -0,0 +1,442 @@ +COMPND PolyALA +AUTHOR GENERATED BY OPEN BABEL 2.3.2 +ATOM 1 H1 ACE A 1 -3.054 -3.171 0.465 1.00 0.00 H +ATOM 2 CH3 ACE A 1 -2.917 -2.969 -0.597 1.00 0.00 C +ATOM 3 H2 ACE A 1 -3.815 -3.045 -1.210 1.00 0.00 H +ATOM 4 H3 ACE A 1 -2.106 -3.644 -0.872 1.00 0.00 H +ATOM 5 C ACE A 1 -2.282 -1.553 -0.711 1.00 0.00 C +ATOM 6 O ACE A 1 -2.958 -0.698 -1.252 1.00 0.00 O +ATOM 7 N HID A 2 -1.104 -1.396 -0.185 1.00 0.00 N +ATOM 8 H HID A 2 -0.697 -2.276 0.096 1.00 0.00 H +ATOM 9 CA HID A 2 -0.333 -0.155 -0.121 1.00 0.00 C +ATOM 10 CB HID A 2 -0.870 0.739 0.999 1.00 0.00 C +ATOM 11 HB2 HID A 2 -0.351 1.697 0.995 1.00 0.00 H +ATOM 12 HB3 HID A 2 -1.939 0.904 0.864 1.00 0.00 H +ATOM 13 CG HID A 2 -0.694 0.162 2.369 1.00 0.00 C +ATOM 14 ND1 HID A 2 0.481 0.271 3.078 1.00 0.00 N +ATOM 15 HD1 HID A 2 1.312 0.739 2.745 1.00 0.00 H +ATOM 16 CE1 HID A 2 0.344 -0.330 4.248 1.00 0.00 C +ATOM 17 HE1 HID A 2 1.169 -0.352 4.958 1.00 0.00 H +ATOM 18 NE2 HID A 2 -0.876 -0.824 4.323 1.00 0.00 N +ATOM 19 CD2 HID A 2 -1.547 -0.532 3.161 1.00 0.00 C +ATOM 20 HD2 HID A 2 -2.578 -0.860 3.029 1.00 0.00 H +ATOM 21 HA HID A 2 -0.610 0.298 -1.073 1.00 0.00 H +ATOM 22 C HID A 2 1.131 -0.273 -0.199 1.00 0.00 C +ATOM 23 O HID A 2 1.769 0.539 -0.827 1.00 0.00 O +ATOM 24 N ALA A 3 1.795 -1.211 0.498 1.00 0.00 N +ATOM 25 H ALA A 3 1.221 -1.808 1.076 1.00 0.00 H +ATOM 26 CA ALA A 3 3.262 -1.252 0.419 1.00 0.00 C +ATOM 27 HA ALA A 3 3.652 -0.256 0.628 1.00 0.00 H +ATOM 28 CB ALA A 3 3.827 -2.271 1.436 1.00 0.00 C +ATOM 29 HB1 ALA A 3 3.510 -1.948 2.428 1.00 0.00 H +ATOM 30 HB2 ALA A 3 3.389 -3.228 1.153 1.00 0.00 H +ATOM 31 HB3 ALA A 3 4.910 -2.372 1.514 1.00 0.00 H +ATOM 32 C ALA A 3 3.783 -1.597 -0.986 1.00 0.00 C +ATOM 33 O ALA A 3 4.802 -1.070 -1.378 1.00 0.00 O +ATOM 34 N ALA A 4 3.132 -2.508 -1.712 1.00 0.00 N +ATOM 35 H ALA A 4 2.361 -3.014 -1.299 1.00 0.00 H +ATOM 36 CA ALA A 4 3.470 -2.716 -3.172 1.00 0.00 C +ATOM 37 HA ALA A 4 4.559 -2.699 -3.210 1.00 0.00 H +ATOM 38 CB ALA A 4 2.900 -4.035 -3.564 1.00 0.00 C +ATOM 39 HB1 ALA A 4 3.370 -4.803 -2.950 1.00 0.00 H +ATOM 40 HB2 ALA A 4 1.845 -4.033 -3.290 1.00 0.00 H +ATOM 41 HB3 ALA A 4 3.197 -4.068 -4.612 1.00 0.00 H +ATOM 42 C ALA A 4 3.146 -1.507 -3.992 1.00 0.00 C +ATOM 43 O ALA A 4 4.003 -1.154 -4.830 1.00 0.00 O +ATOM 44 N ALA A 5 2.102 -0.798 -3.719 1.00 0.00 N +ATOM 45 H ALA A 5 1.578 -1.096 -2.909 1.00 0.00 H +ATOM 46 CA ALA A 5 1.798 0.414 -4.360 1.00 0.00 C +ATOM 47 HA ALA A 5 2.033 0.197 -5.403 1.00 0.00 H +ATOM 48 CB ALA A 5 0.257 0.848 -4.179 1.00 0.00 C +ATOM 49 HB1 ALA A 5 -0.434 0.100 -4.566 1.00 0.00 H +ATOM 50 HB2 ALA A 5 0.029 0.931 -3.116 1.00 0.00 H +ATOM 51 HB3 ALA A 5 0.160 1.812 -4.679 1.00 0.00 H +ATOM 52 C ALA A 5 2.753 1.542 -4.006 1.00 0.00 C +ATOM 53 O ALA A 5 3.074 2.358 -4.897 1.00 0.00 O +ATOM 54 N ALA A 6 3.298 1.676 -2.803 1.00 0.00 N +ATOM 55 H ALA A 6 2.836 1.294 -1.990 1.00 0.00 H +ATOM 56 CA ALA A 6 4.273 2.694 -2.399 1.00 0.00 C +ATOM 57 HA ALA A 6 3.991 3.697 -2.721 1.00 0.00 H +ATOM 58 CB ALA A 6 4.338 2.833 -0.890 1.00 0.00 C +ATOM 59 HB1 ALA A 6 3.425 3.266 -0.481 1.00 0.00 H +ATOM 60 HB2 ALA A 6 4.564 1.863 -0.449 1.00 0.00 H +ATOM 61 HB3 ALA A 6 5.247 3.402 -0.697 1.00 0.00 H +ATOM 62 C ALA A 6 5.749 2.356 -2.826 1.00 0.00 C +ATOM 63 O ALA A 6 6.538 3.204 -3.079 1.00 0.00 O +ATOM 64 N ALA A 7 5.959 1.049 -3.048 1.00 0.00 N +ATOM 65 H ALA A 7 5.304 0.423 -2.601 1.00 0.00 H +ATOM 66 CA ALA A 7 7.183 0.475 -3.563 1.00 0.00 C +ATOM 67 HA ALA A 7 7.990 1.166 -3.316 1.00 0.00 H +ATOM 68 CB ALA A 7 7.530 -0.880 -2.926 1.00 0.00 C +ATOM 69 HB1 ALA A 7 7.386 -0.936 -1.847 1.00 0.00 H +ATOM 70 HB2 ALA A 7 6.786 -1.525 -3.395 1.00 0.00 H +ATOM 71 HB3 ALA A 7 8.523 -1.178 -3.261 1.00 0.00 H +ATOM 72 C ALA A 7 7.218 0.417 -5.118 1.00 0.00 C +ATOM 73 O ALA A 7 8.320 0.602 -5.691 1.00 0.00 O +ATOM 74 N ALA A 8 6.093 0.302 -5.750 1.00 0.00 N +ATOM 75 H ALA A 8 5.324 -0.065 -5.206 1.00 0.00 H +ATOM 76 CA ALA A 8 5.982 0.524 -7.158 1.00 0.00 C +ATOM 77 HA ALA A 8 6.812 0.018 -7.650 1.00 0.00 H +ATOM 78 CB ALA A 8 4.784 -0.264 -7.698 1.00 0.00 C +ATOM 79 HB1 ALA A 8 4.911 -1.274 -7.308 1.00 0.00 H +ATOM 80 HB2 ALA A 8 3.881 0.285 -7.430 1.00 0.00 H +ATOM 81 HB3 ALA A 8 4.855 -0.199 -8.784 1.00 0.00 H +ATOM 82 C ALA A 8 5.945 2.036 -7.500 1.00 0.00 C +ATOM 83 O ALA A 8 6.554 2.371 -8.484 1.00 0.00 O +ATOM 84 N ALA A 9 5.406 2.871 -6.588 1.00 0.00 N +ATOM 85 H ALA A 9 4.829 2.524 -5.835 1.00 0.00 H +ATOM 86 CA ALA A 9 5.472 4.303 -6.694 1.00 0.00 C +ATOM 87 HA ALA A 9 5.320 4.497 -7.756 1.00 0.00 H +ATOM 88 CB ALA A 9 4.300 5.085 -6.075 1.00 0.00 C +ATOM 89 HB1 ALA A 9 3.330 4.659 -6.333 1.00 0.00 H +ATOM 90 HB2 ALA A 9 4.436 5.008 -4.996 1.00 0.00 H +ATOM 91 HB3 ALA A 9 4.315 6.151 -6.302 1.00 0.00 H +ATOM 92 C ALA A 9 6.893 4.859 -6.381 1.00 0.00 C +ATOM 93 O ALA A 9 7.444 5.619 -7.164 1.00 0.00 O +ATOM 94 N ALA A 10 7.541 4.364 -5.327 1.00 0.00 N +ATOM 95 H ALA A 10 7.021 3.870 -4.617 1.00 0.00 H +ATOM 96 CA ALA A 10 8.960 4.713 -5.050 1.00 0.00 C +ATOM 97 HA ALA A 10 8.966 5.797 -5.163 1.00 0.00 H +ATOM 98 CB ALA A 10 9.288 4.389 -3.622 1.00 0.00 C +ATOM 99 HB1 ALA A 10 8.642 4.839 -2.869 1.00 0.00 H +ATOM 100 HB2 ALA A 10 9.230 3.307 -3.504 1.00 0.00 H +ATOM 101 HB3 ALA A 10 10.344 4.615 -3.471 1.00 0.00 H +ATOM 102 C ALA A 10 9.986 4.042 -6.032 1.00 0.00 C +ATOM 103 O ALA A 10 11.142 4.565 -6.147 1.00 0.00 O +ATOM 104 N ALA A 11 9.656 2.896 -6.701 1.00 0.00 N +ATOM 105 H ALA A 11 8.894 2.276 -6.470 1.00 0.00 H +ATOM 106 CA ALA A 11 10.445 2.411 -7.813 1.00 0.00 C +ATOM 107 HA ALA A 11 11.510 2.566 -7.640 1.00 0.00 H +ATOM 108 CB ALA A 11 10.164 0.914 -8.040 1.00 0.00 C +ATOM 109 HB1 ALA A 11 10.615 0.443 -7.166 1.00 0.00 H +ATOM 110 HB2 ALA A 11 9.107 0.669 -8.142 1.00 0.00 H +ATOM 111 HB3 ALA A 11 10.719 0.516 -8.889 1.00 0.00 H +ATOM 112 C ALA A 11 10.151 3.103 -9.155 1.00 0.00 C +ATOM 113 O ALA A 11 11.041 3.166 -9.980 1.00 0.00 O +ATOM 114 N ALA A 12 8.962 3.622 -9.346 1.00 0.00 N +ATOM 115 H ALA A 12 8.246 3.385 -8.673 1.00 0.00 H +ATOM 116 CA ALA A 12 8.644 4.359 -10.533 1.00 0.00 C +ATOM 117 HA ALA A 12 9.114 3.991 -11.446 1.00 0.00 H +ATOM 118 CB ALA A 12 7.143 4.275 -10.773 1.00 0.00 C +ATOM 119 HB1 ALA A 12 6.835 3.230 -10.811 1.00 0.00 H +ATOM 120 HB2 ALA A 12 6.547 4.719 -9.976 1.00 0.00 H +ATOM 121 HB3 ALA A 12 6.930 4.661 -11.770 1.00 0.00 H +ATOM 122 C ALA A 12 8.998 5.845 -10.408 1.00 0.00 C +ATOM 123 O ALA A 12 9.206 6.435 -11.479 1.00 0.00 O +ATOM 124 N ALA A 13 9.060 6.373 -9.150 1.00 0.00 N +ATOM 125 H ALA A 13 8.710 5.815 -8.384 1.00 0.00 H +ATOM 126 CA ALA A 13 9.644 7.589 -8.707 1.00 0.00 C +ATOM 127 HA ALA A 13 9.378 8.325 -9.466 1.00 0.00 H +ATOM 128 CB ALA A 13 8.979 8.114 -7.362 1.00 0.00 C +ATOM 129 HB1 ALA A 13 7.893 8.188 -7.300 1.00 0.00 H +ATOM 130 HB2 ALA A 13 9.391 7.514 -6.550 1.00 0.00 H +ATOM 131 HB3 ALA A 13 9.297 9.138 -7.165 1.00 0.00 H +ATOM 132 C ALA A 13 11.163 7.561 -8.544 1.00 0.00 C +ATOM 133 O ALA A 13 11.753 8.643 -8.809 1.00 0.00 O +ATOM 134 N ALA A 14 11.711 6.438 -8.195 1.00 0.00 N +ATOM 135 H ALA A 14 11.201 5.708 -7.719 1.00 0.00 H +ATOM 136 CA ALA A 14 13.187 6.178 -8.377 1.00 0.00 C +ATOM 137 HA ALA A 14 13.746 7.056 -8.055 1.00 0.00 H +ATOM 138 CB ALA A 14 13.659 4.995 -7.481 1.00 0.00 C +ATOM 139 HB1 ALA A 14 13.670 5.270 -6.427 1.00 0.00 H +ATOM 140 HB2 ALA A 14 13.140 4.041 -7.573 1.00 0.00 H +ATOM 141 HB3 ALA A 14 14.732 4.857 -7.614 1.00 0.00 H +ATOM 142 C ALA A 14 13.540 5.894 -9.914 1.00 0.00 C +ATOM 143 O ALA A 14 14.638 6.393 -10.399 1.00 0.00 O +ATOM 144 N ALA A 15 12.747 5.180 -10.675 1.00 0.00 N +ATOM 145 H ALA A 15 11.928 4.701 -10.329 1.00 0.00 H +ATOM 146 CA ALA A 15 13.062 5.067 -12.046 1.00 0.00 C +ATOM 147 HA ALA A 15 14.076 4.746 -12.284 1.00 0.00 H +ATOM 148 CB ALA A 15 12.198 3.975 -12.711 1.00 0.00 C +ATOM 149 HB1 ALA A 15 12.343 3.040 -12.170 1.00 0.00 H +ATOM 150 HB2 ALA A 15 11.153 4.203 -12.506 1.00 0.00 H +ATOM 151 HB3 ALA A 15 12.380 3.968 -13.786 1.00 0.00 H +ATOM 152 C ALA A 15 12.703 6.348 -12.778 1.00 0.00 C +ATOM 153 O ALA A 15 13.510 6.684 -13.678 1.00 0.00 O +ATOM 154 N ALA A 16 11.645 7.130 -12.475 1.00 0.00 N +ATOM 155 H ALA A 16 10.893 6.780 -11.898 1.00 0.00 H +ATOM 156 CA ALA A 16 11.461 8.455 -13.029 1.00 0.00 C +ATOM 157 HA ALA A 16 11.491 8.353 -14.114 1.00 0.00 H +ATOM 158 CB ALA A 16 10.149 9.085 -12.685 1.00 0.00 C +ATOM 159 HB1 ALA A 16 9.388 8.398 -13.054 1.00 0.00 H +ATOM 160 HB2 ALA A 16 10.052 9.148 -11.601 1.00 0.00 H +ATOM 161 HB3 ALA A 16 10.063 10.057 -13.171 1.00 0.00 H +ATOM 162 C ALA A 16 12.608 9.384 -12.612 1.00 0.00 C +ATOM 163 O ALA A 16 13.039 10.222 -13.473 1.00 0.00 O +ATOM 164 N ALA A 17 13.138 9.241 -11.388 1.00 0.00 N +ATOM 165 H ALA A 17 12.604 8.788 -10.661 1.00 0.00 H +ATOM 166 CA ALA A 17 14.326 10.028 -10.964 1.00 0.00 C +ATOM 167 HA ALA A 17 14.114 11.052 -11.270 1.00 0.00 H +ATOM 168 CB ALA A 17 14.275 10.145 -9.531 1.00 0.00 C +ATOM 169 HB1 ALA A 17 13.375 10.647 -9.177 1.00 0.00 H +ATOM 170 HB2 ALA A 17 14.478 9.222 -8.988 1.00 0.00 H +ATOM 171 HB3 ALA A 17 15.023 10.861 -9.189 1.00 0.00 H +ATOM 172 C ALA A 17 15.611 9.623 -11.594 1.00 0.00 C +ATOM 173 O ALA A 17 16.445 10.488 -11.882 1.00 0.00 O +ATOM 174 N ALA A 18 15.812 8.347 -11.791 1.00 0.00 N +ATOM 175 H ALA A 18 15.210 7.647 -11.382 1.00 0.00 H +ATOM 176 CA ALA A 18 17.039 7.928 -12.446 1.00 0.00 C +ATOM 177 HA ALA A 18 17.935 8.483 -12.170 1.00 0.00 H +ATOM 178 CB ALA A 18 17.358 6.480 -12.029 1.00 0.00 C +ATOM 179 HB1 ALA A 18 17.561 6.449 -10.958 1.00 0.00 H +ATOM 180 HB2 ALA A 18 16.536 5.820 -12.307 1.00 0.00 H +ATOM 181 HB3 ALA A 18 18.323 6.159 -12.422 1.00 0.00 H +ATOM 182 C ALA A 18 16.968 8.017 -13.999 1.00 0.00 C +ATOM 183 O ALA A 18 18.024 8.143 -14.660 1.00 0.00 O +ATOM 184 N ALA A 19 15.774 8.031 -14.539 1.00 0.00 N +ATOM 185 H ALA A 19 15.110 7.729 -13.840 1.00 0.00 H +ATOM 186 CA ALA A 19 15.508 8.397 -15.942 1.00 0.00 C +ATOM 187 HA ALA A 19 16.274 7.890 -16.528 1.00 0.00 H +ATOM 188 CB ALA A 19 14.132 7.825 -16.381 1.00 0.00 C +ATOM 189 HB1 ALA A 19 14.000 6.748 -16.279 1.00 0.00 H +ATOM 190 HB2 ALA A 19 13.326 8.274 -15.801 1.00 0.00 H +ATOM 191 HB3 ALA A 19 14.129 8.183 -17.411 1.00 0.00 H +ATOM 192 C ALA A 19 15.616 9.879 -16.218 1.00 0.00 C +ATOM 193 O ALA A 19 15.925 10.312 -17.349 1.00 0.00 O +ATOM 194 N ALA A 20 15.342 10.748 -15.240 1.00 0.00 N +ATOM 195 H ALA A 20 15.274 10.304 -14.336 1.00 0.00 H +ATOM 196 CA ALA A 20 15.539 12.186 -15.310 1.00 0.00 C +ATOM 197 HA ALA A 20 15.392 12.510 -16.340 1.00 0.00 H +ATOM 198 CB ALA A 20 14.470 12.874 -14.390 1.00 0.00 C +ATOM 199 HB1 ALA A 20 13.502 12.406 -14.574 1.00 0.00 H +ATOM 200 HB2 ALA A 20 14.667 12.751 -13.325 1.00 0.00 H +ATOM 201 HB3 ALA A 20 14.411 13.936 -14.630 1.00 0.00 H +ATOM 202 C ALA A 20 16.976 12.596 -14.911 1.00 0.00 C +ATOM 203 O ALA A 20 17.474 13.502 -15.583 1.00 0.00 O +ATOM 204 N ALA A 21 17.617 12.028 -13.914 1.00 0.00 N +ATOM 205 H ALA A 21 17.079 11.380 -13.356 1.00 0.00 H +ATOM 206 CA ALA A 21 19.140 12.093 -13.649 1.00 0.00 C +ATOM 207 HA ALA A 21 19.393 13.153 -13.607 1.00 0.00 H +ATOM 208 CB ALA A 21 19.438 11.428 -12.300 1.00 0.00 C +ATOM 209 HB1 ALA A 21 18.876 12.017 -11.575 1.00 0.00 H +ATOM 210 HB2 ALA A 21 19.196 10.366 -12.277 1.00 0.00 H +ATOM 211 HB3 ALA A 21 20.473 11.677 -12.068 1.00 0.00 H +ATOM 212 C ALA A 21 19.911 11.369 -14.740 1.00 0.00 C +ATOM 213 O ALA A 21 19.370 10.700 -15.601 1.00 0.00 O +ATOM 214 N NME A 22 21.266 11.506 -14.654 1.00 0.00 N +ATOM 215 H NME A 22 21.663 12.119 -13.956 1.00 0.00 H +ATOM 216 CH3 NME A 22 22.261 10.909 -15.537 1.00 0.00 C +ATOM 217 HH31 NME A 22 21.787 10.285 -16.294 1.00 0.00 H +ATOM 218 HH32 NME A 22 22.939 11.631 -15.993 1.00 0.00 H +ATOM 219 HH33 NME A 22 22.893 10.275 -14.916 1.00 0.00 H +CONECT 1 2 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 7 +CONECT 6 5 +CONECT 7 5 8 9 +CONECT 8 7 +CONECT 9 7 21 22 10 +CONECT 10 11 12 13 9 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 19 +CONECT 14 13 15 16 +CONECT 15 14 +CONECT 16 14 17 18 +CONECT 17 16 +CONECT 18 16 19 +CONECT 19 13 18 20 +CONECT 20 19 +CONECT 21 9 +CONECT 22 9 23 24 +CONECT 23 22 +CONECT 24 22 25 26 +CONECT 25 24 +CONECT 26 24 27 28 32 +CONECT 27 26 +CONECT 28 26 29 30 31 +CONECT 29 28 +CONECT 30 28 +CONECT 31 28 +CONECT 32 26 33 34 +CONECT 33 32 +CONECT 34 32 35 36 +CONECT 35 34 +CONECT 36 34 37 38 42 +CONECT 37 36 +CONECT 38 36 39 40 41 +CONECT 39 38 +CONECT 40 38 +CONECT 41 38 +CONECT 42 36 43 44 +CONECT 43 42 +CONECT 44 42 45 46 +CONECT 45 44 +CONECT 46 44 47 48 52 +CONECT 47 46 +CONECT 48 46 49 50 51 +CONECT 49 48 +CONECT 50 48 +CONECT 51 48 +CONECT 52 46 53 54 +CONECT 53 52 +CONECT 54 52 55 56 +CONECT 55 54 +CONECT 56 54 57 58 62 +CONECT 57 56 +CONECT 58 56 59 60 61 +CONECT 59 58 +CONECT 60 58 +CONECT 61 58 +CONECT 62 56 63 64 +CONECT 63 62 +CONECT 64 62 65 66 +CONECT 65 64 +CONECT 66 64 67 68 72 +CONECT 67 66 +CONECT 68 66 69 70 71 +CONECT 69 68 +CONECT 70 68 +CONECT 71 68 +CONECT 72 66 73 74 +CONECT 73 72 +CONECT 74 72 75 76 +CONECT 75 74 +CONECT 76 74 77 78 82 +CONECT 77 76 +CONECT 78 76 79 80 81 +CONECT 79 78 +CONECT 80 78 +CONECT 81 78 +CONECT 82 76 83 84 +CONECT 83 82 +CONECT 84 82 85 86 +CONECT 85 84 +CONECT 86 84 87 88 92 +CONECT 87 86 +CONECT 88 86 89 90 91 +CONECT 89 88 +CONECT 90 88 +CONECT 91 88 +CONECT 92 86 93 94 +CONECT 93 92 +CONECT 94 92 95 96 +CONECT 95 94 +CONECT 96 94 97 98 102 +CONECT 97 96 +CONECT 98 96 99 100 101 +CONECT 99 98 +CONECT 100 98 +CONECT 101 98 +CONECT 102 96 103 104 +CONECT 103 102 +CONECT 104 102 105 106 +CONECT 105 104 +CONECT 106 104 107 108 112 +CONECT 107 106 +CONECT 108 106 109 110 111 +CONECT 109 108 +CONECT 110 108 +CONECT 111 108 +CONECT 112 106 113 114 +CONECT 113 112 +CONECT 114 112 115 116 +CONECT 115 114 +CONECT 116 114 117 118 122 +CONECT 117 116 +CONECT 118 116 119 120 121 +CONECT 119 118 +CONECT 120 118 +CONECT 121 118 +CONECT 122 116 123 124 +CONECT 123 122 +CONECT 124 122 125 126 +CONECT 125 124 +CONECT 126 124 127 128 132 +CONECT 127 126 +CONECT 128 126 129 130 131 +CONECT 129 128 +CONECT 130 128 +CONECT 131 128 +CONECT 132 126 133 134 +CONECT 133 132 +CONECT 134 132 135 136 +CONECT 135 134 +CONECT 136 134 137 138 142 +CONECT 137 136 +CONECT 138 136 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 144 +CONECT 143 142 +CONECT 144 142 145 146 +CONECT 145 144 +CONECT 146 144 147 148 152 +CONECT 147 146 +CONECT 148 146 149 150 151 +CONECT 149 148 +CONECT 150 148 +CONECT 151 148 +CONECT 152 146 153 154 +CONECT 153 152 +CONECT 154 152 155 156 +CONECT 155 154 +CONECT 156 154 157 158 162 +CONECT 157 156 +CONECT 158 156 159 160 161 +CONECT 159 158 +CONECT 160 158 +CONECT 161 158 +CONECT 162 156 163 164 +CONECT 163 162 +CONECT 164 162 165 166 +CONECT 165 164 +CONECT 166 164 167 168 172 +CONECT 167 166 +CONECT 168 166 169 170 171 +CONECT 169 168 +CONECT 170 168 +CONECT 171 168 +CONECT 172 166 173 174 +CONECT 173 172 +CONECT 174 172 175 176 +CONECT 175 174 +CONECT 176 174 177 178 182 +CONECT 177 176 +CONECT 178 176 179 180 181 +CONECT 179 178 +CONECT 180 178 +CONECT 181 178 +CONECT 182 176 183 184 +CONECT 183 182 +CONECT 184 182 185 186 +CONECT 185 184 +CONECT 186 184 187 188 192 +CONECT 187 186 +CONECT 188 186 189 190 191 +CONECT 189 188 +CONECT 190 188 +CONECT 191 188 +CONECT 192 186 193 194 +CONECT 193 192 +CONECT 194 192 195 196 +CONECT 195 194 +CONECT 196 194 197 198 202 +CONECT 197 196 +CONECT 198 196 199 200 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 +CONECT 202 196 203 204 +CONECT 203 202 +CONECT 204 202 205 206 +CONECT 205 204 +CONECT 206 204 207 208 212 +CONECT 207 206 +CONECT 208 206 209 210 211 +CONECT 209 208 +CONECT 210 208 +CONECT 211 208 +CONECT 212 206 213 214 +CONECT 213 212 +CONECT 214 212 215 216 +CONECT 215 214 +CONECT 216 214 217 218 219 +CONECT 217 216 +CONECT 218 216 +CONECT 219 216 +MASTER 0 0 0 0 0 0 0 0 219 0 219 0 +END diff --git a/unittests/example_files/H1A19_resname.pdb b/unittests/example_files/H1A19_resname.pdb new file mode 100644 index 0000000..7165682 --- /dev/null +++ b/unittests/example_files/H1A19_resname.pdb @@ -0,0 +1,442 @@ +COMPND PolyALA +AUTHOR GENERATED BY OPEN BABEL 2.3.2 +ATOM 1 H1 ACE A 1 -3.054 -3.171 0.465 1.00 0.00 H +ATOM 2 CH3 ACE A 1 -2.917 -2.969 -0.597 1.00 0.00 C +ATOM 3 H2 ACE A 1 -3.815 -3.045 -1.210 1.00 0.00 H +ATOM 4 H3 ACE A 1 -2.106 -3.644 -0.872 1.00 0.00 H +ATOM 5 C ACE A 1 -2.282 -1.553 -0.711 1.00 0.00 C +ATOM 6 O ACE A 1 -2.958 -0.698 -1.252 1.00 0.00 O +ATOM 7 N HID A 2 -1.104 -1.396 -0.185 1.00 0.00 N +ATOM 8 H HID A 2 -0.697 -2.276 0.096 1.00 0.00 H +ATOM 9 CA HID A 2 -0.333 -0.155 -0.121 1.00 0.00 C +ATOM 10 CB HID A 2 -0.870 0.739 0.999 1.00 0.00 C +ATOM 11 HB2 HID A 2 -0.352 1.697 0.995 1.00 0.00 H +ATOM 12 HB3 HID A 2 -1.939 0.904 0.864 1.00 0.00 H +ATOM 13 CG HID A 2 -0.695 0.162 2.369 1.00 0.00 C +ATOM 14 ND1 HID A 2 0.481 0.272 3.078 1.00 0.00 N +ATOM 15 HD1 HID A 2 1.312 0.740 2.745 1.00 0.00 H +ATOM 16 CE1 HID A 2 0.343 -0.328 4.248 1.00 0.00 C +ATOM 17 HE1 HID A 2 1.169 -0.351 4.958 1.00 0.00 H +ATOM 18 NE2 HID A 2 -0.877 -0.823 4.323 1.00 0.00 N +ATOM 19 CD2 HID A 2 -1.547 -0.531 3.160 1.00 0.00 C +ATOM 20 HD2 HID A 2 -2.579 -0.859 3.029 1.00 0.00 H +ATOM 21 HA HID A 2 -0.610 0.298 -1.073 1.00 0.00 H +ATOM 22 C HID A 2 1.131 -0.273 -0.199 1.00 0.00 C +ATOM 23 O HID A 2 1.769 0.539 -0.827 1.00 0.00 O +ATOM 24 N ALA A 3 1.795 -1.211 0.498 1.00 0.00 N +ATOM 25 H ALA A 3 1.221 -1.808 1.076 1.00 0.00 H +ATOM 26 CA ALA A 3 3.262 -1.252 0.419 1.00 0.00 C +ATOM 27 HA ALA A 3 3.652 -0.256 0.628 1.00 0.00 H +ATOM 28 CB ALA A 3 3.827 -2.271 1.436 1.00 0.00 C +ATOM 29 HB1 ALA A 3 3.510 -1.948 2.428 1.00 0.00 H +ATOM 30 HB2 ALA A 3 3.389 -3.228 1.153 1.00 0.00 H +ATOM 31 HB3 ALA A 3 4.910 -2.372 1.514 1.00 0.00 H +ATOM 32 C ALA A 3 3.783 -1.597 -0.986 1.00 0.00 C +ATOM 33 O ALA A 3 4.802 -1.070 -1.378 1.00 0.00 O +ATOM 34 N ALA A 4 3.132 -2.508 -1.712 1.00 0.00 N +ATOM 35 H ALA A 4 2.361 -3.014 -1.299 1.00 0.00 H +ATOM 36 CA ALA A 4 3.470 -2.716 -3.172 1.00 0.00 C +ATOM 37 HA ALA A 4 4.559 -2.699 -3.210 1.00 0.00 H +ATOM 38 CB ALA A 4 2.900 -4.035 -3.564 1.00 0.00 C +ATOM 39 HB1 ALA A 4 3.370 -4.803 -2.950 1.00 0.00 H +ATOM 40 HB2 ALA A 4 1.845 -4.033 -3.290 1.00 0.00 H +ATOM 41 HB3 ALA A 4 3.197 -4.068 -4.612 1.00 0.00 H +ATOM 42 C ALA A 4 3.146 -1.507 -3.992 1.00 0.00 C +ATOM 43 O ALA A 4 4.003 -1.154 -4.830 1.00 0.00 O +ATOM 44 N ALA A 5 2.102 -0.798 -3.719 1.00 0.00 N +ATOM 45 H ALA A 5 1.578 -1.096 -2.909 1.00 0.00 H +ATOM 46 CA ALA A 5 1.798 0.414 -4.360 1.00 0.00 C +ATOM 47 HA ALA A 5 2.033 0.197 -5.403 1.00 0.00 H +ATOM 48 CB ALA A 5 0.257 0.848 -4.179 1.00 0.00 C +ATOM 49 HB1 ALA A 5 -0.434 0.100 -4.566 1.00 0.00 H +ATOM 50 HB2 ALA A 5 0.029 0.931 -3.116 1.00 0.00 H +ATOM 51 HB3 ALA A 5 0.160 1.812 -4.679 1.00 0.00 H +ATOM 52 C ALA A 5 2.753 1.542 -4.006 1.00 0.00 C +ATOM 53 O ALA A 5 3.074 2.358 -4.897 1.00 0.00 O +ATOM 54 N ALA A 6 3.298 1.676 -2.803 1.00 0.00 N +ATOM 55 H ALA A 6 2.836 1.294 -1.990 1.00 0.00 H +ATOM 56 CA ALA A 6 4.273 2.694 -2.399 1.00 0.00 C +ATOM 57 HA ALA A 6 3.991 3.697 -2.721 1.00 0.00 H +ATOM 58 CB ALA A 6 4.338 2.833 -0.890 1.00 0.00 C +ATOM 59 HB1 ALA A 6 3.425 3.266 -0.481 1.00 0.00 H +ATOM 60 HB2 ALA A 6 4.564 1.863 -0.449 1.00 0.00 H +ATOM 61 HB3 ALA A 6 5.247 3.402 -0.697 1.00 0.00 H +ATOM 62 C ALA A 6 5.749 2.356 -2.826 1.00 0.00 C +ATOM 63 O ALA A 6 6.538 3.204 -3.079 1.00 0.00 O +ATOM 64 N ALA A 7 5.959 1.049 -3.048 1.00 0.00 N +ATOM 65 H ALA A 7 5.304 0.423 -2.601 1.00 0.00 H +ATOM 66 CA ALA A 7 7.183 0.475 -3.563 1.00 0.00 C +ATOM 67 HA ALA A 7 7.990 1.166 -3.316 1.00 0.00 H +ATOM 68 CB ALA A 7 7.530 -0.880 -2.926 1.00 0.00 C +ATOM 69 HB1 ALA A 7 7.386 -0.936 -1.847 1.00 0.00 H +ATOM 70 HB2 ALA A 7 6.786 -1.525 -3.395 1.00 0.00 H +ATOM 71 HB3 ALA A 7 8.523 -1.178 -3.261 1.00 0.00 H +ATOM 72 C ALA A 7 7.218 0.417 -5.118 1.00 0.00 C +ATOM 73 O ALA A 7 8.320 0.602 -5.691 1.00 0.00 O +ATOM 74 N ALA A 8 6.093 0.302 -5.750 1.00 0.00 N +ATOM 75 H ALA A 8 5.324 -0.065 -5.206 1.00 0.00 H +ATOM 76 CA ALA A 8 5.982 0.524 -7.158 1.00 0.00 C +ATOM 77 HA ALA A 8 6.812 0.018 -7.650 1.00 0.00 H +ATOM 78 CB ALA A 8 4.784 -0.264 -7.698 1.00 0.00 C +ATOM 79 HB1 ALA A 8 4.911 -1.274 -7.308 1.00 0.00 H +ATOM 80 HB2 ALA A 8 3.881 0.285 -7.430 1.00 0.00 H +ATOM 81 HB3 ALA A 8 4.855 -0.199 -8.784 1.00 0.00 H +ATOM 82 C ALA A 8 5.945 2.036 -7.500 1.00 0.00 C +ATOM 83 O ALA A 8 6.554 2.371 -8.484 1.00 0.00 O +ATOM 84 N ALA A 9 5.406 2.871 -6.588 1.00 0.00 N +ATOM 85 H ALA A 9 4.829 2.524 -5.835 1.00 0.00 H +ATOM 86 CA ALA A 9 5.472 4.303 -6.694 1.00 0.00 C +ATOM 87 HA ALA A 9 5.320 4.497 -7.756 1.00 0.00 H +ATOM 88 CB ALA A 9 4.300 5.085 -6.075 1.00 0.00 C +ATOM 89 HB1 ALA A 9 3.330 4.659 -6.333 1.00 0.00 H +ATOM 90 HB2 ALA A 9 4.436 5.008 -4.996 1.00 0.00 H +ATOM 91 HB3 ALA A 9 4.315 6.151 -6.302 1.00 0.00 H +ATOM 92 C ALA A 9 6.893 4.859 -6.381 1.00 0.00 C +ATOM 93 O ALA A 9 7.444 5.619 -7.164 1.00 0.00 O +ATOM 94 N ALA A 10 7.541 4.364 -5.327 1.00 0.00 N +ATOM 95 H ALA A 10 7.021 3.870 -4.617 1.00 0.00 H +ATOM 96 CA ALA A 10 8.960 4.713 -5.050 1.00 0.00 C +ATOM 97 HA ALA A 10 8.966 5.797 -5.163 1.00 0.00 H +ATOM 98 CB ALA A 10 9.288 4.389 -3.622 1.00 0.00 C +ATOM 99 HB1 ALA A 10 8.642 4.839 -2.869 1.00 0.00 H +ATOM 100 HB2 ALA A 10 9.230 3.307 -3.504 1.00 0.00 H +ATOM 101 HB3 ALA A 10 10.344 4.615 -3.471 1.00 0.00 H +ATOM 102 C ALA A 10 9.986 4.042 -6.032 1.00 0.00 C +ATOM 103 O ALA A 10 11.142 4.565 -6.147 1.00 0.00 O +ATOM 104 N ALA A 11 9.656 2.896 -6.701 1.00 0.00 N +ATOM 105 H ALA A 11 8.894 2.276 -6.470 1.00 0.00 H +ATOM 106 CA ALA A 11 10.445 2.411 -7.813 1.00 0.00 C +ATOM 107 HA ALA A 11 11.510 2.566 -7.640 1.00 0.00 H +ATOM 108 CB ALA A 11 10.164 0.914 -8.040 1.00 0.00 C +ATOM 109 HB1 ALA A 11 10.615 0.443 -7.166 1.00 0.00 H +ATOM 110 HB2 ALA A 11 9.107 0.669 -8.142 1.00 0.00 H +ATOM 111 HB3 ALA A 11 10.719 0.516 -8.889 1.00 0.00 H +ATOM 112 C ALA A 11 10.151 3.103 -9.155 1.00 0.00 C +ATOM 113 O ALA A 11 11.041 3.166 -9.980 1.00 0.00 O +ATOM 114 N ALA A 12 8.962 3.622 -9.346 1.00 0.00 N +ATOM 115 H ALA A 12 8.246 3.385 -8.673 1.00 0.00 H +ATOM 116 CA ALA A 12 8.644 4.359 -10.533 1.00 0.00 C +ATOM 117 HA ALA A 12 9.114 3.991 -11.446 1.00 0.00 H +ATOM 118 CB ALA A 12 7.143 4.275 -10.773 1.00 0.00 C +ATOM 119 HB1 ALA A 12 6.835 3.230 -10.811 1.00 0.00 H +ATOM 120 HB2 ALA A 12 6.547 4.719 -9.976 1.00 0.00 H +ATOM 121 HB3 ALA A 12 6.930 4.661 -11.770 1.00 0.00 H +ATOM 122 C ALA A 12 8.998 5.845 -10.408 1.00 0.00 C +ATOM 123 O ALA A 12 9.206 6.435 -11.479 1.00 0.00 O +ATOM 124 N ALA A 13 9.060 6.373 -9.150 1.00 0.00 N +ATOM 125 H ALA A 13 8.710 5.815 -8.384 1.00 0.00 H +ATOM 126 CA ALA A 13 9.644 7.589 -8.707 1.00 0.00 C +ATOM 127 HA ALA A 13 9.378 8.325 -9.466 1.00 0.00 H +ATOM 128 CB ALA A 13 8.979 8.114 -7.362 1.00 0.00 C +ATOM 129 HB1 ALA A 13 7.893 8.188 -7.300 1.00 0.00 H +ATOM 130 HB2 ALA A 13 9.391 7.514 -6.550 1.00 0.00 H +ATOM 131 HB3 ALA A 13 9.297 9.138 -7.165 1.00 0.00 H +ATOM 132 C ALA A 13 11.163 7.561 -8.544 1.00 0.00 C +ATOM 133 O ALA A 13 11.753 8.643 -8.809 1.00 0.00 O +ATOM 134 N ALA A 14 11.711 6.438 -8.195 1.00 0.00 N +ATOM 135 H ALA A 14 11.201 5.708 -7.719 1.00 0.00 H +ATOM 136 CA ALA A 14 13.187 6.178 -8.377 1.00 0.00 C +ATOM 137 HA ALA A 14 13.746 7.056 -8.055 1.00 0.00 H +ATOM 138 CB ALA A 14 13.659 4.995 -7.481 1.00 0.00 C +ATOM 139 HB1 ALA A 14 13.670 5.270 -6.427 1.00 0.00 H +ATOM 140 HB2 ALA A 14 13.140 4.041 -7.573 1.00 0.00 H +ATOM 141 HB3 ALA A 14 14.732 4.857 -7.614 1.00 0.00 H +ATOM 142 C ALA A 14 13.540 5.894 -9.914 1.00 0.00 C +ATOM 143 O ALA A 14 14.638 6.393 -10.399 1.00 0.00 O +ATOM 144 N ALA A 15 12.747 5.180 -10.675 1.00 0.00 N +ATOM 145 H ALA A 15 11.928 4.701 -10.329 1.00 0.00 H +ATOM 146 CA ALA A 15 13.062 5.067 -12.046 1.00 0.00 C +ATOM 147 HA ALA A 15 14.076 4.746 -12.284 1.00 0.00 H +ATOM 148 CB ALA A 15 12.198 3.975 -12.711 1.00 0.00 C +ATOM 149 HB1 ALA A 15 12.343 3.040 -12.170 1.00 0.00 H +ATOM 150 HB2 ALA A 15 11.153 4.203 -12.506 1.00 0.00 H +ATOM 151 HB3 ALA A 15 12.380 3.968 -13.786 1.00 0.00 H +ATOM 152 C ALA A 15 12.703 6.348 -12.778 1.00 0.00 C +ATOM 153 O ALA A 15 13.510 6.684 -13.678 1.00 0.00 O +ATOM 154 N ALA A 16 11.645 7.130 -12.475 1.00 0.00 N +ATOM 155 H ALA A 16 10.893 6.780 -11.898 1.00 0.00 H +ATOM 156 CA ALA A 16 11.461 8.455 -13.029 1.00 0.00 C +ATOM 157 HA ALA A 16 11.491 8.353 -14.114 1.00 0.00 H +ATOM 158 CB ALA A 16 10.149 9.085 -12.685 1.00 0.00 C +ATOM 159 HB1 ALA A 16 9.388 8.398 -13.054 1.00 0.00 H +ATOM 160 HB2 ALA A 16 10.052 9.148 -11.601 1.00 0.00 H +ATOM 161 HB3 ALA A 16 10.063 10.057 -13.171 1.00 0.00 H +ATOM 162 C ALA A 16 12.608 9.384 -12.612 1.00 0.00 C +ATOM 163 O ALA A 16 13.039 10.222 -13.473 1.00 0.00 O +ATOM 164 N ALA A 17 13.138 9.241 -11.388 1.00 0.00 N +ATOM 165 H ALA A 17 12.604 8.788 -10.661 1.00 0.00 H +ATOM 166 CA ALA A 17 14.326 10.028 -10.964 1.00 0.00 C +ATOM 167 HA ALA A 17 14.114 11.052 -11.270 1.00 0.00 H +ATOM 168 CB ALA A 17 14.275 10.145 -9.531 1.00 0.00 C +ATOM 169 HB1 ALA A 17 13.375 10.647 -9.177 1.00 0.00 H +ATOM 170 HB2 ALA A 17 14.478 9.222 -8.988 1.00 0.00 H +ATOM 171 HB3 ALA A 17 15.023 10.861 -9.189 1.00 0.00 H +ATOM 172 C ALA A 17 15.611 9.623 -11.594 1.00 0.00 C +ATOM 173 O ALA A 17 16.445 10.488 -11.882 1.00 0.00 O +ATOM 174 N ALA A 18 15.812 8.347 -11.791 1.00 0.00 N +ATOM 175 H ALA A 18 15.210 7.647 -11.382 1.00 0.00 H +ATOM 176 CA ALA A 18 17.039 7.928 -12.446 1.00 0.00 C +ATOM 177 HA ALA A 18 17.935 8.483 -12.170 1.00 0.00 H +ATOM 178 CB ALA A 18 17.358 6.480 -12.029 1.00 0.00 C +ATOM 179 HB1 ALA A 18 17.561 6.449 -10.958 1.00 0.00 H +ATOM 180 HB2 ALA A 18 16.536 5.820 -12.307 1.00 0.00 H +ATOM 181 HB3 ALA A 18 18.323 6.159 -12.422 1.00 0.00 H +ATOM 182 C ALA A 18 16.968 8.017 -13.999 1.00 0.00 C +ATOM 183 O ALA A 18 18.024 8.143 -14.660 1.00 0.00 O +ATOM 184 N ALA A 19 15.774 8.031 -14.539 1.00 0.00 N +ATOM 185 H ALA A 19 15.110 7.729 -13.840 1.00 0.00 H +ATOM 186 CA ALA A 19 15.508 8.397 -15.942 1.00 0.00 C +ATOM 187 HA ALA A 19 16.274 7.890 -16.528 1.00 0.00 H +ATOM 188 CB ALA A 19 14.132 7.825 -16.381 1.00 0.00 C +ATOM 189 HB1 ALA A 19 14.000 6.748 -16.279 1.00 0.00 H +ATOM 190 HB2 ALA A 19 13.326 8.274 -15.801 1.00 0.00 H +ATOM 191 HB3 ALA A 19 14.129 8.183 -17.411 1.00 0.00 H +ATOM 192 C ALA A 19 15.616 9.879 -16.218 1.00 0.00 C +ATOM 193 O ALA A 19 15.925 10.312 -17.349 1.00 0.00 O +ATOM 194 N ALA A 20 15.342 10.748 -15.240 1.00 0.00 N +ATOM 195 H ALA A 20 15.274 10.304 -14.336 1.00 0.00 H +ATOM 196 CA ALA A 20 15.539 12.186 -15.310 1.00 0.00 C +ATOM 197 HA ALA A 20 15.392 12.510 -16.340 1.00 0.00 H +ATOM 198 CB ALA A 20 14.470 12.874 -14.390 1.00 0.00 C +ATOM 199 HB1 ALA A 20 13.502 12.406 -14.574 1.00 0.00 H +ATOM 200 HB2 ALA A 20 14.667 12.751 -13.325 1.00 0.00 H +ATOM 201 HB3 ALA A 20 14.411 13.936 -14.630 1.00 0.00 H +ATOM 202 C ALA A 20 16.976 12.596 -14.911 1.00 0.00 C +ATOM 203 O ALA A 20 17.474 13.502 -15.583 1.00 0.00 O +ATOM 204 N ALA A 21 17.617 12.028 -13.914 1.00 0.00 N +ATOM 205 H ALA A 21 17.079 11.380 -13.356 1.00 0.00 H +ATOM 206 CA ALA A 21 19.140 12.093 -13.649 1.00 0.00 C +ATOM 207 HA ALA A 21 19.393 13.153 -13.607 1.00 0.00 H +ATOM 208 CB ALA A 21 19.438 11.428 -12.300 1.00 0.00 C +ATOM 209 HB1 ALA A 21 18.876 12.017 -11.575 1.00 0.00 H +ATOM 210 HB2 ALA A 21 19.196 10.366 -12.277 1.00 0.00 H +ATOM 211 HB3 ALA A 21 20.473 11.677 -12.068 1.00 0.00 H +ATOM 212 C ALA A 21 19.911 11.369 -14.740 1.00 0.00 C +ATOM 213 O ALA A 21 19.370 10.700 -15.601 1.00 0.00 O +ATOM 214 N NME A 22 21.266 11.506 -14.654 1.00 0.00 N +ATOM 215 H NME A 22 21.663 12.119 -13.956 1.00 0.00 H +ATOM 216 CH3 NME A 22 22.261 10.909 -15.537 1.00 0.00 C +ATOM 217 HH31 NME A 22 21.787 10.285 -16.294 1.00 0.00 H +ATOM 218 HH32 NME A 22 22.939 11.631 -15.993 1.00 0.00 H +ATOM 219 HH33 NME A 22 22.893 10.275 -14.916 1.00 0.00 H +CONECT 1 2 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 6 7 +CONECT 6 5 5 +CONECT 7 5 8 9 +CONECT 8 7 +CONECT 9 7 21 22 10 +CONECT 10 9 11 12 13 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 19 19 +CONECT 14 13 15 16 +CONECT 15 14 +CONECT 16 14 17 18 18 +CONECT 17 16 +CONECT 18 16 16 19 +CONECT 19 13 13 18 20 +CONECT 20 19 +CONECT 21 9 +CONECT 22 9 23 23 24 +CONECT 23 22 22 +CONECT 24 22 25 26 +CONECT 25 24 +CONECT 26 24 27 28 32 +CONECT 27 26 +CONECT 28 26 29 30 31 +CONECT 29 28 +CONECT 30 28 +CONECT 31 28 +CONECT 32 26 33 33 34 +CONECT 33 32 32 +CONECT 34 32 35 36 +CONECT 35 34 +CONECT 36 34 37 38 42 +CONECT 37 36 +CONECT 38 36 39 40 41 +CONECT 39 38 +CONECT 40 38 +CONECT 41 38 +CONECT 42 36 43 43 44 +CONECT 43 42 42 +CONECT 44 42 45 46 +CONECT 45 44 +CONECT 46 44 47 48 52 +CONECT 47 46 +CONECT 48 46 49 50 51 +CONECT 49 48 +CONECT 50 48 +CONECT 51 48 +CONECT 52 46 53 53 54 +CONECT 53 52 52 +CONECT 54 52 55 56 +CONECT 55 54 +CONECT 56 54 57 58 62 +CONECT 57 56 +CONECT 58 56 59 60 61 +CONECT 59 58 +CONECT 60 58 +CONECT 61 58 +CONECT 62 56 63 63 64 +CONECT 63 62 62 +CONECT 64 62 65 66 +CONECT 65 64 +CONECT 66 64 67 68 72 +CONECT 67 66 +CONECT 68 66 69 70 71 +CONECT 69 68 +CONECT 70 68 +CONECT 71 68 +CONECT 72 66 73 73 74 +CONECT 73 72 72 +CONECT 74 72 75 76 +CONECT 75 74 +CONECT 76 74 77 78 82 +CONECT 77 76 +CONECT 78 76 79 80 81 +CONECT 79 78 +CONECT 80 78 +CONECT 81 78 +CONECT 82 76 83 83 84 +CONECT 83 82 82 +CONECT 84 82 85 86 +CONECT 85 84 +CONECT 86 84 87 88 92 +CONECT 87 86 +CONECT 88 86 89 90 91 +CONECT 89 88 +CONECT 90 88 +CONECT 91 88 +CONECT 92 86 93 93 94 +CONECT 93 92 92 +CONECT 94 92 95 96 +CONECT 95 94 +CONECT 96 94 97 98 102 +CONECT 97 96 +CONECT 98 96 99 100 101 +CONECT 99 98 +CONECT 100 98 +CONECT 101 98 +CONECT 102 96 103 103 104 +CONECT 103 102 102 +CONECT 104 102 105 106 +CONECT 105 104 +CONECT 106 104 107 108 112 +CONECT 107 106 +CONECT 108 106 109 110 111 +CONECT 109 108 +CONECT 110 108 +CONECT 111 108 +CONECT 112 106 113 113 114 +CONECT 113 112 112 +CONECT 114 112 115 116 +CONECT 115 114 +CONECT 116 114 117 118 122 +CONECT 117 116 +CONECT 118 116 119 120 121 +CONECT 119 118 +CONECT 120 118 +CONECT 121 118 +CONECT 122 116 123 123 124 +CONECT 123 122 122 +CONECT 124 122 125 126 +CONECT 125 124 +CONECT 126 124 127 128 132 +CONECT 127 126 +CONECT 128 126 129 130 131 +CONECT 129 128 +CONECT 130 128 +CONECT 131 128 +CONECT 132 126 133 133 134 +CONECT 133 132 132 +CONECT 134 132 135 136 +CONECT 135 134 +CONECT 136 134 137 138 142 +CONECT 137 136 +CONECT 138 136 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 +CONECT 142 136 143 143 144 +CONECT 143 142 142 +CONECT 144 142 145 146 +CONECT 145 144 +CONECT 146 144 147 148 152 +CONECT 147 146 +CONECT 148 146 149 150 151 +CONECT 149 148 +CONECT 150 148 +CONECT 151 148 +CONECT 152 146 153 153 154 +CONECT 153 152 152 +CONECT 154 152 155 156 +CONECT 155 154 +CONECT 156 154 157 158 162 +CONECT 157 156 +CONECT 158 156 159 160 161 +CONECT 159 158 +CONECT 160 158 +CONECT 161 158 +CONECT 162 156 163 163 164 +CONECT 163 162 162 +CONECT 164 162 165 166 +CONECT 165 164 +CONECT 166 164 167 168 172 +CONECT 167 166 +CONECT 168 166 169 170 171 +CONECT 169 168 +CONECT 170 168 +CONECT 171 168 +CONECT 172 166 173 173 174 +CONECT 173 172 172 +CONECT 174 172 175 176 +CONECT 175 174 +CONECT 176 174 177 178 182 +CONECT 177 176 +CONECT 178 176 179 180 181 +CONECT 179 178 +CONECT 180 178 +CONECT 181 178 +CONECT 182 176 183 183 184 +CONECT 183 182 182 +CONECT 184 182 185 186 +CONECT 185 184 +CONECT 186 184 187 188 192 +CONECT 187 186 +CONECT 188 186 189 190 191 +CONECT 189 188 +CONECT 190 188 +CONECT 191 188 +CONECT 192 186 193 193 194 +CONECT 193 192 192 +CONECT 194 192 195 196 +CONECT 195 194 +CONECT 196 194 197 198 202 +CONECT 197 196 +CONECT 198 196 199 200 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 +CONECT 202 196 203 203 204 +CONECT 203 202 202 +CONECT 204 202 205 206 +CONECT 205 204 +CONECT 206 204 207 208 212 +CONECT 207 206 +CONECT 208 206 209 210 211 +CONECT 209 208 +CONECT 210 208 +CONECT 211 208 +CONECT 212 206 213 213 214 +CONECT 213 212 212 +CONECT 214 212 215 216 +CONECT 215 214 +CONECT 216 214 217 218 219 +CONECT 217 216 +CONECT 218 216 +CONECT 219 216 +MASTER 0 0 0 0 0 0 0 0 219 0 219 0 +END diff --git a/unittests/example_files/amber_minimization.in b/unittests/example_files/amber_minimization.in new file mode 100644 index 0000000..f794efd --- /dev/null +++ b/unittests/example_files/amber_minimization.in @@ -0,0 +1,12 @@ +Minimize using Amber FF + &cntrl + imin = 1, + drms= 0.0001, + maxcyc =9000, + ncyc = 1000, + ntmin = 1, + ntb = 0, + igb = 5, + extdiel = 80.0, + cut = 16.0 + / diff --git a/unittests/example_files/ga_input.in b/unittests/example_files/ga_input.in new file mode 100644 index 0000000..36bf1ba --- /dev/null +++ b/unittests/example_files/ga_input.in @@ -0,0 +1,52 @@ +[OPTIMIZATION] +dihedral_optimization = False +composition_optimization = True +composition_residue_indexes = 1 2 +composition_lower_bounds = 1 175 +composition_upper_bounds = 176 176 +composition_library = ../share/flat/ + + +[MOLECULE] +initial_molecule = example_files/ALA20.pdb + +[IO] +store_intermediate_mol = True +output_path = . +output_file = final.pdb + +[GA_GLOBAL] +seed_population = False +population_file_path = None +population_size = 10 +max_iteration = 10 + +[EVALUATOR] +evaluators = helical_stability +tleap_template = example_files/tleap_template.in +amber_params = example_files/amber_minimization.in +mpi_processors = 20 +dielectric = 80.0 + +[GA_SELECTION] +selector = tournament_wor +tournament_size = 2 + +[GA_CROSSOVER] +crossover = sbx +sbx_distribution_index = 7.0 +mating_probability = 0.7 +genewise_crossover_probability = 0.4 + +[GA_MUTATION] +mutator = polynomial_mutation +mutation_probability = 0.3 +genewise__mutation_probability = 0.15 +poly_eta = 7.0 + +[GA_REPLACER] +replacer = elitism +elitist_factor = 0.25 + +[DEBUG] +verbose = True diff --git a/unittests/example_files/individual2.pdb b/unittests/example_files/individual2.pdb new file mode 100644 index 0000000..2ff8fc5 --- /dev/null +++ b/unittests/example_files/individual2.pdb @@ -0,0 +1,736 @@ +COMPND ./amber_run/min_struct.pdb +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +ATOM 1 H1 ACE 1 -3.244 -3.622 -0.732 1.00 0.00 H +ATOM 2 CH3 ACE 1 -2.169 -3.787 -0.782 1.00 0.00 C +ATOM 3 H2 ACE 1 -1.911 -4.228 -1.744 1.00 0.00 H +ATOM 4 H3 ACE 1 -1.866 -4.461 0.019 1.00 0.00 H +ATOM 5 C ACE 1 -1.452 -2.467 -0.623 1.00 0.00 C +ATOM 6 O ACE 1 -0.754 -2.029 -1.536 1.00 0.00 O +ATOM 7 N W01 2 -1.635 -1.824 0.532 1.00 0.00 N +ATOM 8 H W01 2 -2.194 -2.275 1.240 1.00 0.00 H +ATOM 9 CA W01 2 -1.100 -0.485 0.823 1.00 0.00 C +ATOM 10 HA W01 2 -1.481 0.209 0.075 1.00 0.00 H +ATOM 11 CB W01 2 -1.612 -0.004 2.190 1.00 0.00 C +ATOM 12 HB2 W01 2 -1.195 0.985 2.388 1.00 0.00 H +ATOM 13 HB3 W01 2 -2.694 0.116 2.125 1.00 0.00 H +ATOM 14 CG W01 2 -1.319 -0.892 3.365 1.00 0.00 C +ATOM 15 CD1 W01 2 -0.239 -0.794 4.174 1.00 0.00 C +ATOM 16 HD1 W01 2 0.545 -0.048 4.077 1.00 0.00 H +ATOM 17 NE1 W01 2 -0.275 -1.796 5.125 1.00 0.00 N +ATOM 18 HE1 W01 2 0.439 -1.915 5.837 1.00 0.00 H +ATOM 19 CE2 W01 2 -1.392 -2.592 4.981 1.00 0.00 C +ATOM 20 CZ2 W01 2 -1.872 -3.705 5.687 1.00 0.00 C +ATOM 21 HZ2 W01 2 -1.316 -4.099 6.528 1.00 0.00 H +ATOM 22 CH2 W01 2 -3.082 -4.299 5.289 1.00 0.00 C +ATOM 23 HH2 W01 2 -3.467 -5.159 5.823 1.00 0.00 H +ATOM 24 CZ3 W01 2 -3.796 -3.768 4.199 1.00 0.00 C +ATOM 25 HZ3 W01 2 -4.734 -4.224 3.902 1.00 0.00 H +ATOM 26 CE3 W01 2 -3.307 -2.648 3.497 1.00 0.00 C +ATOM 27 HE3 W01 2 -3.879 -2.242 2.674 1.00 0.00 H +ATOM 28 CD2 W01 2 -2.087 -2.034 3.864 1.00 0.00 C +ATOM 29 C W01 2 0.436 -0.432 0.757 1.00 0.00 C +ATOM 30 O W01 2 0.999 0.505 0.188 1.00 0.00 O +ATOM 31 N E02 3 1.125 -1.453 1.275 1.00 0.00 N +ATOM 32 H E02 3 0.603 -2.198 1.716 1.00 0.00 H +ATOM 33 CA E02 3 2.587 -1.560 1.185 1.00 0.00 C +ATOM 34 HA E02 3 3.003 -0.600 1.498 1.00 0.00 H +ATOM 35 CB E02 3 3.134 -2.613 2.171 1.00 0.00 C +ATOM 36 HB2 E02 3 4.201 -2.422 2.288 1.00 0.00 H +ATOM 37 HB3 E02 3 2.672 -2.454 3.146 1.00 0.00 H +ATOM 38 CG E02 3 2.982 -4.094 1.788 1.00 0.00 C +ATOM 39 HG2 E02 3 3.492 -4.279 0.840 1.00 0.00 H +ATOM 40 HG3 E02 3 3.503 -4.691 2.541 1.00 0.00 H +ATOM 41 CD E02 3 1.512 -4.549 1.706 1.00 0.00 C +ATOM 42 OE1 E02 3 0.946 -4.972 2.743 1.00 0.00 O +ATOM 43 OE2 E02 3 0.927 -4.493 0.599 1.00 0.00 O +ATOM 44 C E02 3 3.061 -1.787 -0.261 1.00 0.00 C +ATOM 45 O E02 3 4.035 -1.163 -0.691 1.00 0.00 O +ATOM 46 N HP6 4 2.342 -2.604 -1.046 1.00 0.00 N +ATOM 47 H HP6 4 1.577 -3.125 -0.616 1.00 0.00 H +ATOM 48 CA HP6 4 2.646 -2.830 -2.463 1.00 0.00 C +ATOM 49 HA HP6 4 3.689 -3.146 -2.537 1.00 0.00 H +ATOM 50 CB HP6 4 1.770 -3.950 -3.058 1.00 0.00 C +ATOM 51 HB2 HP6 4 1.951 -4.880 -2.515 1.00 0.00 H +ATOM 52 HB3 HP6 4 0.713 -3.702 -2.950 1.00 0.00 H +ATOM 53 CG HP6 4 2.079 -4.165 -4.523 1.00 0.00 C +ATOM 54 ND1 HP6 4 3.191 -4.817 -5.032 1.00 0.00 N +ATOM 55 HD1 HP6 4 3.863 -5.360 -4.497 1.00 0.00 H +ATOM 56 CE1 HP6 4 3.248 -4.577 -6.358 1.00 0.00 C +ATOM 57 HE1 HP6 4 4.033 -4.915 -7.031 1.00 0.00 H +ATOM 58 NE2 HP6 4 2.207 -3.792 -6.703 1.00 0.00 N +ATOM 59 HE2 HP6 4 2.086 -3.335 -7.619 1.00 0.00 H +ATOM 60 CD2 HP6 4 1.460 -3.531 -5.567 1.00 0.00 C +ATOM 61 HD2 HP6 4 0.604 -2.868 -5.502 1.00 0.00 H +ATOM 62 C HP6 4 2.526 -1.543 -3.283 1.00 0.00 C +ATOM 63 O HP6 4 3.467 -1.203 -3.994 1.00 0.00 O +ATOM 64 N I03 5 1.415 -0.802 -3.187 1.00 0.00 N +ATOM 65 H I03 5 0.659 -1.127 -2.590 1.00 0.00 H +ATOM 66 CA I03 5 1.245 0.436 -3.975 1.00 0.00 C +ATOM 67 HA I03 5 1.492 0.193 -5.011 1.00 0.00 H +ATOM 68 CB I03 5 -0.211 0.955 -3.992 1.00 0.00 C +ATOM 69 HB I03 5 -0.229 1.835 -4.638 1.00 0.00 H +ATOM 70 CG2 I03 5 -1.124 -0.101 -4.643 1.00 0.00 C +ATOM 71 HG21 I03 5 -1.243 -0.964 -3.988 1.00 0.00 H +ATOM 72 HG22 I03 5 -2.106 0.326 -4.847 1.00 0.00 H +ATOM 73 HG23 I03 5 -0.700 -0.426 -5.594 1.00 0.00 H +ATOM 74 CG1 I03 5 -0.715 1.392 -2.601 1.00 0.00 C +ATOM 75 HG12 I03 5 -0.686 0.539 -1.932 1.00 0.00 H +ATOM 76 HG13 I03 5 -0.051 2.161 -2.205 1.00 0.00 H +ATOM 77 CD1 I03 5 -2.136 1.968 -2.592 1.00 0.00 C +ATOM 78 HD11 I03 5 -2.863 1.193 -2.836 1.00 0.00 H +ATOM 79 HD12 I03 5 -2.361 2.351 -1.596 1.00 0.00 H +ATOM 80 HD13 I03 5 -2.212 2.784 -3.311 1.00 0.00 H +ATOM 81 C I03 5 2.246 1.527 -3.564 1.00 0.00 C +ATOM 82 O I03 5 2.739 2.245 -4.430 1.00 0.00 O +ATOM 83 N L03 6 2.632 1.604 -2.282 1.00 0.00 N +ATOM 84 H L03 6 2.168 1.022 -1.594 1.00 0.00 H +ATOM 85 CA L03 6 3.705 2.497 -1.827 1.00 0.00 C +ATOM 86 HA L03 6 3.469 3.507 -2.169 1.00 0.00 H +ATOM 87 CB L03 6 3.733 2.497 -0.287 1.00 0.00 C +ATOM 88 HB2 L03 6 2.756 2.822 0.076 1.00 0.00 H +ATOM 89 HB3 L03 6 3.894 1.476 0.061 1.00 0.00 H +ATOM 90 CG L03 6 4.814 3.397 0.343 1.00 0.00 C +ATOM 91 HG L03 6 5.798 3.045 0.037 1.00 0.00 H +ATOM 92 CD1 L03 6 4.672 4.867 -0.056 1.00 0.00 C +ATOM 93 HD11 L03 6 3.675 5.230 0.194 1.00 0.00 H +ATOM 94 HD12 L03 6 5.415 5.465 0.472 1.00 0.00 H +ATOM 95 HD13 L03 6 4.845 4.985 -1.126 1.00 0.00 H +ATOM 96 CD2 L03 6 4.733 3.302 1.866 1.00 0.00 C +ATOM 97 HD21 L03 6 4.863 2.266 2.179 1.00 0.00 H +ATOM 98 HD22 L03 6 5.523 3.903 2.317 1.00 0.00 H +ATOM 99 HD23 L03 6 3.764 3.663 2.215 1.00 0.00 H +ATOM 100 C L03 6 5.062 2.110 -2.444 1.00 0.00 C +ATOM 101 O L03 6 5.760 2.970 -2.982 1.00 0.00 O +ATOM 102 N R23 7 5.421 0.817 -2.432 1.00 0.00 N +ATOM 103 H R23 7 4.814 0.158 -1.949 1.00 0.00 H +ATOM 104 CA R23 7 6.642 0.300 -3.079 1.00 0.00 C +ATOM 105 HA R23 7 7.501 0.846 -2.687 1.00 0.00 H +ATOM 106 CB R23 7 6.805 -1.189 -2.717 1.00 0.00 C +ATOM 107 HB2 R23 7 6.731 -1.291 -1.633 1.00 0.00 H +ATOM 108 HB3 R23 7 5.997 -1.767 -3.169 1.00 0.00 H +ATOM 109 CG R23 7 8.157 -1.765 -3.178 1.00 0.00 C +ATOM 110 HG2 R23 7 8.220 -1.707 -4.265 1.00 0.00 H +ATOM 111 HG3 R23 7 8.972 -1.176 -2.755 1.00 0.00 H +ATOM 112 CD R23 7 8.330 -3.234 -2.769 1.00 0.00 C +ATOM 113 HD2 R23 7 7.477 -3.803 -3.144 1.00 0.00 H +ATOM 114 HD3 R23 7 9.237 -3.616 -3.243 1.00 0.00 H +ATOM 115 NE R23 7 8.447 -3.397 -1.303 1.00 0.00 N +ATOM 116 HE R23 7 8.545 -2.556 -0.753 1.00 0.00 H +ATOM 117 CZ R23 7 8.477 -4.538 -0.635 1.00 0.00 C +ATOM 118 NH1 R23 7 8.582 -4.539 0.663 1.00 0.00 N +ATOM 119 HH11 R23 7 8.644 -3.671 1.171 1.00 0.00 H +ATOM 120 HH12 R23 7 8.610 -5.408 1.172 1.00 0.00 H +ATOM 121 NH2 R23 7 8.405 -5.694 -1.233 1.00 0.00 N +ATOM 122 HH21 R23 7 8.344 -5.726 -2.236 1.00 0.00 H +ATOM 123 HH22 R23 7 8.434 -6.551 -0.704 1.00 0.00 H +ATOM 124 C R23 7 6.635 0.535 -4.594 1.00 0.00 C +ATOM 125 O R23 7 7.645 0.955 -5.149 1.00 0.00 O +ATOM 126 N E04 8 5.498 0.325 -5.251 1.00 0.00 N +ATOM 127 H E04 8 4.722 -0.064 -4.726 1.00 0.00 H +ATOM 128 CA E04 8 5.313 0.548 -6.691 1.00 0.00 C +ATOM 129 HA E04 8 6.087 -0.004 -7.227 1.00 0.00 H +ATOM 130 CB E04 8 3.946 -0.025 -7.102 1.00 0.00 C +ATOM 131 HB2 E04 8 3.852 -1.029 -6.686 1.00 0.00 H +ATOM 132 HB3 E04 8 3.151 0.595 -6.688 1.00 0.00 H +ATOM 133 CG E04 8 3.767 -0.129 -8.620 1.00 0.00 C +ATOM 134 HG2 E04 8 3.815 0.872 -9.057 1.00 0.00 H +ATOM 135 HG3 E04 8 4.589 -0.716 -9.037 1.00 0.00 H +ATOM 136 CD E04 8 2.421 -0.798 -8.967 1.00 0.00 C +ATOM 137 OE1 E04 8 1.465 -0.086 -9.359 1.00 0.00 O +ATOM 138 OE2 E04 8 2.307 -2.045 -8.849 1.00 0.00 O +ATOM 139 C E04 8 5.454 2.036 -7.073 1.00 0.00 C +ATOM 140 O E04 8 6.119 2.353 -8.059 1.00 0.00 O +ATOM 141 N E07 9 4.914 2.961 -6.272 1.00 0.00 N +ATOM 142 H E07 9 4.332 2.655 -5.498 1.00 0.00 H +ATOM 143 CA E07 9 5.105 4.408 -6.458 1.00 0.00 C +ATOM 144 HA E07 9 4.860 4.669 -7.488 1.00 0.00 H +ATOM 145 CB E07 9 4.173 5.195 -5.518 1.00 0.00 C +ATOM 146 HB2 E07 9 4.231 4.767 -4.516 1.00 0.00 H +ATOM 147 HB3 E07 9 4.519 6.227 -5.455 1.00 0.00 H +ATOM 148 CG E07 9 2.708 5.208 -5.978 1.00 0.00 C +ATOM 149 HG2 E07 9 2.378 4.191 -6.201 1.00 0.00 H +ATOM 150 HG3 E07 9 2.094 5.575 -5.152 1.00 0.00 H +ATOM 151 CD E07 9 2.505 6.115 -7.208 1.00 0.00 C +ATOM 152 OE1 E07 9 2.349 7.349 -7.038 1.00 0.00 O +ATOM 153 OE2 E07 9 2.486 5.603 -8.355 1.00 0.00 O +ATOM 154 C E07 9 6.563 4.846 -6.231 1.00 0.00 C +ATOM 155 O E07 9 7.086 5.651 -7.005 1.00 0.00 O +ATOM 156 N M12 10 7.254 4.302 -5.218 1.00 0.00 N +ATOM 157 H M12 10 6.771 3.677 -4.580 1.00 0.00 H +ATOM 158 CA M12 10 8.687 4.563 -5.013 1.00 0.00 C +ATOM 159 HA M12 10 8.844 5.643 -4.993 1.00 0.00 H +ATOM 160 CB M12 10 9.161 3.991 -3.667 1.00 0.00 C +ATOM 161 HB2 M12 10 8.874 2.942 -3.592 1.00 0.00 H +ATOM 162 HB3 M12 10 10.250 4.055 -3.625 1.00 0.00 H +ATOM 163 CG M12 10 8.593 4.778 -2.477 1.00 0.00 C +ATOM 164 HG2 M12 10 8.796 5.837 -2.640 1.00 0.00 H +ATOM 165 HG3 M12 10 7.512 4.654 -2.447 1.00 0.00 H +ATOM 166 SD M12 10 9.272 4.338 -0.849 1.00 0.00 S +ATOM 167 CE M12 10 8.825 2.583 -0.737 1.00 0.00 C +ATOM 168 HE1 M12 10 9.394 2.009 -1.468 1.00 0.00 H +ATOM 169 HE2 M12 10 9.057 2.212 0.262 1.00 0.00 H +ATOM 170 HE3 M12 10 7.760 2.461 -0.927 1.00 0.00 H +ATOM 171 C M12 10 9.543 4.010 -6.166 1.00 0.00 C +ATOM 172 O M12 10 10.455 4.694 -6.629 1.00 0.00 O +ATOM 173 N K32 11 9.226 2.815 -6.679 1.00 0.00 N +ATOM 174 H K32 11 8.488 2.281 -6.231 1.00 0.00 H +ATOM 175 CA K32 11 9.887 2.228 -7.850 1.00 0.00 C +ATOM 176 HA K32 11 10.963 2.210 -7.665 1.00 0.00 H +ATOM 177 CB K32 11 9.400 0.779 -8.017 1.00 0.00 C +ATOM 178 HB2 K32 11 9.574 0.243 -7.082 1.00 0.00 H +ATOM 179 HB3 K32 11 8.330 0.776 -8.223 1.00 0.00 H +ATOM 180 CG K32 11 10.131 0.037 -9.146 1.00 0.00 C +ATOM 181 HG2 K32 11 9.919 0.523 -10.099 1.00 0.00 H +ATOM 182 HG3 K32 11 11.205 0.072 -8.960 1.00 0.00 H +ATOM 183 CD K32 11 9.667 -1.425 -9.222 1.00 0.00 C +ATOM 184 HD2 K32 11 9.894 -1.935 -8.284 1.00 0.00 H +ATOM 185 HD3 K32 11 8.586 -1.443 -9.368 1.00 0.00 H +ATOM 186 CE K32 11 10.316 -2.184 -10.387 1.00 0.00 C +ATOM 187 HE2 K32 11 9.840 -3.160 -10.477 1.00 0.00 H +ATOM 188 HE3 K32 11 10.155 -1.628 -11.310 1.00 0.00 H +ATOM 189 NZ K32 11 11.764 -2.391 -10.201 1.00 0.00 N +ATOM 190 HZ2 K32 11 12.110 -2.902 -11.007 1.00 0.00 H +ATOM 191 HZ3 K32 11 12.214 -1.484 -10.217 1.00 0.00 H +ATOM 192 C K32 11 9.654 3.070 -9.116 1.00 0.00 C +ATOM 193 O K32 11 10.595 3.320 -9.865 1.00 0.00 O +ATOM 194 N D02 12 8.436 3.571 -9.340 1.00 0.00 N +ATOM 195 H D02 12 7.677 3.296 -8.724 1.00 0.00 H +ATOM 196 CA D02 12 8.142 4.501 -10.436 1.00 0.00 C +ATOM 197 HA D02 12 8.424 4.029 -11.378 1.00 0.00 H +ATOM 198 CB D02 12 6.636 4.780 -10.488 1.00 0.00 C +ATOM 199 HB2 D02 12 6.099 3.834 -10.579 1.00 0.00 H +ATOM 200 HB3 D02 12 6.321 5.257 -9.559 1.00 0.00 H +ATOM 201 CG D02 12 6.283 5.678 -11.685 1.00 0.00 C +ATOM 202 OD1 D02 12 6.269 5.172 -12.834 1.00 0.00 O +ATOM 203 OD2 D02 12 6.014 6.887 -11.485 1.00 0.00 O +ATOM 204 C D02 12 8.945 5.812 -10.312 1.00 0.00 C +ATOM 205 O D02 12 9.529 6.274 -11.297 1.00 0.00 O +ATOM 206 N R16 13 9.057 6.370 -9.096 1.00 0.00 N +ATOM 207 H R16 13 8.523 5.955 -8.335 1.00 0.00 H +ATOM 208 CA R16 13 9.862 7.570 -8.814 1.00 0.00 C +ATOM 209 HA R16 13 9.532 8.352 -9.501 1.00 0.00 H +ATOM 210 CB R16 13 9.596 8.039 -7.368 1.00 0.00 C +ATOM 211 HB2 R16 13 8.527 8.226 -7.254 1.00 0.00 H +ATOM 212 HB3 R16 13 9.863 7.241 -6.677 1.00 0.00 H +ATOM 213 CG R16 13 10.355 9.307 -6.936 1.00 0.00 C +ATOM 214 HG2 R16 13 10.069 9.535 -5.908 1.00 0.00 H +ATOM 215 HG3 R16 13 11.429 9.116 -6.950 1.00 0.00 H +ATOM 216 CD R16 13 10.051 10.533 -7.809 1.00 0.00 C +ATOM 217 HD2 R16 13 10.429 10.354 -8.819 1.00 0.00 H +ATOM 218 HD3 R16 13 8.968 10.674 -7.852 1.00 0.00 H +ATOM 219 NE R16 13 10.684 11.751 -7.260 1.00 0.00 N +ATOM 220 HE R16 13 11.164 11.659 -6.377 1.00 0.00 H +ATOM 221 CZ R16 13 10.657 12.964 -7.788 1.00 0.00 C +ATOM 222 NH1 R16 13 10.048 13.219 -8.912 1.00 0.00 N +ATOM 223 HH11 R16 13 9.569 12.477 -9.393 1.00 0.00 H +ATOM 224 HH12 R16 13 10.038 14.151 -9.292 1.00 0.00 H +ATOM 225 NH2 R16 13 11.251 13.956 -7.187 1.00 0.00 N +ATOM 226 HH21 R16 13 11.725 13.811 -6.311 1.00 0.00 H +ATOM 227 HH22 R16 13 11.229 14.879 -7.587 1.00 0.00 H +ATOM 228 C R16 13 11.350 7.351 -9.101 1.00 0.00 C +ATOM 229 O R16 13 11.954 8.188 -9.768 1.00 0.00 O +ATOM 230 N T03 14 11.953 6.240 -8.668 1.00 0.00 N +ATOM 231 H T03 14 11.424 5.573 -8.111 1.00 0.00 H +ATOM 232 CA T03 14 13.374 5.962 -8.970 1.00 0.00 C +ATOM 233 HA T03 14 13.929 6.889 -8.833 1.00 0.00 H +ATOM 234 CB T03 14 14.017 4.944 -8.016 1.00 0.00 C +ATOM 235 HB T03 14 15.074 4.860 -8.269 1.00 0.00 H +ATOM 236 CG2 T03 14 13.923 5.364 -6.550 1.00 0.00 C +ATOM 237 HG21 T03 14 12.886 5.405 -6.224 1.00 0.00 H +ATOM 238 HG22 T03 14 14.467 4.652 -5.928 1.00 0.00 H +ATOM 239 HG23 T03 14 14.374 6.349 -6.423 1.00 0.00 H +ATOM 240 OG1 T03 14 13.423 3.677 -8.184 1.00 0.00 O +ATOM 241 HG1 T03 14 13.504 3.182 -7.346 1.00 0.00 H +ATOM 242 C T03 14 13.601 5.538 -10.423 1.00 0.00 C +ATOM 243 O T03 14 14.677 5.799 -10.956 1.00 0.00 O +ATOM 244 N N07 15 12.618 4.942 -11.108 1.00 0.00 N +ATOM 245 H N07 15 11.796 4.634 -10.595 1.00 0.00 H +ATOM 246 CA N07 15 12.669 4.687 -12.556 1.00 0.00 C +ATOM 247 HA N07 15 13.600 4.172 -12.798 1.00 0.00 H +ATOM 248 CB N07 15 11.497 3.777 -12.976 1.00 0.00 C +ATOM 249 HB2 N07 15 10.569 4.137 -12.535 1.00 0.00 H +ATOM 250 HB3 N07 15 11.386 3.828 -14.060 1.00 0.00 H +ATOM 251 CG N07 15 11.681 2.305 -12.623 1.00 0.00 C +ATOM 252 OD1 N07 15 12.717 1.853 -12.156 1.00 0.00 O +ATOM 253 ND2 N07 15 10.684 1.491 -12.896 1.00 0.00 N +ATOM 254 HD21 N07 15 10.805 0.508 -12.710 1.00 0.00 H +ATOM 255 HD22 N07 15 9.833 1.842 -13.307 1.00 0.00 H +ATOM 256 C N07 15 12.670 6.000 -13.364 1.00 0.00 C +ATOM 257 O N07 15 13.439 6.131 -14.318 1.00 0.00 O +ATOM 258 N A01 16 11.877 6.997 -12.956 1.00 0.00 N +ATOM 259 H A01 16 11.200 6.814 -12.221 1.00 0.00 H +ATOM 260 CA A01 16 11.938 8.346 -13.523 1.00 0.00 C +ATOM 261 HA A01 16 11.852 8.274 -14.610 1.00 0.00 H +ATOM 262 CB A01 16 10.739 9.155 -13.007 1.00 0.00 C +ATOM 263 HB1 A01 16 9.810 8.657 -13.289 1.00 0.00 H +ATOM 264 HB2 A01 16 10.777 9.249 -11.922 1.00 0.00 H +ATOM 265 HB3 A01 16 10.751 10.151 -13.451 1.00 0.00 H +ATOM 266 C A01 16 13.283 9.029 -13.209 1.00 0.00 C +ATOM 267 O A01 16 13.967 9.494 -14.119 1.00 0.00 O +ATOM 268 N M07 17 13.712 9.021 -11.939 1.00 0.00 N +ATOM 269 H M07 17 13.084 8.648 -11.232 1.00 0.00 H +ATOM 270 CA M07 17 14.948 9.680 -11.485 1.00 0.00 C +ATOM 271 HA M07 17 14.867 10.743 -11.715 1.00 0.00 H +ATOM 272 CB M07 17 15.057 9.540 -9.958 1.00 0.00 C +ATOM 273 HB2 M07 17 14.111 9.850 -9.512 1.00 0.00 H +ATOM 274 HB3 M07 17 15.238 8.497 -9.700 1.00 0.00 H +ATOM 275 CG M07 17 16.178 10.400 -9.360 1.00 0.00 C +ATOM 276 HG2 M07 17 17.123 10.120 -9.827 1.00 0.00 H +ATOM 277 HG3 M07 17 15.986 11.448 -9.593 1.00 0.00 H +ATOM 278 SD M07 17 16.384 10.228 -7.563 1.00 0.00 S +ATOM 279 CE M07 17 14.851 10.994 -6.961 1.00 0.00 C +ATOM 280 HE1 M07 17 13.988 10.407 -7.277 1.00 0.00 H +ATOM 281 HE2 M07 17 14.870 11.035 -5.872 1.00 0.00 H +ATOM 282 HE3 M07 17 14.765 12.008 -7.354 1.00 0.00 H +ATOM 283 C M07 17 16.205 9.144 -12.192 1.00 0.00 C +ATOM 284 O M07 17 17.005 9.932 -12.700 1.00 0.00 O +ATOM 285 N R07 18 16.364 7.812 -12.293 1.00 0.00 N +ATOM 286 H R07 18 15.679 7.211 -11.841 1.00 0.00 H +ATOM 287 CA R07 18 17.535 7.183 -12.945 1.00 0.00 C +ATOM 288 HA R07 18 18.429 7.641 -12.515 1.00 0.00 H +ATOM 289 CB R07 18 17.607 5.681 -12.593 1.00 0.00 C +ATOM 290 HB2 R07 18 18.621 5.329 -12.792 1.00 0.00 H +ATOM 291 HB3 R07 18 17.426 5.562 -11.523 1.00 0.00 H +ATOM 292 CG R07 18 16.632 4.793 -13.386 1.00 0.00 C +ATOM 293 HG2 R07 18 15.625 5.191 -13.311 1.00 0.00 H +ATOM 294 HG3 R07 18 16.922 4.802 -14.438 1.00 0.00 H +ATOM 295 CD R07 18 16.642 3.336 -12.907 1.00 0.00 C +ATOM 296 HD2 R07 18 16.129 2.730 -13.657 1.00 0.00 H +ATOM 297 HD3 R07 18 17.678 2.996 -12.837 1.00 0.00 H +ATOM 298 NE R07 18 15.958 3.160 -11.606 1.00 0.00 N +ATOM 299 HE R07 18 15.539 3.983 -11.192 1.00 0.00 H +ATOM 300 CZ R07 18 15.830 2.018 -10.945 1.00 0.00 C +ATOM 301 NH1 R07 18 15.127 1.937 -9.850 1.00 0.00 N +ATOM 302 HH11 R07 18 14.552 2.705 -9.529 1.00 0.00 H +ATOM 303 HH12 R07 18 15.054 1.058 -9.367 1.00 0.00 H +ATOM 304 NH2 R07 18 16.410 0.922 -11.353 1.00 0.00 N +ATOM 305 HH21 R07 18 16.962 0.939 -12.193 1.00 0.00 H +ATOM 306 HH22 R07 18 16.306 0.060 -10.844 1.00 0.00 H +ATOM 307 C R07 18 17.615 7.446 -14.458 1.00 0.00 C +ATOM 308 O R07 18 18.698 7.371 -15.033 1.00 0.00 O +ATOM 309 N D08 19 16.486 7.778 -15.092 1.00 0.00 N +ATOM 310 H D08 19 15.630 7.782 -14.555 1.00 0.00 H +ATOM 311 CA D08 19 16.425 8.210 -16.493 1.00 0.00 C +ATOM 312 HA D08 19 17.193 7.682 -17.063 1.00 0.00 H +ATOM 313 CB D08 19 15.058 7.812 -17.075 1.00 0.00 C +ATOM 314 HB2 D08 19 14.916 6.736 -16.962 1.00 0.00 H +ATOM 315 HB3 D08 19 14.260 8.316 -16.529 1.00 0.00 H +ATOM 316 CG D08 19 14.947 8.156 -18.560 1.00 0.00 C +ATOM 317 OD1 D08 19 15.501 7.530 -19.461 1.00 0.00 O +ATOM 318 OD2 D08 19 14.185 9.248 -18.826 1.00 0.00 O +ATOM 319 HD2 D08 19 14.148 9.401 -19.793 1.00 0.00 H +ATOM 320 C D08 19 16.682 9.722 -16.661 1.00 0.00 C +ATOM 321 O D08 19 17.443 10.120 -17.543 1.00 0.00 O +ATOM 322 N E03 20 16.053 10.572 -15.838 1.00 0.00 N +ATOM 323 H E03 20 15.422 10.190 -15.138 1.00 0.00 H +ATOM 324 CA E03 20 15.992 12.025 -16.077 1.00 0.00 C +ATOM 325 HA E03 20 15.987 12.177 -17.158 1.00 0.00 H +ATOM 326 CB E03 20 14.647 12.579 -15.569 1.00 0.00 C +ATOM 327 HB2 E03 20 14.465 13.544 -16.042 1.00 0.00 H +ATOM 328 HB3 E03 20 13.858 11.908 -15.912 1.00 0.00 H +ATOM 329 CG E03 20 14.521 12.728 -14.043 1.00 0.00 C +ATOM 330 HG2 E03 20 13.486 12.516 -13.763 1.00 0.00 H +ATOM 331 HG3 E03 20 15.145 11.978 -13.555 1.00 0.00 H +ATOM 332 CD E03 20 14.883 14.144 -13.544 1.00 0.00 C +ATOM 333 OE1 E03 20 14.160 15.116 -13.880 1.00 0.00 O +ATOM 334 OE2 E03 20 15.862 14.296 -12.773 1.00 0.00 O +ATOM 335 C E03 20 17.191 12.838 -15.549 1.00 0.00 C +ATOM 336 O E03 20 17.415 13.953 -16.033 1.00 0.00 O +ATOM 337 N R11 21 17.972 12.309 -14.589 1.00 0.00 N +ATOM 338 H R11 21 17.696 11.419 -14.189 1.00 0.00 H +ATOM 339 CA R11 21 19.127 13.028 -14.006 1.00 0.00 C +ATOM 340 HA R11 21 18.737 13.989 -13.664 1.00 0.00 H +ATOM 341 CB R11 21 19.678 12.308 -12.753 1.00 0.00 C +ATOM 342 HB2 R11 21 20.146 13.065 -12.121 1.00 0.00 H +ATOM 343 HB3 R11 21 18.849 11.890 -12.180 1.00 0.00 H +ATOM 344 CG R11 21 20.736 11.213 -12.991 1.00 0.00 C +ATOM 345 HG2 R11 21 21.607 11.651 -13.478 1.00 0.00 H +ATOM 346 HG3 R11 21 21.064 10.835 -12.022 1.00 0.00 H +ATOM 347 CD R11 21 20.231 10.028 -13.821 1.00 0.00 C +ATOM 348 HD2 R11 21 19.487 9.494 -13.232 1.00 0.00 H +ATOM 349 HD3 R11 21 19.744 10.375 -14.731 1.00 0.00 H +ATOM 350 NE R11 21 21.330 9.107 -14.169 1.00 0.00 N +ATOM 351 HE R11 21 21.506 8.348 -13.527 1.00 0.00 H +ATOM 352 CZ R11 21 22.075 9.132 -15.262 1.00 0.00 C +ATOM 353 NH1 R11 21 21.968 10.069 -16.164 1.00 0.00 N +ATOM 354 HH11 R11 21 21.320 10.836 -16.019 1.00 0.00 H +ATOM 355 HH12 R11 21 22.549 10.061 -16.985 1.00 0.00 H +ATOM 356 NH2 R11 21 22.966 8.203 -15.469 1.00 0.00 N +ATOM 357 HH21 R11 21 23.085 7.458 -14.802 1.00 0.00 H +ATOM 358 HH22 R11 21 23.539 8.218 -16.297 1.00 0.00 H +ATOM 359 C R11 21 20.226 13.348 -15.035 1.00 0.00 C +ATOM 360 O R11 21 20.510 12.536 -15.921 1.00 0.00 O +ATOM 361 N NME 22 20.890 14.496 -14.871 1.00 0.00 N +ATOM 362 H NME 22 20.607 15.093 -14.106 1.00 0.00 H +ATOM 363 CH3 NME 22 21.994 14.950 -15.719 1.00 0.00 C +ATOM 364 HH31 NME 22 22.830 14.250 -15.653 1.00 0.00 H +ATOM 365 HH32 NME 22 21.668 15.011 -16.760 1.00 0.00 H +ATOM 366 HH33 NME 22 22.335 15.936 -15.399 1.00 0.00 H +CONECT 1 2 +CONECT 2 3 1 5 4 +CONECT 3 2 +CONECT 4 2 +CONECT 5 6 2 7 +CONECT 6 5 +CONECT 7 5 9 8 +CONECT 8 7 +CONECT 9 10 7 29 11 +CONECT 10 9 +CONECT 11 9 13 12 14 +CONECT 12 11 +CONECT 13 11 +CONECT 14 11 28 15 +CONECT 15 14 16 17 +CONECT 16 15 +CONECT 17 15 19 18 +CONECT 18 17 +CONECT 19 28 17 20 +CONECT 20 19 22 21 +CONECT 21 20 +CONECT 22 24 20 23 +CONECT 23 22 +CONECT 24 26 25 22 +CONECT 25 24 +CONECT 26 27 28 24 +CONECT 27 26 +CONECT 28 14 26 19 +CONECT 29 30 9 31 +CONECT 30 29 +CONECT 31 29 33 32 +CONECT 32 31 +CONECT 33 44 31 34 35 +CONECT 34 33 +CONECT 35 33 38 36 37 +CONECT 36 35 +CONECT 37 35 +CONECT 38 39 41 35 40 +CONECT 39 38 +CONECT 40 38 +CONECT 41 43 38 42 +CONECT 42 41 +CONECT 43 41 +CONECT 44 46 45 33 +CONECT 45 44 +CONECT 46 48 47 44 +CONECT 47 46 +CONECT 48 62 50 49 46 +CONECT 49 48 +CONECT 50 53 52 51 48 +CONECT 51 50 +CONECT 52 50 +CONECT 53 60 54 50 +CONECT 54 56 53 55 +CONECT 55 54 +CONECT 56 57 58 54 +CONECT 57 56 +CONECT 58 59 56 60 +CONECT 59 58 +CONECT 60 58 61 53 +CONECT 61 60 +CONECT 62 63 64 48 +CONECT 63 62 +CONECT 64 66 62 65 +CONECT 65 64 +CONECT 66 67 68 81 64 +CONECT 67 66 +CONECT 68 70 69 66 74 +CONECT 69 68 +CONECT 70 73 72 68 71 +CONECT 71 70 +CONECT 72 70 +CONECT 73 70 +CONECT 74 68 77 76 75 +CONECT 75 74 +CONECT 76 74 +CONECT 77 80 78 74 79 +CONECT 78 77 +CONECT 79 77 +CONECT 80 77 +CONECT 81 82 66 83 +CONECT 82 81 +CONECT 83 81 85 84 +CONECT 84 83 +CONECT 85 100 83 86 87 +CONECT 86 85 +CONECT 87 85 89 88 90 +CONECT 88 87 +CONECT 89 87 +CONECT 90 87 92 91 96 +CONECT 91 90 +CONECT 92 95 93 90 94 +CONECT 93 92 +CONECT 94 92 +CONECT 95 92 +CONECT 96 90 97 99 98 +CONECT 97 96 +CONECT 98 96 +CONECT 99 96 +CONECT 100 101 102 85 +CONECT 101 100 +CONECT 102 104 100 103 +CONECT 103 102 +CONECT 104 124 106 105 102 +CONECT 105 104 +CONECT 106 109 108 104 107 +CONECT 107 106 +CONECT 108 106 +CONECT 109 110 112 111 106 +CONECT 110 109 +CONECT 111 109 +CONECT 112 114 109 113 115 +CONECT 113 112 +CONECT 114 112 +CONECT 115 112 116 117 +CONECT 116 115 +CONECT 117 115 121 118 +CONECT 118 117 119 120 +CONECT 119 118 +CONECT 120 118 +CONECT 121 122 123 117 +CONECT 122 121 +CONECT 123 121 +CONECT 124 126 125 104 +CONECT 125 124 +CONECT 126 128 127 124 +CONECT 127 126 +CONECT 128 129 130 139 126 +CONECT 129 128 +CONECT 130 133 128 132 131 +CONECT 131 130 +CONECT 132 130 +CONECT 133 134 135 136 130 +CONECT 134 133 +CONECT 135 133 +CONECT 136 137 138 133 +CONECT 137 136 +CONECT 138 136 +CONECT 139 140 128 141 +CONECT 140 139 +CONECT 141 139 143 142 +CONECT 142 141 +CONECT 143 144 141 154 145 +CONECT 144 143 +CONECT 145 143 148 147 146 +CONECT 146 145 +CONECT 147 145 +CONECT 148 151 149 145 150 +CONECT 149 148 +CONECT 150 148 +CONECT 151 153 152 148 +CONECT 152 151 +CONECT 153 151 +CONECT 154 155 143 156 +CONECT 155 154 +CONECT 156 154 158 157 +CONECT 157 156 +CONECT 158 171 156 159 160 +CONECT 159 158 +CONECT 160 158 162 161 163 +CONECT 161 160 +CONECT 162 160 +CONECT 163 160 164 165 166 +CONECT 164 163 +CONECT 165 163 +CONECT 166 163 167 +CONECT 167 168 170 166 169 +CONECT 168 167 +CONECT 169 167 +CONECT 170 167 +CONECT 171 173 172 158 +CONECT 172 171 +CONECT 173 175 174 171 +CONECT 174 173 +CONECT 175 192 177 176 173 +CONECT 176 175 +CONECT 177 180 179 175 178 +CONECT 178 177 +CONECT 179 177 +CONECT 180 181 183 182 177 +CONECT 181 180 +CONECT 182 180 +CONECT 183 186 185 180 184 +CONECT 184 183 +CONECT 185 183 +CONECT 186 188 187 189 183 +CONECT 187 186 +CONECT 188 186 +CONECT 189 190 186 191 +CONECT 190 189 +CONECT 191 189 +CONECT 192 193 194 175 +CONECT 193 192 +CONECT 194 196 192 195 +CONECT 195 194 +CONECT 196 197 198 204 194 +CONECT 197 196 +CONECT 198 201 199 196 200 +CONECT 199 198 +CONECT 200 198 +CONECT 201 202 203 198 +CONECT 202 201 +CONECT 203 201 +CONECT 204 205 196 206 +CONECT 205 204 +CONECT 206 204 208 207 +CONECT 207 206 +CONECT 208 209 228 206 210 +CONECT 209 208 +CONECT 210 208 211 213 212 +CONECT 211 210 +CONECT 212 210 +CONECT 213 216 210 215 214 +CONECT 214 213 +CONECT 215 213 +CONECT 216 217 218 219 213 +CONECT 217 216 +CONECT 218 216 +CONECT 219 216 221 220 +CONECT 220 219 +CONECT 221 222 219 225 +CONECT 222 223 224 221 +CONECT 223 222 +CONECT 224 222 +CONECT 225 221 227 226 +CONECT 226 225 +CONECT 227 225 +CONECT 228 229 208 230 +CONECT 229 228 +CONECT 230 228 232 231 +CONECT 231 230 +CONECT 232 242 233 230 234 +CONECT 233 232 +CONECT 234 232 235 240 236 +CONECT 235 234 +CONECT 236 234 239 237 238 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 234 241 +CONECT 241 240 +CONECT 242 244 243 232 +CONECT 243 242 +CONECT 244 246 245 242 +CONECT 245 244 +CONECT 246 256 248 247 244 +CONECT 247 246 +CONECT 248 250 251 246 249 +CONECT 249 248 +CONECT 250 248 +CONECT 251 248 253 252 +CONECT 252 251 +CONECT 253 255 254 251 +CONECT 254 253 +CONECT 255 253 +CONECT 256 257 258 246 +CONECT 257 256 +CONECT 258 260 256 259 +CONECT 259 258 +CONECT 260 261 266 262 258 +CONECT 261 260 +CONECT 262 260 265 263 264 +CONECT 263 262 +CONECT 264 262 +CONECT 265 262 +CONECT 266 267 260 268 +CONECT 267 266 +CONECT 268 266 270 269 +CONECT 269 268 +CONECT 270 283 268 271 272 +CONECT 271 270 +CONECT 272 270 274 273 275 +CONECT 273 272 +CONECT 274 272 +CONECT 275 272 276 277 278 +CONECT 276 275 +CONECT 277 275 +CONECT 278 275 279 +CONECT 279 278 282 280 281 +CONECT 280 279 +CONECT 281 279 +CONECT 282 279 +CONECT 283 284 285 270 +CONECT 284 283 +CONECT 285 287 283 286 +CONECT 286 285 +CONECT 287 307 289 288 285 +CONECT 288 287 +CONECT 289 292 287 290 291 +CONECT 290 289 +CONECT 291 289 +CONECT 292 294 293 295 289 +CONECT 293 292 +CONECT 294 292 +CONECT 295 296 292 297 298 +CONECT 296 295 +CONECT 297 295 +CONECT 298 295 299 300 +CONECT 299 298 +CONECT 300 298 304 301 +CONECT 301 300 302 303 +CONECT 302 301 +CONECT 303 301 +CONECT 304 305 300 306 +CONECT 305 304 +CONECT 306 304 +CONECT 307 309 308 287 +CONECT 308 307 +CONECT 309 311 310 307 +CONECT 310 309 +CONECT 311 313 312 320 309 +CONECT 312 311 +CONECT 313 316 314 315 311 +CONECT 314 313 +CONECT 315 313 +CONECT 316 317 318 313 +CONECT 317 316 +CONECT 318 319 316 +CONECT 319 318 +CONECT 320 321 311 322 +CONECT 321 320 +CONECT 322 320 324 323 +CONECT 323 322 +CONECT 324 325 322 326 335 +CONECT 325 324 +CONECT 326 324 327 328 329 +CONECT 327 326 +CONECT 328 326 +CONECT 329 326 330 331 332 +CONECT 330 329 +CONECT 331 329 +CONECT 332 329 333 334 +CONECT 333 332 +CONECT 334 332 +CONECT 335 324 336 337 +CONECT 336 335 +CONECT 337 335 338 339 +CONECT 338 337 +CONECT 339 359 337 340 341 +CONECT 340 339 +CONECT 341 339 344 343 342 +CONECT 342 341 +CONECT 343 341 +CONECT 344 347 345 341 346 +CONECT 345 344 +CONECT 346 344 +CONECT 347 349 350 348 344 +CONECT 348 347 +CONECT 349 347 +CONECT 350 352 347 351 +CONECT 351 350 +CONECT 352 353 356 350 +CONECT 353 355 354 352 +CONECT 354 353 +CONECT 355 353 +CONECT 356 358 352 357 +CONECT 357 356 +CONECT 358 356 +CONECT 359 360 361 339 +CONECT 360 359 +CONECT 361 363 359 362 +CONECT 362 361 +CONECT 363 365 364 366 361 +CONECT 364 363 +CONECT 365 363 +CONECT 366 363 +MASTER 0 0 0 0 0 0 0 0 366 0 366 0 +END diff --git a/unittests/example_files/leap_glycine.in b/unittests/example_files/leap_glycine.in new file mode 100644 index 0000000..191111d --- /dev/null +++ b/unittests/example_files/leap_glycine.in @@ -0,0 +1,189 @@ +source oldff/leaprc.ff10 +source leaprc.gaff + + +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +loadOff 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b/unittests/example_files/openmm.in new file mode 100644 index 0000000..c406d75 --- /dev/null +++ b/unittests/example_files/openmm.in @@ -0,0 +1,53 @@ +[OPTIMIZATION] +dihedral_optimization = False +composition_optimization = True +composition_residue_indexes = 1 2 +composition_lower_bounds = 1 175 +composition_upper_bounds = 2 176 +composition_library = ../share/flat/ + + +[MOLECULE] +initial_molecule = example_files/ALA20.pdb + +[IO] +store_intermediate_mol = True +output_path = . +output_file = final.pdb + +[GA_GLOBAL] +seed_population = False +population_file_path = None +population_size = 10 +max_iteration = 10 + +[EVALUATOR] +evaluators = helical_stability +tleap_template = example_files/tleap_template.in +amber_params = example_files/amber_minimization.in +mpi_processors = 20 +dielectric = 80.0 +gpu_openmm=True + +[GA_SELECTION] +selector = tournament_wor +tournament_size = 2 + +[GA_CROSSOVER] +crossover = sbx +sbx_distribution_index = 7.0 +mating_probability = 0.7 +genewise_crossover_probability = 0.4 + +[GA_MUTATION] +mutator = polynomial_mutation +mutation_probability = 0.3 +genewise__mutation_probability = 0.15 +poly_eta = 7.0 + +[GA_REPLACER] +replacer = elitism +elitist_factor = 0.25 + +[DEBUG] +verbose = True diff --git a/unittests/example_files/openmm_entropy.in b/unittests/example_files/openmm_entropy.in new file mode 100644 index 0000000..1c67064 --- /dev/null +++ b/unittests/example_files/openmm_entropy.in @@ -0,0 +1,55 @@ +[OPTIMIZATION] +dihedral_optimization = False +composition_optimization = True +composition_residue_indexes = 1 2 +composition_lower_bounds = 1 174 +composition_upper_bounds = 2 176 +composition_library = ../share/flat/ + + +[MOLECULE] +initial_molecule = example_files/ALA20.pdb + +[IO] +store_intermediate_mol = True +output_path = . +output_file = final.pdb + +[GA_GLOBAL] +seed_population = False +population_file_path = None +population_size = 10 +max_iteration = 10 + +[EVALUATOR] +evaluators = helical_stability +tleap_template = example_files/tleap_template.in +amber_params = example_files/amber_minimization.in +mpi_processors = 20 +dielectric = 80.0 +gpu_openmm=True +entropy_correction = KoehlDelarue + + +[GA_SELECTION] +selector = tournament_wor +tournament_size = 2 + +[GA_CROSSOVER] +crossover = sbx +sbx_distribution_index = 7.0 +mating_probability = 0.7 +genewise_crossover_probability = 0.4 + +[GA_MUTATION] +mutator = polynomial_mutation +mutation_probability = 0.3 +genewise__mutation_probability = 0.15 +poly_eta = 7.0 + +[GA_REPLACER] +replacer = elitism +elitist_factor = 0.25 + +[DEBUG] +verbose = True diff --git a/unittests/example_files/test_gly.mol2 b/unittests/example_files/test_gly.mol2 new file mode 100644 index 0000000..41f973f --- /dev/null +++ b/unittests/example_files/test_gly.mol2 @@ -0,0 +1,1727 @@ +@MOLECULE +MET + 855 861 1 0 0 +SMALL +No Charge or Current Charge + + +@ATOM + 1 N 19.1570 32.5760 19.1400 N.4 1 MET 0.000000 + 2 H1 18.4350 31.8700 19.1290 H 1 MET 0.000000 + 3 H2 18.9000 33.2600 18.4410 H 1 MET 0.000000 + 4 H3 19.2290 33.0730 20.0160 H 1 MET 0.000000 + 5 CA 20.4580 31.9390 18.9310 C.3 1 MET 0.000000 + 6 HA 20.4200 31.3030 18.0460 H 1 MET 0.000000 + 7 CB 21.5040 33.0150 18.7220 C.3 1 MET 0.000000 + 8 HB2 21.3520 33.5190 17.7680 H 1 MET 0.000000 + 9 HB3 21.3900 33.7640 19.5050 H 1 MET 0.000000 + 10 CG 22.9040 32.5170 18.6560 C.3 1 MET 0.000000 + 11 HG2 23.5900 33.3620 18.6010 H 1 MET 0.000000 + 12 HG3 23.1540 32.0950 19.6300 H 1 MET 0.000000 + 13 SD 23.2050 31.2690 17.3860 S.3 1 MET 0.000000 + 14 CE 22.9900 32.1370 15.8700 C.3 1 MET 0.000000 + 15 HE1 23.3390 33.1630 15.9830 H 1 MET 0.000000 + 16 HE2 21.9680 32.1280 15.4900 H 1 MET 0.000000 + 17 HE3 23.5720 31.5860 15.1320 H 1 MET 0.000000 + 18 C 20.7960 31.0170 20.1330 C.2 1 MET 0.000000 + 19 O 20.6740 31.4400 21.2970 O.2 1 MET 0.000000 + 20 N 21.1240 29.7740 19.8190 N.am 2 THR 0.000000 + 21 H 21.2790 29.5270 18.8510 H 2 THR 0.000000 + 22 CA 21.4430 28.7040 20.8610 C.3 2 THR 0.000000 + 23 HA 20.9090 28.9980 21.7640 H 2 THR 0.000000 + 24 CB 21.1140 27.2410 20.5220 C.3 2 THR 0.000000 + 25 HB 21.9450 26.8250 19.9550 H 2 THR 0.000000 + 26 CG2 20.7150 26.5580 21.8170 C.3 2 THR 0.000000 + 27 HG21 20.2030 25.6090 21.6560 H 2 THR 0.000000 + 28 HG22 20.0010 27.1370 22.4030 H 2 THR 0.000000 + 29 HG23 21.6330 26.3440 22.3630 H 2 THR 0.000000 + 30 OG1 19.9570 27.2310 19.6580 O.3 2 THR 0.000000 + 31 HG1 19.3860 27.9760 19.8640 H 2 THR 0.000000 + 32 C 22.9370 28.8920 21.0860 C.2 2 THR 0.000000 + 33 O 23.7730 28.8670 20.1810 O.2 2 THR 0.000000 + 34 N 23.2440 29.1550 22.3440 N.am 3 TYR 0.000000 + 35 H 22.5130 29.0850 23.0380 H 3 TYR 0.000000 + 36 CA 24.6280 29.3050 22.8880 C.3 3 TYR 0.000000 + 37 HA 25.2620 29.3910 22.0040 H 3 TYR 0.000000 + 38 CB 24.7440 30.5790 23.6750 C.3 3 TYR 0.000000 + 39 HB2 24.1310 30.4950 24.5720 H 3 TYR 0.000000 + 40 HB3 25.7800 30.5050 24.0080 H 3 TYR 0.000000 + 41 CG 24.4680 31.8620 22.9280 C.ar 3 TYR 0.000000 + 42 CD1 25.5250 32.5440 22.3170 C.ar 3 TYR 0.000000 + 43 HD1 26.4770 32.0390 22.3790 H 3 TYR 0.000000 + 44 CE1 25.2890 33.7610 21.6190 C.ar 3 TYR 0.000000 + 45 HE1 26.1000 34.2750 21.1220 H 3 TYR 0.000000 + 46 CZ 23.9360 34.2600 21.5790 C.ar 3 TYR 0.000000 + 47 OH 23.7740 35.2680 20.7740 O.3 3 TYR 0.000000 + 48 HH 24.4860 35.1610 20.1400 H 3 TYR 0.000000 + 49 CE2 22.8490 33.5370 22.1760 C.ar 3 TYR 0.000000 + 50 HE2 21.8680 33.9650 22.0360 H 3 TYR 0.000000 + 51 CD2 23.1100 32.2910 22.8530 C.ar 3 TYR 0.000000 + 52 HD2 22.2350 31.7520 23.1870 H 3 TYR 0.000000 + 53 C 25.0660 28.1360 23.7740 C.2 3 TYR 0.000000 + 54 O 24.2330 27.4360 24.3380 O.2 3 TYR 0.000000 + 55 N 26.3390 27.9340 23.8110 N.am 4 LYS 0.000000 + 56 H 26.9440 28.5140 23.2480 H 4 LYS 0.000000 + 57 CA 26.9820 26.9180 24.6870 C.3 4 LYS 0.000000 + 58 HA 26.2120 26.4880 25.3280 H 4 LYS 0.000000 + 59 CB 27.6430 25.8010 23.8030 C.3 4 LYS 0.000000 + 60 HB2 26.8680 25.4650 23.1130 H 4 LYS 0.000000 + 61 HB3 28.4220 26.1960 23.1510 H 4 LYS 0.000000 + 62 CG 28.2050 24.6250 24.5060 C.3 4 LYS 0.000000 + 63 HG2 29.0540 24.9160 25.1250 H 4 LYS 0.000000 + 64 HG3 27.4520 24.2780 25.2130 H 4 LYS 0.000000 + 65 CD 28.6350 23.4070 23.6780 C.3 4 LYS 0.000000 + 66 HD2 29.0030 22.6910 24.4140 H 4 LYS 0.000000 + 67 HD3 27.7370 22.9540 23.2550 H 4 LYS 0.000000 + 68 CE 29.5540 23.5750 22.5060 C.3 4 LYS 0.000000 + 69 HE2 28.8990 24.1200 21.8270 H 4 LYS 0.000000 + 70 HE3 30.4580 24.1140 22.7940 H 4 LYS 0.000000 + 71 NZ 30.0520 22.2790 21.8880 N.4 4 LYS 0.000000 + 72 HZ1 30.8310 21.8960 22.4020 H 4 LYS 0.000000 + 73 HZ2 30.4430 22.4230 20.9680 H 4 LYS 0.000000 + 74 HZ3 29.3280 21.5790 21.8050 H 4 LYS 0.000000 + 75 C 28.0030 27.5160 25.6550 C.2 4 LYS 0.000000 + 76 O 28.5790 28.5530 25.3100 O.2 4 LYS 0.000000 + 77 N 28.2450 26.7730 26.7410 N.am 5 LEU 0.000000 + 78 H 27.5440 26.0840 26.9770 H 5 LEU 0.000000 + 79 CA 29.2440 27.1180 27.7660 C.3 5 LEU 0.000000 + 80 HA 29.9160 27.8840 27.3800 H 5 LEU 0.000000 + 81 CB 28.5790 27.5070 29.0970 C.3 5 LEU 0.000000 + 82 HB2 28.0580 28.4380 28.8720 H 5 LEU 0.000000 + 83 HB3 27.8590 26.7790 29.4690 H 5 LEU 0.000000 + 84 CG 29.5510 27.7200 30.2350 C.3 5 LEU 0.000000 + 85 HG 30.1660 26.8410 30.4290 H 5 LEU 0.000000 + 86 CD1 30.4270 28.9520 29.9860 C.3 5 LEU 0.000000 + 87 HD11 31.1140 28.6830 29.1840 H 5 LEU 0.000000 + 88 HD12 31.0080 29.1200 30.8940 H 5 LEU 0.000000 + 89 HD13 29.8480 29.8610 29.8250 H 5 LEU 0.000000 + 90 CD2 28.6780 28.1150 31.4570 C.3 5 LEU 0.000000 + 91 HD21 28.2350 29.0960 31.2840 H 5 LEU 0.000000 + 92 HD22 29.3270 28.2870 32.3150 H 5 LEU 0.000000 + 93 HD23 27.9070 27.3900 31.7200 H 5 LEU 0.000000 + 94 C 30.0650 25.8160 27.9900 C.2 5 LEU 0.000000 + 95 O 29.4890 24.7680 28.3020 O.2 5 LEU 0.000000 + 96 N 31.4150 25.9540 27.9590 N.am 6 ILE 0.000000 + 97 H 31.8340 26.8220 27.6580 H 6 ILE 0.000000 + 98 CA 32.3520 24.9440 28.4380 C.3 6 ILE 0.000000 + 99 HA 31.8510 23.9780 28.4940 H 6 ILE 0.000000 + 100 CB 33.5350 24.7360 27.4340 C.3 6 ILE 0.000000 + 101 HB 34.0020 25.7060 27.2610 H 6 ILE 0.000000 + 102 CG2 34.6580 23.7960 27.9520 C.3 6 ILE 0.000000 + 103 HG21 35.0110 24.0490 28.9530 H 6 ILE 0.000000 + 104 HG22 35.6100 23.7730 27.4230 H 6 ILE 0.000000 + 105 HG23 34.3150 22.7680 28.0650 H 6 ILE 0.000000 + 106 CG1 32.9670 24.0830 26.1350 C.3 6 ILE 0.000000 + 107 HG12 32.8150 23.0140 26.2810 H 6 ILE 0.000000 + 108 HG13 32.0160 24.5480 25.8750 H 6 ILE 0.000000 + 109 CD1 33.9640 24.2280 24.9830 C.3 6 ILE 0.000000 + 110 HD11 34.2030 25.2800 24.8310 H 6 ILE 0.000000 + 111 HD12 33.5210 23.6460 24.1740 H 6 ILE 0.000000 + 112 HD13 34.8900 23.7440 25.2930 H 6 ILE 0.000000 + 113 C 32.8780 25.3800 29.8250 C.2 6 ILE 0.000000 + 114 O 33.5170 26.4490 29.9560 O.2 6 ILE 0.000000 + 115 N 32.7560 24.5480 30.8230 N.am 7 LEU 0.000000 + 116 H 32.3370 23.6490 30.6320 H 7 LEU 0.000000 + 117 CA 33.4180 24.6780 32.1280 C.3 7 LEU 0.000000 + 118 HA 33.7720 25.7020 32.2430 H 7 LEU 0.000000 + 119 CB 32.4520 24.2870 33.2690 C.3 7 LEU 0.000000 + 120 HB2 32.2350 23.2190 33.2800 H 7 LEU 0.000000 + 121 HB3 33.0250 24.4910 34.1730 H 7 LEU 0.000000 + 122 CG 31.0680 25.0800 33.2940 C.3 7 LEU 0.000000 + 123 HG 31.2340 26.0000 32.7310 H 7 LEU 0.000000 + 124 CD1 29.9570 24.1850 32.7370 C.3 7 LEU 0.000000 + 125 HD11 29.0910 24.7910 32.4720 H 7 LEU 0.000000 + 126 HD12 29.6750 23.4580 33.4970 H 7 LEU 0.000000 + 127 HD13 30.2420 23.5980 31.8630 H 7 LEU 0.000000 + 128 CD2 30.6790 25.5000 34.6660 C.3 7 LEU 0.000000 + 129 HD21 30.6920 24.6790 35.3840 H 7 LEU 0.000000 + 130 HD22 29.6780 25.9260 34.6040 H 7 LEU 0.000000 + 131 HD23 31.2660 26.3490 35.0140 H 7 LEU 0.000000 + 132 C 34.7040 23.8320 31.9820 C.2 7 LEU 0.000000 + 133 O 34.6080 22.7120 31.4340 O.2 7 LEU 0.000000 + 134 N 35.7410 24.3550 32.5660 N.am 8 ASN 0.000000 + 135 H 35.6570 25.2890 32.9430 H 8 ASN 0.000000 + 136 CA 37.0870 23.9380 32.3400 C.3 8 ASN 0.000000 + 137 HA 37.1950 22.8750 32.1280 H 8 ASN 0.000000 + 138 CB 37.6830 24.6480 31.0790 C.3 8 ASN 0.000000 + 139 HB2 37.0520 24.5140 30.1990 H 8 ASN 0.000000 + 140 HB3 37.6970 25.7010 31.3580 H 8 ASN 0.000000 + 141 CG 39.0690 24.1720 30.7530 C.2 8 ASN 0.000000 + 142 OD1 39.2930 22.9720 30.6160 O.2 8 ASN 0.000000 + 143 ND2 40.1710 24.9660 30.8340 N.am 8 ASN 0.000000 + 144 HD21 40.0640 25.9680 30.8800 H 8 ASN 0.000000 + 145 HD22 41.0730 24.5640 30.6180 H 8 ASN 0.000000 + 146 C 37.9290 24.2620 33.6020 C.2 8 ASN 0.000000 + 147 O 37.7360 25.2990 34.2340 O.2 8 ASN 0.000000 + 148 N 38.8930 23.4110 33.9370 N.am 9 GLY 0.000000 + 149 H 38.8720 22.5590 33.3940 H 9 GLY 0.000000 + 150 CA 39.9370 23.6670 34.9460 C.3 9 GLY 0.000000 + 151 HA2 40.5630 24.4960 34.6190 H 9 GLY 0.000000 + 152 HA3 39.5250 24.0580 35.8760 H 9 GLY 0.000000 + 153 C 40.8200 22.5040 35.2100 C.2 9 GLY 0.000000 + 154 O 40.8260 21.5060 34.4460 O.2 9 GLY 0.000000 + 155 N 41.4770 22.4730 36.3560 N.am 10 LYS 0.000000 + 156 H 41.4390 23.2560 36.9920 H 10 LYS 0.000000 + 157 CA 42.3210 21.3630 36.7660 C.3 10 LYS 0.000000 + 158 HA 42.8380 21.0360 35.8640 H 10 LYS 0.000000 + 159 CB 43.4350 21.8390 37.7360 C.3 10 LYS 0.000000 + 160 HB2 42.9600 22.1300 38.6730 H 10 LYS 0.000000 + 161 HB3 44.1510 21.0180 37.7870 H 10 LYS 0.000000 + 162 CG 44.1460 23.1210 37.2280 C.3 10 LYS 0.000000 + 163 HG2 44.5810 22.9590 36.2420 H 10 LYS 0.000000 + 164 HG3 43.4240 23.9340 37.1510 H 10 LYS 0.000000 + 165 CD 45.2060 23.4740 38.2690 C.3 10 LYS 0.000000 + 166 HD2 44.8340 23.3760 39.2900 H 10 LYS 0.000000 + 167 HD3 46.0450 22.7810 38.2650 H 10 LYS 0.000000 + 168 CE 45.8330 24.8660 37.9360 C.3 10 LYS 0.000000 + 169 HE2 46.8980 24.8670 38.1720 H 10 LYS 0.000000 + 170 HE3 45.6150 25.1390 36.9040 H 10 LYS 0.000000 + 171 NZ 45.3140 25.8850 38.9150 N.4 10 LYS 0.000000 + 172 HZ1 44.3180 26.0490 38.8850 H 10 LYS 0.000000 + 173 HZ2 45.8050 26.7560 38.7650 H 10 LYS 0.000000 + 174 HZ3 45.4340 25.6940 39.8990 H 10 LYS 0.000000 + 175 C 41.6080 20.1420 37.3690 C.2 10 LYS 0.000000 + 176 O 42.1360 19.0170 37.4320 O.2 10 LYS 0.000000 + 177 N 40.3160 20.4070 37.7090 N.am 11 THR 0.000000 + 178 H 40.0180 21.3730 37.7390 H 11 THR 0.000000 + 179 CA 39.3330 19.4280 38.1900 C.3 11 THR 0.000000 + 180 HA 39.6270 18.4390 37.8410 H 11 THR 0.000000 + 181 CB 39.3190 19.4970 39.7400 C.3 11 THR 0.000000 + 182 HB 38.5380 18.8090 40.0630 H 11 THR 0.000000 + 183 CG2 40.6560 18.9940 40.1970 C.3 11 THR 0.000000 + 184 HG21 40.9540 17.9910 39.8960 H 11 THR 0.000000 + 185 HG22 40.6950 18.9840 41.2860 H 11 THR 0.000000 + 186 HG23 41.4530 19.6620 39.8690 H 11 THR 0.000000 + 187 OG1 39.1180 20.7380 40.2290 O.3 11 THR 0.000000 + 188 HG1 39.3210 20.7280 41.1680 H 11 THR 0.000000 + 189 C 37.9370 19.7040 37.7500 C.2 11 THR 0.000000 + 190 O 37.1800 18.7440 37.5920 O.2 11 THR 0.000000 + 191 N 37.5720 20.9090 37.3600 N.am 12 LEU 0.000000 + 192 H 38.1000 21.7450 37.5690 H 12 LEU 0.000000 + 193 CA 36.2620 21.2940 36.7600 C.3 12 LEU 0.000000 + 194 HA 35.4270 20.8870 37.3290 H 12 LEU 0.000000 + 195 CB 36.1690 22.8730 36.7850 C.3 12 LEU 0.000000 + 196 HB2 36.5310 23.2380 37.7460 H 12 LEU 0.000000 + 197 HB3 36.8590 23.2680 36.0410 H 12 LEU 0.000000 + 198 CG 34.8240 23.4830 36.3570 C.3 12 LEU 0.000000 + 199 HG 34.4790 23.0280 35.4280 H 12 LEU 0.000000 + 200 CD1 33.8670 23.3210 37.4770 C.3 12 LEU 0.000000 + 201 HD11 32.9970 23.8770 37.1260 H 12 LEU 0.000000 + 202 HD12 34.3040 23.6910 38.4040 H 12 LEU 0.000000 + 203 HD13 33.5940 22.2650 37.5030 H 12 LEU 0.000000 + 204 CD2 34.9260 25.0520 36.1810 C.3 12 LEU 0.000000 + 205 HD21 35.3340 25.5600 37.0540 H 12 LEU 0.000000 + 206 HD22 33.9260 25.4420 35.9970 H 12 LEU 0.000000 + 207 HD23 35.5550 25.3550 35.3440 H 12 LEU 0.000000 + 208 C 36.0920 20.8050 35.2830 C.2 12 LEU 0.000000 + 209 O 36.9410 21.1020 34.4410 O.2 12 LEU 0.000000 + 210 N 35.0160 20.0800 34.9060 N.am 13 LYS 0.000000 + 211 H 34.3910 19.6970 35.6020 H 13 LYS 0.000000 + 212 CA 34.6420 19.7040 33.5710 C.3 13 LYS 0.000000 + 213 HA 35.0630 20.4210 32.8660 H 13 LYS 0.000000 + 214 CB 35.0340 18.2260 33.2440 C.3 13 LYS 0.000000 + 215 HB2 34.4970 17.5790 33.9380 H 13 LYS 0.000000 + 216 HB3 34.8490 17.9220 32.2140 H 13 LYS 0.000000 + 217 CG 36.5150 17.9230 33.4720 C.3 13 LYS 0.000000 + 218 HG2 37.1620 18.6580 32.9940 H 13 LYS 0.000000 + 219 HG3 36.7010 17.7680 34.5350 H 13 LYS 0.000000 + 220 CD 36.8040 16.4870 32.9940 C.3 13 LYS 0.000000 + 221 HD2 36.1570 15.7470 33.4650 H 13 LYS 0.000000 + 222 HD3 36.4560 16.5060 31.9620 H 13 LYS 0.000000 + 223 CE 38.2640 16.1630 32.9970 C.3 13 LYS 0.000000 + 224 HE2 38.7410 16.7320 32.1990 H 13 LYS 0.000000 + 225 HE3 38.6860 16.4240 33.9670 H 13 LYS 0.000000 + 226 NZ 38.3970 14.6720 32.8370 N.4 13 LYS 0.000000 + 227 HZ1 37.9440 14.3240 32.0050 H 13 LYS 0.000000 + 228 HZ2 37.8880 14.2390 33.5950 H 13 LYS 0.000000 + 229 HZ3 39.3670 14.3910 32.8170 H 13 LYS 0.000000 + 230 C 33.1190 19.8750 33.4000 C.2 13 LYS 0.000000 + 231 O 32.5220 20.2180 34.4480 O.2 13 LYS 0.000000 + 232 N 32.5410 19.9290 32.1820 N.am 14 GLY 0.000000 + 233 H 33.0850 19.6110 31.3920 H 14 GLY 0.000000 + 234 CA 31.1410 20.1350 31.9510 C.3 14 GLY 0.000000 + 235 HA2 30.6960 19.1430 31.8770 H 14 GLY 0.000000 + 236 HA3 30.7070 20.5000 32.8830 H 14 GLY 0.000000 + 237 C 30.7260 21.0300 30.8030 C.2 14 GLY 0.000000 + 238 O 31.4590 21.9860 30.4780 O.2 14 GLY 0.000000 + 239 N 29.6020 20.6610 30.1750 N.am 15 GLU 0.000000 + 240 H 29.2330 19.8010 30.5570 H 15 GLU 0.000000 + 241 CA 29.0530 21.5950 29.1150 C.3 15 GLU 0.000000 + 242 HA 29.4570 22.5920 29.2920 H 15 GLU 0.000000 + 243 CB 29.4520 21.1510 27.7050 C.3 15 GLU 0.000000 + 244 HB2 28.8860 21.7700 27.0090 H 15 GLU 0.000000 + 245 HB3 30.4970 21.3960 27.5120 H 15 GLU 0.000000 + 246 CG 29.1570 19.6680 27.4100 C.3 15 GLU 0.000000 + 247 HG2 29.8650 19.1040 28.0170 H 15 GLU 0.000000 + 248 HG3 28.1090 19.4560 27.6190 H 15 GLU 0.000000 + 249 CD 29.4230 19.3850 25.9680 C.2 15 GLU 0.000000 + 250 OE1 28.4580 19.2500 25.1770 O.co2 15 GLU 0.000000 + 251 OE2 30.5960 19.2970 25.5210 O.co2 15 GLU 0.000000 + 252 C 27.5630 21.8430 29.3530 C.2 15 GLU 0.000000 + 253 O 26.8140 21.0200 29.7960 O.2 15 GLU 0.000000 + 254 N 27.0800 22.9660 28.8630 N.am 16 THR 0.000000 + 255 H 27.7180 23.6470 28.4770 H 16 THR 0.000000 + 256 CA 25.6180 23.3420 28.9870 C.3 16 THR 0.000000 + 257 HA 24.9870 22.4660 28.8320 H 16 THR 0.000000 + 258 CB 25.3000 23.7550 30.4630 C.3 16 THR 0.000000 + 259 HB 25.6640 23.0280 31.1900 H 16 THR 0.000000 + 260 CG2 26.0790 25.0290 30.8510 C.3 16 THR 0.000000 + 261 HG21 26.0020 25.2120 31.9230 H 16 THR 0.000000 + 262 HG22 25.8270 25.9990 30.4200 H 16 THR 0.000000 + 263 HG23 27.1390 24.8330 30.6860 H 16 THR 0.000000 + 264 OG1 23.9190 23.8700 30.5910 O.3 16 THR 0.000000 + 265 HG1 23.6050 22.9660 30.6540 H 16 THR 0.000000 + 266 C 25.1360 24.3870 27.9560 C.2 16 THR 0.000000 + 267 O 25.8470 25.3920 27.6860 O.2 16 THR 0.000000 + 268 N 23.9440 24.1260 27.3740 N.am 17 THR 0.000000 + 269 H 23.4140 23.3000 27.6150 H 17 THR 0.000000 + 270 CA 23.3410 25.0880 26.4180 C.3 17 THR 0.000000 + 271 HA 24.1390 25.6970 25.9920 H 17 THR 0.000000 + 272 CB 22.6340 24.3990 25.2500 C.3 17 THR 0.000000 + 273 HB 22.1940 25.1420 24.5850 H 17 THR 0.000000 + 274 CG2 23.5340 23.4660 24.4060 C.3 17 THR 0.000000 + 275 HG21 22.9810 22.8750 23.6770 H 17 THR 0.000000 + 276 HG22 24.0160 22.7890 25.1120 H 17 THR 0.000000 + 277 HG23 24.3050 24.1190 23.9980 H 17 THR 0.000000 + 278 OG1 21.6180 23.5160 25.7400 O.3 17 THR 0.000000 + 279 HG1 21.1580 23.2100 24.9550 H 17 THR 0.000000 + 280 C 22.4090 26.0840 27.0800 C.2 17 THR 0.000000 + 281 O 21.8650 25.8800 28.1710 O.2 17 THR 0.000000 + 282 N 22.2840 27.1860 26.3670 N.am 18 THR 0.000000 + 283 H 22.9180 27.2110 25.5810 H 18 THR 0.000000 + 284 CA 21.3410 28.3460 26.6650 C.3 18 THR 0.000000 + 285 HA 20.4470 28.0470 27.2130 H 18 THR 0.000000 + 286 CB 21.9680 29.4240 27.6060 C.3 18 THR 0.000000 + 287 HB 22.9260 29.8000 27.2510 H 18 THR 0.000000 + 288 CG2 20.9590 30.5650 27.7470 C.3 18 THR 0.000000 + 289 HG21 21.1770 31.2320 28.5810 H 18 THR 0.000000 + 290 HG22 19.9320 30.2140 27.8380 H 18 THR 0.000000 + 291 HG23 21.0570 31.1490 26.8310 H 18 THR 0.000000 + 292 OG1 21.9830 28.9740 29.0510 O.3 18 THR 0.000000 + 293 HG1 22.8660 29.1230 29.4000 H 18 THR 0.000000 + 294 C 20.8290 28.9560 25.3540 C.2 18 THR 0.000000 + 295 O 21.5530 29.4580 24.5280 O.2 18 THR 0.000000 + 296 N 19.5420 28.8720 25.0830 N.am 19 GLU 0.000000 + 297 H 18.9190 28.5790 25.8230 H 19 GLU 0.000000 + 298 CA 18.9320 29.5760 23.9870 C.3 19 GLU 0.000000 + 299 HA 19.6790 29.5080 23.1970 H 19 GLU 0.000000 + 300 CB 17.6860 28.7850 23.6270 C.3 19 GLU 0.000000 + 301 HB2 17.8990 27.7220 23.5140 H 19 GLU 0.000000 + 302 HB3 16.9980 28.8420 24.4710 H 19 GLU 0.000000 + 303 CG 16.8520 29.2840 22.4770 C.3 19 GLU 0.000000 + 304 HG2 16.2460 28.4470 22.1280 H 19 GLU 0.000000 + 305 HG3 16.1330 30.0570 22.7480 H 19 GLU 0.000000 + 306 CD 17.7360 29.7310 21.2810 C.2 19 GLU 0.000000 + 307 OE1 18.3630 28.8000 20.6790 O.co2 19 GLU 0.000000 + 308 OE2 17.8250 30.9440 20.9200 O.co2 19 GLU 0.000000 + 309 C 18.6310 31.0490 24.3110 C.2 19 GLU 0.000000 + 310 O 17.9510 31.3360 25.2400 O.2 19 GLU 0.000000 + 311 N 19.1090 32.0520 23.6090 N.am 20 ALA 0.000000 + 312 H 19.6590 31.7660 22.8100 H 20 ALA 0.000000 + 313 CA 18.9620 33.5050 23.8850 C.3 20 ALA 0.000000 + 314 HA 17.9800 33.7420 24.2950 H 20 ALA 0.000000 + 315 CB 19.9780 33.9790 24.9610 C.3 20 ALA 0.000000 + 316 HB1 19.8070 35.0260 25.2140 H 20 ALA 0.000000 + 317 HB2 20.9830 33.9230 24.5440 H 20 ALA 0.000000 + 318 HB3 19.8000 33.4040 25.8690 H 20 ALA 0.000000 + 319 C 19.1210 34.3520 22.5950 C.2 20 ALA 0.000000 + 320 O 19.5650 33.8670 21.5410 O.2 20 ALA 0.000000 + 321 N 18.8190 35.6980 22.6660 N.am 21 VAL 0.000000 + 322 H 18.4660 36.0070 23.5610 H 21 VAL 0.000000 + 323 CA 18.7270 36.6070 21.5050 C.3 21 VAL 0.000000 + 324 HA 18.5540 36.0390 20.5920 H 21 VAL 0.000000 + 325 CB 17.4370 37.4640 21.7800 C.3 21 VAL 0.000000 + 326 HB 17.4770 38.1300 22.6420 H 21 VAL 0.000000 + 327 CG1 17.0720 38.3790 20.6730 C.3 21 VAL 0.000000 + 328 HG11 16.9910 37.8050 19.7500 H 21 VAL 0.000000 + 329 HG12 17.6850 39.2690 20.5330 H 21 VAL 0.000000 + 330 HG13 16.0810 38.7870 20.8740 H 21 VAL 0.000000 + 331 CG2 16.2510 36.5360 21.9200 C.3 21 VAL 0.000000 + 332 HG21 15.3330 37.0330 21.6050 H 21 VAL 0.000000 + 333 HG22 16.1280 36.2190 22.9560 H 21 VAL 0.000000 + 334 HG23 16.4770 35.6810 21.2840 H 21 VAL 0.000000 + 335 C 19.9760 37.5210 21.4050 C.2 21 VAL 0.000000 + 336 O 20.2950 38.0220 20.3060 O.2 21 VAL 0.000000 + 337 N 20.7280 37.6510 22.4570 N.am 22 ASP 0.000000 + 338 H 20.4600 37.1040 23.2620 H 22 ASP 0.000000 + 339 CA 21.9200 38.5170 22.5610 C.3 22 ASP 0.000000 + 340 HA 22.2180 38.7210 21.5320 H 22 ASP 0.000000 + 341 CB 21.4830 39.7010 23.3500 C.3 22 ASP 0.000000 + 342 HB2 20.6320 40.1560 22.8430 H 22 ASP 0.000000 + 343 HB3 21.1330 39.4210 24.3440 H 22 ASP 0.000000 + 344 CG 22.5760 40.7460 23.5900 C.2 22 ASP 0.000000 + 345 OD1 23.6810 40.5880 23.0430 O.co2 22 ASP 0.000000 + 346 OD2 22.3400 41.7510 24.2640 O.co2 22 ASP 0.000000 + 347 C 23.0190 37.7030 23.2940 C.2 22 ASP 0.000000 + 348 O 22.8390 37.1840 24.4120 O.2 22 ASP 0.000000 + 349 N 24.2100 37.6490 22.6940 N.am 23 ALA 0.000000 + 350 H 24.3580 38.0650 21.7860 H 23 ALA 0.000000 + 351 CA 25.4930 37.1720 23.2150 C.3 23 ALA 0.000000 + 352 HA 25.3710 36.0890 23.2210 H 23 ALA 0.000000 + 353 CB 26.7010 37.4860 22.3260 C.3 23 ALA 0.000000 + 354 HB1 26.4460 37.3090 21.2800 H 23 ALA 0.000000 + 355 HB2 27.3790 36.7080 22.6760 H 23 ALA 0.000000 + 356 HB3 27.0910 38.4940 22.4680 H 23 ALA 0.000000 + 357 C 25.7480 37.7570 24.6420 C.2 23 ALA 0.000000 + 358 O 26.0910 36.9530 25.5180 O.2 23 ALA 0.000000 + 359 N 25.5640 39.0500 24.8460 N.am 24 ALA 0.000000 + 360 H 25.2140 39.6740 24.1330 H 24 ALA 0.000000 + 361 CA 25.7450 39.6870 26.1530 C.3 24 ALA 0.000000 + 362 HA 26.7610 39.4190 26.4450 H 24 ALA 0.000000 + 363 CB 25.4900 41.1890 25.9380 C.3 24 ALA 0.000000 + 364 HB1 26.2470 41.6760 25.3250 H 24 ALA 0.000000 + 365 HB2 25.6330 41.7290 26.8740 H 24 ALA 0.000000 + 366 HB3 24.5610 41.4670 25.4400 H 24 ALA 0.000000 + 367 C 24.7960 39.1010 27.1370 C.2 24 ALA 0.000000 + 368 O 25.1160 38.9750 28.3290 O.2 24 ALA 0.000000 + 369 N 23.5770 38.6590 26.7360 N.am 25 THR 0.000000 + 370 H 23.3980 38.6810 25.7430 H 25 THR 0.000000 + 371 CA 22.5870 38.0940 27.6800 C.3 25 THR 0.000000 + 372 HA 22.7550 38.4950 28.6810 H 25 THR 0.000000 + 373 CB 21.1960 38.5490 27.2620 C.3 25 THR 0.000000 + 374 HB 20.7970 37.8830 26.4970 H 25 THR 0.000000 + 375 CG2 20.2460 38.3690 28.4380 C.3 25 THR 0.000000 + 376 HG21 20.2030 37.3290 28.7630 H 25 THR 0.000000 + 377 HG22 19.2550 38.7400 28.1760 H 25 THR 0.000000 + 378 HG23 20.5740 38.9770 29.2800 H 25 THR 0.000000 + 379 OG1 21.1990 39.9310 27.0300 O.3 25 THR 0.000000 + 380 HG1 20.2930 40.1560 26.8070 H 25 THR 0.000000 + 381 C 22.7880 36.6180 27.9280 C.2 25 THR 0.000000 + 382 O 22.6180 36.1640 29.0500 O.2 25 THR 0.000000 + 383 N 23.2160 35.8540 26.9290 N.am 26 ALA 0.000000 + 384 H 23.3150 36.2080 25.9880 H 26 ALA 0.000000 + 385 CA 23.6520 34.5130 27.1590 C.3 26 ALA 0.000000 + 386 HA 22.7810 33.9400 27.4760 H 26 ALA 0.000000 + 387 CB 24.0620 33.9130 25.7340 C.3 26 ALA 0.000000 + 388 HB1 23.1200 33.7320 25.2150 H 26 ALA 0.000000 + 389 HB2 24.6950 33.0290 25.8040 H 26 ALA 0.000000 + 390 HB3 24.7150 34.6130 25.2110 H 26 ALA 0.000000 + 391 C 24.8560 34.5230 28.0620 C.2 26 ALA 0.000000 + 392 O 24.8890 33.7450 28.9850 O.2 26 ALA 0.000000 + 393 N 25.7490 35.5000 28.0270 N.am 27 GLU 0.000000 + 394 H 25.9400 35.9330 27.1350 H 27 GLU 0.000000 + 395 CA 26.7120 35.6710 29.0370 C.3 27 GLU 0.000000 + 396 HA 27.3060 34.7570 29.0970 H 27 GLU 0.000000 + 397 CB 27.6840 36.8330 28.6050 C.3 27 GLU 0.000000 + 398 HB2 28.2700 36.5610 27.7280 H 27 GLU 0.000000 + 399 HB3 27.1780 37.7730 28.3870 H 27 GLU 0.000000 + 400 CG 28.7420 37.1650 29.6640 C.3 27 GLU 0.000000 + 401 HG2 28.1930 37.5370 30.5290 H 27 GLU 0.000000 + 402 HG3 29.2670 36.2440 29.9140 H 27 GLU 0.000000 + 403 CD 29.8870 38.2420 29.2690 C.2 27 GLU 0.000000 + 404 OE1 31.1080 37.8270 29.1640 O.co2 27 GLU 0.000000 + 405 OE2 29.5290 39.4200 29.1100 O.co2 27 GLU 0.000000 + 406 C 26.0990 35.7420 30.4500 C.2 27 GLU 0.000000 + 407 O 26.5530 35.1620 31.4140 O.2 27 GLU 0.000000 + 408 N 25.1240 36.6090 30.6040 N.am 28 LYS 0.000000 + 409 H 24.7100 37.1060 29.8270 H 28 LYS 0.000000 + 410 CA 24.5380 36.9470 31.9500 C.3 28 LYS 0.000000 + 411 HA 25.3240 37.3000 32.6180 H 28 LYS 0.000000 + 412 CB 23.5590 38.0520 31.7280 C.3 28 LYS 0.000000 + 413 HB2 24.0960 38.9430 31.4030 H 28 LYS 0.000000 + 414 HB3 22.7610 37.8110 31.0250 H 28 LYS 0.000000 + 415 CG 22.8850 38.4010 33.1500 C.3 28 LYS 0.000000 + 416 HG2 22.3430 37.5420 33.5450 H 28 LYS 0.000000 + 417 HG3 23.6380 38.6980 33.8790 H 28 LYS 0.000000 + 418 CD 21.8260 39.5790 33.0630 C.3 28 LYS 0.000000 + 419 HD2 20.9300 39.1460 32.6160 H 28 LYS 0.000000 + 420 HD3 21.6560 39.9890 34.0580 H 28 LYS 0.000000 + 421 CE 22.3590 40.8500 32.2670 C.3 28 LYS 0.000000 + 422 HE2 23.4320 40.8990 32.4490 H 28 LYS 0.000000 + 423 HE3 22.1990 40.7560 31.1930 H 28 LYS 0.000000 + 424 NZ 21.5210 42.0130 32.7150 N.4 28 LYS 0.000000 + 425 HZ1 21.6960 42.2940 33.6700 H 28 LYS 0.000000 + 426 HZ2 20.5410 41.7770 32.6530 H 28 LYS 0.000000 + 427 HZ3 21.6510 42.8270 32.1310 H 28 LYS 0.000000 + 428 C 23.8660 35.7780 32.5350 C.2 28 LYS 0.000000 + 429 O 23.9940 35.6650 33.7420 O.2 28 LYS 0.000000 + 430 N 23.3290 34.8850 31.7120 N.am 29 VAL 0.000000 + 431 H 23.2290 35.1110 30.7330 H 29 VAL 0.000000 + 432 CA 22.7360 33.6500 32.0970 C.3 29 VAL 0.000000 + 433 HA 21.9990 33.8790 32.8660 H 29 VAL 0.000000 + 434 CB 21.7350 33.1660 30.9620 C.3 29 VAL 0.000000 + 435 HB 22.3750 32.9510 30.1060 H 29 VAL 0.000000 + 436 CG1 21.1390 31.7830 31.4450 C.3 29 VAL 0.000000 + 437 HG11 20.5920 31.4130 30.5790 H 29 VAL 0.000000 + 438 HG12 20.5750 31.9080 32.3700 H 29 VAL 0.000000 + 439 HG13 21.9930 31.1130 31.5340 H 29 VAL 0.000000 + 440 CG2 20.4820 33.9920 30.5470 C.3 29 VAL 0.000000 + 441 HG21 19.9660 33.6180 29.6620 H 29 VAL 0.000000 + 442 HG22 20.7390 35.0190 30.2860 H 29 VAL 0.000000 + 443 HG23 19.8380 34.1100 31.4190 H 29 VAL 0.000000 + 444 C 23.7810 32.6420 32.4840 C.2 29 VAL 0.000000 + 445 O 23.6040 31.8760 33.4620 O.2 29 VAL 0.000000 + 446 N 24.9620 32.6410 31.7580 N.am 30 PHE 0.000000 + 447 H 24.9970 33.2870 30.9810 H 30 PHE 0.000000 + 448 CA 26.1120 31.7010 32.0330 C.3 30 PHE 0.000000 + 449 HA 25.6920 30.7530 32.3710 H 30 PHE 0.000000 + 450 CB 26.9010 31.5820 30.7130 C.3 30 PHE 0.000000 + 451 HB2 26.9660 32.5370 30.1910 H 30 PHE 0.000000 + 452 HB3 27.9280 31.2660 30.8880 H 30 PHE 0.000000 + 453 CG 26.3480 30.6000 29.6560 C.ar 30 PHE 0.000000 + 454 CD1 25.7510 29.2960 29.8780 C.ar 30 PHE 0.000000 + 455 HD1 25.7050 28.9430 30.8970 H 30 PHE 0.000000 + 456 CE1 25.3450 28.3770 28.8170 C.ar 30 PHE 0.000000 + 457 HE1 24.8100 27.4640 29.0390 H 30 PHE 0.000000 + 458 CZ 25.5340 28.8400 27.5150 C.ar 30 PHE 0.000000 + 459 HZ 25.1960 28.2670 26.6660 H 30 PHE 0.000000 + 460 CE2 26.0960 30.0990 27.2710 C.ar 30 PHE 0.000000 + 461 HE2 26.2120 30.3190 26.2190 H 30 PHE 0.000000 + 462 CD2 26.5330 30.9240 28.2970 C.ar 30 PHE 0.000000 + 463 HD2 27.1350 31.7780 28.0290 H 30 PHE 0.000000 + 464 C 26.9880 32.1890 33.2460 C.2 30 PHE 0.000000 + 465 O 27.6090 31.3440 33.9050 O.2 30 PHE 0.000000 + 466 N 27.0380 33.4460 33.5400 N.am 31 LYS 0.000000 + 467 H 26.7100 34.1050 32.8490 H 31 LYS 0.000000 + 468 CA 27.4050 34.0220 34.8540 C.3 31 LYS 0.000000 + 469 HA 28.4370 33.7640 35.0920 H 31 LYS 0.000000 + 470 CB 27.2740 35.5990 34.8580 C.3 31 LYS 0.000000 + 471 HB2 26.2420 35.7140 34.5270 H 31 LYS 0.000000 + 472 HB3 27.2920 36.0980 35.8270 H 31 LYS 0.000000 + 473 CG 28.3780 36.2750 33.9190 C.3 31 LYS 0.000000 + 474 HG2 28.5220 35.7100 32.9970 H 31 LYS 0.000000 + 475 HG3 27.9260 37.2290 33.6490 H 31 LYS 0.000000 + 476 CD 29.8230 36.4870 34.4390 C.3 31 LYS 0.000000 + 477 HD2 29.7550 36.9770 35.4110 H 31 LYS 0.000000 + 478 HD3 30.1320 35.4720 34.6840 H 31 LYS 0.000000 + 479 CE 30.7770 37.1500 33.3940 C.3 31 LYS 0.000000 + 480 HE2 30.6330 36.6300 32.4470 H 31 LYS 0.000000 + 481 HE3 30.4360 38.1580 33.1580 H 31 LYS 0.000000 + 482 NZ 32.1380 37.1210 33.9260 N.4 31 LYS 0.000000 + 483 HZ1 32.2720 37.4580 34.8690 H 31 LYS 0.000000 + 484 HZ2 32.6760 37.7770 33.3760 H 31 LYS 0.000000 + 485 HZ3 32.5550 36.2100 33.8050 H 31 LYS 0.000000 + 486 C 26.5160 33.5620 35.9830 C.2 31 LYS 0.000000 + 487 O 27.0180 32.9930 36.9430 O.2 31 LYS 0.000000 + 488 N 25.1850 33.7450 35.9530 N.am 32 GLN 0.000000 + 489 H 24.7370 34.1940 35.1660 H 32 GLN 0.000000 + 490 CA 24.3650 33.1970 37.0270 C.3 32 GLN 0.000000 + 491 HA 24.6790 33.8220 37.8630 H 32 GLN 0.000000 + 492 CB 22.8910 33.4270 36.6880 C.3 32 GLN 0.000000 + 493 HB2 22.8450 33.3660 35.6010 H 32 GLN 0.000000 + 494 HB3 22.2850 32.6850 37.2090 H 32 GLN 0.000000 + 495 CG 22.2800 34.8400 37.0280 C.3 32 GLN 0.000000 + 496 HG2 22.0390 34.8810 38.0900 H 32 GLN 0.000000 + 497 HG3 22.8990 35.7100 36.8070 H 32 GLN 0.000000 + 498 CD 20.9580 35.1240 36.1950 C.2 32 GLN 0.000000 + 499 OE1 19.8830 34.8230 36.7380 O.2 32 GLN 0.000000 + 500 NE2 20.9880 35.5300 34.9740 N.am 32 GLN 0.000000 + 501 HE21 21.9020 35.7870 34.6280 H 32 GLN 0.000000 + 502 HE22 20.1770 35.7140 34.4000 H 32 GLN 0.000000 + 503 C 24.5980 31.7070 37.2320 C.2 32 GLN 0.000000 + 504 O 24.7940 31.2930 38.3840 O.2 32 GLN 0.000000 + 505 N 24.5300 30.8750 36.1420 N.am 33 TYR 0.000000 + 506 H 24.5870 31.2740 35.2160 H 33 TYR 0.000000 + 507 CA 24.7220 29.4590 36.2170 C.3 33 TYR 0.000000 + 508 HA 23.8810 29.0420 36.7720 H 33 TYR 0.000000 + 509 CB 24.6220 28.8480 34.8420 C.3 33 TYR 0.000000 + 510 HB2 23.6210 29.0060 34.4420 H 33 TYR 0.000000 + 511 HB3 25.3530 29.3880 34.2400 H 33 TYR 0.000000 + 512 CG 24.8770 27.3040 34.7040 C.ar 33 TYR 0.000000 + 513 CD1 23.8080 26.3830 34.9380 C.ar 33 TYR 0.000000 + 514 HD1 22.8140 26.7540 35.1400 H 33 TYR 0.000000 + 515 CE1 24.0540 24.9910 35.0750 C.ar 33 TYR 0.000000 + 516 HE1 23.3000 24.2510 35.3000 H 33 TYR 0.000000 + 517 CZ 25.3990 24.5620 34.9340 C.ar 33 TYR 0.000000 + 518 OH 25.6580 23.2120 34.9830 O.3 33 TYR 0.000000 + 519 HH 26.6080 23.0800 35.0300 H 33 TYR 0.000000 + 520 CE2 26.4100 25.4590 34.7230 C.ar 33 TYR 0.000000 + 521 HE2 27.4430 25.1570 34.6300 H 33 TYR 0.000000 + 522 CD2 26.1460 26.8180 34.6020 C.ar 33 TYR 0.000000 + 523 HD2 26.9920 27.4690 34.4350 H 33 TYR 0.000000 + 524 C 26.0780 29.1550 36.8540 C.2 33 TYR 0.000000 + 525 O 26.1790 28.1860 37.5660 O.2 33 TYR 0.000000 + 526 N 27.1590 29.7880 36.5080 N.am 34 ALA 0.000000 + 527 H 26.9970 30.5630 35.8810 H 34 ALA 0.000000 + 528 CA 28.4730 29.5350 37.1000 C.3 34 ALA 0.000000 + 529 HA 28.7170 28.4760 37.0230 H 34 ALA 0.000000 + 530 CB 29.6510 30.2650 36.4020 C.3 34 ALA 0.000000 + 531 HB1 30.5770 29.8130 36.7570 H 34 ALA 0.000000 + 532 HB2 29.6190 31.2960 36.7520 H 34 ALA 0.000000 + 533 HB3 29.6810 30.1590 35.3170 H 34 ALA 0.000000 + 534 C 28.5080 29.8350 38.6140 C.2 34 ALA 0.000000 + 535 O 29.0970 29.0770 39.3890 O.2 34 ALA 0.000000 + 536 N 27.8140 30.8640 39.0240 N.am 35 ASN 0.000000 + 537 H 27.5940 31.5350 38.3010 H 35 ASN 0.000000 + 538 CA 27.7430 31.2520 40.4450 C.3 35 ASN 0.000000 + 539 HA 28.7130 31.1680 40.9350 H 35 ASN 0.000000 + 540 CB 27.2540 32.6840 40.5410 C.3 35 ASN 0.000000 + 541 HB2 27.7980 33.3610 39.8830 H 35 ASN 0.000000 + 542 HB3 26.1920 32.7270 40.3000 H 35 ASN 0.000000 + 543 CG 27.3260 33.1690 41.9470 C.2 35 ASN 0.000000 + 544 OD1 26.4930 32.7430 42.7630 O.2 35 ASN 0.000000 + 545 ND2 28.0990 34.1830 42.2230 N.am 35 ASN 0.000000 + 546 HD21 28.8670 34.3500 41.5890 H 35 ASN 0.000000 + 547 HD22 28.2760 34.3970 43.1930 H 35 ASN 0.000000 + 548 C 26.8330 30.2000 41.1270 C.2 35 ASN 0.000000 + 549 O 27.1140 29.6860 42.2380 O.2 35 ASN 0.000000 + 550 N 25.8190 29.6160 40.3950 N.am 36 ASP 0.000000 + 551 H 25.6080 30.1440 39.5600 H 36 ASP 0.000000 + 552 CA 25.0040 28.4010 40.8670 C.3 36 ASP 0.000000 + 553 HA 24.4910 28.8190 41.7330 H 36 ASP 0.000000 + 554 CB 23.8190 28.1750 39.9480 C.3 36 ASP 0.000000 + 555 HB2 23.3790 29.1170 39.6230 H 36 ASP 0.000000 + 556 HB3 24.2790 27.5860 39.1540 H 36 ASP 0.000000 + 557 CG 22.7200 27.3500 40.4700 C.2 36 ASP 0.000000 + 558 OD1 22.2140 26.4850 39.7140 O.co2 36 ASP 0.000000 + 559 OD2 22.3610 27.4550 41.6530 O.co2 36 ASP 0.000000 + 560 C 25.7930 27.1130 41.2440 C.2 36 ASP 0.000000 + 561 O 25.3570 26.3910 42.1120 O.2 36 ASP 0.000000 + 562 N 26.9910 27.0060 40.6660 N.am 37 ASN 0.000000 + 563 H 27.3060 27.7790 40.0980 H 37 ASN 0.000000 + 564 CA 27.8290 25.8140 40.6360 C.3 37 ASN 0.000000 + 565 HA 27.3780 25.1300 41.3540 H 37 ASN 0.000000 + 566 CB 27.8730 25.2810 39.1950 C.3 37 ASN 0.000000 + 567 HB2 27.9360 26.1060 38.4870 H 37 ASN 0.000000 + 568 HB3 28.7020 24.5790 39.1010 H 37 ASN 0.000000 + 569 CG 26.6520 24.4920 38.8420 C.2 37 ASN 0.000000 + 570 OD1 26.4320 23.3570 39.2820 O.2 37 ASN 0.000000 + 571 ND2 25.7060 25.0570 38.1770 N.am 37 ASN 0.000000 + 572 HD21 25.8040 26.0500 38.0160 H 37 ASN 0.000000 + 573 HD22 24.8950 24.5020 37.9470 H 37 ASN 0.000000 + 574 C 29.1960 26.0530 41.2610 C.2 37 ASN 0.000000 + 575 O 30.0640 25.1710 41.1820 O.2 37 ASN 0.000000 + 576 N 29.3580 27.1760 42.0120 N.am 38 GLY 0.000000 + 577 H 28.5560 27.7650 42.1890 H 38 GLY 0.000000 + 578 CA 30.6370 27.4600 42.6810 C.3 38 GLY 0.000000 + 579 HA2 30.4440 28.2960 43.3540 H 38 GLY 0.000000 + 580 HA3 30.9000 26.6550 43.3680 H 38 GLY 0.000000 + 581 C 31.8940 27.7740 41.7850 C.2 38 GLY 0.000000 + 582 O 33.0270 27.4290 42.1240 O.2 38 GLY 0.000000 + 583 N 31.7310 28.2870 40.5790 N.am 39 VAL 0.000000 + 584 H 30.7940 28.6240 40.4080 H 39 VAL 0.000000 + 585 CA 32.6640 28.4490 39.4030 C.3 39 VAL 0.000000 + 586 HA 33.5980 27.9110 39.5700 H 39 VAL 0.000000 + 587 CB 32.0150 27.7780 38.1790 C.3 39 VAL 0.000000 + 588 HB 31.0050 28.1580 38.0270 H 39 VAL 0.000000 + 589 CG1 32.9890 28.1210 37.0140 C.3 39 VAL 0.000000 + 590 HG11 32.6360 27.5190 36.1760 H 39 VAL 0.000000 + 591 HG12 34.0190 27.9630 37.3340 H 39 VAL 0.000000 + 592 HG13 32.8690 29.1170 36.5880 H 39 VAL 0.000000 + 593 CG2 31.9430 26.2740 38.4370 C.3 39 VAL 0.000000 + 594 HG21 31.5400 25.7290 37.5830 H 39 VAL 0.000000 + 595 HG22 31.3560 26.0860 39.3370 H 39 VAL 0.000000 + 596 HG23 32.9070 25.8630 38.7380 H 39 VAL 0.000000 + 597 C 33.0290 29.9090 39.2350 C.2 39 VAL 0.000000 + 598 O 32.1860 30.6830 38.7570 O.2 39 VAL 0.000000 + 599 N 34.2680 30.2810 39.5580 N.am 40 ASP 0.000000 + 600 H 34.8380 29.5430 39.9470 H 40 ASP 0.000000 + 601 CA 34.8750 31.5510 39.0960 C.3 40 ASP 0.000000 + 602 HA 34.1430 32.0780 38.4870 H 40 ASP 0.000000 + 603 CB 35.1830 32.4180 40.3450 C.3 40 ASP 0.000000 + 604 HB2 34.1840 32.6570 40.7100 H 40 ASP 0.000000 + 605 HB3 35.7070 31.7880 41.0650 H 40 ASP 0.000000 + 606 CG 35.8790 33.6830 40.0090 C.2 40 ASP 0.000000 + 607 OD1 35.3930 34.4100 39.0760 O.co2 40 ASP 0.000000 + 608 OD2 37.0250 33.8970 40.4600 O.co2 40 ASP 0.000000 + 609 C 36.0620 31.1690 38.2380 C.2 40 ASP 0.000000 + 610 O 36.8500 30.2750 38.6300 O.2 40 ASP 0.000000 + 611 N 36.1720 31.7510 37.1020 N.am 41 GLY 0.000000 + 612 H 35.4430 32.4080 36.8580 H 41 GLY 0.000000 + 613 CA 37.2140 31.4840 36.1890 C.3 41 GLY 0.000000 + 614 HA2 38.0720 31.0140 36.6700 H 41 GLY 0.000000 + 615 HA3 36.7610 30.6720 35.6200 H 41 GLY 0.000000 + 616 C 37.6230 32.7090 35.3790 C.2 41 GLY 0.000000 + 617 O 37.2880 33.8620 35.6860 O.2 41 GLY 0.000000 + 618 N 38.3540 32.4220 34.3160 N.am 42 GLU 0.000000 + 619 H 38.7890 31.5120 34.3680 H 42 GLU 0.000000 + 620 CA 38.6030 33.3100 33.2280 C.3 42 GLU 0.000000 + 621 HA 38.3290 34.3180 33.5410 H 42 GLU 0.000000 + 622 CB 40.1580 33.2940 33.0400 C.3 42 GLU 0.000000 + 623 HB2 40.6560 33.3980 34.0040 H 42 GLU 0.000000 + 624 HB3 40.4170 32.3260 32.6110 H 42 GLU 0.000000 + 625 CG 40.6730 34.3280 32.0460 C.3 42 GLU 0.000000 + 626 HG2 41.6060 34.0150 31.5800 H 42 GLU 0.000000 + 627 HG3 39.9700 34.5010 31.2310 H 42 GLU 0.000000 + 628 CD 41.0140 35.6130 32.8040 C.2 42 GLU 0.000000 + 629 OE1 41.9440 35.6930 33.6440 O.co2 42 GLU 0.000000 + 630 OE2 40.2180 36.6020 32.6560 O.co2 42 GLU 0.000000 + 631 C 37.7800 33.0330 32.0330 C.2 42 GLU 0.000000 + 632 O 37.5770 31.8700 31.6900 O.2 42 GLU 0.000000 + 633 N 37.2280 34.0690 31.4120 N.am 43 TRP 0.000000 + 634 H 37.4230 35.0350 31.6340 H 43 TRP 0.000000 + 635 CA 36.2330 33.9510 30.3540 C.3 43 TRP 0.000000 + 636 HA 35.8500 32.9310 30.3480 H 43 TRP 0.000000 + 637 CB 34.9840 34.8890 30.6160 C.3 43 TRP 0.000000 + 638 HB2 35.4360 35.8680 30.7710 H 43 TRP 0.000000 + 639 HB3 34.4270 34.9180 29.6790 H 43 TRP 0.000000 + 640 CG 34.1150 34.5360 31.8380 C.2 43 TRP 0.000000 + 641 CD1 34.4280 34.7080 33.1540 C.2 43 TRP 0.000000 + 642 HD1 35.3870 35.0520 33.5110 H 43 TRP 0.000000 + 643 NE1 33.3990 34.1100 33.8770 N.pl3 43 TRP 0.000000 + 644 HE1 33.5110 34.0660 34.8800 H 43 TRP 0.000000 + 645 CE2 32.4440 33.4630 33.0730 C.ar 43 TRP 0.000000 + 646 CZ2 31.2480 32.7450 33.2960 C.ar 43 TRP 0.000000 + 647 HZ2 31.0070 32.4290 34.3010 H 43 TRP 0.000000 + 648 CH2 30.5750 32.1940 32.1990 C.ar 43 TRP 0.000000 + 649 HH2 29.7400 31.5270 32.3550 H 43 TRP 0.000000 + 650 CZ3 30.9880 32.5410 30.9090 C.ar 43 TRP 0.000000 + 651 HZ3 30.4120 32.2360 30.0470 H 43 TRP 0.000000 + 652 CE3 32.1090 33.3270 30.6820 C.ar 43 TRP 0.000000 + 653 HE3 32.3970 33.6790 29.7030 H 43 TRP 0.000000 + 654 CD2 32.8700 33.8170 31.7650 C.ar 43 TRP 0.000000 + 655 C 36.9100 34.2350 29.0340 C.2 43 TRP 0.000000 + 656 O 37.6600 35.2020 28.8230 O.2 43 TRP 0.000000 + 657 N 36.4680 33.3980 28.1130 N.am 44 THR 0.000000 + 658 H 35.9190 32.5900 28.3670 H 44 THR 0.000000 + 659 CA 36.6270 33.5260 26.6680 C.3 44 THR 0.000000 + 660 HA 36.8250 34.5800 26.4740 H 44 THR 0.000000 + 661 CB 37.8130 32.7940 26.0620 C.3 44 THR 0.000000 + 662 HB 37.6950 32.7890 24.9780 H 44 THR 0.000000 + 663 CG2 39.1420 33.4110 26.4700 C.3 44 THR 0.000000 + 664 HG21 39.9710 32.8140 26.0900 H 44 THR 0.000000 + 665 HG22 39.2770 33.3950 27.5520 H 44 THR 0.000000 + 666 HG23 39.3600 34.4080 26.0880 H 44 THR 0.000000 + 667 OG1 37.8540 31.5070 26.6040 O.3 44 THR 0.000000 + 668 HG1 37.6290 30.9070 25.8890 H 44 THR 0.000000 + 669 C 35.2670 33.2950 26.0050 C.2 44 THR 0.000000 + 670 O 34.4800 32.5770 26.4440 O.2 44 THR 0.000000 + 671 N 35.1370 33.9190 24.8480 N.am 45 TYR 0.000000 + 672 H 35.9000 34.5260 24.5850 H 45 TYR 0.000000 + 673 CA 34.0510 33.6790 23.8140 C.3 45 TYR 0.000000 + 674 HA 33.5650 32.7480 24.1090 H 45 TYR 0.000000 + 675 CB 33.0610 34.8900 23.8360 C.3 45 TYR 0.000000 + 676 HB2 32.6890 35.0850 24.8430 H 45 TYR 0.000000 + 677 HB3 33.6700 35.7620 23.5960 H 45 TYR 0.000000 + 678 CG 31.8250 34.7470 22.9620 C.ar 45 TYR 0.000000 + 679 CD1 30.9550 33.6840 23.0610 C.ar 45 TYR 0.000000 + 680 HD1 31.0400 32.9450 23.8450 H 45 TYR 0.000000 + 681 CE1 29.9080 33.5560 22.1160 C.ar 45 TYR 0.000000 + 682 HE1 29.1130 32.8490 22.2910 H 45 TYR 0.000000 + 683 CZ 29.7180 34.5060 21.0940 C.ar 45 TYR 0.000000 + 684 OH 28.6580 34.3380 20.2680 O.3 45 TYR 0.000000 + 685 HH 28.4960 35.0520 19.6480 H 45 TYR 0.000000 + 686 CE2 30.6530 35.5740 21.0280 C.ar 45 TYR 0.000000 + 687 HE2 30.4900 36.2880 20.2340 H 45 TYR 0.000000 + 688 CD2 31.7520 35.6430 21.9110 C.ar 45 TYR 0.000000 + 689 HD2 32.5370 36.3460 21.6790 H 45 TYR 0.000000 + 690 C 34.5450 33.5290 22.3360 C.2 45 TYR 0.000000 + 691 O 35.2600 34.4120 21.8090 O.2 45 TYR 0.000000 + 692 N 33.9240 32.5670 21.6400 N.am 46 ASP 0.000000 + 693 H 33.2150 32.0060 22.0880 H 46 ASP 0.000000 + 694 CA 34.1090 32.2890 20.2040 C.3 46 ASP 0.000000 + 695 HA 34.8050 32.8960 19.6250 H 46 ASP 0.000000 + 696 CB 34.8180 30.9170 20.2400 C.3 46 ASP 0.000000 + 697 HB2 35.7000 31.0320 20.8710 H 46 ASP 0.000000 + 698 HB3 34.2520 30.2000 20.8340 H 46 ASP 0.000000 + 699 CG 35.2160 30.2820 18.9120 C.2 46 ASP 0.000000 + 700 OD1 34.4050 29.5070 18.3230 O.co2 46 ASP 0.000000 + 701 OD2 36.1560 30.8570 18.3650 O.co2 46 ASP 0.000000 + 702 C 32.8770 32.2750 19.3190 C.2 46 ASP 0.000000 + 703 O 31.9310 31.5170 19.5290 O.2 46 ASP 0.000000 + 704 N 32.8330 33.2200 18.4130 N.am 47 ASP 0.000000 + 705 H 33.6220 33.8520 18.4290 H 47 ASP 0.000000 + 706 CA 31.6880 33.4560 17.5540 C.3 47 ASP 0.000000 + 707 HA 30.7730 33.5610 18.1370 H 47 ASP 0.000000 + 708 CB 31.9070 34.7380 16.7470 C.3 47 ASP 0.000000 + 709 HB2 32.1130 35.5100 17.4880 H 47 ASP 0.000000 + 710 HB3 32.8530 34.6970 16.2070 H 47 ASP 0.000000 + 711 CG 30.7290 35.1870 15.8440 C.2 47 ASP 0.000000 + 712 OD1 29.5510 35.0400 16.1740 O.co2 47 ASP 0.000000 + 713 OD2 31.1170 35.7270 14.7550 O.co2 47 ASP 0.000000 + 714 C 31.5220 32.3260 16.5570 C.2 47 ASP 0.000000 + 715 O 30.3900 32.0690 16.1340 O.2 47 ASP 0.000000 + 716 N 32.5550 31.6570 16.0920 N.am 48 ALA 0.000000 + 717 H 33.4900 31.9310 16.3570 H 48 ALA 0.000000 + 718 CA 32.4370 30.6470 15.0150 C.3 48 ALA 0.000000 + 719 HA 31.7070 31.1080 14.3490 H 48 ALA 0.000000 + 720 CB 33.8210 30.4670 14.3400 C.3 48 ALA 0.000000 + 721 HB1 34.2440 31.3990 13.9640 H 48 ALA 0.000000 + 722 HB2 33.6750 29.7060 13.5730 H 48 ALA 0.000000 + 723 HB3 34.4210 29.9860 15.1120 H 48 ALA 0.000000 + 724 C 31.8550 29.3010 15.5490 C.2 48 ALA 0.000000 + 725 O 31.5480 28.4450 14.7200 O.2 48 ALA 0.000000 + 726 N 31.6190 29.1630 16.8850 N.am 49 THR 0.000000 + 727 H 31.9750 29.9290 17.4390 H 49 THR 0.000000 + 728 CA 30.8110 28.1260 17.5760 C.3 49 THR 0.000000 + 729 HA 30.3710 27.5440 16.7670 H 49 THR 0.000000 + 730 CB 31.7130 27.1000 18.3100 C.3 49 THR 0.000000 + 731 HB 31.1340 26.4200 18.9350 H 49 THR 0.000000 + 732 CG2 32.6140 26.2800 17.4360 C.3 49 THR 0.000000 + 733 HG21 33.3290 26.8680 16.8590 H 49 THR 0.000000 + 734 HG22 32.0020 25.5930 16.8530 H 49 THR 0.000000 + 735 HG23 33.3540 25.7600 18.0440 H 49 THR 0.000000 + 736 OG1 32.5070 27.8340 19.2220 O.3 49 THR 0.000000 + 737 HG1 33.1510 28.3360 18.7150 H 49 THR 0.000000 + 738 C 29.7130 28.6440 18.4680 C.2 49 THR 0.000000 + 739 O 28.9410 27.9120 19.1030 O.2 49 THR 0.000000 + 740 N 29.6280 29.9770 18.6490 N.am 50 LYS 0.000000 + 741 H 30.4190 30.5220 18.3340 H 50 LYS 0.000000 + 742 CA 28.6630 30.6950 19.5410 C.3 50 LYS 0.000000 + 743 HA 28.8470 31.7690 19.5010 H 50 LYS 0.000000 + 744 CB 27.1890 30.6250 19.0330 C.3 50 LYS 0.000000 + 745 HB2 26.9360 29.5720 19.1630 H 50 LYS 0.000000 + 746 HB3 26.4690 31.0810 19.7120 H 50 LYS 0.000000 + 747 CG 27.1190 30.9840 17.4650 C.3 50 LYS 0.000000 + 748 HG2 27.9610 30.5900 16.8950 H 50 LYS 0.000000 + 749 HG3 26.1880 30.5510 17.1000 H 50 LYS 0.000000 + 750 CD 27.0250 32.5470 17.3220 C.3 50 LYS 0.000000 + 751 HD2 26.3370 33.0990 17.9640 H 50 LYS 0.000000 + 752 HD3 28.0050 32.9130 17.6230 H 50 LYS 0.000000 + 753 CE 26.6860 32.9330 15.9300 C.3 50 LYS 0.000000 + 754 HE2 25.8290 32.3630 15.5720 H 50 LYS 0.000000 + 755 HE3 26.3040 33.9530 15.9860 H 50 LYS 0.000000 + 756 NZ 27.8610 32.9050 14.9900 N.4 50 LYS 0.000000 + 757 HZ1 28.5620 33.5070 15.3970 H 50 LYS 0.000000 + 758 HZ2 27.5970 33.3210 14.1080 H 50 LYS 0.000000 + 759 HZ3 28.2690 32.0170 14.7360 H 50 LYS 0.000000 + 760 C 28.8840 30.2500 21.0330 C.2 50 LYS 0.000000 + 761 O 27.9580 30.2060 21.8260 O.2 50 LYS 0.000000 + 762 N 30.1480 29.8200 21.3280 N.am 51 THR 0.000000 + 763 H 30.9400 30.1000 20.7660 H 51 THR 0.000000 + 764 CA 30.5030 29.2140 22.6320 C.3 51 THR 0.000000 + 765 HA 29.6800 28.7140 23.1420 H 51 THR 0.000000 + 766 CB 31.3130 27.9440 22.3690 C.3 51 THR 0.000000 + 767 HB 32.2450 28.1020 21.8260 H 51 THR 0.000000 + 768 CG2 31.7030 27.0880 23.5900 C.3 51 THR 0.000000 + 769 HG21 32.1770 26.1600 23.2720 H 51 THR 0.000000 + 770 HG22 30.7450 26.9770 24.1000 H 51 THR 0.000000 + 771 HG23 32.4010 27.6770 24.1860 H 51 THR 0.000000 + 772 OG1 30.4040 27.1610 21.6590 O.3 51 THR 0.000000 + 773 HG1 29.7570 27.6830 21.1790 H 51 THR 0.000000 + 774 C 31.2020 30.1200 23.5490 C.2 51 THR 0.000000 + 775 O 32.2000 30.7210 23.1430 O.2 51 THR 0.000000 + 776 N 31.0090 29.9260 24.8450 N.am 52 PHE 0.000000 + 777 H 30.1250 29.4790 25.0420 H 52 PHE 0.000000 + 778 CA 31.8210 30.3910 25.9410 C.3 52 PHE 0.000000 + 779 HA 32.4900 31.1920 25.6280 H 52 PHE 0.000000 + 780 CB 30.7150 30.9790 27.0070 C.3 52 PHE 0.000000 + 781 HB2 29.9880 30.2000 27.2380 H 52 PHE 0.000000 + 782 HB3 31.2500 31.2980 27.9010 H 52 PHE 0.000000 + 783 CG 30.0490 32.2220 26.5340 C.ar 52 PHE 0.000000 + 784 CD1 28.8760 32.1420 25.7810 C.ar 52 PHE 0.000000 + 785 HD1 28.4130 31.2040 25.5150 H 52 PHE 0.000000 + 786 CE1 28.3000 33.3500 25.3040 C.ar 52 PHE 0.000000 + 787 HE1 27.3030 33.3160 24.8900 H 52 PHE 0.000000 + 788 CZ 28.8800 34.5930 25.5000 C.ar 52 PHE 0.000000 + 789 HZ 28.4170 35.4600 25.0540 H 52 PHE 0.000000 + 790 CE2 30.1220 34.6650 26.1920 C.ar 52 PHE 0.000000 + 791 HE2 30.6500 35.5970 26.3330 H 52 PHE 0.000000 + 792 CD2 30.5970 33.4950 26.7950 C.ar 52 PHE 0.000000 + 793 HD2 31.4350 33.5810 27.4710 H 52 PHE 0.000000 + 794 C 32.7210 29.3430 26.5530 C.2 52 PHE 0.000000 + 795 O 32.2800 28.2400 26.6740 O.2 52 PHE 0.000000 + 796 N 33.9080 29.8290 27.0870 N.am 53 THR 0.000000 + 797 H 34.2030 30.7840 26.9380 H 53 THR 0.000000 + 798 CA 34.5770 29.0440 28.1320 C.3 53 THR 0.000000 + 799 HA 34.0030 28.1900 28.4920 H 53 THR 0.000000 + 800 CB 35.8810 28.4430 27.6840 C.3 53 THR 0.000000 + 801 HB 36.5130 29.2340 27.2800 H 53 THR 0.000000 + 802 CG2 36.6200 27.5710 28.7520 C.3 53 THR 0.000000 + 803 HG21 36.8140 28.2360 29.5950 H 53 THR 0.000000 + 804 HG22 37.5350 27.1740 28.3130 H 53 THR 0.000000 + 805 HG23 35.9240 26.7950 29.0680 H 53 THR 0.000000 + 806 OG1 35.6050 27.6490 26.5840 O.3 53 THR 0.000000 + 807 HG1 35.4590 28.1770 25.7960 H 53 THR 0.000000 + 808 C 34.7760 29.7480 29.4430 C.2 53 THR 0.000000 + 809 O 35.1460 30.9390 29.4370 O.2 53 THR 0.000000 + 810 N 34.4990 29.1350 30.6390 N.am 54 VAL 0.000000 + 811 H 34.2090 28.1730 30.5380 H 54 VAL 0.000000 + 812 CA 34.8610 29.5360 31.9820 C.3 54 VAL 0.000000 + 813 HA 35.3820 30.4930 31.9780 H 54 VAL 0.000000 + 814 CB 33.6970 29.7160 32.8690 C.3 54 VAL 0.000000 + 815 HB 32.9130 30.3350 32.4340 H 54 VAL 0.000000 + 816 CG1 33.0020 28.3940 33.2890 C.3 54 VAL 0.000000 + 817 HG11 33.6900 27.6660 33.7180 H 54 VAL 0.000000 + 818 HG12 32.6180 28.0140 32.3420 H 54 VAL 0.000000 + 819 HG13 32.0930 28.5250 33.8770 H 54 VAL 0.000000 + 820 CG2 34.1180 30.3200 34.2240 C.3 54 VAL 0.000000 + 821 HG21 34.7110 31.2280 34.1230 H 54 VAL 0.000000 + 822 HG22 34.6910 29.6640 34.8800 H 54 VAL 0.000000 + 823 HG23 33.2020 30.5510 34.7670 H 54 VAL 0.000000 + 824 C 35.9500 28.5900 32.4680 C.2 54 VAL 0.000000 + 825 O 35.7380 27.3850 32.6600 O.2 54 VAL 0.000000 + 826 N 37.1870 29.0850 32.6510 N.am 55 THR 0.000000 + 827 H 37.3260 30.0380 32.3450 H 55 THR 0.000000 + 828 CA 38.4180 28.3630 33.0710 C.3 55 THR 0.000000 + 829 HA 38.1970 27.2990 32.9910 H 55 THR 0.000000 + 830 CB 39.5740 28.5160 32.1610 C.3 55 THR 0.000000 + 831 HB 39.7570 29.5810 32.0190 H 55 THR 0.000000 + 832 CG2 40.8700 27.8980 32.7860 C.3 55 THR 0.000000 + 833 HG21 40.5830 26.8490 32.8550 H 55 THR 0.000000 + 834 HG22 41.0230 28.1900 33.8260 H 55 THR 0.000000 + 835 HG23 41.8250 28.0440 32.2800 H 55 THR 0.000000 + 836 OG1 39.2150 27.9700 30.8180 O.3 55 THR 0.000000 + 837 HG1 38.7920 28.7250 30.4010 H 55 THR 0.000000 + 838 C 38.7790 28.7250 34.4580 C.2 55 THR 0.000000 + 839 O 39.2630 29.8410 34.7350 O.2 55 THR 0.000000 + 840 N 38.7570 27.7730 35.4160 N.am 56 GLU 0.000000 + 841 H 38.4590 26.8690 35.0790 H 56 GLU 0.000000 + 842 CA 39.0450 27.9930 36.8880 C.3 56 GLU 0.000000 + 843 HA 38.6180 28.9210 37.2670 H 56 GLU 0.000000 + 844 CB 38.4020 26.9110 37.7490 C.3 56 GLU 0.000000 + 845 HB2 37.3290 27.0190 37.5930 H 56 GLU 0.000000 + 846 HB3 38.7800 25.9050 37.5630 H 56 GLU 0.000000 + 847 CG 38.4360 27.0780 39.2670 C.3 56 GLU 0.000000 + 848 HG2 39.4550 26.9680 39.6360 H 56 GLU 0.000000 + 849 HG3 38.0940 28.0970 39.4450 H 56 GLU 0.000000 + 850 CD 37.5140 26.0140 39.9180 C.2 56 GLU 0.000000 + 851 OE1 37.9050 24.8230 39.8700 O.co2 56 GLU 0.000000 + 852 OE2 36.5290 26.3270 40.6640 O.co2 56 GLU 0.000000 + 853 C 40.4880 28.1370 37.3010 C.2 56 GLU 0.000000 + 854 O 40.8070 29.0900 38.0250 O.co2 56 GLU 0.000000 + 855 OXT 41.3770 27.2710 37.0310 O.co2 56 GLU 0.000000 +@BOND + 1 1 2 1 + 2 1 3 1 + 3 1 4 1 + 4 1 5 1 + 5 5 6 1 + 6 5 7 1 + 7 5 18 1 + 8 7 8 1 + 9 7 9 1 + 10 7 10 1 + 11 10 11 1 + 12 10 12 1 + 13 10 13 1 + 14 13 14 1 + 15 14 15 1 + 16 14 16 1 + 17 14 17 1 + 18 18 19 2 + 19 18 20 am + 20 20 21 1 + 21 20 22 1 + 22 22 23 1 + 23 22 24 1 + 24 22 32 1 + 25 24 25 1 + 26 24 26 1 + 27 24 30 1 + 28 26 27 1 + 29 26 28 1 + 30 26 29 1 + 31 30 31 1 + 32 32 33 2 + 33 32 34 am + 34 34 35 1 + 35 34 36 1 + 36 36 37 1 + 37 36 38 1 + 38 36 53 1 + 39 38 39 1 + 40 38 40 1 + 41 38 41 1 + 42 41 42 ar + 43 41 51 ar + 44 42 43 1 + 45 42 44 ar + 46 44 45 1 + 47 44 46 ar + 48 46 47 1 + 49 46 49 ar + 50 47 48 1 + 51 49 50 1 + 52 49 51 ar + 53 51 52 1 + 54 53 54 2 + 55 53 55 am + 56 55 56 1 + 57 55 57 1 + 58 57 58 1 + 59 57 59 1 + 60 57 75 1 + 61 59 60 1 + 62 59 61 1 + 63 59 62 1 + 64 62 63 1 + 65 62 64 1 + 66 62 65 1 + 67 65 66 1 + 68 65 67 1 + 69 65 68 1 + 70 68 69 1 + 71 68 70 1 + 72 68 71 1 + 73 71 72 1 + 74 71 73 1 + 75 71 74 1 + 76 75 76 2 + 77 75 77 am + 78 77 78 1 + 79 77 79 1 + 80 79 80 1 + 81 79 81 1 + 82 79 94 1 + 83 81 82 1 + 84 81 83 1 + 85 81 84 1 + 86 84 85 1 + 87 84 86 1 + 88 84 90 1 + 89 86 87 1 + 90 86 88 1 + 91 86 89 1 + 92 90 91 1 + 93 90 92 1 + 94 90 93 1 + 95 94 95 2 + 96 94 96 am + 97 96 97 1 + 98 96 98 1 + 99 98 99 1 + 100 98 100 1 + 101 98 113 1 + 102 100 101 1 + 103 100 102 1 + 104 100 106 1 + 105 102 103 1 + 106 102 104 1 + 107 102 105 1 + 108 106 107 1 + 109 106 108 1 + 110 106 109 1 + 111 109 110 1 + 112 109 111 1 + 113 109 112 1 + 114 113 114 2 + 115 113 115 am + 116 115 116 1 + 117 115 117 1 + 118 117 118 1 + 119 117 119 1 + 120 117 132 1 + 121 119 120 1 + 122 119 121 1 + 123 119 122 1 + 124 122 123 1 + 125 122 124 1 + 126 122 128 1 + 127 124 125 1 + 128 124 126 1 + 129 124 127 1 + 130 128 129 1 + 131 128 130 1 + 132 128 131 1 + 133 132 133 2 + 134 132 134 am + 135 134 135 1 + 136 134 136 1 + 137 136 137 1 + 138 136 138 1 + 139 136 146 1 + 140 138 139 1 + 141 138 140 1 + 142 138 141 1 + 143 141 142 2 + 144 141 143 am + 145 143 144 1 + 146 143 145 1 + 147 146 147 2 + 148 146 148 am + 149 148 149 1 + 150 148 150 1 + 151 150 151 1 + 152 150 152 1 + 153 150 153 1 + 154 153 154 2 + 155 153 155 am + 156 155 156 1 + 157 155 157 1 + 158 157 158 1 + 159 157 159 1 + 160 157 175 1 + 161 159 160 1 + 162 159 161 1 + 163 159 162 1 + 164 162 163 1 + 165 162 164 1 + 166 162 165 1 + 167 165 166 1 + 168 165 167 1 + 169 165 168 1 + 170 168 169 1 + 171 168 170 1 + 172 168 171 1 + 173 171 172 1 + 174 171 173 1 + 175 171 174 1 + 176 175 176 2 + 177 175 177 am + 178 177 178 1 + 179 177 179 1 + 180 179 180 1 + 181 179 181 1 + 182 179 189 1 + 183 181 182 1 + 184 181 183 1 + 185 181 187 1 + 186 183 184 1 + 187 183 185 1 + 188 183 186 1 + 189 187 188 1 + 190 189 190 2 + 191 189 191 am + 192 191 192 1 + 193 191 193 1 + 194 193 194 1 + 195 193 195 1 + 196 193 208 1 + 197 195 196 1 + 198 195 197 1 + 199 195 198 1 + 200 198 199 1 + 201 198 200 1 + 202 198 204 1 + 203 200 201 1 + 204 200 202 1 + 205 200 203 1 + 206 204 205 1 + 207 204 206 1 + 208 204 207 1 + 209 208 209 2 + 210 208 210 am + 211 210 211 1 + 212 210 212 1 + 213 212 213 1 + 214 212 214 1 + 215 212 230 1 + 216 214 215 1 + 217 214 216 1 + 218 214 217 1 + 219 217 218 1 + 220 217 219 1 + 221 217 220 1 + 222 220 221 1 + 223 220 222 1 + 224 220 223 1 + 225 223 224 1 + 226 223 225 1 + 227 223 226 1 + 228 226 227 1 + 229 226 228 1 + 230 226 229 1 + 231 230 231 2 + 232 230 232 am + 233 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+ 854 844 847 1 + 855 847 848 1 + 856 847 849 1 + 857 847 850 1 + 858 850 851 1 + 859 850 852 1 + 860 853 854 1 + 861 853 855 1 +@SUBSTRUCTURE + 1 MET 1 TEMP 0 **** **** 0 ROOT diff --git a/unittests/example_files/test_gly.pdb b/unittests/example_files/test_gly.pdb new file mode 100644 index 0000000..2bb3c09 --- /dev/null +++ b/unittests/example_files/test_gly.pdb @@ -0,0 +1,1734 @@ +COMPND MET +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +ATOM 1 N MET A 1 19.157 32.576 19.140 1.00 0.00 N1+ +ATOM 2 H1 MET A 1 18.435 31.870 19.129 1.00 0.00 H +ATOM 3 H2 MET A 1 18.900 33.260 18.441 1.00 0.00 H +ATOM 4 H3 MET A 1 19.229 33.073 20.016 1.00 0.00 H +ATOM 5 CA MET A 1 20.458 31.939 18.931 1.00 0.00 C +ATOM 6 HA MET A 1 20.420 31.303 18.046 1.00 0.00 H +ATOM 7 CB MET A 1 21.504 33.015 18.722 1.00 0.00 C +ATOM 8 HB2 MET A 1 21.352 33.519 17.768 1.00 0.00 H +ATOM 9 HB3 MET A 1 21.390 33.764 19.505 1.00 0.00 H +ATOM 10 CG MET A 1 22.904 32.517 18.656 1.00 0.00 C +ATOM 11 HG2 MET A 1 23.590 33.362 18.601 1.00 0.00 H +ATOM 12 HG3 MET A 1 23.154 32.095 19.630 1.00 0.00 H +ATOM 13 SD MET A 1 23.205 31.269 17.386 1.00 0.00 S +ATOM 14 CE MET A 1 22.990 32.137 15.870 1.00 0.00 C +ATOM 15 HE1 MET A 1 23.339 33.163 15.983 1.00 0.00 H +ATOM 16 HE2 MET A 1 21.968 32.128 15.490 1.00 0.00 H +ATOM 17 HE3 MET A 1 23.572 31.586 15.132 1.00 0.00 H +ATOM 18 C MET A 1 20.796 31.017 20.133 1.00 0.00 C +ATOM 19 O MET A 1 20.674 31.440 21.297 1.00 0.00 O +ATOM 20 N THR A 2 21.124 29.774 19.819 1.00 0.00 N +ATOM 21 H THR A 2 21.279 29.527 18.851 1.00 0.00 H +ATOM 22 CA THR A 2 21.443 28.704 20.861 1.00 0.00 C +ATOM 23 HA THR A 2 20.909 28.998 21.764 1.00 0.00 H +ATOM 24 CB THR A 2 21.114 27.241 20.522 1.00 0.00 C +ATOM 25 HB THR A 2 21.945 26.825 19.955 1.00 0.00 H +ATOM 26 CG2 THR A 2 20.715 26.558 21.817 1.00 0.00 C +ATOM 27 HG21 THR A 2 20.203 25.609 21.656 1.00 0.00 H +ATOM 28 HG22 THR A 2 20.001 27.137 22.403 1.00 0.00 H +ATOM 29 HG23 THR A 2 21.633 26.344 22.363 1.00 0.00 H +ATOM 30 OG1 THR A 2 19.957 27.231 19.658 1.00 0.00 O +ATOM 31 HG1 THR A 2 19.386 27.976 19.864 1.00 0.00 H +ATOM 32 C THR A 2 22.937 28.892 21.086 1.00 0.00 C +ATOM 33 O THR A 2 23.773 28.867 20.181 1.00 0.00 O +ATOM 34 N TYR A 3 23.244 29.155 22.344 1.00 0.00 N +ATOM 35 H TYR A 3 22.513 29.085 23.038 1.00 0.00 H +ATOM 36 CA TYR A 3 24.628 29.305 22.888 1.00 0.00 C +ATOM 37 HA TYR A 3 25.262 29.391 22.004 1.00 0.00 H +ATOM 38 CB TYR A 3 24.744 30.579 23.675 1.00 0.00 C +ATOM 39 HB2 TYR A 3 24.131 30.495 24.572 1.00 0.00 H +ATOM 40 HB3 TYR A 3 25.780 30.505 24.008 1.00 0.00 H +ATOM 41 CG TYR A 3 24.468 31.862 22.928 1.00 0.00 C +ATOM 42 CD1 TYR A 3 25.525 32.544 22.317 1.00 0.00 C +ATOM 43 HD1 TYR A 3 26.477 32.039 22.379 1.00 0.00 H +ATOM 44 CE1 TYR A 3 25.289 33.761 21.619 1.00 0.00 C +ATOM 45 HE1 TYR A 3 26.100 34.275 21.122 1.00 0.00 H +ATOM 46 CZ TYR A 3 23.936 34.260 21.579 1.00 0.00 C +ATOM 47 OH TYR A 3 23.774 35.268 20.774 1.00 0.00 O +ATOM 48 HH TYR A 3 24.486 35.161 20.140 1.00 0.00 H +ATOM 49 CE2 TYR A 3 22.849 33.537 22.176 1.00 0.00 C +ATOM 50 HE2 TYR A 3 21.868 33.965 22.036 1.00 0.00 H +ATOM 51 CD2 TYR A 3 23.110 32.291 22.853 1.00 0.00 C +ATOM 52 HD2 TYR A 3 22.235 31.752 23.187 1.00 0.00 H +ATOM 53 C TYR A 3 25.066 28.136 23.774 1.00 0.00 C +ATOM 54 O TYR A 3 24.233 27.436 24.338 1.00 0.00 O +ATOM 55 N LYS A 4 26.339 27.934 23.811 1.00 0.00 N +ATOM 56 H LYS A 4 26.944 28.514 23.248 1.00 0.00 H +ATOM 57 CA LYS A 4 26.982 26.918 24.687 1.00 0.00 C +ATOM 58 HA LYS A 4 26.212 26.488 25.328 1.00 0.00 H +ATOM 59 CB LYS A 4 27.643 25.801 23.803 1.00 0.00 C +ATOM 60 HB2 LYS A 4 26.868 25.465 23.113 1.00 0.00 H +ATOM 61 HB3 LYS A 4 28.422 26.196 23.151 1.00 0.00 H +ATOM 62 CG LYS A 4 28.205 24.625 24.506 1.00 0.00 C +ATOM 63 HG2 LYS A 4 29.054 24.916 25.125 1.00 0.00 H +ATOM 64 HG3 LYS A 4 27.452 24.278 25.213 1.00 0.00 H +ATOM 65 CD LYS A 4 28.635 23.407 23.678 1.00 0.00 C +ATOM 66 HD2 LYS A 4 29.003 22.691 24.414 1.00 0.00 H +ATOM 67 HD3 LYS A 4 27.737 22.954 23.255 1.00 0.00 H +ATOM 68 CE LYS A 4 29.554 23.575 22.506 1.00 0.00 C +ATOM 69 HE2 LYS A 4 28.899 24.120 21.827 1.00 0.00 H +ATOM 70 HE3 LYS A 4 30.458 24.114 22.794 1.00 0.00 H +ATOM 71 NZ LYS A 4 30.052 22.279 21.888 1.00 0.00 N1+ +ATOM 72 HZ1 LYS A 4 30.831 21.896 22.402 1.00 0.00 H +ATOM 73 HZ2 LYS A 4 30.443 22.423 20.968 1.00 0.00 H +ATOM 74 HZ3 LYS A 4 29.328 21.579 21.805 1.00 0.00 H +ATOM 75 C LYS A 4 28.003 27.516 25.655 1.00 0.00 C +ATOM 76 O LYS A 4 28.579 28.553 25.310 1.00 0.00 O +ATOM 77 N LEU A 5 28.245 26.773 26.741 1.00 0.00 N +ATOM 78 H LEU A 5 27.544 26.084 26.977 1.00 0.00 H +ATOM 79 CA LEU A 5 29.244 27.118 27.766 1.00 0.00 C +ATOM 80 HA LEU A 5 29.916 27.884 27.380 1.00 0.00 H +ATOM 81 CB LEU A 5 28.579 27.507 29.097 1.00 0.00 C +ATOM 82 HB2 LEU A 5 28.058 28.438 28.872 1.00 0.00 H +ATOM 83 HB3 LEU A 5 27.859 26.779 29.469 1.00 0.00 H +ATOM 84 CG LEU A 5 29.551 27.720 30.235 1.00 0.00 C +ATOM 85 HG LEU A 5 30.166 26.841 30.429 1.00 0.00 H +ATOM 86 CD1 LEU A 5 30.427 28.952 29.986 1.00 0.00 C +ATOM 87 HD11 LEU A 5 31.114 28.683 29.184 1.00 0.00 H +ATOM 88 HD12 LEU A 5 31.008 29.120 30.894 1.00 0.00 H +ATOM 89 HD13 LEU A 5 29.848 29.861 29.825 1.00 0.00 H +ATOM 90 CD2 LEU A 5 28.678 28.115 31.457 1.00 0.00 C +ATOM 91 HD21 LEU A 5 28.235 29.096 31.284 1.00 0.00 H +ATOM 92 HD22 LEU A 5 29.327 28.287 32.315 1.00 0.00 H +ATOM 93 HD23 LEU A 5 27.907 27.390 31.720 1.00 0.00 H +ATOM 94 C LEU A 5 30.065 25.816 27.990 1.00 0.00 C +ATOM 95 O LEU A 5 29.489 24.768 28.302 1.00 0.00 O +ATOM 96 N ILE A 6 31.415 25.954 27.959 1.00 0.00 N +ATOM 97 H ILE A 6 31.834 26.822 27.658 1.00 0.00 H +ATOM 98 CA ILE A 6 32.352 24.944 28.438 1.00 0.00 C +ATOM 99 HA ILE A 6 31.851 23.978 28.494 1.00 0.00 H +ATOM 100 CB ILE A 6 33.535 24.736 27.434 1.00 0.00 C +ATOM 101 HB ILE A 6 34.002 25.706 27.261 1.00 0.00 H +ATOM 102 CG2 ILE A 6 34.658 23.796 27.952 1.00 0.00 C +ATOM 103 HG21 ILE A 6 35.011 24.049 28.953 1.00 0.00 H +ATOM 104 HG22 ILE A 6 35.610 23.773 27.423 1.00 0.00 H +ATOM 105 HG23 ILE A 6 34.315 22.768 28.065 1.00 0.00 H +ATOM 106 CG1 ILE A 6 32.967 24.083 26.135 1.00 0.00 C +ATOM 107 HG12 ILE A 6 32.815 23.014 26.281 1.00 0.00 H +ATOM 108 HG13 ILE A 6 32.016 24.548 25.875 1.00 0.00 H +ATOM 109 CD1 ILE A 6 33.964 24.228 24.983 1.00 0.00 C +ATOM 110 HD11 ILE A 6 34.203 25.280 24.831 1.00 0.00 H +ATOM 111 HD12 ILE A 6 33.521 23.646 24.174 1.00 0.00 H +ATOM 112 HD13 ILE A 6 34.890 23.744 25.293 1.00 0.00 H +ATOM 113 C ILE A 6 32.878 25.380 29.825 1.00 0.00 C +ATOM 114 O ILE A 6 33.517 26.449 29.956 1.00 0.00 O +ATOM 115 N LEU A 7 32.756 24.548 30.823 1.00 0.00 N +ATOM 116 H LEU A 7 32.337 23.649 30.632 1.00 0.00 H +ATOM 117 CA LEU A 7 33.418 24.678 32.128 1.00 0.00 C +ATOM 118 HA LEU A 7 33.772 25.702 32.243 1.00 0.00 H +ATOM 119 CB LEU A 7 32.452 24.287 33.269 1.00 0.00 C +ATOM 120 HB2 LEU A 7 32.235 23.219 33.280 1.00 0.00 H +ATOM 121 HB3 LEU A 7 33.025 24.491 34.173 1.00 0.00 H +ATOM 122 CG LEU A 7 31.068 25.080 33.294 1.00 0.00 C +ATOM 123 HG LEU A 7 31.234 26.000 32.731 1.00 0.00 H +ATOM 124 CD1 LEU A 7 29.957 24.185 32.737 1.00 0.00 C +ATOM 125 HD11 LEU A 7 29.091 24.791 32.472 1.00 0.00 H +ATOM 126 HD12 LEU A 7 29.675 23.458 33.497 1.00 0.00 H +ATOM 127 HD13 LEU A 7 30.242 23.598 31.863 1.00 0.00 H +ATOM 128 CD2 LEU A 7 30.679 25.500 34.666 1.00 0.00 C +ATOM 129 HD21 LEU A 7 30.692 24.679 35.384 1.00 0.00 H +ATOM 130 HD22 LEU A 7 29.678 25.926 34.604 1.00 0.00 H +ATOM 131 HD23 LEU A 7 31.266 26.349 35.014 1.00 0.00 H +ATOM 132 C LEU A 7 34.704 23.832 31.982 1.00 0.00 C +ATOM 133 O LEU A 7 34.608 22.712 31.434 1.00 0.00 O +ATOM 134 N ASN A 8 35.741 24.355 32.566 1.00 0.00 N +ATOM 135 H ASN A 8 35.657 25.289 32.943 1.00 0.00 H +ATOM 136 CA ASN A 8 37.087 23.938 32.340 1.00 0.00 C +ATOM 137 HA ASN A 8 37.195 22.875 32.128 1.00 0.00 H +ATOM 138 CB ASN A 8 37.683 24.648 31.079 1.00 0.00 C +ATOM 139 HB2 ASN A 8 37.052 24.514 30.199 1.00 0.00 H +ATOM 140 HB3 ASN A 8 37.697 25.701 31.358 1.00 0.00 H +ATOM 141 CG ASN A 8 39.069 24.172 30.753 1.00 0.00 C +ATOM 142 OD1 ASN A 8 39.293 22.972 30.616 1.00 0.00 O +ATOM 143 ND2 ASN A 8 40.171 24.966 30.834 1.00 0.00 N +ATOM 144 HD21 ASN A 8 40.064 25.968 30.880 1.00 0.00 H +ATOM 145 HD22 ASN A 8 41.073 24.564 30.618 1.00 0.00 H +ATOM 146 C ASN A 8 37.929 24.262 33.602 1.00 0.00 C +ATOM 147 O ASN A 8 37.736 25.299 34.234 1.00 0.00 O +ATOM 148 N HD7 A 9 38.893 23.411 33.937 1.00 0.00 N +ATOM 149 H HD7 A 9 38.872 22.559 33.394 1.00 0.00 H +ATOM 150 CA HD7 A 9 39.937 23.667 34.946 1.00 0.00 C +ATOM 151 CB HD7 A 9 39.359 24.216 36.252 1.00 0.00 C +ATOM 152 HB2 HD7 A 9 38.622 23.522 36.654 1.00 0.00 H +ATOM 153 HB3 HD7 A 9 40.155 24.364 36.981 1.00 0.00 H +ATOM 154 CG HD7 A 9 38.666 25.534 36.099 1.00 0.00 C +ATOM 155 ND1 HD7 A 9 39.350 26.719 35.934 1.00 0.00 N +ATOM 156 HD7 HD7 A 9 40.356 26.803 35.902 1.00 0.00 H +ATOM 157 CE1 HD7 A 9 38.483 27.711 35.827 1.00 0.00 C +ATOM 158 HE1 HD7 A 9 38.830 28.735 35.691 1.00 0.00 H +ATOM 159 NE2 HD7 A 9 37.266 27.215 35.914 1.00 0.00 N +ATOM 160 CD2 HD7 A 9 37.351 25.855 36.085 1.00 0.00 C +ATOM 161 HD2 HD7 A 9 36.443 25.259 36.180 1.00 0.00 H +ATOM 162 HA2 HD7 A 9 40.563 24.496 34.619 1.00 0.00 H +ATOM 163 C HD7 A 9 40.820 22.504 35.210 1.00 0.00 C +ATOM 164 O HD7 A 9 40.826 21.506 34.446 1.00 0.00 O +ATOM 165 N LYS A 10 41.477 22.473 36.356 1.00 0.00 N +ATOM 166 H LYS A 10 41.439 23.256 36.992 1.00 0.00 H +ATOM 167 CA LYS A 10 42.321 21.363 36.766 1.00 0.00 C +ATOM 168 HA LYS A 10 42.838 21.036 35.864 1.00 0.00 H +ATOM 169 CB LYS A 10 43.435 21.839 37.736 1.00 0.00 C +ATOM 170 HB2 LYS A 10 42.960 22.130 38.673 1.00 0.00 H +ATOM 171 HB3 LYS A 10 44.151 21.018 37.787 1.00 0.00 H +ATOM 172 CG LYS A 10 44.146 23.121 37.228 1.00 0.00 C +ATOM 173 HG2 LYS A 10 44.581 22.959 36.242 1.00 0.00 H +ATOM 174 HG3 LYS A 10 43.424 23.934 37.151 1.00 0.00 H +ATOM 175 CD LYS A 10 45.206 23.474 38.269 1.00 0.00 C +ATOM 176 HD2 LYS A 10 44.834 23.376 39.290 1.00 0.00 H +ATOM 177 HD3 LYS A 10 46.045 22.781 38.265 1.00 0.00 H +ATOM 178 CE LYS A 10 45.833 24.866 37.936 1.00 0.00 C +ATOM 179 HE2 LYS A 10 46.898 24.867 38.172 1.00 0.00 H +ATOM 180 HE3 LYS A 10 45.615 25.139 36.904 1.00 0.00 H +ATOM 181 NZ LYS A 10 45.314 25.885 38.915 1.00 0.00 N1+ +ATOM 182 HZ1 LYS A 10 44.318 26.049 38.885 1.00 0.00 H +ATOM 183 HZ2 LYS A 10 45.805 26.756 38.765 1.00 0.00 H +ATOM 184 HZ3 LYS A 10 45.434 25.694 39.899 1.00 0.00 H +ATOM 185 C LYS A 10 41.608 20.142 37.369 1.00 0.00 C +ATOM 186 O LYS A 10 42.136 19.017 37.432 1.00 0.00 O +ATOM 187 N THR A 11 40.316 20.407 37.709 1.00 0.00 N +ATOM 188 H THR A 11 40.018 21.373 37.739 1.00 0.00 H +ATOM 189 CA THR A 11 39.333 19.428 38.190 1.00 0.00 C +ATOM 190 HA THR A 11 39.627 18.439 37.841 1.00 0.00 H +ATOM 191 CB THR A 11 39.319 19.497 39.740 1.00 0.00 C +ATOM 192 HB THR A 11 38.538 18.809 40.063 1.00 0.00 H +ATOM 193 CG2 THR A 11 40.656 18.994 40.197 1.00 0.00 C +ATOM 194 HG21 THR A 11 40.954 17.991 39.896 1.00 0.00 H +ATOM 195 HG22 THR A 11 40.695 18.984 41.286 1.00 0.00 H +ATOM 196 HG23 THR A 11 41.453 19.662 39.869 1.00 0.00 H +ATOM 197 OG1 THR A 11 39.118 20.738 40.229 1.00 0.00 O +ATOM 198 HG1 THR A 11 39.321 20.728 41.168 1.00 0.00 H +ATOM 199 C THR A 11 37.937 19.704 37.750 1.00 0.00 C +ATOM 200 O THR A 11 37.180 18.744 37.592 1.00 0.00 O +ATOM 201 N LEU A 12 37.572 20.909 37.360 1.00 0.00 N +ATOM 202 H LEU A 12 38.100 21.745 37.569 1.00 0.00 H +ATOM 203 CA LEU A 12 36.262 21.294 36.760 1.00 0.00 C +ATOM 204 HA LEU A 12 35.427 20.887 37.329 1.00 0.00 H +ATOM 205 CB LEU A 12 36.169 22.873 36.785 1.00 0.00 C +ATOM 206 HB2 LEU A 12 36.531 23.238 37.746 1.00 0.00 H +ATOM 207 HB3 LEU A 12 36.859 23.268 36.041 1.00 0.00 H +ATOM 208 CG LEU A 12 34.824 23.483 36.357 1.00 0.00 C +ATOM 209 HG LEU A 12 34.479 23.028 35.428 1.00 0.00 H +ATOM 210 CD1 LEU A 12 33.867 23.321 37.477 1.00 0.00 C +ATOM 211 HD11 LEU A 12 32.997 23.877 37.126 1.00 0.00 H +ATOM 212 HD12 LEU A 12 34.304 23.691 38.404 1.00 0.00 H +ATOM 213 HD13 LEU A 12 33.594 22.265 37.503 1.00 0.00 H +ATOM 214 CD2 LEU A 12 34.926 25.052 36.181 1.00 0.00 C +ATOM 215 HD21 LEU A 12 35.334 25.560 37.054 1.00 0.00 H +ATOM 216 HD22 LEU A 12 33.926 25.442 35.997 1.00 0.00 H +ATOM 217 HD23 LEU A 12 35.555 25.355 35.344 1.00 0.00 H +ATOM 218 C LEU A 12 36.092 20.805 35.283 1.00 0.00 C +ATOM 219 O LEU A 12 36.941 21.102 34.441 1.00 0.00 O +ATOM 220 N LYS A 13 35.016 20.080 34.906 1.00 0.00 N +ATOM 221 H LYS A 13 34.391 19.697 35.602 1.00 0.00 H +ATOM 222 CA LYS A 13 34.642 19.704 33.571 1.00 0.00 C +ATOM 223 HA LYS A 13 35.063 20.421 32.866 1.00 0.00 H +ATOM 224 CB LYS A 13 35.034 18.226 33.244 1.00 0.00 C +ATOM 225 HB2 LYS A 13 34.497 17.579 33.938 1.00 0.00 H +ATOM 226 HB3 LYS A 13 34.849 17.922 32.214 1.00 0.00 H +ATOM 227 CG LYS A 13 36.515 17.923 33.472 1.00 0.00 C +ATOM 228 HG2 LYS A 13 37.162 18.658 32.994 1.00 0.00 H +ATOM 229 HG3 LYS A 13 36.701 17.768 34.535 1.00 0.00 H +ATOM 230 CD LYS A 13 36.804 16.487 32.994 1.00 0.00 C +ATOM 231 HD2 LYS A 13 36.157 15.747 33.465 1.00 0.00 H +ATOM 232 HD3 LYS A 13 36.456 16.506 31.962 1.00 0.00 H +ATOM 233 CE LYS A 13 38.264 16.163 32.997 1.00 0.00 C +ATOM 234 HE2 LYS A 13 38.741 16.732 32.199 1.00 0.00 H +ATOM 235 HE3 LYS A 13 38.686 16.424 33.967 1.00 0.00 H +ATOM 236 NZ LYS A 13 38.397 14.672 32.837 1.00 0.00 N1+ +ATOM 237 HZ1 LYS A 13 37.944 14.324 32.005 1.00 0.00 H +ATOM 238 HZ2 LYS A 13 37.888 14.239 33.595 1.00 0.00 H +ATOM 239 HZ3 LYS A 13 39.367 14.391 32.817 1.00 0.00 H +ATOM 240 C LYS A 13 33.119 19.875 33.400 1.00 0.00 C +ATOM 241 O LYS A 13 32.522 20.218 34.448 1.00 0.00 O +ATOM 242 N GLY A 14 32.541 19.929 32.182 1.00 0.00 N +ATOM 243 H GLY A 14 33.085 19.611 31.392 1.00 0.00 H +ATOM 244 CA GLY A 14 31.141 20.135 31.951 1.00 0.00 C +ATOM 245 HA2 GLY A 14 30.696 19.143 31.877 1.00 0.00 H +ATOM 246 HA3 GLY A 14 30.707 20.500 32.883 1.00 0.00 H +ATOM 247 C GLY A 14 30.726 21.030 30.803 1.00 0.00 C +ATOM 248 O GLY A 14 31.459 21.986 30.478 1.00 0.00 O +ATOM 249 N GLU A 15 29.602 20.661 30.175 1.00 0.00 N +ATOM 250 H GLU A 15 29.233 19.801 30.557 1.00 0.00 H +ATOM 251 CA GLU A 15 29.053 21.595 29.115 1.00 0.00 C +ATOM 252 HA GLU A 15 29.457 22.592 29.292 1.00 0.00 H +ATOM 253 CB GLU A 15 29.452 21.151 27.705 1.00 0.00 C +ATOM 254 HB2 GLU A 15 28.886 21.770 27.009 1.00 0.00 H +ATOM 255 HB3 GLU A 15 30.497 21.396 27.512 1.00 0.00 H +ATOM 256 CG GLU A 15 29.157 19.668 27.410 1.00 0.00 C +ATOM 257 HG2 GLU A 15 29.865 19.104 28.017 1.00 0.00 H +ATOM 258 HG3 GLU A 15 28.109 19.456 27.619 1.00 0.00 H +ATOM 259 CD GLU A 15 29.423 19.385 25.968 1.00 0.00 C +ATOM 260 OE1 GLU A 15 28.458 19.250 25.177 1.00 0.00 O +ATOM 261 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O +ATOM 262 C GLU A 15 27.563 21.843 29.353 1.00 0.00 C +ATOM 263 O GLU A 15 26.814 21.020 29.796 1.00 0.00 O +ATOM 264 N THR A 16 27.080 22.966 28.863 1.00 0.00 N +ATOM 265 H THR A 16 27.718 23.647 28.477 1.00 0.00 H +ATOM 266 CA THR A 16 25.618 23.342 28.987 1.00 0.00 C +ATOM 267 HA THR A 16 24.987 22.466 28.832 1.00 0.00 H +ATOM 268 CB THR A 16 25.300 23.755 30.463 1.00 0.00 C +ATOM 269 HB THR A 16 25.664 23.028 31.190 1.00 0.00 H +ATOM 270 CG2 THR A 16 26.079 25.029 30.851 1.00 0.00 C +ATOM 271 HG21 THR A 16 26.002 25.212 31.923 1.00 0.00 H +ATOM 272 HG22 THR A 16 25.827 25.999 30.420 1.00 0.00 H +ATOM 273 HG23 THR A 16 27.139 24.833 30.686 1.00 0.00 H +ATOM 274 OG1 THR A 16 23.919 23.870 30.591 1.00 0.00 O +ATOM 275 HG1 THR A 16 23.605 22.966 30.654 1.00 0.00 H +ATOM 276 C THR A 16 25.136 24.387 27.956 1.00 0.00 C +ATOM 277 O THR A 16 25.847 25.392 27.686 1.00 0.00 O +ATOM 278 N THR A 17 23.944 24.126 27.374 1.00 0.00 N +ATOM 279 H THR A 17 23.414 23.300 27.615 1.00 0.00 H +ATOM 280 CA THR A 17 23.341 25.088 26.418 1.00 0.00 C +ATOM 281 HA THR A 17 24.139 25.697 25.992 1.00 0.00 H +ATOM 282 CB THR A 17 22.634 24.399 25.250 1.00 0.00 C +ATOM 283 HB THR A 17 22.194 25.142 24.585 1.00 0.00 H +ATOM 284 CG2 THR A 17 23.534 23.466 24.406 1.00 0.00 C +ATOM 285 HG21 THR A 17 22.981 22.875 23.677 1.00 0.00 H +ATOM 286 HG22 THR A 17 24.016 22.789 25.112 1.00 0.00 H +ATOM 287 HG23 THR A 17 24.305 24.119 23.998 1.00 0.00 H +ATOM 288 OG1 THR A 17 21.618 23.516 25.740 1.00 0.00 O +ATOM 289 HG1 THR A 17 21.158 23.210 24.955 1.00 0.00 H +ATOM 290 C THR A 17 22.409 26.084 27.080 1.00 0.00 C +ATOM 291 O THR A 17 21.865 25.880 28.171 1.00 0.00 O +ATOM 292 N THR A 18 22.284 27.186 26.367 1.00 0.00 N +ATOM 293 H THR A 18 22.918 27.211 25.581 1.00 0.00 H +ATOM 294 CA THR A 18 21.341 28.346 26.665 1.00 0.00 C +ATOM 295 HA THR A 18 20.447 28.047 27.213 1.00 0.00 H +ATOM 296 CB THR A 18 21.968 29.424 27.606 1.00 0.00 C +ATOM 297 HB THR A 18 22.926 29.800 27.251 1.00 0.00 H +ATOM 298 CG2 THR A 18 20.959 30.565 27.747 1.00 0.00 C +ATOM 299 HG21 THR A 18 21.177 31.232 28.581 1.00 0.00 H +ATOM 300 HG22 THR A 18 19.932 30.214 27.838 1.00 0.00 H +ATOM 301 HG23 THR A 18 21.057 31.149 26.831 1.00 0.00 H +ATOM 302 OG1 THR A 18 21.983 28.974 29.051 1.00 0.00 O +ATOM 303 HG1 THR A 18 22.866 29.123 29.400 1.00 0.00 H +ATOM 304 C THR A 18 20.829 28.956 25.354 1.00 0.00 C +ATOM 305 O THR A 18 21.553 29.458 24.528 1.00 0.00 O +ATOM 306 N GLU A 19 19.542 28.872 25.083 1.00 0.00 N +ATOM 307 H GLU A 19 18.919 28.579 25.823 1.00 0.00 H +ATOM 308 CA GLU A 19 18.932 29.576 23.987 1.00 0.00 C +ATOM 309 HA GLU A 19 19.679 29.508 23.197 1.00 0.00 H +ATOM 310 CB GLU A 19 17.686 28.785 23.627 1.00 0.00 C +ATOM 311 HB2 GLU A 19 17.899 27.722 23.514 1.00 0.00 H +ATOM 312 HB3 GLU A 19 16.998 28.842 24.471 1.00 0.00 H +ATOM 313 CG GLU A 19 16.852 29.284 22.477 1.00 0.00 C +ATOM 314 HG2 GLU A 19 16.246 28.447 22.128 1.00 0.00 H +ATOM 315 HG3 GLU A 19 16.133 30.057 22.748 1.00 0.00 H +ATOM 316 CD GLU A 19 17.736 29.731 21.281 1.00 0.00 C +ATOM 317 OE1 GLU A 19 18.363 28.800 20.679 1.00 0.00 O +ATOM 318 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O +ATOM 319 C GLU A 19 18.631 31.049 24.311 1.00 0.00 C +ATOM 320 O GLU A 19 17.951 31.336 25.240 1.00 0.00 O +ATOM 321 N ALA A 20 19.109 32.052 23.609 1.00 0.00 N +ATOM 322 H ALA A 20 19.659 31.766 22.810 1.00 0.00 H +ATOM 323 CA ALA A 20 18.962 33.505 23.885 1.00 0.00 C +ATOM 324 HA ALA A 20 17.980 33.742 24.295 1.00 0.00 H +ATOM 325 CB ALA A 20 19.978 33.979 24.961 1.00 0.00 C +ATOM 326 HB1 ALA A 20 19.807 35.026 25.214 1.00 0.00 H +ATOM 327 HB2 ALA A 20 20.983 33.923 24.544 1.00 0.00 H +ATOM 328 HB3 ALA A 20 19.800 33.404 25.869 1.00 0.00 H +ATOM 329 C ALA A 20 19.121 34.352 22.595 1.00 0.00 C +ATOM 330 O ALA A 20 19.565 33.867 21.541 1.00 0.00 O +ATOM 331 N VAL A 21 18.819 35.698 22.666 1.00 0.00 N +ATOM 332 H VAL A 21 18.466 36.007 23.561 1.00 0.00 H +ATOM 333 CA VAL A 21 18.727 36.607 21.505 1.00 0.00 C +ATOM 334 HA VAL A 21 18.554 36.039 20.592 1.00 0.00 H +ATOM 335 CB VAL A 21 17.437 37.464 21.780 1.00 0.00 C +ATOM 336 HB VAL A 21 17.477 38.130 22.642 1.00 0.00 H +ATOM 337 CG1 VAL A 21 17.072 38.379 20.673 1.00 0.00 C +ATOM 338 HG11 VAL A 21 16.991 37.805 19.750 1.00 0.00 H +ATOM 339 HG12 VAL A 21 17.685 39.269 20.533 1.00 0.00 H +ATOM 340 HG13 VAL A 21 16.081 38.787 20.874 1.00 0.00 H +ATOM 341 CG2 VAL A 21 16.251 36.536 21.920 1.00 0.00 C +ATOM 342 HG21 VAL A 21 15.333 37.033 21.605 1.00 0.00 H +ATOM 343 HG22 VAL A 21 16.128 36.219 22.956 1.00 0.00 H +ATOM 344 HG23 VAL A 21 16.477 35.681 21.284 1.00 0.00 H +ATOM 345 C VAL A 21 19.976 37.521 21.405 1.00 0.00 C +ATOM 346 O VAL A 21 20.295 38.022 20.306 1.00 0.00 O +ATOM 347 N ASP A 22 20.728 37.651 22.457 1.00 0.00 N +ATOM 348 H ASP A 22 20.460 37.104 23.262 1.00 0.00 H +ATOM 349 CA ASP A 22 21.920 38.517 22.561 1.00 0.00 C +ATOM 350 HA ASP A 22 22.218 38.721 21.532 1.00 0.00 H +ATOM 351 CB ASP A 22 21.483 39.701 23.350 1.00 0.00 C +ATOM 352 HB2 ASP A 22 20.632 40.156 22.843 1.00 0.00 H +ATOM 353 HB3 ASP A 22 21.133 39.421 24.344 1.00 0.00 H +ATOM 354 CG ASP A 22 22.576 40.746 23.590 1.00 0.00 C +ATOM 355 OD1 ASP A 22 23.681 40.588 23.043 1.00 0.00 O +ATOM 356 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O +ATOM 357 C ASP A 22 23.019 37.703 23.294 1.00 0.00 C +ATOM 358 O ASP A 22 22.839 37.184 24.412 1.00 0.00 O +ATOM 359 N ALA A 23 24.210 37.649 22.694 1.00 0.00 N +ATOM 360 H ALA A 23 24.358 38.065 21.786 1.00 0.00 H +ATOM 361 CA ALA A 23 25.493 37.172 23.215 1.00 0.00 C +ATOM 362 HA ALA A 23 25.371 36.089 23.221 1.00 0.00 H +ATOM 363 CB ALA A 23 26.701 37.486 22.326 1.00 0.00 C +ATOM 364 HB1 ALA A 23 26.446 37.309 21.280 1.00 0.00 H +ATOM 365 HB2 ALA A 23 27.379 36.708 22.676 1.00 0.00 H +ATOM 366 HB3 ALA A 23 27.091 38.494 22.468 1.00 0.00 H +ATOM 367 C ALA A 23 25.748 37.757 24.642 1.00 0.00 C +ATOM 368 O ALA A 23 26.091 36.953 25.518 1.00 0.00 O +ATOM 369 N ALA A 24 25.564 39.050 24.846 1.00 0.00 N +ATOM 370 H ALA A 24 25.214 39.674 24.133 1.00 0.00 H +ATOM 371 CA ALA A 24 25.745 39.687 26.153 1.00 0.00 C +ATOM 372 HA ALA A 24 26.761 39.419 26.445 1.00 0.00 H +ATOM 373 CB ALA A 24 25.490 41.189 25.938 1.00 0.00 C +ATOM 374 HB1 ALA A 24 26.247 41.676 25.325 1.00 0.00 H +ATOM 375 HB2 ALA A 24 25.633 41.729 26.874 1.00 0.00 H +ATOM 376 HB3 ALA A 24 24.561 41.467 25.440 1.00 0.00 H +ATOM 377 C ALA A 24 24.796 39.101 27.137 1.00 0.00 C +ATOM 378 O ALA A 24 25.116 38.975 28.329 1.00 0.00 O +ATOM 379 N THR A 25 23.577 38.659 26.736 1.00 0.00 N +ATOM 380 H THR A 25 23.398 38.681 25.743 1.00 0.00 H +ATOM 381 CA THR A 25 22.587 38.094 27.680 1.00 0.00 C +ATOM 382 HA THR A 25 22.755 38.495 28.681 1.00 0.00 H +ATOM 383 CB THR A 25 21.196 38.549 27.262 1.00 0.00 C +ATOM 384 HB THR A 25 20.797 37.883 26.497 1.00 0.00 H +ATOM 385 CG2 THR A 25 20.246 38.369 28.438 1.00 0.00 C +ATOM 386 HG21 THR A 25 20.203 37.329 28.763 1.00 0.00 H +ATOM 387 HG22 THR A 25 19.255 38.740 28.176 1.00 0.00 H +ATOM 388 HG23 THR A 25 20.574 38.977 29.280 1.00 0.00 H +ATOM 389 OG1 THR A 25 21.199 39.931 27.030 1.00 0.00 O +ATOM 390 HG1 THR A 25 20.293 40.156 26.807 1.00 0.00 H +ATOM 391 C THR A 25 22.788 36.618 27.928 1.00 0.00 C +ATOM 392 O THR A 25 22.618 36.164 29.050 1.00 0.00 O +ATOM 393 N ALA A 26 23.216 35.854 26.929 1.00 0.00 N +ATOM 394 H ALA A 26 23.315 36.208 25.988 1.00 0.00 H +ATOM 395 CA ALA A 26 23.652 34.513 27.159 1.00 0.00 C +ATOM 396 HA ALA A 26 22.781 33.940 27.476 1.00 0.00 H +ATOM 397 CB ALA A 26 24.062 33.913 25.734 1.00 0.00 C +ATOM 398 HB1 ALA A 26 23.120 33.732 25.215 1.00 0.00 H +ATOM 399 HB2 ALA A 26 24.695 33.029 25.804 1.00 0.00 H +ATOM 400 HB3 ALA A 26 24.715 34.613 25.211 1.00 0.00 H +ATOM 401 C ALA A 26 24.856 34.523 28.062 1.00 0.00 C +ATOM 402 O ALA A 26 24.889 33.745 28.985 1.00 0.00 O +ATOM 403 N GLU A 27 25.749 35.500 28.027 1.00 0.00 N +ATOM 404 H GLU A 27 25.940 35.933 27.135 1.00 0.00 H +ATOM 405 CA GLU A 27 26.712 35.671 29.037 1.00 0.00 C +ATOM 406 HA GLU A 27 27.306 34.757 29.097 1.00 0.00 H +ATOM 407 CB GLU A 27 27.684 36.833 28.605 1.00 0.00 C +ATOM 408 HB2 GLU A 27 28.270 36.561 27.728 1.00 0.00 H +ATOM 409 HB3 GLU A 27 27.178 37.773 28.387 1.00 0.00 H +ATOM 410 CG GLU A 27 28.742 37.165 29.664 1.00 0.00 C +ATOM 411 HG2 GLU A 27 28.193 37.537 30.529 1.00 0.00 H +ATOM 412 HG3 GLU A 27 29.267 36.244 29.914 1.00 0.00 H +ATOM 413 CD GLU A 27 29.887 38.242 29.269 1.00 0.00 C +ATOM 414 OE1 GLU A 27 31.108 37.827 29.164 1.00 0.00 O +ATOM 415 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O +ATOM 416 C GLU A 27 26.099 35.742 30.450 1.00 0.00 C +ATOM 417 O GLU A 27 26.553 35.162 31.414 1.00 0.00 O +ATOM 418 N LYS A 28 25.124 36.609 30.604 1.00 0.00 N +ATOM 419 H LYS A 28 24.710 37.106 29.827 1.00 0.00 H +ATOM 420 CA LYS A 28 24.538 36.947 31.950 1.00 0.00 C +ATOM 421 HA LYS A 28 25.324 37.300 32.618 1.00 0.00 H +ATOM 422 CB LYS A 28 23.559 38.052 31.728 1.00 0.00 C +ATOM 423 HB2 LYS A 28 24.096 38.943 31.403 1.00 0.00 H +ATOM 424 HB3 LYS A 28 22.761 37.811 31.025 1.00 0.00 H +ATOM 425 CG LYS A 28 22.885 38.401 33.150 1.00 0.00 C +ATOM 426 HG2 LYS A 28 22.343 37.542 33.545 1.00 0.00 H +ATOM 427 HG3 LYS A 28 23.638 38.698 33.879 1.00 0.00 H +ATOM 428 CD LYS A 28 21.826 39.579 33.063 1.00 0.00 C +ATOM 429 HD2 LYS A 28 20.930 39.146 32.616 1.00 0.00 H +ATOM 430 HD3 LYS A 28 21.656 39.989 34.058 1.00 0.00 H +ATOM 431 CE LYS A 28 22.359 40.850 32.267 1.00 0.00 C +ATOM 432 HE2 LYS A 28 23.432 40.899 32.449 1.00 0.00 H +ATOM 433 HE3 LYS A 28 22.199 40.756 31.193 1.00 0.00 H +ATOM 434 NZ LYS A 28 21.521 42.013 32.715 1.00 0.00 N1+ +ATOM 435 HZ1 LYS A 28 21.696 42.294 33.670 1.00 0.00 H +ATOM 436 HZ2 LYS A 28 20.541 41.777 32.653 1.00 0.00 H +ATOM 437 HZ3 LYS A 28 21.651 42.827 32.131 1.00 0.00 H +ATOM 438 C LYS A 28 23.866 35.778 32.535 1.00 0.00 C +ATOM 439 O LYS A 28 23.994 35.665 33.742 1.00 0.00 O +ATOM 440 N VAL A 29 23.329 34.885 31.712 1.00 0.00 N +ATOM 441 H VAL A 29 23.229 35.111 30.733 1.00 0.00 H +ATOM 442 CA VAL A 29 22.736 33.650 32.097 1.00 0.00 C +ATOM 443 HA VAL A 29 21.999 33.879 32.866 1.00 0.00 H +ATOM 444 CB VAL A 29 21.735 33.166 30.962 1.00 0.00 C +ATOM 445 HB VAL A 29 22.375 32.951 30.106 1.00 0.00 H +ATOM 446 CG1 VAL A 29 21.139 31.783 31.445 1.00 0.00 C +ATOM 447 HG11 VAL A 29 20.592 31.413 30.579 1.00 0.00 H +ATOM 448 HG12 VAL A 29 20.575 31.908 32.370 1.00 0.00 H +ATOM 449 HG13 VAL A 29 21.993 31.113 31.534 1.00 0.00 H +ATOM 450 CG2 VAL A 29 20.482 33.992 30.547 1.00 0.00 C +ATOM 451 HG21 VAL A 29 19.966 33.618 29.662 1.00 0.00 H +ATOM 452 HG22 VAL A 29 20.739 35.019 30.286 1.00 0.00 H +ATOM 453 HG23 VAL A 29 19.838 34.110 31.419 1.00 0.00 H +ATOM 454 C VAL A 29 23.781 32.642 32.484 1.00 0.00 C +ATOM 455 O VAL A 29 23.604 31.876 33.462 1.00 0.00 O +ATOM 456 N PHE A 30 24.962 32.641 31.758 1.00 0.00 N +ATOM 457 H PHE A 30 24.997 33.287 30.981 1.00 0.00 H +ATOM 458 CA PHE A 30 26.112 31.701 32.033 1.00 0.00 C +ATOM 459 HA PHE A 30 25.692 30.753 32.371 1.00 0.00 H +ATOM 460 CB PHE A 30 26.901 31.582 30.713 1.00 0.00 C +ATOM 461 HB2 PHE A 30 26.966 32.537 30.191 1.00 0.00 H +ATOM 462 HB3 PHE A 30 27.928 31.266 30.888 1.00 0.00 H +ATOM 463 CG PHE A 30 26.348 30.600 29.656 1.00 0.00 C +ATOM 464 CD1 PHE A 30 25.751 29.296 29.878 1.00 0.00 C +ATOM 465 HD1 PHE A 30 25.705 28.943 30.897 1.00 0.00 H +ATOM 466 CE1 PHE A 30 25.345 28.377 28.817 1.00 0.00 C +ATOM 467 HE1 PHE A 30 24.810 27.464 29.039 1.00 0.00 H +ATOM 468 CZ PHE A 30 25.534 28.840 27.515 1.00 0.00 C +ATOM 469 HZ PHE A 30 25.196 28.267 26.666 1.00 0.00 H +ATOM 470 CE2 PHE A 30 26.096 30.099 27.271 1.00 0.00 C +ATOM 471 HE2 PHE A 30 26.212 30.319 26.219 1.00 0.00 H +ATOM 472 CD2 PHE A 30 26.533 30.924 28.297 1.00 0.00 C +ATOM 473 HD2 PHE A 30 27.135 31.778 28.029 1.00 0.00 H +ATOM 474 C PHE A 30 26.988 32.189 33.246 1.00 0.00 C +ATOM 475 O PHE A 30 27.609 31.344 33.905 1.00 0.00 O +ATOM 476 N LYS A 31 27.038 33.446 33.540 1.00 0.00 N +ATOM 477 H LYS A 31 26.710 34.105 32.849 1.00 0.00 H +ATOM 478 CA LYS A 31 27.405 34.022 34.854 1.00 0.00 C +ATOM 479 HA LYS A 31 28.437 33.764 35.092 1.00 0.00 H +ATOM 480 CB LYS A 31 27.274 35.599 34.858 1.00 0.00 C +ATOM 481 HB2 LYS A 31 26.242 35.714 34.527 1.00 0.00 H +ATOM 482 HB3 LYS A 31 27.292 36.098 35.827 1.00 0.00 H +ATOM 483 CG LYS A 31 28.378 36.275 33.919 1.00 0.00 C +ATOM 484 HG2 LYS A 31 28.522 35.710 32.997 1.00 0.00 H +ATOM 485 HG3 LYS A 31 27.926 37.229 33.649 1.00 0.00 H +ATOM 486 CD LYS A 31 29.823 36.487 34.439 1.00 0.00 C +ATOM 487 HD2 LYS A 31 29.755 36.977 35.411 1.00 0.00 H +ATOM 488 HD3 LYS A 31 30.132 35.472 34.684 1.00 0.00 H +ATOM 489 CE LYS A 31 30.777 37.150 33.394 1.00 0.00 C +ATOM 490 HE2 LYS A 31 30.633 36.630 32.447 1.00 0.00 H +ATOM 491 HE3 LYS A 31 30.436 38.158 33.158 1.00 0.00 H +ATOM 492 NZ LYS A 31 32.138 37.121 33.926 1.00 0.00 N1+ +ATOM 493 HZ1 LYS A 31 32.272 37.458 34.869 1.00 0.00 H +ATOM 494 HZ2 LYS A 31 32.676 37.777 33.376 1.00 0.00 H +ATOM 495 HZ3 LYS A 31 32.555 36.210 33.805 1.00 0.00 H +ATOM 496 C LYS A 31 26.516 33.562 35.983 1.00 0.00 C +ATOM 497 O LYS A 31 27.018 32.993 36.943 1.00 0.00 O +ATOM 498 N GLN A 32 25.185 33.745 35.953 1.00 0.00 N +ATOM 499 H GLN A 32 24.737 34.194 35.166 1.00 0.00 H +ATOM 500 CA GLN A 32 24.365 33.197 37.027 1.00 0.00 C +ATOM 501 HA GLN A 32 24.679 33.822 37.863 1.00 0.00 H +ATOM 502 CB GLN A 32 22.891 33.427 36.688 1.00 0.00 C +ATOM 503 HB2 GLN A 32 22.845 33.366 35.601 1.00 0.00 H +ATOM 504 HB3 GLN A 32 22.285 32.685 37.209 1.00 0.00 H +ATOM 505 CG GLN A 32 22.280 34.840 37.028 1.00 0.00 C +ATOM 506 HG2 GLN A 32 22.039 34.881 38.090 1.00 0.00 H +ATOM 507 HG3 GLN A 32 22.899 35.710 36.807 1.00 0.00 H +ATOM 508 CD GLN A 32 20.958 35.124 36.195 1.00 0.00 C +ATOM 509 OE1 GLN A 32 19.883 34.823 36.738 1.00 0.00 O +ATOM 510 NE2 GLN A 32 20.988 35.530 34.974 1.00 0.00 N +ATOM 511 HE21 GLN A 32 21.902 35.787 34.628 1.00 0.00 H +ATOM 512 HE22 GLN A 32 20.177 35.714 34.400 1.00 0.00 H +ATOM 513 C GLN A 32 24.598 31.707 37.232 1.00 0.00 C +ATOM 514 O GLN A 32 24.794 31.293 38.384 1.00 0.00 O +ATOM 515 N TYR A 33 24.530 30.875 36.142 1.00 0.00 N +ATOM 516 H TYR A 33 24.587 31.274 35.216 1.00 0.00 H +ATOM 517 CA TYR A 33 24.722 29.459 36.217 1.00 0.00 C +ATOM 518 HA TYR A 33 23.881 29.042 36.772 1.00 0.00 H +ATOM 519 CB TYR A 33 24.622 28.848 34.842 1.00 0.00 C +ATOM 520 HB2 TYR A 33 23.621 29.006 34.442 1.00 0.00 H +ATOM 521 HB3 TYR A 33 25.353 29.388 34.240 1.00 0.00 H +ATOM 522 CG TYR A 33 24.877 27.304 34.704 1.00 0.00 C +ATOM 523 CD1 TYR A 33 23.808 26.383 34.938 1.00 0.00 C +ATOM 524 HD1 TYR A 33 22.814 26.754 35.140 1.00 0.00 H +ATOM 525 CE1 TYR A 33 24.054 24.991 35.075 1.00 0.00 C +ATOM 526 HE1 TYR A 33 23.300 24.251 35.300 1.00 0.00 H +ATOM 527 CZ TYR A 33 25.399 24.562 34.934 1.00 0.00 C +ATOM 528 OH TYR A 33 25.658 23.212 34.983 1.00 0.00 O +ATOM 529 HH TYR A 33 26.608 23.080 35.030 1.00 0.00 H +ATOM 530 CE2 TYR A 33 26.410 25.459 34.723 1.00 0.00 C +ATOM 531 HE2 TYR A 33 27.443 25.157 34.630 1.00 0.00 H +ATOM 532 CD2 TYR A 33 26.146 26.818 34.602 1.00 0.00 C +ATOM 533 HD2 TYR A 33 26.992 27.469 34.435 1.00 0.00 H +ATOM 534 C TYR A 33 26.078 29.155 36.854 1.00 0.00 C +ATOM 535 O TYR A 33 26.179 28.186 37.566 1.00 0.00 O +ATOM 536 N ALA A 34 27.159 29.788 36.508 1.00 0.00 N +ATOM 537 H ALA A 34 26.997 30.563 35.881 1.00 0.00 H +ATOM 538 CA ALA A 34 28.473 29.535 37.100 1.00 0.00 C +ATOM 539 HA ALA A 34 28.717 28.476 37.023 1.00 0.00 H +ATOM 540 CB ALA A 34 29.651 30.265 36.402 1.00 0.00 C +ATOM 541 HB1 ALA A 34 30.577 29.813 36.757 1.00 0.00 H +ATOM 542 HB2 ALA A 34 29.619 31.296 36.752 1.00 0.00 H +ATOM 543 HB3 ALA A 34 29.681 30.159 35.317 1.00 0.00 H +ATOM 544 C ALA A 34 28.508 29.835 38.614 1.00 0.00 C +ATOM 545 O ALA A 34 29.097 29.077 39.389 1.00 0.00 O +ATOM 546 N ASN A 35 27.814 30.864 39.024 1.00 0.00 N +ATOM 547 H ASN A 35 27.594 31.535 38.301 1.00 0.00 H +ATOM 548 CA ASN A 35 27.743 31.252 40.445 1.00 0.00 C +ATOM 549 HA ASN A 35 28.713 31.168 40.935 1.00 0.00 H +ATOM 550 CB ASN A 35 27.254 32.684 40.541 1.00 0.00 C +ATOM 551 HB2 ASN A 35 27.798 33.361 39.883 1.00 0.00 H +ATOM 552 HB3 ASN A 35 26.192 32.727 40.300 1.00 0.00 H +ATOM 553 CG ASN A 35 27.326 33.169 41.947 1.00 0.00 C +ATOM 554 OD1 ASN A 35 26.493 32.743 42.763 1.00 0.00 O +ATOM 555 ND2 ASN A 35 28.099 34.183 42.223 1.00 0.00 N +ATOM 556 HD21 ASN A 35 28.867 34.350 41.589 1.00 0.00 H +ATOM 557 HD22 ASN A 35 28.276 34.397 43.193 1.00 0.00 H +ATOM 558 C ASN A 35 26.833 30.200 41.127 1.00 0.00 C +ATOM 559 O ASN A 35 27.114 29.686 42.238 1.00 0.00 O +ATOM 560 N ASP A 36 25.819 29.616 40.395 1.00 0.00 N +ATOM 561 H ASP A 36 25.608 30.144 39.560 1.00 0.00 H +ATOM 562 CA ASP A 36 25.004 28.401 40.867 1.00 0.00 C +ATOM 563 HA ASP A 36 24.491 28.819 41.733 1.00 0.00 H +ATOM 564 CB ASP A 36 23.819 28.175 39.948 1.00 0.00 C +ATOM 565 HB2 ASP A 36 23.379 29.117 39.623 1.00 0.00 H +ATOM 566 HB3 ASP A 36 24.279 27.586 39.154 1.00 0.00 H +ATOM 567 CG ASP A 36 22.720 27.350 40.470 1.00 0.00 C +ATOM 568 OD1 ASP A 36 22.214 26.485 39.714 1.00 0.00 O +ATOM 569 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O +ATOM 570 C ASP A 36 25.793 27.113 41.244 1.00 0.00 C +ATOM 571 O ASP A 36 25.357 26.391 42.112 1.00 0.00 O +ATOM 572 N ASN A 37 26.991 27.006 40.666 1.00 0.00 N +ATOM 573 H ASN A 37 27.306 27.779 40.098 1.00 0.00 H +ATOM 574 CA ASN A 37 27.829 25.814 40.636 1.00 0.00 C +ATOM 575 HA ASN A 37 27.378 25.130 41.354 1.00 0.00 H +ATOM 576 CB ASN A 37 27.873 25.281 39.195 1.00 0.00 C +ATOM 577 HB2 ASN A 37 27.936 26.106 38.487 1.00 0.00 H +ATOM 578 HB3 ASN A 37 28.702 24.579 39.101 1.00 0.00 H +ATOM 579 CG ASN A 37 26.652 24.492 38.842 1.00 0.00 C +ATOM 580 OD1 ASN A 37 26.432 23.357 39.282 1.00 0.00 O +ATOM 581 ND2 ASN A 37 25.706 25.057 38.177 1.00 0.00 N +ATOM 582 HD21 ASN A 37 25.804 26.050 38.016 1.00 0.00 H +ATOM 583 HD22 ASN A 37 24.895 24.502 37.947 1.00 0.00 H +ATOM 584 C ASN A 37 29.196 26.053 41.261 1.00 0.00 C +ATOM 585 O ASN A 37 30.064 25.171 41.182 1.00 0.00 O +ATOM 586 N GLY A 38 29.358 27.176 42.012 1.00 0.00 N +ATOM 587 H GLY A 38 28.556 27.765 42.189 1.00 0.00 H +ATOM 588 CA GLY A 38 30.637 27.460 42.681 1.00 0.00 C +ATOM 589 HA2 GLY A 38 30.444 28.296 43.354 1.00 0.00 H +ATOM 590 HA3 GLY A 38 30.900 26.655 43.368 1.00 0.00 H +ATOM 591 C GLY A 38 31.894 27.774 41.785 1.00 0.00 C +ATOM 592 O GLY A 38 33.027 27.429 42.124 1.00 0.00 O +ATOM 593 N VAL A 39 31.731 28.287 40.579 1.00 0.00 N +ATOM 594 H VAL A 39 30.794 28.624 40.408 1.00 0.00 H +ATOM 595 CA VAL A 39 32.664 28.449 39.403 1.00 0.00 C +ATOM 596 HA VAL A 39 33.598 27.911 39.570 1.00 0.00 H +ATOM 597 CB VAL A 39 32.015 27.778 38.179 1.00 0.00 C +ATOM 598 HB VAL A 39 31.005 28.158 38.027 1.00 0.00 H +ATOM 599 CG1 VAL A 39 32.989 28.121 37.014 1.00 0.00 C +ATOM 600 HG11 VAL A 39 32.636 27.519 36.176 1.00 0.00 H +ATOM 601 HG12 VAL A 39 34.019 27.963 37.334 1.00 0.00 H +ATOM 602 HG13 VAL A 39 32.869 29.117 36.588 1.00 0.00 H +ATOM 603 CG2 VAL A 39 31.943 26.274 38.437 1.00 0.00 C +ATOM 604 HG21 VAL A 39 31.540 25.729 37.583 1.00 0.00 H +ATOM 605 HG22 VAL A 39 31.356 26.086 39.337 1.00 0.00 H +ATOM 606 HG23 VAL A 39 32.907 25.863 38.738 1.00 0.00 H +ATOM 607 C VAL A 39 33.029 29.909 39.235 1.00 0.00 C +ATOM 608 O VAL A 39 32.186 30.683 38.757 1.00 0.00 O +ATOM 609 N ASP A 40 34.268 30.281 39.558 1.00 0.00 N +ATOM 610 H ASP A 40 34.838 29.543 39.947 1.00 0.00 H +ATOM 611 CA ASP A 40 34.875 31.551 39.096 1.00 0.00 C +ATOM 612 HA ASP A 40 34.143 32.078 38.487 1.00 0.00 H +ATOM 613 CB ASP A 40 35.183 32.418 40.345 1.00 0.00 C +ATOM 614 HB2 ASP A 40 34.184 32.657 40.710 1.00 0.00 H +ATOM 615 HB3 ASP A 40 35.707 31.788 41.065 1.00 0.00 H +ATOM 616 CG ASP A 40 35.879 33.683 40.009 1.00 0.00 C +ATOM 617 OD1 ASP A 40 35.393 34.410 39.076 1.00 0.00 O +ATOM 618 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O +ATOM 619 C ASP A 40 36.062 31.169 38.238 1.00 0.00 C +ATOM 620 O ASP A 40 36.850 30.275 38.630 1.00 0.00 O +ATOM 621 N GLY A 41 36.172 31.751 37.102 1.00 0.00 N +ATOM 622 H GLY A 41 35.443 32.408 36.858 1.00 0.00 H +ATOM 623 CA GLY A 41 37.214 31.484 36.189 1.00 0.00 C +ATOM 624 HA2 GLY A 41 38.072 31.014 36.670 1.00 0.00 H +ATOM 625 HA3 GLY A 41 36.761 30.672 35.620 1.00 0.00 H +ATOM 626 C GLY A 41 37.623 32.709 35.379 1.00 0.00 C +ATOM 627 O GLY A 41 37.288 33.862 35.686 1.00 0.00 O +ATOM 628 N GLU A 42 38.354 32.422 34.316 1.00 0.00 N +ATOM 629 H GLU A 42 38.789 31.512 34.368 1.00 0.00 H +ATOM 630 CA GLU A 42 38.603 33.310 33.228 1.00 0.00 C +ATOM 631 HA GLU A 42 38.329 34.318 33.541 1.00 0.00 H +ATOM 632 CB GLU A 42 40.158 33.294 33.040 1.00 0.00 C +ATOM 633 HB2 GLU A 42 40.656 33.398 34.004 1.00 0.00 H +ATOM 634 HB3 GLU A 42 40.417 32.326 32.611 1.00 0.00 H +ATOM 635 CG GLU A 42 40.673 34.328 32.046 1.00 0.00 C +ATOM 636 HG2 GLU A 42 41.606 34.015 31.580 1.00 0.00 H +ATOM 637 HG3 GLU A 42 39.970 34.501 31.231 1.00 0.00 H +ATOM 638 CD GLU A 42 41.014 35.613 32.804 1.00 0.00 C +ATOM 639 OE1 GLU A 42 41.944 35.693 33.644 1.00 0.00 O +ATOM 640 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O +ATOM 641 C GLU A 42 37.780 33.033 32.033 1.00 0.00 C +ATOM 642 O GLU A 42 37.577 31.870 31.690 1.00 0.00 O +ATOM 643 N TRP A 43 37.228 34.069 31.412 1.00 0.00 N +ATOM 644 H TRP A 43 37.423 35.035 31.634 1.00 0.00 H +ATOM 645 CA TRP A 43 36.233 33.951 30.354 1.00 0.00 C +ATOM 646 HA TRP A 43 35.850 32.931 30.348 1.00 0.00 H +ATOM 647 CB TRP A 43 34.984 34.889 30.616 1.00 0.00 C +ATOM 648 HB2 TRP A 43 35.436 35.868 30.771 1.00 0.00 H +ATOM 649 HB3 TRP A 43 34.427 34.918 29.679 1.00 0.00 H +ATOM 650 CG TRP A 43 34.115 34.536 31.838 1.00 0.00 C +ATOM 651 CD1 TRP A 43 34.428 34.708 33.154 1.00 0.00 C +ATOM 652 HD1 TRP A 43 35.387 35.052 33.511 1.00 0.00 H +ATOM 653 NE1 TRP A 43 33.399 34.110 33.877 1.00 0.00 N +ATOM 654 HE1 TRP A 43 33.511 34.066 34.880 1.00 0.00 H +ATOM 655 CE2 TRP A 43 32.444 33.463 33.073 1.00 0.00 C +ATOM 656 CZ2 TRP A 43 31.248 32.745 33.296 1.00 0.00 C +ATOM 657 HZ2 TRP A 43 31.007 32.429 34.301 1.00 0.00 H +ATOM 658 CH2 TRP A 43 30.575 32.194 32.199 1.00 0.00 C +ATOM 659 HH2 TRP A 43 29.740 31.527 32.355 1.00 0.00 H +ATOM 660 CZ3 TRP A 43 30.988 32.541 30.909 1.00 0.00 C +ATOM 661 HZ3 TRP A 43 30.412 32.236 30.047 1.00 0.00 H +ATOM 662 CE3 TRP A 43 32.109 33.327 30.682 1.00 0.00 C +ATOM 663 HE3 TRP A 43 32.397 33.679 29.703 1.00 0.00 H +ATOM 664 CD2 TRP A 43 32.870 33.817 31.765 1.00 0.00 C +ATOM 665 C TRP A 43 36.910 34.235 29.034 1.00 0.00 C +ATOM 666 O TRP A 43 37.660 35.202 28.823 1.00 0.00 O +ATOM 667 N THR A 44 36.468 33.398 28.113 1.00 0.00 N +ATOM 668 H THR A 44 35.919 32.590 28.367 1.00 0.00 H +ATOM 669 CA THR A 44 36.627 33.526 26.668 1.00 0.00 C +ATOM 670 HA THR A 44 36.825 34.580 26.474 1.00 0.00 H +ATOM 671 CB THR A 44 37.813 32.794 26.062 1.00 0.00 C +ATOM 672 HB THR A 44 37.695 32.789 24.978 1.00 0.00 H +ATOM 673 CG2 THR A 44 39.142 33.411 26.470 1.00 0.00 C +ATOM 674 HG21 THR A 44 39.971 32.814 26.090 1.00 0.00 H +ATOM 675 HG22 THR A 44 39.277 33.395 27.552 1.00 0.00 H +ATOM 676 HG23 THR A 44 39.360 34.408 26.088 1.00 0.00 H +ATOM 677 OG1 THR A 44 37.854 31.507 26.604 1.00 0.00 O +ATOM 678 HG1 THR A 44 37.629 30.907 25.889 1.00 0.00 H +ATOM 679 C THR A 44 35.267 33.295 26.005 1.00 0.00 C +ATOM 680 O THR A 44 34.480 32.577 26.444 1.00 0.00 O +ATOM 681 N TYR A 45 35.137 33.919 24.848 1.00 0.00 N +ATOM 682 H TYR A 45 35.900 34.526 24.585 1.00 0.00 H +ATOM 683 CA TYR A 45 34.051 33.679 23.814 1.00 0.00 C +ATOM 684 HA TYR A 45 33.565 32.748 24.109 1.00 0.00 H +ATOM 685 CB TYR A 45 33.061 34.890 23.836 1.00 0.00 C +ATOM 686 HB2 TYR A 45 32.689 35.085 24.843 1.00 0.00 H +ATOM 687 HB3 TYR A 45 33.670 35.762 23.596 1.00 0.00 H +ATOM 688 CG TYR A 45 31.825 34.747 22.962 1.00 0.00 C +ATOM 689 CD1 TYR A 45 30.955 33.684 23.061 1.00 0.00 C +ATOM 690 HD1 TYR A 45 31.040 32.945 23.845 1.00 0.00 H +ATOM 691 CE1 TYR A 45 29.908 33.556 22.116 1.00 0.00 C +ATOM 692 HE1 TYR A 45 29.113 32.849 22.291 1.00 0.00 H +ATOM 693 CZ TYR A 45 29.718 34.506 21.094 1.00 0.00 C +ATOM 694 OH TYR A 45 28.658 34.338 20.268 1.00 0.00 O +ATOM 695 HH TYR A 45 28.496 35.052 19.648 1.00 0.00 H +ATOM 696 CE2 TYR A 45 30.653 35.574 21.028 1.00 0.00 C +ATOM 697 HE2 TYR A 45 30.490 36.288 20.234 1.00 0.00 H +ATOM 698 CD2 TYR A 45 31.752 35.643 21.911 1.00 0.00 C +ATOM 699 HD2 TYR A 45 32.537 36.346 21.679 1.00 0.00 H +ATOM 700 C TYR A 45 34.545 33.529 22.336 1.00 0.00 C +ATOM 701 O TYR A 45 35.260 34.412 21.809 1.00 0.00 O +ATOM 702 N ASP A 46 33.924 32.567 21.640 1.00 0.00 N +ATOM 703 H ASP A 46 33.215 32.006 22.088 1.00 0.00 H +ATOM 704 CA ASP A 46 34.109 32.289 20.204 1.00 0.00 C +ATOM 705 HA ASP A 46 34.805 32.896 19.625 1.00 0.00 H +ATOM 706 CB ASP A 46 34.818 30.917 20.240 1.00 0.00 C +ATOM 707 HB2 ASP A 46 35.700 31.032 20.871 1.00 0.00 H +ATOM 708 HB3 ASP A 46 34.252 30.200 20.834 1.00 0.00 H +ATOM 709 CG ASP A 46 35.216 30.282 18.912 1.00 0.00 C +ATOM 710 OD1 ASP A 46 34.405 29.507 18.323 1.00 0.00 O +ATOM 711 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O +ATOM 712 C ASP A 46 32.877 32.275 19.319 1.00 0.00 C +ATOM 713 O ASP A 46 31.931 31.517 19.529 1.00 0.00 O +ATOM 714 N ASP A 47 32.833 33.220 18.413 1.00 0.00 N +ATOM 715 H ASP A 47 33.622 33.852 18.429 1.00 0.00 H +ATOM 716 CA ASP A 47 31.688 33.456 17.554 1.00 0.00 C +ATOM 717 HA ASP A 47 30.773 33.561 18.137 1.00 0.00 H +ATOM 718 CB ASP A 47 31.907 34.738 16.747 1.00 0.00 C +ATOM 719 HB2 ASP A 47 32.113 35.510 17.488 1.00 0.00 H +ATOM 720 HB3 ASP A 47 32.853 34.697 16.207 1.00 0.00 H +ATOM 721 CG ASP A 47 30.729 35.187 15.844 1.00 0.00 C +ATOM 722 OD1 ASP A 47 29.551 35.040 16.174 1.00 0.00 O +ATOM 723 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O +ATOM 724 C ASP A 47 31.522 32.326 16.557 1.00 0.00 C +ATOM 725 O ASP A 47 30.390 32.069 16.134 1.00 0.00 O +ATOM 726 N ALA A 48 32.555 31.657 16.092 1.00 0.00 N +ATOM 727 H ALA A 48 33.490 31.931 16.357 1.00 0.00 H +ATOM 728 CA ALA A 48 32.437 30.647 15.015 1.00 0.00 C +ATOM 729 HA ALA A 48 31.707 31.108 14.349 1.00 0.00 H +ATOM 730 CB ALA A 48 33.821 30.467 14.340 1.00 0.00 C +ATOM 731 HB1 ALA A 48 34.244 31.399 13.964 1.00 0.00 H +ATOM 732 HB2 ALA A 48 33.675 29.706 13.573 1.00 0.00 H +ATOM 733 HB3 ALA A 48 34.421 29.986 15.112 1.00 0.00 H +ATOM 734 C ALA A 48 31.855 29.301 15.549 1.00 0.00 C +ATOM 735 O ALA A 48 31.548 28.445 14.720 1.00 0.00 O +ATOM 736 N THR A 49 31.619 29.163 16.885 1.00 0.00 N +ATOM 737 H THR A 49 31.975 29.929 17.439 1.00 0.00 H +ATOM 738 CA THR A 49 30.811 28.126 17.576 1.00 0.00 C +ATOM 739 HA THR A 49 30.371 27.544 16.767 1.00 0.00 H +ATOM 740 CB THR A 49 31.713 27.100 18.310 1.00 0.00 C +ATOM 741 HB THR A 49 31.134 26.420 18.935 1.00 0.00 H +ATOM 742 CG2 THR A 49 32.614 26.280 17.436 1.00 0.00 C +ATOM 743 HG21 THR A 49 33.329 26.868 16.859 1.00 0.00 H +ATOM 744 HG22 THR A 49 32.002 25.593 16.853 1.00 0.00 H +ATOM 745 HG23 THR A 49 33.354 25.760 18.044 1.00 0.00 H +ATOM 746 OG1 THR A 49 32.507 27.834 19.222 1.00 0.00 O +ATOM 747 HG1 THR A 49 33.151 28.336 18.715 1.00 0.00 H +ATOM 748 C THR A 49 29.713 28.644 18.468 1.00 0.00 C +ATOM 749 O THR A 49 28.941 27.912 19.103 1.00 0.00 O +ATOM 750 N LYS A 50 29.628 29.977 18.649 1.00 0.00 N +ATOM 751 H LYS A 50 30.419 30.522 18.334 1.00 0.00 H +ATOM 752 CA LYS A 50 28.663 30.695 19.541 1.00 0.00 C +ATOM 753 HA LYS A 50 28.847 31.769 19.501 1.00 0.00 H +ATOM 754 CB LYS A 50 27.189 30.625 19.033 1.00 0.00 C +ATOM 755 HB2 LYS A 50 26.936 29.572 19.163 1.00 0.00 H +ATOM 756 HB3 LYS A 50 26.469 31.081 19.712 1.00 0.00 H +ATOM 757 CG LYS A 50 27.119 30.984 17.465 1.00 0.00 C +ATOM 758 HG2 LYS A 50 27.961 30.590 16.895 1.00 0.00 H +ATOM 759 HG3 LYS A 50 26.188 30.551 17.100 1.00 0.00 H +ATOM 760 CD LYS A 50 27.025 32.547 17.322 1.00 0.00 C +ATOM 761 HD2 LYS A 50 26.337 33.099 17.964 1.00 0.00 H +ATOM 762 HD3 LYS A 50 28.005 32.913 17.623 1.00 0.00 H +ATOM 763 CE LYS A 50 26.686 32.933 15.930 1.00 0.00 C +ATOM 764 HE2 LYS A 50 25.829 32.363 15.572 1.00 0.00 H +ATOM 765 HE3 LYS A 50 26.304 33.953 15.986 1.00 0.00 H +ATOM 766 NZ LYS A 50 27.861 32.905 14.990 1.00 0.00 N1+ +ATOM 767 HZ1 LYS A 50 28.562 33.507 15.397 1.00 0.00 H +ATOM 768 HZ2 LYS A 50 27.597 33.321 14.108 1.00 0.00 H +ATOM 769 HZ3 LYS A 50 28.269 32.017 14.736 1.00 0.00 H +ATOM 770 C LYS A 50 28.884 30.250 21.033 1.00 0.00 C +ATOM 771 O LYS A 50 27.958 30.206 21.826 1.00 0.00 O +ATOM 772 N THR A 51 30.148 29.820 21.328 1.00 0.00 N +ATOM 773 H THR A 51 30.940 30.100 20.766 1.00 0.00 H +ATOM 774 CA THR A 51 30.503 29.214 22.632 1.00 0.00 C +ATOM 775 HA THR A 51 29.680 28.714 23.142 1.00 0.00 H +ATOM 776 CB THR A 51 31.313 27.944 22.369 1.00 0.00 C +ATOM 777 HB THR A 51 32.245 28.102 21.826 1.00 0.00 H +ATOM 778 CG2 THR A 51 31.703 27.088 23.590 1.00 0.00 C +ATOM 779 HG21 THR A 51 32.177 26.160 23.272 1.00 0.00 H +ATOM 780 HG22 THR A 51 30.745 26.977 24.100 1.00 0.00 H +ATOM 781 HG23 THR A 51 32.401 27.677 24.186 1.00 0.00 H +ATOM 782 OG1 THR A 51 30.404 27.161 21.659 1.00 0.00 O +ATOM 783 HG1 THR A 51 29.757 27.683 21.179 1.00 0.00 H +ATOM 784 C THR A 51 31.202 30.120 23.549 1.00 0.00 C +ATOM 785 O THR A 51 32.200 30.721 23.143 1.00 0.00 O +ATOM 786 N PHE A 52 31.009 29.926 24.845 1.00 0.00 N +ATOM 787 H PHE A 52 30.125 29.479 25.042 1.00 0.00 H +ATOM 788 CA PHE A 52 31.821 30.391 25.941 1.00 0.00 C +ATOM 789 HA PHE A 52 32.490 31.192 25.628 1.00 0.00 H +ATOM 790 CB PHE A 52 30.715 30.979 27.007 1.00 0.00 C +ATOM 791 HB2 PHE A 52 29.988 30.200 27.238 1.00 0.00 H +ATOM 792 HB3 PHE A 52 31.250 31.298 27.901 1.00 0.00 H +ATOM 793 CG PHE A 52 30.049 32.222 26.534 1.00 0.00 C +ATOM 794 CD1 PHE A 52 28.876 32.142 25.781 1.00 0.00 C +ATOM 795 HD1 PHE A 52 28.413 31.204 25.515 1.00 0.00 H +ATOM 796 CE1 PHE A 52 28.300 33.350 25.304 1.00 0.00 C +ATOM 797 HE1 PHE A 52 27.303 33.316 24.890 1.00 0.00 H +ATOM 798 CZ PHE A 52 28.880 34.593 25.500 1.00 0.00 C +ATOM 799 HZ PHE A 52 28.417 35.460 25.054 1.00 0.00 H +ATOM 800 CE2 PHE A 52 30.122 34.665 26.192 1.00 0.00 C +ATOM 801 HE2 PHE A 52 30.650 35.597 26.333 1.00 0.00 H +ATOM 802 CD2 PHE A 52 30.597 33.495 26.795 1.00 0.00 C +ATOM 803 HD2 PHE A 52 31.435 33.581 27.471 1.00 0.00 H +ATOM 804 C PHE A 52 32.721 29.343 26.553 1.00 0.00 C +ATOM 805 O PHE A 52 32.280 28.240 26.674 1.00 0.00 O +ATOM 806 N THR A 53 33.908 29.829 27.087 1.00 0.00 N +ATOM 807 H THR A 53 34.203 30.784 26.938 1.00 0.00 H +ATOM 808 CA THR A 53 34.577 29.044 28.132 1.00 0.00 C +ATOM 809 HA THR A 53 34.003 28.190 28.492 1.00 0.00 H +ATOM 810 CB THR A 53 35.881 28.443 27.684 1.00 0.00 C +ATOM 811 HB THR A 53 36.513 29.234 27.280 1.00 0.00 H +ATOM 812 CG2 THR A 53 36.620 27.571 28.752 1.00 0.00 C +ATOM 813 HG21 THR A 53 36.814 28.236 29.595 1.00 0.00 H +ATOM 814 HG22 THR A 53 37.535 27.174 28.313 1.00 0.00 H +ATOM 815 HG23 THR A 53 35.924 26.795 29.068 1.00 0.00 H +ATOM 816 OG1 THR A 53 35.605 27.649 26.584 1.00 0.00 O +ATOM 817 HG1 THR A 53 35.459 28.177 25.796 1.00 0.00 H +ATOM 818 C THR A 53 34.776 29.748 29.443 1.00 0.00 C +ATOM 819 O THR A 53 35.146 30.939 29.437 1.00 0.00 O +ATOM 820 N VAL A 54 34.499 29.135 30.639 1.00 0.00 N +ATOM 821 H VAL A 54 34.209 28.173 30.538 1.00 0.00 H +ATOM 822 CA VAL A 54 34.861 29.536 31.982 1.00 0.00 C +ATOM 823 HA VAL A 54 35.382 30.493 31.978 1.00 0.00 H +ATOM 824 CB VAL A 54 33.697 29.716 32.869 1.00 0.00 C +ATOM 825 HB VAL A 54 32.913 30.335 32.434 1.00 0.00 H +ATOM 826 CG1 VAL A 54 33.002 28.394 33.289 1.00 0.00 C +ATOM 827 HG11 VAL A 54 33.690 27.666 33.718 1.00 0.00 H +ATOM 828 HG12 VAL A 54 32.618 28.014 32.342 1.00 0.00 H +ATOM 829 HG13 VAL A 54 32.093 28.525 33.877 1.00 0.00 H +ATOM 830 CG2 VAL A 54 34.118 30.320 34.224 1.00 0.00 C +ATOM 831 HG21 VAL A 54 34.711 31.228 34.123 1.00 0.00 H +ATOM 832 HG22 VAL A 54 34.691 29.664 34.880 1.00 0.00 H +ATOM 833 HG23 VAL A 54 33.202 30.551 34.767 1.00 0.00 H +ATOM 834 C VAL A 54 35.950 28.590 32.468 1.00 0.00 C +ATOM 835 O VAL A 54 35.738 27.385 32.660 1.00 0.00 O +ATOM 836 N THR A 55 37.187 29.085 32.651 1.00 0.00 N +ATOM 837 H THR A 55 37.326 30.038 32.345 1.00 0.00 H +ATOM 838 CA THR A 55 38.418 28.363 33.071 1.00 0.00 C +ATOM 839 HA THR A 55 38.197 27.299 32.991 1.00 0.00 H +ATOM 840 CB THR A 55 39.574 28.516 32.161 1.00 0.00 C +ATOM 841 HB THR A 55 39.757 29.581 32.019 1.00 0.00 H +ATOM 842 CG2 THR A 55 40.870 27.898 32.786 1.00 0.00 C +ATOM 843 HG21 THR A 55 40.583 26.849 32.855 1.00 0.00 H +ATOM 844 HG22 THR A 55 41.023 28.190 33.826 1.00 0.00 H +ATOM 845 HG23 THR A 55 41.825 28.044 32.280 1.00 0.00 H +ATOM 846 OG1 THR A 55 39.215 27.970 30.818 1.00 0.00 O +ATOM 847 HG1 THR A 55 38.792 28.725 30.401 1.00 0.00 H +ATOM 848 C THR A 55 38.779 28.725 34.458 1.00 0.00 C +ATOM 849 O THR A 55 39.263 29.841 34.735 1.00 0.00 O +ATOM 850 N GLU A 56 38.757 27.773 35.416 1.00 0.00 N +ATOM 851 H GLU A 56 38.459 26.869 35.079 1.00 0.00 H +ATOM 852 CA GLU A 56 39.045 27.993 36.888 1.00 0.00 C +ATOM 853 HA GLU A 56 38.618 28.921 37.267 1.00 0.00 H +ATOM 854 CB GLU A 56 38.402 26.911 37.749 1.00 0.00 C +ATOM 855 HB2 GLU A 56 37.329 27.019 37.593 1.00 0.00 H +ATOM 856 HB3 GLU A 56 38.780 25.905 37.563 1.00 0.00 H +ATOM 857 CG GLU A 56 38.436 27.078 39.267 1.00 0.00 C +ATOM 858 HG2 GLU A 56 39.455 26.968 39.636 1.00 0.00 H +ATOM 859 HG3 GLU A 56 38.094 28.097 39.445 1.00 0.00 H +ATOM 860 CD GLU A 56 37.514 26.014 39.918 1.00 0.00 C +ATOM 861 OE1 GLU A 56 37.905 24.823 39.870 1.00 0.00 O +ATOM 862 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O +ATOM 863 C GLU A 56 40.488 28.137 37.301 1.00 0.00 C +ATOM 864 O GLU A 56 40.807 29.090 38.025 1.00 0.00 O +ATOM 865 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O +CONECT 1 2 3 4 5 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 1 6 7 18 +CONECT 6 5 +CONECT 7 5 8 9 10 +CONECT 8 7 +CONECT 9 7 +CONECT 10 7 11 12 13 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 +CONECT 14 13 15 16 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 20 +CONECT 19 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 23 24 32 +CONECT 23 22 +CONECT 24 22 25 26 30 +CONECT 25 24 +CONECT 26 24 27 28 29 +CONECT 27 26 +CONECT 28 26 +CONECT 29 26 +CONECT 30 24 31 +CONECT 31 30 +CONECT 32 22 33 34 +CONECT 33 32 +CONECT 34 32 35 36 +CONECT 35 34 +CONECT 36 34 37 38 53 +CONECT 37 36 +CONECT 38 36 39 40 41 +CONECT 39 38 +CONECT 40 38 +CONECT 41 38 42 51 +CONECT 42 41 43 44 +CONECT 43 42 +CONECT 44 42 45 46 +CONECT 45 44 +CONECT 46 44 47 49 +CONECT 47 46 48 +CONECT 48 47 +CONECT 49 46 50 51 +CONECT 50 49 +CONECT 51 41 49 52 +CONECT 52 51 +CONECT 53 36 54 55 +CONECT 54 53 +CONECT 55 53 56 57 +CONECT 56 55 +CONECT 57 55 58 59 75 +CONECT 58 57 +CONECT 59 57 60 61 62 +CONECT 60 59 +CONECT 61 59 +CONECT 62 59 63 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 67 68 +CONECT 66 65 +CONECT 67 65 +CONECT 68 65 69 70 71 +CONECT 69 68 +CONECT 70 68 +CONECT 71 68 72 73 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 +CONECT 75 57 76 77 +CONECT 76 75 +CONECT 77 75 78 79 +CONECT 78 77 +CONECT 79 77 80 81 94 +CONECT 80 79 +CONECT 81 79 82 83 84 +CONECT 82 81 +CONECT 83 81 +CONECT 84 81 85 86 90 +CONECT 85 84 +CONECT 86 84 87 88 89 +CONECT 87 86 +CONECT 88 86 +CONECT 89 86 +CONECT 90 84 91 92 93 +CONECT 91 90 +CONECT 92 90 +CONECT 93 90 +CONECT 94 79 95 96 +CONECT 95 94 +CONECT 96 94 97 98 +CONECT 97 96 +CONECT 98 96 99 100 113 +CONECT 99 98 +CONECT 100 98 101 102 106 +CONECT 101 100 +CONECT 102 100 103 104 105 +CONECT 103 102 +CONECT 104 102 +CONECT 105 102 +CONECT 106 100 107 108 109 +CONECT 107 106 +CONECT 108 106 +CONECT 109 106 110 111 112 +CONECT 110 109 +CONECT 111 109 +CONECT 112 109 +CONECT 113 98 114 115 +CONECT 114 113 +CONECT 115 113 116 117 +CONECT 116 115 +CONECT 117 115 118 119 132 +CONECT 118 117 +CONECT 119 117 120 121 122 +CONECT 120 119 +CONECT 121 119 +CONECT 122 119 123 124 128 +CONECT 123 122 +CONECT 124 122 125 126 127 +CONECT 125 124 +CONECT 126 124 +CONECT 127 124 +CONECT 128 122 129 130 131 +CONECT 129 128 +CONECT 130 128 +CONECT 131 128 +CONECT 132 117 133 134 +CONECT 133 132 +CONECT 134 132 135 136 +CONECT 135 134 +CONECT 136 134 137 138 146 +CONECT 137 136 +CONECT 138 136 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 142 143 +CONECT 142 141 +CONECT 143 141 144 145 +CONECT 144 143 +CONECT 145 143 +CONECT 146 136 147 148 +CONECT 147 146 +CONECT 148 146 149 150 +CONECT 149 148 +CONECT 150 148 162 163 151 +CONECT 151 152 153 154 150 +CONECT 152 151 +CONECT 153 151 +CONECT 154 151 155 160 +CONECT 155 154 156 157 +CONECT 156 155 +CONECT 157 155 158 159 +CONECT 158 157 +CONECT 159 157 160 +CONECT 160 154 159 161 +CONECT 161 160 +CONECT 162 150 +CONECT 163 150 164 165 +CONECT 164 163 +CONECT 165 163 166 167 +CONECT 166 165 +CONECT 167 165 168 169 185 +CONECT 168 167 +CONECT 169 167 170 171 172 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 173 174 175 +CONECT 173 172 +CONECT 174 172 +CONECT 175 172 176 177 178 +CONECT 176 175 +CONECT 177 175 +CONECT 178 175 179 180 181 +CONECT 179 178 +CONECT 180 178 +CONECT 181 178 182 183 184 +CONECT 182 181 +CONECT 183 181 +CONECT 184 181 +CONECT 185 167 186 187 +CONECT 186 185 +CONECT 187 185 188 189 +CONECT 188 187 +CONECT 189 187 190 191 199 +CONECT 190 189 +CONECT 191 189 192 193 197 +CONECT 192 191 +CONECT 193 191 194 195 196 +CONECT 194 193 +CONECT 195 193 +CONECT 196 193 +CONECT 197 191 198 +CONECT 198 197 +CONECT 199 189 200 201 +CONECT 200 199 +CONECT 201 199 202 203 +CONECT 202 201 +CONECT 203 201 204 205 218 +CONECT 204 203 +CONECT 205 203 206 207 208 +CONECT 206 205 +CONECT 207 205 +CONECT 208 205 209 210 214 +CONECT 209 208 +CONECT 210 208 211 212 213 +CONECT 211 210 +CONECT 212 210 +CONECT 213 210 +CONECT 214 208 215 216 217 +CONECT 215 214 +CONECT 216 214 +CONECT 217 214 +CONECT 218 203 219 220 +CONECT 219 218 +CONECT 220 218 221 222 +CONECT 221 220 +CONECT 222 220 223 224 240 +CONECT 223 222 +CONECT 224 222 225 226 227 +CONECT 225 224 +CONECT 226 224 +CONECT 227 224 228 229 230 +CONECT 228 227 +CONECT 229 227 +CONECT 230 227 231 232 233 +CONECT 231 230 +CONECT 232 230 +CONECT 233 230 234 235 236 +CONECT 234 233 +CONECT 235 233 +CONECT 236 233 237 238 239 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 +CONECT 240 222 241 242 +CONECT 241 240 +CONECT 242 240 243 244 +CONECT 243 242 +CONECT 244 242 245 246 247 +CONECT 245 244 +CONECT 246 244 +CONECT 247 244 248 249 +CONECT 248 247 +CONECT 249 247 250 251 +CONECT 250 249 +CONECT 251 249 252 253 262 +CONECT 252 251 +CONECT 253 251 254 255 256 +CONECT 254 253 +CONECT 255 253 +CONECT 256 253 257 258 259 +CONECT 257 256 +CONECT 258 256 +CONECT 259 256 260 261 +CONECT 260 259 +CONECT 261 259 +CONECT 262 251 263 264 +CONECT 263 262 +CONECT 264 262 265 266 +CONECT 265 264 +CONECT 266 264 267 268 276 +CONECT 267 266 +CONECT 268 266 269 270 274 +CONECT 269 268 +CONECT 270 268 271 272 273 +CONECT 271 270 +CONECT 272 270 +CONECT 273 270 +CONECT 274 268 275 +CONECT 275 274 +CONECT 276 266 277 278 +CONECT 277 276 +CONECT 278 276 279 280 +CONECT 279 278 +CONECT 280 278 281 282 290 +CONECT 281 280 +CONECT 282 280 283 284 288 +CONECT 283 282 +CONECT 284 282 285 286 287 +CONECT 285 284 +CONECT 286 284 +CONECT 287 284 +CONECT 288 282 289 +CONECT 289 288 +CONECT 290 280 291 292 +CONECT 291 290 +CONECT 292 290 293 294 +CONECT 293 292 +CONECT 294 292 295 296 304 +CONECT 295 294 +CONECT 296 294 297 298 302 +CONECT 297 296 +CONECT 298 296 299 300 301 +CONECT 299 298 +CONECT 300 298 +CONECT 301 298 +CONECT 302 296 303 +CONECT 303 302 +CONECT 304 294 305 306 +CONECT 305 304 +CONECT 306 304 307 308 +CONECT 307 306 +CONECT 308 306 309 310 319 +CONECT 309 308 +CONECT 310 308 311 312 313 +CONECT 311 310 +CONECT 312 310 +CONECT 313 310 314 315 316 +CONECT 314 313 +CONECT 315 313 +CONECT 316 313 317 318 +CONECT 317 316 +CONECT 318 316 +CONECT 319 308 320 321 +CONECT 320 319 +CONECT 321 319 322 323 +CONECT 322 321 +CONECT 323 321 324 325 329 +CONECT 324 323 +CONECT 325 323 326 327 328 +CONECT 326 325 +CONECT 327 325 +CONECT 328 325 +CONECT 329 323 330 331 +CONECT 330 329 +CONECT 331 329 332 333 +CONECT 332 331 +CONECT 333 331 334 335 345 +CONECT 334 333 +CONECT 335 333 336 337 341 +CONECT 336 335 +CONECT 337 335 338 339 340 +CONECT 338 337 +CONECT 339 337 +CONECT 340 337 +CONECT 341 335 342 343 344 +CONECT 342 341 +CONECT 343 341 +CONECT 344 341 +CONECT 345 333 346 347 +CONECT 346 345 +CONECT 347 345 348 349 +CONECT 348 347 +CONECT 349 347 350 351 357 +CONECT 350 349 +CONECT 351 349 352 353 354 +CONECT 352 351 +CONECT 353 351 +CONECT 354 351 355 356 +CONECT 355 354 +CONECT 356 354 +CONECT 357 349 358 359 +CONECT 358 357 +CONECT 359 357 360 361 +CONECT 360 359 +CONECT 361 359 362 363 367 +CONECT 362 361 +CONECT 363 361 364 365 366 +CONECT 364 363 +CONECT 365 363 +CONECT 366 363 +CONECT 367 361 368 369 +CONECT 368 367 +CONECT 369 367 370 371 +CONECT 370 369 +CONECT 371 369 372 373 377 +CONECT 372 371 +CONECT 373 371 374 375 376 +CONECT 374 373 +CONECT 375 373 +CONECT 376 373 +CONECT 377 371 378 379 +CONECT 378 377 +CONECT 379 377 380 381 +CONECT 380 379 +CONECT 381 379 382 383 391 +CONECT 382 381 +CONECT 383 381 384 385 389 +CONECT 384 383 +CONECT 385 383 386 387 388 +CONECT 386 385 +CONECT 387 385 +CONECT 388 385 +CONECT 389 383 390 +CONECT 390 389 +CONECT 391 381 392 393 +CONECT 392 391 +CONECT 393 391 394 395 +CONECT 394 393 +CONECT 395 393 396 397 401 +CONECT 396 395 +CONECT 397 395 398 399 400 +CONECT 398 397 +CONECT 399 397 +CONECT 400 397 +CONECT 401 395 402 403 +CONECT 402 401 +CONECT 403 401 404 405 +CONECT 404 403 +CONECT 405 403 406 407 416 +CONECT 406 405 +CONECT 407 405 408 409 410 +CONECT 408 407 +CONECT 409 407 +CONECT 410 407 411 412 413 +CONECT 411 410 +CONECT 412 410 +CONECT 413 410 414 415 +CONECT 414 413 +CONECT 415 413 +CONECT 416 405 417 418 +CONECT 417 416 +CONECT 418 416 419 420 +CONECT 419 418 +CONECT 420 418 421 422 438 +CONECT 421 420 +CONECT 422 420 423 424 425 +CONECT 423 422 +CONECT 424 422 +CONECT 425 422 426 427 428 +CONECT 426 425 +CONECT 427 425 +CONECT 428 425 429 430 431 +CONECT 429 428 +CONECT 430 428 +CONECT 431 428 432 433 434 +CONECT 432 431 +CONECT 433 431 +CONECT 434 431 435 436 437 +CONECT 435 434 +CONECT 436 434 +CONECT 437 434 +CONECT 438 420 439 440 +CONECT 439 438 +CONECT 440 438 441 442 +CONECT 441 440 +CONECT 442 440 443 444 454 +CONECT 443 442 +CONECT 444 442 445 446 450 +CONECT 445 444 +CONECT 446 444 447 448 449 +CONECT 447 446 +CONECT 448 446 +CONECT 449 446 +CONECT 450 444 451 452 453 +CONECT 451 450 +CONECT 452 450 +CONECT 453 450 +CONECT 454 442 455 456 +CONECT 455 454 +CONECT 456 454 457 458 +CONECT 457 456 +CONECT 458 456 459 460 474 +CONECT 459 458 +CONECT 460 458 461 462 463 +CONECT 461 460 +CONECT 462 460 +CONECT 463 460 464 472 +CONECT 464 463 465 466 +CONECT 465 464 +CONECT 466 464 467 468 +CONECT 467 466 +CONECT 468 466 469 470 +CONECT 469 468 +CONECT 470 468 471 472 +CONECT 471 470 +CONECT 472 463 470 473 +CONECT 473 472 +CONECT 474 458 475 476 +CONECT 475 474 +CONECT 476 474 477 478 +CONECT 477 476 +CONECT 478 476 479 480 496 +CONECT 479 478 +CONECT 480 478 481 482 483 +CONECT 481 480 +CONECT 482 480 +CONECT 483 480 484 485 486 +CONECT 484 483 +CONECT 485 483 +CONECT 486 483 487 488 489 +CONECT 487 486 +CONECT 488 486 +CONECT 489 486 490 491 492 +CONECT 490 489 +CONECT 491 489 +CONECT 492 489 493 494 495 +CONECT 493 492 +CONECT 494 492 +CONECT 495 492 +CONECT 496 478 497 498 +CONECT 497 496 +CONECT 498 496 499 500 +CONECT 499 498 +CONECT 500 498 501 502 513 +CONECT 501 500 +CONECT 502 500 503 504 505 +CONECT 503 502 +CONECT 504 502 +CONECT 505 502 506 507 508 +CONECT 506 505 +CONECT 507 505 +CONECT 508 505 509 510 +CONECT 509 508 +CONECT 510 508 511 512 +CONECT 511 510 +CONECT 512 510 +CONECT 513 500 514 515 +CONECT 514 513 +CONECT 515 513 516 517 +CONECT 516 515 +CONECT 517 515 518 519 534 +CONECT 518 517 +CONECT 519 517 520 521 522 +CONECT 520 519 +CONECT 521 519 +CONECT 522 519 523 532 +CONECT 523 522 524 525 +CONECT 524 523 +CONECT 525 523 526 527 +CONECT 526 525 +CONECT 527 525 528 530 +CONECT 528 527 529 +CONECT 529 528 +CONECT 530 527 531 532 +CONECT 531 530 +CONECT 532 522 530 533 +CONECT 533 532 +CONECT 534 517 535 536 +CONECT 535 534 +CONECT 536 534 537 538 +CONECT 537 536 +CONECT 538 536 539 540 544 +CONECT 539 538 +CONECT 540 538 541 542 543 +CONECT 541 540 +CONECT 542 540 +CONECT 543 540 +CONECT 544 538 545 546 +CONECT 545 544 +CONECT 546 544 547 548 +CONECT 547 546 +CONECT 548 546 549 550 558 +CONECT 549 548 +CONECT 550 548 551 552 553 +CONECT 551 550 +CONECT 552 550 +CONECT 553 550 554 555 +CONECT 554 553 +CONECT 555 553 556 557 +CONECT 556 555 +CONECT 557 555 +CONECT 558 548 559 560 +CONECT 559 558 +CONECT 560 558 561 562 +CONECT 561 560 +CONECT 562 560 563 564 570 +CONECT 563 562 +CONECT 564 562 565 566 567 +CONECT 565 564 +CONECT 566 564 +CONECT 567 564 568 569 +CONECT 568 567 +CONECT 569 567 +CONECT 570 562 571 572 +CONECT 571 570 +CONECT 572 570 573 574 +CONECT 573 572 +CONECT 574 572 575 576 584 +CONECT 575 574 +CONECT 576 574 577 578 579 +CONECT 577 576 +CONECT 578 576 +CONECT 579 576 580 581 +CONECT 580 579 +CONECT 581 579 582 583 +CONECT 582 581 +CONECT 583 581 +CONECT 584 574 585 586 +CONECT 585 584 +CONECT 586 584 587 588 +CONECT 587 586 +CONECT 588 586 589 590 591 +CONECT 589 588 +CONECT 590 588 +CONECT 591 588 592 593 +CONECT 592 591 +CONECT 593 591 594 595 +CONECT 594 593 +CONECT 595 593 596 597 607 +CONECT 596 595 +CONECT 597 595 598 599 603 +CONECT 598 597 +CONECT 599 597 600 601 602 +CONECT 600 599 +CONECT 601 599 +CONECT 602 599 +CONECT 603 597 604 605 606 +CONECT 604 603 +CONECT 605 603 +CONECT 606 603 +CONECT 607 595 608 609 +CONECT 608 607 +CONECT 609 607 610 611 +CONECT 610 609 +CONECT 611 609 612 613 619 +CONECT 612 611 +CONECT 613 611 614 615 616 +CONECT 614 613 +CONECT 615 613 +CONECT 616 613 617 618 +CONECT 617 616 +CONECT 618 616 +CONECT 619 611 620 621 +CONECT 620 619 +CONECT 621 619 622 623 +CONECT 622 621 +CONECT 623 621 624 625 626 +CONECT 624 623 +CONECT 625 623 +CONECT 626 623 627 628 +CONECT 627 626 +CONECT 628 626 629 630 +CONECT 629 628 +CONECT 630 628 631 632 641 +CONECT 631 630 +CONECT 632 630 633 634 635 +CONECT 633 632 +CONECT 634 632 +CONECT 635 632 636 637 638 +CONECT 636 635 +CONECT 637 635 +CONECT 638 635 639 640 +CONECT 639 638 +CONECT 640 638 +CONECT 641 630 642 643 +CONECT 642 641 +CONECT 643 641 644 645 +CONECT 644 643 +CONECT 645 643 646 647 665 +CONECT 646 645 +CONECT 647 645 648 649 650 +CONECT 648 647 +CONECT 649 647 +CONECT 650 647 651 664 +CONECT 651 650 652 653 +CONECT 652 651 +CONECT 653 651 654 655 +CONECT 654 653 +CONECT 655 653 656 664 +CONECT 656 655 657 658 +CONECT 657 656 +CONECT 658 656 659 660 +CONECT 659 658 +CONECT 660 658 661 662 +CONECT 661 660 +CONECT 662 660 663 664 +CONECT 663 662 +CONECT 664 650 655 662 +CONECT 665 645 666 667 +CONECT 666 665 +CONECT 667 665 668 669 +CONECT 668 667 +CONECT 669 667 670 671 679 +CONECT 670 669 +CONECT 671 669 672 673 677 +CONECT 672 671 +CONECT 673 671 674 675 676 +CONECT 674 673 +CONECT 675 673 +CONECT 676 673 +CONECT 677 671 678 +CONECT 678 677 +CONECT 679 669 680 681 +CONECT 680 679 +CONECT 681 679 682 683 +CONECT 682 681 +CONECT 683 681 684 685 700 +CONECT 684 683 +CONECT 685 683 686 687 688 +CONECT 686 685 +CONECT 687 685 +CONECT 688 685 689 698 +CONECT 689 688 690 691 +CONECT 690 689 +CONECT 691 689 692 693 +CONECT 692 691 +CONECT 693 691 694 696 +CONECT 694 693 695 +CONECT 695 694 +CONECT 696 693 697 698 +CONECT 697 696 +CONECT 698 688 696 699 +CONECT 699 698 +CONECT 700 683 701 702 +CONECT 701 700 +CONECT 702 700 703 704 +CONECT 703 702 +CONECT 704 702 705 706 712 +CONECT 705 704 +CONECT 706 704 707 708 709 +CONECT 707 706 +CONECT 708 706 +CONECT 709 706 710 711 +CONECT 710 709 +CONECT 711 709 +CONECT 712 704 713 714 +CONECT 713 712 +CONECT 714 712 715 716 +CONECT 715 714 +CONECT 716 714 717 718 724 +CONECT 717 716 +CONECT 718 716 719 720 721 +CONECT 719 718 +CONECT 720 718 +CONECT 721 718 722 723 +CONECT 722 721 +CONECT 723 721 +CONECT 724 716 725 726 +CONECT 725 724 +CONECT 726 724 727 728 +CONECT 727 726 +CONECT 728 726 729 730 734 +CONECT 729 728 +CONECT 730 728 731 732 733 +CONECT 731 730 +CONECT 732 730 +CONECT 733 730 +CONECT 734 728 735 736 +CONECT 735 734 +CONECT 736 734 737 738 +CONECT 737 736 +CONECT 738 736 739 740 748 +CONECT 739 738 +CONECT 740 738 741 742 746 +CONECT 741 740 +CONECT 742 740 743 744 745 +CONECT 743 742 +CONECT 744 742 +CONECT 745 742 +CONECT 746 740 747 +CONECT 747 746 +CONECT 748 738 749 750 +CONECT 749 748 +CONECT 750 748 751 752 +CONECT 751 750 +CONECT 752 750 753 754 770 +CONECT 753 752 +CONECT 754 752 755 756 757 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 758 759 760 +CONECT 758 757 +CONECT 759 757 +CONECT 760 757 761 762 763 +CONECT 761 760 +CONECT 762 760 +CONECT 763 760 764 765 766 +CONECT 764 763 +CONECT 765 763 +CONECT 766 763 767 768 769 +CONECT 767 766 +CONECT 768 766 +CONECT 769 766 +CONECT 770 752 771 772 +CONECT 771 770 +CONECT 772 770 773 774 +CONECT 773 772 +CONECT 774 772 775 776 784 +CONECT 775 774 +CONECT 776 774 777 778 782 +CONECT 777 776 +CONECT 778 776 779 780 781 +CONECT 779 778 +CONECT 780 778 +CONECT 781 778 +CONECT 782 776 783 +CONECT 783 782 +CONECT 784 774 785 786 +CONECT 785 784 +CONECT 786 784 787 788 +CONECT 787 786 +CONECT 788 786 789 790 804 +CONECT 789 788 +CONECT 790 788 791 792 793 +CONECT 791 790 +CONECT 792 790 +CONECT 793 790 794 802 +CONECT 794 793 795 796 +CONECT 795 794 +CONECT 796 794 797 798 +CONECT 797 796 +CONECT 798 796 799 800 +CONECT 799 798 +CONECT 800 798 801 802 +CONECT 801 800 +CONECT 802 793 800 803 +CONECT 803 802 +CONECT 804 788 805 806 +CONECT 805 804 +CONECT 806 804 807 808 +CONECT 807 806 +CONECT 808 806 809 810 818 +CONECT 809 808 +CONECT 810 808 811 812 816 +CONECT 811 810 +CONECT 812 810 813 814 815 +CONECT 813 812 +CONECT 814 812 +CONECT 815 812 +CONECT 816 810 817 +CONECT 817 816 +CONECT 818 808 819 820 +CONECT 819 818 +CONECT 820 818 821 822 +CONECT 821 820 +CONECT 822 820 823 824 834 +CONECT 823 822 +CONECT 824 822 825 826 830 +CONECT 825 824 +CONECT 826 824 827 828 829 +CONECT 827 826 +CONECT 828 826 +CONECT 829 826 +CONECT 830 824 831 832 833 +CONECT 831 830 +CONECT 832 830 +CONECT 833 830 +CONECT 834 822 835 836 +CONECT 835 834 +CONECT 836 834 837 838 +CONECT 837 836 +CONECT 838 836 839 840 848 +CONECT 839 838 +CONECT 840 838 841 842 846 +CONECT 841 840 +CONECT 842 840 843 844 845 +CONECT 843 842 +CONECT 844 842 +CONECT 845 842 +CONECT 846 840 847 +CONECT 847 846 +CONECT 848 838 849 850 +CONECT 849 848 +CONECT 850 848 851 852 +CONECT 851 850 +CONECT 852 850 853 854 863 +CONECT 853 852 +CONECT 854 852 855 856 857 +CONECT 855 854 +CONECT 856 854 +CONECT 857 854 858 859 860 +CONECT 858 857 +CONECT 859 857 +CONECT 860 857 861 862 +CONECT 861 860 +CONECT 862 860 +CONECT 863 852 864 865 +CONECT 864 863 +CONECT 865 863 +MASTER 0 0 0 0 0 0 0 0 865 0 865 0 +END diff --git a/unittests/example_files/test_individual.in b/unittests/example_files/test_individual.in new file mode 100644 index 0000000..36bf1ba --- /dev/null +++ b/unittests/example_files/test_individual.in @@ -0,0 +1,52 @@ +[OPTIMIZATION] +dihedral_optimization = False +composition_optimization = True +composition_residue_indexes = 1 2 +composition_lower_bounds = 1 175 +composition_upper_bounds = 176 176 +composition_library = ../share/flat/ + + +[MOLECULE] +initial_molecule = example_files/ALA20.pdb + +[IO] +store_intermediate_mol = True +output_path = . +output_file = final.pdb + +[GA_GLOBAL] +seed_population = False +population_file_path = None +population_size = 10 +max_iteration = 10 + +[EVALUATOR] +evaluators = helical_stability +tleap_template = example_files/tleap_template.in +amber_params = example_files/amber_minimization.in +mpi_processors = 20 +dielectric = 80.0 + +[GA_SELECTION] +selector = tournament_wor +tournament_size = 2 + +[GA_CROSSOVER] +crossover = sbx +sbx_distribution_index = 7.0 +mating_probability = 0.7 +genewise_crossover_probability = 0.4 + +[GA_MUTATION] +mutator = polynomial_mutation +mutation_probability = 0.3 +genewise__mutation_probability = 0.15 +poly_eta = 7.0 + +[GA_REPLACER] +replacer = elitism +elitist_factor = 0.25 + +[DEBUG] +verbose = True diff --git a/unittests/example_files/tleap_template.in b/unittests/example_files/tleap_template.in new file mode 100644 index 0000000..327e8e9 --- /dev/null +++ b/unittests/example_files/tleap_template.in @@ -0,0 +1,187 @@ +source leaprc.protein.ff14SB +#source /software/amber/18/intel-17.0.4/dat/leap/cmd/oldff/leaprc.ff99SB +#source /software/amber/14/amber14-intelmpi/dat/leap/cmd/leaprc.ff12SB + +loadOff ../share/off/ALA/A01.off +loadOff ../share/off/ARG/R01.off +loadOff ../share/off/ARG/R02.off +loadOff ../share/off/ARG/R03.off +loadOff ../share/off/ARG/R04.off +loadOff ../share/off/ARG/R05.off +loadOff ../share/off/ARG/R06.off +loadOff ../share/off/ARG/R07.off +loadOff ../share/off/ARG/R08.off +loadOff ../share/off/ARG/R09.off +loadOff ../share/off/ARG/R10.off +loadOff ../share/off/ARG/R11.off +loadOff ../share/off/ARG/R12.off +loadOff ../share/off/ARG/R13.off +loadOff ../share/off/ARG/R14.off +loadOff ../share/off/ARG/R15.off +loadOff ../share/off/ARG/R16.off +loadOff ../share/off/ARG/R17.off +loadOff ../share/off/ARG/R18.off +loadOff ../share/off/ARG/R19.off +loadOff ../share/off/ARG/R20.off +loadOff ../share/off/ARG/R21.off +loadOff ../share/off/ARG/R22.off +loadOff ../share/off/ARG/R23.off +loadOff ../share/off/ARG/R24.off +loadOff ../share/off/ARG/R25.off +loadOff ../share/off/ARG/R26.off +loadOff ../share/off/ARG/R27.off +loadOff ../share/off/ARG/R28.off +loadOff ../share/off/ASP/D01.off +loadOff ../share/off/ASP/D02.off +loadOff ../share/off/ASP/D03.off +loadOff ../share/off/ASP/D04.off +loadOff ../share/off/ASP/D05.off +loadOff ../share/off/ASH/D06.off +loadOff ../share/off/ASH/D07.off +loadOff ../share/off/ASH/D08.off +loadOff ../share/off/ASH/D09.off +loadOff ../share/off/ASH/D10.off +loadOff ../share/off/ASN/N01.off +loadOff ../share/off/ASN/N02.off +loadOff ../share/off/ASN/N03.off +loadOff ../share/off/ASN/N04.off +loadOff ../share/off/ASN/N05.off +loadOff ../share/off/ASN/N06.off +loadOff ../share/off/ASN/N07.off +loadOff ../share/off/CYS/C01.off +loadOff ../share/off/CYS/C02.off +loadOff ../share/off/CYS/C03.off +loadOff ../share/off/GLU/E01.off +loadOff ../share/off/GLU/E02.off +loadOff ../share/off/GLU/E03.off +loadOff ../share/off/GLU/E04.off +loadOff ../share/off/GLU/E05.off +loadOff ../share/off/GLU/E06.off +loadOff ../share/off/GLU/E07.off +loadOff ../share/off/GLH/E08.off +loadOff ../share/off/GLH/E09.off +loadOff ../share/off/GLH/E10.off +loadOff ../share/off/GLH/E11.off +loadOff ../share/off/GLH/E12.off +loadOff ../share/off/GLH/E13.off +loadOff ../share/off/GLH/E14.off +loadOff ../share/off/GLN/Q01.off +loadOff ../share/off/GLN/Q02.off +loadOff ../share/off/GLN/Q03.off +loadOff ../share/off/GLN/Q04.off +loadOff ../share/off/GLN/Q05.off +loadOff ../share/off/GLY/G01.off +loadOff ../share/off/HID/HD1.off +loadOff ../share/off/HID/HD2.off +loadOff ../share/off/HID/HD3.off +loadOff ../share/off/HID/HD4.off +loadOff ../share/off/HID/HD5.off +loadOff ../share/off/HID/HD6.off +loadOff ../share/off/HID/HD7.off +loadOff ../share/off/HID/HD8.off +loadOff ../share/off/HIE/HE1.off +loadOff ../share/off/HIE/HE2.off +loadOff ../share/off/HIE/HE3.off +loadOff ../share/off/HIE/HE4.off +loadOff ../share/off/HIE/HE5.off +loadOff ../share/off/HIE/HE6.off +loadOff ../share/off/HIE/HE7.off +loadOff ../share/off/HIE/HE8.off +loadOff ../share/off/HIP/HP1.off +loadOff ../share/off/HIP/HP2.off +loadOff ../share/off/HIP/HP3.off +loadOff ../share/off/HIP/HP4.off +loadOff ../share/off/HIP/HP5.off +loadOff ../share/off/HIP/HP6.off +loadOff ../share/off/HIP/HP7.off +loadOff ../share/off/HIP/HP8.off +loadOff ../share/off/ILE/I01.off +loadOff ../share/off/ILE/I02.off +loadOff ../share/off/ILE/I03.off +loadOff ../share/off/ILE/I04.off +loadOff ../share/off/ILE/I05.off +loadOff ../share/off/LEU/L01.off +loadOff ../share/off/LEU/L02.off +loadOff ../share/off/LEU/L03.off +loadOff ../share/off/LEU/L04.off +loadOff ../share/off/MET/M01.off +loadOff ../share/off/MET/M02.off +loadOff ../share/off/MET/M03.off +loadOff ../share/off/MET/M04.off +loadOff ../share/off/MET/M05.off +loadOff ../share/off/MET/M06.off +loadOff ../share/off/MET/M07.off +loadOff ../share/off/MET/M08.off +loadOff ../share/off/MET/M09.off +loadOff ../share/off/MET/M10.off +loadOff ../share/off/MET/M11.off +loadOff ../share/off/MET/M12.off +loadOff ../share/off/MET/M13.off +loadOff ../share/off/PHE/P01.off +loadOff ../share/off/PHE/P02.off +loadOff ../share/off/PHE/P03.off +loadOff ../share/off/PHE/P04.off +loadOff ../share/off/SER/S01.off +loadOff ../share/off/SER/S02.off +loadOff ../share/off/SER/S03.off +loadOff ../share/off/THR/T01.off +loadOff ../share/off/THR/T02.off +loadOff ../share/off/THR/T03.off +loadOff ../share/off/TRP/W01.off +loadOff ../share/off/TRP/W02.off +loadOff ../share/off/TRP/W03.off +loadOff ../share/off/TRP/W04.off +loadOff ../share/off/TRP/W05.off +loadOff ../share/off/TRP/W06.off +loadOff ../share/off/TRP/W07.off +loadOff ../share/off/TYR/Y01.off +loadOff ../share/off/TYR/Y02.off +loadOff ../share/off/TYR/Y03.off +loadOff ../share/off/TYR/Y04.off +loadOff ../share/off/VAL/V01.off +loadOff ../share/off/VAL/V02.off +loadOff ../share/off/VAL/V03.off +loadOff ../share/off/LYS/K01.off +loadOff ../share/off/LYS/K02.off +loadOff ../share/off/LYS/K03.off +loadOff ../share/off/LYS/K04.off +loadOff ../share/off/LYS/K05.off +loadOff ../share/off/LYS/K06.off +loadOff ../share/off/LYS/K07.off +loadOff ../share/off/LYS/K08.off +loadOff ../share/off/LYS/K09.off +loadOff ../share/off/LYS/K10.off +loadOff ../share/off/LYS/K11.off +loadOff ../share/off/LYS/K12.off +loadOff ../share/off/LYS/K13.off +loadOff ../share/off/LYS/K14.off +loadOff ../share/off/LYS/K15.off +loadOff ../share/off/LYS/K16.off +loadOff ../share/off/LYS/K17.off +loadOff ../share/off/LYS/K18.off +loadOff ../share/off/LYS/K19.off +loadOff ../share/off/LYN/K20.off +loadOff ../share/off/LYN/K21.off +loadOff ../share/off/LYN/K22.off +loadOff ../share/off/LYN/K23.off +loadOff ../share/off/LYN/K24.off +loadOff ../share/off/LYN/K25.off +loadOff ../share/off/LYN/K26.off +loadOff ../share/off/LYN/K27.off +loadOff ../share/off/LYN/K28.off +loadOff ../share/off/LYN/K29.off +loadOff ../share/off/LYN/K30.off +loadOff ../share/off/LYN/K31.off +loadOff ../share/off/LYN/K32.off +loadOff ../share/off/LYN/K33.off +loadOff ../share/off/LYN/K34.off +loadOff ../share/off/LYN/K35.off +loadOff ../share/off/LYN/K36.off +loadOff ../share/off/LYN/K37.off +loadOff ../share/off/LYN/K38.off + +mol = loadpdb "ALA20_mut.pdb" + +saveamberparm mol ALA20.prmtop ALA20.inpcrd + +quit diff --git a/unittests/output_files/applied_composition.pdb b/unittests/output_files/applied_composition.pdb new file mode 100644 index 0000000..2615b60 --- /dev/null +++ b/unittests/output_files/applied_composition.pdb @@ -0,0 +1,416 @@ +COMPND PolyALA +AUTHOR GENERATED BY OPEN BABEL 2.3.2 +ATOM 1 H1 ACE A 1 -3.054 -3.171 0.465 1.00 0.00 H +ATOM 2 CH3 ACE A 1 -2.917 -2.969 -0.597 1.00 0.00 C +ATOM 3 H2 ACE A 1 -3.815 -3.045 -1.210 1.00 0.00 H +ATOM 4 H3 ACE A 1 -2.106 -3.644 -0.872 1.00 0.00 H +ATOM 5 C ACE A 1 -2.282 -1.553 -0.711 1.00 0.00 C +ATOM 6 O ACE A 1 -2.958 -0.698 -1.252 1.00 0.00 O +ATOM 7 N G01 A 2 -1.104 -1.396 -0.185 1.00 0.00 N +ATOM 8 H G01 A 2 -0.697 -2.276 0.096 1.00 0.00 H +ATOM 9 CA G01 A 2 -0.333 -0.155 -0.121 1.00 0.00 C +ATOM 10 HA3 G01 A 2 -0.715 0.482 0.677 1.00 0.00 H +ATOM 11 HA G01 A 2 -0.610 0.298 -1.073 1.00 0.00 H +ATOM 12 C G01 A 2 1.131 -0.273 -0.199 1.00 0.00 C +ATOM 13 O G01 A 2 1.769 0.539 -0.827 1.00 0.00 O +ATOM 14 N G01 A 3 1.795 -1.211 0.498 1.00 0.00 N +ATOM 15 H G01 A 3 1.221 -1.808 1.076 1.00 0.00 H +ATOM 16 CA G01 A 3 3.262 -1.252 0.419 1.00 0.00 C +ATOM 17 HA3 G01 A 3 3.660 -1.970 1.136 1.00 0.00 H +ATOM 18 HA G01 A 3 3.652 -0.256 0.628 1.00 0.00 H +ATOM 19 C G01 A 3 3.783 -1.597 -0.986 1.00 0.00 C +ATOM 20 O G01 A 3 4.802 -1.070 -1.378 1.00 0.00 O +ATOM 21 N ALA A 4 3.132 -2.508 -1.712 1.00 0.00 N +ATOM 22 H ALA A 4 2.361 -3.014 -1.299 1.00 0.00 H +ATOM 23 CA ALA A 4 3.470 -2.716 -3.172 1.00 0.00 C +ATOM 24 HA ALA A 4 4.559 -2.699 -3.210 1.00 0.00 H +ATOM 25 CB ALA A 4 2.900 -4.035 -3.564 1.00 0.00 C +ATOM 26 HB1 ALA A 4 3.370 -4.803 -2.950 1.00 0.00 H +ATOM 27 HB2 ALA A 4 1.845 -4.033 -3.290 1.00 0.00 H +ATOM 28 HB3 ALA A 4 3.197 -4.068 -4.612 1.00 0.00 H +ATOM 29 C ALA A 4 3.146 -1.507 -3.992 1.00 0.00 C +ATOM 30 O ALA A 4 4.003 -1.154 -4.830 1.00 0.00 O +ATOM 31 N ALA A 5 2.102 -0.798 -3.719 1.00 0.00 N +ATOM 32 H ALA A 5 1.578 -1.096 -2.909 1.00 0.00 H +ATOM 33 CA ALA A 5 1.798 0.414 -4.360 1.00 0.00 C +ATOM 34 HA ALA A 5 2.033 0.197 -5.403 1.00 0.00 H +ATOM 35 CB ALA A 5 0.257 0.848 -4.179 1.00 0.00 C +ATOM 36 HB1 ALA A 5 -0.434 0.100 -4.566 1.00 0.00 H +ATOM 37 HB2 ALA A 5 0.029 0.931 -3.116 1.00 0.00 H +ATOM 38 HB3 ALA A 5 0.160 1.812 -4.679 1.00 0.00 H +ATOM 39 C ALA A 5 2.753 1.542 -4.006 1.00 0.00 C +ATOM 40 O ALA A 5 3.074 2.358 -4.897 1.00 0.00 O +ATOM 41 N ALA A 6 3.298 1.676 -2.803 1.00 0.00 N +ATOM 42 H ALA A 6 2.836 1.294 -1.990 1.00 0.00 H +ATOM 43 CA ALA A 6 4.273 2.694 -2.399 1.00 0.00 C +ATOM 44 HA ALA A 6 3.991 3.697 -2.721 1.00 0.00 H +ATOM 45 CB ALA A 6 4.338 2.833 -0.890 1.00 0.00 C +ATOM 46 HB1 ALA A 6 3.425 3.266 -0.481 1.00 0.00 H +ATOM 47 HB2 ALA A 6 4.564 1.863 -0.449 1.00 0.00 H +ATOM 48 HB3 ALA A 6 5.247 3.402 -0.697 1.00 0.00 H +ATOM 49 C ALA A 6 5.749 2.356 -2.826 1.00 0.00 C +ATOM 50 O ALA A 6 6.538 3.204 -3.079 1.00 0.00 O +ATOM 51 N ALA A 7 5.959 1.049 -3.048 1.00 0.00 N +ATOM 52 H ALA A 7 5.304 0.423 -2.601 1.00 0.00 H +ATOM 53 CA ALA A 7 7.183 0.475 -3.563 1.00 0.00 C +ATOM 54 HA ALA A 7 7.990 1.166 -3.316 1.00 0.00 H +ATOM 55 CB ALA A 7 7.530 -0.880 -2.926 1.00 0.00 C +ATOM 56 HB1 ALA A 7 7.386 -0.936 -1.847 1.00 0.00 H +ATOM 57 HB2 ALA A 7 6.786 -1.525 -3.395 1.00 0.00 H +ATOM 58 HB3 ALA A 7 8.523 -1.178 -3.261 1.00 0.00 H +ATOM 59 C ALA A 7 7.218 0.417 -5.118 1.00 0.00 C +ATOM 60 O ALA A 7 8.320 0.602 -5.691 1.00 0.00 O +ATOM 61 N ALA A 8 6.093 0.302 -5.750 1.00 0.00 N +ATOM 62 H ALA A 8 5.324 -0.065 -5.206 1.00 0.00 H +ATOM 63 CA ALA A 8 5.982 0.524 -7.158 1.00 0.00 C +ATOM 64 HA ALA A 8 6.812 0.018 -7.650 1.00 0.00 H +ATOM 65 CB ALA A 8 4.784 -0.264 -7.698 1.00 0.00 C +ATOM 66 HB1 ALA A 8 4.911 -1.274 -7.308 1.00 0.00 H +ATOM 67 HB2 ALA A 8 3.881 0.285 -7.430 1.00 0.00 H +ATOM 68 HB3 ALA A 8 4.855 -0.199 -8.784 1.00 0.00 H +ATOM 69 C ALA A 8 5.945 2.036 -7.500 1.00 0.00 C +ATOM 70 O ALA A 8 6.554 2.371 -8.484 1.00 0.00 O +ATOM 71 N ALA A 9 5.406 2.871 -6.588 1.00 0.00 N +ATOM 72 H ALA A 9 4.829 2.524 -5.835 1.00 0.00 H +ATOM 73 CA ALA A 9 5.472 4.303 -6.694 1.00 0.00 C +ATOM 74 HA ALA A 9 5.320 4.497 -7.756 1.00 0.00 H +ATOM 75 CB ALA A 9 4.300 5.085 -6.075 1.00 0.00 C +ATOM 76 HB1 ALA A 9 3.330 4.659 -6.333 1.00 0.00 H +ATOM 77 HB2 ALA A 9 4.436 5.008 -4.996 1.00 0.00 H +ATOM 78 HB3 ALA A 9 4.315 6.151 -6.302 1.00 0.00 H +ATOM 79 C ALA A 9 6.893 4.859 -6.381 1.00 0.00 C +ATOM 80 O ALA A 9 7.444 5.619 -7.164 1.00 0.00 O +ATOM 81 N ALA A 10 7.541 4.364 -5.327 1.00 0.00 N +ATOM 82 H ALA A 10 7.021 3.870 -4.617 1.00 0.00 H +ATOM 83 CA ALA A 10 8.960 4.713 -5.050 1.00 0.00 C +ATOM 84 HA ALA A 10 8.966 5.797 -5.163 1.00 0.00 H +ATOM 85 CB ALA A 10 9.288 4.389 -3.622 1.00 0.00 C +ATOM 86 HB1 ALA A 10 8.642 4.839 -2.869 1.00 0.00 H +ATOM 87 HB2 ALA A 10 9.230 3.307 -3.504 1.00 0.00 H +ATOM 88 HB3 ALA A 10 10.344 4.615 -3.471 1.00 0.00 H +ATOM 89 C ALA A 10 9.986 4.042 -6.032 1.00 0.00 C +ATOM 90 O ALA A 10 11.142 4.565 -6.147 1.00 0.00 O +ATOM 91 N ALA A 11 9.656 2.896 -6.701 1.00 0.00 N +ATOM 92 H ALA A 11 8.894 2.276 -6.470 1.00 0.00 H +ATOM 93 CA ALA A 11 10.445 2.411 -7.813 1.00 0.00 C +ATOM 94 HA ALA A 11 11.510 2.566 -7.640 1.00 0.00 H +ATOM 95 CB ALA A 11 10.164 0.914 -8.040 1.00 0.00 C +ATOM 96 HB1 ALA A 11 10.615 0.443 -7.166 1.00 0.00 H +ATOM 97 HB2 ALA A 11 9.107 0.669 -8.142 1.00 0.00 H +ATOM 98 HB3 ALA A 11 10.719 0.516 -8.889 1.00 0.00 H +ATOM 99 C ALA A 11 10.151 3.103 -9.155 1.00 0.00 C +ATOM 100 O ALA A 11 11.041 3.166 -9.980 1.00 0.00 O +ATOM 101 N ALA A 12 8.962 3.622 -9.346 1.00 0.00 N +ATOM 102 H ALA A 12 8.246 3.385 -8.673 1.00 0.00 H +ATOM 103 CA ALA A 12 8.644 4.359 -10.533 1.00 0.00 C +ATOM 104 HA ALA A 12 9.114 3.991 -11.446 1.00 0.00 H +ATOM 105 CB ALA A 12 7.143 4.275 -10.773 1.00 0.00 C +ATOM 106 HB1 ALA A 12 6.835 3.230 -10.811 1.00 0.00 H +ATOM 107 HB2 ALA A 12 6.547 4.719 -9.976 1.00 0.00 H +ATOM 108 HB3 ALA A 12 6.930 4.661 -11.770 1.00 0.00 H +ATOM 109 C ALA A 12 8.998 5.845 -10.408 1.00 0.00 C +ATOM 110 O ALA A 12 9.206 6.435 -11.479 1.00 0.00 O +ATOM 111 N ALA A 13 9.060 6.373 -9.150 1.00 0.00 N +ATOM 112 H ALA A 13 8.710 5.815 -8.384 1.00 0.00 H +ATOM 113 CA ALA A 13 9.644 7.589 -8.707 1.00 0.00 C +ATOM 114 HA ALA A 13 9.378 8.325 -9.466 1.00 0.00 H +ATOM 115 CB ALA A 13 8.979 8.114 -7.362 1.00 0.00 C +ATOM 116 HB1 ALA A 13 7.893 8.188 -7.300 1.00 0.00 H +ATOM 117 HB2 ALA A 13 9.391 7.514 -6.550 1.00 0.00 H +ATOM 118 HB3 ALA A 13 9.297 9.138 -7.165 1.00 0.00 H +ATOM 119 C ALA A 13 11.163 7.561 -8.544 1.00 0.00 C +ATOM 120 O ALA A 13 11.753 8.643 -8.809 1.00 0.00 O +ATOM 121 N ALA A 14 11.711 6.438 -8.195 1.00 0.00 N +ATOM 122 H ALA A 14 11.201 5.708 -7.719 1.00 0.00 H +ATOM 123 CA ALA A 14 13.187 6.178 -8.377 1.00 0.00 C +ATOM 124 HA ALA A 14 13.746 7.056 -8.055 1.00 0.00 H +ATOM 125 CB ALA A 14 13.659 4.995 -7.481 1.00 0.00 C +ATOM 126 HB1 ALA A 14 13.670 5.270 -6.427 1.00 0.00 H +ATOM 127 HB2 ALA A 14 13.140 4.041 -7.573 1.00 0.00 H +ATOM 128 HB3 ALA A 14 14.732 4.857 -7.614 1.00 0.00 H +ATOM 129 C ALA A 14 13.540 5.894 -9.914 1.00 0.00 C +ATOM 130 O ALA A 14 14.638 6.393 -10.399 1.00 0.00 O +ATOM 131 N ALA A 15 12.747 5.180 -10.675 1.00 0.00 N +ATOM 132 H ALA A 15 11.928 4.701 -10.329 1.00 0.00 H +ATOM 133 CA ALA A 15 13.062 5.067 -12.046 1.00 0.00 C +ATOM 134 HA ALA A 15 14.076 4.746 -12.284 1.00 0.00 H +ATOM 135 CB ALA A 15 12.198 3.975 -12.711 1.00 0.00 C +ATOM 136 HB1 ALA A 15 12.343 3.040 -12.170 1.00 0.00 H +ATOM 137 HB2 ALA A 15 11.153 4.203 -12.506 1.00 0.00 H +ATOM 138 HB3 ALA A 15 12.380 3.968 -13.786 1.00 0.00 H +ATOM 139 C ALA A 15 12.703 6.348 -12.778 1.00 0.00 C +ATOM 140 O ALA A 15 13.510 6.684 -13.678 1.00 0.00 O +ATOM 141 N ALA A 16 11.645 7.130 -12.475 1.00 0.00 N +ATOM 142 H ALA A 16 10.893 6.780 -11.898 1.00 0.00 H +ATOM 143 CA ALA A 16 11.461 8.455 -13.029 1.00 0.00 C +ATOM 144 HA ALA A 16 11.491 8.353 -14.114 1.00 0.00 H +ATOM 145 CB ALA A 16 10.149 9.085 -12.685 1.00 0.00 C +ATOM 146 HB1 ALA A 16 9.388 8.398 -13.054 1.00 0.00 H +ATOM 147 HB2 ALA A 16 10.052 9.148 -11.601 1.00 0.00 H +ATOM 148 HB3 ALA A 16 10.063 10.057 -13.171 1.00 0.00 H +ATOM 149 C ALA A 16 12.608 9.384 -12.612 1.00 0.00 C +ATOM 150 O ALA A 16 13.039 10.222 -13.473 1.00 0.00 O +ATOM 151 N ALA A 17 13.138 9.241 -11.388 1.00 0.00 N +ATOM 152 H ALA A 17 12.604 8.788 -10.661 1.00 0.00 H +ATOM 153 CA ALA A 17 14.326 10.028 -10.964 1.00 0.00 C +ATOM 154 HA ALA A 17 14.114 11.052 -11.270 1.00 0.00 H +ATOM 155 CB ALA A 17 14.275 10.145 -9.531 1.00 0.00 C +ATOM 156 HB1 ALA A 17 13.375 10.647 -9.177 1.00 0.00 H +ATOM 157 HB2 ALA A 17 14.478 9.222 -8.988 1.00 0.00 H +ATOM 158 HB3 ALA A 17 15.023 10.861 -9.189 1.00 0.00 H +ATOM 159 C ALA A 17 15.611 9.623 -11.594 1.00 0.00 C +ATOM 160 O ALA A 17 16.445 10.488 -11.882 1.00 0.00 O +ATOM 161 N ALA A 18 15.812 8.347 -11.791 1.00 0.00 N +ATOM 162 H ALA A 18 15.210 7.647 -11.382 1.00 0.00 H +ATOM 163 CA ALA A 18 17.039 7.928 -12.446 1.00 0.00 C +ATOM 164 HA ALA A 18 17.935 8.483 -12.170 1.00 0.00 H +ATOM 165 CB ALA A 18 17.358 6.480 -12.029 1.00 0.00 C +ATOM 166 HB1 ALA A 18 17.561 6.449 -10.958 1.00 0.00 H +ATOM 167 HB2 ALA A 18 16.536 5.820 -12.307 1.00 0.00 H +ATOM 168 HB3 ALA A 18 18.323 6.159 -12.422 1.00 0.00 H +ATOM 169 C ALA A 18 16.968 8.017 -13.999 1.00 0.00 C +ATOM 170 O ALA A 18 18.024 8.143 -14.660 1.00 0.00 O +ATOM 171 N ALA A 19 15.774 8.031 -14.539 1.00 0.00 N +ATOM 172 H ALA A 19 15.110 7.729 -13.840 1.00 0.00 H +ATOM 173 CA ALA A 19 15.508 8.397 -15.942 1.00 0.00 C +ATOM 174 HA ALA A 19 16.274 7.890 -16.528 1.00 0.00 H +ATOM 175 CB ALA A 19 14.132 7.825 -16.381 1.00 0.00 C +ATOM 176 HB1 ALA A 19 14.000 6.748 -16.279 1.00 0.00 H +ATOM 177 HB2 ALA A 19 13.326 8.274 -15.801 1.00 0.00 H +ATOM 178 HB3 ALA A 19 14.129 8.183 -17.411 1.00 0.00 H +ATOM 179 C ALA A 19 15.616 9.879 -16.218 1.00 0.00 C +ATOM 180 O ALA A 19 15.925 10.312 -17.349 1.00 0.00 O +ATOM 181 N ALA A 20 15.342 10.748 -15.240 1.00 0.00 N +ATOM 182 H ALA A 20 15.274 10.304 -14.336 1.00 0.00 H +ATOM 183 CA ALA A 20 15.539 12.186 -15.310 1.00 0.00 C +ATOM 184 HA ALA A 20 15.392 12.510 -16.340 1.00 0.00 H +ATOM 185 CB ALA A 20 14.470 12.874 -14.390 1.00 0.00 C +ATOM 186 HB1 ALA A 20 13.502 12.406 -14.574 1.00 0.00 H +ATOM 187 HB2 ALA A 20 14.667 12.751 -13.325 1.00 0.00 H +ATOM 188 HB3 ALA A 20 14.411 13.936 -14.630 1.00 0.00 H +ATOM 189 C ALA A 20 16.976 12.596 -14.911 1.00 0.00 C +ATOM 190 O ALA A 20 17.474 13.502 -15.583 1.00 0.00 O +ATOM 191 N ALA A 21 17.617 12.028 -13.914 1.00 0.00 N +ATOM 192 H ALA A 21 17.079 11.380 -13.356 1.00 0.00 H +ATOM 193 CA ALA A 21 19.140 12.093 -13.649 1.00 0.00 C +ATOM 194 HA ALA A 21 19.393 13.153 -13.607 1.00 0.00 H +ATOM 195 CB ALA A 21 19.438 11.428 -12.300 1.00 0.00 C +ATOM 196 HB1 ALA A 21 18.876 12.017 -11.575 1.00 0.00 H +ATOM 197 HB2 ALA A 21 19.196 10.366 -12.277 1.00 0.00 H +ATOM 198 HB3 ALA A 21 20.473 11.677 -12.068 1.00 0.00 H +ATOM 199 C ALA A 21 19.911 11.369 -14.740 1.00 0.00 C +ATOM 200 O ALA A 21 19.370 10.700 -15.601 1.00 0.00 O +ATOM 201 N NME A 22 21.266 11.506 -14.654 1.00 0.00 N +ATOM 202 H NME A 22 21.663 12.119 -13.956 1.00 0.00 H +ATOM 203 CH3 NME A 22 22.261 10.909 -15.537 1.00 0.00 C +ATOM 204 HH31 NME A 22 21.787 10.285 -16.294 1.00 0.00 H +ATOM 205 HH32 NME A 22 22.939 11.631 -15.993 1.00 0.00 H +ATOM 206 HH33 NME A 22 22.893 10.275 -14.916 1.00 0.00 H +CONECT 1 2 +CONECT 2 1 3 4 5 +CONECT 3 2 +CONECT 4 2 +CONECT 5 2 6 6 7 +CONECT 6 5 5 +CONECT 7 5 8 9 +CONECT 8 7 +CONECT 9 7 11 12 10 +CONECT 10 9 +CONECT 11 9 +CONECT 12 9 13 13 14 +CONECT 13 12 12 +CONECT 14 12 15 16 +CONECT 15 14 +CONECT 16 14 18 19 17 +CONECT 17 16 +CONECT 18 16 +CONECT 19 16 20 20 21 +CONECT 20 19 19 +CONECT 21 19 22 23 +CONECT 22 21 +CONECT 23 21 24 25 29 +CONECT 24 23 +CONECT 25 23 26 27 28 +CONECT 26 25 +CONECT 27 25 +CONECT 28 25 +CONECT 29 23 30 30 31 +CONECT 30 29 29 +CONECT 31 29 32 33 +CONECT 32 31 +CONECT 33 31 34 35 39 +CONECT 34 33 +CONECT 35 33 36 37 38 +CONECT 36 35 +CONECT 37 35 +CONECT 38 35 +CONECT 39 33 40 40 41 +CONECT 40 39 39 +CONECT 41 39 42 43 +CONECT 42 41 +CONECT 43 41 44 45 49 +CONECT 44 43 +CONECT 45 43 46 47 48 +CONECT 46 45 +CONECT 47 45 +CONECT 48 45 +CONECT 49 43 50 50 51 +CONECT 50 49 49 +CONECT 51 49 52 53 +CONECT 52 51 +CONECT 53 51 54 55 59 +CONECT 54 53 +CONECT 55 53 56 57 58 +CONECT 56 55 +CONECT 57 55 +CONECT 58 55 +CONECT 59 53 60 60 61 +CONECT 60 59 59 +CONECT 61 59 62 63 +CONECT 62 61 +CONECT 63 61 64 65 69 +CONECT 64 63 +CONECT 65 63 66 67 68 +CONECT 66 65 +CONECT 67 65 +CONECT 68 65 +CONECT 69 63 70 70 71 +CONECT 70 69 69 +CONECT 71 69 72 73 +CONECT 72 71 +CONECT 73 71 74 75 79 +CONECT 74 73 +CONECT 75 73 76 77 78 +CONECT 76 75 +CONECT 77 75 +CONECT 78 75 +CONECT 79 73 80 80 81 +CONECT 80 79 79 +CONECT 81 79 82 83 +CONECT 82 81 +CONECT 83 81 84 85 89 +CONECT 84 83 +CONECT 85 83 86 87 88 +CONECT 86 85 +CONECT 87 85 +CONECT 88 85 +CONECT 89 83 90 90 91 +CONECT 90 89 89 +CONECT 91 89 92 93 +CONECT 92 91 +CONECT 93 91 94 95 99 +CONECT 94 93 +CONECT 95 93 96 97 98 +CONECT 96 95 +CONECT 97 95 +CONECT 98 95 +CONECT 99 93 100 100 101 +CONECT 100 99 99 +CONECT 101 99 102 103 +CONECT 102 101 +CONECT 103 101 104 105 109 +CONECT 104 103 +CONECT 105 103 106 107 108 +CONECT 106 105 +CONECT 107 105 +CONECT 108 105 +CONECT 109 103 110 110 111 +CONECT 110 109 109 +CONECT 111 109 112 113 +CONECT 112 111 +CONECT 113 111 114 115 119 +CONECT 114 113 +CONECT 115 113 116 117 118 +CONECT 116 115 +CONECT 117 115 +CONECT 118 115 +CONECT 119 113 120 120 121 +CONECT 120 119 119 +CONECT 121 119 122 123 +CONECT 122 121 +CONECT 123 121 124 125 129 +CONECT 124 123 +CONECT 125 123 126 127 128 +CONECT 126 125 +CONECT 127 125 +CONECT 128 125 +CONECT 129 123 130 130 131 +CONECT 130 129 129 +CONECT 131 129 132 133 +CONECT 132 131 +CONECT 133 131 134 135 139 +CONECT 134 133 +CONECT 135 133 136 137 138 +CONECT 136 135 +CONECT 137 135 +CONECT 138 135 +CONECT 139 133 140 140 141 +CONECT 140 139 139 +CONECT 141 139 142 143 +CONECT 142 141 +CONECT 143 141 144 145 149 +CONECT 144 143 +CONECT 145 143 146 147 148 +CONECT 146 145 +CONECT 147 145 +CONECT 148 145 +CONECT 149 143 150 150 151 +CONECT 150 149 149 +CONECT 151 149 152 153 +CONECT 152 151 +CONECT 153 151 154 155 159 +CONECT 154 153 +CONECT 155 153 156 157 158 +CONECT 156 155 +CONECT 157 155 +CONECT 158 155 +CONECT 159 153 160 160 161 +CONECT 160 159 159 +CONECT 161 159 162 163 +CONECT 162 161 +CONECT 163 161 164 165 169 +CONECT 164 163 +CONECT 165 163 166 167 168 +CONECT 166 165 +CONECT 167 165 +CONECT 168 165 +CONECT 169 163 170 170 171 +CONECT 170 169 169 +CONECT 171 169 172 173 +CONECT 172 171 +CONECT 173 171 174 175 179 +CONECT 174 173 +CONECT 175 173 176 177 178 +CONECT 176 175 +CONECT 177 175 +CONECT 178 175 +CONECT 179 173 180 180 181 +CONECT 180 179 179 +CONECT 181 179 182 183 +CONECT 182 181 +CONECT 183 181 184 185 189 +CONECT 184 183 +CONECT 185 183 186 187 188 +CONECT 186 185 +CONECT 187 185 +CONECT 188 185 +CONECT 189 183 190 190 191 +CONECT 190 189 189 +CONECT 191 189 192 193 +CONECT 192 191 +CONECT 193 191 194 195 199 +CONECT 194 193 +CONECT 195 193 196 197 198 +CONECT 196 195 +CONECT 197 195 +CONECT 198 195 +CONECT 199 193 200 200 201 +CONECT 200 199 199 +CONECT 201 199 202 203 +CONECT 202 201 +CONECT 203 201 204 205 206 +CONECT 204 203 +CONECT 205 203 +CONECT 206 203 +MASTER 0 0 0 0 0 0 0 0 206 0 206 0 +END diff --git a/unittests/output_files/leap.log b/unittests/output_files/leap.log new file mode 100644 index 0000000..17223dd --- /dev/null +++ b/unittests/output_files/leap.log @@ -0,0 +1,717072 @@ +log started: Mon Jun 15 20:56:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 15 20:56:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 15 20:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 15 20:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 15 20:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 15 20:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 15 20:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 15 20:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 15 20:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 15 20:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 15 20:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 15 20:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 15 20:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 15 20:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 15 20:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 15 20:56:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:20:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:20:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:20:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:20:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:20:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:20:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:20:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:20:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:20:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:20:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:20:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:20:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:20:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:20:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:20:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:20:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:21:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:21:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:21:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:21:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:21:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:21:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:21:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:21:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:21:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:21:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:21:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:21:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. +Created a new atom named: HD6 within residue: .R + total atoms in file: 858 + Leap added 1 missing atom according to residue templates: + 1 H / lone pairs + The file contained 1 atoms not in residue templates + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +Since the number of added atoms equals the number of missing atoms, it is likely +that some atoms had incorrect names; you may want to use addPdbAtomMap to map +these names, or change the names in the PDB file. + +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. +FATAL: Atom .R.A does not have a type. + +/software/amber/18/intel-17.0.4/bin/teLeap: Fatal Error! +Failed to generate parameters + +Exiting LEaP: Errors = 1; Warnings = 2; Notes = 0. +log started: Mon Jun 22 11:22:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:22:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:22:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:22:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:22:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:22:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:22:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:22:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:22:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:22:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:22:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:22:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:22:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:22:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:22:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:23:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:23:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:23:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:23:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:23:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:23:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:23:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:23:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:23:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:23:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:23:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:23:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:23:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:23:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:23:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. +Created a new atom named: HE7 within residue: .R +Bond: Maximum coordination exceeded on .R.A + -- setting atoms pert=true overrides default limits +ATOMS NOT BONDED: .R.A .R.A +log started: Mon Jun 22 11:24:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:24:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:24:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:24:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:24:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:24:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:24:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:24:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:24:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:24:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:24:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:24:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:24:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:24:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:24:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +-- residue 2: duplicate [ HE1] atoms (total 2) + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +Atom names in each residue should be unique. + (Same-name atoms are handled by using the first + occurrence and by ignoring the rest. + Frequently duplicate atom names stem from alternate + conformations in the PDB file.) + +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. +Bond: Maximum coordination exceeded on .R.A + -- setting atoms pert=true overrides default limits +ATOMS NOT BONDED: .R.A .R.A +log started: Mon Jun 22 11:27:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:27:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:27:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:27:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:27:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:27:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:27:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:27:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:27:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:27:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:27:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:27:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:27:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:27:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:27:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. +Created a new atom named: HE7 within residue: .R +Bond: Maximum coordination exceeded on .R.A + -- setting atoms pert=true overrides default limits +ATOMS NOT BONDED: .R.A .R.A +log started: Mon Jun 22 11:31:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:31:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:31:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:31:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:31:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:31:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:31:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:31:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:31:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:31:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:31:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:31:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:31:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +-- residue 2: duplicate [ HE2] atoms (total 2) + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +Atom names in each residue should be unique. + (Same-name atoms are handled by using the first + occurrence and by ignoring the rest. + Frequently duplicate atom names stem from alternate + conformations in the PDB file.) + +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. +Bond: Maximum coordination exceeded on .R.A + -- setting atoms pert=true overrides default limits +ATOMS NOT BONDED: .R.A .R.A +log started: Mon Jun 22 11:33:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:33:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:33:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:33:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:33:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:33:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:33:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:33:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:33:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:33:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:33:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:33:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:33:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:33:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:33:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:33:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:33:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:12 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:12 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:15 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:15 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:15 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:15 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:15 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:16 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:16 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:16 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:16 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:34:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:34:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:34:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. +Created a new atom named: H1 within residue: .R +Bond: Maximum coordination exceeded on .R.A + -- setting atoms pert=true overrides default limits +ATOMS NOT BONDED: .R.A .R.A +log started: Mon Jun 22 11:36:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:36:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:36:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:36:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:36:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:36:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:36:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:36:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:36:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:36:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:36:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:36:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +-- residue 2: duplicate [ HD1] atoms (total 2) + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +Atom names in each residue should be unique. + (Same-name atoms are handled by using the first + occurrence and by ignoring the rest. + Frequently duplicate atom names stem from alternate + conformations in the PDB file.) + +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. +Bond: Maximum coordination exceeded on .R.A + -- setting atoms pert=true overrides default limits +ATOMS NOT BONDED: .R.A .R.A +log started: Mon Jun 22 11:38:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:38:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:38:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:38:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:38:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:38:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:38:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:38:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:38:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:38:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:38:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:38:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:38:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:38:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:45 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:45 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:45 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:45 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:45 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Mon Jun 22 11:39:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Mon Jun 22 11:39:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Mon Jun 22 11:39:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 10:59:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 10:59:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 11:00:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 11:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 11:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 11:00:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 11:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 11:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 11:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 11:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 11:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jun 23 11:00:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jun 23 11:00:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jun 23 11:00:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Jul 14 14:36:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Jul 14 14:36:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Jul 14 14:36:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:15:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:15:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:15:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:15:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:15:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:15:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:15:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:15:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:15:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:15:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:15:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:15:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:16:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:16:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:16:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:16:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:16:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:16:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:16:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:16:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:16:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:16:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:16:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:16:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:23 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:23 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:24 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:24 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 166 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:24 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:24 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:24 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:19:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Tue Oct 13 18:19:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:19:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Tue Oct 13 18:28:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Tue Oct 13 18:28:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG11 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HA1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HA1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HA1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HA1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R + total atoms in file: 858 + Leap added 62 missing atoms according to residue templates: + 62 H / lone pairs + The file contained 62 atoms not in residue templates + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +Since the number of added atoms equals the number of missing atoms, it is likely +that some atoms had incorrect names; you may want to use addPdbAtomMap to map +these names, or change the names in the PDB file. + +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. + +/software/amber/18/intel-17.0.4/bin/teLeap: Fatal Error! +Failed to generate parameters + +Exiting LEaP: Errors = 1; Warnings = 2; Notes = 0. +log started: Wed Oct 14 10:16:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Oct 14 10:16:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Oct 14 10:16:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Oct 14 10:16:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Oct 14 10:16:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Oct 14 10:16:19 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:19 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Oct 14 10:16:19 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:19 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Oct 14 10:16:19 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:19 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Oct 14 10:16:19 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:20 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Oct 14 10:16:20 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:20 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Oct 14 10:16:20 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:20 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Oct 14 10:16:20 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:21 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Oct 14 10:16:21 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:21 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Oct 14 10:16:21 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:21 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Oct 14 10:16:21 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:21 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Oct 14 10:16:22 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:22 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 170 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Oct 14 10:16:22 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:22 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Oct 14 10:16:22 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:22 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Oct 14 10:16:23 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:23 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Oct 14 10:16:23 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:16:23 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/software/amber/18/intel-17.0.4/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + ** Warning: No sp2 improper torsion term for C*-CN-CB-CA + atoms are: CG CE2 CD2 CE3 + ** Warning: No sp2 improper torsion term for NA-CA-CN-CB + atoms are: NE1 CZ2 CE2 CD2 + total 171 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Oct 14 10:50:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +(UNKNOWN ATOM TYPE: Zn) +(UNKNOWN ATOM TYPE: EP) +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /software/amber/18/intel-17.0.4/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff +----- Source of /software/amber/18/intel-17.0.4/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Oct 14 10:50:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /software/amber/18/intel-17.0.4/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +(UNKNOWN ATOM TYPE: oq) +(UNKNOWN ATOM TYPE: ni) +(UNKNOWN ATOM TYPE: nj) +(UNKNOWN ATOM TYPE: nk) +(UNKNOWN ATOM TYPE: nl) +(UNKNOWN ATOM TYPE: nm) +(UNKNOWN ATOM TYPE: nn) +(UNKNOWN ATOM TYPE: sp) +(UNKNOWN ATOM TYPE: sq) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG11 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HA1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HA1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HA1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HA1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R +Created a new atom named: HD1 within residue: .R +Created a new atom named: HE1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HB1 within residue: .R +Created a new atom named: HG1 within residue: .R + total atoms in file: 858 + Leap added 62 missing atoms according to residue templates: + 62 H / lone pairs + The file contained 62 atoms not in residue templates + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +Since the number of added atoms equals the number of missing atoms, it is likely +that some atoms had incorrect names; you may want to use addPdbAtomMap to map +these names, or change the names in the PDB file. + +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/software/amber/18/intel-17.0.4/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. +FATAL: Atom .R.A does not have a type. + +/software/amber/18/intel-17.0.4/bin/teLeap: Fatal Error! +Failed to generate parameters + +Exiting LEaP: Errors = 1; Warnings = 2; Notes = 0. +log started: Wed Nov 4 15:57:22 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:22 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 15:57:24 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:24 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 15:57:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 15:57:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 15:57:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 15:57:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 15:57:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 15:57:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 15:57:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 15:57:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 15:57:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 15:57:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 15:57:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 15:57:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 15:57:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 15:57:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 15:57:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 15:57:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 15:57:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 15:57:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 15:57:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:40:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:40:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:40:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:40:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:40:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:40:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:40:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:40:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:40:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:40:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:40:09 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:09 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:40:09 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:09 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:40:10 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:40:10 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:41:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:41:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:41:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:41:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:41:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:41:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:41:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:41:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:41:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:41:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:41:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:41:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:41:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:41:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:41:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:41:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:41:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:41:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:41:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:41:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:41:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:42:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:42:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:42:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:42:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:42:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:42:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:42:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:42:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:42:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:42:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:42:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:42:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:42:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:42:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:42:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:42:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:42:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:42:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:42:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:42:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:42:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:43:10 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:10 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:43:10 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:11 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:43:11 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:11 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:43:11 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:11 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:43:12 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:12 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:43:12 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:12 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:43:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:43:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:13 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:43:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:43:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:43:14 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:15 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:43:15 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:15 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:43:15 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:16 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:43:16 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:16 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:43:16 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:16 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:43:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:43:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:17 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:43:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:43:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:18 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:43:19 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:43:19 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:59:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:59:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:59:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:59:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:59:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:59:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:59:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:59:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:59:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:59:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 16:59:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 16:59:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 16:59:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 17:00:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 17:00:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 17:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 17:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 17:00:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 17:00:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 17:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 17:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 17:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 17:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 17:00:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Wed Nov 4 17:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Wed Nov 4 17:00:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Wed Nov 4 17:00:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 11:58:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:25 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 11:58:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:26 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 11:58:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 11:58:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:27 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 11:58:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 11:58:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:28 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 11:58:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 11:58:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 11:58:29 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 11:58:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 11:58:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 11:58:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 11:58:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 11:58:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 11:58:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 11:58:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 11:58:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 11:58:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 11:58:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 11:58:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 11:58:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:08:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:08:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:08:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:08:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:08:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:08:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:08:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:08:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:08:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:08:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:08:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:08:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:08:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:08:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:08:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:08:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:08:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:08:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:08:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:08:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:08:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:54:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:54:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:55:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:55:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:55:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:55:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:55:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:55:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:55:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:55:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:55:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:55:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:55:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:55:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:55:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:55:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:55:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:55:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:55:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:55:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:55:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:55:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:30 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:58 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:56:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:56:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:56:59 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:57:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:57:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:00 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:57:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:57:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:57:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:57:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:57:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:57:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:57:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:57:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:57:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:57:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 12:57:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 12:57:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 12:57:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:40 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:41 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:42 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:43 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 13:11:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 13:11:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 13:11:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:53 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:54 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:55 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:38:56 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:38:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:38:57 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:01 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:02 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:03 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:04 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:05 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:06 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:07 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:08 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:09 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:09 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:09 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:31 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:32 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:33 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:34 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:35 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:36 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:37 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:38 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 14:40:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 14:40:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 14:40:39 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + G01 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:44 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:45 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 848 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 168 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:45 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:45 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD1 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:45 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:45 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:46 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:47 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD6 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD5 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:48 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HD8 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:49 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE2 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HE7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:50 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 858 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-4.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 172 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP7 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:51 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. +log started: Thu Nov 5 16:13:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading: R05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R06.off +Loading: R06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R07.off +Loading: R07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R08.off +Loading: R08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R09.off +Loading: R09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R10.off +Loading: R10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R11.off +Loading: R11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R12.off +Loading: R12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R13.off +Loading: R13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R14.off +Loading: R14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R15.off +Loading: R15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R16.off +Loading: R16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R17.off +Loading: R17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R18.off +Loading: R18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R19.off +Loading: R19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R20.off +Loading: R20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R21.off +Loading: R21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R22.off +Loading: R22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R23.off +Loading: R23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R24.off +Loading: R24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R25.off +Loading: R25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R26.off +Loading: R26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R27.off +Loading: R27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R28.off +Loading: R28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D01.off +Loading: D01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D02.off +Loading: D02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D03.off +Loading: D03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D04.off +Loading: D04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASP/D05.off +Loading: D05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D06.off +Loading: D06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D07.off +Loading: D07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D08.off +Loading: D08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D09.off +Loading: D09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASH/D10.off +Loading: D10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N01.off +Loading: N01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N02.off +Loading: N02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N03.off +Loading: N03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N04.off +Loading: N04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N05.off +Loading: N05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N06.off +Loading: N06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ASN/N07.off +Loading: N07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C01.off +Loading: C01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C02.off +Loading: C02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/CYS/C03.off +Loading: C03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E01.off +Loading: E01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The perturbed charge (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warnings from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + HP3 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 2; Notes = 1. +log started: Thu Nov 5 16:13:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the ff10 force field +>> # ----- NOTE: this is designed for PDB format 3! +>> # ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA +>> # phosphoaa parms from N. Homeyer, A.H.C. Horn, H. Lanig, H. Sticht +>> # J. Mol. Model. 2006, 12, 281-289. OP vdW parameters modified +>> # by T. Steinbrecher and J. Latzer. +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "H" "H" "sp3" } +>> { "HO" "H" "sp3" } +>> { "HS" "H" "sp3" } +>> { "H1" "H" "sp3" } +>> { "H2" "H" "sp3" } +>> { "H3" "H" "sp3" } +>> { "H4" "H" "sp3" } +>> { "H5" "H" "sp3" } +>> { "HW" "H" "sp3" } +>> { "HC" "H" "sp3" } +>> { "HA" "H" "sp3" } +>> { "HP" "H" "sp3" } +>> { "HZ" "H" "sp3" } +>> { "OH" "O" "sp3" } +>> { "OS" "O" "sp3" } +>> { "O" "O" "sp2" } +>> { "O2" "O" "sp2" } +>> { "OP" "O" "sp2" } +>> { "OW" "O" "sp3" } +>> { "CT" "C" "sp3" } +>> { "CX" "C" "sp3" } +>> { "CH" "C" "sp3" } +>> { "CS" "C" "sp2" } +>> { "C" "C" "sp2" } +>> { "C*" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CB" "C" "sp2" } +>> { "CC" "C" "sp2" } +>> { "CN" "C" "sp2" } +>> { "CM" "C" "sp2" } +>> { "CK" "C" "sp2" } +>> { "CQ" "C" "sp2" } +>> { "CD" "C" "sp2" } +>> { "C5" "C" "sp2" } +>> { "C4" "C" "sp2" } +>> { "CP" "C" "sp2" } +>> { "CI" "C" "sp3" } +>> { "CJ" "C" "sp2" } +>> { "CW" "C" "sp2" } +>> { "CV" "C" "sp2" } +>> { "CR" "C" "sp2" } +>> { "CA" "C" "sp2" } +>> { "CY" "C" "sp2" } +>> { "C0" "Ca" "sp2" } +>> { "MG" "Mg" "sp3" } +>> { "N" "N" "sp2" } +>> { "NA" "N" "sp2" } +>> { "N2" "N" "sp2" } +>> { "N*" "N" "sp2" } +>> { "NP" "N" "sp2" } +>> { "NQ" "N" "sp2" } +>> { "NB" "N" "sp2" } +>> { "NC" "N" "sp2" } +>> { "NT" "N" "sp3" } +>> { "NY" "N" "sp2" } +>> { "N3" "N" "sp3" } +>> { "S" "S" "sp3" } +>> { "SH" "S" "sp3" } +>> { "P" "P" "sp3" } +>> { "LP" "" "sp3" } +>> { "EP" "" "sp3" } +>> { "F" "F" "sp3" } +>> { "Cl" "Cl" "sp3" } +>> { "Br" "Br" "sp3" } +>> { "I" "I" "sp3" } +>> { "F-" "F" "sp3" } +>> { "Cl-" "Cl" "sp3" } +>> { "Br-" "Br" "sp3" } +>> { "I-" "I" "sp3" } +>> { "Li+" "Li" "sp3" } +>> { "Na+" "Na" "sp3" } +>> { "K+" "K" "sp3" } +>> { "Rb+" "Rb" "sp3" } +>> { "Cs+" "Cs" "sp3" } +>> { "Mg+" "Mg" "sp3" } +>> # glycam +>> { "OG" "O" "sp3" } +>> { "OL" "O" "sp3" } +>> { "AC" "C" "sp3" } +>> { "EC" "C" "sp3" } +>> } +>> # +>> # Load the main parameter set. +>> # +>> parm10 = loadamberparams parm10.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/parm10.dat +Reading title: +PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA +>> # +>> # Load main chain and terminating amino acid libraries, nucleic acids +>> # +>> loadOff amino10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/amino10.lib +Loading: ALA +Loading: ARG +Loading: ASH +Loading: ASN +Loading: ASP +Loading: CYM +Loading: CYS +Loading: CYX +Loading: GLH +Loading: GLN +Loading: GLU +Loading: GLY +Loading: HID +Loading: HIE +Loading: HIP +Loading: HYP +Loading: ILE +Loading: LEU +Loading: LYN +Loading: LYS +Loading: MET +Loading: PHE +Loading: PRO +Loading: SER +Loading: THR +Loading: TRP +Loading: TYR +Loading: VAL +>> loadOff aminoct10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminoct10.lib +Loading: CALA +Loading: CARG +Loading: CASN +Loading: CASP +Loading: CCYS +Loading: CCYX +Loading: CGLN +Loading: CGLU +Loading: CGLY +Loading: CHID +Loading: CHIE +Loading: CHIP +Loading: CILE +Loading: CLEU +Loading: CLYS +Loading: CMET +Loading: CPHE +Loading: CPRO +Loading: CSER +Loading: CTHR +Loading: CTRP +Loading: CTYR +Loading: CVAL +Loading: NHE +Loading: NME +>> loadOff aminont10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/aminont10.lib +Loading: ACE +Loading: NALA +Loading: NARG +Loading: NASN +Loading: NASP +Loading: NCYS +Loading: NCYX +Loading: NGLN +Loading: NGLU +Loading: NGLY +Loading: NHID +Loading: NHIE +Loading: NHIP +Loading: NILE +Loading: NLEU +Loading: NLYS +Loading: NMET +Loading: NPHE +Loading: NPRO +Loading: NSER +Loading: NTHR +Loading: NTRP +Loading: NTYR +Loading: NVAL +>> loadOff oldff/phosphoaa10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/oldff/phosphoaa10.lib +Loading: H2D +Loading: PTR +Loading: S1P +Loading: SEP +Loading: T1P +Loading: TPO +Loading: Y1P +>> loadOff nucleic10.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/nucleic10.lib +Loading: A +Loading: A3 +Loading: A5 +Loading: AN +Loading: C +Loading: C3 +Loading: C5 +Loading: CN +Loading: DA +Loading: DA3 +Loading: DA5 +Loading: DAN +Loading: DC +Loading: DC3 +Loading: DC5 +Loading: DCN +Loading: DG +Loading: DG3 +Loading: DG5 +Loading: DGN +Loading: DT +Loading: DT3 +Loading: DT5 +Loading: DTN +Loading: G +Loading: G3 +Loading: G5 +Loading: GN +Loading: OHE +Loading: U +Loading: U3 +Loading: U5 +Loading: UN +>> # +>> # Load water and ions +>> # +>> loadOff atomic_ions.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/atomic_ions.lib +Loading: AG +Loading: AL +Loading: Ag +Loading: BA +Loading: BR +Loading: Be +Loading: CA +Loading: CD +Loading: CE +Loading: CL +Loading: CO +Loading: CR +Loading: CS +Loading: CU +Loading: CU1 +Loading: Ce +Loading: Cl- +Loading: Cr +Loading: Dy +Loading: EU +Loading: EU3 +Loading: Er +Loading: F +Loading: FE +Loading: FE2 +Loading: GD3 +Loading: H3O+ +Loading: HE+ +Loading: HG +Loading: HZ+ +Loading: Hf +Loading: IN +Loading: IOD +Loading: K +Loading: K+ +Loading: LA +Loading: LI +Loading: LU +Loading: MG +Loading: MN +Loading: NA +Loading: NH4 +Loading: NI +Loading: Na+ +Loading: Nd +Loading: PB +Loading: PD +Loading: PR +Loading: PT +Loading: Pu +Loading: RB +Loading: Ra +Loading: SM +Loading: SR +Loading: Sm +Loading: Sn +Loading: TB +Loading: TL +Loading: Th +Loading: Tl +Loading: Tm +Loading: U4+ +Loading: V2+ +Loading: Y +Loading: YB2 +Loading: ZN +Loading: Zr +>> loadOff solvents.lib +Loading library: /home/duerr/miniconda3/envs/openmm/dat/leap/lib/solvents.lib +Loading: CHCL3BOX +Loading: DC4 +Loading: FB3 +Loading: FB3BOX +Loading: FB4 +Loading: FB4BOX +Loading: MEOHBOX +Loading: NMABOX +Loading: OP3 +Loading: OPC +Loading: OPC3BOX +Loading: OPCBOX +Loading: PL3 +Loading: POL3BOX +Loading: QSPCFWBOX +Loading: SPC +Loading: SPCBOX +Loading: SPCFWBOX +Loading: SPF +Loading: SPG +Loading: T4E +Loading: TIP3PBOX +Loading: TIP3PFBOX +Loading: TIP4PBOX +Loading: TIP4PEWBOX +Loading: TIP5PBOX +Loading: TP3 +Loading: TP4 +Loading: TP5 +Loading: TPF +>> HOH = TP3 +>> WAT = TP3 +>> +>> # +>> # Define the PDB name map for the amino acids and nucleic acids +>> # +>> addPdbResMap { +>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" } +>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" } +>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" } +>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" } +>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" } +>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" } +>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" } +>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" } +>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" } +>> { 0 "HID" "NHID" } { 1 "HID" "CHID" } +>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" } +>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" } +>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" } +>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" } +>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" } +>> { 0 "MET" "NMET" } { 1 "MET" "CMET" } +>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" } +>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" } +>> { 0 "SER" "NSER" } { 1 "SER" "CSER" } +>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" } +>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" } +>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" } +>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" } +>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" } +>> { 0 "G" "G5" } { 1 "G" "G3" } +>> { 0 "A" "A5" } { 1 "A" "A3" } +>> { 0 "C" "C5" } { 1 "C" "C3" } +>> { 0 "U" "U5" } { 1 "U" "U3" } +>> { 0 "DG" "DG5" } { 1 "DG" "DG3" } +>> { 0 "DA" "DA5" } { 1 "DA" "DA3" } +>> { 0 "DC" "DC5" } { 1 "DC" "DC3" } +>> { 0 "DT" "DT5" } { 1 "DT" "DT3" } +>> # some old Amber residue names for RNA: +>> { 0 "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" } +>> { 0 "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" } +>> { 0 "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" } +>> { 0 "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" } +>> # some really old Amber residue names, assuming DNA: +>> { 0 "GUA" "DG5" } { 1 "GUA" "DG3" } { "GUA" "DG" } +>> { 0 "ADE" "DA5" } { 1 "ADE" "DA3" } { "ADE" "DA" } +>> { 0 "CYT" "DC5" } { 1 "CYT" "DC3" } { "CYT" "DC" } +>> { 0 "THY" "DT5" } { 1 "THY" "DT3" } { "THY" "DT" } +>> # uncomment out the following if you have this old style RNA files: +>> # { 0 "GUA" "G5" } { 1 "GUA" "G3" } { "GUA" "G" } +>> # { 0 "ADE" "A5" } { 1 "ADE" "A3" } { "ADE" "A" } +>> # { 0 "CYT" "C5" } { 1 "CYT" "C3" } { "CYT" "C" } +>> # { 0 "THY" "T5" } { 1 "THY" "T3" } { "THY" "T" } +>> +>> } +>> +>> # try to be good about reading in really old atom names as well: +>> addPdbAtomMap { +>> { "O5*" "O5'" } +>> { "C5*" "C5'" } +>> { "C4*" "C4'" } +>> { "O4*" "O4'" } +>> { "C3*" "C3'" } +>> { "O3*" "O3'" } +>> { "C2*" "C2'" } +>> { "O2*" "O2'" } +>> { "C1*" "C1'" } +>> { "C5M" "C7" } +>> { "H1*" "H1'" } +>> { "H2*1" "H2'" } +>> { "H2*2" "H2''" } +>> { "H2'1" "H2'" } +>> { "H2'2" "H2''" } +>> { "H3*" "H3'" } +>> { "H4*" "H4'" } +>> { "H5*1" "H5'" } +>> { "H5*2" "H5''" } +>> { "H5'1" "H5'" } +>> { "H5'2" "H5''" } +>> { "HO'2" "HO2'" } +>> { "H5T" "HO5'" } +>> { "H3T" "HO3'" } +>> { "O1'" "O4'" } +>> { "OA" "OP1" } +>> { "OB" "OP2" } +>> { "O1P" "OP1" } +>> { "O2P" "OP2" } +>> } +>> +>> # +>> # assume that most often proteins use HIE +>> # +>> NHIS = NHIE +>> HIS = HIE +>> CHIS = CHIE +> +> source leaprc.gaff +----- Source: /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff +----- Source of /home/duerr/miniconda3/envs/openmm/dat/leap/cmd/leaprc.gaff done +>> logFile leap.log +log started: Thu Nov 5 16:13:52 2020 + +Log file: ./leap.log +>> # +>> # ----- leaprc for loading the general Amber Force field. +>> # This file is mostly for use with Antechamber +>> # +>> # load atom type hybridizations +>> # +>> addAtomTypes { +>> { "h1" "H" "sp3" } +>> { "h2" "H" "sp3" } +>> { "h3" "H" "sp3" } +>> { "h4" "H" "sp3" } +>> { "h5" "H" "sp3" } +>> { "ha" "H" "sp3" } +>> { "hc" "H" "sp3" } +>> { "hn" "H" "sp3" } +>> { "ho" "H" "sp3" } +>> { "hp" "H" "sp3" } +>> { "hs" "H" "sp3" } +>> { "hw" "H" "sp3" } +>> { "hx" "H" "sp3" } +>> { "o" "O" "sp2" } +>> { "o2" "O" "sp2" } +>> { "oh" "O" "sp3" } +>> { "op" "O" "sp3" } +>> { "oq" "O" "sp3" } +>> { "os" "O" "sp3" } +>> { "ow" "O" "sp3" } +>> { "c" "C" "sp2" } +>> { "c1" "C" "sp2" } +>> { "c2" "C" "sp2" } +>> { "c3" "C" "sp3" } +>> { "ca" "C" "sp2" } +>> { "cc" "C" "sp2" } +>> { "cd" "C" "sp2" } +>> { "ce" "C" "sp2" } +>> { "cf" "C" "sp2" } +>> { "cg" "C" "sp2" } +>> { "ch" "C" "sp2" } +>> { "cp" "C" "sp2" } +>> { "cq" "C" "sp2" } +>> { "cu" "C" "sp2" } +>> { "cv" "C" "sp2" } +>> { "cx" "C" "sp2" } +>> { "cy" "C" "sp2" } +>> { "cz" "C" "sp2" } +>> { "n" "N" "sp2" } +>> { "n1" "N" "sp2" } +>> { "n2" "N" "sp2" } +>> { "n3" "N" "sp3" } +>> { "n4" "N" "sp3" } +>> { "na" "N" "sp2" } +>> { "nb" "N" "sp2" } +>> { "nc" "N" "sp2" } +>> { "nd" "N" "sp2" } +>> { "ne" "N" "sp2" } +>> { "nf" "N" "sp2" } +>> { "nh" "N" "sp2" } +>> { "ni" "N" "sp2" } +>> { "nj" "N" "sp2" } +>> { "nk" "N" "sp3" } +>> { "nl" "N" "sp3" } +>> { "nm" "N" "sp2" } +>> { "nn" "N" "sp2" } +>> { "no" "N" "sp2" } +>> { "np" "N" "sp3" } +>> { "nq" "N" "sp3" } +>> { "s" "S" "sp2" } +>> { "s2" "S" "sp2" } +>> { "s3" "S" "sp3" } +>> { "s4" "S" "sp3" } +>> { "s6" "S" "sp3" } +>> { "sh" "S" "sp3" } +>> { "sp" "S" "sp3" } +>> { "sq" "S" "sp3" } +>> { "ss" "S" "sp3" } +>> { "sx" "S" "sp3" } +>> { "sy" "S" "sp3" } +>> { "p2" "P" "sp2" } +>> { "p3" "P" "sp3" } +>> { "p4" "P" "sp3" } +>> { "p5" "P" "sp3" } +>> { "pb" "P" "sp3" } +>> { "pc" "P" "sp3" } +>> { "pd" "P" "sp3" } +>> { "pe" "P" "sp3" } +>> { "pf" "P" "sp3" } +>> { "px" "P" "sp3" } +>> { "py" "P" "sp3" } +>> { "f" "F" "sp3" } +>> { "cl" "Cl" "sp3" } +>> { "br" "Br" "sp3" } +>> { "i" "I" "sp3" } +>> } +>> # +>> # Load the general force field parameter set. +>> # +>> gaff = loadamberparams gaff.dat +Loading parameters: /home/duerr/miniconda3/envs/openmm/dat/leap/parm/gaff.dat +Reading title: +AMBER General Force Field for organic molecules (Version 1.81, May 2017) +> +> +> +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ALA/A01.off +Loading: A01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R01.off +Loading: R01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R02.off +Loading: R02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R03.off +Loading: R03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R04.off +Loading: R04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ARG/R05.off +Loading library: 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/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E02.off +Loading: E02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E03.off +Loading: E03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E04.off +Loading: E04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E05.off +Loading: E05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E06.off +Loading: E06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLU/E07.off +Loading: E07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E08.off +Loading: E08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E09.off +Loading: E09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E10.off +Loading: E10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E11.off +Loading: E11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E12.off +Loading: E12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E13.off +Loading: E13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLH/E14.off +Loading: E14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q01.off +Loading: Q01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q02.off +Loading: Q02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q03.off +Loading: Q03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q04.off +Loading: Q04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLN/Q05.off +Loading: Q05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/GLY/G01.off +Loading: G01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD1.off +Loading: HD1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD2.off +Loading: HD2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD3.off +Loading: HD3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD4.off +Loading: HD4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD5.off +Loading: HD5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD6.off +Loading: HD6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD7.off +Loading: HD7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HID/HD8.off +Loading: HD8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE1.off +Loading: HE1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE2.off +Loading: HE2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE3.off +Loading: HE3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE4.off +Loading: HE4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE5.off +Loading: HE5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE6.off +Loading: HE6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE7.off +Loading: HE7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIE/HE8.off +Loading: HE8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP1.off +Loading: HP1 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP2.off +Loading: HP2 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP3.off +Loading: HP3 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP4.off +Loading: HP4 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP5.off +Loading: HP5 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP6.off +Loading: HP6 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP7.off +Loading: HP7 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/HIP/HP8.off +Loading: HP8 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I01.off +Loading: I01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I02.off +Loading: I02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I03.off +Loading: I03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I04.off +Loading: I04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/ILE/I05.off +Loading: I05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L01.off +Loading: L01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L02.off +Loading: L02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L03.off +Loading: L03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LEU/L04.off +Loading: L04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M01.off +Loading: M01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M02.off +Loading: M02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M03.off +Loading: M03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M04.off +Loading: M04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M05.off +Loading: M05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M06.off +Loading: M06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M07.off +Loading: M07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M08.off +Loading: M08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M09.off +Loading: M09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M10.off +Loading: M10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M11.off +Loading: M11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M12.off +Loading: M12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/MET/M13.off +Loading: M13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P01.off +Loading: P01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P02.off +Loading: P02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P03.off +Loading: P03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/PHE/P04.off +Loading: P04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S01.off +Loading: S01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S02.off +Loading: S02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/SER/S03.off +Loading: S03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T01.off +Loading: T01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T02.off +Loading: T02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/THR/T03.off +Loading: T03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W01.off +Loading: W01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W02.off +Loading: W02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W03.off +Loading: W03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W04.off +Loading: W04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W05.off +Loading: W05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W06.off +Loading: W06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TRP/W07.off +Loading: W07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y01.off +Loading: Y01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y02.off +Loading: Y02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y03.off +Loading: Y03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/TYR/Y04.off +Loading: Y04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V01.off +Loading: V01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V02.off +Loading: V02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/VAL/V03.off +Loading: V03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K01.off +Loading: K01 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K02.off +Loading: K02 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K03.off +Loading: K03 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K04.off +Loading: K04 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K05.off +Loading: K05 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K06.off +Loading: K06 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K07.off +Loading: K07 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K08.off +Loading: K08 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K09.off +Loading: K09 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K10.off +Loading: K10 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K11.off +Loading: K11 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K12.off +Loading: K12 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K13.off +Loading: K13 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K14.off +Loading: K14 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K15.off +Loading: K15 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K16.off +Loading: K16 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K17.off +Loading: K17 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K18.off +Loading: K18 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYS/K19.off +Loading: K19 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K20.off +Loading: K20 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K21.off +Loading: K21 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K22.off +Loading: K22 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K23.off +Loading: K23 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K24.off +Loading: K24 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K25.off +Loading: K25 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K26.off +Loading: K26 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K27.off +Loading: K27 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K28.off +Loading: K28 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K29.off +Loading: K29 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K30.off +Loading: K30 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K31.off +Loading: K31 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K32.off +Loading: K32 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K33.off +Loading: K33 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K34.off +Loading: K34 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K35.off +Loading: K35 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K36.off +Loading: K36 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K37.off +Loading: K37 +> loadOff /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading library: /home/duerr/phd/02_Projects/EVOLVE/Development/evolve/share/off/LYN/K38.off +Loading: K38 +> +> mol = loadpdb mol.pdb +Loading PDB file: ./mol.pdb +Matching PDB residue names to LEaP variables. +Mapped residue MET, term: Terminal/beginning, seq. number: 0 to: NMET. +Mapped residue GLU, term: Terminal/last, seq. number: 55 to: CGLU. + total atoms in file: 859 +> +> saveamberparm mol mol.prmtop mol.inpcrd +Checking Unit. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Warning! +The unperturbed charge of the unit (-3.000000) is not zero. + +/home/duerr/miniconda3/envs/openmm/bin/teLeap: Note. +Ignoring the warning from Unit Checking. + +Building topology. +Building atom parameters. +Building bond parameters. +Building angle parameters. +Building proper torsion parameters. +Building improper torsion parameters. + total 173 improper torsions applied +Building H-Bond parameters. +Incorporating Non-Bonded adjustments. +Not Marking per-residue atom chain types. +Marking per-residue atom chain types. + (Residues lacking connect0/connect1 - + these don't have chain types marked: + + res total affected + + CGLU 1 + NMET 1 + ) + (no restraints) +> +> +> quit + Quit + +Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1. diff --git a/unittests/output_files/mol.pdb b/unittests/output_files/mol.pdb new file mode 100644 index 0000000..20a1049 --- /dev/null +++ b/unittests/output_files/mol.pdb @@ -0,0 +1,1722 @@ +COMPND MET +AUTHOR GENERATED BY OPEN BABEL 3.0.0 +ATOM 1 N MET A 1 19.157 32.576 19.140 1.00 0.00 N1+ +ATOM 2 H1 MET A 1 18.435 31.870 19.129 1.00 0.00 H +ATOM 3 H2 MET A 1 18.900 33.260 18.441 1.00 0.00 H +ATOM 4 H3 MET A 1 19.229 33.073 20.016 1.00 0.00 H +ATOM 5 CA MET A 1 20.458 31.939 18.931 1.00 0.00 C +ATOM 6 HA MET A 1 20.420 31.303 18.046 1.00 0.00 H +ATOM 7 CB MET A 1 21.504 33.015 18.722 1.00 0.00 C +ATOM 8 HB2 MET A 1 21.352 33.519 17.768 1.00 0.00 H +ATOM 9 HB3 MET A 1 21.390 33.764 19.505 1.00 0.00 H +ATOM 10 CG MET A 1 22.904 32.517 18.656 1.00 0.00 C +ATOM 11 HG2 MET A 1 23.590 33.362 18.601 1.00 0.00 H +ATOM 12 HG3 MET A 1 23.154 32.095 19.630 1.00 0.00 H +ATOM 13 SD MET A 1 23.205 31.269 17.386 1.00 0.00 S +ATOM 14 CE MET A 1 22.990 32.137 15.870 1.00 0.00 C +ATOM 15 HE1 MET A 1 23.339 33.163 15.983 1.00 0.00 H +ATOM 16 HE2 MET A 1 21.968 32.128 15.490 1.00 0.00 H +ATOM 17 HE3 MET A 1 23.572 31.586 15.132 1.00 0.00 H +ATOM 18 C MET A 1 20.796 31.017 20.133 1.00 0.00 C +ATOM 19 O MET A 1 20.674 31.440 21.297 1.00 0.00 O +ATOM 20 N HIP A 2 21.124 29.774 19.819 1.00 0.00 N +ATOM 21 H HIP A 2 21.279 29.527 18.851 1.00 0.00 H +ATOM 22 CA HIP A 2 21.443 28.704 20.861 1.00 0.00 C +ATOM 23 CB HIP A 2 21.116 27.248 20.524 1.00 0.00 C +ATOM 24 HB2 HIP A 2 21.319 26.609 21.384 1.00 0.00 H +ATOM 25 HB3 HIP A 2 20.067 27.156 20.245 1.00 0.00 H +ATOM 26 CG HIP A 2 21.914 26.697 19.384 1.00 0.00 C +ATOM 27 ND1 HIP A 2 23.189 26.197 19.539 1.00 0.00 N +ATOM 28 HD1 HIP A 2 23.687 26.157 20.416 1.00 0.00 H +ATOM 29 CE1 HIP A 2 23.642 25.784 18.368 1.00 0.00 C +ATOM 30 HE1 HIP A 2 24.637 25.352 18.282 1.00 0.00 H +ATOM 31 NE2 HIP A 2 22.710 25.999 17.460 1.00 0.00 N +ATOM 32 HE2 HIP A 2 22.777 25.784 16.475 1.00 0.00 H +ATOM 33 CD2 HIP A 2 21.619 26.570 18.068 1.00 0.00 C +ATOM 34 HD2 HIP A 2 20.738 26.826 17.479 1.00 0.00 H +ATOM 35 HA HIP A 2 20.909 28.998 21.764 1.00 0.00 H +ATOM 36 C HIP A 2 22.937 28.892 21.086 1.00 0.00 C +ATOM 37 O HIP A 2 23.773 28.867 20.181 1.00 0.00 O +ATOM 38 N TYR A 3 23.244 29.155 22.344 1.00 0.00 N +ATOM 39 H TYR A 3 22.513 29.085 23.038 1.00 0.00 H +ATOM 40 CA TYR A 3 24.628 29.305 22.888 1.00 0.00 C +ATOM 41 HA TYR A 3 25.262 29.391 22.004 1.00 0.00 H +ATOM 42 CB TYR A 3 24.744 30.579 23.675 1.00 0.00 C +ATOM 43 HB2 TYR A 3 24.131 30.495 24.572 1.00 0.00 H +ATOM 44 HB3 TYR A 3 25.780 30.505 24.008 1.00 0.00 H +ATOM 45 CG TYR A 3 24.468 31.862 22.928 1.00 0.00 C +ATOM 46 CD1 TYR A 3 25.525 32.544 22.317 1.00 0.00 C +ATOM 47 HD1 TYR A 3 26.477 32.039 22.379 1.00 0.00 H +ATOM 48 CE1 TYR A 3 25.289 33.761 21.619 1.00 0.00 C +ATOM 49 HE1 TYR A 3 26.100 34.275 21.122 1.00 0.00 H +ATOM 50 CZ TYR A 3 23.936 34.260 21.579 1.00 0.00 C +ATOM 51 OH TYR A 3 23.774 35.268 20.774 1.00 0.00 O +ATOM 52 HH TYR A 3 24.486 35.161 20.140 1.00 0.00 H +ATOM 53 CE2 TYR A 3 22.849 33.537 22.176 1.00 0.00 C +ATOM 54 HE2 TYR A 3 21.868 33.965 22.036 1.00 0.00 H +ATOM 55 CD2 TYR A 3 23.110 32.291 22.853 1.00 0.00 C +ATOM 56 HD2 TYR A 3 22.235 31.752 23.187 1.00 0.00 H +ATOM 57 C TYR A 3 25.066 28.136 23.774 1.00 0.00 C +ATOM 58 O TYR A 3 24.233 27.436 24.338 1.00 0.00 O +ATOM 59 N LYS A 4 26.339 27.934 23.811 1.00 0.00 N +ATOM 60 H LYS A 4 26.944 28.514 23.248 1.00 0.00 H +ATOM 61 CA LYS A 4 26.982 26.918 24.687 1.00 0.00 C +ATOM 62 HA LYS A 4 26.212 26.488 25.328 1.00 0.00 H +ATOM 63 CB LYS A 4 27.643 25.801 23.803 1.00 0.00 C +ATOM 64 HB2 LYS A 4 26.868 25.465 23.113 1.00 0.00 H +ATOM 65 HB3 LYS A 4 28.422 26.196 23.151 1.00 0.00 H +ATOM 66 CG LYS A 4 28.205 24.625 24.506 1.00 0.00 C +ATOM 67 HG2 LYS A 4 29.054 24.916 25.125 1.00 0.00 H +ATOM 68 HG3 LYS A 4 27.452 24.278 25.213 1.00 0.00 H +ATOM 69 CD LYS A 4 28.635 23.407 23.678 1.00 0.00 C +ATOM 70 HD2 LYS A 4 29.003 22.691 24.414 1.00 0.00 H +ATOM 71 HD3 LYS A 4 27.737 22.954 23.255 1.00 0.00 H +ATOM 72 CE LYS A 4 29.554 23.575 22.506 1.00 0.00 C +ATOM 73 HE2 LYS A 4 28.899 24.120 21.827 1.00 0.00 H +ATOM 74 HE3 LYS A 4 30.458 24.114 22.794 1.00 0.00 H +ATOM 75 NZ LYS A 4 30.052 22.279 21.888 1.00 0.00 N1+ +ATOM 76 HZ1 LYS A 4 30.831 21.896 22.402 1.00 0.00 H +ATOM 77 HZ2 LYS A 4 30.443 22.423 20.968 1.00 0.00 H +ATOM 78 HZ3 LYS A 4 29.328 21.579 21.805 1.00 0.00 H +ATOM 79 C LYS A 4 28.003 27.516 25.655 1.00 0.00 C +ATOM 80 O LYS A 4 28.579 28.553 25.310 1.00 0.00 O +ATOM 81 N LEU A 5 28.245 26.773 26.741 1.00 0.00 N +ATOM 82 H LEU A 5 27.544 26.084 26.977 1.00 0.00 H +ATOM 83 CA LEU A 5 29.244 27.118 27.766 1.00 0.00 C +ATOM 84 HA LEU A 5 29.916 27.884 27.380 1.00 0.00 H +ATOM 85 CB LEU A 5 28.579 27.507 29.097 1.00 0.00 C +ATOM 86 HB2 LEU A 5 28.058 28.438 28.872 1.00 0.00 H +ATOM 87 HB3 LEU A 5 27.859 26.779 29.469 1.00 0.00 H +ATOM 88 CG LEU A 5 29.551 27.720 30.235 1.00 0.00 C +ATOM 89 HG LEU A 5 30.166 26.841 30.429 1.00 0.00 H +ATOM 90 CD1 LEU A 5 30.427 28.952 29.986 1.00 0.00 C +ATOM 91 HD11 LEU A 5 31.114 28.683 29.184 1.00 0.00 H +ATOM 92 HD12 LEU A 5 31.008 29.120 30.894 1.00 0.00 H +ATOM 93 HD13 LEU A 5 29.848 29.861 29.825 1.00 0.00 H +ATOM 94 CD2 LEU A 5 28.678 28.115 31.457 1.00 0.00 C +ATOM 95 HD21 LEU A 5 28.235 29.096 31.284 1.00 0.00 H +ATOM 96 HD22 LEU A 5 29.327 28.287 32.315 1.00 0.00 H +ATOM 97 HD23 LEU A 5 27.907 27.390 31.720 1.00 0.00 H +ATOM 98 C LEU A 5 30.065 25.816 27.990 1.00 0.00 C +ATOM 99 O LEU A 5 29.489 24.768 28.302 1.00 0.00 O +ATOM 100 N ILE A 6 31.415 25.954 27.959 1.00 0.00 N +ATOM 101 H ILE A 6 31.834 26.822 27.658 1.00 0.00 H +ATOM 102 CA ILE A 6 32.352 24.944 28.438 1.00 0.00 C +ATOM 103 HA ILE A 6 31.851 23.978 28.494 1.00 0.00 H +ATOM 104 CB ILE A 6 33.535 24.736 27.434 1.00 0.00 C +ATOM 105 HB ILE A 6 34.002 25.706 27.261 1.00 0.00 H +ATOM 106 CG2 ILE A 6 34.658 23.796 27.952 1.00 0.00 C +ATOM 107 HG21 ILE A 6 35.011 24.049 28.953 1.00 0.00 H +ATOM 108 HG22 ILE A 6 35.610 23.773 27.423 1.00 0.00 H +ATOM 109 HG23 ILE A 6 34.315 22.768 28.065 1.00 0.00 H +ATOM 110 CG1 ILE A 6 32.967 24.083 26.135 1.00 0.00 C +ATOM 111 HG12 ILE A 6 32.815 23.014 26.281 1.00 0.00 H +ATOM 112 HG13 ILE A 6 32.016 24.548 25.875 1.00 0.00 H +ATOM 113 CD1 ILE A 6 33.964 24.228 24.983 1.00 0.00 C +ATOM 114 HD11 ILE A 6 34.203 25.280 24.831 1.00 0.00 H +ATOM 115 HD12 ILE A 6 33.521 23.646 24.174 1.00 0.00 H +ATOM 116 HD13 ILE A 6 34.890 23.744 25.293 1.00 0.00 H +ATOM 117 C ILE A 6 32.878 25.380 29.825 1.00 0.00 C +ATOM 118 O ILE A 6 33.517 26.449 29.956 1.00 0.00 O +ATOM 119 N LEU A 7 32.756 24.548 30.823 1.00 0.00 N +ATOM 120 H LEU A 7 32.337 23.649 30.632 1.00 0.00 H +ATOM 121 CA LEU A 7 33.418 24.678 32.128 1.00 0.00 C +ATOM 122 HA LEU A 7 33.772 25.702 32.243 1.00 0.00 H +ATOM 123 CB LEU A 7 32.452 24.287 33.269 1.00 0.00 C +ATOM 124 HB2 LEU A 7 32.235 23.219 33.280 1.00 0.00 H +ATOM 125 HB3 LEU A 7 33.025 24.491 34.173 1.00 0.00 H +ATOM 126 CG LEU A 7 31.068 25.080 33.294 1.00 0.00 C +ATOM 127 HG LEU A 7 31.234 26.000 32.731 1.00 0.00 H +ATOM 128 CD1 LEU A 7 29.957 24.185 32.737 1.00 0.00 C +ATOM 129 HD11 LEU A 7 29.091 24.791 32.472 1.00 0.00 H +ATOM 130 HD12 LEU A 7 29.675 23.458 33.497 1.00 0.00 H +ATOM 131 HD13 LEU A 7 30.242 23.598 31.863 1.00 0.00 H +ATOM 132 CD2 LEU A 7 30.679 25.500 34.666 1.00 0.00 C +ATOM 133 HD21 LEU A 7 30.692 24.679 35.384 1.00 0.00 H +ATOM 134 HD22 LEU A 7 29.678 25.926 34.604 1.00 0.00 H +ATOM 135 HD23 LEU A 7 31.266 26.349 35.014 1.00 0.00 H +ATOM 136 C LEU A 7 34.704 23.832 31.982 1.00 0.00 C +ATOM 137 O LEU A 7 34.608 22.712 31.434 1.00 0.00 O +ATOM 138 N ASN A 8 35.741 24.355 32.566 1.00 0.00 N +ATOM 139 H ASN A 8 35.657 25.289 32.943 1.00 0.00 H +ATOM 140 CA ASN A 8 37.087 23.938 32.340 1.00 0.00 C +ATOM 141 HA ASN A 8 37.195 22.875 32.128 1.00 0.00 H +ATOM 142 CB ASN A 8 37.683 24.648 31.079 1.00 0.00 C +ATOM 143 HB2 ASN A 8 37.052 24.514 30.199 1.00 0.00 H +ATOM 144 HB3 ASN A 8 37.697 25.701 31.358 1.00 0.00 H +ATOM 145 CG ASN A 8 39.069 24.172 30.753 1.00 0.00 C +ATOM 146 OD1 ASN A 8 39.293 22.972 30.616 1.00 0.00 O +ATOM 147 ND2 ASN A 8 40.171 24.966 30.834 1.00 0.00 N +ATOM 148 HD21 ASN A 8 40.064 25.968 30.880 1.00 0.00 H +ATOM 149 HD22 ASN A 8 41.073 24.564 30.618 1.00 0.00 H +ATOM 150 C ASN A 8 37.929 24.262 33.602 1.00 0.00 C +ATOM 151 O ASN A 8 37.736 25.299 34.234 1.00 0.00 O +ATOM 152 N GLY A 9 38.893 23.411 33.937 1.00 0.00 N +ATOM 153 H GLY A 9 38.872 22.559 33.394 1.00 0.00 H +ATOM 154 CA GLY A 9 39.937 23.667 34.946 1.00 0.00 C +ATOM 155 HA2 GLY A 9 40.563 24.496 34.619 1.00 0.00 H +ATOM 156 HA3 GLY A 9 39.525 24.058 35.876 1.00 0.00 H +ATOM 157 C GLY A 9 40.820 22.504 35.210 1.00 0.00 C +ATOM 158 O GLY A 9 40.826 21.506 34.446 1.00 0.00 O +ATOM 159 N LYS A 10 41.477 22.473 36.356 1.00 0.00 N +ATOM 160 H LYS A 10 41.439 23.256 36.992 1.00 0.00 H +ATOM 161 CA LYS A 10 42.321 21.363 36.766 1.00 0.00 C +ATOM 162 HA LYS A 10 42.838 21.036 35.864 1.00 0.00 H +ATOM 163 CB LYS A 10 43.435 21.839 37.736 1.00 0.00 C +ATOM 164 HB2 LYS A 10 42.960 22.130 38.673 1.00 0.00 H +ATOM 165 HB3 LYS A 10 44.151 21.018 37.787 1.00 0.00 H +ATOM 166 CG LYS A 10 44.146 23.121 37.228 1.00 0.00 C +ATOM 167 HG2 LYS A 10 44.581 22.959 36.242 1.00 0.00 H +ATOM 168 HG3 LYS A 10 43.424 23.934 37.151 1.00 0.00 H +ATOM 169 CD LYS A 10 45.206 23.474 38.269 1.00 0.00 C +ATOM 170 HD2 LYS A 10 44.834 23.376 39.290 1.00 0.00 H +ATOM 171 HD3 LYS A 10 46.045 22.781 38.265 1.00 0.00 H +ATOM 172 CE LYS A 10 45.833 24.866 37.936 1.00 0.00 C +ATOM 173 HE2 LYS A 10 46.898 24.867 38.172 1.00 0.00 H +ATOM 174 HE3 LYS A 10 45.615 25.139 36.904 1.00 0.00 H +ATOM 175 NZ LYS A 10 45.314 25.885 38.915 1.00 0.00 N1+ +ATOM 176 HZ1 LYS A 10 44.318 26.049 38.885 1.00 0.00 H +ATOM 177 HZ2 LYS A 10 45.805 26.756 38.765 1.00 0.00 H +ATOM 178 HZ3 LYS A 10 45.434 25.694 39.899 1.00 0.00 H +ATOM 179 C LYS A 10 41.608 20.142 37.369 1.00 0.00 C +ATOM 180 O LYS A 10 42.136 19.017 37.432 1.00 0.00 O +ATOM 181 N THR A 11 40.316 20.407 37.709 1.00 0.00 N +ATOM 182 H THR A 11 40.018 21.373 37.739 1.00 0.00 H +ATOM 183 CA THR A 11 39.333 19.428 38.190 1.00 0.00 C +ATOM 184 HA THR A 11 39.627 18.439 37.841 1.00 0.00 H +ATOM 185 CB THR A 11 39.319 19.497 39.740 1.00 0.00 C +ATOM 186 HB THR A 11 38.538 18.809 40.063 1.00 0.00 H +ATOM 187 CG2 THR A 11 40.656 18.994 40.197 1.00 0.00 C +ATOM 188 HG21 THR A 11 40.954 17.991 39.896 1.00 0.00 H +ATOM 189 HG22 THR A 11 40.695 18.984 41.286 1.00 0.00 H +ATOM 190 HG23 THR A 11 41.453 19.662 39.869 1.00 0.00 H +ATOM 191 OG1 THR A 11 39.118 20.738 40.229 1.00 0.00 O +ATOM 192 HG1 THR A 11 39.321 20.728 41.168 1.00 0.00 H +ATOM 193 C THR A 11 37.937 19.704 37.750 1.00 0.00 C +ATOM 194 O THR A 11 37.180 18.744 37.592 1.00 0.00 O +ATOM 195 N LEU A 12 37.572 20.909 37.360 1.00 0.00 N +ATOM 196 H LEU A 12 38.100 21.745 37.569 1.00 0.00 H +ATOM 197 CA LEU A 12 36.262 21.294 36.760 1.00 0.00 C +ATOM 198 HA LEU A 12 35.427 20.887 37.329 1.00 0.00 H +ATOM 199 CB LEU A 12 36.169 22.873 36.785 1.00 0.00 C +ATOM 200 HB2 LEU A 12 36.531 23.238 37.746 1.00 0.00 H +ATOM 201 HB3 LEU A 12 36.859 23.268 36.041 1.00 0.00 H +ATOM 202 CG LEU A 12 34.824 23.483 36.357 1.00 0.00 C +ATOM 203 HG LEU A 12 34.479 23.028 35.428 1.00 0.00 H +ATOM 204 CD1 LEU A 12 33.867 23.321 37.477 1.00 0.00 C +ATOM 205 HD11 LEU A 12 32.997 23.877 37.126 1.00 0.00 H +ATOM 206 HD12 LEU A 12 34.304 23.691 38.404 1.00 0.00 H +ATOM 207 HD13 LEU A 12 33.594 22.265 37.503 1.00 0.00 H +ATOM 208 CD2 LEU A 12 34.926 25.052 36.181 1.00 0.00 C +ATOM 209 HD21 LEU A 12 35.334 25.560 37.054 1.00 0.00 H +ATOM 210 HD22 LEU A 12 33.926 25.442 35.997 1.00 0.00 H +ATOM 211 HD23 LEU A 12 35.555 25.355 35.344 1.00 0.00 H +ATOM 212 C LEU A 12 36.092 20.805 35.283 1.00 0.00 C +ATOM 213 O LEU A 12 36.941 21.102 34.441 1.00 0.00 O +ATOM 214 N LYS A 13 35.016 20.080 34.906 1.00 0.00 N +ATOM 215 H LYS A 13 34.391 19.697 35.602 1.00 0.00 H +ATOM 216 CA LYS A 13 34.642 19.704 33.571 1.00 0.00 C +ATOM 217 HA LYS A 13 35.063 20.421 32.866 1.00 0.00 H +ATOM 218 CB LYS A 13 35.034 18.226 33.244 1.00 0.00 C +ATOM 219 HB2 LYS A 13 34.497 17.579 33.938 1.00 0.00 H +ATOM 220 HB3 LYS A 13 34.849 17.922 32.214 1.00 0.00 H +ATOM 221 CG LYS A 13 36.515 17.923 33.472 1.00 0.00 C +ATOM 222 HG2 LYS A 13 37.162 18.658 32.994 1.00 0.00 H +ATOM 223 HG3 LYS A 13 36.701 17.768 34.535 1.00 0.00 H +ATOM 224 CD LYS A 13 36.804 16.487 32.994 1.00 0.00 C +ATOM 225 HD2 LYS A 13 36.157 15.747 33.465 1.00 0.00 H +ATOM 226 HD3 LYS A 13 36.456 16.506 31.962 1.00 0.00 H +ATOM 227 CE LYS A 13 38.264 16.163 32.997 1.00 0.00 C +ATOM 228 HE2 LYS A 13 38.741 16.732 32.199 1.00 0.00 H +ATOM 229 HE3 LYS A 13 38.686 16.424 33.967 1.00 0.00 H +ATOM 230 NZ LYS A 13 38.397 14.672 32.837 1.00 0.00 N1+ +ATOM 231 HZ1 LYS A 13 37.944 14.324 32.005 1.00 0.00 H +ATOM 232 HZ2 LYS A 13 37.888 14.239 33.595 1.00 0.00 H +ATOM 233 HZ3 LYS A 13 39.367 14.391 32.817 1.00 0.00 H +ATOM 234 C LYS A 13 33.119 19.875 33.400 1.00 0.00 C +ATOM 235 O LYS A 13 32.522 20.218 34.448 1.00 0.00 O +ATOM 236 N GLY A 14 32.541 19.929 32.182 1.00 0.00 N +ATOM 237 H GLY A 14 33.085 19.611 31.392 1.00 0.00 H +ATOM 238 CA GLY A 14 31.141 20.135 31.951 1.00 0.00 C +ATOM 239 HA2 GLY A 14 30.696 19.143 31.877 1.00 0.00 H +ATOM 240 HA3 GLY A 14 30.707 20.500 32.883 1.00 0.00 H +ATOM 241 C GLY A 14 30.726 21.030 30.803 1.00 0.00 C +ATOM 242 O GLY A 14 31.459 21.986 30.478 1.00 0.00 O +ATOM 243 N GLU A 15 29.602 20.661 30.175 1.00 0.00 N +ATOM 244 H GLU A 15 29.233 19.801 30.557 1.00 0.00 H +ATOM 245 CA GLU A 15 29.053 21.595 29.115 1.00 0.00 C +ATOM 246 HA GLU A 15 29.457 22.592 29.292 1.00 0.00 H +ATOM 247 CB GLU A 15 29.452 21.151 27.705 1.00 0.00 C +ATOM 248 HB2 GLU A 15 28.886 21.770 27.009 1.00 0.00 H +ATOM 249 HB3 GLU A 15 30.497 21.396 27.512 1.00 0.00 H +ATOM 250 CG GLU A 15 29.157 19.668 27.410 1.00 0.00 C +ATOM 251 HG2 GLU A 15 29.865 19.104 28.017 1.00 0.00 H +ATOM 252 HG3 GLU A 15 28.109 19.456 27.619 1.00 0.00 H +ATOM 253 CD GLU A 15 29.423 19.385 25.968 1.00 0.00 C +ATOM 254 OE1 GLU A 15 28.458 19.250 25.177 1.00 0.00 O1- +ATOM 255 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O1- +ATOM 256 C GLU A 15 27.563 21.843 29.353 1.00 0.00 C +ATOM 257 O GLU A 15 26.814 21.020 29.796 1.00 0.00 O +ATOM 258 N THR A 16 27.080 22.966 28.863 1.00 0.00 N +ATOM 259 H THR A 16 27.718 23.647 28.477 1.00 0.00 H +ATOM 260 CA THR A 16 25.618 23.342 28.987 1.00 0.00 C +ATOM 261 HA THR A 16 24.987 22.466 28.832 1.00 0.00 H +ATOM 262 CB THR A 16 25.300 23.755 30.463 1.00 0.00 C +ATOM 263 HB THR A 16 25.664 23.028 31.190 1.00 0.00 H +ATOM 264 CG2 THR A 16 26.079 25.029 30.851 1.00 0.00 C +ATOM 265 HG21 THR A 16 26.002 25.212 31.923 1.00 0.00 H +ATOM 266 HG22 THR A 16 25.827 25.999 30.420 1.00 0.00 H +ATOM 267 HG23 THR A 16 27.139 24.833 30.686 1.00 0.00 H +ATOM 268 OG1 THR A 16 23.919 23.870 30.591 1.00 0.00 O +ATOM 269 HG1 THR A 16 23.605 22.966 30.654 1.00 0.00 H +ATOM 270 C THR A 16 25.136 24.387 27.956 1.00 0.00 C +ATOM 271 O THR A 16 25.847 25.392 27.686 1.00 0.00 O +ATOM 272 N THR A 17 23.944 24.126 27.374 1.00 0.00 N +ATOM 273 H THR A 17 23.414 23.300 27.615 1.00 0.00 H +ATOM 274 CA THR A 17 23.341 25.088 26.418 1.00 0.00 C +ATOM 275 HA THR A 17 24.139 25.697 25.992 1.00 0.00 H +ATOM 276 CB THR A 17 22.634 24.399 25.250 1.00 0.00 C +ATOM 277 HB THR A 17 22.194 25.142 24.585 1.00 0.00 H +ATOM 278 CG2 THR A 17 23.534 23.466 24.406 1.00 0.00 C +ATOM 279 HG21 THR A 17 22.981 22.875 23.677 1.00 0.00 H +ATOM 280 HG22 THR A 17 24.016 22.789 25.112 1.00 0.00 H +ATOM 281 HG23 THR A 17 24.305 24.119 23.998 1.00 0.00 H +ATOM 282 OG1 THR A 17 21.618 23.516 25.740 1.00 0.00 O +ATOM 283 HG1 THR A 17 21.158 23.210 24.955 1.00 0.00 H +ATOM 284 C THR A 17 22.409 26.084 27.080 1.00 0.00 C +ATOM 285 O THR A 17 21.865 25.880 28.171 1.00 0.00 O +ATOM 286 N THR A 18 22.284 27.186 26.367 1.00 0.00 N +ATOM 287 H THR A 18 22.918 27.211 25.581 1.00 0.00 H +ATOM 288 CA THR A 18 21.341 28.346 26.665 1.00 0.00 C +ATOM 289 HA THR A 18 20.447 28.047 27.213 1.00 0.00 H +ATOM 290 CB THR A 18 21.968 29.424 27.606 1.00 0.00 C +ATOM 291 HB THR A 18 22.926 29.800 27.251 1.00 0.00 H +ATOM 292 CG2 THR A 18 20.959 30.565 27.747 1.00 0.00 C +ATOM 293 HG21 THR A 18 21.177 31.232 28.581 1.00 0.00 H +ATOM 294 HG22 THR A 18 19.932 30.214 27.838 1.00 0.00 H +ATOM 295 HG23 THR A 18 21.057 31.149 26.831 1.00 0.00 H +ATOM 296 OG1 THR A 18 21.983 28.974 29.051 1.00 0.00 O +ATOM 297 HG1 THR A 18 22.866 29.123 29.400 1.00 0.00 H +ATOM 298 C THR A 18 20.829 28.956 25.354 1.00 0.00 C +ATOM 299 O THR A 18 21.553 29.458 24.528 1.00 0.00 O +ATOM 300 N GLU A 19 19.542 28.872 25.083 1.00 0.00 N +ATOM 301 H GLU A 19 18.919 28.579 25.823 1.00 0.00 H +ATOM 302 CA GLU A 19 18.932 29.576 23.987 1.00 0.00 C +ATOM 303 HA GLU A 19 19.679 29.508 23.197 1.00 0.00 H +ATOM 304 CB GLU A 19 17.686 28.785 23.627 1.00 0.00 C +ATOM 305 HB2 GLU A 19 17.899 27.722 23.514 1.00 0.00 H +ATOM 306 HB3 GLU A 19 16.998 28.842 24.471 1.00 0.00 H +ATOM 307 CG GLU A 19 16.852 29.284 22.477 1.00 0.00 C +ATOM 308 HG2 GLU A 19 16.246 28.447 22.128 1.00 0.00 H +ATOM 309 HG3 GLU A 19 16.133 30.057 22.748 1.00 0.00 H +ATOM 310 CD GLU A 19 17.736 29.731 21.281 1.00 0.00 C +ATOM 311 OE1 GLU A 19 18.363 28.800 20.679 1.00 0.00 O1- +ATOM 312 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O1- +ATOM 313 C GLU A 19 18.631 31.049 24.311 1.00 0.00 C +ATOM 314 O GLU A 19 17.951 31.336 25.240 1.00 0.00 O +ATOM 315 N ALA A 20 19.109 32.052 23.609 1.00 0.00 N +ATOM 316 H ALA A 20 19.659 31.766 22.810 1.00 0.00 H +ATOM 317 CA ALA A 20 18.962 33.505 23.885 1.00 0.00 C +ATOM 318 HA ALA A 20 17.980 33.742 24.295 1.00 0.00 H +ATOM 319 CB ALA A 20 19.978 33.979 24.961 1.00 0.00 C +ATOM 320 HB1 ALA A 20 19.807 35.026 25.214 1.00 0.00 H +ATOM 321 HB2 ALA A 20 20.983 33.923 24.544 1.00 0.00 H +ATOM 322 HB3 ALA A 20 19.800 33.404 25.869 1.00 0.00 H +ATOM 323 C ALA A 20 19.121 34.352 22.595 1.00 0.00 C +ATOM 324 O ALA A 20 19.565 33.867 21.541 1.00 0.00 O +ATOM 325 N VAL A 21 18.819 35.698 22.666 1.00 0.00 N +ATOM 326 H VAL A 21 18.466 36.007 23.561 1.00 0.00 H +ATOM 327 CA VAL A 21 18.727 36.607 21.505 1.00 0.00 C +ATOM 328 HA VAL A 21 18.554 36.039 20.592 1.00 0.00 H +ATOM 329 CB VAL A 21 17.437 37.464 21.780 1.00 0.00 C +ATOM 330 HB VAL A 21 17.477 38.130 22.642 1.00 0.00 H +ATOM 331 CG1 VAL A 21 17.072 38.379 20.673 1.00 0.00 C +ATOM 332 HG11 VAL A 21 16.991 37.805 19.750 1.00 0.00 H +ATOM 333 HG12 VAL A 21 17.685 39.269 20.533 1.00 0.00 H +ATOM 334 HG13 VAL A 21 16.081 38.787 20.874 1.00 0.00 H +ATOM 335 CG2 VAL A 21 16.251 36.536 21.920 1.00 0.00 C +ATOM 336 HG21 VAL A 21 15.333 37.033 21.605 1.00 0.00 H +ATOM 337 HG22 VAL A 21 16.128 36.219 22.956 1.00 0.00 H +ATOM 338 HG23 VAL A 21 16.477 35.681 21.284 1.00 0.00 H +ATOM 339 C VAL A 21 19.976 37.521 21.405 1.00 0.00 C +ATOM 340 O VAL A 21 20.295 38.022 20.306 1.00 0.00 O +ATOM 341 N ASP A 22 20.728 37.651 22.457 1.00 0.00 N +ATOM 342 H ASP A 22 20.460 37.104 23.262 1.00 0.00 H +ATOM 343 CA ASP A 22 21.920 38.517 22.561 1.00 0.00 C +ATOM 344 HA ASP A 22 22.218 38.721 21.532 1.00 0.00 H +ATOM 345 CB ASP A 22 21.483 39.701 23.350 1.00 0.00 C +ATOM 346 HB2 ASP A 22 20.632 40.156 22.843 1.00 0.00 H +ATOM 347 HB3 ASP A 22 21.133 39.421 24.344 1.00 0.00 H +ATOM 348 CG ASP A 22 22.576 40.746 23.590 1.00 0.00 C +ATOM 349 OD1 ASP A 22 23.681 40.588 23.043 1.00 0.00 O1- +ATOM 350 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O1- +ATOM 351 C ASP A 22 23.019 37.703 23.294 1.00 0.00 C +ATOM 352 O ASP A 22 22.839 37.184 24.412 1.00 0.00 O +ATOM 353 N ALA A 23 24.210 37.649 22.694 1.00 0.00 N +ATOM 354 H ALA A 23 24.358 38.065 21.786 1.00 0.00 H +ATOM 355 CA ALA A 23 25.493 37.172 23.215 1.00 0.00 C +ATOM 356 HA ALA A 23 25.371 36.089 23.221 1.00 0.00 H +ATOM 357 CB ALA A 23 26.701 37.486 22.326 1.00 0.00 C +ATOM 358 HB1 ALA A 23 26.446 37.309 21.280 1.00 0.00 H +ATOM 359 HB2 ALA A 23 27.379 36.708 22.676 1.00 0.00 H +ATOM 360 HB3 ALA A 23 27.091 38.494 22.468 1.00 0.00 H +ATOM 361 C ALA A 23 25.748 37.757 24.642 1.00 0.00 C +ATOM 362 O ALA A 23 26.091 36.953 25.518 1.00 0.00 O +ATOM 363 N ALA A 24 25.564 39.050 24.846 1.00 0.00 N +ATOM 364 H ALA A 24 25.214 39.674 24.133 1.00 0.00 H +ATOM 365 CA ALA A 24 25.745 39.687 26.153 1.00 0.00 C +ATOM 366 HA ALA A 24 26.761 39.419 26.445 1.00 0.00 H +ATOM 367 CB ALA A 24 25.490 41.189 25.938 1.00 0.00 C +ATOM 368 HB1 ALA A 24 26.247 41.676 25.325 1.00 0.00 H +ATOM 369 HB2 ALA A 24 25.633 41.729 26.874 1.00 0.00 H +ATOM 370 HB3 ALA A 24 24.561 41.467 25.440 1.00 0.00 H +ATOM 371 C ALA A 24 24.796 39.101 27.137 1.00 0.00 C +ATOM 372 O ALA A 24 25.116 38.975 28.329 1.00 0.00 O +ATOM 373 N THR A 25 23.577 38.659 26.736 1.00 0.00 N +ATOM 374 H THR A 25 23.398 38.681 25.743 1.00 0.00 H +ATOM 375 CA THR A 25 22.587 38.094 27.680 1.00 0.00 C +ATOM 376 HA THR A 25 22.755 38.495 28.681 1.00 0.00 H +ATOM 377 CB THR A 25 21.196 38.549 27.262 1.00 0.00 C +ATOM 378 HB THR A 25 20.797 37.883 26.497 1.00 0.00 H +ATOM 379 CG2 THR A 25 20.246 38.369 28.438 1.00 0.00 C +ATOM 380 HG21 THR A 25 20.203 37.329 28.763 1.00 0.00 H +ATOM 381 HG22 THR A 25 19.255 38.740 28.176 1.00 0.00 H +ATOM 382 HG23 THR A 25 20.574 38.977 29.280 1.00 0.00 H +ATOM 383 OG1 THR A 25 21.199 39.931 27.030 1.00 0.00 O +ATOM 384 HG1 THR A 25 20.293 40.156 26.807 1.00 0.00 H +ATOM 385 C THR A 25 22.788 36.618 27.928 1.00 0.00 C +ATOM 386 O THR A 25 22.618 36.164 29.050 1.00 0.00 O +ATOM 387 N ALA A 26 23.216 35.854 26.929 1.00 0.00 N +ATOM 388 H ALA A 26 23.315 36.208 25.988 1.00 0.00 H +ATOM 389 CA ALA A 26 23.652 34.513 27.159 1.00 0.00 C +ATOM 390 HA ALA A 26 22.781 33.940 27.476 1.00 0.00 H +ATOM 391 CB ALA A 26 24.062 33.913 25.734 1.00 0.00 C +ATOM 392 HB1 ALA A 26 23.120 33.732 25.215 1.00 0.00 H +ATOM 393 HB2 ALA A 26 24.695 33.029 25.804 1.00 0.00 H +ATOM 394 HB3 ALA A 26 24.715 34.613 25.211 1.00 0.00 H +ATOM 395 C ALA A 26 24.856 34.523 28.062 1.00 0.00 C +ATOM 396 O ALA A 26 24.889 33.745 28.985 1.00 0.00 O +ATOM 397 N GLU A 27 25.749 35.500 28.027 1.00 0.00 N +ATOM 398 H GLU A 27 25.940 35.933 27.135 1.00 0.00 H +ATOM 399 CA GLU A 27 26.712 35.671 29.037 1.00 0.00 C +ATOM 400 HA GLU A 27 27.306 34.757 29.097 1.00 0.00 H +ATOM 401 CB GLU A 27 27.684 36.833 28.605 1.00 0.00 C +ATOM 402 HB2 GLU A 27 28.270 36.561 27.728 1.00 0.00 H +ATOM 403 HB3 GLU A 27 27.178 37.773 28.387 1.00 0.00 H +ATOM 404 CG GLU A 27 28.742 37.165 29.664 1.00 0.00 C +ATOM 405 HG2 GLU A 27 28.193 37.537 30.529 1.00 0.00 H +ATOM 406 HG3 GLU A 27 29.267 36.244 29.914 1.00 0.00 H +ATOM 407 CD GLU A 27 29.887 38.242 29.269 1.00 0.00 C +ATOM 408 OE1 GLU A 27 31.108 37.827 29.164 1.00 0.00 O1- +ATOM 409 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O1- +ATOM 410 C GLU A 27 26.099 35.742 30.450 1.00 0.00 C +ATOM 411 O GLU A 27 26.553 35.162 31.414 1.00 0.00 O +ATOM 412 N LYS A 28 25.124 36.609 30.604 1.00 0.00 N +ATOM 413 H LYS A 28 24.710 37.106 29.827 1.00 0.00 H +ATOM 414 CA LYS A 28 24.538 36.947 31.950 1.00 0.00 C +ATOM 415 HA LYS A 28 25.324 37.300 32.618 1.00 0.00 H +ATOM 416 CB LYS A 28 23.559 38.052 31.728 1.00 0.00 C +ATOM 417 HB2 LYS A 28 24.096 38.943 31.403 1.00 0.00 H +ATOM 418 HB3 LYS A 28 22.761 37.811 31.025 1.00 0.00 H +ATOM 419 CG LYS A 28 22.885 38.401 33.150 1.00 0.00 C +ATOM 420 HG2 LYS A 28 22.343 37.542 33.545 1.00 0.00 H +ATOM 421 HG3 LYS A 28 23.638 38.698 33.879 1.00 0.00 H +ATOM 422 CD LYS A 28 21.826 39.579 33.063 1.00 0.00 C +ATOM 423 HD2 LYS A 28 20.930 39.146 32.616 1.00 0.00 H +ATOM 424 HD3 LYS A 28 21.656 39.989 34.058 1.00 0.00 H +ATOM 425 CE LYS A 28 22.359 40.850 32.267 1.00 0.00 C +ATOM 426 HE2 LYS A 28 23.432 40.899 32.449 1.00 0.00 H +ATOM 427 HE3 LYS A 28 22.199 40.756 31.193 1.00 0.00 H +ATOM 428 NZ LYS A 28 21.521 42.013 32.715 1.00 0.00 N1+ +ATOM 429 HZ1 LYS A 28 21.696 42.294 33.670 1.00 0.00 H +ATOM 430 HZ2 LYS A 28 20.541 41.777 32.653 1.00 0.00 H +ATOM 431 HZ3 LYS A 28 21.651 42.827 32.131 1.00 0.00 H +ATOM 432 C LYS A 28 23.866 35.778 32.535 1.00 0.00 C +ATOM 433 O LYS A 28 23.994 35.665 33.742 1.00 0.00 O +ATOM 434 N VAL A 29 23.329 34.885 31.712 1.00 0.00 N +ATOM 435 H VAL A 29 23.229 35.111 30.733 1.00 0.00 H +ATOM 436 CA VAL A 29 22.736 33.650 32.097 1.00 0.00 C +ATOM 437 HA VAL A 29 21.999 33.879 32.866 1.00 0.00 H +ATOM 438 CB VAL A 29 21.735 33.166 30.962 1.00 0.00 C +ATOM 439 HB VAL A 29 22.375 32.951 30.106 1.00 0.00 H +ATOM 440 CG1 VAL A 29 21.139 31.783 31.445 1.00 0.00 C +ATOM 441 HG11 VAL A 29 20.592 31.413 30.579 1.00 0.00 H +ATOM 442 HG12 VAL A 29 20.575 31.908 32.370 1.00 0.00 H +ATOM 443 HG13 VAL A 29 21.993 31.113 31.534 1.00 0.00 H +ATOM 444 CG2 VAL A 29 20.482 33.992 30.547 1.00 0.00 C +ATOM 445 HG21 VAL A 29 19.966 33.618 29.662 1.00 0.00 H +ATOM 446 HG22 VAL A 29 20.739 35.019 30.286 1.00 0.00 H +ATOM 447 HG23 VAL A 29 19.838 34.110 31.419 1.00 0.00 H +ATOM 448 C VAL A 29 23.781 32.642 32.484 1.00 0.00 C +ATOM 449 O VAL A 29 23.604 31.876 33.462 1.00 0.00 O +ATOM 450 N PHE A 30 24.962 32.641 31.758 1.00 0.00 N +ATOM 451 H PHE A 30 24.997 33.287 30.981 1.00 0.00 H +ATOM 452 CA PHE A 30 26.112 31.701 32.033 1.00 0.00 C +ATOM 453 HA PHE A 30 25.692 30.753 32.371 1.00 0.00 H +ATOM 454 CB PHE A 30 26.901 31.582 30.713 1.00 0.00 C +ATOM 455 HB2 PHE A 30 26.966 32.537 30.191 1.00 0.00 H +ATOM 456 HB3 PHE A 30 27.928 31.266 30.888 1.00 0.00 H +ATOM 457 CG PHE A 30 26.348 30.600 29.656 1.00 0.00 C +ATOM 458 CD1 PHE A 30 25.751 29.296 29.878 1.00 0.00 C +ATOM 459 HD1 PHE A 30 25.705 28.943 30.897 1.00 0.00 H +ATOM 460 CE1 PHE A 30 25.345 28.377 28.817 1.00 0.00 C +ATOM 461 HE1 PHE A 30 24.810 27.464 29.039 1.00 0.00 H +ATOM 462 CZ PHE A 30 25.534 28.840 27.515 1.00 0.00 C +ATOM 463 HZ PHE A 30 25.196 28.267 26.666 1.00 0.00 H +ATOM 464 CE2 PHE A 30 26.096 30.099 27.271 1.00 0.00 C +ATOM 465 HE2 PHE A 30 26.212 30.319 26.219 1.00 0.00 H +ATOM 466 CD2 PHE A 30 26.533 30.924 28.297 1.00 0.00 C +ATOM 467 HD2 PHE A 30 27.135 31.778 28.029 1.00 0.00 H +ATOM 468 C PHE A 30 26.988 32.189 33.246 1.00 0.00 C +ATOM 469 O PHE A 30 27.609 31.344 33.905 1.00 0.00 O +ATOM 470 N LYS A 31 27.038 33.446 33.540 1.00 0.00 N +ATOM 471 H LYS A 31 26.710 34.105 32.849 1.00 0.00 H +ATOM 472 CA LYS A 31 27.405 34.022 34.854 1.00 0.00 C +ATOM 473 HA LYS A 31 28.437 33.764 35.092 1.00 0.00 H +ATOM 474 CB LYS A 31 27.274 35.599 34.858 1.00 0.00 C +ATOM 475 HB2 LYS A 31 26.242 35.714 34.527 1.00 0.00 H +ATOM 476 HB3 LYS A 31 27.292 36.098 35.827 1.00 0.00 H +ATOM 477 CG LYS A 31 28.378 36.275 33.919 1.00 0.00 C +ATOM 478 HG2 LYS A 31 28.522 35.710 32.997 1.00 0.00 H +ATOM 479 HG3 LYS A 31 27.926 37.229 33.649 1.00 0.00 H +ATOM 480 CD LYS A 31 29.823 36.487 34.439 1.00 0.00 C +ATOM 481 HD2 LYS A 31 29.755 36.977 35.411 1.00 0.00 H +ATOM 482 HD3 LYS A 31 30.132 35.472 34.684 1.00 0.00 H +ATOM 483 CE LYS A 31 30.777 37.150 33.394 1.00 0.00 C +ATOM 484 HE2 LYS A 31 30.633 36.630 32.447 1.00 0.00 H +ATOM 485 HE3 LYS A 31 30.436 38.158 33.158 1.00 0.00 H +ATOM 486 NZ LYS A 31 32.138 37.121 33.926 1.00 0.00 N1+ +ATOM 487 HZ1 LYS A 31 32.272 37.458 34.869 1.00 0.00 H +ATOM 488 HZ2 LYS A 31 32.676 37.777 33.376 1.00 0.00 H +ATOM 489 HZ3 LYS A 31 32.555 36.210 33.805 1.00 0.00 H +ATOM 490 C LYS A 31 26.516 33.562 35.983 1.00 0.00 C +ATOM 491 O LYS A 31 27.018 32.993 36.943 1.00 0.00 O +ATOM 492 N GLN A 32 25.185 33.745 35.953 1.00 0.00 N +ATOM 493 H GLN A 32 24.737 34.194 35.166 1.00 0.00 H +ATOM 494 CA GLN A 32 24.365 33.197 37.027 1.00 0.00 C +ATOM 495 HA GLN A 32 24.679 33.822 37.863 1.00 0.00 H +ATOM 496 CB GLN A 32 22.891 33.427 36.688 1.00 0.00 C +ATOM 497 HB2 GLN A 32 22.845 33.366 35.601 1.00 0.00 H +ATOM 498 HB3 GLN A 32 22.285 32.685 37.209 1.00 0.00 H +ATOM 499 CG GLN A 32 22.280 34.840 37.028 1.00 0.00 C +ATOM 500 HG2 GLN A 32 22.039 34.881 38.090 1.00 0.00 H +ATOM 501 HG3 GLN A 32 22.899 35.710 36.807 1.00 0.00 H +ATOM 502 CD GLN A 32 20.958 35.124 36.195 1.00 0.00 C +ATOM 503 OE1 GLN A 32 19.883 34.823 36.738 1.00 0.00 O +ATOM 504 NE2 GLN A 32 20.988 35.530 34.974 1.00 0.00 N +ATOM 505 HE21 GLN A 32 21.902 35.787 34.628 1.00 0.00 H +ATOM 506 HE22 GLN A 32 20.177 35.714 34.400 1.00 0.00 H +ATOM 507 C GLN A 32 24.598 31.707 37.232 1.00 0.00 C +ATOM 508 O GLN A 32 24.794 31.293 38.384 1.00 0.00 O +ATOM 509 N TYR A 33 24.530 30.875 36.142 1.00 0.00 N +ATOM 510 H TYR A 33 24.587 31.274 35.216 1.00 0.00 H +ATOM 511 CA TYR A 33 24.722 29.459 36.217 1.00 0.00 C +ATOM 512 HA TYR A 33 23.881 29.042 36.772 1.00 0.00 H +ATOM 513 CB TYR A 33 24.622 28.848 34.842 1.00 0.00 C +ATOM 514 HB2 TYR A 33 23.621 29.006 34.442 1.00 0.00 H +ATOM 515 HB3 TYR A 33 25.353 29.388 34.240 1.00 0.00 H +ATOM 516 CG TYR A 33 24.877 27.304 34.704 1.00 0.00 C +ATOM 517 CD1 TYR A 33 23.808 26.383 34.938 1.00 0.00 C +ATOM 518 HD1 TYR A 33 22.814 26.754 35.140 1.00 0.00 H +ATOM 519 CE1 TYR A 33 24.054 24.991 35.075 1.00 0.00 C +ATOM 520 HE1 TYR A 33 23.300 24.251 35.300 1.00 0.00 H +ATOM 521 CZ TYR A 33 25.399 24.562 34.934 1.00 0.00 C +ATOM 522 OH TYR A 33 25.658 23.212 34.983 1.00 0.00 O +ATOM 523 HH TYR A 33 26.608 23.080 35.030 1.00 0.00 H +ATOM 524 CE2 TYR A 33 26.410 25.459 34.723 1.00 0.00 C +ATOM 525 HE2 TYR A 33 27.443 25.157 34.630 1.00 0.00 H +ATOM 526 CD2 TYR A 33 26.146 26.818 34.602 1.00 0.00 C +ATOM 527 HD2 TYR A 33 26.992 27.469 34.435 1.00 0.00 H +ATOM 528 C TYR A 33 26.078 29.155 36.854 1.00 0.00 C +ATOM 529 O TYR A 33 26.179 28.186 37.566 1.00 0.00 O +ATOM 530 N ALA A 34 27.159 29.788 36.508 1.00 0.00 N +ATOM 531 H ALA A 34 26.997 30.563 35.881 1.00 0.00 H +ATOM 532 CA ALA A 34 28.473 29.535 37.100 1.00 0.00 C +ATOM 533 HA ALA A 34 28.717 28.476 37.023 1.00 0.00 H +ATOM 534 CB ALA A 34 29.651 30.265 36.402 1.00 0.00 C +ATOM 535 HB1 ALA A 34 30.577 29.813 36.757 1.00 0.00 H +ATOM 536 HB2 ALA A 34 29.619 31.296 36.752 1.00 0.00 H +ATOM 537 HB3 ALA A 34 29.681 30.159 35.317 1.00 0.00 H +ATOM 538 C ALA A 34 28.508 29.835 38.614 1.00 0.00 C +ATOM 539 O ALA A 34 29.097 29.077 39.389 1.00 0.00 O +ATOM 540 N ASN A 35 27.814 30.864 39.024 1.00 0.00 N +ATOM 541 H ASN A 35 27.594 31.535 38.301 1.00 0.00 H +ATOM 542 CA ASN A 35 27.743 31.252 40.445 1.00 0.00 C +ATOM 543 HA ASN A 35 28.713 31.168 40.935 1.00 0.00 H +ATOM 544 CB ASN A 35 27.254 32.684 40.541 1.00 0.00 C +ATOM 545 HB2 ASN A 35 27.798 33.361 39.883 1.00 0.00 H +ATOM 546 HB3 ASN A 35 26.192 32.727 40.300 1.00 0.00 H +ATOM 547 CG ASN A 35 27.326 33.169 41.947 1.00 0.00 C +ATOM 548 OD1 ASN A 35 26.493 32.743 42.763 1.00 0.00 O +ATOM 549 ND2 ASN A 35 28.099 34.183 42.223 1.00 0.00 N +ATOM 550 HD21 ASN A 35 28.867 34.350 41.589 1.00 0.00 H +ATOM 551 HD22 ASN A 35 28.276 34.397 43.193 1.00 0.00 H +ATOM 552 C ASN A 35 26.833 30.200 41.127 1.00 0.00 C +ATOM 553 O ASN A 35 27.114 29.686 42.238 1.00 0.00 O +ATOM 554 N ASP A 36 25.819 29.616 40.395 1.00 0.00 N +ATOM 555 H ASP A 36 25.608 30.144 39.560 1.00 0.00 H +ATOM 556 CA ASP A 36 25.004 28.401 40.867 1.00 0.00 C +ATOM 557 HA ASP A 36 24.491 28.819 41.733 1.00 0.00 H +ATOM 558 CB ASP A 36 23.819 28.175 39.948 1.00 0.00 C +ATOM 559 HB2 ASP A 36 23.379 29.117 39.623 1.00 0.00 H +ATOM 560 HB3 ASP A 36 24.279 27.586 39.154 1.00 0.00 H +ATOM 561 CG ASP A 36 22.720 27.350 40.470 1.00 0.00 C +ATOM 562 OD1 ASP A 36 22.214 26.485 39.714 1.00 0.00 O1- +ATOM 563 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O1- +ATOM 564 C ASP A 36 25.793 27.113 41.244 1.00 0.00 C +ATOM 565 O ASP A 36 25.357 26.391 42.112 1.00 0.00 O +ATOM 566 N ASN A 37 26.991 27.006 40.666 1.00 0.00 N +ATOM 567 H ASN A 37 27.306 27.779 40.098 1.00 0.00 H +ATOM 568 CA ASN A 37 27.829 25.814 40.636 1.00 0.00 C +ATOM 569 HA ASN A 37 27.378 25.130 41.354 1.00 0.00 H +ATOM 570 CB ASN A 37 27.873 25.281 39.195 1.00 0.00 C +ATOM 571 HB2 ASN A 37 27.936 26.106 38.487 1.00 0.00 H +ATOM 572 HB3 ASN A 37 28.702 24.579 39.101 1.00 0.00 H +ATOM 573 CG ASN A 37 26.652 24.492 38.842 1.00 0.00 C +ATOM 574 OD1 ASN A 37 26.432 23.357 39.282 1.00 0.00 O +ATOM 575 ND2 ASN A 37 25.706 25.057 38.177 1.00 0.00 N +ATOM 576 HD21 ASN A 37 25.804 26.050 38.016 1.00 0.00 H +ATOM 577 HD22 ASN A 37 24.895 24.502 37.947 1.00 0.00 H +ATOM 578 C ASN A 37 29.196 26.053 41.261 1.00 0.00 C +ATOM 579 O ASN A 37 30.064 25.171 41.182 1.00 0.00 O +ATOM 580 N GLY A 38 29.358 27.176 42.012 1.00 0.00 N +ATOM 581 H GLY A 38 28.556 27.765 42.189 1.00 0.00 H +ATOM 582 CA GLY A 38 30.637 27.460 42.681 1.00 0.00 C +ATOM 583 HA2 GLY A 38 30.444 28.296 43.354 1.00 0.00 H +ATOM 584 HA3 GLY A 38 30.900 26.655 43.368 1.00 0.00 H +ATOM 585 C GLY A 38 31.894 27.774 41.785 1.00 0.00 C +ATOM 586 O GLY A 38 33.027 27.429 42.124 1.00 0.00 O +ATOM 587 N VAL A 39 31.731 28.287 40.579 1.00 0.00 N +ATOM 588 H VAL A 39 30.794 28.624 40.408 1.00 0.00 H +ATOM 589 CA VAL A 39 32.664 28.449 39.403 1.00 0.00 C +ATOM 590 HA VAL A 39 33.598 27.911 39.570 1.00 0.00 H +ATOM 591 CB VAL A 39 32.015 27.778 38.179 1.00 0.00 C +ATOM 592 HB VAL A 39 31.005 28.158 38.027 1.00 0.00 H +ATOM 593 CG1 VAL A 39 32.989 28.121 37.014 1.00 0.00 C +ATOM 594 HG11 VAL A 39 32.636 27.519 36.176 1.00 0.00 H +ATOM 595 HG12 VAL A 39 34.019 27.963 37.334 1.00 0.00 H +ATOM 596 HG13 VAL A 39 32.869 29.117 36.588 1.00 0.00 H +ATOM 597 CG2 VAL A 39 31.943 26.274 38.437 1.00 0.00 C +ATOM 598 HG21 VAL A 39 31.540 25.729 37.583 1.00 0.00 H +ATOM 599 HG22 VAL A 39 31.356 26.086 39.337 1.00 0.00 H +ATOM 600 HG23 VAL A 39 32.907 25.863 38.738 1.00 0.00 H +ATOM 601 C VAL A 39 33.029 29.909 39.235 1.00 0.00 C +ATOM 602 O VAL A 39 32.186 30.683 38.757 1.00 0.00 O +ATOM 603 N ASP A 40 34.268 30.281 39.558 1.00 0.00 N +ATOM 604 H ASP A 40 34.838 29.543 39.947 1.00 0.00 H +ATOM 605 CA ASP A 40 34.875 31.551 39.096 1.00 0.00 C +ATOM 606 HA ASP A 40 34.143 32.078 38.487 1.00 0.00 H +ATOM 607 CB ASP A 40 35.183 32.418 40.345 1.00 0.00 C +ATOM 608 HB2 ASP A 40 34.184 32.657 40.710 1.00 0.00 H +ATOM 609 HB3 ASP A 40 35.707 31.788 41.065 1.00 0.00 H +ATOM 610 CG ASP A 40 35.879 33.683 40.009 1.00 0.00 C +ATOM 611 OD1 ASP A 40 35.393 34.410 39.076 1.00 0.00 O1- +ATOM 612 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O1- +ATOM 613 C ASP A 40 36.062 31.169 38.238 1.00 0.00 C +ATOM 614 O ASP A 40 36.850 30.275 38.630 1.00 0.00 O +ATOM 615 N GLY A 41 36.172 31.751 37.102 1.00 0.00 N +ATOM 616 H GLY A 41 35.443 32.408 36.858 1.00 0.00 H +ATOM 617 CA GLY A 41 37.214 31.484 36.189 1.00 0.00 C +ATOM 618 HA2 GLY A 41 38.072 31.014 36.670 1.00 0.00 H +ATOM 619 HA3 GLY A 41 36.761 30.672 35.620 1.00 0.00 H +ATOM 620 C GLY A 41 37.623 32.709 35.379 1.00 0.00 C +ATOM 621 O GLY A 41 37.288 33.862 35.686 1.00 0.00 O +ATOM 622 N GLU A 42 38.354 32.422 34.316 1.00 0.00 N +ATOM 623 H GLU A 42 38.789 31.512 34.368 1.00 0.00 H +ATOM 624 CA GLU A 42 38.603 33.310 33.228 1.00 0.00 C +ATOM 625 HA GLU A 42 38.329 34.318 33.541 1.00 0.00 H +ATOM 626 CB GLU A 42 40.158 33.294 33.040 1.00 0.00 C +ATOM 627 HB2 GLU A 42 40.656 33.398 34.004 1.00 0.00 H +ATOM 628 HB3 GLU A 42 40.417 32.326 32.611 1.00 0.00 H +ATOM 629 CG GLU A 42 40.673 34.328 32.046 1.00 0.00 C +ATOM 630 HG2 GLU A 42 41.606 34.015 31.580 1.00 0.00 H +ATOM 631 HG3 GLU A 42 39.970 34.501 31.231 1.00 0.00 H +ATOM 632 CD GLU A 42 41.014 35.613 32.804 1.00 0.00 C +ATOM 633 OE1 GLU A 42 41.944 35.693 33.644 1.00 0.00 O1- +ATOM 634 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O1- +ATOM 635 C GLU A 42 37.780 33.033 32.033 1.00 0.00 C +ATOM 636 O GLU A 42 37.577 31.870 31.690 1.00 0.00 O +ATOM 637 N TRP A 43 37.228 34.069 31.412 1.00 0.00 N +ATOM 638 H TRP A 43 37.423 35.035 31.634 1.00 0.00 H +ATOM 639 CA TRP A 43 36.233 33.951 30.354 1.00 0.00 C +ATOM 640 HA TRP A 43 35.850 32.931 30.348 1.00 0.00 H +ATOM 641 CB TRP A 43 34.984 34.889 30.616 1.00 0.00 C +ATOM 642 HB2 TRP A 43 35.436 35.868 30.771 1.00 0.00 H +ATOM 643 HB3 TRP A 43 34.427 34.918 29.679 1.00 0.00 H +ATOM 644 CG TRP A 43 34.115 34.536 31.838 1.00 0.00 C +ATOM 645 CD1 TRP A 43 34.428 34.708 33.154 1.00 0.00 C +ATOM 646 HD1 TRP A 43 35.387 35.052 33.511 1.00 0.00 H +ATOM 647 NE1 TRP A 43 33.399 34.110 33.877 1.00 0.00 N +ATOM 648 HE1 TRP A 43 33.511 34.066 34.880 1.00 0.00 H +ATOM 649 CE2 TRP A 43 32.444 33.463 33.073 1.00 0.00 C +ATOM 650 CZ2 TRP A 43 31.248 32.745 33.296 1.00 0.00 C +ATOM 651 HZ2 TRP A 43 31.007 32.429 34.301 1.00 0.00 H +ATOM 652 CH2 TRP A 43 30.575 32.194 32.199 1.00 0.00 C +ATOM 653 HH2 TRP A 43 29.740 31.527 32.355 1.00 0.00 H +ATOM 654 CZ3 TRP A 43 30.988 32.541 30.909 1.00 0.00 C +ATOM 655 HZ3 TRP A 43 30.412 32.236 30.047 1.00 0.00 H +ATOM 656 CE3 TRP A 43 32.109 33.327 30.682 1.00 0.00 C +ATOM 657 HE3 TRP A 43 32.397 33.679 29.703 1.00 0.00 H +ATOM 658 CD2 TRP A 43 32.870 33.817 31.765 1.00 0.00 C +ATOM 659 C TRP A 43 36.910 34.235 29.034 1.00 0.00 C +ATOM 660 O TRP A 43 37.660 35.202 28.823 1.00 0.00 O +ATOM 661 N THR A 44 36.468 33.398 28.113 1.00 0.00 N +ATOM 662 H THR A 44 35.919 32.590 28.367 1.00 0.00 H +ATOM 663 CA THR A 44 36.627 33.526 26.668 1.00 0.00 C +ATOM 664 HA THR A 44 36.825 34.580 26.474 1.00 0.00 H +ATOM 665 CB THR A 44 37.813 32.794 26.062 1.00 0.00 C +ATOM 666 HB THR A 44 37.695 32.789 24.978 1.00 0.00 H +ATOM 667 CG2 THR A 44 39.142 33.411 26.470 1.00 0.00 C +ATOM 668 HG21 THR A 44 39.971 32.814 26.090 1.00 0.00 H +ATOM 669 HG22 THR A 44 39.277 33.395 27.552 1.00 0.00 H +ATOM 670 HG23 THR A 44 39.360 34.408 26.088 1.00 0.00 H +ATOM 671 OG1 THR A 44 37.854 31.507 26.604 1.00 0.00 O +ATOM 672 HG1 THR A 44 37.629 30.907 25.889 1.00 0.00 H +ATOM 673 C THR A 44 35.267 33.295 26.005 1.00 0.00 C +ATOM 674 O THR A 44 34.480 32.577 26.444 1.00 0.00 O +ATOM 675 N TYR A 45 35.137 33.919 24.848 1.00 0.00 N +ATOM 676 H TYR A 45 35.900 34.526 24.585 1.00 0.00 H +ATOM 677 CA TYR A 45 34.051 33.679 23.814 1.00 0.00 C +ATOM 678 HA TYR A 45 33.565 32.748 24.109 1.00 0.00 H +ATOM 679 CB TYR A 45 33.061 34.890 23.836 1.00 0.00 C +ATOM 680 HB2 TYR A 45 32.689 35.085 24.843 1.00 0.00 H +ATOM 681 HB3 TYR A 45 33.670 35.762 23.596 1.00 0.00 H +ATOM 682 CG TYR A 45 31.825 34.747 22.962 1.00 0.00 C +ATOM 683 CD1 TYR A 45 30.955 33.684 23.061 1.00 0.00 C +ATOM 684 HD1 TYR A 45 31.040 32.945 23.845 1.00 0.00 H +ATOM 685 CE1 TYR A 45 29.908 33.556 22.116 1.00 0.00 C +ATOM 686 HE1 TYR A 45 29.113 32.849 22.291 1.00 0.00 H +ATOM 687 CZ TYR A 45 29.718 34.506 21.094 1.00 0.00 C +ATOM 688 OH TYR A 45 28.658 34.338 20.268 1.00 0.00 O +ATOM 689 HH TYR A 45 28.496 35.052 19.648 1.00 0.00 H +ATOM 690 CE2 TYR A 45 30.653 35.574 21.028 1.00 0.00 C +ATOM 691 HE2 TYR A 45 30.490 36.288 20.234 1.00 0.00 H +ATOM 692 CD2 TYR A 45 31.752 35.643 21.911 1.00 0.00 C +ATOM 693 HD2 TYR A 45 32.537 36.346 21.679 1.00 0.00 H +ATOM 694 C TYR A 45 34.545 33.529 22.336 1.00 0.00 C +ATOM 695 O TYR A 45 35.260 34.412 21.809 1.00 0.00 O +ATOM 696 N ASP A 46 33.924 32.567 21.640 1.00 0.00 N +ATOM 697 H ASP A 46 33.215 32.006 22.088 1.00 0.00 H +ATOM 698 CA ASP A 46 34.109 32.289 20.204 1.00 0.00 C +ATOM 699 HA ASP A 46 34.805 32.896 19.625 1.00 0.00 H +ATOM 700 CB ASP A 46 34.818 30.917 20.240 1.00 0.00 C +ATOM 701 HB2 ASP A 46 35.700 31.032 20.871 1.00 0.00 H +ATOM 702 HB3 ASP A 46 34.252 30.200 20.834 1.00 0.00 H +ATOM 703 CG ASP A 46 35.216 30.282 18.912 1.00 0.00 C +ATOM 704 OD1 ASP A 46 34.405 29.507 18.323 1.00 0.00 O1- +ATOM 705 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O1- +ATOM 706 C ASP A 46 32.877 32.275 19.319 1.00 0.00 C +ATOM 707 O ASP A 46 31.931 31.517 19.529 1.00 0.00 O +ATOM 708 N ASP A 47 32.833 33.220 18.413 1.00 0.00 N +ATOM 709 H ASP A 47 33.622 33.852 18.429 1.00 0.00 H +ATOM 710 CA ASP A 47 31.688 33.456 17.554 1.00 0.00 C +ATOM 711 HA ASP A 47 30.773 33.561 18.137 1.00 0.00 H +ATOM 712 CB ASP A 47 31.907 34.738 16.747 1.00 0.00 C +ATOM 713 HB2 ASP A 47 32.113 35.510 17.488 1.00 0.00 H +ATOM 714 HB3 ASP A 47 32.853 34.697 16.207 1.00 0.00 H +ATOM 715 CG ASP A 47 30.729 35.187 15.844 1.00 0.00 C +ATOM 716 OD1 ASP A 47 29.551 35.040 16.174 1.00 0.00 O1- +ATOM 717 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O1- +ATOM 718 C ASP A 47 31.522 32.326 16.557 1.00 0.00 C +ATOM 719 O ASP A 47 30.390 32.069 16.134 1.00 0.00 O +ATOM 720 N ALA A 48 32.555 31.657 16.092 1.00 0.00 N +ATOM 721 H ALA A 48 33.490 31.931 16.357 1.00 0.00 H +ATOM 722 CA ALA A 48 32.437 30.647 15.015 1.00 0.00 C +ATOM 723 HA ALA A 48 31.707 31.108 14.349 1.00 0.00 H +ATOM 724 CB ALA A 48 33.821 30.467 14.340 1.00 0.00 C +ATOM 725 HB1 ALA A 48 34.244 31.399 13.964 1.00 0.00 H +ATOM 726 HB2 ALA A 48 33.675 29.706 13.573 1.00 0.00 H +ATOM 727 HB3 ALA A 48 34.421 29.986 15.112 1.00 0.00 H +ATOM 728 C ALA A 48 31.855 29.301 15.549 1.00 0.00 C +ATOM 729 O ALA A 48 31.548 28.445 14.720 1.00 0.00 O +ATOM 730 N THR A 49 31.619 29.163 16.885 1.00 0.00 N +ATOM 731 H THR A 49 31.975 29.929 17.439 1.00 0.00 H +ATOM 732 CA THR A 49 30.811 28.126 17.576 1.00 0.00 C +ATOM 733 HA THR A 49 30.371 27.544 16.767 1.00 0.00 H +ATOM 734 CB THR A 49 31.713 27.100 18.310 1.00 0.00 C +ATOM 735 HB THR A 49 31.134 26.420 18.935 1.00 0.00 H +ATOM 736 CG2 THR A 49 32.614 26.280 17.436 1.00 0.00 C +ATOM 737 HG21 THR A 49 33.329 26.868 16.859 1.00 0.00 H +ATOM 738 HG22 THR A 49 32.002 25.593 16.853 1.00 0.00 H +ATOM 739 HG23 THR A 49 33.354 25.760 18.044 1.00 0.00 H +ATOM 740 OG1 THR A 49 32.507 27.834 19.222 1.00 0.00 O +ATOM 741 HG1 THR A 49 33.151 28.336 18.715 1.00 0.00 H +ATOM 742 C THR A 49 29.713 28.644 18.468 1.00 0.00 C +ATOM 743 O THR A 49 28.941 27.912 19.103 1.00 0.00 O +ATOM 744 N LYS A 50 29.628 29.977 18.649 1.00 0.00 N +ATOM 745 H LYS A 50 30.419 30.522 18.334 1.00 0.00 H +ATOM 746 CA LYS A 50 28.663 30.695 19.541 1.00 0.00 C +ATOM 747 HA LYS A 50 28.847 31.769 19.501 1.00 0.00 H +ATOM 748 CB LYS A 50 27.189 30.625 19.033 1.00 0.00 C +ATOM 749 HB2 LYS A 50 26.936 29.572 19.163 1.00 0.00 H +ATOM 750 HB3 LYS A 50 26.469 31.081 19.712 1.00 0.00 H +ATOM 751 CG LYS A 50 27.119 30.984 17.465 1.00 0.00 C +ATOM 752 HG2 LYS A 50 27.961 30.590 16.895 1.00 0.00 H +ATOM 753 HG3 LYS A 50 26.188 30.551 17.100 1.00 0.00 H +ATOM 754 CD LYS A 50 27.025 32.547 17.322 1.00 0.00 C +ATOM 755 HD2 LYS A 50 26.337 33.099 17.964 1.00 0.00 H +ATOM 756 HD3 LYS A 50 28.005 32.913 17.623 1.00 0.00 H +ATOM 757 CE LYS A 50 26.686 32.933 15.930 1.00 0.00 C +ATOM 758 HE2 LYS A 50 25.829 32.363 15.572 1.00 0.00 H +ATOM 759 HE3 LYS A 50 26.304 33.953 15.986 1.00 0.00 H +ATOM 760 NZ LYS A 50 27.861 32.905 14.990 1.00 0.00 N1+ +ATOM 761 HZ1 LYS A 50 28.562 33.507 15.397 1.00 0.00 H +ATOM 762 HZ2 LYS A 50 27.597 33.321 14.108 1.00 0.00 H +ATOM 763 HZ3 LYS A 50 28.269 32.017 14.736 1.00 0.00 H +ATOM 764 C LYS A 50 28.884 30.250 21.033 1.00 0.00 C +ATOM 765 O LYS A 50 27.958 30.206 21.826 1.00 0.00 O +ATOM 766 N THR A 51 30.148 29.820 21.328 1.00 0.00 N +ATOM 767 H THR A 51 30.940 30.100 20.766 1.00 0.00 H +ATOM 768 CA THR A 51 30.503 29.214 22.632 1.00 0.00 C +ATOM 769 HA THR A 51 29.680 28.714 23.142 1.00 0.00 H +ATOM 770 CB THR A 51 31.313 27.944 22.369 1.00 0.00 C +ATOM 771 HB THR A 51 32.245 28.102 21.826 1.00 0.00 H +ATOM 772 CG2 THR A 51 31.703 27.088 23.590 1.00 0.00 C +ATOM 773 HG21 THR A 51 32.177 26.160 23.272 1.00 0.00 H +ATOM 774 HG22 THR A 51 30.745 26.977 24.100 1.00 0.00 H +ATOM 775 HG23 THR A 51 32.401 27.677 24.186 1.00 0.00 H +ATOM 776 OG1 THR A 51 30.404 27.161 21.659 1.00 0.00 O +ATOM 777 HG1 THR A 51 29.757 27.683 21.179 1.00 0.00 H +ATOM 778 C THR A 51 31.202 30.120 23.549 1.00 0.00 C +ATOM 779 O THR A 51 32.200 30.721 23.143 1.00 0.00 O +ATOM 780 N PHE A 52 31.009 29.926 24.845 1.00 0.00 N +ATOM 781 H PHE A 52 30.125 29.479 25.042 1.00 0.00 H +ATOM 782 CA PHE A 52 31.821 30.391 25.941 1.00 0.00 C +ATOM 783 HA PHE A 52 32.490 31.192 25.628 1.00 0.00 H +ATOM 784 CB PHE A 52 30.715 30.979 27.007 1.00 0.00 C +ATOM 785 HB2 PHE A 52 29.988 30.200 27.238 1.00 0.00 H +ATOM 786 HB3 PHE A 52 31.250 31.298 27.901 1.00 0.00 H +ATOM 787 CG PHE A 52 30.049 32.222 26.534 1.00 0.00 C +ATOM 788 CD1 PHE A 52 28.876 32.142 25.781 1.00 0.00 C +ATOM 789 HD1 PHE A 52 28.413 31.204 25.515 1.00 0.00 H +ATOM 790 CE1 PHE A 52 28.300 33.350 25.304 1.00 0.00 C +ATOM 791 HE1 PHE A 52 27.303 33.316 24.890 1.00 0.00 H +ATOM 792 CZ PHE A 52 28.880 34.593 25.500 1.00 0.00 C +ATOM 793 HZ PHE A 52 28.417 35.460 25.054 1.00 0.00 H +ATOM 794 CE2 PHE A 52 30.122 34.665 26.192 1.00 0.00 C +ATOM 795 HE2 PHE A 52 30.650 35.597 26.333 1.00 0.00 H +ATOM 796 CD2 PHE A 52 30.597 33.495 26.795 1.00 0.00 C +ATOM 797 HD2 PHE A 52 31.435 33.581 27.471 1.00 0.00 H +ATOM 798 C PHE A 52 32.721 29.343 26.553 1.00 0.00 C +ATOM 799 O PHE A 52 32.280 28.240 26.674 1.00 0.00 O +ATOM 800 N THR A 53 33.908 29.829 27.087 1.00 0.00 N +ATOM 801 H THR A 53 34.203 30.784 26.938 1.00 0.00 H +ATOM 802 CA THR A 53 34.577 29.044 28.132 1.00 0.00 C +ATOM 803 HA THR A 53 34.003 28.190 28.492 1.00 0.00 H +ATOM 804 CB THR A 53 35.881 28.443 27.684 1.00 0.00 C +ATOM 805 HB THR A 53 36.513 29.234 27.280 1.00 0.00 H +ATOM 806 CG2 THR A 53 36.620 27.571 28.752 1.00 0.00 C +ATOM 807 HG21 THR A 53 36.814 28.236 29.595 1.00 0.00 H +ATOM 808 HG22 THR A 53 37.535 27.174 28.313 1.00 0.00 H +ATOM 809 HG23 THR A 53 35.924 26.795 29.068 1.00 0.00 H +ATOM 810 OG1 THR A 53 35.605 27.649 26.584 1.00 0.00 O +ATOM 811 HG1 THR A 53 35.459 28.177 25.796 1.00 0.00 H +ATOM 812 C THR A 53 34.776 29.748 29.443 1.00 0.00 C +ATOM 813 O THR A 53 35.146 30.939 29.437 1.00 0.00 O +ATOM 814 N VAL A 54 34.499 29.135 30.639 1.00 0.00 N +ATOM 815 H VAL A 54 34.209 28.173 30.538 1.00 0.00 H +ATOM 816 CA VAL A 54 34.861 29.536 31.982 1.00 0.00 C +ATOM 817 HA VAL A 54 35.382 30.493 31.978 1.00 0.00 H +ATOM 818 CB VAL A 54 33.697 29.716 32.869 1.00 0.00 C +ATOM 819 HB VAL A 54 32.913 30.335 32.434 1.00 0.00 H +ATOM 820 CG1 VAL A 54 33.002 28.394 33.289 1.00 0.00 C +ATOM 821 HG11 VAL A 54 33.690 27.666 33.718 1.00 0.00 H +ATOM 822 HG12 VAL A 54 32.618 28.014 32.342 1.00 0.00 H +ATOM 823 HG13 VAL A 54 32.093 28.525 33.877 1.00 0.00 H +ATOM 824 CG2 VAL A 54 34.118 30.320 34.224 1.00 0.00 C +ATOM 825 HG21 VAL A 54 34.711 31.228 34.123 1.00 0.00 H +ATOM 826 HG22 VAL A 54 34.691 29.664 34.880 1.00 0.00 H +ATOM 827 HG23 VAL A 54 33.202 30.551 34.767 1.00 0.00 H +ATOM 828 C VAL A 54 35.950 28.590 32.468 1.00 0.00 C +ATOM 829 O VAL A 54 35.738 27.385 32.660 1.00 0.00 O +ATOM 830 N THR A 55 37.187 29.085 32.651 1.00 0.00 N +ATOM 831 H THR A 55 37.326 30.038 32.345 1.00 0.00 H +ATOM 832 CA THR A 55 38.418 28.363 33.071 1.00 0.00 C +ATOM 833 HA THR A 55 38.197 27.299 32.991 1.00 0.00 H +ATOM 834 CB THR A 55 39.574 28.516 32.161 1.00 0.00 C +ATOM 835 HB THR A 55 39.757 29.581 32.019 1.00 0.00 H +ATOM 836 CG2 THR A 55 40.870 27.898 32.786 1.00 0.00 C +ATOM 837 HG21 THR A 55 40.583 26.849 32.855 1.00 0.00 H +ATOM 838 HG22 THR A 55 41.023 28.190 33.826 1.00 0.00 H +ATOM 839 HG23 THR A 55 41.825 28.044 32.280 1.00 0.00 H +ATOM 840 OG1 THR A 55 39.215 27.970 30.818 1.00 0.00 O +ATOM 841 HG1 THR A 55 38.792 28.725 30.401 1.00 0.00 H +ATOM 842 C THR A 55 38.779 28.725 34.458 1.00 0.00 C +ATOM 843 O THR A 55 39.263 29.841 34.735 1.00 0.00 O +ATOM 844 N GLU A 56 38.757 27.773 35.416 1.00 0.00 N +ATOM 845 H GLU A 56 38.459 26.869 35.079 1.00 0.00 H +ATOM 846 CA GLU A 56 39.045 27.993 36.888 1.00 0.00 C +ATOM 847 HA GLU A 56 38.618 28.921 37.267 1.00 0.00 H +ATOM 848 CB GLU A 56 38.402 26.911 37.749 1.00 0.00 C +ATOM 849 HB2 GLU A 56 37.329 27.019 37.593 1.00 0.00 H +ATOM 850 HB3 GLU A 56 38.780 25.905 37.563 1.00 0.00 H +ATOM 851 CG GLU A 56 38.436 27.078 39.267 1.00 0.00 C +ATOM 852 HG2 GLU A 56 39.455 26.968 39.636 1.00 0.00 H +ATOM 853 HG3 GLU A 56 38.094 28.097 39.445 1.00 0.00 H +ATOM 854 CD GLU A 56 37.514 26.014 39.918 1.00 0.00 C +ATOM 855 OE1 GLU A 56 37.905 24.823 39.870 1.00 0.00 O1- +ATOM 856 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O1- +ATOM 857 C GLU A 56 40.488 28.137 37.301 1.00 0.00 C +ATOM 858 O GLU A 56 40.807 29.090 38.025 1.00 0.00 O1- +ATOM 859 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O1- +CONECT 1 2 3 4 5 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 1 6 7 18 +CONECT 6 5 +CONECT 7 5 8 9 10 +CONECT 8 7 +CONECT 9 7 +CONECT 10 7 11 12 13 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 +CONECT 14 13 15 16 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 19 20 +CONECT 19 18 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 36 23 +CONECT 23 22 24 25 26 +CONECT 24 23 +CONECT 25 23 +CONECT 26 23 27 33 33 +CONECT 27 26 28 29 +CONECT 28 27 +CONECT 29 27 30 31 +CONECT 30 29 +CONECT 31 29 32 33 +CONECT 32 31 +CONECT 33 26 26 31 34 +CONECT 34 33 +CONECT 35 22 +CONECT 36 22 37 37 38 +CONECT 37 36 36 +CONECT 38 36 39 40 +CONECT 39 38 +CONECT 40 38 41 42 57 +CONECT 41 40 +CONECT 42 40 43 44 45 +CONECT 43 42 +CONECT 44 42 +CONECT 45 42 46 46 55 +CONECT 46 45 45 47 48 +CONECT 47 46 +CONECT 48 46 49 50 50 +CONECT 49 48 +CONECT 50 48 48 51 53 +CONECT 51 50 52 +CONECT 52 51 +CONECT 53 50 54 55 55 +CONECT 54 53 +CONECT 55 45 53 53 56 +CONECT 56 55 +CONECT 57 40 58 58 59 +CONECT 58 57 57 +CONECT 59 57 60 61 +CONECT 60 59 +CONECT 61 59 62 63 79 +CONECT 62 61 +CONECT 63 61 64 65 66 +CONECT 64 63 +CONECT 65 63 +CONECT 66 63 67 68 69 +CONECT 67 66 +CONECT 68 66 +CONECT 69 66 70 71 72 +CONECT 70 69 +CONECT 71 69 +CONECT 72 69 73 74 75 +CONECT 73 72 +CONECT 74 72 +CONECT 75 72 76 77 78 +CONECT 76 75 +CONECT 77 75 +CONECT 78 75 +CONECT 79 61 80 80 81 +CONECT 80 79 79 +CONECT 81 79 82 83 +CONECT 82 81 +CONECT 83 81 84 85 98 +CONECT 84 83 +CONECT 85 83 86 87 88 +CONECT 86 85 +CONECT 87 85 +CONECT 88 85 89 90 94 +CONECT 89 88 +CONECT 90 88 91 92 93 +CONECT 91 90 +CONECT 92 90 +CONECT 93 90 +CONECT 94 88 95 96 97 +CONECT 95 94 +CONECT 96 94 +CONECT 97 94 +CONECT 98 83 99 99 100 +CONECT 99 98 98 +CONECT 100 98 101 102 +CONECT 101 100 +CONECT 102 100 103 104 117 +CONECT 103 102 +CONECT 104 102 105 106 110 +CONECT 105 104 +CONECT 106 104 107 108 109 +CONECT 107 106 +CONECT 108 106 +CONECT 109 106 +CONECT 110 104 111 112 113 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 114 115 116 +CONECT 114 113 +CONECT 115 113 +CONECT 116 113 +CONECT 117 102 118 118 119 +CONECT 118 117 117 +CONECT 119 117 120 121 +CONECT 120 119 +CONECT 121 119 122 123 136 +CONECT 122 121 +CONECT 123 121 124 125 126 +CONECT 124 123 +CONECT 125 123 +CONECT 126 123 127 128 132 +CONECT 127 126 +CONECT 128 126 129 130 131 +CONECT 129 128 +CONECT 130 128 +CONECT 131 128 +CONECT 132 126 133 134 135 +CONECT 133 132 +CONECT 134 132 +CONECT 135 132 +CONECT 136 121 137 137 138 +CONECT 137 136 136 +CONECT 138 136 139 140 +CONECT 139 138 +CONECT 140 138 141 142 150 +CONECT 141 140 +CONECT 142 140 143 144 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 146 147 +CONECT 146 145 145 +CONECT 147 145 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 140 151 151 152 +CONECT 151 150 150 +CONECT 152 150 153 154 +CONECT 153 152 +CONECT 154 152 155 156 157 +CONECT 155 154 +CONECT 156 154 +CONECT 157 154 158 158 159 +CONECT 158 157 157 +CONECT 159 157 160 161 +CONECT 160 159 +CONECT 161 159 162 163 179 +CONECT 162 161 +CONECT 163 161 164 165 166 +CONECT 164 163 +CONECT 165 163 +CONECT 166 163 167 168 169 +CONECT 167 166 +CONECT 168 166 +CONECT 169 166 170 171 172 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 173 174 175 +CONECT 173 172 +CONECT 174 172 +CONECT 175 172 176 177 178 +CONECT 176 175 +CONECT 177 175 +CONECT 178 175 +CONECT 179 161 180 180 181 +CONECT 180 179 179 +CONECT 181 179 182 183 +CONECT 182 181 +CONECT 183 181 184 185 193 +CONECT 184 183 +CONECT 185 183 186 187 191 +CONECT 186 185 +CONECT 187 185 188 189 190 +CONECT 188 187 +CONECT 189 187 +CONECT 190 187 +CONECT 191 185 192 +CONECT 192 191 +CONECT 193 183 194 194 195 +CONECT 194 193 193 +CONECT 195 193 196 197 +CONECT 196 195 +CONECT 197 195 198 199 212 +CONECT 198 197 +CONECT 199 197 200 201 202 +CONECT 200 199 +CONECT 201 199 +CONECT 202 199 203 204 208 +CONECT 203 202 +CONECT 204 202 205 206 207 +CONECT 205 204 +CONECT 206 204 +CONECT 207 204 +CONECT 208 202 209 210 211 +CONECT 209 208 +CONECT 210 208 +CONECT 211 208 +CONECT 212 197 213 213 214 +CONECT 213 212 212 +CONECT 214 212 215 216 +CONECT 215 214 +CONECT 216 214 217 218 234 +CONECT 217 216 +CONECT 218 216 219 220 221 +CONECT 219 218 +CONECT 220 218 +CONECT 221 218 222 223 224 +CONECT 222 221 +CONECT 223 221 +CONECT 224 221 225 226 227 +CONECT 225 224 +CONECT 226 224 +CONECT 227 224 228 229 230 +CONECT 228 227 +CONECT 229 227 +CONECT 230 227 231 232 233 +CONECT 231 230 +CONECT 232 230 +CONECT 233 230 +CONECT 234 216 235 235 236 +CONECT 235 234 234 +CONECT 236 234 237 238 +CONECT 237 236 +CONECT 238 236 239 240 241 +CONECT 239 238 +CONECT 240 238 +CONECT 241 238 242 242 243 +CONECT 242 241 241 +CONECT 243 241 244 245 +CONECT 244 243 +CONECT 245 243 246 247 256 +CONECT 246 245 +CONECT 247 245 248 249 250 +CONECT 248 247 +CONECT 249 247 +CONECT 250 247 251 252 253 +CONECT 251 250 +CONECT 252 250 +CONECT 253 250 254 254 255 +CONECT 254 253 253 +CONECT 255 253 +CONECT 256 245 257 257 258 +CONECT 257 256 256 +CONECT 258 256 259 260 +CONECT 259 258 +CONECT 260 258 261 262 270 +CONECT 261 260 +CONECT 262 260 263 264 268 +CONECT 263 262 +CONECT 264 262 265 266 267 +CONECT 265 264 +CONECT 266 264 +CONECT 267 264 +CONECT 268 262 269 +CONECT 269 268 +CONECT 270 260 271 271 272 +CONECT 271 270 270 +CONECT 272 270 273 274 +CONECT 273 272 +CONECT 274 272 275 276 284 +CONECT 275 274 +CONECT 276 274 277 278 282 +CONECT 277 276 +CONECT 278 276 279 280 281 +CONECT 279 278 +CONECT 280 278 +CONECT 281 278 +CONECT 282 276 283 +CONECT 283 282 +CONECT 284 274 285 285 286 +CONECT 285 284 284 +CONECT 286 284 287 288 +CONECT 287 286 +CONECT 288 286 289 290 298 +CONECT 289 288 +CONECT 290 288 291 292 296 +CONECT 291 290 +CONECT 292 290 293 294 295 +CONECT 293 292 +CONECT 294 292 +CONECT 295 292 +CONECT 296 290 297 +CONECT 297 296 +CONECT 298 288 299 299 300 +CONECT 299 298 298 +CONECT 300 298 301 302 +CONECT 301 300 +CONECT 302 300 303 304 313 +CONECT 303 302 +CONECT 304 302 305 306 307 +CONECT 305 304 +CONECT 306 304 +CONECT 307 304 308 309 310 +CONECT 308 307 +CONECT 309 307 +CONECT 310 307 311 311 312 +CONECT 311 310 310 +CONECT 312 310 +CONECT 313 302 314 314 315 +CONECT 314 313 313 +CONECT 315 313 316 317 +CONECT 316 315 +CONECT 317 315 318 319 323 +CONECT 318 317 +CONECT 319 317 320 321 322 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 317 324 324 325 +CONECT 324 323 323 +CONECT 325 323 326 327 +CONECT 326 325 +CONECT 327 325 328 329 339 +CONECT 328 327 +CONECT 329 327 330 331 335 +CONECT 330 329 +CONECT 331 329 332 333 334 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 329 336 337 338 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 327 340 340 341 +CONECT 340 339 339 +CONECT 341 339 342 343 +CONECT 342 341 +CONECT 343 341 344 345 351 +CONECT 344 343 +CONECT 345 343 346 347 348 +CONECT 346 345 +CONECT 347 345 +CONECT 348 345 349 349 350 +CONECT 349 348 348 +CONECT 350 348 +CONECT 351 343 352 352 353 +CONECT 352 351 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 356 357 361 +CONECT 356 355 +CONECT 357 355 358 359 360 +CONECT 358 357 +CONECT 359 357 +CONECT 360 357 +CONECT 361 355 362 362 363 +CONECT 362 361 361 +CONECT 363 361 364 365 +CONECT 364 363 +CONECT 365 363 366 367 371 +CONECT 366 365 +CONECT 367 365 368 369 370 +CONECT 368 367 +CONECT 369 367 +CONECT 370 367 +CONECT 371 365 372 372 373 +CONECT 372 371 371 +CONECT 373 371 374 375 +CONECT 374 373 +CONECT 375 373 376 377 385 +CONECT 376 375 +CONECT 377 375 378 379 383 +CONECT 378 377 +CONECT 379 377 380 381 382 +CONECT 380 379 +CONECT 381 379 +CONECT 382 379 +CONECT 383 377 384 +CONECT 384 383 +CONECT 385 375 386 386 387 +CONECT 386 385 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 390 391 395 +CONECT 390 389 +CONECT 391 389 392 393 394 +CONECT 392 391 +CONECT 393 391 +CONECT 394 391 +CONECT 395 389 396 396 397 +CONECT 396 395 395 +CONECT 397 395 398 399 +CONECT 398 397 +CONECT 399 397 400 401 410 +CONECT 400 399 +CONECT 401 399 402 403 404 +CONECT 402 401 +CONECT 403 401 +CONECT 404 401 405 406 407 +CONECT 405 404 +CONECT 406 404 +CONECT 407 404 408 408 409 +CONECT 408 407 407 +CONECT 409 407 +CONECT 410 399 411 411 412 +CONECT 411 410 410 +CONECT 412 410 413 414 +CONECT 413 412 +CONECT 414 412 415 416 432 +CONECT 415 414 +CONECT 416 414 417 418 419 +CONECT 417 416 +CONECT 418 416 +CONECT 419 416 420 421 422 +CONECT 420 419 +CONECT 421 419 +CONECT 422 419 423 424 425 +CONECT 423 422 +CONECT 424 422 +CONECT 425 422 426 427 428 +CONECT 426 425 +CONECT 427 425 +CONECT 428 425 429 430 431 +CONECT 429 428 +CONECT 430 428 +CONECT 431 428 +CONECT 432 414 433 433 434 +CONECT 433 432 432 +CONECT 434 432 435 436 +CONECT 435 434 +CONECT 436 434 437 438 448 +CONECT 437 436 +CONECT 438 436 439 440 444 +CONECT 439 438 +CONECT 440 438 441 442 443 +CONECT 441 440 +CONECT 442 440 +CONECT 443 440 +CONECT 444 438 445 446 447 +CONECT 445 444 +CONECT 446 444 +CONECT 447 444 +CONECT 448 436 449 449 450 +CONECT 449 448 448 +CONECT 450 448 451 452 +CONECT 451 450 +CONECT 452 450 453 454 468 +CONECT 453 452 +CONECT 454 452 455 456 457 +CONECT 455 454 +CONECT 456 454 +CONECT 457 454 458 458 466 +CONECT 458 457 457 459 460 +CONECT 459 458 +CONECT 460 458 461 462 462 +CONECT 461 460 +CONECT 462 460 460 463 464 +CONECT 463 462 +CONECT 464 462 465 466 466 +CONECT 465 464 +CONECT 466 457 464 464 467 +CONECT 467 466 +CONECT 468 452 469 469 470 +CONECT 469 468 468 +CONECT 470 468 471 472 +CONECT 471 470 +CONECT 472 470 473 474 490 +CONECT 473 472 +CONECT 474 472 475 476 477 +CONECT 475 474 +CONECT 476 474 +CONECT 477 474 478 479 480 +CONECT 478 477 +CONECT 479 477 +CONECT 480 477 481 482 483 +CONECT 481 480 +CONECT 482 480 +CONECT 483 480 484 485 486 +CONECT 484 483 +CONECT 485 483 +CONECT 486 483 487 488 489 +CONECT 487 486 +CONECT 488 486 +CONECT 489 486 +CONECT 490 472 491 491 492 +CONECT 491 490 490 +CONECT 492 490 493 494 +CONECT 493 492 +CONECT 494 492 495 496 507 +CONECT 495 494 +CONECT 496 494 497 498 499 +CONECT 497 496 +CONECT 498 496 +CONECT 499 496 500 501 502 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8.50000000E-01 7.90000000E-01 + 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 + 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 + 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 + 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01 + 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 + 8.50000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 + 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 + 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01 + 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 + 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 + 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01 8.50000000E-01 + 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 + 8.50000000E-01 8.50000000E-01 8.50000000E-01 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+COMPND MET +AUTHOR GENERATED BY OPEN BABEL 3.0.0 +ATOM 1 N MET A 1 19.157 32.576 19.140 1.00 0.00 N1+ +ATOM 2 H1 MET A 1 18.435 31.870 19.129 1.00 0.00 H +ATOM 3 H2 MET A 1 18.900 33.260 18.441 1.00 0.00 H +ATOM 4 H3 MET A 1 19.229 33.073 20.016 1.00 0.00 H +ATOM 5 CA MET A 1 20.458 31.939 18.931 1.00 0.00 C +ATOM 6 HA MET A 1 20.420 31.303 18.046 1.00 0.00 H +ATOM 7 CB MET A 1 21.504 33.015 18.722 1.00 0.00 C +ATOM 8 HB2 MET A 1 21.352 33.519 17.768 1.00 0.00 H +ATOM 9 HB3 MET A 1 21.390 33.764 19.505 1.00 0.00 H +ATOM 10 CG MET A 1 22.904 32.517 18.656 1.00 0.00 C +ATOM 11 HG2 MET A 1 23.590 33.362 18.601 1.00 0.00 H +ATOM 12 HG3 MET A 1 23.154 32.095 19.630 1.00 0.00 H +ATOM 13 SD MET A 1 23.205 31.269 17.386 1.00 0.00 S +ATOM 14 CE MET A 1 22.990 32.137 15.870 1.00 0.00 C +ATOM 15 HE1 MET A 1 23.339 33.163 15.983 1.00 0.00 H +ATOM 16 HE2 MET A 1 21.968 32.128 15.490 1.00 0.00 H +ATOM 17 HE3 MET A 1 23.572 31.586 15.132 1.00 0.00 H +ATOM 18 C MET A 1 20.796 31.017 20.133 1.00 0.00 C +ATOM 19 O MET A 1 20.674 31.440 21.297 1.00 0.00 O +ATOM 20 N THR A 2 21.124 29.774 19.819 1.00 0.00 N +ATOM 21 H THR A 2 21.279 29.527 18.851 1.00 0.00 H +ATOM 22 CA THR A 2 21.443 28.704 20.861 1.00 0.00 C +ATOM 23 HA THR A 2 20.909 28.998 21.764 1.00 0.00 H +ATOM 24 CB THR A 2 21.114 27.241 20.522 1.00 0.00 C +ATOM 25 HB THR A 2 21.945 26.825 19.955 1.00 0.00 H +ATOM 26 CG2 THR A 2 20.715 26.558 21.817 1.00 0.00 C +ATOM 27 HG21 THR A 2 20.203 25.609 21.656 1.00 0.00 H +ATOM 28 HG22 THR A 2 20.001 27.137 22.403 1.00 0.00 H +ATOM 29 HG23 THR A 2 21.633 26.344 22.363 1.00 0.00 H +ATOM 30 OG1 THR A 2 19.957 27.231 19.658 1.00 0.00 O +ATOM 31 HG1 THR A 2 19.386 27.976 19.864 1.00 0.00 H +ATOM 32 C THR A 2 22.937 28.892 21.086 1.00 0.00 C +ATOM 33 O THR A 2 23.773 28.867 20.181 1.00 0.00 O +ATOM 34 N TYR A 3 23.244 29.155 22.344 1.00 0.00 N +ATOM 35 H TYR A 3 22.513 29.085 23.038 1.00 0.00 H +ATOM 36 CA TYR A 3 24.628 29.305 22.888 1.00 0.00 C +ATOM 37 HA TYR A 3 25.262 29.391 22.004 1.00 0.00 H +ATOM 38 CB TYR A 3 24.744 30.579 23.675 1.00 0.00 C +ATOM 39 HB2 TYR A 3 24.131 30.495 24.572 1.00 0.00 H +ATOM 40 HB3 TYR A 3 25.780 30.505 24.008 1.00 0.00 H +ATOM 41 CG TYR A 3 24.468 31.862 22.928 1.00 0.00 C +ATOM 42 CD1 TYR A 3 25.525 32.544 22.317 1.00 0.00 C +ATOM 43 HD1 TYR A 3 26.477 32.039 22.379 1.00 0.00 H +ATOM 44 CE1 TYR A 3 25.289 33.761 21.619 1.00 0.00 C +ATOM 45 HE1 TYR A 3 26.100 34.275 21.122 1.00 0.00 H +ATOM 46 CZ TYR A 3 23.936 34.260 21.579 1.00 0.00 C +ATOM 47 OH TYR A 3 23.774 35.268 20.774 1.00 0.00 O +ATOM 48 HH TYR A 3 24.486 35.161 20.140 1.00 0.00 H +ATOM 49 CE2 TYR A 3 22.849 33.537 22.176 1.00 0.00 C +ATOM 50 HE2 TYR A 3 21.868 33.965 22.036 1.00 0.00 H +ATOM 51 CD2 TYR A 3 23.110 32.291 22.853 1.00 0.00 C +ATOM 52 HD2 TYR A 3 22.235 31.752 23.187 1.00 0.00 H +ATOM 53 C TYR A 3 25.066 28.136 23.774 1.00 0.00 C +ATOM 54 O TYR A 3 24.233 27.436 24.338 1.00 0.00 O +ATOM 55 N LYS A 4 26.339 27.934 23.811 1.00 0.00 N +ATOM 56 H LYS A 4 26.944 28.514 23.248 1.00 0.00 H +ATOM 57 CA LYS A 4 26.982 26.918 24.687 1.00 0.00 C +ATOM 58 HA LYS A 4 26.212 26.488 25.328 1.00 0.00 H +ATOM 59 CB LYS A 4 27.643 25.801 23.803 1.00 0.00 C +ATOM 60 HB2 LYS A 4 26.868 25.465 23.113 1.00 0.00 H +ATOM 61 HB3 LYS A 4 28.422 26.196 23.151 1.00 0.00 H +ATOM 62 CG LYS A 4 28.205 24.625 24.506 1.00 0.00 C +ATOM 63 HG2 LYS A 4 29.054 24.916 25.125 1.00 0.00 H +ATOM 64 HG3 LYS A 4 27.452 24.278 25.213 1.00 0.00 H +ATOM 65 CD LYS A 4 28.635 23.407 23.678 1.00 0.00 C +ATOM 66 HD2 LYS A 4 29.003 22.691 24.414 1.00 0.00 H +ATOM 67 HD3 LYS A 4 27.737 22.954 23.255 1.00 0.00 H +ATOM 68 CE LYS A 4 29.554 23.575 22.506 1.00 0.00 C +ATOM 69 HE2 LYS A 4 28.899 24.120 21.827 1.00 0.00 H +ATOM 70 HE3 LYS A 4 30.458 24.114 22.794 1.00 0.00 H +ATOM 71 NZ LYS A 4 30.052 22.279 21.888 1.00 0.00 N1+ +ATOM 72 HZ1 LYS A 4 30.831 21.896 22.402 1.00 0.00 H +ATOM 73 HZ2 LYS A 4 30.443 22.423 20.968 1.00 0.00 H +ATOM 74 HZ3 LYS A 4 29.328 21.579 21.805 1.00 0.00 H +ATOM 75 C LYS A 4 28.003 27.516 25.655 1.00 0.00 C +ATOM 76 O LYS A 4 28.579 28.553 25.310 1.00 0.00 O +ATOM 77 N LEU A 5 28.245 26.773 26.741 1.00 0.00 N +ATOM 78 H LEU A 5 27.544 26.084 26.977 1.00 0.00 H +ATOM 79 CA LEU A 5 29.244 27.118 27.766 1.00 0.00 C +ATOM 80 HA LEU A 5 29.916 27.884 27.380 1.00 0.00 H +ATOM 81 CB LEU A 5 28.579 27.507 29.097 1.00 0.00 C +ATOM 82 HB2 LEU A 5 28.058 28.438 28.872 1.00 0.00 H +ATOM 83 HB3 LEU A 5 27.859 26.779 29.469 1.00 0.00 H +ATOM 84 CG LEU A 5 29.551 27.720 30.235 1.00 0.00 C +ATOM 85 HG LEU A 5 30.166 26.841 30.429 1.00 0.00 H +ATOM 86 CD1 LEU A 5 30.427 28.952 29.986 1.00 0.00 C +ATOM 87 HD11 LEU A 5 31.114 28.683 29.184 1.00 0.00 H +ATOM 88 HD12 LEU A 5 31.008 29.120 30.894 1.00 0.00 H +ATOM 89 HD13 LEU A 5 29.848 29.861 29.825 1.00 0.00 H +ATOM 90 CD2 LEU A 5 28.678 28.115 31.457 1.00 0.00 C +ATOM 91 HD21 LEU A 5 28.235 29.096 31.284 1.00 0.00 H +ATOM 92 HD22 LEU A 5 29.327 28.287 32.315 1.00 0.00 H +ATOM 93 HD23 LEU A 5 27.907 27.390 31.720 1.00 0.00 H +ATOM 94 C LEU A 5 30.065 25.816 27.990 1.00 0.00 C +ATOM 95 O LEU A 5 29.489 24.768 28.302 1.00 0.00 O +ATOM 96 N ILE A 6 31.415 25.954 27.959 1.00 0.00 N +ATOM 97 H ILE A 6 31.834 26.822 27.658 1.00 0.00 H +ATOM 98 CA ILE A 6 32.352 24.944 28.438 1.00 0.00 C +ATOM 99 HA ILE A 6 31.851 23.978 28.494 1.00 0.00 H +ATOM 100 CB ILE A 6 33.535 24.736 27.434 1.00 0.00 C +ATOM 101 HB ILE A 6 34.002 25.706 27.261 1.00 0.00 H +ATOM 102 CG2 ILE A 6 34.658 23.796 27.952 1.00 0.00 C +ATOM 103 HG21 ILE A 6 35.011 24.049 28.953 1.00 0.00 H +ATOM 104 HG22 ILE A 6 35.610 23.773 27.423 1.00 0.00 H +ATOM 105 HG23 ILE A 6 34.315 22.768 28.065 1.00 0.00 H +ATOM 106 CG1 ILE A 6 32.967 24.083 26.135 1.00 0.00 C +ATOM 107 HG12 ILE A 6 32.815 23.014 26.281 1.00 0.00 H +ATOM 108 HG13 ILE A 6 32.016 24.548 25.875 1.00 0.00 H +ATOM 109 CD1 ILE A 6 33.964 24.228 24.983 1.00 0.00 C +ATOM 110 HD11 ILE A 6 34.203 25.280 24.831 1.00 0.00 H +ATOM 111 HD12 ILE A 6 33.521 23.646 24.174 1.00 0.00 H +ATOM 112 HD13 ILE A 6 34.890 23.744 25.293 1.00 0.00 H +ATOM 113 C ILE A 6 32.878 25.380 29.825 1.00 0.00 C +ATOM 114 O ILE A 6 33.517 26.449 29.956 1.00 0.00 O +ATOM 115 N LEU A 7 32.756 24.548 30.823 1.00 0.00 N +ATOM 116 H LEU A 7 32.337 23.649 30.632 1.00 0.00 H +ATOM 117 CA LEU A 7 33.418 24.678 32.128 1.00 0.00 C +ATOM 118 HA LEU A 7 33.772 25.702 32.243 1.00 0.00 H +ATOM 119 CB LEU A 7 32.452 24.287 33.269 1.00 0.00 C +ATOM 120 HB2 LEU A 7 32.235 23.219 33.280 1.00 0.00 H +ATOM 121 HB3 LEU A 7 33.025 24.491 34.173 1.00 0.00 H +ATOM 122 CG LEU A 7 31.068 25.080 33.294 1.00 0.00 C +ATOM 123 HG LEU A 7 31.234 26.000 32.731 1.00 0.00 H +ATOM 124 CD1 LEU A 7 29.957 24.185 32.737 1.00 0.00 C +ATOM 125 HD11 LEU A 7 29.091 24.791 32.472 1.00 0.00 H +ATOM 126 HD12 LEU A 7 29.675 23.458 33.497 1.00 0.00 H +ATOM 127 HD13 LEU A 7 30.242 23.598 31.863 1.00 0.00 H +ATOM 128 CD2 LEU A 7 30.679 25.500 34.666 1.00 0.00 C +ATOM 129 HD21 LEU A 7 30.692 24.679 35.384 1.00 0.00 H +ATOM 130 HD22 LEU A 7 29.678 25.926 34.604 1.00 0.00 H +ATOM 131 HD23 LEU A 7 31.266 26.349 35.014 1.00 0.00 H +ATOM 132 C LEU A 7 34.704 23.832 31.982 1.00 0.00 C +ATOM 133 O LEU A 7 34.608 22.712 31.434 1.00 0.00 O +ATOM 134 N ASN A 8 35.741 24.355 32.566 1.00 0.00 N +ATOM 135 H ASN A 8 35.657 25.289 32.943 1.00 0.00 H +ATOM 136 CA ASN A 8 37.087 23.938 32.340 1.00 0.00 C +ATOM 137 HA ASN A 8 37.195 22.875 32.128 1.00 0.00 H +ATOM 138 CB ASN A 8 37.683 24.648 31.079 1.00 0.00 C +ATOM 139 HB2 ASN A 8 37.052 24.514 30.199 1.00 0.00 H +ATOM 140 HB3 ASN A 8 37.697 25.701 31.358 1.00 0.00 H +ATOM 141 CG ASN A 8 39.069 24.172 30.753 1.00 0.00 C +ATOM 142 OD1 ASN A 8 39.293 22.972 30.616 1.00 0.00 O +ATOM 143 ND2 ASN A 8 40.171 24.966 30.834 1.00 0.00 N +ATOM 144 HD21 ASN A 8 40.064 25.968 30.880 1.00 0.00 H +ATOM 145 HD22 ASN A 8 41.073 24.564 30.618 1.00 0.00 H +ATOM 146 C ASN A 8 37.929 24.262 33.602 1.00 0.00 C +ATOM 147 O ASN A 8 37.736 25.299 34.234 1.00 0.00 O +ATOM 148 N A01 A 9 38.893 23.411 33.937 1.00 0.00 N +ATOM 149 H A01 A 9 38.872 22.559 33.394 1.00 0.00 H +ATOM 150 CA A01 A 9 39.937 23.667 34.946 1.00 0.00 C +ATOM 151 CB A01 A 9 39.356 24.218 36.257 1.00 0.00 C +ATOM 152 HB1 A01 A 9 38.859 25.168 36.064 1.00 0.00 H +ATOM 153 HB2 A01 A 9 38.635 23.507 36.663 1.00 0.00 H +ATOM 154 HB3 A01 A 9 40.160 24.369 36.977 1.00 0.00 H +ATOM 155 HA A01 A 9 40.563 24.496 34.619 1.00 0.00 H +ATOM 156 C A01 A 9 40.820 22.504 35.210 1.00 0.00 C +ATOM 157 O A01 A 9 40.826 21.506 34.446 1.00 0.00 O +ATOM 158 N LYS A 10 41.477 22.473 36.356 1.00 0.00 N +ATOM 159 H LYS A 10 41.439 23.256 36.992 1.00 0.00 H +ATOM 160 CA LYS A 10 42.321 21.363 36.766 1.00 0.00 C +ATOM 161 HA LYS A 10 42.838 21.036 35.864 1.00 0.00 H +ATOM 162 CB LYS A 10 43.435 21.839 37.736 1.00 0.00 C +ATOM 163 HB2 LYS A 10 42.960 22.130 38.673 1.00 0.00 H +ATOM 164 HB3 LYS A 10 44.151 21.018 37.787 1.00 0.00 H +ATOM 165 CG LYS A 10 44.146 23.121 37.228 1.00 0.00 C +ATOM 166 HG2 LYS A 10 44.581 22.959 36.242 1.00 0.00 H +ATOM 167 HG3 LYS A 10 43.424 23.934 37.151 1.00 0.00 H +ATOM 168 CD LYS A 10 45.206 23.474 38.269 1.00 0.00 C +ATOM 169 HD2 LYS A 10 44.834 23.376 39.290 1.00 0.00 H +ATOM 170 HD3 LYS A 10 46.045 22.781 38.265 1.00 0.00 H +ATOM 171 CE LYS A 10 45.833 24.866 37.936 1.00 0.00 C +ATOM 172 HE2 LYS A 10 46.898 24.867 38.172 1.00 0.00 H +ATOM 173 HE3 LYS A 10 45.615 25.139 36.904 1.00 0.00 H +ATOM 174 NZ LYS A 10 45.314 25.885 38.915 1.00 0.00 N1+ +ATOM 175 HZ1 LYS A 10 44.318 26.049 38.885 1.00 0.00 H +ATOM 176 HZ2 LYS A 10 45.805 26.756 38.765 1.00 0.00 H +ATOM 177 HZ3 LYS A 10 45.434 25.694 39.899 1.00 0.00 H +ATOM 178 C LYS A 10 41.608 20.142 37.369 1.00 0.00 C +ATOM 179 O LYS A 10 42.136 19.017 37.432 1.00 0.00 O +ATOM 180 N THR A 11 40.316 20.407 37.709 1.00 0.00 N +ATOM 181 H THR A 11 40.018 21.373 37.739 1.00 0.00 H +ATOM 182 CA THR A 11 39.333 19.428 38.190 1.00 0.00 C +ATOM 183 HA THR A 11 39.627 18.439 37.841 1.00 0.00 H +ATOM 184 CB THR A 11 39.319 19.497 39.740 1.00 0.00 C +ATOM 185 HB THR A 11 38.538 18.809 40.063 1.00 0.00 H +ATOM 186 CG2 THR A 11 40.656 18.994 40.197 1.00 0.00 C +ATOM 187 HG21 THR A 11 40.954 17.991 39.896 1.00 0.00 H +ATOM 188 HG22 THR A 11 40.695 18.984 41.286 1.00 0.00 H +ATOM 189 HG23 THR A 11 41.453 19.662 39.869 1.00 0.00 H +ATOM 190 OG1 THR A 11 39.118 20.738 40.229 1.00 0.00 O +ATOM 191 HG1 THR A 11 39.321 20.728 41.168 1.00 0.00 H +ATOM 192 C THR A 11 37.937 19.704 37.750 1.00 0.00 C +ATOM 193 O THR A 11 37.180 18.744 37.592 1.00 0.00 O +ATOM 194 N LEU A 12 37.572 20.909 37.360 1.00 0.00 N +ATOM 195 H LEU A 12 38.100 21.745 37.569 1.00 0.00 H +ATOM 196 CA LEU A 12 36.262 21.294 36.760 1.00 0.00 C +ATOM 197 HA LEU A 12 35.427 20.887 37.329 1.00 0.00 H +ATOM 198 CB LEU A 12 36.169 22.873 36.785 1.00 0.00 C +ATOM 199 HB2 LEU A 12 36.531 23.238 37.746 1.00 0.00 H +ATOM 200 HB3 LEU A 12 36.859 23.268 36.041 1.00 0.00 H +ATOM 201 CG LEU A 12 34.824 23.483 36.357 1.00 0.00 C +ATOM 202 HG LEU A 12 34.479 23.028 35.428 1.00 0.00 H +ATOM 203 CD1 LEU A 12 33.867 23.321 37.477 1.00 0.00 C +ATOM 204 HD11 LEU A 12 32.997 23.877 37.126 1.00 0.00 H +ATOM 205 HD12 LEU A 12 34.304 23.691 38.404 1.00 0.00 H +ATOM 206 HD13 LEU A 12 33.594 22.265 37.503 1.00 0.00 H +ATOM 207 CD2 LEU A 12 34.926 25.052 36.181 1.00 0.00 C +ATOM 208 HD21 LEU A 12 35.334 25.560 37.054 1.00 0.00 H +ATOM 209 HD22 LEU A 12 33.926 25.442 35.997 1.00 0.00 H +ATOM 210 HD23 LEU A 12 35.555 25.355 35.344 1.00 0.00 H +ATOM 211 C LEU A 12 36.092 20.805 35.283 1.00 0.00 C +ATOM 212 O LEU A 12 36.941 21.102 34.441 1.00 0.00 O +ATOM 213 N LYS A 13 35.016 20.080 34.906 1.00 0.00 N +ATOM 214 H LYS A 13 34.391 19.697 35.602 1.00 0.00 H +ATOM 215 CA LYS A 13 34.642 19.704 33.571 1.00 0.00 C +ATOM 216 HA LYS A 13 35.063 20.421 32.866 1.00 0.00 H +ATOM 217 CB LYS A 13 35.034 18.226 33.244 1.00 0.00 C +ATOM 218 HB2 LYS A 13 34.497 17.579 33.938 1.00 0.00 H +ATOM 219 HB3 LYS A 13 34.849 17.922 32.214 1.00 0.00 H +ATOM 220 CG LYS A 13 36.515 17.923 33.472 1.00 0.00 C +ATOM 221 HG2 LYS A 13 37.162 18.658 32.994 1.00 0.00 H +ATOM 222 HG3 LYS A 13 36.701 17.768 34.535 1.00 0.00 H +ATOM 223 CD LYS A 13 36.804 16.487 32.994 1.00 0.00 C +ATOM 224 HD2 LYS A 13 36.157 15.747 33.465 1.00 0.00 H +ATOM 225 HD3 LYS A 13 36.456 16.506 31.962 1.00 0.00 H +ATOM 226 CE LYS A 13 38.264 16.163 32.997 1.00 0.00 C +ATOM 227 HE2 LYS A 13 38.741 16.732 32.199 1.00 0.00 H +ATOM 228 HE3 LYS A 13 38.686 16.424 33.967 1.00 0.00 H +ATOM 229 NZ LYS A 13 38.397 14.672 32.837 1.00 0.00 N1+ +ATOM 230 HZ1 LYS A 13 37.944 14.324 32.005 1.00 0.00 H +ATOM 231 HZ2 LYS A 13 37.888 14.239 33.595 1.00 0.00 H +ATOM 232 HZ3 LYS A 13 39.367 14.391 32.817 1.00 0.00 H +ATOM 233 C LYS A 13 33.119 19.875 33.400 1.00 0.00 C +ATOM 234 O LYS A 13 32.522 20.218 34.448 1.00 0.00 O +ATOM 235 N GLY A 14 32.541 19.929 32.182 1.00 0.00 N +ATOM 236 H GLY A 14 33.085 19.611 31.392 1.00 0.00 H +ATOM 237 CA GLY A 14 31.141 20.135 31.951 1.00 0.00 C +ATOM 238 HA2 GLY A 14 30.696 19.143 31.877 1.00 0.00 H +ATOM 239 HA3 GLY A 14 30.707 20.500 32.883 1.00 0.00 H +ATOM 240 C GLY A 14 30.726 21.030 30.803 1.00 0.00 C +ATOM 241 O GLY A 14 31.459 21.986 30.478 1.00 0.00 O +ATOM 242 N GLU A 15 29.602 20.661 30.175 1.00 0.00 N +ATOM 243 H GLU A 15 29.233 19.801 30.557 1.00 0.00 H +ATOM 244 CA GLU A 15 29.053 21.595 29.115 1.00 0.00 C +ATOM 245 HA GLU A 15 29.457 22.592 29.292 1.00 0.00 H +ATOM 246 CB GLU A 15 29.452 21.151 27.705 1.00 0.00 C +ATOM 247 HB2 GLU A 15 28.886 21.770 27.009 1.00 0.00 H +ATOM 248 HB3 GLU A 15 30.497 21.396 27.512 1.00 0.00 H +ATOM 249 CG GLU A 15 29.157 19.668 27.410 1.00 0.00 C +ATOM 250 HG2 GLU A 15 29.865 19.104 28.017 1.00 0.00 H +ATOM 251 HG3 GLU A 15 28.109 19.456 27.619 1.00 0.00 H +ATOM 252 CD GLU A 15 29.423 19.385 25.968 1.00 0.00 C +ATOM 253 OE1 GLU A 15 28.458 19.250 25.177 1.00 0.00 O1- +ATOM 254 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O1- +ATOM 255 C GLU A 15 27.563 21.843 29.353 1.00 0.00 C +ATOM 256 O GLU A 15 26.814 21.020 29.796 1.00 0.00 O +ATOM 257 N THR A 16 27.080 22.966 28.863 1.00 0.00 N +ATOM 258 H THR A 16 27.718 23.647 28.477 1.00 0.00 H +ATOM 259 CA THR A 16 25.618 23.342 28.987 1.00 0.00 C +ATOM 260 HA THR A 16 24.987 22.466 28.832 1.00 0.00 H +ATOM 261 CB THR A 16 25.300 23.755 30.463 1.00 0.00 C +ATOM 262 HB THR A 16 25.664 23.028 31.190 1.00 0.00 H +ATOM 263 CG2 THR A 16 26.079 25.029 30.851 1.00 0.00 C +ATOM 264 HG21 THR A 16 26.002 25.212 31.923 1.00 0.00 H +ATOM 265 HG22 THR A 16 25.827 25.999 30.420 1.00 0.00 H +ATOM 266 HG23 THR A 16 27.139 24.833 30.686 1.00 0.00 H +ATOM 267 OG1 THR A 16 23.919 23.870 30.591 1.00 0.00 O +ATOM 268 HG1 THR A 16 23.605 22.966 30.654 1.00 0.00 H +ATOM 269 C THR A 16 25.136 24.387 27.956 1.00 0.00 C +ATOM 270 O THR A 16 25.847 25.392 27.686 1.00 0.00 O +ATOM 271 N THR A 17 23.944 24.126 27.374 1.00 0.00 N +ATOM 272 H THR A 17 23.414 23.300 27.615 1.00 0.00 H +ATOM 273 CA THR A 17 23.341 25.088 26.418 1.00 0.00 C +ATOM 274 HA THR A 17 24.139 25.697 25.992 1.00 0.00 H +ATOM 275 CB THR A 17 22.634 24.399 25.250 1.00 0.00 C +ATOM 276 HB THR A 17 22.194 25.142 24.585 1.00 0.00 H +ATOM 277 CG2 THR A 17 23.534 23.466 24.406 1.00 0.00 C +ATOM 278 HG21 THR A 17 22.981 22.875 23.677 1.00 0.00 H +ATOM 279 HG22 THR A 17 24.016 22.789 25.112 1.00 0.00 H +ATOM 280 HG23 THR A 17 24.305 24.119 23.998 1.00 0.00 H +ATOM 281 OG1 THR A 17 21.618 23.516 25.740 1.00 0.00 O +ATOM 282 HG1 THR A 17 21.158 23.210 24.955 1.00 0.00 H +ATOM 283 C THR A 17 22.409 26.084 27.080 1.00 0.00 C +ATOM 284 O THR A 17 21.865 25.880 28.171 1.00 0.00 O +ATOM 285 N THR A 18 22.284 27.186 26.367 1.00 0.00 N +ATOM 286 H THR A 18 22.918 27.211 25.581 1.00 0.00 H +ATOM 287 CA THR A 18 21.341 28.346 26.665 1.00 0.00 C +ATOM 288 HA THR A 18 20.447 28.047 27.213 1.00 0.00 H +ATOM 289 CB THR A 18 21.968 29.424 27.606 1.00 0.00 C +ATOM 290 HB THR A 18 22.926 29.800 27.251 1.00 0.00 H +ATOM 291 CG2 THR A 18 20.959 30.565 27.747 1.00 0.00 C +ATOM 292 HG21 THR A 18 21.177 31.232 28.581 1.00 0.00 H +ATOM 293 HG22 THR A 18 19.932 30.214 27.838 1.00 0.00 H +ATOM 294 HG23 THR A 18 21.057 31.149 26.831 1.00 0.00 H +ATOM 295 OG1 THR A 18 21.983 28.974 29.051 1.00 0.00 O +ATOM 296 HG1 THR A 18 22.866 29.123 29.400 1.00 0.00 H +ATOM 297 C THR A 18 20.829 28.956 25.354 1.00 0.00 C +ATOM 298 O THR A 18 21.553 29.458 24.528 1.00 0.00 O +ATOM 299 N GLU A 19 19.542 28.872 25.083 1.00 0.00 N +ATOM 300 H GLU A 19 18.919 28.579 25.823 1.00 0.00 H +ATOM 301 CA GLU A 19 18.932 29.576 23.987 1.00 0.00 C +ATOM 302 HA GLU A 19 19.679 29.508 23.197 1.00 0.00 H +ATOM 303 CB GLU A 19 17.686 28.785 23.627 1.00 0.00 C +ATOM 304 HB2 GLU A 19 17.899 27.722 23.514 1.00 0.00 H +ATOM 305 HB3 GLU A 19 16.998 28.842 24.471 1.00 0.00 H +ATOM 306 CG GLU A 19 16.852 29.284 22.477 1.00 0.00 C +ATOM 307 HG2 GLU A 19 16.246 28.447 22.128 1.00 0.00 H +ATOM 308 HG3 GLU A 19 16.133 30.057 22.748 1.00 0.00 H +ATOM 309 CD GLU A 19 17.736 29.731 21.281 1.00 0.00 C +ATOM 310 OE1 GLU A 19 18.363 28.800 20.679 1.00 0.00 O1- +ATOM 311 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O1- +ATOM 312 C GLU A 19 18.631 31.049 24.311 1.00 0.00 C +ATOM 313 O GLU A 19 17.951 31.336 25.240 1.00 0.00 O +ATOM 314 N ALA A 20 19.109 32.052 23.609 1.00 0.00 N +ATOM 315 H ALA A 20 19.659 31.766 22.810 1.00 0.00 H +ATOM 316 CA ALA A 20 18.962 33.505 23.885 1.00 0.00 C +ATOM 317 HA ALA A 20 17.980 33.742 24.295 1.00 0.00 H +ATOM 318 CB ALA A 20 19.978 33.979 24.961 1.00 0.00 C +ATOM 319 HB1 ALA A 20 19.807 35.026 25.214 1.00 0.00 H +ATOM 320 HB2 ALA A 20 20.983 33.923 24.544 1.00 0.00 H +ATOM 321 HB3 ALA A 20 19.800 33.404 25.869 1.00 0.00 H +ATOM 322 C ALA A 20 19.121 34.352 22.595 1.00 0.00 C +ATOM 323 O ALA A 20 19.565 33.867 21.541 1.00 0.00 O +ATOM 324 N VAL A 21 18.819 35.698 22.666 1.00 0.00 N +ATOM 325 H VAL A 21 18.466 36.007 23.561 1.00 0.00 H +ATOM 326 CA VAL A 21 18.727 36.607 21.505 1.00 0.00 C +ATOM 327 HA VAL A 21 18.554 36.039 20.592 1.00 0.00 H +ATOM 328 CB VAL A 21 17.437 37.464 21.780 1.00 0.00 C +ATOM 329 HB VAL A 21 17.477 38.130 22.642 1.00 0.00 H +ATOM 330 CG1 VAL A 21 17.072 38.379 20.673 1.00 0.00 C +ATOM 331 HG11 VAL A 21 16.991 37.805 19.750 1.00 0.00 H +ATOM 332 HG12 VAL A 21 17.685 39.269 20.533 1.00 0.00 H +ATOM 333 HG13 VAL A 21 16.081 38.787 20.874 1.00 0.00 H +ATOM 334 CG2 VAL A 21 16.251 36.536 21.920 1.00 0.00 C +ATOM 335 HG21 VAL A 21 15.333 37.033 21.605 1.00 0.00 H +ATOM 336 HG22 VAL A 21 16.128 36.219 22.956 1.00 0.00 H +ATOM 337 HG23 VAL A 21 16.477 35.681 21.284 1.00 0.00 H +ATOM 338 C VAL A 21 19.976 37.521 21.405 1.00 0.00 C +ATOM 339 O VAL A 21 20.295 38.022 20.306 1.00 0.00 O +ATOM 340 N ASP A 22 20.728 37.651 22.457 1.00 0.00 N +ATOM 341 H ASP A 22 20.460 37.104 23.262 1.00 0.00 H +ATOM 342 CA ASP A 22 21.920 38.517 22.561 1.00 0.00 C +ATOM 343 HA ASP A 22 22.218 38.721 21.532 1.00 0.00 H +ATOM 344 CB ASP A 22 21.483 39.701 23.350 1.00 0.00 C +ATOM 345 HB2 ASP A 22 20.632 40.156 22.843 1.00 0.00 H +ATOM 346 HB3 ASP A 22 21.133 39.421 24.344 1.00 0.00 H +ATOM 347 CG ASP A 22 22.576 40.746 23.590 1.00 0.00 C +ATOM 348 OD1 ASP A 22 23.681 40.588 23.043 1.00 0.00 O1- +ATOM 349 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O1- +ATOM 350 C ASP A 22 23.019 37.703 23.294 1.00 0.00 C +ATOM 351 O ASP A 22 22.839 37.184 24.412 1.00 0.00 O +ATOM 352 N ALA A 23 24.210 37.649 22.694 1.00 0.00 N +ATOM 353 H ALA A 23 24.358 38.065 21.786 1.00 0.00 H +ATOM 354 CA ALA A 23 25.493 37.172 23.215 1.00 0.00 C +ATOM 355 HA ALA A 23 25.371 36.089 23.221 1.00 0.00 H +ATOM 356 CB ALA A 23 26.701 37.486 22.326 1.00 0.00 C +ATOM 357 HB1 ALA A 23 26.446 37.309 21.280 1.00 0.00 H +ATOM 358 HB2 ALA A 23 27.379 36.708 22.676 1.00 0.00 H +ATOM 359 HB3 ALA A 23 27.091 38.494 22.468 1.00 0.00 H +ATOM 360 C ALA A 23 25.748 37.757 24.642 1.00 0.00 C +ATOM 361 O ALA A 23 26.091 36.953 25.518 1.00 0.00 O +ATOM 362 N ALA A 24 25.564 39.050 24.846 1.00 0.00 N +ATOM 363 H ALA A 24 25.214 39.674 24.133 1.00 0.00 H +ATOM 364 CA ALA A 24 25.745 39.687 26.153 1.00 0.00 C +ATOM 365 HA ALA A 24 26.761 39.419 26.445 1.00 0.00 H +ATOM 366 CB ALA A 24 25.490 41.189 25.938 1.00 0.00 C +ATOM 367 HB1 ALA A 24 26.247 41.676 25.325 1.00 0.00 H +ATOM 368 HB2 ALA A 24 25.633 41.729 26.874 1.00 0.00 H +ATOM 369 HB3 ALA A 24 24.561 41.467 25.440 1.00 0.00 H +ATOM 370 C ALA A 24 24.796 39.101 27.137 1.00 0.00 C +ATOM 371 O ALA A 24 25.116 38.975 28.329 1.00 0.00 O +ATOM 372 N THR A 25 23.577 38.659 26.736 1.00 0.00 N +ATOM 373 H THR A 25 23.398 38.681 25.743 1.00 0.00 H +ATOM 374 CA THR A 25 22.587 38.094 27.680 1.00 0.00 C +ATOM 375 HA THR A 25 22.755 38.495 28.681 1.00 0.00 H +ATOM 376 CB THR A 25 21.196 38.549 27.262 1.00 0.00 C +ATOM 377 HB THR A 25 20.797 37.883 26.497 1.00 0.00 H +ATOM 378 CG2 THR A 25 20.246 38.369 28.438 1.00 0.00 C +ATOM 379 HG21 THR A 25 20.203 37.329 28.763 1.00 0.00 H +ATOM 380 HG22 THR A 25 19.255 38.740 28.176 1.00 0.00 H +ATOM 381 HG23 THR A 25 20.574 38.977 29.280 1.00 0.00 H +ATOM 382 OG1 THR A 25 21.199 39.931 27.030 1.00 0.00 O +ATOM 383 HG1 THR A 25 20.293 40.156 26.807 1.00 0.00 H +ATOM 384 C THR A 25 22.788 36.618 27.928 1.00 0.00 C +ATOM 385 O THR A 25 22.618 36.164 29.050 1.00 0.00 O +ATOM 386 N ALA A 26 23.216 35.854 26.929 1.00 0.00 N +ATOM 387 H ALA A 26 23.315 36.208 25.988 1.00 0.00 H +ATOM 388 CA ALA A 26 23.652 34.513 27.159 1.00 0.00 C +ATOM 389 HA ALA A 26 22.781 33.940 27.476 1.00 0.00 H +ATOM 390 CB ALA A 26 24.062 33.913 25.734 1.00 0.00 C +ATOM 391 HB1 ALA A 26 23.120 33.732 25.215 1.00 0.00 H +ATOM 392 HB2 ALA A 26 24.695 33.029 25.804 1.00 0.00 H +ATOM 393 HB3 ALA A 26 24.715 34.613 25.211 1.00 0.00 H +ATOM 394 C ALA A 26 24.856 34.523 28.062 1.00 0.00 C +ATOM 395 O ALA A 26 24.889 33.745 28.985 1.00 0.00 O +ATOM 396 N GLU A 27 25.749 35.500 28.027 1.00 0.00 N +ATOM 397 H GLU A 27 25.940 35.933 27.135 1.00 0.00 H +ATOM 398 CA GLU A 27 26.712 35.671 29.037 1.00 0.00 C +ATOM 399 HA GLU A 27 27.306 34.757 29.097 1.00 0.00 H +ATOM 400 CB GLU A 27 27.684 36.833 28.605 1.00 0.00 C +ATOM 401 HB2 GLU A 27 28.270 36.561 27.728 1.00 0.00 H +ATOM 402 HB3 GLU A 27 27.178 37.773 28.387 1.00 0.00 H +ATOM 403 CG GLU A 27 28.742 37.165 29.664 1.00 0.00 C +ATOM 404 HG2 GLU A 27 28.193 37.537 30.529 1.00 0.00 H +ATOM 405 HG3 GLU A 27 29.267 36.244 29.914 1.00 0.00 H +ATOM 406 CD GLU A 27 29.887 38.242 29.269 1.00 0.00 C +ATOM 407 OE1 GLU A 27 31.108 37.827 29.164 1.00 0.00 O1- +ATOM 408 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O1- +ATOM 409 C GLU A 27 26.099 35.742 30.450 1.00 0.00 C +ATOM 410 O GLU A 27 26.553 35.162 31.414 1.00 0.00 O +ATOM 411 N LYS A 28 25.124 36.609 30.604 1.00 0.00 N +ATOM 412 H LYS A 28 24.710 37.106 29.827 1.00 0.00 H +ATOM 413 CA LYS A 28 24.538 36.947 31.950 1.00 0.00 C +ATOM 414 HA LYS A 28 25.324 37.300 32.618 1.00 0.00 H +ATOM 415 CB LYS A 28 23.559 38.052 31.728 1.00 0.00 C +ATOM 416 HB2 LYS A 28 24.096 38.943 31.403 1.00 0.00 H +ATOM 417 HB3 LYS A 28 22.761 37.811 31.025 1.00 0.00 H +ATOM 418 CG LYS A 28 22.885 38.401 33.150 1.00 0.00 C +ATOM 419 HG2 LYS A 28 22.343 37.542 33.545 1.00 0.00 H +ATOM 420 HG3 LYS A 28 23.638 38.698 33.879 1.00 0.00 H +ATOM 421 CD LYS A 28 21.826 39.579 33.063 1.00 0.00 C +ATOM 422 HD2 LYS A 28 20.930 39.146 32.616 1.00 0.00 H +ATOM 423 HD3 LYS A 28 21.656 39.989 34.058 1.00 0.00 H +ATOM 424 CE LYS A 28 22.359 40.850 32.267 1.00 0.00 C +ATOM 425 HE2 LYS A 28 23.432 40.899 32.449 1.00 0.00 H +ATOM 426 HE3 LYS A 28 22.199 40.756 31.193 1.00 0.00 H +ATOM 427 NZ LYS A 28 21.521 42.013 32.715 1.00 0.00 N1+ +ATOM 428 HZ1 LYS A 28 21.696 42.294 33.670 1.00 0.00 H +ATOM 429 HZ2 LYS A 28 20.541 41.777 32.653 1.00 0.00 H +ATOM 430 HZ3 LYS A 28 21.651 42.827 32.131 1.00 0.00 H +ATOM 431 C LYS A 28 23.866 35.778 32.535 1.00 0.00 C +ATOM 432 O LYS A 28 23.994 35.665 33.742 1.00 0.00 O +ATOM 433 N VAL A 29 23.329 34.885 31.712 1.00 0.00 N +ATOM 434 H VAL A 29 23.229 35.111 30.733 1.00 0.00 H +ATOM 435 CA VAL A 29 22.736 33.650 32.097 1.00 0.00 C +ATOM 436 HA VAL A 29 21.999 33.879 32.866 1.00 0.00 H +ATOM 437 CB VAL A 29 21.735 33.166 30.962 1.00 0.00 C +ATOM 438 HB VAL A 29 22.375 32.951 30.106 1.00 0.00 H +ATOM 439 CG1 VAL A 29 21.139 31.783 31.445 1.00 0.00 C +ATOM 440 HG11 VAL A 29 20.592 31.413 30.579 1.00 0.00 H +ATOM 441 HG12 VAL A 29 20.575 31.908 32.370 1.00 0.00 H +ATOM 442 HG13 VAL A 29 21.993 31.113 31.534 1.00 0.00 H +ATOM 443 CG2 VAL A 29 20.482 33.992 30.547 1.00 0.00 C +ATOM 444 HG21 VAL A 29 19.966 33.618 29.662 1.00 0.00 H +ATOM 445 HG22 VAL A 29 20.739 35.019 30.286 1.00 0.00 H +ATOM 446 HG23 VAL A 29 19.838 34.110 31.419 1.00 0.00 H +ATOM 447 C VAL A 29 23.781 32.642 32.484 1.00 0.00 C +ATOM 448 O VAL A 29 23.604 31.876 33.462 1.00 0.00 O +ATOM 449 N PHE A 30 24.962 32.641 31.758 1.00 0.00 N +ATOM 450 H PHE A 30 24.997 33.287 30.981 1.00 0.00 H +ATOM 451 CA PHE A 30 26.112 31.701 32.033 1.00 0.00 C +ATOM 452 HA PHE A 30 25.692 30.753 32.371 1.00 0.00 H +ATOM 453 CB PHE A 30 26.901 31.582 30.713 1.00 0.00 C +ATOM 454 HB2 PHE A 30 26.966 32.537 30.191 1.00 0.00 H +ATOM 455 HB3 PHE A 30 27.928 31.266 30.888 1.00 0.00 H +ATOM 456 CG PHE A 30 26.348 30.600 29.656 1.00 0.00 C +ATOM 457 CD1 PHE A 30 25.751 29.296 29.878 1.00 0.00 C +ATOM 458 HD1 PHE A 30 25.705 28.943 30.897 1.00 0.00 H +ATOM 459 CE1 PHE A 30 25.345 28.377 28.817 1.00 0.00 C +ATOM 460 HE1 PHE A 30 24.810 27.464 29.039 1.00 0.00 H +ATOM 461 CZ PHE A 30 25.534 28.840 27.515 1.00 0.00 C +ATOM 462 HZ PHE A 30 25.196 28.267 26.666 1.00 0.00 H +ATOM 463 CE2 PHE A 30 26.096 30.099 27.271 1.00 0.00 C +ATOM 464 HE2 PHE A 30 26.212 30.319 26.219 1.00 0.00 H +ATOM 465 CD2 PHE A 30 26.533 30.924 28.297 1.00 0.00 C +ATOM 466 HD2 PHE A 30 27.135 31.778 28.029 1.00 0.00 H +ATOM 467 C PHE A 30 26.988 32.189 33.246 1.00 0.00 C +ATOM 468 O PHE A 30 27.609 31.344 33.905 1.00 0.00 O +ATOM 469 N LYS A 31 27.038 33.446 33.540 1.00 0.00 N +ATOM 470 H LYS A 31 26.710 34.105 32.849 1.00 0.00 H +ATOM 471 CA LYS A 31 27.405 34.022 34.854 1.00 0.00 C +ATOM 472 HA LYS A 31 28.437 33.764 35.092 1.00 0.00 H +ATOM 473 CB LYS A 31 27.274 35.599 34.858 1.00 0.00 C +ATOM 474 HB2 LYS A 31 26.242 35.714 34.527 1.00 0.00 H +ATOM 475 HB3 LYS A 31 27.292 36.098 35.827 1.00 0.00 H +ATOM 476 CG LYS A 31 28.378 36.275 33.919 1.00 0.00 C +ATOM 477 HG2 LYS A 31 28.522 35.710 32.997 1.00 0.00 H +ATOM 478 HG3 LYS A 31 27.926 37.229 33.649 1.00 0.00 H +ATOM 479 CD LYS A 31 29.823 36.487 34.439 1.00 0.00 C +ATOM 480 HD2 LYS A 31 29.755 36.977 35.411 1.00 0.00 H +ATOM 481 HD3 LYS A 31 30.132 35.472 34.684 1.00 0.00 H +ATOM 482 CE LYS A 31 30.777 37.150 33.394 1.00 0.00 C +ATOM 483 HE2 LYS A 31 30.633 36.630 32.447 1.00 0.00 H +ATOM 484 HE3 LYS A 31 30.436 38.158 33.158 1.00 0.00 H +ATOM 485 NZ LYS A 31 32.138 37.121 33.926 1.00 0.00 N1+ +ATOM 486 HZ1 LYS A 31 32.272 37.458 34.869 1.00 0.00 H +ATOM 487 HZ2 LYS A 31 32.676 37.777 33.376 1.00 0.00 H +ATOM 488 HZ3 LYS A 31 32.555 36.210 33.805 1.00 0.00 H +ATOM 489 C LYS A 31 26.516 33.562 35.983 1.00 0.00 C +ATOM 490 O LYS A 31 27.018 32.993 36.943 1.00 0.00 O +ATOM 491 N GLN A 32 25.185 33.745 35.953 1.00 0.00 N +ATOM 492 H GLN A 32 24.737 34.194 35.166 1.00 0.00 H +ATOM 493 CA GLN A 32 24.365 33.197 37.027 1.00 0.00 C +ATOM 494 HA GLN A 32 24.679 33.822 37.863 1.00 0.00 H +ATOM 495 CB GLN A 32 22.891 33.427 36.688 1.00 0.00 C +ATOM 496 HB2 GLN A 32 22.845 33.366 35.601 1.00 0.00 H +ATOM 497 HB3 GLN A 32 22.285 32.685 37.209 1.00 0.00 H +ATOM 498 CG GLN A 32 22.280 34.840 37.028 1.00 0.00 C +ATOM 499 HG2 GLN A 32 22.039 34.881 38.090 1.00 0.00 H +ATOM 500 HG3 GLN A 32 22.899 35.710 36.807 1.00 0.00 H +ATOM 501 CD GLN A 32 20.958 35.124 36.195 1.00 0.00 C +ATOM 502 OE1 GLN A 32 19.883 34.823 36.738 1.00 0.00 O +ATOM 503 NE2 GLN A 32 20.988 35.530 34.974 1.00 0.00 N +ATOM 504 HE21 GLN A 32 21.902 35.787 34.628 1.00 0.00 H +ATOM 505 HE22 GLN A 32 20.177 35.714 34.400 1.00 0.00 H +ATOM 506 C GLN A 32 24.598 31.707 37.232 1.00 0.00 C +ATOM 507 O GLN A 32 24.794 31.293 38.384 1.00 0.00 O +ATOM 508 N TYR A 33 24.530 30.875 36.142 1.00 0.00 N +ATOM 509 H TYR A 33 24.587 31.274 35.216 1.00 0.00 H +ATOM 510 CA TYR A 33 24.722 29.459 36.217 1.00 0.00 C +ATOM 511 HA TYR A 33 23.881 29.042 36.772 1.00 0.00 H +ATOM 512 CB TYR A 33 24.622 28.848 34.842 1.00 0.00 C +ATOM 513 HB2 TYR A 33 23.621 29.006 34.442 1.00 0.00 H +ATOM 514 HB3 TYR A 33 25.353 29.388 34.240 1.00 0.00 H +ATOM 515 CG TYR A 33 24.877 27.304 34.704 1.00 0.00 C +ATOM 516 CD1 TYR A 33 23.808 26.383 34.938 1.00 0.00 C +ATOM 517 HD1 TYR A 33 22.814 26.754 35.140 1.00 0.00 H +ATOM 518 CE1 TYR A 33 24.054 24.991 35.075 1.00 0.00 C +ATOM 519 HE1 TYR A 33 23.300 24.251 35.300 1.00 0.00 H +ATOM 520 CZ TYR A 33 25.399 24.562 34.934 1.00 0.00 C +ATOM 521 OH TYR A 33 25.658 23.212 34.983 1.00 0.00 O +ATOM 522 HH TYR A 33 26.608 23.080 35.030 1.00 0.00 H +ATOM 523 CE2 TYR A 33 26.410 25.459 34.723 1.00 0.00 C +ATOM 524 HE2 TYR A 33 27.443 25.157 34.630 1.00 0.00 H +ATOM 525 CD2 TYR A 33 26.146 26.818 34.602 1.00 0.00 C +ATOM 526 HD2 TYR A 33 26.992 27.469 34.435 1.00 0.00 H +ATOM 527 C TYR A 33 26.078 29.155 36.854 1.00 0.00 C +ATOM 528 O TYR A 33 26.179 28.186 37.566 1.00 0.00 O +ATOM 529 N ALA A 34 27.159 29.788 36.508 1.00 0.00 N +ATOM 530 H ALA A 34 26.997 30.563 35.881 1.00 0.00 H +ATOM 531 CA ALA A 34 28.473 29.535 37.100 1.00 0.00 C +ATOM 532 HA ALA A 34 28.717 28.476 37.023 1.00 0.00 H +ATOM 533 CB ALA A 34 29.651 30.265 36.402 1.00 0.00 C +ATOM 534 HB1 ALA A 34 30.577 29.813 36.757 1.00 0.00 H +ATOM 535 HB2 ALA A 34 29.619 31.296 36.752 1.00 0.00 H +ATOM 536 HB3 ALA A 34 29.681 30.159 35.317 1.00 0.00 H +ATOM 537 C ALA A 34 28.508 29.835 38.614 1.00 0.00 C +ATOM 538 O ALA A 34 29.097 29.077 39.389 1.00 0.00 O +ATOM 539 N ASN A 35 27.814 30.864 39.024 1.00 0.00 N +ATOM 540 H ASN A 35 27.594 31.535 38.301 1.00 0.00 H +ATOM 541 CA ASN A 35 27.743 31.252 40.445 1.00 0.00 C +ATOM 542 HA ASN A 35 28.713 31.168 40.935 1.00 0.00 H +ATOM 543 CB ASN A 35 27.254 32.684 40.541 1.00 0.00 C +ATOM 544 HB2 ASN A 35 27.798 33.361 39.883 1.00 0.00 H +ATOM 545 HB3 ASN A 35 26.192 32.727 40.300 1.00 0.00 H +ATOM 546 CG ASN A 35 27.326 33.169 41.947 1.00 0.00 C +ATOM 547 OD1 ASN A 35 26.493 32.743 42.763 1.00 0.00 O +ATOM 548 ND2 ASN A 35 28.099 34.183 42.223 1.00 0.00 N +ATOM 549 HD21 ASN A 35 28.867 34.350 41.589 1.00 0.00 H +ATOM 550 HD22 ASN A 35 28.276 34.397 43.193 1.00 0.00 H +ATOM 551 C ASN A 35 26.833 30.200 41.127 1.00 0.00 C +ATOM 552 O ASN A 35 27.114 29.686 42.238 1.00 0.00 O +ATOM 553 N ASP A 36 25.819 29.616 40.395 1.00 0.00 N +ATOM 554 H ASP A 36 25.608 30.144 39.560 1.00 0.00 H +ATOM 555 CA ASP A 36 25.004 28.401 40.867 1.00 0.00 C +ATOM 556 HA ASP A 36 24.491 28.819 41.733 1.00 0.00 H +ATOM 557 CB ASP A 36 23.819 28.175 39.948 1.00 0.00 C +ATOM 558 HB2 ASP A 36 23.379 29.117 39.623 1.00 0.00 H +ATOM 559 HB3 ASP A 36 24.279 27.586 39.154 1.00 0.00 H +ATOM 560 CG ASP A 36 22.720 27.350 40.470 1.00 0.00 C +ATOM 561 OD1 ASP A 36 22.214 26.485 39.714 1.00 0.00 O1- +ATOM 562 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O1- +ATOM 563 C ASP A 36 25.793 27.113 41.244 1.00 0.00 C +ATOM 564 O ASP A 36 25.357 26.391 42.112 1.00 0.00 O +ATOM 565 N ASN A 37 26.991 27.006 40.666 1.00 0.00 N +ATOM 566 H ASN A 37 27.306 27.779 40.098 1.00 0.00 H +ATOM 567 CA ASN A 37 27.829 25.814 40.636 1.00 0.00 C +ATOM 568 HA ASN A 37 27.378 25.130 41.354 1.00 0.00 H +ATOM 569 CB ASN A 37 27.873 25.281 39.195 1.00 0.00 C +ATOM 570 HB2 ASN A 37 27.936 26.106 38.487 1.00 0.00 H +ATOM 571 HB3 ASN A 37 28.702 24.579 39.101 1.00 0.00 H +ATOM 572 CG ASN A 37 26.652 24.492 38.842 1.00 0.00 C +ATOM 573 OD1 ASN A 37 26.432 23.357 39.282 1.00 0.00 O +ATOM 574 ND2 ASN A 37 25.706 25.057 38.177 1.00 0.00 N +ATOM 575 HD21 ASN A 37 25.804 26.050 38.016 1.00 0.00 H +ATOM 576 HD22 ASN A 37 24.895 24.502 37.947 1.00 0.00 H +ATOM 577 C ASN A 37 29.196 26.053 41.261 1.00 0.00 C +ATOM 578 O ASN A 37 30.064 25.171 41.182 1.00 0.00 O +ATOM 579 N GLY A 38 29.358 27.176 42.012 1.00 0.00 N +ATOM 580 H GLY A 38 28.556 27.765 42.189 1.00 0.00 H +ATOM 581 CA GLY A 38 30.637 27.460 42.681 1.00 0.00 C +ATOM 582 HA2 GLY A 38 30.444 28.296 43.354 1.00 0.00 H +ATOM 583 HA3 GLY A 38 30.900 26.655 43.368 1.00 0.00 H +ATOM 584 C GLY A 38 31.894 27.774 41.785 1.00 0.00 C +ATOM 585 O GLY A 38 33.027 27.429 42.124 1.00 0.00 O +ATOM 586 N VAL A 39 31.731 28.287 40.579 1.00 0.00 N +ATOM 587 H VAL A 39 30.794 28.624 40.408 1.00 0.00 H +ATOM 588 CA VAL A 39 32.664 28.449 39.403 1.00 0.00 C +ATOM 589 HA VAL A 39 33.598 27.911 39.570 1.00 0.00 H +ATOM 590 CB VAL A 39 32.015 27.778 38.179 1.00 0.00 C +ATOM 591 HB VAL A 39 31.005 28.158 38.027 1.00 0.00 H +ATOM 592 CG1 VAL A 39 32.989 28.121 37.014 1.00 0.00 C +ATOM 593 HG11 VAL A 39 32.636 27.519 36.176 1.00 0.00 H +ATOM 594 HG12 VAL A 39 34.019 27.963 37.334 1.00 0.00 H +ATOM 595 HG13 VAL A 39 32.869 29.117 36.588 1.00 0.00 H +ATOM 596 CG2 VAL A 39 31.943 26.274 38.437 1.00 0.00 C +ATOM 597 HG21 VAL A 39 31.540 25.729 37.583 1.00 0.00 H +ATOM 598 HG22 VAL A 39 31.356 26.086 39.337 1.00 0.00 H +ATOM 599 HG23 VAL A 39 32.907 25.863 38.738 1.00 0.00 H +ATOM 600 C VAL A 39 33.029 29.909 39.235 1.00 0.00 C +ATOM 601 O VAL A 39 32.186 30.683 38.757 1.00 0.00 O +ATOM 602 N ASP A 40 34.268 30.281 39.558 1.00 0.00 N +ATOM 603 H ASP A 40 34.838 29.543 39.947 1.00 0.00 H +ATOM 604 CA ASP A 40 34.875 31.551 39.096 1.00 0.00 C +ATOM 605 HA ASP A 40 34.143 32.078 38.487 1.00 0.00 H +ATOM 606 CB ASP A 40 35.183 32.418 40.345 1.00 0.00 C +ATOM 607 HB2 ASP A 40 34.184 32.657 40.710 1.00 0.00 H +ATOM 608 HB3 ASP A 40 35.707 31.788 41.065 1.00 0.00 H +ATOM 609 CG ASP A 40 35.879 33.683 40.009 1.00 0.00 C +ATOM 610 OD1 ASP A 40 35.393 34.410 39.076 1.00 0.00 O1- +ATOM 611 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O1- +ATOM 612 C ASP A 40 36.062 31.169 38.238 1.00 0.00 C +ATOM 613 O ASP A 40 36.850 30.275 38.630 1.00 0.00 O +ATOM 614 N GLY A 41 36.172 31.751 37.102 1.00 0.00 N +ATOM 615 H GLY A 41 35.443 32.408 36.858 1.00 0.00 H +ATOM 616 CA GLY A 41 37.214 31.484 36.189 1.00 0.00 C +ATOM 617 HA2 GLY A 41 38.072 31.014 36.670 1.00 0.00 H +ATOM 618 HA3 GLY A 41 36.761 30.672 35.620 1.00 0.00 H +ATOM 619 C GLY A 41 37.623 32.709 35.379 1.00 0.00 C +ATOM 620 O GLY A 41 37.288 33.862 35.686 1.00 0.00 O +ATOM 621 N GLU A 42 38.354 32.422 34.316 1.00 0.00 N +ATOM 622 H GLU A 42 38.789 31.512 34.368 1.00 0.00 H +ATOM 623 CA GLU A 42 38.603 33.310 33.228 1.00 0.00 C +ATOM 624 HA GLU A 42 38.329 34.318 33.541 1.00 0.00 H +ATOM 625 CB GLU A 42 40.158 33.294 33.040 1.00 0.00 C +ATOM 626 HB2 GLU A 42 40.656 33.398 34.004 1.00 0.00 H +ATOM 627 HB3 GLU A 42 40.417 32.326 32.611 1.00 0.00 H +ATOM 628 CG GLU A 42 40.673 34.328 32.046 1.00 0.00 C +ATOM 629 HG2 GLU A 42 41.606 34.015 31.580 1.00 0.00 H +ATOM 630 HG3 GLU A 42 39.970 34.501 31.231 1.00 0.00 H +ATOM 631 CD GLU A 42 41.014 35.613 32.804 1.00 0.00 C +ATOM 632 OE1 GLU A 42 41.944 35.693 33.644 1.00 0.00 O1- +ATOM 633 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O1- +ATOM 634 C GLU A 42 37.780 33.033 32.033 1.00 0.00 C +ATOM 635 O GLU A 42 37.577 31.870 31.690 1.00 0.00 O +ATOM 636 N TRP A 43 37.228 34.069 31.412 1.00 0.00 N +ATOM 637 H TRP A 43 37.423 35.035 31.634 1.00 0.00 H +ATOM 638 CA TRP A 43 36.233 33.951 30.354 1.00 0.00 C +ATOM 639 HA TRP A 43 35.850 32.931 30.348 1.00 0.00 H +ATOM 640 CB TRP A 43 34.984 34.889 30.616 1.00 0.00 C +ATOM 641 HB2 TRP A 43 35.436 35.868 30.771 1.00 0.00 H +ATOM 642 HB3 TRP A 43 34.427 34.918 29.679 1.00 0.00 H +ATOM 643 CG TRP A 43 34.115 34.536 31.838 1.00 0.00 C +ATOM 644 CD1 TRP A 43 34.428 34.708 33.154 1.00 0.00 C +ATOM 645 HD1 TRP A 43 35.387 35.052 33.511 1.00 0.00 H +ATOM 646 NE1 TRP A 43 33.399 34.110 33.877 1.00 0.00 N +ATOM 647 HE1 TRP A 43 33.511 34.066 34.880 1.00 0.00 H +ATOM 648 CE2 TRP A 43 32.444 33.463 33.073 1.00 0.00 C +ATOM 649 CZ2 TRP A 43 31.248 32.745 33.296 1.00 0.00 C +ATOM 650 HZ2 TRP A 43 31.007 32.429 34.301 1.00 0.00 H +ATOM 651 CH2 TRP A 43 30.575 32.194 32.199 1.00 0.00 C +ATOM 652 HH2 TRP A 43 29.740 31.527 32.355 1.00 0.00 H +ATOM 653 CZ3 TRP A 43 30.988 32.541 30.909 1.00 0.00 C +ATOM 654 HZ3 TRP A 43 30.412 32.236 30.047 1.00 0.00 H +ATOM 655 CE3 TRP A 43 32.109 33.327 30.682 1.00 0.00 C +ATOM 656 HE3 TRP A 43 32.397 33.679 29.703 1.00 0.00 H +ATOM 657 CD2 TRP A 43 32.870 33.817 31.765 1.00 0.00 C +ATOM 658 C TRP A 43 36.910 34.235 29.034 1.00 0.00 C +ATOM 659 O TRP A 43 37.660 35.202 28.823 1.00 0.00 O +ATOM 660 N THR A 44 36.468 33.398 28.113 1.00 0.00 N +ATOM 661 H THR A 44 35.919 32.590 28.367 1.00 0.00 H +ATOM 662 CA THR A 44 36.627 33.526 26.668 1.00 0.00 C +ATOM 663 HA THR A 44 36.825 34.580 26.474 1.00 0.00 H +ATOM 664 CB THR A 44 37.813 32.794 26.062 1.00 0.00 C +ATOM 665 HB THR A 44 37.695 32.789 24.978 1.00 0.00 H +ATOM 666 CG2 THR A 44 39.142 33.411 26.470 1.00 0.00 C +ATOM 667 HG21 THR A 44 39.971 32.814 26.090 1.00 0.00 H +ATOM 668 HG22 THR A 44 39.277 33.395 27.552 1.00 0.00 H +ATOM 669 HG23 THR A 44 39.360 34.408 26.088 1.00 0.00 H +ATOM 670 OG1 THR A 44 37.854 31.507 26.604 1.00 0.00 O +ATOM 671 HG1 THR A 44 37.629 30.907 25.889 1.00 0.00 H +ATOM 672 C THR A 44 35.267 33.295 26.005 1.00 0.00 C +ATOM 673 O THR A 44 34.480 32.577 26.444 1.00 0.00 O +ATOM 674 N TYR A 45 35.137 33.919 24.848 1.00 0.00 N +ATOM 675 H TYR A 45 35.900 34.526 24.585 1.00 0.00 H +ATOM 676 CA TYR A 45 34.051 33.679 23.814 1.00 0.00 C +ATOM 677 HA TYR A 45 33.565 32.748 24.109 1.00 0.00 H +ATOM 678 CB TYR A 45 33.061 34.890 23.836 1.00 0.00 C +ATOM 679 HB2 TYR A 45 32.689 35.085 24.843 1.00 0.00 H +ATOM 680 HB3 TYR A 45 33.670 35.762 23.596 1.00 0.00 H +ATOM 681 CG TYR A 45 31.825 34.747 22.962 1.00 0.00 C +ATOM 682 CD1 TYR A 45 30.955 33.684 23.061 1.00 0.00 C +ATOM 683 HD1 TYR A 45 31.040 32.945 23.845 1.00 0.00 H +ATOM 684 CE1 TYR A 45 29.908 33.556 22.116 1.00 0.00 C +ATOM 685 HE1 TYR A 45 29.113 32.849 22.291 1.00 0.00 H +ATOM 686 CZ TYR A 45 29.718 34.506 21.094 1.00 0.00 C +ATOM 687 OH TYR A 45 28.658 34.338 20.268 1.00 0.00 O +ATOM 688 HH TYR A 45 28.496 35.052 19.648 1.00 0.00 H +ATOM 689 CE2 TYR A 45 30.653 35.574 21.028 1.00 0.00 C +ATOM 690 HE2 TYR A 45 30.490 36.288 20.234 1.00 0.00 H +ATOM 691 CD2 TYR A 45 31.752 35.643 21.911 1.00 0.00 C +ATOM 692 HD2 TYR A 45 32.537 36.346 21.679 1.00 0.00 H +ATOM 693 C TYR A 45 34.545 33.529 22.336 1.00 0.00 C +ATOM 694 O TYR A 45 35.260 34.412 21.809 1.00 0.00 O +ATOM 695 N ASP A 46 33.924 32.567 21.640 1.00 0.00 N +ATOM 696 H ASP A 46 33.215 32.006 22.088 1.00 0.00 H +ATOM 697 CA ASP A 46 34.109 32.289 20.204 1.00 0.00 C +ATOM 698 HA ASP A 46 34.805 32.896 19.625 1.00 0.00 H +ATOM 699 CB ASP A 46 34.818 30.917 20.240 1.00 0.00 C +ATOM 700 HB2 ASP A 46 35.700 31.032 20.871 1.00 0.00 H +ATOM 701 HB3 ASP A 46 34.252 30.200 20.834 1.00 0.00 H +ATOM 702 CG ASP A 46 35.216 30.282 18.912 1.00 0.00 C +ATOM 703 OD1 ASP A 46 34.405 29.507 18.323 1.00 0.00 O1- +ATOM 704 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O1- +ATOM 705 C ASP A 46 32.877 32.275 19.319 1.00 0.00 C +ATOM 706 O ASP A 46 31.931 31.517 19.529 1.00 0.00 O +ATOM 707 N ASP A 47 32.833 33.220 18.413 1.00 0.00 N +ATOM 708 H ASP A 47 33.622 33.852 18.429 1.00 0.00 H +ATOM 709 CA ASP A 47 31.688 33.456 17.554 1.00 0.00 C +ATOM 710 HA ASP A 47 30.773 33.561 18.137 1.00 0.00 H +ATOM 711 CB ASP A 47 31.907 34.738 16.747 1.00 0.00 C +ATOM 712 HB2 ASP A 47 32.113 35.510 17.488 1.00 0.00 H +ATOM 713 HB3 ASP A 47 32.853 34.697 16.207 1.00 0.00 H +ATOM 714 CG ASP A 47 30.729 35.187 15.844 1.00 0.00 C +ATOM 715 OD1 ASP A 47 29.551 35.040 16.174 1.00 0.00 O1- +ATOM 716 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O1- +ATOM 717 C ASP A 47 31.522 32.326 16.557 1.00 0.00 C +ATOM 718 O ASP A 47 30.390 32.069 16.134 1.00 0.00 O +ATOM 719 N ALA A 48 32.555 31.657 16.092 1.00 0.00 N +ATOM 720 H ALA A 48 33.490 31.931 16.357 1.00 0.00 H +ATOM 721 CA ALA A 48 32.437 30.647 15.015 1.00 0.00 C +ATOM 722 HA ALA A 48 31.707 31.108 14.349 1.00 0.00 H +ATOM 723 CB ALA A 48 33.821 30.467 14.340 1.00 0.00 C +ATOM 724 HB1 ALA A 48 34.244 31.399 13.964 1.00 0.00 H +ATOM 725 HB2 ALA A 48 33.675 29.706 13.573 1.00 0.00 H +ATOM 726 HB3 ALA A 48 34.421 29.986 15.112 1.00 0.00 H +ATOM 727 C ALA A 48 31.855 29.301 15.549 1.00 0.00 C +ATOM 728 O ALA A 48 31.548 28.445 14.720 1.00 0.00 O +ATOM 729 N THR A 49 31.619 29.163 16.885 1.00 0.00 N +ATOM 730 H THR A 49 31.975 29.929 17.439 1.00 0.00 H +ATOM 731 CA THR A 49 30.811 28.126 17.576 1.00 0.00 C +ATOM 732 HA THR A 49 30.371 27.544 16.767 1.00 0.00 H +ATOM 733 CB THR A 49 31.713 27.100 18.310 1.00 0.00 C +ATOM 734 HB THR A 49 31.134 26.420 18.935 1.00 0.00 H +ATOM 735 CG2 THR A 49 32.614 26.280 17.436 1.00 0.00 C +ATOM 736 HG21 THR A 49 33.329 26.868 16.859 1.00 0.00 H +ATOM 737 HG22 THR A 49 32.002 25.593 16.853 1.00 0.00 H +ATOM 738 HG23 THR A 49 33.354 25.760 18.044 1.00 0.00 H +ATOM 739 OG1 THR A 49 32.507 27.834 19.222 1.00 0.00 O +ATOM 740 HG1 THR A 49 33.151 28.336 18.715 1.00 0.00 H +ATOM 741 C THR A 49 29.713 28.644 18.468 1.00 0.00 C +ATOM 742 O THR A 49 28.941 27.912 19.103 1.00 0.00 O +ATOM 743 N LYS A 50 29.628 29.977 18.649 1.00 0.00 N +ATOM 744 H LYS A 50 30.419 30.522 18.334 1.00 0.00 H +ATOM 745 CA LYS A 50 28.663 30.695 19.541 1.00 0.00 C +ATOM 746 HA LYS A 50 28.847 31.769 19.501 1.00 0.00 H +ATOM 747 CB LYS A 50 27.189 30.625 19.033 1.00 0.00 C +ATOM 748 HB2 LYS A 50 26.936 29.572 19.163 1.00 0.00 H +ATOM 749 HB3 LYS A 50 26.469 31.081 19.712 1.00 0.00 H +ATOM 750 CG LYS A 50 27.119 30.984 17.465 1.00 0.00 C +ATOM 751 HG2 LYS A 50 27.961 30.590 16.895 1.00 0.00 H +ATOM 752 HG3 LYS A 50 26.188 30.551 17.100 1.00 0.00 H +ATOM 753 CD LYS A 50 27.025 32.547 17.322 1.00 0.00 C +ATOM 754 HD2 LYS A 50 26.337 33.099 17.964 1.00 0.00 H +ATOM 755 HD3 LYS A 50 28.005 32.913 17.623 1.00 0.00 H +ATOM 756 CE LYS A 50 26.686 32.933 15.930 1.00 0.00 C +ATOM 757 HE2 LYS A 50 25.829 32.363 15.572 1.00 0.00 H +ATOM 758 HE3 LYS A 50 26.304 33.953 15.986 1.00 0.00 H +ATOM 759 NZ LYS A 50 27.861 32.905 14.990 1.00 0.00 N1+ +ATOM 760 HZ1 LYS A 50 28.562 33.507 15.397 1.00 0.00 H +ATOM 761 HZ2 LYS A 50 27.597 33.321 14.108 1.00 0.00 H +ATOM 762 HZ3 LYS A 50 28.269 32.017 14.736 1.00 0.00 H +ATOM 763 C LYS A 50 28.884 30.250 21.033 1.00 0.00 C +ATOM 764 O LYS A 50 27.958 30.206 21.826 1.00 0.00 O +ATOM 765 N THR A 51 30.148 29.820 21.328 1.00 0.00 N +ATOM 766 H THR A 51 30.940 30.100 20.766 1.00 0.00 H +ATOM 767 CA THR A 51 30.503 29.214 22.632 1.00 0.00 C +ATOM 768 HA THR A 51 29.680 28.714 23.142 1.00 0.00 H +ATOM 769 CB THR A 51 31.313 27.944 22.369 1.00 0.00 C +ATOM 770 HB THR A 51 32.245 28.102 21.826 1.00 0.00 H +ATOM 771 CG2 THR A 51 31.703 27.088 23.590 1.00 0.00 C +ATOM 772 HG21 THR A 51 32.177 26.160 23.272 1.00 0.00 H +ATOM 773 HG22 THR A 51 30.745 26.977 24.100 1.00 0.00 H +ATOM 774 HG23 THR A 51 32.401 27.677 24.186 1.00 0.00 H +ATOM 775 OG1 THR A 51 30.404 27.161 21.659 1.00 0.00 O +ATOM 776 HG1 THR A 51 29.757 27.683 21.179 1.00 0.00 H +ATOM 777 C THR A 51 31.202 30.120 23.549 1.00 0.00 C +ATOM 778 O THR A 51 32.200 30.721 23.143 1.00 0.00 O +ATOM 779 N PHE A 52 31.009 29.926 24.845 1.00 0.00 N +ATOM 780 H PHE A 52 30.125 29.479 25.042 1.00 0.00 H +ATOM 781 CA PHE A 52 31.821 30.391 25.941 1.00 0.00 C +ATOM 782 HA PHE A 52 32.490 31.192 25.628 1.00 0.00 H +ATOM 783 CB PHE A 52 30.715 30.979 27.007 1.00 0.00 C +ATOM 784 HB2 PHE A 52 29.988 30.200 27.238 1.00 0.00 H +ATOM 785 HB3 PHE A 52 31.250 31.298 27.901 1.00 0.00 H +ATOM 786 CG PHE A 52 30.049 32.222 26.534 1.00 0.00 C +ATOM 787 CD1 PHE A 52 28.876 32.142 25.781 1.00 0.00 C +ATOM 788 HD1 PHE A 52 28.413 31.204 25.515 1.00 0.00 H +ATOM 789 CE1 PHE A 52 28.300 33.350 25.304 1.00 0.00 C +ATOM 790 HE1 PHE A 52 27.303 33.316 24.890 1.00 0.00 H +ATOM 791 CZ PHE A 52 28.880 34.593 25.500 1.00 0.00 C +ATOM 792 HZ PHE A 52 28.417 35.460 25.054 1.00 0.00 H +ATOM 793 CE2 PHE A 52 30.122 34.665 26.192 1.00 0.00 C +ATOM 794 HE2 PHE A 52 30.650 35.597 26.333 1.00 0.00 H +ATOM 795 CD2 PHE A 52 30.597 33.495 26.795 1.00 0.00 C +ATOM 796 HD2 PHE A 52 31.435 33.581 27.471 1.00 0.00 H +ATOM 797 C PHE A 52 32.721 29.343 26.553 1.00 0.00 C +ATOM 798 O PHE A 52 32.280 28.240 26.674 1.00 0.00 O +ATOM 799 N THR A 53 33.908 29.829 27.087 1.00 0.00 N +ATOM 800 H THR A 53 34.203 30.784 26.938 1.00 0.00 H +ATOM 801 CA THR A 53 34.577 29.044 28.132 1.00 0.00 C +ATOM 802 HA THR A 53 34.003 28.190 28.492 1.00 0.00 H +ATOM 803 CB THR A 53 35.881 28.443 27.684 1.00 0.00 C +ATOM 804 HB THR A 53 36.513 29.234 27.280 1.00 0.00 H +ATOM 805 CG2 THR A 53 36.620 27.571 28.752 1.00 0.00 C +ATOM 806 HG21 THR A 53 36.814 28.236 29.595 1.00 0.00 H +ATOM 807 HG22 THR A 53 37.535 27.174 28.313 1.00 0.00 H +ATOM 808 HG23 THR A 53 35.924 26.795 29.068 1.00 0.00 H +ATOM 809 OG1 THR A 53 35.605 27.649 26.584 1.00 0.00 O +ATOM 810 HG1 THR A 53 35.459 28.177 25.796 1.00 0.00 H +ATOM 811 C THR A 53 34.776 29.748 29.443 1.00 0.00 C +ATOM 812 O THR A 53 35.146 30.939 29.437 1.00 0.00 O +ATOM 813 N VAL A 54 34.499 29.135 30.639 1.00 0.00 N +ATOM 814 H VAL A 54 34.209 28.173 30.538 1.00 0.00 H +ATOM 815 CA VAL A 54 34.861 29.536 31.982 1.00 0.00 C +ATOM 816 HA VAL A 54 35.382 30.493 31.978 1.00 0.00 H +ATOM 817 CB VAL A 54 33.697 29.716 32.869 1.00 0.00 C +ATOM 818 HB VAL A 54 32.913 30.335 32.434 1.00 0.00 H +ATOM 819 CG1 VAL A 54 33.002 28.394 33.289 1.00 0.00 C +ATOM 820 HG11 VAL A 54 33.690 27.666 33.718 1.00 0.00 H +ATOM 821 HG12 VAL A 54 32.618 28.014 32.342 1.00 0.00 H +ATOM 822 HG13 VAL A 54 32.093 28.525 33.877 1.00 0.00 H +ATOM 823 CG2 VAL A 54 34.118 30.320 34.224 1.00 0.00 C +ATOM 824 HG21 VAL A 54 34.711 31.228 34.123 1.00 0.00 H +ATOM 825 HG22 VAL A 54 34.691 29.664 34.880 1.00 0.00 H +ATOM 826 HG23 VAL A 54 33.202 30.551 34.767 1.00 0.00 H +ATOM 827 C VAL A 54 35.950 28.590 32.468 1.00 0.00 C +ATOM 828 O VAL A 54 35.738 27.385 32.660 1.00 0.00 O +ATOM 829 N THR A 55 37.187 29.085 32.651 1.00 0.00 N +ATOM 830 H THR A 55 37.326 30.038 32.345 1.00 0.00 H +ATOM 831 CA THR A 55 38.418 28.363 33.071 1.00 0.00 C +ATOM 832 HA THR A 55 38.197 27.299 32.991 1.00 0.00 H +ATOM 833 CB THR A 55 39.574 28.516 32.161 1.00 0.00 C +ATOM 834 HB THR A 55 39.757 29.581 32.019 1.00 0.00 H +ATOM 835 CG2 THR A 55 40.870 27.898 32.786 1.00 0.00 C +ATOM 836 HG21 THR A 55 40.583 26.849 32.855 1.00 0.00 H +ATOM 837 HG22 THR A 55 41.023 28.190 33.826 1.00 0.00 H +ATOM 838 HG23 THR A 55 41.825 28.044 32.280 1.00 0.00 H +ATOM 839 OG1 THR A 55 39.215 27.970 30.818 1.00 0.00 O +ATOM 840 HG1 THR A 55 38.792 28.725 30.401 1.00 0.00 H +ATOM 841 C THR A 55 38.779 28.725 34.458 1.00 0.00 C +ATOM 842 O THR A 55 39.263 29.841 34.735 1.00 0.00 O +ATOM 843 N GLU A 56 38.757 27.773 35.416 1.00 0.00 N +ATOM 844 H GLU A 56 38.459 26.869 35.079 1.00 0.00 H +ATOM 845 CA GLU A 56 39.045 27.993 36.888 1.00 0.00 C +ATOM 846 HA GLU A 56 38.618 28.921 37.267 1.00 0.00 H +ATOM 847 CB GLU A 56 38.402 26.911 37.749 1.00 0.00 C +ATOM 848 HB2 GLU A 56 37.329 27.019 37.593 1.00 0.00 H +ATOM 849 HB3 GLU A 56 38.780 25.905 37.563 1.00 0.00 H +ATOM 850 CG GLU A 56 38.436 27.078 39.267 1.00 0.00 C +ATOM 851 HG2 GLU A 56 39.455 26.968 39.636 1.00 0.00 H +ATOM 852 HG3 GLU A 56 38.094 28.097 39.445 1.00 0.00 H +ATOM 853 CD GLU A 56 37.514 26.014 39.918 1.00 0.00 C +ATOM 854 OE1 GLU A 56 37.905 24.823 39.870 1.00 0.00 O1- +ATOM 855 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O1- +ATOM 856 C GLU A 56 40.488 28.137 37.301 1.00 0.00 C +ATOM 857 O GLU A 56 40.807 29.090 38.025 1.00 0.00 O1- +ATOM 858 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O1- +CONECT 1 2 3 4 5 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 1 6 7 18 +CONECT 6 5 +CONECT 7 5 8 9 10 +CONECT 8 7 +CONECT 9 7 +CONECT 10 7 11 12 13 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 +CONECT 14 13 15 16 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 19 20 +CONECT 19 18 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 23 24 32 +CONECT 23 22 +CONECT 24 22 25 26 30 +CONECT 25 24 +CONECT 26 24 27 28 29 +CONECT 27 26 +CONECT 28 26 +CONECT 29 26 +CONECT 30 24 31 +CONECT 31 30 +CONECT 32 22 33 33 34 +CONECT 33 32 32 +CONECT 34 32 35 36 +CONECT 35 34 +CONECT 36 34 37 38 53 +CONECT 37 36 +CONECT 38 36 39 40 41 +CONECT 39 38 +CONECT 40 38 +CONECT 41 38 42 42 51 +CONECT 42 41 41 43 44 +CONECT 43 42 +CONECT 44 42 45 46 46 +CONECT 45 44 +CONECT 46 44 44 47 49 +CONECT 47 46 48 +CONECT 48 47 +CONECT 49 46 50 51 51 +CONECT 50 49 +CONECT 51 41 49 49 52 +CONECT 52 51 +CONECT 53 36 54 54 55 +CONECT 54 53 53 +CONECT 55 53 56 57 +CONECT 56 55 +CONECT 57 55 58 59 75 +CONECT 58 57 +CONECT 59 57 60 61 62 +CONECT 60 59 +CONECT 61 59 +CONECT 62 59 63 64 65 +CONECT 63 62 +CONECT 64 62 +CONECT 65 62 66 67 68 +CONECT 66 65 +CONECT 67 65 +CONECT 68 65 69 70 71 +CONECT 69 68 +CONECT 70 68 +CONECT 71 68 72 73 74 +CONECT 72 71 +CONECT 73 71 +CONECT 74 71 +CONECT 75 57 76 76 77 +CONECT 76 75 75 +CONECT 77 75 78 79 +CONECT 78 77 +CONECT 79 77 80 81 94 +CONECT 80 79 +CONECT 81 79 82 83 84 +CONECT 82 81 +CONECT 83 81 +CONECT 84 81 85 86 90 +CONECT 85 84 +CONECT 86 84 87 88 89 +CONECT 87 86 +CONECT 88 86 +CONECT 89 86 +CONECT 90 84 91 92 93 +CONECT 91 90 +CONECT 92 90 +CONECT 93 90 +CONECT 94 79 95 95 96 +CONECT 95 94 94 +CONECT 96 94 97 98 +CONECT 97 96 +CONECT 98 96 99 100 113 +CONECT 99 98 +CONECT 100 98 101 102 106 +CONECT 101 100 +CONECT 102 100 103 104 105 +CONECT 103 102 +CONECT 104 102 +CONECT 105 102 +CONECT 106 100 107 108 109 +CONECT 107 106 +CONECT 108 106 +CONECT 109 106 110 111 112 +CONECT 110 109 +CONECT 111 109 +CONECT 112 109 +CONECT 113 98 114 114 115 +CONECT 114 113 113 +CONECT 115 113 116 117 +CONECT 116 115 +CONECT 117 115 118 119 132 +CONECT 118 117 +CONECT 119 117 120 121 122 +CONECT 120 119 +CONECT 121 119 +CONECT 122 119 123 124 128 +CONECT 123 122 +CONECT 124 122 125 126 127 +CONECT 125 124 +CONECT 126 124 +CONECT 127 124 +CONECT 128 122 129 130 131 +CONECT 129 128 +CONECT 130 128 +CONECT 131 128 +CONECT 132 117 133 133 134 +CONECT 133 132 132 +CONECT 134 132 135 136 +CONECT 135 134 +CONECT 136 134 137 138 146 +CONECT 137 136 +CONECT 138 136 139 140 141 +CONECT 139 138 +CONECT 140 138 +CONECT 141 138 142 142 143 +CONECT 142 141 141 +CONECT 143 141 144 145 +CONECT 144 143 +CONECT 145 143 +CONECT 146 136 147 147 148 +CONECT 147 146 146 +CONECT 148 146 149 150 +CONECT 149 148 +CONECT 150 148 155 156 151 +CONECT 151 150 152 153 154 +CONECT 152 151 +CONECT 153 151 +CONECT 154 151 +CONECT 155 150 +CONECT 156 150 157 157 158 +CONECT 157 156 156 +CONECT 158 156 159 160 +CONECT 159 158 +CONECT 160 158 161 162 178 +CONECT 161 160 +CONECT 162 160 163 164 165 +CONECT 163 162 +CONECT 164 162 +CONECT 165 162 166 167 168 +CONECT 166 165 +CONECT 167 165 +CONECT 168 165 169 170 171 +CONECT 169 168 +CONECT 170 168 +CONECT 171 168 172 173 174 +CONECT 172 171 +CONECT 173 171 +CONECT 174 171 175 176 177 +CONECT 175 174 +CONECT 176 174 +CONECT 177 174 +CONECT 178 160 179 179 180 +CONECT 179 178 178 +CONECT 180 178 181 182 +CONECT 181 180 +CONECT 182 180 183 184 192 +CONECT 183 182 +CONECT 184 182 185 186 190 +CONECT 185 184 +CONECT 186 184 187 188 189 +CONECT 187 186 +CONECT 188 186 +CONECT 189 186 +CONECT 190 184 191 +CONECT 191 190 +CONECT 192 182 193 193 194 +CONECT 193 192 192 +CONECT 194 192 195 196 +CONECT 195 194 +CONECT 196 194 197 198 211 +CONECT 197 196 +CONECT 198 196 199 200 201 +CONECT 199 198 +CONECT 200 198 +CONECT 201 198 202 203 207 +CONECT 202 201 +CONECT 203 201 204 205 206 +CONECT 204 203 +CONECT 205 203 +CONECT 206 203 +CONECT 207 201 208 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 207 +CONECT 211 196 212 212 213 +CONECT 212 211 211 +CONECT 213 211 214 215 +CONECT 214 213 +CONECT 215 213 216 217 233 +CONECT 216 215 +CONECT 217 215 218 219 220 +CONECT 218 217 +CONECT 219 217 +CONECT 220 217 221 222 223 +CONECT 221 220 +CONECT 222 220 +CONECT 223 220 224 225 226 +CONECT 224 223 +CONECT 225 223 +CONECT 226 223 227 228 229 +CONECT 227 226 +CONECT 228 226 +CONECT 229 226 230 231 232 +CONECT 230 229 +CONECT 231 229 +CONECT 232 229 +CONECT 233 215 234 234 235 +CONECT 234 233 233 +CONECT 235 233 236 237 +CONECT 236 235 +CONECT 237 235 238 239 240 +CONECT 238 237 +CONECT 239 237 +CONECT 240 237 241 241 242 +CONECT 241 240 240 +CONECT 242 240 243 244 +CONECT 243 242 +CONECT 244 242 245 246 255 +CONECT 245 244 +CONECT 246 244 247 248 249 +CONECT 247 246 +CONECT 248 246 +CONECT 249 246 250 251 252 +CONECT 250 249 +CONECT 251 249 +CONECT 252 249 253 253 254 +CONECT 253 252 252 +CONECT 254 252 +CONECT 255 244 256 256 257 +CONECT 256 255 255 +CONECT 257 255 258 259 +CONECT 258 257 +CONECT 259 257 260 261 269 +CONECT 260 259 +CONECT 261 259 262 263 267 +CONECT 262 261 +CONECT 263 261 264 265 266 +CONECT 264 263 +CONECT 265 263 +CONECT 266 263 +CONECT 267 261 268 +CONECT 268 267 +CONECT 269 259 270 270 271 +CONECT 270 269 269 +CONECT 271 269 272 273 +CONECT 272 271 +CONECT 273 271 274 275 283 +CONECT 274 273 +CONECT 275 273 276 277 281 +CONECT 276 275 +CONECT 277 275 278 279 280 +CONECT 278 277 +CONECT 279 277 +CONECT 280 277 +CONECT 281 275 282 +CONECT 282 281 +CONECT 283 273 284 284 285 +CONECT 284 283 283 +CONECT 285 283 286 287 +CONECT 286 285 +CONECT 287 285 288 289 297 +CONECT 288 287 +CONECT 289 287 290 291 295 +CONECT 290 289 +CONECT 291 289 292 293 294 +CONECT 292 291 +CONECT 293 291 +CONECT 294 291 +CONECT 295 289 296 +CONECT 296 295 +CONECT 297 287 298 298 299 +CONECT 298 297 297 +CONECT 299 297 300 301 +CONECT 300 299 +CONECT 301 299 302 303 312 +CONECT 302 301 +CONECT 303 301 304 305 306 +CONECT 304 303 +CONECT 305 303 +CONECT 306 303 307 308 309 +CONECT 307 306 +CONECT 308 306 +CONECT 309 306 310 310 311 +CONECT 310 309 309 +CONECT 311 309 +CONECT 312 301 313 313 314 +CONECT 313 312 312 +CONECT 314 312 315 316 +CONECT 315 314 +CONECT 316 314 317 318 322 +CONECT 317 316 +CONECT 318 316 319 320 321 +CONECT 319 318 +CONECT 320 318 +CONECT 321 318 +CONECT 322 316 323 323 324 +CONECT 323 322 322 +CONECT 324 322 325 326 +CONECT 325 324 +CONECT 326 324 327 328 338 +CONECT 327 326 +CONECT 328 326 329 330 334 +CONECT 329 328 +CONECT 330 328 331 332 333 +CONECT 331 330 +CONECT 332 330 +CONECT 333 330 +CONECT 334 328 335 336 337 +CONECT 335 334 +CONECT 336 334 +CONECT 337 334 +CONECT 338 326 339 339 340 +CONECT 339 338 338 +CONECT 340 338 341 342 +CONECT 341 340 +CONECT 342 340 343 344 350 +CONECT 343 342 +CONECT 344 342 345 346 347 +CONECT 345 344 +CONECT 346 344 +CONECT 347 344 348 348 349 +CONECT 348 347 347 +CONECT 349 347 +CONECT 350 342 351 351 352 +CONECT 351 350 350 +CONECT 352 350 353 354 +CONECT 353 352 +CONECT 354 352 355 356 360 +CONECT 355 354 +CONECT 356 354 357 358 359 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 +CONECT 360 354 361 361 362 +CONECT 361 360 360 +CONECT 362 360 363 364 +CONECT 363 362 +CONECT 364 362 365 366 370 +CONECT 365 364 +CONECT 366 364 367 368 369 +CONECT 367 366 +CONECT 368 366 +CONECT 369 366 +CONECT 370 364 371 371 372 +CONECT 371 370 370 +CONECT 372 370 373 374 +CONECT 373 372 +CONECT 374 372 375 376 384 +CONECT 375 374 +CONECT 376 374 377 378 382 +CONECT 377 376 +CONECT 378 376 379 380 381 +CONECT 379 378 +CONECT 380 378 +CONECT 381 378 +CONECT 382 376 383 +CONECT 383 382 +CONECT 384 374 385 385 386 +CONECT 385 384 384 +CONECT 386 384 387 388 +CONECT 387 386 +CONECT 388 386 389 390 394 +CONECT 389 388 +CONECT 390 388 391 392 393 +CONECT 391 390 +CONECT 392 390 +CONECT 393 390 +CONECT 394 388 395 395 396 +CONECT 395 394 394 +CONECT 396 394 397 398 +CONECT 397 396 +CONECT 398 396 399 400 409 +CONECT 399 398 +CONECT 400 398 401 402 403 +CONECT 401 400 +CONECT 402 400 +CONECT 403 400 404 405 406 +CONECT 404 403 +CONECT 405 403 +CONECT 406 403 407 407 408 +CONECT 407 406 406 +CONECT 408 406 +CONECT 409 398 410 410 411 +CONECT 410 409 409 +CONECT 411 409 412 413 +CONECT 412 411 +CONECT 413 411 414 415 431 +CONECT 414 413 +CONECT 415 413 416 417 418 +CONECT 416 415 +CONECT 417 415 +CONECT 418 415 419 420 421 +CONECT 419 418 +CONECT 420 418 +CONECT 421 418 422 423 424 +CONECT 422 421 +CONECT 423 421 +CONECT 424 421 425 426 427 +CONECT 425 424 +CONECT 426 424 +CONECT 427 424 428 429 430 +CONECT 428 427 +CONECT 429 427 +CONECT 430 427 +CONECT 431 413 432 432 433 +CONECT 432 431 431 +CONECT 433 431 434 435 +CONECT 434 433 +CONECT 435 433 436 437 447 +CONECT 436 435 +CONECT 437 435 438 439 443 +CONECT 438 437 +CONECT 439 437 440 441 442 +CONECT 440 439 +CONECT 441 439 +CONECT 442 439 +CONECT 443 437 444 445 446 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 +CONECT 447 435 448 448 449 +CONECT 448 447 447 +CONECT 449 447 450 451 +CONECT 450 449 +CONECT 451 449 452 453 467 +CONECT 452 451 +CONECT 453 451 454 455 456 +CONECT 454 453 +CONECT 455 453 +CONECT 456 453 457 457 465 +CONECT 457 456 456 458 459 +CONECT 458 457 +CONECT 459 457 460 461 461 +CONECT 460 459 +CONECT 461 459 459 462 463 +CONECT 462 461 +CONECT 463 461 464 465 465 +CONECT 464 463 +CONECT 465 456 463 463 466 +CONECT 466 465 +CONECT 467 451 468 468 469 +CONECT 468 467 467 +CONECT 469 467 470 471 +CONECT 470 469 +CONECT 471 469 472 473 489 +CONECT 472 471 +CONECT 473 471 474 475 476 +CONECT 474 473 +CONECT 475 473 +CONECT 476 473 477 478 479 +CONECT 477 476 +CONECT 478 476 +CONECT 479 476 480 481 482 +CONECT 480 479 +CONECT 481 479 +CONECT 482 479 483 484 485 +CONECT 483 482 +CONECT 484 482 +CONECT 485 482 486 487 488 +CONECT 486 485 +CONECT 487 485 +CONECT 488 485 +CONECT 489 471 490 490 491 +CONECT 490 489 489 +CONECT 491 489 492 493 +CONECT 492 491 +CONECT 493 491 494 495 506 +CONECT 494 493 +CONECT 495 493 496 497 498 +CONECT 496 495 +CONECT 497 495 +CONECT 498 495 499 500 501 +CONECT 499 498 +CONECT 500 498 +CONECT 501 498 502 502 503 +CONECT 502 501 501 +CONECT 503 501 504 505 +CONECT 504 503 +CONECT 505 503 +CONECT 506 493 507 507 508 +CONECT 507 506 506 +CONECT 508 506 509 510 +CONECT 509 508 +CONECT 510 508 511 512 527 +CONECT 511 510 +CONECT 512 510 513 514 515 +CONECT 513 512 +CONECT 514 512 +CONECT 515 512 516 516 525 +CONECT 516 515 515 517 518 +CONECT 517 516 +CONECT 518 516 519 520 520 +CONECT 519 518 +CONECT 520 518 518 521 523 +CONECT 521 520 522 +CONECT 522 521 +CONECT 523 520 524 525 525 +CONECT 524 523 +CONECT 525 515 523 523 526 +CONECT 526 525 +CONECT 527 510 528 528 529 +CONECT 528 527 527 +CONECT 529 527 530 531 +CONECT 530 529 +CONECT 531 529 532 533 537 +CONECT 532 531 +CONECT 533 531 534 535 536 +CONECT 534 533 +CONECT 535 533 +CONECT 536 533 +CONECT 537 531 538 538 539 +CONECT 538 537 537 +CONECT 539 537 540 541 +CONECT 540 539 +CONECT 541 539 542 543 551 +CONECT 542 541 +CONECT 543 541 544 545 546 +CONECT 544 543 +CONECT 545 543 +CONECT 546 543 547 547 548 +CONECT 547 546 546 +CONECT 548 546 549 550 +CONECT 549 548 +CONECT 550 548 +CONECT 551 541 552 552 553 +CONECT 552 551 551 +CONECT 553 551 554 555 +CONECT 554 553 +CONECT 555 553 556 557 563 +CONECT 556 555 +CONECT 557 555 558 559 560 +CONECT 558 557 +CONECT 559 557 +CONECT 560 557 561 561 562 +CONECT 561 560 560 +CONECT 562 560 +CONECT 563 555 564 564 565 +CONECT 564 563 563 +CONECT 565 563 566 567 +CONECT 566 565 +CONECT 567 565 568 569 577 +CONECT 568 567 +CONECT 569 567 570 571 572 +CONECT 570 569 +CONECT 571 569 +CONECT 572 569 573 573 574 +CONECT 573 572 572 +CONECT 574 572 575 576 +CONECT 575 574 +CONECT 576 574 +CONECT 577 567 578 578 579 +CONECT 578 577 577 +CONECT 579 577 580 581 +CONECT 580 579 +CONECT 581 579 582 583 584 +CONECT 582 581 +CONECT 583 581 +CONECT 584 581 585 585 586 +CONECT 585 584 584 +CONECT 586 584 587 588 +CONECT 587 586 +CONECT 588 586 589 590 600 +CONECT 589 588 +CONECT 590 588 591 592 596 +CONECT 591 590 +CONECT 592 590 593 594 595 +CONECT 593 592 +CONECT 594 592 +CONECT 595 592 +CONECT 596 590 597 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 +CONECT 600 588 601 601 602 +CONECT 601 600 600 +CONECT 602 600 603 604 +CONECT 603 602 +CONECT 604 602 605 606 612 +CONECT 605 604 +CONECT 606 604 607 608 609 +CONECT 607 606 +CONECT 608 606 +CONECT 609 606 610 610 611 +CONECT 610 609 609 +CONECT 611 609 +CONECT 612 604 613 613 614 +CONECT 613 612 612 +CONECT 614 612 615 616 +CONECT 615 614 +CONECT 616 614 617 618 619 +CONECT 617 616 +CONECT 618 616 +CONECT 619 616 620 620 621 +CONECT 620 619 619 +CONECT 621 619 622 623 +CONECT 622 621 +CONECT 623 621 624 625 634 +CONECT 624 623 +CONECT 625 623 626 627 628 +CONECT 626 625 +CONECT 627 625 +CONECT 628 625 629 630 631 +CONECT 629 628 +CONECT 630 628 +CONECT 631 628 632 632 633 +CONECT 632 631 631 +CONECT 633 631 +CONECT 634 623 635 635 636 +CONECT 635 634 634 +CONECT 636 634 637 638 +CONECT 637 636 +CONECT 638 636 639 640 658 +CONECT 639 638 +CONECT 640 638 641 642 643 +CONECT 641 640 +CONECT 642 640 +CONECT 643 640 644 644 657 +CONECT 644 643 643 645 646 +CONECT 645 644 +CONECT 646 644 647 648 +CONECT 647 646 +CONECT 648 646 649 649 657 +CONECT 649 648 648 650 651 +CONECT 650 649 +CONECT 651 649 652 653 653 +CONECT 652 651 +CONECT 653 651 651 654 655 +CONECT 654 653 +CONECT 655 653 656 657 657 +CONECT 656 655 +CONECT 657 643 648 655 655 +CONECT 658 638 659 659 660 +CONECT 659 658 658 +CONECT 660 658 661 662 +CONECT 661 660 +CONECT 662 660 663 664 672 +CONECT 663 662 +CONECT 664 662 665 666 670 +CONECT 665 664 +CONECT 666 664 667 668 669 +CONECT 667 666 +CONECT 668 666 +CONECT 669 666 +CONECT 670 664 671 +CONECT 671 670 +CONECT 672 662 673 673 674 +CONECT 673 672 672 +CONECT 674 672 675 676 +CONECT 675 674 +CONECT 676 674 677 678 693 +CONECT 677 676 +CONECT 678 676 679 680 681 +CONECT 679 678 +CONECT 680 678 +CONECT 681 678 682 682 691 +CONECT 682 681 681 683 684 +CONECT 683 682 +CONECT 684 682 685 686 686 +CONECT 685 684 +CONECT 686 684 684 687 689 +CONECT 687 686 688 +CONECT 688 687 +CONECT 689 686 690 691 691 +CONECT 690 689 +CONECT 691 681 689 689 692 +CONECT 692 691 +CONECT 693 676 694 694 695 +CONECT 694 693 693 +CONECT 695 693 696 697 +CONECT 696 695 +CONECT 697 695 698 699 705 +CONECT 698 697 +CONECT 699 697 700 701 702 +CONECT 700 699 +CONECT 701 699 +CONECT 702 699 703 703 704 +CONECT 703 702 702 +CONECT 704 702 +CONECT 705 697 706 706 707 +CONECT 706 705 705 +CONECT 707 705 708 709 +CONECT 708 707 +CONECT 709 707 710 711 717 +CONECT 710 709 +CONECT 711 709 712 713 714 +CONECT 712 711 +CONECT 713 711 +CONECT 714 711 715 715 716 +CONECT 715 714 714 +CONECT 716 714 +CONECT 717 709 718 718 719 +CONECT 718 717 717 +CONECT 719 717 720 721 +CONECT 720 719 +CONECT 721 719 722 723 727 +CONECT 722 721 +CONECT 723 721 724 725 726 +CONECT 724 723 +CONECT 725 723 +CONECT 726 723 +CONECT 727 721 728 728 729 +CONECT 728 727 727 +CONECT 729 727 730 731 +CONECT 730 729 +CONECT 731 729 732 733 741 +CONECT 732 731 +CONECT 733 731 734 735 739 +CONECT 734 733 +CONECT 735 733 736 737 738 +CONECT 736 735 +CONECT 737 735 +CONECT 738 735 +CONECT 739 733 740 +CONECT 740 739 +CONECT 741 731 742 742 743 +CONECT 742 741 741 +CONECT 743 741 744 745 +CONECT 744 743 +CONECT 745 743 746 747 763 +CONECT 746 745 +CONECT 747 745 748 749 750 +CONECT 748 747 +CONECT 749 747 +CONECT 750 747 751 752 753 +CONECT 751 750 +CONECT 752 750 +CONECT 753 750 754 755 756 +CONECT 754 753 +CONECT 755 753 +CONECT 756 753 757 758 759 +CONECT 757 756 +CONECT 758 756 +CONECT 759 756 760 761 762 +CONECT 760 759 +CONECT 761 759 +CONECT 762 759 +CONECT 763 745 764 764 765 +CONECT 764 763 763 +CONECT 765 763 766 767 +CONECT 766 765 +CONECT 767 765 768 769 777 +CONECT 768 767 +CONECT 769 767 770 771 775 +CONECT 770 769 +CONECT 771 769 772 773 774 +CONECT 772 771 +CONECT 773 771 +CONECT 774 771 +CONECT 775 769 776 +CONECT 776 775 +CONECT 777 767 778 778 779 +CONECT 778 777 777 +CONECT 779 777 780 781 +CONECT 780 779 +CONECT 781 779 782 783 797 +CONECT 782 781 +CONECT 783 781 784 785 786 +CONECT 784 783 +CONECT 785 783 +CONECT 786 783 787 787 795 +CONECT 787 786 786 788 789 +CONECT 788 787 +CONECT 789 787 790 791 791 +CONECT 790 789 +CONECT 791 789 789 792 793 +CONECT 792 791 +CONECT 793 791 794 795 795 +CONECT 794 793 +CONECT 795 786 793 793 796 +CONECT 796 795 +CONECT 797 781 798 798 799 +CONECT 798 797 797 +CONECT 799 797 800 801 +CONECT 800 799 +CONECT 801 799 802 803 811 +CONECT 802 801 +CONECT 803 801 804 805 809 +CONECT 804 803 +CONECT 805 803 806 807 808 +CONECT 806 805 +CONECT 807 805 +CONECT 808 805 +CONECT 809 803 810 +CONECT 810 809 +CONECT 811 801 812 812 813 +CONECT 812 811 811 +CONECT 813 811 814 815 +CONECT 814 813 +CONECT 815 813 816 817 827 +CONECT 816 815 +CONECT 817 815 818 819 823 +CONECT 818 817 +CONECT 819 817 820 821 822 +CONECT 820 819 +CONECT 821 819 +CONECT 822 819 +CONECT 823 817 824 825 826 +CONECT 824 823 +CONECT 825 823 +CONECT 826 823 +CONECT 827 815 828 828 829 +CONECT 828 827 827 +CONECT 829 827 830 831 +CONECT 830 829 +CONECT 831 829 832 833 841 +CONECT 832 831 +CONECT 833 831 834 835 839 +CONECT 834 833 +CONECT 835 833 836 837 838 +CONECT 836 835 +CONECT 837 835 +CONECT 838 835 +CONECT 839 833 840 +CONECT 840 839 +CONECT 841 831 842 842 843 +CONECT 842 841 841 +CONECT 843 841 844 845 +CONECT 844 843 +CONECT 845 843 846 847 856 +CONECT 846 845 +CONECT 847 845 848 849 850 +CONECT 848 847 +CONECT 849 847 +CONECT 850 847 851 852 853 +CONECT 851 850 +CONECT 852 850 +CONECT 853 850 854 854 855 +CONECT 854 853 853 +CONECT 855 853 +CONECT 856 845 857 857 858 +CONECT 857 856 856 +CONECT 858 856 +MASTER 0 0 0 0 0 0 0 0 858 0 858 0 +END diff --git a/unittests/output_files/test_thr_to_gly_restypeFalse.pdb b/unittests/output_files/test_thr_to_gly_restypeFalse.pdb new file mode 100644 index 0000000..23c4be5 --- /dev/null +++ b/unittests/output_files/test_thr_to_gly_restypeFalse.pdb @@ -0,0 +1,1700 @@ +COMPND MET +AUTHOR GENERATED BY OPEN BABEL 3.0.0 +ATOM 1 N MET A 1 19.157 32.576 19.140 1.00 0.00 N1+ +ATOM 2 H1 MET A 1 18.435 31.870 19.129 1.00 0.00 H +ATOM 3 H2 MET A 1 18.900 33.260 18.441 1.00 0.00 H +ATOM 4 H3 MET A 1 19.229 33.073 20.016 1.00 0.00 H +ATOM 5 CA MET A 1 20.458 31.939 18.931 1.00 0.00 C +ATOM 6 HA MET A 1 20.420 31.303 18.046 1.00 0.00 H +ATOM 7 CB MET A 1 21.504 33.015 18.722 1.00 0.00 C +ATOM 8 HB2 MET A 1 21.352 33.519 17.768 1.00 0.00 H +ATOM 9 HB3 MET A 1 21.390 33.764 19.505 1.00 0.00 H +ATOM 10 CG MET A 1 22.904 32.517 18.656 1.00 0.00 C +ATOM 11 HG2 MET A 1 23.590 33.362 18.601 1.00 0.00 H +ATOM 12 HG3 MET A 1 23.154 32.095 19.630 1.00 0.00 H +ATOM 13 SD MET A 1 23.205 31.269 17.386 1.00 0.00 S +ATOM 14 CE MET A 1 22.990 32.137 15.870 1.00 0.00 C +ATOM 15 HE1 MET A 1 23.339 33.163 15.983 1.00 0.00 H +ATOM 16 HE2 MET A 1 21.968 32.128 15.490 1.00 0.00 H +ATOM 17 HE3 MET A 1 23.572 31.586 15.132 1.00 0.00 H +ATOM 18 C MET A 1 20.796 31.017 20.133 1.00 0.00 C +ATOM 19 O MET A 1 20.674 31.440 21.297 1.00 0.00 O +ATOM 20 N G01 A 2 21.124 29.774 19.819 1.00 0.00 N +ATOM 21 H G01 A 2 21.279 29.527 18.851 1.00 0.00 H +ATOM 22 CA G01 A 2 21.443 28.704 20.861 1.00 0.00 C +ATOM 23 HA3 G01 A 2 21.210 27.667 20.621 1.00 0.00 H +ATOM 24 HA G01 A 2 20.909 28.998 21.764 1.00 0.00 H +ATOM 25 C G01 A 2 22.937 28.892 21.086 1.00 0.00 C +ATOM 26 O G01 A 2 23.773 28.867 20.181 1.00 0.00 O +ATOM 27 N TYR A 3 23.244 29.155 22.344 1.00 0.00 N +ATOM 28 H TYR A 3 22.513 29.085 23.038 1.00 0.00 H +ATOM 29 CA TYR A 3 24.628 29.305 22.888 1.00 0.00 C +ATOM 30 HA TYR A 3 25.262 29.391 22.004 1.00 0.00 H +ATOM 31 CB TYR A 3 24.744 30.579 23.675 1.00 0.00 C +ATOM 32 HB2 TYR A 3 24.131 30.495 24.572 1.00 0.00 H +ATOM 33 HB3 TYR A 3 25.780 30.505 24.008 1.00 0.00 H +ATOM 34 CG TYR A 3 24.468 31.862 22.928 1.00 0.00 C +ATOM 35 CD1 TYR A 3 25.525 32.544 22.317 1.00 0.00 C +ATOM 36 HD1 TYR A 3 26.477 32.039 22.379 1.00 0.00 H +ATOM 37 CE1 TYR A 3 25.289 33.761 21.619 1.00 0.00 C +ATOM 38 HE1 TYR A 3 26.100 34.275 21.122 1.00 0.00 H +ATOM 39 CZ TYR A 3 23.936 34.260 21.579 1.00 0.00 C +ATOM 40 OH TYR A 3 23.774 35.268 20.774 1.00 0.00 O +ATOM 41 HH TYR A 3 24.486 35.161 20.140 1.00 0.00 H +ATOM 42 CE2 TYR A 3 22.849 33.537 22.176 1.00 0.00 C +ATOM 43 HE2 TYR A 3 21.868 33.965 22.036 1.00 0.00 H +ATOM 44 CD2 TYR A 3 23.110 32.291 22.853 1.00 0.00 C +ATOM 45 HD2 TYR A 3 22.235 31.752 23.187 1.00 0.00 H +ATOM 46 C TYR A 3 25.066 28.136 23.774 1.00 0.00 C +ATOM 47 O TYR A 3 24.233 27.436 24.338 1.00 0.00 O +ATOM 48 N LYS A 4 26.339 27.934 23.811 1.00 0.00 N +ATOM 49 H LYS A 4 26.944 28.514 23.248 1.00 0.00 H +ATOM 50 CA LYS A 4 26.982 26.918 24.687 1.00 0.00 C +ATOM 51 HA LYS A 4 26.212 26.488 25.328 1.00 0.00 H +ATOM 52 CB LYS A 4 27.643 25.801 23.803 1.00 0.00 C +ATOM 53 HB2 LYS A 4 26.868 25.465 23.113 1.00 0.00 H +ATOM 54 HB3 LYS A 4 28.422 26.196 23.151 1.00 0.00 H +ATOM 55 CG LYS A 4 28.205 24.625 24.506 1.00 0.00 C +ATOM 56 HG2 LYS A 4 29.054 24.916 25.125 1.00 0.00 H +ATOM 57 HG3 LYS A 4 27.452 24.278 25.213 1.00 0.00 H +ATOM 58 CD LYS A 4 28.635 23.407 23.678 1.00 0.00 C +ATOM 59 HD2 LYS A 4 29.003 22.691 24.414 1.00 0.00 H +ATOM 60 HD3 LYS A 4 27.737 22.954 23.255 1.00 0.00 H +ATOM 61 CE LYS A 4 29.554 23.575 22.506 1.00 0.00 C +ATOM 62 HE2 LYS A 4 28.899 24.120 21.827 1.00 0.00 H +ATOM 63 HE3 LYS A 4 30.458 24.114 22.794 1.00 0.00 H +ATOM 64 NZ LYS A 4 30.052 22.279 21.888 1.00 0.00 N1+ +ATOM 65 HZ1 LYS A 4 30.831 21.896 22.402 1.00 0.00 H +ATOM 66 HZ2 LYS A 4 30.443 22.423 20.968 1.00 0.00 H +ATOM 67 HZ3 LYS A 4 29.328 21.579 21.805 1.00 0.00 H +ATOM 68 C LYS A 4 28.003 27.516 25.655 1.00 0.00 C +ATOM 69 O LYS A 4 28.579 28.553 25.310 1.00 0.00 O +ATOM 70 N LEU A 5 28.245 26.773 26.741 1.00 0.00 N +ATOM 71 H LEU A 5 27.544 26.084 26.977 1.00 0.00 H +ATOM 72 CA LEU A 5 29.244 27.118 27.766 1.00 0.00 C +ATOM 73 HA LEU A 5 29.916 27.884 27.380 1.00 0.00 H +ATOM 74 CB LEU A 5 28.579 27.507 29.097 1.00 0.00 C +ATOM 75 HB2 LEU A 5 28.058 28.438 28.872 1.00 0.00 H +ATOM 76 HB3 LEU A 5 27.859 26.779 29.469 1.00 0.00 H +ATOM 77 CG LEU A 5 29.551 27.720 30.235 1.00 0.00 C +ATOM 78 HG LEU A 5 30.166 26.841 30.429 1.00 0.00 H +ATOM 79 CD1 LEU A 5 30.427 28.952 29.986 1.00 0.00 C +ATOM 80 HD11 LEU A 5 31.114 28.683 29.184 1.00 0.00 H +ATOM 81 HD12 LEU A 5 31.008 29.120 30.894 1.00 0.00 H +ATOM 82 HD13 LEU A 5 29.848 29.861 29.825 1.00 0.00 H +ATOM 83 CD2 LEU A 5 28.678 28.115 31.457 1.00 0.00 C +ATOM 84 HD21 LEU A 5 28.235 29.096 31.284 1.00 0.00 H +ATOM 85 HD22 LEU A 5 29.327 28.287 32.315 1.00 0.00 H +ATOM 86 HD23 LEU A 5 27.907 27.390 31.720 1.00 0.00 H +ATOM 87 C LEU A 5 30.065 25.816 27.990 1.00 0.00 C +ATOM 88 O LEU A 5 29.489 24.768 28.302 1.00 0.00 O +ATOM 89 N ILE A 6 31.415 25.954 27.959 1.00 0.00 N +ATOM 90 H ILE A 6 31.834 26.822 27.658 1.00 0.00 H +ATOM 91 CA ILE A 6 32.352 24.944 28.438 1.00 0.00 C +ATOM 92 HA ILE A 6 31.851 23.978 28.494 1.00 0.00 H +ATOM 93 CB ILE A 6 33.535 24.736 27.434 1.00 0.00 C +ATOM 94 HB ILE A 6 34.002 25.706 27.261 1.00 0.00 H +ATOM 95 CG2 ILE A 6 34.658 23.796 27.952 1.00 0.00 C +ATOM 96 HG21 ILE A 6 35.011 24.049 28.953 1.00 0.00 H +ATOM 97 HG22 ILE A 6 35.610 23.773 27.423 1.00 0.00 H +ATOM 98 HG23 ILE A 6 34.315 22.768 28.065 1.00 0.00 H +ATOM 99 CG1 ILE A 6 32.967 24.083 26.135 1.00 0.00 C +ATOM 100 HG12 ILE A 6 32.815 23.014 26.281 1.00 0.00 H +ATOM 101 HG13 ILE A 6 32.016 24.548 25.875 1.00 0.00 H +ATOM 102 CD1 ILE A 6 33.964 24.228 24.983 1.00 0.00 C +ATOM 103 HD11 ILE A 6 34.203 25.280 24.831 1.00 0.00 H +ATOM 104 HD12 ILE A 6 33.521 23.646 24.174 1.00 0.00 H +ATOM 105 HD13 ILE A 6 34.890 23.744 25.293 1.00 0.00 H +ATOM 106 C ILE A 6 32.878 25.380 29.825 1.00 0.00 C +ATOM 107 O ILE A 6 33.517 26.449 29.956 1.00 0.00 O +ATOM 108 N LEU A 7 32.756 24.548 30.823 1.00 0.00 N +ATOM 109 H LEU A 7 32.337 23.649 30.632 1.00 0.00 H +ATOM 110 CA LEU A 7 33.418 24.678 32.128 1.00 0.00 C +ATOM 111 HA LEU A 7 33.772 25.702 32.243 1.00 0.00 H +ATOM 112 CB LEU A 7 32.452 24.287 33.269 1.00 0.00 C +ATOM 113 HB2 LEU A 7 32.235 23.219 33.280 1.00 0.00 H +ATOM 114 HB3 LEU A 7 33.025 24.491 34.173 1.00 0.00 H +ATOM 115 CG LEU A 7 31.068 25.080 33.294 1.00 0.00 C +ATOM 116 HG LEU A 7 31.234 26.000 32.731 1.00 0.00 H +ATOM 117 CD1 LEU A 7 29.957 24.185 32.737 1.00 0.00 C +ATOM 118 HD11 LEU A 7 29.091 24.791 32.472 1.00 0.00 H +ATOM 119 HD12 LEU A 7 29.675 23.458 33.497 1.00 0.00 H +ATOM 120 HD13 LEU A 7 30.242 23.598 31.863 1.00 0.00 H +ATOM 121 CD2 LEU A 7 30.679 25.500 34.666 1.00 0.00 C +ATOM 122 HD21 LEU A 7 30.692 24.679 35.384 1.00 0.00 H +ATOM 123 HD22 LEU A 7 29.678 25.926 34.604 1.00 0.00 H +ATOM 124 HD23 LEU A 7 31.266 26.349 35.014 1.00 0.00 H +ATOM 125 C LEU A 7 34.704 23.832 31.982 1.00 0.00 C +ATOM 126 O LEU A 7 34.608 22.712 31.434 1.00 0.00 O +ATOM 127 N ASN A 8 35.741 24.355 32.566 1.00 0.00 N +ATOM 128 H ASN A 8 35.657 25.289 32.943 1.00 0.00 H +ATOM 129 CA ASN A 8 37.087 23.938 32.340 1.00 0.00 C +ATOM 130 HA ASN A 8 37.195 22.875 32.128 1.00 0.00 H +ATOM 131 CB ASN A 8 37.683 24.648 31.079 1.00 0.00 C +ATOM 132 HB2 ASN A 8 37.052 24.514 30.199 1.00 0.00 H +ATOM 133 HB3 ASN A 8 37.697 25.701 31.358 1.00 0.00 H +ATOM 134 CG ASN A 8 39.069 24.172 30.753 1.00 0.00 C +ATOM 135 OD1 ASN A 8 39.293 22.972 30.616 1.00 0.00 O +ATOM 136 ND2 ASN A 8 40.171 24.966 30.834 1.00 0.00 N +ATOM 137 HD21 ASN A 8 40.064 25.968 30.880 1.00 0.00 H +ATOM 138 HD22 ASN A 8 41.073 24.564 30.618 1.00 0.00 H +ATOM 139 C ASN A 8 37.929 24.262 33.602 1.00 0.00 C +ATOM 140 O ASN A 8 37.736 25.299 34.234 1.00 0.00 O +ATOM 141 N GLY A 9 38.893 23.411 33.937 1.00 0.00 N +ATOM 142 H GLY A 9 38.872 22.559 33.394 1.00 0.00 H +ATOM 143 CA GLY A 9 39.937 23.667 34.946 1.00 0.00 C +ATOM 144 HA2 GLY A 9 40.563 24.496 34.619 1.00 0.00 H +ATOM 145 HA3 GLY A 9 39.525 24.058 35.876 1.00 0.00 H +ATOM 146 C GLY A 9 40.820 22.504 35.210 1.00 0.00 C +ATOM 147 O GLY A 9 40.826 21.506 34.446 1.00 0.00 O +ATOM 148 N LYS A 10 41.477 22.473 36.356 1.00 0.00 N +ATOM 149 H LYS A 10 41.439 23.256 36.992 1.00 0.00 H +ATOM 150 CA LYS A 10 42.321 21.363 36.766 1.00 0.00 C +ATOM 151 HA LYS A 10 42.838 21.036 35.864 1.00 0.00 H +ATOM 152 CB LYS A 10 43.435 21.839 37.736 1.00 0.00 C +ATOM 153 HB2 LYS A 10 42.960 22.130 38.673 1.00 0.00 H +ATOM 154 HB3 LYS A 10 44.151 21.018 37.787 1.00 0.00 H +ATOM 155 CG LYS A 10 44.146 23.121 37.228 1.00 0.00 C +ATOM 156 HG2 LYS A 10 44.581 22.959 36.242 1.00 0.00 H +ATOM 157 HG3 LYS A 10 43.424 23.934 37.151 1.00 0.00 H +ATOM 158 CD LYS A 10 45.206 23.474 38.269 1.00 0.00 C +ATOM 159 HD2 LYS A 10 44.834 23.376 39.290 1.00 0.00 H +ATOM 160 HD3 LYS A 10 46.045 22.781 38.265 1.00 0.00 H +ATOM 161 CE LYS A 10 45.833 24.866 37.936 1.00 0.00 C +ATOM 162 HE2 LYS A 10 46.898 24.867 38.172 1.00 0.00 H +ATOM 163 HE3 LYS A 10 45.615 25.139 36.904 1.00 0.00 H +ATOM 164 NZ LYS A 10 45.314 25.885 38.915 1.00 0.00 N1+ +ATOM 165 HZ1 LYS A 10 44.318 26.049 38.885 1.00 0.00 H +ATOM 166 HZ2 LYS A 10 45.805 26.756 38.765 1.00 0.00 H +ATOM 167 HZ3 LYS A 10 45.434 25.694 39.899 1.00 0.00 H +ATOM 168 C LYS A 10 41.608 20.142 37.369 1.00 0.00 C +ATOM 169 O LYS A 10 42.136 19.017 37.432 1.00 0.00 O +ATOM 170 N THR A 11 40.316 20.407 37.709 1.00 0.00 N +ATOM 171 H THR A 11 40.018 21.373 37.739 1.00 0.00 H +ATOM 172 CA THR A 11 39.333 19.428 38.190 1.00 0.00 C +ATOM 173 HA THR A 11 39.627 18.439 37.841 1.00 0.00 H +ATOM 174 CB THR A 11 39.319 19.497 39.740 1.00 0.00 C +ATOM 175 HB THR A 11 38.538 18.809 40.063 1.00 0.00 H +ATOM 176 CG2 THR A 11 40.656 18.994 40.197 1.00 0.00 C +ATOM 177 HG21 THR A 11 40.954 17.991 39.896 1.00 0.00 H +ATOM 178 HG22 THR A 11 40.695 18.984 41.286 1.00 0.00 H +ATOM 179 HG23 THR A 11 41.453 19.662 39.869 1.00 0.00 H +ATOM 180 OG1 THR A 11 39.118 20.738 40.229 1.00 0.00 O +ATOM 181 HG1 THR A 11 39.321 20.728 41.168 1.00 0.00 H +ATOM 182 C THR A 11 37.937 19.704 37.750 1.00 0.00 C +ATOM 183 O THR A 11 37.180 18.744 37.592 1.00 0.00 O +ATOM 184 N LEU A 12 37.572 20.909 37.360 1.00 0.00 N +ATOM 185 H LEU A 12 38.100 21.745 37.569 1.00 0.00 H +ATOM 186 CA LEU A 12 36.262 21.294 36.760 1.00 0.00 C +ATOM 187 HA LEU A 12 35.427 20.887 37.329 1.00 0.00 H +ATOM 188 CB LEU A 12 36.169 22.873 36.785 1.00 0.00 C +ATOM 189 HB2 LEU A 12 36.531 23.238 37.746 1.00 0.00 H +ATOM 190 HB3 LEU A 12 36.859 23.268 36.041 1.00 0.00 H +ATOM 191 CG LEU A 12 34.824 23.483 36.357 1.00 0.00 C +ATOM 192 HG LEU A 12 34.479 23.028 35.428 1.00 0.00 H +ATOM 193 CD1 LEU A 12 33.867 23.321 37.477 1.00 0.00 C +ATOM 194 HD11 LEU A 12 32.997 23.877 37.126 1.00 0.00 H +ATOM 195 HD12 LEU A 12 34.304 23.691 38.404 1.00 0.00 H +ATOM 196 HD13 LEU A 12 33.594 22.265 37.503 1.00 0.00 H +ATOM 197 CD2 LEU A 12 34.926 25.052 36.181 1.00 0.00 C +ATOM 198 HD21 LEU A 12 35.334 25.560 37.054 1.00 0.00 H +ATOM 199 HD22 LEU A 12 33.926 25.442 35.997 1.00 0.00 H +ATOM 200 HD23 LEU A 12 35.555 25.355 35.344 1.00 0.00 H +ATOM 201 C LEU A 12 36.092 20.805 35.283 1.00 0.00 C +ATOM 202 O LEU A 12 36.941 21.102 34.441 1.00 0.00 O +ATOM 203 N LYS A 13 35.016 20.080 34.906 1.00 0.00 N +ATOM 204 H LYS A 13 34.391 19.697 35.602 1.00 0.00 H +ATOM 205 CA LYS A 13 34.642 19.704 33.571 1.00 0.00 C +ATOM 206 HA LYS A 13 35.063 20.421 32.866 1.00 0.00 H +ATOM 207 CB LYS A 13 35.034 18.226 33.244 1.00 0.00 C +ATOM 208 HB2 LYS A 13 34.497 17.579 33.938 1.00 0.00 H +ATOM 209 HB3 LYS A 13 34.849 17.922 32.214 1.00 0.00 H +ATOM 210 CG LYS A 13 36.515 17.923 33.472 1.00 0.00 C +ATOM 211 HG2 LYS A 13 37.162 18.658 32.994 1.00 0.00 H +ATOM 212 HG3 LYS A 13 36.701 17.768 34.535 1.00 0.00 H +ATOM 213 CD LYS A 13 36.804 16.487 32.994 1.00 0.00 C +ATOM 214 HD2 LYS A 13 36.157 15.747 33.465 1.00 0.00 H +ATOM 215 HD3 LYS A 13 36.456 16.506 31.962 1.00 0.00 H +ATOM 216 CE LYS A 13 38.264 16.163 32.997 1.00 0.00 C +ATOM 217 HE2 LYS A 13 38.741 16.732 32.199 1.00 0.00 H +ATOM 218 HE3 LYS A 13 38.686 16.424 33.967 1.00 0.00 H +ATOM 219 NZ LYS A 13 38.397 14.672 32.837 1.00 0.00 N1+ +ATOM 220 HZ1 LYS A 13 37.944 14.324 32.005 1.00 0.00 H +ATOM 221 HZ2 LYS A 13 37.888 14.239 33.595 1.00 0.00 H +ATOM 222 HZ3 LYS A 13 39.367 14.391 32.817 1.00 0.00 H +ATOM 223 C LYS A 13 33.119 19.875 33.400 1.00 0.00 C +ATOM 224 O LYS A 13 32.522 20.218 34.448 1.00 0.00 O +ATOM 225 N GLY A 14 32.541 19.929 32.182 1.00 0.00 N +ATOM 226 H GLY A 14 33.085 19.611 31.392 1.00 0.00 H +ATOM 227 CA GLY A 14 31.141 20.135 31.951 1.00 0.00 C +ATOM 228 HA2 GLY A 14 30.696 19.143 31.877 1.00 0.00 H +ATOM 229 HA3 GLY A 14 30.707 20.500 32.883 1.00 0.00 H +ATOM 230 C GLY A 14 30.726 21.030 30.803 1.00 0.00 C +ATOM 231 O GLY A 14 31.459 21.986 30.478 1.00 0.00 O +ATOM 232 N GLU A 15 29.602 20.661 30.175 1.00 0.00 N +ATOM 233 H GLU A 15 29.233 19.801 30.557 1.00 0.00 H +ATOM 234 CA GLU A 15 29.053 21.595 29.115 1.00 0.00 C +ATOM 235 HA GLU A 15 29.457 22.592 29.292 1.00 0.00 H +ATOM 236 CB GLU A 15 29.452 21.151 27.705 1.00 0.00 C +ATOM 237 HB2 GLU A 15 28.886 21.770 27.009 1.00 0.00 H +ATOM 238 HB3 GLU A 15 30.497 21.396 27.512 1.00 0.00 H +ATOM 239 CG GLU A 15 29.157 19.668 27.410 1.00 0.00 C +ATOM 240 HG2 GLU A 15 29.865 19.104 28.017 1.00 0.00 H +ATOM 241 HG3 GLU A 15 28.109 19.456 27.619 1.00 0.00 H +ATOM 242 CD GLU A 15 29.423 19.385 25.968 1.00 0.00 C +ATOM 243 OE1 GLU A 15 28.458 19.250 25.177 1.00 0.00 O1- +ATOM 244 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O1- +ATOM 245 C GLU A 15 27.563 21.843 29.353 1.00 0.00 C +ATOM 246 O GLU A 15 26.814 21.020 29.796 1.00 0.00 O +ATOM 247 N THR A 16 27.080 22.966 28.863 1.00 0.00 N +ATOM 248 H THR A 16 27.718 23.647 28.477 1.00 0.00 H +ATOM 249 CA THR A 16 25.618 23.342 28.987 1.00 0.00 C +ATOM 250 HA THR A 16 24.987 22.466 28.832 1.00 0.00 H +ATOM 251 CB THR A 16 25.300 23.755 30.463 1.00 0.00 C +ATOM 252 HB THR A 16 25.664 23.028 31.190 1.00 0.00 H +ATOM 253 CG2 THR A 16 26.079 25.029 30.851 1.00 0.00 C +ATOM 254 HG21 THR A 16 26.002 25.212 31.923 1.00 0.00 H +ATOM 255 HG22 THR A 16 25.827 25.999 30.420 1.00 0.00 H +ATOM 256 HG23 THR A 16 27.139 24.833 30.686 1.00 0.00 H +ATOM 257 OG1 THR A 16 23.919 23.870 30.591 1.00 0.00 O +ATOM 258 HG1 THR A 16 23.605 22.966 30.654 1.00 0.00 H +ATOM 259 C THR A 16 25.136 24.387 27.956 1.00 0.00 C +ATOM 260 O THR A 16 25.847 25.392 27.686 1.00 0.00 O +ATOM 261 N THR A 17 23.944 24.126 27.374 1.00 0.00 N +ATOM 262 H THR A 17 23.414 23.300 27.615 1.00 0.00 H +ATOM 263 CA THR A 17 23.341 25.088 26.418 1.00 0.00 C +ATOM 264 HA THR A 17 24.139 25.697 25.992 1.00 0.00 H +ATOM 265 CB THR A 17 22.634 24.399 25.250 1.00 0.00 C +ATOM 266 HB THR A 17 22.194 25.142 24.585 1.00 0.00 H +ATOM 267 CG2 THR A 17 23.534 23.466 24.406 1.00 0.00 C +ATOM 268 HG21 THR A 17 22.981 22.875 23.677 1.00 0.00 H +ATOM 269 HG22 THR A 17 24.016 22.789 25.112 1.00 0.00 H +ATOM 270 HG23 THR A 17 24.305 24.119 23.998 1.00 0.00 H +ATOM 271 OG1 THR A 17 21.618 23.516 25.740 1.00 0.00 O +ATOM 272 HG1 THR A 17 21.158 23.210 24.955 1.00 0.00 H +ATOM 273 C THR A 17 22.409 26.084 27.080 1.00 0.00 C +ATOM 274 O THR A 17 21.865 25.880 28.171 1.00 0.00 O +ATOM 275 N THR A 18 22.284 27.186 26.367 1.00 0.00 N +ATOM 276 H THR A 18 22.918 27.211 25.581 1.00 0.00 H +ATOM 277 CA THR A 18 21.341 28.346 26.665 1.00 0.00 C +ATOM 278 HA THR A 18 20.447 28.047 27.213 1.00 0.00 H +ATOM 279 CB THR A 18 21.968 29.424 27.606 1.00 0.00 C +ATOM 280 HB THR A 18 22.926 29.800 27.251 1.00 0.00 H +ATOM 281 CG2 THR A 18 20.959 30.565 27.747 1.00 0.00 C +ATOM 282 HG21 THR A 18 21.177 31.232 28.581 1.00 0.00 H +ATOM 283 HG22 THR A 18 19.932 30.214 27.838 1.00 0.00 H +ATOM 284 HG23 THR A 18 21.057 31.149 26.831 1.00 0.00 H +ATOM 285 OG1 THR A 18 21.983 28.974 29.051 1.00 0.00 O +ATOM 286 HG1 THR A 18 22.866 29.123 29.400 1.00 0.00 H +ATOM 287 C THR A 18 20.829 28.956 25.354 1.00 0.00 C +ATOM 288 O THR A 18 21.553 29.458 24.528 1.00 0.00 O +ATOM 289 N GLU A 19 19.542 28.872 25.083 1.00 0.00 N +ATOM 290 H GLU A 19 18.919 28.579 25.823 1.00 0.00 H +ATOM 291 CA GLU A 19 18.932 29.576 23.987 1.00 0.00 C +ATOM 292 HA GLU A 19 19.679 29.508 23.197 1.00 0.00 H +ATOM 293 CB GLU A 19 17.686 28.785 23.627 1.00 0.00 C +ATOM 294 HB2 GLU A 19 17.899 27.722 23.514 1.00 0.00 H +ATOM 295 HB3 GLU A 19 16.998 28.842 24.471 1.00 0.00 H +ATOM 296 CG GLU A 19 16.852 29.284 22.477 1.00 0.00 C +ATOM 297 HG2 GLU A 19 16.246 28.447 22.128 1.00 0.00 H +ATOM 298 HG3 GLU A 19 16.133 30.057 22.748 1.00 0.00 H +ATOM 299 CD GLU A 19 17.736 29.731 21.281 1.00 0.00 C +ATOM 300 OE1 GLU A 19 18.363 28.800 20.679 1.00 0.00 O1- +ATOM 301 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O1- +ATOM 302 C GLU A 19 18.631 31.049 24.311 1.00 0.00 C +ATOM 303 O GLU A 19 17.951 31.336 25.240 1.00 0.00 O +ATOM 304 N ALA A 20 19.109 32.052 23.609 1.00 0.00 N +ATOM 305 H ALA A 20 19.659 31.766 22.810 1.00 0.00 H +ATOM 306 CA ALA A 20 18.962 33.505 23.885 1.00 0.00 C +ATOM 307 HA ALA A 20 17.980 33.742 24.295 1.00 0.00 H +ATOM 308 CB ALA A 20 19.978 33.979 24.961 1.00 0.00 C +ATOM 309 HB1 ALA A 20 19.807 35.026 25.214 1.00 0.00 H +ATOM 310 HB2 ALA A 20 20.983 33.923 24.544 1.00 0.00 H +ATOM 311 HB3 ALA A 20 19.800 33.404 25.869 1.00 0.00 H +ATOM 312 C ALA A 20 19.121 34.352 22.595 1.00 0.00 C +ATOM 313 O ALA A 20 19.565 33.867 21.541 1.00 0.00 O +ATOM 314 N VAL A 21 18.819 35.698 22.666 1.00 0.00 N +ATOM 315 H VAL A 21 18.466 36.007 23.561 1.00 0.00 H +ATOM 316 CA VAL A 21 18.727 36.607 21.505 1.00 0.00 C +ATOM 317 HA VAL A 21 18.554 36.039 20.592 1.00 0.00 H +ATOM 318 CB VAL A 21 17.437 37.464 21.780 1.00 0.00 C +ATOM 319 HB VAL A 21 17.477 38.130 22.642 1.00 0.00 H +ATOM 320 CG1 VAL A 21 17.072 38.379 20.673 1.00 0.00 C +ATOM 321 HG11 VAL A 21 16.991 37.805 19.750 1.00 0.00 H +ATOM 322 HG12 VAL A 21 17.685 39.269 20.533 1.00 0.00 H +ATOM 323 HG13 VAL A 21 16.081 38.787 20.874 1.00 0.00 H +ATOM 324 CG2 VAL A 21 16.251 36.536 21.920 1.00 0.00 C +ATOM 325 HG21 VAL A 21 15.333 37.033 21.605 1.00 0.00 H +ATOM 326 HG22 VAL A 21 16.128 36.219 22.956 1.00 0.00 H +ATOM 327 HG23 VAL A 21 16.477 35.681 21.284 1.00 0.00 H +ATOM 328 C VAL A 21 19.976 37.521 21.405 1.00 0.00 C +ATOM 329 O VAL A 21 20.295 38.022 20.306 1.00 0.00 O +ATOM 330 N ASP A 22 20.728 37.651 22.457 1.00 0.00 N +ATOM 331 H ASP A 22 20.460 37.104 23.262 1.00 0.00 H +ATOM 332 CA ASP A 22 21.920 38.517 22.561 1.00 0.00 C +ATOM 333 HA ASP A 22 22.218 38.721 21.532 1.00 0.00 H +ATOM 334 CB ASP A 22 21.483 39.701 23.350 1.00 0.00 C +ATOM 335 HB2 ASP A 22 20.632 40.156 22.843 1.00 0.00 H +ATOM 336 HB3 ASP A 22 21.133 39.421 24.344 1.00 0.00 H +ATOM 337 CG ASP A 22 22.576 40.746 23.590 1.00 0.00 C +ATOM 338 OD1 ASP A 22 23.681 40.588 23.043 1.00 0.00 O1- +ATOM 339 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O1- +ATOM 340 C ASP A 22 23.019 37.703 23.294 1.00 0.00 C +ATOM 341 O ASP A 22 22.839 37.184 24.412 1.00 0.00 O +ATOM 342 N ALA A 23 24.210 37.649 22.694 1.00 0.00 N +ATOM 343 H ALA A 23 24.358 38.065 21.786 1.00 0.00 H +ATOM 344 CA ALA A 23 25.493 37.172 23.215 1.00 0.00 C +ATOM 345 HA ALA A 23 25.371 36.089 23.221 1.00 0.00 H +ATOM 346 CB ALA A 23 26.701 37.486 22.326 1.00 0.00 C +ATOM 347 HB1 ALA A 23 26.446 37.309 21.280 1.00 0.00 H +ATOM 348 HB2 ALA A 23 27.379 36.708 22.676 1.00 0.00 H +ATOM 349 HB3 ALA A 23 27.091 38.494 22.468 1.00 0.00 H +ATOM 350 C ALA A 23 25.748 37.757 24.642 1.00 0.00 C +ATOM 351 O ALA A 23 26.091 36.953 25.518 1.00 0.00 O +ATOM 352 N ALA A 24 25.564 39.050 24.846 1.00 0.00 N +ATOM 353 H ALA A 24 25.214 39.674 24.133 1.00 0.00 H +ATOM 354 CA ALA A 24 25.745 39.687 26.153 1.00 0.00 C +ATOM 355 HA ALA A 24 26.761 39.419 26.445 1.00 0.00 H +ATOM 356 CB ALA A 24 25.490 41.189 25.938 1.00 0.00 C +ATOM 357 HB1 ALA A 24 26.247 41.676 25.325 1.00 0.00 H +ATOM 358 HB2 ALA A 24 25.633 41.729 26.874 1.00 0.00 H +ATOM 359 HB3 ALA A 24 24.561 41.467 25.440 1.00 0.00 H +ATOM 360 C ALA A 24 24.796 39.101 27.137 1.00 0.00 C +ATOM 361 O ALA A 24 25.116 38.975 28.329 1.00 0.00 O +ATOM 362 N THR A 25 23.577 38.659 26.736 1.00 0.00 N +ATOM 363 H THR A 25 23.398 38.681 25.743 1.00 0.00 H +ATOM 364 CA THR A 25 22.587 38.094 27.680 1.00 0.00 C +ATOM 365 HA THR A 25 22.755 38.495 28.681 1.00 0.00 H +ATOM 366 CB THR A 25 21.196 38.549 27.262 1.00 0.00 C +ATOM 367 HB THR A 25 20.797 37.883 26.497 1.00 0.00 H +ATOM 368 CG2 THR A 25 20.246 38.369 28.438 1.00 0.00 C +ATOM 369 HG21 THR A 25 20.203 37.329 28.763 1.00 0.00 H +ATOM 370 HG22 THR A 25 19.255 38.740 28.176 1.00 0.00 H +ATOM 371 HG23 THR A 25 20.574 38.977 29.280 1.00 0.00 H +ATOM 372 OG1 THR A 25 21.199 39.931 27.030 1.00 0.00 O +ATOM 373 HG1 THR A 25 20.293 40.156 26.807 1.00 0.00 H +ATOM 374 C THR A 25 22.788 36.618 27.928 1.00 0.00 C +ATOM 375 O THR A 25 22.618 36.164 29.050 1.00 0.00 O +ATOM 376 N ALA A 26 23.216 35.854 26.929 1.00 0.00 N +ATOM 377 H ALA A 26 23.315 36.208 25.988 1.00 0.00 H +ATOM 378 CA ALA A 26 23.652 34.513 27.159 1.00 0.00 C +ATOM 379 HA ALA A 26 22.781 33.940 27.476 1.00 0.00 H +ATOM 380 CB ALA A 26 24.062 33.913 25.734 1.00 0.00 C +ATOM 381 HB1 ALA A 26 23.120 33.732 25.215 1.00 0.00 H +ATOM 382 HB2 ALA A 26 24.695 33.029 25.804 1.00 0.00 H +ATOM 383 HB3 ALA A 26 24.715 34.613 25.211 1.00 0.00 H +ATOM 384 C ALA A 26 24.856 34.523 28.062 1.00 0.00 C +ATOM 385 O ALA A 26 24.889 33.745 28.985 1.00 0.00 O +ATOM 386 N GLU A 27 25.749 35.500 28.027 1.00 0.00 N +ATOM 387 H GLU A 27 25.940 35.933 27.135 1.00 0.00 H +ATOM 388 CA GLU A 27 26.712 35.671 29.037 1.00 0.00 C +ATOM 389 HA GLU A 27 27.306 34.757 29.097 1.00 0.00 H +ATOM 390 CB GLU A 27 27.684 36.833 28.605 1.00 0.00 C +ATOM 391 HB2 GLU A 27 28.270 36.561 27.728 1.00 0.00 H +ATOM 392 HB3 GLU A 27 27.178 37.773 28.387 1.00 0.00 H +ATOM 393 CG GLU A 27 28.742 37.165 29.664 1.00 0.00 C +ATOM 394 HG2 GLU A 27 28.193 37.537 30.529 1.00 0.00 H +ATOM 395 HG3 GLU A 27 29.267 36.244 29.914 1.00 0.00 H +ATOM 396 CD GLU A 27 29.887 38.242 29.269 1.00 0.00 C +ATOM 397 OE1 GLU A 27 31.108 37.827 29.164 1.00 0.00 O1- +ATOM 398 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O1- +ATOM 399 C GLU A 27 26.099 35.742 30.450 1.00 0.00 C +ATOM 400 O GLU A 27 26.553 35.162 31.414 1.00 0.00 O +ATOM 401 N LYS A 28 25.124 36.609 30.604 1.00 0.00 N +ATOM 402 H LYS A 28 24.710 37.106 29.827 1.00 0.00 H +ATOM 403 CA LYS A 28 24.538 36.947 31.950 1.00 0.00 C +ATOM 404 HA LYS A 28 25.324 37.300 32.618 1.00 0.00 H +ATOM 405 CB LYS A 28 23.559 38.052 31.728 1.00 0.00 C +ATOM 406 HB2 LYS A 28 24.096 38.943 31.403 1.00 0.00 H +ATOM 407 HB3 LYS A 28 22.761 37.811 31.025 1.00 0.00 H +ATOM 408 CG LYS A 28 22.885 38.401 33.150 1.00 0.00 C +ATOM 409 HG2 LYS A 28 22.343 37.542 33.545 1.00 0.00 H +ATOM 410 HG3 LYS A 28 23.638 38.698 33.879 1.00 0.00 H +ATOM 411 CD LYS A 28 21.826 39.579 33.063 1.00 0.00 C +ATOM 412 HD2 LYS A 28 20.930 39.146 32.616 1.00 0.00 H +ATOM 413 HD3 LYS A 28 21.656 39.989 34.058 1.00 0.00 H +ATOM 414 CE LYS A 28 22.359 40.850 32.267 1.00 0.00 C +ATOM 415 HE2 LYS A 28 23.432 40.899 32.449 1.00 0.00 H +ATOM 416 HE3 LYS A 28 22.199 40.756 31.193 1.00 0.00 H +ATOM 417 NZ LYS A 28 21.521 42.013 32.715 1.00 0.00 N1+ +ATOM 418 HZ1 LYS A 28 21.696 42.294 33.670 1.00 0.00 H +ATOM 419 HZ2 LYS A 28 20.541 41.777 32.653 1.00 0.00 H +ATOM 420 HZ3 LYS A 28 21.651 42.827 32.131 1.00 0.00 H +ATOM 421 C LYS A 28 23.866 35.778 32.535 1.00 0.00 C +ATOM 422 O LYS A 28 23.994 35.665 33.742 1.00 0.00 O +ATOM 423 N VAL A 29 23.329 34.885 31.712 1.00 0.00 N +ATOM 424 H VAL A 29 23.229 35.111 30.733 1.00 0.00 H +ATOM 425 CA VAL A 29 22.736 33.650 32.097 1.00 0.00 C +ATOM 426 HA VAL A 29 21.999 33.879 32.866 1.00 0.00 H +ATOM 427 CB VAL A 29 21.735 33.166 30.962 1.00 0.00 C +ATOM 428 HB VAL A 29 22.375 32.951 30.106 1.00 0.00 H +ATOM 429 CG1 VAL A 29 21.139 31.783 31.445 1.00 0.00 C +ATOM 430 HG11 VAL A 29 20.592 31.413 30.579 1.00 0.00 H +ATOM 431 HG12 VAL A 29 20.575 31.908 32.370 1.00 0.00 H +ATOM 432 HG13 VAL A 29 21.993 31.113 31.534 1.00 0.00 H +ATOM 433 CG2 VAL A 29 20.482 33.992 30.547 1.00 0.00 C +ATOM 434 HG21 VAL A 29 19.966 33.618 29.662 1.00 0.00 H +ATOM 435 HG22 VAL A 29 20.739 35.019 30.286 1.00 0.00 H +ATOM 436 HG23 VAL A 29 19.838 34.110 31.419 1.00 0.00 H +ATOM 437 C VAL A 29 23.781 32.642 32.484 1.00 0.00 C +ATOM 438 O VAL A 29 23.604 31.876 33.462 1.00 0.00 O +ATOM 439 N PHE A 30 24.962 32.641 31.758 1.00 0.00 N +ATOM 440 H PHE A 30 24.997 33.287 30.981 1.00 0.00 H +ATOM 441 CA PHE A 30 26.112 31.701 32.033 1.00 0.00 C +ATOM 442 HA PHE A 30 25.692 30.753 32.371 1.00 0.00 H +ATOM 443 CB PHE A 30 26.901 31.582 30.713 1.00 0.00 C +ATOM 444 HB2 PHE A 30 26.966 32.537 30.191 1.00 0.00 H +ATOM 445 HB3 PHE A 30 27.928 31.266 30.888 1.00 0.00 H +ATOM 446 CG PHE A 30 26.348 30.600 29.656 1.00 0.00 C +ATOM 447 CD1 PHE A 30 25.751 29.296 29.878 1.00 0.00 C +ATOM 448 HD1 PHE A 30 25.705 28.943 30.897 1.00 0.00 H +ATOM 449 CE1 PHE A 30 25.345 28.377 28.817 1.00 0.00 C +ATOM 450 HE1 PHE A 30 24.810 27.464 29.039 1.00 0.00 H +ATOM 451 CZ PHE A 30 25.534 28.840 27.515 1.00 0.00 C +ATOM 452 HZ PHE A 30 25.196 28.267 26.666 1.00 0.00 H +ATOM 453 CE2 PHE A 30 26.096 30.099 27.271 1.00 0.00 C +ATOM 454 HE2 PHE A 30 26.212 30.319 26.219 1.00 0.00 H +ATOM 455 CD2 PHE A 30 26.533 30.924 28.297 1.00 0.00 C +ATOM 456 HD2 PHE A 30 27.135 31.778 28.029 1.00 0.00 H +ATOM 457 C PHE A 30 26.988 32.189 33.246 1.00 0.00 C +ATOM 458 O PHE A 30 27.609 31.344 33.905 1.00 0.00 O +ATOM 459 N LYS A 31 27.038 33.446 33.540 1.00 0.00 N +ATOM 460 H LYS A 31 26.710 34.105 32.849 1.00 0.00 H +ATOM 461 CA LYS A 31 27.405 34.022 34.854 1.00 0.00 C +ATOM 462 HA LYS A 31 28.437 33.764 35.092 1.00 0.00 H +ATOM 463 CB LYS A 31 27.274 35.599 34.858 1.00 0.00 C +ATOM 464 HB2 LYS A 31 26.242 35.714 34.527 1.00 0.00 H +ATOM 465 HB3 LYS A 31 27.292 36.098 35.827 1.00 0.00 H +ATOM 466 CG LYS A 31 28.378 36.275 33.919 1.00 0.00 C +ATOM 467 HG2 LYS A 31 28.522 35.710 32.997 1.00 0.00 H +ATOM 468 HG3 LYS A 31 27.926 37.229 33.649 1.00 0.00 H +ATOM 469 CD LYS A 31 29.823 36.487 34.439 1.00 0.00 C +ATOM 470 HD2 LYS A 31 29.755 36.977 35.411 1.00 0.00 H +ATOM 471 HD3 LYS A 31 30.132 35.472 34.684 1.00 0.00 H +ATOM 472 CE LYS A 31 30.777 37.150 33.394 1.00 0.00 C +ATOM 473 HE2 LYS A 31 30.633 36.630 32.447 1.00 0.00 H +ATOM 474 HE3 LYS A 31 30.436 38.158 33.158 1.00 0.00 H +ATOM 475 NZ LYS A 31 32.138 37.121 33.926 1.00 0.00 N1+ +ATOM 476 HZ1 LYS A 31 32.272 37.458 34.869 1.00 0.00 H +ATOM 477 HZ2 LYS A 31 32.676 37.777 33.376 1.00 0.00 H +ATOM 478 HZ3 LYS A 31 32.555 36.210 33.805 1.00 0.00 H +ATOM 479 C LYS A 31 26.516 33.562 35.983 1.00 0.00 C +ATOM 480 O LYS A 31 27.018 32.993 36.943 1.00 0.00 O +ATOM 481 N GLN A 32 25.185 33.745 35.953 1.00 0.00 N +ATOM 482 H GLN A 32 24.737 34.194 35.166 1.00 0.00 H +ATOM 483 CA GLN A 32 24.365 33.197 37.027 1.00 0.00 C +ATOM 484 HA GLN A 32 24.679 33.822 37.863 1.00 0.00 H +ATOM 485 CB GLN A 32 22.891 33.427 36.688 1.00 0.00 C +ATOM 486 HB2 GLN A 32 22.845 33.366 35.601 1.00 0.00 H +ATOM 487 HB3 GLN A 32 22.285 32.685 37.209 1.00 0.00 H +ATOM 488 CG GLN A 32 22.280 34.840 37.028 1.00 0.00 C +ATOM 489 HG2 GLN A 32 22.039 34.881 38.090 1.00 0.00 H +ATOM 490 HG3 GLN A 32 22.899 35.710 36.807 1.00 0.00 H +ATOM 491 CD GLN A 32 20.958 35.124 36.195 1.00 0.00 C +ATOM 492 OE1 GLN A 32 19.883 34.823 36.738 1.00 0.00 O +ATOM 493 NE2 GLN A 32 20.988 35.530 34.974 1.00 0.00 N +ATOM 494 HE21 GLN A 32 21.902 35.787 34.628 1.00 0.00 H +ATOM 495 HE22 GLN A 32 20.177 35.714 34.400 1.00 0.00 H +ATOM 496 C GLN A 32 24.598 31.707 37.232 1.00 0.00 C +ATOM 497 O GLN A 32 24.794 31.293 38.384 1.00 0.00 O +ATOM 498 N TYR A 33 24.530 30.875 36.142 1.00 0.00 N +ATOM 499 H TYR A 33 24.587 31.274 35.216 1.00 0.00 H +ATOM 500 CA TYR A 33 24.722 29.459 36.217 1.00 0.00 C +ATOM 501 HA TYR A 33 23.881 29.042 36.772 1.00 0.00 H +ATOM 502 CB TYR A 33 24.622 28.848 34.842 1.00 0.00 C +ATOM 503 HB2 TYR A 33 23.621 29.006 34.442 1.00 0.00 H +ATOM 504 HB3 TYR A 33 25.353 29.388 34.240 1.00 0.00 H +ATOM 505 CG TYR A 33 24.877 27.304 34.704 1.00 0.00 C +ATOM 506 CD1 TYR A 33 23.808 26.383 34.938 1.00 0.00 C +ATOM 507 HD1 TYR A 33 22.814 26.754 35.140 1.00 0.00 H +ATOM 508 CE1 TYR A 33 24.054 24.991 35.075 1.00 0.00 C +ATOM 509 HE1 TYR A 33 23.300 24.251 35.300 1.00 0.00 H +ATOM 510 CZ TYR A 33 25.399 24.562 34.934 1.00 0.00 C +ATOM 511 OH TYR A 33 25.658 23.212 34.983 1.00 0.00 O +ATOM 512 HH TYR A 33 26.608 23.080 35.030 1.00 0.00 H +ATOM 513 CE2 TYR A 33 26.410 25.459 34.723 1.00 0.00 C +ATOM 514 HE2 TYR A 33 27.443 25.157 34.630 1.00 0.00 H +ATOM 515 CD2 TYR A 33 26.146 26.818 34.602 1.00 0.00 C +ATOM 516 HD2 TYR A 33 26.992 27.469 34.435 1.00 0.00 H +ATOM 517 C TYR A 33 26.078 29.155 36.854 1.00 0.00 C +ATOM 518 O TYR A 33 26.179 28.186 37.566 1.00 0.00 O +ATOM 519 N ALA A 34 27.159 29.788 36.508 1.00 0.00 N +ATOM 520 H ALA A 34 26.997 30.563 35.881 1.00 0.00 H +ATOM 521 CA ALA A 34 28.473 29.535 37.100 1.00 0.00 C +ATOM 522 HA ALA A 34 28.717 28.476 37.023 1.00 0.00 H +ATOM 523 CB ALA A 34 29.651 30.265 36.402 1.00 0.00 C +ATOM 524 HB1 ALA A 34 30.577 29.813 36.757 1.00 0.00 H +ATOM 525 HB2 ALA A 34 29.619 31.296 36.752 1.00 0.00 H +ATOM 526 HB3 ALA A 34 29.681 30.159 35.317 1.00 0.00 H +ATOM 527 C ALA A 34 28.508 29.835 38.614 1.00 0.00 C +ATOM 528 O ALA A 34 29.097 29.077 39.389 1.00 0.00 O +ATOM 529 N ASN A 35 27.814 30.864 39.024 1.00 0.00 N +ATOM 530 H ASN A 35 27.594 31.535 38.301 1.00 0.00 H +ATOM 531 CA ASN A 35 27.743 31.252 40.445 1.00 0.00 C +ATOM 532 HA ASN A 35 28.713 31.168 40.935 1.00 0.00 H +ATOM 533 CB ASN A 35 27.254 32.684 40.541 1.00 0.00 C +ATOM 534 HB2 ASN A 35 27.798 33.361 39.883 1.00 0.00 H +ATOM 535 HB3 ASN A 35 26.192 32.727 40.300 1.00 0.00 H +ATOM 536 CG ASN A 35 27.326 33.169 41.947 1.00 0.00 C +ATOM 537 OD1 ASN A 35 26.493 32.743 42.763 1.00 0.00 O +ATOM 538 ND2 ASN A 35 28.099 34.183 42.223 1.00 0.00 N +ATOM 539 HD21 ASN A 35 28.867 34.350 41.589 1.00 0.00 H +ATOM 540 HD22 ASN A 35 28.276 34.397 43.193 1.00 0.00 H +ATOM 541 C ASN A 35 26.833 30.200 41.127 1.00 0.00 C +ATOM 542 O ASN A 35 27.114 29.686 42.238 1.00 0.00 O +ATOM 543 N ASP A 36 25.819 29.616 40.395 1.00 0.00 N +ATOM 544 H ASP A 36 25.608 30.144 39.560 1.00 0.00 H +ATOM 545 CA ASP A 36 25.004 28.401 40.867 1.00 0.00 C +ATOM 546 HA ASP A 36 24.491 28.819 41.733 1.00 0.00 H +ATOM 547 CB ASP A 36 23.819 28.175 39.948 1.00 0.00 C +ATOM 548 HB2 ASP A 36 23.379 29.117 39.623 1.00 0.00 H +ATOM 549 HB3 ASP A 36 24.279 27.586 39.154 1.00 0.00 H +ATOM 550 CG ASP A 36 22.720 27.350 40.470 1.00 0.00 C +ATOM 551 OD1 ASP A 36 22.214 26.485 39.714 1.00 0.00 O1- +ATOM 552 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O1- +ATOM 553 C ASP A 36 25.793 27.113 41.244 1.00 0.00 C +ATOM 554 O ASP A 36 25.357 26.391 42.112 1.00 0.00 O +ATOM 555 N ASN A 37 26.991 27.006 40.666 1.00 0.00 N +ATOM 556 H ASN A 37 27.306 27.779 40.098 1.00 0.00 H +ATOM 557 CA ASN A 37 27.829 25.814 40.636 1.00 0.00 C +ATOM 558 HA ASN A 37 27.378 25.130 41.354 1.00 0.00 H +ATOM 559 CB ASN A 37 27.873 25.281 39.195 1.00 0.00 C +ATOM 560 HB2 ASN A 37 27.936 26.106 38.487 1.00 0.00 H +ATOM 561 HB3 ASN A 37 28.702 24.579 39.101 1.00 0.00 H +ATOM 562 CG ASN A 37 26.652 24.492 38.842 1.00 0.00 C +ATOM 563 OD1 ASN A 37 26.432 23.357 39.282 1.00 0.00 O +ATOM 564 ND2 ASN A 37 25.706 25.057 38.177 1.00 0.00 N +ATOM 565 HD21 ASN A 37 25.804 26.050 38.016 1.00 0.00 H +ATOM 566 HD22 ASN A 37 24.895 24.502 37.947 1.00 0.00 H +ATOM 567 C ASN A 37 29.196 26.053 41.261 1.00 0.00 C +ATOM 568 O ASN A 37 30.064 25.171 41.182 1.00 0.00 O +ATOM 569 N GLY A 38 29.358 27.176 42.012 1.00 0.00 N +ATOM 570 H GLY A 38 28.556 27.765 42.189 1.00 0.00 H +ATOM 571 CA GLY A 38 30.637 27.460 42.681 1.00 0.00 C +ATOM 572 HA2 GLY A 38 30.444 28.296 43.354 1.00 0.00 H +ATOM 573 HA3 GLY A 38 30.900 26.655 43.368 1.00 0.00 H +ATOM 574 C GLY A 38 31.894 27.774 41.785 1.00 0.00 C +ATOM 575 O GLY A 38 33.027 27.429 42.124 1.00 0.00 O +ATOM 576 N VAL A 39 31.731 28.287 40.579 1.00 0.00 N +ATOM 577 H VAL A 39 30.794 28.624 40.408 1.00 0.00 H +ATOM 578 CA VAL A 39 32.664 28.449 39.403 1.00 0.00 C +ATOM 579 HA VAL A 39 33.598 27.911 39.570 1.00 0.00 H +ATOM 580 CB VAL A 39 32.015 27.778 38.179 1.00 0.00 C +ATOM 581 HB VAL A 39 31.005 28.158 38.027 1.00 0.00 H +ATOM 582 CG1 VAL A 39 32.989 28.121 37.014 1.00 0.00 C +ATOM 583 HG11 VAL A 39 32.636 27.519 36.176 1.00 0.00 H +ATOM 584 HG12 VAL A 39 34.019 27.963 37.334 1.00 0.00 H +ATOM 585 HG13 VAL A 39 32.869 29.117 36.588 1.00 0.00 H +ATOM 586 CG2 VAL A 39 31.943 26.274 38.437 1.00 0.00 C +ATOM 587 HG21 VAL A 39 31.540 25.729 37.583 1.00 0.00 H +ATOM 588 HG22 VAL A 39 31.356 26.086 39.337 1.00 0.00 H +ATOM 589 HG23 VAL A 39 32.907 25.863 38.738 1.00 0.00 H +ATOM 590 C VAL A 39 33.029 29.909 39.235 1.00 0.00 C +ATOM 591 O VAL A 39 32.186 30.683 38.757 1.00 0.00 O +ATOM 592 N ASP A 40 34.268 30.281 39.558 1.00 0.00 N +ATOM 593 H ASP A 40 34.838 29.543 39.947 1.00 0.00 H +ATOM 594 CA ASP A 40 34.875 31.551 39.096 1.00 0.00 C +ATOM 595 HA ASP A 40 34.143 32.078 38.487 1.00 0.00 H +ATOM 596 CB ASP A 40 35.183 32.418 40.345 1.00 0.00 C +ATOM 597 HB2 ASP A 40 34.184 32.657 40.710 1.00 0.00 H +ATOM 598 HB3 ASP A 40 35.707 31.788 41.065 1.00 0.00 H +ATOM 599 CG ASP A 40 35.879 33.683 40.009 1.00 0.00 C +ATOM 600 OD1 ASP A 40 35.393 34.410 39.076 1.00 0.00 O1- +ATOM 601 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O1- +ATOM 602 C ASP A 40 36.062 31.169 38.238 1.00 0.00 C +ATOM 603 O ASP A 40 36.850 30.275 38.630 1.00 0.00 O +ATOM 604 N GLY A 41 36.172 31.751 37.102 1.00 0.00 N +ATOM 605 H GLY A 41 35.443 32.408 36.858 1.00 0.00 H +ATOM 606 CA GLY A 41 37.214 31.484 36.189 1.00 0.00 C +ATOM 607 HA2 GLY A 41 38.072 31.014 36.670 1.00 0.00 H +ATOM 608 HA3 GLY A 41 36.761 30.672 35.620 1.00 0.00 H +ATOM 609 C GLY A 41 37.623 32.709 35.379 1.00 0.00 C +ATOM 610 O GLY A 41 37.288 33.862 35.686 1.00 0.00 O +ATOM 611 N GLU A 42 38.354 32.422 34.316 1.00 0.00 N +ATOM 612 H GLU A 42 38.789 31.512 34.368 1.00 0.00 H +ATOM 613 CA GLU A 42 38.603 33.310 33.228 1.00 0.00 C +ATOM 614 HA GLU A 42 38.329 34.318 33.541 1.00 0.00 H +ATOM 615 CB GLU A 42 40.158 33.294 33.040 1.00 0.00 C +ATOM 616 HB2 GLU A 42 40.656 33.398 34.004 1.00 0.00 H +ATOM 617 HB3 GLU A 42 40.417 32.326 32.611 1.00 0.00 H +ATOM 618 CG GLU A 42 40.673 34.328 32.046 1.00 0.00 C +ATOM 619 HG2 GLU A 42 41.606 34.015 31.580 1.00 0.00 H +ATOM 620 HG3 GLU A 42 39.970 34.501 31.231 1.00 0.00 H +ATOM 621 CD GLU A 42 41.014 35.613 32.804 1.00 0.00 C +ATOM 622 OE1 GLU A 42 41.944 35.693 33.644 1.00 0.00 O1- +ATOM 623 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O1- +ATOM 624 C GLU A 42 37.780 33.033 32.033 1.00 0.00 C +ATOM 625 O GLU A 42 37.577 31.870 31.690 1.00 0.00 O +ATOM 626 N TRP A 43 37.228 34.069 31.412 1.00 0.00 N +ATOM 627 H TRP A 43 37.423 35.035 31.634 1.00 0.00 H +ATOM 628 CA TRP A 43 36.233 33.951 30.354 1.00 0.00 C +ATOM 629 HA TRP A 43 35.850 32.931 30.348 1.00 0.00 H +ATOM 630 CB TRP A 43 34.984 34.889 30.616 1.00 0.00 C +ATOM 631 HB2 TRP A 43 35.436 35.868 30.771 1.00 0.00 H +ATOM 632 HB3 TRP A 43 34.427 34.918 29.679 1.00 0.00 H +ATOM 633 CG TRP A 43 34.115 34.536 31.838 1.00 0.00 C +ATOM 634 CD1 TRP A 43 34.428 34.708 33.154 1.00 0.00 C +ATOM 635 HD1 TRP A 43 35.387 35.052 33.511 1.00 0.00 H +ATOM 636 NE1 TRP A 43 33.399 34.110 33.877 1.00 0.00 N +ATOM 637 HE1 TRP A 43 33.511 34.066 34.880 1.00 0.00 H +ATOM 638 CE2 TRP A 43 32.444 33.463 33.073 1.00 0.00 C +ATOM 639 CZ2 TRP A 43 31.248 32.745 33.296 1.00 0.00 C +ATOM 640 HZ2 TRP A 43 31.007 32.429 34.301 1.00 0.00 H +ATOM 641 CH2 TRP A 43 30.575 32.194 32.199 1.00 0.00 C +ATOM 642 HH2 TRP A 43 29.740 31.527 32.355 1.00 0.00 H +ATOM 643 CZ3 TRP A 43 30.988 32.541 30.909 1.00 0.00 C +ATOM 644 HZ3 TRP A 43 30.412 32.236 30.047 1.00 0.00 H +ATOM 645 CE3 TRP A 43 32.109 33.327 30.682 1.00 0.00 C +ATOM 646 HE3 TRP A 43 32.397 33.679 29.703 1.00 0.00 H +ATOM 647 CD2 TRP A 43 32.870 33.817 31.765 1.00 0.00 C +ATOM 648 C TRP A 43 36.910 34.235 29.034 1.00 0.00 C +ATOM 649 O TRP A 43 37.660 35.202 28.823 1.00 0.00 O +ATOM 650 N THR A 44 36.468 33.398 28.113 1.00 0.00 N +ATOM 651 H THR A 44 35.919 32.590 28.367 1.00 0.00 H +ATOM 652 CA THR A 44 36.627 33.526 26.668 1.00 0.00 C +ATOM 653 HA THR A 44 36.825 34.580 26.474 1.00 0.00 H +ATOM 654 CB THR A 44 37.813 32.794 26.062 1.00 0.00 C +ATOM 655 HB THR A 44 37.695 32.789 24.978 1.00 0.00 H +ATOM 656 CG2 THR A 44 39.142 33.411 26.470 1.00 0.00 C +ATOM 657 HG21 THR A 44 39.971 32.814 26.090 1.00 0.00 H +ATOM 658 HG22 THR A 44 39.277 33.395 27.552 1.00 0.00 H +ATOM 659 HG23 THR A 44 39.360 34.408 26.088 1.00 0.00 H +ATOM 660 OG1 THR A 44 37.854 31.507 26.604 1.00 0.00 O +ATOM 661 HG1 THR A 44 37.629 30.907 25.889 1.00 0.00 H +ATOM 662 C THR A 44 35.267 33.295 26.005 1.00 0.00 C +ATOM 663 O THR A 44 34.480 32.577 26.444 1.00 0.00 O +ATOM 664 N TYR A 45 35.137 33.919 24.848 1.00 0.00 N +ATOM 665 H TYR A 45 35.900 34.526 24.585 1.00 0.00 H +ATOM 666 CA TYR A 45 34.051 33.679 23.814 1.00 0.00 C +ATOM 667 HA TYR A 45 33.565 32.748 24.109 1.00 0.00 H +ATOM 668 CB TYR A 45 33.061 34.890 23.836 1.00 0.00 C +ATOM 669 HB2 TYR A 45 32.689 35.085 24.843 1.00 0.00 H +ATOM 670 HB3 TYR A 45 33.670 35.762 23.596 1.00 0.00 H +ATOM 671 CG TYR A 45 31.825 34.747 22.962 1.00 0.00 C +ATOM 672 CD1 TYR A 45 30.955 33.684 23.061 1.00 0.00 C +ATOM 673 HD1 TYR A 45 31.040 32.945 23.845 1.00 0.00 H +ATOM 674 CE1 TYR A 45 29.908 33.556 22.116 1.00 0.00 C +ATOM 675 HE1 TYR A 45 29.113 32.849 22.291 1.00 0.00 H +ATOM 676 CZ TYR A 45 29.718 34.506 21.094 1.00 0.00 C +ATOM 677 OH TYR A 45 28.658 34.338 20.268 1.00 0.00 O +ATOM 678 HH TYR A 45 28.496 35.052 19.648 1.00 0.00 H +ATOM 679 CE2 TYR A 45 30.653 35.574 21.028 1.00 0.00 C +ATOM 680 HE2 TYR A 45 30.490 36.288 20.234 1.00 0.00 H +ATOM 681 CD2 TYR A 45 31.752 35.643 21.911 1.00 0.00 C +ATOM 682 HD2 TYR A 45 32.537 36.346 21.679 1.00 0.00 H +ATOM 683 C TYR A 45 34.545 33.529 22.336 1.00 0.00 C +ATOM 684 O TYR A 45 35.260 34.412 21.809 1.00 0.00 O +ATOM 685 N ASP A 46 33.924 32.567 21.640 1.00 0.00 N +ATOM 686 H ASP A 46 33.215 32.006 22.088 1.00 0.00 H +ATOM 687 CA ASP A 46 34.109 32.289 20.204 1.00 0.00 C +ATOM 688 HA ASP A 46 34.805 32.896 19.625 1.00 0.00 H +ATOM 689 CB ASP A 46 34.818 30.917 20.240 1.00 0.00 C +ATOM 690 HB2 ASP A 46 35.700 31.032 20.871 1.00 0.00 H +ATOM 691 HB3 ASP A 46 34.252 30.200 20.834 1.00 0.00 H +ATOM 692 CG ASP A 46 35.216 30.282 18.912 1.00 0.00 C +ATOM 693 OD1 ASP A 46 34.405 29.507 18.323 1.00 0.00 O1- +ATOM 694 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O1- +ATOM 695 C ASP A 46 32.877 32.275 19.319 1.00 0.00 C +ATOM 696 O ASP A 46 31.931 31.517 19.529 1.00 0.00 O +ATOM 697 N ASP A 47 32.833 33.220 18.413 1.00 0.00 N +ATOM 698 H ASP A 47 33.622 33.852 18.429 1.00 0.00 H +ATOM 699 CA ASP A 47 31.688 33.456 17.554 1.00 0.00 C +ATOM 700 HA ASP A 47 30.773 33.561 18.137 1.00 0.00 H +ATOM 701 CB ASP A 47 31.907 34.738 16.747 1.00 0.00 C +ATOM 702 HB2 ASP A 47 32.113 35.510 17.488 1.00 0.00 H +ATOM 703 HB3 ASP A 47 32.853 34.697 16.207 1.00 0.00 H +ATOM 704 CG ASP A 47 30.729 35.187 15.844 1.00 0.00 C +ATOM 705 OD1 ASP A 47 29.551 35.040 16.174 1.00 0.00 O1- +ATOM 706 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O1- +ATOM 707 C ASP A 47 31.522 32.326 16.557 1.00 0.00 C +ATOM 708 O ASP A 47 30.390 32.069 16.134 1.00 0.00 O +ATOM 709 N ALA A 48 32.555 31.657 16.092 1.00 0.00 N +ATOM 710 H ALA A 48 33.490 31.931 16.357 1.00 0.00 H +ATOM 711 CA ALA A 48 32.437 30.647 15.015 1.00 0.00 C +ATOM 712 HA ALA A 48 31.707 31.108 14.349 1.00 0.00 H +ATOM 713 CB ALA A 48 33.821 30.467 14.340 1.00 0.00 C +ATOM 714 HB1 ALA A 48 34.244 31.399 13.964 1.00 0.00 H +ATOM 715 HB2 ALA A 48 33.675 29.706 13.573 1.00 0.00 H +ATOM 716 HB3 ALA A 48 34.421 29.986 15.112 1.00 0.00 H +ATOM 717 C ALA A 48 31.855 29.301 15.549 1.00 0.00 C +ATOM 718 O ALA A 48 31.548 28.445 14.720 1.00 0.00 O +ATOM 719 N THR A 49 31.619 29.163 16.885 1.00 0.00 N +ATOM 720 H THR A 49 31.975 29.929 17.439 1.00 0.00 H +ATOM 721 CA THR A 49 30.811 28.126 17.576 1.00 0.00 C +ATOM 722 HA THR A 49 30.371 27.544 16.767 1.00 0.00 H +ATOM 723 CB THR A 49 31.713 27.100 18.310 1.00 0.00 C +ATOM 724 HB THR A 49 31.134 26.420 18.935 1.00 0.00 H +ATOM 725 CG2 THR A 49 32.614 26.280 17.436 1.00 0.00 C +ATOM 726 HG21 THR A 49 33.329 26.868 16.859 1.00 0.00 H +ATOM 727 HG22 THR A 49 32.002 25.593 16.853 1.00 0.00 H +ATOM 728 HG23 THR A 49 33.354 25.760 18.044 1.00 0.00 H +ATOM 729 OG1 THR A 49 32.507 27.834 19.222 1.00 0.00 O +ATOM 730 HG1 THR A 49 33.151 28.336 18.715 1.00 0.00 H +ATOM 731 C THR A 49 29.713 28.644 18.468 1.00 0.00 C +ATOM 732 O THR A 49 28.941 27.912 19.103 1.00 0.00 O +ATOM 733 N LYS A 50 29.628 29.977 18.649 1.00 0.00 N +ATOM 734 H LYS A 50 30.419 30.522 18.334 1.00 0.00 H +ATOM 735 CA LYS A 50 28.663 30.695 19.541 1.00 0.00 C +ATOM 736 HA LYS A 50 28.847 31.769 19.501 1.00 0.00 H +ATOM 737 CB LYS A 50 27.189 30.625 19.033 1.00 0.00 C +ATOM 738 HB2 LYS A 50 26.936 29.572 19.163 1.00 0.00 H +ATOM 739 HB3 LYS A 50 26.469 31.081 19.712 1.00 0.00 H +ATOM 740 CG LYS A 50 27.119 30.984 17.465 1.00 0.00 C +ATOM 741 HG2 LYS A 50 27.961 30.590 16.895 1.00 0.00 H +ATOM 742 HG3 LYS A 50 26.188 30.551 17.100 1.00 0.00 H +ATOM 743 CD LYS A 50 27.025 32.547 17.322 1.00 0.00 C +ATOM 744 HD2 LYS A 50 26.337 33.099 17.964 1.00 0.00 H +ATOM 745 HD3 LYS A 50 28.005 32.913 17.623 1.00 0.00 H +ATOM 746 CE LYS A 50 26.686 32.933 15.930 1.00 0.00 C +ATOM 747 HE2 LYS A 50 25.829 32.363 15.572 1.00 0.00 H +ATOM 748 HE3 LYS A 50 26.304 33.953 15.986 1.00 0.00 H +ATOM 749 NZ LYS A 50 27.861 32.905 14.990 1.00 0.00 N1+ +ATOM 750 HZ1 LYS A 50 28.562 33.507 15.397 1.00 0.00 H +ATOM 751 HZ2 LYS A 50 27.597 33.321 14.108 1.00 0.00 H +ATOM 752 HZ3 LYS A 50 28.269 32.017 14.736 1.00 0.00 H +ATOM 753 C LYS A 50 28.884 30.250 21.033 1.00 0.00 C +ATOM 754 O LYS A 50 27.958 30.206 21.826 1.00 0.00 O +ATOM 755 N THR A 51 30.148 29.820 21.328 1.00 0.00 N +ATOM 756 H THR A 51 30.940 30.100 20.766 1.00 0.00 H +ATOM 757 CA THR A 51 30.503 29.214 22.632 1.00 0.00 C +ATOM 758 HA THR A 51 29.680 28.714 23.142 1.00 0.00 H +ATOM 759 CB THR A 51 31.313 27.944 22.369 1.00 0.00 C +ATOM 760 HB THR A 51 32.245 28.102 21.826 1.00 0.00 H +ATOM 761 CG2 THR A 51 31.703 27.088 23.590 1.00 0.00 C +ATOM 762 HG21 THR A 51 32.177 26.160 23.272 1.00 0.00 H +ATOM 763 HG22 THR A 51 30.745 26.977 24.100 1.00 0.00 H +ATOM 764 HG23 THR A 51 32.401 27.677 24.186 1.00 0.00 H +ATOM 765 OG1 THR A 51 30.404 27.161 21.659 1.00 0.00 O +ATOM 766 HG1 THR A 51 29.757 27.683 21.179 1.00 0.00 H +ATOM 767 C THR A 51 31.202 30.120 23.549 1.00 0.00 C +ATOM 768 O THR A 51 32.200 30.721 23.143 1.00 0.00 O +ATOM 769 N PHE A 52 31.009 29.926 24.845 1.00 0.00 N +ATOM 770 H PHE A 52 30.125 29.479 25.042 1.00 0.00 H +ATOM 771 CA PHE A 52 31.821 30.391 25.941 1.00 0.00 C +ATOM 772 HA PHE A 52 32.490 31.192 25.628 1.00 0.00 H +ATOM 773 CB PHE A 52 30.715 30.979 27.007 1.00 0.00 C +ATOM 774 HB2 PHE A 52 29.988 30.200 27.238 1.00 0.00 H +ATOM 775 HB3 PHE A 52 31.250 31.298 27.901 1.00 0.00 H +ATOM 776 CG PHE A 52 30.049 32.222 26.534 1.00 0.00 C +ATOM 777 CD1 PHE A 52 28.876 32.142 25.781 1.00 0.00 C +ATOM 778 HD1 PHE A 52 28.413 31.204 25.515 1.00 0.00 H +ATOM 779 CE1 PHE A 52 28.300 33.350 25.304 1.00 0.00 C +ATOM 780 HE1 PHE A 52 27.303 33.316 24.890 1.00 0.00 H +ATOM 781 CZ PHE A 52 28.880 34.593 25.500 1.00 0.00 C +ATOM 782 HZ PHE A 52 28.417 35.460 25.054 1.00 0.00 H +ATOM 783 CE2 PHE A 52 30.122 34.665 26.192 1.00 0.00 C +ATOM 784 HE2 PHE A 52 30.650 35.597 26.333 1.00 0.00 H +ATOM 785 CD2 PHE A 52 30.597 33.495 26.795 1.00 0.00 C +ATOM 786 HD2 PHE A 52 31.435 33.581 27.471 1.00 0.00 H +ATOM 787 C PHE A 52 32.721 29.343 26.553 1.00 0.00 C +ATOM 788 O PHE A 52 32.280 28.240 26.674 1.00 0.00 O +ATOM 789 N THR A 53 33.908 29.829 27.087 1.00 0.00 N +ATOM 790 H THR A 53 34.203 30.784 26.938 1.00 0.00 H +ATOM 791 CA THR A 53 34.577 29.044 28.132 1.00 0.00 C +ATOM 792 HA THR A 53 34.003 28.190 28.492 1.00 0.00 H +ATOM 793 CB THR A 53 35.881 28.443 27.684 1.00 0.00 C +ATOM 794 HB THR A 53 36.513 29.234 27.280 1.00 0.00 H +ATOM 795 CG2 THR A 53 36.620 27.571 28.752 1.00 0.00 C +ATOM 796 HG21 THR A 53 36.814 28.236 29.595 1.00 0.00 H +ATOM 797 HG22 THR A 53 37.535 27.174 28.313 1.00 0.00 H +ATOM 798 HG23 THR A 53 35.924 26.795 29.068 1.00 0.00 H +ATOM 799 OG1 THR A 53 35.605 27.649 26.584 1.00 0.00 O +ATOM 800 HG1 THR A 53 35.459 28.177 25.796 1.00 0.00 H +ATOM 801 C THR A 53 34.776 29.748 29.443 1.00 0.00 C +ATOM 802 O THR A 53 35.146 30.939 29.437 1.00 0.00 O +ATOM 803 N VAL A 54 34.499 29.135 30.639 1.00 0.00 N +ATOM 804 H VAL A 54 34.209 28.173 30.538 1.00 0.00 H +ATOM 805 CA VAL A 54 34.861 29.536 31.982 1.00 0.00 C +ATOM 806 HA VAL A 54 35.382 30.493 31.978 1.00 0.00 H +ATOM 807 CB VAL A 54 33.697 29.716 32.869 1.00 0.00 C +ATOM 808 HB VAL A 54 32.913 30.335 32.434 1.00 0.00 H +ATOM 809 CG1 VAL A 54 33.002 28.394 33.289 1.00 0.00 C +ATOM 810 HG11 VAL A 54 33.690 27.666 33.718 1.00 0.00 H +ATOM 811 HG12 VAL A 54 32.618 28.014 32.342 1.00 0.00 H +ATOM 812 HG13 VAL A 54 32.093 28.525 33.877 1.00 0.00 H +ATOM 813 CG2 VAL A 54 34.118 30.320 34.224 1.00 0.00 C +ATOM 814 HG21 VAL A 54 34.711 31.228 34.123 1.00 0.00 H +ATOM 815 HG22 VAL A 54 34.691 29.664 34.880 1.00 0.00 H +ATOM 816 HG23 VAL A 54 33.202 30.551 34.767 1.00 0.00 H +ATOM 817 C VAL A 54 35.950 28.590 32.468 1.00 0.00 C +ATOM 818 O VAL A 54 35.738 27.385 32.660 1.00 0.00 O +ATOM 819 N THR A 55 37.187 29.085 32.651 1.00 0.00 N +ATOM 820 H THR A 55 37.326 30.038 32.345 1.00 0.00 H +ATOM 821 CA THR A 55 38.418 28.363 33.071 1.00 0.00 C +ATOM 822 HA THR A 55 38.197 27.299 32.991 1.00 0.00 H +ATOM 823 CB THR A 55 39.574 28.516 32.161 1.00 0.00 C +ATOM 824 HB THR A 55 39.757 29.581 32.019 1.00 0.00 H +ATOM 825 CG2 THR A 55 40.870 27.898 32.786 1.00 0.00 C +ATOM 826 HG21 THR A 55 40.583 26.849 32.855 1.00 0.00 H +ATOM 827 HG22 THR A 55 41.023 28.190 33.826 1.00 0.00 H +ATOM 828 HG23 THR A 55 41.825 28.044 32.280 1.00 0.00 H +ATOM 829 OG1 THR A 55 39.215 27.970 30.818 1.00 0.00 O +ATOM 830 HG1 THR A 55 38.792 28.725 30.401 1.00 0.00 H +ATOM 831 C THR A 55 38.779 28.725 34.458 1.00 0.00 C +ATOM 832 O THR A 55 39.263 29.841 34.735 1.00 0.00 O +ATOM 833 N GLU A 56 38.757 27.773 35.416 1.00 0.00 N +ATOM 834 H GLU A 56 38.459 26.869 35.079 1.00 0.00 H +ATOM 835 CA GLU A 56 39.045 27.993 36.888 1.00 0.00 C +ATOM 836 HA GLU A 56 38.618 28.921 37.267 1.00 0.00 H +ATOM 837 CB GLU A 56 38.402 26.911 37.749 1.00 0.00 C +ATOM 838 HB2 GLU A 56 37.329 27.019 37.593 1.00 0.00 H +ATOM 839 HB3 GLU A 56 38.780 25.905 37.563 1.00 0.00 H +ATOM 840 CG GLU A 56 38.436 27.078 39.267 1.00 0.00 C +ATOM 841 HG2 GLU A 56 39.455 26.968 39.636 1.00 0.00 H +ATOM 842 HG3 GLU A 56 38.094 28.097 39.445 1.00 0.00 H +ATOM 843 CD GLU A 56 37.514 26.014 39.918 1.00 0.00 C +ATOM 844 OE1 GLU A 56 37.905 24.823 39.870 1.00 0.00 O1- +ATOM 845 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O1- +ATOM 846 C GLU A 56 40.488 28.137 37.301 1.00 0.00 C +ATOM 847 O GLU A 56 40.807 29.090 38.025 1.00 0.00 O1- +ATOM 848 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O1- +CONECT 1 2 3 4 5 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 1 6 7 18 +CONECT 6 5 +CONECT 7 5 8 9 10 +CONECT 8 7 +CONECT 9 7 +CONECT 10 7 11 12 13 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 +CONECT 14 13 15 16 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 19 20 +CONECT 19 18 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 24 25 23 +CONECT 23 22 +CONECT 24 22 +CONECT 25 22 26 26 27 +CONECT 26 25 25 +CONECT 27 25 28 29 +CONECT 28 27 +CONECT 29 27 30 31 46 +CONECT 30 29 +CONECT 31 29 32 33 34 +CONECT 32 31 +CONECT 33 31 +CONECT 34 31 35 35 44 +CONECT 35 34 34 36 37 +CONECT 36 35 +CONECT 37 35 38 39 39 +CONECT 38 37 +CONECT 39 37 37 40 42 +CONECT 40 39 41 +CONECT 41 40 +CONECT 42 39 43 44 44 +CONECT 43 42 +CONECT 44 34 42 42 45 +CONECT 45 44 +CONECT 46 29 47 47 48 +CONECT 47 46 46 +CONECT 48 46 49 50 +CONECT 49 48 +CONECT 50 48 51 52 68 +CONECT 51 50 +CONECT 52 50 53 54 55 +CONECT 53 52 +CONECT 54 52 +CONECT 55 52 56 57 58 +CONECT 56 55 +CONECT 57 55 +CONECT 58 55 59 60 61 +CONECT 59 58 +CONECT 60 58 +CONECT 61 58 62 63 64 +CONECT 62 61 +CONECT 63 61 +CONECT 64 61 65 66 67 +CONECT 65 64 +CONECT 66 64 +CONECT 67 64 +CONECT 68 50 69 69 70 +CONECT 69 68 68 +CONECT 70 68 71 72 +CONECT 71 70 +CONECT 72 70 73 74 87 +CONECT 73 72 +CONECT 74 72 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 78 79 83 +CONECT 78 77 +CONECT 79 77 80 81 82 +CONECT 80 79 +CONECT 81 79 +CONECT 82 79 +CONECT 83 77 84 85 86 +CONECT 84 83 +CONECT 85 83 +CONECT 86 83 +CONECT 87 72 88 88 89 +CONECT 88 87 87 +CONECT 89 87 90 91 +CONECT 90 89 +CONECT 91 89 92 93 106 +CONECT 92 91 +CONECT 93 91 94 95 99 +CONECT 94 93 +CONECT 95 93 96 97 98 +CONECT 96 95 +CONECT 97 95 +CONECT 98 95 +CONECT 99 93 100 101 102 +CONECT 100 99 +CONECT 101 99 +CONECT 102 99 103 104 105 +CONECT 103 102 +CONECT 104 102 +CONECT 105 102 +CONECT 106 91 107 107 108 +CONECT 107 106 106 +CONECT 108 106 109 110 +CONECT 109 108 +CONECT 110 108 111 112 125 +CONECT 111 110 +CONECT 112 110 113 114 115 +CONECT 113 112 +CONECT 114 112 +CONECT 115 112 116 117 121 +CONECT 116 115 +CONECT 117 115 118 119 120 +CONECT 118 117 +CONECT 119 117 +CONECT 120 117 +CONECT 121 115 122 123 124 +CONECT 122 121 +CONECT 123 121 +CONECT 124 121 +CONECT 125 110 126 126 127 +CONECT 126 125 125 +CONECT 127 125 128 129 +CONECT 128 127 +CONECT 129 127 130 131 139 +CONECT 130 129 +CONECT 131 129 132 133 134 +CONECT 132 131 +CONECT 133 131 +CONECT 134 131 135 135 136 +CONECT 135 134 134 +CONECT 136 134 137 138 +CONECT 137 136 +CONECT 138 136 +CONECT 139 129 140 140 141 +CONECT 140 139 139 +CONECT 141 139 142 143 +CONECT 142 141 +CONECT 143 141 144 145 146 +CONECT 144 143 +CONECT 145 143 +CONECT 146 143 147 147 148 +CONECT 147 146 146 +CONECT 148 146 149 150 +CONECT 149 148 +CONECT 150 148 151 152 168 +CONECT 151 150 +CONECT 152 150 153 154 155 +CONECT 153 152 +CONECT 154 152 +CONECT 155 152 156 157 158 +CONECT 156 155 +CONECT 157 155 +CONECT 158 155 159 160 161 +CONECT 159 158 +CONECT 160 158 +CONECT 161 158 162 163 164 +CONECT 162 161 +CONECT 163 161 +CONECT 164 161 165 166 167 +CONECT 165 164 +CONECT 166 164 +CONECT 167 164 +CONECT 168 150 169 169 170 +CONECT 169 168 168 +CONECT 170 168 171 172 +CONECT 171 170 +CONECT 172 170 173 174 182 +CONECT 173 172 +CONECT 174 172 175 176 180 +CONECT 175 174 +CONECT 176 174 177 178 179 +CONECT 177 176 +CONECT 178 176 +CONECT 179 176 +CONECT 180 174 181 +CONECT 181 180 +CONECT 182 172 183 183 184 +CONECT 183 182 182 +CONECT 184 182 185 186 +CONECT 185 184 +CONECT 186 184 187 188 201 +CONECT 187 186 +CONECT 188 186 189 190 191 +CONECT 189 188 +CONECT 190 188 +CONECT 191 188 192 193 197 +CONECT 192 191 +CONECT 193 191 194 195 196 +CONECT 194 193 +CONECT 195 193 +CONECT 196 193 +CONECT 197 191 198 199 200 +CONECT 198 197 +CONECT 199 197 +CONECT 200 197 +CONECT 201 186 202 202 203 +CONECT 202 201 201 +CONECT 203 201 204 205 +CONECT 204 203 +CONECT 205 203 206 207 223 +CONECT 206 205 +CONECT 207 205 208 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 207 211 212 213 +CONECT 211 210 +CONECT 212 210 +CONECT 213 210 214 215 216 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 217 218 219 +CONECT 217 216 +CONECT 218 216 +CONECT 219 216 220 221 222 +CONECT 220 219 +CONECT 221 219 +CONECT 222 219 +CONECT 223 205 224 224 225 +CONECT 224 223 223 +CONECT 225 223 226 227 +CONECT 226 225 +CONECT 227 225 228 229 230 +CONECT 228 227 +CONECT 229 227 +CONECT 230 227 231 231 232 +CONECT 231 230 230 +CONECT 232 230 233 234 +CONECT 233 232 +CONECT 234 232 235 236 245 +CONECT 235 234 +CONECT 236 234 237 238 239 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 240 241 242 +CONECT 240 239 +CONECT 241 239 +CONECT 242 239 243 243 244 +CONECT 243 242 242 +CONECT 244 242 +CONECT 245 234 246 246 247 +CONECT 246 245 245 +CONECT 247 245 248 249 +CONECT 248 247 +CONECT 249 247 250 251 259 +CONECT 250 249 +CONECT 251 249 252 253 257 +CONECT 252 251 +CONECT 253 251 254 255 256 +CONECT 254 253 +CONECT 255 253 +CONECT 256 253 +CONECT 257 251 258 +CONECT 258 257 +CONECT 259 249 260 260 261 +CONECT 260 259 259 +CONECT 261 259 262 263 +CONECT 262 261 +CONECT 263 261 264 265 273 +CONECT 264 263 +CONECT 265 263 266 267 271 +CONECT 266 265 +CONECT 267 265 268 269 270 +CONECT 268 267 +CONECT 269 267 +CONECT 270 267 +CONECT 271 265 272 +CONECT 272 271 +CONECT 273 263 274 274 275 +CONECT 274 273 273 +CONECT 275 273 276 277 +CONECT 276 275 +CONECT 277 275 278 279 287 +CONECT 278 277 +CONECT 279 277 280 281 285 +CONECT 280 279 +CONECT 281 279 282 283 284 +CONECT 282 281 +CONECT 283 281 +CONECT 284 281 +CONECT 285 279 286 +CONECT 286 285 +CONECT 287 277 288 288 289 +CONECT 288 287 287 +CONECT 289 287 290 291 +CONECT 290 289 +CONECT 291 289 292 293 302 +CONECT 292 291 +CONECT 293 291 294 295 296 +CONECT 294 293 +CONECT 295 293 +CONECT 296 293 297 298 299 +CONECT 297 296 +CONECT 298 296 +CONECT 299 296 300 300 301 +CONECT 300 299 299 +CONECT 301 299 +CONECT 302 291 303 303 304 +CONECT 303 302 302 +CONECT 304 302 305 306 +CONECT 305 304 +CONECT 306 304 307 308 312 +CONECT 307 306 +CONECT 308 306 309 310 311 +CONECT 309 308 +CONECT 310 308 +CONECT 311 308 +CONECT 312 306 313 313 314 +CONECT 313 312 312 +CONECT 314 312 315 316 +CONECT 315 314 +CONECT 316 314 317 318 328 +CONECT 317 316 +CONECT 318 316 319 320 324 +CONECT 319 318 +CONECT 320 318 321 322 323 +CONECT 321 320 +CONECT 322 320 +CONECT 323 320 +CONECT 324 318 325 326 327 +CONECT 325 324 +CONECT 326 324 +CONECT 327 324 +CONECT 328 316 329 329 330 +CONECT 329 328 328 +CONECT 330 328 331 332 +CONECT 331 330 +CONECT 332 330 333 334 340 +CONECT 333 332 +CONECT 334 332 335 336 337 +CONECT 335 334 +CONECT 336 334 +CONECT 337 334 338 338 339 +CONECT 338 337 337 +CONECT 339 337 +CONECT 340 332 341 341 342 +CONECT 341 340 340 +CONECT 342 340 343 344 +CONECT 343 342 +CONECT 344 342 345 346 350 +CONECT 345 344 +CONECT 346 344 347 348 349 +CONECT 347 346 +CONECT 348 346 +CONECT 349 346 +CONECT 350 344 351 351 352 +CONECT 351 350 350 +CONECT 352 350 353 354 +CONECT 353 352 +CONECT 354 352 355 356 360 +CONECT 355 354 +CONECT 356 354 357 358 359 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 +CONECT 360 354 361 361 362 +CONECT 361 360 360 +CONECT 362 360 363 364 +CONECT 363 362 +CONECT 364 362 365 366 374 +CONECT 365 364 +CONECT 366 364 367 368 372 +CONECT 367 366 +CONECT 368 366 369 370 371 +CONECT 369 368 +CONECT 370 368 +CONECT 371 368 +CONECT 372 366 373 +CONECT 373 372 +CONECT 374 364 375 375 376 +CONECT 375 374 374 +CONECT 376 374 377 378 +CONECT 377 376 +CONECT 378 376 379 380 384 +CONECT 379 378 +CONECT 380 378 381 382 383 +CONECT 381 380 +CONECT 382 380 +CONECT 383 380 +CONECT 384 378 385 385 386 +CONECT 385 384 384 +CONECT 386 384 387 388 +CONECT 387 386 +CONECT 388 386 389 390 399 +CONECT 389 388 +CONECT 390 388 391 392 393 +CONECT 391 390 +CONECT 392 390 +CONECT 393 390 394 395 396 +CONECT 394 393 +CONECT 395 393 +CONECT 396 393 397 397 398 +CONECT 397 396 396 +CONECT 398 396 +CONECT 399 388 400 400 401 +CONECT 400 399 399 +CONECT 401 399 402 403 +CONECT 402 401 +CONECT 403 401 404 405 421 +CONECT 404 403 +CONECT 405 403 406 407 408 +CONECT 406 405 +CONECT 407 405 +CONECT 408 405 409 410 411 +CONECT 409 408 +CONECT 410 408 +CONECT 411 408 412 413 414 +CONECT 412 411 +CONECT 413 411 +CONECT 414 411 415 416 417 +CONECT 415 414 +CONECT 416 414 +CONECT 417 414 418 419 420 +CONECT 418 417 +CONECT 419 417 +CONECT 420 417 +CONECT 421 403 422 422 423 +CONECT 422 421 421 +CONECT 423 421 424 425 +CONECT 424 423 +CONECT 425 423 426 427 437 +CONECT 426 425 +CONECT 427 425 428 429 433 +CONECT 428 427 +CONECT 429 427 430 431 432 +CONECT 430 429 +CONECT 431 429 +CONECT 432 429 +CONECT 433 427 434 435 436 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 425 438 438 439 +CONECT 438 437 437 +CONECT 439 437 440 441 +CONECT 440 439 +CONECT 441 439 442 443 457 +CONECT 442 441 +CONECT 443 441 444 445 446 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 447 447 455 +CONECT 447 446 446 448 449 +CONECT 448 447 +CONECT 449 447 450 451 451 +CONECT 450 449 +CONECT 451 449 449 452 453 +CONECT 452 451 +CONECT 453 451 454 455 455 +CONECT 454 453 +CONECT 455 446 453 453 456 +CONECT 456 455 +CONECT 457 441 458 458 459 +CONECT 458 457 457 +CONECT 459 457 460 461 +CONECT 460 459 +CONECT 461 459 462 463 479 +CONECT 462 461 +CONECT 463 461 464 465 466 +CONECT 464 463 +CONECT 465 463 +CONECT 466 463 467 468 469 +CONECT 467 466 +CONECT 468 466 +CONECT 469 466 470 471 472 +CONECT 470 469 +CONECT 471 469 +CONECT 472 469 473 474 475 +CONECT 473 472 +CONECT 474 472 +CONECT 475 472 476 477 478 +CONECT 476 475 +CONECT 477 475 +CONECT 478 475 +CONECT 479 461 480 480 481 +CONECT 480 479 479 +CONECT 481 479 482 483 +CONECT 482 481 +CONECT 483 481 484 485 496 +CONECT 484 483 +CONECT 485 483 486 487 488 +CONECT 486 485 +CONECT 487 485 +CONECT 488 485 489 490 491 +CONECT 489 488 +CONECT 490 488 +CONECT 491 488 492 492 493 +CONECT 492 491 491 +CONECT 493 491 494 495 +CONECT 494 493 +CONECT 495 493 +CONECT 496 483 497 497 498 +CONECT 497 496 496 +CONECT 498 496 499 500 +CONECT 499 498 +CONECT 500 498 501 502 517 +CONECT 501 500 +CONECT 502 500 503 504 505 +CONECT 503 502 +CONECT 504 502 +CONECT 505 502 506 506 515 +CONECT 506 505 505 507 508 +CONECT 507 506 +CONECT 508 506 509 510 510 +CONECT 509 508 +CONECT 510 508 508 511 513 +CONECT 511 510 512 +CONECT 512 511 +CONECT 513 510 514 515 515 +CONECT 514 513 +CONECT 515 505 513 513 516 +CONECT 516 515 +CONECT 517 500 518 518 519 +CONECT 518 517 517 +CONECT 519 517 520 521 +CONECT 520 519 +CONECT 521 519 522 523 527 +CONECT 522 521 +CONECT 523 521 524 525 526 +CONECT 524 523 +CONECT 525 523 +CONECT 526 523 +CONECT 527 521 528 528 529 +CONECT 528 527 527 +CONECT 529 527 530 531 +CONECT 530 529 +CONECT 531 529 532 533 541 +CONECT 532 531 +CONECT 533 531 534 535 536 +CONECT 534 533 +CONECT 535 533 +CONECT 536 533 537 537 538 +CONECT 537 536 536 +CONECT 538 536 539 540 +CONECT 539 538 +CONECT 540 538 +CONECT 541 531 542 542 543 +CONECT 542 541 541 +CONECT 543 541 544 545 +CONECT 544 543 +CONECT 545 543 546 547 553 +CONECT 546 545 +CONECT 547 545 548 549 550 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 551 551 552 +CONECT 551 550 550 +CONECT 552 550 +CONECT 553 545 554 554 555 +CONECT 554 553 553 +CONECT 555 553 556 557 +CONECT 556 555 +CONECT 557 555 558 559 567 +CONECT 558 557 +CONECT 559 557 560 561 562 +CONECT 560 559 +CONECT 561 559 +CONECT 562 559 563 563 564 +CONECT 563 562 562 +CONECT 564 562 565 566 +CONECT 565 564 +CONECT 566 564 +CONECT 567 557 568 568 569 +CONECT 568 567 567 +CONECT 569 567 570 571 +CONECT 570 569 +CONECT 571 569 572 573 574 +CONECT 572 571 +CONECT 573 571 +CONECT 574 571 575 575 576 +CONECT 575 574 574 +CONECT 576 574 577 578 +CONECT 577 576 +CONECT 578 576 579 580 590 +CONECT 579 578 +CONECT 580 578 581 582 586 +CONECT 581 580 +CONECT 582 580 583 584 585 +CONECT 583 582 +CONECT 584 582 +CONECT 585 582 +CONECT 586 580 587 588 589 +CONECT 587 586 +CONECT 588 586 +CONECT 589 586 +CONECT 590 578 591 591 592 +CONECT 591 590 590 +CONECT 592 590 593 594 +CONECT 593 592 +CONECT 594 592 595 596 602 +CONECT 595 594 +CONECT 596 594 597 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 600 600 601 +CONECT 600 599 599 +CONECT 601 599 +CONECT 602 594 603 603 604 +CONECT 603 602 602 +CONECT 604 602 605 606 +CONECT 605 604 +CONECT 606 604 607 608 609 +CONECT 607 606 +CONECT 608 606 +CONECT 609 606 610 610 611 +CONECT 610 609 609 +CONECT 611 609 612 613 +CONECT 612 611 +CONECT 613 611 614 615 624 +CONECT 614 613 +CONECT 615 613 616 617 618 +CONECT 616 615 +CONECT 617 615 +CONECT 618 615 619 620 621 +CONECT 619 618 +CONECT 620 618 +CONECT 621 618 622 622 623 +CONECT 622 621 621 +CONECT 623 621 +CONECT 624 613 625 625 626 +CONECT 625 624 624 +CONECT 626 624 627 628 +CONECT 627 626 +CONECT 628 626 629 630 648 +CONECT 629 628 +CONECT 630 628 631 632 633 +CONECT 631 630 +CONECT 632 630 +CONECT 633 630 634 634 647 +CONECT 634 633 633 635 636 +CONECT 635 634 +CONECT 636 634 637 638 +CONECT 637 636 +CONECT 638 636 639 639 647 +CONECT 639 638 638 640 641 +CONECT 640 639 +CONECT 641 639 642 643 643 +CONECT 642 641 +CONECT 643 641 641 644 645 +CONECT 644 643 +CONECT 645 643 646 647 647 +CONECT 646 645 +CONECT 647 633 638 645 645 +CONECT 648 628 649 649 650 +CONECT 649 648 648 +CONECT 650 648 651 652 +CONECT 651 650 +CONECT 652 650 653 654 662 +CONECT 653 652 +CONECT 654 652 655 656 660 +CONECT 655 654 +CONECT 656 654 657 658 659 +CONECT 657 656 +CONECT 658 656 +CONECT 659 656 +CONECT 660 654 661 +CONECT 661 660 +CONECT 662 652 663 663 664 +CONECT 663 662 662 +CONECT 664 662 665 666 +CONECT 665 664 +CONECT 666 664 667 668 683 +CONECT 667 666 +CONECT 668 666 669 670 671 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 672 672 681 +CONECT 672 671 671 673 674 +CONECT 673 672 +CONECT 674 672 675 676 676 +CONECT 675 674 +CONECT 676 674 674 677 679 +CONECT 677 676 678 +CONECT 678 677 +CONECT 679 676 680 681 681 +CONECT 680 679 +CONECT 681 671 679 679 682 +CONECT 682 681 +CONECT 683 666 684 684 685 +CONECT 684 683 683 +CONECT 685 683 686 687 +CONECT 686 685 +CONECT 687 685 688 689 695 +CONECT 688 687 +CONECT 689 687 690 691 692 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 693 693 694 +CONECT 693 692 692 +CONECT 694 692 +CONECT 695 687 696 696 697 +CONECT 696 695 695 +CONECT 697 695 698 699 +CONECT 698 697 +CONECT 699 697 700 701 707 +CONECT 700 699 +CONECT 701 699 702 703 704 +CONECT 702 701 +CONECT 703 701 +CONECT 704 701 705 705 706 +CONECT 705 704 704 +CONECT 706 704 +CONECT 707 699 708 708 709 +CONECT 708 707 707 +CONECT 709 707 710 711 +CONECT 710 709 +CONECT 711 709 712 713 717 +CONECT 712 711 +CONECT 713 711 714 715 716 +CONECT 714 713 +CONECT 715 713 +CONECT 716 713 +CONECT 717 711 718 718 719 +CONECT 718 717 717 +CONECT 719 717 720 721 +CONECT 720 719 +CONECT 721 719 722 723 731 +CONECT 722 721 +CONECT 723 721 724 725 729 +CONECT 724 723 +CONECT 725 723 726 727 728 +CONECT 726 725 +CONECT 727 725 +CONECT 728 725 +CONECT 729 723 730 +CONECT 730 729 +CONECT 731 721 732 732 733 +CONECT 732 731 731 +CONECT 733 731 734 735 +CONECT 734 733 +CONECT 735 733 736 737 753 +CONECT 736 735 +CONECT 737 735 738 739 740 +CONECT 738 737 +CONECT 739 737 +CONECT 740 737 741 742 743 +CONECT 741 740 +CONECT 742 740 +CONECT 743 740 744 745 746 +CONECT 744 743 +CONECT 745 743 +CONECT 746 743 747 748 749 +CONECT 747 746 +CONECT 748 746 +CONECT 749 746 750 751 752 +CONECT 750 749 +CONECT 751 749 +CONECT 752 749 +CONECT 753 735 754 754 755 +CONECT 754 753 753 +CONECT 755 753 756 757 +CONECT 756 755 +CONECT 757 755 758 759 767 +CONECT 758 757 +CONECT 759 757 760 761 765 +CONECT 760 759 +CONECT 761 759 762 763 764 +CONECT 762 761 +CONECT 763 761 +CONECT 764 761 +CONECT 765 759 766 +CONECT 766 765 +CONECT 767 757 768 768 769 +CONECT 768 767 767 +CONECT 769 767 770 771 +CONECT 770 769 +CONECT 771 769 772 773 787 +CONECT 772 771 +CONECT 773 771 774 775 776 +CONECT 774 773 +CONECT 775 773 +CONECT 776 773 777 777 785 +CONECT 777 776 776 778 779 +CONECT 778 777 +CONECT 779 777 780 781 781 +CONECT 780 779 +CONECT 781 779 779 782 783 +CONECT 782 781 +CONECT 783 781 784 785 785 +CONECT 784 783 +CONECT 785 776 783 783 786 +CONECT 786 785 +CONECT 787 771 788 788 789 +CONECT 788 787 787 +CONECT 789 787 790 791 +CONECT 790 789 +CONECT 791 789 792 793 801 +CONECT 792 791 +CONECT 793 791 794 795 799 +CONECT 794 793 +CONECT 795 793 796 797 798 +CONECT 796 795 +CONECT 797 795 +CONECT 798 795 +CONECT 799 793 800 +CONECT 800 799 +CONECT 801 791 802 802 803 +CONECT 802 801 801 +CONECT 803 801 804 805 +CONECT 804 803 +CONECT 805 803 806 807 817 +CONECT 806 805 +CONECT 807 805 808 809 813 +CONECT 808 807 +CONECT 809 807 810 811 812 +CONECT 810 809 +CONECT 811 809 +CONECT 812 809 +CONECT 813 807 814 815 816 +CONECT 814 813 +CONECT 815 813 +CONECT 816 813 +CONECT 817 805 818 818 819 +CONECT 818 817 817 +CONECT 819 817 820 821 +CONECT 820 819 +CONECT 821 819 822 823 831 +CONECT 822 821 +CONECT 823 821 824 825 829 +CONECT 824 823 +CONECT 825 823 826 827 828 +CONECT 826 825 +CONECT 827 825 +CONECT 828 825 +CONECT 829 823 830 +CONECT 830 829 +CONECT 831 821 832 832 833 +CONECT 832 831 831 +CONECT 833 831 834 835 +CONECT 834 833 +CONECT 835 833 836 837 846 +CONECT 836 835 +CONECT 837 835 838 839 840 +CONECT 838 837 +CONECT 839 837 +CONECT 840 837 841 842 843 +CONECT 841 840 +CONECT 842 840 +CONECT 843 840 844 844 845 +CONECT 844 843 843 +CONECT 845 843 +CONECT 846 835 847 847 848 +CONECT 847 846 846 +CONECT 848 846 +MASTER 0 0 0 0 0 0 0 0 848 0 848 0 +END diff --git a/unittests/output_files/test_thr_to_gly_restypeTrue.pdb b/unittests/output_files/test_thr_to_gly_restypeTrue.pdb new file mode 100644 index 0000000..5370589 --- /dev/null +++ b/unittests/output_files/test_thr_to_gly_restypeTrue.pdb @@ -0,0 +1,1700 @@ +COMPND MET +AUTHOR GENERATED BY OPEN BABEL 3.0.0 +ATOM 1 N MET A 1 19.157 32.576 19.140 1.00 0.00 N1+ +ATOM 2 H1 MET A 1 18.435 31.870 19.129 1.00 0.00 H +ATOM 3 H2 MET A 1 18.900 33.260 18.441 1.00 0.00 H +ATOM 4 H3 MET A 1 19.229 33.073 20.016 1.00 0.00 H +ATOM 5 CA MET A 1 20.458 31.939 18.931 1.00 0.00 C +ATOM 6 HA MET A 1 20.420 31.303 18.046 1.00 0.00 H +ATOM 7 CB MET A 1 21.504 33.015 18.722 1.00 0.00 C +ATOM 8 HB2 MET A 1 21.352 33.519 17.768 1.00 0.00 H +ATOM 9 HB3 MET A 1 21.390 33.764 19.505 1.00 0.00 H +ATOM 10 CG MET A 1 22.904 32.517 18.656 1.00 0.00 C +ATOM 11 HG2 MET A 1 23.590 33.362 18.601 1.00 0.00 H +ATOM 12 HG3 MET A 1 23.154 32.095 19.630 1.00 0.00 H +ATOM 13 SD MET A 1 23.205 31.269 17.386 1.00 0.00 S +ATOM 14 CE MET A 1 22.990 32.137 15.870 1.00 0.00 C +ATOM 15 HE1 MET A 1 23.339 33.163 15.983 1.00 0.00 H +ATOM 16 HE2 MET A 1 21.968 32.128 15.490 1.00 0.00 H +ATOM 17 HE3 MET A 1 23.572 31.586 15.132 1.00 0.00 H +ATOM 18 C MET A 1 20.796 31.017 20.133 1.00 0.00 C +ATOM 19 O MET A 1 20.674 31.440 21.297 1.00 0.00 O +ATOM 20 N GLY A 2 21.124 29.774 19.819 1.00 0.00 N +ATOM 21 H GLY A 2 21.279 29.527 18.851 1.00 0.00 H +ATOM 22 CA GLY A 2 21.443 28.704 20.861 1.00 0.00 C +ATOM 23 HA3 GLY A 2 21.210 27.667 20.621 1.00 0.00 H +ATOM 24 HA2 GLY A 2 20.909 28.998 21.764 1.00 0.00 H +ATOM 25 C GLY A 2 22.937 28.892 21.086 1.00 0.00 C +ATOM 26 O GLY A 2 23.773 28.867 20.181 1.00 0.00 O +ATOM 27 N TYR A 3 23.244 29.155 22.344 1.00 0.00 N +ATOM 28 H TYR A 3 22.513 29.085 23.038 1.00 0.00 H +ATOM 29 CA TYR A 3 24.628 29.305 22.888 1.00 0.00 C +ATOM 30 HA TYR A 3 25.262 29.391 22.004 1.00 0.00 H +ATOM 31 CB TYR A 3 24.744 30.579 23.675 1.00 0.00 C +ATOM 32 HB2 TYR A 3 24.131 30.495 24.572 1.00 0.00 H +ATOM 33 HB3 TYR A 3 25.780 30.505 24.008 1.00 0.00 H +ATOM 34 CG TYR A 3 24.468 31.862 22.928 1.00 0.00 C +ATOM 35 CD1 TYR A 3 25.525 32.544 22.317 1.00 0.00 C +ATOM 36 HD1 TYR A 3 26.477 32.039 22.379 1.00 0.00 H +ATOM 37 CE1 TYR A 3 25.289 33.761 21.619 1.00 0.00 C +ATOM 38 HE1 TYR A 3 26.100 34.275 21.122 1.00 0.00 H +ATOM 39 CZ TYR A 3 23.936 34.260 21.579 1.00 0.00 C +ATOM 40 OH TYR A 3 23.774 35.268 20.774 1.00 0.00 O +ATOM 41 HH TYR A 3 24.486 35.161 20.140 1.00 0.00 H +ATOM 42 CE2 TYR A 3 22.849 33.537 22.176 1.00 0.00 C +ATOM 43 HE2 TYR A 3 21.868 33.965 22.036 1.00 0.00 H +ATOM 44 CD2 TYR A 3 23.110 32.291 22.853 1.00 0.00 C +ATOM 45 HD2 TYR A 3 22.235 31.752 23.187 1.00 0.00 H +ATOM 46 C TYR A 3 25.066 28.136 23.774 1.00 0.00 C +ATOM 47 O TYR A 3 24.233 27.436 24.338 1.00 0.00 O +ATOM 48 N LYS A 4 26.339 27.934 23.811 1.00 0.00 N +ATOM 49 H LYS A 4 26.944 28.514 23.248 1.00 0.00 H +ATOM 50 CA LYS A 4 26.982 26.918 24.687 1.00 0.00 C +ATOM 51 HA LYS A 4 26.212 26.488 25.328 1.00 0.00 H +ATOM 52 CB LYS A 4 27.643 25.801 23.803 1.00 0.00 C +ATOM 53 HB2 LYS A 4 26.868 25.465 23.113 1.00 0.00 H +ATOM 54 HB3 LYS A 4 28.422 26.196 23.151 1.00 0.00 H +ATOM 55 CG LYS A 4 28.205 24.625 24.506 1.00 0.00 C +ATOM 56 HG2 LYS A 4 29.054 24.916 25.125 1.00 0.00 H +ATOM 57 HG3 LYS A 4 27.452 24.278 25.213 1.00 0.00 H +ATOM 58 CD LYS A 4 28.635 23.407 23.678 1.00 0.00 C +ATOM 59 HD2 LYS A 4 29.003 22.691 24.414 1.00 0.00 H +ATOM 60 HD3 LYS A 4 27.737 22.954 23.255 1.00 0.00 H +ATOM 61 CE LYS A 4 29.554 23.575 22.506 1.00 0.00 C +ATOM 62 HE2 LYS A 4 28.899 24.120 21.827 1.00 0.00 H +ATOM 63 HE3 LYS A 4 30.458 24.114 22.794 1.00 0.00 H +ATOM 64 NZ LYS A 4 30.052 22.279 21.888 1.00 0.00 N1+ +ATOM 65 HZ1 LYS A 4 30.831 21.896 22.402 1.00 0.00 H +ATOM 66 HZ2 LYS A 4 30.443 22.423 20.968 1.00 0.00 H +ATOM 67 HZ3 LYS A 4 29.328 21.579 21.805 1.00 0.00 H +ATOM 68 C LYS A 4 28.003 27.516 25.655 1.00 0.00 C +ATOM 69 O LYS A 4 28.579 28.553 25.310 1.00 0.00 O +ATOM 70 N LEU A 5 28.245 26.773 26.741 1.00 0.00 N +ATOM 71 H LEU A 5 27.544 26.084 26.977 1.00 0.00 H +ATOM 72 CA LEU A 5 29.244 27.118 27.766 1.00 0.00 C +ATOM 73 HA LEU A 5 29.916 27.884 27.380 1.00 0.00 H +ATOM 74 CB LEU A 5 28.579 27.507 29.097 1.00 0.00 C +ATOM 75 HB2 LEU A 5 28.058 28.438 28.872 1.00 0.00 H +ATOM 76 HB3 LEU A 5 27.859 26.779 29.469 1.00 0.00 H +ATOM 77 CG LEU A 5 29.551 27.720 30.235 1.00 0.00 C +ATOM 78 HG LEU A 5 30.166 26.841 30.429 1.00 0.00 H +ATOM 79 CD1 LEU A 5 30.427 28.952 29.986 1.00 0.00 C +ATOM 80 HD11 LEU A 5 31.114 28.683 29.184 1.00 0.00 H +ATOM 81 HD12 LEU A 5 31.008 29.120 30.894 1.00 0.00 H +ATOM 82 HD13 LEU A 5 29.848 29.861 29.825 1.00 0.00 H +ATOM 83 CD2 LEU A 5 28.678 28.115 31.457 1.00 0.00 C +ATOM 84 HD21 LEU A 5 28.235 29.096 31.284 1.00 0.00 H +ATOM 85 HD22 LEU A 5 29.327 28.287 32.315 1.00 0.00 H +ATOM 86 HD23 LEU A 5 27.907 27.390 31.720 1.00 0.00 H +ATOM 87 C LEU A 5 30.065 25.816 27.990 1.00 0.00 C +ATOM 88 O LEU A 5 29.489 24.768 28.302 1.00 0.00 O +ATOM 89 N ILE A 6 31.415 25.954 27.959 1.00 0.00 N +ATOM 90 H ILE A 6 31.834 26.822 27.658 1.00 0.00 H +ATOM 91 CA ILE A 6 32.352 24.944 28.438 1.00 0.00 C +ATOM 92 HA ILE A 6 31.851 23.978 28.494 1.00 0.00 H +ATOM 93 CB ILE A 6 33.535 24.736 27.434 1.00 0.00 C +ATOM 94 HB ILE A 6 34.002 25.706 27.261 1.00 0.00 H +ATOM 95 CG2 ILE A 6 34.658 23.796 27.952 1.00 0.00 C +ATOM 96 HG21 ILE A 6 35.011 24.049 28.953 1.00 0.00 H +ATOM 97 HG22 ILE A 6 35.610 23.773 27.423 1.00 0.00 H +ATOM 98 HG23 ILE A 6 34.315 22.768 28.065 1.00 0.00 H +ATOM 99 CG1 ILE A 6 32.967 24.083 26.135 1.00 0.00 C +ATOM 100 HG12 ILE A 6 32.815 23.014 26.281 1.00 0.00 H +ATOM 101 HG13 ILE A 6 32.016 24.548 25.875 1.00 0.00 H +ATOM 102 CD1 ILE A 6 33.964 24.228 24.983 1.00 0.00 C +ATOM 103 HD11 ILE A 6 34.203 25.280 24.831 1.00 0.00 H +ATOM 104 HD12 ILE A 6 33.521 23.646 24.174 1.00 0.00 H +ATOM 105 HD13 ILE A 6 34.890 23.744 25.293 1.00 0.00 H +ATOM 106 C ILE A 6 32.878 25.380 29.825 1.00 0.00 C +ATOM 107 O ILE A 6 33.517 26.449 29.956 1.00 0.00 O +ATOM 108 N LEU A 7 32.756 24.548 30.823 1.00 0.00 N +ATOM 109 H LEU A 7 32.337 23.649 30.632 1.00 0.00 H +ATOM 110 CA LEU A 7 33.418 24.678 32.128 1.00 0.00 C +ATOM 111 HA LEU A 7 33.772 25.702 32.243 1.00 0.00 H +ATOM 112 CB LEU A 7 32.452 24.287 33.269 1.00 0.00 C +ATOM 113 HB2 LEU A 7 32.235 23.219 33.280 1.00 0.00 H +ATOM 114 HB3 LEU A 7 33.025 24.491 34.173 1.00 0.00 H +ATOM 115 CG LEU A 7 31.068 25.080 33.294 1.00 0.00 C +ATOM 116 HG LEU A 7 31.234 26.000 32.731 1.00 0.00 H +ATOM 117 CD1 LEU A 7 29.957 24.185 32.737 1.00 0.00 C +ATOM 118 HD11 LEU A 7 29.091 24.791 32.472 1.00 0.00 H +ATOM 119 HD12 LEU A 7 29.675 23.458 33.497 1.00 0.00 H +ATOM 120 HD13 LEU A 7 30.242 23.598 31.863 1.00 0.00 H +ATOM 121 CD2 LEU A 7 30.679 25.500 34.666 1.00 0.00 C +ATOM 122 HD21 LEU A 7 30.692 24.679 35.384 1.00 0.00 H +ATOM 123 HD22 LEU A 7 29.678 25.926 34.604 1.00 0.00 H +ATOM 124 HD23 LEU A 7 31.266 26.349 35.014 1.00 0.00 H +ATOM 125 C LEU A 7 34.704 23.832 31.982 1.00 0.00 C +ATOM 126 O LEU A 7 34.608 22.712 31.434 1.00 0.00 O +ATOM 127 N ASN A 8 35.741 24.355 32.566 1.00 0.00 N +ATOM 128 H ASN A 8 35.657 25.289 32.943 1.00 0.00 H +ATOM 129 CA ASN A 8 37.087 23.938 32.340 1.00 0.00 C +ATOM 130 HA ASN A 8 37.195 22.875 32.128 1.00 0.00 H +ATOM 131 CB ASN A 8 37.683 24.648 31.079 1.00 0.00 C +ATOM 132 HB2 ASN A 8 37.052 24.514 30.199 1.00 0.00 H +ATOM 133 HB3 ASN A 8 37.697 25.701 31.358 1.00 0.00 H +ATOM 134 CG ASN A 8 39.069 24.172 30.753 1.00 0.00 C +ATOM 135 OD1 ASN A 8 39.293 22.972 30.616 1.00 0.00 O +ATOM 136 ND2 ASN A 8 40.171 24.966 30.834 1.00 0.00 N +ATOM 137 HD21 ASN A 8 40.064 25.968 30.880 1.00 0.00 H +ATOM 138 HD22 ASN A 8 41.073 24.564 30.618 1.00 0.00 H +ATOM 139 C ASN A 8 37.929 24.262 33.602 1.00 0.00 C +ATOM 140 O ASN A 8 37.736 25.299 34.234 1.00 0.00 O +ATOM 141 N GLY A 9 38.893 23.411 33.937 1.00 0.00 N +ATOM 142 H GLY A 9 38.872 22.559 33.394 1.00 0.00 H +ATOM 143 CA GLY A 9 39.937 23.667 34.946 1.00 0.00 C +ATOM 144 HA2 GLY A 9 40.563 24.496 34.619 1.00 0.00 H +ATOM 145 HA3 GLY A 9 39.525 24.058 35.876 1.00 0.00 H +ATOM 146 C GLY A 9 40.820 22.504 35.210 1.00 0.00 C +ATOM 147 O GLY A 9 40.826 21.506 34.446 1.00 0.00 O +ATOM 148 N LYS A 10 41.477 22.473 36.356 1.00 0.00 N +ATOM 149 H LYS A 10 41.439 23.256 36.992 1.00 0.00 H +ATOM 150 CA LYS A 10 42.321 21.363 36.766 1.00 0.00 C +ATOM 151 HA LYS A 10 42.838 21.036 35.864 1.00 0.00 H +ATOM 152 CB LYS A 10 43.435 21.839 37.736 1.00 0.00 C +ATOM 153 HB2 LYS A 10 42.960 22.130 38.673 1.00 0.00 H +ATOM 154 HB3 LYS A 10 44.151 21.018 37.787 1.00 0.00 H +ATOM 155 CG LYS A 10 44.146 23.121 37.228 1.00 0.00 C +ATOM 156 HG2 LYS A 10 44.581 22.959 36.242 1.00 0.00 H +ATOM 157 HG3 LYS A 10 43.424 23.934 37.151 1.00 0.00 H +ATOM 158 CD LYS A 10 45.206 23.474 38.269 1.00 0.00 C +ATOM 159 HD2 LYS A 10 44.834 23.376 39.290 1.00 0.00 H +ATOM 160 HD3 LYS A 10 46.045 22.781 38.265 1.00 0.00 H +ATOM 161 CE LYS A 10 45.833 24.866 37.936 1.00 0.00 C +ATOM 162 HE2 LYS A 10 46.898 24.867 38.172 1.00 0.00 H +ATOM 163 HE3 LYS A 10 45.615 25.139 36.904 1.00 0.00 H +ATOM 164 NZ LYS A 10 45.314 25.885 38.915 1.00 0.00 N1+ +ATOM 165 HZ1 LYS A 10 44.318 26.049 38.885 1.00 0.00 H +ATOM 166 HZ2 LYS A 10 45.805 26.756 38.765 1.00 0.00 H +ATOM 167 HZ3 LYS A 10 45.434 25.694 39.899 1.00 0.00 H +ATOM 168 C LYS A 10 41.608 20.142 37.369 1.00 0.00 C +ATOM 169 O LYS A 10 42.136 19.017 37.432 1.00 0.00 O +ATOM 170 N THR A 11 40.316 20.407 37.709 1.00 0.00 N +ATOM 171 H THR A 11 40.018 21.373 37.739 1.00 0.00 H +ATOM 172 CA THR A 11 39.333 19.428 38.190 1.00 0.00 C +ATOM 173 HA THR A 11 39.627 18.439 37.841 1.00 0.00 H +ATOM 174 CB THR A 11 39.319 19.497 39.740 1.00 0.00 C +ATOM 175 HB THR A 11 38.538 18.809 40.063 1.00 0.00 H +ATOM 176 CG2 THR A 11 40.656 18.994 40.197 1.00 0.00 C +ATOM 177 HG21 THR A 11 40.954 17.991 39.896 1.00 0.00 H +ATOM 178 HG22 THR A 11 40.695 18.984 41.286 1.00 0.00 H +ATOM 179 HG23 THR A 11 41.453 19.662 39.869 1.00 0.00 H +ATOM 180 OG1 THR A 11 39.118 20.738 40.229 1.00 0.00 O +ATOM 181 HG1 THR A 11 39.321 20.728 41.168 1.00 0.00 H +ATOM 182 C THR A 11 37.937 19.704 37.750 1.00 0.00 C +ATOM 183 O THR A 11 37.180 18.744 37.592 1.00 0.00 O +ATOM 184 N LEU A 12 37.572 20.909 37.360 1.00 0.00 N +ATOM 185 H LEU A 12 38.100 21.745 37.569 1.00 0.00 H +ATOM 186 CA LEU A 12 36.262 21.294 36.760 1.00 0.00 C +ATOM 187 HA LEU A 12 35.427 20.887 37.329 1.00 0.00 H +ATOM 188 CB LEU A 12 36.169 22.873 36.785 1.00 0.00 C +ATOM 189 HB2 LEU A 12 36.531 23.238 37.746 1.00 0.00 H +ATOM 190 HB3 LEU A 12 36.859 23.268 36.041 1.00 0.00 H +ATOM 191 CG LEU A 12 34.824 23.483 36.357 1.00 0.00 C +ATOM 192 HG LEU A 12 34.479 23.028 35.428 1.00 0.00 H +ATOM 193 CD1 LEU A 12 33.867 23.321 37.477 1.00 0.00 C +ATOM 194 HD11 LEU A 12 32.997 23.877 37.126 1.00 0.00 H +ATOM 195 HD12 LEU A 12 34.304 23.691 38.404 1.00 0.00 H +ATOM 196 HD13 LEU A 12 33.594 22.265 37.503 1.00 0.00 H +ATOM 197 CD2 LEU A 12 34.926 25.052 36.181 1.00 0.00 C +ATOM 198 HD21 LEU A 12 35.334 25.560 37.054 1.00 0.00 H +ATOM 199 HD22 LEU A 12 33.926 25.442 35.997 1.00 0.00 H +ATOM 200 HD23 LEU A 12 35.555 25.355 35.344 1.00 0.00 H +ATOM 201 C LEU A 12 36.092 20.805 35.283 1.00 0.00 C +ATOM 202 O LEU A 12 36.941 21.102 34.441 1.00 0.00 O +ATOM 203 N LYS A 13 35.016 20.080 34.906 1.00 0.00 N +ATOM 204 H LYS A 13 34.391 19.697 35.602 1.00 0.00 H +ATOM 205 CA LYS A 13 34.642 19.704 33.571 1.00 0.00 C +ATOM 206 HA LYS A 13 35.063 20.421 32.866 1.00 0.00 H +ATOM 207 CB LYS A 13 35.034 18.226 33.244 1.00 0.00 C +ATOM 208 HB2 LYS A 13 34.497 17.579 33.938 1.00 0.00 H +ATOM 209 HB3 LYS A 13 34.849 17.922 32.214 1.00 0.00 H +ATOM 210 CG LYS A 13 36.515 17.923 33.472 1.00 0.00 C +ATOM 211 HG2 LYS A 13 37.162 18.658 32.994 1.00 0.00 H +ATOM 212 HG3 LYS A 13 36.701 17.768 34.535 1.00 0.00 H +ATOM 213 CD LYS A 13 36.804 16.487 32.994 1.00 0.00 C +ATOM 214 HD2 LYS A 13 36.157 15.747 33.465 1.00 0.00 H +ATOM 215 HD3 LYS A 13 36.456 16.506 31.962 1.00 0.00 H +ATOM 216 CE LYS A 13 38.264 16.163 32.997 1.00 0.00 C +ATOM 217 HE2 LYS A 13 38.741 16.732 32.199 1.00 0.00 H +ATOM 218 HE3 LYS A 13 38.686 16.424 33.967 1.00 0.00 H +ATOM 219 NZ LYS A 13 38.397 14.672 32.837 1.00 0.00 N1+ +ATOM 220 HZ1 LYS A 13 37.944 14.324 32.005 1.00 0.00 H +ATOM 221 HZ2 LYS A 13 37.888 14.239 33.595 1.00 0.00 H +ATOM 222 HZ3 LYS A 13 39.367 14.391 32.817 1.00 0.00 H +ATOM 223 C LYS A 13 33.119 19.875 33.400 1.00 0.00 C +ATOM 224 O LYS A 13 32.522 20.218 34.448 1.00 0.00 O +ATOM 225 N GLY A 14 32.541 19.929 32.182 1.00 0.00 N +ATOM 226 H GLY A 14 33.085 19.611 31.392 1.00 0.00 H +ATOM 227 CA GLY A 14 31.141 20.135 31.951 1.00 0.00 C +ATOM 228 HA2 GLY A 14 30.696 19.143 31.877 1.00 0.00 H +ATOM 229 HA3 GLY A 14 30.707 20.500 32.883 1.00 0.00 H +ATOM 230 C GLY A 14 30.726 21.030 30.803 1.00 0.00 C +ATOM 231 O GLY A 14 31.459 21.986 30.478 1.00 0.00 O +ATOM 232 N GLU A 15 29.602 20.661 30.175 1.00 0.00 N +ATOM 233 H GLU A 15 29.233 19.801 30.557 1.00 0.00 H +ATOM 234 CA GLU A 15 29.053 21.595 29.115 1.00 0.00 C +ATOM 235 HA GLU A 15 29.457 22.592 29.292 1.00 0.00 H +ATOM 236 CB GLU A 15 29.452 21.151 27.705 1.00 0.00 C +ATOM 237 HB2 GLU A 15 28.886 21.770 27.009 1.00 0.00 H +ATOM 238 HB3 GLU A 15 30.497 21.396 27.512 1.00 0.00 H +ATOM 239 CG GLU A 15 29.157 19.668 27.410 1.00 0.00 C +ATOM 240 HG2 GLU A 15 29.865 19.104 28.017 1.00 0.00 H +ATOM 241 HG3 GLU A 15 28.109 19.456 27.619 1.00 0.00 H +ATOM 242 CD GLU A 15 29.423 19.385 25.968 1.00 0.00 C +ATOM 243 OE1 GLU A 15 28.458 19.250 25.177 1.00 0.00 O1- +ATOM 244 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O1- +ATOM 245 C GLU A 15 27.563 21.843 29.353 1.00 0.00 C +ATOM 246 O GLU A 15 26.814 21.020 29.796 1.00 0.00 O +ATOM 247 N THR A 16 27.080 22.966 28.863 1.00 0.00 N +ATOM 248 H THR A 16 27.718 23.647 28.477 1.00 0.00 H +ATOM 249 CA THR A 16 25.618 23.342 28.987 1.00 0.00 C +ATOM 250 HA THR A 16 24.987 22.466 28.832 1.00 0.00 H +ATOM 251 CB THR A 16 25.300 23.755 30.463 1.00 0.00 C +ATOM 252 HB THR A 16 25.664 23.028 31.190 1.00 0.00 H +ATOM 253 CG2 THR A 16 26.079 25.029 30.851 1.00 0.00 C +ATOM 254 HG21 THR A 16 26.002 25.212 31.923 1.00 0.00 H +ATOM 255 HG22 THR A 16 25.827 25.999 30.420 1.00 0.00 H +ATOM 256 HG23 THR A 16 27.139 24.833 30.686 1.00 0.00 H +ATOM 257 OG1 THR A 16 23.919 23.870 30.591 1.00 0.00 O +ATOM 258 HG1 THR A 16 23.605 22.966 30.654 1.00 0.00 H +ATOM 259 C THR A 16 25.136 24.387 27.956 1.00 0.00 C +ATOM 260 O THR A 16 25.847 25.392 27.686 1.00 0.00 O +ATOM 261 N THR A 17 23.944 24.126 27.374 1.00 0.00 N +ATOM 262 H THR A 17 23.414 23.300 27.615 1.00 0.00 H +ATOM 263 CA THR A 17 23.341 25.088 26.418 1.00 0.00 C +ATOM 264 HA THR A 17 24.139 25.697 25.992 1.00 0.00 H +ATOM 265 CB THR A 17 22.634 24.399 25.250 1.00 0.00 C +ATOM 266 HB THR A 17 22.194 25.142 24.585 1.00 0.00 H +ATOM 267 CG2 THR A 17 23.534 23.466 24.406 1.00 0.00 C +ATOM 268 HG21 THR A 17 22.981 22.875 23.677 1.00 0.00 H +ATOM 269 HG22 THR A 17 24.016 22.789 25.112 1.00 0.00 H +ATOM 270 HG23 THR A 17 24.305 24.119 23.998 1.00 0.00 H +ATOM 271 OG1 THR A 17 21.618 23.516 25.740 1.00 0.00 O +ATOM 272 HG1 THR A 17 21.158 23.210 24.955 1.00 0.00 H +ATOM 273 C THR A 17 22.409 26.084 27.080 1.00 0.00 C +ATOM 274 O THR A 17 21.865 25.880 28.171 1.00 0.00 O +ATOM 275 N THR A 18 22.284 27.186 26.367 1.00 0.00 N +ATOM 276 H THR A 18 22.918 27.211 25.581 1.00 0.00 H +ATOM 277 CA THR A 18 21.341 28.346 26.665 1.00 0.00 C +ATOM 278 HA THR A 18 20.447 28.047 27.213 1.00 0.00 H +ATOM 279 CB THR A 18 21.968 29.424 27.606 1.00 0.00 C +ATOM 280 HB THR A 18 22.926 29.800 27.251 1.00 0.00 H +ATOM 281 CG2 THR A 18 20.959 30.565 27.747 1.00 0.00 C +ATOM 282 HG21 THR A 18 21.177 31.232 28.581 1.00 0.00 H +ATOM 283 HG22 THR A 18 19.932 30.214 27.838 1.00 0.00 H +ATOM 284 HG23 THR A 18 21.057 31.149 26.831 1.00 0.00 H +ATOM 285 OG1 THR A 18 21.983 28.974 29.051 1.00 0.00 O +ATOM 286 HG1 THR A 18 22.866 29.123 29.400 1.00 0.00 H +ATOM 287 C THR A 18 20.829 28.956 25.354 1.00 0.00 C +ATOM 288 O THR A 18 21.553 29.458 24.528 1.00 0.00 O +ATOM 289 N GLU A 19 19.542 28.872 25.083 1.00 0.00 N +ATOM 290 H GLU A 19 18.919 28.579 25.823 1.00 0.00 H +ATOM 291 CA GLU A 19 18.932 29.576 23.987 1.00 0.00 C +ATOM 292 HA GLU A 19 19.679 29.508 23.197 1.00 0.00 H +ATOM 293 CB GLU A 19 17.686 28.785 23.627 1.00 0.00 C +ATOM 294 HB2 GLU A 19 17.899 27.722 23.514 1.00 0.00 H +ATOM 295 HB3 GLU A 19 16.998 28.842 24.471 1.00 0.00 H +ATOM 296 CG GLU A 19 16.852 29.284 22.477 1.00 0.00 C +ATOM 297 HG2 GLU A 19 16.246 28.447 22.128 1.00 0.00 H +ATOM 298 HG3 GLU A 19 16.133 30.057 22.748 1.00 0.00 H +ATOM 299 CD GLU A 19 17.736 29.731 21.281 1.00 0.00 C +ATOM 300 OE1 GLU A 19 18.363 28.800 20.679 1.00 0.00 O1- +ATOM 301 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O1- +ATOM 302 C GLU A 19 18.631 31.049 24.311 1.00 0.00 C +ATOM 303 O GLU A 19 17.951 31.336 25.240 1.00 0.00 O +ATOM 304 N ALA A 20 19.109 32.052 23.609 1.00 0.00 N +ATOM 305 H ALA A 20 19.659 31.766 22.810 1.00 0.00 H +ATOM 306 CA ALA A 20 18.962 33.505 23.885 1.00 0.00 C +ATOM 307 HA ALA A 20 17.980 33.742 24.295 1.00 0.00 H +ATOM 308 CB ALA A 20 19.978 33.979 24.961 1.00 0.00 C +ATOM 309 HB1 ALA A 20 19.807 35.026 25.214 1.00 0.00 H +ATOM 310 HB2 ALA A 20 20.983 33.923 24.544 1.00 0.00 H +ATOM 311 HB3 ALA A 20 19.800 33.404 25.869 1.00 0.00 H +ATOM 312 C ALA A 20 19.121 34.352 22.595 1.00 0.00 C +ATOM 313 O ALA A 20 19.565 33.867 21.541 1.00 0.00 O +ATOM 314 N VAL A 21 18.819 35.698 22.666 1.00 0.00 N +ATOM 315 H VAL A 21 18.466 36.007 23.561 1.00 0.00 H +ATOM 316 CA VAL A 21 18.727 36.607 21.505 1.00 0.00 C +ATOM 317 HA VAL A 21 18.554 36.039 20.592 1.00 0.00 H +ATOM 318 CB VAL A 21 17.437 37.464 21.780 1.00 0.00 C +ATOM 319 HB VAL A 21 17.477 38.130 22.642 1.00 0.00 H +ATOM 320 CG1 VAL A 21 17.072 38.379 20.673 1.00 0.00 C +ATOM 321 HG11 VAL A 21 16.991 37.805 19.750 1.00 0.00 H +ATOM 322 HG12 VAL A 21 17.685 39.269 20.533 1.00 0.00 H +ATOM 323 HG13 VAL A 21 16.081 38.787 20.874 1.00 0.00 H +ATOM 324 CG2 VAL A 21 16.251 36.536 21.920 1.00 0.00 C +ATOM 325 HG21 VAL A 21 15.333 37.033 21.605 1.00 0.00 H +ATOM 326 HG22 VAL A 21 16.128 36.219 22.956 1.00 0.00 H +ATOM 327 HG23 VAL A 21 16.477 35.681 21.284 1.00 0.00 H +ATOM 328 C VAL A 21 19.976 37.521 21.405 1.00 0.00 C +ATOM 329 O VAL A 21 20.295 38.022 20.306 1.00 0.00 O +ATOM 330 N ASP A 22 20.728 37.651 22.457 1.00 0.00 N +ATOM 331 H ASP A 22 20.460 37.104 23.262 1.00 0.00 H +ATOM 332 CA ASP A 22 21.920 38.517 22.561 1.00 0.00 C +ATOM 333 HA ASP A 22 22.218 38.721 21.532 1.00 0.00 H +ATOM 334 CB ASP A 22 21.483 39.701 23.350 1.00 0.00 C +ATOM 335 HB2 ASP A 22 20.632 40.156 22.843 1.00 0.00 H +ATOM 336 HB3 ASP A 22 21.133 39.421 24.344 1.00 0.00 H +ATOM 337 CG ASP A 22 22.576 40.746 23.590 1.00 0.00 C +ATOM 338 OD1 ASP A 22 23.681 40.588 23.043 1.00 0.00 O1- +ATOM 339 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O1- +ATOM 340 C ASP A 22 23.019 37.703 23.294 1.00 0.00 C +ATOM 341 O ASP A 22 22.839 37.184 24.412 1.00 0.00 O +ATOM 342 N ALA A 23 24.210 37.649 22.694 1.00 0.00 N +ATOM 343 H ALA A 23 24.358 38.065 21.786 1.00 0.00 H +ATOM 344 CA ALA A 23 25.493 37.172 23.215 1.00 0.00 C +ATOM 345 HA ALA A 23 25.371 36.089 23.221 1.00 0.00 H +ATOM 346 CB ALA A 23 26.701 37.486 22.326 1.00 0.00 C +ATOM 347 HB1 ALA A 23 26.446 37.309 21.280 1.00 0.00 H +ATOM 348 HB2 ALA A 23 27.379 36.708 22.676 1.00 0.00 H +ATOM 349 HB3 ALA A 23 27.091 38.494 22.468 1.00 0.00 H +ATOM 350 C ALA A 23 25.748 37.757 24.642 1.00 0.00 C +ATOM 351 O ALA A 23 26.091 36.953 25.518 1.00 0.00 O +ATOM 352 N ALA A 24 25.564 39.050 24.846 1.00 0.00 N +ATOM 353 H ALA A 24 25.214 39.674 24.133 1.00 0.00 H +ATOM 354 CA ALA A 24 25.745 39.687 26.153 1.00 0.00 C +ATOM 355 HA ALA A 24 26.761 39.419 26.445 1.00 0.00 H +ATOM 356 CB ALA A 24 25.490 41.189 25.938 1.00 0.00 C +ATOM 357 HB1 ALA A 24 26.247 41.676 25.325 1.00 0.00 H +ATOM 358 HB2 ALA A 24 25.633 41.729 26.874 1.00 0.00 H +ATOM 359 HB3 ALA A 24 24.561 41.467 25.440 1.00 0.00 H +ATOM 360 C ALA A 24 24.796 39.101 27.137 1.00 0.00 C +ATOM 361 O ALA A 24 25.116 38.975 28.329 1.00 0.00 O +ATOM 362 N THR A 25 23.577 38.659 26.736 1.00 0.00 N +ATOM 363 H THR A 25 23.398 38.681 25.743 1.00 0.00 H +ATOM 364 CA THR A 25 22.587 38.094 27.680 1.00 0.00 C +ATOM 365 HA THR A 25 22.755 38.495 28.681 1.00 0.00 H +ATOM 366 CB THR A 25 21.196 38.549 27.262 1.00 0.00 C +ATOM 367 HB THR A 25 20.797 37.883 26.497 1.00 0.00 H +ATOM 368 CG2 THR A 25 20.246 38.369 28.438 1.00 0.00 C +ATOM 369 HG21 THR A 25 20.203 37.329 28.763 1.00 0.00 H +ATOM 370 HG22 THR A 25 19.255 38.740 28.176 1.00 0.00 H +ATOM 371 HG23 THR A 25 20.574 38.977 29.280 1.00 0.00 H +ATOM 372 OG1 THR A 25 21.199 39.931 27.030 1.00 0.00 O +ATOM 373 HG1 THR A 25 20.293 40.156 26.807 1.00 0.00 H +ATOM 374 C THR A 25 22.788 36.618 27.928 1.00 0.00 C +ATOM 375 O THR A 25 22.618 36.164 29.050 1.00 0.00 O +ATOM 376 N ALA A 26 23.216 35.854 26.929 1.00 0.00 N +ATOM 377 H ALA A 26 23.315 36.208 25.988 1.00 0.00 H +ATOM 378 CA ALA A 26 23.652 34.513 27.159 1.00 0.00 C +ATOM 379 HA ALA A 26 22.781 33.940 27.476 1.00 0.00 H +ATOM 380 CB ALA A 26 24.062 33.913 25.734 1.00 0.00 C +ATOM 381 HB1 ALA A 26 23.120 33.732 25.215 1.00 0.00 H +ATOM 382 HB2 ALA A 26 24.695 33.029 25.804 1.00 0.00 H +ATOM 383 HB3 ALA A 26 24.715 34.613 25.211 1.00 0.00 H +ATOM 384 C ALA A 26 24.856 34.523 28.062 1.00 0.00 C +ATOM 385 O ALA A 26 24.889 33.745 28.985 1.00 0.00 O +ATOM 386 N GLU A 27 25.749 35.500 28.027 1.00 0.00 N +ATOM 387 H GLU A 27 25.940 35.933 27.135 1.00 0.00 H +ATOM 388 CA GLU A 27 26.712 35.671 29.037 1.00 0.00 C +ATOM 389 HA GLU A 27 27.306 34.757 29.097 1.00 0.00 H +ATOM 390 CB GLU A 27 27.684 36.833 28.605 1.00 0.00 C +ATOM 391 HB2 GLU A 27 28.270 36.561 27.728 1.00 0.00 H +ATOM 392 HB3 GLU A 27 27.178 37.773 28.387 1.00 0.00 H +ATOM 393 CG GLU A 27 28.742 37.165 29.664 1.00 0.00 C +ATOM 394 HG2 GLU A 27 28.193 37.537 30.529 1.00 0.00 H +ATOM 395 HG3 GLU A 27 29.267 36.244 29.914 1.00 0.00 H +ATOM 396 CD GLU A 27 29.887 38.242 29.269 1.00 0.00 C +ATOM 397 OE1 GLU A 27 31.108 37.827 29.164 1.00 0.00 O1- +ATOM 398 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O1- +ATOM 399 C GLU A 27 26.099 35.742 30.450 1.00 0.00 C +ATOM 400 O GLU A 27 26.553 35.162 31.414 1.00 0.00 O +ATOM 401 N LYS A 28 25.124 36.609 30.604 1.00 0.00 N +ATOM 402 H LYS A 28 24.710 37.106 29.827 1.00 0.00 H +ATOM 403 CA LYS A 28 24.538 36.947 31.950 1.00 0.00 C +ATOM 404 HA LYS A 28 25.324 37.300 32.618 1.00 0.00 H +ATOM 405 CB LYS A 28 23.559 38.052 31.728 1.00 0.00 C +ATOM 406 HB2 LYS A 28 24.096 38.943 31.403 1.00 0.00 H +ATOM 407 HB3 LYS A 28 22.761 37.811 31.025 1.00 0.00 H +ATOM 408 CG LYS A 28 22.885 38.401 33.150 1.00 0.00 C +ATOM 409 HG2 LYS A 28 22.343 37.542 33.545 1.00 0.00 H +ATOM 410 HG3 LYS A 28 23.638 38.698 33.879 1.00 0.00 H +ATOM 411 CD LYS A 28 21.826 39.579 33.063 1.00 0.00 C +ATOM 412 HD2 LYS A 28 20.930 39.146 32.616 1.00 0.00 H +ATOM 413 HD3 LYS A 28 21.656 39.989 34.058 1.00 0.00 H +ATOM 414 CE LYS A 28 22.359 40.850 32.267 1.00 0.00 C +ATOM 415 HE2 LYS A 28 23.432 40.899 32.449 1.00 0.00 H +ATOM 416 HE3 LYS A 28 22.199 40.756 31.193 1.00 0.00 H +ATOM 417 NZ LYS A 28 21.521 42.013 32.715 1.00 0.00 N1+ +ATOM 418 HZ1 LYS A 28 21.696 42.294 33.670 1.00 0.00 H +ATOM 419 HZ2 LYS A 28 20.541 41.777 32.653 1.00 0.00 H +ATOM 420 HZ3 LYS A 28 21.651 42.827 32.131 1.00 0.00 H +ATOM 421 C LYS A 28 23.866 35.778 32.535 1.00 0.00 C +ATOM 422 O LYS A 28 23.994 35.665 33.742 1.00 0.00 O +ATOM 423 N VAL A 29 23.329 34.885 31.712 1.00 0.00 N +ATOM 424 H VAL A 29 23.229 35.111 30.733 1.00 0.00 H +ATOM 425 CA VAL A 29 22.736 33.650 32.097 1.00 0.00 C +ATOM 426 HA VAL A 29 21.999 33.879 32.866 1.00 0.00 H +ATOM 427 CB VAL A 29 21.735 33.166 30.962 1.00 0.00 C +ATOM 428 HB VAL A 29 22.375 32.951 30.106 1.00 0.00 H +ATOM 429 CG1 VAL A 29 21.139 31.783 31.445 1.00 0.00 C +ATOM 430 HG11 VAL A 29 20.592 31.413 30.579 1.00 0.00 H +ATOM 431 HG12 VAL A 29 20.575 31.908 32.370 1.00 0.00 H +ATOM 432 HG13 VAL A 29 21.993 31.113 31.534 1.00 0.00 H +ATOM 433 CG2 VAL A 29 20.482 33.992 30.547 1.00 0.00 C +ATOM 434 HG21 VAL A 29 19.966 33.618 29.662 1.00 0.00 H +ATOM 435 HG22 VAL A 29 20.739 35.019 30.286 1.00 0.00 H +ATOM 436 HG23 VAL A 29 19.838 34.110 31.419 1.00 0.00 H +ATOM 437 C VAL A 29 23.781 32.642 32.484 1.00 0.00 C +ATOM 438 O VAL A 29 23.604 31.876 33.462 1.00 0.00 O +ATOM 439 N PHE A 30 24.962 32.641 31.758 1.00 0.00 N +ATOM 440 H PHE A 30 24.997 33.287 30.981 1.00 0.00 H +ATOM 441 CA PHE A 30 26.112 31.701 32.033 1.00 0.00 C +ATOM 442 HA PHE A 30 25.692 30.753 32.371 1.00 0.00 H +ATOM 443 CB PHE A 30 26.901 31.582 30.713 1.00 0.00 C +ATOM 444 HB2 PHE A 30 26.966 32.537 30.191 1.00 0.00 H +ATOM 445 HB3 PHE A 30 27.928 31.266 30.888 1.00 0.00 H +ATOM 446 CG PHE A 30 26.348 30.600 29.656 1.00 0.00 C +ATOM 447 CD1 PHE A 30 25.751 29.296 29.878 1.00 0.00 C +ATOM 448 HD1 PHE A 30 25.705 28.943 30.897 1.00 0.00 H +ATOM 449 CE1 PHE A 30 25.345 28.377 28.817 1.00 0.00 C +ATOM 450 HE1 PHE A 30 24.810 27.464 29.039 1.00 0.00 H +ATOM 451 CZ PHE A 30 25.534 28.840 27.515 1.00 0.00 C +ATOM 452 HZ PHE A 30 25.196 28.267 26.666 1.00 0.00 H +ATOM 453 CE2 PHE A 30 26.096 30.099 27.271 1.00 0.00 C +ATOM 454 HE2 PHE A 30 26.212 30.319 26.219 1.00 0.00 H +ATOM 455 CD2 PHE A 30 26.533 30.924 28.297 1.00 0.00 C +ATOM 456 HD2 PHE A 30 27.135 31.778 28.029 1.00 0.00 H +ATOM 457 C PHE A 30 26.988 32.189 33.246 1.00 0.00 C +ATOM 458 O PHE A 30 27.609 31.344 33.905 1.00 0.00 O +ATOM 459 N LYS A 31 27.038 33.446 33.540 1.00 0.00 N +ATOM 460 H LYS A 31 26.710 34.105 32.849 1.00 0.00 H +ATOM 461 CA LYS A 31 27.405 34.022 34.854 1.00 0.00 C +ATOM 462 HA LYS A 31 28.437 33.764 35.092 1.00 0.00 H +ATOM 463 CB LYS A 31 27.274 35.599 34.858 1.00 0.00 C +ATOM 464 HB2 LYS A 31 26.242 35.714 34.527 1.00 0.00 H +ATOM 465 HB3 LYS A 31 27.292 36.098 35.827 1.00 0.00 H +ATOM 466 CG LYS A 31 28.378 36.275 33.919 1.00 0.00 C +ATOM 467 HG2 LYS A 31 28.522 35.710 32.997 1.00 0.00 H +ATOM 468 HG3 LYS A 31 27.926 37.229 33.649 1.00 0.00 H +ATOM 469 CD LYS A 31 29.823 36.487 34.439 1.00 0.00 C +ATOM 470 HD2 LYS A 31 29.755 36.977 35.411 1.00 0.00 H +ATOM 471 HD3 LYS A 31 30.132 35.472 34.684 1.00 0.00 H +ATOM 472 CE LYS A 31 30.777 37.150 33.394 1.00 0.00 C +ATOM 473 HE2 LYS A 31 30.633 36.630 32.447 1.00 0.00 H +ATOM 474 HE3 LYS A 31 30.436 38.158 33.158 1.00 0.00 H +ATOM 475 NZ LYS A 31 32.138 37.121 33.926 1.00 0.00 N1+ +ATOM 476 HZ1 LYS A 31 32.272 37.458 34.869 1.00 0.00 H +ATOM 477 HZ2 LYS A 31 32.676 37.777 33.376 1.00 0.00 H +ATOM 478 HZ3 LYS A 31 32.555 36.210 33.805 1.00 0.00 H +ATOM 479 C LYS A 31 26.516 33.562 35.983 1.00 0.00 C +ATOM 480 O LYS A 31 27.018 32.993 36.943 1.00 0.00 O +ATOM 481 N GLN A 32 25.185 33.745 35.953 1.00 0.00 N +ATOM 482 H GLN A 32 24.737 34.194 35.166 1.00 0.00 H +ATOM 483 CA GLN A 32 24.365 33.197 37.027 1.00 0.00 C +ATOM 484 HA GLN A 32 24.679 33.822 37.863 1.00 0.00 H +ATOM 485 CB GLN A 32 22.891 33.427 36.688 1.00 0.00 C +ATOM 486 HB2 GLN A 32 22.845 33.366 35.601 1.00 0.00 H +ATOM 487 HB3 GLN A 32 22.285 32.685 37.209 1.00 0.00 H +ATOM 488 CG GLN A 32 22.280 34.840 37.028 1.00 0.00 C +ATOM 489 HG2 GLN A 32 22.039 34.881 38.090 1.00 0.00 H +ATOM 490 HG3 GLN A 32 22.899 35.710 36.807 1.00 0.00 H +ATOM 491 CD GLN A 32 20.958 35.124 36.195 1.00 0.00 C +ATOM 492 OE1 GLN A 32 19.883 34.823 36.738 1.00 0.00 O +ATOM 493 NE2 GLN A 32 20.988 35.530 34.974 1.00 0.00 N +ATOM 494 HE21 GLN A 32 21.902 35.787 34.628 1.00 0.00 H +ATOM 495 HE22 GLN A 32 20.177 35.714 34.400 1.00 0.00 H +ATOM 496 C GLN A 32 24.598 31.707 37.232 1.00 0.00 C +ATOM 497 O GLN A 32 24.794 31.293 38.384 1.00 0.00 O +ATOM 498 N TYR A 33 24.530 30.875 36.142 1.00 0.00 N +ATOM 499 H TYR A 33 24.587 31.274 35.216 1.00 0.00 H +ATOM 500 CA TYR A 33 24.722 29.459 36.217 1.00 0.00 C +ATOM 501 HA TYR A 33 23.881 29.042 36.772 1.00 0.00 H +ATOM 502 CB TYR A 33 24.622 28.848 34.842 1.00 0.00 C +ATOM 503 HB2 TYR A 33 23.621 29.006 34.442 1.00 0.00 H +ATOM 504 HB3 TYR A 33 25.353 29.388 34.240 1.00 0.00 H +ATOM 505 CG TYR A 33 24.877 27.304 34.704 1.00 0.00 C +ATOM 506 CD1 TYR A 33 23.808 26.383 34.938 1.00 0.00 C +ATOM 507 HD1 TYR A 33 22.814 26.754 35.140 1.00 0.00 H +ATOM 508 CE1 TYR A 33 24.054 24.991 35.075 1.00 0.00 C +ATOM 509 HE1 TYR A 33 23.300 24.251 35.300 1.00 0.00 H +ATOM 510 CZ TYR A 33 25.399 24.562 34.934 1.00 0.00 C +ATOM 511 OH TYR A 33 25.658 23.212 34.983 1.00 0.00 O +ATOM 512 HH TYR A 33 26.608 23.080 35.030 1.00 0.00 H +ATOM 513 CE2 TYR A 33 26.410 25.459 34.723 1.00 0.00 C +ATOM 514 HE2 TYR A 33 27.443 25.157 34.630 1.00 0.00 H +ATOM 515 CD2 TYR A 33 26.146 26.818 34.602 1.00 0.00 C +ATOM 516 HD2 TYR A 33 26.992 27.469 34.435 1.00 0.00 H +ATOM 517 C TYR A 33 26.078 29.155 36.854 1.00 0.00 C +ATOM 518 O TYR A 33 26.179 28.186 37.566 1.00 0.00 O +ATOM 519 N ALA A 34 27.159 29.788 36.508 1.00 0.00 N +ATOM 520 H ALA A 34 26.997 30.563 35.881 1.00 0.00 H +ATOM 521 CA ALA A 34 28.473 29.535 37.100 1.00 0.00 C +ATOM 522 HA ALA A 34 28.717 28.476 37.023 1.00 0.00 H +ATOM 523 CB ALA A 34 29.651 30.265 36.402 1.00 0.00 C +ATOM 524 HB1 ALA A 34 30.577 29.813 36.757 1.00 0.00 H +ATOM 525 HB2 ALA A 34 29.619 31.296 36.752 1.00 0.00 H +ATOM 526 HB3 ALA A 34 29.681 30.159 35.317 1.00 0.00 H +ATOM 527 C ALA A 34 28.508 29.835 38.614 1.00 0.00 C +ATOM 528 O ALA A 34 29.097 29.077 39.389 1.00 0.00 O +ATOM 529 N ASN A 35 27.814 30.864 39.024 1.00 0.00 N +ATOM 530 H ASN A 35 27.594 31.535 38.301 1.00 0.00 H +ATOM 531 CA ASN A 35 27.743 31.252 40.445 1.00 0.00 C +ATOM 532 HA ASN A 35 28.713 31.168 40.935 1.00 0.00 H +ATOM 533 CB ASN A 35 27.254 32.684 40.541 1.00 0.00 C +ATOM 534 HB2 ASN A 35 27.798 33.361 39.883 1.00 0.00 H +ATOM 535 HB3 ASN A 35 26.192 32.727 40.300 1.00 0.00 H +ATOM 536 CG ASN A 35 27.326 33.169 41.947 1.00 0.00 C +ATOM 537 OD1 ASN A 35 26.493 32.743 42.763 1.00 0.00 O +ATOM 538 ND2 ASN A 35 28.099 34.183 42.223 1.00 0.00 N +ATOM 539 HD21 ASN A 35 28.867 34.350 41.589 1.00 0.00 H +ATOM 540 HD22 ASN A 35 28.276 34.397 43.193 1.00 0.00 H +ATOM 541 C ASN A 35 26.833 30.200 41.127 1.00 0.00 C +ATOM 542 O ASN A 35 27.114 29.686 42.238 1.00 0.00 O +ATOM 543 N ASP A 36 25.819 29.616 40.395 1.00 0.00 N +ATOM 544 H ASP A 36 25.608 30.144 39.560 1.00 0.00 H +ATOM 545 CA ASP A 36 25.004 28.401 40.867 1.00 0.00 C +ATOM 546 HA ASP A 36 24.491 28.819 41.733 1.00 0.00 H +ATOM 547 CB ASP A 36 23.819 28.175 39.948 1.00 0.00 C +ATOM 548 HB2 ASP A 36 23.379 29.117 39.623 1.00 0.00 H +ATOM 549 HB3 ASP A 36 24.279 27.586 39.154 1.00 0.00 H +ATOM 550 CG ASP A 36 22.720 27.350 40.470 1.00 0.00 C +ATOM 551 OD1 ASP A 36 22.214 26.485 39.714 1.00 0.00 O1- +ATOM 552 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O1- +ATOM 553 C ASP A 36 25.793 27.113 41.244 1.00 0.00 C +ATOM 554 O ASP A 36 25.357 26.391 42.112 1.00 0.00 O +ATOM 555 N ASN A 37 26.991 27.006 40.666 1.00 0.00 N +ATOM 556 H ASN A 37 27.306 27.779 40.098 1.00 0.00 H +ATOM 557 CA ASN A 37 27.829 25.814 40.636 1.00 0.00 C +ATOM 558 HA ASN A 37 27.378 25.130 41.354 1.00 0.00 H +ATOM 559 CB ASN A 37 27.873 25.281 39.195 1.00 0.00 C +ATOM 560 HB2 ASN A 37 27.936 26.106 38.487 1.00 0.00 H +ATOM 561 HB3 ASN A 37 28.702 24.579 39.101 1.00 0.00 H +ATOM 562 CG ASN A 37 26.652 24.492 38.842 1.00 0.00 C +ATOM 563 OD1 ASN A 37 26.432 23.357 39.282 1.00 0.00 O +ATOM 564 ND2 ASN A 37 25.706 25.057 38.177 1.00 0.00 N +ATOM 565 HD21 ASN A 37 25.804 26.050 38.016 1.00 0.00 H +ATOM 566 HD22 ASN A 37 24.895 24.502 37.947 1.00 0.00 H +ATOM 567 C ASN A 37 29.196 26.053 41.261 1.00 0.00 C +ATOM 568 O ASN A 37 30.064 25.171 41.182 1.00 0.00 O +ATOM 569 N GLY A 38 29.358 27.176 42.012 1.00 0.00 N +ATOM 570 H GLY A 38 28.556 27.765 42.189 1.00 0.00 H +ATOM 571 CA GLY A 38 30.637 27.460 42.681 1.00 0.00 C +ATOM 572 HA2 GLY A 38 30.444 28.296 43.354 1.00 0.00 H +ATOM 573 HA3 GLY A 38 30.900 26.655 43.368 1.00 0.00 H +ATOM 574 C GLY A 38 31.894 27.774 41.785 1.00 0.00 C +ATOM 575 O GLY A 38 33.027 27.429 42.124 1.00 0.00 O +ATOM 576 N VAL A 39 31.731 28.287 40.579 1.00 0.00 N +ATOM 577 H VAL A 39 30.794 28.624 40.408 1.00 0.00 H +ATOM 578 CA VAL A 39 32.664 28.449 39.403 1.00 0.00 C +ATOM 579 HA VAL A 39 33.598 27.911 39.570 1.00 0.00 H +ATOM 580 CB VAL A 39 32.015 27.778 38.179 1.00 0.00 C +ATOM 581 HB VAL A 39 31.005 28.158 38.027 1.00 0.00 H +ATOM 582 CG1 VAL A 39 32.989 28.121 37.014 1.00 0.00 C +ATOM 583 HG11 VAL A 39 32.636 27.519 36.176 1.00 0.00 H +ATOM 584 HG12 VAL A 39 34.019 27.963 37.334 1.00 0.00 H +ATOM 585 HG13 VAL A 39 32.869 29.117 36.588 1.00 0.00 H +ATOM 586 CG2 VAL A 39 31.943 26.274 38.437 1.00 0.00 C +ATOM 587 HG21 VAL A 39 31.540 25.729 37.583 1.00 0.00 H +ATOM 588 HG22 VAL A 39 31.356 26.086 39.337 1.00 0.00 H +ATOM 589 HG23 VAL A 39 32.907 25.863 38.738 1.00 0.00 H +ATOM 590 C VAL A 39 33.029 29.909 39.235 1.00 0.00 C +ATOM 591 O VAL A 39 32.186 30.683 38.757 1.00 0.00 O +ATOM 592 N ASP A 40 34.268 30.281 39.558 1.00 0.00 N +ATOM 593 H ASP A 40 34.838 29.543 39.947 1.00 0.00 H +ATOM 594 CA ASP A 40 34.875 31.551 39.096 1.00 0.00 C +ATOM 595 HA ASP A 40 34.143 32.078 38.487 1.00 0.00 H +ATOM 596 CB ASP A 40 35.183 32.418 40.345 1.00 0.00 C +ATOM 597 HB2 ASP A 40 34.184 32.657 40.710 1.00 0.00 H +ATOM 598 HB3 ASP A 40 35.707 31.788 41.065 1.00 0.00 H +ATOM 599 CG ASP A 40 35.879 33.683 40.009 1.00 0.00 C +ATOM 600 OD1 ASP A 40 35.393 34.410 39.076 1.00 0.00 O1- +ATOM 601 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O1- +ATOM 602 C ASP A 40 36.062 31.169 38.238 1.00 0.00 C +ATOM 603 O ASP A 40 36.850 30.275 38.630 1.00 0.00 O +ATOM 604 N GLY A 41 36.172 31.751 37.102 1.00 0.00 N +ATOM 605 H GLY A 41 35.443 32.408 36.858 1.00 0.00 H +ATOM 606 CA GLY A 41 37.214 31.484 36.189 1.00 0.00 C +ATOM 607 HA2 GLY A 41 38.072 31.014 36.670 1.00 0.00 H +ATOM 608 HA3 GLY A 41 36.761 30.672 35.620 1.00 0.00 H +ATOM 609 C GLY A 41 37.623 32.709 35.379 1.00 0.00 C +ATOM 610 O GLY A 41 37.288 33.862 35.686 1.00 0.00 O +ATOM 611 N GLU A 42 38.354 32.422 34.316 1.00 0.00 N +ATOM 612 H GLU A 42 38.789 31.512 34.368 1.00 0.00 H +ATOM 613 CA GLU A 42 38.603 33.310 33.228 1.00 0.00 C +ATOM 614 HA GLU A 42 38.329 34.318 33.541 1.00 0.00 H +ATOM 615 CB GLU A 42 40.158 33.294 33.040 1.00 0.00 C +ATOM 616 HB2 GLU A 42 40.656 33.398 34.004 1.00 0.00 H +ATOM 617 HB3 GLU A 42 40.417 32.326 32.611 1.00 0.00 H +ATOM 618 CG GLU A 42 40.673 34.328 32.046 1.00 0.00 C +ATOM 619 HG2 GLU A 42 41.606 34.015 31.580 1.00 0.00 H +ATOM 620 HG3 GLU A 42 39.970 34.501 31.231 1.00 0.00 H +ATOM 621 CD GLU A 42 41.014 35.613 32.804 1.00 0.00 C +ATOM 622 OE1 GLU A 42 41.944 35.693 33.644 1.00 0.00 O1- +ATOM 623 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O1- +ATOM 624 C GLU A 42 37.780 33.033 32.033 1.00 0.00 C +ATOM 625 O GLU A 42 37.577 31.870 31.690 1.00 0.00 O +ATOM 626 N TRP A 43 37.228 34.069 31.412 1.00 0.00 N +ATOM 627 H TRP A 43 37.423 35.035 31.634 1.00 0.00 H +ATOM 628 CA TRP A 43 36.233 33.951 30.354 1.00 0.00 C +ATOM 629 HA TRP A 43 35.850 32.931 30.348 1.00 0.00 H +ATOM 630 CB TRP A 43 34.984 34.889 30.616 1.00 0.00 C +ATOM 631 HB2 TRP A 43 35.436 35.868 30.771 1.00 0.00 H +ATOM 632 HB3 TRP A 43 34.427 34.918 29.679 1.00 0.00 H +ATOM 633 CG TRP A 43 34.115 34.536 31.838 1.00 0.00 C +ATOM 634 CD1 TRP A 43 34.428 34.708 33.154 1.00 0.00 C +ATOM 635 HD1 TRP A 43 35.387 35.052 33.511 1.00 0.00 H +ATOM 636 NE1 TRP A 43 33.399 34.110 33.877 1.00 0.00 N +ATOM 637 HE1 TRP A 43 33.511 34.066 34.880 1.00 0.00 H +ATOM 638 CE2 TRP A 43 32.444 33.463 33.073 1.00 0.00 C +ATOM 639 CZ2 TRP A 43 31.248 32.745 33.296 1.00 0.00 C +ATOM 640 HZ2 TRP A 43 31.007 32.429 34.301 1.00 0.00 H +ATOM 641 CH2 TRP A 43 30.575 32.194 32.199 1.00 0.00 C +ATOM 642 HH2 TRP A 43 29.740 31.527 32.355 1.00 0.00 H +ATOM 643 CZ3 TRP A 43 30.988 32.541 30.909 1.00 0.00 C +ATOM 644 HZ3 TRP A 43 30.412 32.236 30.047 1.00 0.00 H +ATOM 645 CE3 TRP A 43 32.109 33.327 30.682 1.00 0.00 C +ATOM 646 HE3 TRP A 43 32.397 33.679 29.703 1.00 0.00 H +ATOM 647 CD2 TRP A 43 32.870 33.817 31.765 1.00 0.00 C +ATOM 648 C TRP A 43 36.910 34.235 29.034 1.00 0.00 C +ATOM 649 O TRP A 43 37.660 35.202 28.823 1.00 0.00 O +ATOM 650 N THR A 44 36.468 33.398 28.113 1.00 0.00 N +ATOM 651 H THR A 44 35.919 32.590 28.367 1.00 0.00 H +ATOM 652 CA THR A 44 36.627 33.526 26.668 1.00 0.00 C +ATOM 653 HA THR A 44 36.825 34.580 26.474 1.00 0.00 H +ATOM 654 CB THR A 44 37.813 32.794 26.062 1.00 0.00 C +ATOM 655 HB THR A 44 37.695 32.789 24.978 1.00 0.00 H +ATOM 656 CG2 THR A 44 39.142 33.411 26.470 1.00 0.00 C +ATOM 657 HG21 THR A 44 39.971 32.814 26.090 1.00 0.00 H +ATOM 658 HG22 THR A 44 39.277 33.395 27.552 1.00 0.00 H +ATOM 659 HG23 THR A 44 39.360 34.408 26.088 1.00 0.00 H +ATOM 660 OG1 THR A 44 37.854 31.507 26.604 1.00 0.00 O +ATOM 661 HG1 THR A 44 37.629 30.907 25.889 1.00 0.00 H +ATOM 662 C THR A 44 35.267 33.295 26.005 1.00 0.00 C +ATOM 663 O THR A 44 34.480 32.577 26.444 1.00 0.00 O +ATOM 664 N TYR A 45 35.137 33.919 24.848 1.00 0.00 N +ATOM 665 H TYR A 45 35.900 34.526 24.585 1.00 0.00 H +ATOM 666 CA TYR A 45 34.051 33.679 23.814 1.00 0.00 C +ATOM 667 HA TYR A 45 33.565 32.748 24.109 1.00 0.00 H +ATOM 668 CB TYR A 45 33.061 34.890 23.836 1.00 0.00 C +ATOM 669 HB2 TYR A 45 32.689 35.085 24.843 1.00 0.00 H +ATOM 670 HB3 TYR A 45 33.670 35.762 23.596 1.00 0.00 H +ATOM 671 CG TYR A 45 31.825 34.747 22.962 1.00 0.00 C +ATOM 672 CD1 TYR A 45 30.955 33.684 23.061 1.00 0.00 C +ATOM 673 HD1 TYR A 45 31.040 32.945 23.845 1.00 0.00 H +ATOM 674 CE1 TYR A 45 29.908 33.556 22.116 1.00 0.00 C +ATOM 675 HE1 TYR A 45 29.113 32.849 22.291 1.00 0.00 H +ATOM 676 CZ TYR A 45 29.718 34.506 21.094 1.00 0.00 C +ATOM 677 OH TYR A 45 28.658 34.338 20.268 1.00 0.00 O +ATOM 678 HH TYR A 45 28.496 35.052 19.648 1.00 0.00 H +ATOM 679 CE2 TYR A 45 30.653 35.574 21.028 1.00 0.00 C +ATOM 680 HE2 TYR A 45 30.490 36.288 20.234 1.00 0.00 H +ATOM 681 CD2 TYR A 45 31.752 35.643 21.911 1.00 0.00 C +ATOM 682 HD2 TYR A 45 32.537 36.346 21.679 1.00 0.00 H +ATOM 683 C TYR A 45 34.545 33.529 22.336 1.00 0.00 C +ATOM 684 O TYR A 45 35.260 34.412 21.809 1.00 0.00 O +ATOM 685 N ASP A 46 33.924 32.567 21.640 1.00 0.00 N +ATOM 686 H ASP A 46 33.215 32.006 22.088 1.00 0.00 H +ATOM 687 CA ASP A 46 34.109 32.289 20.204 1.00 0.00 C +ATOM 688 HA ASP A 46 34.805 32.896 19.625 1.00 0.00 H +ATOM 689 CB ASP A 46 34.818 30.917 20.240 1.00 0.00 C +ATOM 690 HB2 ASP A 46 35.700 31.032 20.871 1.00 0.00 H +ATOM 691 HB3 ASP A 46 34.252 30.200 20.834 1.00 0.00 H +ATOM 692 CG ASP A 46 35.216 30.282 18.912 1.00 0.00 C +ATOM 693 OD1 ASP A 46 34.405 29.507 18.323 1.00 0.00 O1- +ATOM 694 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O1- +ATOM 695 C ASP A 46 32.877 32.275 19.319 1.00 0.00 C +ATOM 696 O ASP A 46 31.931 31.517 19.529 1.00 0.00 O +ATOM 697 N ASP A 47 32.833 33.220 18.413 1.00 0.00 N +ATOM 698 H ASP A 47 33.622 33.852 18.429 1.00 0.00 H +ATOM 699 CA ASP A 47 31.688 33.456 17.554 1.00 0.00 C +ATOM 700 HA ASP A 47 30.773 33.561 18.137 1.00 0.00 H +ATOM 701 CB ASP A 47 31.907 34.738 16.747 1.00 0.00 C +ATOM 702 HB2 ASP A 47 32.113 35.510 17.488 1.00 0.00 H +ATOM 703 HB3 ASP A 47 32.853 34.697 16.207 1.00 0.00 H +ATOM 704 CG ASP A 47 30.729 35.187 15.844 1.00 0.00 C +ATOM 705 OD1 ASP A 47 29.551 35.040 16.174 1.00 0.00 O1- +ATOM 706 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O1- +ATOM 707 C ASP A 47 31.522 32.326 16.557 1.00 0.00 C +ATOM 708 O ASP A 47 30.390 32.069 16.134 1.00 0.00 O +ATOM 709 N ALA A 48 32.555 31.657 16.092 1.00 0.00 N +ATOM 710 H ALA A 48 33.490 31.931 16.357 1.00 0.00 H +ATOM 711 CA ALA A 48 32.437 30.647 15.015 1.00 0.00 C +ATOM 712 HA ALA A 48 31.707 31.108 14.349 1.00 0.00 H +ATOM 713 CB ALA A 48 33.821 30.467 14.340 1.00 0.00 C +ATOM 714 HB1 ALA A 48 34.244 31.399 13.964 1.00 0.00 H +ATOM 715 HB2 ALA A 48 33.675 29.706 13.573 1.00 0.00 H +ATOM 716 HB3 ALA A 48 34.421 29.986 15.112 1.00 0.00 H +ATOM 717 C ALA A 48 31.855 29.301 15.549 1.00 0.00 C +ATOM 718 O ALA A 48 31.548 28.445 14.720 1.00 0.00 O +ATOM 719 N THR A 49 31.619 29.163 16.885 1.00 0.00 N +ATOM 720 H THR A 49 31.975 29.929 17.439 1.00 0.00 H +ATOM 721 CA THR A 49 30.811 28.126 17.576 1.00 0.00 C +ATOM 722 HA THR A 49 30.371 27.544 16.767 1.00 0.00 H +ATOM 723 CB THR A 49 31.713 27.100 18.310 1.00 0.00 C +ATOM 724 HB THR A 49 31.134 26.420 18.935 1.00 0.00 H +ATOM 725 CG2 THR A 49 32.614 26.280 17.436 1.00 0.00 C +ATOM 726 HG21 THR A 49 33.329 26.868 16.859 1.00 0.00 H +ATOM 727 HG22 THR A 49 32.002 25.593 16.853 1.00 0.00 H +ATOM 728 HG23 THR A 49 33.354 25.760 18.044 1.00 0.00 H +ATOM 729 OG1 THR A 49 32.507 27.834 19.222 1.00 0.00 O +ATOM 730 HG1 THR A 49 33.151 28.336 18.715 1.00 0.00 H +ATOM 731 C THR A 49 29.713 28.644 18.468 1.00 0.00 C +ATOM 732 O THR A 49 28.941 27.912 19.103 1.00 0.00 O +ATOM 733 N LYS A 50 29.628 29.977 18.649 1.00 0.00 N +ATOM 734 H LYS A 50 30.419 30.522 18.334 1.00 0.00 H +ATOM 735 CA LYS A 50 28.663 30.695 19.541 1.00 0.00 C +ATOM 736 HA LYS A 50 28.847 31.769 19.501 1.00 0.00 H +ATOM 737 CB LYS A 50 27.189 30.625 19.033 1.00 0.00 C +ATOM 738 HB2 LYS A 50 26.936 29.572 19.163 1.00 0.00 H +ATOM 739 HB3 LYS A 50 26.469 31.081 19.712 1.00 0.00 H +ATOM 740 CG LYS A 50 27.119 30.984 17.465 1.00 0.00 C +ATOM 741 HG2 LYS A 50 27.961 30.590 16.895 1.00 0.00 H +ATOM 742 HG3 LYS A 50 26.188 30.551 17.100 1.00 0.00 H +ATOM 743 CD LYS A 50 27.025 32.547 17.322 1.00 0.00 C +ATOM 744 HD2 LYS A 50 26.337 33.099 17.964 1.00 0.00 H +ATOM 745 HD3 LYS A 50 28.005 32.913 17.623 1.00 0.00 H +ATOM 746 CE LYS A 50 26.686 32.933 15.930 1.00 0.00 C +ATOM 747 HE2 LYS A 50 25.829 32.363 15.572 1.00 0.00 H +ATOM 748 HE3 LYS A 50 26.304 33.953 15.986 1.00 0.00 H +ATOM 749 NZ LYS A 50 27.861 32.905 14.990 1.00 0.00 N1+ +ATOM 750 HZ1 LYS A 50 28.562 33.507 15.397 1.00 0.00 H +ATOM 751 HZ2 LYS A 50 27.597 33.321 14.108 1.00 0.00 H +ATOM 752 HZ3 LYS A 50 28.269 32.017 14.736 1.00 0.00 H +ATOM 753 C LYS A 50 28.884 30.250 21.033 1.00 0.00 C +ATOM 754 O LYS A 50 27.958 30.206 21.826 1.00 0.00 O +ATOM 755 N THR A 51 30.148 29.820 21.328 1.00 0.00 N +ATOM 756 H THR A 51 30.940 30.100 20.766 1.00 0.00 H +ATOM 757 CA THR A 51 30.503 29.214 22.632 1.00 0.00 C +ATOM 758 HA THR A 51 29.680 28.714 23.142 1.00 0.00 H +ATOM 759 CB THR A 51 31.313 27.944 22.369 1.00 0.00 C +ATOM 760 HB THR A 51 32.245 28.102 21.826 1.00 0.00 H +ATOM 761 CG2 THR A 51 31.703 27.088 23.590 1.00 0.00 C +ATOM 762 HG21 THR A 51 32.177 26.160 23.272 1.00 0.00 H +ATOM 763 HG22 THR A 51 30.745 26.977 24.100 1.00 0.00 H +ATOM 764 HG23 THR A 51 32.401 27.677 24.186 1.00 0.00 H +ATOM 765 OG1 THR A 51 30.404 27.161 21.659 1.00 0.00 O +ATOM 766 HG1 THR A 51 29.757 27.683 21.179 1.00 0.00 H +ATOM 767 C THR A 51 31.202 30.120 23.549 1.00 0.00 C +ATOM 768 O THR A 51 32.200 30.721 23.143 1.00 0.00 O +ATOM 769 N PHE A 52 31.009 29.926 24.845 1.00 0.00 N +ATOM 770 H PHE A 52 30.125 29.479 25.042 1.00 0.00 H +ATOM 771 CA PHE A 52 31.821 30.391 25.941 1.00 0.00 C +ATOM 772 HA PHE A 52 32.490 31.192 25.628 1.00 0.00 H +ATOM 773 CB PHE A 52 30.715 30.979 27.007 1.00 0.00 C +ATOM 774 HB2 PHE A 52 29.988 30.200 27.238 1.00 0.00 H +ATOM 775 HB3 PHE A 52 31.250 31.298 27.901 1.00 0.00 H +ATOM 776 CG PHE A 52 30.049 32.222 26.534 1.00 0.00 C +ATOM 777 CD1 PHE A 52 28.876 32.142 25.781 1.00 0.00 C +ATOM 778 HD1 PHE A 52 28.413 31.204 25.515 1.00 0.00 H +ATOM 779 CE1 PHE A 52 28.300 33.350 25.304 1.00 0.00 C +ATOM 780 HE1 PHE A 52 27.303 33.316 24.890 1.00 0.00 H +ATOM 781 CZ PHE A 52 28.880 34.593 25.500 1.00 0.00 C +ATOM 782 HZ PHE A 52 28.417 35.460 25.054 1.00 0.00 H +ATOM 783 CE2 PHE A 52 30.122 34.665 26.192 1.00 0.00 C +ATOM 784 HE2 PHE A 52 30.650 35.597 26.333 1.00 0.00 H +ATOM 785 CD2 PHE A 52 30.597 33.495 26.795 1.00 0.00 C +ATOM 786 HD2 PHE A 52 31.435 33.581 27.471 1.00 0.00 H +ATOM 787 C PHE A 52 32.721 29.343 26.553 1.00 0.00 C +ATOM 788 O PHE A 52 32.280 28.240 26.674 1.00 0.00 O +ATOM 789 N THR A 53 33.908 29.829 27.087 1.00 0.00 N +ATOM 790 H THR A 53 34.203 30.784 26.938 1.00 0.00 H +ATOM 791 CA THR A 53 34.577 29.044 28.132 1.00 0.00 C +ATOM 792 HA THR A 53 34.003 28.190 28.492 1.00 0.00 H +ATOM 793 CB THR A 53 35.881 28.443 27.684 1.00 0.00 C +ATOM 794 HB THR A 53 36.513 29.234 27.280 1.00 0.00 H +ATOM 795 CG2 THR A 53 36.620 27.571 28.752 1.00 0.00 C +ATOM 796 HG21 THR A 53 36.814 28.236 29.595 1.00 0.00 H +ATOM 797 HG22 THR A 53 37.535 27.174 28.313 1.00 0.00 H +ATOM 798 HG23 THR A 53 35.924 26.795 29.068 1.00 0.00 H +ATOM 799 OG1 THR A 53 35.605 27.649 26.584 1.00 0.00 O +ATOM 800 HG1 THR A 53 35.459 28.177 25.796 1.00 0.00 H +ATOM 801 C THR A 53 34.776 29.748 29.443 1.00 0.00 C +ATOM 802 O THR A 53 35.146 30.939 29.437 1.00 0.00 O +ATOM 803 N VAL A 54 34.499 29.135 30.639 1.00 0.00 N +ATOM 804 H VAL A 54 34.209 28.173 30.538 1.00 0.00 H +ATOM 805 CA VAL A 54 34.861 29.536 31.982 1.00 0.00 C +ATOM 806 HA VAL A 54 35.382 30.493 31.978 1.00 0.00 H +ATOM 807 CB VAL A 54 33.697 29.716 32.869 1.00 0.00 C +ATOM 808 HB VAL A 54 32.913 30.335 32.434 1.00 0.00 H +ATOM 809 CG1 VAL A 54 33.002 28.394 33.289 1.00 0.00 C +ATOM 810 HG11 VAL A 54 33.690 27.666 33.718 1.00 0.00 H +ATOM 811 HG12 VAL A 54 32.618 28.014 32.342 1.00 0.00 H +ATOM 812 HG13 VAL A 54 32.093 28.525 33.877 1.00 0.00 H +ATOM 813 CG2 VAL A 54 34.118 30.320 34.224 1.00 0.00 C +ATOM 814 HG21 VAL A 54 34.711 31.228 34.123 1.00 0.00 H +ATOM 815 HG22 VAL A 54 34.691 29.664 34.880 1.00 0.00 H +ATOM 816 HG23 VAL A 54 33.202 30.551 34.767 1.00 0.00 H +ATOM 817 C VAL A 54 35.950 28.590 32.468 1.00 0.00 C +ATOM 818 O VAL A 54 35.738 27.385 32.660 1.00 0.00 O +ATOM 819 N THR A 55 37.187 29.085 32.651 1.00 0.00 N +ATOM 820 H THR A 55 37.326 30.038 32.345 1.00 0.00 H +ATOM 821 CA THR A 55 38.418 28.363 33.071 1.00 0.00 C +ATOM 822 HA THR A 55 38.197 27.299 32.991 1.00 0.00 H +ATOM 823 CB THR A 55 39.574 28.516 32.161 1.00 0.00 C +ATOM 824 HB THR A 55 39.757 29.581 32.019 1.00 0.00 H +ATOM 825 CG2 THR A 55 40.870 27.898 32.786 1.00 0.00 C +ATOM 826 HG21 THR A 55 40.583 26.849 32.855 1.00 0.00 H +ATOM 827 HG22 THR A 55 41.023 28.190 33.826 1.00 0.00 H +ATOM 828 HG23 THR A 55 41.825 28.044 32.280 1.00 0.00 H +ATOM 829 OG1 THR A 55 39.215 27.970 30.818 1.00 0.00 O +ATOM 830 HG1 THR A 55 38.792 28.725 30.401 1.00 0.00 H +ATOM 831 C THR A 55 38.779 28.725 34.458 1.00 0.00 C +ATOM 832 O THR A 55 39.263 29.841 34.735 1.00 0.00 O +ATOM 833 N GLU A 56 38.757 27.773 35.416 1.00 0.00 N +ATOM 834 H GLU A 56 38.459 26.869 35.079 1.00 0.00 H +ATOM 835 CA GLU A 56 39.045 27.993 36.888 1.00 0.00 C +ATOM 836 HA GLU A 56 38.618 28.921 37.267 1.00 0.00 H +ATOM 837 CB GLU A 56 38.402 26.911 37.749 1.00 0.00 C +ATOM 838 HB2 GLU A 56 37.329 27.019 37.593 1.00 0.00 H +ATOM 839 HB3 GLU A 56 38.780 25.905 37.563 1.00 0.00 H +ATOM 840 CG GLU A 56 38.436 27.078 39.267 1.00 0.00 C +ATOM 841 HG2 GLU A 56 39.455 26.968 39.636 1.00 0.00 H +ATOM 842 HG3 GLU A 56 38.094 28.097 39.445 1.00 0.00 H +ATOM 843 CD GLU A 56 37.514 26.014 39.918 1.00 0.00 C +ATOM 844 OE1 GLU A 56 37.905 24.823 39.870 1.00 0.00 O1- +ATOM 845 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O1- +ATOM 846 C GLU A 56 40.488 28.137 37.301 1.00 0.00 C +ATOM 847 O GLU A 56 40.807 29.090 38.025 1.00 0.00 O1- +ATOM 848 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O1- +CONECT 1 2 3 4 5 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 1 6 7 18 +CONECT 6 5 +CONECT 7 5 8 9 10 +CONECT 8 7 +CONECT 9 7 +CONECT 10 7 11 12 13 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 +CONECT 14 13 15 16 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 19 20 +CONECT 19 18 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 24 25 23 +CONECT 23 22 +CONECT 24 22 +CONECT 25 22 26 26 27 +CONECT 26 25 25 +CONECT 27 25 28 29 +CONECT 28 27 +CONECT 29 27 30 31 46 +CONECT 30 29 +CONECT 31 29 32 33 34 +CONECT 32 31 +CONECT 33 31 +CONECT 34 31 35 35 44 +CONECT 35 34 34 36 37 +CONECT 36 35 +CONECT 37 35 38 39 39 +CONECT 38 37 +CONECT 39 37 37 40 42 +CONECT 40 39 41 +CONECT 41 40 +CONECT 42 39 43 44 44 +CONECT 43 42 +CONECT 44 34 42 42 45 +CONECT 45 44 +CONECT 46 29 47 47 48 +CONECT 47 46 46 +CONECT 48 46 49 50 +CONECT 49 48 +CONECT 50 48 51 52 68 +CONECT 51 50 +CONECT 52 50 53 54 55 +CONECT 53 52 +CONECT 54 52 +CONECT 55 52 56 57 58 +CONECT 56 55 +CONECT 57 55 +CONECT 58 55 59 60 61 +CONECT 59 58 +CONECT 60 58 +CONECT 61 58 62 63 64 +CONECT 62 61 +CONECT 63 61 +CONECT 64 61 65 66 67 +CONECT 65 64 +CONECT 66 64 +CONECT 67 64 +CONECT 68 50 69 69 70 +CONECT 69 68 68 +CONECT 70 68 71 72 +CONECT 71 70 +CONECT 72 70 73 74 87 +CONECT 73 72 +CONECT 74 72 75 76 77 +CONECT 75 74 +CONECT 76 74 +CONECT 77 74 78 79 83 +CONECT 78 77 +CONECT 79 77 80 81 82 +CONECT 80 79 +CONECT 81 79 +CONECT 82 79 +CONECT 83 77 84 85 86 +CONECT 84 83 +CONECT 85 83 +CONECT 86 83 +CONECT 87 72 88 88 89 +CONECT 88 87 87 +CONECT 89 87 90 91 +CONECT 90 89 +CONECT 91 89 92 93 106 +CONECT 92 91 +CONECT 93 91 94 95 99 +CONECT 94 93 +CONECT 95 93 96 97 98 +CONECT 96 95 +CONECT 97 95 +CONECT 98 95 +CONECT 99 93 100 101 102 +CONECT 100 99 +CONECT 101 99 +CONECT 102 99 103 104 105 +CONECT 103 102 +CONECT 104 102 +CONECT 105 102 +CONECT 106 91 107 107 108 +CONECT 107 106 106 +CONECT 108 106 109 110 +CONECT 109 108 +CONECT 110 108 111 112 125 +CONECT 111 110 +CONECT 112 110 113 114 115 +CONECT 113 112 +CONECT 114 112 +CONECT 115 112 116 117 121 +CONECT 116 115 +CONECT 117 115 118 119 120 +CONECT 118 117 +CONECT 119 117 +CONECT 120 117 +CONECT 121 115 122 123 124 +CONECT 122 121 +CONECT 123 121 +CONECT 124 121 +CONECT 125 110 126 126 127 +CONECT 126 125 125 +CONECT 127 125 128 129 +CONECT 128 127 +CONECT 129 127 130 131 139 +CONECT 130 129 +CONECT 131 129 132 133 134 +CONECT 132 131 +CONECT 133 131 +CONECT 134 131 135 135 136 +CONECT 135 134 134 +CONECT 136 134 137 138 +CONECT 137 136 +CONECT 138 136 +CONECT 139 129 140 140 141 +CONECT 140 139 139 +CONECT 141 139 142 143 +CONECT 142 141 +CONECT 143 141 144 145 146 +CONECT 144 143 +CONECT 145 143 +CONECT 146 143 147 147 148 +CONECT 147 146 146 +CONECT 148 146 149 150 +CONECT 149 148 +CONECT 150 148 151 152 168 +CONECT 151 150 +CONECT 152 150 153 154 155 +CONECT 153 152 +CONECT 154 152 +CONECT 155 152 156 157 158 +CONECT 156 155 +CONECT 157 155 +CONECT 158 155 159 160 161 +CONECT 159 158 +CONECT 160 158 +CONECT 161 158 162 163 164 +CONECT 162 161 +CONECT 163 161 +CONECT 164 161 165 166 167 +CONECT 165 164 +CONECT 166 164 +CONECT 167 164 +CONECT 168 150 169 169 170 +CONECT 169 168 168 +CONECT 170 168 171 172 +CONECT 171 170 +CONECT 172 170 173 174 182 +CONECT 173 172 +CONECT 174 172 175 176 180 +CONECT 175 174 +CONECT 176 174 177 178 179 +CONECT 177 176 +CONECT 178 176 +CONECT 179 176 +CONECT 180 174 181 +CONECT 181 180 +CONECT 182 172 183 183 184 +CONECT 183 182 182 +CONECT 184 182 185 186 +CONECT 185 184 +CONECT 186 184 187 188 201 +CONECT 187 186 +CONECT 188 186 189 190 191 +CONECT 189 188 +CONECT 190 188 +CONECT 191 188 192 193 197 +CONECT 192 191 +CONECT 193 191 194 195 196 +CONECT 194 193 +CONECT 195 193 +CONECT 196 193 +CONECT 197 191 198 199 200 +CONECT 198 197 +CONECT 199 197 +CONECT 200 197 +CONECT 201 186 202 202 203 +CONECT 202 201 201 +CONECT 203 201 204 205 +CONECT 204 203 +CONECT 205 203 206 207 223 +CONECT 206 205 +CONECT 207 205 208 209 210 +CONECT 208 207 +CONECT 209 207 +CONECT 210 207 211 212 213 +CONECT 211 210 +CONECT 212 210 +CONECT 213 210 214 215 216 +CONECT 214 213 +CONECT 215 213 +CONECT 216 213 217 218 219 +CONECT 217 216 +CONECT 218 216 +CONECT 219 216 220 221 222 +CONECT 220 219 +CONECT 221 219 +CONECT 222 219 +CONECT 223 205 224 224 225 +CONECT 224 223 223 +CONECT 225 223 226 227 +CONECT 226 225 +CONECT 227 225 228 229 230 +CONECT 228 227 +CONECT 229 227 +CONECT 230 227 231 231 232 +CONECT 231 230 230 +CONECT 232 230 233 234 +CONECT 233 232 +CONECT 234 232 235 236 245 +CONECT 235 234 +CONECT 236 234 237 238 239 +CONECT 237 236 +CONECT 238 236 +CONECT 239 236 240 241 242 +CONECT 240 239 +CONECT 241 239 +CONECT 242 239 243 243 244 +CONECT 243 242 242 +CONECT 244 242 +CONECT 245 234 246 246 247 +CONECT 246 245 245 +CONECT 247 245 248 249 +CONECT 248 247 +CONECT 249 247 250 251 259 +CONECT 250 249 +CONECT 251 249 252 253 257 +CONECT 252 251 +CONECT 253 251 254 255 256 +CONECT 254 253 +CONECT 255 253 +CONECT 256 253 +CONECT 257 251 258 +CONECT 258 257 +CONECT 259 249 260 260 261 +CONECT 260 259 259 +CONECT 261 259 262 263 +CONECT 262 261 +CONECT 263 261 264 265 273 +CONECT 264 263 +CONECT 265 263 266 267 271 +CONECT 266 265 +CONECT 267 265 268 269 270 +CONECT 268 267 +CONECT 269 267 +CONECT 270 267 +CONECT 271 265 272 +CONECT 272 271 +CONECT 273 263 274 274 275 +CONECT 274 273 273 +CONECT 275 273 276 277 +CONECT 276 275 +CONECT 277 275 278 279 287 +CONECT 278 277 +CONECT 279 277 280 281 285 +CONECT 280 279 +CONECT 281 279 282 283 284 +CONECT 282 281 +CONECT 283 281 +CONECT 284 281 +CONECT 285 279 286 +CONECT 286 285 +CONECT 287 277 288 288 289 +CONECT 288 287 287 +CONECT 289 287 290 291 +CONECT 290 289 +CONECT 291 289 292 293 302 +CONECT 292 291 +CONECT 293 291 294 295 296 +CONECT 294 293 +CONECT 295 293 +CONECT 296 293 297 298 299 +CONECT 297 296 +CONECT 298 296 +CONECT 299 296 300 300 301 +CONECT 300 299 299 +CONECT 301 299 +CONECT 302 291 303 303 304 +CONECT 303 302 302 +CONECT 304 302 305 306 +CONECT 305 304 +CONECT 306 304 307 308 312 +CONECT 307 306 +CONECT 308 306 309 310 311 +CONECT 309 308 +CONECT 310 308 +CONECT 311 308 +CONECT 312 306 313 313 314 +CONECT 313 312 312 +CONECT 314 312 315 316 +CONECT 315 314 +CONECT 316 314 317 318 328 +CONECT 317 316 +CONECT 318 316 319 320 324 +CONECT 319 318 +CONECT 320 318 321 322 323 +CONECT 321 320 +CONECT 322 320 +CONECT 323 320 +CONECT 324 318 325 326 327 +CONECT 325 324 +CONECT 326 324 +CONECT 327 324 +CONECT 328 316 329 329 330 +CONECT 329 328 328 +CONECT 330 328 331 332 +CONECT 331 330 +CONECT 332 330 333 334 340 +CONECT 333 332 +CONECT 334 332 335 336 337 +CONECT 335 334 +CONECT 336 334 +CONECT 337 334 338 338 339 +CONECT 338 337 337 +CONECT 339 337 +CONECT 340 332 341 341 342 +CONECT 341 340 340 +CONECT 342 340 343 344 +CONECT 343 342 +CONECT 344 342 345 346 350 +CONECT 345 344 +CONECT 346 344 347 348 349 +CONECT 347 346 +CONECT 348 346 +CONECT 349 346 +CONECT 350 344 351 351 352 +CONECT 351 350 350 +CONECT 352 350 353 354 +CONECT 353 352 +CONECT 354 352 355 356 360 +CONECT 355 354 +CONECT 356 354 357 358 359 +CONECT 357 356 +CONECT 358 356 +CONECT 359 356 +CONECT 360 354 361 361 362 +CONECT 361 360 360 +CONECT 362 360 363 364 +CONECT 363 362 +CONECT 364 362 365 366 374 +CONECT 365 364 +CONECT 366 364 367 368 372 +CONECT 367 366 +CONECT 368 366 369 370 371 +CONECT 369 368 +CONECT 370 368 +CONECT 371 368 +CONECT 372 366 373 +CONECT 373 372 +CONECT 374 364 375 375 376 +CONECT 375 374 374 +CONECT 376 374 377 378 +CONECT 377 376 +CONECT 378 376 379 380 384 +CONECT 379 378 +CONECT 380 378 381 382 383 +CONECT 381 380 +CONECT 382 380 +CONECT 383 380 +CONECT 384 378 385 385 386 +CONECT 385 384 384 +CONECT 386 384 387 388 +CONECT 387 386 +CONECT 388 386 389 390 399 +CONECT 389 388 +CONECT 390 388 391 392 393 +CONECT 391 390 +CONECT 392 390 +CONECT 393 390 394 395 396 +CONECT 394 393 +CONECT 395 393 +CONECT 396 393 397 397 398 +CONECT 397 396 396 +CONECT 398 396 +CONECT 399 388 400 400 401 +CONECT 400 399 399 +CONECT 401 399 402 403 +CONECT 402 401 +CONECT 403 401 404 405 421 +CONECT 404 403 +CONECT 405 403 406 407 408 +CONECT 406 405 +CONECT 407 405 +CONECT 408 405 409 410 411 +CONECT 409 408 +CONECT 410 408 +CONECT 411 408 412 413 414 +CONECT 412 411 +CONECT 413 411 +CONECT 414 411 415 416 417 +CONECT 415 414 +CONECT 416 414 +CONECT 417 414 418 419 420 +CONECT 418 417 +CONECT 419 417 +CONECT 420 417 +CONECT 421 403 422 422 423 +CONECT 422 421 421 +CONECT 423 421 424 425 +CONECT 424 423 +CONECT 425 423 426 427 437 +CONECT 426 425 +CONECT 427 425 428 429 433 +CONECT 428 427 +CONECT 429 427 430 431 432 +CONECT 430 429 +CONECT 431 429 +CONECT 432 429 +CONECT 433 427 434 435 436 +CONECT 434 433 +CONECT 435 433 +CONECT 436 433 +CONECT 437 425 438 438 439 +CONECT 438 437 437 +CONECT 439 437 440 441 +CONECT 440 439 +CONECT 441 439 442 443 457 +CONECT 442 441 +CONECT 443 441 444 445 446 +CONECT 444 443 +CONECT 445 443 +CONECT 446 443 447 447 455 +CONECT 447 446 446 448 449 +CONECT 448 447 +CONECT 449 447 450 451 451 +CONECT 450 449 +CONECT 451 449 449 452 453 +CONECT 452 451 +CONECT 453 451 454 455 455 +CONECT 454 453 +CONECT 455 446 453 453 456 +CONECT 456 455 +CONECT 457 441 458 458 459 +CONECT 458 457 457 +CONECT 459 457 460 461 +CONECT 460 459 +CONECT 461 459 462 463 479 +CONECT 462 461 +CONECT 463 461 464 465 466 +CONECT 464 463 +CONECT 465 463 +CONECT 466 463 467 468 469 +CONECT 467 466 +CONECT 468 466 +CONECT 469 466 470 471 472 +CONECT 470 469 +CONECT 471 469 +CONECT 472 469 473 474 475 +CONECT 473 472 +CONECT 474 472 +CONECT 475 472 476 477 478 +CONECT 476 475 +CONECT 477 475 +CONECT 478 475 +CONECT 479 461 480 480 481 +CONECT 480 479 479 +CONECT 481 479 482 483 +CONECT 482 481 +CONECT 483 481 484 485 496 +CONECT 484 483 +CONECT 485 483 486 487 488 +CONECT 486 485 +CONECT 487 485 +CONECT 488 485 489 490 491 +CONECT 489 488 +CONECT 490 488 +CONECT 491 488 492 492 493 +CONECT 492 491 491 +CONECT 493 491 494 495 +CONECT 494 493 +CONECT 495 493 +CONECT 496 483 497 497 498 +CONECT 497 496 496 +CONECT 498 496 499 500 +CONECT 499 498 +CONECT 500 498 501 502 517 +CONECT 501 500 +CONECT 502 500 503 504 505 +CONECT 503 502 +CONECT 504 502 +CONECT 505 502 506 506 515 +CONECT 506 505 505 507 508 +CONECT 507 506 +CONECT 508 506 509 510 510 +CONECT 509 508 +CONECT 510 508 508 511 513 +CONECT 511 510 512 +CONECT 512 511 +CONECT 513 510 514 515 515 +CONECT 514 513 +CONECT 515 505 513 513 516 +CONECT 516 515 +CONECT 517 500 518 518 519 +CONECT 518 517 517 +CONECT 519 517 520 521 +CONECT 520 519 +CONECT 521 519 522 523 527 +CONECT 522 521 +CONECT 523 521 524 525 526 +CONECT 524 523 +CONECT 525 523 +CONECT 526 523 +CONECT 527 521 528 528 529 +CONECT 528 527 527 +CONECT 529 527 530 531 +CONECT 530 529 +CONECT 531 529 532 533 541 +CONECT 532 531 +CONECT 533 531 534 535 536 +CONECT 534 533 +CONECT 535 533 +CONECT 536 533 537 537 538 +CONECT 537 536 536 +CONECT 538 536 539 540 +CONECT 539 538 +CONECT 540 538 +CONECT 541 531 542 542 543 +CONECT 542 541 541 +CONECT 543 541 544 545 +CONECT 544 543 +CONECT 545 543 546 547 553 +CONECT 546 545 +CONECT 547 545 548 549 550 +CONECT 548 547 +CONECT 549 547 +CONECT 550 547 551 551 552 +CONECT 551 550 550 +CONECT 552 550 +CONECT 553 545 554 554 555 +CONECT 554 553 553 +CONECT 555 553 556 557 +CONECT 556 555 +CONECT 557 555 558 559 567 +CONECT 558 557 +CONECT 559 557 560 561 562 +CONECT 560 559 +CONECT 561 559 +CONECT 562 559 563 563 564 +CONECT 563 562 562 +CONECT 564 562 565 566 +CONECT 565 564 +CONECT 566 564 +CONECT 567 557 568 568 569 +CONECT 568 567 567 +CONECT 569 567 570 571 +CONECT 570 569 +CONECT 571 569 572 573 574 +CONECT 572 571 +CONECT 573 571 +CONECT 574 571 575 575 576 +CONECT 575 574 574 +CONECT 576 574 577 578 +CONECT 577 576 +CONECT 578 576 579 580 590 +CONECT 579 578 +CONECT 580 578 581 582 586 +CONECT 581 580 +CONECT 582 580 583 584 585 +CONECT 583 582 +CONECT 584 582 +CONECT 585 582 +CONECT 586 580 587 588 589 +CONECT 587 586 +CONECT 588 586 +CONECT 589 586 +CONECT 590 578 591 591 592 +CONECT 591 590 590 +CONECT 592 590 593 594 +CONECT 593 592 +CONECT 594 592 595 596 602 +CONECT 595 594 +CONECT 596 594 597 598 599 +CONECT 597 596 +CONECT 598 596 +CONECT 599 596 600 600 601 +CONECT 600 599 599 +CONECT 601 599 +CONECT 602 594 603 603 604 +CONECT 603 602 602 +CONECT 604 602 605 606 +CONECT 605 604 +CONECT 606 604 607 608 609 +CONECT 607 606 +CONECT 608 606 +CONECT 609 606 610 610 611 +CONECT 610 609 609 +CONECT 611 609 612 613 +CONECT 612 611 +CONECT 613 611 614 615 624 +CONECT 614 613 +CONECT 615 613 616 617 618 +CONECT 616 615 +CONECT 617 615 +CONECT 618 615 619 620 621 +CONECT 619 618 +CONECT 620 618 +CONECT 621 618 622 622 623 +CONECT 622 621 621 +CONECT 623 621 +CONECT 624 613 625 625 626 +CONECT 625 624 624 +CONECT 626 624 627 628 +CONECT 627 626 +CONECT 628 626 629 630 648 +CONECT 629 628 +CONECT 630 628 631 632 633 +CONECT 631 630 +CONECT 632 630 +CONECT 633 630 634 634 647 +CONECT 634 633 633 635 636 +CONECT 635 634 +CONECT 636 634 637 638 +CONECT 637 636 +CONECT 638 636 639 639 647 +CONECT 639 638 638 640 641 +CONECT 640 639 +CONECT 641 639 642 643 643 +CONECT 642 641 +CONECT 643 641 641 644 645 +CONECT 644 643 +CONECT 645 643 646 647 647 +CONECT 646 645 +CONECT 647 633 638 645 645 +CONECT 648 628 649 649 650 +CONECT 649 648 648 +CONECT 650 648 651 652 +CONECT 651 650 +CONECT 652 650 653 654 662 +CONECT 653 652 +CONECT 654 652 655 656 660 +CONECT 655 654 +CONECT 656 654 657 658 659 +CONECT 657 656 +CONECT 658 656 +CONECT 659 656 +CONECT 660 654 661 +CONECT 661 660 +CONECT 662 652 663 663 664 +CONECT 663 662 662 +CONECT 664 662 665 666 +CONECT 665 664 +CONECT 666 664 667 668 683 +CONECT 667 666 +CONECT 668 666 669 670 671 +CONECT 669 668 +CONECT 670 668 +CONECT 671 668 672 672 681 +CONECT 672 671 671 673 674 +CONECT 673 672 +CONECT 674 672 675 676 676 +CONECT 675 674 +CONECT 676 674 674 677 679 +CONECT 677 676 678 +CONECT 678 677 +CONECT 679 676 680 681 681 +CONECT 680 679 +CONECT 681 671 679 679 682 +CONECT 682 681 +CONECT 683 666 684 684 685 +CONECT 684 683 683 +CONECT 685 683 686 687 +CONECT 686 685 +CONECT 687 685 688 689 695 +CONECT 688 687 +CONECT 689 687 690 691 692 +CONECT 690 689 +CONECT 691 689 +CONECT 692 689 693 693 694 +CONECT 693 692 692 +CONECT 694 692 +CONECT 695 687 696 696 697 +CONECT 696 695 695 +CONECT 697 695 698 699 +CONECT 698 697 +CONECT 699 697 700 701 707 +CONECT 700 699 +CONECT 701 699 702 703 704 +CONECT 702 701 +CONECT 703 701 +CONECT 704 701 705 705 706 +CONECT 705 704 704 +CONECT 706 704 +CONECT 707 699 708 708 709 +CONECT 708 707 707 +CONECT 709 707 710 711 +CONECT 710 709 +CONECT 711 709 712 713 717 +CONECT 712 711 +CONECT 713 711 714 715 716 +CONECT 714 713 +CONECT 715 713 +CONECT 716 713 +CONECT 717 711 718 718 719 +CONECT 718 717 717 +CONECT 719 717 720 721 +CONECT 720 719 +CONECT 721 719 722 723 731 +CONECT 722 721 +CONECT 723 721 724 725 729 +CONECT 724 723 +CONECT 725 723 726 727 728 +CONECT 726 725 +CONECT 727 725 +CONECT 728 725 +CONECT 729 723 730 +CONECT 730 729 +CONECT 731 721 732 732 733 +CONECT 732 731 731 +CONECT 733 731 734 735 +CONECT 734 733 +CONECT 735 733 736 737 753 +CONECT 736 735 +CONECT 737 735 738 739 740 +CONECT 738 737 +CONECT 739 737 +CONECT 740 737 741 742 743 +CONECT 741 740 +CONECT 742 740 +CONECT 743 740 744 745 746 +CONECT 744 743 +CONECT 745 743 +CONECT 746 743 747 748 749 +CONECT 747 746 +CONECT 748 746 +CONECT 749 746 750 751 752 +CONECT 750 749 +CONECT 751 749 +CONECT 752 749 +CONECT 753 735 754 754 755 +CONECT 754 753 753 +CONECT 755 753 756 757 +CONECT 756 755 +CONECT 757 755 758 759 767 +CONECT 758 757 +CONECT 759 757 760 761 765 +CONECT 760 759 +CONECT 761 759 762 763 764 +CONECT 762 761 +CONECT 763 761 +CONECT 764 761 +CONECT 765 759 766 +CONECT 766 765 +CONECT 767 757 768 768 769 +CONECT 768 767 767 +CONECT 769 767 770 771 +CONECT 770 769 +CONECT 771 769 772 773 787 +CONECT 772 771 +CONECT 773 771 774 775 776 +CONECT 774 773 +CONECT 775 773 +CONECT 776 773 777 777 785 +CONECT 777 776 776 778 779 +CONECT 778 777 +CONECT 779 777 780 781 781 +CONECT 780 779 +CONECT 781 779 779 782 783 +CONECT 782 781 +CONECT 783 781 784 785 785 +CONECT 784 783 +CONECT 785 776 783 783 786 +CONECT 786 785 +CONECT 787 771 788 788 789 +CONECT 788 787 787 +CONECT 789 787 790 791 +CONECT 790 789 +CONECT 791 789 792 793 801 +CONECT 792 791 +CONECT 793 791 794 795 799 +CONECT 794 793 +CONECT 795 793 796 797 798 +CONECT 796 795 +CONECT 797 795 +CONECT 798 795 +CONECT 799 793 800 +CONECT 800 799 +CONECT 801 791 802 802 803 +CONECT 802 801 801 +CONECT 803 801 804 805 +CONECT 804 803 +CONECT 805 803 806 807 817 +CONECT 806 805 +CONECT 807 805 808 809 813 +CONECT 808 807 +CONECT 809 807 810 811 812 +CONECT 810 809 +CONECT 811 809 +CONECT 812 809 +CONECT 813 807 814 815 816 +CONECT 814 813 +CONECT 815 813 +CONECT 816 813 +CONECT 817 805 818 818 819 +CONECT 818 817 817 +CONECT 819 817 820 821 +CONECT 820 819 +CONECT 821 819 822 823 831 +CONECT 822 821 +CONECT 823 821 824 825 829 +CONECT 824 823 +CONECT 825 823 826 827 828 +CONECT 826 825 +CONECT 827 825 +CONECT 828 825 +CONECT 829 823 830 +CONECT 830 829 +CONECT 831 821 832 832 833 +CONECT 832 831 831 +CONECT 833 831 834 835 +CONECT 834 833 +CONECT 835 833 836 837 846 +CONECT 836 835 +CONECT 837 835 838 839 840 +CONECT 838 837 +CONECT 839 837 +CONECT 840 837 841 842 843 +CONECT 841 840 +CONECT 842 840 +CONECT 843 840 844 844 845 +CONECT 844 843 843 +CONECT 845 843 +CONECT 846 835 847 847 848 +CONECT 847 846 846 +CONECT 848 846 +MASTER 0 0 0 0 0 0 0 0 848 0 848 0 +END diff --git a/unittests/output_files/test_thr_to_his_restypeFalse.pdb b/unittests/output_files/test_thr_to_his_restypeFalse.pdb new file mode 100644 index 0000000..92913fa --- /dev/null +++ b/unittests/output_files/test_thr_to_his_restypeFalse.pdb @@ -0,0 +1,1722 @@ +COMPND MET +AUTHOR GENERATED BY OPEN BABEL 3.0.0 +ATOM 1 N MET A 1 19.157 32.576 19.140 1.00 0.00 N1+ +ATOM 2 H1 MET A 1 18.435 31.870 19.129 1.00 0.00 H +ATOM 3 H2 MET A 1 18.900 33.260 18.441 1.00 0.00 H +ATOM 4 H3 MET A 1 19.229 33.073 20.016 1.00 0.00 H +ATOM 5 CA MET A 1 20.458 31.939 18.931 1.00 0.00 C +ATOM 6 HA MET A 1 20.420 31.303 18.046 1.00 0.00 H +ATOM 7 CB MET A 1 21.504 33.015 18.722 1.00 0.00 C +ATOM 8 HB2 MET A 1 21.352 33.519 17.768 1.00 0.00 H +ATOM 9 HB3 MET A 1 21.390 33.764 19.505 1.00 0.00 H +ATOM 10 CG MET A 1 22.904 32.517 18.656 1.00 0.00 C +ATOM 11 HG2 MET A 1 23.590 33.362 18.601 1.00 0.00 H +ATOM 12 HG3 MET A 1 23.154 32.095 19.630 1.00 0.00 H +ATOM 13 SD MET A 1 23.205 31.269 17.386 1.00 0.00 S +ATOM 14 CE MET A 1 22.990 32.137 15.870 1.00 0.00 C +ATOM 15 HE1 MET A 1 23.339 33.163 15.983 1.00 0.00 H +ATOM 16 HE2 MET A 1 21.968 32.128 15.490 1.00 0.00 H +ATOM 17 HE3 MET A 1 23.572 31.586 15.132 1.00 0.00 H +ATOM 18 C MET A 1 20.796 31.017 20.133 1.00 0.00 C +ATOM 19 O MET A 1 20.674 31.440 21.297 1.00 0.00 O +ATOM 20 N HP3 A 2 21.124 29.774 19.819 1.00 0.00 N +ATOM 21 H HP3 A 2 21.279 29.527 18.851 1.00 0.00 H +ATOM 22 CA HP3 A 2 21.443 28.704 20.861 1.00 0.00 C +ATOM 23 CB HP3 A 2 21.116 27.248 20.524 1.00 0.00 C +ATOM 24 HB2 HP3 A 2 21.319 26.609 21.384 1.00 0.00 H +ATOM 25 HB3 HP3 A 2 20.067 27.156 20.245 1.00 0.00 H +ATOM 26 CG HP3 A 2 21.914 26.697 19.384 1.00 0.00 C +ATOM 27 ND1 HP3 A 2 23.189 26.197 19.539 1.00 0.00 N +ATOM 28 HD1 HP3 A 2 23.687 26.157 20.416 1.00 0.00 H +ATOM 29 CE1 HP3 A 2 23.642 25.784 18.368 1.00 0.00 C +ATOM 30 HE1 HP3 A 2 24.637 25.352 18.282 1.00 0.00 H +ATOM 31 NE2 HP3 A 2 22.710 25.999 17.460 1.00 0.00 N +ATOM 32 HE2 HP3 A 2 22.777 25.784 16.475 1.00 0.00 H +ATOM 33 CD2 HP3 A 2 21.619 26.570 18.068 1.00 0.00 C +ATOM 34 HD2 HP3 A 2 20.738 26.826 17.479 1.00 0.00 H +ATOM 35 HA HP3 A 2 20.909 28.998 21.764 1.00 0.00 H +ATOM 36 C HP3 A 2 22.937 28.892 21.086 1.00 0.00 C +ATOM 37 O HP3 A 2 23.773 28.867 20.181 1.00 0.00 O +ATOM 38 N TYR A 3 23.244 29.155 22.344 1.00 0.00 N +ATOM 39 H TYR A 3 22.513 29.085 23.038 1.00 0.00 H +ATOM 40 CA TYR A 3 24.628 29.305 22.888 1.00 0.00 C +ATOM 41 HA TYR A 3 25.262 29.391 22.004 1.00 0.00 H +ATOM 42 CB TYR A 3 24.744 30.579 23.675 1.00 0.00 C +ATOM 43 HB2 TYR A 3 24.131 30.495 24.572 1.00 0.00 H +ATOM 44 HB3 TYR A 3 25.780 30.505 24.008 1.00 0.00 H +ATOM 45 CG TYR A 3 24.468 31.862 22.928 1.00 0.00 C +ATOM 46 CD1 TYR A 3 25.525 32.544 22.317 1.00 0.00 C +ATOM 47 HD1 TYR A 3 26.477 32.039 22.379 1.00 0.00 H +ATOM 48 CE1 TYR A 3 25.289 33.761 21.619 1.00 0.00 C +ATOM 49 HE1 TYR A 3 26.100 34.275 21.122 1.00 0.00 H +ATOM 50 CZ TYR A 3 23.936 34.260 21.579 1.00 0.00 C +ATOM 51 OH TYR A 3 23.774 35.268 20.774 1.00 0.00 O +ATOM 52 HH TYR A 3 24.486 35.161 20.140 1.00 0.00 H +ATOM 53 CE2 TYR A 3 22.849 33.537 22.176 1.00 0.00 C +ATOM 54 HE2 TYR A 3 21.868 33.965 22.036 1.00 0.00 H +ATOM 55 CD2 TYR A 3 23.110 32.291 22.853 1.00 0.00 C +ATOM 56 HD2 TYR A 3 22.235 31.752 23.187 1.00 0.00 H +ATOM 57 C TYR A 3 25.066 28.136 23.774 1.00 0.00 C +ATOM 58 O TYR A 3 24.233 27.436 24.338 1.00 0.00 O +ATOM 59 N LYS A 4 26.339 27.934 23.811 1.00 0.00 N +ATOM 60 H LYS A 4 26.944 28.514 23.248 1.00 0.00 H +ATOM 61 CA LYS A 4 26.982 26.918 24.687 1.00 0.00 C +ATOM 62 HA LYS A 4 26.212 26.488 25.328 1.00 0.00 H +ATOM 63 CB LYS A 4 27.643 25.801 23.803 1.00 0.00 C +ATOM 64 HB2 LYS A 4 26.868 25.465 23.113 1.00 0.00 H +ATOM 65 HB3 LYS A 4 28.422 26.196 23.151 1.00 0.00 H +ATOM 66 CG LYS A 4 28.205 24.625 24.506 1.00 0.00 C +ATOM 67 HG2 LYS A 4 29.054 24.916 25.125 1.00 0.00 H +ATOM 68 HG3 LYS A 4 27.452 24.278 25.213 1.00 0.00 H +ATOM 69 CD LYS A 4 28.635 23.407 23.678 1.00 0.00 C +ATOM 70 HD2 LYS A 4 29.003 22.691 24.414 1.00 0.00 H +ATOM 71 HD3 LYS A 4 27.737 22.954 23.255 1.00 0.00 H +ATOM 72 CE LYS A 4 29.554 23.575 22.506 1.00 0.00 C +ATOM 73 HE2 LYS A 4 28.899 24.120 21.827 1.00 0.00 H +ATOM 74 HE3 LYS A 4 30.458 24.114 22.794 1.00 0.00 H +ATOM 75 NZ LYS A 4 30.052 22.279 21.888 1.00 0.00 N1+ +ATOM 76 HZ1 LYS A 4 30.831 21.896 22.402 1.00 0.00 H +ATOM 77 HZ2 LYS A 4 30.443 22.423 20.968 1.00 0.00 H +ATOM 78 HZ3 LYS A 4 29.328 21.579 21.805 1.00 0.00 H +ATOM 79 C LYS A 4 28.003 27.516 25.655 1.00 0.00 C +ATOM 80 O LYS A 4 28.579 28.553 25.310 1.00 0.00 O +ATOM 81 N LEU A 5 28.245 26.773 26.741 1.00 0.00 N +ATOM 82 H LEU A 5 27.544 26.084 26.977 1.00 0.00 H +ATOM 83 CA LEU A 5 29.244 27.118 27.766 1.00 0.00 C +ATOM 84 HA LEU A 5 29.916 27.884 27.380 1.00 0.00 H +ATOM 85 CB LEU A 5 28.579 27.507 29.097 1.00 0.00 C +ATOM 86 HB2 LEU A 5 28.058 28.438 28.872 1.00 0.00 H +ATOM 87 HB3 LEU A 5 27.859 26.779 29.469 1.00 0.00 H +ATOM 88 CG LEU A 5 29.551 27.720 30.235 1.00 0.00 C +ATOM 89 HG LEU A 5 30.166 26.841 30.429 1.00 0.00 H +ATOM 90 CD1 LEU A 5 30.427 28.952 29.986 1.00 0.00 C +ATOM 91 HD11 LEU A 5 31.114 28.683 29.184 1.00 0.00 H +ATOM 92 HD12 LEU A 5 31.008 29.120 30.894 1.00 0.00 H +ATOM 93 HD13 LEU A 5 29.848 29.861 29.825 1.00 0.00 H +ATOM 94 CD2 LEU A 5 28.678 28.115 31.457 1.00 0.00 C +ATOM 95 HD21 LEU A 5 28.235 29.096 31.284 1.00 0.00 H +ATOM 96 HD22 LEU A 5 29.327 28.287 32.315 1.00 0.00 H +ATOM 97 HD23 LEU A 5 27.907 27.390 31.720 1.00 0.00 H +ATOM 98 C LEU A 5 30.065 25.816 27.990 1.00 0.00 C +ATOM 99 O LEU A 5 29.489 24.768 28.302 1.00 0.00 O +ATOM 100 N ILE A 6 31.415 25.954 27.959 1.00 0.00 N +ATOM 101 H ILE A 6 31.834 26.822 27.658 1.00 0.00 H +ATOM 102 CA ILE A 6 32.352 24.944 28.438 1.00 0.00 C +ATOM 103 HA ILE A 6 31.851 23.978 28.494 1.00 0.00 H +ATOM 104 CB ILE A 6 33.535 24.736 27.434 1.00 0.00 C +ATOM 105 HB ILE A 6 34.002 25.706 27.261 1.00 0.00 H +ATOM 106 CG2 ILE A 6 34.658 23.796 27.952 1.00 0.00 C +ATOM 107 HG21 ILE A 6 35.011 24.049 28.953 1.00 0.00 H +ATOM 108 HG22 ILE A 6 35.610 23.773 27.423 1.00 0.00 H +ATOM 109 HG23 ILE A 6 34.315 22.768 28.065 1.00 0.00 H +ATOM 110 CG1 ILE A 6 32.967 24.083 26.135 1.00 0.00 C +ATOM 111 HG12 ILE A 6 32.815 23.014 26.281 1.00 0.00 H +ATOM 112 HG13 ILE A 6 32.016 24.548 25.875 1.00 0.00 H +ATOM 113 CD1 ILE A 6 33.964 24.228 24.983 1.00 0.00 C +ATOM 114 HD11 ILE A 6 34.203 25.280 24.831 1.00 0.00 H +ATOM 115 HD12 ILE A 6 33.521 23.646 24.174 1.00 0.00 H +ATOM 116 HD13 ILE A 6 34.890 23.744 25.293 1.00 0.00 H +ATOM 117 C ILE A 6 32.878 25.380 29.825 1.00 0.00 C +ATOM 118 O ILE A 6 33.517 26.449 29.956 1.00 0.00 O +ATOM 119 N LEU A 7 32.756 24.548 30.823 1.00 0.00 N +ATOM 120 H LEU A 7 32.337 23.649 30.632 1.00 0.00 H +ATOM 121 CA LEU A 7 33.418 24.678 32.128 1.00 0.00 C +ATOM 122 HA LEU A 7 33.772 25.702 32.243 1.00 0.00 H +ATOM 123 CB LEU A 7 32.452 24.287 33.269 1.00 0.00 C +ATOM 124 HB2 LEU A 7 32.235 23.219 33.280 1.00 0.00 H +ATOM 125 HB3 LEU A 7 33.025 24.491 34.173 1.00 0.00 H +ATOM 126 CG LEU A 7 31.068 25.080 33.294 1.00 0.00 C +ATOM 127 HG LEU A 7 31.234 26.000 32.731 1.00 0.00 H +ATOM 128 CD1 LEU A 7 29.957 24.185 32.737 1.00 0.00 C +ATOM 129 HD11 LEU A 7 29.091 24.791 32.472 1.00 0.00 H +ATOM 130 HD12 LEU A 7 29.675 23.458 33.497 1.00 0.00 H +ATOM 131 HD13 LEU A 7 30.242 23.598 31.863 1.00 0.00 H +ATOM 132 CD2 LEU A 7 30.679 25.500 34.666 1.00 0.00 C +ATOM 133 HD21 LEU A 7 30.692 24.679 35.384 1.00 0.00 H +ATOM 134 HD22 LEU A 7 29.678 25.926 34.604 1.00 0.00 H +ATOM 135 HD23 LEU A 7 31.266 26.349 35.014 1.00 0.00 H +ATOM 136 C LEU A 7 34.704 23.832 31.982 1.00 0.00 C +ATOM 137 O LEU A 7 34.608 22.712 31.434 1.00 0.00 O +ATOM 138 N ASN A 8 35.741 24.355 32.566 1.00 0.00 N +ATOM 139 H ASN A 8 35.657 25.289 32.943 1.00 0.00 H +ATOM 140 CA ASN A 8 37.087 23.938 32.340 1.00 0.00 C +ATOM 141 HA ASN A 8 37.195 22.875 32.128 1.00 0.00 H +ATOM 142 CB ASN A 8 37.683 24.648 31.079 1.00 0.00 C +ATOM 143 HB2 ASN A 8 37.052 24.514 30.199 1.00 0.00 H +ATOM 144 HB3 ASN A 8 37.697 25.701 31.358 1.00 0.00 H +ATOM 145 CG ASN A 8 39.069 24.172 30.753 1.00 0.00 C +ATOM 146 OD1 ASN A 8 39.293 22.972 30.616 1.00 0.00 O +ATOM 147 ND2 ASN A 8 40.171 24.966 30.834 1.00 0.00 N +ATOM 148 HD21 ASN A 8 40.064 25.968 30.880 1.00 0.00 H +ATOM 149 HD22 ASN A 8 41.073 24.564 30.618 1.00 0.00 H +ATOM 150 C ASN A 8 37.929 24.262 33.602 1.00 0.00 C +ATOM 151 O ASN A 8 37.736 25.299 34.234 1.00 0.00 O +ATOM 152 N GLY A 9 38.893 23.411 33.937 1.00 0.00 N +ATOM 153 H GLY A 9 38.872 22.559 33.394 1.00 0.00 H +ATOM 154 CA GLY A 9 39.937 23.667 34.946 1.00 0.00 C +ATOM 155 HA2 GLY A 9 40.563 24.496 34.619 1.00 0.00 H +ATOM 156 HA3 GLY A 9 39.525 24.058 35.876 1.00 0.00 H +ATOM 157 C GLY A 9 40.820 22.504 35.210 1.00 0.00 C +ATOM 158 O GLY A 9 40.826 21.506 34.446 1.00 0.00 O +ATOM 159 N LYS A 10 41.477 22.473 36.356 1.00 0.00 N +ATOM 160 H LYS A 10 41.439 23.256 36.992 1.00 0.00 H +ATOM 161 CA LYS A 10 42.321 21.363 36.766 1.00 0.00 C +ATOM 162 HA LYS A 10 42.838 21.036 35.864 1.00 0.00 H +ATOM 163 CB LYS A 10 43.435 21.839 37.736 1.00 0.00 C +ATOM 164 HB2 LYS A 10 42.960 22.130 38.673 1.00 0.00 H +ATOM 165 HB3 LYS A 10 44.151 21.018 37.787 1.00 0.00 H +ATOM 166 CG LYS A 10 44.146 23.121 37.228 1.00 0.00 C +ATOM 167 HG2 LYS A 10 44.581 22.959 36.242 1.00 0.00 H +ATOM 168 HG3 LYS A 10 43.424 23.934 37.151 1.00 0.00 H +ATOM 169 CD LYS A 10 45.206 23.474 38.269 1.00 0.00 C +ATOM 170 HD2 LYS A 10 44.834 23.376 39.290 1.00 0.00 H +ATOM 171 HD3 LYS A 10 46.045 22.781 38.265 1.00 0.00 H +ATOM 172 CE LYS A 10 45.833 24.866 37.936 1.00 0.00 C +ATOM 173 HE2 LYS A 10 46.898 24.867 38.172 1.00 0.00 H +ATOM 174 HE3 LYS A 10 45.615 25.139 36.904 1.00 0.00 H +ATOM 175 NZ LYS A 10 45.314 25.885 38.915 1.00 0.00 N1+ +ATOM 176 HZ1 LYS A 10 44.318 26.049 38.885 1.00 0.00 H +ATOM 177 HZ2 LYS A 10 45.805 26.756 38.765 1.00 0.00 H +ATOM 178 HZ3 LYS A 10 45.434 25.694 39.899 1.00 0.00 H +ATOM 179 C LYS A 10 41.608 20.142 37.369 1.00 0.00 C +ATOM 180 O LYS A 10 42.136 19.017 37.432 1.00 0.00 O +ATOM 181 N THR A 11 40.316 20.407 37.709 1.00 0.00 N +ATOM 182 H THR A 11 40.018 21.373 37.739 1.00 0.00 H +ATOM 183 CA THR A 11 39.333 19.428 38.190 1.00 0.00 C +ATOM 184 HA THR A 11 39.627 18.439 37.841 1.00 0.00 H +ATOM 185 CB THR A 11 39.319 19.497 39.740 1.00 0.00 C +ATOM 186 HB THR A 11 38.538 18.809 40.063 1.00 0.00 H +ATOM 187 CG2 THR A 11 40.656 18.994 40.197 1.00 0.00 C +ATOM 188 HG21 THR A 11 40.954 17.991 39.896 1.00 0.00 H +ATOM 189 HG22 THR A 11 40.695 18.984 41.286 1.00 0.00 H +ATOM 190 HG23 THR A 11 41.453 19.662 39.869 1.00 0.00 H +ATOM 191 OG1 THR A 11 39.118 20.738 40.229 1.00 0.00 O +ATOM 192 HG1 THR A 11 39.321 20.728 41.168 1.00 0.00 H +ATOM 193 C THR A 11 37.937 19.704 37.750 1.00 0.00 C +ATOM 194 O THR A 11 37.180 18.744 37.592 1.00 0.00 O +ATOM 195 N LEU A 12 37.572 20.909 37.360 1.00 0.00 N +ATOM 196 H LEU A 12 38.100 21.745 37.569 1.00 0.00 H +ATOM 197 CA LEU A 12 36.262 21.294 36.760 1.00 0.00 C +ATOM 198 HA LEU A 12 35.427 20.887 37.329 1.00 0.00 H +ATOM 199 CB LEU A 12 36.169 22.873 36.785 1.00 0.00 C +ATOM 200 HB2 LEU A 12 36.531 23.238 37.746 1.00 0.00 H +ATOM 201 HB3 LEU A 12 36.859 23.268 36.041 1.00 0.00 H +ATOM 202 CG LEU A 12 34.824 23.483 36.357 1.00 0.00 C +ATOM 203 HG LEU A 12 34.479 23.028 35.428 1.00 0.00 H +ATOM 204 CD1 LEU A 12 33.867 23.321 37.477 1.00 0.00 C +ATOM 205 HD11 LEU A 12 32.997 23.877 37.126 1.00 0.00 H +ATOM 206 HD12 LEU A 12 34.304 23.691 38.404 1.00 0.00 H +ATOM 207 HD13 LEU A 12 33.594 22.265 37.503 1.00 0.00 H +ATOM 208 CD2 LEU A 12 34.926 25.052 36.181 1.00 0.00 C +ATOM 209 HD21 LEU A 12 35.334 25.560 37.054 1.00 0.00 H +ATOM 210 HD22 LEU A 12 33.926 25.442 35.997 1.00 0.00 H +ATOM 211 HD23 LEU A 12 35.555 25.355 35.344 1.00 0.00 H +ATOM 212 C LEU A 12 36.092 20.805 35.283 1.00 0.00 C +ATOM 213 O LEU A 12 36.941 21.102 34.441 1.00 0.00 O +ATOM 214 N LYS A 13 35.016 20.080 34.906 1.00 0.00 N +ATOM 215 H LYS A 13 34.391 19.697 35.602 1.00 0.00 H +ATOM 216 CA LYS A 13 34.642 19.704 33.571 1.00 0.00 C +ATOM 217 HA LYS A 13 35.063 20.421 32.866 1.00 0.00 H +ATOM 218 CB LYS A 13 35.034 18.226 33.244 1.00 0.00 C +ATOM 219 HB2 LYS A 13 34.497 17.579 33.938 1.00 0.00 H +ATOM 220 HB3 LYS A 13 34.849 17.922 32.214 1.00 0.00 H +ATOM 221 CG LYS A 13 36.515 17.923 33.472 1.00 0.00 C +ATOM 222 HG2 LYS A 13 37.162 18.658 32.994 1.00 0.00 H +ATOM 223 HG3 LYS A 13 36.701 17.768 34.535 1.00 0.00 H +ATOM 224 CD LYS A 13 36.804 16.487 32.994 1.00 0.00 C +ATOM 225 HD2 LYS A 13 36.157 15.747 33.465 1.00 0.00 H +ATOM 226 HD3 LYS A 13 36.456 16.506 31.962 1.00 0.00 H +ATOM 227 CE LYS A 13 38.264 16.163 32.997 1.00 0.00 C +ATOM 228 HE2 LYS A 13 38.741 16.732 32.199 1.00 0.00 H +ATOM 229 HE3 LYS A 13 38.686 16.424 33.967 1.00 0.00 H +ATOM 230 NZ LYS A 13 38.397 14.672 32.837 1.00 0.00 N1+ +ATOM 231 HZ1 LYS A 13 37.944 14.324 32.005 1.00 0.00 H +ATOM 232 HZ2 LYS A 13 37.888 14.239 33.595 1.00 0.00 H +ATOM 233 HZ3 LYS A 13 39.367 14.391 32.817 1.00 0.00 H +ATOM 234 C LYS A 13 33.119 19.875 33.400 1.00 0.00 C +ATOM 235 O LYS A 13 32.522 20.218 34.448 1.00 0.00 O +ATOM 236 N GLY A 14 32.541 19.929 32.182 1.00 0.00 N +ATOM 237 H GLY A 14 33.085 19.611 31.392 1.00 0.00 H +ATOM 238 CA GLY A 14 31.141 20.135 31.951 1.00 0.00 C +ATOM 239 HA2 GLY A 14 30.696 19.143 31.877 1.00 0.00 H +ATOM 240 HA3 GLY A 14 30.707 20.500 32.883 1.00 0.00 H +ATOM 241 C GLY A 14 30.726 21.030 30.803 1.00 0.00 C +ATOM 242 O GLY A 14 31.459 21.986 30.478 1.00 0.00 O +ATOM 243 N GLU A 15 29.602 20.661 30.175 1.00 0.00 N +ATOM 244 H GLU A 15 29.233 19.801 30.557 1.00 0.00 H +ATOM 245 CA GLU A 15 29.053 21.595 29.115 1.00 0.00 C +ATOM 246 HA GLU A 15 29.457 22.592 29.292 1.00 0.00 H +ATOM 247 CB GLU A 15 29.452 21.151 27.705 1.00 0.00 C +ATOM 248 HB2 GLU A 15 28.886 21.770 27.009 1.00 0.00 H +ATOM 249 HB3 GLU A 15 30.497 21.396 27.512 1.00 0.00 H +ATOM 250 CG GLU A 15 29.157 19.668 27.410 1.00 0.00 C +ATOM 251 HG2 GLU A 15 29.865 19.104 28.017 1.00 0.00 H +ATOM 252 HG3 GLU A 15 28.109 19.456 27.619 1.00 0.00 H +ATOM 253 CD GLU A 15 29.423 19.385 25.968 1.00 0.00 C +ATOM 254 OE1 GLU A 15 28.458 19.250 25.177 1.00 0.00 O1- +ATOM 255 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O1- +ATOM 256 C GLU A 15 27.563 21.843 29.353 1.00 0.00 C +ATOM 257 O GLU A 15 26.814 21.020 29.796 1.00 0.00 O +ATOM 258 N THR A 16 27.080 22.966 28.863 1.00 0.00 N +ATOM 259 H THR A 16 27.718 23.647 28.477 1.00 0.00 H +ATOM 260 CA THR A 16 25.618 23.342 28.987 1.00 0.00 C +ATOM 261 HA THR A 16 24.987 22.466 28.832 1.00 0.00 H +ATOM 262 CB THR A 16 25.300 23.755 30.463 1.00 0.00 C +ATOM 263 HB THR A 16 25.664 23.028 31.190 1.00 0.00 H +ATOM 264 CG2 THR A 16 26.079 25.029 30.851 1.00 0.00 C +ATOM 265 HG21 THR A 16 26.002 25.212 31.923 1.00 0.00 H +ATOM 266 HG22 THR A 16 25.827 25.999 30.420 1.00 0.00 H +ATOM 267 HG23 THR A 16 27.139 24.833 30.686 1.00 0.00 H +ATOM 268 OG1 THR A 16 23.919 23.870 30.591 1.00 0.00 O +ATOM 269 HG1 THR A 16 23.605 22.966 30.654 1.00 0.00 H +ATOM 270 C THR A 16 25.136 24.387 27.956 1.00 0.00 C +ATOM 271 O THR A 16 25.847 25.392 27.686 1.00 0.00 O +ATOM 272 N THR A 17 23.944 24.126 27.374 1.00 0.00 N +ATOM 273 H THR A 17 23.414 23.300 27.615 1.00 0.00 H +ATOM 274 CA THR A 17 23.341 25.088 26.418 1.00 0.00 C +ATOM 275 HA THR A 17 24.139 25.697 25.992 1.00 0.00 H +ATOM 276 CB THR A 17 22.634 24.399 25.250 1.00 0.00 C +ATOM 277 HB THR A 17 22.194 25.142 24.585 1.00 0.00 H +ATOM 278 CG2 THR A 17 23.534 23.466 24.406 1.00 0.00 C +ATOM 279 HG21 THR A 17 22.981 22.875 23.677 1.00 0.00 H +ATOM 280 HG22 THR A 17 24.016 22.789 25.112 1.00 0.00 H +ATOM 281 HG23 THR A 17 24.305 24.119 23.998 1.00 0.00 H +ATOM 282 OG1 THR A 17 21.618 23.516 25.740 1.00 0.00 O +ATOM 283 HG1 THR A 17 21.158 23.210 24.955 1.00 0.00 H +ATOM 284 C THR A 17 22.409 26.084 27.080 1.00 0.00 C +ATOM 285 O THR A 17 21.865 25.880 28.171 1.00 0.00 O +ATOM 286 N THR A 18 22.284 27.186 26.367 1.00 0.00 N +ATOM 287 H THR A 18 22.918 27.211 25.581 1.00 0.00 H +ATOM 288 CA THR A 18 21.341 28.346 26.665 1.00 0.00 C +ATOM 289 HA THR A 18 20.447 28.047 27.213 1.00 0.00 H +ATOM 290 CB THR A 18 21.968 29.424 27.606 1.00 0.00 C +ATOM 291 HB THR A 18 22.926 29.800 27.251 1.00 0.00 H +ATOM 292 CG2 THR A 18 20.959 30.565 27.747 1.00 0.00 C +ATOM 293 HG21 THR A 18 21.177 31.232 28.581 1.00 0.00 H +ATOM 294 HG22 THR A 18 19.932 30.214 27.838 1.00 0.00 H +ATOM 295 HG23 THR A 18 21.057 31.149 26.831 1.00 0.00 H +ATOM 296 OG1 THR A 18 21.983 28.974 29.051 1.00 0.00 O +ATOM 297 HG1 THR A 18 22.866 29.123 29.400 1.00 0.00 H +ATOM 298 C THR A 18 20.829 28.956 25.354 1.00 0.00 C +ATOM 299 O THR A 18 21.553 29.458 24.528 1.00 0.00 O +ATOM 300 N GLU A 19 19.542 28.872 25.083 1.00 0.00 N +ATOM 301 H GLU A 19 18.919 28.579 25.823 1.00 0.00 H +ATOM 302 CA GLU A 19 18.932 29.576 23.987 1.00 0.00 C +ATOM 303 HA GLU A 19 19.679 29.508 23.197 1.00 0.00 H +ATOM 304 CB GLU A 19 17.686 28.785 23.627 1.00 0.00 C +ATOM 305 HB2 GLU A 19 17.899 27.722 23.514 1.00 0.00 H +ATOM 306 HB3 GLU A 19 16.998 28.842 24.471 1.00 0.00 H +ATOM 307 CG GLU A 19 16.852 29.284 22.477 1.00 0.00 C +ATOM 308 HG2 GLU A 19 16.246 28.447 22.128 1.00 0.00 H +ATOM 309 HG3 GLU A 19 16.133 30.057 22.748 1.00 0.00 H +ATOM 310 CD GLU A 19 17.736 29.731 21.281 1.00 0.00 C +ATOM 311 OE1 GLU A 19 18.363 28.800 20.679 1.00 0.00 O1- +ATOM 312 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O1- +ATOM 313 C GLU A 19 18.631 31.049 24.311 1.00 0.00 C +ATOM 314 O GLU A 19 17.951 31.336 25.240 1.00 0.00 O +ATOM 315 N ALA A 20 19.109 32.052 23.609 1.00 0.00 N +ATOM 316 H ALA A 20 19.659 31.766 22.810 1.00 0.00 H +ATOM 317 CA ALA A 20 18.962 33.505 23.885 1.00 0.00 C +ATOM 318 HA ALA A 20 17.980 33.742 24.295 1.00 0.00 H +ATOM 319 CB ALA A 20 19.978 33.979 24.961 1.00 0.00 C +ATOM 320 HB1 ALA A 20 19.807 35.026 25.214 1.00 0.00 H +ATOM 321 HB2 ALA A 20 20.983 33.923 24.544 1.00 0.00 H +ATOM 322 HB3 ALA A 20 19.800 33.404 25.869 1.00 0.00 H +ATOM 323 C ALA A 20 19.121 34.352 22.595 1.00 0.00 C +ATOM 324 O ALA A 20 19.565 33.867 21.541 1.00 0.00 O +ATOM 325 N VAL A 21 18.819 35.698 22.666 1.00 0.00 N +ATOM 326 H VAL A 21 18.466 36.007 23.561 1.00 0.00 H +ATOM 327 CA VAL A 21 18.727 36.607 21.505 1.00 0.00 C +ATOM 328 HA VAL A 21 18.554 36.039 20.592 1.00 0.00 H +ATOM 329 CB VAL A 21 17.437 37.464 21.780 1.00 0.00 C +ATOM 330 HB VAL A 21 17.477 38.130 22.642 1.00 0.00 H +ATOM 331 CG1 VAL A 21 17.072 38.379 20.673 1.00 0.00 C +ATOM 332 HG11 VAL A 21 16.991 37.805 19.750 1.00 0.00 H +ATOM 333 HG12 VAL A 21 17.685 39.269 20.533 1.00 0.00 H +ATOM 334 HG13 VAL A 21 16.081 38.787 20.874 1.00 0.00 H +ATOM 335 CG2 VAL A 21 16.251 36.536 21.920 1.00 0.00 C +ATOM 336 HG21 VAL A 21 15.333 37.033 21.605 1.00 0.00 H +ATOM 337 HG22 VAL A 21 16.128 36.219 22.956 1.00 0.00 H +ATOM 338 HG23 VAL A 21 16.477 35.681 21.284 1.00 0.00 H +ATOM 339 C VAL A 21 19.976 37.521 21.405 1.00 0.00 C +ATOM 340 O VAL A 21 20.295 38.022 20.306 1.00 0.00 O +ATOM 341 N ASP A 22 20.728 37.651 22.457 1.00 0.00 N +ATOM 342 H ASP A 22 20.460 37.104 23.262 1.00 0.00 H +ATOM 343 CA ASP A 22 21.920 38.517 22.561 1.00 0.00 C +ATOM 344 HA ASP A 22 22.218 38.721 21.532 1.00 0.00 H +ATOM 345 CB ASP A 22 21.483 39.701 23.350 1.00 0.00 C +ATOM 346 HB2 ASP A 22 20.632 40.156 22.843 1.00 0.00 H +ATOM 347 HB3 ASP A 22 21.133 39.421 24.344 1.00 0.00 H +ATOM 348 CG ASP A 22 22.576 40.746 23.590 1.00 0.00 C +ATOM 349 OD1 ASP A 22 23.681 40.588 23.043 1.00 0.00 O1- +ATOM 350 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O1- +ATOM 351 C ASP A 22 23.019 37.703 23.294 1.00 0.00 C +ATOM 352 O ASP A 22 22.839 37.184 24.412 1.00 0.00 O +ATOM 353 N ALA A 23 24.210 37.649 22.694 1.00 0.00 N +ATOM 354 H ALA A 23 24.358 38.065 21.786 1.00 0.00 H +ATOM 355 CA ALA A 23 25.493 37.172 23.215 1.00 0.00 C +ATOM 356 HA ALA A 23 25.371 36.089 23.221 1.00 0.00 H +ATOM 357 CB ALA A 23 26.701 37.486 22.326 1.00 0.00 C +ATOM 358 HB1 ALA A 23 26.446 37.309 21.280 1.00 0.00 H +ATOM 359 HB2 ALA A 23 27.379 36.708 22.676 1.00 0.00 H +ATOM 360 HB3 ALA A 23 27.091 38.494 22.468 1.00 0.00 H +ATOM 361 C ALA A 23 25.748 37.757 24.642 1.00 0.00 C +ATOM 362 O ALA A 23 26.091 36.953 25.518 1.00 0.00 O +ATOM 363 N ALA A 24 25.564 39.050 24.846 1.00 0.00 N +ATOM 364 H ALA A 24 25.214 39.674 24.133 1.00 0.00 H +ATOM 365 CA ALA A 24 25.745 39.687 26.153 1.00 0.00 C +ATOM 366 HA ALA A 24 26.761 39.419 26.445 1.00 0.00 H +ATOM 367 CB ALA A 24 25.490 41.189 25.938 1.00 0.00 C +ATOM 368 HB1 ALA A 24 26.247 41.676 25.325 1.00 0.00 H +ATOM 369 HB2 ALA A 24 25.633 41.729 26.874 1.00 0.00 H +ATOM 370 HB3 ALA A 24 24.561 41.467 25.440 1.00 0.00 H +ATOM 371 C ALA A 24 24.796 39.101 27.137 1.00 0.00 C +ATOM 372 O ALA A 24 25.116 38.975 28.329 1.00 0.00 O +ATOM 373 N THR A 25 23.577 38.659 26.736 1.00 0.00 N +ATOM 374 H THR A 25 23.398 38.681 25.743 1.00 0.00 H +ATOM 375 CA THR A 25 22.587 38.094 27.680 1.00 0.00 C +ATOM 376 HA THR A 25 22.755 38.495 28.681 1.00 0.00 H +ATOM 377 CB THR A 25 21.196 38.549 27.262 1.00 0.00 C +ATOM 378 HB THR A 25 20.797 37.883 26.497 1.00 0.00 H +ATOM 379 CG2 THR A 25 20.246 38.369 28.438 1.00 0.00 C +ATOM 380 HG21 THR A 25 20.203 37.329 28.763 1.00 0.00 H +ATOM 381 HG22 THR A 25 19.255 38.740 28.176 1.00 0.00 H +ATOM 382 HG23 THR A 25 20.574 38.977 29.280 1.00 0.00 H +ATOM 383 OG1 THR A 25 21.199 39.931 27.030 1.00 0.00 O +ATOM 384 HG1 THR A 25 20.293 40.156 26.807 1.00 0.00 H +ATOM 385 C THR A 25 22.788 36.618 27.928 1.00 0.00 C +ATOM 386 O THR A 25 22.618 36.164 29.050 1.00 0.00 O +ATOM 387 N ALA A 26 23.216 35.854 26.929 1.00 0.00 N +ATOM 388 H ALA A 26 23.315 36.208 25.988 1.00 0.00 H +ATOM 389 CA ALA A 26 23.652 34.513 27.159 1.00 0.00 C +ATOM 390 HA ALA A 26 22.781 33.940 27.476 1.00 0.00 H +ATOM 391 CB ALA A 26 24.062 33.913 25.734 1.00 0.00 C +ATOM 392 HB1 ALA A 26 23.120 33.732 25.215 1.00 0.00 H +ATOM 393 HB2 ALA A 26 24.695 33.029 25.804 1.00 0.00 H +ATOM 394 HB3 ALA A 26 24.715 34.613 25.211 1.00 0.00 H +ATOM 395 C ALA A 26 24.856 34.523 28.062 1.00 0.00 C +ATOM 396 O ALA A 26 24.889 33.745 28.985 1.00 0.00 O +ATOM 397 N GLU A 27 25.749 35.500 28.027 1.00 0.00 N +ATOM 398 H GLU A 27 25.940 35.933 27.135 1.00 0.00 H +ATOM 399 CA GLU A 27 26.712 35.671 29.037 1.00 0.00 C +ATOM 400 HA GLU A 27 27.306 34.757 29.097 1.00 0.00 H +ATOM 401 CB GLU A 27 27.684 36.833 28.605 1.00 0.00 C +ATOM 402 HB2 GLU A 27 28.270 36.561 27.728 1.00 0.00 H +ATOM 403 HB3 GLU A 27 27.178 37.773 28.387 1.00 0.00 H +ATOM 404 CG GLU A 27 28.742 37.165 29.664 1.00 0.00 C +ATOM 405 HG2 GLU A 27 28.193 37.537 30.529 1.00 0.00 H +ATOM 406 HG3 GLU A 27 29.267 36.244 29.914 1.00 0.00 H +ATOM 407 CD GLU A 27 29.887 38.242 29.269 1.00 0.00 C +ATOM 408 OE1 GLU A 27 31.108 37.827 29.164 1.00 0.00 O1- +ATOM 409 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O1- +ATOM 410 C GLU A 27 26.099 35.742 30.450 1.00 0.00 C +ATOM 411 O GLU A 27 26.553 35.162 31.414 1.00 0.00 O +ATOM 412 N LYS A 28 25.124 36.609 30.604 1.00 0.00 N +ATOM 413 H LYS A 28 24.710 37.106 29.827 1.00 0.00 H +ATOM 414 CA LYS A 28 24.538 36.947 31.950 1.00 0.00 C +ATOM 415 HA LYS A 28 25.324 37.300 32.618 1.00 0.00 H +ATOM 416 CB LYS A 28 23.559 38.052 31.728 1.00 0.00 C +ATOM 417 HB2 LYS A 28 24.096 38.943 31.403 1.00 0.00 H +ATOM 418 HB3 LYS A 28 22.761 37.811 31.025 1.00 0.00 H +ATOM 419 CG LYS A 28 22.885 38.401 33.150 1.00 0.00 C +ATOM 420 HG2 LYS A 28 22.343 37.542 33.545 1.00 0.00 H +ATOM 421 HG3 LYS A 28 23.638 38.698 33.879 1.00 0.00 H +ATOM 422 CD LYS A 28 21.826 39.579 33.063 1.00 0.00 C +ATOM 423 HD2 LYS A 28 20.930 39.146 32.616 1.00 0.00 H +ATOM 424 HD3 LYS A 28 21.656 39.989 34.058 1.00 0.00 H +ATOM 425 CE LYS A 28 22.359 40.850 32.267 1.00 0.00 C +ATOM 426 HE2 LYS A 28 23.432 40.899 32.449 1.00 0.00 H +ATOM 427 HE3 LYS A 28 22.199 40.756 31.193 1.00 0.00 H +ATOM 428 NZ LYS A 28 21.521 42.013 32.715 1.00 0.00 N1+ +ATOM 429 HZ1 LYS A 28 21.696 42.294 33.670 1.00 0.00 H +ATOM 430 HZ2 LYS A 28 20.541 41.777 32.653 1.00 0.00 H +ATOM 431 HZ3 LYS A 28 21.651 42.827 32.131 1.00 0.00 H +ATOM 432 C LYS A 28 23.866 35.778 32.535 1.00 0.00 C +ATOM 433 O LYS A 28 23.994 35.665 33.742 1.00 0.00 O +ATOM 434 N VAL A 29 23.329 34.885 31.712 1.00 0.00 N +ATOM 435 H VAL A 29 23.229 35.111 30.733 1.00 0.00 H +ATOM 436 CA VAL A 29 22.736 33.650 32.097 1.00 0.00 C +ATOM 437 HA VAL A 29 21.999 33.879 32.866 1.00 0.00 H +ATOM 438 CB VAL A 29 21.735 33.166 30.962 1.00 0.00 C +ATOM 439 HB VAL A 29 22.375 32.951 30.106 1.00 0.00 H +ATOM 440 CG1 VAL A 29 21.139 31.783 31.445 1.00 0.00 C +ATOM 441 HG11 VAL A 29 20.592 31.413 30.579 1.00 0.00 H +ATOM 442 HG12 VAL A 29 20.575 31.908 32.370 1.00 0.00 H +ATOM 443 HG13 VAL A 29 21.993 31.113 31.534 1.00 0.00 H +ATOM 444 CG2 VAL A 29 20.482 33.992 30.547 1.00 0.00 C +ATOM 445 HG21 VAL A 29 19.966 33.618 29.662 1.00 0.00 H +ATOM 446 HG22 VAL A 29 20.739 35.019 30.286 1.00 0.00 H +ATOM 447 HG23 VAL A 29 19.838 34.110 31.419 1.00 0.00 H +ATOM 448 C VAL A 29 23.781 32.642 32.484 1.00 0.00 C +ATOM 449 O VAL A 29 23.604 31.876 33.462 1.00 0.00 O +ATOM 450 N PHE A 30 24.962 32.641 31.758 1.00 0.00 N +ATOM 451 H PHE A 30 24.997 33.287 30.981 1.00 0.00 H +ATOM 452 CA PHE A 30 26.112 31.701 32.033 1.00 0.00 C +ATOM 453 HA PHE A 30 25.692 30.753 32.371 1.00 0.00 H +ATOM 454 CB PHE A 30 26.901 31.582 30.713 1.00 0.00 C +ATOM 455 HB2 PHE A 30 26.966 32.537 30.191 1.00 0.00 H +ATOM 456 HB3 PHE A 30 27.928 31.266 30.888 1.00 0.00 H +ATOM 457 CG PHE A 30 26.348 30.600 29.656 1.00 0.00 C +ATOM 458 CD1 PHE A 30 25.751 29.296 29.878 1.00 0.00 C +ATOM 459 HD1 PHE A 30 25.705 28.943 30.897 1.00 0.00 H +ATOM 460 CE1 PHE A 30 25.345 28.377 28.817 1.00 0.00 C +ATOM 461 HE1 PHE A 30 24.810 27.464 29.039 1.00 0.00 H +ATOM 462 CZ PHE A 30 25.534 28.840 27.515 1.00 0.00 C +ATOM 463 HZ PHE A 30 25.196 28.267 26.666 1.00 0.00 H +ATOM 464 CE2 PHE A 30 26.096 30.099 27.271 1.00 0.00 C +ATOM 465 HE2 PHE A 30 26.212 30.319 26.219 1.00 0.00 H +ATOM 466 CD2 PHE A 30 26.533 30.924 28.297 1.00 0.00 C +ATOM 467 HD2 PHE A 30 27.135 31.778 28.029 1.00 0.00 H +ATOM 468 C PHE A 30 26.988 32.189 33.246 1.00 0.00 C +ATOM 469 O PHE A 30 27.609 31.344 33.905 1.00 0.00 O +ATOM 470 N LYS A 31 27.038 33.446 33.540 1.00 0.00 N +ATOM 471 H LYS A 31 26.710 34.105 32.849 1.00 0.00 H +ATOM 472 CA LYS A 31 27.405 34.022 34.854 1.00 0.00 C +ATOM 473 HA LYS A 31 28.437 33.764 35.092 1.00 0.00 H +ATOM 474 CB LYS A 31 27.274 35.599 34.858 1.00 0.00 C +ATOM 475 HB2 LYS A 31 26.242 35.714 34.527 1.00 0.00 H +ATOM 476 HB3 LYS A 31 27.292 36.098 35.827 1.00 0.00 H +ATOM 477 CG LYS A 31 28.378 36.275 33.919 1.00 0.00 C +ATOM 478 HG2 LYS A 31 28.522 35.710 32.997 1.00 0.00 H +ATOM 479 HG3 LYS A 31 27.926 37.229 33.649 1.00 0.00 H +ATOM 480 CD LYS A 31 29.823 36.487 34.439 1.00 0.00 C +ATOM 481 HD2 LYS A 31 29.755 36.977 35.411 1.00 0.00 H +ATOM 482 HD3 LYS A 31 30.132 35.472 34.684 1.00 0.00 H +ATOM 483 CE LYS A 31 30.777 37.150 33.394 1.00 0.00 C +ATOM 484 HE2 LYS A 31 30.633 36.630 32.447 1.00 0.00 H +ATOM 485 HE3 LYS A 31 30.436 38.158 33.158 1.00 0.00 H +ATOM 486 NZ LYS A 31 32.138 37.121 33.926 1.00 0.00 N1+ +ATOM 487 HZ1 LYS A 31 32.272 37.458 34.869 1.00 0.00 H +ATOM 488 HZ2 LYS A 31 32.676 37.777 33.376 1.00 0.00 H +ATOM 489 HZ3 LYS A 31 32.555 36.210 33.805 1.00 0.00 H +ATOM 490 C LYS A 31 26.516 33.562 35.983 1.00 0.00 C +ATOM 491 O LYS A 31 27.018 32.993 36.943 1.00 0.00 O +ATOM 492 N GLN A 32 25.185 33.745 35.953 1.00 0.00 N +ATOM 493 H GLN A 32 24.737 34.194 35.166 1.00 0.00 H +ATOM 494 CA GLN A 32 24.365 33.197 37.027 1.00 0.00 C +ATOM 495 HA GLN A 32 24.679 33.822 37.863 1.00 0.00 H +ATOM 496 CB GLN A 32 22.891 33.427 36.688 1.00 0.00 C +ATOM 497 HB2 GLN A 32 22.845 33.366 35.601 1.00 0.00 H +ATOM 498 HB3 GLN A 32 22.285 32.685 37.209 1.00 0.00 H +ATOM 499 CG GLN A 32 22.280 34.840 37.028 1.00 0.00 C +ATOM 500 HG2 GLN A 32 22.039 34.881 38.090 1.00 0.00 H +ATOM 501 HG3 GLN A 32 22.899 35.710 36.807 1.00 0.00 H +ATOM 502 CD GLN A 32 20.958 35.124 36.195 1.00 0.00 C +ATOM 503 OE1 GLN A 32 19.883 34.823 36.738 1.00 0.00 O +ATOM 504 NE2 GLN A 32 20.988 35.530 34.974 1.00 0.00 N +ATOM 505 HE21 GLN A 32 21.902 35.787 34.628 1.00 0.00 H +ATOM 506 HE22 GLN A 32 20.177 35.714 34.400 1.00 0.00 H +ATOM 507 C GLN A 32 24.598 31.707 37.232 1.00 0.00 C +ATOM 508 O GLN A 32 24.794 31.293 38.384 1.00 0.00 O +ATOM 509 N TYR A 33 24.530 30.875 36.142 1.00 0.00 N +ATOM 510 H TYR A 33 24.587 31.274 35.216 1.00 0.00 H +ATOM 511 CA TYR A 33 24.722 29.459 36.217 1.00 0.00 C +ATOM 512 HA TYR A 33 23.881 29.042 36.772 1.00 0.00 H +ATOM 513 CB TYR A 33 24.622 28.848 34.842 1.00 0.00 C +ATOM 514 HB2 TYR A 33 23.621 29.006 34.442 1.00 0.00 H +ATOM 515 HB3 TYR A 33 25.353 29.388 34.240 1.00 0.00 H +ATOM 516 CG TYR A 33 24.877 27.304 34.704 1.00 0.00 C +ATOM 517 CD1 TYR A 33 23.808 26.383 34.938 1.00 0.00 C +ATOM 518 HD1 TYR A 33 22.814 26.754 35.140 1.00 0.00 H +ATOM 519 CE1 TYR A 33 24.054 24.991 35.075 1.00 0.00 C +ATOM 520 HE1 TYR A 33 23.300 24.251 35.300 1.00 0.00 H +ATOM 521 CZ TYR A 33 25.399 24.562 34.934 1.00 0.00 C +ATOM 522 OH TYR A 33 25.658 23.212 34.983 1.00 0.00 O +ATOM 523 HH TYR A 33 26.608 23.080 35.030 1.00 0.00 H +ATOM 524 CE2 TYR A 33 26.410 25.459 34.723 1.00 0.00 C +ATOM 525 HE2 TYR A 33 27.443 25.157 34.630 1.00 0.00 H +ATOM 526 CD2 TYR A 33 26.146 26.818 34.602 1.00 0.00 C +ATOM 527 HD2 TYR A 33 26.992 27.469 34.435 1.00 0.00 H +ATOM 528 C TYR A 33 26.078 29.155 36.854 1.00 0.00 C +ATOM 529 O TYR A 33 26.179 28.186 37.566 1.00 0.00 O +ATOM 530 N ALA A 34 27.159 29.788 36.508 1.00 0.00 N +ATOM 531 H ALA A 34 26.997 30.563 35.881 1.00 0.00 H +ATOM 532 CA ALA A 34 28.473 29.535 37.100 1.00 0.00 C +ATOM 533 HA ALA A 34 28.717 28.476 37.023 1.00 0.00 H +ATOM 534 CB ALA A 34 29.651 30.265 36.402 1.00 0.00 C +ATOM 535 HB1 ALA A 34 30.577 29.813 36.757 1.00 0.00 H +ATOM 536 HB2 ALA A 34 29.619 31.296 36.752 1.00 0.00 H +ATOM 537 HB3 ALA A 34 29.681 30.159 35.317 1.00 0.00 H +ATOM 538 C ALA A 34 28.508 29.835 38.614 1.00 0.00 C +ATOM 539 O ALA A 34 29.097 29.077 39.389 1.00 0.00 O +ATOM 540 N ASN A 35 27.814 30.864 39.024 1.00 0.00 N +ATOM 541 H ASN A 35 27.594 31.535 38.301 1.00 0.00 H +ATOM 542 CA ASN A 35 27.743 31.252 40.445 1.00 0.00 C +ATOM 543 HA ASN A 35 28.713 31.168 40.935 1.00 0.00 H +ATOM 544 CB ASN A 35 27.254 32.684 40.541 1.00 0.00 C +ATOM 545 HB2 ASN A 35 27.798 33.361 39.883 1.00 0.00 H +ATOM 546 HB3 ASN A 35 26.192 32.727 40.300 1.00 0.00 H +ATOM 547 CG ASN A 35 27.326 33.169 41.947 1.00 0.00 C +ATOM 548 OD1 ASN A 35 26.493 32.743 42.763 1.00 0.00 O +ATOM 549 ND2 ASN A 35 28.099 34.183 42.223 1.00 0.00 N +ATOM 550 HD21 ASN A 35 28.867 34.350 41.589 1.00 0.00 H +ATOM 551 HD22 ASN A 35 28.276 34.397 43.193 1.00 0.00 H +ATOM 552 C ASN A 35 26.833 30.200 41.127 1.00 0.00 C +ATOM 553 O ASN A 35 27.114 29.686 42.238 1.00 0.00 O +ATOM 554 N ASP A 36 25.819 29.616 40.395 1.00 0.00 N +ATOM 555 H ASP A 36 25.608 30.144 39.560 1.00 0.00 H +ATOM 556 CA ASP A 36 25.004 28.401 40.867 1.00 0.00 C +ATOM 557 HA ASP A 36 24.491 28.819 41.733 1.00 0.00 H +ATOM 558 CB ASP A 36 23.819 28.175 39.948 1.00 0.00 C +ATOM 559 HB2 ASP A 36 23.379 29.117 39.623 1.00 0.00 H +ATOM 560 HB3 ASP A 36 24.279 27.586 39.154 1.00 0.00 H +ATOM 561 CG ASP A 36 22.720 27.350 40.470 1.00 0.00 C +ATOM 562 OD1 ASP A 36 22.214 26.485 39.714 1.00 0.00 O1- +ATOM 563 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O1- +ATOM 564 C ASP A 36 25.793 27.113 41.244 1.00 0.00 C +ATOM 565 O ASP A 36 25.357 26.391 42.112 1.00 0.00 O +ATOM 566 N ASN A 37 26.991 27.006 40.666 1.00 0.00 N +ATOM 567 H ASN A 37 27.306 27.779 40.098 1.00 0.00 H +ATOM 568 CA ASN A 37 27.829 25.814 40.636 1.00 0.00 C +ATOM 569 HA ASN A 37 27.378 25.130 41.354 1.00 0.00 H +ATOM 570 CB ASN A 37 27.873 25.281 39.195 1.00 0.00 C +ATOM 571 HB2 ASN A 37 27.936 26.106 38.487 1.00 0.00 H +ATOM 572 HB3 ASN A 37 28.702 24.579 39.101 1.00 0.00 H +ATOM 573 CG ASN A 37 26.652 24.492 38.842 1.00 0.00 C +ATOM 574 OD1 ASN A 37 26.432 23.357 39.282 1.00 0.00 O +ATOM 575 ND2 ASN A 37 25.706 25.057 38.177 1.00 0.00 N +ATOM 576 HD21 ASN A 37 25.804 26.050 38.016 1.00 0.00 H +ATOM 577 HD22 ASN A 37 24.895 24.502 37.947 1.00 0.00 H +ATOM 578 C ASN A 37 29.196 26.053 41.261 1.00 0.00 C +ATOM 579 O ASN A 37 30.064 25.171 41.182 1.00 0.00 O +ATOM 580 N GLY A 38 29.358 27.176 42.012 1.00 0.00 N +ATOM 581 H GLY A 38 28.556 27.765 42.189 1.00 0.00 H +ATOM 582 CA GLY A 38 30.637 27.460 42.681 1.00 0.00 C +ATOM 583 HA2 GLY A 38 30.444 28.296 43.354 1.00 0.00 H +ATOM 584 HA3 GLY A 38 30.900 26.655 43.368 1.00 0.00 H +ATOM 585 C GLY A 38 31.894 27.774 41.785 1.00 0.00 C +ATOM 586 O GLY A 38 33.027 27.429 42.124 1.00 0.00 O +ATOM 587 N VAL A 39 31.731 28.287 40.579 1.00 0.00 N +ATOM 588 H VAL A 39 30.794 28.624 40.408 1.00 0.00 H +ATOM 589 CA VAL A 39 32.664 28.449 39.403 1.00 0.00 C +ATOM 590 HA VAL A 39 33.598 27.911 39.570 1.00 0.00 H +ATOM 591 CB VAL A 39 32.015 27.778 38.179 1.00 0.00 C +ATOM 592 HB VAL A 39 31.005 28.158 38.027 1.00 0.00 H +ATOM 593 CG1 VAL A 39 32.989 28.121 37.014 1.00 0.00 C +ATOM 594 HG11 VAL A 39 32.636 27.519 36.176 1.00 0.00 H +ATOM 595 HG12 VAL A 39 34.019 27.963 37.334 1.00 0.00 H +ATOM 596 HG13 VAL A 39 32.869 29.117 36.588 1.00 0.00 H +ATOM 597 CG2 VAL A 39 31.943 26.274 38.437 1.00 0.00 C +ATOM 598 HG21 VAL A 39 31.540 25.729 37.583 1.00 0.00 H +ATOM 599 HG22 VAL A 39 31.356 26.086 39.337 1.00 0.00 H +ATOM 600 HG23 VAL A 39 32.907 25.863 38.738 1.00 0.00 H +ATOM 601 C VAL A 39 33.029 29.909 39.235 1.00 0.00 C +ATOM 602 O VAL A 39 32.186 30.683 38.757 1.00 0.00 O +ATOM 603 N ASP A 40 34.268 30.281 39.558 1.00 0.00 N +ATOM 604 H ASP A 40 34.838 29.543 39.947 1.00 0.00 H +ATOM 605 CA ASP A 40 34.875 31.551 39.096 1.00 0.00 C +ATOM 606 HA ASP A 40 34.143 32.078 38.487 1.00 0.00 H +ATOM 607 CB ASP A 40 35.183 32.418 40.345 1.00 0.00 C +ATOM 608 HB2 ASP A 40 34.184 32.657 40.710 1.00 0.00 H +ATOM 609 HB3 ASP A 40 35.707 31.788 41.065 1.00 0.00 H +ATOM 610 CG ASP A 40 35.879 33.683 40.009 1.00 0.00 C +ATOM 611 OD1 ASP A 40 35.393 34.410 39.076 1.00 0.00 O1- +ATOM 612 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O1- +ATOM 613 C ASP A 40 36.062 31.169 38.238 1.00 0.00 C +ATOM 614 O ASP A 40 36.850 30.275 38.630 1.00 0.00 O +ATOM 615 N GLY A 41 36.172 31.751 37.102 1.00 0.00 N +ATOM 616 H GLY A 41 35.443 32.408 36.858 1.00 0.00 H +ATOM 617 CA GLY A 41 37.214 31.484 36.189 1.00 0.00 C +ATOM 618 HA2 GLY A 41 38.072 31.014 36.670 1.00 0.00 H +ATOM 619 HA3 GLY A 41 36.761 30.672 35.620 1.00 0.00 H +ATOM 620 C GLY A 41 37.623 32.709 35.379 1.00 0.00 C +ATOM 621 O GLY A 41 37.288 33.862 35.686 1.00 0.00 O +ATOM 622 N GLU A 42 38.354 32.422 34.316 1.00 0.00 N +ATOM 623 H GLU A 42 38.789 31.512 34.368 1.00 0.00 H +ATOM 624 CA GLU A 42 38.603 33.310 33.228 1.00 0.00 C +ATOM 625 HA GLU A 42 38.329 34.318 33.541 1.00 0.00 H +ATOM 626 CB GLU A 42 40.158 33.294 33.040 1.00 0.00 C +ATOM 627 HB2 GLU A 42 40.656 33.398 34.004 1.00 0.00 H +ATOM 628 HB3 GLU A 42 40.417 32.326 32.611 1.00 0.00 H +ATOM 629 CG GLU A 42 40.673 34.328 32.046 1.00 0.00 C +ATOM 630 HG2 GLU A 42 41.606 34.015 31.580 1.00 0.00 H +ATOM 631 HG3 GLU A 42 39.970 34.501 31.231 1.00 0.00 H +ATOM 632 CD GLU A 42 41.014 35.613 32.804 1.00 0.00 C +ATOM 633 OE1 GLU A 42 41.944 35.693 33.644 1.00 0.00 O1- +ATOM 634 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O1- +ATOM 635 C GLU A 42 37.780 33.033 32.033 1.00 0.00 C +ATOM 636 O GLU A 42 37.577 31.870 31.690 1.00 0.00 O +ATOM 637 N TRP A 43 37.228 34.069 31.412 1.00 0.00 N +ATOM 638 H TRP A 43 37.423 35.035 31.634 1.00 0.00 H +ATOM 639 CA TRP A 43 36.233 33.951 30.354 1.00 0.00 C +ATOM 640 HA TRP A 43 35.850 32.931 30.348 1.00 0.00 H +ATOM 641 CB TRP A 43 34.984 34.889 30.616 1.00 0.00 C +ATOM 642 HB2 TRP A 43 35.436 35.868 30.771 1.00 0.00 H +ATOM 643 HB3 TRP A 43 34.427 34.918 29.679 1.00 0.00 H +ATOM 644 CG TRP A 43 34.115 34.536 31.838 1.00 0.00 C +ATOM 645 CD1 TRP A 43 34.428 34.708 33.154 1.00 0.00 C +ATOM 646 HD1 TRP A 43 35.387 35.052 33.511 1.00 0.00 H +ATOM 647 NE1 TRP A 43 33.399 34.110 33.877 1.00 0.00 N +ATOM 648 HE1 TRP A 43 33.511 34.066 34.880 1.00 0.00 H +ATOM 649 CE2 TRP A 43 32.444 33.463 33.073 1.00 0.00 C +ATOM 650 CZ2 TRP A 43 31.248 32.745 33.296 1.00 0.00 C +ATOM 651 HZ2 TRP A 43 31.007 32.429 34.301 1.00 0.00 H +ATOM 652 CH2 TRP A 43 30.575 32.194 32.199 1.00 0.00 C +ATOM 653 HH2 TRP A 43 29.740 31.527 32.355 1.00 0.00 H +ATOM 654 CZ3 TRP A 43 30.988 32.541 30.909 1.00 0.00 C +ATOM 655 HZ3 TRP A 43 30.412 32.236 30.047 1.00 0.00 H +ATOM 656 CE3 TRP A 43 32.109 33.327 30.682 1.00 0.00 C +ATOM 657 HE3 TRP A 43 32.397 33.679 29.703 1.00 0.00 H +ATOM 658 CD2 TRP A 43 32.870 33.817 31.765 1.00 0.00 C +ATOM 659 C TRP A 43 36.910 34.235 29.034 1.00 0.00 C +ATOM 660 O TRP A 43 37.660 35.202 28.823 1.00 0.00 O +ATOM 661 N THR A 44 36.468 33.398 28.113 1.00 0.00 N +ATOM 662 H THR A 44 35.919 32.590 28.367 1.00 0.00 H +ATOM 663 CA THR A 44 36.627 33.526 26.668 1.00 0.00 C +ATOM 664 HA THR A 44 36.825 34.580 26.474 1.00 0.00 H +ATOM 665 CB THR A 44 37.813 32.794 26.062 1.00 0.00 C +ATOM 666 HB THR A 44 37.695 32.789 24.978 1.00 0.00 H +ATOM 667 CG2 THR A 44 39.142 33.411 26.470 1.00 0.00 C +ATOM 668 HG21 THR A 44 39.971 32.814 26.090 1.00 0.00 H +ATOM 669 HG22 THR A 44 39.277 33.395 27.552 1.00 0.00 H +ATOM 670 HG23 THR A 44 39.360 34.408 26.088 1.00 0.00 H +ATOM 671 OG1 THR A 44 37.854 31.507 26.604 1.00 0.00 O +ATOM 672 HG1 THR A 44 37.629 30.907 25.889 1.00 0.00 H +ATOM 673 C THR A 44 35.267 33.295 26.005 1.00 0.00 C +ATOM 674 O THR A 44 34.480 32.577 26.444 1.00 0.00 O +ATOM 675 N TYR A 45 35.137 33.919 24.848 1.00 0.00 N +ATOM 676 H TYR A 45 35.900 34.526 24.585 1.00 0.00 H +ATOM 677 CA TYR A 45 34.051 33.679 23.814 1.00 0.00 C +ATOM 678 HA TYR A 45 33.565 32.748 24.109 1.00 0.00 H +ATOM 679 CB TYR A 45 33.061 34.890 23.836 1.00 0.00 C +ATOM 680 HB2 TYR A 45 32.689 35.085 24.843 1.00 0.00 H +ATOM 681 HB3 TYR A 45 33.670 35.762 23.596 1.00 0.00 H +ATOM 682 CG TYR A 45 31.825 34.747 22.962 1.00 0.00 C +ATOM 683 CD1 TYR A 45 30.955 33.684 23.061 1.00 0.00 C +ATOM 684 HD1 TYR A 45 31.040 32.945 23.845 1.00 0.00 H +ATOM 685 CE1 TYR A 45 29.908 33.556 22.116 1.00 0.00 C +ATOM 686 HE1 TYR A 45 29.113 32.849 22.291 1.00 0.00 H +ATOM 687 CZ TYR A 45 29.718 34.506 21.094 1.00 0.00 C +ATOM 688 OH TYR A 45 28.658 34.338 20.268 1.00 0.00 O +ATOM 689 HH TYR A 45 28.496 35.052 19.648 1.00 0.00 H +ATOM 690 CE2 TYR A 45 30.653 35.574 21.028 1.00 0.00 C +ATOM 691 HE2 TYR A 45 30.490 36.288 20.234 1.00 0.00 H +ATOM 692 CD2 TYR A 45 31.752 35.643 21.911 1.00 0.00 C +ATOM 693 HD2 TYR A 45 32.537 36.346 21.679 1.00 0.00 H +ATOM 694 C TYR A 45 34.545 33.529 22.336 1.00 0.00 C +ATOM 695 O TYR A 45 35.260 34.412 21.809 1.00 0.00 O +ATOM 696 N ASP A 46 33.924 32.567 21.640 1.00 0.00 N +ATOM 697 H ASP A 46 33.215 32.006 22.088 1.00 0.00 H +ATOM 698 CA ASP A 46 34.109 32.289 20.204 1.00 0.00 C +ATOM 699 HA ASP A 46 34.805 32.896 19.625 1.00 0.00 H +ATOM 700 CB ASP A 46 34.818 30.917 20.240 1.00 0.00 C +ATOM 701 HB2 ASP A 46 35.700 31.032 20.871 1.00 0.00 H +ATOM 702 HB3 ASP A 46 34.252 30.200 20.834 1.00 0.00 H +ATOM 703 CG ASP A 46 35.216 30.282 18.912 1.00 0.00 C +ATOM 704 OD1 ASP A 46 34.405 29.507 18.323 1.00 0.00 O1- +ATOM 705 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O1- +ATOM 706 C ASP A 46 32.877 32.275 19.319 1.00 0.00 C +ATOM 707 O ASP A 46 31.931 31.517 19.529 1.00 0.00 O +ATOM 708 N ASP A 47 32.833 33.220 18.413 1.00 0.00 N +ATOM 709 H ASP A 47 33.622 33.852 18.429 1.00 0.00 H +ATOM 710 CA ASP A 47 31.688 33.456 17.554 1.00 0.00 C +ATOM 711 HA ASP A 47 30.773 33.561 18.137 1.00 0.00 H +ATOM 712 CB ASP A 47 31.907 34.738 16.747 1.00 0.00 C +ATOM 713 HB2 ASP A 47 32.113 35.510 17.488 1.00 0.00 H +ATOM 714 HB3 ASP A 47 32.853 34.697 16.207 1.00 0.00 H +ATOM 715 CG ASP A 47 30.729 35.187 15.844 1.00 0.00 C +ATOM 716 OD1 ASP A 47 29.551 35.040 16.174 1.00 0.00 O1- +ATOM 717 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O1- +ATOM 718 C ASP A 47 31.522 32.326 16.557 1.00 0.00 C +ATOM 719 O ASP A 47 30.390 32.069 16.134 1.00 0.00 O +ATOM 720 N ALA A 48 32.555 31.657 16.092 1.00 0.00 N +ATOM 721 H ALA A 48 33.490 31.931 16.357 1.00 0.00 H +ATOM 722 CA ALA A 48 32.437 30.647 15.015 1.00 0.00 C +ATOM 723 HA ALA A 48 31.707 31.108 14.349 1.00 0.00 H +ATOM 724 CB ALA A 48 33.821 30.467 14.340 1.00 0.00 C +ATOM 725 HB1 ALA A 48 34.244 31.399 13.964 1.00 0.00 H +ATOM 726 HB2 ALA A 48 33.675 29.706 13.573 1.00 0.00 H +ATOM 727 HB3 ALA A 48 34.421 29.986 15.112 1.00 0.00 H +ATOM 728 C ALA A 48 31.855 29.301 15.549 1.00 0.00 C +ATOM 729 O ALA A 48 31.548 28.445 14.720 1.00 0.00 O +ATOM 730 N THR A 49 31.619 29.163 16.885 1.00 0.00 N +ATOM 731 H THR A 49 31.975 29.929 17.439 1.00 0.00 H +ATOM 732 CA THR A 49 30.811 28.126 17.576 1.00 0.00 C +ATOM 733 HA THR A 49 30.371 27.544 16.767 1.00 0.00 H +ATOM 734 CB THR A 49 31.713 27.100 18.310 1.00 0.00 C +ATOM 735 HB THR A 49 31.134 26.420 18.935 1.00 0.00 H +ATOM 736 CG2 THR A 49 32.614 26.280 17.436 1.00 0.00 C +ATOM 737 HG21 THR A 49 33.329 26.868 16.859 1.00 0.00 H +ATOM 738 HG22 THR A 49 32.002 25.593 16.853 1.00 0.00 H +ATOM 739 HG23 THR A 49 33.354 25.760 18.044 1.00 0.00 H +ATOM 740 OG1 THR A 49 32.507 27.834 19.222 1.00 0.00 O +ATOM 741 HG1 THR A 49 33.151 28.336 18.715 1.00 0.00 H +ATOM 742 C THR A 49 29.713 28.644 18.468 1.00 0.00 C +ATOM 743 O THR A 49 28.941 27.912 19.103 1.00 0.00 O +ATOM 744 N LYS A 50 29.628 29.977 18.649 1.00 0.00 N +ATOM 745 H LYS A 50 30.419 30.522 18.334 1.00 0.00 H +ATOM 746 CA LYS A 50 28.663 30.695 19.541 1.00 0.00 C +ATOM 747 HA LYS A 50 28.847 31.769 19.501 1.00 0.00 H +ATOM 748 CB LYS A 50 27.189 30.625 19.033 1.00 0.00 C +ATOM 749 HB2 LYS A 50 26.936 29.572 19.163 1.00 0.00 H +ATOM 750 HB3 LYS A 50 26.469 31.081 19.712 1.00 0.00 H +ATOM 751 CG LYS A 50 27.119 30.984 17.465 1.00 0.00 C +ATOM 752 HG2 LYS A 50 27.961 30.590 16.895 1.00 0.00 H +ATOM 753 HG3 LYS A 50 26.188 30.551 17.100 1.00 0.00 H +ATOM 754 CD LYS A 50 27.025 32.547 17.322 1.00 0.00 C +ATOM 755 HD2 LYS A 50 26.337 33.099 17.964 1.00 0.00 H +ATOM 756 HD3 LYS A 50 28.005 32.913 17.623 1.00 0.00 H +ATOM 757 CE LYS A 50 26.686 32.933 15.930 1.00 0.00 C +ATOM 758 HE2 LYS A 50 25.829 32.363 15.572 1.00 0.00 H +ATOM 759 HE3 LYS A 50 26.304 33.953 15.986 1.00 0.00 H +ATOM 760 NZ LYS A 50 27.861 32.905 14.990 1.00 0.00 N1+ +ATOM 761 HZ1 LYS A 50 28.562 33.507 15.397 1.00 0.00 H +ATOM 762 HZ2 LYS A 50 27.597 33.321 14.108 1.00 0.00 H +ATOM 763 HZ3 LYS A 50 28.269 32.017 14.736 1.00 0.00 H +ATOM 764 C LYS A 50 28.884 30.250 21.033 1.00 0.00 C +ATOM 765 O LYS A 50 27.958 30.206 21.826 1.00 0.00 O +ATOM 766 N THR A 51 30.148 29.820 21.328 1.00 0.00 N +ATOM 767 H THR A 51 30.940 30.100 20.766 1.00 0.00 H +ATOM 768 CA THR A 51 30.503 29.214 22.632 1.00 0.00 C +ATOM 769 HA THR A 51 29.680 28.714 23.142 1.00 0.00 H +ATOM 770 CB THR A 51 31.313 27.944 22.369 1.00 0.00 C +ATOM 771 HB THR A 51 32.245 28.102 21.826 1.00 0.00 H +ATOM 772 CG2 THR A 51 31.703 27.088 23.590 1.00 0.00 C +ATOM 773 HG21 THR A 51 32.177 26.160 23.272 1.00 0.00 H +ATOM 774 HG22 THR A 51 30.745 26.977 24.100 1.00 0.00 H +ATOM 775 HG23 THR A 51 32.401 27.677 24.186 1.00 0.00 H +ATOM 776 OG1 THR A 51 30.404 27.161 21.659 1.00 0.00 O +ATOM 777 HG1 THR A 51 29.757 27.683 21.179 1.00 0.00 H +ATOM 778 C THR A 51 31.202 30.120 23.549 1.00 0.00 C +ATOM 779 O THR A 51 32.200 30.721 23.143 1.00 0.00 O +ATOM 780 N PHE A 52 31.009 29.926 24.845 1.00 0.00 N +ATOM 781 H PHE A 52 30.125 29.479 25.042 1.00 0.00 H +ATOM 782 CA PHE A 52 31.821 30.391 25.941 1.00 0.00 C +ATOM 783 HA PHE A 52 32.490 31.192 25.628 1.00 0.00 H +ATOM 784 CB PHE A 52 30.715 30.979 27.007 1.00 0.00 C +ATOM 785 HB2 PHE A 52 29.988 30.200 27.238 1.00 0.00 H +ATOM 786 HB3 PHE A 52 31.250 31.298 27.901 1.00 0.00 H +ATOM 787 CG PHE A 52 30.049 32.222 26.534 1.00 0.00 C +ATOM 788 CD1 PHE A 52 28.876 32.142 25.781 1.00 0.00 C +ATOM 789 HD1 PHE A 52 28.413 31.204 25.515 1.00 0.00 H +ATOM 790 CE1 PHE A 52 28.300 33.350 25.304 1.00 0.00 C +ATOM 791 HE1 PHE A 52 27.303 33.316 24.890 1.00 0.00 H +ATOM 792 CZ PHE A 52 28.880 34.593 25.500 1.00 0.00 C +ATOM 793 HZ PHE A 52 28.417 35.460 25.054 1.00 0.00 H +ATOM 794 CE2 PHE A 52 30.122 34.665 26.192 1.00 0.00 C +ATOM 795 HE2 PHE A 52 30.650 35.597 26.333 1.00 0.00 H +ATOM 796 CD2 PHE A 52 30.597 33.495 26.795 1.00 0.00 C +ATOM 797 HD2 PHE A 52 31.435 33.581 27.471 1.00 0.00 H +ATOM 798 C PHE A 52 32.721 29.343 26.553 1.00 0.00 C +ATOM 799 O PHE A 52 32.280 28.240 26.674 1.00 0.00 O +ATOM 800 N THR A 53 33.908 29.829 27.087 1.00 0.00 N +ATOM 801 H THR A 53 34.203 30.784 26.938 1.00 0.00 H +ATOM 802 CA THR A 53 34.577 29.044 28.132 1.00 0.00 C +ATOM 803 HA THR A 53 34.003 28.190 28.492 1.00 0.00 H +ATOM 804 CB THR A 53 35.881 28.443 27.684 1.00 0.00 C +ATOM 805 HB THR A 53 36.513 29.234 27.280 1.00 0.00 H +ATOM 806 CG2 THR A 53 36.620 27.571 28.752 1.00 0.00 C +ATOM 807 HG21 THR A 53 36.814 28.236 29.595 1.00 0.00 H +ATOM 808 HG22 THR A 53 37.535 27.174 28.313 1.00 0.00 H +ATOM 809 HG23 THR A 53 35.924 26.795 29.068 1.00 0.00 H +ATOM 810 OG1 THR A 53 35.605 27.649 26.584 1.00 0.00 O +ATOM 811 HG1 THR A 53 35.459 28.177 25.796 1.00 0.00 H +ATOM 812 C THR A 53 34.776 29.748 29.443 1.00 0.00 C +ATOM 813 O THR A 53 35.146 30.939 29.437 1.00 0.00 O +ATOM 814 N VAL A 54 34.499 29.135 30.639 1.00 0.00 N +ATOM 815 H VAL A 54 34.209 28.173 30.538 1.00 0.00 H +ATOM 816 CA VAL A 54 34.861 29.536 31.982 1.00 0.00 C +ATOM 817 HA VAL A 54 35.382 30.493 31.978 1.00 0.00 H +ATOM 818 CB VAL A 54 33.697 29.716 32.869 1.00 0.00 C +ATOM 819 HB VAL A 54 32.913 30.335 32.434 1.00 0.00 H +ATOM 820 CG1 VAL A 54 33.002 28.394 33.289 1.00 0.00 C +ATOM 821 HG11 VAL A 54 33.690 27.666 33.718 1.00 0.00 H +ATOM 822 HG12 VAL A 54 32.618 28.014 32.342 1.00 0.00 H +ATOM 823 HG13 VAL A 54 32.093 28.525 33.877 1.00 0.00 H +ATOM 824 CG2 VAL A 54 34.118 30.320 34.224 1.00 0.00 C +ATOM 825 HG21 VAL A 54 34.711 31.228 34.123 1.00 0.00 H +ATOM 826 HG22 VAL A 54 34.691 29.664 34.880 1.00 0.00 H +ATOM 827 HG23 VAL A 54 33.202 30.551 34.767 1.00 0.00 H +ATOM 828 C VAL A 54 35.950 28.590 32.468 1.00 0.00 C +ATOM 829 O VAL A 54 35.738 27.385 32.660 1.00 0.00 O +ATOM 830 N THR A 55 37.187 29.085 32.651 1.00 0.00 N +ATOM 831 H THR A 55 37.326 30.038 32.345 1.00 0.00 H +ATOM 832 CA THR A 55 38.418 28.363 33.071 1.00 0.00 C +ATOM 833 HA THR A 55 38.197 27.299 32.991 1.00 0.00 H +ATOM 834 CB THR A 55 39.574 28.516 32.161 1.00 0.00 C +ATOM 835 HB THR A 55 39.757 29.581 32.019 1.00 0.00 H +ATOM 836 CG2 THR A 55 40.870 27.898 32.786 1.00 0.00 C +ATOM 837 HG21 THR A 55 40.583 26.849 32.855 1.00 0.00 H +ATOM 838 HG22 THR A 55 41.023 28.190 33.826 1.00 0.00 H +ATOM 839 HG23 THR A 55 41.825 28.044 32.280 1.00 0.00 H +ATOM 840 OG1 THR A 55 39.215 27.970 30.818 1.00 0.00 O +ATOM 841 HG1 THR A 55 38.792 28.725 30.401 1.00 0.00 H +ATOM 842 C THR A 55 38.779 28.725 34.458 1.00 0.00 C +ATOM 843 O THR A 55 39.263 29.841 34.735 1.00 0.00 O +ATOM 844 N GLU A 56 38.757 27.773 35.416 1.00 0.00 N +ATOM 845 H GLU A 56 38.459 26.869 35.079 1.00 0.00 H +ATOM 846 CA GLU A 56 39.045 27.993 36.888 1.00 0.00 C +ATOM 847 HA GLU A 56 38.618 28.921 37.267 1.00 0.00 H +ATOM 848 CB GLU A 56 38.402 26.911 37.749 1.00 0.00 C +ATOM 849 HB2 GLU A 56 37.329 27.019 37.593 1.00 0.00 H +ATOM 850 HB3 GLU A 56 38.780 25.905 37.563 1.00 0.00 H +ATOM 851 CG GLU A 56 38.436 27.078 39.267 1.00 0.00 C +ATOM 852 HG2 GLU A 56 39.455 26.968 39.636 1.00 0.00 H +ATOM 853 HG3 GLU A 56 38.094 28.097 39.445 1.00 0.00 H +ATOM 854 CD GLU A 56 37.514 26.014 39.918 1.00 0.00 C +ATOM 855 OE1 GLU A 56 37.905 24.823 39.870 1.00 0.00 O1- +ATOM 856 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O1- +ATOM 857 C GLU A 56 40.488 28.137 37.301 1.00 0.00 C +ATOM 858 O GLU A 56 40.807 29.090 38.025 1.00 0.00 O1- +ATOM 859 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O1- +CONECT 1 2 3 4 5 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 1 6 7 18 +CONECT 6 5 +CONECT 7 5 8 9 10 +CONECT 8 7 +CONECT 9 7 +CONECT 10 7 11 12 13 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 +CONECT 14 13 15 16 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 19 20 +CONECT 19 18 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 36 23 +CONECT 23 22 24 25 26 +CONECT 24 23 +CONECT 25 23 +CONECT 26 23 27 33 33 +CONECT 27 26 28 29 +CONECT 28 27 +CONECT 29 27 30 31 +CONECT 30 29 +CONECT 31 29 32 33 +CONECT 32 31 +CONECT 33 26 26 31 34 +CONECT 34 33 +CONECT 35 22 +CONECT 36 22 37 37 38 +CONECT 37 36 36 +CONECT 38 36 39 40 +CONECT 39 38 +CONECT 40 38 41 42 57 +CONECT 41 40 +CONECT 42 40 43 44 45 +CONECT 43 42 +CONECT 44 42 +CONECT 45 42 46 46 55 +CONECT 46 45 45 47 48 +CONECT 47 46 +CONECT 48 46 49 50 50 +CONECT 49 48 +CONECT 50 48 48 51 53 +CONECT 51 50 52 +CONECT 52 51 +CONECT 53 50 54 55 55 +CONECT 54 53 +CONECT 55 45 53 53 56 +CONECT 56 55 +CONECT 57 40 58 58 59 +CONECT 58 57 57 +CONECT 59 57 60 61 +CONECT 60 59 +CONECT 61 59 62 63 79 +CONECT 62 61 +CONECT 63 61 64 65 66 +CONECT 64 63 +CONECT 65 63 +CONECT 66 63 67 68 69 +CONECT 67 66 +CONECT 68 66 +CONECT 69 66 70 71 72 +CONECT 70 69 +CONECT 71 69 +CONECT 72 69 73 74 75 +CONECT 73 72 +CONECT 74 72 +CONECT 75 72 76 77 78 +CONECT 76 75 +CONECT 77 75 +CONECT 78 75 +CONECT 79 61 80 80 81 +CONECT 80 79 79 +CONECT 81 79 82 83 +CONECT 82 81 +CONECT 83 81 84 85 98 +CONECT 84 83 +CONECT 85 83 86 87 88 +CONECT 86 85 +CONECT 87 85 +CONECT 88 85 89 90 94 +CONECT 89 88 +CONECT 90 88 91 92 93 +CONECT 91 90 +CONECT 92 90 +CONECT 93 90 +CONECT 94 88 95 96 97 +CONECT 95 94 +CONECT 96 94 +CONECT 97 94 +CONECT 98 83 99 99 100 +CONECT 99 98 98 +CONECT 100 98 101 102 +CONECT 101 100 +CONECT 102 100 103 104 117 +CONECT 103 102 +CONECT 104 102 105 106 110 +CONECT 105 104 +CONECT 106 104 107 108 109 +CONECT 107 106 +CONECT 108 106 +CONECT 109 106 +CONECT 110 104 111 112 113 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 114 115 116 +CONECT 114 113 +CONECT 115 113 +CONECT 116 113 +CONECT 117 102 118 118 119 +CONECT 118 117 117 +CONECT 119 117 120 121 +CONECT 120 119 +CONECT 121 119 122 123 136 +CONECT 122 121 +CONECT 123 121 124 125 126 +CONECT 124 123 +CONECT 125 123 +CONECT 126 123 127 128 132 +CONECT 127 126 +CONECT 128 126 129 130 131 +CONECT 129 128 +CONECT 130 128 +CONECT 131 128 +CONECT 132 126 133 134 135 +CONECT 133 132 +CONECT 134 132 +CONECT 135 132 +CONECT 136 121 137 137 138 +CONECT 137 136 136 +CONECT 138 136 139 140 +CONECT 139 138 +CONECT 140 138 141 142 150 +CONECT 141 140 +CONECT 142 140 143 144 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 146 147 +CONECT 146 145 145 +CONECT 147 145 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 140 151 151 152 +CONECT 151 150 150 +CONECT 152 150 153 154 +CONECT 153 152 +CONECT 154 152 155 156 157 +CONECT 155 154 +CONECT 156 154 +CONECT 157 154 158 158 159 +CONECT 158 157 157 +CONECT 159 157 160 161 +CONECT 160 159 +CONECT 161 159 162 163 179 +CONECT 162 161 +CONECT 163 161 164 165 166 +CONECT 164 163 +CONECT 165 163 +CONECT 166 163 167 168 169 +CONECT 167 166 +CONECT 168 166 +CONECT 169 166 170 171 172 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 173 174 175 +CONECT 173 172 +CONECT 174 172 +CONECT 175 172 176 177 178 +CONECT 176 175 +CONECT 177 175 +CONECT 178 175 +CONECT 179 161 180 180 181 +CONECT 180 179 179 +CONECT 181 179 182 183 +CONECT 182 181 +CONECT 183 181 184 185 193 +CONECT 184 183 +CONECT 185 183 186 187 191 +CONECT 186 185 +CONECT 187 185 188 189 190 +CONECT 188 187 +CONECT 189 187 +CONECT 190 187 +CONECT 191 185 192 +CONECT 192 191 +CONECT 193 183 194 194 195 +CONECT 194 193 193 +CONECT 195 193 196 197 +CONECT 196 195 +CONECT 197 195 198 199 212 +CONECT 198 197 +CONECT 199 197 200 201 202 +CONECT 200 199 +CONECT 201 199 +CONECT 202 199 203 204 208 +CONECT 203 202 +CONECT 204 202 205 206 207 +CONECT 205 204 +CONECT 206 204 +CONECT 207 204 +CONECT 208 202 209 210 211 +CONECT 209 208 +CONECT 210 208 +CONECT 211 208 +CONECT 212 197 213 213 214 +CONECT 213 212 212 +CONECT 214 212 215 216 +CONECT 215 214 +CONECT 216 214 217 218 234 +CONECT 217 216 +CONECT 218 216 219 220 221 +CONECT 219 218 +CONECT 220 218 +CONECT 221 218 222 223 224 +CONECT 222 221 +CONECT 223 221 +CONECT 224 221 225 226 227 +CONECT 225 224 +CONECT 226 224 +CONECT 227 224 228 229 230 +CONECT 228 227 +CONECT 229 227 +CONECT 230 227 231 232 233 +CONECT 231 230 +CONECT 232 230 +CONECT 233 230 +CONECT 234 216 235 235 236 +CONECT 235 234 234 +CONECT 236 234 237 238 +CONECT 237 236 +CONECT 238 236 239 240 241 +CONECT 239 238 +CONECT 240 238 +CONECT 241 238 242 242 243 +CONECT 242 241 241 +CONECT 243 241 244 245 +CONECT 244 243 +CONECT 245 243 246 247 256 +CONECT 246 245 +CONECT 247 245 248 249 250 +CONECT 248 247 +CONECT 249 247 +CONECT 250 247 251 252 253 +CONECT 251 250 +CONECT 252 250 +CONECT 253 250 254 254 255 +CONECT 254 253 253 +CONECT 255 253 +CONECT 256 245 257 257 258 +CONECT 257 256 256 +CONECT 258 256 259 260 +CONECT 259 258 +CONECT 260 258 261 262 270 +CONECT 261 260 +CONECT 262 260 263 264 268 +CONECT 263 262 +CONECT 264 262 265 266 267 +CONECT 265 264 +CONECT 266 264 +CONECT 267 264 +CONECT 268 262 269 +CONECT 269 268 +CONECT 270 260 271 271 272 +CONECT 271 270 270 +CONECT 272 270 273 274 +CONECT 273 272 +CONECT 274 272 275 276 284 +CONECT 275 274 +CONECT 276 274 277 278 282 +CONECT 277 276 +CONECT 278 276 279 280 281 +CONECT 279 278 +CONECT 280 278 +CONECT 281 278 +CONECT 282 276 283 +CONECT 283 282 +CONECT 284 274 285 285 286 +CONECT 285 284 284 +CONECT 286 284 287 288 +CONECT 287 286 +CONECT 288 286 289 290 298 +CONECT 289 288 +CONECT 290 288 291 292 296 +CONECT 291 290 +CONECT 292 290 293 294 295 +CONECT 293 292 +CONECT 294 292 +CONECT 295 292 +CONECT 296 290 297 +CONECT 297 296 +CONECT 298 288 299 299 300 +CONECT 299 298 298 +CONECT 300 298 301 302 +CONECT 301 300 +CONECT 302 300 303 304 313 +CONECT 303 302 +CONECT 304 302 305 306 307 +CONECT 305 304 +CONECT 306 304 +CONECT 307 304 308 309 310 +CONECT 308 307 +CONECT 309 307 +CONECT 310 307 311 311 312 +CONECT 311 310 310 +CONECT 312 310 +CONECT 313 302 314 314 315 +CONECT 314 313 313 +CONECT 315 313 316 317 +CONECT 316 315 +CONECT 317 315 318 319 323 +CONECT 318 317 +CONECT 319 317 320 321 322 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 317 324 324 325 +CONECT 324 323 323 +CONECT 325 323 326 327 +CONECT 326 325 +CONECT 327 325 328 329 339 +CONECT 328 327 +CONECT 329 327 330 331 335 +CONECT 330 329 +CONECT 331 329 332 333 334 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 329 336 337 338 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 327 340 340 341 +CONECT 340 339 339 +CONECT 341 339 342 343 +CONECT 342 341 +CONECT 343 341 344 345 351 +CONECT 344 343 +CONECT 345 343 346 347 348 +CONECT 346 345 +CONECT 347 345 +CONECT 348 345 349 349 350 +CONECT 349 348 348 +CONECT 350 348 +CONECT 351 343 352 352 353 +CONECT 352 351 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 356 357 361 +CONECT 356 355 +CONECT 357 355 358 359 360 +CONECT 358 357 +CONECT 359 357 +CONECT 360 357 +CONECT 361 355 362 362 363 +CONECT 362 361 361 +CONECT 363 361 364 365 +CONECT 364 363 +CONECT 365 363 366 367 371 +CONECT 366 365 +CONECT 367 365 368 369 370 +CONECT 368 367 +CONECT 369 367 +CONECT 370 367 +CONECT 371 365 372 372 373 +CONECT 372 371 371 +CONECT 373 371 374 375 +CONECT 374 373 +CONECT 375 373 376 377 385 +CONECT 376 375 +CONECT 377 375 378 379 383 +CONECT 378 377 +CONECT 379 377 380 381 382 +CONECT 380 379 +CONECT 381 379 +CONECT 382 379 +CONECT 383 377 384 +CONECT 384 383 +CONECT 385 375 386 386 387 +CONECT 386 385 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 390 391 395 +CONECT 390 389 +CONECT 391 389 392 393 394 +CONECT 392 391 +CONECT 393 391 +CONECT 394 391 +CONECT 395 389 396 396 397 +CONECT 396 395 395 +CONECT 397 395 398 399 +CONECT 398 397 +CONECT 399 397 400 401 410 +CONECT 400 399 +CONECT 401 399 402 403 404 +CONECT 402 401 +CONECT 403 401 +CONECT 404 401 405 406 407 +CONECT 405 404 +CONECT 406 404 +CONECT 407 404 408 408 409 +CONECT 408 407 407 +CONECT 409 407 +CONECT 410 399 411 411 412 +CONECT 411 410 410 +CONECT 412 410 413 414 +CONECT 413 412 +CONECT 414 412 415 416 432 +CONECT 415 414 +CONECT 416 414 417 418 419 +CONECT 417 416 +CONECT 418 416 +CONECT 419 416 420 421 422 +CONECT 420 419 +CONECT 421 419 +CONECT 422 419 423 424 425 +CONECT 423 422 +CONECT 424 422 +CONECT 425 422 426 427 428 +CONECT 426 425 +CONECT 427 425 +CONECT 428 425 429 430 431 +CONECT 429 428 +CONECT 430 428 +CONECT 431 428 +CONECT 432 414 433 433 434 +CONECT 433 432 432 +CONECT 434 432 435 436 +CONECT 435 434 +CONECT 436 434 437 438 448 +CONECT 437 436 +CONECT 438 436 439 440 444 +CONECT 439 438 +CONECT 440 438 441 442 443 +CONECT 441 440 +CONECT 442 440 +CONECT 443 440 +CONECT 444 438 445 446 447 +CONECT 445 444 +CONECT 446 444 +CONECT 447 444 +CONECT 448 436 449 449 450 +CONECT 449 448 448 +CONECT 450 448 451 452 +CONECT 451 450 +CONECT 452 450 453 454 468 +CONECT 453 452 +CONECT 454 452 455 456 457 +CONECT 455 454 +CONECT 456 454 +CONECT 457 454 458 458 466 +CONECT 458 457 457 459 460 +CONECT 459 458 +CONECT 460 458 461 462 462 +CONECT 461 460 +CONECT 462 460 460 463 464 +CONECT 463 462 +CONECT 464 462 465 466 466 +CONECT 465 464 +CONECT 466 457 464 464 467 +CONECT 467 466 +CONECT 468 452 469 469 470 +CONECT 469 468 468 +CONECT 470 468 471 472 +CONECT 471 470 +CONECT 472 470 473 474 490 +CONECT 473 472 +CONECT 474 472 475 476 477 +CONECT 475 474 +CONECT 476 474 +CONECT 477 474 478 479 480 +CONECT 478 477 +CONECT 479 477 +CONECT 480 477 481 482 483 +CONECT 481 480 +CONECT 482 480 +CONECT 483 480 484 485 486 +CONECT 484 483 +CONECT 485 483 +CONECT 486 483 487 488 489 +CONECT 487 486 +CONECT 488 486 +CONECT 489 486 +CONECT 490 472 491 491 492 +CONECT 491 490 490 +CONECT 492 490 493 494 +CONECT 493 492 +CONECT 494 492 495 496 507 +CONECT 495 494 +CONECT 496 494 497 498 499 +CONECT 497 496 +CONECT 498 496 +CONECT 499 496 500 501 502 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 503 503 504 +CONECT 503 502 502 +CONECT 504 502 505 506 +CONECT 505 504 +CONECT 506 504 +CONECT 507 494 508 508 509 +CONECT 508 507 507 +CONECT 509 507 510 511 +CONECT 510 509 +CONECT 511 509 512 513 528 +CONECT 512 511 +CONECT 513 511 514 515 516 +CONECT 514 513 +CONECT 515 513 +CONECT 516 513 517 517 526 +CONECT 517 516 516 518 519 +CONECT 518 517 +CONECT 519 517 520 521 521 +CONECT 520 519 +CONECT 521 519 519 522 524 +CONECT 522 521 523 +CONECT 523 522 +CONECT 524 521 525 526 526 +CONECT 525 524 +CONECT 526 516 524 524 527 +CONECT 527 526 +CONECT 528 511 529 529 530 +CONECT 529 528 528 +CONECT 530 528 531 532 +CONECT 531 530 +CONECT 532 530 533 534 538 +CONECT 533 532 +CONECT 534 532 535 536 537 +CONECT 535 534 +CONECT 536 534 +CONECT 537 534 +CONECT 538 532 539 539 540 +CONECT 539 538 538 +CONECT 540 538 541 542 +CONECT 541 540 +CONECT 542 540 543 544 552 +CONECT 543 542 +CONECT 544 542 545 546 547 +CONECT 545 544 +CONECT 546 544 +CONECT 547 544 548 548 549 +CONECT 548 547 547 +CONECT 549 547 550 551 +CONECT 550 549 +CONECT 551 549 +CONECT 552 542 553 553 554 +CONECT 553 552 552 +CONECT 554 552 555 556 +CONECT 555 554 +CONECT 556 554 557 558 564 +CONECT 557 556 +CONECT 558 556 559 560 561 +CONECT 559 558 +CONECT 560 558 +CONECT 561 558 562 562 563 +CONECT 562 561 561 +CONECT 563 561 +CONECT 564 556 565 565 566 +CONECT 565 564 564 +CONECT 566 564 567 568 +CONECT 567 566 +CONECT 568 566 569 570 578 +CONECT 569 568 +CONECT 570 568 571 572 573 +CONECT 571 570 +CONECT 572 570 +CONECT 573 570 574 574 575 +CONECT 574 573 573 +CONECT 575 573 576 577 +CONECT 576 575 +CONECT 577 575 +CONECT 578 568 579 579 580 +CONECT 579 578 578 +CONECT 580 578 581 582 +CONECT 581 580 +CONECT 582 580 583 584 585 +CONECT 583 582 +CONECT 584 582 +CONECT 585 582 586 586 587 +CONECT 586 585 585 +CONECT 587 585 588 589 +CONECT 588 587 +CONECT 589 587 590 591 601 +CONECT 590 589 +CONECT 591 589 592 593 597 +CONECT 592 591 +CONECT 593 591 594 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 593 +CONECT 597 591 598 599 600 +CONECT 598 597 +CONECT 599 597 +CONECT 600 597 +CONECT 601 589 602 602 603 +CONECT 602 601 601 +CONECT 603 601 604 605 +CONECT 604 603 +CONECT 605 603 606 607 613 +CONECT 606 605 +CONECT 607 605 608 609 610 +CONECT 608 607 +CONECT 609 607 +CONECT 610 607 611 611 612 +CONECT 611 610 610 +CONECT 612 610 +CONECT 613 605 614 614 615 +CONECT 614 613 613 +CONECT 615 613 616 617 +CONECT 616 615 +CONECT 617 615 618 619 620 +CONECT 618 617 +CONECT 619 617 +CONECT 620 617 621 621 622 +CONECT 621 620 620 +CONECT 622 620 623 624 +CONECT 623 622 +CONECT 624 622 625 626 635 +CONECT 625 624 +CONECT 626 624 627 628 629 +CONECT 627 626 +CONECT 628 626 +CONECT 629 626 630 631 632 +CONECT 630 629 +CONECT 631 629 +CONECT 632 629 633 633 634 +CONECT 633 632 632 +CONECT 634 632 +CONECT 635 624 636 636 637 +CONECT 636 635 635 +CONECT 637 635 638 639 +CONECT 638 637 +CONECT 639 637 640 641 659 +CONECT 640 639 +CONECT 641 639 642 643 644 +CONECT 642 641 +CONECT 643 641 +CONECT 644 641 645 645 658 +CONECT 645 644 644 646 647 +CONECT 646 645 +CONECT 647 645 648 649 +CONECT 648 647 +CONECT 649 647 650 650 658 +CONECT 650 649 649 651 652 +CONECT 651 650 +CONECT 652 650 653 654 654 +CONECT 653 652 +CONECT 654 652 652 655 656 +CONECT 655 654 +CONECT 656 654 657 658 658 +CONECT 657 656 +CONECT 658 644 649 656 656 +CONECT 659 639 660 660 661 +CONECT 660 659 659 +CONECT 661 659 662 663 +CONECT 662 661 +CONECT 663 661 664 665 673 +CONECT 664 663 +CONECT 665 663 666 667 671 +CONECT 666 665 +CONECT 667 665 668 669 670 +CONECT 668 667 +CONECT 669 667 +CONECT 670 667 +CONECT 671 665 672 +CONECT 672 671 +CONECT 673 663 674 674 675 +CONECT 674 673 673 +CONECT 675 673 676 677 +CONECT 676 675 +CONECT 677 675 678 679 694 +CONECT 678 677 +CONECT 679 677 680 681 682 +CONECT 680 679 +CONECT 681 679 +CONECT 682 679 683 683 692 +CONECT 683 682 682 684 685 +CONECT 684 683 +CONECT 685 683 686 687 687 +CONECT 686 685 +CONECT 687 685 685 688 690 +CONECT 688 687 689 +CONECT 689 688 +CONECT 690 687 691 692 692 +CONECT 691 690 +CONECT 692 682 690 690 693 +CONECT 693 692 +CONECT 694 677 695 695 696 +CONECT 695 694 694 +CONECT 696 694 697 698 +CONECT 697 696 +CONECT 698 696 699 700 706 +CONECT 699 698 +CONECT 700 698 701 702 703 +CONECT 701 700 +CONECT 702 700 +CONECT 703 700 704 704 705 +CONECT 704 703 703 +CONECT 705 703 +CONECT 706 698 707 707 708 +CONECT 707 706 706 +CONECT 708 706 709 710 +CONECT 709 708 +CONECT 710 708 711 712 718 +CONECT 711 710 +CONECT 712 710 713 714 715 +CONECT 713 712 +CONECT 714 712 +CONECT 715 712 716 716 717 +CONECT 716 715 715 +CONECT 717 715 +CONECT 718 710 719 719 720 +CONECT 719 718 718 +CONECT 720 718 721 722 +CONECT 721 720 +CONECT 722 720 723 724 728 +CONECT 723 722 +CONECT 724 722 725 726 727 +CONECT 725 724 +CONECT 726 724 +CONECT 727 724 +CONECT 728 722 729 729 730 +CONECT 729 728 728 +CONECT 730 728 731 732 +CONECT 731 730 +CONECT 732 730 733 734 742 +CONECT 733 732 +CONECT 734 732 735 736 740 +CONECT 735 734 +CONECT 736 734 737 738 739 +CONECT 737 736 +CONECT 738 736 +CONECT 739 736 +CONECT 740 734 741 +CONECT 741 740 +CONECT 742 732 743 743 744 +CONECT 743 742 742 +CONECT 744 742 745 746 +CONECT 745 744 +CONECT 746 744 747 748 764 +CONECT 747 746 +CONECT 748 746 749 750 751 +CONECT 749 748 +CONECT 750 748 +CONECT 751 748 752 753 754 +CONECT 752 751 +CONECT 753 751 +CONECT 754 751 755 756 757 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 758 759 760 +CONECT 758 757 +CONECT 759 757 +CONECT 760 757 761 762 763 +CONECT 761 760 +CONECT 762 760 +CONECT 763 760 +CONECT 764 746 765 765 766 +CONECT 765 764 764 +CONECT 766 764 767 768 +CONECT 767 766 +CONECT 768 766 769 770 778 +CONECT 769 768 +CONECT 770 768 771 772 776 +CONECT 771 770 +CONECT 772 770 773 774 775 +CONECT 773 772 +CONECT 774 772 +CONECT 775 772 +CONECT 776 770 777 +CONECT 777 776 +CONECT 778 768 779 779 780 +CONECT 779 778 778 +CONECT 780 778 781 782 +CONECT 781 780 +CONECT 782 780 783 784 798 +CONECT 783 782 +CONECT 784 782 785 786 787 +CONECT 785 784 +CONECT 786 784 +CONECT 787 784 788 788 796 +CONECT 788 787 787 789 790 +CONECT 789 788 +CONECT 790 788 791 792 792 +CONECT 791 790 +CONECT 792 790 790 793 794 +CONECT 793 792 +CONECT 794 792 795 796 796 +CONECT 795 794 +CONECT 796 787 794 794 797 +CONECT 797 796 +CONECT 798 782 799 799 800 +CONECT 799 798 798 +CONECT 800 798 801 802 +CONECT 801 800 +CONECT 802 800 803 804 812 +CONECT 803 802 +CONECT 804 802 805 806 810 +CONECT 805 804 +CONECT 806 804 807 808 809 +CONECT 807 806 +CONECT 808 806 +CONECT 809 806 +CONECT 810 804 811 +CONECT 811 810 +CONECT 812 802 813 813 814 +CONECT 813 812 812 +CONECT 814 812 815 816 +CONECT 815 814 +CONECT 816 814 817 818 828 +CONECT 817 816 +CONECT 818 816 819 820 824 +CONECT 819 818 +CONECT 820 818 821 822 823 +CONECT 821 820 +CONECT 822 820 +CONECT 823 820 +CONECT 824 818 825 826 827 +CONECT 825 824 +CONECT 826 824 +CONECT 827 824 +CONECT 828 816 829 829 830 +CONECT 829 828 828 +CONECT 830 828 831 832 +CONECT 831 830 +CONECT 832 830 833 834 842 +CONECT 833 832 +CONECT 834 832 835 836 840 +CONECT 835 834 +CONECT 836 834 837 838 839 +CONECT 837 836 +CONECT 838 836 +CONECT 839 836 +CONECT 840 834 841 +CONECT 841 840 +CONECT 842 832 843 843 844 +CONECT 843 842 842 +CONECT 844 842 845 846 +CONECT 845 844 +CONECT 846 844 847 848 857 +CONECT 847 846 +CONECT 848 846 849 850 851 +CONECT 849 848 +CONECT 850 848 +CONECT 851 848 852 853 854 +CONECT 852 851 +CONECT 853 851 +CONECT 854 851 855 855 856 +CONECT 855 854 854 +CONECT 856 854 +CONECT 857 846 858 858 859 +CONECT 858 857 857 +CONECT 859 857 +MASTER 0 0 0 0 0 0 0 0 859 0 859 0 +END diff --git a/unittests/output_files/test_thr_to_his_restypeTrue.pdb b/unittests/output_files/test_thr_to_his_restypeTrue.pdb new file mode 100644 index 0000000..20a1049 --- /dev/null +++ b/unittests/output_files/test_thr_to_his_restypeTrue.pdb @@ -0,0 +1,1722 @@ +COMPND MET +AUTHOR GENERATED BY OPEN BABEL 3.0.0 +ATOM 1 N MET A 1 19.157 32.576 19.140 1.00 0.00 N1+ +ATOM 2 H1 MET A 1 18.435 31.870 19.129 1.00 0.00 H +ATOM 3 H2 MET A 1 18.900 33.260 18.441 1.00 0.00 H +ATOM 4 H3 MET A 1 19.229 33.073 20.016 1.00 0.00 H +ATOM 5 CA MET A 1 20.458 31.939 18.931 1.00 0.00 C +ATOM 6 HA MET A 1 20.420 31.303 18.046 1.00 0.00 H +ATOM 7 CB MET A 1 21.504 33.015 18.722 1.00 0.00 C +ATOM 8 HB2 MET A 1 21.352 33.519 17.768 1.00 0.00 H +ATOM 9 HB3 MET A 1 21.390 33.764 19.505 1.00 0.00 H +ATOM 10 CG MET A 1 22.904 32.517 18.656 1.00 0.00 C +ATOM 11 HG2 MET A 1 23.590 33.362 18.601 1.00 0.00 H +ATOM 12 HG3 MET A 1 23.154 32.095 19.630 1.00 0.00 H +ATOM 13 SD MET A 1 23.205 31.269 17.386 1.00 0.00 S +ATOM 14 CE MET A 1 22.990 32.137 15.870 1.00 0.00 C +ATOM 15 HE1 MET A 1 23.339 33.163 15.983 1.00 0.00 H +ATOM 16 HE2 MET A 1 21.968 32.128 15.490 1.00 0.00 H +ATOM 17 HE3 MET A 1 23.572 31.586 15.132 1.00 0.00 H +ATOM 18 C MET A 1 20.796 31.017 20.133 1.00 0.00 C +ATOM 19 O MET A 1 20.674 31.440 21.297 1.00 0.00 O +ATOM 20 N HIP A 2 21.124 29.774 19.819 1.00 0.00 N +ATOM 21 H HIP A 2 21.279 29.527 18.851 1.00 0.00 H +ATOM 22 CA HIP A 2 21.443 28.704 20.861 1.00 0.00 C +ATOM 23 CB HIP A 2 21.116 27.248 20.524 1.00 0.00 C +ATOM 24 HB2 HIP A 2 21.319 26.609 21.384 1.00 0.00 H +ATOM 25 HB3 HIP A 2 20.067 27.156 20.245 1.00 0.00 H +ATOM 26 CG HIP A 2 21.914 26.697 19.384 1.00 0.00 C +ATOM 27 ND1 HIP A 2 23.189 26.197 19.539 1.00 0.00 N +ATOM 28 HD1 HIP A 2 23.687 26.157 20.416 1.00 0.00 H +ATOM 29 CE1 HIP A 2 23.642 25.784 18.368 1.00 0.00 C +ATOM 30 HE1 HIP A 2 24.637 25.352 18.282 1.00 0.00 H +ATOM 31 NE2 HIP A 2 22.710 25.999 17.460 1.00 0.00 N +ATOM 32 HE2 HIP A 2 22.777 25.784 16.475 1.00 0.00 H +ATOM 33 CD2 HIP A 2 21.619 26.570 18.068 1.00 0.00 C +ATOM 34 HD2 HIP A 2 20.738 26.826 17.479 1.00 0.00 H +ATOM 35 HA HIP A 2 20.909 28.998 21.764 1.00 0.00 H +ATOM 36 C HIP A 2 22.937 28.892 21.086 1.00 0.00 C +ATOM 37 O HIP A 2 23.773 28.867 20.181 1.00 0.00 O +ATOM 38 N TYR A 3 23.244 29.155 22.344 1.00 0.00 N +ATOM 39 H TYR A 3 22.513 29.085 23.038 1.00 0.00 H +ATOM 40 CA TYR A 3 24.628 29.305 22.888 1.00 0.00 C +ATOM 41 HA TYR A 3 25.262 29.391 22.004 1.00 0.00 H +ATOM 42 CB TYR A 3 24.744 30.579 23.675 1.00 0.00 C +ATOM 43 HB2 TYR A 3 24.131 30.495 24.572 1.00 0.00 H +ATOM 44 HB3 TYR A 3 25.780 30.505 24.008 1.00 0.00 H +ATOM 45 CG TYR A 3 24.468 31.862 22.928 1.00 0.00 C +ATOM 46 CD1 TYR A 3 25.525 32.544 22.317 1.00 0.00 C +ATOM 47 HD1 TYR A 3 26.477 32.039 22.379 1.00 0.00 H +ATOM 48 CE1 TYR A 3 25.289 33.761 21.619 1.00 0.00 C +ATOM 49 HE1 TYR A 3 26.100 34.275 21.122 1.00 0.00 H +ATOM 50 CZ TYR A 3 23.936 34.260 21.579 1.00 0.00 C +ATOM 51 OH TYR A 3 23.774 35.268 20.774 1.00 0.00 O +ATOM 52 HH TYR A 3 24.486 35.161 20.140 1.00 0.00 H +ATOM 53 CE2 TYR A 3 22.849 33.537 22.176 1.00 0.00 C +ATOM 54 HE2 TYR A 3 21.868 33.965 22.036 1.00 0.00 H +ATOM 55 CD2 TYR A 3 23.110 32.291 22.853 1.00 0.00 C +ATOM 56 HD2 TYR A 3 22.235 31.752 23.187 1.00 0.00 H +ATOM 57 C TYR A 3 25.066 28.136 23.774 1.00 0.00 C +ATOM 58 O TYR A 3 24.233 27.436 24.338 1.00 0.00 O +ATOM 59 N LYS A 4 26.339 27.934 23.811 1.00 0.00 N +ATOM 60 H LYS A 4 26.944 28.514 23.248 1.00 0.00 H +ATOM 61 CA LYS A 4 26.982 26.918 24.687 1.00 0.00 C +ATOM 62 HA LYS A 4 26.212 26.488 25.328 1.00 0.00 H +ATOM 63 CB LYS A 4 27.643 25.801 23.803 1.00 0.00 C +ATOM 64 HB2 LYS A 4 26.868 25.465 23.113 1.00 0.00 H +ATOM 65 HB3 LYS A 4 28.422 26.196 23.151 1.00 0.00 H +ATOM 66 CG LYS A 4 28.205 24.625 24.506 1.00 0.00 C +ATOM 67 HG2 LYS A 4 29.054 24.916 25.125 1.00 0.00 H +ATOM 68 HG3 LYS A 4 27.452 24.278 25.213 1.00 0.00 H +ATOM 69 CD LYS A 4 28.635 23.407 23.678 1.00 0.00 C +ATOM 70 HD2 LYS A 4 29.003 22.691 24.414 1.00 0.00 H +ATOM 71 HD3 LYS A 4 27.737 22.954 23.255 1.00 0.00 H +ATOM 72 CE LYS A 4 29.554 23.575 22.506 1.00 0.00 C +ATOM 73 HE2 LYS A 4 28.899 24.120 21.827 1.00 0.00 H +ATOM 74 HE3 LYS A 4 30.458 24.114 22.794 1.00 0.00 H +ATOM 75 NZ LYS A 4 30.052 22.279 21.888 1.00 0.00 N1+ +ATOM 76 HZ1 LYS A 4 30.831 21.896 22.402 1.00 0.00 H +ATOM 77 HZ2 LYS A 4 30.443 22.423 20.968 1.00 0.00 H +ATOM 78 HZ3 LYS A 4 29.328 21.579 21.805 1.00 0.00 H +ATOM 79 C LYS A 4 28.003 27.516 25.655 1.00 0.00 C +ATOM 80 O LYS A 4 28.579 28.553 25.310 1.00 0.00 O +ATOM 81 N LEU A 5 28.245 26.773 26.741 1.00 0.00 N +ATOM 82 H LEU A 5 27.544 26.084 26.977 1.00 0.00 H +ATOM 83 CA LEU A 5 29.244 27.118 27.766 1.00 0.00 C +ATOM 84 HA LEU A 5 29.916 27.884 27.380 1.00 0.00 H +ATOM 85 CB LEU A 5 28.579 27.507 29.097 1.00 0.00 C +ATOM 86 HB2 LEU A 5 28.058 28.438 28.872 1.00 0.00 H +ATOM 87 HB3 LEU A 5 27.859 26.779 29.469 1.00 0.00 H +ATOM 88 CG LEU A 5 29.551 27.720 30.235 1.00 0.00 C +ATOM 89 HG LEU A 5 30.166 26.841 30.429 1.00 0.00 H +ATOM 90 CD1 LEU A 5 30.427 28.952 29.986 1.00 0.00 C +ATOM 91 HD11 LEU A 5 31.114 28.683 29.184 1.00 0.00 H +ATOM 92 HD12 LEU A 5 31.008 29.120 30.894 1.00 0.00 H +ATOM 93 HD13 LEU A 5 29.848 29.861 29.825 1.00 0.00 H +ATOM 94 CD2 LEU A 5 28.678 28.115 31.457 1.00 0.00 C +ATOM 95 HD21 LEU A 5 28.235 29.096 31.284 1.00 0.00 H +ATOM 96 HD22 LEU A 5 29.327 28.287 32.315 1.00 0.00 H +ATOM 97 HD23 LEU A 5 27.907 27.390 31.720 1.00 0.00 H +ATOM 98 C LEU A 5 30.065 25.816 27.990 1.00 0.00 C +ATOM 99 O LEU A 5 29.489 24.768 28.302 1.00 0.00 O +ATOM 100 N ILE A 6 31.415 25.954 27.959 1.00 0.00 N +ATOM 101 H ILE A 6 31.834 26.822 27.658 1.00 0.00 H +ATOM 102 CA ILE A 6 32.352 24.944 28.438 1.00 0.00 C +ATOM 103 HA ILE A 6 31.851 23.978 28.494 1.00 0.00 H +ATOM 104 CB ILE A 6 33.535 24.736 27.434 1.00 0.00 C +ATOM 105 HB ILE A 6 34.002 25.706 27.261 1.00 0.00 H +ATOM 106 CG2 ILE A 6 34.658 23.796 27.952 1.00 0.00 C +ATOM 107 HG21 ILE A 6 35.011 24.049 28.953 1.00 0.00 H +ATOM 108 HG22 ILE A 6 35.610 23.773 27.423 1.00 0.00 H +ATOM 109 HG23 ILE A 6 34.315 22.768 28.065 1.00 0.00 H +ATOM 110 CG1 ILE A 6 32.967 24.083 26.135 1.00 0.00 C +ATOM 111 HG12 ILE A 6 32.815 23.014 26.281 1.00 0.00 H +ATOM 112 HG13 ILE A 6 32.016 24.548 25.875 1.00 0.00 H +ATOM 113 CD1 ILE A 6 33.964 24.228 24.983 1.00 0.00 C +ATOM 114 HD11 ILE A 6 34.203 25.280 24.831 1.00 0.00 H +ATOM 115 HD12 ILE A 6 33.521 23.646 24.174 1.00 0.00 H +ATOM 116 HD13 ILE A 6 34.890 23.744 25.293 1.00 0.00 H +ATOM 117 C ILE A 6 32.878 25.380 29.825 1.00 0.00 C +ATOM 118 O ILE A 6 33.517 26.449 29.956 1.00 0.00 O +ATOM 119 N LEU A 7 32.756 24.548 30.823 1.00 0.00 N +ATOM 120 H LEU A 7 32.337 23.649 30.632 1.00 0.00 H +ATOM 121 CA LEU A 7 33.418 24.678 32.128 1.00 0.00 C +ATOM 122 HA LEU A 7 33.772 25.702 32.243 1.00 0.00 H +ATOM 123 CB LEU A 7 32.452 24.287 33.269 1.00 0.00 C +ATOM 124 HB2 LEU A 7 32.235 23.219 33.280 1.00 0.00 H +ATOM 125 HB3 LEU A 7 33.025 24.491 34.173 1.00 0.00 H +ATOM 126 CG LEU A 7 31.068 25.080 33.294 1.00 0.00 C +ATOM 127 HG LEU A 7 31.234 26.000 32.731 1.00 0.00 H +ATOM 128 CD1 LEU A 7 29.957 24.185 32.737 1.00 0.00 C +ATOM 129 HD11 LEU A 7 29.091 24.791 32.472 1.00 0.00 H +ATOM 130 HD12 LEU A 7 29.675 23.458 33.497 1.00 0.00 H +ATOM 131 HD13 LEU A 7 30.242 23.598 31.863 1.00 0.00 H +ATOM 132 CD2 LEU A 7 30.679 25.500 34.666 1.00 0.00 C +ATOM 133 HD21 LEU A 7 30.692 24.679 35.384 1.00 0.00 H +ATOM 134 HD22 LEU A 7 29.678 25.926 34.604 1.00 0.00 H +ATOM 135 HD23 LEU A 7 31.266 26.349 35.014 1.00 0.00 H +ATOM 136 C LEU A 7 34.704 23.832 31.982 1.00 0.00 C +ATOM 137 O LEU A 7 34.608 22.712 31.434 1.00 0.00 O +ATOM 138 N ASN A 8 35.741 24.355 32.566 1.00 0.00 N +ATOM 139 H ASN A 8 35.657 25.289 32.943 1.00 0.00 H +ATOM 140 CA ASN A 8 37.087 23.938 32.340 1.00 0.00 C +ATOM 141 HA ASN A 8 37.195 22.875 32.128 1.00 0.00 H +ATOM 142 CB ASN A 8 37.683 24.648 31.079 1.00 0.00 C +ATOM 143 HB2 ASN A 8 37.052 24.514 30.199 1.00 0.00 H +ATOM 144 HB3 ASN A 8 37.697 25.701 31.358 1.00 0.00 H +ATOM 145 CG ASN A 8 39.069 24.172 30.753 1.00 0.00 C +ATOM 146 OD1 ASN A 8 39.293 22.972 30.616 1.00 0.00 O +ATOM 147 ND2 ASN A 8 40.171 24.966 30.834 1.00 0.00 N +ATOM 148 HD21 ASN A 8 40.064 25.968 30.880 1.00 0.00 H +ATOM 149 HD22 ASN A 8 41.073 24.564 30.618 1.00 0.00 H +ATOM 150 C ASN A 8 37.929 24.262 33.602 1.00 0.00 C +ATOM 151 O ASN A 8 37.736 25.299 34.234 1.00 0.00 O +ATOM 152 N GLY A 9 38.893 23.411 33.937 1.00 0.00 N +ATOM 153 H GLY A 9 38.872 22.559 33.394 1.00 0.00 H +ATOM 154 CA GLY A 9 39.937 23.667 34.946 1.00 0.00 C +ATOM 155 HA2 GLY A 9 40.563 24.496 34.619 1.00 0.00 H +ATOM 156 HA3 GLY A 9 39.525 24.058 35.876 1.00 0.00 H +ATOM 157 C GLY A 9 40.820 22.504 35.210 1.00 0.00 C +ATOM 158 O GLY A 9 40.826 21.506 34.446 1.00 0.00 O +ATOM 159 N LYS A 10 41.477 22.473 36.356 1.00 0.00 N +ATOM 160 H LYS A 10 41.439 23.256 36.992 1.00 0.00 H +ATOM 161 CA LYS A 10 42.321 21.363 36.766 1.00 0.00 C +ATOM 162 HA LYS A 10 42.838 21.036 35.864 1.00 0.00 H +ATOM 163 CB LYS A 10 43.435 21.839 37.736 1.00 0.00 C +ATOM 164 HB2 LYS A 10 42.960 22.130 38.673 1.00 0.00 H +ATOM 165 HB3 LYS A 10 44.151 21.018 37.787 1.00 0.00 H +ATOM 166 CG LYS A 10 44.146 23.121 37.228 1.00 0.00 C +ATOM 167 HG2 LYS A 10 44.581 22.959 36.242 1.00 0.00 H +ATOM 168 HG3 LYS A 10 43.424 23.934 37.151 1.00 0.00 H +ATOM 169 CD LYS A 10 45.206 23.474 38.269 1.00 0.00 C +ATOM 170 HD2 LYS A 10 44.834 23.376 39.290 1.00 0.00 H +ATOM 171 HD3 LYS A 10 46.045 22.781 38.265 1.00 0.00 H +ATOM 172 CE LYS A 10 45.833 24.866 37.936 1.00 0.00 C +ATOM 173 HE2 LYS A 10 46.898 24.867 38.172 1.00 0.00 H +ATOM 174 HE3 LYS A 10 45.615 25.139 36.904 1.00 0.00 H +ATOM 175 NZ LYS A 10 45.314 25.885 38.915 1.00 0.00 N1+ +ATOM 176 HZ1 LYS A 10 44.318 26.049 38.885 1.00 0.00 H +ATOM 177 HZ2 LYS A 10 45.805 26.756 38.765 1.00 0.00 H +ATOM 178 HZ3 LYS A 10 45.434 25.694 39.899 1.00 0.00 H +ATOM 179 C LYS A 10 41.608 20.142 37.369 1.00 0.00 C +ATOM 180 O LYS A 10 42.136 19.017 37.432 1.00 0.00 O +ATOM 181 N THR A 11 40.316 20.407 37.709 1.00 0.00 N +ATOM 182 H THR A 11 40.018 21.373 37.739 1.00 0.00 H +ATOM 183 CA THR A 11 39.333 19.428 38.190 1.00 0.00 C +ATOM 184 HA THR A 11 39.627 18.439 37.841 1.00 0.00 H +ATOM 185 CB THR A 11 39.319 19.497 39.740 1.00 0.00 C +ATOM 186 HB THR A 11 38.538 18.809 40.063 1.00 0.00 H +ATOM 187 CG2 THR A 11 40.656 18.994 40.197 1.00 0.00 C +ATOM 188 HG21 THR A 11 40.954 17.991 39.896 1.00 0.00 H +ATOM 189 HG22 THR A 11 40.695 18.984 41.286 1.00 0.00 H +ATOM 190 HG23 THR A 11 41.453 19.662 39.869 1.00 0.00 H +ATOM 191 OG1 THR A 11 39.118 20.738 40.229 1.00 0.00 O +ATOM 192 HG1 THR A 11 39.321 20.728 41.168 1.00 0.00 H +ATOM 193 C THR A 11 37.937 19.704 37.750 1.00 0.00 C +ATOM 194 O THR A 11 37.180 18.744 37.592 1.00 0.00 O +ATOM 195 N LEU A 12 37.572 20.909 37.360 1.00 0.00 N +ATOM 196 H LEU A 12 38.100 21.745 37.569 1.00 0.00 H +ATOM 197 CA LEU A 12 36.262 21.294 36.760 1.00 0.00 C +ATOM 198 HA LEU A 12 35.427 20.887 37.329 1.00 0.00 H +ATOM 199 CB LEU A 12 36.169 22.873 36.785 1.00 0.00 C +ATOM 200 HB2 LEU A 12 36.531 23.238 37.746 1.00 0.00 H +ATOM 201 HB3 LEU A 12 36.859 23.268 36.041 1.00 0.00 H +ATOM 202 CG LEU A 12 34.824 23.483 36.357 1.00 0.00 C +ATOM 203 HG LEU A 12 34.479 23.028 35.428 1.00 0.00 H +ATOM 204 CD1 LEU A 12 33.867 23.321 37.477 1.00 0.00 C +ATOM 205 HD11 LEU A 12 32.997 23.877 37.126 1.00 0.00 H +ATOM 206 HD12 LEU A 12 34.304 23.691 38.404 1.00 0.00 H +ATOM 207 HD13 LEU A 12 33.594 22.265 37.503 1.00 0.00 H +ATOM 208 CD2 LEU A 12 34.926 25.052 36.181 1.00 0.00 C +ATOM 209 HD21 LEU A 12 35.334 25.560 37.054 1.00 0.00 H +ATOM 210 HD22 LEU A 12 33.926 25.442 35.997 1.00 0.00 H +ATOM 211 HD23 LEU A 12 35.555 25.355 35.344 1.00 0.00 H +ATOM 212 C LEU A 12 36.092 20.805 35.283 1.00 0.00 C +ATOM 213 O LEU A 12 36.941 21.102 34.441 1.00 0.00 O +ATOM 214 N LYS A 13 35.016 20.080 34.906 1.00 0.00 N +ATOM 215 H LYS A 13 34.391 19.697 35.602 1.00 0.00 H +ATOM 216 CA LYS A 13 34.642 19.704 33.571 1.00 0.00 C +ATOM 217 HA LYS A 13 35.063 20.421 32.866 1.00 0.00 H +ATOM 218 CB LYS A 13 35.034 18.226 33.244 1.00 0.00 C +ATOM 219 HB2 LYS A 13 34.497 17.579 33.938 1.00 0.00 H +ATOM 220 HB3 LYS A 13 34.849 17.922 32.214 1.00 0.00 H +ATOM 221 CG LYS A 13 36.515 17.923 33.472 1.00 0.00 C +ATOM 222 HG2 LYS A 13 37.162 18.658 32.994 1.00 0.00 H +ATOM 223 HG3 LYS A 13 36.701 17.768 34.535 1.00 0.00 H +ATOM 224 CD LYS A 13 36.804 16.487 32.994 1.00 0.00 C +ATOM 225 HD2 LYS A 13 36.157 15.747 33.465 1.00 0.00 H +ATOM 226 HD3 LYS A 13 36.456 16.506 31.962 1.00 0.00 H +ATOM 227 CE LYS A 13 38.264 16.163 32.997 1.00 0.00 C +ATOM 228 HE2 LYS A 13 38.741 16.732 32.199 1.00 0.00 H +ATOM 229 HE3 LYS A 13 38.686 16.424 33.967 1.00 0.00 H +ATOM 230 NZ LYS A 13 38.397 14.672 32.837 1.00 0.00 N1+ +ATOM 231 HZ1 LYS A 13 37.944 14.324 32.005 1.00 0.00 H +ATOM 232 HZ2 LYS A 13 37.888 14.239 33.595 1.00 0.00 H +ATOM 233 HZ3 LYS A 13 39.367 14.391 32.817 1.00 0.00 H +ATOM 234 C LYS A 13 33.119 19.875 33.400 1.00 0.00 C +ATOM 235 O LYS A 13 32.522 20.218 34.448 1.00 0.00 O +ATOM 236 N GLY A 14 32.541 19.929 32.182 1.00 0.00 N +ATOM 237 H GLY A 14 33.085 19.611 31.392 1.00 0.00 H +ATOM 238 CA GLY A 14 31.141 20.135 31.951 1.00 0.00 C +ATOM 239 HA2 GLY A 14 30.696 19.143 31.877 1.00 0.00 H +ATOM 240 HA3 GLY A 14 30.707 20.500 32.883 1.00 0.00 H +ATOM 241 C GLY A 14 30.726 21.030 30.803 1.00 0.00 C +ATOM 242 O GLY A 14 31.459 21.986 30.478 1.00 0.00 O +ATOM 243 N GLU A 15 29.602 20.661 30.175 1.00 0.00 N +ATOM 244 H GLU A 15 29.233 19.801 30.557 1.00 0.00 H +ATOM 245 CA GLU A 15 29.053 21.595 29.115 1.00 0.00 C +ATOM 246 HA GLU A 15 29.457 22.592 29.292 1.00 0.00 H +ATOM 247 CB GLU A 15 29.452 21.151 27.705 1.00 0.00 C +ATOM 248 HB2 GLU A 15 28.886 21.770 27.009 1.00 0.00 H +ATOM 249 HB3 GLU A 15 30.497 21.396 27.512 1.00 0.00 H +ATOM 250 CG GLU A 15 29.157 19.668 27.410 1.00 0.00 C +ATOM 251 HG2 GLU A 15 29.865 19.104 28.017 1.00 0.00 H +ATOM 252 HG3 GLU A 15 28.109 19.456 27.619 1.00 0.00 H +ATOM 253 CD GLU A 15 29.423 19.385 25.968 1.00 0.00 C +ATOM 254 OE1 GLU A 15 28.458 19.250 25.177 1.00 0.00 O1- +ATOM 255 OE2 GLU A 15 30.596 19.297 25.521 1.00 0.00 O1- +ATOM 256 C GLU A 15 27.563 21.843 29.353 1.00 0.00 C +ATOM 257 O GLU A 15 26.814 21.020 29.796 1.00 0.00 O +ATOM 258 N THR A 16 27.080 22.966 28.863 1.00 0.00 N +ATOM 259 H THR A 16 27.718 23.647 28.477 1.00 0.00 H +ATOM 260 CA THR A 16 25.618 23.342 28.987 1.00 0.00 C +ATOM 261 HA THR A 16 24.987 22.466 28.832 1.00 0.00 H +ATOM 262 CB THR A 16 25.300 23.755 30.463 1.00 0.00 C +ATOM 263 HB THR A 16 25.664 23.028 31.190 1.00 0.00 H +ATOM 264 CG2 THR A 16 26.079 25.029 30.851 1.00 0.00 C +ATOM 265 HG21 THR A 16 26.002 25.212 31.923 1.00 0.00 H +ATOM 266 HG22 THR A 16 25.827 25.999 30.420 1.00 0.00 H +ATOM 267 HG23 THR A 16 27.139 24.833 30.686 1.00 0.00 H +ATOM 268 OG1 THR A 16 23.919 23.870 30.591 1.00 0.00 O +ATOM 269 HG1 THR A 16 23.605 22.966 30.654 1.00 0.00 H +ATOM 270 C THR A 16 25.136 24.387 27.956 1.00 0.00 C +ATOM 271 O THR A 16 25.847 25.392 27.686 1.00 0.00 O +ATOM 272 N THR A 17 23.944 24.126 27.374 1.00 0.00 N +ATOM 273 H THR A 17 23.414 23.300 27.615 1.00 0.00 H +ATOM 274 CA THR A 17 23.341 25.088 26.418 1.00 0.00 C +ATOM 275 HA THR A 17 24.139 25.697 25.992 1.00 0.00 H +ATOM 276 CB THR A 17 22.634 24.399 25.250 1.00 0.00 C +ATOM 277 HB THR A 17 22.194 25.142 24.585 1.00 0.00 H +ATOM 278 CG2 THR A 17 23.534 23.466 24.406 1.00 0.00 C +ATOM 279 HG21 THR A 17 22.981 22.875 23.677 1.00 0.00 H +ATOM 280 HG22 THR A 17 24.016 22.789 25.112 1.00 0.00 H +ATOM 281 HG23 THR A 17 24.305 24.119 23.998 1.00 0.00 H +ATOM 282 OG1 THR A 17 21.618 23.516 25.740 1.00 0.00 O +ATOM 283 HG1 THR A 17 21.158 23.210 24.955 1.00 0.00 H +ATOM 284 C THR A 17 22.409 26.084 27.080 1.00 0.00 C +ATOM 285 O THR A 17 21.865 25.880 28.171 1.00 0.00 O +ATOM 286 N THR A 18 22.284 27.186 26.367 1.00 0.00 N +ATOM 287 H THR A 18 22.918 27.211 25.581 1.00 0.00 H +ATOM 288 CA THR A 18 21.341 28.346 26.665 1.00 0.00 C +ATOM 289 HA THR A 18 20.447 28.047 27.213 1.00 0.00 H +ATOM 290 CB THR A 18 21.968 29.424 27.606 1.00 0.00 C +ATOM 291 HB THR A 18 22.926 29.800 27.251 1.00 0.00 H +ATOM 292 CG2 THR A 18 20.959 30.565 27.747 1.00 0.00 C +ATOM 293 HG21 THR A 18 21.177 31.232 28.581 1.00 0.00 H +ATOM 294 HG22 THR A 18 19.932 30.214 27.838 1.00 0.00 H +ATOM 295 HG23 THR A 18 21.057 31.149 26.831 1.00 0.00 H +ATOM 296 OG1 THR A 18 21.983 28.974 29.051 1.00 0.00 O +ATOM 297 HG1 THR A 18 22.866 29.123 29.400 1.00 0.00 H +ATOM 298 C THR A 18 20.829 28.956 25.354 1.00 0.00 C +ATOM 299 O THR A 18 21.553 29.458 24.528 1.00 0.00 O +ATOM 300 N GLU A 19 19.542 28.872 25.083 1.00 0.00 N +ATOM 301 H GLU A 19 18.919 28.579 25.823 1.00 0.00 H +ATOM 302 CA GLU A 19 18.932 29.576 23.987 1.00 0.00 C +ATOM 303 HA GLU A 19 19.679 29.508 23.197 1.00 0.00 H +ATOM 304 CB GLU A 19 17.686 28.785 23.627 1.00 0.00 C +ATOM 305 HB2 GLU A 19 17.899 27.722 23.514 1.00 0.00 H +ATOM 306 HB3 GLU A 19 16.998 28.842 24.471 1.00 0.00 H +ATOM 307 CG GLU A 19 16.852 29.284 22.477 1.00 0.00 C +ATOM 308 HG2 GLU A 19 16.246 28.447 22.128 1.00 0.00 H +ATOM 309 HG3 GLU A 19 16.133 30.057 22.748 1.00 0.00 H +ATOM 310 CD GLU A 19 17.736 29.731 21.281 1.00 0.00 C +ATOM 311 OE1 GLU A 19 18.363 28.800 20.679 1.00 0.00 O1- +ATOM 312 OE2 GLU A 19 17.825 30.944 20.920 1.00 0.00 O1- +ATOM 313 C GLU A 19 18.631 31.049 24.311 1.00 0.00 C +ATOM 314 O GLU A 19 17.951 31.336 25.240 1.00 0.00 O +ATOM 315 N ALA A 20 19.109 32.052 23.609 1.00 0.00 N +ATOM 316 H ALA A 20 19.659 31.766 22.810 1.00 0.00 H +ATOM 317 CA ALA A 20 18.962 33.505 23.885 1.00 0.00 C +ATOM 318 HA ALA A 20 17.980 33.742 24.295 1.00 0.00 H +ATOM 319 CB ALA A 20 19.978 33.979 24.961 1.00 0.00 C +ATOM 320 HB1 ALA A 20 19.807 35.026 25.214 1.00 0.00 H +ATOM 321 HB2 ALA A 20 20.983 33.923 24.544 1.00 0.00 H +ATOM 322 HB3 ALA A 20 19.800 33.404 25.869 1.00 0.00 H +ATOM 323 C ALA A 20 19.121 34.352 22.595 1.00 0.00 C +ATOM 324 O ALA A 20 19.565 33.867 21.541 1.00 0.00 O +ATOM 325 N VAL A 21 18.819 35.698 22.666 1.00 0.00 N +ATOM 326 H VAL A 21 18.466 36.007 23.561 1.00 0.00 H +ATOM 327 CA VAL A 21 18.727 36.607 21.505 1.00 0.00 C +ATOM 328 HA VAL A 21 18.554 36.039 20.592 1.00 0.00 H +ATOM 329 CB VAL A 21 17.437 37.464 21.780 1.00 0.00 C +ATOM 330 HB VAL A 21 17.477 38.130 22.642 1.00 0.00 H +ATOM 331 CG1 VAL A 21 17.072 38.379 20.673 1.00 0.00 C +ATOM 332 HG11 VAL A 21 16.991 37.805 19.750 1.00 0.00 H +ATOM 333 HG12 VAL A 21 17.685 39.269 20.533 1.00 0.00 H +ATOM 334 HG13 VAL A 21 16.081 38.787 20.874 1.00 0.00 H +ATOM 335 CG2 VAL A 21 16.251 36.536 21.920 1.00 0.00 C +ATOM 336 HG21 VAL A 21 15.333 37.033 21.605 1.00 0.00 H +ATOM 337 HG22 VAL A 21 16.128 36.219 22.956 1.00 0.00 H +ATOM 338 HG23 VAL A 21 16.477 35.681 21.284 1.00 0.00 H +ATOM 339 C VAL A 21 19.976 37.521 21.405 1.00 0.00 C +ATOM 340 O VAL A 21 20.295 38.022 20.306 1.00 0.00 O +ATOM 341 N ASP A 22 20.728 37.651 22.457 1.00 0.00 N +ATOM 342 H ASP A 22 20.460 37.104 23.262 1.00 0.00 H +ATOM 343 CA ASP A 22 21.920 38.517 22.561 1.00 0.00 C +ATOM 344 HA ASP A 22 22.218 38.721 21.532 1.00 0.00 H +ATOM 345 CB ASP A 22 21.483 39.701 23.350 1.00 0.00 C +ATOM 346 HB2 ASP A 22 20.632 40.156 22.843 1.00 0.00 H +ATOM 347 HB3 ASP A 22 21.133 39.421 24.344 1.00 0.00 H +ATOM 348 CG ASP A 22 22.576 40.746 23.590 1.00 0.00 C +ATOM 349 OD1 ASP A 22 23.681 40.588 23.043 1.00 0.00 O1- +ATOM 350 OD2 ASP A 22 22.340 41.751 24.264 1.00 0.00 O1- +ATOM 351 C ASP A 22 23.019 37.703 23.294 1.00 0.00 C +ATOM 352 O ASP A 22 22.839 37.184 24.412 1.00 0.00 O +ATOM 353 N ALA A 23 24.210 37.649 22.694 1.00 0.00 N +ATOM 354 H ALA A 23 24.358 38.065 21.786 1.00 0.00 H +ATOM 355 CA ALA A 23 25.493 37.172 23.215 1.00 0.00 C +ATOM 356 HA ALA A 23 25.371 36.089 23.221 1.00 0.00 H +ATOM 357 CB ALA A 23 26.701 37.486 22.326 1.00 0.00 C +ATOM 358 HB1 ALA A 23 26.446 37.309 21.280 1.00 0.00 H +ATOM 359 HB2 ALA A 23 27.379 36.708 22.676 1.00 0.00 H +ATOM 360 HB3 ALA A 23 27.091 38.494 22.468 1.00 0.00 H +ATOM 361 C ALA A 23 25.748 37.757 24.642 1.00 0.00 C +ATOM 362 O ALA A 23 26.091 36.953 25.518 1.00 0.00 O +ATOM 363 N ALA A 24 25.564 39.050 24.846 1.00 0.00 N +ATOM 364 H ALA A 24 25.214 39.674 24.133 1.00 0.00 H +ATOM 365 CA ALA A 24 25.745 39.687 26.153 1.00 0.00 C +ATOM 366 HA ALA A 24 26.761 39.419 26.445 1.00 0.00 H +ATOM 367 CB ALA A 24 25.490 41.189 25.938 1.00 0.00 C +ATOM 368 HB1 ALA A 24 26.247 41.676 25.325 1.00 0.00 H +ATOM 369 HB2 ALA A 24 25.633 41.729 26.874 1.00 0.00 H +ATOM 370 HB3 ALA A 24 24.561 41.467 25.440 1.00 0.00 H +ATOM 371 C ALA A 24 24.796 39.101 27.137 1.00 0.00 C +ATOM 372 O ALA A 24 25.116 38.975 28.329 1.00 0.00 O +ATOM 373 N THR A 25 23.577 38.659 26.736 1.00 0.00 N +ATOM 374 H THR A 25 23.398 38.681 25.743 1.00 0.00 H +ATOM 375 CA THR A 25 22.587 38.094 27.680 1.00 0.00 C +ATOM 376 HA THR A 25 22.755 38.495 28.681 1.00 0.00 H +ATOM 377 CB THR A 25 21.196 38.549 27.262 1.00 0.00 C +ATOM 378 HB THR A 25 20.797 37.883 26.497 1.00 0.00 H +ATOM 379 CG2 THR A 25 20.246 38.369 28.438 1.00 0.00 C +ATOM 380 HG21 THR A 25 20.203 37.329 28.763 1.00 0.00 H +ATOM 381 HG22 THR A 25 19.255 38.740 28.176 1.00 0.00 H +ATOM 382 HG23 THR A 25 20.574 38.977 29.280 1.00 0.00 H +ATOM 383 OG1 THR A 25 21.199 39.931 27.030 1.00 0.00 O +ATOM 384 HG1 THR A 25 20.293 40.156 26.807 1.00 0.00 H +ATOM 385 C THR A 25 22.788 36.618 27.928 1.00 0.00 C +ATOM 386 O THR A 25 22.618 36.164 29.050 1.00 0.00 O +ATOM 387 N ALA A 26 23.216 35.854 26.929 1.00 0.00 N +ATOM 388 H ALA A 26 23.315 36.208 25.988 1.00 0.00 H +ATOM 389 CA ALA A 26 23.652 34.513 27.159 1.00 0.00 C +ATOM 390 HA ALA A 26 22.781 33.940 27.476 1.00 0.00 H +ATOM 391 CB ALA A 26 24.062 33.913 25.734 1.00 0.00 C +ATOM 392 HB1 ALA A 26 23.120 33.732 25.215 1.00 0.00 H +ATOM 393 HB2 ALA A 26 24.695 33.029 25.804 1.00 0.00 H +ATOM 394 HB3 ALA A 26 24.715 34.613 25.211 1.00 0.00 H +ATOM 395 C ALA A 26 24.856 34.523 28.062 1.00 0.00 C +ATOM 396 O ALA A 26 24.889 33.745 28.985 1.00 0.00 O +ATOM 397 N GLU A 27 25.749 35.500 28.027 1.00 0.00 N +ATOM 398 H GLU A 27 25.940 35.933 27.135 1.00 0.00 H +ATOM 399 CA GLU A 27 26.712 35.671 29.037 1.00 0.00 C +ATOM 400 HA GLU A 27 27.306 34.757 29.097 1.00 0.00 H +ATOM 401 CB GLU A 27 27.684 36.833 28.605 1.00 0.00 C +ATOM 402 HB2 GLU A 27 28.270 36.561 27.728 1.00 0.00 H +ATOM 403 HB3 GLU A 27 27.178 37.773 28.387 1.00 0.00 H +ATOM 404 CG GLU A 27 28.742 37.165 29.664 1.00 0.00 C +ATOM 405 HG2 GLU A 27 28.193 37.537 30.529 1.00 0.00 H +ATOM 406 HG3 GLU A 27 29.267 36.244 29.914 1.00 0.00 H +ATOM 407 CD GLU A 27 29.887 38.242 29.269 1.00 0.00 C +ATOM 408 OE1 GLU A 27 31.108 37.827 29.164 1.00 0.00 O1- +ATOM 409 OE2 GLU A 27 29.529 39.420 29.110 1.00 0.00 O1- +ATOM 410 C GLU A 27 26.099 35.742 30.450 1.00 0.00 C +ATOM 411 O GLU A 27 26.553 35.162 31.414 1.00 0.00 O +ATOM 412 N LYS A 28 25.124 36.609 30.604 1.00 0.00 N +ATOM 413 H LYS A 28 24.710 37.106 29.827 1.00 0.00 H +ATOM 414 CA LYS A 28 24.538 36.947 31.950 1.00 0.00 C +ATOM 415 HA LYS A 28 25.324 37.300 32.618 1.00 0.00 H +ATOM 416 CB LYS A 28 23.559 38.052 31.728 1.00 0.00 C +ATOM 417 HB2 LYS A 28 24.096 38.943 31.403 1.00 0.00 H +ATOM 418 HB3 LYS A 28 22.761 37.811 31.025 1.00 0.00 H +ATOM 419 CG LYS A 28 22.885 38.401 33.150 1.00 0.00 C +ATOM 420 HG2 LYS A 28 22.343 37.542 33.545 1.00 0.00 H +ATOM 421 HG3 LYS A 28 23.638 38.698 33.879 1.00 0.00 H +ATOM 422 CD LYS A 28 21.826 39.579 33.063 1.00 0.00 C +ATOM 423 HD2 LYS A 28 20.930 39.146 32.616 1.00 0.00 H +ATOM 424 HD3 LYS A 28 21.656 39.989 34.058 1.00 0.00 H +ATOM 425 CE LYS A 28 22.359 40.850 32.267 1.00 0.00 C +ATOM 426 HE2 LYS A 28 23.432 40.899 32.449 1.00 0.00 H +ATOM 427 HE3 LYS A 28 22.199 40.756 31.193 1.00 0.00 H +ATOM 428 NZ LYS A 28 21.521 42.013 32.715 1.00 0.00 N1+ +ATOM 429 HZ1 LYS A 28 21.696 42.294 33.670 1.00 0.00 H +ATOM 430 HZ2 LYS A 28 20.541 41.777 32.653 1.00 0.00 H +ATOM 431 HZ3 LYS A 28 21.651 42.827 32.131 1.00 0.00 H +ATOM 432 C LYS A 28 23.866 35.778 32.535 1.00 0.00 C +ATOM 433 O LYS A 28 23.994 35.665 33.742 1.00 0.00 O +ATOM 434 N VAL A 29 23.329 34.885 31.712 1.00 0.00 N +ATOM 435 H VAL A 29 23.229 35.111 30.733 1.00 0.00 H +ATOM 436 CA VAL A 29 22.736 33.650 32.097 1.00 0.00 C +ATOM 437 HA VAL A 29 21.999 33.879 32.866 1.00 0.00 H +ATOM 438 CB VAL A 29 21.735 33.166 30.962 1.00 0.00 C +ATOM 439 HB VAL A 29 22.375 32.951 30.106 1.00 0.00 H +ATOM 440 CG1 VAL A 29 21.139 31.783 31.445 1.00 0.00 C +ATOM 441 HG11 VAL A 29 20.592 31.413 30.579 1.00 0.00 H +ATOM 442 HG12 VAL A 29 20.575 31.908 32.370 1.00 0.00 H +ATOM 443 HG13 VAL A 29 21.993 31.113 31.534 1.00 0.00 H +ATOM 444 CG2 VAL A 29 20.482 33.992 30.547 1.00 0.00 C +ATOM 445 HG21 VAL A 29 19.966 33.618 29.662 1.00 0.00 H +ATOM 446 HG22 VAL A 29 20.739 35.019 30.286 1.00 0.00 H +ATOM 447 HG23 VAL A 29 19.838 34.110 31.419 1.00 0.00 H +ATOM 448 C VAL A 29 23.781 32.642 32.484 1.00 0.00 C +ATOM 449 O VAL A 29 23.604 31.876 33.462 1.00 0.00 O +ATOM 450 N PHE A 30 24.962 32.641 31.758 1.00 0.00 N +ATOM 451 H PHE A 30 24.997 33.287 30.981 1.00 0.00 H +ATOM 452 CA PHE A 30 26.112 31.701 32.033 1.00 0.00 C +ATOM 453 HA PHE A 30 25.692 30.753 32.371 1.00 0.00 H +ATOM 454 CB PHE A 30 26.901 31.582 30.713 1.00 0.00 C +ATOM 455 HB2 PHE A 30 26.966 32.537 30.191 1.00 0.00 H +ATOM 456 HB3 PHE A 30 27.928 31.266 30.888 1.00 0.00 H +ATOM 457 CG PHE A 30 26.348 30.600 29.656 1.00 0.00 C +ATOM 458 CD1 PHE A 30 25.751 29.296 29.878 1.00 0.00 C +ATOM 459 HD1 PHE A 30 25.705 28.943 30.897 1.00 0.00 H +ATOM 460 CE1 PHE A 30 25.345 28.377 28.817 1.00 0.00 C +ATOM 461 HE1 PHE A 30 24.810 27.464 29.039 1.00 0.00 H +ATOM 462 CZ PHE A 30 25.534 28.840 27.515 1.00 0.00 C +ATOM 463 HZ PHE A 30 25.196 28.267 26.666 1.00 0.00 H +ATOM 464 CE2 PHE A 30 26.096 30.099 27.271 1.00 0.00 C +ATOM 465 HE2 PHE A 30 26.212 30.319 26.219 1.00 0.00 H +ATOM 466 CD2 PHE A 30 26.533 30.924 28.297 1.00 0.00 C +ATOM 467 HD2 PHE A 30 27.135 31.778 28.029 1.00 0.00 H +ATOM 468 C PHE A 30 26.988 32.189 33.246 1.00 0.00 C +ATOM 469 O PHE A 30 27.609 31.344 33.905 1.00 0.00 O +ATOM 470 N LYS A 31 27.038 33.446 33.540 1.00 0.00 N +ATOM 471 H LYS A 31 26.710 34.105 32.849 1.00 0.00 H +ATOM 472 CA LYS A 31 27.405 34.022 34.854 1.00 0.00 C +ATOM 473 HA LYS A 31 28.437 33.764 35.092 1.00 0.00 H +ATOM 474 CB LYS A 31 27.274 35.599 34.858 1.00 0.00 C +ATOM 475 HB2 LYS A 31 26.242 35.714 34.527 1.00 0.00 H +ATOM 476 HB3 LYS A 31 27.292 36.098 35.827 1.00 0.00 H +ATOM 477 CG LYS A 31 28.378 36.275 33.919 1.00 0.00 C +ATOM 478 HG2 LYS A 31 28.522 35.710 32.997 1.00 0.00 H +ATOM 479 HG3 LYS A 31 27.926 37.229 33.649 1.00 0.00 H +ATOM 480 CD LYS A 31 29.823 36.487 34.439 1.00 0.00 C +ATOM 481 HD2 LYS A 31 29.755 36.977 35.411 1.00 0.00 H +ATOM 482 HD3 LYS A 31 30.132 35.472 34.684 1.00 0.00 H +ATOM 483 CE LYS A 31 30.777 37.150 33.394 1.00 0.00 C +ATOM 484 HE2 LYS A 31 30.633 36.630 32.447 1.00 0.00 H +ATOM 485 HE3 LYS A 31 30.436 38.158 33.158 1.00 0.00 H +ATOM 486 NZ LYS A 31 32.138 37.121 33.926 1.00 0.00 N1+ +ATOM 487 HZ1 LYS A 31 32.272 37.458 34.869 1.00 0.00 H +ATOM 488 HZ2 LYS A 31 32.676 37.777 33.376 1.00 0.00 H +ATOM 489 HZ3 LYS A 31 32.555 36.210 33.805 1.00 0.00 H +ATOM 490 C LYS A 31 26.516 33.562 35.983 1.00 0.00 C +ATOM 491 O LYS A 31 27.018 32.993 36.943 1.00 0.00 O +ATOM 492 N GLN A 32 25.185 33.745 35.953 1.00 0.00 N +ATOM 493 H GLN A 32 24.737 34.194 35.166 1.00 0.00 H +ATOM 494 CA GLN A 32 24.365 33.197 37.027 1.00 0.00 C +ATOM 495 HA GLN A 32 24.679 33.822 37.863 1.00 0.00 H +ATOM 496 CB GLN A 32 22.891 33.427 36.688 1.00 0.00 C +ATOM 497 HB2 GLN A 32 22.845 33.366 35.601 1.00 0.00 H +ATOM 498 HB3 GLN A 32 22.285 32.685 37.209 1.00 0.00 H +ATOM 499 CG GLN A 32 22.280 34.840 37.028 1.00 0.00 C +ATOM 500 HG2 GLN A 32 22.039 34.881 38.090 1.00 0.00 H +ATOM 501 HG3 GLN A 32 22.899 35.710 36.807 1.00 0.00 H +ATOM 502 CD GLN A 32 20.958 35.124 36.195 1.00 0.00 C +ATOM 503 OE1 GLN A 32 19.883 34.823 36.738 1.00 0.00 O +ATOM 504 NE2 GLN A 32 20.988 35.530 34.974 1.00 0.00 N +ATOM 505 HE21 GLN A 32 21.902 35.787 34.628 1.00 0.00 H +ATOM 506 HE22 GLN A 32 20.177 35.714 34.400 1.00 0.00 H +ATOM 507 C GLN A 32 24.598 31.707 37.232 1.00 0.00 C +ATOM 508 O GLN A 32 24.794 31.293 38.384 1.00 0.00 O +ATOM 509 N TYR A 33 24.530 30.875 36.142 1.00 0.00 N +ATOM 510 H TYR A 33 24.587 31.274 35.216 1.00 0.00 H +ATOM 511 CA TYR A 33 24.722 29.459 36.217 1.00 0.00 C +ATOM 512 HA TYR A 33 23.881 29.042 36.772 1.00 0.00 H +ATOM 513 CB TYR A 33 24.622 28.848 34.842 1.00 0.00 C +ATOM 514 HB2 TYR A 33 23.621 29.006 34.442 1.00 0.00 H +ATOM 515 HB3 TYR A 33 25.353 29.388 34.240 1.00 0.00 H +ATOM 516 CG TYR A 33 24.877 27.304 34.704 1.00 0.00 C +ATOM 517 CD1 TYR A 33 23.808 26.383 34.938 1.00 0.00 C +ATOM 518 HD1 TYR A 33 22.814 26.754 35.140 1.00 0.00 H +ATOM 519 CE1 TYR A 33 24.054 24.991 35.075 1.00 0.00 C +ATOM 520 HE1 TYR A 33 23.300 24.251 35.300 1.00 0.00 H +ATOM 521 CZ TYR A 33 25.399 24.562 34.934 1.00 0.00 C +ATOM 522 OH TYR A 33 25.658 23.212 34.983 1.00 0.00 O +ATOM 523 HH TYR A 33 26.608 23.080 35.030 1.00 0.00 H +ATOM 524 CE2 TYR A 33 26.410 25.459 34.723 1.00 0.00 C +ATOM 525 HE2 TYR A 33 27.443 25.157 34.630 1.00 0.00 H +ATOM 526 CD2 TYR A 33 26.146 26.818 34.602 1.00 0.00 C +ATOM 527 HD2 TYR A 33 26.992 27.469 34.435 1.00 0.00 H +ATOM 528 C TYR A 33 26.078 29.155 36.854 1.00 0.00 C +ATOM 529 O TYR A 33 26.179 28.186 37.566 1.00 0.00 O +ATOM 530 N ALA A 34 27.159 29.788 36.508 1.00 0.00 N +ATOM 531 H ALA A 34 26.997 30.563 35.881 1.00 0.00 H +ATOM 532 CA ALA A 34 28.473 29.535 37.100 1.00 0.00 C +ATOM 533 HA ALA A 34 28.717 28.476 37.023 1.00 0.00 H +ATOM 534 CB ALA A 34 29.651 30.265 36.402 1.00 0.00 C +ATOM 535 HB1 ALA A 34 30.577 29.813 36.757 1.00 0.00 H +ATOM 536 HB2 ALA A 34 29.619 31.296 36.752 1.00 0.00 H +ATOM 537 HB3 ALA A 34 29.681 30.159 35.317 1.00 0.00 H +ATOM 538 C ALA A 34 28.508 29.835 38.614 1.00 0.00 C +ATOM 539 O ALA A 34 29.097 29.077 39.389 1.00 0.00 O +ATOM 540 N ASN A 35 27.814 30.864 39.024 1.00 0.00 N +ATOM 541 H ASN A 35 27.594 31.535 38.301 1.00 0.00 H +ATOM 542 CA ASN A 35 27.743 31.252 40.445 1.00 0.00 C +ATOM 543 HA ASN A 35 28.713 31.168 40.935 1.00 0.00 H +ATOM 544 CB ASN A 35 27.254 32.684 40.541 1.00 0.00 C +ATOM 545 HB2 ASN A 35 27.798 33.361 39.883 1.00 0.00 H +ATOM 546 HB3 ASN A 35 26.192 32.727 40.300 1.00 0.00 H +ATOM 547 CG ASN A 35 27.326 33.169 41.947 1.00 0.00 C +ATOM 548 OD1 ASN A 35 26.493 32.743 42.763 1.00 0.00 O +ATOM 549 ND2 ASN A 35 28.099 34.183 42.223 1.00 0.00 N +ATOM 550 HD21 ASN A 35 28.867 34.350 41.589 1.00 0.00 H +ATOM 551 HD22 ASN A 35 28.276 34.397 43.193 1.00 0.00 H +ATOM 552 C ASN A 35 26.833 30.200 41.127 1.00 0.00 C +ATOM 553 O ASN A 35 27.114 29.686 42.238 1.00 0.00 O +ATOM 554 N ASP A 36 25.819 29.616 40.395 1.00 0.00 N +ATOM 555 H ASP A 36 25.608 30.144 39.560 1.00 0.00 H +ATOM 556 CA ASP A 36 25.004 28.401 40.867 1.00 0.00 C +ATOM 557 HA ASP A 36 24.491 28.819 41.733 1.00 0.00 H +ATOM 558 CB ASP A 36 23.819 28.175 39.948 1.00 0.00 C +ATOM 559 HB2 ASP A 36 23.379 29.117 39.623 1.00 0.00 H +ATOM 560 HB3 ASP A 36 24.279 27.586 39.154 1.00 0.00 H +ATOM 561 CG ASP A 36 22.720 27.350 40.470 1.00 0.00 C +ATOM 562 OD1 ASP A 36 22.214 26.485 39.714 1.00 0.00 O1- +ATOM 563 OD2 ASP A 36 22.361 27.455 41.653 1.00 0.00 O1- +ATOM 564 C ASP A 36 25.793 27.113 41.244 1.00 0.00 C +ATOM 565 O ASP A 36 25.357 26.391 42.112 1.00 0.00 O +ATOM 566 N ASN A 37 26.991 27.006 40.666 1.00 0.00 N +ATOM 567 H ASN A 37 27.306 27.779 40.098 1.00 0.00 H +ATOM 568 CA ASN A 37 27.829 25.814 40.636 1.00 0.00 C +ATOM 569 HA ASN A 37 27.378 25.130 41.354 1.00 0.00 H +ATOM 570 CB ASN A 37 27.873 25.281 39.195 1.00 0.00 C +ATOM 571 HB2 ASN A 37 27.936 26.106 38.487 1.00 0.00 H +ATOM 572 HB3 ASN A 37 28.702 24.579 39.101 1.00 0.00 H +ATOM 573 CG ASN A 37 26.652 24.492 38.842 1.00 0.00 C +ATOM 574 OD1 ASN A 37 26.432 23.357 39.282 1.00 0.00 O +ATOM 575 ND2 ASN A 37 25.706 25.057 38.177 1.00 0.00 N +ATOM 576 HD21 ASN A 37 25.804 26.050 38.016 1.00 0.00 H +ATOM 577 HD22 ASN A 37 24.895 24.502 37.947 1.00 0.00 H +ATOM 578 C ASN A 37 29.196 26.053 41.261 1.00 0.00 C +ATOM 579 O ASN A 37 30.064 25.171 41.182 1.00 0.00 O +ATOM 580 N GLY A 38 29.358 27.176 42.012 1.00 0.00 N +ATOM 581 H GLY A 38 28.556 27.765 42.189 1.00 0.00 H +ATOM 582 CA GLY A 38 30.637 27.460 42.681 1.00 0.00 C +ATOM 583 HA2 GLY A 38 30.444 28.296 43.354 1.00 0.00 H +ATOM 584 HA3 GLY A 38 30.900 26.655 43.368 1.00 0.00 H +ATOM 585 C GLY A 38 31.894 27.774 41.785 1.00 0.00 C +ATOM 586 O GLY A 38 33.027 27.429 42.124 1.00 0.00 O +ATOM 587 N VAL A 39 31.731 28.287 40.579 1.00 0.00 N +ATOM 588 H VAL A 39 30.794 28.624 40.408 1.00 0.00 H +ATOM 589 CA VAL A 39 32.664 28.449 39.403 1.00 0.00 C +ATOM 590 HA VAL A 39 33.598 27.911 39.570 1.00 0.00 H +ATOM 591 CB VAL A 39 32.015 27.778 38.179 1.00 0.00 C +ATOM 592 HB VAL A 39 31.005 28.158 38.027 1.00 0.00 H +ATOM 593 CG1 VAL A 39 32.989 28.121 37.014 1.00 0.00 C +ATOM 594 HG11 VAL A 39 32.636 27.519 36.176 1.00 0.00 H +ATOM 595 HG12 VAL A 39 34.019 27.963 37.334 1.00 0.00 H +ATOM 596 HG13 VAL A 39 32.869 29.117 36.588 1.00 0.00 H +ATOM 597 CG2 VAL A 39 31.943 26.274 38.437 1.00 0.00 C +ATOM 598 HG21 VAL A 39 31.540 25.729 37.583 1.00 0.00 H +ATOM 599 HG22 VAL A 39 31.356 26.086 39.337 1.00 0.00 H +ATOM 600 HG23 VAL A 39 32.907 25.863 38.738 1.00 0.00 H +ATOM 601 C VAL A 39 33.029 29.909 39.235 1.00 0.00 C +ATOM 602 O VAL A 39 32.186 30.683 38.757 1.00 0.00 O +ATOM 603 N ASP A 40 34.268 30.281 39.558 1.00 0.00 N +ATOM 604 H ASP A 40 34.838 29.543 39.947 1.00 0.00 H +ATOM 605 CA ASP A 40 34.875 31.551 39.096 1.00 0.00 C +ATOM 606 HA ASP A 40 34.143 32.078 38.487 1.00 0.00 H +ATOM 607 CB ASP A 40 35.183 32.418 40.345 1.00 0.00 C +ATOM 608 HB2 ASP A 40 34.184 32.657 40.710 1.00 0.00 H +ATOM 609 HB3 ASP A 40 35.707 31.788 41.065 1.00 0.00 H +ATOM 610 CG ASP A 40 35.879 33.683 40.009 1.00 0.00 C +ATOM 611 OD1 ASP A 40 35.393 34.410 39.076 1.00 0.00 O1- +ATOM 612 OD2 ASP A 40 37.025 33.897 40.460 1.00 0.00 O1- +ATOM 613 C ASP A 40 36.062 31.169 38.238 1.00 0.00 C +ATOM 614 O ASP A 40 36.850 30.275 38.630 1.00 0.00 O +ATOM 615 N GLY A 41 36.172 31.751 37.102 1.00 0.00 N +ATOM 616 H GLY A 41 35.443 32.408 36.858 1.00 0.00 H +ATOM 617 CA GLY A 41 37.214 31.484 36.189 1.00 0.00 C +ATOM 618 HA2 GLY A 41 38.072 31.014 36.670 1.00 0.00 H +ATOM 619 HA3 GLY A 41 36.761 30.672 35.620 1.00 0.00 H +ATOM 620 C GLY A 41 37.623 32.709 35.379 1.00 0.00 C +ATOM 621 O GLY A 41 37.288 33.862 35.686 1.00 0.00 O +ATOM 622 N GLU A 42 38.354 32.422 34.316 1.00 0.00 N +ATOM 623 H GLU A 42 38.789 31.512 34.368 1.00 0.00 H +ATOM 624 CA GLU A 42 38.603 33.310 33.228 1.00 0.00 C +ATOM 625 HA GLU A 42 38.329 34.318 33.541 1.00 0.00 H +ATOM 626 CB GLU A 42 40.158 33.294 33.040 1.00 0.00 C +ATOM 627 HB2 GLU A 42 40.656 33.398 34.004 1.00 0.00 H +ATOM 628 HB3 GLU A 42 40.417 32.326 32.611 1.00 0.00 H +ATOM 629 CG GLU A 42 40.673 34.328 32.046 1.00 0.00 C +ATOM 630 HG2 GLU A 42 41.606 34.015 31.580 1.00 0.00 H +ATOM 631 HG3 GLU A 42 39.970 34.501 31.231 1.00 0.00 H +ATOM 632 CD GLU A 42 41.014 35.613 32.804 1.00 0.00 C +ATOM 633 OE1 GLU A 42 41.944 35.693 33.644 1.00 0.00 O1- +ATOM 634 OE2 GLU A 42 40.218 36.602 32.656 1.00 0.00 O1- +ATOM 635 C GLU A 42 37.780 33.033 32.033 1.00 0.00 C +ATOM 636 O GLU A 42 37.577 31.870 31.690 1.00 0.00 O +ATOM 637 N TRP A 43 37.228 34.069 31.412 1.00 0.00 N +ATOM 638 H TRP A 43 37.423 35.035 31.634 1.00 0.00 H +ATOM 639 CA TRP A 43 36.233 33.951 30.354 1.00 0.00 C +ATOM 640 HA TRP A 43 35.850 32.931 30.348 1.00 0.00 H +ATOM 641 CB TRP A 43 34.984 34.889 30.616 1.00 0.00 C +ATOM 642 HB2 TRP A 43 35.436 35.868 30.771 1.00 0.00 H +ATOM 643 HB3 TRP A 43 34.427 34.918 29.679 1.00 0.00 H +ATOM 644 CG TRP A 43 34.115 34.536 31.838 1.00 0.00 C +ATOM 645 CD1 TRP A 43 34.428 34.708 33.154 1.00 0.00 C +ATOM 646 HD1 TRP A 43 35.387 35.052 33.511 1.00 0.00 H +ATOM 647 NE1 TRP A 43 33.399 34.110 33.877 1.00 0.00 N +ATOM 648 HE1 TRP A 43 33.511 34.066 34.880 1.00 0.00 H +ATOM 649 CE2 TRP A 43 32.444 33.463 33.073 1.00 0.00 C +ATOM 650 CZ2 TRP A 43 31.248 32.745 33.296 1.00 0.00 C +ATOM 651 HZ2 TRP A 43 31.007 32.429 34.301 1.00 0.00 H +ATOM 652 CH2 TRP A 43 30.575 32.194 32.199 1.00 0.00 C +ATOM 653 HH2 TRP A 43 29.740 31.527 32.355 1.00 0.00 H +ATOM 654 CZ3 TRP A 43 30.988 32.541 30.909 1.00 0.00 C +ATOM 655 HZ3 TRP A 43 30.412 32.236 30.047 1.00 0.00 H +ATOM 656 CE3 TRP A 43 32.109 33.327 30.682 1.00 0.00 C +ATOM 657 HE3 TRP A 43 32.397 33.679 29.703 1.00 0.00 H +ATOM 658 CD2 TRP A 43 32.870 33.817 31.765 1.00 0.00 C +ATOM 659 C TRP A 43 36.910 34.235 29.034 1.00 0.00 C +ATOM 660 O TRP A 43 37.660 35.202 28.823 1.00 0.00 O +ATOM 661 N THR A 44 36.468 33.398 28.113 1.00 0.00 N +ATOM 662 H THR A 44 35.919 32.590 28.367 1.00 0.00 H +ATOM 663 CA THR A 44 36.627 33.526 26.668 1.00 0.00 C +ATOM 664 HA THR A 44 36.825 34.580 26.474 1.00 0.00 H +ATOM 665 CB THR A 44 37.813 32.794 26.062 1.00 0.00 C +ATOM 666 HB THR A 44 37.695 32.789 24.978 1.00 0.00 H +ATOM 667 CG2 THR A 44 39.142 33.411 26.470 1.00 0.00 C +ATOM 668 HG21 THR A 44 39.971 32.814 26.090 1.00 0.00 H +ATOM 669 HG22 THR A 44 39.277 33.395 27.552 1.00 0.00 H +ATOM 670 HG23 THR A 44 39.360 34.408 26.088 1.00 0.00 H +ATOM 671 OG1 THR A 44 37.854 31.507 26.604 1.00 0.00 O +ATOM 672 HG1 THR A 44 37.629 30.907 25.889 1.00 0.00 H +ATOM 673 C THR A 44 35.267 33.295 26.005 1.00 0.00 C +ATOM 674 O THR A 44 34.480 32.577 26.444 1.00 0.00 O +ATOM 675 N TYR A 45 35.137 33.919 24.848 1.00 0.00 N +ATOM 676 H TYR A 45 35.900 34.526 24.585 1.00 0.00 H +ATOM 677 CA TYR A 45 34.051 33.679 23.814 1.00 0.00 C +ATOM 678 HA TYR A 45 33.565 32.748 24.109 1.00 0.00 H +ATOM 679 CB TYR A 45 33.061 34.890 23.836 1.00 0.00 C +ATOM 680 HB2 TYR A 45 32.689 35.085 24.843 1.00 0.00 H +ATOM 681 HB3 TYR A 45 33.670 35.762 23.596 1.00 0.00 H +ATOM 682 CG TYR A 45 31.825 34.747 22.962 1.00 0.00 C +ATOM 683 CD1 TYR A 45 30.955 33.684 23.061 1.00 0.00 C +ATOM 684 HD1 TYR A 45 31.040 32.945 23.845 1.00 0.00 H +ATOM 685 CE1 TYR A 45 29.908 33.556 22.116 1.00 0.00 C +ATOM 686 HE1 TYR A 45 29.113 32.849 22.291 1.00 0.00 H +ATOM 687 CZ TYR A 45 29.718 34.506 21.094 1.00 0.00 C +ATOM 688 OH TYR A 45 28.658 34.338 20.268 1.00 0.00 O +ATOM 689 HH TYR A 45 28.496 35.052 19.648 1.00 0.00 H +ATOM 690 CE2 TYR A 45 30.653 35.574 21.028 1.00 0.00 C +ATOM 691 HE2 TYR A 45 30.490 36.288 20.234 1.00 0.00 H +ATOM 692 CD2 TYR A 45 31.752 35.643 21.911 1.00 0.00 C +ATOM 693 HD2 TYR A 45 32.537 36.346 21.679 1.00 0.00 H +ATOM 694 C TYR A 45 34.545 33.529 22.336 1.00 0.00 C +ATOM 695 O TYR A 45 35.260 34.412 21.809 1.00 0.00 O +ATOM 696 N ASP A 46 33.924 32.567 21.640 1.00 0.00 N +ATOM 697 H ASP A 46 33.215 32.006 22.088 1.00 0.00 H +ATOM 698 CA ASP A 46 34.109 32.289 20.204 1.00 0.00 C +ATOM 699 HA ASP A 46 34.805 32.896 19.625 1.00 0.00 H +ATOM 700 CB ASP A 46 34.818 30.917 20.240 1.00 0.00 C +ATOM 701 HB2 ASP A 46 35.700 31.032 20.871 1.00 0.00 H +ATOM 702 HB3 ASP A 46 34.252 30.200 20.834 1.00 0.00 H +ATOM 703 CG ASP A 46 35.216 30.282 18.912 1.00 0.00 C +ATOM 704 OD1 ASP A 46 34.405 29.507 18.323 1.00 0.00 O1- +ATOM 705 OD2 ASP A 46 36.156 30.857 18.365 1.00 0.00 O1- +ATOM 706 C ASP A 46 32.877 32.275 19.319 1.00 0.00 C +ATOM 707 O ASP A 46 31.931 31.517 19.529 1.00 0.00 O +ATOM 708 N ASP A 47 32.833 33.220 18.413 1.00 0.00 N +ATOM 709 H ASP A 47 33.622 33.852 18.429 1.00 0.00 H +ATOM 710 CA ASP A 47 31.688 33.456 17.554 1.00 0.00 C +ATOM 711 HA ASP A 47 30.773 33.561 18.137 1.00 0.00 H +ATOM 712 CB ASP A 47 31.907 34.738 16.747 1.00 0.00 C +ATOM 713 HB2 ASP A 47 32.113 35.510 17.488 1.00 0.00 H +ATOM 714 HB3 ASP A 47 32.853 34.697 16.207 1.00 0.00 H +ATOM 715 CG ASP A 47 30.729 35.187 15.844 1.00 0.00 C +ATOM 716 OD1 ASP A 47 29.551 35.040 16.174 1.00 0.00 O1- +ATOM 717 OD2 ASP A 47 31.117 35.727 14.755 1.00 0.00 O1- +ATOM 718 C ASP A 47 31.522 32.326 16.557 1.00 0.00 C +ATOM 719 O ASP A 47 30.390 32.069 16.134 1.00 0.00 O +ATOM 720 N ALA A 48 32.555 31.657 16.092 1.00 0.00 N +ATOM 721 H ALA A 48 33.490 31.931 16.357 1.00 0.00 H +ATOM 722 CA ALA A 48 32.437 30.647 15.015 1.00 0.00 C +ATOM 723 HA ALA A 48 31.707 31.108 14.349 1.00 0.00 H +ATOM 724 CB ALA A 48 33.821 30.467 14.340 1.00 0.00 C +ATOM 725 HB1 ALA A 48 34.244 31.399 13.964 1.00 0.00 H +ATOM 726 HB2 ALA A 48 33.675 29.706 13.573 1.00 0.00 H +ATOM 727 HB3 ALA A 48 34.421 29.986 15.112 1.00 0.00 H +ATOM 728 C ALA A 48 31.855 29.301 15.549 1.00 0.00 C +ATOM 729 O ALA A 48 31.548 28.445 14.720 1.00 0.00 O +ATOM 730 N THR A 49 31.619 29.163 16.885 1.00 0.00 N +ATOM 731 H THR A 49 31.975 29.929 17.439 1.00 0.00 H +ATOM 732 CA THR A 49 30.811 28.126 17.576 1.00 0.00 C +ATOM 733 HA THR A 49 30.371 27.544 16.767 1.00 0.00 H +ATOM 734 CB THR A 49 31.713 27.100 18.310 1.00 0.00 C +ATOM 735 HB THR A 49 31.134 26.420 18.935 1.00 0.00 H +ATOM 736 CG2 THR A 49 32.614 26.280 17.436 1.00 0.00 C +ATOM 737 HG21 THR A 49 33.329 26.868 16.859 1.00 0.00 H +ATOM 738 HG22 THR A 49 32.002 25.593 16.853 1.00 0.00 H +ATOM 739 HG23 THR A 49 33.354 25.760 18.044 1.00 0.00 H +ATOM 740 OG1 THR A 49 32.507 27.834 19.222 1.00 0.00 O +ATOM 741 HG1 THR A 49 33.151 28.336 18.715 1.00 0.00 H +ATOM 742 C THR A 49 29.713 28.644 18.468 1.00 0.00 C +ATOM 743 O THR A 49 28.941 27.912 19.103 1.00 0.00 O +ATOM 744 N LYS A 50 29.628 29.977 18.649 1.00 0.00 N +ATOM 745 H LYS A 50 30.419 30.522 18.334 1.00 0.00 H +ATOM 746 CA LYS A 50 28.663 30.695 19.541 1.00 0.00 C +ATOM 747 HA LYS A 50 28.847 31.769 19.501 1.00 0.00 H +ATOM 748 CB LYS A 50 27.189 30.625 19.033 1.00 0.00 C +ATOM 749 HB2 LYS A 50 26.936 29.572 19.163 1.00 0.00 H +ATOM 750 HB3 LYS A 50 26.469 31.081 19.712 1.00 0.00 H +ATOM 751 CG LYS A 50 27.119 30.984 17.465 1.00 0.00 C +ATOM 752 HG2 LYS A 50 27.961 30.590 16.895 1.00 0.00 H +ATOM 753 HG3 LYS A 50 26.188 30.551 17.100 1.00 0.00 H +ATOM 754 CD LYS A 50 27.025 32.547 17.322 1.00 0.00 C +ATOM 755 HD2 LYS A 50 26.337 33.099 17.964 1.00 0.00 H +ATOM 756 HD3 LYS A 50 28.005 32.913 17.623 1.00 0.00 H +ATOM 757 CE LYS A 50 26.686 32.933 15.930 1.00 0.00 C +ATOM 758 HE2 LYS A 50 25.829 32.363 15.572 1.00 0.00 H +ATOM 759 HE3 LYS A 50 26.304 33.953 15.986 1.00 0.00 H +ATOM 760 NZ LYS A 50 27.861 32.905 14.990 1.00 0.00 N1+ +ATOM 761 HZ1 LYS A 50 28.562 33.507 15.397 1.00 0.00 H +ATOM 762 HZ2 LYS A 50 27.597 33.321 14.108 1.00 0.00 H +ATOM 763 HZ3 LYS A 50 28.269 32.017 14.736 1.00 0.00 H +ATOM 764 C LYS A 50 28.884 30.250 21.033 1.00 0.00 C +ATOM 765 O LYS A 50 27.958 30.206 21.826 1.00 0.00 O +ATOM 766 N THR A 51 30.148 29.820 21.328 1.00 0.00 N +ATOM 767 H THR A 51 30.940 30.100 20.766 1.00 0.00 H +ATOM 768 CA THR A 51 30.503 29.214 22.632 1.00 0.00 C +ATOM 769 HA THR A 51 29.680 28.714 23.142 1.00 0.00 H +ATOM 770 CB THR A 51 31.313 27.944 22.369 1.00 0.00 C +ATOM 771 HB THR A 51 32.245 28.102 21.826 1.00 0.00 H +ATOM 772 CG2 THR A 51 31.703 27.088 23.590 1.00 0.00 C +ATOM 773 HG21 THR A 51 32.177 26.160 23.272 1.00 0.00 H +ATOM 774 HG22 THR A 51 30.745 26.977 24.100 1.00 0.00 H +ATOM 775 HG23 THR A 51 32.401 27.677 24.186 1.00 0.00 H +ATOM 776 OG1 THR A 51 30.404 27.161 21.659 1.00 0.00 O +ATOM 777 HG1 THR A 51 29.757 27.683 21.179 1.00 0.00 H +ATOM 778 C THR A 51 31.202 30.120 23.549 1.00 0.00 C +ATOM 779 O THR A 51 32.200 30.721 23.143 1.00 0.00 O +ATOM 780 N PHE A 52 31.009 29.926 24.845 1.00 0.00 N +ATOM 781 H PHE A 52 30.125 29.479 25.042 1.00 0.00 H +ATOM 782 CA PHE A 52 31.821 30.391 25.941 1.00 0.00 C +ATOM 783 HA PHE A 52 32.490 31.192 25.628 1.00 0.00 H +ATOM 784 CB PHE A 52 30.715 30.979 27.007 1.00 0.00 C +ATOM 785 HB2 PHE A 52 29.988 30.200 27.238 1.00 0.00 H +ATOM 786 HB3 PHE A 52 31.250 31.298 27.901 1.00 0.00 H +ATOM 787 CG PHE A 52 30.049 32.222 26.534 1.00 0.00 C +ATOM 788 CD1 PHE A 52 28.876 32.142 25.781 1.00 0.00 C +ATOM 789 HD1 PHE A 52 28.413 31.204 25.515 1.00 0.00 H +ATOM 790 CE1 PHE A 52 28.300 33.350 25.304 1.00 0.00 C +ATOM 791 HE1 PHE A 52 27.303 33.316 24.890 1.00 0.00 H +ATOM 792 CZ PHE A 52 28.880 34.593 25.500 1.00 0.00 C +ATOM 793 HZ PHE A 52 28.417 35.460 25.054 1.00 0.00 H +ATOM 794 CE2 PHE A 52 30.122 34.665 26.192 1.00 0.00 C +ATOM 795 HE2 PHE A 52 30.650 35.597 26.333 1.00 0.00 H +ATOM 796 CD2 PHE A 52 30.597 33.495 26.795 1.00 0.00 C +ATOM 797 HD2 PHE A 52 31.435 33.581 27.471 1.00 0.00 H +ATOM 798 C PHE A 52 32.721 29.343 26.553 1.00 0.00 C +ATOM 799 O PHE A 52 32.280 28.240 26.674 1.00 0.00 O +ATOM 800 N THR A 53 33.908 29.829 27.087 1.00 0.00 N +ATOM 801 H THR A 53 34.203 30.784 26.938 1.00 0.00 H +ATOM 802 CA THR A 53 34.577 29.044 28.132 1.00 0.00 C +ATOM 803 HA THR A 53 34.003 28.190 28.492 1.00 0.00 H +ATOM 804 CB THR A 53 35.881 28.443 27.684 1.00 0.00 C +ATOM 805 HB THR A 53 36.513 29.234 27.280 1.00 0.00 H +ATOM 806 CG2 THR A 53 36.620 27.571 28.752 1.00 0.00 C +ATOM 807 HG21 THR A 53 36.814 28.236 29.595 1.00 0.00 H +ATOM 808 HG22 THR A 53 37.535 27.174 28.313 1.00 0.00 H +ATOM 809 HG23 THR A 53 35.924 26.795 29.068 1.00 0.00 H +ATOM 810 OG1 THR A 53 35.605 27.649 26.584 1.00 0.00 O +ATOM 811 HG1 THR A 53 35.459 28.177 25.796 1.00 0.00 H +ATOM 812 C THR A 53 34.776 29.748 29.443 1.00 0.00 C +ATOM 813 O THR A 53 35.146 30.939 29.437 1.00 0.00 O +ATOM 814 N VAL A 54 34.499 29.135 30.639 1.00 0.00 N +ATOM 815 H VAL A 54 34.209 28.173 30.538 1.00 0.00 H +ATOM 816 CA VAL A 54 34.861 29.536 31.982 1.00 0.00 C +ATOM 817 HA VAL A 54 35.382 30.493 31.978 1.00 0.00 H +ATOM 818 CB VAL A 54 33.697 29.716 32.869 1.00 0.00 C +ATOM 819 HB VAL A 54 32.913 30.335 32.434 1.00 0.00 H +ATOM 820 CG1 VAL A 54 33.002 28.394 33.289 1.00 0.00 C +ATOM 821 HG11 VAL A 54 33.690 27.666 33.718 1.00 0.00 H +ATOM 822 HG12 VAL A 54 32.618 28.014 32.342 1.00 0.00 H +ATOM 823 HG13 VAL A 54 32.093 28.525 33.877 1.00 0.00 H +ATOM 824 CG2 VAL A 54 34.118 30.320 34.224 1.00 0.00 C +ATOM 825 HG21 VAL A 54 34.711 31.228 34.123 1.00 0.00 H +ATOM 826 HG22 VAL A 54 34.691 29.664 34.880 1.00 0.00 H +ATOM 827 HG23 VAL A 54 33.202 30.551 34.767 1.00 0.00 H +ATOM 828 C VAL A 54 35.950 28.590 32.468 1.00 0.00 C +ATOM 829 O VAL A 54 35.738 27.385 32.660 1.00 0.00 O +ATOM 830 N THR A 55 37.187 29.085 32.651 1.00 0.00 N +ATOM 831 H THR A 55 37.326 30.038 32.345 1.00 0.00 H +ATOM 832 CA THR A 55 38.418 28.363 33.071 1.00 0.00 C +ATOM 833 HA THR A 55 38.197 27.299 32.991 1.00 0.00 H +ATOM 834 CB THR A 55 39.574 28.516 32.161 1.00 0.00 C +ATOM 835 HB THR A 55 39.757 29.581 32.019 1.00 0.00 H +ATOM 836 CG2 THR A 55 40.870 27.898 32.786 1.00 0.00 C +ATOM 837 HG21 THR A 55 40.583 26.849 32.855 1.00 0.00 H +ATOM 838 HG22 THR A 55 41.023 28.190 33.826 1.00 0.00 H +ATOM 839 HG23 THR A 55 41.825 28.044 32.280 1.00 0.00 H +ATOM 840 OG1 THR A 55 39.215 27.970 30.818 1.00 0.00 O +ATOM 841 HG1 THR A 55 38.792 28.725 30.401 1.00 0.00 H +ATOM 842 C THR A 55 38.779 28.725 34.458 1.00 0.00 C +ATOM 843 O THR A 55 39.263 29.841 34.735 1.00 0.00 O +ATOM 844 N GLU A 56 38.757 27.773 35.416 1.00 0.00 N +ATOM 845 H GLU A 56 38.459 26.869 35.079 1.00 0.00 H +ATOM 846 CA GLU A 56 39.045 27.993 36.888 1.00 0.00 C +ATOM 847 HA GLU A 56 38.618 28.921 37.267 1.00 0.00 H +ATOM 848 CB GLU A 56 38.402 26.911 37.749 1.00 0.00 C +ATOM 849 HB2 GLU A 56 37.329 27.019 37.593 1.00 0.00 H +ATOM 850 HB3 GLU A 56 38.780 25.905 37.563 1.00 0.00 H +ATOM 851 CG GLU A 56 38.436 27.078 39.267 1.00 0.00 C +ATOM 852 HG2 GLU A 56 39.455 26.968 39.636 1.00 0.00 H +ATOM 853 HG3 GLU A 56 38.094 28.097 39.445 1.00 0.00 H +ATOM 854 CD GLU A 56 37.514 26.014 39.918 1.00 0.00 C +ATOM 855 OE1 GLU A 56 37.905 24.823 39.870 1.00 0.00 O1- +ATOM 856 OE2 GLU A 56 36.529 26.327 40.664 1.00 0.00 O1- +ATOM 857 C GLU A 56 40.488 28.137 37.301 1.00 0.00 C +ATOM 858 O GLU A 56 40.807 29.090 38.025 1.00 0.00 O1- +ATOM 859 OXT GLU A 56 41.377 27.271 37.031 1.00 0.00 O1- +CONECT 1 2 3 4 5 +CONECT 2 1 +CONECT 3 1 +CONECT 4 1 +CONECT 5 1 6 7 18 +CONECT 6 5 +CONECT 7 5 8 9 10 +CONECT 8 7 +CONECT 9 7 +CONECT 10 7 11 12 13 +CONECT 11 10 +CONECT 12 10 +CONECT 13 10 14 +CONECT 14 13 15 16 17 +CONECT 15 14 +CONECT 16 14 +CONECT 17 14 +CONECT 18 5 19 19 20 +CONECT 19 18 18 +CONECT 20 18 21 22 +CONECT 21 20 +CONECT 22 20 35 36 23 +CONECT 23 22 24 25 26 +CONECT 24 23 +CONECT 25 23 +CONECT 26 23 27 33 33 +CONECT 27 26 28 29 +CONECT 28 27 +CONECT 29 27 30 31 +CONECT 30 29 +CONECT 31 29 32 33 +CONECT 32 31 +CONECT 33 26 26 31 34 +CONECT 34 33 +CONECT 35 22 +CONECT 36 22 37 37 38 +CONECT 37 36 36 +CONECT 38 36 39 40 +CONECT 39 38 +CONECT 40 38 41 42 57 +CONECT 41 40 +CONECT 42 40 43 44 45 +CONECT 43 42 +CONECT 44 42 +CONECT 45 42 46 46 55 +CONECT 46 45 45 47 48 +CONECT 47 46 +CONECT 48 46 49 50 50 +CONECT 49 48 +CONECT 50 48 48 51 53 +CONECT 51 50 52 +CONECT 52 51 +CONECT 53 50 54 55 55 +CONECT 54 53 +CONECT 55 45 53 53 56 +CONECT 56 55 +CONECT 57 40 58 58 59 +CONECT 58 57 57 +CONECT 59 57 60 61 +CONECT 60 59 +CONECT 61 59 62 63 79 +CONECT 62 61 +CONECT 63 61 64 65 66 +CONECT 64 63 +CONECT 65 63 +CONECT 66 63 67 68 69 +CONECT 67 66 +CONECT 68 66 +CONECT 69 66 70 71 72 +CONECT 70 69 +CONECT 71 69 +CONECT 72 69 73 74 75 +CONECT 73 72 +CONECT 74 72 +CONECT 75 72 76 77 78 +CONECT 76 75 +CONECT 77 75 +CONECT 78 75 +CONECT 79 61 80 80 81 +CONECT 80 79 79 +CONECT 81 79 82 83 +CONECT 82 81 +CONECT 83 81 84 85 98 +CONECT 84 83 +CONECT 85 83 86 87 88 +CONECT 86 85 +CONECT 87 85 +CONECT 88 85 89 90 94 +CONECT 89 88 +CONECT 90 88 91 92 93 +CONECT 91 90 +CONECT 92 90 +CONECT 93 90 +CONECT 94 88 95 96 97 +CONECT 95 94 +CONECT 96 94 +CONECT 97 94 +CONECT 98 83 99 99 100 +CONECT 99 98 98 +CONECT 100 98 101 102 +CONECT 101 100 +CONECT 102 100 103 104 117 +CONECT 103 102 +CONECT 104 102 105 106 110 +CONECT 105 104 +CONECT 106 104 107 108 109 +CONECT 107 106 +CONECT 108 106 +CONECT 109 106 +CONECT 110 104 111 112 113 +CONECT 111 110 +CONECT 112 110 +CONECT 113 110 114 115 116 +CONECT 114 113 +CONECT 115 113 +CONECT 116 113 +CONECT 117 102 118 118 119 +CONECT 118 117 117 +CONECT 119 117 120 121 +CONECT 120 119 +CONECT 121 119 122 123 136 +CONECT 122 121 +CONECT 123 121 124 125 126 +CONECT 124 123 +CONECT 125 123 +CONECT 126 123 127 128 132 +CONECT 127 126 +CONECT 128 126 129 130 131 +CONECT 129 128 +CONECT 130 128 +CONECT 131 128 +CONECT 132 126 133 134 135 +CONECT 133 132 +CONECT 134 132 +CONECT 135 132 +CONECT 136 121 137 137 138 +CONECT 137 136 136 +CONECT 138 136 139 140 +CONECT 139 138 +CONECT 140 138 141 142 150 +CONECT 141 140 +CONECT 142 140 143 144 145 +CONECT 143 142 +CONECT 144 142 +CONECT 145 142 146 146 147 +CONECT 146 145 145 +CONECT 147 145 148 149 +CONECT 148 147 +CONECT 149 147 +CONECT 150 140 151 151 152 +CONECT 151 150 150 +CONECT 152 150 153 154 +CONECT 153 152 +CONECT 154 152 155 156 157 +CONECT 155 154 +CONECT 156 154 +CONECT 157 154 158 158 159 +CONECT 158 157 157 +CONECT 159 157 160 161 +CONECT 160 159 +CONECT 161 159 162 163 179 +CONECT 162 161 +CONECT 163 161 164 165 166 +CONECT 164 163 +CONECT 165 163 +CONECT 166 163 167 168 169 +CONECT 167 166 +CONECT 168 166 +CONECT 169 166 170 171 172 +CONECT 170 169 +CONECT 171 169 +CONECT 172 169 173 174 175 +CONECT 173 172 +CONECT 174 172 +CONECT 175 172 176 177 178 +CONECT 176 175 +CONECT 177 175 +CONECT 178 175 +CONECT 179 161 180 180 181 +CONECT 180 179 179 +CONECT 181 179 182 183 +CONECT 182 181 +CONECT 183 181 184 185 193 +CONECT 184 183 +CONECT 185 183 186 187 191 +CONECT 186 185 +CONECT 187 185 188 189 190 +CONECT 188 187 +CONECT 189 187 +CONECT 190 187 +CONECT 191 185 192 +CONECT 192 191 +CONECT 193 183 194 194 195 +CONECT 194 193 193 +CONECT 195 193 196 197 +CONECT 196 195 +CONECT 197 195 198 199 212 +CONECT 198 197 +CONECT 199 197 200 201 202 +CONECT 200 199 +CONECT 201 199 +CONECT 202 199 203 204 208 +CONECT 203 202 +CONECT 204 202 205 206 207 +CONECT 205 204 +CONECT 206 204 +CONECT 207 204 +CONECT 208 202 209 210 211 +CONECT 209 208 +CONECT 210 208 +CONECT 211 208 +CONECT 212 197 213 213 214 +CONECT 213 212 212 +CONECT 214 212 215 216 +CONECT 215 214 +CONECT 216 214 217 218 234 +CONECT 217 216 +CONECT 218 216 219 220 221 +CONECT 219 218 +CONECT 220 218 +CONECT 221 218 222 223 224 +CONECT 222 221 +CONECT 223 221 +CONECT 224 221 225 226 227 +CONECT 225 224 +CONECT 226 224 +CONECT 227 224 228 229 230 +CONECT 228 227 +CONECT 229 227 +CONECT 230 227 231 232 233 +CONECT 231 230 +CONECT 232 230 +CONECT 233 230 +CONECT 234 216 235 235 236 +CONECT 235 234 234 +CONECT 236 234 237 238 +CONECT 237 236 +CONECT 238 236 239 240 241 +CONECT 239 238 +CONECT 240 238 +CONECT 241 238 242 242 243 +CONECT 242 241 241 +CONECT 243 241 244 245 +CONECT 244 243 +CONECT 245 243 246 247 256 +CONECT 246 245 +CONECT 247 245 248 249 250 +CONECT 248 247 +CONECT 249 247 +CONECT 250 247 251 252 253 +CONECT 251 250 +CONECT 252 250 +CONECT 253 250 254 254 255 +CONECT 254 253 253 +CONECT 255 253 +CONECT 256 245 257 257 258 +CONECT 257 256 256 +CONECT 258 256 259 260 +CONECT 259 258 +CONECT 260 258 261 262 270 +CONECT 261 260 +CONECT 262 260 263 264 268 +CONECT 263 262 +CONECT 264 262 265 266 267 +CONECT 265 264 +CONECT 266 264 +CONECT 267 264 +CONECT 268 262 269 +CONECT 269 268 +CONECT 270 260 271 271 272 +CONECT 271 270 270 +CONECT 272 270 273 274 +CONECT 273 272 +CONECT 274 272 275 276 284 +CONECT 275 274 +CONECT 276 274 277 278 282 +CONECT 277 276 +CONECT 278 276 279 280 281 +CONECT 279 278 +CONECT 280 278 +CONECT 281 278 +CONECT 282 276 283 +CONECT 283 282 +CONECT 284 274 285 285 286 +CONECT 285 284 284 +CONECT 286 284 287 288 +CONECT 287 286 +CONECT 288 286 289 290 298 +CONECT 289 288 +CONECT 290 288 291 292 296 +CONECT 291 290 +CONECT 292 290 293 294 295 +CONECT 293 292 +CONECT 294 292 +CONECT 295 292 +CONECT 296 290 297 +CONECT 297 296 +CONECT 298 288 299 299 300 +CONECT 299 298 298 +CONECT 300 298 301 302 +CONECT 301 300 +CONECT 302 300 303 304 313 +CONECT 303 302 +CONECT 304 302 305 306 307 +CONECT 305 304 +CONECT 306 304 +CONECT 307 304 308 309 310 +CONECT 308 307 +CONECT 309 307 +CONECT 310 307 311 311 312 +CONECT 311 310 310 +CONECT 312 310 +CONECT 313 302 314 314 315 +CONECT 314 313 313 +CONECT 315 313 316 317 +CONECT 316 315 +CONECT 317 315 318 319 323 +CONECT 318 317 +CONECT 319 317 320 321 322 +CONECT 320 319 +CONECT 321 319 +CONECT 322 319 +CONECT 323 317 324 324 325 +CONECT 324 323 323 +CONECT 325 323 326 327 +CONECT 326 325 +CONECT 327 325 328 329 339 +CONECT 328 327 +CONECT 329 327 330 331 335 +CONECT 330 329 +CONECT 331 329 332 333 334 +CONECT 332 331 +CONECT 333 331 +CONECT 334 331 +CONECT 335 329 336 337 338 +CONECT 336 335 +CONECT 337 335 +CONECT 338 335 +CONECT 339 327 340 340 341 +CONECT 340 339 339 +CONECT 341 339 342 343 +CONECT 342 341 +CONECT 343 341 344 345 351 +CONECT 344 343 +CONECT 345 343 346 347 348 +CONECT 346 345 +CONECT 347 345 +CONECT 348 345 349 349 350 +CONECT 349 348 348 +CONECT 350 348 +CONECT 351 343 352 352 353 +CONECT 352 351 351 +CONECT 353 351 354 355 +CONECT 354 353 +CONECT 355 353 356 357 361 +CONECT 356 355 +CONECT 357 355 358 359 360 +CONECT 358 357 +CONECT 359 357 +CONECT 360 357 +CONECT 361 355 362 362 363 +CONECT 362 361 361 +CONECT 363 361 364 365 +CONECT 364 363 +CONECT 365 363 366 367 371 +CONECT 366 365 +CONECT 367 365 368 369 370 +CONECT 368 367 +CONECT 369 367 +CONECT 370 367 +CONECT 371 365 372 372 373 +CONECT 372 371 371 +CONECT 373 371 374 375 +CONECT 374 373 +CONECT 375 373 376 377 385 +CONECT 376 375 +CONECT 377 375 378 379 383 +CONECT 378 377 +CONECT 379 377 380 381 382 +CONECT 380 379 +CONECT 381 379 +CONECT 382 379 +CONECT 383 377 384 +CONECT 384 383 +CONECT 385 375 386 386 387 +CONECT 386 385 385 +CONECT 387 385 388 389 +CONECT 388 387 +CONECT 389 387 390 391 395 +CONECT 390 389 +CONECT 391 389 392 393 394 +CONECT 392 391 +CONECT 393 391 +CONECT 394 391 +CONECT 395 389 396 396 397 +CONECT 396 395 395 +CONECT 397 395 398 399 +CONECT 398 397 +CONECT 399 397 400 401 410 +CONECT 400 399 +CONECT 401 399 402 403 404 +CONECT 402 401 +CONECT 403 401 +CONECT 404 401 405 406 407 +CONECT 405 404 +CONECT 406 404 +CONECT 407 404 408 408 409 +CONECT 408 407 407 +CONECT 409 407 +CONECT 410 399 411 411 412 +CONECT 411 410 410 +CONECT 412 410 413 414 +CONECT 413 412 +CONECT 414 412 415 416 432 +CONECT 415 414 +CONECT 416 414 417 418 419 +CONECT 417 416 +CONECT 418 416 +CONECT 419 416 420 421 422 +CONECT 420 419 +CONECT 421 419 +CONECT 422 419 423 424 425 +CONECT 423 422 +CONECT 424 422 +CONECT 425 422 426 427 428 +CONECT 426 425 +CONECT 427 425 +CONECT 428 425 429 430 431 +CONECT 429 428 +CONECT 430 428 +CONECT 431 428 +CONECT 432 414 433 433 434 +CONECT 433 432 432 +CONECT 434 432 435 436 +CONECT 435 434 +CONECT 436 434 437 438 448 +CONECT 437 436 +CONECT 438 436 439 440 444 +CONECT 439 438 +CONECT 440 438 441 442 443 +CONECT 441 440 +CONECT 442 440 +CONECT 443 440 +CONECT 444 438 445 446 447 +CONECT 445 444 +CONECT 446 444 +CONECT 447 444 +CONECT 448 436 449 449 450 +CONECT 449 448 448 +CONECT 450 448 451 452 +CONECT 451 450 +CONECT 452 450 453 454 468 +CONECT 453 452 +CONECT 454 452 455 456 457 +CONECT 455 454 +CONECT 456 454 +CONECT 457 454 458 458 466 +CONECT 458 457 457 459 460 +CONECT 459 458 +CONECT 460 458 461 462 462 +CONECT 461 460 +CONECT 462 460 460 463 464 +CONECT 463 462 +CONECT 464 462 465 466 466 +CONECT 465 464 +CONECT 466 457 464 464 467 +CONECT 467 466 +CONECT 468 452 469 469 470 +CONECT 469 468 468 +CONECT 470 468 471 472 +CONECT 471 470 +CONECT 472 470 473 474 490 +CONECT 473 472 +CONECT 474 472 475 476 477 +CONECT 475 474 +CONECT 476 474 +CONECT 477 474 478 479 480 +CONECT 478 477 +CONECT 479 477 +CONECT 480 477 481 482 483 +CONECT 481 480 +CONECT 482 480 +CONECT 483 480 484 485 486 +CONECT 484 483 +CONECT 485 483 +CONECT 486 483 487 488 489 +CONECT 487 486 +CONECT 488 486 +CONECT 489 486 +CONECT 490 472 491 491 492 +CONECT 491 490 490 +CONECT 492 490 493 494 +CONECT 493 492 +CONECT 494 492 495 496 507 +CONECT 495 494 +CONECT 496 494 497 498 499 +CONECT 497 496 +CONECT 498 496 +CONECT 499 496 500 501 502 +CONECT 500 499 +CONECT 501 499 +CONECT 502 499 503 503 504 +CONECT 503 502 502 +CONECT 504 502 505 506 +CONECT 505 504 +CONECT 506 504 +CONECT 507 494 508 508 509 +CONECT 508 507 507 +CONECT 509 507 510 511 +CONECT 510 509 +CONECT 511 509 512 513 528 +CONECT 512 511 +CONECT 513 511 514 515 516 +CONECT 514 513 +CONECT 515 513 +CONECT 516 513 517 517 526 +CONECT 517 516 516 518 519 +CONECT 518 517 +CONECT 519 517 520 521 521 +CONECT 520 519 +CONECT 521 519 519 522 524 +CONECT 522 521 523 +CONECT 523 522 +CONECT 524 521 525 526 526 +CONECT 525 524 +CONECT 526 516 524 524 527 +CONECT 527 526 +CONECT 528 511 529 529 530 +CONECT 529 528 528 +CONECT 530 528 531 532 +CONECT 531 530 +CONECT 532 530 533 534 538 +CONECT 533 532 +CONECT 534 532 535 536 537 +CONECT 535 534 +CONECT 536 534 +CONECT 537 534 +CONECT 538 532 539 539 540 +CONECT 539 538 538 +CONECT 540 538 541 542 +CONECT 541 540 +CONECT 542 540 543 544 552 +CONECT 543 542 +CONECT 544 542 545 546 547 +CONECT 545 544 +CONECT 546 544 +CONECT 547 544 548 548 549 +CONECT 548 547 547 +CONECT 549 547 550 551 +CONECT 550 549 +CONECT 551 549 +CONECT 552 542 553 553 554 +CONECT 553 552 552 +CONECT 554 552 555 556 +CONECT 555 554 +CONECT 556 554 557 558 564 +CONECT 557 556 +CONECT 558 556 559 560 561 +CONECT 559 558 +CONECT 560 558 +CONECT 561 558 562 562 563 +CONECT 562 561 561 +CONECT 563 561 +CONECT 564 556 565 565 566 +CONECT 565 564 564 +CONECT 566 564 567 568 +CONECT 567 566 +CONECT 568 566 569 570 578 +CONECT 569 568 +CONECT 570 568 571 572 573 +CONECT 571 570 +CONECT 572 570 +CONECT 573 570 574 574 575 +CONECT 574 573 573 +CONECT 575 573 576 577 +CONECT 576 575 +CONECT 577 575 +CONECT 578 568 579 579 580 +CONECT 579 578 578 +CONECT 580 578 581 582 +CONECT 581 580 +CONECT 582 580 583 584 585 +CONECT 583 582 +CONECT 584 582 +CONECT 585 582 586 586 587 +CONECT 586 585 585 +CONECT 587 585 588 589 +CONECT 588 587 +CONECT 589 587 590 591 601 +CONECT 590 589 +CONECT 591 589 592 593 597 +CONECT 592 591 +CONECT 593 591 594 595 596 +CONECT 594 593 +CONECT 595 593 +CONECT 596 593 +CONECT 597 591 598 599 600 +CONECT 598 597 +CONECT 599 597 +CONECT 600 597 +CONECT 601 589 602 602 603 +CONECT 602 601 601 +CONECT 603 601 604 605 +CONECT 604 603 +CONECT 605 603 606 607 613 +CONECT 606 605 +CONECT 607 605 608 609 610 +CONECT 608 607 +CONECT 609 607 +CONECT 610 607 611 611 612 +CONECT 611 610 610 +CONECT 612 610 +CONECT 613 605 614 614 615 +CONECT 614 613 613 +CONECT 615 613 616 617 +CONECT 616 615 +CONECT 617 615 618 619 620 +CONECT 618 617 +CONECT 619 617 +CONECT 620 617 621 621 622 +CONECT 621 620 620 +CONECT 622 620 623 624 +CONECT 623 622 +CONECT 624 622 625 626 635 +CONECT 625 624 +CONECT 626 624 627 628 629 +CONECT 627 626 +CONECT 628 626 +CONECT 629 626 630 631 632 +CONECT 630 629 +CONECT 631 629 +CONECT 632 629 633 633 634 +CONECT 633 632 632 +CONECT 634 632 +CONECT 635 624 636 636 637 +CONECT 636 635 635 +CONECT 637 635 638 639 +CONECT 638 637 +CONECT 639 637 640 641 659 +CONECT 640 639 +CONECT 641 639 642 643 644 +CONECT 642 641 +CONECT 643 641 +CONECT 644 641 645 645 658 +CONECT 645 644 644 646 647 +CONECT 646 645 +CONECT 647 645 648 649 +CONECT 648 647 +CONECT 649 647 650 650 658 +CONECT 650 649 649 651 652 +CONECT 651 650 +CONECT 652 650 653 654 654 +CONECT 653 652 +CONECT 654 652 652 655 656 +CONECT 655 654 +CONECT 656 654 657 658 658 +CONECT 657 656 +CONECT 658 644 649 656 656 +CONECT 659 639 660 660 661 +CONECT 660 659 659 +CONECT 661 659 662 663 +CONECT 662 661 +CONECT 663 661 664 665 673 +CONECT 664 663 +CONECT 665 663 666 667 671 +CONECT 666 665 +CONECT 667 665 668 669 670 +CONECT 668 667 +CONECT 669 667 +CONECT 670 667 +CONECT 671 665 672 +CONECT 672 671 +CONECT 673 663 674 674 675 +CONECT 674 673 673 +CONECT 675 673 676 677 +CONECT 676 675 +CONECT 677 675 678 679 694 +CONECT 678 677 +CONECT 679 677 680 681 682 +CONECT 680 679 +CONECT 681 679 +CONECT 682 679 683 683 692 +CONECT 683 682 682 684 685 +CONECT 684 683 +CONECT 685 683 686 687 687 +CONECT 686 685 +CONECT 687 685 685 688 690 +CONECT 688 687 689 +CONECT 689 688 +CONECT 690 687 691 692 692 +CONECT 691 690 +CONECT 692 682 690 690 693 +CONECT 693 692 +CONECT 694 677 695 695 696 +CONECT 695 694 694 +CONECT 696 694 697 698 +CONECT 697 696 +CONECT 698 696 699 700 706 +CONECT 699 698 +CONECT 700 698 701 702 703 +CONECT 701 700 +CONECT 702 700 +CONECT 703 700 704 704 705 +CONECT 704 703 703 +CONECT 705 703 +CONECT 706 698 707 707 708 +CONECT 707 706 706 +CONECT 708 706 709 710 +CONECT 709 708 +CONECT 710 708 711 712 718 +CONECT 711 710 +CONECT 712 710 713 714 715 +CONECT 713 712 +CONECT 714 712 +CONECT 715 712 716 716 717 +CONECT 716 715 715 +CONECT 717 715 +CONECT 718 710 719 719 720 +CONECT 719 718 718 +CONECT 720 718 721 722 +CONECT 721 720 +CONECT 722 720 723 724 728 +CONECT 723 722 +CONECT 724 722 725 726 727 +CONECT 725 724 +CONECT 726 724 +CONECT 727 724 +CONECT 728 722 729 729 730 +CONECT 729 728 728 +CONECT 730 728 731 732 +CONECT 731 730 +CONECT 732 730 733 734 742 +CONECT 733 732 +CONECT 734 732 735 736 740 +CONECT 735 734 +CONECT 736 734 737 738 739 +CONECT 737 736 +CONECT 738 736 +CONECT 739 736 +CONECT 740 734 741 +CONECT 741 740 +CONECT 742 732 743 743 744 +CONECT 743 742 742 +CONECT 744 742 745 746 +CONECT 745 744 +CONECT 746 744 747 748 764 +CONECT 747 746 +CONECT 748 746 749 750 751 +CONECT 749 748 +CONECT 750 748 +CONECT 751 748 752 753 754 +CONECT 752 751 +CONECT 753 751 +CONECT 754 751 755 756 757 +CONECT 755 754 +CONECT 756 754 +CONECT 757 754 758 759 760 +CONECT 758 757 +CONECT 759 757 +CONECT 760 757 761 762 763 +CONECT 761 760 +CONECT 762 760 +CONECT 763 760 +CONECT 764 746 765 765 766 +CONECT 765 764 764 +CONECT 766 764 767 768 +CONECT 767 766 +CONECT 768 766 769 770 778 +CONECT 769 768 +CONECT 770 768 771 772 776 +CONECT 771 770 +CONECT 772 770 773 774 775 +CONECT 773 772 +CONECT 774 772 +CONECT 775 772 +CONECT 776 770 777 +CONECT 777 776 +CONECT 778 768 779 779 780 +CONECT 779 778 778 +CONECT 780 778 781 782 +CONECT 781 780 +CONECT 782 780 783 784 798 +CONECT 783 782 +CONECT 784 782 785 786 787 +CONECT 785 784 +CONECT 786 784 +CONECT 787 784 788 788 796 +CONECT 788 787 787 789 790 +CONECT 789 788 +CONECT 790 788 791 792 792 +CONECT 791 790 +CONECT 792 790 790 793 794 +CONECT 793 792 +CONECT 794 792 795 796 796 +CONECT 795 794 +CONECT 796 787 794 794 797 +CONECT 797 796 +CONECT 798 782 799 799 800 +CONECT 799 798 798 +CONECT 800 798 801 802 +CONECT 801 800 +CONECT 802 800 803 804 812 +CONECT 803 802 +CONECT 804 802 805 806 810 +CONECT 805 804 +CONECT 806 804 807 808 809 +CONECT 807 806 +CONECT 808 806 +CONECT 809 806 +CONECT 810 804 811 +CONECT 811 810 +CONECT 812 802 813 813 814 +CONECT 813 812 812 +CONECT 814 812 815 816 +CONECT 815 814 +CONECT 816 814 817 818 828 +CONECT 817 816 +CONECT 818 816 819 820 824 +CONECT 819 818 +CONECT 820 818 821 822 823 +CONECT 821 820 +CONECT 822 820 +CONECT 823 820 +CONECT 824 818 825 826 827 +CONECT 825 824 +CONECT 826 824 +CONECT 827 824 +CONECT 828 816 829 829 830 +CONECT 829 828 828 +CONECT 830 828 831 832 +CONECT 831 830 +CONECT 832 830 833 834 842 +CONECT 833 832 +CONECT 834 832 835 836 840 +CONECT 835 834 +CONECT 836 834 837 838 839 +CONECT 837 836 +CONECT 838 836 +CONECT 839 836 +CONECT 840 834 841 +CONECT 841 840 +CONECT 842 832 843 843 844 +CONECT 843 842 842 +CONECT 844 842 845 846 +CONECT 845 844 +CONECT 846 844 847 848 857 +CONECT 847 846 +CONECT 848 846 849 850 851 +CONECT 849 848 +CONECT 850 848 +CONECT 851 848 852 853 854 +CONECT 852 851 +CONECT 853 851 +CONECT 854 851 855 855 856 +CONECT 855 854 854 +CONECT 856 854 +CONECT 857 846 858 858 859 +CONECT 858 857 857 +CONECT 859 857 +MASTER 0 0 0 0 0 0 0 0 859 0 859 0 +END diff --git a/unittests/run_unitests.sh b/unittests/run_unitests.sh new file mode 100755 index 0000000..16eab6a --- /dev/null +++ b/unittests/run_unitests.sh @@ -0,0 +1,16 @@ + +source /software/ENV/modules + +module load amber/18/intel-17.0.4 +module load openbabel/2.4.1/gcc-6.3.0 +module unload anaconda/5.0.1/python-3.6 + +module load cuda/10.1 + +source /home/duerr/miniconda3/bin/activate openmm +export PYTHONPATH=/home/duerr/phd/02_Projects/EVOLVE/Development/evolve/:$PYTHONPATH + + +python test_openbabel.py +python test_gaapi.py +python test_StartGA_Run.py diff --git a/unittests/test_StartGA_Run.py b/unittests/test_StartGA_Run.py new file mode 100644 index 0000000..b248ce7 --- /dev/null +++ b/unittests/test_StartGA_Run.py @@ -0,0 +1,178 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- + +''' + +Unittests for starting a job + +''' + +import unittest +from openbabel import openbabel +from src import JobConfig +from src.gaapi import operator_types +from src.gaapi import generators +from src.gaapi import Individual +import main as main_program +import shutil +import os +from pathlib import Path + +def setUpModule(): + pass + + +def tearDownModule(): + try: + os.remove("mdinfo") + os.remove("logfile") + os.remove("leap.log") + os.remove("new_mol.pdb") + shutil.rmtree("amber_run") + except: + print("One of temporary files written by AMBER could not be deleted.") + pass + + + +class TestJobConfig(unittest.TestCase): + """Unittest.""" + + def setUp(self): + """Method to prepare the test fixture. Run BEFORE the test methods.""" + pass + + def tearDown(self): + """Method to tear down the test fixture. Run AFTER the test methods.""" + pass + + def addCleanup(self, function, *args, **kwargs): + """Function called AFTER tearDown() to clean resources used on test.""" + + pass + + @classmethod + def setUpClass(cls): + """Class method called BEFORE tests in an individual class run. """ + pass # Probably you may not use this one. See setUp(). + + @classmethod + def tearDownClass(cls): + """Class method called AFTER tests in an individual class run. """ + pass # Probably you may not use this one. See tearDown(). + + def test_general_loading(self): + print('Running tests for general parsing of input file') + print("-" * 50) + settings = JobConfig.Settings('example_files/ga_input.in') + + self.assertEqual(settings.verbose, True) + self.assertEqual(settings.composition_optimization, True) + self.assertEqual(len(settings.composition_lower_bounds), 2) + self.assertEqual(len(settings.composition_lower_bounds), len(settings.composition_upper_bounds)) + self.assertEqual(settings.selector, operator_types.TOURNAMENT_WOR ) + self.assertEqual(settings.replacer, operator_types.ELITIST) + + @unittest.skipIf(os.environ["EVOLVE_CPU"]=='FALSE', "no gpu/mpi environment available") + def test_initPop_helicalstability(self): + print('Running tests for initalizing of population for evaluator helical stability') + print("-"*50) + settings = JobConfig.Settings('example_files/ga_input.in') + ga =main_program.initialise_ga(settings) + parent_population= generators.initialisePopulation(settings) + self.assertEqual(len(parent_population), 10) + self.assertIsInstance(parent_population[0], Individual.Individual ) + + generators.unbiased_protein_composition_generator(settings, parent_population) + + for i, indiv in enumerate(parent_population): + self.assertEqual(indiv.composition[1], 175) + self.assertEqual(len(indiv.fitnesses), len(settings.evaluators)) + self.assertEqual(len(indiv.composition), 2) + # TODO + # Test for length of indiv.mol + + # do an example fitness calculation of a defined individual = initial fitness test + initial_indiv = Individual.Individual(settings) + settings.originalResidues=['ALA', 'ALA'] + ga["evaluators"][0](settings, [initial_indiv], 0) + self.assertAlmostEqual(initial_indiv.fitnesses[0], -64.173) + f = open("amber_run/amber.out", 'r') + print('AMBER outputfile') + for lineno, line in enumerate(f): + if lineno==1606: + + final_energy=float(line[10:26]) + f.close() + + self.assertEqual(initial_indiv.fitnesses[0], final_energy) + # check that new molecule file is identical to minimized file + obConversion = openbabel.OBConversion() + obConversion.SetOutFormat("pdb") + obConversion.WriteFile(initial_indiv.mol, "new_mol.pdb") + + def read_atom_lines(infile): + out='' + for lineno, line in enumerate(infile): + if line[:4] == "ATOM": + out+=line + return out + + f1=open("new_mol.pdb", 'r') + f2=open('amber_run/min_struct.pdb', 'r') + f1content=read_atom_lines(f1) + f2content = read_atom_lines(f2) + self.assertTrue(f1content==f2content) + f1.close() + f2.close() + + + # set predefined fitnesses and compare individuals to compare whether replacing works + @unittest.skipIf(os.environ["EVOLVE_GPU"]=='FALSE', "no gpu/mpi environment available") + def test_initPop_helicalstability_openmm(self): + print('OpenMM test') + print("-"*50) + settings = JobConfig.Settings('example_files/openmm.in') + ga=main_program.initialise_ga(settings) + parent_population= generators.initialisePopulation(settings) + self.assertEqual(len(parent_population), 10) + self.assertIsInstance(parent_population[0], Individual.Individual ) + + generators.unbiased_protein_composition_generator(settings, parent_population) + + for i, indiv in enumerate(parent_population): + self.assertEqual(indiv.composition[1], 175) + self.assertEqual(len(indiv.fitnesses), len(settings.evaluators)) + self.assertEqual(len(indiv.composition), 2) + + # do an example fitness calculation of a defined individual = initial fitness test + initial_indiv = Individual.Individual(settings) + settings.originalResidues=['ALA', 'ALA'] # need to set this here, otherwise done in evaluator method. + settings.gpu_openmm=True + + ga["evaluators"][0](settings, [initial_indiv], 0) + print("openMM", initial_indiv.fitnesses[0]) + + @unittest.skipIf(os.environ["EVOLVE_GPU"]=='FALSE', "no gpu/mpi environment available") + def test_initPop_helicalstability_openmm_entropy(self): + print('OpenMM test with entropy corrections') + print("-"*50) + settings = JobConfig.Settings('example_files/openmm_entropy.in') + ga=main_program.initialise_ga(settings) + parent_population= generators.initialisePopulation(settings) + generators.unbiased_protein_composition_generator(settings, parent_population) + + # do an example fitness calculation of a defined individual = initial fitness test + initial_indiv = Individual.Individual(settings) + settings.originalResidues=['ALA', 'ALA'] # need to set this here, otherwise done in evaluator method. + settings.gpu_openmm=True + print(settings) + ga["evaluators"][0](settings, [initial_indiv], 0) + settings.initial_energy=initial_indiv.fitnesses[0] + for i, eval in enumerate(ga["evaluators"]): + print("EVALUATORS {}".format(ga["evaluators"][i].__name__)) + eval(settings, parent_population, i) + +if __name__.__contains__("__main__"): + print(__doc__) + unittest.main() diff --git a/unittests/test_gaapi.py b/unittests/test_gaapi.py new file mode 100644 index 0000000..eb56055 --- /dev/null +++ b/unittests/test_gaapi.py @@ -0,0 +1,92 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- + +''' + +Unittests for the gaapi modules + +Tests +- crossovers +- generators +- Inidividual +- mutators +- replacers +- selectors + +''' + +import unittest +import openbabel +#from openbabel import openbabel +from src import JobConfig +from src.gaapi import operator_types +from src.gaapi import generators +from src.gaapi import Individual +import main as main_program +import shutil +import os + + +def setUpModule(): + pass + + +def tearDownModule(): + pass + + + +class TestGAAPI(unittest.TestCase): + """Unittest.""" + + def setUp(self): + """Method to prepare the test fixture. Run BEFORE the test methods.""" + + self.settings = JobConfig.Settings('example_files/test_individual.in') + ga = main_program.initialise_ga(self.settings) + self.individualone= Individual.Individual(self.settings) + self.individualtwo = Individual.Individual(self.settings) + pass + + def tearDown(self): + """Method to tear down the test fixture. Run AFTER the test methods.""" + pass + + def addCleanup(self, function, *args, **kwargs): + """Function called AFTER tearDown() to clean resources used on test.""" + pass + + + #@unittest.skip("do not execute") + def test_comparison_onedim(self): + #test dominiation for one fitness + self.individualone.fitnesses=[-10] + self.individualtwo.fitnesses=[10] + self.assertLess(self.individualone, self.individualtwo) + self.assertGreater(self.individualtwo, self.individualone) + + ##@unittest.expectedFailure #multidim not implented yet + #@unittest.skip("do not execute") + def test_comparison_multidim(self): + # test dominiation for multiple fitnesses + self.individualone.fitnesses = [-10, -10, -10] + self.individualtwo.fitnesses = [10, 10, 10] + self.assertLess(self.individualone, self.individualtwo) + self.assertGreater(self.individualtwo, self.individualone) + + def test_applyComposition(self): + print('applying compostion') + #print(composition_residue_indexes) + print(self.settings) + self.composition_residue_indexes=[2, 4] + self.composition_lower_bounds=[4, 5] + self.composition_upper_bounds=[5, 6] + print(self.composition_residue_indexes) + self.individualone.applyComposition(self.settings) + self.individualone.saveMol('output_files/applied_composition.pdb') + + + +if __name__.__contains__("__main__"): + print(__doc__) + unittest.main() diff --git a/unittests/test_openbabel.py b/unittests/test_openbabel.py new file mode 100644 index 0000000..ed146bb --- /dev/null +++ b/unittests/test_openbabel.py @@ -0,0 +1,237 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- + +''' + +Unittests for the openbabel based modules + +Tests +- MoleculeCreator +- MoleculeInfo + +''' + +import unittest +import openbabel +#from openbabel import openbabel +from src import MoleculeInfo as mi +from src import MoleculeCreator as mc +import filecmp +import os +import subprocess + +def setUpModule(): + pass + + +def tearDownModule(): + pass + + + +class TestGAAPI(unittest.TestCase): + """Unittest.""" + + def setUp(self): + """Method to prepare the test fixture. Run BEFORE the test methods.""" + pass + + def tearDown(self): + """Method to tear down the test fixture. Run AFTER the test methods.""" + pass + + def addCleanup(self, function, *args, **kwargs): + """Function called AFTER tearDown() to clean resources used on test.""" + try: + os.remove("mdinfo") + os.remove("logfile") + os.remove("leap.log") + os.remove("new_mol.pdb") + except: + print("One of temporary files written by AMBER could not be deleted.") + pass + + @classmethod + def setUpClass(cls): + """Class method called BEFORE tests in an individual class run. """ + pass # Probably you may not use this one. See setUp(). + + @classmethod + def tearDownClass(cls): + """Class method called AFTER tests in an individual class run. """ + pass # Probably you may not use this one. See tearDown(). + + + def test_MoleculeInfo(self): + obConversion = openbabel.OBConversion() + obConversion.SetInAndOutFormats("pdb", "pdb") + + mol = openbabel.OBMol() + obConversion.ReadFile(mol, "example_files/ALA20.pdb") + obres = mol.GetResidue(0) + self.assertTrue(obres.GetName()=="ACE") + obres = mol.GetResidue(1) + self.assertTrue(mi.getResType(obres) == 'ALA') + #beta_atom = getBetaAtom(obres) + # # TODO + # test for proline and glycine + + # AlphaCarbon + self.assertIs(mi.getAlphaCarbon(obres).GetIdx(),9) + + # bb carboxzl + self.assertIs(mi.getBBCarboxyl(obres).GetIdx(),15) + + #bb nitrogen + self.assertIs(mi.getBBNitrogen(obres).GetIdx(),7) + + + # Dihedral tests + + # TODO + self.assertAlmostEqual(mi.getChi1DihedralAngle(mol, obres),-58.54682580446737) + + x,y,z=mi.getPosition(mi.getAlphaCarbon(obres)) + self.assertTrue(x==-0.333) + self.assertTrue(y==-0.155) + self.assertTrue(z==-0.121) + + self.assertIs(mi.countBonds(mi.getAlphaCarbon(obres)),4) + + + def test_MoleculeCreator_rotname(self): + + # TODO + # rotatematrix + class DemoSettings(object): + pass + settings=DemoSettings() + settings.use_res_type = False + obConversion = openbabel.OBConversion() + obConversion.SetInAndOutFormats("pdb", "pdb") + + mol = openbabel.OBMol() + obConversion.ReadFile(mol, "example_files/ALA20.pdb") + + frag = openbabel.OBMol() + obConversion.SetInAndOutFormats("mol2", "pdb") + obConversion.ReadFile(frag, "../share/HID/HD3.mol2") + + mc.swapsidechain(settings, mol, 1, frag) + + obConversion.WriteFile(mol, "output_files/test_swap.pdb") + + self.assertTrue(filecmp.cmp('output_files/test_swap.pdb', 'example_files/H1A19.pdb', shallow=False), 'MoleculeCreator.swapsidechain has not yielded the same file') + try: + os.remove("output_files/test_swap.pdb") + except: + print("test_swap could not be deleted.") + + def test_MoleculeCreator_resname(self): + + # TODO + # rotatematrix + class DemoSettings(object): + pass + settings=DemoSettings() + settings.use_res_type = True + obConversion = openbabel.OBConversion() + obConversion.SetInAndOutFormats("pdb", "pdb") + + mol = openbabel.OBMol() + obConversion.ReadFile(mol, "example_files/ALA20.pdb") + + frag = openbabel.OBMol() + obConversion.SetInAndOutFormats("mol2", "pdb") + obConversion.ReadFile(frag, "../share/HID/HD3.mol2") + + mc.swapsidechain(settings, mol, 1, frag) + + obConversion.WriteFile(mol, "output_files/test_swap_resname.pdb") + + self.assertTrue(filecmp.cmp('output_files/test_swap_resname.pdb', 'example_files/H1A19_resname.pdb', shallow=False), 'MoleculeCreator.swapsidechain has not yielded the same file') + try: + os.remove("output_files/test_swap_resname.pdb") + except: + print("test_swap could not be deleted.") + + #@unittest.skip("see if this one fails") + def test_MoleculeCreator_glycine(self): + + class DemoSettings(object): + pass + settings=DemoSettings() + settings.use_res_type = False + obConversion = openbabel.OBConversion() + obConversion.SetInAndOutFormats("mol2", "pdb") + + mol = openbabel.OBMol() + obConversion.ReadFile(mol, "example_files/test_gly.mol2") + + frag = openbabel.OBMol() + obConversion.SetInAndOutFormats("mol2", "pdb") + obConversion.ReadFile(frag, "../share/ALA/A01.mol2") + print('test') + mc.swapsidechain(settings, mol, 8, frag) + + obConversion.WriteFile(mol, "output_files/test_gly_to_K.pdb") + + + for rot_or_type in [False, True]: + settings.use_res_type = rot_or_type + mol = openbabel.OBMol() + obConversion.ReadFile(mol, "example_files/3GB1WT_2clust2.mol2") + frag = openbabel.OBMol() + obConversion.ReadFile(frag, "../share/GLY/G01.mol2") + mc.swapsidechain(settings, mol, 1, frag) + obConversion.WriteFile(mol, "output_files/test_thr_to_gly_restype"+str(rot_or_type)+".pdb") + obConversion.WriteFile(mol, "output_files/mol.pdb") + os.chdir("./output_files/") + print(os.getcwd()) + subprocess.call("tleap -f ../example_files/leap_glycine.in", shell=True) + WasInputFileGenerated=os.path.isfile("mol.inpcrd") + if WasInputFileGenerated: + os.remove("mol.inpcrd") + os.chdir("../") + print("For ResType =", rot_or_type, "the result was ",WasInputFileGenerated) + self.assertTrue(WasInputFileGenerated) + + def test_MoleculeCreator_histidine(self): + + class DemoSettings(object): + pass + settings=DemoSettings() + settings.use_res_type = False + obConversion = openbabel.OBConversion() + obConversion.SetInAndOutFormats("mol2", "pdb") + + for his in [("HID", "HD1"),("HID", "HD2"),("HID", "HD3"), ("HID", "HD6"), ("HID", "HD5"), ("HID", "HD8"), ("HIE", "HE2"), ("HIE", "HE7"), ("HIP", "HP7"), ("HIP", "HP3")]: + for rot_or_type in [False, True]: + settings.use_res_type = rot_or_type + mol = openbabel.OBMol() + obConversion.ReadFile(mol, "example_files/3GB1WT_2clust2.mol2") + frag = openbabel.OBMol() + obConversion.ReadFile(frag, "../share/"+his[0]+"/"+his[1]+".mol2") + mc.swapsidechain(settings, mol, 1, frag) + obConversion.WriteFile(mol, "output_files/test_thr_to_his_restype"+str(rot_or_type)+".pdb") + obConversion.WriteFile(mol, "output_files/mol.pdb") + os.chdir("./output_files/") + print(os.getcwd()) + subprocess.call("tleap -f ../example_files/leap_glycine.in", shell=True) + WasInputFileGenerated=os.path.isfile("mol.inpcrd") + if WasInputFileGenerated: + os.remove("mol.inpcrd") + os.chdir("../") + print("For "+his[0]+" "+his[1]+" ResType =", rot_or_type, "the result was ",WasInputFileGenerated) + self.assertTrue(WasInputFileGenerated) + # self.assertTrue(filecmp.cmp('test_swap.pdb', 'example_files/H1A19.pdb', shallow=False), 'MoleculeCreator.swapsidechain has not yielded the same file') + # try: + # os.remove("test_swap.pdb") + # except: + # print("test_swap could not be deleted.") + + + +if __name__.__contains__("__main__"): + print(__doc__) + unittest.main()